From a4f214e684aebaa6f7974ffe82bb1649f529f41b Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 21 Feb 2025 12:04:43 +0100
Subject: [PATCH 01/80] fix(CI): find correct upstream prefix when it's padded
---
install_spack_env.sh | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/install_spack_env.sh b/install_spack_env.sh
index 3bb01936..bb7fb9be 100644
--- a/install_spack_env.sh
+++ b/install_spack_env.sh
@@ -52,10 +52,11 @@ fi
if [[ $UPSTREAM_INSTANCE ]]
then
+ UPSTREAM_PREFIX=$(find $UPSTREAM_INSTANCE/spack/opt/spack/ -type d -name ".spack-db" 2>/dev/null | xargs -I {} dirname {})
cat <<EOF > ${CI_SPACK_ROOT}/etc/spack/defaults/upstreams.yaml
upstreams:
upstream-spack-instance:
- install_tree: $UPSTREAM_INSTANCE/spack/opt/spack
+ install_tree: $UPSTREAM_PREFIX
EOF
fi
--
GitLab
From d3bc5d9491eb8e3d4e213799581dfd6df67aff55 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Sat, 22 Feb 2025 15:47:45 +0000
Subject: [PATCH 02/80] fix(CI): only trigger CI build jobs on push
---
.gitlab-ci.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 766dfb9d..be25c7c8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -102,7 +102,7 @@ variables:
SPACK_ENV: test
RELEASE_NAME: EBRAINS-test
rules:
- - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE != "schedule"
+ - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE == "push"
# deploy the experimental release of tools once a week from latest working version of int release
.deploy-exp-release:
@@ -210,7 +210,7 @@ build-spack-env-on-runner:
when: always
timeout: 2 days
rules:
- - if: $CI_PIPELINE_SOURCE != "schedule" && $CI_PIPELINE_SOURCE != "merge_request_event"
+ - if: $CI_PIPELINE_SOURCE == "push"
# this one fills the spack caches and updates the ESD (ebrainslab-variant) images on harbor
sync-esd-image:
@@ -262,7 +262,7 @@ sync-esd-image:
resource_group: registry-esd-master-image
rules:
# branches that update the gitlab-runner upstream (read-only) installation and the spack OCI caches
- - if: ($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "experimental_rel" || $CI_COMMIT_BRANCH =~ /^ebrains/) && $CI_PROJECT_PATH =~ /platform\/esd\/ebrains-spack-builds/ && $CI_PIPELINE_SOURCE != "schedule"
+ - if: ($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "experimental_rel" || $CI_COMMIT_BRANCH =~ /^ebrains/) && $CI_PROJECT_PATH =~ /platform\/esd\/ebrains-spack-builds/ && $CI_PIPELINE_SOURCE == "push"
when: manual
# update gitlab-runner upstream (read-only) installation
@@ -307,7 +307,7 @@ sync-gitlab-spack-instance:
when: always
rules:
# branches that update the gitlab-runner upstream (read-only) installation
- - if: ($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "experimental_rel" || $CI_COMMIT_BRANCH =~ /^ebrains/) && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE != "schedule"
+ - if: ($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "experimental_rel" || $CI_COMMIT_BRANCH =~ /^ebrains/) && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE == "push"
when: manual
# run (scheduled) standalone tests for environment
--
GitLab
From 13bff2c40533a2264de5ddace89ffd609d2eb9bb Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 18 Feb 2025 07:34:08 +0000
Subject: [PATCH 03/80] feat: update Spack to v0.23.0
---
.gitlab-ci.yml | 6 +++---
README.md | 4 ++--
install_spack_env.sh | 4 ----
vendor/spack | 2 +-
4 files changed, 6 insertions(+), 10 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index be25c7c8..d76a5319 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,7 +4,7 @@ stages:
variables:
BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/ebrains-spack-build-env/base:24.12
- SPACK_PATH_GITLAB: /mnt/spack_v0.21.1
+ SPACK_PATH_GITLAB: /mnt/spack_v0.23.0
SYSTEMNAME: ebrainslab
GIT_SUBMODULE_STRATEGY: recursive
GIT_CLEAN_FLAGS: -ffdxq
@@ -62,14 +62,14 @@ variables:
extends: .deploy-build-environment
variables:
LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/int
- INSTALLATION_ROOT: /srv/test-build-2402
+ INSTALLATION_ROOT: /srv/test-build-2502
# deploy to a prod lab environment
.deploy-prod-server:
extends: .deploy-build-environment
variables:
LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod
- INSTALLATION_ROOT: /srv/main-spack-instance-2402
+ INSTALLATION_ROOT: /srv/main-spack-instance-2502
# deploy to the dev lab environment at CINECA
.deploy-dev-server-cineca:
diff --git a/README.md b/README.md
index 1f567131..36bce891 100644
--- a/README.md
+++ b/README.md
@@ -38,9 +38,9 @@ Clone this repository. You can use the `ebrains-yy-mm` branches to install the E
git clone --branch {branch-name} https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git
```
-Clone Spack. We currently use version v0.21.1:
+Clone Spack. We currently use version v0.23.0:
```
-git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.21.1 https://github.com/spack/spack
+git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.23.0 https://github.com/spack/spack
```
Activate Spack:
diff --git a/install_spack_env.sh b/install_spack_env.sh
index bb7fb9be..faf7ef8b 100644
--- a/install_spack_env.sh
+++ b/install_spack_env.sh
@@ -44,10 +44,6 @@ SPACK_ROOT_EXISTED=1
if [ ! -d ${CI_SPACK_ROOT} ]; then
ln -s ${EBRAINS_REPO}/vendor/spack ${CI_SPACK_ROOT}
SPACK_ROOT_EXISTED=0
-
- # SPACK PATCH: the post-build logs on install-time-test-logs.txt gets ovewritten by the post-install logs.
- # quick fix for that: (TODO: investigate more and open PR)
- sed -i "s/self.file_like, \"w\"/self.file_like, \"a\"/g" ${CI_SPACK_ROOT}/lib/spack/llnl/util/tty/log.py
fi
if [[ $UPSTREAM_INSTANCE ]]
diff --git a/vendor/spack b/vendor/spack
index 904e1a73..65abf4d1 160000
--- a/vendor/spack
+++ b/vendor/spack
@@ -1 +1 @@
-Subproject commit 904e1a73567bc17d43fe0e4615ca0d7f1d50e2ed
+Subproject commit 65abf4d14071280c6d4a183e20c0f6991ed49986
--
GitLab
From 1b33064ba357250db73ec862f24df637ed180c30 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 18 Feb 2025 07:35:13 +0000
Subject: [PATCH 04/80] feat: align packages with Spack v0.23.0 upstream
---
packages/ambertools/package.py | 78 --
packages/bazel/bazelconfiguration-0.3.patch | 16 -
.../bazel/bazelruleclassprovider-0.14.patch | 16 -
packages/bazel/build-0.29.1.patch | 61 -
packages/bazel/cc_configure-0.3.0.patch | 24 -
packages/bazel/cc_configure-0.5.0.patch | 24 -
packages/bazel/compile-0.13.patch | 11 -
packages/bazel/compile-0.16.patch | 11 -
packages/bazel/compile-0.21.patch | 11 -
packages/bazel/compile-0.3.patch | 11 -
packages/bazel/compile-0.9.patch | 11 -
packages/bazel/cppcompileaction-0.3.0.patch | 11 -
packages/bazel/cppcompileaction-7.0.0.patch | 12 +
packages/bazel/package.py | 514 ++------
packages/bazel/unix_cc_configure-0.10.patch | 22 -
packages/bazel/unix_cc_configure-0.5.3.patch | 24 -
packages/gcc/darwin/apfs.patch | 12 -
packages/gcc/darwin/clang13.patch | 32 -
packages/gcc/darwin/gcc-4.9.patch1 | 42 -
packages/gcc/darwin/gcc-4.9.patch2 | 28 -
packages/gcc/darwin/gcc-6.1.0-jit.patch | 21 -
packages/gcc/darwin/gcc-7.1.0-headerpad.patch | 19 -
packages/gcc/darwin/headers-10.13-fix.patch | 127 --
packages/gcc/detection_test.yaml | 38 -
packages/gcc/gcc-backport.patch | 138 --
.../gcc/glibc-2.31-libsanitizer-1-gcc-6.patch | 39 -
packages/gcc/glibc-2.31-libsanitizer-1.patch | 37 -
.../gcc/glibc-2.31-libsanitizer-2-gcc-6.patch | 69 -
.../gcc/glibc-2.31-libsanitizer-2-gcc-7.patch | 69 -
packages/gcc/glibc-2.31-libsanitizer-2.patch | 73 --
.../gcc/glibc-2.31-libsanitizer-3-gcc-5.patch | 81 --
.../glibc-2.36-libsanitizer-gcc-10-12.patch | 27 -
.../gcc/glibc-2.36-libsanitizer-gcc-5-9.patch | 27 -
packages/gcc/package.py | 1114 -----------------
...941d23b1570cdd90083b58fa0f66aa58c86e.patch | 121 --
...ae5923aba02982563481d75a21595df22ff8.patch | 123 --
...b74046e0feb0596b93bbb822fae02940a90e.patch | 133 --
...0b3010bd0de899a3da3209eab20664ddb703.patch | 133 --
packages/gcc/piclibs.patch | 62 -
packages/gcc/signal.patch | 28 -
packages/gcc/stack_t-4.9.patch | 80 --
packages/gcc/stack_t.patch | 88 --
packages/gcc/sys_ustat-4.9.patch | 34 -
packages/gcc/sys_ustat.h.patch | 63 -
packages/gcc/ucontext_t-java.patch | 60 -
packages/gcc/ucontext_t.patch | 189 ---
packages/gcc/zstd.patch | 43 -
packages/libvips/package.py | 23 +-
packages/libxcb/package.py | 54 +-
packages/llvm/constexpr_longdouble.patch | 28 -
packages/llvm/constexpr_longdouble_9.0.patch | 38 -
packages/llvm/detection_test.yaml | 104 ++
packages/llvm/libomp-libflags-as-list.patch | 14 -
packages/llvm/lldb_external_ncurses-10.patch | 31 -
packages/llvm/llvm-gcc11.patch | 9 -
packages/llvm/llvm13-thread.patch | 19 -
packages/llvm/llvm14-hwloc-ompd.patch | 13 -
packages/llvm/llvm17-18-thread.patch | 22 +
packages/llvm/llvm17-fujitsu.patch | 28 +
packages/llvm/llvm4-lld-ELF-Symbols.patch | 112 --
packages/llvm/llvm5-lld-ELF-Symbols.patch | 33 -
packages/llvm/llvm5-sanitizer-ustat.patch | 25 -
packages/llvm/llvm_py37.patch | 37 -
packages/llvm/llvm_python_path.patch | 14 -
packages/llvm/missing-includes.patch | 23 -
packages/llvm/no_cyclades.patch | 81 --
packages/llvm/package.py | 369 ++++--
...izer-platform-limits-posix-xdr-macos.patch | 11 +
packages/llvm/thread-p9.patch | 16 -
packages/log4cxx/package.py | 35 +-
packages/nanoflann/package.py | 26 -
packages/netlib-xblas/package.py | 74 --
packages/nglview/package.py | 36 -
packages/open3d/package.py | 35 +-
packages/openbabel/gcc12-cmake.patch | 37 -
packages/openbabel/package.py | 97 --
.../openbabel/python-3.6-rtld-global.patch | 42 -
.../testpdbformat-tabs-to-spaces.patch | 47 -
packages/py-astropy/package.py | 25 +-
packages/py-autopep8/package.py | 2 +
packages/py-bokeh/package.py | 23 +-
packages/py-chex/package.py | 34 -
packages/py-dash/package.py | 29 -
packages/py-flit-core/package.py | 40 -
packages/py-ipycanvas/package.py | 2 +
packages/py-ipympl/package.py | 53 +-
packages/py-jax/package.py | 70 --
packages/py-jaxlib/package.py | 125 --
packages/py-numba/package.py | 30 +-
packages/py-optax/package.py | 24 -
packages/py-pycuda/package.py | 4 +
packages/py-pyvista/package.py | 44 -
packages/py-pyviz-comms/package.py | 2 +
packages/py-ray/package.py | 6 +
packages/py-sympy/package.py | 9 +-
packages/py-tree-math/package.py | 26 -
packages/sbml/package.py | 5 +
packages/simpletraj/package.py | 32 -
packages/sleef/package.py | 63 -
packages/wf-biobb/package.py | 4 +-
100 files changed, 772 insertions(+), 5420 deletions(-)
delete mode 100644 packages/ambertools/package.py
delete mode 100644 packages/bazel/bazelconfiguration-0.3.patch
delete mode 100644 packages/bazel/bazelruleclassprovider-0.14.patch
delete mode 100644 packages/bazel/build-0.29.1.patch
delete mode 100644 packages/bazel/cc_configure-0.3.0.patch
delete mode 100644 packages/bazel/cc_configure-0.5.0.patch
delete mode 100644 packages/bazel/compile-0.13.patch
delete mode 100644 packages/bazel/compile-0.16.patch
delete mode 100644 packages/bazel/compile-0.21.patch
delete mode 100644 packages/bazel/compile-0.3.patch
delete mode 100644 packages/bazel/compile-0.9.patch
delete mode 100644 packages/bazel/cppcompileaction-0.3.0.patch
create mode 100644 packages/bazel/cppcompileaction-7.0.0.patch
delete mode 100644 packages/bazel/unix_cc_configure-0.10.patch
delete mode 100644 packages/bazel/unix_cc_configure-0.5.3.patch
delete mode 100644 packages/gcc/darwin/apfs.patch
delete mode 100644 packages/gcc/darwin/clang13.patch
delete mode 100644 packages/gcc/darwin/gcc-4.9.patch1
delete mode 100644 packages/gcc/darwin/gcc-4.9.patch2
delete mode 100644 packages/gcc/darwin/gcc-6.1.0-jit.patch
delete mode 100644 packages/gcc/darwin/gcc-7.1.0-headerpad.patch
delete mode 100644 packages/gcc/darwin/headers-10.13-fix.patch
delete mode 100644 packages/gcc/detection_test.yaml
delete mode 100644 packages/gcc/gcc-backport.patch
delete mode 100644 packages/gcc/glibc-2.31-libsanitizer-1-gcc-6.patch
delete mode 100644 packages/gcc/glibc-2.31-libsanitizer-1.patch
delete mode 100644 packages/gcc/glibc-2.31-libsanitizer-2-gcc-6.patch
delete mode 100644 packages/gcc/glibc-2.31-libsanitizer-2-gcc-7.patch
delete mode 100644 packages/gcc/glibc-2.31-libsanitizer-2.patch
delete mode 100644 packages/gcc/glibc-2.31-libsanitizer-3-gcc-5.patch
delete mode 100644 packages/gcc/glibc-2.36-libsanitizer-gcc-10-12.patch
delete mode 100644 packages/gcc/glibc-2.36-libsanitizer-gcc-5-9.patch
delete mode 100644 packages/gcc/package.py
delete mode 100644 packages/gcc/patch-2b40941d23b1570cdd90083b58fa0f66aa58c86e.patch
delete mode 100644 packages/gcc/patch-745dae5923aba02982563481d75a21595df22ff8.patch
delete mode 100644 packages/gcc/patch-f1feb74046e0feb0596b93bbb822fae02940a90e.patch
delete mode 100644 packages/gcc/patch-fc930b3010bd0de899a3da3209eab20664ddb703.patch
delete mode 100644 packages/gcc/piclibs.patch
delete mode 100644 packages/gcc/signal.patch
delete mode 100644 packages/gcc/stack_t-4.9.patch
delete mode 100644 packages/gcc/stack_t.patch
delete mode 100644 packages/gcc/sys_ustat-4.9.patch
delete mode 100644 packages/gcc/sys_ustat.h.patch
delete mode 100644 packages/gcc/ucontext_t-java.patch
delete mode 100644 packages/gcc/ucontext_t.patch
delete mode 100644 packages/gcc/zstd.patch
delete mode 100644 packages/llvm/constexpr_longdouble.patch
delete mode 100644 packages/llvm/constexpr_longdouble_9.0.patch
create mode 100644 packages/llvm/detection_test.yaml
delete mode 100644 packages/llvm/libomp-libflags-as-list.patch
delete mode 100644 packages/llvm/lldb_external_ncurses-10.patch
delete mode 100644 packages/llvm/llvm-gcc11.patch
delete mode 100644 packages/llvm/llvm13-thread.patch
delete mode 100644 packages/llvm/llvm14-hwloc-ompd.patch
create mode 100644 packages/llvm/llvm17-18-thread.patch
create mode 100644 packages/llvm/llvm17-fujitsu.patch
delete mode 100644 packages/llvm/llvm4-lld-ELF-Symbols.patch
delete mode 100644 packages/llvm/llvm5-lld-ELF-Symbols.patch
delete mode 100644 packages/llvm/llvm5-sanitizer-ustat.patch
delete mode 100644 packages/llvm/llvm_py37.patch
delete mode 100644 packages/llvm/llvm_python_path.patch
delete mode 100644 packages/llvm/missing-includes.patch
delete mode 100644 packages/llvm/no_cyclades.patch
create mode 100644 packages/llvm/sanitizer-platform-limits-posix-xdr-macos.patch
delete mode 100644 packages/llvm/thread-p9.patch
delete mode 100644 packages/nanoflann/package.py
delete mode 100644 packages/netlib-xblas/package.py
delete mode 100644 packages/nglview/package.py
delete mode 100644 packages/openbabel/gcc12-cmake.patch
delete mode 100644 packages/openbabel/package.py
delete mode 100644 packages/openbabel/python-3.6-rtld-global.patch
delete mode 100644 packages/openbabel/testpdbformat-tabs-to-spaces.patch
delete mode 100644 packages/py-chex/package.py
delete mode 100644 packages/py-dash/package.py
delete mode 100644 packages/py-flit-core/package.py
delete mode 100644 packages/py-jax/package.py
delete mode 100644 packages/py-jaxlib/package.py
delete mode 100644 packages/py-optax/package.py
delete mode 100644 packages/py-pyvista/package.py
delete mode 100644 packages/py-tree-math/package.py
delete mode 100644 packages/simpletraj/package.py
delete mode 100644 packages/sleef/package.py
diff --git a/packages/ambertools/package.py b/packages/ambertools/package.py
deleted file mode 100644
index 4e4552cd..00000000
--- a/packages/ambertools/package.py
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class Ambertools (CMakePackage):
- """AmberTools is a free, useful standalone package and a prerequisite for installing Amber itself.
- The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL).
- A few components are included that are in the public domain or which have other, open-source, licenses.
- The libsander and libpbsa libraries use the LGPL license."""
-
- # Set the homepage and download url
- homepage = "http://ambermd.org/AmberTools.php"
- url = "http://ambermd.org/downloads/AmberTools22jlmrcc.tar.bz2"
-
- # Set the gitlab accounts of this package maintainers
- maintainers = ['dbeltran', 'elmath']
-
- version('22jlmrcc', sha256='1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121')
-
- # Dependencies
- depends_on("flex", type="build") # This is necessary for sure (experimentally tested)
- depends_on("bison", type="build") # This is necessary for sure (experimentally tested)
- depends_on("tcsh", type="build")
- depends_on("zlib", type=("build", "link", "run"))
- depends_on("bzip2", type=("build", "run"))
- depends_on("blas", type=("build", "run"))
- depends_on("lapack", type=("build", "run"))
- depends_on("arpack-ng", type=("build", "run"))
- depends_on("netcdf-c", type=("build", "run"))
- depends_on("netcdf-fortran", type=("build", "run"))
- depends_on("fftw", type=("build", "run"))
- depends_on("readline", type=("build", "run"))
- depends_on("netlib-xblas~plain_blas", type=("build", "run"))
- # specific variants needed for boost - from the build log "Could NOT find Boost (missing: thread system program_options iostreams regex timer chrono filesystem graph)"
- depends_on("boost+thread+system+program_options+iostreams+regex+timer+chrono+filesystem+graph", type=("build", "run"))
-
- # Python dependencies
- # WARNING: If a python 3.8 version is already installed in spack then the '+tkinter' variant makes spack ignore the version
- # WARNING: Spack may try to install the preferred python version (i.e. python 3.10.8)
- # WARNING: The soultion is uninstall python and reinstall with this variant
- depends_on('python@3.8: +tkinter', type=('build', 'run'))
- depends_on("py-numpy", type=("build", "run"))
- depends_on("py-matplotlib", type=("build", "run"))
- depends_on("py-scipy", type=("build", "run"))
-
- def cmake_args(self):
- # Translated from ambertools build/run_cmake script
- # We also add the TRUST_SYSTEM_LIBS argument that is mentioned in the ambertools CMake guide
- # https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Guide-to-Options
- args = [
- self.define("COMPILER", "GNU"),
- self.define("MPI", False),
- self.define("CUDA", False),
- self.define("INSTALL_TESTS", True),
- self.define("DOWNLOAD_MINICONDA", False),
- self.define("TRUST_SYSTEM_LIBS", True),
- # This is to avoid the x11 (X11_Xext_LIB) error
- # It is equivalent to the '-noX11' flag accoridng to the docs:
- # https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
- self.define("BUILD_GUI", False)
- ]
- return args
-
- def setup_run_environment(self, env):
- env.set("AMBER_PREFIX", self.prefix)
- env.set("AMBERHOME", self.prefix)
-
- def setup_build_environment(self, env):
- env.set("AMBER_PREFIX", self.prefix)
- env.set("AMBERHOME", self.prefix)
-
- @run_after('install')
- @on_package_attributes(run_tests=True)
- def check_install(self):
- make("test.serial")
diff --git a/packages/bazel/bazelconfiguration-0.3.patch b/packages/bazel/bazelconfiguration-0.3.patch
deleted file mode 100644
index e6a974a9..00000000
--- a/packages/bazel/bazelconfiguration-0.3.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
-+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
-@@ -150,6 +150,13 @@
- builder.put("PATH", null);
- builder.put("LD_LIBRARY_PATH", null);
- }
-+
-+ Map<String, String> spackEnv = System.getenv();
-+ for (String envName : spackEnv.keySet()) {
-+ if (envName.startsWith("SPACK_")) {
-+ builder.put(envName, spackEnv.get(envName));
-+ }
-+ }
- }
-
- private static PathFragment determineShellExecutable(OS os, PathFragment fromOption) {
diff --git a/packages/bazel/bazelruleclassprovider-0.14.patch b/packages/bazel/bazelruleclassprovider-0.14.patch
deleted file mode 100644
index b0aebdf3..00000000
--- a/packages/bazel/bazelruleclassprovider-0.14.patch
+++ /dev/null
@@ -1,16 +0,0 @@
---- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
-+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
-@@ -168,6 +168,13 @@ public class BazelRuleClassProvider {
- env.put("PATH", null);
- }
-
-+ Map<String, String> spackEnv = System.getenv();
-+ for (String envName : spackEnv.keySet()) {
-+ if (envName.startsWith("SPACK_")) {
-+ env.put(envName, spackEnv.get(envName));
-+ }
-+ }
-+
- // Shell environment variables specified via options take precedence over the
- // ones inherited from the fragments. In the long run, these fragments will
- // be replaced by appropriate default rc files anyway.
diff --git a/packages/bazel/build-0.29.1.patch b/packages/bazel/build-0.29.1.patch
deleted file mode 100644
index c3ed9ab2..00000000
--- a/packages/bazel/build-0.29.1.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-From 9c9d27561780bc56d9f0867e325c7421a94ee1cb Mon Sep 17 00:00:00 2001
-From: Harsh Bhatia <bhatia4@llnl.gov>
-Date: Tue, 15 Dec 2020 15:56:10 -0800
-Subject: [PATCH] https://github.com/bazelbuild/bazel/commit/ab62a6e097590dac5ec946ad7a796ea0e8593ae0
-
----
- src/conditions/BUILD | 6 ++++++
- third_party/BUILD | 8 ++++++--
- 2 files changed, 12 insertions(+), 2 deletions(-)
-
-diff --git a/src/conditions/BUILD b/src/conditions/BUILD
-index 2b28e28057..faa41a439d 100644
---- a/src/conditions/BUILD
-+++ b/src/conditions/BUILD
-@@ -10,6 +10,12 @@ filegroup(
- visibility = ["//src:__pkg__"],
- )
-
-+config_setting(
-+ name = "linux_ppc",
-+ values = {"cpu": "ppc"},
-+ visibility = ["//visibility:public"],
-+)
-+
- config_setting(
- name = "linux_x86_64",
- values = {"cpu": "k8"},
-diff --git a/third_party/BUILD b/third_party/BUILD
-index 159006d741..4fcae54c00 100644
---- a/third_party/BUILD
-+++ b/third_party/BUILD
-@@ -523,12 +523,13 @@ UNNECESSARY_DYNAMIC_LIBRARIES = select({
- "//src/conditions:darwin": "*.so *.dll",
- "//src/conditions:darwin_x86_64": "*.so *.dll",
- "//src/conditions:linux_x86_64": "*.jnilib *.dll",
-+ "//src/conditions:linux_ppc": "*.so *.jnilib *.dll",
- # The .so file is an x86 one, so we can just remove it if the CPU is not x86
- "//src/conditions:arm": "*.so *.jnilib *.dll",
- "//src/conditions:linux_aarch64": "*.so *.jnilib *.dll",
- # Play it safe -- better have a big binary than a slow binary
- # zip -d does require an argument. Supply something bogus.
-- "//conditions:default": "*.bogusextension",
-+ "//conditions:default": "",
- })
-
- # Remove native libraries that are for a platform different from the one we are
-@@ -537,7 +538,10 @@ genrule(
- name = "filter_netty_dynamic_libs",
- srcs = ["netty_tcnative/netty-tcnative-boringssl-static-2.0.24.Final.jar"],
- outs = ["netty_tcnative/netty-tcnative-filtered.jar"],
-- cmd = "cp $< $@ && zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES,
-+ cmd = "cp $< $@ && " +
-+ # End successfully if there is nothing to be deleted from the archive
-+ "if [ -n '" + UNNECESSARY_DYNAMIC_LIBRARIES + "' ]; then " +
-+ "zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES + "; fi",
- )
-
- java_import(
---
-2.21.0 (Apple Git-122.2)
-
diff --git a/packages/bazel/cc_configure-0.3.0.patch b/packages/bazel/cc_configure-0.3.0.patch
deleted file mode 100644
index 79e12269..00000000
--- a/packages/bazel/cc_configure-0.3.0.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- a/tools/cpp/cc_configure.bzl
-+++ b/tools/cpp/cc_configure.bzl
-@@ -173,8 +173,19 @@
- else:
- inc_dirs = result.stderr[index1 + 1:index2].strip()
-
-- return [repository_ctx.path(_cxx_inc_convert(p))
-- for p in inc_dirs.split("\n")]
-+ default_inc_directories = [
-+ repository_ctx.path(_cxx_inc_convert(p))
-+ for p in inc_dirs.split("\n")
-+ ]
-+
-+ env = repository_ctx.os.environ
-+ if "SPACK_INCLUDE_DIRS" in env:
-+ for path in env["SPACK_INCLUDE_DIRS"].split(":"):
-+ default_inc_directories.append(
-+ repository_ctx.path(_cxx_inc_convert(path))
-+ )
-+
-+ return default_inc_directories
-
- def _add_option_if_supported(repository_ctx, cc, option):
- """Checks that `option` is supported by the C compiler."""
diff --git a/packages/bazel/cc_configure-0.5.0.patch b/packages/bazel/cc_configure-0.5.0.patch
deleted file mode 100644
index 470986be..00000000
--- a/packages/bazel/cc_configure-0.5.0.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- a/tools/cpp/cc_configure.bzl
-+++ b/tools/cpp/cc_configure.bzl
-@@ -200,8 +200,19 @@
- else:
- inc_dirs = result.stderr[index1 + 1:index2].strip()
-
-- return [_escape_string(repository_ctx.path(_cxx_inc_convert(p)))
-- for p in inc_dirs.split("\n")]
-+ default_inc_directories = [
-+ _escape_string(repository_ctx.path(_cxx_inc_convert(p)))
-+ for p in inc_dirs.split("\n")
-+ ]
-+
-+ env = repository_ctx.os.environ
-+ if "SPACK_INCLUDE_DIRS" in env:
-+ for path in env["SPACK_INCLUDE_DIRS"].split(":"):
-+ default_inc_directories.append(
-+ repository_ctx.path(_cxx_inc_convert(path))
-+ )
-+
-+ return default_inc_directories
-
-
- def _add_option_if_supported(repository_ctx, cc, option):
diff --git a/packages/bazel/compile-0.13.patch b/packages/bazel/compile-0.13.patch
deleted file mode 100644
index 13c82e76..00000000
--- a/packages/bazel/compile-0.13.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/compile.sh
-+++ b/compile.sh
-@@ -92,7 +92,7 @@
- log "Building output/bazel"
- # We set host and target platform directly since the defaults in @bazel_tools
- # have not yet been generated.
--bazel_build "src:bazel${EXE_EXT}" \
-+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \
- --host_platform=@bazel_tools//platforms:host_platform \
- --platforms=@bazel_tools//platforms:target_platform \
- || fail "Could not build Bazel"
diff --git a/packages/bazel/compile-0.16.patch b/packages/bazel/compile-0.16.patch
deleted file mode 100644
index f61f521a..00000000
--- a/packages/bazel/compile-0.16.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/compile.sh
-+++ b/compile.sh
-@@ -92,7 +92,7 @@ display "."
- log "Building output/bazel"
- # We set host and target platform directly since the defaults in @bazel_tools
- # have not yet been generated.
--bazel_build "src:bazel_nojdk${EXE_EXT}" \
-+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \
- --host_platform=@bazel_tools//platforms:host_platform \
- --platforms=@bazel_tools//platforms:target_platform \
- || fail "Could not build Bazel"
diff --git a/packages/bazel/compile-0.21.patch b/packages/bazel/compile-0.21.patch
deleted file mode 100644
index d666a0f0..00000000
--- a/packages/bazel/compile-0.21.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/compile.sh
-+++ b/compile.sh
-@@ -92,7 +92,7 @@ display "."
- log "Building output/bazel"
- # We set host and target platform directly since the defaults in @bazel_tools
- # have not yet been generated.
--bazel_build "src:bazel_nojdk${EXE_EXT}" \
-+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \
- --action_env=PATH \
- --host_platform=@bazel_tools//platforms:host_platform \
- --platforms=@bazel_tools//platforms:target_platform \
diff --git a/packages/bazel/compile-0.3.patch b/packages/bazel/compile-0.3.patch
deleted file mode 100644
index 82db6efb..00000000
--- a/packages/bazel/compile-0.3.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/compile.sh
-+++ b/compile.sh
-@@ -99,7 +99,7 @@
- new_step 'Building Bazel with Bazel'
- display "."
- log "Building output/bazel"
-- bazel_build "src:bazel${EXE_EXT}"
-+ CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}"
- cp -f "bazel-bin/src/bazel${EXE_EXT}" "output/bazel${EXE_EXT}"
- chmod 0755 "output/bazel${EXE_EXT}"
- BAZEL="$(pwd)/output/bazel${EXE_EXT}"
diff --git a/packages/bazel/compile-0.9.patch b/packages/bazel/compile-0.9.patch
deleted file mode 100644
index 135de3a0..00000000
--- a/packages/bazel/compile-0.9.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/compile.sh
-+++ b/compile.sh
-@@ -92,7 +92,7 @@
- log "Building output/bazel"
- # We set host and target platform directly since the defaults in @bazel_tools
- # have not yet been generated.
--bazel_build "src:bazel${EXE_EXT}" \
-+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \
- --host_platform=//tools/platforms:host_platform \
- --platforms=//tools/platforms:target_platform \
- || fail "Could not build Bazel"
diff --git a/packages/bazel/cppcompileaction-0.3.0.patch b/packages/bazel/cppcompileaction-0.3.0.patch
deleted file mode 100644
index dd23972d..00000000
--- a/packages/bazel/cppcompileaction-0.3.0.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java.orig 2020-06-08 13:42:14.035342560 -0400
-+++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java 2020-06-08 13:42:25.149375458 -0400
-@@ -963,7 +963,7 @@
- // are, it's probably due to a non-hermetic #include, & we should stop
- // the build with an error.
- if (execPath.startsWith(execRoot)) {
-- execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
-+ // execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
- } else {
- problems.add(execPathFragment.getPathString());
- continue;
diff --git a/packages/bazel/cppcompileaction-7.0.0.patch b/packages/bazel/cppcompileaction-7.0.0.patch
new file mode 100644
index 00000000..b182f98f
--- /dev/null
+++ b/packages/bazel/cppcompileaction-7.0.0.patch
@@ -0,0 +1,12 @@
+diff --color=auto --color=auto -Naur a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java
+--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java 1980-01-01 00:00:00
++++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java 2024-02-15 13:36:37
+@@ -143,7 +143,7 @@
+ LabelConstants.EXPERIMENTAL_EXTERNAL_PATH_PREFIX.getRelative(
+ execPath.relativeTo(execRoot.getParentDirectory()));
+ } else {
+- absolutePathProblems.add(execPathFragment.getPathString());
++ // absolutePathProblems.add(execPathFragment.getPathString());
+ continue;
+ }
+ }
diff --git a/packages/bazel/package.py b/packages/bazel/package.py
index 102bb5c5..9d548b61 100644
--- a/packages/bazel/package.py
+++ b/packages/bazel/package.py
@@ -18,8 +18,23 @@ class Bazel(Package):
homepage = "https://bazel.build/"
url = "https://github.com/bazelbuild/bazel/releases/download/3.1.0/bazel-3.1.0-dist.zip"
+ maintainers("LydDeb")
+
tags = ["build-tools"]
+ license("Apache-2.0")
+
+ version("7.0.2", sha256="dea2b90575d43ef3e41c402f64c2481844ecbf0b40f8548b75a204a4d504e035")
+ version("7.0.1", sha256="596b13e071d27c43343ec8f5d263cb5312fafe7ef8702401f7ed492f182f4e6c")
+ version("7.0.0", sha256="477e54f6374001f439a9471ba1de9d7824daf129db95510849ecc5e19ce88170")
+ version("6.5.0", sha256="fc89da919415289f29e4ff18a5e01270ece9a6fe83cb60967218bac4a3bb3ed2")
+ version("6.4.0", sha256="bd88ff602c8bbb29ee82ba2a6b12ad092d51ec668c6577f9628f18e48ff4e51e")
+ version("6.3.2", sha256="8cd7feac58193be2bcba451ba6688a46824d37ca6359ff58e0d44eb98f042948")
+ version("6.3.1", sha256="2676319e86c5aeab142dccd42434364a33aa330a091c13562b7de87a10e68775")
+ version("6.3.0", sha256="902198981b1d26112fc05913e79f1b3e9772c3f95594caf85619d041ba06ede0")
+ version("6.2.1", sha256="4cf4d264bff388ee0012735728630d23832d3c9d021383b2fadceadb0775dd6b")
+ version("6.2.0", sha256="f1e8f788637ac574d471d619d2096baaca04a19b57a034399e079633db441945")
+ version("6.1.2", sha256="6fb3ee22fe9fa86d82e173572d504c089f10825d749725592626e090b38c9679")
version("6.1.1", sha256="6b900f26d676c7eca1d2e7dff9b71890dabd3ff59cab2a2d2178bc8a0395342a")
version("6.1.0", sha256="c4b85675541cf66ee7cb71514097fdd6c5fc0e02527243617a4f20ca6b4f2932")
version("6.0.0", sha256="7bc0c5145c19a56d82a08fce6908c5e1a0e75e4fbfb3b6f12b4deae7f4b38cbc")
@@ -31,6 +46,7 @@ class Bazel(Package):
version("5.1.1", sha256="7f5d3bc1d344692b2400f3765fd4b5c0b636eb4e7a8a7b17923095c7b56a4f78")
version("5.1.0", sha256="4de301f509fc6d0cbc697b2017384ecdc94df8f36245bbcbedc7ea6780acc9f5")
version("5.0.0", sha256="072dd62d237dbc11e0bac02e118d8c2db4d0ba3ba09f1a0eb1e2a460fb8419db")
+ version("4.2.4", sha256="d5ba2ef28da5275f22e832aaa7f9319c61ea5db9b6a3e23b28a6a64ad03078f3")
version("4.2.3", sha256="b0e84d0538f3ec2b95a49bae31a5066f0967281a3ca99965016fbe178acd2d3d")
version("4.2.2", sha256="9981d0d53a356c4e87962847750a97c9e8054e460854748006c80f0d7e2b2d33")
version("4.2.1", sha256="12ea7aa11e2bdb12de1dceb9939a22e96f5a480437cb17c123379d8e0fdf5e82")
@@ -55,356 +71,6 @@ class Bazel(Package):
version("2.1.0", sha256="3371cd9050989173a3b27364668328653a65653a50a85c320adc53953b4d5f46")
version("2.0.1", sha256="a863ed9e6fc420fbd92e63a12fe1a5b9be1a7a36f11f61f1fdc582c813bbe543")
version("2.0.0", sha256="724da3c656f68e787a86ebb9844773aa1c2e3a873cc39462a8f1b336153d6cbb")
- version(
- "1.2.1",
- sha256="255da49d0f012bc4f2c1d6d3ccdbe578e22fe97b8d124e1629a486fe2a09d3e1",
- deprecated=True,
- )
- version(
- "1.2.0",
- sha256="9cb46b0a18b9166730307a0e82bf4c02281a1cc6da0fb11239e6fe4147bdee6e",
- deprecated=True,
- )
- version(
- "1.1.0",
- sha256="4b66a8c93af7832ed32e7236cf454a05f3aa06d25a8576fc3f83114f142f95ab",
- deprecated=True,
- )
- version(
- "1.0.1",
- sha256="f4d2dfad011ff03a5fae41b9b02cd96cd7297c1205d496603d66516934fbcfee",
- deprecated=True,
- )
- version(
- "1.0.0",
- sha256="c61daf0b69dd95205c695b2f9022d296d052c727062cfd396d54ffb2154f8cac",
- deprecated=True,
- )
- version(
- "0.29.1",
- sha256="872a52cff208676e1169b3e1cae71b1fe572c4109cbd66eab107d8607c378de5",
- deprecated=True,
- )
- version(
- "0.29.0",
- sha256="01cb6f2e808bd016cf0e217e12373c9efb808123e58b37885be8364458d3a40a",
- deprecated=True,
- )
- version(
- "0.28.1",
- sha256="2cea463d611f5255d2f3d41c8de5dcc0961adccb39cf0ac036f07070ba720314",
- deprecated=True,
- )
- version(
- "0.28.0",
- sha256="26ad8cdadd413b8432cf46d9fc3801e8db85d9922f85dd8a7f5a92fec876557f",
- deprecated=True,
- )
- version(
- "0.27.2",
- sha256="5e1bf2b48e54eb7e518430667d29aef53695d6dd7c718665a52131ab27aadab2",
- deprecated=True,
- )
- version(
- "0.27.1",
- sha256="8051d77da4ec338acd91770f853e4c25f4407115ed86fd35a6de25921673e779",
- deprecated=True,
- )
- version(
- "0.27.0",
- sha256="c3080d3b959ac08502ad5c84a51608c291accb1481baad88a628bbf79b30c67a",
- deprecated=True,
- )
- version(
- "0.26.1",
- sha256="c0e94f8f818759f3f67af798c38683520c540f469cb41aea8f5e5a0e43f11600",
- deprecated=True,
- )
- version(
- "0.26.0",
- sha256="d26dadf62959255d58e523da3448a6222af768fe1224e321b120c1d5bbe4b4f2",
- deprecated=True,
- )
- version(
- "0.25.3",
- sha256="23eafd3e439bc71baba9c592b52cb742dabc8640a13b9da1751fec090a2dda99",
- deprecated=True,
- )
- version(
- "0.25.2",
- sha256="7456032199852c043e6c5b3e4c71dd8089c1158f72ec554e6ec1c77007f0ab51",
- deprecated=True,
- )
- version(
- "0.25.1",
- sha256="a52bb31aeb1f821e649d25ef48023cfb54a12887aff875c6349ebcac36c2f056",
- deprecated=True,
- )
- version(
- "0.25.0",
- sha256="f624fe9ca8d51de192655369ac538c420afb7cde16e1ad052554b582fff09287",
- deprecated=True,
- )
- version(
- "0.24.1",
- sha256="56ea1b199003ad832813621744178e42b39e6206d34fbae342562c287da0cd54",
- deprecated=True,
- )
- version(
- "0.24.0",
- sha256="621d2a97899a88850a913eabf9285778331a309fd4658b225b1377f80060fa85",
- deprecated=True,
- )
- version(
- "0.23.2",
- sha256="293a5a7d851e0618eeb5e6958d94a11d45b6a00f2ba9376de61ac2bd5f917439",
- deprecated=True,
- )
- version(
- "0.23.1",
- sha256="dd47199f92452bf67b2c5d60ad4b7143554eaf2c6196ab6e8713449d81a0491d",
- deprecated=True,
- )
- version(
- "0.23.0",
- sha256="2daf9c2c6498836ed4ebae7706abb809748b1350cacd35b9f89452f31ac0acc1",
- deprecated=True,
- )
- version(
- "0.22.0",
- sha256="6860a226c8123770b122189636fb0c156c6e5c9027b5b245ac3b2315b7b55641",
- deprecated=True,
- )
- version(
- "0.21.0",
- sha256="6ccb831e683179e0cfb351cb11ea297b4db48f9eab987601c038aa0f83037db4",
- deprecated=True,
- )
- version(
- "0.20.0",
- sha256="1945afa84fd8858b0a3c68c09915a4bc81065c61df2591387b2985e2297d30bd",
- deprecated=True,
- )
- version(
- "0.19.2",
- sha256="11234cce4f6bdc62c3ac688f41c7b5c178eecb6f7e2c4ba0bcf00ba8565b1d19",
- deprecated=True,
- )
- version(
- "0.19.1",
- sha256="c9405f7b8c79ebc81f9f0e49bb656df4a0da246771d010c2cdd6bb30e2500ac0",
- deprecated=True,
- )
- version(
- "0.19.0",
- sha256="ee6135c5c47306c8421d43ad83aabc4f219cb065376ee37797f2c8ba9a615315",
- deprecated=True,
- )
- version(
- "0.18.1",
- sha256="baed9f28c317000a4ec1ad2571b3939356d22746ca945ac2109148d7abb860d4",
- deprecated=True,
- )
- version(
- "0.18.0",
- sha256="d0e86d2f7881ec8742a9823a986017452d2da0dfe4e989111da787cb89257155",
- deprecated=True,
- )
- version(
- "0.17.2",
- sha256="b6e87acfa0a405bb8b3417c58477b66d5bc27dc0d31ba6fa12bc255b9278d33b",
- deprecated=True,
- )
- version(
- "0.17.1",
- sha256="23e4281c3628cbd746da3f51330109bbf69780bd64461b63b386efae37203f20",
- deprecated=True,
- )
- version(
- "0.16.1",
- sha256="09c66b94356c82c52f212af52a81ac28eb06de1313755a2f23eeef84d167b36c",
- deprecated=True,
- )
- version(
- "0.16.0",
- sha256="c730593916ef0ba62f3d113cc3a268e45f7e8039daf7b767c8641b6999bd49b1",
- deprecated=True,
- )
- version(
- "0.15.2",
- sha256="bf53ec73be3a6d412d85ef612cec6e9c85db45da42001fab0cf1dad44cfc03f1",
- deprecated=True,
- )
- version(
- "0.15.1",
- sha256="c62b351fa4c1ba5aeb34d0a137176f8e8f1d89a32f548a10e96c11df176ffc6c",
- deprecated=True,
- )
- version(
- "0.15.0",
- sha256="c3b716e6625e6b8c323350c95cd3ae0f56aeb00458dddd10544d5bead8a7b602",
- deprecated=True,
- )
- version(
- "0.14.1",
- sha256="d49cdcd82618ae7a7a190e6f0a80d9bf85c1a66b732f994f37732dc14ffb0025",
- deprecated=True,
- )
- version(
- "0.14.0",
- sha256="259627de8b9d415cc80904523facf3d50e6e8e68448ab968eb1c9cb8ca1ef843",
- deprecated=True,
- )
- version(
- "0.13.1",
- sha256="b0269e75b40d87ff87886e5f3432cbf88f70c96f907ab588e6c21b2922d72db0",
- deprecated=True,
- )
- version(
- "0.13.0",
- sha256="82e9035084660b9c683187618a29aa896f8b05b5f16ae4be42a80b5e5b6a7690",
- deprecated=True,
- )
- version(
- "0.12.0",
- sha256="3b3e7dc76d145046fdc78db7cac9a82bc8939d3b291e53a7ce85315feb827754",
- deprecated=True,
- )
- version(
- "0.11.1",
- sha256="e8d762bcc01566fa50952c8028e95cfbe7545a39b8ceb3a0d0d6df33b25b333f",
- deprecated=True,
- )
- version(
- "0.11.0",
- sha256="abfeccc94728cb46be8dbb3507a23ccffbacef9fbda96a977ef4ea8d6ab0d384",
- deprecated=True,
- )
- version(
- "0.10.1",
- sha256="708248f6d92f2f4d6342006c520f22dffa2f8adb0a9dc06a058e3effe7fee667",
- deprecated=True,
- )
- version(
- "0.10.0",
- sha256="47e0798caaac4df499bce5fe554a914abd884a855a27085a4473de1d737d9548",
- deprecated=True,
- )
- version(
- "0.9.0",
- sha256="efb28fed4ffcfaee653e0657f6500fc4cbac61e32104f4208da385676e76312a",
- deprecated=True,
- )
- version(
- "0.8.1",
- sha256="dfd0761e0b7e36c1d74c928ad986500c905be5ebcfbc29914d574af1db7218cf",
- deprecated=True,
- )
- version(
- "0.8.0",
- sha256="aa840321d056abd3c6be10c4a1e98a64f9f73fff9aa89c468dae8c003974a078",
- deprecated=True,
- )
- version(
- "0.7.0",
- sha256="a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416",
- deprecated=True,
- )
- version(
- "0.6.1",
- sha256="dada1f60a512789747011184b2767d2b44136ef3b036d86947f1896d200d2ba7",
- deprecated=True,
- )
- version(
- "0.6.0",
- sha256="a0e53728a9541ef87934831f3d05f2ccfdc3b8aeffe3e037be2b92b12400598e",
- deprecated=True,
- )
- version(
- "0.5.4",
- sha256="2157b05309614d6af0e4bbc6065987aede590822634a0522161f3af5d647abc9",
- deprecated=True,
- )
- version(
- "0.5.3",
- sha256="76b5c5880a0b15f5b91f7d626c5bc3b76ce7e5d21456963c117ab711bf1c5333",
- deprecated=True,
- )
- version(
- "0.5.2",
- sha256="2418c619bdd44257a170b85b9d2ecb75def29e751b725e27186468ada2e009ea",
- deprecated=True,
- )
- version(
- "0.5.1",
- sha256="85e6a18b111afeea2e475fe991db2a441ec3824211d659bee7b0012c36be9a40",
- deprecated=True,
- )
- version(
- "0.5.0",
- sha256="ebba7330a8715e96a6d6dc0aa085125d529d0740d788f0544c6169d892e4f861",
- deprecated=True,
- )
- version(
- "0.4.5",
- sha256="2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b",
- deprecated=True,
- )
- version(
- "0.4.4",
- sha256="d52a21dda271ae645711ce99c70cf44c5d3a809138e656bbff00998827548ebb",
- deprecated=True,
- )
- version(
- "0.4.3",
- sha256="cbd2ab580181c17317cf18b2bf825bcded2d97cab01cd5b5fe4f4d520b64f90f",
- deprecated=True,
- )
- version(
- "0.4.2",
- sha256="8e6f41252abadcdb2cc7a07f910ec4b45fb12c46f0a578672c6a186c7efcdb36",
- deprecated=True,
- )
- version(
- "0.4.1",
- sha256="008c648d3c46ece063ae8b5008480d8ae6d359d35967356685d1c09da07e1064",
- deprecated=True,
- )
- version(
- "0.4.0",
- sha256="6474714eee72ba2d4e271ed00ce8c05d67a9d15327bc03962b821b2af2c5ca36",
- deprecated=True,
- )
- version(
- "0.3.2",
- sha256="ca5caf7b2b48c7639f45d815b32e76d69650f3199eb8caa541d402722e3f6c10",
- deprecated=True,
- )
- version(
- "0.3.1",
- sha256="218d0e28b4d1ee34585f2ac6b18d169c81404d93958815e73e60cc0368efcbb7",
- deprecated=True,
- )
- version(
- "0.3.0",
- sha256="357fd8bdf86034b93902616f0844bd52e9304cccca22971ab7007588bf9d5fb3",
- deprecated=True,
- )
- version(
- "0.2.0",
- sha256="e9ba2740d9727ae6d0f9b1ac0c5df331814fd03518fe4b511396ed10780d5272",
- deprecated=True,
- )
- version(
- "0.1.4",
- sha256="f3c395f5cd78cfef96f4008fe842f327bc8b03b77f46999387bc0ad223b5d970",
- deprecated=True,
- )
- version(
- "0.1.1",
- sha256="c6ae19610b936a0aa940b44a3626d6e660fc457a8187d295cdf0b21169453d20",
- deprecated=True,
- )
variant(
"nodepfail",
@@ -418,45 +84,30 @@ class Bazel(Package):
# end EBRAINS
# https://bazel.build/install/compile-source#bootstrap-unix-prereq
- depends_on("java", type=("build", "run"))
depends_on("java@11", when="@5.3:", type=("build", "run"))
depends_on("java@8,11", when="@3.3:5.2", type=("build", "run"))
depends_on("java@8", when="@0.6:3.2", type=("build", "run"))
- depends_on("java@7:8", when="@:0.5", type=("build", "run"))
depends_on("python+pythoncmd", type=("build", "run"))
depends_on("zip", when="platform=linux", type=("build", "run"))
# Pass Spack environment variables to the build
- patch("bazelruleclassprovider-0.25.patch", when="@0.25:")
- patch("bazelruleclassprovider-0.14.patch", when="@0.14:0.24")
- patch("bazelconfiguration-0.3.patch", when="@:0.13")
+ patch("bazelruleclassprovider-0.25.patch")
# Inject include paths
patch("unix_cc_configure-3.0.patch", when="@3:")
- patch("unix_cc_configure-0.15.patch", when="@0.15:2")
- patch("unix_cc_configure-0.10.patch", when="@0.10:0.14")
- patch("unix_cc_configure-0.5.3.patch", when="@0.5.3:0.9")
- patch("cc_configure-0.5.0.patch", when="@0.5.0:0.5.2")
- patch("cc_configure-0.3.0.patch", when="@0.3:0.4")
+ patch("unix_cc_configure-0.15.patch", when="@:2")
# Set CC and CXX
# begin EBRAINS (modified): bring upstream after checking since when this is breaking the build
- patch("compile-0.29.patch", when="@0.29:5.3")
+ patch("compile-0.29.patch", when="@:5.3")
# end EBRAINS
- patch("compile-0.21.patch", when="@0.21:0.28")
- patch("compile-0.16.patch", when="@0.16:0.20")
- patch("compile-0.13.patch", when="@0.13:0.15")
- patch("compile-0.9.patch", when="@0.9:0.12")
- patch("compile-0.6.patch", when="@0.6:0.8")
- patch("compile-0.4.patch", when="@0.4:0.5")
- patch("compile-0.3.patch", when="@0.2:0.3")
# Disable dependency search
- patch("cppcompileaction-0.3.2.patch", when="@0.3.2:+nodepfail")
- patch("cppcompileaction-0.3.0.patch", when="@0.3.0:0.3.1+nodepfail")
+ patch("cppcompileaction-7.0.0.patch", when="@7: +nodepfail")
+ patch("cppcompileaction-0.3.2.patch", when="@:6 +nodepfail")
# https://github.com/bazelbuild/bazel/issues/17956
- patch("apple-clang-14.0.3.patch", when="@0.3:5.4.0,6.0:6.1")
+ patch("apple-clang-14.0.3.patch", when="@:4.2.3,5:6.1.1")
# https://github.com/bazelbuild/bazel/issues/17958
patch(
@@ -465,56 +116,85 @@ class Bazel(Package):
when="@5.0:5.4.0,6.0",
)
- # Fix build on power9 (2x commits)
- # https://github.com/bazelbuild/bazel/commit/5cff4f1edf8b95bf0612791632255852332f72b5
- # https://github.com/bazelbuild/bazel/commit/ab62a6e097590dac5ec946ad7a796ea0e8593ae0
- patch("build-0.29.1.patch", when="@0.29.1")
-
# Fix build with Fujitsu compiler
- patch("blaze_util_posix-0.29.1.patch", when="@0.29.1:%fj")
+ patch("blaze_util_posix-0.29.1.patch", when="%fj")
patch("unix_cc_configure_fj-5.2.patch", when="@5.2:%fj")
patch("unix_cc_configure_fj-5.0.patch", when="@5.0:5.1%fj")
- patch("unix_cc_configure_fj-0.29.1.patch", when="@0.29.1:4%fj")
- patch("bazelruleclassprovider_fj-0.25.patch", when="@0.25:%fj")
- conflicts(
- "%fj",
- when="@:0.24.1",
- msg="Fujitsu Compiler cannot build 0.24.1 or less, " "please use a newer release.",
- )
+ patch("unix_cc_configure_fj-0.29.1.patch", when="@:4%fj")
+ patch("bazelruleclassprovider_fj-0.25.patch", when="%fj")
# https://blog.bazel.build/2021/05/21/bazel-4-1.html
conflicts("platform=darwin target=aarch64:", when="@:4.0")
- # patches for compiling various older bazels which had ICWYU
- # violations revealed by (but not unique to) GCC 11 header changes.
- # these are derived from
+ # https://github.com/bazelbuild/bazel/issues/18642
+ patch(
+ "https://github.com/bazelbuild/bazel/pull/20785.patch?full_index=1",
+ sha256="85dde31d129bbd31e004c5c87f23cdda9295fbb22946dc6d362f23d83bae1fd8",
+ when="@6.0:6.4",
+ )
+ conflicts("%gcc@13:", when="@:5")
+
+ # Patches for compiling various older bazels which had ICWYU violations revealed by
+ # (but not unique to) GCC 11 header changes. These are derived from
# https://gitlab.alpinelinux.org/alpine/aports/-/merge_requests/29084/
- patch("gcc11_1.patch", when="@0.3.2:4")
- patch("gcc11_2.patch", when="@0.3.2:4")
- patch("gcc11_3.patch", when="@0.3:4")
+ patch("gcc11_1.patch", when="@:4")
+ patch("gcc11_2.patch", when="@:4")
+ patch("gcc11_3.patch", when="@:4")
patch("gcc11_4.patch", when="@4.1:4")
- # bazel-4.0.0 does not compile with gcc-11
- # newer versions of grpc and abseil dependencies are needed but are not in
- # bazel-4.0.0
- conflicts("@:0.2,4.0.0", when="%gcc@11:")
+ # Bazel-4.0.0 does not compile with gcc-11
+ # Newer versions of grpc and abseil dependencies are needed but are not in bazel-4.0.0
+ conflicts("@4.0.0", when="%gcc@11:")
+
+ # https://github.com/bazelbuild/bazel/pull/23667
+ conflicts("%apple-clang@16:", when="@:7.3")
executables = ["^bazel$"]
+ # Download resources to perform offline build with bazel.
+ # The following URLs and sha256 are in the file distdir_deps.bzl at the root of bazel sources.
+ resource_dictionary = {}
+ resource_dictionary["bazel_skylib"] = {
+ "url": "https://github.com/bazelbuild/bazel-skylib/releases/download/1.0.1/bazel-skylib-1.0.1.tar.gz",
+ "sha256": "f1c8360c01fcf276778d3519394805dc2a71a64274a3a0908bc9edff7b5aebc8",
+ "when": "@4:6",
+ }
+ resource_dictionary["com_google_absl"] = {
+ "url": "https://github.com/abseil/abseil-cpp/archive/refs/tags/20230802.0.tar.gz",
+ "sha256": "59d2976af9d6ecf001a81a35749a6e551a335b949d34918cfade07737b9d93c5",
+ "when": "@6.0:6.4",
+ }
+ resource_dictionary["zulu_11_56_19"] = {
+ "url": "https://mirror.bazel.build/cdn.azul.com/zulu/bin/zulu11.56.19-ca-jdk11.0.15-linux_x64.tar.gz",
+ "sha256": "e064b61d93304012351242bf0823c6a2e41d9e28add7ea7f05378b7243d34247",
+ "when": "@6",
+ }
+ resource_dictionary["zulu_11_50_19"] = {
+ "url": "https://mirror.bazel.build/openjdk/azul-zulu11.50.19-ca-jdk11.0.12/zulu11.50.19-ca-jdk11.0.12-linux_x64.tar.gz",
+ "sha256": "b8e8a63b79bc312aa90f3558edbea59e71495ef1a9c340e38900dd28a1c579f3",
+ "when": "@5",
+ }
+ resource_dictionary["zulu_11_37_17"] = {
+ "url": "https://mirror.bazel.build/openjdk/azul-zulu11.37.17-ca-jdk11.0.6/zulu11.37.17-ca-jdk11.0.6-linux_x64.tar.gz",
+ "sha256": "360626cc19063bc411bfed2914301b908a8f77a7919aaea007a977fa8fb3cde1",
+ "when": "@4",
+ }
+ for resource_name in resource_dictionary.keys():
+ resource(
+ when=resource_dictionary[resource_name]["when"],
+ name=resource_name,
+ url=resource_dictionary[resource_name]["url"],
+ sha256=resource_dictionary[resource_name]["sha256"],
+ destination="archive",
+ expand=False,
+ )
+
@classmethod
def determine_version(cls, exe):
output = Executable(exe)("version", output=str, error=str)
match = re.search(r"Build label: ([\d.]+)", output)
return match.group(1) if match else None
- def url_for_version(self, version):
- if version >= Version("0.4.1"):
- url = "https://github.com/bazelbuild/bazel/releases/download/{0}/bazel-{0}-dist.zip"
- else:
- url = "https://github.com/bazelbuild/bazel/archive/{0}.tar.gz"
-
- return url.format(version)
-
# begin EBRAINS (added)
def setup_dependent_build_environment(self, env, dependent_spec):
env.prepend_path("GCC_HOST_COMPILER_PREFIX", self.spec['binutils'].prefix.bin)
@@ -526,19 +206,25 @@ class Bazel(Package):
env.set("BAZEL_LINKOPTS", "")
env.set("BAZEL_LINKLIBS", "-lstdc++")
- env.set(
- "EXTRA_BAZEL_ARGS",
- # Spack's logs don't handle colored output well
- "--color=no --host_javabase=@local_jdk//:jdk"
- # Enable verbose output for failures
- " --verbose_failures"
- # begin EBRAINS (modified): bring upstream after checking since when the compile-x.patch is breaking the build
- # expose CC and CXX (the spack compiler wrappers)
- " --action_env=CC"
- " --action_env=CXX"
- # end EBRAINS
- " --jobs={0}".format(make_jobs),
+ # .WARNING: Option 'host_javabase' is deprecated
+ # Use local java installation
+ # begin EBRAINS (modified): expose CC and CXX (the spack compiler wrappers)
+ args = "--color=no --define=ABSOLUTE_JAVABASE={0} --verbose_failures --action_env=CC --action_env=CXX --jobs={1}".format(
+ self.spec["java"].prefix, make_jobs
)
+ # end EBRAINS
+
+ resource_stages = self.stage[1:]
+ for _resource in resource_stages:
+ try:
+ resource_name = _resource.resource.name
+ if self.spec.satisfies(self.resource_dictionary[resource_name]["when"]):
+ archive_path = _resource.source_path
+ args += " --distdir={0}".format(archive_path)
+ except AttributeError:
+ continue
+
+ env.set("EXTRA_BAZEL_ARGS", args)
@run_before("install")
def bootstrap(self):
diff --git a/packages/bazel/unix_cc_configure-0.10.patch b/packages/bazel/unix_cc_configure-0.10.patch
deleted file mode 100644
index bdd24e11..00000000
--- a/packages/bazel/unix_cc_configure-0.10.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/tools/cpp/unix_cc_configure.bzl
-+++ b/tools/cpp/unix_cc_configure.bzl
-@@ -147,9 +147,18 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, additional_flags = []):
- else:
- inc_dirs = result.stderr[index1 + 1:index2].strip()
-
-- return [_prepare_include_path(repository_ctx, _cxx_inc_convert(p))
-- for p in inc_dirs.split("\n")]
-+ default_inc_directories = [
-+ _prepare_include_path(repository_ctx, _cxx_inc_convert(p))
-+ for p in inc_dirs.split("\n")
-+ ]
-+
-+ env = repository_ctx.os.environ
-+ if "SPACK_INCLUDE_DIRS" in env:
-+ for path in env["SPACK_INCLUDE_DIRS"].split(":"):
-+ default_inc_directories.append(path)
-+
-+ return default_inc_directories
-
-
- def _is_option_supported(repository_ctx, cc, option):
diff --git a/packages/bazel/unix_cc_configure-0.5.3.patch b/packages/bazel/unix_cc_configure-0.5.3.patch
deleted file mode 100644
index 79b583ba..00000000
--- a/packages/bazel/unix_cc_configure-0.5.3.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- a/tools/cpp/unix_cc_configure.bzl
-+++ b/tools/cpp/unix_cc_configure.bzl
-@@ -117,9 +117,19 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc):
- else:
- inc_dirs = result.stderr[index1 + 1:index2].strip()
-
-- return [escape_string(repository_ctx.path(_cxx_inc_convert(p)))
-- for p in inc_dirs.split("\n")]
-+ default_inc_directories = [
-+ escape_string(repository_ctx.path(_cxx_inc_convert(p)))
-+ for p in inc_dirs.split("\n")
-+ ]
-
-+ env = repository_ctx.os.environ
-+ if "SPACK_INCLUDE_DIRS" in env:
-+ for path in env["SPACK_INCLUDE_DIRS"].split(":"):
-+ default_inc_directories.append(
-+ repository_ctx.path(_cxx_inc_convert(path))
-+ )
-+
-+ return default_inc_directories
-
- def _add_option_if_supported(repository_ctx, cc, option):
- """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
diff --git a/packages/gcc/darwin/apfs.patch b/packages/gcc/darwin/apfs.patch
deleted file mode 100644
index d1f9d566..00000000
--- a/packages/gcc/darwin/apfs.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -uNr gcc-7.2.0.orig/libstdc++-v3/include/Makefile.in gcc-7.2.0/libstdc++-v3/include/Makefile.in
---- gcc-7.2.0.orig/libstdc++-v3/include/Makefile.in 2017-07-25 14:05:07.000000000 -0400
-+++ gcc-7.2.0/libstdc++-v3/include/Makefile.in 2017-09-02 12:22:08.000000000 -0400
-@@ -1764,6 +1764,8 @@
- @GLIBCXX_HOSTED_TRUE@install-data-local: install-headers
- @GLIBCXX_HOSTED_FALSE@install-data-local: install-freestanding-headers
-
-+.NOTPARALLEL: install-headers
-+
- # This is a subset of the full install-headers rule. We only need <ciso646>,
- # <cstddef>, <cfloat>, <limits>, <climits>, <cstdint>, <cstdlib>, <new>,
- # <typeinfo>, <exception>, <initializer_list>, <cstdalign>, <cstdarg>,
diff --git a/packages/gcc/darwin/clang13.patch b/packages/gcc/darwin/clang13.patch
deleted file mode 100644
index ac3bfcbe..00000000
--- a/packages/gcc/darwin/clang13.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- a/gcc/genconditions.c 2019-01-01 12:37:19.064943662 +0100
-+++ b/gcc/genconditions.c 2019-10-11 10:57:11.464595789 +0200
-@@ -57,8 +57,9 @@ write_header (void)
- \n\
- /* It is necessary, but not entirely safe, to include the headers below\n\
- in a generator program. As a defensive measure, don't do so when the\n\
-- table isn't going to have anything in it. */\n\
--#if GCC_VERSION >= 3001\n\
-+ table isn't going to have anything in it.\n\
-+ Clang 9 is buggy and doesn't handle __builtin_constant_p correctly. */\n\
-+#if GCC_VERSION >= 3001 && __clang_major__ < 9\n\
- \n\
- /* Do not allow checking to confuse the issue. */\n\
- #undef CHECKING_P\n\
-@@ -170,7 +171,7 @@ struct c_test\n\
- vary at run time. It works in 3.0.1 and later; 3.0 only when not\n\
- optimizing. */\n\
- \n\
--#if GCC_VERSION >= 3001\n\
-+#if GCC_VERSION >= 3001 && __clang_major__ < 9\n\
- static const struct c_test insn_conditions[] = {\n");
-
- traverse_c_tests (write_one_condition, 0);
-@@ -191,7 +192,7 @@ write_writer (void)
- " unsigned int i;\n"
- " const char *p;\n"
- " puts (\"(define_conditions [\");\n"
-- "#if GCC_VERSION >= 3001\n"
-+ "#if GCC_VERSION >= 3001 && __clang_major__ < 9\n"
- " for (i = 0; i < ARRAY_SIZE (insn_conditions); i++)\n"
- " {\n"
- " printf (\" (%d \\\"\", insn_conditions[i].value);\n"
diff --git a/packages/gcc/darwin/gcc-4.9.patch1 b/packages/gcc/darwin/gcc-4.9.patch1
deleted file mode 100644
index 444e2927..00000000
--- a/packages/gcc/darwin/gcc-4.9.patch1
+++ /dev/null
@@ -1,42 +0,0 @@
-diff --git a/gcc/configure b/gcc/configure
-index 9523773..52b0bf7 100755
---- a/gcc/configure
-+++ b/gcc/configure
-@@ -24884,7 +24884,7 @@ if test "${gcc_cv_as_ix86_filds+set}" = set; then :
- else
- gcc_cv_as_ix86_filds=no
- if test x$gcc_cv_as != x; then
-- $as_echo 'filds mem; fists mem' > conftest.s
-+ $as_echo 'filds (%ebp); fists (%ebp)' > conftest.s
- if { ac_try='$gcc_cv_as $gcc_cv_as_flags -o conftest.o conftest.s >&5'
- { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5
- (eval $ac_try) 2>&5
-@@ -24915,7 +24915,7 @@ if test "${gcc_cv_as_ix86_fildq+set}" = set; then :
- else
- gcc_cv_as_ix86_fildq=no
- if test x$gcc_cv_as != x; then
-- $as_echo 'fildq mem; fistpq mem' > conftest.s
-+ $as_echo 'fildq (%ebp); fistpq (%ebp)' > conftest.s
- if { ac_try='$gcc_cv_as $gcc_cv_as_flags -o conftest.o conftest.s >&5'
- { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5
- (eval $ac_try) 2>&5
-diff --git a/gcc/configure.ac b/gcc/configure.ac
-index 68b0ee8..bd53978 100644
---- a/gcc/configure.ac
-+++ b/gcc/configure.ac
-@@ -3869,13 +3869,13 @@ foo: nop
-
- gcc_GAS_CHECK_FEATURE([filds and fists mnemonics],
- gcc_cv_as_ix86_filds,,,
-- [filds mem; fists mem],,
-+ [filds (%ebp); fists (%ebp)],,
- [AC_DEFINE(HAVE_AS_IX86_FILDS, 1,
- [Define if your assembler uses filds and fists mnemonics.])])
-
- gcc_GAS_CHECK_FEATURE([fildq and fistpq mnemonics],
- gcc_cv_as_ix86_fildq,,,
-- [fildq mem; fistpq mem],,
-+ [fildq (%ebp); fistpq (%ebp)],,
- [AC_DEFINE(HAVE_AS_IX86_FILDQ, 1,
- [Define if your assembler uses fildq and fistq mnemonics.])])
-
diff --git a/packages/gcc/darwin/gcc-4.9.patch2 b/packages/gcc/darwin/gcc-4.9.patch2
deleted file mode 100644
index b065997f..00000000
--- a/packages/gcc/darwin/gcc-4.9.patch2
+++ /dev/null
@@ -1,28 +0,0 @@
-From 82f81877458ea372176eabb5de36329431dce99b Mon Sep 17 00:00:00 2001
-From: Iain Sandoe <iain@codesourcery.com>
-Date: Sat, 21 Dec 2013 00:30:18 +0000
-Subject: [PATCH] don't try to mark local symbols as no-dead-strip
-
----
- gcc/config/darwin.c | 5 +++++
- 1 file changed, 5 insertions(+)
-
-diff --git a/gcc/config/darwin.c b/gcc/config/darwin.c
-index 40804b8..0080299 100644
---- a/gcc/config/darwin.c
-+++ b/gcc/config/darwin.c
-@@ -1259,6 +1259,11 @@ darwin_encode_section_info (tree decl, rtx rtl, int first ATTRIBUTE_UNUSED)
- void
- darwin_mark_decl_preserved (const char *name)
- {
-+ /* Actually we shouldn't mark any local symbol this way, but for now
-+ this only happens with ObjC meta-data. */
-+ if (darwin_label_is_anonymous_local_objc_name (name))
-+ return;
-+
- fprintf (asm_out_file, "\t.no_dead_strip ");
- assemble_name (asm_out_file, name);
- fputc ('\n', asm_out_file);
---
-2.2.1
-
diff --git a/packages/gcc/darwin/gcc-6.1.0-jit.patch b/packages/gcc/darwin/gcc-6.1.0-jit.patch
deleted file mode 100644
index 8cc4405d..00000000
--- a/packages/gcc/darwin/gcc-6.1.0-jit.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-# Fix for libgccjit.so linkage on Darwin
-# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=64089
-# https://github.com/Homebrew/homebrew-core/issues/1872#issuecomment-225625332
-# https://github.com/Homebrew/homebrew-core/issues/1872#issuecomment-225626490
-
-# Stolen from Homebrew:
-# https://raw.githubusercontent.com/Homebrew/formula-patches/e9e0ee09389a54cc4c8fe1c24ebca3cd765ed0ba/gcc/6.1.0-jit.patch
-diff --git a/gcc/jit/Make-lang.in b/gcc/jit/Make-lang.in
-index 44d0750..4df2a9c 100644
---- a/gcc/jit/Make-lang.in
-+++ b/gcc/jit/Make-lang.in
-@@ -85,8 +85,7 @@ $(LIBGCCJIT_FILENAME): $(jit_OBJS) \
- $(jit_OBJS) libbackend.a libcommon-target.a libcommon.a \
- $(CPPLIB) $(LIBDECNUMBER) $(LIBS) $(BACKENDLIBS) \
- $(EXTRA_GCC_OBJS) \
-- -Wl,--version-script=$(srcdir)/jit/libgccjit.map \
-- -Wl,-soname,$(LIBGCCJIT_SONAME)
-+ -Wl,-install_name,$(LIBGCCJIT_SONAME)
-
- $(LIBGCCJIT_SONAME_SYMLINK): $(LIBGCCJIT_FILENAME)
- ln -sf $(LIBGCCJIT_FILENAME) $(LIBGCCJIT_SONAME_SYMLINK)
diff --git a/packages/gcc/darwin/gcc-7.1.0-headerpad.patch b/packages/gcc/darwin/gcc-7.1.0-headerpad.patch
deleted file mode 100644
index 11ca2d0e..00000000
--- a/packages/gcc/darwin/gcc-7.1.0-headerpad.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-# Use -headerpad_max_install_names in the build,
-# otherwise lto1 load commands cannot be edited on El Capitan
-
-# Stolen from Homebrew:
-# https://raw.githubusercontent.com/Homebrew/formula-patches/32cf103/gcc/7.1.0-headerpad.patch
-
-diff --git a/config/mh-darwin b/config/mh-darwin
-index 148b730..c2318b5 100644
---- a/config/mh-darwin
-+++ b/config/mh-darwin
-@@ -16,7 +16,7 @@ DARWIN_GCC_MDYNAMIC_NO_PIC := \
- DARWIN_NO_PIE := `case ${host} in *-*-darwin[1][1-9]*) echo -Wl,-no_pie ;; esac;`
-
- BOOT_CFLAGS += $(DARWIN_MDYNAMIC_NO_PIC)
--BOOT_LDFLAGS += $(DARWIN_NO_PIE)
-+BOOT_LDFLAGS += $(DARWIN_NO_PIE) -Wl,-headerpad_max_install_names
-
- # Similarly, for cross-compilation.
- STAGE1_CFLAGS += $(DARWIN_MDYNAMIC_NO_PIC)
diff --git a/packages/gcc/darwin/headers-10.13-fix.patch b/packages/gcc/darwin/headers-10.13-fix.patch
deleted file mode 100644
index 3dbfde02..00000000
--- a/packages/gcc/darwin/headers-10.13-fix.patch
+++ /dev/null
@@ -1,127 +0,0 @@
-diff -pur fixincludes/fixincl.x gcc-5.5.0/fixincludes/fixincl.x
---- a/fixincludes/fixincl.x 2017-01-30 17:08:42.000000000 +0100
-+++ b/fixincludes/fixincl.x 2017-12-21 14:34:35.000000000 +0100
-@@ -1,12 +1,12 @@
- /* -*- buffer-read-only: t -*- vi: set ro:
-- *
-+ *
- * DO NOT EDIT THIS FILE (fixincl.x)
-- *
-- * It has been AutoGen-ed January 5, 2017 at 06:05:06 PM by AutoGen 5.16.2
-+ *
-+ * It has been AutoGen-ed December 21, 2017 at 02:34:35 PM by AutoGen 5.18.7
- * From the definitions inclhack.def
- * and the template file fixincl
- */
--/* DO NOT SVN-MERGE THIS FILE, EITHER Thu Jan 5 18:05:06 CET 2017
-+/* DO NOT SVN-MERGE THIS FILE, EITHER Thu Dec 21 14:34:35 CET 2017
- *
- * You must regenerate it. Use the ./genfixes script.
- *
-@@ -15,7 +15,7 @@
- * certain ANSI-incompatible system header files which are fixed to work
- * correctly with ANSI C and placed in a directory that GNU C will search.
- *
-- * This file contains 240 fixup descriptions.
-+ * This file contains 241 fixup descriptions.
- *
- * See README for more information.
- *
-@@ -2579,6 +2579,43 @@ extern \"C\" {\n\
-
- /* * * * * * * * * * * * * * * * * * * * * * * * * *
- *
-+ * Description of Darwin_Osavailability fix
-+ */
-+tSCC zDarwin_OsavailabilityName[] =
-+ "darwin_osavailability";
-+
-+/*
-+ * File name selection pattern
-+ */
-+tSCC zDarwin_OsavailabilityList[] =
-+ "os/availability.h\0";
-+/*
-+ * Machine/OS name selection pattern
-+ */
-+tSCC* apzDarwin_OsavailabilityMachs[] = {
-+ "*-*-darwin*",
-+ (const char*)NULL };
-+
-+/*
-+ * content selection pattern - do fix if pattern found
-+ */
-+tSCC zDarwin_OsavailabilitySelect0[] =
-+ "#define[ \t]+__(API_[A-Z_]*)\\(\\.\\.\\.\\)";
-+
-+#define DARWIN_OSAVAILABILITY_TEST_CT 1
-+static tTestDesc aDarwin_OsavailabilityTests[] = {
-+ { TT_EGREP, zDarwin_OsavailabilitySelect0, (regex_t*)NULL }, };
-+
-+/*
-+ * Fix Command Arguments for Darwin_Osavailability
-+ */
-+static const char* apzDarwin_OsavailabilityPatch[] = {
-+ "format",
-+ "#define %1(...)",
-+ (char*)NULL };
-+
-+/* * * * * * * * * * * * * * * * * * * * * * * * * *
-+ *
- * Description of Darwin_9_Long_Double_Funcs_2 fix
- */
- tSCC zDarwin_9_Long_Double_Funcs_2Name[] =
-@@ -9818,9 +9855,9 @@ static const char* apzX11_SprintfPatch[]
- *
- * List of all fixes
- */
--#define REGEX_COUNT 276
-+#define REGEX_COUNT 277
- #define MACH_LIST_SIZE_LIMIT 187
--#define FIX_COUNT 240
-+#define FIX_COUNT 241
-
- /*
- * Enumerate the fixes
-@@ -9885,6 +9922,7 @@ typedef enum {
- CTRL_QUOTES_DEF_FIXIDX,
- CTRL_QUOTES_USE_FIXIDX,
- CXX_UNREADY_FIXIDX,
-+ DARWIN_OSAVAILABILITY_FIXIDX,
- DARWIN_9_LONG_DOUBLE_FUNCS_2_FIXIDX,
- DARWIN_EXTERNC_FIXIDX,
- DARWIN_GCC4_BREAKAGE_FIXIDX,
-@@ -10364,6 +10402,11 @@ tFixDesc fixDescList[ FIX_COUNT ] = {
- CXX_UNREADY_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,
- aCxx_UnreadyTests, apzCxx_UnreadyPatch, 0 },
-
-+ { zDarwin_OsavailabilityName, zDarwin_OsavailabilityList,
-+ apzDarwin_OsavailabilityMachs,
-+ DARWIN_OSAVAILABILITY_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,
-+ aDarwin_OsavailabilityTests, apzDarwin_OsavailabilityPatch, 0 },
-+
- { zDarwin_9_Long_Double_Funcs_2Name, zDarwin_9_Long_Double_Funcs_2List,
- apzDarwin_9_Long_Double_Funcs_2Machs,
- DARWIN_9_LONG_DOUBLE_FUNCS_2_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,
-diff -pur fixincludes/inclhack.def gcc-5.5.0/fixincludes/inclhack.def
---- a/fixincludes/inclhack.def 2017-01-30 17:08:42.000000000 +0100
-+++ b/fixincludes/inclhack.def 2017-12-21 14:34:28.000000000 +0100
-@@ -1337,6 +1337,18 @@ fix = {
- test_text = "extern void* malloc( size_t );";
- };
-
-+fix = {
-+ hackname = darwin_osavailability;
-+ mach = "*-*-darwin*";
-+ files = os/availability.h;
-+ select = "#define[ \t]+__(API_[A-Z_]*)\\(\\.\\.\\.\\)";
-+ c_fix = format;
-+ c_fix_arg = "#define %1(...)";
-+
-+ test_text = "#define __API_AVAILABLE(...)\n"
-+ "#define API_AVAILABLE(...)\n";
-+};
-+
- /*
- * For the AAB_darwin7_9_long_double_funcs fix to be useful,
- * you have to not use "" includes.
diff --git a/packages/gcc/detection_test.yaml b/packages/gcc/detection_test.yaml
deleted file mode 100644
index 5e53101a..00000000
--- a/packages/gcc/detection_test.yaml
+++ /dev/null
@@ -1,38 +0,0 @@
-paths:
- # Ubuntu 18.04, system compilers without Fortran
- - layout:
- - executables:
- - "bin/gcc"
- - "bin/g++"
- script: "echo 7.5.0"
- results:
- - spec: "gcc@7.5.0 languages=c,c++"
- # Mock a version < 7 of GCC that requires -dumpversion and
- # errors with -dumpfullversion
- - layout:
- - executables:
- - "bin/gcc-5"
- - "bin/g++-5"
- - "bin/gfortran-5"
- script: |
- if [[ "$1" == "-dumpversion" ]] ; then
- echo "5.5.0"
- else
- echo "gcc-5: fatal error: no input files"
- echo "compilation terminated."
- exit 1
- fi
- results:
- - spec: "gcc@5.5.0 languages=c,c++,fortran"
- # Multiple compilers present at the same time
- - layout:
- - executables:
- - "bin/x86_64-linux-gnu-gcc-6"
- script: 'echo 6.5.0'
- - executables:
- - "bin/x86_64-linux-gnu-gcc-10"
- - "bin/x86_64-linux-gnu-g++-10"
- script: "echo 10.1.0"
- results:
- - spec: "gcc@6.5.0 languages=c"
- - spec: "gcc@10.1.0 languages=c,c++"
\ No newline at end of file
diff --git a/packages/gcc/gcc-backport.patch b/packages/gcc/gcc-backport.patch
deleted file mode 100644
index f9fab68f..00000000
--- a/packages/gcc/gcc-backport.patch
+++ /dev/null
@@ -1,138 +0,0 @@
-2016-02-20 Bernd Edlinger <bernd.edlinger@hotmail.de>
-
- Backported from mainline
- 2016-02-19 Jakub Jelinek <jakub@redhat.com>
- Bernd Edlinger <bernd.edlinger@hotmail.de>
-
- * Make-lang.in: Invoke gperf with -L C++.
- * cfns.gperf: Remove prototypes for hash and libc_name_p
- inlines.
- * cfns.h: Regenerated.
- * except.c (nothrow_libfn_p): Adjust.
-
-Index: gcc/cp/Make-lang.in
-===================================================================
---- a/gcc/cp/Make-lang.in (revision 233574)
-+++ b/gcc/cp/Make-lang.in (working copy)
-@@ -111,7 +111,7 @@ else
- # deleting the $(srcdir)/cp/cfns.h file.
- $(srcdir)/cp/cfns.h:
- endif
-- gperf -o -C -E -k '1-6,$$' -j1 -D -N 'libc_name_p' -L ANSI-C \
-+ gperf -o -C -E -k '1-6,$$' -j1 -D -N 'libc_name_p' -L C++ \
- $(srcdir)/cp/cfns.gperf --output-file $(srcdir)/cp/cfns.h
-
- #
-Index: gcc/cp/cfns.gperf
-===================================================================
---- a/gcc/cp/cfns.gperf (revision 233574)
-+++ b/gcc/cp/cfns.gperf (working copy)
-@@ -1,3 +1,5 @@
-+%language=C++
-+%define class-name libc_name
- %{
- /* Copyright (C) 2000-2015 Free Software Foundation, Inc.
-
-@@ -16,14 +18,6 @@ for more details.
- You should have received a copy of the GNU General Public License
- along with GCC; see the file COPYING3. If not see
- <http://www.gnu.org/licenses/>. */
--#ifdef __GNUC__
--__inline
--#endif
--static unsigned int hash (const char *, unsigned int);
--#ifdef __GNUC__
--__inline
--#endif
--const char * libc_name_p (const char *, unsigned int);
- %}
- %%
- # The standard C library functions, for feeding to gperf; the result is used
-Index: gcc/cp/cfns.h
-===================================================================
---- a/gcc/cp/cfns.h (revision 233574)
-+++ b/gcc/cp/cfns.h (working copy)
-@@ -1,5 +1,5 @@
--/* ANSI-C code produced by gperf version 3.0.3 */
--/* Command-line: gperf -o -C -E -k '1-6,$' -j1 -D -N libc_name_p -L ANSI-C cfns.gperf */
-+/* C++ code produced by gperf version 3.0.4 */
-+/* Command-line: gperf -o -C -E -k '1-6,$' -j1 -D -N libc_name_p -L C++ --output-file cfns.h cfns.gperf */
-
- #if !((' ' == 32) && ('!' == 33) && ('"' == 34) && ('#' == 35) \
- && ('%' == 37) && ('&' == 38) && ('\'' == 39) && ('(' == 40) \
-@@ -28,7 +28,7 @@
- #error "gperf generated tables don't work with this execution character set. Please report a bug to <bug-gnu-gperf@gnu.org>."
- #endif
-
--#line 1 "cfns.gperf"
-+#line 3 "cfns.gperf"
-
- /* Copyright (C) 2000-2015 Free Software Foundation, Inc.
-
-@@ -47,26 +47,19 @@ for more details.
- You should have received a copy of the GNU General Public License
- along with GCC; see the file COPYING3. If not see
- <http://www.gnu.org/licenses/>. */
--#ifdef __GNUC__
--__inline
--#endif
--static unsigned int hash (const char *, unsigned int);
--#ifdef __GNUC__
--__inline
--#endif
--const char * libc_name_p (const char *, unsigned int);
- /* maximum key range = 391, duplicates = 0 */
-
--#ifdef __GNUC__
--__inline
--#else
--#ifdef __cplusplus
--inline
--#endif
--#endif
--static unsigned int
--hash (register const char *str, register unsigned int len)
-+class libc_name
- {
-+private:
-+ static inline unsigned int hash (const char *str, unsigned int len);
-+public:
-+ static const char *libc_name_p (const char *str, unsigned int len);
-+};
-+
-+inline unsigned int
-+libc_name::hash (register const char *str, register unsigned int len)
-+{
- static const unsigned short asso_values[] =
- {
- 400, 400, 400, 400, 400, 400, 400, 400, 400, 400,
-@@ -122,14 +115,8 @@ along with GCC; see the file COPYING3. If not see
- return hval + asso_values[(unsigned char)str[len - 1]];
- }
-
--#ifdef __GNUC__
--__inline
--#ifdef __GNUC_STDC_INLINE__
--__attribute__ ((__gnu_inline__))
--#endif
--#endif
- const char *
--libc_name_p (register const char *str, register unsigned int len)
-+libc_name::libc_name_p (register const char *str, register unsigned int len)
- {
- enum
- {
-Index: gcc/cp/except.c
-===================================================================
---- a/gcc/cp/except.c (revision 233574)
-+++ b/gcc/cp/except.c (working copy)
-@@ -1040,7 +1040,8 @@ nothrow_libfn_p (const_tree fn)
- unless the system headers are playing rename tricks, and if
- they are, we don't want to be confused by them. */
- id = DECL_NAME (fn);
-- return !!libc_name_p (IDENTIFIER_POINTER (id), IDENTIFIER_LENGTH (id));
-+ return !!libc_name::libc_name_p (IDENTIFIER_POINTER (id),
-+ IDENTIFIER_LENGTH (id));
- }
-
- /* Returns nonzero if an exception of type FROM will be caught by a
diff --git a/packages/gcc/glibc-2.31-libsanitizer-1-gcc-6.patch b/packages/gcc/glibc-2.31-libsanitizer-1-gcc-6.patch
deleted file mode 100644
index 4187b812..00000000
--- a/packages/gcc/glibc-2.31-libsanitizer-1-gcc-6.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-From ce9568e9e9cf6094be30e748821421e703754ffc Mon Sep 17 00:00:00 2001
-From: Jakub Jelinek <jakub@redhat.com>
-Date: Fri, 8 Nov 2019 19:53:18 +0100
-Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm
- bootstrap due to libsanitizer)
-
- Backported from mainline
- 2019-10-22 Tamar Christina <tamar.christina@arm.com>
- Backported for version 5.3.0 <= gcc <= 6.5.0
- 2020-06-05 John L. Jolly <john.jolly@gmail.com>
-
- PR sanitizer/92154
- * sanitizer_common/sanitizer_platform_limits_posix.cc:
- Cherry-pick compiler-rt revision r375220.
-
-From-SVN: r277981
----
- libsanitizer/ChangeLog | 9 +++++++++
- .../sanitizer_common/sanitizer_platform_limits_posix.cc | 6 +++++-
- 2 files changed, 14 insertions(+), 1 deletion(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-index 6cd4a5bac8b0..06a605ff4670 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-@@ -1130,8 +1130,12 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);
- #ifndef __GLIBC_PREREQ
- #define __GLIBC_PREREQ(x, y) 0
- #endif
--#if !defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)
-+#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \
-+ !defined(__arm__)
- /* On aarch64 glibc 2.20 and earlier provided incorrect mode field. */
-+/* On Arm glibc 2.31 and later provide a different mode field, this field is
-+ never used by libsanitizer so we can simply ignore this assert for all glibc
-+ versions. */
- CHECK_SIZE_AND_OFFSET(ipc_perm, mode);
- #endif
-
diff --git a/packages/gcc/glibc-2.31-libsanitizer-1.patch b/packages/gcc/glibc-2.31-libsanitizer-1.patch
deleted file mode 100644
index 96037707..00000000
--- a/packages/gcc/glibc-2.31-libsanitizer-1.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-From ce9568e9e9cf6094be30e748821421e703754ffc Mon Sep 17 00:00:00 2001
-From: Jakub Jelinek <jakub@redhat.com>
-Date: Fri, 8 Nov 2019 19:53:18 +0100
-Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm
- bootstrap due to libsanitizer)
-
- Backported from mainline
- 2019-10-22 Tamar Christina <tamar.christina@arm.com>
-
- PR sanitizer/92154
- * sanitizer_common/sanitizer_platform_limits_posix.cc:
- Cherry-pick compiler-rt revision r375220.
-
-From-SVN: r277981
----
- libsanitizer/ChangeLog | 9 +++++++++
- .../sanitizer_common/sanitizer_platform_limits_posix.cc | 6 +++++-
- 2 files changed, 14 insertions(+), 1 deletion(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-index 6cd4a5bac8b0..06a605ff4670 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-@@ -1156,8 +1156,12 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);
- CHECK_SIZE_AND_OFFSET(ipc_perm, gid);
- CHECK_SIZE_AND_OFFSET(ipc_perm, cuid);
- CHECK_SIZE_AND_OFFSET(ipc_perm, cgid);
--#if !defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)
-+#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \
-+ !defined(__arm__)
- /* On aarch64 glibc 2.20 and earlier provided incorrect mode field. */
-+/* On Arm glibc 2.31 and later provide a different mode field, this field is
-+ never used by libsanitizer so we can simply ignore this assert for all glibc
-+ versions. */
- CHECK_SIZE_AND_OFFSET(ipc_perm, mode);
- #endif
-
diff --git a/packages/gcc/glibc-2.31-libsanitizer-2-gcc-6.patch b/packages/gcc/glibc-2.31-libsanitizer-2-gcc-6.patch
deleted file mode 100644
index 755db173..00000000
--- a/packages/gcc/glibc-2.31-libsanitizer-2-gcc-6.patch
+++ /dev/null
@@ -1,69 +0,0 @@
-From 75003cdd23c310ec385344e8040d490e8dd6d2be Mon Sep 17 00:00:00 2001
-From: Jakub Jelinek <jakub@redhat.com>
-Date: Fri, 20 Dec 2019 17:58:35 +0100
-Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm
- bootstrap due to libsanitizer)
-
- Backported from mainline
- 2019-11-26 Jakub Jelinek <jakub@redhat.com>
- Backported for version 5.3.0 <= gcc <= 6.5.0
- 2020-06-05 John L. Jolly <john.jolly@gmail.com>
-
- PR sanitizer/92154
- * sanitizer_common/sanitizer_platform_limits_posix.h: Cherry-pick
- llvm-project revision 947f9692440836dcb8d88b74b69dd379d85974ce.
- * sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.
-
-From-SVN: r279653
----
- libsanitizer/ChangeLog | 10 ++++++++++
- .../sanitizer_platform_limits_posix.cc | 9 +++------
- .../sanitizer_platform_limits_posix.h | 15 +--------------
- 3 files changed, 14 insertions(+), 20 deletions(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-index 06a605ff4670..d823a12190c0 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-@@ -1130,12 +1130,9 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);
- #ifndef __GLIBC_PREREQ
- #define __GLIBC_PREREQ(x, y) 0
- #endif
--#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \
-- !defined(__arm__)
--/* On aarch64 glibc 2.20 and earlier provided incorrect mode field. */
--/* On Arm glibc 2.31 and later provide a different mode field, this field is
-- never used by libsanitizer so we can simply ignore this assert for all glibc
-- versions. */
-+#if !SANITIZER_LINUX || __GLIBC_PREREQ (2, 31)
-+/* glibc 2.30 and earlier provided 16-bit mode field instead of 32-bit
-+ on many architectures. */
- CHECK_SIZE_AND_OFFSET(ipc_perm, mode);
- #endif
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-index 73af92af1e8f..6a673a7c9959 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-@@ -211,20 +211,13 @@ namespace __sanitizer {
- unsigned long __unused1;
- unsigned long __unused2;
- #elif defined(__sparc__)
--# if defined(__arch64__)
- unsigned mode;
-- unsigned short __pad1;
--# else
-- unsigned short __pad1;
-- unsigned short mode;
- unsigned short __pad2;
--# endif
- unsigned short __seq;
- unsigned long long __unused1;
- unsigned long long __unused2;
- #else
-- unsigned short mode;
-- unsigned short __pad1;
-+ unsigned int mode;
- unsigned short __seq;
- unsigned short __pad2;
- #if defined(__x86_64__) && !defined(_LP64)
diff --git a/packages/gcc/glibc-2.31-libsanitizer-2-gcc-7.patch b/packages/gcc/glibc-2.31-libsanitizer-2-gcc-7.patch
deleted file mode 100644
index 07cbb3fd..00000000
--- a/packages/gcc/glibc-2.31-libsanitizer-2-gcc-7.patch
+++ /dev/null
@@ -1,69 +0,0 @@
-From 75003cdd23c310ec385344e8040d490e8dd6d2be Mon Sep 17 00:00:00 2001
-From: Jakub Jelinek <jakub@redhat.com>
-Date: Fri, 20 Dec 2019 17:58:35 +0100
-Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm
- bootstrap due to libsanitizer)
-
- Backported from mainline
- 2019-11-26 Jakub Jelinek <jakub@redhat.com>
- Backported for version 7.1.0 <= gcc <= 7.4.0
- 2020-06-05 John L. Jolly <john.jolly@gmail.com>
-
- PR sanitizer/92154
- * sanitizer_common/sanitizer_platform_limits_posix.h: Cherry-pick
- llvm-project revision 947f9692440836dcb8d88b74b69dd379d85974ce.
- * sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.
-
-From-SVN: r279653
----
- libsanitizer/ChangeLog | 10 ++++++++++
- .../sanitizer_platform_limits_posix.cc | 9 +++------
- .../sanitizer_platform_limits_posix.h | 15 +--------------
- 3 files changed, 14 insertions(+), 20 deletions(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-index 06a605ff4670..d823a12190c0 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-@@ -1156,12 +1156,9 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);
- CHECK_SIZE_AND_OFFSET(ipc_perm, gid);
- CHECK_SIZE_AND_OFFSET(ipc_perm, cuid);
- CHECK_SIZE_AND_OFFSET(ipc_perm, cgid);
--#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \
-- !defined(__arm__)
--/* On aarch64 glibc 2.20 and earlier provided incorrect mode field. */
--/* On Arm glibc 2.31 and later provide a different mode field, this field is
-- never used by libsanitizer so we can simply ignore this assert for all glibc
-- versions. */
-+#if !SANITIZER_LINUX || __GLIBC_PREREQ (2, 31)
-+/* glibc 2.30 and earlier provided 16-bit mode field instead of 32-bit
-+ on many architectures. */
- CHECK_SIZE_AND_OFFSET(ipc_perm, mode);
- #endif
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-index 73af92af1e8f..6a673a7c9959 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-@@ -211,20 +211,13 @@ namespace __sanitizer {
- unsigned long __unused1;
- unsigned long __unused2;
- #elif defined(__sparc__)
--# if defined(__arch64__)
- unsigned mode;
-- unsigned short __pad1;
--# else
-- unsigned short __pad1;
-- unsigned short mode;
- unsigned short __pad2;
--# endif
- unsigned short __seq;
- unsigned long long __unused1;
- unsigned long long __unused2;
- #else
-- unsigned short mode;
-- unsigned short __pad1;
-+ unsigned int mode;
- unsigned short __seq;
- unsigned short __pad2;
- #if defined(__x86_64__) && !defined(_LP64)
diff --git a/packages/gcc/glibc-2.31-libsanitizer-2.patch b/packages/gcc/glibc-2.31-libsanitizer-2.patch
deleted file mode 100644
index 75234436..00000000
--- a/packages/gcc/glibc-2.31-libsanitizer-2.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-From 75003cdd23c310ec385344e8040d490e8dd6d2be Mon Sep 17 00:00:00 2001
-From: Jakub Jelinek <jakub@redhat.com>
-Date: Fri, 20 Dec 2019 17:58:35 +0100
-Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm
- bootstrap due to libsanitizer)
-
- Backported from mainline
- 2019-11-26 Jakub Jelinek <jakub@redhat.com>
-
- PR sanitizer/92154
- * sanitizer_common/sanitizer_platform_limits_posix.h: Cherry-pick
- llvm-project revision 947f9692440836dcb8d88b74b69dd379d85974ce.
- * sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.
-
-From-SVN: r279653
----
- libsanitizer/ChangeLog | 10 ++++++++++
- .../sanitizer_platform_limits_posix.cc | 9 +++------
- .../sanitizer_platform_limits_posix.h | 15 +--------------
- 3 files changed, 14 insertions(+), 20 deletions(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-index 06a605ff4670..d823a12190c0 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-@@ -1156,12 +1156,9 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);
- CHECK_SIZE_AND_OFFSET(ipc_perm, gid);
- CHECK_SIZE_AND_OFFSET(ipc_perm, cuid);
- CHECK_SIZE_AND_OFFSET(ipc_perm, cgid);
--#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \
-- !defined(__arm__)
--/* On aarch64 glibc 2.20 and earlier provided incorrect mode field. */
--/* On Arm glibc 2.31 and later provide a different mode field, this field is
-- never used by libsanitizer so we can simply ignore this assert for all glibc
-- versions. */
-+#if !SANITIZER_LINUX || __GLIBC_PREREQ (2, 31)
-+/* glibc 2.30 and earlier provided 16-bit mode field instead of 32-bit
-+ on many architectures. */
- CHECK_SIZE_AND_OFFSET(ipc_perm, mode);
- #endif
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-index 73af92af1e8f..6a673a7c9959 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-@@ -211,26 +211,13 @@ namespace __sanitizer {
- u64 __unused1;
- u64 __unused2;
- #elif defined(__sparc__)
--#if defined(__arch64__)
- unsigned mode;
-- unsigned short __pad1;
--#else
-- unsigned short __pad1;
-- unsigned short mode;
- unsigned short __pad2;
--#endif
- unsigned short __seq;
- unsigned long long __unused1;
- unsigned long long __unused2;
--#elif defined(__mips__) || defined(__aarch64__) || defined(__s390x__)
-- unsigned int mode;
-- unsigned short __seq;
-- unsigned short __pad1;
-- unsigned long __unused1;
-- unsigned long __unused2;
- #else
-- unsigned short mode;
-- unsigned short __pad1;
-+ unsigned int mode;
- unsigned short __seq;
- unsigned short __pad2;
- #if defined(__x86_64__) && !defined(_LP64)
diff --git a/packages/gcc/glibc-2.31-libsanitizer-3-gcc-5.patch b/packages/gcc/glibc-2.31-libsanitizer-3-gcc-5.patch
deleted file mode 100644
index e1df265a..00000000
--- a/packages/gcc/glibc-2.31-libsanitizer-3-gcc-5.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-diff -ru a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
---- a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc 2014-09-23 17:59:53.000000000 +0000
-+++ b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc 2021-10-30 19:48:38.690007561 +0000
-@@ -358,15 +358,6 @@
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
- // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE
-- _(CYGETDEFTHRESH, WRITE, sizeof(int));
-- _(CYGETDEFTIMEOUT, WRITE, sizeof(int));
-- _(CYGETMON, WRITE, struct_cyclades_monitor_sz);
-- _(CYGETTHRESH, WRITE, sizeof(int));
-- _(CYGETTIMEOUT, WRITE, sizeof(int));
-- _(CYSETDEFTHRESH, NONE, 0);
-- _(CYSETDEFTIMEOUT, NONE, 0);
-- _(CYSETTHRESH, NONE, 0);
-- _(CYSETTIMEOUT, NONE, 0);
- _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz);
- _(EQL_ENSLAVE, WRITE, struct_ifreq_sz);
- _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz);
-diff -ru a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc 2021-10-30 19:40:51.805824323 +0000
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc 2021-10-30 19:51:13.640403192 +0000
-@@ -143,7 +143,6 @@
- #include <sys/statvfs.h>
- #include <sys/timex.h>
- #include <sys/user.h>
--#include <linux/cyclades.h>
- #include <linux/if_eql.h>
- #include <linux/if_plip.h>
- #include <linux/lp.h>
-@@ -392,7 +391,6 @@
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
- unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct);
-- unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor);
- #if EV_VERSION > (0x010000)
- unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry);
- #else
-@@ -759,15 +757,6 @@
- #endif // SANITIZER_LINUX || SANITIZER_FREEBSD
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
-- unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH;
-- unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT;
-- unsigned IOCTL_CYGETMON = CYGETMON;
-- unsigned IOCTL_CYGETTHRESH = CYGETTHRESH;
-- unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT;
-- unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH;
-- unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT;
-- unsigned IOCTL_CYSETTHRESH = CYSETTHRESH;
-- unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT;
- unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE;
- unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE;
- unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG;
-diff -ru a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h 2021-10-30 19:40:51.698824053 +0000
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h 2021-10-30 19:51:39.680469814 +0000
-@@ -875,7 +875,6 @@
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
- extern unsigned struct_ax25_parms_struct_sz;
-- extern unsigned struct_cyclades_monitor_sz;
- extern unsigned struct_input_keymap_entry_sz;
- extern unsigned struct_ipx_config_data_sz;
- extern unsigned struct_kbdiacrs_sz;
-@@ -1220,15 +1219,6 @@
- #endif // SANITIZER_LINUX || SANITIZER_FREEBSD
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
-- extern unsigned IOCTL_CYGETDEFTHRESH;
-- extern unsigned IOCTL_CYGETDEFTIMEOUT;
-- extern unsigned IOCTL_CYGETMON;
-- extern unsigned IOCTL_CYGETTHRESH;
-- extern unsigned IOCTL_CYGETTIMEOUT;
-- extern unsigned IOCTL_CYSETDEFTHRESH;
-- extern unsigned IOCTL_CYSETDEFTIMEOUT;
-- extern unsigned IOCTL_CYSETTHRESH;
-- extern unsigned IOCTL_CYSETTIMEOUT;
- extern unsigned IOCTL_EQL_EMANCIPATE;
- extern unsigned IOCTL_EQL_ENSLAVE;
- extern unsigned IOCTL_EQL_GETMASTRCFG;
diff --git a/packages/gcc/glibc-2.36-libsanitizer-gcc-10-12.patch b/packages/gcc/glibc-2.36-libsanitizer-gcc-10-12.patch
deleted file mode 100644
index 90df6b04..00000000
--- a/packages/gcc/glibc-2.36-libsanitizer-gcc-10-12.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
-index badf6a401cc..b43733033a6 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
-@@ -72,7 +72,6 @@
- #include <sys/vt.h>
- #include <linux/cdrom.h>
- #include <linux/fd.h>
--#include <linux/fs.h>
- #include <linux/hdreg.h>
- #include <linux/input.h>
- #include <linux/ioctl.h>
-@@ -822,10 +821,10 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);
- unsigned IOCTL_EVIOCGPROP = IOCTL_NOT_PRESENT;
- unsigned IOCTL_EVIOCSKEYCODE_V2 = IOCTL_NOT_PRESENT;
- #endif
-- unsigned IOCTL_FS_IOC_GETFLAGS = FS_IOC_GETFLAGS;
-- unsigned IOCTL_FS_IOC_GETVERSION = FS_IOC_GETVERSION;
-- unsigned IOCTL_FS_IOC_SETFLAGS = FS_IOC_SETFLAGS;
-- unsigned IOCTL_FS_IOC_SETVERSION = FS_IOC_SETVERSION;
-+ unsigned IOCTL_FS_IOC_GETFLAGS = _IOR('f', 1, long);
-+ unsigned IOCTL_FS_IOC_GETVERSION = _IOR('v', 1, long);
-+ unsigned IOCTL_FS_IOC_SETFLAGS = _IOW('f', 2, long);
-+ unsigned IOCTL_FS_IOC_SETVERSION = _IOW('v', 2, long);
- unsigned IOCTL_GIO_CMAP = GIO_CMAP;
- unsigned IOCTL_GIO_FONT = GIO_FONT;
- unsigned IOCTL_GIO_UNIMAP = GIO_UNIMAP;
diff --git a/packages/gcc/glibc-2.36-libsanitizer-gcc-5-9.patch b/packages/gcc/glibc-2.36-libsanitizer-gcc-5-9.patch
deleted file mode 100644
index 2cd2bc4e..00000000
--- a/packages/gcc/glibc-2.36-libsanitizer-gcc-5-9.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-index e8fce8a02..5122baa46 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-@@ -65,7 +65,6 @@
- #include <sys/vt.h>
- #include <linux/cdrom.h>
- #include <linux/fd.h>
--#include <linux/fs.h>
- #include <linux/hdreg.h>
- #include <linux/input.h>
- #include <linux/ioctl.h>
-@@ -846,10 +845,10 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);
- unsigned IOCTL_EVIOCGPROP = IOCTL_NOT_PRESENT;
- unsigned IOCTL_EVIOCSKEYCODE_V2 = IOCTL_NOT_PRESENT;
- #endif
-- unsigned IOCTL_FS_IOC_GETFLAGS = FS_IOC_GETFLAGS;
-- unsigned IOCTL_FS_IOC_GETVERSION = FS_IOC_GETVERSION;
-- unsigned IOCTL_FS_IOC_SETFLAGS = FS_IOC_SETFLAGS;
-- unsigned IOCTL_FS_IOC_SETVERSION = FS_IOC_SETVERSION;
-+ unsigned IOCTL_FS_IOC_GETFLAGS = _IOR('f', 1, long);
-+ unsigned IOCTL_FS_IOC_GETVERSION = _IOR('v', 1, long);
-+ unsigned IOCTL_FS_IOC_SETFLAGS = _IOW('f', 2, long);
-+ unsigned IOCTL_FS_IOC_SETVERSION = _IOW('v', 2, long);
- unsigned IOCTL_GIO_CMAP = GIO_CMAP;
- unsigned IOCTL_GIO_FONT = GIO_FONT;
- unsigned IOCTL_GIO_UNIMAP = GIO_UNIMAP;
diff --git a/packages/gcc/package.py b/packages/gcc/package.py
deleted file mode 100644
index 4eb88a25..00000000
--- a/packages/gcc/package.py
+++ /dev/null
@@ -1,1114 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-import glob
-import itertools
-import os
-import re
-import sys
-
-from archspec.cpu import UnsupportedMicroarchitecture
-
-import llnl.util.tty as tty
-from llnl.util.lang import classproperty
-
-import spack.platforms
-import spack.util.executable
-from spack.build_environment import dso_suffix
-from spack.operating_systems.mac_os import macos_sdk_path, macos_version
-from spack.package import *
-
-
-class Gcc(AutotoolsPackage, GNUMirrorPackage):
- """The GNU Compiler Collection includes front ends for C, C++, Objective-C,
- Fortran, Ada, and Go, as well as libraries for these languages."""
-
- homepage = "https://gcc.gnu.org"
- gnu_mirror_path = "gcc/gcc-9.2.0/gcc-9.2.0.tar.xz"
- git = "git://gcc.gnu.org/git/gcc.git"
- list_url = "https://ftp.gnu.org/gnu/gcc/"
- list_depth = 1
- keep_werror = "all"
-
- maintainers("michaelkuhn", "alalazo")
-
- version("master", branch="master")
-
- version("13.2.0", sha256="e275e76442a6067341a27f04c5c6b83d8613144004c0413528863dc6b5c743da")
- version("13.1.0", sha256="61d684f0aa5e76ac6585ad8898a2427aade8979ed5e7f85492286c4dfc13ee86")
-
- version("12.3.0", sha256="949a5d4f99e786421a93b532b22ffab5578de7321369975b91aec97adfda8c3b")
- version("12.2.0", sha256="e549cf9cf3594a00e27b6589d4322d70e0720cdd213f39beb4181e06926230ff")
- version("12.1.0", sha256="62fd634889f31c02b64af2c468f064b47ad1ca78411c45abe6ac4b5f8dd19c7b")
-
- version("11.4.0", sha256="3f2db222b007e8a4a23cd5ba56726ef08e8b1f1eb2055ee72c1402cea73a8dd9")
- version("11.3.0", sha256="b47cf2818691f5b1e21df2bb38c795fac2cfbd640ede2d0a5e1c89e338a3ac39")
- version("11.2.0", sha256="d08edc536b54c372a1010ff6619dd274c0f1603aa49212ba20f7aa2cda36fa8b")
- version("11.1.0", sha256="4c4a6fb8a8396059241c2e674b85b351c26a5d678274007f076957afa1cc9ddf")
-
- version("10.5.0", sha256="25109543fdf46f397c347b5d8b7a2c7e5694a5a51cce4b9c6e1ea8a71ca307c1")
- version("10.4.0", sha256="c9297d5bcd7cb43f3dfc2fed5389e948c9312fd962ef6a4ce455cff963ebe4f1")
- version("10.3.0", sha256="64f404c1a650f27fc33da242e1f2df54952e3963a49e06e73f6940f3223ac344")
- version("10.2.0", sha256="b8dd4368bb9c7f0b98188317ee0254dd8cc99d1e3a18d0ff146c855fe16c1d8c")
- version("10.1.0", sha256="b6898a23844b656f1b68691c5c012036c2e694ac4b53a8918d4712ad876e7ea2")
-
- version("9.5.0", sha256="27769f64ef1d4cd5e2be8682c0c93f9887983e6cfd1a927ce5a0a2915a95cf8f")
- version("9.4.0", sha256="c95da32f440378d7751dd95533186f7fc05ceb4fb65eb5b85234e6299eb9838e")
- version("9.3.0", sha256="71e197867611f6054aa1119b13a0c0abac12834765fe2d81f35ac57f84f742d1")
- version("9.2.0", sha256="ea6ef08f121239da5695f76c9b33637a118dcf63e24164422231917fa61fb206")
- version("9.1.0", sha256="79a66834e96a6050d8fe78db2c3b32fb285b230b855d0a66288235bc04b327a0")
-
- version("8.5.0", sha256="d308841a511bb830a6100397b0042db24ce11f642dab6ea6ee44842e5325ed50")
- version("8.4.0", sha256="e30a6e52d10e1f27ed55104ad233c30bd1e99cfb5ff98ab022dc941edd1b2dd4")
- version("8.3.0", sha256="64baadfe6cc0f4947a84cb12d7f0dfaf45bb58b7e92461639596c21e02d97d2c")
- version("8.2.0", sha256="196c3c04ba2613f893283977e6011b2345d1cd1af9abeac58e916b1aab3e0080")
- version("8.1.0", sha256="1d1866f992626e61349a1ccd0b8d5253816222cdc13390dcfaa74b093aa2b153")
-
- version("7.5.0", sha256="b81946e7f01f90528a1f7352ab08cc602b9ccc05d4e44da4bd501c5a189ee661")
- version("7.4.0", sha256="eddde28d04f334aec1604456e536416549e9b1aa137fc69204e65eb0c009fe51")
- version("7.3.0", sha256="832ca6ae04636adbb430e865a1451adf6979ab44ca1c8374f61fba65645ce15c")
- version("7.2.0", sha256="1cf7adf8ff4b5aa49041c8734bbcf1ad18cc4c94d0029aae0f4e48841088479a")
- version("7.1.0", sha256="8a8136c235f64c6fef69cac0d73a46a1a09bb250776a050aec8f9fc880bebc17")
-
- version("6.5.0", sha256="7ef1796ce497e89479183702635b14bb7a46b53249209a5e0f999bebf4740945")
- version("6.4.0", sha256="850bf21eafdfe5cd5f6827148184c08c4a0852a37ccf36ce69855334d2c914d4")
- version("6.3.0", sha256="f06ae7f3f790fbf0f018f6d40e844451e6bc3b7bc96e128e63b09825c1f8b29f")
- version("6.2.0", sha256="9944589fc722d3e66308c0ce5257788ebd7872982a718aa2516123940671b7c5")
- version("6.1.0", sha256="09c4c85cabebb971b1de732a0219609f93fc0af5f86f6e437fd8d7f832f1a351")
-
- version("5.5.0", sha256="530cea139d82fe542b358961130c69cfde8b3d14556370b65823d2f91f0ced87")
- version("5.4.0", sha256="608df76dec2d34de6558249d8af4cbee21eceddbcb580d666f7a5a583ca3303a")
- version("5.3.0", sha256="b84f5592e9218b73dbae612b5253035a7b34a9a1f7688d2e1bfaaf7267d5c4db")
- version("5.2.0", sha256="5f835b04b5f7dd4f4d2dc96190ec1621b8d89f2dc6f638f9f8bc1b1014ba8cad")
- version("5.1.0", sha256="b7dafdf89cbb0e20333dbf5b5349319ae06e3d1a30bf3515b5488f7e89dca5ad")
-
- version("4.9.4", sha256="6c11d292cd01b294f9f84c9a59c230d80e9e4a47e5c6355f046bb36d4f358092")
- version("4.9.3", sha256="2332b2a5a321b57508b9031354a8503af6fdfb868b8c1748d33028d100a8b67e")
- version("4.9.2", sha256="2020c98295856aa13fda0f2f3a4794490757fc24bcca918d52cc8b4917b972dd")
- version("4.9.1", sha256="d334781a124ada6f38e63b545e2a3b8c2183049515a1abab6d513f109f1d717e")
- version("4.8.5", sha256="22fb1e7e0f68a63cee631d85b20461d1ea6bda162f03096350e38c8d427ecf23")
- version("4.8.4", sha256="4a80aa23798b8e9b5793494b8c976b39b8d9aa2e53cd5ed5534aff662a7f8695")
- version("4.7.4", sha256="92e61c6dc3a0a449e62d72a38185fda550168a86702dea07125ebd3ec3996282")
- version("4.6.4", sha256="35af16afa0b67af9b8eb15cafb76d2bc5f568540552522f5dc2c88dd45d977e8")
- version("4.5.4", sha256="eef3f0456db8c3d992cbb51d5d32558190bc14f3bc19383dd93acc27acc6befc")
-
- # We specifically do not add 'all' variant here because:
- # (i) Ada, D, Go, Jit, and Objective-C++ are not default languages.
- # In that respect, the name 'all' is rather misleading.
- # (ii) Languages other than c,c++,fortran are prone to configure bug in GCC
- # For example, 'java' appears to ignore custom location of zlib
- # (iii) meaning of 'all' changes with GCC version, i.e. 'java' is not part
- # of gcc7. Correctly specifying conflicts() and depends_on() in such a
- # case is a PITA.
- #
- # Also note that some languages get enabled by the configure scripts even if not listed in the
- # arguments. For example, c++ is enabled when the bootstrapping is enabled and lto is enabled
- # when the link time optimization support is enabled.
- variant(
- "languages",
- default="c,c++,fortran",
- values=(
- "ada",
- "brig",
- "c",
- "c++",
- "d",
- "fortran",
- "go",
- "java",
- "jit",
- "lto",
- "objc",
- "obj-c++",
- ),
- multi=True,
- description="Compilers and runtime libraries to build",
- )
- variant("binutils", default=False, description="Build via binutils")
- variant(
- "piclibs", default=False, description="Build PIC versions of libgfortran.a and libstdc++.a"
- )
- variant("strip", default=False, description="Strip executables to reduce installation size")
- variant("nvptx", default=False, description="Target nvptx offloading to NVIDIA GPUs")
- variant("bootstrap", default=True, description="Enable 3-stage bootstrap")
- variant(
- "graphite", default=False, description="Enable Graphite loop optimizations (requires ISL)"
- )
- variant(
- "build_type",
- default="RelWithDebInfo",
- values=("Debug", "Release", "RelWithDebInfo", "MinSizeRel"),
- description="CMake-like build type. "
- "Debug: -O0 -g; Release: -O3; "
- "RelWithDebInfo: -O2 -g; MinSizeRel: -Os",
- )
- variant(
- "profiled",
- default=False,
- description="Use Profile Guided Optimization",
- when="+bootstrap %gcc",
- )
-
- depends_on("flex", type="build", when="@master")
-
- # https://gcc.gnu.org/install/prerequisites.html
- depends_on("gmp@4.3.2:")
- # mawk is not sufficient for go support
- depends_on("gawk@3.1.5:", type="build")
- depends_on("texinfo@4.7:", type="build")
- depends_on("libtool", type="build")
- # dependencies required for git versions
- depends_on("m4@1.4.6:", when="@master", type="build")
- depends_on("automake@1.15.1:", when="@master", type="build")
- depends_on("autoconf@2.69:", when="@master", type="build")
-
- depends_on("gmake@3.80:", type="build")
- depends_on("perl@5", type="build")
-
- # GCC 7.3 does not compile with newer releases on some platforms, see
- # https://github.com/spack/spack/issues/6902#issuecomment-433030376
- depends_on("mpfr@2.4.2:3.1.6", when="@:9.9")
- depends_on("mpfr@3.1.0:", when="@10:")
- depends_on("mpc@1.0.1:", when="@4.5:")
- # Already released GCC versions do not support any newer version of ISL
- # GCC 5.4 https://github.com/spack/spack/issues/6902#issuecomment-433072097
- # GCC 7.3 https://github.com/spack/spack/issues/6902#issuecomment-433030376
- # GCC 9+ https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86724
- with when("+graphite"):
- depends_on("isl@0.14", when="@5.0:5.2")
- depends_on("isl@0.15", when="@5.3:5.9")
- depends_on("isl@0.15:0.18", when="@6:8.9")
- depends_on("isl@0.15:0.20", when="@9:9.9")
- depends_on("isl@0.15:", when="@10:")
-
- depends_on("zlib-api", when="@6:")
- depends_on("zstd", when="@10:")
- depends_on("diffutils", type="build")
- depends_on("iconv", when="platform=darwin")
- depends_on("gnat", when="languages=ada")
- depends_on(
- "binutils+gas+ld+plugins~libiberty", when="+binutils", type=("build", "link", "run")
- )
- depends_on("zip", type="build", when="languages=java")
-
- # The server is sometimes a bit slow to respond
- timeout = {"timeout": 60}
-
- # TODO: integrate these libraries.
- # depends_on('ppl')
- # depends_on('cloog')
-
- # https://gcc.gnu.org/install/test.html
- depends_on("dejagnu@1.4.4", type="test")
- depends_on("expect", type="test")
- depends_on("tcl", type="test")
- depends_on("autogen@5.5.4:", type="test")
- depends_on("guile@1.4.1:", type="test")
-
- # See https://go.dev/doc/install/gccgo#Releases
- with when("languages=go"):
- provides("go-or-gccgo-bootstrap@:1.0", when="@4.7.1:")
- provides("go-or-gccgo-bootstrap@:1.2", when="@4.9:")
- provides("go-or-gccgo-bootstrap@:1.4", when="@5:")
- provides("go-or-gccgo-bootstrap@:1.6.1", when="@6:")
- provides("go-or-gccgo-bootstrap@:1.8.1", when="@7:")
- provides("go-or-gccgo-bootstrap@:1.10.1", when="@8:")
- provides("go-or-gccgo-bootstrap@:1.12.2", when="@9:")
- provides("go-or-gccgo-bootstrap@:1.14.6", when="@10:")
- provides("go-or-gccgo-bootstrap@1.16.3:1.16.5", when="@11:")
-
- provides("golang@:1.0", when="@4.7.1:")
- provides("golang@:1.2", when="@4.9:")
- provides("golang@:1.4", when="@5:")
- provides("golang@:1.6.1", when="@6:")
- provides("golang@:1.8.1", when="@7:")
- provides("golang@:1.10.1", when="@8:")
- provides("golang@:1.12.2", when="@9:")
- provides("golang@:1.14.6", when="@10:")
- provides("golang@1.16.3:1.16.5", when="@11:")
-
- # GCC 4.7.1 added full support for the Go 1.x programming language.
- conflicts("@:4.7.0")
-
- # Go is not supported on macOS
- conflicts("platform=darwin", msg="GCC cannot build Go support on MacOS")
-
- # For a list of valid languages for a specific release,
- # run the following command in the GCC source directory:
- # $ grep ^language= gcc/*/config-lang.in
- # See https://gcc.gnu.org/install/configure.html
-
- # Support for processing BRIG 1.0 files was added in GCC 7
- # BRIG is a binary format for HSAIL:
- # (Heterogeneous System Architecture Intermediate Language).
- # See https://gcc.gnu.org/gcc-7/changes.html
- conflicts("languages=brig", when="@:6")
-
- # BRIG does not seem to be supported on macOS
- conflicts("languages=brig", when="platform=darwin")
-
- # GCC 4.8 added a 'c' language. I'm sure C was always built,
- # but this is the first version that accepts 'c' as a valid language.
- conflicts("languages=c", when="@:4.7")
-
- # The GCC Java frontend and associated libjava runtime library
- # have been removed from GCC as of GCC 7.
- # See https://gcc.gnu.org/gcc-7/changes.html
- conflicts("languages=java", when="@7:")
-
- # GCC 5 added the ability to build GCC as a Just-In-Time compiler.
- # See https://gcc.gnu.org/gcc-5/changes.html
- conflicts("languages=jit", when="@:4")
-
- with when("languages=d"):
- # The very first version of GDC that became part of GCC already supported version 2.076 of
- # the language and runtime.
- # See https://wiki.dlang.org/GDC#Status
- provides("D@2")
-
- # Support for the D programming language has been added to GCC 9.
- # See https://gcc.gnu.org/gcc-9/changes.html#d
- conflicts("@:8", msg="support for D has been added in GCC 9.1")
-
- # Versions of GDC prior to 12 can be built with an ISO C++11 compiler. Starting version 12,
- # the D frontend requires a working GDC. Moreover, it is strongly recommended to use an
- # older version of GDC to build GDC.
- # See https://gcc.gnu.org/install/prerequisites.html#GDC-prerequisite
- with when("@12:"):
- # All versions starting 12 have to be built GCC:
- requires("%gcc")
-
- # And it has to be GCC older than the version we build:
- vv = ["11", "12.1.0", "12.2.0"]
- for prev_v, curr_v in zip(vv, vv[1:]):
- conflicts(
- "%gcc@{0}:".format(curr_v),
- when="@{0}".format(curr_v),
- msg="'gcc@{0} languages=d' requires '%gcc@:{1}' "
- "with the D language support".format(curr_v, prev_v),
- )
-
- # In principle, it is possible to have GDC even with GCC 5.
- # See https://github.com/D-Programming-GDC/gdc
- # We, however, require at least the oldest version that officially supports GDC. It is
- # also a good opportunity to tell the users that they need a working GDC:
- conflicts(
- "%gcc@:8",
- msg="'gcc@12: languages=d' requires '%gcc@9:' with the D language support",
- )
-
- with when("+nvptx"):
- depends_on("cuda")
- resource(
- name="newlib",
- url="ftp://sourceware.org/pub/newlib/newlib-3.0.0.20180831.tar.gz",
- sha256="3ad3664f227357df15ff34e954bfd9f501009a647667cd307bf0658aefd6eb5b",
- destination="newlibsource",
- fetch_options=timeout,
- )
- # nvptx-tools does not seem to work as a dependency,
- # but does fine when the source is inside the gcc build directory
- # nvptx-tools doesn't have any releases, so grabbing the last commit
- resource(
- name="nvptx-tools",
- git="https://github.com/MentorEmbedded/nvptx-tools",
- commit="d0524fbdc86dfca068db5a21cc78ac255b335be5",
- )
- # NVPTX offloading supported in 7 and later by limited languages
- conflicts("@:6", msg="NVPTX only supported in gcc 7 and above")
- conflicts("languages=ada")
- conflicts("languages=brig")
- conflicts("languages=go")
- conflicts("languages=java")
- conflicts("languages=jit")
- conflicts("languages=objc")
- conflicts("languages=obj-c++")
- conflicts("languages=d")
- # NVPTX build disables bootstrap
- conflicts("+bootstrap")
-
- # Binutils can't build ld on macOS
- conflicts("+binutils", when="platform=darwin")
-
- # Bootstrap comparison failure:
- # see https://github.com/spack/spack/issues/23296
- # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100340
- # on XCode 12.5
- conflicts("+bootstrap", when="@:11.1 %apple-clang@12.0.5")
-
- # aarch64/M1 is supported in GCC 11.3-12.2 and 13
- requires(
- "@11.3,12.2,13.1:",
- when="target=aarch64: platform=darwin",
- msg="Only GCC 11.3-12.2, 13.1+ support macOS M1 (aarch64)",
- )
-
- # Newer binutils than RHEL's is required to run `as` on some instructions
- # generated by new GCC (see https://github.com/spack/spack/issues/12235)
- conflicts("~binutils", when="@7: os=rhel6", msg="New GCC cannot use system assembler on RHEL6")
- # Ditto for RHEL7/8: OpenBLAS uses flags which the RHEL system-binutils don't have:
- # https://github.com/xianyi/OpenBLAS/issues/3805#issuecomment-1319878852
- conflicts(
- "~binutils", when="@10: os=rhel7", msg="gcc: Add +binutils - preinstalled as might be old"
- )
- conflicts(
- "~binutils", when="@10: os=rhel8", msg="gcc: Add +binutils - preinstalled as might be old"
- )
-
- # GCC 11 requires GCC 4.8 or later (https://gcc.gnu.org/gcc-11/changes.html)
- conflicts("%gcc@:4.7", when="@11:")
-
- # https://github.com/iains/gcc-12-branch/issues/6
- conflicts("@:12", when="%apple-clang@14:14.0")
-
- if sys.platform == "darwin":
- # Fix parallel build on APFS filesystem
- # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81797
- if macos_version() >= Version("10.13"):
- patch("darwin/apfs.patch", when="@5.5.0,6.1:6.4,7.1:7.3")
- # from homebrew via macports
- # https://trac.macports.org/ticket/56502#no1
- # see also: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=83531
- patch("darwin/headers-10.13-fix.patch", when="@5.5.0")
- if macos_version() >= Version("10.14"):
- # Fix system headers for Mojave SDK:
- # https://github.com/Homebrew/homebrew-core/pull/39041
- patch(
- "https://raw.githubusercontent.com/Homebrew/formula-patches/b8b8e65e/gcc/8.3.0-xcode-bug-_Atomic-fix.patch",
- sha256="33ee92bf678586357ee8ab9d2faddf807e671ad37b97afdd102d5d153d03ca84",
- when="@6:8.3",
- )
- if macos_version() >= Version("10.15"):
- # Fix system headers for Catalina SDK
- # (otherwise __OSX_AVAILABLE_STARTING ends up undefined)
- patch(
- "https://raw.githubusercontent.com/Homebrew/formula-patches/b8b8e65e/gcc/9.2.0-catalina.patch",
- sha256="0b8d14a7f3c6a2f0d2498526e86e088926671b5da50a554ffa6b7f73ac4f132b",
- when="@9.2.0",
- )
-
- # See https://raw.githubusercontent.com/Homebrew/homebrew-core/3b7db4457ac64a31e3bbffc54b04c4bd824a4a4a/Formula/gcc.rb
- patch(
- "https://github.com/iains/gcc-darwin-arm64/commit/20f61faaed3b335d792e38892d826054d2ac9f15.patch?full_index=1",
- sha256="c0605179a856ca046d093c13cea4d2e024809ec2ad4bf3708543fc3d2e60504b",
- when="@11.2.0",
- )
-
- # Apple M1 support, created from branch of Darwin maintainer for GCC:
- # https://github.com/iains/gcc-11-branch
- patch(
- "https://raw.githubusercontent.com/Homebrew/formula-patches/22dec3fc/gcc/gcc-11.3.0-arm.diff",
- sha256="e02006b7ec917cc1390645d95735a6a866caed0dfe506d5bef742f7862cab218",
- when="@11.3.0 target=aarch64:",
- )
- # https://github.com/iains/gcc-12-branch
- patch(
- "https://raw.githubusercontent.com/Homebrew/formula-patches/76677f2b/gcc/gcc-12.1.0-arm.diff",
- sha256="a000f1d9cb1dd98c7c4ef00df31435cd5d712d2f9d037ddc044f8bf82a16cf35",
- when="@12.1.0 target=aarch64:",
- )
- patch(
- "https://raw.githubusercontent.com/Homebrew/formula-patches/1d184289/gcc/gcc-12.2.0-arm.diff",
- sha256="a7843b5c6bf1401e40c20c72af69c8f6fc9754ae980bb4a5f0540220b3dcb62d",
- when="@12.2.0 target=aarch64:",
- )
- patch(
- "https://raw.githubusercontent.com/Homebrew/formula-patches/5c206c47/gcc/gcc-13.1.0.diff",
- sha256="cb4e8a89387f748a744da0273025d0dc2e3c76780cc390b18ada704676afea11",
- when="@13.1.0 target=aarch64:",
- )
- patch(
- "https://raw.githubusercontent.com/Homebrew/formula-patches/3c5cbc8e9cf444a1967786af48e430588e1eb481/gcc/gcc-13.2.0.diff",
- sha256="2df7ef067871a30b2531a2013b3db661ec9e61037341977bfc451e30bf2c1035",
- when="@13.2.0 target=aarch64:",
- )
- conflicts("+bootstrap", when="@11.3.0,13.1: target=aarch64:")
-
- # Use -headerpad_max_install_names in the build,
- # otherwise updated load commands won't fit in the Mach-O header.
- # This is needed because `gcc` avoids the superenv shim.
- patch("darwin/gcc-7.1.0-headerpad.patch", when="@5:11.2")
- patch("darwin/gcc-6.1.0-jit.patch", when="@5:7")
- patch("darwin/gcc-4.9.patch1", when="@4.9.0:4.9.3")
- patch("darwin/gcc-4.9.patch2", when="@4.9.0:4.9.3")
-
- # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=92061
- patch("darwin/clang13.patch", when="@:11.1 %apple-clang@13")
-
- patch("piclibs.patch", when="+piclibs")
- patch("gcc-backport.patch", when="@4.7:4.9.3,5:5.3")
-
- # Backport libsanitizer patch for glibc >= 2.31 and 5.3.0 <= gcc <= 9.2.0
- # https://bugs.gentoo.org/708346
- patch("glibc-2.31-libsanitizer-1.patch", when="@7.1.0:7.5.0,8.1.0:8.3.0,9.0.0:9.2.0")
- patch("glibc-2.31-libsanitizer-1-gcc-6.patch", when="@5.3.0:5.5.0,6.1.0:6.5.0")
- patch("glibc-2.31-libsanitizer-2.patch", when="@8.1.0:8.3.0,9.0.0:9.2.0")
- patch("glibc-2.31-libsanitizer-2-gcc-6.patch", when="@5.3.0:5.5.0,6.1.0:6.5.0")
- patch("glibc-2.31-libsanitizer-2-gcc-7.patch", when="@7.1.0:7.5.0")
- patch(
- "patch-2b40941d23b1570cdd90083b58fa0f66aa58c86e.patch",
- when="@6.5.0,7.4.0:7.5.0,8.2.0:9.3.0",
- )
- patch("patch-745dae5923aba02982563481d75a21595df22ff8.patch", when="@10.1.0:10.3.0,11.1.0")
-
- # Backport libsanitizer patch for glibc >= 2.36
- # https://reviews.llvm.org/D129471
- patch("glibc-2.36-libsanitizer-gcc-5-9.patch", when="@5.1:5.5,6.1:6.5,7.1:7.5,8.1:8.5,9.1:9.5")
- patch("glibc-2.36-libsanitizer-gcc-10-12.patch", when="@10.1:10.4,11.1:11.3,12.1.0")
-
- # Older versions do not compile with newer versions of glibc
- # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81712
- patch("ucontext_t.patch", when="@4.9,5.1:5.4,6.1:6.4,7.1")
- patch("ucontext_t-java.patch", when="@4.9,5.1:5.4,6.1:6.4 languages=java")
- # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81066
- patch("stack_t-4.9.patch", when="@4.9")
- patch("stack_t.patch", when="@5.1:5.4,6.1:6.4,7.1")
- # https://bugs.busybox.net/show_bug.cgi?id=10061
- patch("signal.patch", when="@4.9,5.1:5.4")
- # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85835
- patch("sys_ustat.h.patch", when="@5.0:6.4,7.0:7.3,8.1")
- patch("sys_ustat-4.9.patch", when="@4.9")
-
- # this patch removes cylades support from gcc-5 and allows gcc-5 to be built
- # with newer glibc versions.
- patch("glibc-2.31-libsanitizer-3-gcc-5.patch", when="@5.3.0:5.5.0")
-
- # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=95005
- patch("zstd.patch", when="@10")
-
- # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100102
- patch("patch-fc930b3010bd0de899a3da3209eab20664ddb703.patch", when="@10.1:10.3")
- patch("patch-f1feb74046e0feb0596b93bbb822fae02940a90e.patch", when="@11.1")
-
- # libstdc++: Fix inconsistent noexcept-specific for valarray begin/end
- # begin EBRAINS (modified)
- patch(
- "https://github.com/gcc-mirror/gcc/commit/423cd47cfc9640ba3d6811b780e8a0b94b704dcb.patch?full_index=1",
- sha256="0d136226eb07bc43f1b15284f48bd252e3748a0426b5d7ac9084ebc406e15490",
- when="@9.5.0,10.4.0",
- )
- # end EBRAINS
-
- build_directory = "spack-build"
-
- @classproperty
- def executables(cls):
- names = [r"gcc", r"[^\w]?g\+\+", r"gfortran", r"gdc", r"gccgo"]
- suffixes = [r"", r"-mp-\d+\.\d", r"-\d+\.\d", r"-\d+", r"\d\d"]
- return [r"".join(x) for x in itertools.product(names, suffixes)]
-
- @classmethod
- def filter_detected_exes(cls, prefix, exes_in_prefix):
- result = []
- for exe in exes_in_prefix:
- # On systems like Ubuntu we might get multiple executables
- # with the string "gcc" in them. See:
- # https://helpmanual.io/packages/apt/gcc/
- basename = os.path.basename(exe)
- substring_to_be_filtered = [
- "c99-gcc",
- "c89-gcc",
- "-nm",
- "-ar",
- "ranlib",
- "clang", # clang++ matches g++ -> clan[g++]
- ]
- if any(x in basename for x in substring_to_be_filtered):
- continue
- # Filter out links in favor of real executables on
- # all systems but Cray
- host_platform = str(spack.platforms.host())
- if os.path.islink(exe) and host_platform != "cray":
- continue
-
- result.append(exe)
-
- return result
-
- @classmethod
- def determine_version(cls, exe):
- try:
- output = spack.compiler.get_compiler_version_output(exe, "--version")
- except Exception:
- output = ""
- # Apple's gcc is actually apple clang, so skip it.
- # Users can add it manually to compilers.yaml at their own risk.
- if "Apple" in output:
- return None
-
- version_regex = re.compile(r"([\d\.]+)")
- for vargs in ("-dumpfullversion", "-dumpversion"):
- try:
- output = spack.compiler.get_compiler_version_output(exe, vargs)
- match = version_regex.search(output)
- if match:
- return match.group(1)
- except spack.util.executable.ProcessError:
- pass
- except Exception as e:
- tty.debug(e)
-
- return None
-
- @classmethod
- def determine_variants(cls, exes, version_str):
- languages, compilers = set(), {}
- # There are often at least two copies (not symlinks) of each compiler executable in the
- # same directory: one with a canonical name, e.g. "gfortran", and another one with the
- # target prefix, e.g. "x86_64-pc-linux-gnu-gfortran". There also might be a copy of "gcc"
- # with the version suffix, e.g. "x86_64-pc-linux-gnu-gcc-6.3.0". To ensure the consistency
- # of values in the "compilers" dictionary (i.e. we prefer all of them to reference copies
- # with canonical names if possible), we iterate over the executables in the reversed sorted
- # order:
- for exe in sorted(exes, reverse=True):
- basename = os.path.basename(exe)
- if "g++" in basename:
- languages.add("c++")
- compilers["cxx"] = exe
- elif "gfortran" in basename:
- languages.add("fortran")
- compilers["fortran"] = exe
- elif "gcc" in basename:
- languages.add("c")
- compilers["c"] = exe
- elif "gccgo" in basename:
- languages.add("go")
- compilers["go"] = exe
- elif "gdc" in basename:
- languages.add("d")
- compilers["d"] = exe
- variant_str = "languages={0}".format(",".join(languages))
- return variant_str, {"compilers": compilers}
-
- @classmethod
- def validate_detected_spec(cls, spec, extra_attributes):
- # For GCC 'compilers' is a mandatory attribute
- msg = 'the extra attribute "compilers" must be set for ' 'the detected spec "{0}"'.format(
- spec
- )
- assert "compilers" in extra_attributes, msg
-
- compilers = extra_attributes["compilers"]
- for constraint, key in {
- "languages=c": "c",
- "languages=c++": "cxx",
- "languages=d": "d",
- "languages=fortran": "fortran",
- }.items():
- if spec.satisfies(constraint):
- msg = "{0} not in {1}"
- assert key in compilers, msg.format(key, spec)
-
- @property
- def cc(self):
- msg = "cannot retrieve C compiler [spec is not concrete]"
- assert self.spec.concrete, msg
- if self.spec.external:
- return self.spec.extra_attributes["compilers"].get("c", None)
- result = None
- if "languages=c" in self.spec:
- result = str(self.spec.prefix.bin.gcc)
- return result
-
- @property
- def cxx(self):
- msg = "cannot retrieve C++ compiler [spec is not concrete]"
- assert self.spec.concrete, msg
- if self.spec.external:
- return self.spec.extra_attributes["compilers"].get("cxx", None)
- result = None
- if "languages=c++" in self.spec:
- result = os.path.join(self.spec.prefix.bin, "g++")
- return result
-
- @property
- def fortran(self):
- msg = "cannot retrieve Fortran compiler [spec is not concrete]"
- assert self.spec.concrete, msg
- if self.spec.external:
- return self.spec.extra_attributes["compilers"].get("fortran", None)
- result = None
- if "languages=fortran" in self.spec:
- result = str(self.spec.prefix.bin.gfortran)
- return result
-
- def url_for_version(self, version):
- # This function will be called when trying to fetch from url, before
- # mirrors are tried. It takes care of modifying the suffix of gnu
- # mirror path so that Spack will also look for the correct file in
- # the mirrors
- if (version < Version("6.4.0") and version != Version("5.5.0")) or version == Version(
- "7.1.0"
- ):
- self.gnu_mirror_path = self.gnu_mirror_path.replace("xz", "bz2")
- return super().url_for_version(version)
-
- def patch(self):
- spec = self.spec
- prefix = self.spec.prefix
-
- # Fix a standard header file for OS X Yosemite that
- # is GCC incompatible by replacing non-GCC compliant macros
- if "yosemite" in spec.architecture:
- if os.path.isfile("/usr/include/dispatch/object.h"):
- new_dispatch_dir = join_path(prefix, "include", "dispatch")
- mkdirp(new_dispatch_dir)
- new_header = join_path(new_dispatch_dir, "object.h")
- install("/usr/include/dispatch/object.h", new_header)
- filter_file(
- r"typedef void \(\^dispatch_block_t\)\(void\)",
- "typedef void* dispatch_block_t",
- new_header,
- )
-
- # Use installed libz
- if self.version >= Version("6"):
- filter_file(
- "@zlibdir@", "-L{0}".format(spec["zlib-api"].prefix.lib), "gcc/Makefile.in"
- )
- filter_file(
- "@zlibinc@", "-I{0}".format(spec["zlib-api"].prefix.include), "gcc/Makefile.in"
- )
-
- if spec.satisfies("+nvptx"):
- # backport of 383400a6078d upstream to allow support of cuda@11:
- filter_file(
- '#define ASM_SPEC "%{misa=*:-m %*}"',
- '#define ASM_SPEC "%{misa=*:-m %*; :-m sm_35}"',
- "gcc/config/nvptx/nvptx.h",
- string=True,
- )
- filter_file(
- "Target RejectNegative ToLower Joined "
- "Enum(ptx_isa) Var(ptx_isa_option) Init(PTX_ISA_SM30)",
- "Target RejectNegative ToLower Joined "
- "Enum(ptx_isa) Var(ptx_isa_option) Init(PTX_ISA_SM35)",
- "gcc/config/nvptx/nvptx.opt",
- string=True,
- )
- self.build_optimization_config()
-
- def get_common_target_flags(self, spec):
- """Get the right (but pessimistic) architecture specific flags supported by
- both host gcc and to-be-built gcc. For example: gcc@7 %gcc@12 target=znver3
- should pick -march=znver1, since that's what gcc@7 supports."""
- archs = [spec.target] + spec.target.ancestors
- for arch in archs:
- try:
- return arch.optimization_flags("gcc", spec.version)
- except UnsupportedMicroarchitecture:
- pass
- # no arch specific flags in common, unlikely to happen.
- return ""
-
- def build_optimization_config(self):
- """Write a config/spack.mk file with sensible optimization flags, taking into
- account bootstrapping subtleties."""
- build_type_flags = {
- "Debug": "-O0 -g",
- "Release": "-O3",
- "RelWithDebInfo": "-O2 -g",
- "MinSizeRel": "-Os",
- }
-
- # Generic optimization flags.
- flags = build_type_flags[self.spec.variants["build_type"].value]
-
- # Pessimistic target specific flags. For example, when building
- # gcc@11 %gcc@7 on znver3, Spack will fix the target to znver1 during
- # concretization, so we'll stick to that. The other way around however can
- # result in compilation errors, when gcc@7 is built with gcc@11, and znver3
- # is taken as a the target, which gcc@7 doesn't support.
- # Note we're not adding this for aarch64 because of
- # https://github.com/spack/spack/issues/31184
- if "+bootstrap %gcc" in self.spec and self.spec.target.family != "aarch64":
- flags += " " + self.get_common_target_flags(self.spec)
-
- if "+bootstrap" in self.spec:
- variables = ["BOOT_CFLAGS", "CFLAGS_FOR_TARGET", "CXXFLAGS_FOR_TARGET"]
- else:
- variables = ["CFLAGS", "CXXFLAGS"]
-
- # Redefine a few variables without losing other defaults:
- # BOOT_CFLAGS = $(filter-out -O% -g%, $(BOOT_CFLAGS)) -O3
- # This makes sure that build_type=Release is really -O3, not -O3 -g.
- fmt_string = "{} := $(filter-out -O% -g%, $({})) {}\n"
- with open("config/spack.mk", "w") as f:
- for var in variables:
- f.write(fmt_string.format(var, var, flags))
- # Improve the build time for stage 2 a bit by enabling -O1 in stage 1.
- # Note: this is ignored under ~bootstrap.
- f.write("STAGE1_CFLAGS += -O1\n")
-
- # https://gcc.gnu.org/install/configure.html
- def configure_args(self):
- spec = self.spec
-
- # Generic options to compile GCC
- options = [
- # Distributor options
- "--with-pkgversion=Spack GCC",
- "--with-bugurl=https://github.com/spack/spack/issues",
- # Xcode 10 dropped 32-bit support
- "--disable-multilib",
- "--enable-languages={0}".format(",".join(spec.variants["languages"].value)),
- # Drop gettext dependency
- "--disable-nls",
- ]
-
- # Avoid excessive realpath/stat calls for every system header
- # by making -fno-canonical-system-headers the default.
- if self.version >= Version("4.8.0"):
- options.append("--disable-canonical-system-headers")
-
- # Use installed libz
- if self.version >= Version("6"):
- options.append("--with-system-zlib")
-
- if "zstd" in spec:
- options.append("--with-zstd-include={0}".format(spec["zstd"].headers.directories[0]))
- options.append("--with-zstd-lib={0}".format(spec["zstd"].libs.directories[0]))
-
- # Enabling language "jit" requires --enable-host-shared.
- if "languages=jit" in spec:
- options.append("--enable-host-shared")
-
- # Binutils
- if spec.satisfies("+binutils"):
- binutils = spec["binutils"].prefix.bin
- options.extend(
- [
- "--with-gnu-ld",
- "--with-ld=" + binutils.ld,
- "--with-gnu-as",
- "--with-as=" + binutils.join("as"),
- ]
- )
- elif spec.satisfies("%apple-clang@15:"):
- # https://github.com/iains/gcc-darwin-arm64/issues/117
- # https://github.com/iains/gcc-12-branch/issues/22
- # https://github.com/iains/gcc-13-branch/issues/8
- options.append("--with-ld=/Library/Developer/CommandLineTools/usr/bin/ld-classic")
-
- # enable_bootstrap
- if spec.satisfies("+bootstrap"):
- options.extend(["--enable-bootstrap"])
- else:
- options.extend(["--disable-bootstrap"])
-
- # Configure include and lib directories explicitly for these
- # dependencies since the short GCC option assumes that libraries
- # are installed in "/lib" which might not be true on all OS
- # (see #10842)
- #
- # More info at: https://gcc.gnu.org/install/configure.html
- for dep_str in ("mpfr", "gmp", "mpc", "isl"):
- if dep_str not in spec:
- options.append("--without-{0}".format(dep_str))
- continue
-
- dep_spec = spec[dep_str]
- include_dir = dep_spec.headers.directories[0]
- lib_dir = dep_spec.libs.directories[0]
- options.extend(
- [
- "--with-{0}-include={1}".format(dep_str, include_dir),
- "--with-{0}-lib={1}".format(dep_str, lib_dir),
- ]
- )
-
- # nvptx-none offloading for host compiler
- if spec.satisfies("+nvptx"):
- options.extend(
- [
- "--enable-offload-targets=nvptx-none",
- "--with-cuda-driver-include={0}".format(spec["cuda"].prefix.include),
- "--with-cuda-driver-lib={0}".format(spec["cuda"].libs.directories[0]),
- "--disable-bootstrap",
- "--disable-multilib",
- ]
- )
-
- if sys.platform == "darwin":
- options.extend(
- [
- "--with-native-system-header-dir=/usr/include",
- "--with-sysroot={0}".format(macos_sdk_path()),
- "--with-libiconv-prefix={0}".format(spec["iconv"].prefix),
- ]
- )
-
- # enable appropriate bootstrapping flags
- stage1_ldflags = str(self.rpath_args)
- boot_ldflags = stage1_ldflags + " -static-libstdc++ -static-libgcc"
- options.append("--with-stage1-ldflags=" + stage1_ldflags)
- options.append("--with-boot-ldflags=" + boot_ldflags)
- options.append("--with-build-config=spack")
-
- if "languages=d" in spec:
- # Phobos is the standard library for the D Programming Language. The documentation says
- # that on some targets, 'libphobos' is not enabled by default, but compiles and works
- # if '--enable-libphobos' is used. Specifics are documented for affected targets.
- # See https://gcc.gnu.org/install/prerequisites.html#GDC-prerequisite
- # Unfortunately, it is unclear where exactly the aforementioned specifics are
- # documented but GDC seems to be unusable without the library, therefore we enable it
- # explicitly:
- options.append("--enable-libphobos")
- if spec.satisfies("@12:"):
- options.append("GDC={0}".format(self.detect_gdc()))
-
- return options
-
- # run configure/make/make(install) for the nvptx-none target
- # before running the host compiler phases
- @run_before("configure")
- def nvptx_install(self):
- spec = self.spec
- prefix = self.prefix
-
- if not spec.satisfies("+nvptx"):
- return
-
- # config.guess returns the host triple, e.g. "x86_64-pc-linux-gnu"
- guess = Executable("./config.guess")
- targetguess = guess(output=str).rstrip("\n")
-
- options = getattr(self, "configure_flag_args", [])
- options += ["--prefix={0}".format(prefix)]
-
- options += [
- "--with-cuda-driver-include={0}".format(spec["cuda"].prefix.include),
- "--with-cuda-driver-lib={0}".format(spec["cuda"].libs.directories[0]),
- ]
-
- with working_dir("nvptx-tools"):
- configure = Executable("./configure")
- configure(*options)
- make()
- make("install")
-
- pattern = join_path(self.stage.source_path, "newlibsource", "*")
- files = glob.glob(pattern)
-
- if files:
- symlink(join_path(files[0], "newlib"), "newlib")
-
- # self.build_directory = 'spack-build-nvptx'
- with working_dir("spack-build-nvptx", create=True):
- options = [
- "--prefix={0}".format(prefix),
- "--enable-languages={0}".format(",".join(spec.variants["languages"].value)),
- "--with-mpfr={0}".format(spec["mpfr"].prefix),
- "--with-gmp={0}".format(spec["gmp"].prefix),
- "--target=nvptx-none",
- "--with-build-time-tools={0}".format(join_path(prefix, "nvptx-none", "bin")),
- "--enable-as-accelerator-for={0}".format(targetguess),
- "--disable-sjlj-exceptions",
- "--enable-newlib-io-long-long",
- ]
-
- configure = Executable("../configure")
- configure(*options)
- make()
- make("install")
-
- @property
- def build_targets(self):
- if "+profiled" in self.spec:
- return ["profiledbootstrap"]
- return []
-
- @property
- def install_targets(self):
- if "+strip" in self.spec:
- return ["install-strip"]
- return ["install"]
-
- @property
- def spec_dir(self):
- # e.g. lib/gcc/x86_64-unknown-linux-gnu/4.9.2
- spec_dir = glob.glob("{0}/gcc/*/*".format(self.prefix.lib))
- return spec_dir[0] if spec_dir else None
-
- @run_after("install")
- def write_rpath_specs(self):
- """Generate a spec file so the linker adds a rpath to the libs
- the compiler used to build the executable.
-
- .. caution::
-
- The custom spec file by default with *always* pass ``-Wl,-rpath
- ...`` to the linker, which will cause the linker to *ignore* the
- value of ``LD_RUN_PATH``, which otherwise would be saved to the
- binary as the default rpath. See the mitigation below for how to
- temporarily disable this behavior.
-
- Structure the specs file so that users can define a custom spec file
- to suppress the spack-linked rpaths to facilitate rpath adjustment
- for relocatable binaries. The custom spec file
- :file:`{norpath}.spec` will have a single
- line followed by two blanks lines::
-
- *link_libgcc_rpath:
-
-
-
- It can be passed to the GCC linker using the argument
- ``--specs=norpath.spec`` to disable the automatic rpath and restore
- the behavior of ``LD_RUN_PATH``."""
- if not self.spec_dir:
- tty.warn(
- "Could not install specs for {0}.".format(self.spec.format("{name}{@version}"))
- )
- return
-
- gcc = self.spec["gcc"].command
- lines = gcc("-dumpspecs", output=str).splitlines(True)
- specs_file = join_path(self.spec_dir, "specs")
-
- # Save a backup
- with open(specs_file + ".orig", "w") as out:
- out.writelines(lines)
-
- # Find which directories have shared libraries
- rpath_libdirs = []
- for dir in ["lib", "lib64"]:
- libdir = join_path(self.prefix, dir)
- if glob.glob(join_path(libdir, "*." + dso_suffix)):
- rpath_libdirs.append(libdir)
-
- if not rpath_libdirs:
- # No shared libraries
- tty.warn("No dynamic libraries found in lib/lib64")
- return
-
- # Overwrite the specs file
- with open(specs_file, "w") as out:
- for line in lines:
- out.write(line)
- if line.startswith("*link_libgcc:"):
- # Insert at start of line following link_libgcc, which gets
- # inserted into every call to the linker
- out.write("%(link_libgcc_rpath) ")
-
- # Add easily-overridable rpath string at the end
- out.write("*link_libgcc_rpath:\n")
- out.write(" ".join("-rpath " + lib for lib in rpath_libdirs))
- out.write("\n")
- set_install_permissions(specs_file)
- tty.info("Wrote new spec file to {0}".format(specs_file))
-
- def setup_run_environment(self, env):
- # Search prefix directory for possibly modified compiler names
- from spack.compilers.gcc import Gcc as Compiler
-
- # Get the contents of the installed binary directory
- bin_path = self.spec.prefix.bin
-
- if not os.path.isdir(bin_path):
- return
-
- bin_contents = os.listdir(bin_path)
-
- # Find the first non-symlink compiler binary present for each language
- for lang in ["cc", "cxx", "fc", "f77"]:
- for filename, regexp in itertools.product(bin_contents, Compiler.search_regexps(lang)):
- if not regexp.match(filename):
- continue
-
- abspath = os.path.join(bin_path, filename)
- if os.path.islink(abspath):
- continue
-
- # Set the proper environment variable
- env.set(lang.upper(), abspath)
- # Stop searching filename/regex combos for this language
- break
-
- def detect_gdc(self):
- """Detect and return the path to GDC that belongs to the same instance of GCC that is used
- by self.compiler.
-
- If the path cannot be detected, raise InstallError with recommendations for the users on
- how to circumvent the problem.
-
- Should be use only if self.spec.satisfies("@12: languages=d")
- """
- # Detect GCC package in the directory of the GCC compiler
- # or in the $PATH if self.compiler.cc is not an absolute path:
- from spack.detection import by_path
-
- compiler_dir = os.path.dirname(self.compiler.cc)
- detected_packages = by_path(
- [self.name], path_hints=([compiler_dir] if os.path.isdir(compiler_dir) else None)
- )
-
- # We consider only packages that satisfy the following constraint:
- required_spec = Spec("languages=c,c++,d")
- candidate_specs = [
- p.spec
- for p in filter(
- lambda p: p.spec.satisfies(required_spec), detected_packages.get(self.name, ())
- )
- ]
-
- if candidate_specs:
- # We now need to filter specs that match the compiler version:
- compiler_spec = Spec(repr(self.compiler.spec))
-
- # First, try to filter specs that satisfy the compiler spec:
- new_candidate_specs = list(
- filter(lambda s: s.satisfies(compiler_spec), candidate_specs)
- )
-
- # The compiler version might be more specific than what we can detect. For example, the
- # user might have "gcc@10.2.1-sys" as the compiler spec in compilers.yaml. In that
- # case, we end up with an empty list of candidates. To circumvent the problem, we try
- # to filter specs that are satisfied by the compiler spec:
- if not new_candidate_specs:
- new_candidate_specs = list(
- filter(lambda s: compiler_spec.satisfies(s), candidate_specs)
- )
-
- candidate_specs = new_candidate_specs
-
- error_nl = "\n " # see SpackError.__str__()
-
- if not candidate_specs:
- raise InstallError(
- "Cannot detect GDC",
- long_msg="Starting version 12, the D frontend requires a working GDC."
- "{0}You can install it with Spack by running:"
- "{0}{0}spack install gcc@9:11 languages=c,c++,d"
- "{0}{0}Once that has finished, you will need to add it to your compilers.yaml file"
- "{0}and use it to install this spec (i.e. {1} ...).".format(
- error_nl, self.spec.format("{name}{@version} {variants.languages}")
- ),
- )
- elif len(candidate_specs) == 0:
- return candidate_specs[0].extra_attributes["compilers"]["d"]
- else:
- # It is rather unlikely to end up here but let us try to resolve the ambiguity:
- candidate_gdc = candidate_specs[0].extra_attributes["compilers"]["d"]
- if all(
- candidate_gdc == s.extra_attributes["compilers"]["d"] for s in candidate_specs[1:]
- ):
- # It does not matter which one we take if they are all the same:
- return candidate_gdc
- else:
- raise InstallError(
- "Cannot resolve ambiguity when detecting GDC that belongs to "
- "%{0}".format(self.compiler.spec),
- long_msg="The candidates are:{0}{0}{1}{0}".format(
- error_nl,
- error_nl.join(
- "{0} (cc: {1})".format(
- s.extra_attributes["compilers"]["d"],
- s.extra_attributes["compilers"]["c"],
- )
- for s in candidate_specs
- ),
- ),
- )
diff --git a/packages/gcc/patch-2b40941d23b1570cdd90083b58fa0f66aa58c86e.patch b/packages/gcc/patch-2b40941d23b1570cdd90083b58fa0f66aa58c86e.patch
deleted file mode 100644
index 3d76c47b..00000000
--- a/packages/gcc/patch-2b40941d23b1570cdd90083b58fa0f66aa58c86e.patch
+++ /dev/null
@@ -1,121 +0,0 @@
-From 2b40941d23b1570cdd90083b58fa0f66aa58c86e Mon Sep 17 00:00:00 2001
-From: Tamar Christina <tamar.christina@arm.com>
-Date: Fri, 21 May 2021 12:16:56 +0100
-Subject: [PATCH] libsanitizer: Remove cyclades from libsanitizer
-
-The Linux kernel has removed the interface to cyclades from
-the latest kernel headers[1] due to them being orphaned for the
-past 13 years.
-
-libsanitizer uses this header when compiling against glibc, but
-glibcs itself doesn't seem to have any references to cyclades.
-
-Further more it seems that the driver is broken in the kernel and
-the firmware doesn't seem to be available anymore.
-
-As such since this is breaking the build of libsanitizer (and so the
-GCC bootstrap[2]) I propose to remove this.
-
-[1] https://lkml.org/lkml/2021/3/2/153
-[2] https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100379
-
-libsanitizer/ChangeLog:
-
- PR sanitizer/100379
- * sanitizer_common/sanitizer_common_interceptors_ioctl.inc: Cherry-pick
- llvm-project revision f7c5351552387bd43f6ca3631016d7f0dfe0f135.
- * sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.
- * sanitizer_common/sanitizer_platform_limits_posix.h: Likewise.
----
- .../sanitizer_common_interceptors_ioctl.inc | 9 ---------
- .../sanitizer_platform_limits_posix.cc | 11 -----------
- .../sanitizer_platform_limits_posix.h | 10 ----------
- 3 files changed, 30 deletions(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
-index 5408ea17c59..7a9cd3f5968 100644
---- a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
-+++ b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
-@@ -365,15 +365,6 @@ static void ioctl_table_fill() {
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
- // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE
-- _(CYGETDEFTHRESH, WRITE, sizeof(int));
-- _(CYGETDEFTIMEOUT, WRITE, sizeof(int));
-- _(CYGETMON, WRITE, struct_cyclades_monitor_sz);
-- _(CYGETTHRESH, WRITE, sizeof(int));
-- _(CYGETTIMEOUT, WRITE, sizeof(int));
-- _(CYSETDEFTHRESH, NONE, 0);
-- _(CYSETDEFTIMEOUT, NONE, 0);
-- _(CYSETTHRESH, NONE, 0);
-- _(CYSETTIMEOUT, NONE, 0);
- _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz);
- _(EQL_ENSLAVE, WRITE, struct_ifreq_sz);
- _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz);
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-index d823a12190c..e8fce8a0287 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-@@ -157,7 +157,6 @@ typedef struct user_fpregs elf_fpregset_t;
- # include <sys/procfs.h>
- #endif
- #include <sys/user.h>
--#include <linux/cyclades.h>
- #include <linux/if_eql.h>
- #include <linux/if_plip.h>
- #include <linux/lp.h>
-@@ -466,7 +465,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
- unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct);
-- unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor);
- #if EV_VERSION > (0x010000)
- unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry);
- #else
-@@ -833,15 +831,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);
- #endif // SANITIZER_LINUX || SANITIZER_FREEBSD
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
-- unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH;
-- unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT;
-- unsigned IOCTL_CYGETMON = CYGETMON;
-- unsigned IOCTL_CYGETTHRESH = CYGETTHRESH;
-- unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT;
-- unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH;
-- unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT;
-- unsigned IOCTL_CYSETTHRESH = CYSETTHRESH;
-- unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT;
- unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE;
- unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE;
- unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG;
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-index 6a673a7c995..f921bf2b5b5 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-@@ -1040,7 +1040,6 @@ struct __sanitizer_cookie_io_functions_t {
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
- extern unsigned struct_ax25_parms_struct_sz;
-- extern unsigned struct_cyclades_monitor_sz;
- extern unsigned struct_input_keymap_entry_sz;
- extern unsigned struct_ipx_config_data_sz;
- extern unsigned struct_kbdiacrs_sz;
-@@ -1385,15 +1384,6 @@ struct __sanitizer_cookie_io_functions_t {
- #endif // SANITIZER_LINUX || SANITIZER_FREEBSD
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
-- extern unsigned IOCTL_CYGETDEFTHRESH;
-- extern unsigned IOCTL_CYGETDEFTIMEOUT;
-- extern unsigned IOCTL_CYGETMON;
-- extern unsigned IOCTL_CYGETTHRESH;
-- extern unsigned IOCTL_CYGETTIMEOUT;
-- extern unsigned IOCTL_CYSETDEFTHRESH;
-- extern unsigned IOCTL_CYSETDEFTIMEOUT;
-- extern unsigned IOCTL_CYSETTHRESH;
-- extern unsigned IOCTL_CYSETTIMEOUT;
- extern unsigned IOCTL_EQL_EMANCIPATE;
- extern unsigned IOCTL_EQL_ENSLAVE;
- extern unsigned IOCTL_EQL_GETMASTRCFG;
---
-2.31.1
-
diff --git a/packages/gcc/patch-745dae5923aba02982563481d75a21595df22ff8.patch b/packages/gcc/patch-745dae5923aba02982563481d75a21595df22ff8.patch
deleted file mode 100644
index 57c51eb2..00000000
--- a/packages/gcc/patch-745dae5923aba02982563481d75a21595df22ff8.patch
+++ /dev/null
@@ -1,123 +0,0 @@
-From 745dae5923aba02982563481d75a21595df22ff8 Mon Sep 17 00:00:00 2001
-From: Tamar Christina <tamar.christina@arm.com>
-Date: Fri, 21 May 2021 10:30:59 +0100
-Subject: [PATCH] libsanitizer: Remove cyclades from libsanitizer
-
-The Linux kernel has removed the interface to cyclades from
-the latest kernel headers[1] due to them being orphaned for the
-past 13 years.
-
-libsanitizer uses this header when compiling against glibc, but
-glibcs itself doesn't seem to have any references to cyclades.
-
-Further more it seems that the driver is broken in the kernel and
-the firmware doesn't seem to be available anymore.
-
-As such since this is breaking the build of libsanitizer (and so the
-GCC bootstrap[2]) I propose to remove this.
-
-[1] https://lkml.org/lkml/2021/3/2/153
-[2] https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100379
-
-(cherry picked from commit f7c5351552387bd43f6ca3631016d7f0dfe0f135)
-
-libsanitizer/ChangeLog:
-
- PR sanitizer/100379
- * sanitizer_common/sanitizer_common_interceptors_ioctl.inc: Cherry-pick
- llvm-project revision f7c5351552387bd43f6ca3631016d7f0dfe0f135.
- * sanitizer_common/sanitizer_platform_limits_posix.cpp: Likewise.
- * sanitizer_common/sanitizer_platform_limits_posix.h: Likewise.
----
- .../sanitizer_common_interceptors_ioctl.inc | 9 ---------
- .../sanitizer_platform_limits_posix.cpp | 11 -----------
- .../sanitizer_platform_limits_posix.h | 10 ----------
- 3 files changed, 30 deletions(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
-index 7f181258eab..b7da6598755 100644
---- a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
-+++ b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
-@@ -370,15 +370,6 @@ static void ioctl_table_fill() {
-
- #if SANITIZER_GLIBC
- // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE
-- _(CYGETDEFTHRESH, WRITE, sizeof(int));
-- _(CYGETDEFTIMEOUT, WRITE, sizeof(int));
-- _(CYGETMON, WRITE, struct_cyclades_monitor_sz);
-- _(CYGETTHRESH, WRITE, sizeof(int));
-- _(CYGETTIMEOUT, WRITE, sizeof(int));
-- _(CYSETDEFTHRESH, NONE, 0);
-- _(CYSETDEFTIMEOUT, NONE, 0);
-- _(CYSETTHRESH, NONE, 0);
-- _(CYSETTIMEOUT, NONE, 0);
- _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz);
- _(EQL_ENSLAVE, WRITE, struct_ifreq_sz);
- _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz);
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
-index 35a690cba5c..6e5c330b98e 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
-@@ -143,7 +143,6 @@ typedef struct user_fpregs elf_fpregset_t;
- # include <sys/procfs.h>
- #endif
- #include <sys/user.h>
--#include <linux/cyclades.h>
- #include <linux/if_eql.h>
- #include <linux/if_plip.h>
- #include <linux/lp.h>
-@@ -460,7 +459,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);
-
- #if SANITIZER_GLIBC
- unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct);
-- unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor);
- #if EV_VERSION > (0x010000)
- unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry);
- #else
-@@ -824,15 +822,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);
- #endif // SANITIZER_LINUX
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
-- unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH;
-- unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT;
-- unsigned IOCTL_CYGETMON = CYGETMON;
-- unsigned IOCTL_CYGETTHRESH = CYGETTHRESH;
-- unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT;
-- unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH;
-- unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT;
-- unsigned IOCTL_CYSETTHRESH = CYSETTHRESH;
-- unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT;
- unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE;
- unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE;
- unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG;
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-index ad358eef8b7..cba41ba5494 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h
-@@ -983,7 +983,6 @@ extern unsigned struct_vt_mode_sz;
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
- extern unsigned struct_ax25_parms_struct_sz;
--extern unsigned struct_cyclades_monitor_sz;
- extern unsigned struct_input_keymap_entry_sz;
- extern unsigned struct_ipx_config_data_sz;
- extern unsigned struct_kbdiacrs_sz;
-@@ -1328,15 +1327,6 @@ extern unsigned IOCTL_VT_WAITACTIVE;
- #endif // SANITIZER_LINUX
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
--extern unsigned IOCTL_CYGETDEFTHRESH;
--extern unsigned IOCTL_CYGETDEFTIMEOUT;
--extern unsigned IOCTL_CYGETMON;
--extern unsigned IOCTL_CYGETTHRESH;
--extern unsigned IOCTL_CYGETTIMEOUT;
--extern unsigned IOCTL_CYSETDEFTHRESH;
--extern unsigned IOCTL_CYSETDEFTIMEOUT;
--extern unsigned IOCTL_CYSETTHRESH;
--extern unsigned IOCTL_CYSETTIMEOUT;
- extern unsigned IOCTL_EQL_EMANCIPATE;
- extern unsigned IOCTL_EQL_ENSLAVE;
- extern unsigned IOCTL_EQL_GETMASTRCFG;
---
-2.31.1
-
diff --git a/packages/gcc/patch-f1feb74046e0feb0596b93bbb822fae02940a90e.patch b/packages/gcc/patch-f1feb74046e0feb0596b93bbb822fae02940a90e.patch
deleted file mode 100644
index 2448be07..00000000
--- a/packages/gcc/patch-f1feb74046e0feb0596b93bbb822fae02940a90e.patch
+++ /dev/null
@@ -1,133 +0,0 @@
-From f1feb74046e0feb0596b93bbb822fae02940a90e Mon Sep 17 00:00:00 2001
-From: Patrick Palka <ppalka@redhat.com>
-Date: Fri, 4 Jun 2021 13:46:53 -0400
-Subject: [PATCH] c++: tsubst_function_decl and excess arg levels [PR100102]
-
-Here, when instantiating the dependent alias template
-duration::__is_harmonic with args={{T,U},{int}}, we find ourselves
-substituting the function decl _S_gcd. Since we have more arg levels
-than _S_gcd has parm levels, an old special case in tsubst_function_decl
-causes us to unwantedly reduce args to its innermost level, yielding
-args={int}, which leads to a nonsensical substitution into the decl
-context and eventually a crash.
-
-The comment for this special case refers to three examples for which we
-ought to see more arg levels than parm levels here, but none of the
-examples actually demonstrate this. In the first example, when
-defining S<int>::f(U) parms_depth is 2 and args_depth is 1, and
-later when instantiating say S<int>::f<char> both depths are 2. In the
-second example, when substituting the template friend declaration
-parms_depth is 2 and args_depth is 1, and later when instantiating f
-both depths are 1. Finally, the third example is invalid since we can't
-specialize a member template of an unspecialized class template like
-that.
-
-Given that this reduction code seems no longer relevant for its
-documented purpose and that it causes problems as in the PR, this patch
-just removes it. Note that as far as bootstrap/regtest is concerned,
-this code is dead; the below two tests would be the first to reach it.
-
- PR c++/100102
-
-gcc/cp/ChangeLog:
-
- * pt.c (tsubst_function_decl): Remove old code for reducing
- args when it has excess levels.
-
-gcc/testsuite/ChangeLog:
-
- * g++.dg/cpp0x/alias-decl-72.C: New test.
- * g++.dg/cpp0x/alias-decl-72a.C: New test.
-
-(cherry picked from commit 5357ab75dedef403b0eebf9277d61d1cbeb5898f)
----
- gcc/cp/pt.c | 39 ---------------------
- gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C | 9 +++++
- gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C | 9 +++++
- 3 files changed, 18 insertions(+), 39 deletions(-)
- create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C
- create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C
-
-diff --git a/gcc/cp/pt.c b/gcc/cp/pt.c
-index 1434beb80f4..1761a902218 100644
---- a/gcc/cp/pt.c
-+++ b/gcc/cp/pt.c
-@@ -13954,45 +13954,6 @@ tsubst_function_decl (tree t, tree args, tsubst_flags_t complain,
- if (tree spec = retrieve_specialization (gen_tmpl, argvec, hash))
- return spec;
- }
--
-- /* We can see more levels of arguments than parameters if
-- there was a specialization of a member template, like
-- this:
--
-- template <class T> struct S { template <class U> void f(); }
-- template <> template <class U> void S<int>::f(U);
--
-- Here, we'll be substituting into the specialization,
-- because that's where we can find the code we actually
-- want to generate, but we'll have enough arguments for
-- the most general template.
--
-- We also deal with the peculiar case:
--
-- template <class T> struct S {
-- template <class U> friend void f();
-- };
-- template <class U> void f() {}
-- template S<int>;
-- template void f<double>();
--
-- Here, the ARGS for the instantiation of will be {int,
-- double}. But, we only need as many ARGS as there are
-- levels of template parameters in CODE_PATTERN. We are
-- careful not to get fooled into reducing the ARGS in
-- situations like:
--
-- template <class T> struct S { template <class U> void f(U); }
-- template <class T> template <> void S<T>::f(int) {}
--
-- which we can spot because the pattern will be a
-- specialization in this case. */
-- int args_depth = TMPL_ARGS_DEPTH (args);
-- int parms_depth =
-- TMPL_PARMS_DEPTH (DECL_TEMPLATE_PARMS (DECL_TI_TEMPLATE (t)));
--
-- if (args_depth > parms_depth && !DECL_TEMPLATE_SPECIALIZATION (t))
-- args = get_innermost_template_args (args, parms_depth);
- }
- else
- {
-diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C
-new file mode 100644
-index 00000000000..8009756dcba
---- /dev/null
-+++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C
-@@ -0,0 +1,9 @@
-+// PR c++/100102
-+// { dg-do compile { target c++11 } }
-+
-+template<int()> struct ratio;
-+template<class T, class U> struct duration {
-+ static constexpr int _S_gcd();
-+ template<class> using __is_harmonic = ratio<_S_gcd>;
-+ using type = __is_harmonic<int>;
-+};
-diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C
-new file mode 100644
-index 00000000000..a4443e18f9d
---- /dev/null
-+++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C
-@@ -0,0 +1,9 @@
-+// PR c++/100102
-+// { dg-do compile { target c++11 } }
-+
-+template<int> struct ratio;
-+template<class T> struct duration {
-+ static constexpr int _S_gcd();
-+ template<class> using __is_harmonic = ratio<(duration::_S_gcd)()>;
-+ using type = __is_harmonic<int>;
-+};
---
-2.31.1
-
diff --git a/packages/gcc/patch-fc930b3010bd0de899a3da3209eab20664ddb703.patch b/packages/gcc/patch-fc930b3010bd0de899a3da3209eab20664ddb703.patch
deleted file mode 100644
index 27e5a2b5..00000000
--- a/packages/gcc/patch-fc930b3010bd0de899a3da3209eab20664ddb703.patch
+++ /dev/null
@@ -1,133 +0,0 @@
-From fc930b3010bd0de899a3da3209eab20664ddb703 Mon Sep 17 00:00:00 2001
-From: Patrick Palka <ppalka@redhat.com>
-Date: Fri, 4 Jun 2021 13:46:53 -0400
-Subject: [PATCH] c++: tsubst_function_decl and excess arg levels [PR100102]
-
-Here, when instantiating the dependent alias template
-duration::__is_harmonic with args={{T,U},{int}}, we find ourselves
-substituting the function decl _S_gcd. Since we have more arg levels
-than _S_gcd has parm levels, an old special case in tsubst_function_decl
-causes us to unwantedly reduce args to its innermost level, yielding
-args={int}, which leads to a nonsensical substitution into the decl
-context and eventually a crash.
-
-The comment for this special case refers to three examples for which we
-ought to see more arg levels than parm levels here, but none of the
-examples actually demonstrate this. In the first example, when
-defining S<int>::f(U) parms_depth is 2 and args_depth is 1, and
-later when instantiating say S<int>::f<char> both depths are 2. In the
-second example, when substituting the template friend declaration
-parms_depth is 2 and args_depth is 1, and later when instantiating f
-both depths are 1. Finally, the third example is invalid since we can't
-specialize a member template of an unspecialized class template like
-that.
-
-Given that this reduction code seems no longer relevant for its
-documented purpose and that it causes problems as in the PR, this patch
-just removes it. Note that as far as bootstrap/regtest is concerned,
-this code is dead; the below two tests would be the first to reach it.
-
- PR c++/100102
-
-gcc/cp/ChangeLog:
-
- * pt.c (tsubst_function_decl): Remove old code for reducing
- args when it has excess levels.
-
-gcc/testsuite/ChangeLog:
-
- * g++.dg/cpp0x/alias-decl-72.C: New test.
- * g++.dg/cpp0x/alias-decl-72a.C: New test.
-
-(cherry picked from commit 5357ab75dedef403b0eebf9277d61d1cbeb5898f)
----
- gcc/cp/pt.c | 39 ---------------------
- gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C | 9 +++++
- gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C | 9 +++++
- 3 files changed, 18 insertions(+), 39 deletions(-)
- create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C
- create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C
-
-diff --git a/gcc/cp/pt.c b/gcc/cp/pt.c
-index 5a957141ba3..7ce9ac234f8 100644
---- a/gcc/cp/pt.c
-+++ b/gcc/cp/pt.c
-@@ -13811,45 +13811,6 @@ tsubst_function_decl (tree t, tree args, tsubst_flags_t complain,
- if (tree spec = retrieve_specialization (gen_tmpl, argvec, hash))
- return spec;
- }
--
-- /* We can see more levels of arguments than parameters if
-- there was a specialization of a member template, like
-- this:
--
-- template <class T> struct S { template <class U> void f(); }
-- template <> template <class U> void S<int>::f(U);
--
-- Here, we'll be substituting into the specialization,
-- because that's where we can find the code we actually
-- want to generate, but we'll have enough arguments for
-- the most general template.
--
-- We also deal with the peculiar case:
--
-- template <class T> struct S {
-- template <class U> friend void f();
-- };
-- template <class U> void f() {}
-- template S<int>;
-- template void f<double>();
--
-- Here, the ARGS for the instantiation of will be {int,
-- double}. But, we only need as many ARGS as there are
-- levels of template parameters in CODE_PATTERN. We are
-- careful not to get fooled into reducing the ARGS in
-- situations like:
--
-- template <class T> struct S { template <class U> void f(U); }
-- template <class T> template <> void S<T>::f(int) {}
--
-- which we can spot because the pattern will be a
-- specialization in this case. */
-- int args_depth = TMPL_ARGS_DEPTH (args);
-- int parms_depth =
-- TMPL_PARMS_DEPTH (DECL_TEMPLATE_PARMS (DECL_TI_TEMPLATE (t)));
--
-- if (args_depth > parms_depth && !DECL_TEMPLATE_SPECIALIZATION (t))
-- args = get_innermost_template_args (args, parms_depth);
- }
- else
- {
-diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C
-new file mode 100644
-index 00000000000..8009756dcba
---- /dev/null
-+++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C
-@@ -0,0 +1,9 @@
-+// PR c++/100102
-+// { dg-do compile { target c++11 } }
-+
-+template<int()> struct ratio;
-+template<class T, class U> struct duration {
-+ static constexpr int _S_gcd();
-+ template<class> using __is_harmonic = ratio<_S_gcd>;
-+ using type = __is_harmonic<int>;
-+};
-diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C
-new file mode 100644
-index 00000000000..a4443e18f9d
---- /dev/null
-+++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C
-@@ -0,0 +1,9 @@
-+// PR c++/100102
-+// { dg-do compile { target c++11 } }
-+
-+template<int> struct ratio;
-+template<class T> struct duration {
-+ static constexpr int _S_gcd();
-+ template<class> using __is_harmonic = ratio<(duration::_S_gcd)()>;
-+ using type = __is_harmonic<int>;
-+};
---
-2.31.1
-
diff --git a/packages/gcc/piclibs.patch b/packages/gcc/piclibs.patch
deleted file mode 100644
index 0ecb7930..00000000
--- a/packages/gcc/piclibs.patch
+++ /dev/null
@@ -1,62 +0,0 @@
-diff --git a/libgfortran/Makefile.in b/libgfortran/Makefile.in
-index 62b9f7a..7666fdb 100644
---- a/libgfortran/Makefile.in
-+++ b/libgfortran/Makefile.in
-@@ -357,11 +357,11 @@ AUTOMAKE = @AUTOMAKE@
- AWK = @AWK@
- CC = @CC@
- CCDEPMODE = @CCDEPMODE@
--CFLAGS = @CFLAGS@
-+CFLAGS = @CFLAGS@ -fPIC
- CPP = @CPP@
--CPPFLAGS = @CPPFLAGS@
-+CPPFLAGS = @CPPFLAGS@ -fPIC
- CYGPATH_W = @CYGPATH_W@
--DEFS = @DEFS@
-+DEFS = @DEFS@ -fPIC
- DEPDIR = @DEPDIR@
- DSYMUTIL = @DSYMUTIL@
- DUMPBIN = @DUMPBIN@
-@@ -371,7 +371,7 @@ ECHO_T = @ECHO_T@
- EGREP = @EGREP@
- EXEEXT = @EXEEXT@
- FC = @FC@
--FCFLAGS = @FCFLAGS@
-+FCFLAGS = @FCFLAGS@ -fPIC
- FGREP = @FGREP@
- FPU_HOST_HEADER = @FPU_HOST_HEADER@
- GREP = @GREP@
-diff --git a/libstdc++-v3/Makefile.in b/libstdc++-v3/Makefile.in
-index bede542..9b3e442 100644
---- a/libstdc++-v3/Makefile.in
-+++ b/libstdc++-v3/Makefile.in
-@@ -115,7 +115,7 @@ CC = @CC@
- CCODECVT_CC = @CCODECVT_CC@
- CCOLLATE_CC = @CCOLLATE_CC@
- CCTYPE_CC = @CCTYPE_CC@
--CFLAGS = @CFLAGS@
-+CFLAGS = @CFLAGS@ -fPIC
- CLOCALE_CC = @CLOCALE_CC@
- CLOCALE_H = @CLOCALE_H@
- CLOCALE_INTERNAL_H = @CLOCALE_INTERNAL_H@
-@@ -124,7 +124,7 @@ CMESSAGES_H = @CMESSAGES_H@
- CMONEY_CC = @CMONEY_CC@
- CNUMERIC_CC = @CNUMERIC_CC@
- CPP = @CPP@
--CPPFLAGS = @CPPFLAGS@
-+CPPFLAGS = @CPPFLAGS@ -fPIC
- CPU_DEFINES_SRCDIR = @CPU_DEFINES_SRCDIR@
- CPU_OPT_BITS_RANDOM = @CPU_OPT_BITS_RANDOM@
- CPU_OPT_EXT_RANDOM = @CPU_OPT_EXT_RANDOM@
-@@ -139,7 +139,7 @@ CYGPATH_W = @CYGPATH_W@
- C_INCLUDE_DIR = @C_INCLUDE_DIR@
- DBLATEX = @DBLATEX@
- DEBUG_FLAGS = @DEBUG_FLAGS@
--DEFS = @DEFS@
-+DEFS = @DEFS@ -fPIC
- DOT = @DOT@
- DOXYGEN = @DOXYGEN@
- DSYMUTIL = @DSYMUTIL@
---
-2.8.3
-
diff --git a/packages/gcc/signal.patch b/packages/gcc/signal.patch
deleted file mode 100644
index 21bf9e03..00000000
--- a/packages/gcc/signal.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From 6c709b6262e8b6441b1e94526d6d65d4ce7a7dec Mon Sep 17 00:00:00 2001
-From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
-Date: Thu, 7 Sep 2017 07:18:57 +0000
-Subject: [PATCH] 2017-09-07 Matthias Klose <doko@ubuntu.com>
-
- * asan/asan_linux.cc: Include <signal.h>
-
-
-git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251830 138bc75d-0d04-0410-961f-82ee72b054a4
----
- libsanitizer/asan/asan_linux.cc | 1 +
- 2 files changed, 5 insertions(+)
-
-diff --git a/libsanitizer/asan/asan_linux.cc b/libsanitizer/asan/asan_linux.cc
-index c504168..59087b9 100644
---- a/libsanitizer/asan/asan_linux.cc
-+++ b/libsanitizer/asan/asan_linux.cc
-@@ -29,6 +29,7 @@
- #include <dlfcn.h>
- #include <fcntl.h>
- #include <pthread.h>
-+#include <signal.h>
- #include <stdio.h>
- #include <unistd.h>
- #include <unwind.h>
---
-2.9.3
-
diff --git a/packages/gcc/stack_t-4.9.patch b/packages/gcc/stack_t-4.9.patch
deleted file mode 100644
index b894557c..00000000
--- a/packages/gcc/stack_t-4.9.patch
+++ /dev/null
@@ -1,80 +0,0 @@
-From 833e00c01e96f61e24cd7ec97b93fad212dc914b Mon Sep 17 00:00:00 2001
-From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
-Date: Thu, 7 Sep 2017 07:17:17 +0000
-Subject: [PATCH] 2017-09-07 Matthias Klose <doko@ubuntu.com>
-
- Backported from mainline
- 2017-07-14 Jakub Jelinek <jakub@redhat.com>
-
- PR sanitizer/81066
- * sanitizer_common/sanitizer_linux.h: Cherry-pick upstream r307969.
- * sanitizer_common/sanitizer_linux.cc: Likewise.
- * sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc: Likewise.
- * tsan/tsan_platform_linux.cc: Likewise.
-
-
-git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251829 138bc75d-0d04-0410-961f-82ee72b054a4
----
- libsanitizer/sanitizer_common/sanitizer_linux.cc | 3 +--
- libsanitizer/sanitizer_common/sanitizer_linux.h | 4 +---
- .../sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc | 2 +-
- libsanitizer/tsan/tsan_platform_linux.cc | 2 +-
- 5 files changed, 15 insertions(+), 7 deletions(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.cc b/libsanitizer/sanitizer_common/sanitizer_linux.cc
-index 9feb307..821b26d 100644
---- a/libsanitizer/sanitizer_common/sanitizer_linux.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_linux.cc
-@@ -514,8 +514,7 @@ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5) {
- }
- #endif
-
--uptr internal_sigaltstack(const struct sigaltstack *ss,
-- struct sigaltstack *oss) {
-+uptr internal_sigaltstack(const void *ss, void *oss) {
- return internal_syscall(__NR_sigaltstack, (uptr)ss, (uptr)oss);
- }
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.h b/libsanitizer/sanitizer_common/sanitizer_linux.h
-index 086834c..3a6f4cd 100644
---- a/libsanitizer/sanitizer_common/sanitizer_linux.h
-+++ b/libsanitizer/sanitizer_common/sanitizer_linux.h
-@@ -27,8 +26,7 @@ struct linux_dirent;
- // Syscall wrappers.
- uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);
- uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5);
--uptr internal_sigaltstack(const struct sigaltstack* ss,
-- struct sigaltstack* oss);
-+uptr internal_sigaltstack(const void* ss, void* oss);
- uptr internal_sigaction(int signum, const __sanitizer_kernel_sigaction_t *act,
- __sanitizer_kernel_sigaction_t *oldact);
- uptr internal_sigprocmask(int how, __sanitizer_kernel_sigset_t *set,
-diff --git a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
-index 5881202..c54894d 100644
---- a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
-@@ -234,7 +234,7 @@ static int TracerThread(void* argument) {
-
- // Alternate stack for signal handling.
- InternalScopedBuffer<char> handler_stack_memory(kHandlerStackSize);
-- struct sigaltstack handler_stack;
-+ stack_t handler_stack;
- internal_memset(&handler_stack, 0, sizeof(handler_stack));
- handler_stack.ss_sp = handler_stack_memory.data();
- handler_stack.ss_size = kHandlerStackSize;
-diff --git a/libsanitizer/tsan/tsan_platform_linux.cc b/libsanitizer/tsan/tsan_platform_linux.cc
-index 3259131..b8e9078 100644
---- a/libsanitizer/tsan/tsan_platform_linux.cc
-+++ b/libsanitizer/tsan/tsan_platform_linux.cc
-@@ -377,7 +377,7 @@ bool IsGlobalVar(uptr addr) {
- int ExtractResolvFDs(void *state, int *fds, int nfd) {
- #if SANITIZER_LINUX
- int cnt = 0;
-- __res_state *statp = (__res_state*)state;
-+ struct __res_state *statp = (struct __res_state*)state;
- for (int i = 0; i < MAXNS && cnt < nfd; i++) {
- if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)
- fds[cnt++] = statp->_u._ext.nssocks[i];
---
-2.9.3
-
diff --git a/packages/gcc/stack_t.patch b/packages/gcc/stack_t.patch
deleted file mode 100644
index 48a5a47a..00000000
--- a/packages/gcc/stack_t.patch
+++ /dev/null
@@ -1,88 +0,0 @@
-From 833e00c01e96f61e24cd7ec97b93fad212dc914b Mon Sep 17 00:00:00 2001
-From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
-Date: Thu, 7 Sep 2017 07:17:17 +0000
-Subject: [PATCH] 2017-09-07 Matthias Klose <doko@ubuntu.com>
-
- Backported from mainline
- 2017-07-14 Jakub Jelinek <jakub@redhat.com>
-
- PR sanitizer/81066
- * sanitizer_common/sanitizer_linux.h: Cherry-pick upstream r307969.
- * sanitizer_common/sanitizer_linux.cc: Likewise.
- * sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc: Likewise.
- * tsan/tsan_platform_linux.cc: Likewise.
-
-
-git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251829 138bc75d-0d04-0410-961f-82ee72b054a4
----
- libsanitizer/sanitizer_common/sanitizer_linux.cc | 3 +--
- libsanitizer/sanitizer_common/sanitizer_linux.h | 4 +---
- .../sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc | 2 +-
- libsanitizer/tsan/tsan_platform_linux.cc | 2 +-
- 5 files changed, 15 insertions(+), 7 deletions(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.cc b/libsanitizer/sanitizer_common/sanitizer_linux.cc
-index 9feb307..821b26d 100644
---- a/libsanitizer/sanitizer_common/sanitizer_linux.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_linux.cc
-@@ -514,8 +514,7 @@ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5) {
- }
- #endif
-
--uptr internal_sigaltstack(const struct sigaltstack *ss,
-- struct sigaltstack *oss) {
-+uptr internal_sigaltstack(const void *ss, void *oss) {
- return internal_syscall(SYSCALL(sigaltstack), (uptr)ss, (uptr)oss);
- }
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.h b/libsanitizer/sanitizer_common/sanitizer_linux.h
-index 086834c..3a6f4cd 100644
---- a/libsanitizer/sanitizer_common/sanitizer_linux.h
-+++ b/libsanitizer/sanitizer_common/sanitizer_linux.h
-@@ -18,7 +18,6 @@
- #include "sanitizer_platform_limits_posix.h"
-
- struct link_map; // Opaque type returned by dlopen().
--struct sigaltstack;
-
- namespace __sanitizer {
- // Dirent structure for getdents(). Note that this structure is different from
-@@ -27,8 +26,7 @@ struct linux_dirent;
-
- // Syscall wrappers.
- uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);
--uptr internal_sigaltstack(const struct sigaltstack* ss,
-- struct sigaltstack* oss);
-+uptr internal_sigaltstack(const void* ss, void* oss);
- uptr internal_sigprocmask(int how, __sanitizer_sigset_t *set,
- __sanitizer_sigset_t *oldset);
- void internal_sigfillset(__sanitizer_sigset_t *set);
-diff --git a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
-index 5881202..c54894d 100644
---- a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
-@@ -234,7 +234,7 @@ static int TracerThread(void* argument) {
-
- // Alternate stack for signal handling.
- InternalScopedBuffer<char> handler_stack_memory(kHandlerStackSize);
-- struct sigaltstack handler_stack;
-+ stack_t handler_stack;
- internal_memset(&handler_stack, 0, sizeof(handler_stack));
- handler_stack.ss_sp = handler_stack_memory.data();
- handler_stack.ss_size = kHandlerStackSize;
-diff --git a/libsanitizer/tsan/tsan_platform_linux.cc b/libsanitizer/tsan/tsan_platform_linux.cc
-index 3259131..b8e9078 100644
---- a/libsanitizer/tsan/tsan_platform_linux.cc
-+++ b/libsanitizer/tsan/tsan_platform_linux.cc
-@@ -377,7 +377,7 @@ bool IsGlobalVar(uptr addr) {
- int ExtractResolvFDs(void *state, int *fds, int nfd) {
- #if SANITIZER_LINUX
- int cnt = 0;
-- __res_state *statp = (__res_state*)state;
-+ struct __res_state *statp = (struct __res_state*)state;
- for (int i = 0; i < MAXNS && cnt < nfd; i++) {
- if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)
- fds[cnt++] = statp->_u._ext.nssocks[i];
---
-2.9.3
-
diff --git a/packages/gcc/sys_ustat-4.9.patch b/packages/gcc/sys_ustat-4.9.patch
deleted file mode 100644
index 75453af3..00000000
--- a/packages/gcc/sys_ustat-4.9.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-The sys_ustat.h patch modified for gcc 4.9.x.
-
-diff -Naurb gcc-4.9.4.orig/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
---- gcc-4.9.4.orig/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc 2013-12-19 06:54:11.000000000 -0600
-+++ gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc 2018-12-11 15:57:46.901800462 -0600
-@@ -81,7 +81,6 @@
- #include <sys/statvfs.h>
- #include <sys/timex.h>
- #include <sys/user.h>
--#include <sys/ustat.h>
- #include <linux/cyclades.h>
- #include <linux/if_eql.h>
- #include <linux/if_plip.h>
-@@ -163,7 +162,19 @@
- unsigned struct_old_utsname_sz = sizeof(struct old_utsname);
- unsigned struct_oldold_utsname_sz = sizeof(struct oldold_utsname);
- unsigned struct_itimerspec_sz = sizeof(struct itimerspec);
-- unsigned struct_ustat_sz = sizeof(struct ustat);
-+ // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which
-+ // has been removed from glibc 2.28.
-+#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \
-+ || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \
-+ || defined(__x86_64__)
-+#define SIZEOF_STRUCT_USTAT 32
-+#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \
-+ || defined(__powerpc__) || defined(__s390__)
-+#define SIZEOF_STRUCT_USTAT 20
-+#else
-+#error Unknown size of struct ustat
-+#endif
-+ unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT;
- #endif // SANITIZER_LINUX
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
diff --git a/packages/gcc/sys_ustat.h.patch b/packages/gcc/sys_ustat.h.patch
deleted file mode 100644
index c65757b4..00000000
--- a/packages/gcc/sys_ustat.h.patch
+++ /dev/null
@@ -1,63 +0,0 @@
-From 9569b61168b963a6cea7b782fd350dee489ad42c Mon Sep 17 00:00:00 2001
-From: "H.J. Lu" <hjl.tools@gmail.com>
-Date: Mon, 21 May 2018 13:17:55 -0700
-Subject: [PATCH] libsanitizer: Use pre-computed size of struct ustat for Linux
-
-Cherry-pick compiler-rt revision 333213:
-
-<sys/ustat.h> has been removed from glibc 2.28 by:
-
-commit cf2478d53ad7071e84c724a986b56fe17f4f4ca7
-Author: Adhemerval Zanella <adhemerval.zanella@linaro.org>
-Date: Sun Mar 18 11:28:59 2018 +0800
-
- Deprecate ustat syscall interface
-
-This patch uses pre-computed size of struct ustat for Linux.
-
- PR sanitizer/85835
- * sanitizer_common/sanitizer_platform_limits_posix.cc: Don't
- include <sys/ustat.h> for Linux.
- (SIZEOF_STRUCT_USTAT): New.
- (struct_ustat_sz): Use SIZEOF_STRUCT_USTAT for Linux.
----
- .../sanitizer_platform_limits_posix.cc | 15 +++++++++++++--
- 1 file changed, 13 insertions(+), 2 deletions(-)
-
-diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-index 858bb218450..de18e56d11c 100644
---- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc
-@@ -157,7 +157,6 @@ typedef struct user_fpregs elf_fpregset_t;
- # include <sys/procfs.h>
- #endif
- #include <sys/user.h>
--#include <sys/ustat.h>
- #include <linux/cyclades.h>
- #include <linux/if_eql.h>
- #include <linux/if_plip.h>
-@@ -250,7 +249,19 @@ namespace __sanitizer {
- #endif // SANITIZER_LINUX || SANITIZER_FREEBSD
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
-- unsigned struct_ustat_sz = sizeof(struct ustat);
-+ // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which
-+ // has been removed from glibc 2.28.
-+#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \
-+ || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \
-+ || defined(__x86_64__)
-+#define SIZEOF_STRUCT_USTAT 32
-+#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \
-+ || defined(__powerpc__) || defined(__s390__)
-+#define SIZEOF_STRUCT_USTAT 20
-+#else
-+#error Unknown size of struct ustat
-+#endif
-+ unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT;
- unsigned struct_rlimit64_sz = sizeof(struct rlimit64);
- unsigned struct_statvfs64_sz = sizeof(struct statvfs64);
- #endif // SANITIZER_LINUX && !SANITIZER_ANDROID
---
-2.17.0
-
-
diff --git a/packages/gcc/ucontext_t-java.patch b/packages/gcc/ucontext_t-java.patch
deleted file mode 100644
index a43e0b5a..00000000
--- a/packages/gcc/ucontext_t-java.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-From 9b9287cde20ea57578cf07efb2a96ed4cc0da36f Mon Sep 17 00:00:00 2001
-From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
-Date: Thu, 7 Sep 2017 07:22:07 +0000
-Subject: [PATCH] 2017-09-07 Matthias Klose <doko@ubuntu.com>
-
- * include/x86_64-signal.h (HANDLE_DIVIDE_OVERFLOW): Replace
- 'struct ucontext' with ucontext_t.
- * include/i386-signal.h (HANDLE_DIVIDE_OVERFLOW): Likewise.
- * include/s390-signal.h (HANDLE_DIVIDE_OVERFLOW): Likewise.
-
-
-git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251832 138bc75d-0d04-0410-961f-82ee72b054a4
----
- libjava/include/i386-signal.h | 2 +-
- libjava/include/s390-signal.h | 2 +-
- libjava/include/x86_64-signal.h | 2 +-
- 4 files changed, 10 insertions(+), 3 deletions(-)
-
-diff --git a/libjava/include/i386-signal.h b/libjava/include/i386-signal.h
-index c2409b0..ef77e7e 100644
---- a/libjava/include/i386-signal.h
-+++ b/libjava/include/i386-signal.h
-@@ -29,7 +29,7 @@ static void _Jv_##_name (int, siginfo_t *, \
- #define HANDLE_DIVIDE_OVERFLOW \
- do \
- { \
-- struct ucontext *_uc = (struct ucontext *)_p; \
-+ ucontext_t *_uc = (ucontext_t *)_p; \
- gregset_t &_gregs = _uc->uc_mcontext.gregs; \
- unsigned char *_eip = (unsigned char *)_gregs[REG_EIP]; \
- \
-diff --git a/libjava/include/s390-signal.h b/libjava/include/s390-signal.h
-index 4ca4c10..9261b52 100644
---- a/libjava/include/s390-signal.h
-+++ b/libjava/include/s390-signal.h
-@@ -51,7 +51,7 @@ do \
- struct \
- { \
- unsigned long int uc_flags; \
-- struct ucontext *uc_link; \
-+ ucontext_t *uc_link; \
- stack_t uc_stack; \
- mcontext_t uc_mcontext; \
- unsigned long sigmask[2]; \
-diff --git a/libjava/include/x86_64-signal.h b/libjava/include/x86_64-signal.h
-index 12383b5..e36c5a3 100644
---- a/libjava/include/x86_64-signal.h
-+++ b/libjava/include/x86_64-signal.h
-@@ -28,7 +28,7 @@ static void _Jv_##_name (int, siginfo_t *, \
- #define HANDLE_DIVIDE_OVERFLOW \
- do \
- { \
-- struct ucontext *_uc = (struct ucontext *)_p; \
-+ ucontext_t *_uc = (ucontext_t *)_p; \
- gregset_t &_gregs = _uc->uc_mcontext.gregs; \
- unsigned char *_rip = (unsigned char *)_gregs[REG_RIP]; \
- \
---
-2.9.3
-
diff --git a/packages/gcc/ucontext_t.patch b/packages/gcc/ucontext_t.patch
deleted file mode 100644
index a4f04b47..00000000
--- a/packages/gcc/ucontext_t.patch
+++ /dev/null
@@ -1,189 +0,0 @@
-From ecf0d1a107133c715763940c2b197aa814710e1b Mon Sep 17 00:00:00 2001
-From: jsm28 <jsm28@138bc75d-0d04-0410-961f-82ee72b054a4>
-Date: Tue, 4 Jul 2017 10:25:10 +0000
-Subject: [PATCH] Use ucontext_t not struct ucontext in linux-unwind.h files.
-
-Current glibc no longer gives the ucontext_t type the tag struct
-ucontext, to conform with POSIX namespace rules. This requires
-various linux-unwind.h files in libgcc, that were previously using
-struct ucontext, to be fixed to use ucontext_t instead. This is
-similar to the removal of the struct siginfo tag from siginfo_t some
-years ago.
-
-This patch changes those files to use ucontext_t instead. As the
-standard name that should be unconditionally safe, so this is not
-restricted to architectures supported by glibc, or conditioned on the
-glibc version.
-
-Tested compilation together with current glibc with glibc's
-build-many-glibcs.py.
-
- * config/aarch64/linux-unwind.h (aarch64_fallback_frame_state),
- config/alpha/linux-unwind.h (alpha_fallback_frame_state),
- config/bfin/linux-unwind.h (bfin_fallback_frame_state),
- config/i386/linux-unwind.h (x86_64_fallback_frame_state,
- x86_fallback_frame_state), config/m68k/linux-unwind.h (struct
- uw_ucontext), config/nios2/linux-unwind.h (struct nios2_ucontext),
- config/pa/linux-unwind.h (pa32_fallback_frame_state),
- config/sh/linux-unwind.h (sh_fallback_frame_state),
- config/tilepro/linux-unwind.h (tile_fallback_frame_state),
- config/xtensa/linux-unwind.h (xtensa_fallback_frame_state): Use
- ucontext_t instead of struct ucontext.
-
-
-git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@249958 138bc75d-0d04-0410-961f-82ee72b054a4
----
- libgcc/config/aarch64/linux-unwind.h | 2 +-
- libgcc/config/alpha/linux-unwind.h | 2 +-
- libgcc/config/bfin/linux-unwind.h | 2 +-
- libgcc/config/i386/linux-unwind.h | 4 ++--
- libgcc/config/m68k/linux-unwind.h | 2 +-
- libgcc/config/nios2/linux-unwind.h | 2 +-
- libgcc/config/pa/linux-unwind.h | 2 +-
- libgcc/config/sh/linux-unwind.h | 2 +-
- libgcc/config/tilepro/linux-unwind.h | 2 +-
- libgcc/config/xtensa/linux-unwind.h | 2 +-
- 11 files changed, 25 insertions(+), 11 deletions(-)
-
-diff --git a/libgcc/config/aarch64/linux-unwind.h b/libgcc/config/aarch64/linux-unwind.h
-index 86d17b1..909f68f 100644
---- a/libgcc/config/aarch64/linux-unwind.h
-+++ b/libgcc/config/aarch64/linux-unwind.h
-@@ -52,7 +52,7 @@ aarch64_fallback_frame_state (struct _Unwind_Context *context,
- struct rt_sigframe
- {
- siginfo_t info;
-- struct ucontext uc;
-+ ucontext_t uc;
- };
-
- struct rt_sigframe *rt_;
-diff --git a/libgcc/config/alpha/linux-unwind.h b/libgcc/config/alpha/linux-unwind.h
-index d65474f..9a226b1 100644
---- a/libgcc/config/alpha/linux-unwind.h
-+++ b/libgcc/config/alpha/linux-unwind.h
-@@ -51,7 +51,7 @@ alpha_fallback_frame_state (struct _Unwind_Context *context,
- {
- struct rt_sigframe {
- siginfo_t info;
-- struct ucontext uc;
-+ ucontext_t uc;
- } *rt_ = context->cfa;
- sc = &rt_->uc.uc_mcontext;
- }
-diff --git a/libgcc/config/bfin/linux-unwind.h b/libgcc/config/bfin/linux-unwind.h
-index 0c270e4..7fa95d2 100644
---- a/libgcc/config/bfin/linux-unwind.h
-+++ b/libgcc/config/bfin/linux-unwind.h
-@@ -52,7 +52,7 @@ bfin_fallback_frame_state (struct _Unwind_Context *context,
- void *puc;
- char retcode[8];
- siginfo_t info;
-- struct ucontext uc;
-+ ucontext_t uc;
- } *rt_ = context->cfa;
-
- /* The void * cast is necessary to avoid an aliasing warning.
-diff --git a/libgcc/config/i386/linux-unwind.h b/libgcc/config/i386/linux-unwind.h
-index e54bf73..d35fc45 100644
---- a/libgcc/config/i386/linux-unwind.h
-+++ b/libgcc/config/i386/linux-unwind.h
-@@ -58,7 +58,7 @@ x86_64_fallback_frame_state (struct _Unwind_Context *context,
- if (*(unsigned char *)(pc+0) == 0x48
- && *(unsigned long long *)(pc+1) == RT_SIGRETURN_SYSCALL)
- {
-- struct ucontext *uc_ = context->cfa;
-+ ucontext_t *uc_ = context->cfa;
- /* The void * cast is necessary to avoid an aliasing warning.
- The aliasing warning is correct, but should not be a problem
- because it does not alias anything. */
-@@ -138,7 +138,7 @@ x86_fallback_frame_state (struct _Unwind_Context *context,
- siginfo_t *pinfo;
- void *puc;
- siginfo_t info;
-- struct ucontext uc;
-+ ucontext_t uc;
- } *rt_ = context->cfa;
- /* The void * cast is necessary to avoid an aliasing warning.
- The aliasing warning is correct, but should not be a problem
-diff --git a/libgcc/config/m68k/linux-unwind.h b/libgcc/config/m68k/linux-unwind.h
-index fb79a4d..b2f5ea4 100644
---- a/libgcc/config/m68k/linux-unwind.h
-+++ b/libgcc/config/m68k/linux-unwind.h
-@@ -33,7 +33,7 @@ see the files COPYING3 and COPYING.RUNTIME respectively. If not, see
- /* <sys/ucontext.h> is unfortunately broken right now. */
- struct uw_ucontext {
- unsigned long uc_flags;
-- struct ucontext *uc_link;
-+ ucontext_t *uc_link;
- stack_t uc_stack;
- mcontext_t uc_mcontext;
- unsigned long uc_filler[80];
-diff --git a/libgcc/config/nios2/linux-unwind.h b/libgcc/config/nios2/linux-unwind.h
-index dff1c20..1d88afe 100644
---- a/libgcc/config/nios2/linux-unwind.h
-+++ b/libgcc/config/nios2/linux-unwind.h
-@@ -38,7 +38,7 @@ struct nios2_mcontext {
-
- struct nios2_ucontext {
- unsigned long uc_flags;
-- struct ucontext *uc_link;
-+ ucontext_t *uc_link;
- stack_t uc_stack;
- struct nios2_mcontext uc_mcontext;
- sigset_t uc_sigmask; /* mask last for extensibility */
-diff --git a/libgcc/config/pa/linux-unwind.h b/libgcc/config/pa/linux-unwind.h
-index 0149468..9157535 100644
---- a/libgcc/config/pa/linux-unwind.h
-+++ b/libgcc/config/pa/linux-unwind.h
-@@ -80,7 +80,7 @@ pa32_fallback_frame_state (struct _Unwind_Context *context,
- struct sigcontext *sc;
- struct rt_sigframe {
- siginfo_t info;
-- struct ucontext uc;
-+ ucontext_t uc;
- } *frame;
-
- /* rt_sigreturn trampoline:
-diff --git a/libgcc/config/sh/linux-unwind.h b/libgcc/config/sh/linux-unwind.h
-index e63091f..67033f0 100644
---- a/libgcc/config/sh/linux-unwind.h
-+++ b/libgcc/config/sh/linux-unwind.h
-@@ -180,7 +180,7 @@ sh_fallback_frame_state (struct _Unwind_Context *context,
- {
- struct rt_sigframe {
- siginfo_t info;
-- struct ucontext uc;
-+ ucontext_t uc;
- } *rt_ = context->cfa;
- /* The void * cast is necessary to avoid an aliasing warning.
- The aliasing warning is correct, but should not be a problem
-diff --git a/libgcc/config/tilepro/linux-unwind.h b/libgcc/config/tilepro/linux-unwind.h
-index fd83ba7..e3c9ef0 100644
---- a/libgcc/config/tilepro/linux-unwind.h
-+++ b/libgcc/config/tilepro/linux-unwind.h
-@@ -61,7 +61,7 @@ tile_fallback_frame_state (struct _Unwind_Context *context,
- struct rt_sigframe {
- unsigned char save_area[C_ABI_SAVE_AREA_SIZE];
- siginfo_t info;
-- struct ucontext uc;
-+ ucontext_t uc;
- } *rt_;
-
- /* Return if this is not a signal handler. */
-diff --git a/libgcc/config/xtensa/linux-unwind.h b/libgcc/config/xtensa/linux-unwind.h
-index 9a67b5d..98b7ea6 100644
---- a/libgcc/config/xtensa/linux-unwind.h
-+++ b/libgcc/config/xtensa/linux-unwind.h
-@@ -67,7 +67,7 @@ xtensa_fallback_frame_state (struct _Unwind_Context *context,
-
- struct rt_sigframe {
- siginfo_t info;
-- struct ucontext uc;
-+ ucontext_t uc;
- } *rt_;
-
- /* movi a2, __NR_rt_sigreturn; syscall */
---
-2.9.3
-
diff --git a/packages/gcc/zstd.patch b/packages/gcc/zstd.patch
deleted file mode 100644
index 8fb7583a..00000000
--- a/packages/gcc/zstd.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- a/gcc/Makefile.in
-+++ b/gcc/Makefile.in
-@@ -1075,7 +1075,8 @@ GNATMAKE = @GNATMAKE@
- # Libs needed (at present) just for jcf-dump.
- LDEXP_LIB = @LDEXP_LIB@
-
--ZSTD_LIB = @ZSTD_LIB@
-+ZSTD_INC = @ZSTD_CPPFLAGS@
-+ZSTD_LIB = @ZSTD_LDFLAGS@ @ZSTD_LIB@
-
- # Likewise, for use in the tools that must run on this machine
- # even if we are cross-building GCC.
-@@ -2275,7 +2276,7 @@ CFLAGS-version.o += -DBASEVER=$(BASEVER_s) -DDATESTAMP=$(DATESTAMP_s) \
- version.o: $(REVISION) $(DATESTAMP) $(BASEVER) $(DEVPHASE)
-
- # lto-compress.o needs $(ZLIBINC) added to the include flags.
--CFLAGS-lto-compress.o += $(ZLIBINC)
-+CFLAGS-lto-compress.o += $(ZLIBINC) $(ZSTD_INC)
-
- CFLAGS-lto-streamer-in.o += -DTARGET_MACHINE=\"$(target_noncanonical)\"
-
---- a/gcc/configure
-+++ b/gcc/configure
-@@ -786,6 +786,8 @@ LTLIBICONV
- LIBICONV
- ZSTD_LIB
- ZSTD_INCLUDE
-+ZSTD_LDFLAGS
-+ZSTD_CPPFLAGS
- DL_LIB
- LDEXP_LIB
- EXTRA_GCC_LIBS
---- a/gcc/configure.ac
-+++ b/gcc/configure.ac
-@@ -1339,6 +1339,8 @@ AC_SUBST(ZSTD_INCLUDE)
- AC_SUBST(ZSTD_LIB)
- ZSTD_CPPFLAGS=
- ZSTD_LDFLAGS=
-+AC_SUBST(ZSTD_CPPFLAGS)
-+AC_SUBST(ZSTD_LDFLAGS)
- AC_ARG_WITH(zstd,
- [AS_HELP_STRING([--with-zstd=PATH],
- [specify prefix directory for installed zstd library.
diff --git a/packages/libvips/package.py b/packages/libvips/package.py
index ab8a8849..19db301d 100644
--- a/packages/libvips/package.py
+++ b/packages/libvips/package.py
@@ -12,14 +12,26 @@ class Libvips(AutotoolsPackage):
little memory."""
homepage = "https://libvips.github.io/libvips/"
- url = "https://github.com/libvips/libvips/releases/download/v8.9.0/vips-8.9.0.tar.gz"
+ url = "https://github.com/libvips/libvips/releases/download/v8.15.3/vips-8.15.3.tar.xz"
git = "https://github.com/libvips/libvips.git"
+ license("LGPL-2.1-or-later", checked_by="wdconinc")
+
+ version("8.15.3", sha256="3e27d9f536eafad64013958fe9e8a1964c90b564c731d49db7c1a1c11b1052a0")
version("8.13.3", sha256="4eff5cdc8dbe1a05a926290a99014e20ba386f5dcca38d9774bef61413435d4c")
version("8.10.5", sha256="a4eef2f5334ab6dbf133cd3c6d6394d5bdb3e76d5ea4d578b02e1bc3d9e1cfd8")
version("8.9.1", sha256="45633798877839005016c9d3494e98dee065f5cb9e20f4552d3b315b8e8bce91")
version("8.9.0", sha256="97334a5e70aff343d2587f23cb8068fc846a58cd937c89a446142ccf00ea0349")
+ build_system(
+ conditional("autotools", when="@:8.13"),
+ conditional("meson", when="@8.13:"),
+ default="meson",
+ )
+
+ depends_on("c", type="build") # generated
+ depends_on("cxx", type="build") # generated
+
variant("fftw", default=True, description="Uses FFTW3 for fourier transforms.")
variant("jpeg", default=False, description="Enable JPEG support")
@@ -32,10 +44,7 @@ class Libvips(AutotoolsPackage):
# TODO: Add more variants!
- # begin EBRAINS (added)
depends_on("pkgconfig", type="build")
- # end EBRAINS
-
depends_on("glib")
depends_on("expat")
@@ -43,7 +52,7 @@ class Libvips(AutotoolsPackage):
depends_on("libjpeg", when="+jpeg")
depends_on("libtiff", when="+tiff")
depends_on("libpng", when="+png")
- depends_on("poppler", when="+poppler")
+ depends_on("poppler +glib", when="+poppler")
# begin EBRAINS (added): to fix build errors
depends_on("gobject-introspection")
@@ -51,3 +60,7 @@ class Libvips(AutotoolsPackage):
depends_on("pango")
depends_on("libtiff")
# end EBRAINS
+
+ def url_for_version(self, version):
+ ext = "xz" if version >= Version("8.14") else "gz"
+ return f"https://github.com/libvips/libvips/releases/download/v{version}/vips-{version}.tar.{ext}"
diff --git a/packages/libxcb/package.py b/packages/libxcb/package.py
index 2cb1418c..dcaff208 100644
--- a/packages/libxcb/package.py
+++ b/packages/libxcb/package.py
@@ -6,26 +6,44 @@
from spack.package import *
-class Libxcb(AutotoolsPackage):
+class Libxcb(AutotoolsPackage, XorgPackage):
"""The X protocol C-language Binding (XCB) is a replacement
for Xlib featuring a small footprint, latency hiding, direct
access to the protocol, improved threading support, and
extensibility."""
homepage = "https://xcb.freedesktop.org/"
- url = "https://xorg.freedesktop.org/archive/individual/lib/libxcb-1.14.tar.xz"
+ xorg_mirror_path = "lib/libxcb-1.14.tar.xz"
+ license("MIT")
+
+ maintainers("wdconinc")
+
+ version("1.17.0", sha256="599ebf9996710fea71622e6e184f3a8ad5b43d0e5fa8c4e407123c88a59a6d55")
+ version("1.16.1", sha256="f24d187154c8e027b358fc7cb6588e35e33e6a92f11c668fe77396a7ae66e311")
+ version("1.16", sha256="4348566aa0fbf196db5e0a576321c65966189210cb51328ea2bb2be39c711d71")
+ version("1.15", sha256="cc38744f817cf6814c847e2df37fcb8997357d72fa4bcbc228ae0fe47219a059")
version("1.14", sha256="a55ed6db98d43469801262d81dc2572ed124edc3db31059d4e9916eb9f844c34")
- version("1.13", sha256="0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb")
+ version(
+ "1.13",
+ sha256="0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb",
+ url="https://xcb.freedesktop.org/dist/libxcb-1.13.tar.gz",
+ deprecated=True,
+ )
+
+ depends_on("c", type="build") # generated
depends_on("libpthread-stubs")
depends_on("libxau@0.99.2:")
depends_on("libxdmcp")
# libxcb 1.X requires xcb-proto >= 1.X
- depends_on("xcb-proto")
- depends_on("xcb-proto@1.14:", when="@1.14")
- depends_on("xcb-proto@1.13:", when="@1.13")
+ depends_on("xcb-proto", type="build")
+ depends_on("xcb-proto@1.17:", when="@1.17", type="build")
+ depends_on("xcb-proto@1.16:", when="@1.16", type="build")
+ depends_on("xcb-proto@1.15:", when="@1.15", type="build")
+ depends_on("xcb-proto@1.14:", when="@1.14", type="build")
+ depends_on("xcb-proto@1.13:", when="@1.13", type="build")
# begin EBRAINS (deleted): break cyclic dependency in python+tkinter
# depends_on("python", type="build")
@@ -33,14 +51,6 @@ class Libxcb(AutotoolsPackage):
depends_on("pkgconfig", type="build")
depends_on("util-macros", type="build")
- def url_for_version(self, version):
- if version >= Version("1.14"):
- url = "https://xorg.freedesktop.org/archive/individual/lib/libxcb-{0}.tar.xz"
- else:
- url = "https://xcb.freedesktop.org/dist/libxcb-{0}.tar.gz"
-
- return url.format(version)
-
def configure_args(self):
config_args = []
@@ -51,4 +61,18 @@ class Libxcb(AutotoolsPackage):
return config_args
def patch(self):
- filter_file("typedef struct xcb_auth_info_t {", "typedef struct {", "src/xcb.h")
\ No newline at end of file
+ filter_file("typedef struct xcb_auth_info_t {", "typedef struct {", "src/xcb.h")
+
+ # libxcb fails to build with non-UTF-8 locales, see:
+ # https://www.linuxfromscratch.org/blfs/view/git/x/libxcb.html
+ # https://gitlab.freedesktop.org/xorg/lib/libxcb/-/merge_requests/53 (merged in 1.17.0)
+ # https://gitlab.freedesktop.org/xorg/lib/libxcb/-/merge_requests/60
+ # If a newer release can be verified to build with LC_ALL=en_US.ISO-8859-1,
+ # then we can limit the following function, e.g.
+ # when("@:1.17")
+ def setup_build_environment(self, env):
+ env.set("LC_ALL", "C.UTF-8")
+
+ # begin EBRAINS (deleted): break cyclic dependency in python+tkinter
+ # depends_on("python", type="build")
+ # end EBRAINS
diff --git a/packages/llvm/constexpr_longdouble.patch b/packages/llvm/constexpr_longdouble.patch
deleted file mode 100644
index 8b90001d..00000000
--- a/packages/llvm/constexpr_longdouble.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From 3bf63cf3b366d3a57cf5cbad4112a6abf6c0c3b1 Mon Sep 17 00:00:00 2001
-From: Marshall Clow <mclow.lists@gmail.com>
-Date: Tue, 2 Apr 2019 14:46:36 +0000
-Subject: [PATCH] Special case some duration arithmetic for GCC and PPC because
- their long double constant folding is broken. Fixes PR#39696.
-
-llvm-svn: 357478
----
- libcxx/include/thread | 5 +++++
- 1 file changed, 5 insertions(+)
-
-diff --git a/libcxx/include/thread b/libcxx/include/thread
-index df06ff70f8e37f22f4108be8e5e79a38052a11dd..400459ae7f32c4d7cd24b2d85c49d789500e432d 100644
---- a/libcxx/include/thread
-+++ b/libcxx/include/thread
-@@ -434,7 +434,12 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d)
- using namespace chrono;
- if (__d > duration<_Rep, _Period>::zero())
- {
-+#if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__)
-+ // GCC's long double const folding is incomplete for IBM128 long doubles.
-+ _LIBCPP_CONSTEXPR duration<long double> _Max = duration<long double>(ULLONG_MAX/1000000000ULL) ;
-+#else
- _LIBCPP_CONSTEXPR duration<long double> _Max = nanoseconds::max();
-+#endif
- nanoseconds __ns;
- if (__d < _Max)
- {
diff --git a/packages/llvm/constexpr_longdouble_9.0.patch b/packages/llvm/constexpr_longdouble_9.0.patch
deleted file mode 100644
index 9a62f270..00000000
--- a/packages/llvm/constexpr_longdouble_9.0.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-From d9a42ec98adcb1ebc0c3837715df4e5a50c7ccc0 Mon Sep 17 00:00:00 2001
-From: "Joel E. Denny" <jdenny.ornl@gmail.com>
-Date: Wed, 10 Jun 2020 12:40:43 -0400
-Subject: [PATCH] [libc++] Work around gcc/Power9 bug in `include/thread`
-
-This fixes PR39696, which breaks the libcxx build with gcc (I tested
-7.5.0) on Power9. This fix was suggested at
-
-https://bugs.llvm.org/show_bug.cgi?id=39696#c38
-
-but never applied. It just reverts 0583d9ea8d5e, which reverses
-components of the original fix in 3bf63cf3b366, which is correct.
-
-Fixes https://llvm.org/PR39696
-
-Reviewed By: ldionne
-
-Differential Revision: https://reviews.llvm.org/D81438
----
- libcxx/include/thread | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/libcxx/include/thread b/libcxx/include/thread
-index 22aa4f201295867cff57b7a944e6b7bd67b22ad3..6eff1800acdbef09eae4417eee977fa350c596ea 100644
---- a/libcxx/include/thread
-+++ b/libcxx/include/thread
-@@ -365,9 +365,9 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d)
- {
- #if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__)
- // GCC's long double const folding is incomplete for IBM128 long doubles.
-- _LIBCPP_CONSTEXPR duration<long double> _Max = nanoseconds::max();
--#else
- _LIBCPP_CONSTEXPR duration<long double> _Max = duration<long double>(ULLONG_MAX/1000000000ULL) ;
-+#else
-+ _LIBCPP_CONSTEXPR duration<long double> _Max = nanoseconds::max();
- #endif
- nanoseconds __ns;
- if (__d < _Max)
diff --git a/packages/llvm/detection_test.yaml b/packages/llvm/detection_test.yaml
new file mode 100644
index 00000000..860b3061
--- /dev/null
+++ b/packages/llvm/detection_test.yaml
@@ -0,0 +1,104 @@
+paths:
+- layout:
+ - executables:
+ - "bin/clang-3.9"
+ - "bin/clang++-3.9"
+ script: |
+ echo "clang version 3.9.1-19ubuntu1 (tags/RELEASE_391/rc2)"
+ echo "Target: x86_64-pc-linux-gnu"
+ echo "Thread model: posix"
+ echo "InstalledDir: /usr/bin"
+ platforms: ["darwin", "linux"]
+ results:
+ - spec: 'llvm@3.9.1 +clang~lld~lldb'
+ extra_attributes:
+ compilers:
+ c: ".*/bin/clang-3.9$"
+ cxx: ".*/bin/clang[+][+]-3.9$"
+
+# `~` and other weird characters in the version string
+- layout:
+ - executables:
+ - "bin/clang-6.0"
+ - "bin/clang++-6.0"
+ script: |
+ echo "clang version 6.0.1-svn334776-1~exp1~20181018152737.116 (branches/release_60)"
+ echo "Target: x86_64-pc-linux-gnu"
+ echo "Thread model: posix"
+ echo "InstalledDir: /usr/bin",
+
+ platforms: ["darwin", "linux"]
+ results:
+ - spec: 'llvm@6.0.1 +clang~lld~lldb'
+ extra_attributes:
+ compilers:
+ c: ".*/bin/clang-6.0$"
+ cxx: ".*/bin/clang[+][+]-6.0$"
+- layout:
+ - executables:
+ - "bin/clang-9.0"
+ - "bin/clang++-9.0"
+ script: |
+ echo "clang version 9.0.1-+201911131414230800840845a1eea-1~exp1~20191113231141.78"
+ echo "Target: x86_64-pc-linux-gnu"
+ echo "Thread model: posix"
+ echo "InstalledDir: /usr/bin"
+
+ platforms: ["darwin", "linux"]
+ results:
+ - spec: 'llvm@9.0.1 +clang~lld~lldb'
+ extra_attributes:
+ compilers:
+ c: ".*/bin/clang-9.0$"
+ cxx: ".*/bin/clang[+][+]-9.0$"
+
+# Multiple LLVM packages in the same prefix
+- layout:
+ - executables:
+ - "bin/clang-8"
+ - "bin/clang++-8"
+ script: |
+ echo "clang version 8.0.0-3~ubuntu18.04.2 (tags/RELEASE_800/final)"
+ echo "Target: x86_64-pc-linux-gnu"
+ echo "Thread model: posix"
+ echo "InstalledDir: /usr/bin"
+ - executables:
+ - "bin/ld.lld-8"
+ script: 'echo "LLD 8.0.0 (compatible with GNU linkers)"'
+ - executables:
+ - "bin/lldb"
+ script: 'echo "lldb version 8.0.0"'
+ - executables:
+ - "bin/clang-3.9"
+ - "bin/clang++-3.9"
+ script: |
+ echo "clang version 3.9.1-19ubuntu1 (tags/RELEASE_391/rc2)"
+ echo "Target: x86_64-pc-linux-gnu"
+ echo "Thread model: posix"
+ echo "InstalledDir: /usr/bin"
+ platforms: ["darwin", "linux"]
+ results:
+ - spec: 'llvm@8.0.0+clang+lld+lldb'
+ extra_attributes:
+ compilers:
+ c: ".*/bin/clang-8$"
+ cxx: ".*/bin/clang[+][+]-8$"
+
+ - spec: 'llvm@3.9.1+clang~lld~lldb'
+ extra_attributes:
+ compilers:
+ c: ".*/bin/clang-3.9$"
+ cxx: ".*/bin/clang[+][+]-3.9$"
+
+# Apple Clang should not be detected
+- layout:
+ - executables:
+ - "bin/clang"
+ - "bin/clang++"
+ script: |
+ echo "Apple clang version 11.0.0 (clang-1100.0.33.8)"
+ echo "Target: x86_64-apple-darwin19.5.0"
+ echo "Thread model: posix"
+ echo "InstalledDir: /Library/Developer/CommandLineTools/usr/bin"
+ platforms: ["darwin"]
+ results: []
diff --git a/packages/llvm/libomp-libflags-as-list.patch b/packages/llvm/libomp-libflags-as-list.patch
deleted file mode 100644
index 995f55a4..00000000
--- a/packages/llvm/libomp-libflags-as-list.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff --git a/openmp/runtime/cmake/LibompHandleFlags.cmake b/openmp/runtime/cmake/LibompHandleFlags.cmake
-index 9e19e59ba17d..f92fa12d851a 100644
---- a/openmp/runtime/cmake/LibompHandleFlags.cmake
-+++ b/openmp/runtime/cmake/LibompHandleFlags.cmake
-@@ -144,7 +144,8 @@ function(libomp_get_libflags libflags)
- endif()
- set(libflags_local ${libflags_local} ${LIBOMP_LIBFLAGS})
- libomp_setup_flags(libflags_local)
-- set(${libflags} ${libflags_local} PARENT_SCOPE)
-+ libomp_string_to_list("${libflags_local}" libflags_local_list)
-+ set(${libflags} ${libflags_local_list} PARENT_SCOPE)
- endfunction()
-
- # Fortran flags
diff --git a/packages/llvm/lldb_external_ncurses-10.patch b/packages/llvm/lldb_external_ncurses-10.patch
deleted file mode 100644
index 34ed0e3c..00000000
--- a/packages/llvm/lldb_external_ncurses-10.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff --git a/lldb/include/lldb/Host/Config.h.cmake b/lldb/include/lldb/Host/Config.h.cmake
---- a/lldb/include/lldb/Host/Config.h.cmake
-+++ b/lldb/include/lldb/Host/Config.h.cmake
-@@ -38,6 +38,8 @@
-
- #cmakedefine01 LLDB_ENABLE_CURSES
-
-+#cmakedefine01 CURSES_HAVE_NCURSES_CURSES_H
-+
- #cmakedefine01 LLDB_ENABLE_LIBEDIT
-
- #cmakedefine01 LLDB_ENABLE_LIBXML2
-diff --git a/lldb/source/Core/IOHandlerCursesGUI.cpp b/lldb/source/Core/IOHandlerCursesGUI.cpp
---- a/lldb/source/Core/IOHandlerCursesGUI.cpp
-+++ b/lldb/source/Core/IOHandlerCursesGUI.cpp
-@@ -10,9 +10,14 @@
- #include "lldb/Host/Config.h"
-
- #if LLDB_ENABLE_CURSES
-+#if CURSES_HAVE_NCURSES_CURSES_H
-+#include <ncurses/curses.h>
-+#include <ncurses/panel.h>
-+#else
- #include <curses.h>
- #include <panel.h>
- #endif
-+#endif
-
- #if defined(__APPLE__)
- #include <deque>
-
diff --git a/packages/llvm/llvm-gcc11.patch b/packages/llvm/llvm-gcc11.patch
deleted file mode 100644
index 8e081e87..00000000
--- a/packages/llvm/llvm-gcc11.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- a/llvm/utils/benchmark/src/benchmark_register.h
-+++ b/llvm/utils/benchmark/src/benchmark_register.h
-@@ -2,6 +2,7 @@
- #define BENCHMARK_REGISTER_H
-
- #include <vector>
-+#include <limits>
-
- #include "check.h"
diff --git a/packages/llvm/llvm13-thread.patch b/packages/llvm/llvm13-thread.patch
deleted file mode 100644
index 0067a930..00000000
--- a/packages/llvm/llvm13-thread.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- spack-src/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake.org 2022-02-08 14:58:13.000000000 +0900
-+++ spack-src/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake 2022-02-08 13:58:53.000000000 +0900
-@@ -276,4 +276,5 @@
- endif()
- endif()
-
--set(OPENMP_PTHREAD_LIB ${LLVM_PTHREAD_LIB})
-+find_package(Threads REQUIRED)
-+set(OPENMP_PTHREAD_LIB ${CMAKE_THREAD_LIBS_INIT})
---- spack-src/openmp/libomptarget/src/CMakeLists.txt.org 2022-02-09 08:49:35.000000000 +0900
-+++ spack-src/openmp/libomptarget/src/CMakeLists.txt 2022-02-09 08:50:18.000000000 +0900
-@@ -36,6 +36,7 @@
- endif()
- target_link_libraries(omptarget PRIVATE
- ${CMAKE_DL_LIBS}
-+ ${OPENMP_PTHREAD_LIB}
- "-Wl,--version-script=${CMAKE_CURRENT_SOURCE_DIR}/exports")
-
- # Install libomptarget under the lib destination folder.
diff --git a/packages/llvm/llvm14-hwloc-ompd.patch b/packages/llvm/llvm14-hwloc-ompd.patch
deleted file mode 100644
index bdae92e0..00000000
--- a/packages/llvm/llvm14-hwloc-ompd.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- a/openmp/libompd/src/CMakeLists.txt
-+++ b/openmp/libompd/src/CMakeLists.txt
-@@ -44,6 +44,10 @@
- ${LIBOMP_SRC_DIR}
- )
-
-+if(${LIBOMP_USE_HWLOC})
-+ include_directories(${LIBOMP_HWLOC_INSTALL_DIR}/include)
-+endif()
-+
- INSTALL( TARGETS ompd
- LIBRARY DESTINATION ${OPENMP_INSTALL_LIBDIR}
- ARCHIVE DESTINATION ${OPENMP_INSTALL_LIBDIR}
diff --git a/packages/llvm/llvm17-18-thread.patch b/packages/llvm/llvm17-18-thread.patch
new file mode 100644
index 00000000..7e337433
--- /dev/null
+++ b/packages/llvm/llvm17-18-thread.patch
@@ -0,0 +1,22 @@
+diff --git a/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake b/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake
+index 1f2a50667c4f..d3ff232f6bd3 100644
+--- a/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake
++++ b/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake
+@@ -280,4 +280,5 @@ if (NOT LIBOMPTARGET_CUDA_TOOLKIT_ROOT_DIR_PRESET AND
+ endif()
+ endif()
+
+-set(OPENMP_PTHREAD_LIB ${LLVM_PTHREAD_LIB})
++find_package(Threads REQUIRED)
++set(OPENMP_PTHREAD_LIB Threads::Threads)
+diff --git a/openmp/libomptarget/src/CMakeLists.txt b/openmp/libomptarget/src/CMakeLists.txt
+index 071ec61889a2..b782c3b07e6f 100644
+--- a/openmp/libomptarget/src/CMakeLists.txt.orig 2024-03-26 14:30:52.000000000 +0900
++++ b/openmp/libomptarget/src/CMakeLists.txt 2024-03-26 14:34:02.000000000 +0900
+@@ -41,5 +41,6 @@
+
+ if (LIBOMP_HAVE_VERSION_SCRIPT_FLAG)
+ target_link_libraries(omptarget PRIVATE
++ ${OPENMP_PTHREAD_LIB}
+ "-Wl,--version-script=${CMAKE_CURRENT_SOURCE_DIR}/exports")
+ endif()
diff --git a/packages/llvm/llvm17-fujitsu.patch b/packages/llvm/llvm17-fujitsu.patch
new file mode 100644
index 00000000..f960830c
--- /dev/null
+++ b/packages/llvm/llvm17-fujitsu.patch
@@ -0,0 +1,28 @@
+diff --git a/lldb/include/lldb/Utility/LLDBAssert.h_org b/lldb/include/lldb/Utility/LLDBAssert.h
+index aeef3e5..2f14ff3 100644
+--- a/lldb/include/lldb/Utility/LLDBAssert.h_org
++++ b/lldb/include/lldb/Utility/LLDBAssert.h
+@@ -14,7 +14,7 @@
+ #ifndef NDEBUG
+ #define lldbassert(x) assert(x)
+ #else
+-#if defined(__clang__)
++#if defined(__clang__) && !defined(__CLANG_FUJITSU)
+ // __FILE_NAME__ is a Clang-specific extension that functions similar to
+ // __FILE__ but only renders the last path component (the filename) instead of
+ // an invocation dependent full path to that file.
+
+diff --git runtimes/CMakeLists.txt_org runtimes/CMakeLists.txt
+--- a/runtimes/CMakeLists.txt_org
++++ b/runtimes/CMakeLists.txt
+@@ -6,2 +6,2 @@
+ include(${LLVM_COMMON_CMAKE_UTILS}/Modules/CMakePolicy.cmake
+ NO_POLICY_SCOPE)
+
++string(REPLACE "-Nclang" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
++string(REPLACE "-Nnofjprof" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
++string(REPLACE "-Nfjprof" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
++
+ project(Runtimes C CXX ASM)
+
+ list(INSERT CMAKE_MODULE_PATH 0
diff --git a/packages/llvm/llvm4-lld-ELF-Symbols.patch b/packages/llvm/llvm4-lld-ELF-Symbols.patch
deleted file mode 100644
index 1a86cda3..00000000
--- a/packages/llvm/llvm4-lld-ELF-Symbols.patch
+++ /dev/null
@@ -1,112 +0,0 @@
---- a/lldb/include/lldb/Utility/TaskPool.h
-+++ b/lldb/include/lldb/Utility/TaskPool.h
-@@ -33,6 +33,7 @@
- #include <queue>
- #include <thread>
- #include <vector>
-+#include <functional>
-
- // Global TaskPool class for running tasks in parallel on a set of worker thread
- // created the first
-# Fix lld templates: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=230463
---- a/lld/ELF/LTO.cpp
-+++ b/lld/ELF/LTO.cpp
-@@ -158,7 +158,7 @@
- return Ret;
- }
-
--template void BitcodeCompiler::template add<ELF32LE>(BitcodeFile &);
--template void BitcodeCompiler::template add<ELF32BE>(BitcodeFile &);
--template void BitcodeCompiler::template add<ELF64LE>(BitcodeFile &);
--template void BitcodeCompiler::template add<ELF64BE>(BitcodeFile &);
-+template void BitcodeCompiler::add<ELF32LE>(BitcodeFile &);
-+template void BitcodeCompiler::add<ELF32BE>(BitcodeFile &);
-+template void BitcodeCompiler::add<ELF64LE>(BitcodeFile &);
-+template void BitcodeCompiler::add<ELF64BE>(BitcodeFile &);
---- a/lld/ELF/Symbols.cpp
-+++ b/lld/ELF/Symbols.cpp
-@@ -343,45 +343,45 @@
- template bool SymbolBody::hasThunk<ELF64LE>() const;
- template bool SymbolBody::hasThunk<ELF64BE>() const;
-
--template uint32_t SymbolBody::template getVA<ELF32LE>(uint32_t) const;
--template uint32_t SymbolBody::template getVA<ELF32BE>(uint32_t) const;
--template uint64_t SymbolBody::template getVA<ELF64LE>(uint64_t) const;
--template uint64_t SymbolBody::template getVA<ELF64BE>(uint64_t) const;
--
--template uint32_t SymbolBody::template getGotVA<ELF32LE>() const;
--template uint32_t SymbolBody::template getGotVA<ELF32BE>() const;
--template uint64_t SymbolBody::template getGotVA<ELF64LE>() const;
--template uint64_t SymbolBody::template getGotVA<ELF64BE>() const;
--
--template uint32_t SymbolBody::template getGotOffset<ELF32LE>() const;
--template uint32_t SymbolBody::template getGotOffset<ELF32BE>() const;
--template uint64_t SymbolBody::template getGotOffset<ELF64LE>() const;
--template uint64_t SymbolBody::template getGotOffset<ELF64BE>() const;
--
--template uint32_t SymbolBody::template getGotPltVA<ELF32LE>() const;
--template uint32_t SymbolBody::template getGotPltVA<ELF32BE>() const;
--template uint64_t SymbolBody::template getGotPltVA<ELF64LE>() const;
--template uint64_t SymbolBody::template getGotPltVA<ELF64BE>() const;
--
--template uint32_t SymbolBody::template getThunkVA<ELF32LE>() const;
--template uint32_t SymbolBody::template getThunkVA<ELF32BE>() const;
--template uint64_t SymbolBody::template getThunkVA<ELF64LE>() const;
--template uint64_t SymbolBody::template getThunkVA<ELF64BE>() const;
--
--template uint32_t SymbolBody::template getGotPltOffset<ELF32LE>() const;
--template uint32_t SymbolBody::template getGotPltOffset<ELF32BE>() const;
--template uint64_t SymbolBody::template getGotPltOffset<ELF64LE>() const;
--template uint64_t SymbolBody::template getGotPltOffset<ELF64BE>() const;
--
--template uint32_t SymbolBody::template getPltVA<ELF32LE>() const;
--template uint32_t SymbolBody::template getPltVA<ELF32BE>() const;
--template uint64_t SymbolBody::template getPltVA<ELF64LE>() const;
--template uint64_t SymbolBody::template getPltVA<ELF64BE>() const;
--
--template uint32_t SymbolBody::template getSize<ELF32LE>() const;
--template uint32_t SymbolBody::template getSize<ELF32BE>() const;
--template uint64_t SymbolBody::template getSize<ELF64LE>() const;
--template uint64_t SymbolBody::template getSize<ELF64BE>() const;
-+template uint32_t SymbolBody::getVA<ELF32LE>(uint32_t) const;
-+template uint32_t SymbolBody::getVA<ELF32BE>(uint32_t) const;
-+template uint64_t SymbolBody::getVA<ELF64LE>(uint64_t) const;
-+template uint64_t SymbolBody::getVA<ELF64BE>(uint64_t) const;
-+
-+template uint32_t SymbolBody::getGotVA<ELF32LE>() const;
-+template uint32_t SymbolBody::getGotVA<ELF32BE>() const;
-+template uint64_t SymbolBody::getGotVA<ELF64LE>() const;
-+template uint64_t SymbolBody::getGotVA<ELF64BE>() const;
-+
-+template uint32_t SymbolBody::getGotOffset<ELF32LE>() const;
-+template uint32_t SymbolBody::getGotOffset<ELF32BE>() const;
-+template uint64_t SymbolBody::getGotOffset<ELF64LE>() const;
-+template uint64_t SymbolBody::getGotOffset<ELF64BE>() const;
-+
-+template uint32_t SymbolBody::getGotPltVA<ELF32LE>() const;
-+template uint32_t SymbolBody::getGotPltVA<ELF32BE>() const;
-+template uint64_t SymbolBody::getGotPltVA<ELF64LE>() const;
-+template uint64_t SymbolBody::getGotPltVA<ELF64BE>() const;
-+
-+template uint32_t SymbolBody::getThunkVA<ELF32LE>() const;
-+template uint32_t SymbolBody::getThunkVA<ELF32BE>() const;
-+template uint64_t SymbolBody::getThunkVA<ELF64LE>() const;
-+template uint64_t SymbolBody::getThunkVA<ELF64BE>() const;
-+
-+template uint32_t SymbolBody::getGotPltOffset<ELF32LE>() const;
-+template uint32_t SymbolBody::getGotPltOffset<ELF32BE>() const;
-+template uint64_t SymbolBody::getGotPltOffset<ELF64LE>() const;
-+template uint64_t SymbolBody::getGotPltOffset<ELF64BE>() const;
-+
-+template uint32_t SymbolBody::getPltVA<ELF32LE>() const;
-+template uint32_t SymbolBody::getPltVA<ELF32BE>() const;
-+template uint64_t SymbolBody::getPltVA<ELF64LE>() const;
-+template uint64_t SymbolBody::getPltVA<ELF64BE>() const;
-+
-+template uint32_t SymbolBody::getSize<ELF32LE>() const;
-+template uint32_t SymbolBody::getSize<ELF32BE>() const;
-+template uint64_t SymbolBody::getSize<ELF64LE>() const;
-+template uint64_t SymbolBody::getSize<ELF64BE>() const;
-
- template class elf::Undefined<ELF32LE>;
- template class elf::Undefined<ELF32BE>;
diff --git a/packages/llvm/llvm5-lld-ELF-Symbols.patch b/packages/llvm/llvm5-lld-ELF-Symbols.patch
deleted file mode 100644
index 727647d3..00000000
--- a/packages/llvm/llvm5-lld-ELF-Symbols.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-# Fix lld templates: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=230463
---- a/lld/ELF/Symbols.cpp
-+++ b/lld/ELF/Symbols.cpp
-@@ -383,17 +383,17 @@
- return B.getName();
- }
-
--template uint32_t SymbolBody::template getSize<ELF32LE>() const;
--template uint32_t SymbolBody::template getSize<ELF32BE>() const;
--template uint64_t SymbolBody::template getSize<ELF64LE>() const;
--template uint64_t SymbolBody::template getSize<ELF64BE>() const;
-+template uint32_t SymbolBody::getSize<ELF32LE>() const;
-+template uint32_t SymbolBody::getSize<ELF32BE>() const;
-+template uint64_t SymbolBody::getSize<ELF64LE>() const;
-+template uint64_t SymbolBody::getSize<ELF64BE>() const;
-
--template bool DefinedRegular::template isMipsPIC<ELF32LE>() const;
--template bool DefinedRegular::template isMipsPIC<ELF32BE>() const;
--template bool DefinedRegular::template isMipsPIC<ELF64LE>() const;
--template bool DefinedRegular::template isMipsPIC<ELF64BE>() const;
-+template bool DefinedRegular::isMipsPIC<ELF32LE>() const;
-+template bool DefinedRegular::isMipsPIC<ELF32BE>() const;
-+template bool DefinedRegular::isMipsPIC<ELF64LE>() const;
-+template bool DefinedRegular::isMipsPIC<ELF64BE>() const;
-
--template uint32_t SharedSymbol::template getAlignment<ELF32LE>() const;
--template uint32_t SharedSymbol::template getAlignment<ELF32BE>() const;
--template uint32_t SharedSymbol::template getAlignment<ELF64LE>() const;
--template uint32_t SharedSymbol::template getAlignment<ELF64BE>() const;
-+template uint32_t SharedSymbol::getAlignment<ELF32LE>() const;
-+template uint32_t SharedSymbol::getAlignment<ELF32BE>() const;
-+template uint32_t SharedSymbol::getAlignment<ELF64LE>() const;
-+template uint32_t SharedSymbol::getAlignment<ELF64BE>() const;
diff --git a/packages/llvm/llvm5-sanitizer-ustat.patch b/packages/llvm/llvm5-sanitizer-ustat.patch
deleted file mode 100644
index 531a3c5d..00000000
--- a/packages/llvm/llvm5-sanitizer-ustat.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-# <sys/ustat.h> has been removed from glibc 2.28,
-# backport fix from llvm-6.0.1:
---- a/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.cc
-+++ b/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.cc
-@@ -159,1 +159,0 @@
--#include <sys/ustat.h>
-@@ -252,5 +252,17 @@
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
-- unsigned struct_ustat_sz = sizeof(struct ustat);
-+ // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which
-+ // has been removed from glibc 2.28.
-+#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \
-+ || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \
-+ || defined(__x86_64__)
-+#define SIZEOF_STRUCT_USTAT 32
-+#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \
-+ || defined(__powerpc__) || defined(__s390__)
-+#define SIZEOF_STRUCT_USTAT 20
-+#else
-+#error Unknown size of struct ustat
-+#endif
-+ unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT;
- unsigned struct_rlimit64_sz = sizeof(struct rlimit64);
- unsigned struct_statvfs64_sz = sizeof(struct statvfs64);
diff --git a/packages/llvm/llvm_py37.patch b/packages/llvm/llvm_py37.patch
deleted file mode 100644
index 478be879..00000000
--- a/packages/llvm/llvm_py37.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-From ecdefed7f6ba11421fe1ecc6c13a135ab7bcda73 Mon Sep 17 00:00:00 2001
-From: Pavel Labath <labath@google.com>
-Date: Mon, 23 Jul 2018 11:37:36 +0100
-Subject: [PATCH] Fix PythonString::GetString for >=python-3.7
-
-The return value of PyUnicode_AsUTF8AndSize is now "const char *".
----
- .../Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp | 6 ++++--
- 1 file changed, 4 insertions(+), 2 deletions(-)
-
-diff --git a/tools/lldb/source/Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp b/tools/lldb/source/Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp
-index 6a9d57d5a..94f16b2c7 100644
---- a/lldb/source/Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp
-+++ b/lldb/source/Plugins/ScriptInterpreter/Python/PythonDataObjects.cpp
-@@ -404,14 +404,16 @@ llvm::StringRef PythonString::GetString() const {
- return llvm::StringRef();
-
- Py_ssize_t size;
-- char *c;
-+ const char *data;
-
- #if PY_MAJOR_VERSION >= 3
-- c = PyUnicode_AsUTF8AndSize(m_py_obj, &size);
-+ data = PyUnicode_AsUTF8AndSize(m_py_obj, &size);
- #else
-+ char *c;
- PyString_AsStringAndSize(m_py_obj, &c, &size);
-+ data = c;
- #endif
-- return llvm::StringRef(c, size);
-+ return llvm::StringRef(data, size);
- }
-
- size_t PythonString::GetSize() const {
---
-2.18.0.233.g985f88cf7e-goog
-
diff --git a/packages/llvm/llvm_python_path.patch b/packages/llvm/llvm_python_path.patch
deleted file mode 100644
index 9f821cc3..00000000
--- a/packages/llvm/llvm_python_path.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff --git a/compiler-rt/cmake/Modules/AddCompilerRT.cmake b/compiler-rt/cmake/Modules/AddCompilerRT.cmake
-index dab55707338..6f4c6791141 100644
---- a/compiler-rt/cmake/Modules/AddCompilerRT.cmake
-+++ b/compiler-rt/cmake/Modules/AddCompilerRT.cmake
-@@ -612,6 +612,9 @@ macro(add_custom_libcxx name prefix)
- CMAKE_OBJDUMP
- CMAKE_STRIP
- CMAKE_SYSROOT
-+ PYTHON_EXECUTABLE
-+ Python3_EXECUTABLE
-+ Python2_EXECUTABLE
- CMAKE_SYSTEM_NAME)
- foreach(variable ${PASSTHROUGH_VARIABLES})
- get_property(is_value_set CACHE ${variable} PROPERTY VALUE SET)
diff --git a/packages/llvm/missing-includes.patch b/packages/llvm/missing-includes.patch
deleted file mode 100644
index e88b8fcf..00000000
--- a/packages/llvm/missing-includes.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-# https://github.com/spack/spack/issues/24270 (This hunk is upstream since llvm-10)
---- a/llvm/include/llvm/Demangle/MicrosoftDemangleNodes.h
-+++ b/llvm/include/llvm/Demangle/MicrosoftDemangleNodes.h
-@@ -4,6 +4,8 @@
- #include "llvm/Demangle/Compiler.h"
- #include "llvm/Demangle/StringView.h"
- #include <array>
-+#include <cstdint>
-+#include <string>
-
- class OutputStream;
-
-# https://github.com/spack/spack/pull/27233
---- a/llvm/utils/benchmark/src/benchmark_register.h
-+++ b/llvm/utils/benchmark/src/benchmark_register.h
-@@ -2,6 +2,7 @@
- #define BENCHMARK_REGISTER_H
-
- #include <vector>
-+#include <limits>
-
- #include "check.h"
-
diff --git a/packages/llvm/no_cyclades.patch b/packages/llvm/no_cyclades.patch
deleted file mode 100644
index 10f9d079..00000000
--- a/packages/llvm/no_cyclades.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-diff --git a/compiler-rt/lib/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/compiler-rt/lib/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
---- a/compiler-rt/lib/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
-+++ b/compiler-rt/lib/sanitizer_common/sanitizer_common_interceptors_ioctl.inc
-@@ -370,15 +370,6 @@
-
- #if SANITIZER_GLIBC
- // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE
-- _(CYGETDEFTHRESH, WRITE, sizeof(int));
-- _(CYGETDEFTIMEOUT, WRITE, sizeof(int));
-- _(CYGETMON, WRITE, struct_cyclades_monitor_sz);
-- _(CYGETTHRESH, WRITE, sizeof(int));
-- _(CYGETTIMEOUT, WRITE, sizeof(int));
-- _(CYSETDEFTHRESH, NONE, 0);
-- _(CYSETDEFTIMEOUT, NONE, 0);
-- _(CYSETTHRESH, NONE, 0);
-- _(CYSETTIMEOUT, NONE, 0);
- _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz);
- _(EQL_ENSLAVE, WRITE, struct_ifreq_sz);
- _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz);
-diff --git a/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.h b/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.h
---- a/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.h
-+++ b/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.h
-@@ -983,7 +983,6 @@
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
- extern unsigned struct_ax25_parms_struct_sz;
--extern unsigned struct_cyclades_monitor_sz;
- extern unsigned struct_input_keymap_entry_sz;
- extern unsigned struct_ipx_config_data_sz;
- extern unsigned struct_kbdiacrs_sz;
-@@ -1328,15 +1327,6 @@
- #endif // SANITIZER_LINUX
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
--extern unsigned IOCTL_CYGETDEFTHRESH;
--extern unsigned IOCTL_CYGETDEFTIMEOUT;
--extern unsigned IOCTL_CYGETMON;
--extern unsigned IOCTL_CYGETTHRESH;
--extern unsigned IOCTL_CYGETTIMEOUT;
--extern unsigned IOCTL_CYSETDEFTHRESH;
--extern unsigned IOCTL_CYSETDEFTIMEOUT;
--extern unsigned IOCTL_CYSETTHRESH;
--extern unsigned IOCTL_CYSETTIMEOUT;
- extern unsigned IOCTL_EQL_EMANCIPATE;
- extern unsigned IOCTL_EQL_ENSLAVE;
- extern unsigned IOCTL_EQL_GETMASTRCFG;
-diff --git a/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.cpp b/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.cpp
---- a/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.cpp
-+++ b/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.cpp
-@@ -143,7 +143,6 @@
- # include <sys/procfs.h>
- #endif
- #include <sys/user.h>
--#include <linux/cyclades.h>
- #include <linux/if_eql.h>
- #include <linux/if_plip.h>
- #include <linux/lp.h>
-@@ -460,7 +459,6 @@
-
- #if SANITIZER_GLIBC
- unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct);
-- unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor);
- #if EV_VERSION > (0x010000)
- unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry);
- #else
-@@ -824,15 +822,6 @@
- #endif // SANITIZER_LINUX
-
- #if SANITIZER_LINUX && !SANITIZER_ANDROID
-- unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH;
-- unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT;
-- unsigned IOCTL_CYGETMON = CYGETMON;
-- unsigned IOCTL_CYGETTHRESH = CYGETTHRESH;
-- unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT;
-- unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH;
-- unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT;
-- unsigned IOCTL_CYSETTHRESH = CYSETTHRESH;
-- unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT;
- unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE;
- unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE;
- unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG;
diff --git a/packages/llvm/package.py b/packages/llvm/package.py
index c6cf4897..b437b0ee 100644
--- a/packages/llvm/package.py
+++ b/packages/llvm/package.py
@@ -2,20 +2,40 @@
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
import os
import os.path
import re
import sys
import llnl.util.tty as tty
+from llnl.util.lang import classproperty
-import spack.build_environment
import spack.util.executable
+from spack.build_systems.cmake import get_cmake_prefix_path
from spack.package import *
+from spack.package_base import PackageBase
+
+
+class LlvmDetection(PackageBase):
+ """Base class to detect LLVM based compilers"""
+
+ compiler_version_argument = "--version"
+ c_names = ["clang"]
+ cxx_names = ["clang++"]
+
+ @classmethod
+ def filter_detected_exes(cls, prefix, exes_in_prefix):
+ # Executables like lldb-vscode-X are daemon listening on some port and would hang Spack
+ # during detection. clang-cl, clang-cpp, etc. are dev tools that we don't need to test
+ reject = re.compile(
+ r"-(vscode|cpp|cl|ocl|gpu|tidy|rename|scan-deps|format|refactor|offload|"
+ r"check|query|doc|move|extdef|apply|reorder|change-namespace|"
+ r"include-fixer|import-test|dap|server)"
+ )
+ return [x for x in exes_in_prefix if not reject.search(x)]
-class Llvm(CMakePackage, CudaPackage):
+class Llvm(CMakePackage, CudaPackage, LlvmDetection, CompilerPackage):
"""The LLVM Project is a collection of modular and reusable compiler and
toolchain technologies. Despite its name, LLVM has little to do
with traditional virtual machines, though it does provide helpful
@@ -29,13 +49,28 @@ class Llvm(CMakePackage, CudaPackage):
git = "https://github.com/llvm/llvm-project"
maintainers("trws", "haampie", "skosukhin")
- tags = ["e4s"]
+ tags = ["e4s", "compiler"]
generator("ninja")
- family = "compiler" # Used by lmod
+ license("Apache-2.0")
version("main", branch="main")
+ version("19.1.3", sha256="e5106e2bef341b3f5e41340e4b6c6a58259f4021ad801acf14e88f1a84567b05")
+ version("19.1.2", sha256="622cb6c5e95a3bb7e9876c4696a65671f235bd836cfd0c096b272f6c2ada41e7")
+ version("19.1.1", sha256="115dfd98a353d05bffdab3f80db22f159da48aca0124e8c416f437adcd54b77f")
+ version("19.1.0", sha256="0a08341036ca99a106786f50f9c5cb3fbe458b3b74cab6089fd368d0edb2edfe")
+ version("18.1.8", sha256="09c08693a9afd6236f27a2ebae62cda656eba19021ef3f94d59e931d662d4856")
+ version("18.1.7", sha256="b60df7cbe02cef2523f7357120fb0d46cbb443791cde3a5fb36b82c335c0afc9")
+ version("18.1.6", sha256="01390edfae5b809e982b530ff9088e674c62b13aa92cb9dc1e067fa2cf501083")
+ version("18.1.5", sha256="d543309f55ae3f9b422108302b45c40f5696c96862f4bda8f5526955daa54284")
+ version("18.1.4", sha256="deca5a29e8b1d103ecc4badb3c304aca50d5cac6453364d88ee415dc55699dfb")
+ version("18.1.3", sha256="fc5a2fd176d73ceb17f4e522f8fe96d8dde23300b8c233476d3609f55d995a7a")
+ version("18.1.2", sha256="8d686d5ece6f12b09985cb382a3a530dc06bb6e7eb907f57c7f8bf2d868ebb0b")
+ version("18.1.1", sha256="62439f733311869dbbaf704ce2e02141d2a07092d952fc87ef52d1d636a9b1e4")
+ version("18.1.0", sha256="eb18f65a68981e94ea1a5aae4f02321b17da9e99f76bfdb983b953f4ba2d3550")
+ version("17.0.6", sha256="81494d32e6f12ea6f73d6d25424dbd2364646011bb8f7e345ca870750aa27de1")
+ version("17.0.5", sha256="432c1eda3d1c9379cd52a9bee8e0ea6f7b204bff5075895f963fd8e575aa4fb8")
version("17.0.4", sha256="46200b79f52a02fe26d0a43fd856ab6ceff49ab2a0b7c240ac4b700a6ada700c")
version("17.0.3", sha256="1e3d9d04fb5fbd8d0080042ad72c7e2a5c68788b014b186647a604dbbdd625d2")
version("17.0.2", sha256="dcba3eb486973dce45b6edfe618f3f29b703ae7e6ef9df65182fb50fb6fe4235")
@@ -83,6 +118,9 @@ class Llvm(CMakePackage, CudaPackage):
version("5.0.1", sha256="84ca454abf262579814a2a2b846569f6e0cb3e16dc33ca3642b4f1dff6fbafd3")
version("5.0.0", sha256="1f1843315657a4371d8ca37f01265fa9aae17dbcf46d2d0a95c1fdb3c6a4bab6")
+ depends_on("c", type="build")
+ depends_on("cxx", type="build")
+
variant(
"clang", default=True, description="Build the LLVM C/C++/Objective-C compiler frontend"
)
@@ -131,8 +169,12 @@ class Llvm(CMakePackage, CudaPackage):
"or as a project (with the compiler in use)",
)
+ variant("offload", default=True, when="@19:", description="Build the Offload subproject")
+ conflicts("+offload", when="~clang")
+
variant("libomptarget", default=True, description="Build the OpenMP offloading library")
conflicts("+libomptarget", when="~clang")
+ conflicts("+libomptarget", when="~offload @19:")
for _p in ["darwin", "windows"]:
conflicts("+libomptarget", when="platform={0}".format(_p))
del _p
@@ -239,6 +281,8 @@ class Llvm(CMakePackage, CudaPackage):
conflicts("+z3", when="~clang")
conflicts("+lua", when="@:10")
conflicts("+lua", when="~lldb")
+ # Python distutils were removed with 3.12 and are required to build LLVM <= 14
+ conflicts("^python@3.12:", when="@:14")
variant(
"zstd",
@@ -247,6 +291,9 @@ class Llvm(CMakePackage, CudaPackage):
description="Enable zstd support for static analyzer / lld",
)
+ provides("libllvm@19", when="@19.0.0:19")
+ provides("libllvm@18", when="@18.0.0:18")
+ provides("libllvm@17", when="@17.0.0:17")
provides("libllvm@16", when="@16.0.0:16")
provides("libllvm@15", when="@15.0.0:15")
provides("libllvm@14", when="@14.0.0:14")
@@ -308,19 +355,15 @@ class Llvm(CMakePackage, CudaPackage):
depends_on("swig", when="+lua")
depends_on("swig", when="+python")
depends_on("xz")
- # begin VISIONS: modified, bring upstream FIXME: maybe no longer needed
- depends_on("swig@2:4.0", when="@10:")
- depends_on("swig@3:4.0", when="@12:")
- # end VISIONS
-
- # Use ^swig cause it's triggered by both python & lua scripting in lldb
- with when("^swig"):
- depends_on("swig@2:", when="@10:")
- depends_on("swig@3:", when="@12:")
- depends_on("swig@4:", when="@17:")
- # Commits f0a25fe0b746f56295d5c02116ba28d2f965c175 and
- # 81fc5f7909a4ef5a8d4b5da2a10f77f7cb01ba63 fixed swig 4.1 support
- depends_on("swig@:4.0", when="@:15")
+
+ for _when_spec in ("+lldb+python", "+lldb+lua"):
+ with when(_when_spec):
+ depends_on("swig@2:", when="@10:")
+ depends_on("swig@3:", when="@12:")
+ depends_on("swig@4:", when="@17:")
+ # Commits f0a25fe0b746f56295d5c02116ba28d2f965c175 and
+ # 81fc5f7909a4ef5a8d4b5da2a10f77f7cb01ba63 fixed swig 4.1 support
+ depends_on("swig@:4.0", when="@:15")
# gold support, required for some features
depends_on("binutils+gold+ld+plugins+headers", when="+gold")
@@ -384,6 +427,19 @@ class Llvm(CMakePackage, CudaPackage):
# cuda_arch value must be specified
conflicts("cuda_arch=none", when="+cuda", msg="A value for cuda_arch must be specified.")
+ # clang/test/Misc/target-invalid-cpu-note.c
+ conflicts("cuda_arch=10")
+ conflicts("cuda_arch=11")
+ conflicts("cuda_arch=12")
+ conflicts("cuda_arch=13")
+ conflicts("cuda_arch=75", when="@:13")
+ conflicts("cuda_arch=80", when="@:13")
+ conflicts("cuda_arch=86", when="@:13")
+ conflicts("cuda_arch=87", when="@:15")
+ conflicts("cuda_arch=89", when="@:15")
+ conflicts("cuda_arch=90", when="@:15")
+ conflicts("cuda_arch=90a", when="@:17")
+
# LLVM bug https://bugs.llvm.org/show_bug.cgi?id=48234
# CMake bug: https://gitlab.kitware.com/cmake/cmake/-/issues/21469
# Fixed in upstream versions of both
@@ -486,6 +542,12 @@ class Llvm(CMakePackage, CudaPackage):
when="@14:15",
)
+ # missing <cstdint> include
+ patch(
+ "https://github.com/llvm/llvm-project/commit/ff1681ddb303223973653f7f5f3f3435b48a1983.patch?full_index=1",
+ sha256="c6ca6b925f150e8644ce756023797b7f94c9619c62507231f979edab1c09af78",
+ when="@6:13",
+ )
# fix building of older versions of llvm with newer versions of glibc
for compiler_rt_as in ["project", "runtime"]:
with when("compiler-rt={0}".format(compiler_rt_as)):
@@ -583,6 +645,10 @@ class Llvm(CMakePackage, CudaPackage):
# avoid build failed with Fujitsu compiler
patch("llvm13-fujitsu.patch", when="@13 %fj")
+ # avoid build failed with Fujitsu compiler since llvm17
+ patch("llvm17-fujitsu.patch", when="@17: %fj")
+ patch("llvm17-18-thread.patch", when="@17:18 %fj")
+
# patch for missing hwloc.h include for libompd
# see https://reviews.llvm.org/D123888
patch(
@@ -623,6 +689,8 @@ class Llvm(CMakePackage, CudaPackage):
patch("add-include-for-libelf-llvm-12-14.patch", when="@12:14")
patch("add-include-for-libelf-llvm-15.patch", when="@15")
+ patch("sanitizer-platform-limits-posix-xdr-macos.patch", when="@10:14 platform=darwin")
+
@when("@14:17")
def patch(self):
# https://github.com/llvm/llvm-project/pull/69458
@@ -633,47 +701,43 @@ class Llvm(CMakePackage, CudaPackage):
string=True,
)
- # The functions and attributes below implement external package
- # detection for LLVM. See:
- #
- # https://spack.readthedocs.io/en/latest/packaging_guide.html#making-a-package-discoverable-with-spack-external-find
- executables = ["clang", "flang", "ld.lld", "lldb"]
+ compiler_version_regex = (
+ # Normal clang compiler versions are left as-is
+ r"clang version ([^ )\n]+)-svn[~.\w\d-]*|"
+ # Don't include hyphenated patch numbers in the version
+ # (see https://github.com/spack/spack/pull/14365 for details)
+ r"clang version ([^ )\n]+?)-[~.\w\d-]*|"
+ r"clang version ([^ )\n]+)|"
+ # LLDB
+ r"lldb version ([^ )\n]+)|"
+ # LLD
+ r"LLD ([^ )\n]+) \(compatible with GNU linkers\)"
+ )
+ fortran_names = ["flang"]
- @classmethod
- def filter_detected_exes(cls, prefix, exes_in_prefix):
- result = []
- for exe in exes_in_prefix:
- # Executables like lldb-vscode-X are daemon listening
- # on some port and would hang Spack during detection.
- # clang-cl and clang-cpp are dev tools that we don't
- # need to test
- if any(x in exe for x in ("vscode", "cpp", "-cl", "-gpu")):
- continue
- result.append(exe)
- return result
+ @property
+ def supported_languages(self):
+ languages = []
+ if self.spec.satisfies("+clang"):
+ languages.extend(["c", "cxx"])
+ if self.spec.satisfies("+flang"):
+ languages.append("fortran")
+ return languages
+
+ @classproperty
+ def executables(cls):
+ return super().executables + [r"^ld\.lld(-\d+)?$", r"^lldb(-\d+)?$"]
@classmethod
def determine_version(cls, exe):
- version_regex = re.compile(
- # Normal clang compiler versions are left as-is
- r"clang version ([^ )\n]+)-svn[~.\w\d-]*|"
- # Don't include hyphenated patch numbers in the version
- # (see https://github.com/spack/spack/pull/14365 for details)
- r"clang version ([^ )\n]+?)-[~.\w\d-]*|"
- r"clang version ([^ )\n]+)|"
- # LLDB
- r"lldb version ([^ )\n]+)|"
- # LLD
- r"LLD ([^ )\n]+) \(compatible with GNU linkers\)"
- )
try:
compiler = Executable(exe)
- output = compiler("--version", output=str, error=str)
+ output = compiler(cls.compiler_version_argument, output=str, error=str)
if "Apple" in output:
return None
if "AMD" in output:
return None
- match = version_regex.search(output)
+ match = re.search(cls.compiler_version_regex, output)
if match:
return match.group(match.lastindex)
except spack.util.executable.ProcessError:
@@ -685,23 +749,23 @@ class Llvm(CMakePackage, CudaPackage):
@classmethod
def determine_variants(cls, exes, version_str):
+ # Do not need to reuse more general logic from CompilerPackage
+ # because LLVM has kindly named compilers
variants, compilers = ["+clang"], {}
lld_found, lldb_found = False, False
- for exe in exes:
- if "clang++" in exe:
- compilers["cxx"] = exe
- elif "clang" in exe:
- compilers["c"] = exe
- elif "flang" in exe:
+ for exe in sorted(exes, key=len):
+ name = os.path.basename(exe)
+ if "clang++" in name:
+ compilers.setdefault("cxx", exe)
+ elif "clang" in name:
+ compilers.setdefault("c", exe)
+ elif "flang" in name:
variants.append("+flang")
- compilers["fc"] = exe
- compilers["f77"] = exe
- elif "ld.lld" in exe:
+ compilers.setdefault("fortran", exe)
+ elif "ld.lld" in name:
lld_found = True
- compilers["ld"] = exe
- elif "lldb" in exe:
+ elif "lldb" in name:
lldb_found = True
- compilers["lldb"] = exe
variants.append("+lld" if lld_found else "~lld")
variants.append("+lldb" if lldb_found else "~lldb")
@@ -727,7 +791,7 @@ class Llvm(CMakePackage, CudaPackage):
if self.spec.external:
return self.spec.extra_attributes["compilers"].get("c", None)
result = None
- if "+clang" in self.spec:
+ if self.spec.satisfies("+clang"):
result = os.path.join(self.spec.prefix.bin, "clang")
return result
@@ -738,7 +802,7 @@ class Llvm(CMakePackage, CudaPackage):
if self.spec.external:
return self.spec.extra_attributes["compilers"].get("cxx", None)
result = None
- if "+clang" in self.spec:
+ if self.spec.satisfies("+clang"):
result = os.path.join(self.spec.prefix.bin, "clang++")
return result
@@ -749,7 +813,7 @@ class Llvm(CMakePackage, CudaPackage):
if self.spec.external:
return self.spec.extra_attributes["compilers"].get("fc", None)
result = None
- if "+flang" in self.spec:
+ if self.spec.satisfies("+flang"):
result = os.path.join(self.spec.prefix.bin, "flang")
return result
@@ -760,7 +824,7 @@ class Llvm(CMakePackage, CudaPackage):
if self.spec.external:
return self.spec.extra_attributes["compilers"].get("f77", None)
result = None
- if "+flang" in self.spec:
+ if self.spec.satisfies("+flang"):
result = os.path.join(self.spec.prefix.bin, "flang")
return result
@@ -794,10 +858,7 @@ class Llvm(CMakePackage, CudaPackage):
)
def flag_handler(self, name, flags):
- if name == "cxxflags":
- flags.append(self.compiler.cxx11_flag)
- return (None, flags, None)
- elif name == "ldflags" and self.spec.satisfies("%intel"):
+ if name == "ldflags" and self.spec.satisfies("%intel"):
flags.append("-shared-intel")
return (None, flags, None)
return (flags, None, None)
@@ -813,6 +874,14 @@ class Llvm(CMakePackage, CudaPackage):
os.symlink(bin, sym)
env.prepend_path("PATH", self.stage.path)
+ def setup_run_environment(self, env):
+ if self.spec.satisfies("+clang"):
+ env.set("CC", join_path(self.spec.prefix.bin, "clang"))
+ env.set("CXX", join_path(self.spec.prefix.bin, "clang++"))
+ if self.spec.satisfies("+flang"):
+ env.set("FC", join_path(self.spec.prefix.bin, "flang"))
+ env.set("F77", join_path(self.spec.prefix.bin, "flang"))
+
root_cmakelists_dir = "llvm"
def cmake_args(self):
@@ -820,13 +889,11 @@ class Llvm(CMakePackage, CudaPackage):
define = self.define
from_variant = self.define_from_variant
- python = spec["python"]
cmake_args = [
define("LLVM_REQUIRES_RTTI", True),
define("LLVM_ENABLE_RTTI", True),
define("LLVM_ENABLE_LIBXML2", False),
define("CLANG_DEFAULT_OPENMP_RUNTIME", "libomp"),
- define("PYTHON_EXECUTABLE", python.command.path),
define("LIBOMP_USE_HWLOC", True),
define("LIBOMP_HWLOC_INSTALL_DIR", spec["hwloc"].prefix),
from_variant("LLVM_ENABLE_ZSTD", "zstd"),
@@ -850,15 +917,10 @@ class Llvm(CMakePackage, CudaPackage):
if shlib_symbol_version is not None and shlib_symbol_version.value != "none":
cmake_args.append(define("LLVM_SHLIB_SYMBOL_VERSION", shlib_symbol_version.value))
- if python.version >= Version("3"):
- cmake_args.append(define("Python3_EXECUTABLE", python.command.path))
- else:
- cmake_args.append(define("Python2_EXECUTABLE", python.command.path))
-
projects = []
runtimes = []
- if "+cuda" in spec:
+ if spec.satisfies("+cuda"):
cmake_args.extend(
[
define("CUDA_TOOLKIT_ROOT_DIR", spec["cuda"].prefix),
@@ -872,7 +934,7 @@ class Llvm(CMakePackage, CudaPackage):
),
]
)
- if "openmp=runtime" in spec:
+ if spec.satisfies("openmp=runtime"):
cmake_args.append(define("LIBOMPTARGET_NVPTX_ENABLE_BCLIB", True))
else:
# still build libomptarget but disable cuda
@@ -887,7 +949,15 @@ class Llvm(CMakePackage, CudaPackage):
cmake_args.append(from_variant("LIBOMPTARGET_ENABLE_DEBUG", "libomptarget_debug"))
- if "+lldb" in spec:
+ if spec.satisfies("@14:"):
+ # The hsa-rocr-dev package may be pulled in through hwloc, which can lead to cmake
+ # finding libhsa and enabling the AMDGPU plugin. Since we don't support this yet,
+ # disable explicitly. See commit a05a0c3c2f8eefc80d84b7a87a23a4452d4a3087.
+ cmake_args.append(define("LIBOMPTARGET_BUILD_AMDGPU_PLUGIN", False))
+ if "python" in spec: # lit's Python needs to be set with this variable
+ cmake_args.append(define("python_executable", spec["python"].command.path))
+
+ if spec.satisfies("+lldb"):
projects.append("lldb")
cmake_args.extend(
[
@@ -898,59 +968,65 @@ class Llvm(CMakePackage, CudaPackage):
define("LLDB_ENABLE_LZMA", True),
]
)
- if spec["ncurses"].satisfies("+termlib"):
- cmake_args.append(define("LLVM_ENABLE_TERMINFO", True))
+ if spec.satisfies("@19:"):
+ cmake_args.append(define("LLDB_CURSES_LIBS", spec["ncurses"].libs))
else:
- cmake_args.append(define("LLVM_ENABLE_TERMINFO", False))
+ if spec["ncurses"].satisfies("+termlib"):
+ cmake_args.append(define("LLVM_ENABLE_TERMINFO", True))
+ else:
+ cmake_args.append(define("LLVM_ENABLE_TERMINFO", False))
if spec.version >= Version("10"):
cmake_args.append(from_variant("LLDB_ENABLE_PYTHON", "python"))
else:
- cmake_args.append(define("LLDB_DISABLE_PYTHON", "~python" in spec))
+ cmake_args.append(define("LLDB_DISABLE_PYTHON", spec.satisfies("~python")))
if spec.satisfies("@5.0.0: +python"):
cmake_args.append(define("LLDB_USE_SYSTEM_SIX", True))
- else:
+ elif spec.satisfies("@:19"):
cmake_args.append(define("LLVM_ENABLE_TERMINFO", False))
- if "+gold" in spec:
+ if spec.satisfies("+gold"):
cmake_args.append(define("LLVM_BINUTILS_INCDIR", spec["binutils"].prefix.include))
- if "+clang" in spec:
+ if spec.satisfies("+clang"):
projects.append("clang")
projects.append("clang-tools-extra")
- if "openmp=runtime" in spec:
+ if spec.satisfies("openmp=runtime"):
runtimes.append("openmp")
- elif "openmp=project" in spec:
+ elif spec.satisfies("openmp=project"):
projects.append("openmp")
- if "+libomptarget" in spec:
+ if spec.satisfies("+offload"):
+ runtimes.append("offload")
+
+ if spec.satisfies("+libomptarget"):
cmake_args.append(define("OPENMP_ENABLE_LIBOMPTARGET", True))
else:
cmake_args.append(define("OPENMP_ENABLE_LIBOMPTARGET", False))
- if "@8" in spec:
+ if spec.satisfies("@8"):
cmake_args.append(from_variant("CLANG_ANALYZER_ENABLE_Z3_SOLVER", "z3"))
- elif "@9:" in spec:
+ elif spec.satisfies("@9:"):
cmake_args.append(from_variant("LLVM_ENABLE_Z3_SOLVER", "z3"))
- if "+flang" in spec:
+ if spec.satisfies("+flang"):
projects.append("flang")
- if "+lld" in spec:
+ if spec.satisfies("+lld"):
projects.append("lld")
- if "compiler-rt=runtime" in spec:
+ if spec.satisfies("compiler-rt=runtime"):
runtimes.append("compiler-rt")
- elif "compiler-rt=project" in spec:
+ elif spec.satisfies("compiler-rt=project"):
projects.append("compiler-rt")
- if "libcxx=runtime" in spec:
+ if spec.satisfies("libcxx=runtime"):
runtimes.extend(["libcxx", "libcxxabi"])
- elif "libcxx=project" in spec:
+ elif spec.satisfies("libcxx=project"):
projects.extend(["libcxx", "libcxxabi"])
- if "+mlir" in spec:
+ if spec.satisfies("+mlir"):
projects.append("mlir")
- if "libunwind=runtime" in spec:
+ if spec.satisfies("libunwind=runtime"):
runtimes.append("libunwind")
- elif "libunwind=project" in spec:
+ elif spec.satisfies("libunwind=project"):
projects.append("libunwind")
- if "+polly" in spec:
+ if spec.satisfies("+polly"):
projects.append("polly")
cmake_args.append(define("LINK_POLLY_INTO_TOOLS", True))
@@ -964,6 +1040,14 @@ class Llvm(CMakePackage, CudaPackage):
# CMAKE_INSTALL_RPATH to it, which fails. Statically link libc++abi.a
# into libc++.so, linking with -lc++ or -stdlib=libc++ is enough.
define("LIBCXX_ENABLE_STATIC_ABI_LIBRARY", True),
+ # Make sure that CMake does not pick host-installed tools for the build
+ # Until #45535 is merged, prevent CMake from delivering incompatible
+ # system tools like python3.12 to older LLVM versions like LLVM-14:
+ define("CMAKE_FIND_PACKAGE_PREFER_CONFIG", True),
+ define("CMAKE_FIND_USE_PACKAGE_ROOT_PATH", False),
+ define("CMAKE_FIND_USE_SYSTEM_PACKAGE_REGISTRY", False),
+ define("CMAKE_FIND_USE_PACKAGE_REGISTRY", False),
+ define("CMAKE_FIND_USE_SYSTEM_PATH", False),
]
)
@@ -971,14 +1055,16 @@ class Llvm(CMakePackage, CudaPackage):
cmake_args.append(from_variant("LIBOMP_TSAN_SUPPORT", "libomp_tsan"))
- if self.compiler.name == "gcc":
+ # From clang 16 onwards we use a more precise --gcc-install-dir flag in post-install
+ # generated config files.
+ if self.spec.satisfies("@:15 %gcc"):
cmake_args.append(define("GCC_INSTALL_PREFIX", self.compiler.prefix))
if self.spec.satisfies("~code_signing platform=darwin"):
cmake_args.append(define("LLDB_USE_SYSTEM_DEBUGSERVER", True))
# LLDB test suite requires libc++
- if "libcxx=none" in spec:
+ if spec.satisfies("libcxx=none"):
cmake_args.append(define("LLDB_INCLUDE_TESTS", False))
# Enable building with CLT [and not require full Xcode]
@@ -991,12 +1077,44 @@ class Llvm(CMakePackage, CudaPackage):
# Semicolon seperated list of runtimes to enable
if runtimes:
+ # The older versions are not careful enough with the order of the runtimes.
+ # Instead of applying
+ # https://github.com/llvm/llvm-project/commit/06400a0142af8297b5d39b8f34a7c59db6f9910c,
+ # which might be incompatible with the version that we install,
+ # we sort the runtimes here according to the same order as
+ # in the aforementioned commit:
+ if self.spec.satisfies("@:14"):
+ runtimes_order = [
+ "libc",
+ "libunwind",
+ "libcxxabi",
+ "libcxx",
+ "compiler-rt",
+ "openmp",
+ ]
+ runtimes.sort(
+ key=lambda x: (
+ runtimes_order.index(x) if x in runtimes_order else len(runtimes_order)
+ )
+ )
+
+ # CMake args passed just to runtimes
+ runtime_cmake_args = [define("CMAKE_INSTALL_RPATH_USE_LINK_PATH", True)]
+
+ # When building runtimes, just-built clang has to know where GCC is.
+ gcc_install_dir_flag = get_gcc_install_dir_flag(spec, self.compiler)
+ if gcc_install_dir_flag:
+ runtime_cmake_args.extend(
+ [
+ define("CMAKE_C_FLAGS", gcc_install_dir_flag),
+ define("CMAKE_CXX_FLAGS", gcc_install_dir_flag),
+ ]
+ )
+
cmake_args.extend(
[
define("LLVM_ENABLE_RUNTIMES", runtimes),
- define(
- "RUNTIMES_CMAKE_ARGS", [define("CMAKE_INSTALL_RPATH_USE_LINK_PATH", True)]
- ),
+ define("RUNTIMES_CMAKE_ARGS", runtime_cmake_args),
]
)
@@ -1008,9 +1126,9 @@ class Llvm(CMakePackage, CudaPackage):
define = self.define
# unnecessary if we build openmp via LLVM_ENABLE_RUNTIMES
- if "+cuda openmp=project" in self.spec:
+ if self.spec.satisfies("+cuda openmp=project"):
ompdir = "build-bootstrapped-omp"
- prefix_paths = spack.build_environment.get_cmake_prefix_path(self)
+ prefix_paths = get_cmake_prefix_path(self)
prefix_paths.append(str(spec.prefix))
# rebuild libomptarget to get bytecode runtime library files
with working_dir(ompdir, create=True):
@@ -1034,15 +1152,31 @@ class Llvm(CMakePackage, CudaPackage):
cmake(*cmake_args)
ninja()
ninja("install")
- if "+python" in self.spec:
- install_tree("llvm/bindings/python", python_platlib)
+ if self.spec.satisfies("+python"):
+ if spec.version < Version("17.0.0"):
+ # llvm bindings were removed in v17:
+ # https://releases.llvm.org/17.0.1/docs/ReleaseNotes.html#changes-to-the-python-bindings
+ install_tree("llvm/bindings/python", python_platlib)
- if "+clang" in self.spec:
+ if self.spec.satisfies("+clang"):
install_tree("clang/bindings/python", python_platlib)
with working_dir(self.build_directory):
install_tree("bin", join_path(self.prefix, "libexec", "llvm"))
+ cfg_files = []
+ if spec.satisfies("+clang"):
+ cfg_files.extend(("clang.cfg", "clang++.cfg"))
+ if spec.satisfies("@19: +flang"):
+ # The config file is `flang.cfg` even though the executable is `flang-new`.
+ # `--gcc-install-dir` / `--gcc-toolchain` support was only added in LLVM 19.
+ cfg_files.append("flang.cfg")
+ gcc_install_dir_flag = get_gcc_install_dir_flag(spec, self.compiler)
+ if gcc_install_dir_flag:
+ for cfg in cfg_files:
+ with open(os.path.join(self.prefix.bin, cfg), "w") as f:
+ print(gcc_install_dir_flag, file=f)
+
def llvm_config(self, *args, **kwargs):
lc = Executable(self.prefix.bin.join("llvm-config"))
if not kwargs.get("output"):
@@ -1054,6 +1188,18 @@ class Llvm(CMakePackage, CudaPackage):
return ret
+def get_gcc_install_dir_flag(spec: Spec, compiler) -> Optional[str]:
+ """Get the --gcc-install-dir=... flag, so that clang does not do a system scan for GCC."""
+ if not spec.satisfies("@16: %gcc"):
+ return None
+ gcc = Executable(compiler.cc)
+ libgcc_path = gcc("-print-file-name=libgcc.a", output=str, fail_on_error=False).strip()
+ if not os.path.isabs(libgcc_path):
+ return None
+ libgcc_dir = os.path.dirname(libgcc_path)
+ return f"--gcc-install-dir={libgcc_dir}" if os.path.exists(libgcc_dir) else None
+
+
def get_llvm_targets_to_build(spec):
targets = spec.variants["targets"].value
@@ -1100,4 +1246,3 @@ def get_llvm_targets_to_build(spec):
llvm_targets.add("PowerPC")
return list(llvm_targets)
-
diff --git a/packages/llvm/sanitizer-platform-limits-posix-xdr-macos.patch b/packages/llvm/sanitizer-platform-limits-posix-xdr-macos.patch
new file mode 100644
index 00000000..d4477390
--- /dev/null
+++ b/packages/llvm/sanitizer-platform-limits-posix-xdr-macos.patch
@@ -0,0 +1,11 @@
+--- a/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.cpp
++++ b/compiler-rt/lib/sanitizer_common/sanitizer_platform_limits_posix.cpp
+@@ -1250,7 +1250,7 @@ CHECK_SIZE_AND_OFFSET(group, gr_passwd);
+ CHECK_SIZE_AND_OFFSET(group, gr_gid);
+ CHECK_SIZE_AND_OFFSET(group, gr_mem);
+
+-#if HAVE_RPC_XDR_H
++#if HAVE_RPC_XDR_H && !SANITIZER_MAC
+ CHECK_TYPE_SIZE(XDR);
+ CHECK_SIZE_AND_OFFSET(XDR, x_op);
+ CHECK_SIZE_AND_OFFSET(XDR, x_ops);
diff --git a/packages/llvm/thread-p9.patch b/packages/llvm/thread-p9.patch
deleted file mode 100644
index 140473a8..00000000
--- a/packages/llvm/thread-p9.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/libcxx/include/thread b/libcxx/include/thread
-index 02da703..d1677a1 100644
---- a/projects/libcxx/include/thread
-+++ b/projects/libcxx/include/thread
-@@ -368,9 +368,9 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d)
- {
- #if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__)
- // GCC's long double const folding is incomplete for IBM128 long doubles.
-- _LIBCPP_CONSTEXPR duration<long double> _Max = nanoseconds::max();
--#else
- _LIBCPP_CONSTEXPR duration<long double> _Max = duration<long double>(ULLONG_MAX/1000000000ULL) ;
-+#else
-+ _LIBCPP_CONSTEXPR duration<long double> _Max = nanoseconds::max();
- #endif
- nanoseconds __ns;
- if (__d < _Max)
diff --git a/packages/log4cxx/package.py b/packages/log4cxx/package.py
index 0cf8f7a9..eb0c9071 100644
--- a/packages/log4cxx/package.py
+++ b/packages/log4cxx/package.py
@@ -10,18 +10,42 @@ class Log4cxx(CMakePackage):
"""A C++ port of Log4j"""
homepage = "https://logging.apache.org/log4cxx/latest_stable/"
+ # begin EBRAINS (modified): fix url
url = "https://github.com/apache/logging-log4cxx/archive/refs/tags/rel/v1.2.0.tar.gz"
+ # end EBRAINS
maintainers("nicmcd")
- # begin EBRAINS (added): bring upstream (ref. spack@0.21.2)
+ license("Apache-2.0", checked_by="wdconinc")
+
+ # begin EBRAINS (modified): fix checksums
version("1.2.0", sha256="3e0af426011718c634194200cdd79b49ec13c322697bdcddef3d8b2ac9efd7b6")
- version("1.1.0", sha256="feb425ce35a391cf0927356bebb7da53f96c8a7aaf634aaf740e011203c732bb")
+ with default_args(deprecated=True):
+ # https://nvd.nist.gov/vuln/detail/CVE-2023-31038
+ version(
+ "0.12.1", sha256="567a4200c5b005a816c401e798d98294782950c7750eb3e285e851b970c8beed"
+ )
+ version(
+ "0.12.0", sha256="31730a17b8ff3f416256755b7aa6d7e95b167c670eb469eb9ff99aa006376e79"
+ )
# end EBRAINS
- version("0.12.1", sha256="567a4200c5b005a816c401e798d98294782950c7750eb3e285e851b970c8beed")
- version("0.12.0", sha256="31730a17b8ff3f416256755b7aa6d7e95b167c670eb469eb9ff99aa006376e79")
- variant("cxxstd", default="17", description="C++ standard", values=("11", "17"), multi=False)
+ variant(
+ "cxxstd",
+ default="17",
+ description="C++ standard",
+ values=("11", "17"),
+ multi=False,
+ when="@:1.1",
+ )
+ variant(
+ "cxxstd",
+ default="20",
+ description="C++ standard",
+ values=("11", "17", "20"),
+ multi=False,
+ when="@1.2:",
+ )
# begin EBRAINS (added)
variant("events_at_exit",
default=False,
@@ -34,6 +58,7 @@ class Log4cxx(CMakePackage):
depends_on("apr-util")
depends_on("apr")
depends_on("boost+thread+system", when="cxxstd=11")
+ depends_on("expat")
depends_on("zlib-api")
depends_on("zip")
diff --git a/packages/nanoflann/package.py b/packages/nanoflann/package.py
deleted file mode 100644
index 7dd9d7f3..00000000
--- a/packages/nanoflann/package.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class Nanoflann(CMakePackage):
- """a C++ header-only library for Nearest Neighbor (NN) search wih KD-trees."""
-
- homepage = "https://github.com/jlblancoc/nanoflann"
- url = "https://github.com/jlblancoc/nanoflann/archive/v1.2.3.tar.gz"
-
- # begin EBRAINS (added): add version
- version("1.5.4", sha256="a7f64d0bdff42614c561e52680b16de46c0edac9719f21f935c5e1f8b0654afc")
- # end EBRAINS
- version("1.4.3", sha256="cbcecf22bec528a8673a113ee9b0e134f91f1f96be57e913fa1f74e98e4449fa")
- version("1.2.3", sha256="5ef4dfb23872379fe9eb306aabd19c9df4cae852b72a923af01aea5e8d7a59c3")
-
- def patch(self):
- filter_file("-mtune=native", "", "CMakeLists.txt")
-
- def cmake_args(self):
- args = ["-DBUILD_SHARED_LIBS=ON"]
- return args
diff --git a/packages/netlib-xblas/package.py b/packages/netlib-xblas/package.py
deleted file mode 100644
index cc65577f..00000000
--- a/packages/netlib-xblas/package.py
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class NetlibXblas(AutotoolsPackage):
- """XBLAS is a reference implementation for extra precision BLAS.
-
- XBLAS is a reference implementation for the dense and banded BLAS
- routines, along with extended and mixed precision version. Extended
- precision is only used internally; input and output arguments remain
- the same as in the existing BLAS. Extra precisions is implemented as
- double-double (i.e., 128-bit total, 106-bit significand). Mixed
- precision permits some input/output arguments of different types
- (mixing real and complex) or precisions (mixing single and
- double). This implementation is proof of concept, and no attempt was
- made to optimize performance; performance should be as good as
- straightforward but careful code written by hand."""
-
- homepage = "https://www.netlib.org/xblas"
- url = "https://www.netlib.org/xblas/xblas.tar.gz"
-
- version("1.0.248", sha256="b5fe7c71c2da1ed9bcdc5784a12c5fa9fb417577513fe8a38de5de0007f7aaa1")
-
- variant("fortran", default=True, description="Build Fortran interfaces")
- variant("plain_blas", default=True, description="As part of XBLAS, build plain BLAS routines")
-
- provides("blas", when="+plain_blas")
-
- # begin EBRAINS (added)
- depends_on("m4", type="build")
- # end EBRAINS
-
- @property
- def libs(self):
- return find_libraries(["libxblas"], root=self.prefix, shared=False, recursive=True)
-
- def configure_args(self):
- args = []
-
- if self.spec.satisfies("~fortran"):
- args += ["--disable-fortran"]
-
- if self.spec.satisfies("~plain_blas"):
- args += ["--disable-plain-blas"]
-
- return args
-
- def install(self, spec, prefix):
- mkdirp(prefix.lib)
- install("libxblas.a", prefix.lib)
-
- if self.spec.satisfies("+plain_blas"):
- # XBLAS should be a drop-in BLAS replacement
- install("libxblas.a", join_path(prefix.lib, "libblas.a"))
-
- headers = [
- "f2c-bridge.h",
- "blas_dense_proto.h",
- "blas_enum.h",
- "blas_extended.h",
- "blas_extended_private.h",
- "blas_extended_proto.h",
- "blas_fpu.h",
- "blas_malloc.h",
- ]
- mkdirp(prefix.include)
- for h in headers:
- install(join_path("src", h), prefix.include)
-
- return
diff --git a/packages/nglview/package.py b/packages/nglview/package.py
deleted file mode 100644
index e86cd491..00000000
--- a/packages/nglview/package.py
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class Nglview(PythonPackage):
- """An IPython/Jupyter widget to interactively view molecular structures and trajectories.
- Utilizes the embeddable NGL Viewer for rendering."""
-
- # Homepage and download url
- homepage = "https://github.com/nglviewer/nglview"
- git = 'https://github.com/nglviewer/nglview.git'
- url = 'https://github.com/nglviewer/nglview/archive/refs/tags/v3.0.4.tar.gz'
-
- # Set the gitlab accounts of this package maintainers
- maintainers = ['dbeltran']
-
- # Versions
- version('master', branch='master')
- version('3.0.4', sha256='78b4413b796965a94045df0d584ec51e256c3dca5f366020439fe7e9744ce61b')
-
- # Dependencies
- depends_on('python@3.8:', type=('build', 'run'))
- depends_on('py-setuptools')
- depends_on('py-jupyter-packaging')
- depends_on('py-versioneer')
- depends_on('py-numpy', type=('run'))
- depends_on('py-ipywidgets', type=('run'))
-
- # Test
- @run_after('install')
- @on_package_attributes(run_tests=True)
- def check_install (self):
- python("-c", 'import nglview')
diff --git a/packages/open3d/package.py b/packages/open3d/package.py
index f3d2f626..c1faaa0b 100644
--- a/packages/open3d/package.py
+++ b/packages/open3d/package.py
@@ -13,14 +13,24 @@ from spack.package import *
class Open3d(CMakePackage, CudaPackage):
"""Open3D: A Modern Library for 3D Data Processing."""
- homepage = "http://www.open3d.org/"
+ homepage = "https://www.open3d.org/"
url = "https://github.com/isl-org/Open3D/archive/refs/tags/v0.13.0.tar.gz"
git = "https://github.com/isl-org/Open3D.git"
+ license("MIT")
+
# begin EBRAINS (added): add version
- version("0.18.0", tag="v0.18.0", submodules=True)
+ version(
+ "0.18.0", tag="v0.18.0", commit="0f06a149c4fb9406fd3e432a5cb0c024f38e2f0e", submodules=True
+ )
# end EBRAINS
- version("0.13.0", tag="v0.13.0", submodules=True)
+ version(
+ "0.13.0", tag="v0.13.0", commit="c3f9de224e13838a72da0e5565a7ba51038b0f11", submodules=True
+ )
+
+ depends_on("c", type="build") # generated
+ depends_on("cxx", type="build") # generated
+ depends_on("fortran", type="build") # generated
variant("python", default=False, description="Build the Python module")
@@ -159,9 +169,6 @@ class Open3d(CMakePackage, CudaPackage):
args.append(self.define("DEFINE_GLEW_NO_GLU", True))
# end EBRAINS
- if "+python" in self.spec:
- args.append(self.define("PYTHON_EXECUTABLE", self.spec["python"].command.path))
-
return args
def check(self):
@@ -189,11 +196,11 @@ class Open3d(CMakePackage, CudaPackage):
@run_after("install")
@on_package_attributes(run_tests=True)
- def test(self):
- if "+python" in self.spec:
- self.run_test(
- self.spec["python"].command.path,
- ["-c", "import open3d"],
- purpose="checking import of open3d",
- work_dir="spack-test",
- )
+ def test_open3d_import(self):
+ """Checking import of open3d"""
+ if "+python" not in self.spec:
+ return
+
+ with working_dir("spack-test"):
+ python = which(python.path)
+ python("-c", "import open3d")
diff --git a/packages/openbabel/gcc12-cmake.patch b/packages/openbabel/gcc12-cmake.patch
deleted file mode 100644
index c568c899..00000000
--- a/packages/openbabel/gcc12-cmake.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-From c0570bfeb2d7e0a6a6de1f257cf28e7f3cac8739 Mon Sep 17 00:00:00 2001
-From: Sam James <sam@gentoo.org>
-Date: Sun, 12 Jun 2022 11:23:59 +0100
-Subject: [PATCH] CMake: fix time check typo (fixes build failure w/ GCC 12)
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-Without this fixed check, we get a build failure with GCC 12:
-```
-/var/tmp/portage/sci-chemistry/openbabel-3.1.1_p20210225/work/openbabel-08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b/include/openbabel/obutil.h:65:14: error: �~@~Xclock�~@~Y was not declared in this scope; did you mean �~@~Xclock_t�~@~Y?
- 65 | start= clock();
- | ^~~~~
- | clock_t
-```
-
-Bug: https://bugs.gentoo.org/851510
----
- src/config.h.cmake | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/config.h.cmake b/src/config.h.cmake
-index 1c59c67699..26e5dde94f 100644
---- a/src/config.h.cmake
-+++ b/src/config.h.cmake
-@@ -182,8 +182,8 @@
- #define OB_MODULE_PATH "@OB_MODULE_PATH@"
-
- #ifndef TIME_WITH_SYS_TIME
-- #ifdef HAVE_SYS_TIME
-- #ifdef HAVE_TIME
-+ #ifdef HAVE_SYS_TIME_H
-+ #ifdef HAVE_TIME_H
- #define TIME_WITH_SYS_TIME 1
- #else
- #define TIME_WITH_SYS_TIME 0
-
diff --git a/packages/openbabel/package.py b/packages/openbabel/package.py
deleted file mode 100644
index 17641509..00000000
--- a/packages/openbabel/package.py
+++ /dev/null
@@ -1,97 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class Openbabel(CMakePackage):
- """Open Babel is a chemical toolbox designed to speak the many languages
- of chemical data. It's an open, collaborative project allowing anyone to
- search, convert, analyze, or store data from molecular modeling, chemistry,
- solid-state materials, biochemistry, or related areas."""
-
- homepage = "https://openbabel.org/wiki/Main_Page"
- url = "https://github.com/openbabel/openbabel/archive/openbabel-3-0-0.tar.gz"
- git = "https://github.com/openbabel/openbabel.git"
-
- maintainers("RMeli")
-
- version("master", branch="master")
- version("3.1.1", tag="openbabel-3-1-1", commit="cbd4db43f8908b874864280fdc03bf92569eebc1")
- version("3.1.0", tag="openbabel-3-1-0", commit="1e593abc1edf47352d5e8a0887654edf69a2f5f3")
- version("3.0.0", tag="openbabel-3-0-0", commit="49f9cfb32bd0bc6ea440639d338123eb27accbe2")
- version("2.4.1", tag="openbabel-2-4-1", commit="701f6049c483b1349118c2ff736a7f609a84dedd")
- version("2.4.0", tag="openbabel-2-4-0", commit="087f33320e6796f39e6a1da04f4de7ec46bec4af")
-
- variant("python", default=True, description="Build Python bindings")
- variant("gui", default=True, description="Build with GUI")
- variant("cairo", default=True, description="Build with Cairo (PNG output support)")
- variant("openmp", default=False, description="Build with OpenMP")
- variant("maeparser", default=False, description="Built with MAE parser")
- variant("coordgen", default=False, description="Build with Coordgen")
-
- extends("python", when="+python")
-
- depends_on("python", type=("build", "run"), when="+python")
- depends_on("cmake@3.1:", type="build")
- depends_on("pkgconfig", type="build")
- depends_on("swig@2.0:", type="build", when="+python")
-
- depends_on("boost +filesystem +iostreams +test")
- depends_on("cairo", when="+cairo") # required to support PNG depiction
- depends_on("pango", when="+cairo") # custom cairo requires custom pango
- depends_on("eigen@3.0:") # required if using the language bindings
- depends_on("libxml2") # required to read/write CML files, XML formats
- depends_on("zlib-api") # required to support reading gzipped files
- depends_on("rapidjson") # required to support JSON
- depends_on("libsm")
- depends_on("uuid")
-
- depends_on("maeparser", when="+maeparser")
- depends_on("coordgen", when="+coordgen")
-
- # Needed for Python 3.6 support
- patch("python-3.6-rtld-global.patch", when="@:2.4.1+python")
-
- # Convert tabs to spaces. Allows unit tests to pass
- patch("testpdbformat-tabs-to-spaces.patch", when="@:2.4.1")
-
- # begin EBRAINS (added)
- # CMake: fix time check typo (fixes build failure w/ GCC 12)
- patch("gcc12-cmake.patch", when="@:3.1.1")
- # end EBRAINS
-
- def cmake_args(self):
- spec = self.spec
- args = []
-
- if "+python" in spec:
- args.extend(
- [
- "-DPYTHON_BINDINGS=ON",
- "-DPYTHON_EXECUTABLE={0}".format(spec["python"].command.path),
- "-DRUN_SWIG=ON",
- ]
- )
- else:
- args.append("-DPYTHON_BINDINGS=OFF")
-
- args.append(self.define_from_variant("BUILD_GUI", "gui"))
- args.append(self.define_from_variant("ENABLE_OPENMP", "openmp"))
- args.append(self.define_from_variant("WITH_MAEPARSER", "maeparser"))
- args.append(self.define_from_variant("WITH_COORDGEN", "coordgen"))
-
- return args
-
- @run_after("install")
- @on_package_attributes(run_tests=True)
- def check_install(self):
- obabel = Executable(join_path(self.prefix.bin, "obabel"))
- obabel("-:C1=CC=CC=C1Br", "-omol")
-
- if "+python" in self.spec:
- python("-c", "import openbabel")
- if self.spec.version < Version("3.0.0"):
- python("-c", "import pybel")
diff --git a/packages/openbabel/python-3.6-rtld-global.patch b/packages/openbabel/python-3.6-rtld-global.patch
deleted file mode 100644
index 68cd56a1..00000000
--- a/packages/openbabel/python-3.6-rtld-global.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-The DLFCN module has been removed from python 3.6, as it is not
-documented. Same funtionality can be achive with the os module
-that makes available the os.RTLD_GLOBAL variable for dlopen()
-
-See https://github.com/openbabel/openbabel/pull/372 for the
-source of this patch. The original patch only affects the CMake
-file that SWIG uses to generate openbabel.py. This patch also
-includes changes to openbabel.py.
-
-diff -Nuar a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
---- a/scripts/CMakeLists.txt 2017-05-17 10:02:54.408527942 -0500
-+++ b/scripts/CMakeLists.txt 2017-05-17 10:04:09.701598715 -0500
-@@ -81,11 +81,8 @@
- COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
- COMMAND ${CMAKE_COMMAND} -E echo "import sys" > ob.py
- COMMAND ${CMAKE_COMMAND} -E echo "if sys.platform.find('linux'\) != -1:" >> ob.py
-- COMMAND ${CMAKE_COMMAND} -E echo " try:" >> ob.py
-- COMMAND ${CMAKE_COMMAND} -E echo " import dl" >> ob.py
-- COMMAND ${CMAKE_COMMAND} -E echo " except ImportError:" >> ob.py
-- COMMAND ${CMAKE_COMMAND} -E echo " import DLFCN as dl" >> ob.py
-- COMMAND ${CMAKE_COMMAND} -E echo " sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >> ob.py
-+ COMMAND ${CMAKE_COMMAND} -E echo " import os" >> ob.py
-+ COMMAND ${CMAKE_COMMAND} -E echo " sys.setdlopenflags(sys.getdlopenflags() | os.RTLD_GLOBAL)" >> ob.py
- COMMAND cat ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py >> ob.py
- COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py
- COMMAND ${CMAKE_COMMAND} -E remove ob.py
-diff -Nuar a/scripts/python/openbabel.py b/scripts/python/openbabel.py
---- a/scripts/python/openbabel.py 2017-05-17 10:02:54.398527534 -0500
-+++ b/scripts/python/openbabel.py 2017-05-17 10:04:26.705292138 -0500
-@@ -1,10 +1,7 @@
- import sys
- if sys.platform.find('linux') != -1:
-- try:
-- import dl
-- except ImportError:
-- import DLFCN as dl
-- sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
-+ import os
-+ sys.setdlopenflags(sys.getdlopenflags() | os.RTLD_GLOBAL)
- # This file was automatically generated by SWIG (http://www.swig.org).
- # Version 3.0.10
- #
diff --git a/packages/openbabel/testpdbformat-tabs-to-spaces.patch b/packages/openbabel/testpdbformat-tabs-to-spaces.patch
deleted file mode 100644
index 0a71a72e..00000000
--- a/packages/openbabel/testpdbformat-tabs-to-spaces.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-From 08cd38485d4cf1df8802da540f3018921dbc735e Mon Sep 17 00:00:00 2001
-From: "Adam J. Stewart" <ajstewart426@gmail.com>
-Date: Wed, 17 May 2017 10:56:23 -0500
-Subject: [PATCH] Convert tabs to spaces in testpdbformat.py
-
-See https://github.com/openbabel/openbabel/pull/1568
-
----
- test/testpdbformat.py | 12 ++++++------
- 1 file changed, 6 insertions(+), 6 deletions(-)
-
-diff --git a/test/testpdbformat.py b/test/testpdbformat.py
-index 40bd316..ceb8496 100644
---- a/test/testpdbformat.py
-+++ b/test/testpdbformat.py
-@@ -24,12 +24,12 @@ class TestPDBFormat(BaseTest):
-
- def testInsertionCodes(self):
- """
-- Testing a PDB entry with insertion codes to distinguish residues
-- upon conversion to FASTA.
-+ Testing a PDB entry with insertion codes to distinguish residues
-+ upon conversion to FASTA.
- """
- self.canFindExecutable("babel")
-
-- self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
-+ self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
- ATOM 407 CA VAL L 29 57.124 18.088 47.170 1.00 0.00 C
- ATOM 408 C VAL L 29 55.739 17.571 47.538 1.00 0.00 C
- ATOM 409 O VAL L 29 55.535 16.362 47.550 1.00 0.00 O
-@@ -100,9 +100,9 @@ ATOM 473 HE1 TYR L 32 48.512 15.775 42.066 1.00 0.00 H
- ATOM 474 HE2 TYR L 32 48.145 19.172 44.648 1.00 0.00 H
- ATOM 475 HH TYR L 32 46.462 17.658 44.280 1.00 0.00 H
- """
-- output, error = run_exec(self.entryPDBwithInsertioncodes,
-- "babel -ipdb -ofasta")
-- self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
-+ output, error = run_exec(self.entryPDBwithInsertioncodes,
-+ "babel -ipdb -ofasta")
-+ self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY")
-
- if __name__ == "__main__":
- testsuite = []
---
-2.9.4
-
diff --git a/packages/py-astropy/package.py b/packages/py-astropy/package.py
index a58d9ebe..e780f21c 100644
--- a/packages/py-astropy/package.py
+++ b/packages/py-astropy/package.py
@@ -17,9 +17,9 @@ class PyAstropy(PythonPackage):
pypi = "astropy/astropy-4.0.1.post1.tar.gz"
git = "https://github.com/astropy/astropy.git"
- # begin EBRAINS (added): add version
- version("5.2.2", sha256="e6a9e34716bda5945788353c63f0644721ee7e5447d16b1cdcb58c48a96b0d9c")
- # end EBRAINS
+ license("BSD-3-Clause")
+
+ version("6.1.0", sha256="6c3b915f10b1576190730ddce45f6245f9927dda3de6e3f692db45779708950f")
version("5.1", sha256="1db1b2c7eddfc773ca66fa33bd07b25d5b9c3b5eee2b934e0ca277fa5b1b7b7e")
version(
"4.0.1.post1", sha256="5c304a6c1845ca426e7bc319412b0363fccb4928cb4ba59298acd1918eec44b5"
@@ -29,15 +29,24 @@ class PyAstropy(PythonPackage):
version("1.1.2", sha256="6f0d84cd7dfb304bb437dda666406a1d42208c16204043bc920308ff8ffdfad1")
version("1.1.post1", sha256="64427ec132620aeb038e4d8df94d6c30df4cc8b1c42a6d8c5b09907a31566a21")
+ depends_on("c", type="build") # generated
+
variant("all", default=False, when="@3.2:", description="Enable all functionality")
# Required dependencies
+ depends_on("python@3.10:", when="@6.1.0:", type=("build", "run"))
depends_on("python@3.8:", when="@5.1:", type=("build", "run"))
depends_on("py-setuptools", type="build")
+# TODO: probably fix, unrealistic
depends_on("py-cython@0.29.13:", type="build")
+ depends_on("py-cython@0.29.30", when="@5.1:6.0", type="build")
+ depends_on("py-cython@3.0.0", when="@6.1.0:", type="build")
+
# in newer pip versions --install-option does not exist
depends_on("py-pip@:23.0", type="build")
+ depends_on("py-astropy-iers-data", when="@6:", type=("build", "run"))
+ depends_on("py-numpy@1.23:", when="@6.1:", type=("build", "run"))
depends_on("py-numpy@1.18:", when="@5.1:", type=("build", "run"))
depends_on("py-numpy@1.16:", when="@4.0:", type=("build", "run"))
depends_on("py-numpy@1.13:", when="@3.1:", type=("build", "run"))
@@ -45,13 +54,13 @@ class PyAstropy(PythonPackage):
depends_on("py-numpy@1.9:", when="@2.0:", type=("build", "run"))
depends_on("py-numpy@1.7:", when="@1.2:", type=("build", "run"))
depends_on("py-numpy", type=("build", "run"))
+ # https://github.com/astropy/astropy/issues/16200
+ depends_on("py-numpy@:1", when="@:6.0")
depends_on("py-packaging@19.0:", when="@5.1:", type=("build", "run"))
depends_on("py-pyyaml@3.13:", when="@5.1:", type=("build", "run"))
depends_on("py-pyerfa@2.0:", when="@5.1:", type=("build", "run"))
+ depends_on("py-pyerfa@2.0.1.1:", when="@6.1.0:", type=("build", "run"))
depends_on("py-setuptools-scm@6.2:", when="@5.1:", type="build")
- # begin EBRAINS (modified)
- depends_on("py-cython@0.29.30:", when="@5.1:", type="build")
- # end EBRAINS
depends_on("py-extension-helpers", when="@5.1:", type="build")
depends_on("pkgconfig", type="build")
@@ -63,8 +72,10 @@ class PyAstropy(PythonPackage):
# Optional dependencies
with when("+all"):
+ depends_on("py-scipy@1.8:", when="@6:", type=("build", "run"))
depends_on("py-scipy@1.3:", when="@5:", type=("build", "run"))
depends_on("py-scipy@0.18:", type=("build", "run"))
+ depends_on("py-matplotlib@3.3:", when="@6:", type=("build", "run"))
depends_on("py-matplotlib@3.1:", when="@5:", type=("build", "run"))
depends_on("py-matplotlib@2.1:", when="@4:", type=("build", "run"))
depends_on("py-matplotlib@2.0:", type=("build", "run"))
@@ -88,6 +99,8 @@ class PyAstropy(PythonPackage):
depends_on("py-ipython", type=("build", "run"))
depends_on("py-pytest@7:", when="@5.0.2:", type=("build", "run"))
depends_on("py-pytest", type=("build", "run"))
+ depends_on("py-fsspec+http@2023.4:", when="@6.1:", type=("build", "run"))
+ depends_on("py-s3fs@2023.4:", when="@6.1:", type=("build", "run"))
depends_on("py-typing-extensions@3.10.0.1:", when="@5.0.2:", type=("build", "run"))
# Historical optional dependencies
diff --git a/packages/py-autopep8/package.py b/packages/py-autopep8/package.py
index e09fd53f..5e37dec3 100644
--- a/packages/py-autopep8/package.py
+++ b/packages/py-autopep8/package.py
@@ -13,6 +13,8 @@ class PyAutopep8(PythonPackage):
homepage = "https://github.com/hhatto/autopep8"
pypi = "autopep8/autopep8-1.2.4.tar.gz"
+ license("MIT")
+
# begin EBRAINS (added): add version
version("2.0.4", sha256="2913064abd97b3419d1cc83ea71f042cb821f87e45b9c88cad5ad3c4ea87fe0c")
# end EBRAINS
diff --git a/packages/py-bokeh/package.py b/packages/py-bokeh/package.py
index 5c92e166..f6556f83 100644
--- a/packages/py-bokeh/package.py
+++ b/packages/py-bokeh/package.py
@@ -9,9 +9,12 @@ from spack.package import *
class PyBokeh(PythonPackage):
"""Statistical and novel interactive HTML plots for Python"""
- homepage = "https://github.com/bokeh/bokeh"
+ homepage = "https://bokeh.org/"
pypi = "bokeh/bokeh-0.12.2.tar.gz"
+ license("BSD-3-Clause")
+
+ version("3.3.1", sha256="2a7b3702d7e9f03ef4cd801b02b7380196c70cff2773859bcb84fa565218955c")
version("2.4.3", sha256="ef33801161af379665ab7a34684f2209861e3aefd5c803a21fbbb99d94874b03")
version("2.4.1", sha256="d0410717d743a0ac251e62480e2ea860a7341bdcd1dbe01499a904f233c90512")
version("2.4.0", sha256="6fa00ed8baab5cca33f4175792c309fa2536eaae7e90abee884501ba8c90fddb")
@@ -20,6 +23,9 @@ class PyBokeh(PythonPackage):
version("0.12.2", sha256="0a840f6267b6d342e1bd720deee30b693989538c49644142521d247c0f2e6939")
depends_on("py-setuptools", type="build", when="@1.3.4:")
+ depends_on("py-setuptools@64:", type="build", when="@3:")
+ depends_on("py-setuptools-git-versioning", type="build", when="@3:")
+ depends_on("py-colorama", type="build", when="@3:")
# begin EBRAINS (added)
depends_on("npm", type=("build", "run"))
@@ -29,6 +35,8 @@ class PyBokeh(PythonPackage):
depends_on("python@2.7:", type=("build", "run"), when="@1.3.4:")
depends_on("python@3.6:", type=("build", "run"), when="@2.3.3:")
depends_on("python@3.7:", type=("build", "run"), when="@2.4.0:")
+ depends_on("python@3.8:", type=("build", "run"), when="@3.0.0:")
+ depends_on("python@3.9:", type=("build", "run"), when="@3.2.0:")
depends_on("py-requests@1.2.3:", type=("build", "run"), when="@0.12.2")
depends_on("py-six@1.5.2:", type=("build", "run"), when="@:1.3.4")
@@ -37,11 +45,18 @@ class PyBokeh(PythonPackage):
depends_on("py-jinja2@2.7:", type=("build", "run"))
depends_on("py-jinja2@2.9:", type=("build", "run"), when="@2.3.3:")
+ depends_on("py-contourpy@1:", type=("build", "run"), when="@3:")
+
depends_on("py-numpy@1.7.1:", type=("build", "run"))
depends_on("py-numpy@1.11.3:", type=("build", "run"), when="@2.3.3:")
+ depends_on("py-numpy@1.16:", type=("build", "run"), when="@3.1:")
+ # https://github.com/bokeh/bokeh/issues/13835
+ depends_on("py-numpy@:1", when="@:3.4.0", type=("build", "run"))
depends_on("py-packaging@16.8:", type=("build", "run"), when="@1.3.4:")
+ depends_on("py-pandas@1.2:", type=("build", "run"), when="@3:")
+
depends_on("pil@4.0:", type=("build", "run"), when="@1.3.4:")
depends_on("pil@7.1.0:", type=("build", "run"), when="@2.3.3:")
@@ -50,5 +65,7 @@ class PyBokeh(PythonPackage):
depends_on("py-tornado@4.3:", type=("build", "run"))
depends_on("py-tornado@5.1:", type=("build", "run"), when="@2.3.3:")
- depends_on("py-typing-extensions@3.7.4:", type=("build", "run"), when="@2.3.3:")
- depends_on("py-typing-extensions@3.10.0:", type=("build", "run"), when="@2.4.0:")
\ No newline at end of file
+ depends_on("py-typing-extensions@3.7.4:", type=("build", "run"), when="@2.3.3:3.0.0")
+ depends_on("py-typing-extensions@3.10.0:", type=("build", "run"), when="@2.4.0:3.0.0")
+
+ depends_on("py-xyzservices@2021.09.1:", type=("build", "run"), when="@3:")
diff --git a/packages/py-chex/package.py b/packages/py-chex/package.py
deleted file mode 100644
index 86c2f71a..00000000
--- a/packages/py-chex/package.py
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyChex(PythonPackage):
- """Chex is a library of utilities for helping to write reliable JAX code."""
-
- homepage = "https://github.com/deepmind/chex"
- pypi = "chex/chex-0.1.0.tar.gz"
-
- # begin EBRAINS (added): bring upstream
- version("0.1.7", sha256="74ed49799ac4d229881456d468136f1b19a9f9839e3de72b058824e2a4f4dedd")
- # end EBRAINS
- version("0.1.5", sha256="686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e")
- version("0.1.0", sha256="9e032058f5fed2fc1d5e9bf8e12ece5910cf6a478c12d402b6d30984695f2161")
-
- depends_on("python@3.7:", type=("build", "run"))
- depends_on("py-setuptools", type="build")
- depends_on("py-absl-py@0.9.0:", type=("build", "run"))
- # begin EBRAINS (added): bring upstream
- depends_on("py-typing-extensions@4.2.0:", when="@0.1.6: ^python@:3.10", type=("build", "run"))
- # end EBRAINS
- depends_on("py-dm-tree@0.1.5:", type=("build", "run"))
- depends_on("py-jax@0.1.55:", type=("build", "run"))
- # begin EBRAINS (added): bring upstream
- depends_on("py-jax@0.4.6:", when="@0.1.7:", type=("build", "run"))
- # end EBRAINS
- depends_on("py-jaxlib@0.1.37:", type=("build", "run"))
- depends_on("py-numpy@1.18.0:", type=("build", "run"))
- depends_on("py-toolz@0.9.0:", type=("build", "run"))
diff --git a/packages/py-dash/package.py b/packages/py-dash/package.py
deleted file mode 100644
index cca2a47d..00000000
--- a/packages/py-dash/package.py
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyDash(PythonPackage):
- """Python framework for building ML & data science web apps"""
-
- homepage = "https://dash.plotly.com/"
- pypi = "dash/dash-2.16.1.tar.gz"
-
- version("2.16.1", sha256="b2871d6b8d4c9dfd0a64f89f22d001c93292910b41d92d9ff2bb424a28283976")
- version("2.15.0", sha256="d38891337fc855d5673f75e5346354daa063c4ff45a8a6a21f25e858fcae41c2")
-
- depends_on("python@3.8:", type=("build", "run"))
- depends_on("py-setuptools", type="build")
-
- depends_on("py-flask@1.0.4:3.0", type=("build", "run"))
- depends_on("py-werkzeug@:3.0", type=("build", "run"))
- depends_on("py-plotly@5:", type=("build", "run"))
- depends_on("py-importlib-metadata", type=("build", "run"))
- depends_on("py-typing-extensions@4.1.1:", type=("build", "run"))
- depends_on("py-requests", type=("build", "run"))
- depends_on("py-retrying", type=("build", "run"))
- depends_on("py-nest-asyncio", type=("build", "run"))
-
diff --git a/packages/py-flit-core/package.py b/packages/py-flit-core/package.py
deleted file mode 100644
index 9cd30a97..00000000
--- a/packages/py-flit-core/package.py
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyFlitCore(PythonPackage):
- """Distribution-building parts of Flit."""
-
- homepage = "https://github.com/pypa/flit"
- pypi = "flit-core/flit_core-3.9.0.tar.gz"
- # begin EBRAINS (added): tag as build-tool
- tags = ["build-tools"]
- # end EBRAINS
- maintainers("takluyver")
-
- version("3.9.0", sha256="72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba")
- version("3.8.0", sha256="b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3")
- version("3.7.1", sha256="14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f")
- version("3.6.0", sha256="5892962ab8b8ea945835b3a288fe9dd69316f1903d5288c3f5cafdcdd04756ad")
- version("3.5.1", sha256="3083720351a6cb00e0634a1ec0e26eae7b273174c3c6c03d5b597a14203b282e")
- version("3.5.0", sha256="2db800d33ff41e4c6e7c1b594666cb2a11553024106655272c7245933b1d75bd")
- version("3.4.0", sha256="29468fa2330969167d1f5c23eb9c0661cb6dacfcd46f361a274609a7f4197530")
- version("3.3.0", sha256="b1404accffd6504b5f24eeca9ec5d3c877f828d16825348ba81515fa084bd5f0")
- version("3.2.0", sha256="ff87f25c5dbc24ef30ea334074e35030e4885e4c5de3bf4e21f15746f6d99431")
- version("3.1.0", sha256="22ff73be39a2b3c9e0692dfbbea3ad4a9d127e5733736a87dbb8ddcbf7309b1e")
- version("3.0.0", sha256="a465052057e2d6d957e6850e9915245adedfc4fd0dd5737d0791bf3132417c2d")
- version("2.3.0", sha256="a50bcd8bf5785e3a7d95434244f30ba693e794c5204ac1ee908fc07c4acdbf80")
-
- # pyproject.toml
- depends_on("python@3.6:", when="@3.4:", type=("build", "run"))
- depends_on("python@3.4:", when="@3:", type=("build", "run"))
- depends_on("python@2.7,3.4:", type=("build", "run"))
-
- # flit_core/build_thyself.py
- depends_on("py-tomli", when="@3.4:3.5", type="run")
- depends_on("py-toml", when="@3.1:3.3", type="run")
- depends_on("py-pytoml", when="@:3.0", type="run")
diff --git a/packages/py-ipycanvas/package.py b/packages/py-ipycanvas/package.py
index f9cd586a..0883611f 100644
--- a/packages/py-ipycanvas/package.py
+++ b/packages/py-ipycanvas/package.py
@@ -12,6 +12,8 @@ class PyIpycanvas(PythonPackage):
homepage = "https://github.com/martinRenou/ipycanvas"
pypi = "ipycanvas/ipycanvas-0.9.0.tar.gz"
+ license("BSD-3-Clause")
+
# begin EBRAINS (added): add version
version("0.12.0", sha256="3984339cef0c15674e347dd65ffb0cd1edc62e37869cbb5efea46f3259e976f3")
# end EBRAINS
diff --git a/packages/py-ipympl/package.py b/packages/py-ipympl/package.py
index 2bd82b56..a22c00e6 100644
--- a/packages/py-ipympl/package.py
+++ b/packages/py-ipympl/package.py
@@ -1,4 +1,4 @@
-# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -13,19 +13,44 @@ class PyIpympl(PythonPackage):
pypi = "ipympl/ipympl-0.8.8.tar.gz"
maintainers("haralmha")
- version("0.8.8", sha256="5bf5d780b07fafe7924922ac6b2f3abd22721f341e5e196b3b82737dfbd0e1c9")
-
- depends_on("py-setuptools@40.8:", type="build")
- depends_on("py-ipython@:8", type=("build", "run"))
- depends_on("py-numpy", type=("build", "run"))
- depends_on("py-ipython-genutils", type=("build", "run"))
- depends_on("pil", type=("build", "run"))
- depends_on("py-traitlets@:5", type=("build", "run"))
- depends_on("py-ipywidgets@7.6:7", type=("build", "run"))
- depends_on("py-matplotlib@2:3", type=("build", "run"))
- depends_on("py-jupyter-packaging@0.7", type="build")
- depends_on("py-jupyterlab@3", type="build")
- depends_on("yarn", type="build")
+ license("BSD-3-Clause")
+
+ version("0.9.4", sha256="cfb53c5b4fcbcee6d18f095eecfc6c6c474303d5b744e72cc66e7a2804708907")
+ # Build failures
+ version(
+ "0.8.8",
+ sha256="5bf5d780b07fafe7924922ac6b2f3abd22721f341e5e196b3b82737dfbd0e1c9",
+ # begin EBRAINS (modified): don't deprecate to keep compatibility with jupyterlab@3
+ deprecated=False,
+ # end EBRAINS
+ )
+
+ with default_args(type="build"):
+ with when("@0.9:"):
+ depends_on("py-hatchling")
+ depends_on("py-jupyterlab@4")
+ depends_on("py-hatch-nodejs-version@0.3.2:")
+
+ # Historical dependencies
+ with when("@:0.8"):
+ depends_on("py-jupyter-packaging@0.7")
+ depends_on("py-jupyterlab@3")
+ depends_on("py-setuptools@40.8:")
+ depends_on("yarn")
+
+ with default_args(type=("build", "run")):
+ depends_on("py-ipython@:8")
+ depends_on("py-ipython-genutils")
+ depends_on("py-ipywidgets@7.6:8", when="@0.9:")
+ depends_on("py-ipywidgets@7.6:7", when="@:0.8")
+ depends_on("py-matplotlib@3.4:3", when="@0.9:")
+ depends_on("py-matplotlib@2:3", when="@:0.8")
+ depends_on("py-numpy")
+ depends_on("pil")
+ depends_on("py-traitlets@:5")
+
+ # Necessary for jupyter extension env vars
+ depends_on("py-jupyter-core")
# begin EBRAINS (added): use newer typescript
# (see https://github.com/DefinitelyTyped/DefinitelyTyped/issues/69932)
diff --git a/packages/py-jax/package.py b/packages/py-jax/package.py
deleted file mode 100644
index 5d57d7ec..00000000
--- a/packages/py-jax/package.py
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyJax(PythonPackage):
- """JAX is Autograd and XLA, brought together for high-performance
- machine learning research. With its updated version of Autograd,
- JAX can automatically differentiate native Python and NumPy
- functions. It can differentiate through loops, branches,
- recursion, and closures, and it can take derivatives of
- derivatives of derivatives. It supports reverse-mode
- differentiation (a.k.a. backpropagation) via grad as well as
- forward-mode differentiation, and the two can be composed
- arbitrarily to any order."""
-
- homepage = "https://github.com/google/jax"
- pypi = "jax/jax-0.2.25.tar.gz"
-
- # begin EBRAINS (added): bring upstream
- version("0.4.13", sha256="03bfe6749dfe647f16f15f6616638adae6c4a7ca7167c75c21961ecfd3a3baaa")
- # end EBRAINS
- version("0.4.3", sha256="d43f08f940aa30eb339965cfb3d6bee2296537b0dc2f0c65ccae3009279529ae")
- version("0.3.23", sha256="bff436e15552a82c0ebdef32737043b799e1e10124423c57a6ae6118c3a7b6cd")
- version("0.2.25", sha256="822e8d1e06257eaa0fdc4c0a0686c4556e9f33647fa2a766755f984786ae7446")
-
- # begin EBRAINS (modified): bring upstream
- depends_on("python@3.7:", type=("build", "run"))
- depends_on("python@3.8:", when="@0.4:", type=("build", "run"))
- depends_on("python@3.9:", when="@0.4.14:", type=("build", "run"))
- depends_on("py-setuptools", type="build")
- depends_on("py-numpy@1.22:", when="@0.4.14:", type=("build", "run"))
- depends_on("py-numpy@1.21:", when="@0.4.9:", type=("build", "run"))
- depends_on("py-numpy@1.20:", when="@0.3:", type=("build", "run"))
- depends_on("py-numpy@1.18:", type=("build", "run"))
- depends_on("py-opt-einsum", type=("build", "run"))
- depends_on("py-scipy@1.2.1:", type=("build", "run"))
- depends_on("py-scipy@1.5:", when="@0.3:", type=("build", "run"))
- depends_on("py-scipy@1.7:", when="@0.4.7:", type=("build", "run"))
- depends_on("py-ml-dtypes@0.2.0:", when="@0.4.14:", type=("build", "run"))
- depends_on("py-ml-dtypes@0.1.0:", when="@0.4.9:", type=("build", "run"))
- depends_on("py-ml-dtypes@0.0.3:", when="@0.4.7:", type=("build", "run"))
- depends_on("py-importlib-metadata@4.6:", when="@0.4.11: ^python@:3.9", type="run")
- # end EBRAINS
-
- # See _minimum_jaxlib_version in jax/version.py
- # begin EBRAINS (modified): bring upstream
- jax_to_jaxlib = {
- "0.4.14": "0.4.14",
- "0.4.13": "0.4.13",
- "0.4.3": "0.4.2",
- "0.3.23": "0.3.15",
- "0.2.25": "0.1.69",
- }
- # end EBRAINS
-
- for jax, jaxlib in jax_to_jaxlib.items():
- # begin EBRAINS (modified): bring upstream
- depends_on(f"py-jaxlib@{jaxlib}", when=f"@{jax}", type=("build", "run"))
- # end EBRAINS
-
- # Historical dependencies
- depends_on("py-absl-py", when="@:0.3", type=("build", "run"))
- depends_on("py-typing-extensions", when="@:0.3", type=("build", "run"))
- # begin EBRAINS (deleted):
- # depends_on("py-etils+epath", when="@0.3", type=("build", "run"))
- # end EBRAINS
diff --git a/packages/py-jaxlib/package.py b/packages/py-jaxlib/package.py
deleted file mode 100644
index 20b2683c..00000000
--- a/packages/py-jaxlib/package.py
+++ /dev/null
@@ -1,125 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-import tempfile
-
-from spack.package import *
-
-
-class PyJaxlib(PythonPackage, CudaPackage):
- """XLA library for Jax"""
-
- homepage = "https://github.com/google/jax"
- url = "https://github.com/google/jax/archive/refs/tags/jaxlib-v0.1.74.tar.gz"
-
- tmp_path = ""
- buildtmp = ""
-
- # begin EBRAINS (added): bring upstream
- version("0.4.13", sha256="45766238b57b992851763c64bc943858aebafe4cad7b3df6cde844690bc34293")
- # end EBRAINS
- version("0.4.3", sha256="2104735dc22be2b105e5517bd5bc6ae97f40e8e9e54928cac1585c6112a3d910")
- version("0.3.22", sha256="680a6f5265ba26d5515617a95ae47244005366f879a5c321782fde60f34e6d0d")
- version("0.1.74", sha256="bbc78c7a4927012dcb1b7cd135c7521f782d7dad516a2401b56d3190f81afe35")
-
- # begin EBRAINS (deleted): Variant with default=False is provided by CudaPackage
- # variant("cuda", default=True, description="Build with CUDA")
- # end EBRAINS
-
- # jaxlib/setup.py
- # begin EBRAINS (modified): bring upstream
- depends_on("python@3.9:", when="@0.4.14:", type=("build", "run"))
- depends_on("python@3.8:", when="@0.4:", type=("build", "run"))
- depends_on("python@3.7:", type=("build", "run"))
- depends_on("py-setuptools", type="build")
- depends_on("py-numpy@1.22:", when="@0.4.14:", type=("build", "run"))
- depends_on("py-numpy@1.21:", when="@0.4.9:", type=("build", "run"))
- depends_on("py-numpy@1.20:", when="@0.3:", type=("build", "run"))
- depends_on("py-numpy@1.18:", type=("build", "run"))
- depends_on("py-scipy@1.5:", type=("build", "run"))
- depends_on("py-scipy@1.7:", when="@0.4.7:", type=("build", "run"))
- depends_on("py-ml-dtypes@0.2.0:", when="@0.4.14:", type=("build", "run"))
- depends_on("py-ml-dtypes@0.1.0:", when="@0.4.9:", type=("build", "run"))
- depends_on("py-ml-dtypes@0.0.3:", when="@0.4.7:", type=("build", "run"))
- # end EBRAINS
-
- # .bazelversion
- depends_on("bazel@5.1.1:5.9", when="@0.3:", type="build")
- # https://github.com/google/jax/issues/8440
- depends_on("bazel@4.1:4", when="@0.1", type="build")
-
- # README.md
- # begin EBRAINS (added): bring upstream
- depends_on("cuda@11.8:", when="@0.4.8:+cuda")
- # end EBRAINS
- depends_on("cuda@11.4:", when="@0.4:+cuda")
- depends_on("cuda@11.1:", when="@0.3+cuda")
- # https://github.com/google/jax/issues/12614
- depends_on("cuda@11.1:11.7.0", when="@0.1+cuda")
- depends_on("cudnn@8.2:", when="@0.4:+cuda")
- depends_on("cudnn@8.0.5:", when="+cuda")
-
- # Historical dependencies
- depends_on("py-absl-py", when="@:0.3", type=("build", "run"))
- depends_on("py-flatbuffers@1.12:2", when="@0.1", type=("build", "run"))
-
- conflicts(
- "cuda_arch=none",
- when="+cuda",
- msg="Must specify CUDA compute capabilities of your GPU, see "
- "https://developer.nvidia.com/cuda-gpus",
- )
-
- def patch(self):
- self.tmp_path = tempfile.mkdtemp(prefix="spack")
- self.buildtmp = tempfile.mkdtemp(prefix="spack")
- filter_file(
- "build --spawn_strategy=standalone",
- f"""
-# Limit CPU workers to spack jobs instead of using all HOST_CPUS.
-build --spawn_strategy=standalone
-build --local_cpu_resources={make_jobs}
-""".strip(),
- ".bazelrc",
- string=True,
- )
- filter_file(
- 'f"--output_path={output_path}",',
- 'f"--output_path={output_path}",'
- f' "--sources_path={self.tmp_path}",'
- ' "--nohome_rc",'
- ' "--nosystem_rc",'
- f' "--jobs={make_jobs}",',
- "build/build.py",
- string=True,
- )
- filter_file(
- "args = parser.parse_args()",
- "args, junk = parser.parse_known_args()",
- "build/build_wheel.py",
- string=True,
- )
-
- def install(self, spec, prefix):
- args = []
- args.append("build/build.py")
- if "+cuda" in spec:
- args.append("--enable_cuda")
- args.append("--cuda_path={0}".format(self.spec["cuda"].prefix))
- args.append("--cudnn_path={0}".format(self.spec["cudnn"].prefix))
- capabilities = ",".join(
- "{0:.1f}".format(float(i) / 10.0) for i in spec.variants["cuda_arch"].value
- )
- args.append("--cuda_compute_capabilities={0}".format(capabilities))
- args.append(
- "--bazel_startup_options="
- "--output_user_root={0}".format(self.wrapped_package_object.buildtmp)
- )
- python(*args)
- with working_dir(self.wrapped_package_object.tmp_path):
- args = std_pip_args + ["--prefix=" + self.prefix, "."]
- pip(*args)
- remove_linked_tree(self.wrapped_package_object.tmp_path)
- remove_linked_tree(self.wrapped_package_object.buildtmp)
diff --git a/packages/py-numba/package.py b/packages/py-numba/package.py
index 6c0ee7b2..522abe31 100644
--- a/packages/py-numba/package.py
+++ b/packages/py-numba/package.py
@@ -13,6 +13,11 @@ class PyNumba(PythonPackage):
pypi = "numba/numba-0.35.0.tar.gz"
git = "https://github.com/numba/numba.git"
+ skip_modules = ["numba.core.rvsdg_frontend"]
+
+ license("BSD-2-Clause")
+
+ version("0.58.1", sha256="487ded0633efccd9ca3a46364b40006dbdaca0f95e99b8b83e778d1195ebcbaa")
version("0.57.0", sha256="2af6d81067a5bdc13960c6d2519dbabbf4d5d597cf75d640c5aeaefd48c6420a")
version("0.56.4", sha256="32d9fef412c81483d7efe0ceb6cf4d3310fde8b624a9cecca00f790573ac96ee")
version("0.56.0", sha256="87a647dd4b8fce389869ff71f117732de9a519fe07663d9a02d75724eb8e244d")
@@ -22,34 +27,39 @@ class PyNumba(PythonPackage):
version("0.51.1", sha256="1e765b1a41535684bf3b0465c1d0a24dcbbff6af325270c8f4dad924c0940160")
version("0.50.1", sha256="89e81b51b880f9b18c82b7095beaccc6856fcf84ba29c4f0ced42e4e5748a3a7")
version("0.48.0", sha256="9d21bc77e67006b5723052840c88cc59248e079a907cc68f1a1a264e1eaba017")
- version("0.40.1", sha256="52d046c13bcf0de79dbfb936874b7228f141b9b8e3447cc35855e9ad3e12aa33")
- depends_on("python@3.8:3.11", when="@0.57", type=("build", "run"))
+ depends_on("c", type="build") # generated
+ depends_on("cxx", type="build") # generated
+
+ variant("tbb", default=False, description="Build with Intel Threading Building Blocks")
+
+ depends_on("python@3.8:3.11", when="@0.57:", type=("build", "run"))
depends_on("python@3.7:3.10", when="@0.55:0.56", type=("build", "run"))
depends_on("python@3.7:3.9", when="@0.54", type=("build", "run"))
depends_on("python@3.6:3.9", when="@0.53", type=("build", "run"))
depends_on("python@3.6:3.8", when="@0.52", type=("build", "run"))
depends_on("python@3.6:3.8", when="@0.48:0.51", type=("build", "run"))
- depends_on("python@3.3:3.7", when="@0.40.1:0.47", type=("build", "run"))
- depends_on("py-numpy@1.21:1.24", when="@0.57:", type=("build", "run"))
+ depends_on("py-numpy@1.22:1.26", when="@0.58.1:", type=("build", "run"))
+ depends_on("py-numpy@1.21:1.25", when="@0.58.0", type=("build", "run"))
+ depends_on("py-numpy@1.21:1.24", when="@0.57", type=("build", "run"))
depends_on("py-numpy@1.18:1.23", when="@0.56.1:0.56.4", type=("build", "run"))
depends_on("py-numpy@1.18:1.22", when="@0.55.2:0.56.0", type=("build", "run"))
depends_on("py-numpy@1.18:1.21", when="@0.55.0:0.55.1", type=("build", "run"))
depends_on("py-numpy@1.17:1.20", when="@0.54", type=("build", "run"))
depends_on("py-numpy@1.15:1.20", when="@0.48:0.53", type=("build", "run"))
- depends_on("py-numpy@1.10:1.20", when="@:0.47", type=("build", "run"))
depends_on("py-setuptools", type=("build", "run"))
+ depends_on("py-llvmlite@0.41", when="@0.58", type=("build", "run"))
depends_on("py-llvmlite@0.40", when="@0.57", type=("build", "run"))
depends_on("py-llvmlite@0.39", when="@0.56", type=("build", "run"))
depends_on("py-llvmlite@0.38", when="@0.55", type=("build", "run"))
depends_on("py-llvmlite@0.37", when="@0.54.0", type=("build", "run"))
depends_on("py-llvmlite@0.34", when="@0.51.1", type=("build", "run"))
depends_on("py-llvmlite@0.33", when="@0.50.1", type=("build", "run"))
- depends_on("py-llvmlite@0.31", when="@0.47,0.48", type=("build", "run"))
- depends_on("py-llvmlite@0.25", when="@0.40", type=("build", "run"))
- depends_on("py-llvmlite@0.20:0.25", when="@0.35.1", type=("build", "run"))
+ depends_on("py-llvmlite@0.31", when="@0.48", type=("build", "run"))
depends_on("py-importlib-metadata", when="@0.56:^python@:3.8", type=("build", "run"))
+ depends_on("tbb", when="+tbb")
+ conflicts("~tbb", when="@:0.50") # No way to disable TBB
# Version 6.0.0 of llvm had a hidden symbol which breaks numba at runtime.
# See https://reviews.llvm.org/D44140
conflicts("^llvm@6.0.0")
@@ -57,3 +67,7 @@ class PyNumba(PythonPackage):
# begin EBRAINS (added): numba>=0.57 requires at least version 14.0.0 of LLVM
conflicts("llvm@:13", when="@0.57.0:")
# end EBRAINS
+
+ def setup_build_environment(self, env):
+ if self.spec.satisfies("~tbb"):
+ env.set("NUMBA_DISABLE_TBB", "yes")
diff --git a/packages/py-optax/package.py b/packages/py-optax/package.py
deleted file mode 100644
index c5cf8840..00000000
--- a/packages/py-optax/package.py
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class PyOptax(PythonPackage):
- """A gradient processing and optimization library in JAX."""
-
- homepage = "https://github.com/deepmind/optax"
- pypi = "optax/optax-0.1.4.tar.gz"
-
- version("0.1.4", sha256="fb7a0550d57a6636164a3de25986a8a19be8ff6431fcdf1225b4e05175810f22")
-
- depends_on("python@3.8:", type=("build", "run"))
- depends_on("py-setuptools", type="build")
-
- depends_on("py-absl-py@0.7.1:", type=("build", "run"))
- depends_on("py-chex@0.1.5:", type=("build", "run"))
- depends_on("py-jax@0.1.55:", type=("build", "run"))
- depends_on("py-jaxlib@0.1.37:", type=("build", "run"))
- depends_on("py-numpy@1.18:", type=("build", "run"))
diff --git a/packages/py-pycuda/package.py b/packages/py-pycuda/package.py
index 98691d68..3c3d4926 100644
--- a/packages/py-pycuda/package.py
+++ b/packages/py-pycuda/package.py
@@ -15,6 +15,8 @@ class PyPycuda(PythonPackage):
homepage = "https://mathema.tician.de/software/pycuda/"
pypi = "pycuda/pycuda-2019.1.2.tar.gz"
+ license("MIT")
+
# begin EBRAINS (added): add version
version("2023.1", sha256="175ff675f0cf10e38e9adc03ed5df3ed8d8abf7da5134c8dccec752e8a0a3e91")
# end EBRAINS
@@ -23,6 +25,8 @@ class PyPycuda(PythonPackage):
version("2019.1.2", sha256="ada56ce98a41f9f95fe18809f38afbae473a5c62d346cfa126a2d5477f24cc8a")
version("2016.1.2", sha256="a7dbdac7e2f0c0d2ad98f5f281d5a9d29d6673b3c20210e261b96e9a2d0b6e37")
+ depends_on("cxx", type="build") # generated
+
@run_before("install")
def configure(self):
pyver = self.spec["python"].version.up_to(2).joined
diff --git a/packages/py-pyvista/package.py b/packages/py-pyvista/package.py
deleted file mode 100644
index 38054a2f..00000000
--- a/packages/py-pyvista/package.py
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyPyvista(PythonPackage):
- """Easier Pythonic interface to VTK."""
-
- homepage = "https://github.com/pyvista/pyvista"
- pypi = "pyvista/pyvista-0.32.1.tar.gz"
-
- # Requires optional trame dependency
- skip_modules = ["pyvista.ext", "pyvista.jupyter", "pyvista.trame"]
-
- maintainers("banesullivan")
-
- license("MIT")
-
- # begin EBRAINS (added): add version
- version("0.43.0", sha256="0118060d56de7f9b583405723ddd8f77f20d7d8af601ad7c0b0521c6302069cf")
- # end EBRAINS
- version("0.42.3", sha256="00159cf0dea05c1ecfd1695c8c6ccfcfff71b0744c9997fc0276e661dc052351")
- version("0.37.0", sha256="d36a2c6d5f53f473ab6a9241669693acee7a5179394dc97595da14cc1de23141")
- version("0.32.1", sha256="585ac79524e351924730aff9b7207d6c5ac4175dbb5d33f7a9a2de22ae53dbf9")
-
- depends_on("py-setuptools", type="build")
- depends_on("py-matplotlib@3.0.1:", when="@0.39:", type=("build", "run"))
- depends_on("py-numpy", type=("build", "run"))
- depends_on("pil", type=("build", "run"))
- depends_on("py-pooch", when="@0.37:", type=("build", "run"))
- depends_on("py-scooby@0.5.1:", type=("build", "run"))
- depends_on("vtk+python", type=("build", "run"))
- depends_on("py-typing-extensions", when="^python@:3.7", type=("build", "run"))
-
- # Historical dependencies
- depends_on("py-appdirs", when="@:0.36", type=("build", "run"))
- depends_on("py-imageio", when="@:0.38", type=("build", "run"))
- depends_on("py-meshio@4.0.3:4", when="@:0.32", type=("build", "run"))
-
- # '>=3.7.*' in python_requires: setuptools parser changed in v60 and errors.
- depends_on("py-setuptools@:59", when="@:0.37", type="build")
diff --git a/packages/py-pyviz-comms/package.py b/packages/py-pyviz-comms/package.py
index 0e6d6c84..03ed4163 100644
--- a/packages/py-pyviz-comms/package.py
+++ b/packages/py-pyviz-comms/package.py
@@ -12,6 +12,8 @@ class PyPyvizComms(PythonPackage):
homepage = "https://holoviz.org/"
pypi = "pyviz_comms/pyviz_comms-2.2.1.tar.gz"
+ license("BSD-3-Clause")
+
# begin EBRAINS (added): add version
version("2.3.2", sha256="542a10fed8242d3a9d468ed0a14d6a2537e589c3f8a7986c79c374591254d6b4")
# end EBRAINS
diff --git a/packages/py-ray/package.py b/packages/py-ray/package.py
index 6feab9f5..82ba34c4 100644
--- a/packages/py-ray/package.py
+++ b/packages/py-ray/package.py
@@ -3,6 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
from spack.package import *
@@ -12,12 +13,17 @@ class PyRay(PythonPackage):
homepage = "https://github.com/ray-project/ray"
url = "https://github.com/ray-project/ray/archive/ray-0.8.7.tar.gz"
+ license("Apache-2.0")
+
# begin EBRAINS (added): ECM new node-js -> new react whatever -> new py-ray
version("2.4.0", sha256="b0110a84630b2f6d10cd13e8ac955875c3658373eb6cabcc77cf316de3c28066")
# end EBRAINS
version("2.0.1", sha256="b8b2f0a99d2ac4c001ff11c78b4521b217e2a02df95fb6270fd621412143f28b")
version("0.8.7", sha256="2df328f1bcd3eeb4fa33119142ea0d669396f4ab2a3e78db90178757aa61534b")
+ depends_on("c", type="build") # generated
+ depends_on("cxx", type="build") # generated
+
variant("default", default=False, description="Install default extras", when="@2.0.1")
# begin EBRAINS (added): ECM new node-js -> new react whatever -> new py-ray
diff --git a/packages/py-sympy/package.py b/packages/py-sympy/package.py
index b7f5b90e..ffdfe371 100644
--- a/packages/py-sympy/package.py
+++ b/packages/py-sympy/package.py
@@ -11,11 +11,15 @@ class PySympy(PythonPackage):
pypi = "sympy/sympy-0.7.6.tar.gz"
+ license("BSD-3-Clause")
+
+ version("1.13.0", sha256="3b6af8f4d008b9a1a6a4268b335b984b23835f26d1d60b0526ebc71d48a25f57")
+ version("1.12", sha256="ebf595c8dac3e0fdc4152c51878b498396ec7f30e7a914d6071e674d49420fb8")
version("1.11.1", sha256="e32380dce63cb7c0108ed525570092fd45168bdae2faa17e528221ef72e88658")
# begin EBRAINS (added): add versions
version("1.10.1", sha256="5939eeffdf9e152172601463626c022a2c27e75cf6278de8d401d50c9d58787b")
version("1.9", sha256="c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc")
- # end EBRAINS
+ # end EBRAINS
version("1.8", sha256="1ca588a9f6ce6a323c5592f9635159c2093572826668a1022c75c75bdf0297cb")
version("1.7.1", sha256="a3de9261e97535b83bb8607b0da2c7d03126650fafea2b2789657b229c246b2e")
version("1.7", sha256="9104004669cda847f38cfd8cd16dd174952c537349dbae740fea5331d2b3a51b")
@@ -38,4 +42,5 @@ class PySympy(PythonPackage):
# pip silently replaces distutils with setuptools
depends_on("py-setuptools", type="build")
- depends_on("py-mpmath@0.19:", when="@1.0:", type=("build", "run"))
+ depends_on("py-mpmath@0.19:", when="@1.0:1.12", type=("build", "run"))
+ depends_on("py-mpmath@1.1.0:1.3", when="@1.13.0:", type=("build", "run"))
diff --git a/packages/py-tree-math/package.py b/packages/py-tree-math/package.py
deleted file mode 100644
index 69ba02f5..00000000
--- a/packages/py-tree-math/package.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class PyTreeMath(PythonPackage):
- """
- tree-math makes it easy to implement numerical algorithms that work on
- JAX pytrees, such as iterative methods for optimization and equation
- solving. It does so by providing a wrapper class tree_math.Vector that
- defines array operations such as infix arithmetic and dot-products on
- pytrees as if they were vectors.
- """
-
- homepage = "https://github.com/google/tree-math"
- pypi = "tree-math/tree-math-0.1.0.tar.gz"
- git = "https://github.com/google/tree-math.git"
-
- version('0.1.0.post', commit='0af9679125c13cc38dab5159bc8413ed79465344')
- version('0.1.0', sha256='77eb8d6ba4d6cfdd2d986a6bc3fc2d1b16212f0172863a3ca509720babf75929')
-
- depends_on('py-setuptools', type='build')
- depends_on('py-jax', type=('build', 'run'))
diff --git a/packages/sbml/package.py b/packages/sbml/package.py
index e1bfdcef..f54fbb6b 100644
--- a/packages/sbml/package.py
+++ b/packages/sbml/package.py
@@ -14,6 +14,8 @@ class Sbml(CMakePackage):
homepage = "https://sbml.org"
maintainers("rblake-llnl")
+ license("LGPL-2.1-or-later")
+
# begin EBRAINS (added): add version
version("5.19.0", sha256="a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547")
# end EBRAINS
@@ -28,6 +30,9 @@ class Sbml(CMakePackage):
version("5.10.2", sha256="83f32a143cf657672b1050f5f79d3591c418fc59570d180fb1f39b103f4e5286")
version("5.10.0", sha256="2cd8b37018ce8b1df869c8c182803addbce6d451512ae25a7f527b49981f0966")
+ depends_on("c", type="build") # generated
+ depends_on("cxx", type="build") # generated
+
def url_for_version(self, version):
url = "https://downloads.sourceforge.net/project/sbml/libsbml/{0}/stable/libSBML-{1}-core-plus-packages-src.tar.gz".format(
version, version
diff --git a/packages/simpletraj/package.py b/packages/simpletraj/package.py
deleted file mode 100644
index be6fc871..00000000
--- a/packages/simpletraj/package.py
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class Simpletraj(PythonPackage):
- """Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD."""
-
- # Homepage and download url
- homepage = "https://github.com/arose/simpletraj"
- git = 'https://github.com/arose/simpletraj.git'
- url = 'https://github.com/arose/simpletraj/archive/refs/tags/v0.3.tar.gz'
-
- # Set the gitlab accounts of this package maintainers
- maintainers = ['dbeltran']
-
- # Versions
- version('master', branch='master')
- version('0.3', sha256='9ee9b5f3e387f8f8eb74b11f5c5d60bab6f601d190b40e38a7b31afddc3574d0')
-
- # Dependencies
- depends_on('python@3.8:', type=('build', 'run'))
- depends_on('py-setuptools')
- depends_on('py-numpy')
-
- # Test
- @run_after('install')
- @on_package_attributes(run_tests=True)
- def check_install (self):
- python("-c", 'import simpletraj')
diff --git a/packages/sleef/package.py b/packages/sleef/package.py
deleted file mode 100644
index 796219df..00000000
--- a/packages/sleef/package.py
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class Sleef(CMakePackage):
- """SIMD Library for Evaluating Elementary Functions, vectorized libm and DFT."""
-
- homepage = "https://sleef.org"
- url = "https://github.com/shibatch/sleef/archive/3.2.tar.gz"
- git = "https://github.com/shibatch/sleef.git"
-
- version("master", branch="master")
- version("3.5.1_2020-12-22", commit="e0a003ee838b75d11763aa9c3ef17bf71a725bff") # py-torch@1.8:
- version(
- "3.5.1",
- sha256="415ee9b1bcc5816989d3d4d92afd0cd3f9ee89cbd5a33eb008e69751e40438ab",
- preferred=True,
- )
- version(
- "3.4.0_2019-07-30", commit="7f523de651585fe25cade462efccca647dcc8d02"
- ) # py-torch@1.3:1.7
- version(
- "3.4.0_2019-05-13",
- commit="9b249c53a80343cc1a394ca961d7d5696ea76409", # py-torch@1.2
- git="https://github.com/zdevito/sleef.git",
- )
- version(
- "3.3.1_2018-12-09",
- commit="191f655caa25526ae226cf88dd2529265176014a", # py-torch@1.1
- git="https://github.com/zdevito/sleef.git",
- )
- version(
- "3.2_2018-05-09", commit="6ff7a135a1e31979d1e1844a2e7171dfbd34f54f"
- ) # py-torch@0.4.1:1.0
- version("3.2", sha256="3130c5966e204e6d6a3ace81e543d12b5b21f60897f1c185bfa587c1bd77bee2")
-
- # https://github.com/shibatch/sleef/issues/474
- conflicts("%apple-clang@15:")
-
- generator("ninja")
- depends_on("cmake@3.4.3:", type="build")
-
- # # https://github.com/shibatch/sleef/issues/475
- # depends_on("fftw-api")
- # depends_on("mpfr")
- # depends_on("openssl")
-
- # # https://github.com/shibatch/sleef/issues/458
- # conflicts("^mpfr@4.2:")
-
- # begin EBRAINS (modified): removed "disable shared lib build" to fix py-torch
- # this was fixed upstream in 8c061e51.
- def cmake_args(self):
- # https://salsa.debian.org/science-team/sleef/-/blob/master/debian/rules
- return [
- self.define("BUILD_DFT", False),
- self.define("BUILD_TESTS", False),
- ]
- # end EBRAINS
diff --git a/packages/wf-biobb/package.py b/packages/wf-biobb/package.py
index dbcd5b17..28ff7c41 100644
--- a/packages/wf-biobb/package.py
+++ b/packages/wf-biobb/package.py
@@ -16,5 +16,5 @@ class WfBiobb(BundlePackage):
version("0.1")
depends_on("py-plotly")
- depends_on("nglview")
- depends_on("simpletraj")
+ depends_on("py-nglview")
+ depends_on("py-simpletraj")
--
GitLab
From 282c08c57ee8954f685f9ca7d12d822892c74af6 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Wed, 19 Feb 2025 12:52:29 +0000
Subject: [PATCH 05/80] fix(arbor): align with spack.target removal
---
packages/arbor/package.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/packages/arbor/package.py b/packages/arbor/package.py
index 0dc9d0fd..7a4a2c25 100644
--- a/packages/arbor/package.py
+++ b/packages/arbor/package.py
@@ -124,8 +124,8 @@ class Arbor(CMakePackage, CudaPackage):
# query spack for the architecture-specific compiler flags set by its wrapper
args.append("-DARB_ARCH=none")
- opt_flags = self.spec.target.optimization_flags(
- self.spec.compiler.name, self.spec.compiler.version
+ opt_flags = spack.build_environment.optimization_flags(
+ self.compiler, self.spec.target
)
args.append("-DARB_CXX_FLAGS_TARGET=" + opt_flags)
--
GitLab
From c2c96d841c76f2f4d281f8f2b6336b0be15c6940 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Tue, 18 Feb 2025 16:39:12 +0100
Subject: [PATCH 06/80] fix(BSS2): support new spack's
SPACK_STORE_{INCLUDE,LINK}_DIRS
---
packages/build-brainscales/package.py | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/packages/build-brainscales/package.py b/packages/build-brainscales/package.py
index d8349c67..6ea4a370 100644
--- a/packages/build-brainscales/package.py
+++ b/packages/build-brainscales/package.py
@@ -140,10 +140,18 @@ class BuildBrainscales(WafPackage):
# spack tries to find headers and libraries by itself (i.e. it's not
# relying on the compiler to find it); we explicitly expose the
# spack-provided env vars that contain include and library paths
+ if 'SPACK_STORE_INCLUDE_DIRS' in my_env:
+ for dir in reversed(get_path(my_env, "SPACK_STORE_INCLUDE_DIRS")):
+ env.prepend_path("C_INCLUDE_PATH", dir)
+ env.prepend_path("CPLUS_INCLUDE_PATH", dir)
if 'SPACK_INCLUDE_DIRS' in my_env:
for dir in reversed(get_path(my_env, "SPACK_INCLUDE_DIRS")):
env.prepend_path("C_INCLUDE_PATH", dir)
env.prepend_path("CPLUS_INCLUDE_PATH", dir)
+ if 'SPACK_STORE_LINK_DIRS' in my_env:
+ for dir in reversed(get_path(my_env, "SPACK_STORE_LINK_DIRS")):
+ env.prepend_path("LIBRARY_PATH", dir)
+ env.prepend_path("LD_LIBRARY_PATH", dir)
if 'SPACK_LINK_DIRS' in my_env:
for dir in reversed(get_path(my_env, "SPACK_LINK_DIRS")):
env.prepend_path("LIBRARY_PATH", dir)
--
GitLab
From 088e000dd3d3bfba15c2fe44ae53bdcd23c92b98 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 21 Feb 2025 01:39:02 +0000
Subject: [PATCH 07/80] feat(biobb): align packages with Spack upstream
---
packages/biobb-common/package.py | 38 ----------------
packages/biobb-gromacs/package.py | 37 ----------------
packages/biobb-io/package.py | 42 ------------------
packages/biobb-model/package.py | 43 -------------------
packages/biobb-structure-checking/package.py | 36 ----------------
packages/biobb-structure-utils/package.py | 43 -------------------
.../package.py | 4 +-
.../package.py | 4 +-
spack.yaml | 16 +++----
9 files changed, 12 insertions(+), 251 deletions(-)
delete mode 100644 packages/biobb-common/package.py
delete mode 100644 packages/biobb-gromacs/package.py
delete mode 100644 packages/biobb-io/package.py
delete mode 100644 packages/biobb-model/package.py
delete mode 100644 packages/biobb-structure-checking/package.py
delete mode 100644 packages/biobb-structure-utils/package.py
rename packages/{biobb-analysis => py-biobb-analysis}/package.py (95%)
rename packages/{biobb-chemistry => py-biobb-chemistry}/package.py (95%)
diff --git a/packages/biobb-common/package.py b/packages/biobb-common/package.py
deleted file mode 100644
index 44613737..00000000
--- a/packages/biobb-common/package.py
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class BiobbCommon(PythonPackage):
- """Biobb_common is the base package required to use the biobb packages"""
-
- # Homepage and download url
- homepage = "https://github.com/bioexcel/biobb_common"
- git = 'https://github.com/bioexcel/biobb_common.git'
- url = 'https://github.com/bioexcel/biobb_common/archive/refs/tags/v4.0.0.tar.gz'
-
- # Set the gitlab accounts of this package maintainers
- maintainers = ['dbeltran']
-
- # Versions
- version('master', branch='master')
- version('4.0.0', sha256='fff990dce42ded2af3d587567dbf5321b1498f12f24d04d62003f9869d6eb8fe')
-
- # Dependencies
- depends_on('py-setuptools')
- depends_on('python@3.8:', type=('build', 'run'))
- depends_on('py-pyyaml', type=('build', 'run'))
- depends_on('py-requests', type=('build', 'run'))
- depends_on('py-biopython@1.78:1.80', type=('build', 'run'))
-
- # Custom patch to enable python 3.10.8 for this package
- def patch(self):
- filter_file(" python_requires='>=3.7,<=3.10',", " python_requires='>=3.7,<3.11',", "setup.py")
-
- # Test
- @run_after('install')
- @on_package_attributes(run_tests=True)
- def check_install (self):
- python("-c", 'import biobb_common')
diff --git a/packages/biobb-gromacs/package.py b/packages/biobb-gromacs/package.py
deleted file mode 100644
index 1c41dea9..00000000
--- a/packages/biobb-gromacs/package.py
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class BiobbGromacs(PythonPackage):
- """Biobb_gromacs is the Biobb module collection to perform molecular
- dynamics simulations using Gromacs"""
-
- # Homepage and download url
- homepage = "https://github.com/bioexcel/biobb_gromacs"
- git = 'https://github.com/bioexcel/biobb_gromacs.git'
- url = 'https://github.com/bioexcel/biobb_gromacs/archive/refs/tags/v4.0.0.tar.gz'
-
- # Set the gitlab accounts of this package maintainers
- maintainers = ['dbeltran']
-
- # Versions
- version('master', branch='master')
- version('4.0.0', sha256='87f9079ec8b72ff43cd1b388a06fee5b1f64bb4080ffab110941f3c6d155ef0b')
-
- # Dependencies
- depends_on('python@3.8:', type=('build', 'run'))
- depends_on('biobb-common')
- depends_on('gromacs')
-
- # Patching to enable python 3.10 (not official, might not be stable)
- def patch(self):
- filter_file(" python_requires='>=3.7,<=3.10',", " python_requires='>=3.7,<3.11',", "setup.py")
-
- # Test
- @run_after('install')
- @on_package_attributes(run_tests=True)
- def check_install (self):
- python("-c", 'import biobb_gromacs')
diff --git a/packages/biobb-io/package.py b/packages/biobb-io/package.py
deleted file mode 100644
index 807bb205..00000000
--- a/packages/biobb-io/package.py
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class BiobbIo(PythonPackage):
- """Biobb_io is the Biobb module collection to fetch data to be
- consumed by the rest of the Biobb building blocks"""
-
- # Homepage and download url
- homepage = "https://github.com/bioexcel/biobb_io"
- git = 'https://github.com/bioexcel/biobb_io.git'
- url = 'https://github.com/bioexcel/biobb_io/archive/refs/tags/v4.0.0.tar.gz'
-
- # Set the gitlab accounts of this package maintainers
- maintainers = ['dbeltran']
-
- # Versions
- version('master', branch='master')
- version('4.0.0', sha256='600a30f14b1a0e21f57775ba1be695e1595f5702237415fe90d7c531b5a0408a')
-
- # Dependencies
- depends_on('biobb-common')
- depends_on('python@3.8:', type=('build', 'run'))
-
- # Patching to enable python 3.10 (not official, might not be stable)
- def patch(self):
- filter_file(" python_requires='>=3.7,<3.10',", " python_requires='>=3.7,<3.11',", "setup.py")
- filter_file(
- "'Programming Language :: Python :: 3.9'",
- "'Programming Language :: Python :: 3.9',\r\n "
- "'Programming Language :: Python :: 3.10'",
- "setup.py",
- )
-
- # Test
- @run_after('install')
- @on_package_attributes(run_tests=True)
- def check_install (self):
- python("-c", 'import biobb_io')
diff --git a/packages/biobb-model/package.py b/packages/biobb-model/package.py
deleted file mode 100644
index 23bfde29..00000000
--- a/packages/biobb-model/package.py
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class BiobbModel(PythonPackage):
- """Biobb_model is the Biobb module collection to check and model 3d structures,
- create mutations or reconstruct missing atoms"""
-
- # Homepage and download url
- homepage = "https://github.com/bioexcel/biobb_model"
- git = 'https://github.com/bioexcel/biobb_model.git'
- url = 'https://github.com/bioexcel/biobb_model/archive/refs/tags/v4.0.0.tar.gz'
-
- # Set the gitlab accounts of this package maintainers
- maintainers = ['dbeltran']
-
- # Versions
- version('master', branch='master')
- version('4.0.0', sha256='92387725b7ccd3f40d18c1d3e30a6169ca4204ba498ac72e25c9e701b1a89d91')
-
- # Dependencies
- depends_on('python@3.8:', type=('build', 'run'))
- depends_on('biobb-common')
- depends_on('biobb-structure-checking')
-
- # Patching to enable python 3.10 (not official, might not be stable)
- def patch(self):
- filter_file(" python_requires='>=3.7,<=3.10',", " python_requires='>=3.7,<3.11',", "setup.py")
- filter_file(
- "'Programming Language :: Python :: 3.9'",
- "'Programming Language :: Python :: 3.9',\r\n "
- "'Programming Language :: Python :: 3.10'",
- "setup.py",
- )
-
- # Test
- @run_after('install')
- @on_package_attributes(run_tests=True)
- def check_install (self):
- python("-c", 'import biobb_model')
diff --git a/packages/biobb-structure-checking/package.py b/packages/biobb-structure-checking/package.py
deleted file mode 100644
index d298c2b8..00000000
--- a/packages/biobb-structure-checking/package.py
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class BiobbStructureChecking(PythonPackage):
- """Biobb_structure_checking performs a checking of the quality of a
- 3D structure intended to facilitate the setup of molecular dynamics
- simulation of protein or nucleic acids systems"""
-
- # Homepage and download url
- homepage = "https://github.com/bioexcel/biobb_structure_checking"
- git = 'https://github.com/bioexcel/biobb_structure_checking.git'
- url = 'https://github.com/bioexcel/biobb_structure_checking/archive/refs/tags/v3.12.1.tar.gz'
-
- # Set the gitlab accounts of this package maintainers
- maintainers = ['dbeltran']
-
- # Versions
- version('master', branch='master')
- version('3.12.1', sha256='ef3e6fe5f7763e534c91fac00bf873c3d88bcca18be7a63c63608dceb36f3d40')
-
- # Dependencies
- depends_on('py-setuptools')
- depends_on('python@3.8:', type=('build', 'run'))
- depends_on('py-psutil', type=('build', 'run'))
- depends_on('py-numpy', type=('build', 'run'))
- depends_on('py-biopython@1.78:1.80', type=('build', 'run'))
-
- # Test
- @run_after('install')
- @on_package_attributes(run_tests=True)
- def check_install (self):
- python("-c", 'import biobb_structure_checking')
diff --git a/packages/biobb-structure-utils/package.py b/packages/biobb-structure-utils/package.py
deleted file mode 100644
index 063ff341..00000000
--- a/packages/biobb-structure-utils/package.py
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-class BiobbStructureUtils(PythonPackage):
- """Biobb_structure_utils is the Biobb module collection to modify
- or extract information from a PDB structure file."""
-
- # Homepage and download url
- homepage = "https://github.com/bioexcel/biobb_structure_utils"
- git = 'https://github.com/bioexcel/biobb_structure_utils.git'
- url = 'https://github.com/bioexcel/biobb_structure_utils/archive/refs/tags/v4.0.0.tar.gz'
-
- # Set the gitlab accounts of this package maintainers
- maintainers = ['dbeltran']
-
- # Versions
- version('master', branch='master')
- version('4.0.0', sha256='f328eee2166631e1cc514118eb41187620c358c8024431ce2a0b0e4547692c47')
-
- # Dependencies
- depends_on('python@3.8:', type=('build', 'run'))
- depends_on('biobb-common')
- depends_on('biobb-structure-checking')
-
- # Patching to enable python 3.10 (not official, might not be stable)
- def patch(self):
- filter_file(" python_requires='>=3.7,<=3.10',", " python_requires='>=3.7,<3.11',", "setup.py")
- filter_file(
- "'Programming Language :: Python :: 3.9'",
- "'Programming Language :: Python :: 3.9',\r\n "
- "'Programming Language :: Python :: 3.10'",
- "setup.py",
- )
-
- # Test
- @run_after('install')
- @on_package_attributes(run_tests=True)
- def check_install (self):
- python("-c", 'import biobb_structure_utils')
diff --git a/packages/biobb-analysis/package.py b/packages/py-biobb-analysis/package.py
similarity index 95%
rename from packages/biobb-analysis/package.py
rename to packages/py-biobb-analysis/package.py
index 56472b1d..799d4c36 100644
--- a/packages/biobb-analysis/package.py
+++ b/packages/py-biobb-analysis/package.py
@@ -5,7 +5,7 @@
from spack import *
-class BiobbAnalysis(PythonPackage):
+class PyBiobbAnalysis(PythonPackage):
"""Biobb_analysis is the Biobb module collection to perform analysis
of molecular dynamics simulations"""
@@ -23,7 +23,7 @@ class BiobbAnalysis(PythonPackage):
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
- depends_on('biobb-common')
+ depends_on('py-biobb-common')
depends_on('gromacs')
depends_on('ambertools')
diff --git a/packages/biobb-chemistry/package.py b/packages/py-biobb-chemistry/package.py
similarity index 95%
rename from packages/biobb-chemistry/package.py
rename to packages/py-biobb-chemistry/package.py
index 292b6ce1..6ec163b6 100644
--- a/packages/biobb-chemistry/package.py
+++ b/packages/py-biobb-chemistry/package.py
@@ -5,7 +5,7 @@
from spack import *
-class BiobbChemistry(PythonPackage):
+class PyBiobbChemistry(PythonPackage):
"""Biobb_chemistry is the Biobb module collection to perform chemistry
over molecular dynamics simulations."""
@@ -23,7 +23,7 @@ class BiobbChemistry(PythonPackage):
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
- depends_on('biobb-common')
+ depends_on('py-biobb-common')
depends_on('openbabel')
depends_on('ambertools')
depends_on('acpype')
diff --git a/spack.yaml b/spack.yaml
index 79fd41e2..e465a5a4 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -4,14 +4,14 @@ spack:
specs:
# EBRAINS tools
- arbor@0.9.0 +python +mpi
- - biobb-analysis@4.0.1
- - biobb-chemistry@4.0.0
- - biobb-common@4.0.0
- - biobb-gromacs@4.0.0
- - biobb-io@4.0.0
- - biobb-model@4.0.0
- - biobb-structure-checking@3.12.1
- - biobb-structure-utils@4.0.0
+ - py-biobb-analysis@4.0.1
+ - py-biobb-chemistry@4.0.0
+ - py-biobb-common@4.1.0
+ - py-biobb-gromacs@4.1.1
+ - py-biobb-io@4.1.0
+ - py-biobb-model@4.1.0
+ - py-biobb-structure-checking@3.13.4
+ - py-biobb-structure-utils@4.1.0
- hxtorch@9.0-a8
- nest@3.8 +sonata
- neuron@8.2.3 +mpi
--
GitLab
From 2d3dcdba0a51eb9157e0c1d0849671c597d2587f Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 21 Feb 2025 01:54:46 +0000
Subject: [PATCH 08/80] feat(bluebrain): align packages with Spack upstream
---
packages/py-bluepyefe/package.py | 32 ------------------
packages/py-bluepymm/package.py | 5 +--
packages/py-bluepyopt/package.py | 49 ----------------------------
packages/py-bluepyopt/pmi_rank.patch | 17 ----------
packages/py-efel/package.py | 28 ----------------
packages/py-libsonata/package.py | 1 +
packages/py-morph-tool/package.py | 40 -----------------------
packages/py-morphio/package.py | 35 --------------------
packages/py-neurom/package.py | 37 ---------------------
spack.yaml | 10 +++---
10 files changed, 7 insertions(+), 247 deletions(-)
delete mode 100644 packages/py-bluepyefe/package.py
delete mode 100644 packages/py-bluepyopt/package.py
delete mode 100644 packages/py-bluepyopt/pmi_rank.patch
delete mode 100644 packages/py-efel/package.py
delete mode 100644 packages/py-morph-tool/package.py
delete mode 100644 packages/py-morphio/package.py
delete mode 100644 packages/py-neurom/package.py
diff --git a/packages/py-bluepyefe/package.py b/packages/py-bluepyefe/package.py
deleted file mode 100644
index df41cbc8..00000000
--- a/packages/py-bluepyefe/package.py
+++ /dev/null
@@ -1,32 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyBluepyefe(PythonPackage):
- """Blue Brain Python E-feature extraction"""
-
- homepage = "https://github.com/BlueBrain/BluePyEfe"
- pypi = "bluepyefe/bluepyefe-0.3.13.tar.gz"
- git = "https://github.com/BlueBrain/BluePyEfe.git"
-
- version("2.2.18", sha256="bfb50c6482433ec2ffb4b65b072d2778bd89ae50d92dd6830969222aabb30275")
-
- depends_on("py-setuptools", type="build")
-
- depends_on("py-numpy", type=("build", "run"))
- depends_on("py-neo", type=("build", "run"))
- depends_on("py-matplotlib", type=("build", "run"))
- depends_on("py-efel", type=("build", "run"))
- depends_on("py-scipy", type=("build", "run"))
- depends_on("py-h5py", type=("build", "run"))
- depends_on("py-igor", type=("build", "run"))
-
- def setup_run_environment(self, env):
- env.set("NEURON_INIT_MPI", "0")
- env.unset("PMI_RANK")
diff --git a/packages/py-bluepymm/package.py b/packages/py-bluepymm/package.py
index 5fa0d410..7b1a4c2c 100644
--- a/packages/py-bluepymm/package.py
+++ b/packages/py-bluepymm/package.py
@@ -14,15 +14,12 @@ class PyBluepymm(PythonPackage):
homepage = "https://github.com/BlueBrain/BluePyMM"
pypi = "bluepymm/bluepymm-0.7.49.tar.gz"
+ version("0.8.7", sha256="f0e5d4e113b19f71398d0796d5182f322c48c2ab07793ce8d0e4771a251914ab")
version("0.7.65", sha256="024b009decd8d967b3b885421196d53670e3c0a6b75aaaa55559f148b0b0d7d4")
depends_on("py-setuptools", type="build")
depends_on("py-bluepyopt", type="run")
depends_on("py-matplotlib", type="run")
- # The below dependency should disappear once
- # the matplotlib package is fixed
- # not needed with EBRAINS python version:
- # depends_on("py-backports-functools-lru-cache", type="run", when="^python@:3.3.99")
depends_on("py-pandas", type="run")
depends_on("py-numpy", type="run")
depends_on("py-ipyparallel", type="run")
diff --git a/packages/py-bluepyopt/package.py b/packages/py-bluepyopt/package.py
deleted file mode 100644
index 16a10d59..00000000
--- a/packages/py-bluepyopt/package.py
+++ /dev/null
@@ -1,49 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyBluepyopt(PythonPackage):
- """Bluebrain Python Optimisation Library"""
-
- homepage = "https://github.com/BlueBrain/BluePyOpt"
- pypi = "bluepyopt/bluepyopt-1.9.27.tar.gz"
-
- # NOTE : while adding new release check pmi_rank.patch compatibility
- version("1.13.86", sha256="37b4abcc4a53ed5af50fa0b3bc4d0003332b7f2f2b6e4d9f0b9de8638254e753")
- version("1.10.38", sha256="fb1411c6a8fbfac52d36b837225bae882fd6524acfb4d0580189312ef3c1cfcc")
- version("1.9.37", sha256="4399af71de48b288832e92f0de73c431bf88d6e76e2c4ea250c3b38fb38a45a8")
- version("1.9.27", sha256="4cce15b92b32311c808cae5e005b664deb6e8dc5df4ca13ea7b59252ae346522")
- version("1.8.68", sha256="b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c")
- version("1.6.56", sha256="1c57c91465ca4b947fe157692e7004a3e6df02e4151e3dc77a8831382a8f1ab9")
- version("1.8.68", sha256="b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c")
- version("1.9.12", sha256="7b623ab9168f460a85d952719ca5249248fc95e6f7a02658b0673b2baa0a8fc6")
-
- # patch required to avoid hpe-mpi linked mechanism library
- patch("pmi_rank.patch", when="@1.9.27:")
-
- variant("neuron", default=True, description="Use BluePyOpt together with NEURON")
-
- depends_on("py-setuptools", type="build")
- depends_on("py-numpy", type=("build", "run"))
- depends_on("py-pandas", type=("build", "run"))
- depends_on("py-deap", type=("build", "run"))
- depends_on("py-deap@1.3.3:", type=("build","run"), when="@1.13.86:")
- depends_on("py-efel", type=("build", "run"))
- depends_on("py-ipyparallel", type=("build", "run"))
- depends_on("py-pickleshare", type=("build", "run"))
- depends_on("py-jinja2", type=("build", "run"))
- depends_on("py-future", type=("build", "run"))
- depends_on("py-pebble@4.3.10:", type=("build", "run"))
- depends_on("py-scoop@0.7:", type=("build", "run"), when="@:1.9.37")
- depends_on("neuron", type=("build", "run"), when="+neuron")
-
- def setup_run_environment(self, env):
- env.unset("PMI_RANK")
- env.set("NEURON_INIT_MPI", "0")
- env.prepend_path("PATH", self.spec["py-ipyparallel"].prefix.bin)
diff --git a/packages/py-bluepyopt/pmi_rank.patch b/packages/py-bluepyopt/pmi_rank.patch
deleted file mode 100644
index 21a73849..00000000
--- a/packages/py-bluepyopt/pmi_rank.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/bluepyopt/ephys/simulators.py b/bluepyopt/ephys/simulators.py
-index e71ad8b..3c93237 100644
---- a/bluepyopt/ephys/simulators.py
-+++ b/bluepyopt/ephys/simulators.py
-@@ -89,6 +89,12 @@ class NrnSimulator(object):
- NrnSimulator._nrn_disable_banner()
- self.banner_disabled = True
-
-+ # certain mpi libraries (hpe-mpt) use PMI_RANK env variable to initialize
-+ # MPI before calling MPI_Init (which is undesirable). Unset this variable
-+ # if exist to avoid issue with loading neuron and mechanism library.
-+ if 'PMI_RANK' in os.environ:
-+ os.environ.pop("PMI_RANK")
-+
- import neuron # NOQA
-
- return neuron
diff --git a/packages/py-efel/package.py b/packages/py-efel/package.py
deleted file mode 100644
index c7b5d571..00000000
--- a/packages/py-efel/package.py
+++ /dev/null
@@ -1,28 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyEfel(PythonPackage):
- """The Electrophys Feature Extract Library (eFEL) allows
- neuroscientists to automatically extract features from time series data
- recorded from neurons (both in vitro and in silico).
- Examples are the action potential width and amplitude in
- voltage traces recorded during whole-cell patch clamp experiments.
- The user of the library provides a set of traces and selects the
- features to be calculated. The library will then extract the requested
- features and return the values to the user."""
-
- homepage = "https://github.com/BlueBrain/eFEL"
- pypi = "efel/efel-3.0.80.tar.gz"
-
- version("4.0.4", sha256="258c506776df609edc799338fd773e78f0f0315fd6f3e2f969478bda401a8894")
-
- depends_on("py-setuptools", type="build")
- depends_on("py-numpy", type="run")
- depends_on("py-six", type="run")
diff --git a/packages/py-libsonata/package.py b/packages/py-libsonata/package.py
index b8b9695a..80fe984b 100644
--- a/packages/py-libsonata/package.py
+++ b/packages/py-libsonata/package.py
@@ -39,3 +39,4 @@ class PyLibsonata(PythonPackage):
depends_on("py-numpy@1.17:", type=("build", "run"))
depends_on("py-setuptools", type="build", when="@0.1:")
depends_on("py-setuptools-scm", type="build", when="@0.1:")
+
diff --git a/packages/py-morph-tool/package.py b/packages/py-morph-tool/package.py
deleted file mode 100644
index 3c483b74..00000000
--- a/packages/py-morph-tool/package.py
+++ /dev/null
@@ -1,40 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyMorphTool(PythonPackage):
- """Python morphology manipulation toolkit"""
-
- homepage = "https://github.com/BlueBrain/morph-tool"
- git = "https://github.com/BlueBrain/morph-tool.git"
- pypi = "morph-tool/morph-tool-2.9.1.tar.gz"
-
- version("develop", branch="master")
- version("2.9.1", sha256="305e9456c8047726588b23dfa070eb95ccbe5573e9fea3e0a83dc93eacdf61dc")
- version("2.9.0", sha256="c60d4010e17ddcc3f53c864c374fffee05713c8f8fd2ba4eed7706041ce1fa47")
-
- variant("neuron", default=False, description="Enable additional neuron support")
-
- depends_on("py-setuptools", type=("build", "run"))
-
- depends_on("py-click@6.7:", type=("build", "run"))
- depends_on("py-deprecation@2.1.0:", type=("build", "run"))
- depends_on("py-more-itertools@8.6.0:", type=("build", "run"))
- depends_on("py-numpy@1.14:", type=("build", "run"))
- depends_on("py-pandas@1.0.3:", type=("build", "run"))
- depends_on("py-xmltodict@0.12:", type=("build", "run"))
-
- depends_on("py-plotly@4.1:", type=("build", "run"))
- depends_on("py-dask@2.19:", type=("build", "run"))
- depends_on("neuron+python@7.8:", type=("build", "run"))
- depends_on("py-bluepyopt@1.9.37:", type=("build", "run"), when="+neuron")
-
- depends_on("py-neurom@3.0:3.999,develop", type=("build", "run"))
- depends_on("py-morphio@3.3.6:3,develop", type=("build", "run"), when="@2.9.1:")
- depends_on("py-morphio@3.0:3,develop", type=("build", "run"), when="@2.9.0")
diff --git a/packages/py-morphio/package.py b/packages/py-morphio/package.py
deleted file mode 100644
index a2957888..00000000
--- a/packages/py-morphio/package.py
+++ /dev/null
@@ -1,35 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyMorphio(PythonPackage):
- """Python library for reading / writing morphology files"""
-
- homepage = "https://github.com/BlueBrain/MorphIO"
- git = "https://github.com/BlueBrain/MorphIO.git"
- pypi = "morphio/MorphIO-3.3.2.tar.gz"
-
- version("develop", branch="master", submodules=True)
- version("unifurcation", branch="unifurcation", submodules=True)
-
- version("3.3.6", sha256="0f2e55470d92a3d89f2141ae905ee104fd16257b93dafb90682d90171de2f4e6")
- version("3.3.5", sha256="9e6cfebaea32080131b2b08a4a32dfbe92b18427a3e557861e27c4131f7542ac")
- version("3.3.4", sha256="b70c6884e9b835560501f798c75c9cc7eaf3162cba1d930b5a9b854bb9ea60dc")
- version("3.3.3", sha256="f6d91970cfd734b2e5fb8f9239a0bfa00519fe082dd8e403e4cc204dbdf0a9fa")
- version("3.3.2", sha256="fc961defbfbfb3f11360954fb3ec51373eaff25b154fa31d6b31decca6937780")
- version("3.1.1", sha256="ad9f0e363f09f03c6eda54f5f3b006d204236677d2f2c9675421e0441033a503")
- version("2.7.1", sha256="3f3e2229da85e874527775fce080f712b6dc287edc44b90b6de35d17b34badff")
-
- depends_on("py-setuptools", type="build")
- depends_on("py-setuptools-scm", type="build")
-
- depends_on("ninja", type="build")
- depends_on("cmake@3.2:", type="build")
- depends_on("py-numpy@1.14.1:", type="run")
- depends_on("hdf5")
diff --git a/packages/py-neurom/package.py b/packages/py-neurom/package.py
deleted file mode 100644
index b902984e..00000000
--- a/packages/py-neurom/package.py
+++ /dev/null
@@ -1,37 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyNeurom(PythonPackage):
- """Python library neuron morphology analysis"""
-
- homepage = "https://github.com/BlueBrain/NeuroM"
- git = "https://github.com/BlueBrain/NeuroM.git"
- pypi = "neurom/neurom-2.2.1.tar.gz"
-
- version("develop", branch="master")
- version("3.2.2", sha256="bc442cf5193289b893a66d5e541868f84bb120b03395b03ce2423c19729b92de")
-
- variant("plotly", default=False, description="Enable plotly support")
-
- depends_on("py-setuptools@0.42:", type=("build", "run"))
- depends_on("py-setuptools-scm", type="build")
- depends_on("py-wheel", type="build")
-
- depends_on("py-click@7.0:", type=("build", "run"))
- depends_on("py-numpy@1.8.0:", type=("build", "run"))
- depends_on("py-pyyaml@3.10:", type=("build", "run"))
- depends_on("py-tqdm@4.8.4:", type=("build", "run"))
- depends_on("py-matplotlib@3.2.1:", type=("build", "run"))
- depends_on("py-scipy@1.2.0:", type=("build", "run"))
- depends_on("py-plotly@3.6.0:", type=("build", "run"), when="+plotly")
- depends_on("py-psutil@5.5.1:", type=("build", "run"), when="+plotly")
-
- depends_on("py-morphio@3.1.1:", type=("build", "run"))
- depends_on("py-pandas@1.0.5:", type=("build", "run"))
diff --git a/spack.yaml b/spack.yaml
index e465a5a4..99226cda 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -16,14 +16,14 @@ spack:
- nest@3.8 +sonata
- neuron@8.2.3 +mpi
- jaxsnn@9.0-a8
- - py-bluepyefe@2.2.18
- - py-bluepymm@0.7.65
- - py-bluepyopt@1.13.86
+ - py-bluepyefe@2.3.6
+ - py-bluepymm@0.8.7
+ - py-bluepyopt@1.14.11
- py-bsb@4.0.0a57
- py-ebrains-drive@0.6.0
- py-ebrains-kg-core@0.9.15
- py-ebrains-validation-client@0.9.1
- - py-efel@4.0.4
+ - py-efel@5.2.0
- py-elephant@1.1.0
- py-fairgraph@0.12.1
- py-frites@0.4.4
@@ -38,7 +38,7 @@ spack:
- py-neo@0.13.3
- py-nestml@8.0.0
- py-netpyne@1.0.6
- - py-neurom@3.2.2
+ - py-neurom@3.2.4
- py-neuror@1.6.4
- py-pynn@0.12.3 +mpi
- py-pyunicore@1.1.1
--
GitLab
From 1b81fd9363c32ee85ba5ba357af8f728aadd2044 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 21 Feb 2025 02:09:48 +0000
Subject: [PATCH 09/80] fix(py-spynnaker): add missing dependency
---
packages/py-spynnaker/package.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/packages/py-spynnaker/package.py b/packages/py-spynnaker/package.py
index 0e200cb3..836e884e 100644
--- a/packages/py-spynnaker/package.py
+++ b/packages/py-spynnaker/package.py
@@ -34,3 +34,4 @@ class PySpynnaker(PythonPackage):
depends_on("py-lazyarray", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-csa", type=("build", "run"))
+ depends_on("py-typing-extensions", type=("build", "run"))
--
GitLab
From 55097008784dcc4bdc21a8cdeb930b63cc4c80d1 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 21 Feb 2025 02:23:11 +0000
Subject: [PATCH 10/80] fix(py-pytest-benchmark): add missing dependency
---
packages/py-pytest-benchmark/package.py | 26 +++++++++++++++++++++++++
1 file changed, 26 insertions(+)
create mode 100644 packages/py-pytest-benchmark/package.py
diff --git a/packages/py-pytest-benchmark/package.py b/packages/py-pytest-benchmark/package.py
new file mode 100644
index 00000000..ab6f0096
--- /dev/null
+++ b/packages/py-pytest-benchmark/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyPytestBenchmark(PythonPackage):
+ """A pytest fixture for benchmarking code."""
+
+ homepage = "https://github.com/ionelmc/pytest-benchmark"
+ pypi = "pytest-benchmark/pytest-benchmark-3.2.3.tar.gz"
+
+ license("BSD-2-Clause")
+
+ version("3.2.3", sha256="ad4314d093a3089701b24c80a05121994c7765ce373478c8f4ba8d23c9ba9528")
+
+ depends_on("python@2.7:2.8,3.5:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-pytest@3.8:", type=("build", "run"))
+ depends_on("py-py-cpuinfo", type=("build", "run"))
+ # begin EBRAINS (added)
+ depends_on("py-py@1.8.2:", type=("build", "run"))
+ # end EBRAINS
--
GitLab
From 79eb0bd3087e1c3ad029221934d92c9673ee3c74 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Sat, 22 Feb 2025 19:20:56 +0000
Subject: [PATCH 11/80] fix(py-ipympl): add missing dependency
---
packages/py-ipympl/package.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/packages/py-ipympl/package.py b/packages/py-ipympl/package.py
index a22c00e6..285ca93e 100644
--- a/packages/py-ipympl/package.py
+++ b/packages/py-ipympl/package.py
@@ -48,6 +48,9 @@ class PyIpympl(PythonPackage):
depends_on("py-numpy")
depends_on("pil")
depends_on("py-traitlets@:5")
+ # begin EBRAINS (added): add missing dependency
+ depends_on("py-tomli")
+ # end EBRAINS
# Necessary for jupyter extension env vars
depends_on("py-jupyter-core")
--
GitLab
From 0347005182782772981b63b80fbdfebbb47cdf2a Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 21 Feb 2025 02:15:18 +0000
Subject: [PATCH 12/80] fix(py-hbp-validation-client): add missing dependency
---
packages/py-hbp-validation-client/package.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/packages/py-hbp-validation-client/package.py b/packages/py-hbp-validation-client/package.py
index fa315a01..59272cac 100644
--- a/packages/py-hbp-validation-client/package.py
+++ b/packages/py-hbp-validation-client/package.py
@@ -33,4 +33,5 @@ class PyHbpValidationClient(PythonPackage):
depends_on('py-nameparser@1.1.1:', type=('build', 'run'), when='@:0.8.4')
depends_on('py-ebrains-drive@0.4.0:', type=('build', 'run'), when='@:0.8.4')
depends_on('py-simplejson@3.17.2:', type=('build', 'run'), when='@:0.8.4')
+ depends_on('py-sciunit', type=('build', 'run'))
depends_on('py-ebrains-validation-client@0.9.1:', type=('build', 'run'), when='@0.9.0:')
--
GitLab
From 2661d9425666e266e74065c8cfe9a058e7d0f6f9 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Sat, 22 Feb 2025 23:30:36 +0000
Subject: [PATCH 13/80] fix(py-sciunit): add version 0.2.8
for compatibility with Python 3.11
---
packages/py-sciunit/package.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/packages/py-sciunit/package.py b/packages/py-sciunit/package.py
index 8e6479a6..5684040b 100644
--- a/packages/py-sciunit/package.py
+++ b/packages/py-sciunit/package.py
@@ -14,6 +14,7 @@ class PySciunit(PythonPackage):
pypi = "sciunit/sciunit-0.2.5.1.tar.gz"
git = "https://github.com/scidash/sciunit.git"
+ version('0.2.8', sha256='85b7288200e55a3270d2346cc357c19d2c812140a9398eda52152a6cb5a281f5')
version('0.2.5.1', sha256='6148704f92a29c9d6de65ca9455b03ebe1f05101dae5e706aee2186e5a09fab3')
depends_on('python@3.6.9:')
--
GitLab
From 29ae30e788a6639e2978117e4e4021915fdc6d5b Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Sat, 22 Feb 2025 23:32:04 +0000
Subject: [PATCH 14/80] fix(py-cherrypy): add version 18.10.0
for compatibility with Python 3.11
---
packages/py-cherrypy/package.py | 29 ++++++++++++++++++++++
packages/py-jaraco-collections/package.py | 26 ++++++++++++++++++++
packages/py-jaraco-context/package.py | 24 ++++++++++++++++++
packages/py-jaraco-text/package.py | 30 +++++++++++++++++++++++
4 files changed, 109 insertions(+)
create mode 100644 packages/py-cherrypy/package.py
create mode 100644 packages/py-jaraco-collections/package.py
create mode 100644 packages/py-jaraco-context/package.py
create mode 100644 packages/py-jaraco-text/package.py
diff --git a/packages/py-cherrypy/package.py b/packages/py-cherrypy/package.py
new file mode 100644
index 00000000..635e1da7
--- /dev/null
+++ b/packages/py-cherrypy/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyCherrypy(PythonPackage):
+ """CherryPy is a pythonic, object-oriented HTTP framework."""
+
+ homepage = "https://cherrypy.readthedocs.io/en/latest/"
+ pypi = "CherryPy/cherrypy-18.10.0.tar.gz"
+
+ license("BSD-3-Clause")
+
+ # begin EBRAINS(added): new version
+ version("18.10.0", sha256="6c70e78ee11300e8b21c0767c542ae6b102a49cac5cfd4e3e313d7bb907c5891")
+ # end EBRAINS
+ version("18.1.1", sha256="6585c19b5e4faffa3613b5bf02c6a27dcc4c69a30d302aba819639a2af6fa48b")
+
+ depends_on("py-setuptools", type="build")
+ depends_on("py-setuptools-scm", type="build")
+ depends_on("py-more-itertools", type=("build", "run"))
+ depends_on("py-zc-lockfile", type=("build", "run"))
+ depends_on("py-cheroot@6.2.4:", type=("build", "run"))
+ depends_on("py-portend@2.1.1:", type=("build", "run"))
+ depends_on("py-jaraco-collections", type=("build", "run"))
+ depends_on("python@3.5:", when="@18.0.0:", type=("build", "run"))
diff --git a/packages/py-jaraco-collections/package.py b/packages/py-jaraco-collections/package.py
new file mode 100644
index 00000000..df6f5542
--- /dev/null
+++ b/packages/py-jaraco-collections/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyJaracoCollections(PythonPackage):
+ """Collection objects similar to those in stdlib by jaraco"""
+
+ homepage = "https://github.com/jaraco/jaraco.collections"
+ pypi = "jaraco.collections/jaraco.collections-5.1.0.tar.gz"
+
+ license("MIT")
+
+ version("5.0.1", sha256="808631b174b84a4e2a592490d62f62dfc15d8047a0f715726098dc43b81a6cfa")
+ version("5.0.0", sha256="1680e8d09f295f625c7ba926880175a26fdbe7092b4c76d198e30476b21cfe68")
+ version("4.3.0", sha256="74ffc23fccfee4de0a2ebf556a33675b6a3c003d6335947d3122a0bc8822c8e4")
+
+ depends_on("python@3.8:", type=("build", "run"))
+
+ depends_on("py-setuptools@56:", type="build")
+ depends_on("py-setuptools-scm@3.4.1: +toml", type="build")
+ depends_on("py-jaraco-text", type=("build", "run"))
+
diff --git a/packages/py-jaraco-context/package.py b/packages/py-jaraco-context/package.py
new file mode 100644
index 00000000..97655be7
--- /dev/null
+++ b/packages/py-jaraco-context/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyJaracoContext(PythonPackage):
+ """Useful decorators and context managers"""
+
+ homepage = "https://github.com/jaraco/jaraco.context"
+ pypi = "jaraco.context/jaraco.context-5.1.0.tar.gz"
+
+ license("MIT")
+
+ version("5.1.0", sha256="24ec1f739aec2c5766c68027ccc70d91d7b0cb931699442f5c7ed93515b955e7")
+ version("5.0.0", sha256="e0e3a7e5ce2dc17daf5f7a0e9387eebb8f352514fd43418ced34bddc6063c34f")
+ version("4.3.0", sha256="4dad2404540b936a20acedec53355bdaea223acb88fd329fa6de9261c941566e")
+
+ depends_on("python@3.8:", type=("build", "run"))
+
+ depends_on("py-setuptools@56:", type="build")
+ depends_on("py-setuptools-scm@3.4.1: +toml", type="build")
diff --git a/packages/py-jaraco-text/package.py b/packages/py-jaraco-text/package.py
new file mode 100644
index 00000000..0789df05
--- /dev/null
+++ b/packages/py-jaraco-text/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyJaracoText(PythonPackage):
+ """Module for text manipulation"""
+
+ homepage = "https://github.com/jaraco/jaraco.text"
+ pypi = "jaraco.text/jaraco.text-3.12.0.tar.gz"
+
+ license("MIT")
+
+ version("3.12.0", sha256="389e25c8d4b32e9715bf530596fab0f5cd3aa47296e43969392e18a541af592c")
+ version("3.11.1", sha256="333a5df2148f7139718607cdf352fe1d95162971a7299c380dcc24dab0168980")
+ version("3.11.0", sha256="0ddb589595fe176ea8179c801ca4ece2be0aa71f377b91f3ca65b4d741948351")
+
+ depends_on("python@3.8:", type=("build", "run"))
+
+ depends_on("py-setuptools@56:", type="build")
+ depends_on("py-setuptools-scm@3.4.1: +toml", type="build")
+
+ depends_on("py-jaraco-functools", type=("build", "run"))
+ depends_on("py-jaraco-context@4.1:", type=("build", "run"))
+ depends_on("py-importlib-resources@1.3:", when="^python@:3.9", type=("build", "run"))
+ depends_on("py-inflect", type=("build", "run"))
+ depends_on("py-more-itertools", type=("build", "run"))
--
GitLab
From fd473887964d52ecdddb0f51a2eb5ef9de6b2949 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Wed, 19 Feb 2025 13:01:09 +0000
Subject: [PATCH 15/80] fix: add type=test to all run-only dependencies of
top-level packages
---
packages/neuron/package.py | 2 +-
packages/py-bluepymm/package.py | 20 ++++++++++----------
packages/py-tvb-framework/package.py | 2 +-
3 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/packages/neuron/package.py b/packages/neuron/package.py
index a87d6d75..a429e035 100644
--- a/packages/neuron/package.py
+++ b/packages/neuron/package.py
@@ -51,7 +51,7 @@ class Neuron(CMakePackage):
depends_on("py-mpi4py", when="+mpi+python+tests")
depends_on("readline")
depends_on("caliper", when="+caliper")
- depends_on("py-numpy", type="run")
+ depends_on("py-numpy", type=("run","test"))
extends('python', when='+python')
diff --git a/packages/py-bluepymm/package.py b/packages/py-bluepymm/package.py
index 7b1a4c2c..74ed5759 100644
--- a/packages/py-bluepymm/package.py
+++ b/packages/py-bluepymm/package.py
@@ -18,16 +18,16 @@ class PyBluepymm(PythonPackage):
version("0.7.65", sha256="024b009decd8d967b3b885421196d53670e3c0a6b75aaaa55559f148b0b0d7d4")
depends_on("py-setuptools", type="build")
- depends_on("py-bluepyopt", type="run")
- depends_on("py-matplotlib", type="run")
- depends_on("py-pandas", type="run")
- depends_on("py-numpy", type="run")
- depends_on("py-ipyparallel", type="run")
- depends_on("py-lxml", type="run")
- depends_on("py-sh", type="run")
- depends_on("neuron", type="run")
- depends_on("py-h5py", type="run")
- depends_on("py-pyyaml", type="run")
+ depends_on("py-bluepyopt", type=("run","test"))
+ depends_on("py-matplotlib", type=("run","test"))
+ depends_on("py-pandas", type=("run","test"))
+ depends_on("py-numpy", type=("run","test"))
+ depends_on("py-ipyparallel", type=("run","test"))
+ depends_on("py-lxml", type=("run","test"))
+ depends_on("py-sh", type=("run","test"))
+ depends_on("neuron", type=("run","test"))
+ depends_on("py-h5py", type=("run","test"))
+ depends_on("py-pyyaml", type=("run","test"))
def setup_run_environment(self, env):
env.unset("PMI_RANK")
diff --git a/packages/py-tvb-framework/package.py b/packages/py-tvb-framework/package.py
index 764ba19a..fb1ebc2f 100644
--- a/packages/py-tvb-framework/package.py
+++ b/packages/py-tvb-framework/package.py
@@ -59,7 +59,7 @@ class PyTvbFramework(PythonPackage):
depends_on('py-six', type=('build', 'run'))
depends_on('py-sqlalchemy', type=('build', 'run'))
depends_on('py-tvb-data', type=('run', 'test'))
- depends_on('py-tvb-gdist', type='run')
+ depends_on('py-tvb-gdist', type=('run', 'test'))
depends_on('py-tvb-library', type=('build', 'run'))
depends_on('py-tvb-storage', type=('build', 'run'))
depends_on('py-werkzeug', type=('build', 'run'))
--
GitLab
From 63c4f74e103ec2dea78a32892ac0d963f09750cd Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Mon, 17 Feb 2025 18:59:10 +0200
Subject: [PATCH 16/80] feat(ebrainslab): update gcc, python and R version
---
site-config/ebrainslab/packages.yaml | 6 +++---
site-config/ebrainslab/spack.yaml | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/site-config/ebrainslab/packages.yaml b/site-config/ebrainslab/packages.yaml
index 3759479f..44e6777d 100644
--- a/site-config/ebrainslab/packages.yaml
+++ b/site-config/ebrainslab/packages.yaml
@@ -2,13 +2,13 @@ packages:
all:
# collab-specific settings
target: [x86_64]
- compiler: [gcc@10.3.0]
+ compiler: [gcc@13]
python:
# collab-specific settings
- require: "@3.8.11"
+ require: "@3.11"
r:
# EM: +X fixes build for collab
- require: "@4.3.0+X"
+ require: "@4.3.3+X"
py-torch:
# ECM: No cuda nor rocm in collab VMs.
# I did not try to minimize the specification any further.
diff --git a/site-config/ebrainslab/spack.yaml b/site-config/ebrainslab/spack.yaml
index ce36e8bb..5e2f9363 100644
--- a/site-config/ebrainslab/spack.yaml
+++ b/site-config/ebrainslab/spack.yaml
@@ -7,7 +7,7 @@ spack:
- py-notebook
- r-irkernel
# "collab"-specific constraint to match ("jupyterlab_widgets") in the base image
- - py-ipywidgets@:7.7
+ - py-ipywidgets
# Collab utils
- clb-nb-utils@0.1.0
--
GitLab
From 67e211f3b9690d31d57392b3847af7bfccbe2f12 Mon Sep 17 00:00:00 2001
From: Moritz Kern <212-moritzkern@users.noreply.gitlab.ebrains.eu>
Date: Sun, 23 Feb 2025 04:29:51 +0100
Subject: [PATCH 17/80] feat(py-elephant): add version 1.1.1
---
packages/py-elephant/package.py | 11 +++++++----
spack.yaml | 2 +-
2 files changed, 8 insertions(+), 5 deletions(-)
diff --git a/packages/py-elephant/package.py b/packages/py-elephant/package.py
index 1ceebcfb..5b3a984d 100644
--- a/packages/py-elephant/package.py
+++ b/packages/py-elephant/package.py
@@ -16,6 +16,8 @@ class PyElephant(PythonPackage, CudaPackage):
maintainers = ["moritzkern"]
version('develop', branch='master')
+
+ version("1.1.1", sha256="c08b89358b52e826bd081ee5a530728fe487c45f5d0539ec97ebdaed9c106e89")
version("1.1.0", sha256="4085a8fcac3ab855f2585d017d17a1589c74adfbd930f7a1e012f2f5bd994e71")
version("1.0.0", sha256="b1471228821a5b8f3a3137f9facc1a7f2dc355b8e3300490bdc05f0466b80b27")
version("0.14.0", sha256="02ce3b2a8d08dc19828f95384551339ea0946bc405c1db9aace54135417c2b0f")
@@ -61,18 +63,20 @@ class PyElephant(PythonPackage, CudaPackage):
depends_on("py-statsmodels@0.12.1:", type=("build", "run"), when="+extras")
depends_on("py-jinja2@2.11.2:", type=("build", "run"), when="+extras")
depends_on("py-neo@0.10.0:", type=("build", "run"), when="@0.11.0:1.0.0")
+ depends_on("py-neo@0.13.1:", type=("build", "run"), when="@1.1.1:")
depends_on("py-neo@0.13.0:", type=("build", "run"), when="@0.11.0:1.1.0")
depends_on("py-neo@0.9.0", type=("build", "run"), when="@0.9.0:0.10.0")
depends_on("py-neo@0.8.0", type=("build", "run"), when="@0.6.4:0.8.0")
depends_on("py-numpy@1.18.1:1.23.5", type=("build", "run"), when="@0.6.4:0.11.2")
- depends_on("py-numpy@1.18.1:", type=("build", "run"), when="@0.12.0:")
+ depends_on("py-numpy@1.18.1:1.26.4", type=("build", "run"), when="@0.12.0:")
depends_on("py-numpy@1.18.1:", type=("build", "run"), when="@develop")
depends_on("py-quantities@0.12.1:0.13.0", type=("build", "run"), when="@0.6.4:0.11.2")
depends_on("py-quantities@0.14.1:", type=("build", "run"), when="@develop")
depends_on("py-quantities@0.14.1:", type=("build", "run"), when="@0.12.0:")
depends_on("py-scikit-learn", type=("build", "run"), when="@0.3:")
depends_on("py-scipy@1.5.4:", type=("build", "run"), when="@0.6.4:1.0.0")
- depends_on("py-scipy@1.10.0:", type=("build", "run"), when="@1.1.0:")
+ depends_on("py-scipy@1.10.0:", type=("build", "run"), when="@1.1.0")
+ depends_on("py-scipy@1.14.0:", type=("build", "run"), when="@1.1.1:")
depends_on("py-six@1.10.0:", type=("build", "run"), when="@0.6.4:")
depends_on("py-tqdm", type=("build", "run"), when="@0.6.4:")
depends_on("py-pycuda", type=("build", "run"), when="@0.10.0:+cuda")
@@ -86,7 +90,6 @@ class PyElephant(PythonPackage, CudaPackage):
# skip some tests that seem to fail on HPC deployments,
# see https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds/-/issues/38
# test_WPLI_ground_truth_consistency_real_LFP_dataset, test_multitaper_cohere_perfect_cohere
- # skip the following due to issue with neo > 0.13.0 https://github.com/NeuralEnsemble/elephant/pull/634
# ECM (2025-02-05): also disable "test_parallel" test due to some test hang, cf. ESD issue 86
# https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds/-/issues/86
- pytest('-k', 'not test_WPLI_ground_truth_consistency_real_LFP_dataset and not test_multitaper_cohere_perfect_cohere and not test_neo_tools and not test_statistics and not test_trials and not test_parallel')
+ pytest('-k', 'not test_WPLI_ground_truth_consistency_real_LFP_dataset and not test_multitaper_cohere_perfect_cohere and not test_parallel')
diff --git a/spack.yaml b/spack.yaml
index 99226cda..0c13eca8 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -24,7 +24,7 @@ spack:
- py-ebrains-kg-core@0.9.15
- py-ebrains-validation-client@0.9.1
- py-efel@5.2.0
- - py-elephant@1.1.0
+ - py-elephant@1.1.1
- py-fairgraph@0.12.1
- py-frites@0.4.4
- py-hbp-archive@1.1.1
--
GitLab
From 435766da6f1a26b7664c6a9963bf9f676da481d8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Tue, 3 Sep 2024 11:05:32 +0200
Subject: [PATCH 18/80] feat: adds arbor@0.10.0 (and incorporate upstream
changes)
---
packages/arbor/package.py | 46 +++++++++++++++++++++++++++++----------
1 file changed, 35 insertions(+), 11 deletions(-)
diff --git a/packages/arbor/package.py b/packages/arbor/package.py
index 7a4a2c25..c45fa47d 100644
--- a/packages/arbor/package.py
+++ b/packages/arbor/package.py
@@ -15,8 +15,13 @@ class Arbor(CMakePackage, CudaPackage):
url = "https://github.com/arbor-sim/arbor/releases/download/v0.9.0/arbor-v0.9.0-full.tar.gz"
maintainers = ["thorstenhater", "brenthuisman", "haampie"]
- version("master", branch="master")
- version("develop")
+ version("master", branch="master", submodules=True)
+ version("develop", branch="master", submodules=True)
+ version(
+ "0.10.0",
+ sha256="72966b7a2f45ce259b8ba167ca3e4f5ab9f212136a300267aaac0c04ed3fe3fc",
+ url="https://github.com/arbor-sim/arbor/releases/download/v0.10.1/arbor-v0.10.0-full.tar.gz",
+ )
version(
"0.9.0",
sha256="5f9740955c821aca81e23298c17ad64f33f635756ad9b4a0c1444710f564306a",
@@ -75,36 +80,50 @@ class Arbor(CMakePackage, CudaPackage):
conflicts("%cce@:9.1")
conflicts("%intel")
+ # begin EBRAINS (modified: added run dep)
depends_on("cmake@3.19:", type=("build", "run"))
+ # end EBRAINS
# misc dependencies
depends_on("fmt@7.1:", when="@0.5.3:") # required by the modcc compiler
depends_on("fmt@9.1:", when="@0.7.1:")
- depends_on("googletest@1.12.1", when="@0.7.1:")
+ # begin EBRAINS (modified: relaxed (upstream gave no info about update))
+ # upstream adds: depends_on("fmt@10.1:", when="@0.9.1:")
+ depends_on("googletest@1.12.1:", when="@0.7.1:")
depends_on("pugixml@1.11:", when="@0.7.1:")
- depends_on("nlohmann-json@3.11.2")
+ # upstream adds: depends_on("pugixml@1.13:", when="@0.9.1:")
+ depends_on("nlohmann-json@3.11.2:")
depends_on("random123")
+ #upstream adds: depends_on("random123@1.14.0:", when="@0.10:")
+ # end EBRAINS (modified)
with when("+cuda"):
depends_on("cuda@10:")
depends_on("cuda@11:", when="@0.7.1:")
+ depends_on("cuda@12:", when="@0.9.1:")
# mpi
+ # begin EBRAINS (modified: added run dep)
depends_on("mpi", when="+mpi", type=("build", "run"))
+ # end EBRAINS (modified)
depends_on("py-mpi4py", when="+mpi+python", type=("build", "run"))
# python (bindings)
- extends("python", when="+python")
- depends_on("python@3.7:", when="+python", type=("build", "run"))
- depends_on("py-numpy", when="+python", type=("build", "run"))
with when("+python"):
+ extends("python")
+ depends_on("python@3.7:", type=("build", "run"))
+ depends_on("python@3.9:", when="@0.9.1:", type=("build", "run"))
+ depends_on("py-numpy", type=("build", "run"))
depends_on("py-pybind11@2.6:", type="build")
depends_on("py-pybind11@2.8.1:", when="@0.5.3:", type="build")
depends_on("py-pybind11@2.10.1:", when="@0.7.1:", type="build")
+ depends_on("py-pandas", type="test")
+ depends_on("py-seaborn", type="test")
# sphinx based documentation
- depends_on("python@3.7:", when="+doc", type="build")
- depends_on("py-sphinx", when="+doc", type="build")
- depends_on("py-svgwrite", when="+doc", type="build")
+ with when("+doc"):
+ depends_on("python@3.10:", type="build")
+ depends_on("py-sphinx", type="build")
+ depends_on("py-svgwrite", type="build")
@property
def build_targets(self):
@@ -127,7 +146,11 @@ class Arbor(CMakePackage, CudaPackage):
opt_flags = spack.build_environment.optimization_flags(
self.compiler, self.spec.target
)
- args.append("-DARB_CXX_FLAGS_TARGET=" + opt_flags)
+ # Might return nothing
+ if opt_flags:
+ args.append("-DARB_CXX_FLAGS_TARGET=" + opt_flags)
+ # Needed, spack has no units package
+ args.append("-DARB_USE_BUNDLED_UNITS=ON")
return args
@@ -135,3 +158,4 @@ class Arbor(CMakePackage, CudaPackage):
@on_package_attributes(run_tests=True)
def install_test(self):
python("-c", "import arbor")
+ python("python/example/single_cell_model.py")
--
GitLab
From 22896f58a404a2745c0721bf0c64914b2c149dde Mon Sep 17 00:00:00 2001
From: Han Lu <ha.lu@fz-juelich.de>
Date: Fri, 27 Sep 2024 13:55:32 +0200
Subject: [PATCH 19/80] chore(arbor): update maintainers list
---
packages/arbor/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/arbor/package.py b/packages/arbor/package.py
index c45fa47d..8cf2887b 100644
--- a/packages/arbor/package.py
+++ b/packages/arbor/package.py
@@ -13,7 +13,7 @@ class Arbor(CMakePackage, CudaPackage):
homepage = "https://arbor-sim.org"
git = "https://github.com/arbor-sim/arbor.git"
url = "https://github.com/arbor-sim/arbor/releases/download/v0.9.0/arbor-v0.9.0-full.tar.gz"
- maintainers = ["thorstenhater", "brenthuisman", "haampie"]
+ maintainers = ("thorstenhater", "ErbB4", "haampie")
version("master", branch="master", submodules=True)
version("develop", branch="master", submodules=True)
--
GitLab
From c09daae9697f9022e4f1d0f41f20c96075ec2af0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Tue, 3 Sep 2024 11:06:48 +0200
Subject: [PATCH 20/80] feat(ESD): update to arbor@0.10.0
---
spack.yaml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/spack.yaml b/spack.yaml
index 0c13eca8..055df087 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -3,7 +3,7 @@ spack:
- site-config/$SYSTEMNAME
specs:
# EBRAINS tools
- - arbor@0.9.0 +python +mpi
+ - arbor@0.10.0 +python +mpi
- py-biobb-analysis@4.0.1
- py-biobb-chemistry@4.0.0
- py-biobb-common@4.1.0
--
GitLab
From 885811dc5558fc1e5ba4f80a1ab90bb4beef8cae Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 03:57:47 +0100
Subject: [PATCH 21/80] chore(CI): use spack config to set upstream
---
install_spack_env.sh | 15 +++++----------
1 file changed, 5 insertions(+), 10 deletions(-)
diff --git a/install_spack_env.sh b/install_spack_env.sh
index faf7ef8b..e5151a15 100644
--- a/install_spack_env.sh
+++ b/install_spack_env.sh
@@ -46,19 +46,14 @@ if [ ! -d ${CI_SPACK_ROOT} ]; then
SPACK_ROOT_EXISTED=0
fi
-if [[ $UPSTREAM_INSTANCE ]]
-then
- UPSTREAM_PREFIX=$(find $UPSTREAM_INSTANCE/spack/opt/spack/ -type d -name ".spack-db" 2>/dev/null | xargs -I {} dirname {})
- cat <<EOF > ${CI_SPACK_ROOT}/etc/spack/defaults/upstreams.yaml
-upstreams:
- upstream-spack-instance:
- install_tree: $UPSTREAM_PREFIX
-EOF
-fi
-
# activate Spack
source ${CI_SPACK_ROOT}/share/spack/setup-env.sh
+if [[ $UPSTREAM_INSTANCE ]]; then
+ UPSTREAM_PREFIX=$(find $UPSTREAM_INSTANCE/spack/opt/spack/ -type d -name ".spack-db" 2>/dev/null | xargs -I {} dirname {})
+ spack config add upstreams:upstream-spack-instance:install_tree:$UPSTREAM_PREFIX
+fi
+
if [ "${SPACK_ROOT_EXISTED}" -eq 0 ]; then
# for caching purposes it's nice if we can relocate into long paths, but we
# can't do that for existing installations -> else path
--
GitLab
From 011f0a17fa694082bf406e5a0fdb4dafc238a7bd Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 04:06:13 +0100
Subject: [PATCH 22/80] feat(CI): disable local configuration and cache
directories
---
install_spack_env.sh | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/install_spack_env.sh b/install_spack_env.sh
index e5151a15..8de4f7df 100644
--- a/install_spack_env.sh
+++ b/install_spack_env.sh
@@ -21,10 +21,9 @@ export OCI_CACHE_PREFIX=$7
# make sure spack uses the symlinked folder as path
export CI_SPACK_ROOT=${INSTALLATION_ROOT}/spack
-# specify location of .spack dir (by default in ~)
-# this is where cache and configuration settings are stored
-export SPACK_USER_CACHE_PATH=${CI_SPACK_ROOT}/.spack
-export SPACK_USER_CONFIG_PATH=${CI_SPACK_ROOT}/.spack
+# disable local configuration and cache directories
+export SPACK_DISABLE_LOCAL_CONFIG=true
+export SPACK_USER_CACHE_PATH=/tmp/spack
# define SYSTEMNAME variable in sites where it's not already defined
export SYSTEMNAME=${SYSTEMNAME:-${HPC_SYSTEM:-$BSC_MACHINE}}
--
GitLab
From aa3fa88d439c43e245eef75251c01a3d2ea14cd0 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 03:04:47 +0200
Subject: [PATCH 23/80] fix(CI): don't use hardcoded prefix path for log
collection
---
.gitlab-ci.yml | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d76a5319..858211ed 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -197,9 +197,9 @@ build-spack-env-on-runner:
after_script:
- mkdir -p $CI_PROJECT_DIR/spack_logs/installed $CI_PROJECT_DIR/spack_logs/not_installed
# for succesfully installed packages: keep the spack logs for any package modified during this CI job
- - shopt -s globstar
- - PKG_DIR=$CI_PROJECT_DIR/spack/opt/spack/**/linux-ubuntu20.04-x86_64/gcc-10.3.0
- - if cd $PKG_DIR; then find . \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi
+ - . $CI_PROJECT_DIR/spack/share/spack/setup-env.sh
+ - cd $(spack-python -c "print(spack.store.parse_install_tree(spack.config.get('config'))[0])")
+ - find . -mindepth 4 -maxdepth 4 \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;
# for not succesfully installed packages: also keep the spack logs for any packages that failed
- if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 \( -name "*.txt" -o -name ".install_time_tests" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
# - if [ -d /tmp/spack_tests ]; then mv /tmp/spack_tests $CI_PROJECT_DIR; fi
@@ -250,7 +250,7 @@ sync-esd-image:
after_script:
- mkdir -p $CI_PROJECT_DIR/spack_logs/installed $CI_PROJECT_DIR/spack_logs/not_installed
# for succesfully installed packages: keep the spack logs for any package modified during this CI job
- - PKG_DIR=${SANDBOX_ROOT}/${INSTALLATION_ROOT}/spack/opt/spack/**/linux-ubuntu20.04-x86_64/gcc-10.3.0
+ - PKG_DIR=${SANDBOX_ROOT}/${INSTALLATION_ROOT}/spack/opt/spack/**/linux-*/gcc-13.3.0
- if cd $PKG_DIR; then find . \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi
# for not succesfully installed packages: also keep the spack logs for any packages that failed
- if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 \( -name "*.txt" -o -name ".install_time_tests" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
@@ -296,9 +296,9 @@ sync-gitlab-spack-instance:
- mkdir -p $CI_PROJECT_DIR/spack_logs/installed $CI_PROJECT_DIR/spack_logs/not_installed
# for succesfully installed packages: keep the spack logs for any package modified during this CI job
# (we use repo.yaml, that is modified at each start of the pipeline, as a reference file)
- - shopt -s globstar
- - PKG_DIR=$SPACK_PATH_GITLAB/spack/opt/spack/**/linux-ubuntu20.04-x86_64/gcc-10.3.0
- - if cd $PKG_DIR; then find . -newer $SPACK_REPO_PATH/repo.yaml \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi
+ - . $SPACK_PATH_GITLAB/spack/share/spack/setup-env.sh
+ - cd $(spack-python -c "print(spack.store.parse_install_tree(spack.config.get('config'))[0])")
+ - find . -mindepth 4 -maxdepth 4 -newer $SPACK_REPO_PATH/repo.yaml \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;
# for not succesfully installed packages: also keep the spack logs for any packages that failed
- if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 \( -name "*.txt" -o -name ".install_time_tests" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
artifacts:
--
GitLab
From cded6c4b5022f507f491a13def2ec1a8c11e6fab Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 03:08:04 +0200
Subject: [PATCH 24/80] fix(py-viziphant): relax python dependency version
range
---
packages/py-viziphant/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/py-viziphant/package.py b/packages/py-viziphant/package.py
index 439d9051..22281cb4 100644
--- a/packages/py-viziphant/package.py
+++ b/packages/py-viziphant/package.py
@@ -20,7 +20,7 @@ class PyViziphant(PythonPackage):
version('0.1.0', sha256='8fd56ec8633f799396dc33fbace95d2553bedb17f680a8c0e97f43b3a629bf6c')
depends_on('py-setuptools', type='build')
- depends_on('python@3.7:3.10', type=('build', 'run'))
+ depends_on('python@3.7:3.11', type=('build', 'run'))
depends_on('py-neo@0.9.0:', type=('build', 'run'))
depends_on('py-elephant@0.9.0:', type=('build', 'run'))
depends_on('py-numpy@1.18.1:', type=('build', 'run'))
--
GitLab
From 5a2751d09eab350e4d9ff2173b376c8907b7811f Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Wed, 26 Feb 2025 09:31:11 +0000
Subject: [PATCH 25/80] feat(py-llvmlite, py-numba): add new versions
from spack upstream develop (https://github.com/spack/spack/commit/8677bb4d43e84591b00c3293381a169ac3ecf299)
---
packages/py-llvmlite/package.py | 86 +++++++++++++++++++++++++++++++++
packages/py-numba/package.py | 43 ++++++++++++-----
2 files changed, 118 insertions(+), 11 deletions(-)
create mode 100644 packages/py-llvmlite/package.py
diff --git a/packages/py-llvmlite/package.py b/packages/py-llvmlite/package.py
new file mode 100644
index 00000000..a4389d9c
--- /dev/null
+++ b/packages/py-llvmlite/package.py
@@ -0,0 +1,86 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyLlvmlite(PythonPackage):
+ """A lightweight LLVM python binding for writing JIT compilers"""
+
+ homepage = "https://llvmlite.readthedocs.io/en/latest/index.html"
+ pypi = "llvmlite/llvmlite-0.23.0.tar.gz"
+ git = "https://github.com/numba/llvmlite.git"
+
+ license("BSD-2-Clause")
+
+ version("0.44.0", sha256="07667d66a5d150abed9157ab6c0b9393c9356f229784a4385c02f99e94fc94d4")
+ version("0.43.0", sha256="ae2b5b5c3ef67354824fb75517c8db5fbe93bc02cd9671f3c62271626bc041d5")
+ version("0.42.0", sha256="f92b09243c0cc3f457da8b983f67bd8e1295d0f5b3746c7a1861d7a99403854a")
+ version("0.41.1", sha256="f19f767a018e6ec89608e1f6b13348fa2fcde657151137cb64e56d48598a92db")
+ version("0.41.0", sha256="7d41db345d76d2dfa31871178ce0d8e9fd8aa015aa1b7d4dab84b5cb393901e0")
+ version("0.40.1", sha256="5cdb0d45df602099d833d50bd9e81353a5e036242d3c003c5b294fc61d1986b4")
+ version("0.40.0", sha256="c910b8fbfd67b8e9d0b10ebc012b23cd67cbecef1b96f00d391ddd298d71671c")
+ version("0.39.1", sha256="b43abd7c82e805261c425d50335be9a6c4f84264e34d6d6e475207300005d572")
+ version("0.39.0", sha256="01098be54f1aa25e391cebba8ea71cd1533f8cd1f50e34c7dd7540c2560a93af")
+ version("0.38.1", sha256="0622a86301fcf81cc50d7ed5b4bebe992c030580d413a8443b328ed4f4d82561")
+ version("0.38.0", sha256="a99d166ccf3b116f3b9ed23b9b70ba2415640a9c978f3aaa13fad49c58f4965c")
+ version("0.37.0", sha256="6392b870cd018ec0c645d6bbb918d6aa0eeca8c62674baaee30862d6b6865b15")
+ version(
+ "0.34.0",
+ sha256="f03ee0d19bca8f2fe922bb424a909d05c28411983b0c2bc58b020032a0d11f63",
+ deprecated=True,
+ )
+ version(
+ "0.33.0",
+ sha256="9c8aae96f7fba10d9ac864b443d1e8c7ee4765c31569a2b201b3d0b67d8fc596",
+ deprecated=True,
+ )
+ version(
+ "0.31.0",
+ sha256="22ab2b9d7ec79fab66ac8b3d2133347de86addc2e2df1b3793e523ac84baa3c8",
+ deprecated=True,
+ )
+
+ depends_on("cxx", type="build") # generated
+
+ depends_on("py-setuptools", type="build")
+ depends_on("python@3.9:3.12", when="@0.42:", type=("build", "run"))
+ depends_on("python@3.8:3.11", when="@0.40:0.41", type=("build", "run"))
+ depends_on("python@:3.10", when="@0.38:0.39", type=("build", "run"))
+ depends_on("python@:3.9", when="@0.36:0.37", type=("build", "run"))
+ depends_on("python@:3.8", when="@0.31:0.35", type=("build", "run"))
+
+ # https://github.com/numba/llvmlite#compatibility
+ depends_on("llvm@15", when="@0.44:")
+ depends_on("llvm@14", when="@0.41:0.43")
+ depends_on("llvm@11:14", when="@0.40")
+ depends_on("llvm@11", when="@0.37:0.39")
+ for t in [
+ "arm:",
+ "ppc:",
+ "ppc64:",
+ "ppc64le:",
+ "ppcle:",
+ "sparc:",
+ "sparc64:",
+ "x86:",
+ "x86_64:",
+ ]:
+ depends_on("llvm@10.0", when=f"@0.34:0.36 target={t}")
+
+ depends_on("llvm@9.0", when="@0.34:0.36 target=aarch64:")
+ depends_on("llvm@9.0", when="@0.33")
+ depends_on("llvm@7.0:7.1,8.0", when="@0.29:0.32")
+ depends_on("binutils", type="build")
+
+ # TODO: investigate
+ conflicts("%apple-clang@15:")
+
+ def setup_build_environment(self, env):
+ if self.spec.satisfies("%fj"):
+ env.set("CXX_FLTO_FLAGS", "{0}".format(self.compiler.cxx_pic_flag))
+ env.set("LD_FLTO_FLAGS", "-Wl,--exclude-libs=ALL")
+ else:
+ # Need to set PIC flag since this is linking statically with LLVM
+ env.set("CXX_FLTO_FLAGS", "-flto {0}".format(self.compiler.cxx_pic_flag))
diff --git a/packages/py-numba/package.py b/packages/py-numba/package.py
index 522abe31..98b99ab1 100644
--- a/packages/py-numba/package.py
+++ b/packages/py-numba/package.py
@@ -1,5 +1,4 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -17,6 +16,9 @@ class PyNumba(PythonPackage):
license("BSD-2-Clause")
+ version("0.61.0", sha256="888d2e89b8160899e19591467e8fdd4970e07606e1fbc248f239c89818d5f925")
+ version("0.60.0", sha256="5df6158e5584eece5fc83294b949fd30b9f1125df7708862205217e068aabf16")
+ version("0.59.1", sha256="76f69132b96028d2774ed20415e8c528a34e3299a40581bae178f0994a2f370b")
version("0.58.1", sha256="487ded0633efccd9ca3a46364b40006dbdaca0f95e99b8b83e778d1195ebcbaa")
version("0.57.0", sha256="2af6d81067a5bdc13960c6d2519dbabbf4d5d597cf75d640c5aeaefd48c6420a")
version("0.56.4", sha256="32d9fef412c81483d7efe0ceb6cf4d3310fde8b624a9cecca00f790573ac96ee")
@@ -24,22 +26,42 @@ class PyNumba(PythonPackage):
version("0.55.2", sha256="e428d9e11d9ba592849ccc9f7a009003eb7d30612007e365afe743ce7118c6f4")
version("0.55.1", sha256="03e9069a2666d1c84f93b00dbd716fb8fedde8bb2c6efafa2f04842a46442ea3")
version("0.54.0", sha256="bad6bd98ab2e41c34aa9c80b8d9737e07d92a53df4f74d3ada1458b0b516ccff")
- version("0.51.1", sha256="1e765b1a41535684bf3b0465c1d0a24dcbbff6af325270c8f4dad924c0940160")
- version("0.50.1", sha256="89e81b51b880f9b18c82b7095beaccc6856fcf84ba29c4f0ced42e4e5748a3a7")
- version("0.48.0", sha256="9d21bc77e67006b5723052840c88cc59248e079a907cc68f1a1a264e1eaba017")
+ version(
+ "0.51.1",
+ sha256="1e765b1a41535684bf3b0465c1d0a24dcbbff6af325270c8f4dad924c0940160",
+ deprecated=True,
+ )
+ version(
+ "0.50.1",
+ sha256="89e81b51b880f9b18c82b7095beaccc6856fcf84ba29c4f0ced42e4e5748a3a7",
+ deprecated=True,
+ )
+ version(
+ "0.48.0",
+ sha256="9d21bc77e67006b5723052840c88cc59248e079a907cc68f1a1a264e1eaba017",
+ deprecated=True,
+ )
depends_on("c", type="build") # generated
depends_on("cxx", type="build") # generated
variant("tbb", default=False, description="Build with Intel Threading Building Blocks")
- depends_on("python@3.8:3.11", when="@0.57:", type=("build", "run"))
+ # Be careful that the bounds given in setup.py are exclusive on the upper bound
+ # i.e., [min, max)
+ depends_on("python@3.10:3.13", when="@0.61:", type=("build", "run"))
+ depends_on("python@3.9:3.12", when="@0.59:", type=("build", "run"))
+ depends_on("python@3.8:3.11", when="@0.57:0.58", type=("build", "run"))
depends_on("python@3.7:3.10", when="@0.55:0.56", type=("build", "run"))
depends_on("python@3.7:3.9", when="@0.54", type=("build", "run"))
depends_on("python@3.6:3.9", when="@0.53", type=("build", "run"))
depends_on("python@3.6:3.8", when="@0.52", type=("build", "run"))
depends_on("python@3.6:3.8", when="@0.48:0.51", type=("build", "run"))
- depends_on("py-numpy@1.22:1.26", when="@0.58.1:", type=("build", "run"))
+ # begin EBRAINS (added): fix numpy dependency version range
+ depends_on("py-numpy@1.24:1.26,2.0:2.1", when="@0.61:", type=("build", "run"))
+ depends_on("py-numpy@1.22:1.26,2.0", when="@0.60", type=("build", "run"))
+ # end EBRAINS
+ depends_on("py-numpy@1.22:1.26", when="@0.58.1:0.59", type=("build", "run"))
depends_on("py-numpy@1.21:1.25", when="@0.58.0", type=("build", "run"))
depends_on("py-numpy@1.21:1.24", when="@0.57", type=("build", "run"))
depends_on("py-numpy@1.18:1.23", when="@0.56.1:0.56.4", type=("build", "run"))
@@ -48,6 +70,9 @@ class PyNumba(PythonPackage):
depends_on("py-numpy@1.17:1.20", when="@0.54", type=("build", "run"))
depends_on("py-numpy@1.15:1.20", when="@0.48:0.53", type=("build", "run"))
depends_on("py-setuptools", type=("build", "run"))
+ depends_on("py-llvmlite@0.44", when="@0.61", type=("build", "run"))
+ depends_on("py-llvmlite@0.43", when="@0.60", type=("build", "run"))
+ depends_on("py-llvmlite@0.42", when="@0.59", type=("build", "run"))
depends_on("py-llvmlite@0.41", when="@0.58", type=("build", "run"))
depends_on("py-llvmlite@0.40", when="@0.57", type=("build", "run"))
depends_on("py-llvmlite@0.39", when="@0.56", type=("build", "run"))
@@ -64,10 +89,6 @@ class PyNumba(PythonPackage):
# See https://reviews.llvm.org/D44140
conflicts("^llvm@6.0.0")
- # begin EBRAINS (added): numba>=0.57 requires at least version 14.0.0 of LLVM
- conflicts("llvm@:13", when="@0.57.0:")
- # end EBRAINS
-
def setup_build_environment(self, env):
if self.spec.satisfies("~tbb"):
env.set("NUMBA_DISABLE_TBB", "yes")
--
GitLab
From 8df4dc1f4f95ed94ab769a263bd470c9367206a8 Mon Sep 17 00:00:00 2001
From: Abolfazl Ziaeemehr <a.ziaeemehr@gmail.com>
Date: Thu, 20 Feb 2025 14:17:31 +0200
Subject: [PATCH 26/80] feat(py-vbi): add vbi
Co-Authored-By: Eleni Mathioulaki <emathioulaki@athenarc.gr>
---
packages/py-sbi/package.py | 46 ++++++++++++++++++++++++++++++++++++++
packages/py-vbi/package.py | 43 +++++++++++++++++++++++++++++++++++
spack.yaml | 1 +
3 files changed, 90 insertions(+)
create mode 100644 packages/py-sbi/package.py
create mode 100644 packages/py-vbi/package.py
diff --git a/packages/py-sbi/package.py b/packages/py-sbi/package.py
new file mode 100644
index 00000000..a560cd93
--- /dev/null
+++ b/packages/py-sbi/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySbi(PythonPackage):
+ """Python package for simulating biological systems."""
+
+ homepage = "https://sbi-dev.github.io/sbi/v0.23.3/"
+ url = "https://github.com/sbi-dev/sbi/archive/refs/tags/v0.23.3.tar.gz"
+
+ version("0.23.3", "b1ef102e47c90088f2adfff5ea88b18421e84c4641ff4dd4f68c1116c296ba81")
+
+ depends_on("python@3.9:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-wheel", type="build")
+
+ depends_on("py-arviz", type=("build", "run"))
+ depends_on("py-joblib@1.3.0:", type=("build", "run"))
+ depends_on("py-matplotlib", type=("build", "run"))
+ depends_on("py-notebook@:6.4.12", type=("build", "run"))
+ depends_on("py-numpy@:1", type=("build", "run"))
+ depends_on("py-pillow", type=("build", "run"))
+ depends_on("py-pyknos@0.16.0:", type=("build", "run"))
+ depends_on("py-pyro-ppl@1.3.1:", type=("build", "run"))
+ depends_on("py-scikit-learn", type=("build", "run"))
+ depends_on("py-scipy", type=("build", "run"))
+ depends_on("py-tensorboard", type=("build", "run"))
+ depends_on("py-torch@1.13.0:", type=("build", "run"))
+ depends_on("py-tqdm", type=("build", "run"))
+ depends_on("py-pymc@5.0.0:", type=("build", "run"))
+ depends_on("py-zuko@1.2.0:", type=("build", "run"))
+
+ depends_on("py-pytest", type="test")
+ depends_on("py-torchtestcase", type="test")
+
+ skip_modules = ["sbi.inference.snle", "sbi.inference.snpe", "sbi.inference.snre", "sbi.samplers.score", "sbi.samplers.vi"]
+
+ @run_after("install")
+ @on_package_attributes(run_tests=True)
+ def install_test(self):
+ pytest = which("pytest")
+ pytest("-m", "not slow and not gpu")
diff --git a/packages/py-vbi/package.py b/packages/py-vbi/package.py
new file mode 100644
index 00000000..ba2cbebb
--- /dev/null
+++ b/packages/py-vbi/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyVbi(PythonPackage):
+
+ homepage = "https://vbi.readthedocs.io/latest/"
+ git = "https://github.com/ins-amu/vbi"
+ url = "https://github.com/ins-amu/vbi/archive/refs/tags/v0.1.3.tar.gz"
+
+ version("0.1.3", "54fa2062f44c9ec8219fae3c13c52a4bd17141b5467b982987673de0662c5255")
+ version("0.1.2", "6ccfeeec718be62a480002a8370130a3e3344955186f99ecbb15b646b68210d6")
+
+ depends_on("python@3.8:", type=("build","run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-setuptools-scm", type="build")
+ depends_on("py-wheel", type="build")
+ depends_on("swig@4:", type="build")
+ depends_on("py-numpy", type=("build", "run"))
+ depends_on("py-scipy", type=("build", "run"))
+ depends_on("py-numba", type=("build", "run"))
+ depends_on("py-h5py", type=("build", "run"))
+ depends_on("py-pandas", type=("build", "run"))
+ depends_on("py-networkx", type=("build", "run"))
+ depends_on("py-nbconvert", type=("build", "run"))
+ depends_on("py-matplotlib", type=("build", "run"))
+ depends_on("py-tqdm", type=("build", "run"))
+ depends_on("py-sbi", type=("build", "run"))
+ depends_on("py-torch", type=("build", "run"))
+ depends_on("py-parameterized", type=("build", "run"))
+ depends_on("py-scikit-learn", type=("build", "run"))
+ depends_on("py-pycatch22", type=("build", "run"))
+ depends_on("py-pytest", type="test")
+
+ @run_after("install")
+ @on_package_attributes(run_tests=True)
+ def install_test(self):
+ pytest = which("pytest")
+ pytest()
diff --git a/spack.yaml b/spack.yaml
index 055df087..b4322538 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -56,6 +56,7 @@ spack:
- py-tvb-ext-unicore
- py-tvb-ext-xircuits@1.1.0
- py-viziphant@0.4.0
+ - py-vbi
- pynn-brainscales@9.0-a8
- r-rgsl@0.1.1
- r-sbtabvfgen@0.1
--
GitLab
From 243bd1438eb48ec25695cf45dfb88420280df311 Mon Sep 17 00:00:00 2001
From: teodoramisan <teodora.misan@codemart.ro>
Date: Fri, 21 Feb 2025 18:09:01 +0200
Subject: [PATCH 27/80] feat(py-sbi): update dependencies and add missing
packages
Co-Authored-By: Eleni Mathioulaki <emathioulaki@athenarc.gr>
---
packages/py-cons/package.py | 19 +++++++++++++
packages/py-etuples/package.py | 21 +++++++++++++++
packages/py-logical-unification/package.py | 20 ++++++++++++++
packages/py-mini-kanren/package.py | 24 +++++++++++++++++
packages/py-nflows/package.py | 22 +++++++++++++++
packages/py-pycatch22/package.py | 16 +++++++++++
packages/py-pyknos/package.py | 25 +++++++++++++++++
packages/py-pymc/package.py | 31 ++++++++++++++++++++++
packages/py-pytensor/package.py | 27 +++++++++++++++++++
packages/py-torchtestcase/package.py | 20 ++++++++++++++
packages/py-umnn/package.py | 20 ++++++++++++++
packages/py-xarray-einstats/package.py | 23 ++++++++++++++++
packages/py-zuko/package.py | 20 ++++++++++++++
13 files changed, 288 insertions(+)
create mode 100644 packages/py-cons/package.py
create mode 100644 packages/py-etuples/package.py
create mode 100644 packages/py-logical-unification/package.py
create mode 100644 packages/py-mini-kanren/package.py
create mode 100644 packages/py-nflows/package.py
create mode 100644 packages/py-pycatch22/package.py
create mode 100644 packages/py-pyknos/package.py
create mode 100644 packages/py-pymc/package.py
create mode 100644 packages/py-pytensor/package.py
create mode 100644 packages/py-torchtestcase/package.py
create mode 100644 packages/py-umnn/package.py
create mode 100644 packages/py-xarray-einstats/package.py
create mode 100644 packages/py-zuko/package.py
diff --git a/packages/py-cons/package.py b/packages/py-cons/package.py
new file mode 100644
index 00000000..77b2e1ab
--- /dev/null
+++ b/packages/py-cons/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCons(PythonPackage):
+ """An implementation of cons in Python."""
+
+ homepage = "https://github.com/pythological/python-cons"
+ pypi = "cons/cons-0.4.6.tar.gz"
+
+ version("0.4.6", "669fe9d5ee916d5e42b9cac6acc911df803d04f2e945c1604982a04d27a29b47")
+
+ depends_on("python@3.6:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-logical-unification@0.4.0:", type=("build", "run"))
diff --git a/packages/py-etuples/package.py b/packages/py-etuples/package.py
new file mode 100644
index 00000000..d3462437
--- /dev/null
+++ b/packages/py-etuples/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyEtuples(PythonPackage):
+ """Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving
+ multi-dimensional arrays. It provides the computational backend for PyMC."""
+
+ homepage = "http://github.com/pythological/etuples"
+ pypi = "etuples/etuples-0.3.9.tar.gz"
+
+ version("0.3.9", "a474e586683d8ba8d842ba29305005ceed1c08371a4b4b0e0e232527137e5ea3")
+
+ depends_on("python@3.8:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-cons", type=("build", "run"))
+ depends_on("py-multipledispatch", type=("build", "run"))
diff --git a/packages/py-logical-unification/package.py b/packages/py-logical-unification/package.py
new file mode 100644
index 00000000..7ba1620e
--- /dev/null
+++ b/packages/py-logical-unification/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLogicalUnification(PythonPackage):
+ """Logical unification in Python, extensible via dispatch."""
+
+ homepage = "http://github.com/pythological/unification/"
+ pypi = "logical-unification/logical-unification-0.4.6.tar.gz"
+
+ version("0.4.6", "908435123f8a106fa4dcf9bf1b75c7beb309fa2bbecf277868af8f1c212650a0")
+
+ depends_on("python@3.6:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-toolz", type=("build", "run"))
+ depends_on("py-multipledispatch", type=("build", "run"))
diff --git a/packages/py-mini-kanren/package.py b/packages/py-mini-kanren/package.py
new file mode 100644
index 00000000..2d24eb02
--- /dev/null
+++ b/packages/py-mini-kanren/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMiniKanren(PythonPackage):
+ """Logic/relational programming in Python with miniKanren."""
+
+ homepage = "http://github.com/pythological/kanren"
+ pypi = "miniKanren/miniKanren-1.0.3.tar.gz"
+
+ version("1.0.3", "1ec8bdb01144ad5e8752c7c297fb8a122db920f859276d25a72d164e998d7f6e")
+
+ depends_on("python@3.6:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-toolz", type=("build", "run"))
+ depends_on("py-cons@0.4.0:", type=("build", "run"))
+ depends_on("py-multipledispatch", type=("build", "run"))
+ depends_on("py-etuples@0.3.1:", type=("build", "run"))
+ depends_on("py-logical-unification@0.4.1:", type=("build", "run"))
+ depends_on("py-typing-extensions", type=("build", "run"))
diff --git a/packages/py-nflows/package.py b/packages/py-nflows/package.py
new file mode 100644
index 00000000..72f82caf
--- /dev/null
+++ b/packages/py-nflows/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+class PyNflows(PythonPackage):
+ """It is a comprehensive collection of normalizing flows using PyTorch."""
+
+ homepage = "https://github.com/bayesiains/nflows"
+ pypi = "nflows/nflows-0.14.tar.gz"
+
+ version("0.14", "6299844a62f9999fcdf2d95cb2d01c091a50136bd17826e303aba646b2d11b55")
+
+ depends_on("py-setuptools", type="build")
+ depends_on("py-matplotlib", type=("build", "run"))
+ depends_on("py-numpy", type=("build", "run"))
+ depends_on("py-tensorboard", type=("build", "run"))
+ depends_on("py-torch", type=("build", "run"))
+ depends_on("py-tqdm", type=("build", "run"))
+ depends_on("py-umnn", type=("build", "run"))
diff --git a/packages/py-pycatch22/package.py b/packages/py-pycatch22/package.py
new file mode 100644
index 00000000..68c4be09
--- /dev/null
+++ b/packages/py-pycatch22/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPycatch22(PythonPackage):
+
+ homepage = "https://github.com/DynamicsAndNeuralSystems/pycatch22"
+ pypi="pycatch22/pycatch22-0.4.5.tar.gz"
+
+ version("0.4.5", sha256="7ec844c659f22bedc66847ac866ef2bd86ffbbd4d8114b5e97f699f20a6f9f81")
+
+ depends_on("py-setuptools", type="build")
diff --git a/packages/py-pyknos/package.py b/packages/py-pyknos/package.py
new file mode 100644
index 00000000..e9449a6d
--- /dev/null
+++ b/packages/py-pyknos/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyknos(PythonPackage):
+ """Python package for conditional density estimation. It either wraps or implements diverse conditional density
+ estimators."""
+
+ homepage = "https://github.com/sbi-dev/pyknos"
+ pypi = "pyknos/pyknos-0.16.0.tar.gz"
+
+ version("0.16.0", "4e1db834d8a5fd847882a081937732fea6798668b72293ae052765e7bfc371c3")
+
+ depends_on("python@3.8:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-matplotlib", type=("build", "run"))
+ depends_on("py-nflows@0.14", type=("build", "run"))
+ depends_on("py-numpy", type=("build", "run"))
+ depends_on("py-tensorboard", type=("build", "run"))
+ depends_on("py-torch", type=("build", "run"))
+ depends_on("py-tqdm", type=("build", "run"))
diff --git a/packages/py-pymc/package.py b/packages/py-pymc/package.py
new file mode 100644
index 00000000..b7dc999f
--- /dev/null
+++ b/packages/py-pymc/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPymc(PythonPackage):
+ """PyMC (formerly PyMC3) is a Python package for Bayesian statistical modeling focusing on advanced Markov chain Monte
+ Carlo (MCMC) and variational inference (VI) algorithms."""
+
+ homepage = "https://github.com/pymc-devs/pymc"
+ pypi = "pymc/pymc-5.20.1.tar.gz"
+
+ version("5.20.1", "fb5f20d196a1b34eb193a855c611887b2e7b98d3af37d8573a33d112e2278eac")
+
+ depends_on("python@3.10:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-versioneer", type="build")
+
+ depends_on("py-arviz@0.13:", type=("build", "run"))
+ depends_on("py-cachetools@4.2.1:", type=("build", "run"))
+ depends_on("py-cloudpickle", type=("build", "run"))
+ depends_on("py-numpy@1.25.0:", type=("build", "run"))
+ depends_on("py-pandas@0.24.0:", type=("build", "run"))
+ depends_on("py-pytensor@2.26.1:2.27.999", type=("build", "run"))
+ depends_on("py-rich@13.7.1:", type=("build", "run"))
+ depends_on("py-scipy@1.4.1:", type=("build", "run"))
+ depends_on("py-threadpoolctl@3.1.0:3.99", type=("build", "run"))
+ depends_on("py-typing-extensions@3.7.4:", type=("build", "run"))
diff --git a/packages/py-pytensor/package.py b/packages/py-pytensor/package.py
new file mode 100644
index 00000000..4c045393
--- /dev/null
+++ b/packages/py-pytensor/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+class PyPytensor(PythonPackage):
+ """Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving
+ multi-dimensional arrays. It provides the computational backend for PyMC."""
+
+ homepage = "https://github.com/pymc-devs/pytensor"
+ pypi = "pytensor/pytensor-2.27.1.tar.gz"
+
+ version("2.27.1", "ed5075e1504e0e4c2322340111289820c5e1718b70187922777d560a8ef26f75")
+
+ depends_on("python@3.10:3.13", type=("build", "run"))
+ depends_on("py-setuptools@59.0.0:", type="build")
+ depends_on("py-cython", type="build")
+ depends_on("py-versioneer+toml", type="build")
+ depends_on("py-scipy@1.0:1", type=("build", "run"))
+ depends_on("py-numpy@1.17.0:", type=("build", "run"))
+ depends_on("py-filelock", type=("build", "run")) # TODO: it needs filelock>=3.15, but on pypi the latest one is 3.12.4
+ depends_on("py-etuples", type=("build", "run"))
+ depends_on("py-logical-unification", type=("build", "run"))
+ depends_on("py-mini-kanren", type=("build", "run"))
+ depends_on("py-cons", type=("build", "run"))
diff --git a/packages/py-torchtestcase/package.py b/packages/py-torchtestcase/package.py
new file mode 100644
index 00000000..29db01bd
--- /dev/null
+++ b/packages/py-torchtestcase/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyTorchtestcase(PythonPackage):
+ """Extends unittest.TestCase such that assertions support PyTorch tensors and parameters."""
+
+ homepage = "https://github.com/phohenecker/torch-test-case"
+ pypi = "torchtestcase/torchtestcase-2018.2.tar.gz"
+
+ version("2018.2", sha256="0061cde2eb79f09c9501fae675c52c799371606d52afcff8753c44e1a6254a00")
+ version("2018.1", sha256="691b053b0466aed40201e1b41f5a903b4df889a64272a18bcab4b1c8e9091cb4")
+ version("2017.1", sha256="f8bb0c4e3216087130f80c4237bb5e4c1e6de629d553f25fd7b85f6e33bf9b34")
+
+ depends_on("py-numpy@1.13.1:", type=("build", "run"))
+ depends_on("py-torch@0.4.0:", type=("build", "run"))
diff --git a/packages/py-umnn/package.py b/packages/py-umnn/package.py
new file mode 100644
index 00000000..545b1ec0
--- /dev/null
+++ b/packages/py-umnn/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyUmnn(PythonPackage):
+ """Official implementation of Unconstrained Monotonic Neural Networks (UMNN)."""
+
+ homepage = "https://github.com/AWehenkel/UMNN"
+ pypi = "umnn/umnn-1.71.tar.gz"
+
+ version("1.71", "bdd41d941a5d904e2217a960a9584922afad8068304976dc6fb0245e4f834996")
+
+ depends_on("python@3.6:", type=("build", "run"))
+ depends_on("py-hatchling", type="build")
+ depends_on("py-numpy", type=("build", "run"))
+ depends_on("py-torch@1.1:", type=("build", "run"))
diff --git a/packages/py-xarray-einstats/package.py b/packages/py-xarray-einstats/package.py
new file mode 100644
index 00000000..520eb406
--- /dev/null
+++ b/packages/py-xarray-einstats/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyXarrayEinstats(PythonPackage):
+ """Stats, linear algebra and einops for xarray"""
+
+ homepage = "https://github.com/arviz-devs/xarray-einstats"
+ pypi = "xarray_einstats/xarray_einstats-0.8.0.tar.gz"
+
+ version("0.8.0", sha256="7f1573f9bd4d60d6e7ed9fd27c4db39da51ec49bf8ba654d4602a139a6309d7f")
+ version("0.7.0", sha256="2d7b571b3bbad3cf2fd10c6c75fd949d247d14c29574184c8489d9d607278d38")
+ version("0.6.0", sha256="ace90601505cfbe2d374762e674557ed14e1725b024823372f7ef9fd237effad")
+
+ depends_on("python@3.10:", type=("build", "run"))
+ depends_on("py-flit-core@3.4:4", type="build")
+ depends_on("py-numpy@1.23:", type=("build", "run"))
+ depends_on("py-scipy@1.9:", type=("build", "run"))
+ depends_on("py-xarray@2022.09:", type=("build", "run"))
diff --git a/packages/py-zuko/package.py b/packages/py-zuko/package.py
new file mode 100644
index 00000000..9c222273
--- /dev/null
+++ b/packages/py-zuko/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyZuko(PythonPackage):
+ """Python package that implements normalizing flows in PyTorch."""
+
+ homepage = "https://github.com/probabilists/zuko"
+ pypi = "zuko/zuko-1.3.1.tar.gz"
+
+ version("1.3.1", "00f246802d3f486183185529ba22e0b2bf691397e03b28150a5cf713fa0da758")
+
+ depends_on("python@3.9:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-numpy@1.20.0:", type=("build", "run"))
+ depends_on("py-torch@1.12.0:", type=("build", "run"))
--
GitLab
From 176c2a5a618785e017d328b0d36b140bbf32277d Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 01:47:16 +0000
Subject: [PATCH 28/80] feat(py-arviz): copy package from upstream
---
packages/py-arviz/package.py | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
create mode 100644 packages/py-arviz/package.py
diff --git a/packages/py-arviz/package.py b/packages/py-arviz/package.py
new file mode 100644
index 00000000..d16dc45e
--- /dev/null
+++ b/packages/py-arviz/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyArviz(PythonPackage):
+ """ArviZ (pronounced "AR-vees") is a Python package for exploratory
+ analysis of Bayesian models. Includes functions for posterior analysis,
+ model checking, comparison and diagnostics."""
+
+ homepage = "https://github.com/arviz-devs/arviz"
+ pypi = "arviz/arviz-0.6.1.tar.gz"
+
+ license("Apache-2.0")
+
+ version("0.6.1", sha256="435edf8db49c41a8fa198f959e7581063006c49a4efdef4755bb778db6fd4f72")
+
+ depends_on("py-setuptools", type="build")
+ depends_on("py-matplotlib@3.0:", type=("build", "run"))
+ depends_on("py-numpy@1.12:", type=("build", "run"))
+ depends_on("py-scipy@0.19:", type=("build", "run"))
+ depends_on("py-packaging", type=("build", "run"))
+ depends_on("py-pandas@0.23:", type=("build", "run"))
+ depends_on("py-xarray@0.11:", type=("build", "run"))
+ depends_on("py-netcdf4", type=("build", "run"))
--
GitLab
From bed743be961d0d17f738e94b7269af925c6a0155 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 02:12:48 +0000
Subject: [PATCH 29/80] feat(py-arviz): add version 0.20.0
---
packages/py-arviz/package.py | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/packages/py-arviz/package.py b/packages/py-arviz/package.py
index d16dc45e..c127d5f4 100644
--- a/packages/py-arviz/package.py
+++ b/packages/py-arviz/package.py
@@ -16,6 +16,9 @@ class PyArviz(PythonPackage):
license("Apache-2.0")
+ # begin EBRAINS (added): added version
+ version("0.20.0", sha256="a2704e0c141410fcaea1973a90cabf280f5aed5c1e10f44381ebd6c144c10a9c")
+ # end EBRAINS
version("0.6.1", sha256="435edf8db49c41a8fa198f959e7581063006c49a4efdef4755bb778db6fd4f72")
depends_on("py-setuptools", type="build")
@@ -25,4 +28,9 @@ class PyArviz(PythonPackage):
depends_on("py-packaging", type=("build", "run"))
depends_on("py-pandas@0.23:", type=("build", "run"))
depends_on("py-xarray@0.11:", type=("build", "run"))
- depends_on("py-netcdf4", type=("build", "run"))
+ # begin EBRAINS (modified): update dependencies
+ depends_on("py-netcdf4", when="@:0.13", type=("build", "run"))
+ depends_on("py-h5netcdf", when="@0.15:", type=("build", "run"))
+ depends_on("py-typing-extensions", when="@0.11:", type=("build", "run"))
+ depends_on("py-xarray-einstats", type=("build", "run"))
+ # end EBRAINS
--
GitLab
From 4b4bf14f45f1236dba63f36ec4d47df32a1262d3 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 01:47:58 +0000
Subject: [PATCH 30/80] feat(py-parameterized): copy package from upstream
---
packages/py-parameterized/package.py | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
create mode 100644 packages/py-parameterized/package.py
diff --git a/packages/py-parameterized/package.py b/packages/py-parameterized/package.py
new file mode 100644
index 00000000..b5c68b42
--- /dev/null
+++ b/packages/py-parameterized/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyParameterized(PythonPackage):
+ """Parameterized testing with any Python test framework."""
+
+ homepage = "https://github.com/wolever/parameterized"
+ pypi = "parameterized/parameterized-0.7.1.tar.gz"
+
+ version("0.7.1", sha256="6a94dbea30c6abde99fd4c2f2042c1bf7f980e48908bf92ead62394f93cf57ed")
+
+ depends_on("py-setuptools", type="build")
--
GitLab
From 51add17e2da351bd8ed9c847ee0962ebfffbe444 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 02:13:25 +0000
Subject: [PATCH 31/80] feat(py-parameterized): add version 0.9.0
---
packages/py-parameterized/package.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/packages/py-parameterized/package.py b/packages/py-parameterized/package.py
index b5c68b42..1ab00622 100644
--- a/packages/py-parameterized/package.py
+++ b/packages/py-parameterized/package.py
@@ -12,6 +12,9 @@ class PyParameterized(PythonPackage):
homepage = "https://github.com/wolever/parameterized"
pypi = "parameterized/parameterized-0.7.1.tar.gz"
+ # begin EBRAINS (added): new version
+ version("0.9.0", sha256="7fc905272cefa4f364c1a3429cbbe9c0f98b793988efb5bf90aac80f08db09b1")
+ # end EBRAINS
version("0.7.1", sha256="6a94dbea30c6abde99fd4c2f2042c1bf7f980e48908bf92ead62394f93cf57ed")
depends_on("py-setuptools", type="build")
--
GitLab
From 60ad098442d5258c2c0253e568ffbf04db3f477a Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 01:31:59 +0000
Subject: [PATCH 32/80] feat(py-joblib): copy package from upstream
---
packages/py-joblib/package.py | 41 +++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
create mode 100644 packages/py-joblib/package.py
diff --git a/packages/py-joblib/package.py b/packages/py-joblib/package.py
new file mode 100644
index 00000000..4e85d003
--- /dev/null
+++ b/packages/py-joblib/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyJoblib(PythonPackage):
+ """Lightweight pipelining with Python functions."""
+
+ homepage = "https://joblib.readthedocs.io/"
+ pypi = "joblib/joblib-0.14.0.tar.gz"
+ git = "https://github.com/joblib/joblib"
+
+ # 'joblib.test' requires 'pytest'. Leave out of 'import_modules' to avoid
+ # unnecessary dependencies.
+ skip_modules = ["joblib.test"]
+
+ license("BSD-3-Clause")
+
+ version("1.2.0", sha256="e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018")
+ version("1.1.0", sha256="4158fcecd13733f8be669be0683b96ebdbbd38d23559f54dca7205aea1bf1e35")
+ version("1.0.1", sha256="9c17567692206d2f3fb9ecf5e991084254fe631665c450b443761c4186a613f7")
+ version("1.0.0", sha256="7ad866067ac1fdec27d51c8678ea760601b70e32ff1881d4dc8e1171f2b64b24")
+ version("0.17.0", sha256="9e284edd6be6b71883a63c9b7f124738a3c16195513ad940eae7e3438de885d5")
+ version("0.16.0", sha256="8f52bf24c64b608bf0b2563e0e47d6fcf516abc8cfafe10cfd98ad66d94f92d6")
+ version("0.15.1", sha256="61e49189c84b3c5d99a969d314853f4d1d263316cc694bec17548ebaa9c47b6e")
+ version("0.15.0", sha256="f8f84dcef519233be4ede1c64fd1f2d48b1e8bbb632d1013ebca75f8b678ee72")
+ version("0.14.1", sha256="0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8")
+ version("0.14.0", sha256="6fcc57aacb4e89451fd449e9412687c51817c3f48662c3d8f38ba3f8a0a193ff")
+ version("0.13.2", sha256="315d6b19643ec4afd4c41c671f9f2d65ea9d787da093487a81ead7b0bac94524")
+ version("0.11", sha256="7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085")
+ version("0.10.3", sha256="29b2965a9efbc90a5fe66a389ae35ac5b5b0c1feabfc7cab7fd5d19f429a071d")
+ version("0.10.2", sha256="3123553bdad83b143428033537c9e1939caf4a4d8813dade6a2246948c94494b")
+ version("0.10.0", sha256="49b3a0ba956eaa2f077e1ebd230b3c8d7b98afc67520207ada20a4d8b8efd071")
+
+ depends_on("python@3.7:", when="@1.2:", type=("build", "run"))
+ depends_on("python@3.6:", when="@0.15:", type=("build", "run"))
+ depends_on("python@2.7:2.8,3.4:", type=("build", "run"))
+ depends_on("py-setuptools", type=("build", "run"))
--
GitLab
From e1ac13342d7746737c1741052f7395aad501fa28 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 01:36:53 +0000
Subject: [PATCH 33/80] feat(py-joblib): add version 1.4.2
---
packages/py-joblib/package.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/packages/py-joblib/package.py b/packages/py-joblib/package.py
index 4e85d003..41d5602a 100644
--- a/packages/py-joblib/package.py
+++ b/packages/py-joblib/package.py
@@ -19,6 +19,9 @@ class PyJoblib(PythonPackage):
license("BSD-3-Clause")
+ # begin EBRAINS (added): add version
+ version("1.4.2", sha256="2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e")
+ # end EBRAINS
version("1.2.0", sha256="e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018")
version("1.1.0", sha256="4158fcecd13733f8be669be0683b96ebdbbd38d23559f54dca7205aea1bf1e35")
version("1.0.1", sha256="9c17567692206d2f3fb9ecf5e991084254fe631665c450b443761c4186a613f7")
--
GitLab
From dfc46c88d2a8da0e253adff7aed3d7fefea3490f Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 01:25:36 +0000
Subject: [PATCH 34/80] feat(py-torch): copy package from upstream
---
.../detect_omp_of_fujitsu_compiler.patch | 20 +
packages/py-torch/fj-ssl2_1.10.patch | 76 ++
packages/py-torch/fj-ssl2_1.11.patch | 76 ++
packages/py-torch/fj-ssl2_1.3-1.5.patch | 76 ++
packages/py-torch/fj-ssl2_1.6-1.7.patch | 76 ++
packages/py-torch/fj-ssl2_1.8.patch | 76 ++
packages/py-torch/fj-ssl2_1.9.patch | 76 ++
packages/py-torch/package.py | 704 ++++++++++++++++++
packages/py-torch/rocm.patch | 98 +++
packages/py-torch/xnnpack.patch | 47 ++
10 files changed, 1325 insertions(+)
create mode 100644 packages/py-torch/detect_omp_of_fujitsu_compiler.patch
create mode 100644 packages/py-torch/fj-ssl2_1.10.patch
create mode 100644 packages/py-torch/fj-ssl2_1.11.patch
create mode 100644 packages/py-torch/fj-ssl2_1.3-1.5.patch
create mode 100644 packages/py-torch/fj-ssl2_1.6-1.7.patch
create mode 100644 packages/py-torch/fj-ssl2_1.8.patch
create mode 100644 packages/py-torch/fj-ssl2_1.9.patch
create mode 100644 packages/py-torch/package.py
create mode 100644 packages/py-torch/rocm.patch
create mode 100644 packages/py-torch/xnnpack.patch
diff --git a/packages/py-torch/detect_omp_of_fujitsu_compiler.patch b/packages/py-torch/detect_omp_of_fujitsu_compiler.patch
new file mode 100644
index 00000000..519d6686
--- /dev/null
+++ b/packages/py-torch/detect_omp_of_fujitsu_compiler.patch
@@ -0,0 +1,20 @@
+--- pytorch/cmake/Modules/FindOpenMP.cmake.org 2020-05-26 17:43:53.000000000 +0900
++++ pytorch/cmake/Modules/FindOpenMP.cmake 2020-05-26 17:46:37.000000000 +0900
+@@ -84,7 +84,7 @@
+ unset(OpenMP_FLAG_CANDIDATES)
+
+ set(OMP_FLAG_GNU "-fopenmp")
+- set(OMP_FLAG_Clang "-fopenmp=libomp" "-fopenmp=libiomp5" "-fopenmp")
++ set(OMP_FLAG_Clang "-fopenmp" "-fopenmp=libomp" "-fopenmp=libiomp5")
+
+ # AppleClang may need a header file, search for omp.h with hints to brew
+ # default include dir
+@@ -245,7 +245,7 @@
+ set(OpenMP_libomp_LIBRARY "${MKL_OPENMP_LIBRARY}" CACHE STRING "libomp location for OpenMP")
+ else()
+ find_library(OpenMP_libomp_LIBRARY
+- NAMES omp gomp iomp5
++ NAMES fjomp omp gomp iomp5
+ HINTS ${CMAKE_${LANG}_IMPLICIT_LINK_DIRECTORIES}
+ DOC "libomp location for OpenMP"
+ )
diff --git a/packages/py-torch/fj-ssl2_1.10.patch b/packages/py-torch/fj-ssl2_1.10.patch
new file mode 100644
index 00000000..bcd2c378
--- /dev/null
+++ b/packages/py-torch/fj-ssl2_1.10.patch
@@ -0,0 +1,76 @@
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index ca560288a4..f5a29ecf43 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -130,7 +130,7 @@ else()
+ set(AT_MKLDNN_ENABLED 0)
+ set(AT_MKL_ENABLED 0)
+ endif()
+-set_property(CACHE BLAS PROPERTY STRINGS "ATLAS;BLIS;Eigen;FLAME;Generic;MKL;OpenBLAS;vecLib")
++set_property(CACHE BLAS PROPERTY STRINGS "ATLAS;BLIS;Eigen;FLAME;Generic;MKL;OpenBLAS;SSL2;vecLib")
+ message(STATUS "Trying to find preferred BLAS backend of choice: " ${BLAS})
+
+ if(BLAS STREQUAL "Eigen")
+@@ -185,6 +185,20 @@ elseif(BLAS STREQUAL "vecLib")
+ set(BLAS_INFO "veclib")
+ set(BLAS_FOUND 1)
+ set(BLAS_LIBRARIES ${vecLib_LINKER_LIBS})
++elseif(BLAS STREQUAL "SSL2")
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ message(STATUS "SSL2 Selected BLAS library")
++ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS "fjlapackexsve.so")
++ set(SSL2_FOUND ON)
++ message(STATUS "set CMAKE_SHARED_LINKER_FLAGS: -SSL2 --linkfortran")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ set(WITH_BLAS "ssl2")
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
+ elseif(BLAS STREQUAL "Generic")
+ # On Debian family, the CBLAS ABIs have been merged into libblas.so
+ find_library(BLAS_LIBRARIES blas)
+@@ -201,7 +215,7 @@ if(NOT INTERN_BUILD_MOBILE)
+ set(AT_MKL_ENABLED 0)
+ set(AT_MKL_MT 0)
+ set(USE_BLAS 1)
+- if(NOT (ATLAS_FOUND OR BLIS_FOUND OR GENERIC_BLAS_FOUND OR MKL_FOUND OR OpenBLAS_FOUND OR VECLIB_FOUND))
++ if(NOT (ATLAS_FOUND OR BLIS_FOUND OR GENERIC_BLAS_FOUND OR MKL_FOUND OR OpenBLAS_FOUND OR SSL2_FOUND OR VECLIB_FOUND))
+ message(WARNING "Preferred BLAS (" ${BLAS} ") cannot be found, now searching for a general BLAS library")
+ find_package(BLAS)
+ if(NOT BLAS_FOUND)
+diff --git a/cmake/Modules/FindBLAS.cmake b/cmake/Modules/FindBLAS.cmake
+index 47c80b45f6..efd4a87d06 100644
+--- a/cmake/Modules/FindBLAS.cmake
++++ b/cmake/Modules/FindBLAS.cmake
+@@ -276,6 +276,28 @@ if((NOT BLAS_LIBRARIES)
+ endif()
+ endif()
+
++# BLAS in SSL2 library?
++if((NOT BLAS_LIBRARIES)
++ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "ssl2")))
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ check_fortran_libraries(
++ BLAS_LIBRARIES
++ BLAS
++ sgemm
++ "-SSL2;--linkfortran"
++ "fjlapackexsve")
++ if (BLAS_LIBRARIES)
++ set(BLAS_INFO "ssl2")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ endif (BLAS_LIBRARIES)
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
++endif()
++
+ # Generic BLAS library?
+ if((NOT BLAS_LIBRARIES)
+ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "generic")))
diff --git a/packages/py-torch/fj-ssl2_1.11.patch b/packages/py-torch/fj-ssl2_1.11.patch
new file mode 100644
index 00000000..af41e5bb
--- /dev/null
+++ b/packages/py-torch/fj-ssl2_1.11.patch
@@ -0,0 +1,76 @@
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index 557ab649a4..56d1699736 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -174,7 +174,7 @@ else()
+ set(AT_MKLDNN_ENABLED 0)
+ set(AT_MKL_ENABLED 0)
+ endif()
+-set_property(CACHE BLAS PROPERTY STRINGS "ATLAS;BLIS;Eigen;FLAME;Generic;MKL;OpenBLAS;vecLib")
++set_property(CACHE BLAS PROPERTY STRINGS "ATLAS;BLIS;Eigen;FLAME;Generic;MKL;OpenBLAS;SSL2;vecLib")
+ message(STATUS "Trying to find preferred BLAS backend of choice: " ${BLAS})
+
+ if(BLAS STREQUAL "Eigen")
+@@ -229,6 +229,20 @@ elseif(BLAS STREQUAL "vecLib")
+ set(BLAS_INFO "veclib")
+ set(BLAS_FOUND 1)
+ set(BLAS_LIBRARIES ${vecLib_LINKER_LIBS})
++elseif(BLAS STREQUAL "SSL2")
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ message(STATUS "SSL2 Selected BLAS library")
++ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS "fjlapackexsve.so")
++ set(SSL2_FOUND ON)
++ message(STATUS "set CMAKE_SHARED_LINKER_FLAGS: -SSL2 --linkfortran")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ set(WITH_BLAS "ssl2")
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
+ elseif(BLAS STREQUAL "FlexiBLAS")
+ find_package(FlexiBLAS REQUIRED)
+ include_directories(SYSTEM ${FlexiBLAS_INCLUDE_DIR})
+@@ -250,7 +264,7 @@ if(NOT INTERN_BUILD_MOBILE)
+ set(AT_MKL_SEQUENTIAL 0)
+ set(AT_MKL_MT 0)
+ set(USE_BLAS 1)
+- if(NOT (ATLAS_FOUND OR BLIS_FOUND OR GENERIC_BLAS_FOUND OR MKL_FOUND OR OpenBLAS_FOUND OR VECLIB_FOUND OR FlexiBLAS_FOUND))
++ if(NOT (ATLAS_FOUND OR BLIS_FOUND OR GENERIC_BLAS_FOUND OR MKL_FOUND OR OpenBLAS_FOUND OR SSL2_FOUND OR VECLIB_FOUND OR FlexiBLAS_FOUND))
+ message(WARNING "Preferred BLAS (" ${BLAS} ") cannot be found, now searching for a general BLAS library")
+ find_package(BLAS)
+ if(NOT BLAS_FOUND)
+diff --git a/cmake/Modules/FindBLAS.cmake b/cmake/Modules/FindBLAS.cmake
+index 94942d520f..ae5b8db963 100644
+--- a/cmake/Modules/FindBLAS.cmake
++++ b/cmake/Modules/FindBLAS.cmake
+@@ -289,6 +289,28 @@ if((NOT BLAS_LIBRARIES)
+ endif()
+ endif()
+
++# BLAS in SSL2 library?
++if((NOT BLAS_LIBRARIES)
++ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "ssl2")))
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ check_fortran_libraries(
++ BLAS_LIBRARIES
++ BLAS
++ sgemm
++ "-SSL2;--linkfortran"
++ "fjlapackexsve")
++ if (BLAS_LIBRARIES)
++ set(BLAS_INFO "ssl2")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ endif (BLAS_LIBRARIES)
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
++endif()
++
+ # Generic BLAS library?
+ if((NOT BLAS_LIBRARIES)
+ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "generic")))
diff --git a/packages/py-torch/fj-ssl2_1.3-1.5.patch b/packages/py-torch/fj-ssl2_1.3-1.5.patch
new file mode 100644
index 00000000..0ea87500
--- /dev/null
+++ b/packages/py-torch/fj-ssl2_1.3-1.5.patch
@@ -0,0 +1,76 @@
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index a8e9769536..f0f91304c2 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -107,7 +107,7 @@ else()
+ set(AT_MKLDNN_ENABLED 0)
+ set(AT_MKL_ENABLED 0)
+ endif()
+-set_property(CACHE BLAS PROPERTY STRINGS "Eigen;ATLAS;OpenBLAS;MKL;vecLib;FLAME")
++set_property(CACHE BLAS PROPERTY STRINGS "Eigen;ATLAS;OpenBLAS;MKL;vecLib;SSL2;FLAME")
+ message(STATUS "Trying to find preferred BLAS backend of choice: " ${BLAS})
+
+ if(BLAS STREQUAL "Eigen")
+@@ -147,6 +147,20 @@ elseif(BLAS STREQUAL "vecLib")
+ find_package(vecLib REQUIRED)
+ include_directories(SYSTEM ${vecLib_INCLUDE_DIR})
+ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS ${vecLib_LINKER_LIBS})
++elseif(BLAS STREQUAL "SSL2")
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ message(STATUS "SSL2 Selected BLAS library")
++ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS "fjlapackexsve.so")
++ set(SSL2_FOUND ON)
++ message(STATUS "set CMAKE_SHARED_LINKER_FLAGS: -SSL2 --linkfortran")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ set(WITH_BLAS "ssl2")
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
+ else()
+ message(FATAL_ERROR "Unrecognized BLAS option: " ${BLAS})
+ endif()
+@@ -156,7 +170,7 @@ if (NOT INTERN_BUILD_MOBILE)
+ set(AT_MKL_ENABLED 0)
+ set(AT_MKL_MT 0)
+ set(USE_BLAS 1)
+- if(NOT (ATLAS_FOUND OR OpenBLAS_FOUND OR MKL_FOUND OR VECLIB_FOUND))
++ if(NOT (ATLAS_FOUND OR OpenBLAS_FOUND OR MKL_FOUND OR VECLIB_FOUND OR SSL2_FOUND))
+ message(WARNING "Preferred BLAS (" ${BLAS} ") cannot be found, now searching for a general BLAS library")
+ find_package(BLAS)
+ if (NOT BLAS_FOUND)
+diff --git a/cmake/Modules/FindBLAS.cmake b/cmake/Modules/FindBLAS.cmake
+index e93e98a609..d43a6c40bd 100644
+--- a/cmake/Modules/FindBLAS.cmake
++++ b/cmake/Modules/FindBLAS.cmake
+@@ -239,6 +239,28 @@ if((NOT BLAS_LIBRARIES)
+ endif (BLAS_LIBRARIES)
+ endif()
+
++# BLAS in SSL2 library?
++if((NOT BLAS_LIBRARIES)
++ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "ssl2")))
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ check_fortran_libraries(
++ BLAS_LIBRARIES
++ BLAS
++ sgemm
++ "-SSL2;--linkfortran"
++ "fjlapackexsve")
++ if (BLAS_LIBRARIES)
++ set(BLAS_INFO "ssl2")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ endif (BLAS_LIBRARIES)
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
++endif()
++
+ # Generic BLAS library?
+ if((NOT BLAS_LIBRARIES)
+ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "generic")))
diff --git a/packages/py-torch/fj-ssl2_1.6-1.7.patch b/packages/py-torch/fj-ssl2_1.6-1.7.patch
new file mode 100644
index 00000000..423af3f2
--- /dev/null
+++ b/packages/py-torch/fj-ssl2_1.6-1.7.patch
@@ -0,0 +1,76 @@
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index 36e1ab7682..0f02f51c47 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -114,7 +114,7 @@ else()
+ set(AT_MKLDNN_ENABLED 0)
+ set(AT_MKL_ENABLED 0)
+ endif()
+-set_property(CACHE BLAS PROPERTY STRINGS "Eigen;ATLAS;OpenBLAS;MKL;vecLib;FLAME;Generic")
++set_property(CACHE BLAS PROPERTY STRINGS "Eigen;ATLAS;OpenBLAS;MKL;vecLib;SSL2;FLAME;Generic")
+ message(STATUS "Trying to find preferred BLAS backend of choice: " ${BLAS})
+
+ if(BLAS STREQUAL "Eigen")
+@@ -154,6 +154,20 @@ elseif(BLAS STREQUAL "vecLib")
+ find_package(vecLib REQUIRED)
+ include_directories(SYSTEM ${vecLib_INCLUDE_DIR})
+ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS ${vecLib_LINKER_LIBS})
++elseif(BLAS STREQUAL "SSL2")
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ message(STATUS "SSL2 Selected BLAS library")
++ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS "fjlapackexsve.so")
++ set(SSL2_FOUND ON)
++ message(STATUS "set CMAKE_SHARED_LINKER_FLAGS: -SSL2 --linkfortran")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ set(WITH_BLAS "ssl2")
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
+ elseif(BLAS STREQUAL "Generic")
+ # On Debian family, the CBLAS ABIs have been merged into libblas.so
+ find_library(BLAS_LIBRARIES blas)
+@@ -168,7 +182,7 @@ if(NOT INTERN_BUILD_MOBILE)
+ set(AT_MKL_ENABLED 0)
+ set(AT_MKL_MT 0)
+ set(USE_BLAS 1)
+- if(NOT (ATLAS_FOUND OR OpenBLAS_FOUND OR MKL_FOUND OR VECLIB_FOUND OR GENERIC_BLAS_FOUND))
++ if(NOT (ATLAS_FOUND OR OpenBLAS_FOUND OR MKL_FOUND OR VECLIB_FOUND OR SSL2_FOUND OR GENERIC_BLAS_FOUND))
+ message(WARNING "Preferred BLAS (" ${BLAS} ") cannot be found, now searching for a general BLAS library")
+ find_package(BLAS)
+ if(NOT BLAS_FOUND)
+diff --git a/cmake/Modules/FindBLAS.cmake b/cmake/Modules/FindBLAS.cmake
+index e93e98a609..d43a6c40bd 100644
+--- a/cmake/Modules/FindBLAS.cmake
++++ b/cmake/Modules/FindBLAS.cmake
+@@ -239,6 +239,28 @@ if((NOT BLAS_LIBRARIES)
+ endif (BLAS_LIBRARIES)
+ endif()
+
++# BLAS in SSL2 library?
++if((NOT BLAS_LIBRARIES)
++ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "ssl2")))
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ check_fortran_libraries(
++ BLAS_LIBRARIES
++ BLAS
++ sgemm
++ "-SSL2;--linkfortran"
++ "fjlapackexsve")
++ if (BLAS_LIBRARIES)
++ set(BLAS_INFO "ssl2")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ endif (BLAS_LIBRARIES)
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
++endif()
++
+ # Generic BLAS library?
+ if((NOT BLAS_LIBRARIES)
+ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "generic")))
diff --git a/packages/py-torch/fj-ssl2_1.8.patch b/packages/py-torch/fj-ssl2_1.8.patch
new file mode 100644
index 00000000..461c1a29
--- /dev/null
+++ b/packages/py-torch/fj-ssl2_1.8.patch
@@ -0,0 +1,76 @@
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index 06464e799a..7f50bd8fa0 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -118,7 +118,7 @@ else()
+ set(AT_MKLDNN_ENABLED 0)
+ set(AT_MKL_ENABLED 0)
+ endif()
+-set_property(CACHE BLAS PROPERTY STRINGS "Eigen;ATLAS;OpenBLAS;MKL;vecLib;FLAME;Generic")
++set_property(CACHE BLAS PROPERTY STRINGS "Eigen;ATLAS;OpenBLAS;MKL;vecLib;SSL2;FLAME;Generic")
+ message(STATUS "Trying to find preferred BLAS backend of choice: " ${BLAS})
+
+ if(BLAS STREQUAL "Eigen")
+@@ -157,6 +157,20 @@ elseif(BLAS STREQUAL "vecLib")
+ find_package(vecLib REQUIRED)
+ include_directories(SYSTEM ${vecLib_INCLUDE_DIR})
+ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS ${vecLib_LINKER_LIBS})
++elseif(BLAS STREQUAL "SSL2")
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ message(STATUS "SSL2 Selected BLAS library")
++ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS "fjlapackexsve.so")
++ set(SSL2_FOUND ON)
++ message(STATUS "set CMAKE_SHARED_LINKER_FLAGS: -SSL2 --linkfortran")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ set(WITH_BLAS "ssl2")
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
+ elseif(BLAS STREQUAL "Generic")
+ # On Debian family, the CBLAS ABIs have been merged into libblas.so
+ find_library(BLAS_LIBRARIES blas)
+@@ -171,7 +185,7 @@ if(NOT INTERN_BUILD_MOBILE)
+ set(AT_MKL_ENABLED 0)
+ set(AT_MKL_MT 0)
+ set(USE_BLAS 1)
+- if(NOT (ATLAS_FOUND OR OpenBLAS_FOUND OR MKL_FOUND OR VECLIB_FOUND OR GENERIC_BLAS_FOUND))
++ if(NOT (ATLAS_FOUND OR OpenBLAS_FOUND OR MKL_FOUND OR VECLIB_FOUND OR SSL2_FOUND OR GENERIC_BLAS_FOUND))
+ message(WARNING "Preferred BLAS (" ${BLAS} ") cannot be found, now searching for a general BLAS library")
+ find_package(BLAS)
+ if(NOT BLAS_FOUND)
+diff --git a/cmake/Modules/FindBLAS.cmake b/cmake/Modules/FindBLAS.cmake
+index e8f5d7c950..29219e057f 100644
+--- a/cmake/Modules/FindBLAS.cmake
++++ b/cmake/Modules/FindBLAS.cmake
+@@ -257,6 +257,28 @@ if((NOT BLAS_LIBRARIES)
+ endif()
+ endif()
+
++# BLAS in SSL2 library?
++if((NOT BLAS_LIBRARIES)
++ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "ssl2")))
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ check_fortran_libraries(
++ BLAS_LIBRARIES
++ BLAS
++ sgemm
++ "-SSL2;--linkfortran"
++ "fjlapackexsve")
++ if (BLAS_LIBRARIES)
++ set(BLAS_INFO "ssl2")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ endif (BLAS_LIBRARIES)
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
++endif()
++
+ # Generic BLAS library?
+ if((NOT BLAS_LIBRARIES)
+ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "generic")))
diff --git a/packages/py-torch/fj-ssl2_1.9.patch b/packages/py-torch/fj-ssl2_1.9.patch
new file mode 100644
index 00000000..0febb575
--- /dev/null
+++ b/packages/py-torch/fj-ssl2_1.9.patch
@@ -0,0 +1,76 @@
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index 5d57b9ca78..a74fe73b9f 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -118,7 +118,7 @@ else()
+ set(AT_MKLDNN_ENABLED 0)
+ set(AT_MKL_ENABLED 0)
+ endif()
+-set_property(CACHE BLAS PROPERTY STRINGS "ATLAS;BLIS;Eigen;FLAME;Generic;MKL;OpenBLAS;vecLib")
++set_property(CACHE BLAS PROPERTY STRINGS "ATLAS;BLIS;Eigen;FLAME;Generic;MKL;OpenBLAS;SSL2;vecLib")
+ message(STATUS "Trying to find preferred BLAS backend of choice: " ${BLAS})
+
+ if(BLAS STREQUAL "Eigen")
+@@ -161,6 +161,20 @@ elseif(BLAS STREQUAL "vecLib")
+ find_package(vecLib REQUIRED)
+ include_directories(SYSTEM ${vecLib_INCLUDE_DIR})
+ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS ${vecLib_LINKER_LIBS})
++elseif(BLAS STREQUAL "SSL2")
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ message(STATUS "SSL2 Selected BLAS library")
++ list(APPEND Caffe2_PUBLIC_DEPENDENCY_LIBS "fjlapackexsve.so")
++ set(SSL2_FOUND ON)
++ message(STATUS "set CMAKE_SHARED_LINKER_FLAGS: -SSL2 --linkfortran")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ set(WITH_BLAS "ssl2")
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
+ elseif(BLAS STREQUAL "Generic")
+ # On Debian family, the CBLAS ABIs have been merged into libblas.so
+ find_library(BLAS_LIBRARIES blas)
+@@ -175,7 +189,7 @@ if(NOT INTERN_BUILD_MOBILE)
+ set(AT_MKL_ENABLED 0)
+ set(AT_MKL_MT 0)
+ set(USE_BLAS 1)
+- if(NOT (ATLAS_FOUND OR BLIS_FOUND OR GENERIC_BLAS_FOUND OR MKL_FOUND OR OpenBLAS_FOUND OR VECLIB_FOUND))
++ if(NOT (ATLAS_FOUND OR BLIS_FOUND OR GENERIC_BLAS_FOUND OR MKL_FOUND OR OpenBLAS_FOUND OR SSL2_FOUND OR VECLIB_FOUND))
+ message(WARNING "Preferred BLAS (" ${BLAS} ") cannot be found, now searching for a general BLAS library")
+ find_package(BLAS)
+ if(NOT BLAS_FOUND)
+diff --git a/cmake/Modules/FindBLAS.cmake b/cmake/Modules/FindBLAS.cmake
+index eefd6d475a..92ad75d32e 100644
+--- a/cmake/Modules/FindBLAS.cmake
++++ b/cmake/Modules/FindBLAS.cmake
+@@ -276,6 +276,28 @@ if((NOT BLAS_LIBRARIES)
+ endif()
+ endif()
+
++# BLAS in SSL2 library?
++if((NOT BLAS_LIBRARIES)
++ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "ssl2")))
++ if(CMAKE_CXX_COMPILER MATCHES ".*/FCC$"
++ AND CMAKE_C_COMPILER MATCHES ".*/fcc$")
++ check_fortran_libraries(
++ BLAS_LIBRARIES
++ BLAS
++ sgemm
++ "-SSL2;--linkfortran"
++ "fjlapackexsve")
++ if (BLAS_LIBRARIES)
++ set(BLAS_INFO "ssl2")
++ set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -SSL2 --linkfortran")
++ endif (BLAS_LIBRARIES)
++ else()
++ message(STATUS "Not built using fcc and FCC.")
++ message(STATUS "CMAKE_C_COMPILER: ${CMAKE_C_COMPILER}")
++ message(STATUS "CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER}")
++ endif()
++endif()
++
+ # Generic BLAS library?
+ if((NOT BLAS_LIBRARIES)
+ AND ((NOT WITH_BLAS) OR (WITH_BLAS STREQUAL "generic")))
diff --git a/packages/py-torch/package.py b/packages/py-torch/package.py
new file mode 100644
index 00000000..e2bc15b6
--- /dev/null
+++ b/packages/py-torch/package.py
@@ -0,0 +1,704 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import sys
+
+from spack.operating_systems.mac_os import macos_version
+from spack.package import *
+
+
+class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
+ """Tensors and Dynamic neural networks in Python with strong GPU acceleration."""
+
+ homepage = "https://pytorch.org/"
+ git = "https://github.com/pytorch/pytorch.git"
+ submodules = True
+
+ # Exact set of modules is version- and variant-specific, just attempt to import the
+ # core libraries to ensure that the package was successfully installed.
+ import_modules = ["torch", "torch.autograd", "torch.nn", "torch.utils"]
+
+ license("BSD-3-Clause")
+ maintainers("adamjstewart")
+
+ version("main", branch="main")
+ version("2.5.1", tag="v2.5.1", commit="a8d6afb511a69687bbb2b7e88a3cf67917e1697e")
+ version("2.5.0", tag="v2.5.0", commit="32f585d9346e316e554c8d9bf7548af9f62141fc")
+ version("2.4.1", tag="v2.4.1", commit="ee1b6804381c57161c477caa380a840a84167676")
+ version("2.4.0", tag="v2.4.0", commit="d990dada86a8ad94882b5c23e859b88c0c255bda")
+ version("2.3.1", tag="v2.3.1", commit="63d5e9221bedd1546b7d364b5ce4171547db12a9")
+ version("2.3.0", tag="v2.3.0", commit="97ff6cfd9c86c5c09d7ce775ab64ec5c99230f5d")
+ version("2.2.2", tag="v2.2.2", commit="39901f229520a5256505ec24782f716ee7ddc843")
+ version("2.2.1", tag="v2.2.1", commit="6c8c5ad5eaf47a62fafbb4a2747198cbffbf1ff0")
+ version("2.2.0", tag="v2.2.0", commit="8ac9b20d4b090c213799e81acf48a55ea8d437d6")
+ version("2.1.2", tag="v2.1.2", commit="a8e7c98cb95ff97bb30a728c6b2a1ce6bff946eb")
+ version("2.1.1", tag="v2.1.1", commit="4c55dc50355d5e923642c59ad2a23d6ad54711e7")
+ version("2.1.0", tag="v2.1.0", commit="7bcf7da3a268b435777fe87c7794c382f444e86d")
+ version("2.0.1", tag="v2.0.1", commit="e9ebda29d87ce0916ab08c06ab26fd3766a870e5")
+ version("2.0.0", tag="v2.0.0", commit="c263bd43e8e8502d4726643bc6fd046f0130ac0e")
+ version("1.13.1", tag="v1.13.1", commit="49444c3e546bf240bed24a101e747422d1f8a0ee")
+ version("1.13.0", tag="v1.13.0", commit="7c98e70d44abc7a1aead68b6ea6c8adc8c554db5")
+ version("1.12.1", tag="v1.12.1", commit="664058fa83f1d8eede5d66418abff6e20bd76ca8")
+ version("1.12.0", tag="v1.12.0", commit="67ece03c8cd632cce9523cd96efde6f2d1cc8121")
+ version("1.11.0", tag="v1.11.0", commit="bc2c6edaf163b1a1330e37a6e34caf8c553e4755")
+ version("1.10.2", tag="v1.10.2", commit="71f889c7d265b9636b93ede9d651c0a9c4bee191")
+ version("1.10.1", tag="v1.10.1", commit="302ee7bfb604ebef384602c56e3853efed262030")
+ version("1.10.0", tag="v1.10.0", commit="36449ea93134574c2a22b87baad3de0bf8d64d42")
+ version("1.9.1", tag="v1.9.1", commit="dfbd030854359207cb3040b864614affeace11ce")
+ version("1.9.0", tag="v1.9.0", commit="d69c22dd61a2f006dcfe1e3ea8468a3ecaf931aa")
+ version("1.8.2", tag="v1.8.2", commit="e0495a7aa104471d95dc85a1b8f6473fbcc427a8")
+ version("1.8.1", tag="v1.8.1", commit="56b43f4fec1f76953f15a627694d4bba34588969")
+ version("1.8.0", tag="v1.8.0", commit="37c1f4a7fef115d719104e871d0cf39434aa9d56")
+ version("1.7.1", tag="v1.7.1", commit="57bffc3a8e4fee0cce31e1ff1f662ccf7b16db57")
+ version("1.7.0", tag="v1.7.0", commit="e85d494707b835c12165976b8442af54b9afcb26")
+ version("1.6.0", tag="v1.6.0", commit="b31f58de6fa8bbda5353b3c77d9be4914399724d")
+ version("1.5.1", tag="v1.5.1", commit="3c31d73c875d9a4a6ea8a843b9a0d1b19fbe36f3")
+ version("1.5.0", tag="v1.5.0", commit="4ff3872a2099993bf7e8c588f7182f3df777205b")
+ version("1.4.1", tag="v1.4.1", commit="74044638f755cd8667bedc73da4dbda4aa64c948")
+
+ depends_on("c", type="build")
+ depends_on("cxx", type="build")
+
+ is_darwin = sys.platform == "darwin"
+
+ # All options are defined in CMakeLists.txt.
+ # Some are listed in setup.py, but not all.
+ variant("debug", default=False, description="Build with debugging support")
+ variant("caffe2", default=False, description="Build Caffe2", when="@1.7:")
+ variant("test", default=False, description="Build C++ test binaries")
+ variant("cuda", default=not is_darwin, description="Use CUDA")
+ variant("rocm", default=False, description="Use ROCm")
+ variant("cudnn", default=not is_darwin, description="Use cuDNN", when="+cuda")
+ variant("fbgemm", default=True, description="Use FBGEMM (quantized 8-bit server operators)")
+ variant("kineto", default=True, description="Use Kineto profiling library", when="@1.8:")
+ variant("magma", default=not is_darwin, description="Use MAGMA", when="+cuda")
+ variant("metal", default=is_darwin, description="Use Metal for Caffe2 iOS build")
+ variant(
+ "mps",
+ default=is_darwin and macos_version() >= Version("12.3"),
+ description="Use MPS for macOS build (requires full Xcode suite)",
+ when="@1.12: platform=darwin",
+ )
+ variant("nccl", default=True, description="Use NCCL", when="+cuda platform=linux")
+ variant("nccl", default=True, description="Use NCCL", when="+rocm platform=linux")
+ # Requires AVX2: https://discuss.pytorch.org/t/107518
+ variant("nnpack", default=True, description="Use NNPACK", when="target=x86_64_v3:")
+ variant("numa", default=True, description="Use NUMA", when="platform=linux")
+ variant("numpy", default=True, description="Use NumPy")
+ variant("openmp", default=True, description="Use OpenMP for parallel code")
+ variant("qnnpack", default=True, description="Use QNNPACK (quantized 8-bit operators)")
+ variant("valgrind", default=True, description="Use Valgrind", when="@1.8: platform=linux")
+ variant("xnnpack", default=True, description="Use XNNPACK", when="@1.5:")
+ variant("mkldnn", default=True, description="Use MKLDNN")
+ variant("distributed", default=True, description="Use distributed")
+ variant("mpi", default=True, description="Use MPI for Caffe2", when="+distributed")
+ variant("ucc", default=False, description="Use UCC", when="@1.13: +distributed")
+ variant("gloo", default=True, description="Use Gloo", when="+distributed")
+ variant("tensorpipe", default=True, description="Use TensorPipe", when="@1.6: +distributed")
+ variant("onnx_ml", default=True, description="Enable traditional ONNX ML API", when="@1.5:")
+ variant(
+ "breakpad",
+ default=True,
+ description="Enable breakpad crash dump library",
+ when="@1.10:1.11",
+ )
+ # py-torch has strict dependencies on old protobuf/py-protobuf versions that
+ # cause problems with other packages that require newer versions of protobuf
+ # and py-protobuf --> provide an option to use the internal/vendored protobuf.
+ variant("custom-protobuf", default=False, description="Use vendored protobuf")
+
+ conflicts("+cuda+rocm")
+ conflicts("+tensorpipe", when="+rocm ^hip@:5.1", msg="TensorPipe not supported until ROCm 5.2")
+ conflicts("+breakpad", when="target=ppc64:")
+ conflicts("+breakpad", when="target=ppc64le:")
+
+ # https://github.com/pytorch/pytorch/issues/77811
+ conflicts("+qnnpack", when="platform=darwin target=aarch64:")
+
+ # https://github.com/pytorch/pytorch/issues/97397
+ conflicts(
+ "~tensorpipe",
+ when="@1.8: +distributed",
+ msg="TensorPipe must be enabled with +distributed",
+ )
+
+ # https://github.com/pytorch/pytorch/issues/100991
+ conflicts("%apple-clang@14:", when="@:1")
+
+ conflicts(
+ "cuda_arch=none",
+ when="+cuda",
+ msg="Must specify CUDA compute capabilities of your GPU, see "
+ "https://developer.nvidia.com/cuda-gpus",
+ )
+
+ # Required dependencies
+ # Based on PyPI wheel availability
+ with default_args(type=("build", "link", "run")):
+ depends_on("python@3.9:3.13", when="@2.5:")
+ depends_on("python@3.8:3.12", when="@2.2:2.4")
+ depends_on("python@3.8:3.11", when="@2.0:2.1")
+ depends_on("python@:3.10", when="@1.11:1")
+ depends_on("python@:3.9", when="@1.7.1:1.10")
+ depends_on("python@:3.8", when="@1.4:1.7.0")
+
+ # CMakelists.txt
+ with default_args(type="build"):
+ depends_on("cmake@3.18:", when="@2:")
+ depends_on("cmake@3.13:", when="@1.11:")
+ depends_on("cmake@3.10:", when="@1.10:")
+ depends_on("cmake@3.5:")
+ depends_on("ninja@1.5:")
+
+ with default_args(type=("build", "run")):
+ # setup.py
+ depends_on("py-filelock", when="@2:")
+ depends_on("py-typing-extensions@4.8:", when="@2.2:")
+ depends_on("py-typing-extensions@3.6.2.1:", when="@1.7:")
+ depends_on("py-sympy", when="@2:")
+ depends_on("py-networkx", when="@2:")
+ depends_on("py-jinja2", when="@2:")
+ depends_on("py-fsspec", when="@2.1:")
+
+ # pyproject.toml
+ depends_on("py-setuptools")
+ depends_on("py-astunparse", when="@1.13:")
+ depends_on("py-numpy@1.16.6:")
+ # https://github.com/pytorch/pytorch/issues/107302
+ depends_on("py-numpy@:1", when="@:2.2")
+ depends_on("py-pyyaml")
+ depends_on("py-requests", when="@1.13:")
+
+ # Undocumented dependencies
+ depends_on("py-tqdm", type="run")
+ depends_on("blas")
+ depends_on("lapack")
+
+ # Third party dependencies
+ depends_on("fp16@2020-05-14", when="@1.6:")
+ depends_on("fxdiv@2020-04-17", when="@1.6:")
+ # https://github.com/pytorch/pytorch/issues/60332
+ # depends_on("xnnpack@2024-02-29", when="@2.3:+xnnpack")
+ # depends_on("xnnpack@2022-12-21", when="@2.0:2.2+xnnpack")
+ # depends_on("xnnpack@2022-02-16", when="@1.12:1+xnnpack")
+ # depends_on("xnnpack@2021-06-21", when="@1.10:1.11+xnnpack")
+ # depends_on("xnnpack@2021-02-22", when="@1.8:1.9+xnnpack")
+ # depends_on("xnnpack@2020-03-23", when="@1.6:1.7+xnnpack")
+ depends_on("benchmark", when="@1.6:+test")
+ depends_on("cpuinfo@2024-09-06", when="@2.5.1:")
+ depends_on("cpuinfo@2024-08-30", when="@2.5.0")
+ depends_on("cpuinfo@2023-11-04", when="@2.3:2.4")
+ depends_on("cpuinfo@2023-01-13", when="@2.1:2.2")
+ depends_on("cpuinfo@2022-08-19", when="@1.13:2.0")
+ depends_on("cpuinfo@2020-12-17", when="@1.8:1.12")
+ depends_on("cpuinfo@2020-06-11", when="@1.6:1.7")
+ depends_on("eigen")
+ depends_on("gloo@2023-12-03", when="@2.3:+gloo")
+ depends_on("gloo@2023-05-19", when="@2.1:2.2+gloo")
+ depends_on("gloo@2023-01-17", when="@2.0+gloo")
+ depends_on("gloo@2022-05-18", when="@1.13:1+gloo")
+ depends_on("gloo@2021-05-21", when="@1.10:1.12+gloo")
+ depends_on("gloo@2021-05-04", when="@1.9+gloo")
+ depends_on("gloo@2020-09-18", when="@1.7:1.8+gloo")
+ depends_on("gloo@2020-03-17", when="@1.6+gloo")
+ depends_on("gloo+cuda", when="@1.6:+gloo+cuda")
+ depends_on("gloo+libuv", when="@1.6: platform=darwin")
+ depends_on("nccl", when="+nccl+cuda")
+ # https://github.com/pytorch/pytorch/issues/60331
+ # depends_on("onnx@1.16.0", when="@2.3:+onnx_ml")
+ # depends_on("onnx@1.15.0", when="@2.2+onnx_ml")
+ # depends_on("onnx@1.14.1", when="@2.1+onnx_ml")
+ # depends_on("onnx@1.13.1", when="@2.0+onnx_ml")
+ # depends_on("onnx@1.12.0", when="@1.13:1+onnx_ml")
+ # depends_on("onnx@1.11.0", when="@1.12+onnx_ml")
+ # depends_on("onnx@1.10.1_2021-10-08", when="@1.11+onnx_ml")
+ # depends_on("onnx@1.10.1", when="@1.10+onnx_ml")
+ # depends_on("onnx@1.8.0_2020-11-03", when="@1.8:1.9+onnx_ml")
+ # depends_on("onnx@1.7.0_2020-05-31", when="@1.6:1.7+onnx_ml")
+ with when("~custom-protobuf"):
+ depends_on("protobuf@3.13.0", when="@1.10:")
+ depends_on("protobuf@3.11.4", when="@1.6:1.9")
+ depends_on("protobuf@3.6.1", when="@1.1:1.5")
+ depends_on("protobuf@3.5.0", when="@1.0")
+ with default_args(type=("build", "run")):
+ depends_on("py-protobuf@3.13", when="@1.10:")
+ depends_on("py-protobuf@3.11", when="@1.6:1.9")
+ depends_on("py-protobuf@3.6", when="@1.1:1.5")
+ depends_on("py-protobuf@3.5", when="@1.0")
+ depends_on("psimd@2020-05-17", when="@1.6:")
+ depends_on("pthreadpool@2023-08-29", when="@2.2:")
+ depends_on("pthreadpool@2021-04-13", when="@1.9:2.1")
+ depends_on("pthreadpool@2020-10-05", when="@1.8")
+ depends_on("pthreadpool@2020-06-15", when="@1.6:1.7")
+ with default_args(type=("build", "link", "run")):
+ depends_on("py-pybind11@2.13.5:", when="@2.5:")
+ depends_on("py-pybind11@2.12.0:", when="@2.3:2.4")
+ depends_on("py-pybind11@2.11.0:", when="@2.1:2.2")
+ depends_on("py-pybind11@2.10.1:", when="@2.0")
+ depends_on("py-pybind11@2.10.0:", when="@1.13:1")
+ depends_on("py-pybind11@2.6.2:", when="@1.8:1.12")
+ depends_on("py-pybind11@2.3.0:", when="@:1.7")
+ depends_on("sleef@3.6.0_2024-03-20", when="@2.4:")
+ depends_on("sleef@3.5.1_2020-12-22", when="@1.8:2.3")
+ depends_on("sleef@3.4.0_2019-07-30", when="@1.6:1.7")
+
+ # Optional dependencies
+ with default_args(type=("build", "link", "run")):
+ # cmake/public/cuda.cmake
+ depends_on("cuda@11:", when="@2.4:+cuda")
+ # https://github.com/pytorch/pytorch/issues/122169
+ depends_on("cuda@11:12.3", when="@2.0:2.3+cuda")
+ depends_on("cuda@10.2:12.3", when="@1.11:1+cuda")
+ # https://discuss.pytorch.org/t/compiling-1-10-1-from-source-with-gcc-11-and-cuda-11-5/140971
+ depends_on("cuda@10.2:11.4", when="@1.10+cuda")
+ depends_on("cuda@9.2:11.4", when="@1.6:1.9+cuda")
+ depends_on("cuda@9:11.4", when="@:1.5+cuda")
+ # https://github.com/pytorch/pytorch#prerequisites
+ # https://github.com/pytorch/pytorch/issues/119400
+ depends_on("cudnn@8.5:9.0", when="@2.3:+cudnn")
+ depends_on("cudnn@7:8", when="@1.6:2.2+cudnn")
+ depends_on("cudnn@7", when="@:1.5+cudnn")
+ depends_on("magma+cuda", when="+magma+cuda")
+ depends_on("magma+rocm", when="+magma+rocm")
+ depends_on("numactl", when="+numa")
+ depends_on("llvm-openmp", when="%apple-clang +openmp")
+ depends_on("valgrind", when="+valgrind")
+ with when("+rocm"):
+ depends_on("hsa-rocr-dev")
+ depends_on("hip")
+ depends_on("rccl", when="+nccl")
+ depends_on("rocprim")
+ depends_on("hipcub")
+ depends_on("rocthrust")
+ depends_on("roctracer-dev")
+ depends_on("rocrand")
+ depends_on("hipsparse")
+ depends_on("hipfft")
+ depends_on("rocfft")
+ depends_on("rocblas")
+ depends_on("miopen-hip")
+ depends_on("rocminfo")
+ depends_on("mpi", when="+mpi")
+ depends_on("ucc", when="+ucc")
+ depends_on("ucx", when="+ucc")
+ depends_on("mkl", when="+mkldnn")
+
+ # Test dependencies
+ with default_args(type="test"):
+ depends_on("py-hypothesis")
+ depends_on("py-six")
+ depends_on("py-psutil")
+
+ # Historical dependencies
+ with default_args(type=("build", "run")):
+ depends_on("mkl@2021.1.1:2021.4.0", when="@2.3 platform=windows")
+ depends_on("py-cffi", when="@:1")
+ depends_on("py-future", when="@1.5:1")
+ depends_on("py-six", when="@1.13:1")
+
+ conflicts("%gcc@:9.3", when="@2.2:", msg="C++17 support required")
+
+ # https://github.com/pytorch/pytorch/issues/90448
+ patch(
+ "https://github.com/pytorch/pytorch/pull/97270.patch?full_index=1",
+ sha256="beb3fb57746cf8443f5caa6e08b2f8f4d4822c1e11e0c912134bd166c6a0ade7",
+ when="@1.10:2.0",
+ )
+
+ # Fix BLAS being overridden by MKL
+ # https://github.com/pytorch/pytorch/issues/60328
+ patch(
+ "https://github.com/pytorch/pytorch/pull/59220.patch?full_index=1",
+ sha256="6d5717267f901e8ee493dfacd08734d9bcc48ad29a76ca9ef702368e96bee675",
+ when="@:1.11",
+ )
+
+ # Fixes build on older systems with glibc <2.12
+ patch(
+ "https://github.com/pytorch/pytorch/pull/55063.patch?full_index=1",
+ sha256="2229bcbf20fbe88aa9f7318f89c126ec7f527875ffe689a763c78abfa127a65c",
+ when="@:1.8.1",
+ )
+
+ # https://github.com/pytorch/pytorch/issues/70297
+ patch(
+ "https://github.com/google/breakpad/commit/605c51ed96ad44b34c457bbca320e74e194c317e.patch?full_index=1",
+ sha256="694d83db3a2147d543357f22ba5c8d5683d0ed43e693d42bca8f24ec50080f98",
+ when="+breakpad",
+ working_dir="third_party/breakpad",
+ )
+
+ # Fixes CMake configuration error when XNNPACK is disabled
+ # https://github.com/pytorch/pytorch/pull/35607
+ # https://github.com/pytorch/pytorch/pull/37865
+ patch("xnnpack.patch", when="@1.5")
+
+ # Fixes build error when ROCm is enabled for pytorch-1.5 release
+ patch("rocm.patch", when="@1.5+rocm")
+
+ # Fixes compilation with Clang 9.0.0 and Apple Clang 11.0.3
+ # https://github.com/pytorch/pytorch/pull/37086
+ patch(
+ "https://github.com/pytorch/pytorch/commit/e921cd222a8fbeabf5a3e74e83e0d8dfb01aa8b5.patch?full_index=1",
+ sha256="0f3ad037a95af9d34b1d085050c1e7771fd00f0b89e5b3a276097b7c9f4fabf8",
+ when="@:1.5",
+ )
+
+ # Fixes 'FindOpenMP.cmake'
+ # to detect openmp settings used by Fujitsu compiler.
+ patch("detect_omp_of_fujitsu_compiler.patch", when="%fj")
+
+ # Fixes to build with fujitsu-ssl2
+ patch("fj-ssl2_1.11.patch", when="@1.11:^fujitsu-ssl2")
+ patch("fj-ssl2_1.10.patch", when="@1.10^fujitsu-ssl2")
+ patch("fj-ssl2_1.9.patch", when="@1.9^fujitsu-ssl2")
+ patch("fj-ssl2_1.8.patch", when="@1.8^fujitsu-ssl2")
+ patch("fj-ssl2_1.6-1.7.patch", when="@1.6:1.7^fujitsu-ssl2")
+ patch("fj-ssl2_1.3-1.5.patch", when="@:1.5^fujitsu-ssl2")
+
+ # Fix compilation of +distributed~tensorpipe
+ # https://github.com/pytorch/pytorch/issues/68002
+ patch(
+ "https://github.com/pytorch/pytorch/commit/c075f0f633fa0136e68f0a455b5b74d7b500865c.patch?full_index=1",
+ sha256="41271e494a3a60a65a8dd45ac053d1a6e4e4d5b42c2dac589ac67524f61ac41e",
+ when="@1.10.0+distributed~tensorpipe",
+ )
+
+ # Use patches from IBM's Open CE to enable building on Power systems
+ # 01xx patches are specific to open-ce, we only include 03xx patches used in meta.yaml
+ # https://github.com/open-ce/pytorch-feedstock
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.7.4/pytorch-1.10/recipe/0302-cpp-extension.patch",
+ sha256="ecb3973fa7d0f4c8f8ae40433f3ca5622d730a7b16f6cb63325d1e95baff8aa2",
+ when="@1.10:1.11 arch=ppc64le:",
+ )
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.7.4/pytorch-1.10/recipe/0311-PR66085-Remove-unused-dump-method-from-VSX-vec256-methods.patch",
+ sha256="f05db59f3def4c4215db7142d81029c73fe330c660492159b66d65ca5001f4d1",
+ when="@1.10 arch=ppc64le:",
+ )
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.7.4/pytorch-1.10/recipe/0312-PR67331-Dummpy-VSX-bfloat16-implementation.patch",
+ sha256="860b64afa85f5e6647ebc3c91d5a0bb258784770900c9302c3599c98d5cff1ee",
+ when="@1.10 arch=ppc64le:",
+ )
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.7.4/pytorch-1.10/recipe/0313-add-missing-vsx-dispatch.patch",
+ sha256="7393c2bc0b6d41ecc813c829a1e517bee864686652e91f174cb7bcdfb10ba451",
+ when="@1.10 arch=ppc64le:",
+ )
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.7.4/pytorch-1.10/recipe/0314-fix-nullpointer-error.patch",
+ sha256="b9cff8966f316f58514c66a403b7a6786be3cdb252f1380a6b91c722686a4097",
+ when="@1.10 arch=ppc64le:",
+ )
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.7.4/pytorch-1.12/recipe/0302-cpp-extension.patch",
+ sha256="2fac519cca8997f074c263505657ff867e7ba2d6637fc8bda99c70a99be0442a",
+ when="@1.12 arch=ppc64le:",
+ )
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.8.0/pytorch-1.13/recipe/0302-cpp-extension.patch",
+ sha256="a54db63640b90e5833cc1099c0935572f5297d2d8625f62f01ac1fda79ed4569",
+ when="@1.13 arch=ppc64le:",
+ )
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.9.0/pytorch-2.0/recipe/0309-fallback-to-cpu_kernel-with-VSX.patch",
+ sha256="27f41c8d6cb61e69e761be62f03dc1ce023cbca34926e3ba559996821a7ce726",
+ when="@2.0 arch=ppc64le:",
+ )
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.9.0/pytorch-2.0/recipe/0310-PR100149.patch",
+ sha256="1adbd38a9cc1611f1caaa325614695f4349d9ffd236332e0d8f0de5a3880f4dd",
+ when="@2.0 arch=ppc64le:",
+ )
+ patch(
+ "https://github.com/open-ce/pytorch-feedstock/raw/open-ce-v1.10.0/pytorch-2.0/recipe/0311-PR104956.patch",
+ sha256="be27c906924a21be198a3ea6c459739a1daa8b8b89045af339dafa4cd6f90d6c",
+ when="@2.0 arch=ppc64le:",
+ )
+ conflicts("arch=ppc64le:", when="@:1.9")
+
+ # Cherry-pick a patch to allow earlier versions of PyTorch to work with CUDA 11.4
+ patch(
+ "https://github.com/pytorch/pytorch/commit/c74c0c571880df886474be297c556562e95c00e0.patch?full_index=1",
+ sha256="8ff7d285e52e4718bad1ca01ceb3bb6471d7828329036bb94222717fcaa237da",
+ when="@:1.9.1 ^cuda@11.4.100:",
+ )
+
+ # PyTorch does not build with GCC 12 (fixed in 2.0)
+ # See: https://github.com/pytorch/pytorch/issues/77614
+ patch(
+ "https://github.com/facebookincubator/gloo/commit/4a5e339b764261d20fc409071dc7a8b8989aa195.patch?full_index=1",
+ sha256="dc8b3a9bea4693f32d6850ea2ce6ce75e1778538bfba464b50efca92bac425e3",
+ when="@:1 %gcc@12:",
+ working_dir="third_party/gloo",
+ )
+
+ # PyTorch does not build on Linux >=6.0.3 (fixed in master)
+ # See: https://github.com/facebookincubator/gloo/issues/345
+ patch(
+ "https://github.com/facebookincubator/gloo/commit/10909297fedab0a680799211a299203e53515032.patch?full_index=1",
+ sha256="8e6e9a44e0533ba4303a95a651b1934e5d73632cab08cc7d5a9435e1e64aa424",
+ when="@:1",
+ working_dir="third_party/gloo",
+ )
+
+ # Some missing includes
+ # See: https://github.com/pytorch/pytorch/pull/100036
+ patch(
+ "https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/100036.patch?full_index=1",
+ sha256="65060b54c31196b26dcff29bbb178fd17d5677e8481a2a06002c0ca4dd37b3d0",
+ when="@2.0.0:2.0.1",
+ )
+ # See: https://github.com/pytorch/pytorch/pull/100049
+ patch(
+ "https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/100049.patch?full_index=1",
+ sha256="673056141c0ea6ff4411f65a26f1a9d7a7c49ad8fe034a01ef0d56ba8a7a9386",
+ when="@2.0.0:2.0.1",
+ )
+
+ # Use correct OpenBLAS include path under prefix
+ patch(
+ "https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/110063.patch?full_index=1",
+ sha256="23fb4009f7337051fc5303927ff977186a5af960245e7212895406477d8b2f66",
+ when="@:2.1",
+ )
+
+ patch(
+ "https://github.com/pytorch/FBGEMM/commit/da01a59556fec9776733bf20aea8fe8fb29cdd3d.patch?full_index=1",
+ sha256="97d8bd43f8cd8bb203dab3480d609c08499224acaca9915f2bdeb23c62350fb1",
+ when="@2.0.1 +fbgemm",
+ working_dir="third_party/fbgemm",
+ )
+
+ @when("@1.5.0:")
+ def patch(self):
+ # https://github.com/pytorch/pytorch/issues/52208
+ filter_file(
+ "torch_global_deps PROPERTIES LINKER_LANGUAGE C",
+ "torch_global_deps PROPERTIES LINKER_LANGUAGE CXX",
+ "caffe2/CMakeLists.txt",
+ )
+
+ def torch_cuda_arch_list(self, env):
+ if "+cuda" in self.spec:
+ torch_cuda_arch = CudaPackage.compute_capabilities(
+ self.spec.variants["cuda_arch"].value
+ )
+ env.set("TORCH_CUDA_ARCH_LIST", ";".join(torch_cuda_arch))
+
+ def setup_build_environment(self, env):
+ """Set environment variables used to control the build.
+
+ PyTorch's ``setup.py`` is a thin wrapper around ``cmake``.
+ In ``tools/setup_helpers/cmake.py``, you can see that all
+ environment variables that start with ``BUILD_``, ``USE_``,
+ or ``CMAKE_``, plus a few more explicitly specified variable
+ names, are passed directly to the ``cmake`` call. Therefore,
+ most flags defined in ``CMakeLists.txt`` can be specified as
+ environment variables.
+ """
+
+ def enable_or_disable(variant, keyword="USE", var=None):
+ """Set environment variable to enable or disable support for a
+ particular variant.
+
+ Parameters:
+ variant (str): the variant to check
+ keyword (str): the prefix to use for enabling/disabling
+ var (str): CMake variable to set. Defaults to variant.upper()
+ """
+ if var is None:
+ var = variant.upper()
+
+ if "+" + variant in self.spec:
+ env.set(keyword + "_" + var, "ON")
+ elif "~" + variant in self.spec:
+ env.set(keyword + "_" + var, "OFF")
+
+ # Build in parallel to speed up build times
+ env.set("MAX_JOBS", make_jobs)
+
+ # Spack logs have trouble handling colored output
+ env.set("COLORIZE_OUTPUT", "OFF")
+
+ enable_or_disable("test", keyword="BUILD")
+ enable_or_disable("caffe2", keyword="BUILD")
+
+ enable_or_disable("cuda")
+ if "+cuda" in self.spec:
+ env.set("CUDA_TOOLKIT_ROOT_DIR", self.spec["cuda"].prefix) # Linux/macOS
+ env.set("CUDA_HOME", self.spec["cuda"].prefix) # Linux/macOS
+ env.set("CUDA_PATH", self.spec["cuda"].prefix) # Windows
+ self.torch_cuda_arch_list(env)
+
+ if self.spec.satisfies("%clang"):
+ for flag in self.spec.compiler_flags["cxxflags"]:
+ if "gcc-toolchain" in flag:
+ env.set("CMAKE_CUDA_FLAGS", "=-Xcompiler={0}".format(flag))
+
+ enable_or_disable("rocm")
+ if "+rocm" in self.spec:
+ env.set("PYTORCH_ROCM_ARCH", ";".join(self.spec.variants["amdgpu_target"].value))
+ env.set("HSA_PATH", self.spec["hsa-rocr-dev"].prefix)
+ env.set("ROCBLAS_PATH", self.spec["rocblas"].prefix)
+ env.set("ROCFFT_PATH", self.spec["rocfft"].prefix)
+ env.set("HIPFFT_PATH", self.spec["hipfft"].prefix)
+ env.set("HIPSPARSE_PATH", self.spec["hipsparse"].prefix)
+ env.set("HIP_PATH", self.spec["hip"].prefix)
+ env.set("HIPRAND_PATH", self.spec["rocrand"].prefix)
+ env.set("ROCRAND_PATH", self.spec["rocrand"].prefix)
+ env.set("MIOPEN_PATH", self.spec["miopen-hip"].prefix)
+ if "+nccl" in self.spec:
+ env.set("RCCL_PATH", self.spec["rccl"].prefix)
+ env.set("ROCPRIM_PATH", self.spec["rocprim"].prefix)
+ env.set("HIPCUB_PATH", self.spec["hipcub"].prefix)
+ env.set("ROCTHRUST_PATH", self.spec["rocthrust"].prefix)
+ env.set("ROCTRACER_PATH", self.spec["roctracer-dev"].prefix)
+ if self.spec.satisfies("^hip@5.2.0:"):
+ env.set("CMAKE_MODULE_PATH", self.spec["hip"].prefix.lib.cmake.hip)
+
+ enable_or_disable("cudnn")
+ if "+cudnn" in self.spec:
+ # cmake/Modules_CUDA_fix/FindCUDNN.cmake
+ env.set("CUDNN_INCLUDE_DIR", self.spec["cudnn"].prefix.include)
+ env.set("CUDNN_LIBRARY", self.spec["cudnn"].libs[0])
+
+ # Flash attention has very high memory requirements that may cause the build to fail
+ # https://github.com/pytorch/pytorch/issues/111526
+ # https://github.com/pytorch/pytorch/issues/124018
+ env.set("USE_FLASH_ATTENTION", "OFF")
+
+ enable_or_disable("fbgemm")
+ enable_or_disable("kineto")
+ enable_or_disable("magma")
+ enable_or_disable("metal")
+ enable_or_disable("mps")
+ enable_or_disable("breakpad")
+
+ enable_or_disable("nccl")
+ if "+cuda+nccl" in self.spec:
+ env.set("NCCL_LIB_DIR", self.spec["nccl"].libs.directories[0])
+ env.set("NCCL_INCLUDE_DIR", self.spec["nccl"].prefix.include)
+
+ # cmake/External/nnpack.cmake
+ enable_or_disable("nnpack")
+
+ enable_or_disable("numa")
+ if "+numa" in self.spec:
+ # cmake/Modules/FindNuma.cmake
+ env.set("NUMA_ROOT_DIR", self.spec["numactl"].prefix)
+
+ # cmake/Modules/FindNumPy.cmake
+ enable_or_disable("numpy")
+ # cmake/Modules/FindOpenMP.cmake
+ enable_or_disable("openmp")
+ enable_or_disable("qnnpack")
+ enable_or_disable("qnnpack", var="PYTORCH_QNNPACK")
+ enable_or_disable("valgrind")
+ enable_or_disable("xnnpack")
+ enable_or_disable("mkldnn")
+ enable_or_disable("distributed")
+ enable_or_disable("mpi")
+ enable_or_disable("ucc")
+ # cmake/Modules/FindGloo.cmake
+ enable_or_disable("gloo")
+ enable_or_disable("tensorpipe")
+
+ if "+debug" in self.spec:
+ env.set("DEBUG", "ON")
+ else:
+ env.set("DEBUG", "OFF")
+
+ if "+onnx_ml" in self.spec:
+ env.set("ONNX_ML", "ON")
+ elif "~onnx_ml" in self.spec:
+ env.set("ONNX_ML", "OFF")
+
+ if not self.spec.satisfies("@main"):
+ env.set("PYTORCH_BUILD_VERSION", self.version)
+ env.set("PYTORCH_BUILD_NUMBER", 0)
+
+ # BLAS to be used by Caffe2
+ # Options defined in cmake/Dependencies.cmake and cmake/Modules/FindBLAS.cmake
+ if self.spec["blas"].name == "atlas":
+ env.set("BLAS", "ATLAS")
+ env.set("WITH_BLAS", "atlas")
+ env.set("Atlas_ROOT_DIR", self.spec["atlas"].prefix)
+ elif self.spec["blas"].name in ["blis", "amdblis"]:
+ env.set("BLAS", "BLIS")
+ env.set("WITH_BLAS", "blis")
+ env.set("BLIS_HOME", self.spec["blas"].prefix)
+ elif self.spec["blas"].name == "eigen":
+ env.set("BLAS", "Eigen")
+ elif self.spec["lapack"].name in ["libflame", "amdlibflame"]:
+ env.set("BLAS", "FLAME")
+ env.set("WITH_BLAS", "FLAME")
+ elif self.spec["blas"].name in ["intel-mkl", "intel-parallel-studio", "intel-oneapi-mkl"]:
+ env.set("BLAS", "MKL")
+ env.set("WITH_BLAS", "mkl")
+ # help find MKL
+ if self.spec["mkl"].name == "intel-oneapi-mkl":
+ env.set("INTEL_MKL_DIR", self.spec["mkl"].prefix.mkl.latest)
+ else:
+ env.set("INTEL_MKL_DIR", self.spec["mkl"].prefix.mkl)
+ elif self.spec["blas"].name == "openblas":
+ env.set("BLAS", "OpenBLAS")
+ env.set("WITH_BLAS", "open")
+ env.set("OpenBLAS_HOME", self.spec["openblas"].prefix)
+ elif self.spec["blas"].name == "veclibfort":
+ env.set("BLAS", "vecLib")
+ env.set("WITH_BLAS", "veclib")
+ elif self.spec["blas"].name == "fujitsu-ssl2":
+ env.set("BLAS", "SSL2")
+ env.set("WITH_BLAS", "ssl2")
+ else:
+ env.set("BLAS", "Generic")
+ env.set("WITH_BLAS", "generic")
+
+ # Don't use vendored third-party libraries when possible
+ # env.set("USE_SYSTEM_LIBS", "ON")
+ env.set("USE_SYSTEM_BENCHMARK", "ON")
+ env.set("USE_SYSTEM_CPUINFO", "ON")
+ env.set("USE_SYSTEM_EIGEN_INSTALL", "ON")
+ env.set("USE_SYSTEM_FP16", "ON")
+ env.set("USE_SYSTEM_FXDIV", "ON")
+ env.set("USE_SYSTEM_GLOO", "ON")
+ env.set("USE_SYSTEM_NCCL", "ON")
+ # https://github.com/pytorch/pytorch/issues/60331
+ # env.set("USE_SYSTEM_ONNX", "ON")
+ env.set("USE_SYSTEM_PSIMD", "ON")
+ env.set("USE_SYSTEM_PTHREADPOOL", "ON")
+ env.set("USE_SYSTEM_PYBIND11", "ON")
+ env.set("USE_SYSTEM_SLEEF", "ON")
+ env.set("USE_SYSTEM_UCC", "ON")
+ # https://github.com/pytorch/pytorch/issues/60332
+ # env.set("USE_SYSTEM_XNNPACK", "ON")
+
+ if self.spec.satisfies("+custom-protobuf"):
+ env.set("BUILD_CUSTOM_PROTOBUF", "ON")
+ else:
+ env.set("BUILD_CUSTOM_PROTOBUF", "OFF")
+
+ def setup_run_environment(self, env):
+ self.torch_cuda_arch_list(env)
+
+ @run_before("install")
+ def build_amd(self):
+ if "+rocm" in self.spec:
+ python(os.path.join("tools", "amd_build", "build_amd.py"))
+
+ @run_after("install")
+ @on_package_attributes(run_tests=True)
+ def install_test(self):
+ with working_dir("test"):
+ python("run_test.py")
+
+ @property
+ def cmake_prefix_paths(self):
+ cmake_prefix_paths = [join_path(python_platlib, "torch", "share", "cmake")]
+ return cmake_prefix_paths
diff --git a/packages/py-torch/rocm.patch b/packages/py-torch/rocm.patch
new file mode 100644
index 00000000..b50cc7e1
--- /dev/null
+++ b/packages/py-torch/rocm.patch
@@ -0,0 +1,98 @@
+diff --git a/aten/src/ATen/cuda/nvrtc_stub/ATenNVRTC.h b/aten/src/ATen/cuda/nvrtc_stub/ATenNVRTC.h
+index 9cd678dfb4cc7..4630465115c7c 100644
+--- a/aten/src/ATen/cuda/nvrtc_stub/ATenNVRTC.h
++++ b/aten/src/ATen/cuda/nvrtc_stub/ATenNVRTC.h
+@@ -67,6 +67,14 @@ namespace at { namespace cuda {
+ //
+ // HIP doesn't have
+ // cuGetErrorString (maps to non-functional hipGetErrorString___)
++//
++// HIP from ROCm 3.5 on renamed hipOccupancyMaxActiveBlocksPerMultiprocessor
++// to hipModuleOccupancyMaxActiveBlocksPerMultiprocessor.
++#if HIP_VERSION < 305
++#define HIPOCCUPANCYMAXACTIVEBLOCKSPERMULTIPROCESSOR hipOccupancyMaxActiveBlocksPerMultiprocessor
++#else
++#define HIPOCCUPANCYMAXACTIVEBLOCKSPERMULTIPROCESSOR cuOccupancyMaxActiveBlocksPerMultiprocessor
++#endif
+
+ #define AT_FORALL_NVRTC(_) \
+ _(nvrtcVersion) \
+@@ -76,7 +84,7 @@ namespace at { namespace cuda {
+ _(nvrtcGetPTX) \
+ _(cuModuleLoadData) \
+ _(cuModuleGetFunction) \
+- _(cuOccupancyMaxActiveBlocksPerMultiprocessor) \
++ _(HIPOCCUPANCYMAXACTIVEBLOCKSPERMULTIPROCESSOR)\
+ _(nvrtcGetErrorString) \
+ _(nvrtcGetProgramLogSize) \
+ _(nvrtcGetProgramLog) \
+diff --git a/aten/src/ATen/native/cuda/SoftMax.cu b/aten/src/ATen/native/cuda/SoftMax.cu
+index da1995123ecfc..f935eb4ef3d0e 100644
+--- a/aten/src/ATen/native/cuda/SoftMax.cu
++++ b/aten/src/ATen/native/cuda/SoftMax.cu
+@@ -127,8 +127,8 @@ void SpatialSoftMax_getLaunchSizes(
+ uint32_t block_threads = block.x * block.y;
+ smem_size = block.x == 1 ? 0 : block_threads * sizeof(accscalar_t);
+ int max_active_blocks;
+-#ifdef __HIP_PLATFORM_HCC__
+- // XXX HIP function signature is not compatible yet.
++#if defined(__HIP_PLATFORM_HCC__) && HIP_VERSION < 305
++ // HIP function signature is not compatible yet.
+ uint32_t max_blocks;
+ cudaOccupancyMaxActiveBlocksPerMultiprocessor(&max_blocks,
+ k, block_threads, smem_size);
+diff --git a/torch/csrc/jit/codegen/fuser/cuda/fused_kernel.cpp b/torch/csrc/jit/codegen/fuser/cuda/fused_kernel.cpp
+index 5586e49919727..27315ee475277 100644
+--- a/torch/csrc/jit/codegen/fuser/cuda/fused_kernel.cpp
++++ b/torch/csrc/jit/codegen/fuser/cuda/fused_kernel.cpp
+@@ -140,10 +140,10 @@ FusedKernelCUDA::FusedKernelCUDA(
+ nvrtc().cuModuleGetFunction(&function_, module_, name_.c_str()));
+
+ // Computes max blocks
+-#ifdef __HIP_PLATFORM_HCC__
+- // XXX HIP function signature is not compatible yet
++#if defined(__HIP_PLATFORM_HCC__) && HIP_VERSION < 305
++ // HIP function signature is not compatible yet
+ uint32_t max_blocks;
+- AT_CUDA_DRIVER_CHECK(nvrtc().cuOccupancyMaxActiveBlocksPerMultiprocessor(
++ AT_CUDA_DRIVER_CHECK(nvrtc().hipOccupancyMaxActiveBlocksPerMultiprocessor(
+ &max_blocks, function_, 128, 0));
+ maxBlocks_ = max_blocks;
+ #else
+diff --git a/torch/utils/hipify/cuda_to_hip_mappings.py b/torch/utils/hipify/cuda_to_hip_mappings.py
+index 7e21363cbe6af..26f269d92ae38 100644
+--- a/torch/utils/hipify/cuda_to_hip_mappings.py
++++ b/torch/utils/hipify/cuda_to_hip_mappings.py
+@@ -2890,7 +2890,7 @@
+ (
+ "cuOccupancyMaxActiveBlocksPerMultiprocessor",
+ (
+- "hipOccupancyMaxActiveBlocksPerMultiprocessor",
++ "hipModuleOccupancyMaxActiveBlocksPerMultiprocessor",
+ CONV_OCCUPANCY,
+ API_DRIVER,
+ ),
+@@ -2898,7 +2898,7 @@
+ (
+ "cuOccupancyMaxActiveBlocksPerMultiprocessorWithFlags",
+ (
+- "hipOccupancyMaxActiveBlocksPerMultiprocessorWithFlags",
++ "hipModuleOccupancyMaxActiveBlocksPerMultiprocessorWithFlags",
+ CONV_OCCUPANCY,
+ API_DRIVER,
+ HIP_UNSUPPORTED,
+@@ -2906,12 +2906,12 @@
+ ),
+ (
+ "cuOccupancyMaxPotentialBlockSize",
+- ("hipOccupancyMaxPotentialBlockSize", CONV_OCCUPANCY, API_DRIVER),
++ ("hipModuleOccupancyMaxPotentialBlockSize", CONV_OCCUPANCY, API_DRIVER),
+ ),
+ (
+ "cuOccupancyMaxPotentialBlockSizeWithFlags",
+ (
+- "hipOccupancyMaxPotentialBlockSizeWithFlags",
++ "hipModuleOccupancyMaxPotentialBlockSizeWithFlags",
+ CONV_OCCUPANCY,
+ API_DRIVER,
+ HIP_UNSUPPORTED,
diff --git a/packages/py-torch/xnnpack.patch b/packages/py-torch/xnnpack.patch
new file mode 100644
index 00000000..15403308
--- /dev/null
+++ b/packages/py-torch/xnnpack.patch
@@ -0,0 +1,47 @@
+diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt
+index 8025a7de3c..0da37079d6 100644
+--- a/caffe2/CMakeLists.txt
++++ b/caffe2/CMakeLists.txt
+@@ -46,12 +46,19 @@ if (INTERN_BUILD_ATEN_OPS)
+ list(APPEND Caffe2_DEPENDENCY_INCLUDE ${ATen_THIRD_PARTY_INCLUDE})
+ endif()
+
++# {Q/X,etc} NPACK support is enabled by default, if none of these options
++# are selected, turn this flag ON to incidate the support is disabled
++set(NNPACK_AND_FAMILY_DISABLED OFF)
++if(NOT (USE_NNPACK OR USE_QNNPACK OR USE_PYTORCH_QNNPACK OR USE_XNNPACK))
++ set(NNPACK_AND_FAMILY_DISABLED ON)
++endif()
++
+ # ---[ Caffe2 build
+ # Note: the folders that are being commented out have not been properly
+ # addressed yet.
+
+ # For pthreadpool_new_if_impl. TODO: Remove when threadpools are unitied.
+-if (NOT MSVC)
++if (NOT MSVC AND NOT NNPACK_AND_FAMILY_DISABLED)
+ IF(NOT TARGET fxdiv)
+ SET(FXDIV_BUILD_TESTS OFF CACHE BOOL "")
+ SET(FXDIV_BUILD_BENCHMARKS OFF CACHE BOOL "")
+@@ -710,7 +717,7 @@ ELSEIF(USE_CUDA)
+ ENDIF()
+
+
+-if (NOT MSVC)
++if (NOT MSVC AND NOT NNPACK_AND_FAMILY_DISABLED)
+ TARGET_LINK_LIBRARIES(torch_cpu PRIVATE fxdiv)
+ endif()
+
+diff --git a/caffe2/utils/CMakeLists.txt b/caffe2/utils/CMakeLists.txt
+index 27aabb1315..3c7845c67d 100644
+--- a/caffe2/utils/CMakeLists.txt
++++ b/caffe2/utils/CMakeLists.txt
+@@ -36,7 +36,7 @@ list(APPEND Caffe2_CPU_SRCS
+ # ---[ threadpool/pthreadpool* is a local modification of the NNPACK
+ # pthreadpool with a very similar interface. Neither NNPACK, nor this
+ # thread pool supports Windows.
+-if (NOT MSVC)
++if (NOT MSVC AND NOT NNPACK_AND_FAMILY_DISABLED)
+ add_definitions(-DUSE_INTERNAL_THREADPOOL_IMPL)
+ set(Caffe2_CPU_SRCS ${Caffe2_CPU_SRCS}
+ utils/threadpool/pthreadpool.cc
--
GitLab
From 93fc4562cf0a387ce9aa26193c756bada9a67c23 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 01:29:37 +0000
Subject: [PATCH 35/80] fix(py-torch): fixed sympy dependency for py-torch@2.5
---
packages/py-torch/package.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/packages/py-torch/package.py b/packages/py-torch/package.py
index e2bc15b6..6c7f9abd 100644
--- a/packages/py-torch/package.py
+++ b/packages/py-torch/package.py
@@ -159,6 +159,9 @@ class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
depends_on("py-typing-extensions@4.8:", when="@2.2:")
depends_on("py-typing-extensions@3.6.2.1:", when="@1.7:")
depends_on("py-sympy", when="@2:")
+ # begin EBRAINS (added): fix sympy version for py-torch@2.5: (from setup.py)
+ depends_on("py-sympy@1.13.1", when="@2.5:^python@3.9:")
+ # end EBRAINS
depends_on("py-networkx", when="@2:")
depends_on("py-jinja2", when="@2:")
depends_on("py-fsspec", when="@2.1:")
--
GitLab
From 437f31b660bfde29cd36d3001146bf9250d79cee Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 01:30:19 +0000
Subject: [PATCH 36/80] fix(py-torch): fix wrong default install dir
see https://github.com/pytorch/pytorch/issues/129304
---
packages/py-torch/package.py | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/packages/py-torch/package.py b/packages/py-torch/package.py
index 6c7f9abd..b274723b 100644
--- a/packages/py-torch/package.py
+++ b/packages/py-torch/package.py
@@ -478,6 +478,14 @@ class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
working_dir="third_party/fbgemm",
)
+ # begin EBRAINS (added): see https://github.com/pytorch/pytorch/issues/129304
+ patch(
+ "https://github.com/pytorch/pytorch/commit/9174d14551c4c6f594bd1532ab00fb7158b1bbfa.patch?full_index=1",
+ sha256="25204236888f25ea74c081787a01deae1a6fa66ecd77ecbe280e1ce8af6b8116",
+ when="@2.4",
+ )
+ # end EBRAINS
+
@when("@1.5.0:")
def patch(self):
# https://github.com/pytorch/pytorch/issues/52208
--
GitLab
From b2e03f3e15ef613196746c595c10a52e8b92d122 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Wed, 26 Feb 2025 15:31:58 +0000
Subject: [PATCH 37/80] feat(wf-human-multi-area-model): relax notebook
dependency version constraint
---
packages/wf-human-multi-area-model/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/wf-human-multi-area-model/package.py b/packages/wf-human-multi-area-model/package.py
index 7cafb2c1..5bcefe0d 100644
--- a/packages/wf-human-multi-area-model/package.py
+++ b/packages/wf-human-multi-area-model/package.py
@@ -28,7 +28,7 @@ class WfHumanMultiAreaModel(Package):
depends_on("py-nnmt@1.3.0:", type=("run", "test"))
depends_on("py-dicthash@0.0.1:", type=("run", "test"))
depends_on("py-networkx@3.1:", type=("run", "test"))
- depends_on("py-notebook@6.5.4:", type=("run", "test"))
+ depends_on("py-notebook@6.4:", type=("run", "test"))
depends_on("py-future@0.18.2:", type=("run", "test"))
def install(self, spec, prefix):
--
GitLab
From 4ab6eb51593c252b15e70d47242b8d0910625333 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 02:17:52 +0000
Subject: [PATCH 38/80] fix(py-vbi): fix installation of tests
---
packages/py-vbi/fix-install.patch | 12 ++++++++++++
packages/py-vbi/package.py | 2 ++
2 files changed, 14 insertions(+)
create mode 100644 packages/py-vbi/fix-install.patch
diff --git a/packages/py-vbi/fix-install.patch b/packages/py-vbi/fix-install.patch
new file mode 100644
index 00000000..d84cceb0
--- /dev/null
+++ b/packages/py-vbi/fix-install.patch
@@ -0,0 +1,12 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index debc24e..2e0500b 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -58,7 +58,6 @@ path = "vbi/_version.py"
+
+
+ [tool.setuptools]
+-packages = ["vbi"]
+ include-package-data = true
+
+ [tool.setuptools.package-data]
diff --git a/packages/py-vbi/package.py b/packages/py-vbi/package.py
index ba2cbebb..138893c5 100644
--- a/packages/py-vbi/package.py
+++ b/packages/py-vbi/package.py
@@ -15,6 +15,8 @@ class PyVbi(PythonPackage):
version("0.1.3", "54fa2062f44c9ec8219fae3c13c52a4bd17141b5467b982987673de0662c5255")
version("0.1.2", "6ccfeeec718be62a480002a8370130a3e3344955186f99ecbb15b646b68210d6")
+ patch('fix-install.patch')
+
depends_on("python@3.8:", type=("build","run"))
depends_on("py-setuptools", type="build")
depends_on("py-setuptools-scm", type="build")
--
GitLab
From f93d7c434af5cfce526ef0f7a4927e4334618354 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 11:24:36 +0000
Subject: [PATCH 39/80] feat(py-blessed): copy package from upstream
---
packages/py-blessed/package.py | 39 ++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
create mode 100644 packages/py-blessed/package.py
diff --git a/packages/py-blessed/package.py b/packages/py-blessed/package.py
new file mode 100644
index 00000000..d2415b18
--- /dev/null
+++ b/packages/py-blessed/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyBlessed(PythonPackage):
+ """Blessed is a thin, practical wrapper around terminal capabilities in
+ Python."""
+
+ homepage = "https://github.com/jquast/blessed"
+ pypi = "blessed/blessed-1.15.0.tar.gz"
+
+ license("MIT")
+
+ version("1.19.0", sha256="4db0f94e5761aea330b528e84a250027ffe996b5a94bf03e502600c9a5ad7a61")
+ version("1.18.1", sha256="8b09936def6bc06583db99b65636b980075733e13550cb6af262ce724a55da23")
+ version("1.18.0", sha256="1312879f971330a1b7f2c6341f2ae7e2cbac244bfc9d0ecfbbecd4b0293bc755")
+ version("1.17.12", sha256="580429e7e0c6f6a42ea81b0ae5a4993b6205c6ccbb635d034b4277af8175753e")
+ version("1.17.11", sha256="7d4914079a6e8e14fbe080dcaf14dee596a088057cdc598561080e3266123b48")
+ version("1.17.10", sha256="58b9464609f54e2eca5f5926db590a5b01fefef882844ce05064f483b8f96c26")
+ version("1.17.9", sha256="0d497a5be8a808b7300c00bf8303e7ba9fd11f6063a67bb924a475e5bfa7a9bb")
+ version("1.17.8", sha256="7671d057b2df6ddbefd809009fb08feb2f8d2d163d240b5e765088a90519b2f1")
+ version("1.17.7", sha256="0329a3d1db91328986a6dfd36475dbc498c867090f0433cdcc1a45a5eb2067e4")
+ version("1.17.6", sha256="a9a774fc6eda05248735b0d86e866d640ca2fef26038878f7e4d23f7749a1e40")
+ version("1.17.5", sha256="926916492220af741657ec4668aba95f54a8c32445e765cfa38c7ccd3343cc6f")
+ version("1.17.4", sha256="320a619c83298a9c9d632dbd8fafbb90ba9a38b83c7e64726c572fb186dd0781")
+ version("1.17.3", sha256="cc38547175ae0a3a3d4e5dcc7e7478a5a6bf0a6b5f4d9c6b2e5eadbe4475cb0e")
+ version("1.17.0", sha256="38632d60dd384de9e9be0ee5b6e1c6130f96efd0767c6ca530a453da36238c25")
+ version("1.16.1", sha256="a222783b09f266cf76f5a01f4dfd9de79650f07cbefe2cbc67ec7bb9577c1dfa")
+ version("1.16.0", sha256="34b78e9b56c2ba2f6a9a625cc989d6cf4ae8ae87dcc4ed8ad144660ae4cf7784")
+ version("1.15.0", sha256="777b0b6b5ce51f3832e498c22bc6a093b6b5f99148c7cbf866d26e2dec51ef21")
+
+ depends_on("py-setuptools", type="build")
+ depends_on("py-wcwidth@0.1.4:", type=("build", "run"))
+ depends_on("py-six@1.9.0:", type=("build", "run"))
--
GitLab
From efb7995b1da53bb8d3bd301a54cf85f87c6f835a Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 11:24:56 +0000
Subject: [PATCH 40/80] feat(py-blessed): add version 1.20
---
packages/py-blessed/package.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/packages/py-blessed/package.py b/packages/py-blessed/package.py
index d2415b18..c40b13ca 100644
--- a/packages/py-blessed/package.py
+++ b/packages/py-blessed/package.py
@@ -16,6 +16,9 @@ class PyBlessed(PythonPackage):
license("MIT")
+ # begin EBRAINS (added): add version
+ version("1.20.0", sha256="2cdd67f8746e048f00df47a2880f4d6acbcdb399031b604e34ba8f71d5787680")
+ # end EBRAINS
version("1.19.0", sha256="4db0f94e5761aea330b528e84a250027ffe996b5a94bf03e502600c9a5ad7a61")
version("1.18.1", sha256="8b09936def6bc06583db99b65636b980075733e13550cb6af262ce724a55da23")
version("1.18.0", sha256="1312879f971330a1b7f2c6341f2ae7e2cbac244bfc9d0ecfbbecd4b0293bc755")
--
GitLab
From da35a770e5548c1d0066001646a5c8d343aa28e5 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 11:25:16 +0000
Subject: [PATCH 41/80] feat(py-exceptiongroup): copy package from upstream
---
packages/py-exceptiongroup/package.py | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
create mode 100644 packages/py-exceptiongroup/package.py
diff --git a/packages/py-exceptiongroup/package.py b/packages/py-exceptiongroup/package.py
new file mode 100644
index 00000000..7dfb5da6
--- /dev/null
+++ b/packages/py-exceptiongroup/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyExceptiongroup(PythonPackage):
+ """A backport of the BaseExceptionGroup and ExceptionGroup classes from Python 3.11."""
+
+ homepage = "https://github.com/agronholm/exceptiongroup"
+ pypi = "exceptiongroup/exceptiongroup-1.0.4.tar.gz"
+
+ version("1.1.1", sha256="d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785")
+ version("1.0.4", sha256="bd14967b79cd9bdb54d97323216f8fdf533e278df937aa2a90089e7d6e06e5ec")
+
+ depends_on("py-flit-scm", type="build")
--
GitLab
From fe0421c74d54dee9cde3968b96ba2082b7f8104b Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 11:26:04 +0000
Subject: [PATCH 42/80] feat(py-exceptiongroup): add version 1.2.0
---
packages/py-exceptiongroup/package.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/packages/py-exceptiongroup/package.py b/packages/py-exceptiongroup/package.py
index 7dfb5da6..1fe03cd4 100644
--- a/packages/py-exceptiongroup/package.py
+++ b/packages/py-exceptiongroup/package.py
@@ -13,6 +13,9 @@ class PyExceptiongroup(PythonPackage):
homepage = "https://github.com/agronholm/exceptiongroup"
pypi = "exceptiongroup/exceptiongroup-1.0.4.tar.gz"
+ # begin EBRAINS (added): add version
+ version("1.2.0", sha256="91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68")
+ # end EBRAINS
version("1.1.1", sha256="d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785")
version("1.0.4", sha256="bd14967b79cd9bdb54d97323216f8fdf533e278df937aa2a90089e7d6e06e5ec")
--
GitLab
From 4e27a96baf88fa340ab9b42707444586df47c4f3 Mon Sep 17 00:00:00 2001
From: filimarc <oppilif576@msn.com>
Date: Mon, 13 Jan 2025 14:55:57 +0100
Subject: [PATCH 43/80] feat(py-bsb): bump packages for bsb 4.4
Bump bsb-core and bsb-hdf5 to 5.0.2
Add bsb suite python packages and dependencies
Add workflow package for bsb
---
packages/py-arborize/package.py | 26 ++++++++
packages/py-bsb-core/package.py | 59 +++++++++++++++++++
packages/py-bsb-hdf5/package.py | 12 ++--
packages/py-bsb-json/package.py | 22 +++++++
packages/py-bsb-nest/package.py | 24 ++++++++
packages/py-bsb-neuron/package.py | 26 ++++++++
packages/py-bsb-yaml/package.py | 23 ++++++++
packages/py-bsb/package.py | 51 ----------------
packages/py-dashing/package.py | 19 ++++++
packages/py-mpilock/package.py | 21 +++++++
packages/py-mpipool/package.py | 24 ++++++++
packages/py-nmodl-glia/package.py | 25 ++++++++
.../py-nmodl/fix-setup-requirements.patch | 21 +++++++
packages/py-nmodl/package.py | 38 ++++++++++++
packages/py-nrn-patch/package.py | 29 +++++++++
packages/wf-bsb/package.py | 29 +++++++++
16 files changed, 392 insertions(+), 57 deletions(-)
create mode 100644 packages/py-arborize/package.py
create mode 100644 packages/py-bsb-core/package.py
create mode 100644 packages/py-bsb-json/package.py
create mode 100644 packages/py-bsb-nest/package.py
create mode 100644 packages/py-bsb-neuron/package.py
create mode 100644 packages/py-bsb-yaml/package.py
delete mode 100644 packages/py-bsb/package.py
create mode 100644 packages/py-dashing/package.py
create mode 100644 packages/py-mpilock/package.py
create mode 100644 packages/py-mpipool/package.py
create mode 100644 packages/py-nmodl-glia/package.py
create mode 100644 packages/py-nmodl/fix-setup-requirements.patch
create mode 100644 packages/py-nmodl/package.py
create mode 100644 packages/py-nrn-patch/package.py
create mode 100644 packages/wf-bsb/package.py
diff --git a/packages/py-arborize/package.py b/packages/py-arborize/package.py
new file mode 100644
index 00000000..f897963f
--- /dev/null
+++ b/packages/py-arborize/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyArborize(PythonPackage):
+ """
+ A framework to package NEURON cell models following a clear separation between cell model description and its implementation in NEURON.
+ Cell models described using this framework are highly portable, testable and distributable.
+ """
+
+ homepage = "https://github.com/dbbs-lab/arborize"
+ pypi = "arborize/arborize-4.1.0.tar.gz"
+
+ license("GPL-3.0-only")
+ maintainers = ["helveg","filimarc","drodarie"]
+
+ version("4.1.0", sha256="2cb88b890fa69de42a49b38ea4defd0caa4ee91b34f9b75216e1536d9058f57f")
+
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-numpy@1.21:")
+ depends_on("py-errr@1.2:")
+ depends_on("py-morphio@3.3.6:4")
diff --git a/packages/py-bsb-core/package.py b/packages/py-bsb-core/package.py
new file mode 100644
index 00000000..eacb83a4
--- /dev/null
+++ b/packages/py-bsb-core/package.py
@@ -0,0 +1,59 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyBsbCore(PythonPackage):
+ """
+ The BSB is a component framework for neural modeling, which focuses on component
+ declarations to piece together a model.
+ """
+
+ homepage = "https://bsb.readthedocs.io"
+ pypi = "bsb-core/bsb_core-5.0.0.tar.gz"
+
+ license("GPL-3.0-only")
+ maintainers = ["helveg","filimarc","drodarie"]
+
+ version("5.0.2", sha256="414be0f3ba72b2f656b89f8e4636e4a1d19b1f4dc9ba9360cc984020cb1859dc")
+ version("5.0.1", sha256="7cb905ee38419709b4ead2ffb40e1005d813d2c6780706b3f5eb2696aabeb983")
+ version("5.0.0", sha256="08e1776d351a8bb5c056ffbd8108d0bd941f71518b475aecbad9f22050b7cc91")
+
+ variant('parallel', default=True,
+ description='Build with MPI bindings')
+
+ depends_on("python@3.9:3.12", type=("build", "run"))
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-numpy@1.19:")
+ depends_on("py-scipy@1.5:")
+ depends_on("py-scikit-learn@1.0:")
+ depends_on("py-rtree@1.0:")
+ depends_on("py-psutil@5.8:")
+ depends_on("py-pynrrd@1.0:")
+ depends_on("py-toml@0.10:")
+ depends_on("py-requests")
+ depends_on("py-urllib3@2:")
+ depends_on("py-appdirs@1.4:")
+ depends_on("py-neo")
+ depends_on("py-tqdm@4.50:")
+ depends_on("py-shortuuid")
+ depends_on("py-quantities@0.15.0:")
+ depends_on("py-morphio@3.3:")
+ depends_on("py-errr@1.2.0:")
+ depends_on("py-dashing@0.1.0:")
+ depends_on("py-exceptiongroup")
+
+ depends_on('mpi', when='+parallel')
+ depends_on('py-mpi4py', when='+parallel')
+ depends_on('py-mpipool@2.2.1:3', when='+parallel')
+ depends_on('py-mpilock@1.1:', when='+parallel')
+
+
+ def setup_build_environment(self, env):
+ env.set("SPATIALINDEX_C_LIBRARY", self.spec["libspatialindex"].libs[0])
+
+ def setup_run_environment(self, env):
+ self.setup_build_environment(env)
diff --git a/packages/py-bsb-hdf5/package.py b/packages/py-bsb-hdf5/package.py
index 059f2df3..36fbc5d0 100644
--- a/packages/py-bsb-hdf5/package.py
+++ b/packages/py-bsb-hdf5/package.py
@@ -10,13 +10,13 @@ class PyBsbHdf5(PythonPackage):
"""An HDF-5 based storage engine for the BSB framework."""
homepage = "https://github.com/dbbs-lab/bsb-hdf5"
- url = "https://pypi.org/packages/py3/b/bsb_hdf5/bsb_hdf5-0.8.3-py3-none-any.whl"
+ pypi = "bsb-hdf5/bsb_hdf5-5.0.4.tar.gz"
- maintainers = ["helveg"]
+ license("GPL-3.0-only")
+ maintainers = ["helveg","filimarc","drodarie"]
- version('0.8.3', sha256="38162bfe9470b87cb30a2bff78dce68fc1b97f2df7d7e3b288c16b671f7579e5", expand=False)
+ version('5.0.2', sha256='ed11177887848a3f177982201e1adb5770131bd541055a96935af38b39439fac')
- depends_on("py-setuptools", type="build")
- # depends_on("py-bsb@4.0.0a57:")
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-bsb-core@5.0.0:",when='@5.0.2')
depends_on("py-shortuuid")
- depends_on("py-h5py@3.0:")
diff --git a/packages/py-bsb-json/package.py b/packages/py-bsb-json/package.py
new file mode 100644
index 00000000..c692a2c5
--- /dev/null
+++ b/packages/py-bsb-json/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyBsbJson(PythonPackage):
+ """A plugin that allows the user to write their models' configuration in the json format, for the BSB framework."""
+
+ homepage = "https://github.com/dbbs-lab/bsb-json"
+ pypi = "bsb-json/bsb_json-4.2.2.tar.gz"
+
+ license("GPL-3.0-only")
+ maintainers = ["helveg","filimarc","drodarie"]
+
+ version("4.2.2", sha256="0c9e0af2a50f8ebbce353ba19bd11bafaf2536d74f0a79af3b0b6d8241fa6937")
+
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-bsb-core@5.0.0:")
+ depends_on("py-shortuuid")
diff --git a/packages/py-bsb-nest/package.py b/packages/py-bsb-nest/package.py
new file mode 100644
index 00000000..9d81556a
--- /dev/null
+++ b/packages/py-bsb-nest/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyBsbNest(PythonPackage):
+ """
+ The BSB-NEST is a component framework for neural modeling, used for simulate SNN with NEST software.
+ """
+
+ homepage = "https://github.com/dbbs-lab/bsb-nest"
+ pypi = "bsb-nest/bsb_nest-4.3.2.tar.gz"
+
+ license("GPL-3.0-only")
+ maintainers = ["helveg","filimarc","drodarie"]
+
+ version("4.3.2", sha256="478aa2937ca554ff291ce726cc69e1c1b283d7353a56e3b6878b585ed0684041")
+
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-bsb-core@5.0.2:")
+ depends_on("nest")
diff --git a/packages/py-bsb-neuron/package.py b/packages/py-bsb-neuron/package.py
new file mode 100644
index 00000000..6e4ec130
--- /dev/null
+++ b/packages/py-bsb-neuron/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyBsbNeuron(PythonPackage):
+ """
+ The BSB-NEURON is a component framework for neural modeling, used for simulate with NEURON software.
+ """
+
+ homepage = "https://github.com/dbbs-lab/bsb-neuron"
+ pypi = "bsb-neuron/bsb_neuron-4.2.2.tar.gz"
+
+ license("GPL-3.0-only")
+ maintainers = ["helveg","filimarc","drodarie"]
+
+ version("4.2.2", sha256="e7570c0cb17d31349eb8e88487e8ba48653f0fad0d7c232df8815cadde34a941")
+
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-bsb-core@5.0.2:")
+ depends_on("neuron")
+ depends_on("py-arborize@4.1:")
+ depends_on("py-nrn-patch@4:")
diff --git a/packages/py-bsb-yaml/package.py b/packages/py-bsb-yaml/package.py
new file mode 100644
index 00000000..d91b3301
--- /dev/null
+++ b/packages/py-bsb-yaml/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyBsbYaml(PythonPackage):
+ """A plugin that allows the user to write their models' configuration in the yaml format, for the BSB framework."""
+
+ homepage = "https://github.com/dbbs-lab/bsb-yaml"
+ pypi = "bsb-yaml/bsb_yaml-4.2.2.tar.gz"
+
+ license("GPL-3.0-only")
+ maintainers = ["helveg","filimarc","drodarie"]
+
+ version("4.2.2", sha256="c5614bc5fe57b78a445303756819a8d4ba032924484f88a07f6c26dd7e5afbec")
+
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-bsb-core@5.0.0:")
+ depends_on("py-pyyaml@6.0:")
+ depends_on("py-shortuuid")
diff --git a/packages/py-bsb/package.py b/packages/py-bsb/package.py
deleted file mode 100644
index 397bdbd3..00000000
--- a/packages/py-bsb/package.py
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyBsb(PythonPackage):
- """
- The BSB is a component framework for neural modeling, which focuses on component
- declarations to piece together a model.
- """
-
- homepage = "https://bsb.readthedocs.io"
- url = "https://pypi.org/packages/py3/b/bsb/bsb-4.0.0a57-py3-none-any.whl"
-
- maintainers = ["helveg"]
-
- version("4.0.0a57", sha256="5da15799aa8994894ff5371561d534b43beffaa79461189c94080071359f4076", expand=False)
-
- depends_on("python@3.8:", type=("build", "run"))
- depends_on("py-setuptools", type="build")
- depends_on("py-numpy@1.19:")
- depends_on("py-scipy@1.5:")
- depends_on("py-scikit-learn@1.0:")
- depends_on("py-plotly")
- depends_on("py-rtree@1.0:")
- depends_on("py-psutil@5.8:")
- depends_on("py-pynrrd@1.0:")
- depends_on("py-toml")
- depends_on("py-requests")
- depends_on("py-appdirs@1.4:")
- depends_on("py-neo")
- depends_on("py-tqdm@4.50:")
- depends_on("py-shortuuid")
- depends_on("py-quantities")
- depends_on("py-pyyaml@6.0:")
- depends_on("py-morphio@3.3:")
- depends_on("py-bsb-hdf5@0.8.3:")
- depends_on("py-errr@1.2.0:")
- depends_on("py-colour@0.1.5:")
-
- def setup_build_environment(self, env):
- env.set("SPATIALINDEX_C_LIBRARY", self.spec["libspatialindex"].libs[0])
-
- def setup_run_environment(self, env):
- self.setup_build_environment(env)
-
- skip_modules = ['bsb.simulators.arbor', 'bsb.simulators.arbor.devices']
-
diff --git a/packages/py-dashing/package.py b/packages/py-dashing/package.py
new file mode 100644
index 00000000..48d63dc4
--- /dev/null
+++ b/packages/py-dashing/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyDashing(PythonPackage):
+ """Dashing is a library to quickly create terminal-based dashboards in Python."""
+
+ homepage = "https://github.com/FedericoCeratto/dashing"
+ pypi = "dashing-next/dashing_next-0.1.0.tar.gz"
+
+ version("0.1.0", sha256="9d48e97fce430a9cfb47d5627041b001ab306b65e97d6967fe86e2c25e324612")
+
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-blessed@1.20.0:")
diff --git a/packages/py-mpilock/package.py b/packages/py-mpilock/package.py
new file mode 100644
index 00000000..16e9a60c
--- /dev/null
+++ b/packages/py-mpilock/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyMpilock(PythonPackage):
+ """mpilock offers a WindowController class with a high-level API for parallel access to resources. """
+
+ homepage = "https://github.com/Helveg/mpilock"
+ pypi = "mpilock/mpilock-1.1.0-py3-none-any.whl"
+
+ version("1.1.0", sha256="0902ef859a7b3dfb4312a3c46332302493aa14fa398b610554706b0b9e7cb57c", expand=False)
+
+ maintainers=["helveg"]
+
+ depends_on("py-setuptools", type="build")
+ depends_on("py-mpi4py@3.0.3:")
+ depends_on("py-numpy@1.20.0:")
diff --git a/packages/py-mpipool/package.py b/packages/py-mpipool/package.py
new file mode 100644
index 00000000..fb6f112a
--- /dev/null
+++ b/packages/py-mpipool/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyMpipool(PythonPackage):
+ """mpipool offers MPI based parallel execution of tasks through implementations of Python's standard library interfaces"""
+
+ homepage = "https://github.com/mpipool/mpipool"
+ pypi = "mpipool/mpipool-2.2.1.tar.gz"
+
+ version("2.2.1", sha256="dc735b994349ae3e06fce7c3601523ba062125ffa6dd4c6c51a94c168c9ff92c")
+
+ maintainers=["helveg"]
+
+ depends_on("py-flit-core@3.2:4", type="build")
+ depends_on("py-mpi4py@3.0.3:")
+ depends_on("py-errr@1.0:")
+ depends_on("py-tblib@1.7.0:")
+ depends_on("py-dill@0.3.3:")
diff --git a/packages/py-nmodl-glia/package.py b/packages/py-nmodl-glia/package.py
new file mode 100644
index 00000000..acd06eaf
--- /dev/null
+++ b/packages/py-nmodl-glia/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyNmodlGlia(PythonPackage):
+ """
+ Patch to use NMODL within the BSB
+ """
+
+ homepage = "https://github.com/dbbs-lab/glia"
+ pypi = "nmodl-glia/nmodl_glia-4.0.1.tar.gz"
+
+ license("GPL-3.0-only")
+ maintainers = ["helveg","filimarc","drodarie"]
+
+ version("4.0.1", sha256="c3b3dad203eac1f394d6a4ca6e4f42d25d5eebc013970309f1453c7ca3e5c5a3")
+
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-numpy@1.21:")
+ depends_on("py-errr@1.2:")
+ depends_on("py-nmodl@0.5:")
diff --git a/packages/py-nmodl/fix-setup-requirements.patch b/packages/py-nmodl/fix-setup-requirements.patch
new file mode 100644
index 00000000..52ec60c2
--- /dev/null
+++ b/packages/py-nmodl/fix-setup-requirements.patch
@@ -0,0 +1,21 @@
+diff --git a/setup.py b/setup.py
+index c956004c9..671a6619e 100644
+--- a/setup.py
++++ b/setup.py
+@@ -131,16 +131,6 @@ setup(
+ zip_safe=False,
+ setup_requires=[
+ "jinja2>=2.9.3",
+- "jupyter-client",
+- "jupyter",
+- "myst_parser",
+- "mistune<3", # prevents a version conflict with nbconvert
+- "nbconvert",
+- "nbsphinx>=0.3.2",
+- "pytest>=3.7.2",
+- "sphinxcontrib-applehelp<1.0.3",
+- "sphinx<6",
+- "sphinx-rtd-theme",
+ ]
+ + install_requirements,
+ install_requires=install_requirements,
diff --git a/packages/py-nmodl/package.py b/packages/py-nmodl/package.py
new file mode 100644
index 00000000..fd5fb011
--- /dev/null
+++ b/packages/py-nmodl/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyNmodl(PythonPackage):
+ """The NMODL Framework is a code generation engine for NEURON MODeling Language (NMODL)."""
+
+ homepage = "https://github.com/BlueBrain/nmodl"
+
+ git = "https://github.com/BlueBrain/nmodl"
+
+ license("Apache-2.0")
+ maintainers = ["bbp.opensource"]
+
+ version("0.5", tag="0.5", commit="ac272785dc444c8444b085d121f08b7575bb6647", submodules=True)
+
+ patch("fix-setup-requirements.patch", when="@:0.6")
+
+ depends_on("flex@2.6:")
+ depends_on("bison@3.0:")
+ depends_on("cmake@3.15:", type="build")
+ depends_on("python@3.9:", type=("build","run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-scikit-build", type="build")
+ depends_on("py-jinja2@2.9.3:", type="build")
+ depends_on("py-pyyaml@3.13:", type="build")
+ depends_on("py-pytest")
+ depends_on("py-sympy@1.3:", type=("build","run"))
+ depends_on("py-find-libpython", type=("build","run"))
+ depends_on("py-importlib-metadata", when="^python@:3.8", type=("build","run"))
+ depends_on("py-importlib-resources", when="^python@:3.8", type=("build","run"))
+
+ def setup_build_environment(self, env):
+ env.set("NMODL_WHEEL_VERSION", self.version)
diff --git a/packages/py-nrn-patch/package.py b/packages/py-nrn-patch/package.py
new file mode 100644
index 00000000..aaf40362
--- /dev/null
+++ b/packages/py-nrn-patch/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyNrnPatch(PythonPackage):
+ """A patch to make the BSB interface with NEURON software"""
+
+ homepage = "https://github.com/dbbs-lab/patch"
+ pypi = "nrn-patch/nrn_patch-4.0.0.tar.gz"
+
+ license("GPL-3.0-only")
+ maintainers = ["helveg","filimarc","drodarie"]
+
+ version("4.0.0", sha256="0f95243798c7363826d7835023f7c9215577edd8d6695cc7caeb65a7fe8a54c0")
+
+ depends_on("py-flit-core@3.2:4.0", type="build")
+ depends_on("py-numpy@1.21:")
+ depends_on("py-errr@1.2:")
+ depends_on("py-click@8.0:")
+ depends_on("py-appdirs@1.0:")
+ depends_on("py-cookiecutter@2.0:")
+ depends_on("py-black@0.24:")
+ depends_on("py-toml@0.1:")
+ depends_on("py-nmodl-glia@4.0:")
+ depends_on("neuron@8:10")
diff --git a/packages/wf-bsb/package.py b/packages/wf-bsb/package.py
new file mode 100644
index 00000000..2e843818
--- /dev/null
+++ b/packages/wf-bsb/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class WfBsb(BundlePackage):
+ """Meta-package to collect all dependencies for the BSB."""
+
+ homepage="https://github.com/dbbs-lab/bsb"
+
+ maintainers = ["helveg","filimarc","drodarie"]
+
+ version("4.4")
+
+ variant('nest', default=False,
+ description='Build with NEST interface')
+ variant('neuron', default=False,
+ description='Build with NEURON interface')
+
+ depends_on("py-bsb-core@5.0.2:")
+ depends_on("py-bsb-hdf5@5.0.2:")
+ depends_on("py-bsb-json@4.2.2:")
+ depends_on("py-bsb-yaml@4.2.2:")
+
+ depends_on("py-bsb-nest",when="+nest")
+ depends_on("py-bsb-neuron",when="+neuron")
--
GitLab
From ab87efeb322144dea55f283e4b2181b25d7686ba Mon Sep 17 00:00:00 2001
From: filimarc <oppilif576@msn.com>
Date: Mon, 13 Jan 2025 15:12:50 +0100
Subject: [PATCH 44/80] feat(py-bsb): add bsb suite to spack.yaml
Add bsb subpackages
---
spack.yaml | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/spack.yaml b/spack.yaml
index b4322538..274a55d1 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -19,7 +19,12 @@ spack:
- py-bluepyefe@2.3.6
- py-bluepymm@0.8.7
- py-bluepyopt@1.14.11
- - py-bsb@4.0.0a57
+ - py-bsb-core@5.0.2
+ - py-bsb-hdf5@5.0.2
+ - py-bsb-yaml@4.2.2
+ - py-bsb-json@4.2.2
+ - py-bsb-nest@4.3.2
+ - py-bsb-neuron@4.2.2
- py-ebrains-drive@0.6.0
- py-ebrains-kg-core@0.9.15
- py-ebrains-validation-client@0.9.1
@@ -65,6 +70,7 @@ spack:
# Workflows (meta-packages)
- wf-biobb
- wf-brainscales2-demos@9.0-a8
+ - wf-bsb@4.4 +nest +neuron
- wf-protein-association-rates@0.1
- wf-multi-area-model@1.2.0
- wf-human-multi-area-model@2.0.1
--
GitLab
From e290113064c8955562c65f592bbc7bfe509532e4 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 13:57:43 +0000
Subject: [PATCH 45/80] feat(py-annarchy): add version 4.8.2.3
---
packages/py-annarchy/package.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/packages/py-annarchy/package.py b/packages/py-annarchy/package.py
index bf672bb8..4368d1e0 100644
--- a/packages/py-annarchy/package.py
+++ b/packages/py-annarchy/package.py
@@ -13,14 +13,16 @@ class PyAnnarchy(PythonPackage):
"""
homepage = "https://annarchy.readthedocs.io/en/latest/"
- pypi = 'ANNarchy/ANNarchy-4.7.2.5.tar.gz'
+ pypi = 'ANNarchy/annarchy-4.8.2.3.tar.gz'
maintainers = ['dionperd', 'paulapopa', "ldomide"]
+ version('4.8.2.3', '25a4d09905983ce27f7c6b4dd67a54831ea233b6b28943cb67dafd3c351d1dde')
version('4.7.2.5', 'b7ef91cc4415e078e386eb30e595922c9f0ef90ad1340a12dc5ca46e728a7bb2')
# python_requires
- depends_on('python@3.8:3.10', type=('build', 'run'))
+ depends_on('python@3.8:3.10', when='@:4.7.2', type=('build', 'run'))
+ depends_on('python@3.10:', when='@4.7.3:', type=('build', 'run'))
# setup_requires
depends_on('py-pip', type='build')
@@ -34,6 +36,8 @@ class PyAnnarchy(PythonPackage):
depends_on('py-sympy', type=('build', 'run')) # >= 1.6
depends_on('py-matplotlib', type=('build', 'run')) # >= 2.0
depends_on('py-cython', type=('build', 'run')) # >= 0.20
+ depends_on('py-tqdm', when='@4.8:', type=('build', 'run'))
+ depends_on('py-h5py', when='@4.8.2:', type=('build', 'run'))
# Highly recommended:
# pyqtgraph >= 0.9.8 (to visualize some of the provided examples. The OpenGL backend can also be needed)
--
GitLab
From 3885a77eb3eaa4d54ec28f89f81633aea023d1e7 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 13:59:45 +0000
Subject: [PATCH 46/80] feat(py-tvb-multiscale): update dependencies
---
packages/py-tvb-multiscale/package.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/packages/py-tvb-multiscale/package.py b/packages/py-tvb-multiscale/package.py
index 7b78790a..b57b8f03 100644
--- a/packages/py-tvb-multiscale/package.py
+++ b/packages/py-tvb-multiscale/package.py
@@ -21,7 +21,7 @@ class PyTvbMultiscale(PythonPackage):
patch('tvb-multiscale-2.1.0-version-pep440.patch', when='@2.1.0.ebrains')
# python_requires
- depends_on('python@3.8:3.10', type=('build', 'run'))
+ depends_on('python@3.8:3.11', type=('build', 'run'))
# setup_requires
depends_on('py-pip', type='build')
@@ -39,7 +39,7 @@ class PyTvbMultiscale(PythonPackage):
depends_on('py-ray', type=('build', 'run'))
# Test dependency
- depends_on('py-pytest@:7.1', type='test')
+ depends_on('py-pytest', type='test')
@run_after('install')
@on_package_attributes(run_tests=True)
--
GitLab
From 999bfd27be3f33d2aa9fab8166e6d0c7240f4447 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 13:58:58 +0000
Subject: [PATCH 47/80] feat(py-ray): add version 2.30.0
---
packages/py-ray/package.py | 23 ++++++++++++++---------
1 file changed, 14 insertions(+), 9 deletions(-)
diff --git a/packages/py-ray/package.py b/packages/py-ray/package.py
index 82ba34c4..f1bf4b72 100644
--- a/packages/py-ray/package.py
+++ b/packages/py-ray/package.py
@@ -15,7 +15,10 @@ class PyRay(PythonPackage):
license("Apache-2.0")
- # begin EBRAINS (added): ECM new node-js -> new react whatever -> new py-ray
+ # begin EBRAINS (added): new versions
+ # new version to allow building with newer bazel
+ version("2.30.0", sha256="854d549a77f0b0e810d1e9a18e7becf984279e2a0bfad5bed508f500ff770e34")
+ # ECM: new node-js -> new react whatever -> new py-ray
version("2.4.0", sha256="b0110a84630b2f6d10cd13e8ac955875c3658373eb6cabcc77cf316de3c28066")
# end EBRAINS
version("2.0.1", sha256="b8b2f0a99d2ac4c001ff11c78b4521b217e2a02df95fb6270fd621412143f28b")
@@ -30,18 +33,20 @@ class PyRay(PythonPackage):
conflicts("node-js@17:", when="@:2.0.1")
# end EBRAINS
- # begin EBRAINS (added): ElM add missing dependencies/constraints for added version 2.4.0
+ # begin EBRAINS (added): ElM add missing dependencies/constraints for added versions
+ depends_on("python@3.9:3.12", when="@2.30.0", type=("build", "run"))
depends_on("python@3.6:3.11", when="@2.4.0", type=("build", "run"))
+ depends_on("bazel@6.5", when="@2.30.0", type="build")
depends_on("bazel@5", when="@2.4.0", type="build")
- depends_on("py-cython@0.29.32:", when="@2.4.0", type="build")
+ depends_on("py-cython@0.29.32:", when="@2.4.0:", type="build")
depends_on("py-attrs", when="@2.4.0", type=("build", "run"))
- depends_on("py-click@7.0:", when="@2.4.0", type=("build", "run"))
- depends_on("py-grpcio@1.32:1.51.3", when="@2.4.0 ^python@:3.9", type=("build", "run"))
- depends_on("py-grpcio@1.42:1.51.3", when="@2.4.0 ^python@3.10:", type=("build", "run"))
- depends_on("py-protobuf@3.15.3:", when="@2.4.0", type=("build", "run"))
+ depends_on("py-click@7.0:", when="@2.4.0:", type=("build", "run"))
+ depends_on("py-grpcio@1.32:1.51.3", when="@2.4.0: ^python@:3.9", type=("build", "run"))
+ depends_on("py-grpcio@1.42:1.51.3", when="@2.4.0: ^python@3.10:", type=("build", "run"))
+ depends_on("py-protobuf@3.15.3:", when="@2.4.0:", type=("build", "run"))
depends_on("py-frozenlist", when="@2.4.0", type=("build", "run"))
depends_on("py-typing-extensions", when="@2.4.0 ^python@:3.7", type=("build", "run"))
- depends_on("py-virtualenv@20.0.24:", when="@2.4.0", type=("build", "run"))
+ depends_on("py-virtualenv@20.0.24:", when="@2.4.0:", type=("build", "run"))
# end EBRAINS
depends_on("python@3.6:3.10", when="@2.0.1", type=("build", "run"))
@@ -113,7 +118,7 @@ class PyRay(PythonPackage):
build_directory = "python"
# begin EBRAINS (added): fix boost download url
- patch("fix-url-boost.patch", when="@2.4.0:")
+ patch("fix-url-boost.patch", when="@2.4.0")
# end EBRAINS
def patch(self):
--
GitLab
From 69bd1d6c51752ee75a056ddf8cbe7699c01553ab Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Fri, 28 Feb 2025 14:03:27 +0000
Subject: [PATCH 48/80] feat(py-pyspike): patch for py-cython@3
and use source from github, because pypi archives are already patched
---
packages/py-pyspike/cython3.patch | 24 ++++++++++++++++++++++++
packages/py-pyspike/package.py | 14 ++++++++------
2 files changed, 32 insertions(+), 6 deletions(-)
create mode 100644 packages/py-pyspike/cython3.patch
diff --git a/packages/py-pyspike/cython3.patch b/packages/py-pyspike/cython3.patch
new file mode 100644
index 00000000..e3e62eaf
--- /dev/null
+++ b/packages/py-pyspike/cython3.patch
@@ -0,0 +1,24 @@
+diff --git a/setup.py b/setup.py
+index 297746d..b52cf8b 100644
+--- a/setup.py
++++ b/setup.py
+@@ -21,11 +21,14 @@ else:
+ use_cython = True
+
+
+-class numpy_include(object):
+- """Defers import of numpy until install_requires is through"""
+- def __str__(self):
+- import numpy
+- return numpy.get_include()
++class numpy_include(os.PathLike):
++ """Defers import of numpy until install_requires is through"""
++ def __str__(self):
++ import numpy
++ return numpy.get_include()
++
++ def __fspath__(self):
++ return str(self)
+
+
+ if os.path.isfile("pyspike/cython/cython_add.c") and \
diff --git a/packages/py-pyspike/package.py b/packages/py-pyspike/package.py
index 9fbe4128..ddf17e7e 100644
--- a/packages/py-pyspike/package.py
+++ b/packages/py-pyspike/package.py
@@ -12,15 +12,17 @@ class PyPyspike(PythonPackage):
"""
homepage = "https://github.com/mariomulansky/PySpike"
- pypi = 'pyspike/pyspike-0.7.0.tar.gz'
+ url = 'https://github.com/mariomulansky/PySpike/archive/refs/tags/0.8.0.tar.gz'
maintainers = ['dionperd', 'paulapopa', "ldomide"]
- version('0.8.0', '76137b861ed531608aaf55af1a5ebf8a586e98653dab2467b4c1da7b2d9aa4e5')
- version('0.7.0', 'a5d1c1472d3e7c3ac85c8a4ce069d750cca02acf18f185677b29c0a757e78efe')
+ version('0.8.0', '199d41af097e0b6e6583e22d4a9c3cedab51ceba4da2d940682ffefe8120a414')
+ version('0.7.0', '47031ba10a5726845982b62dcae970449ca50c4be9985a1ed0d2a021456bf25a')
+
+ patch("cython3.patch", when="^py-cython@3:")
# python_requires
- depends_on('python@3.8:3.10', type=('build', 'run'))
+ depends_on('python@3.8:', type=('build', 'run'))
# setup_requires
depends_on('py-pip', type='build')
@@ -31,10 +33,10 @@ class PyPyspike(PythonPackage):
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-matplotlib', type=('build', 'run'))
depends_on('py-pytest', type=('build', 'run'))
- depends_on('py-cython@:2', type=('build', 'run'))
+ depends_on('py-cython', type=('build', 'run'))
# Test dependency
- depends_on('py-pytest@:7.1', type='test')
+ depends_on('py-pytest', type='test')
@run_after('install')
@on_package_attributes(run_tests=True)
--
GitLab
From 8e9993028e6e28425e47834bada5016a600cbd91 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Wed, 5 Mar 2025 16:39:46 +0000
Subject: [PATCH 49/80] feat(py-tblib): copy package from upstream
---
packages/py-tblib/package.py | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
create mode 100644 packages/py-tblib/package.py
diff --git a/packages/py-tblib/package.py b/packages/py-tblib/package.py
new file mode 100644
index 00000000..b76e9b84
--- /dev/null
+++ b/packages/py-tblib/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyTblib(PythonPackage):
+ """Traceback fiddling library. Allows you to pickle tracebacks."""
+
+ homepage = "https://github.com/ionelmc/python-tblib"
+ pypi = "tblib/tblib-1.6.0.tar.gz"
+
+ license("BSD-2-Clause")
+
+ version("1.6.0", sha256="229bee3754cb5d98b4837dd5c4405e80cfab57cb9f93220410ad367f8b352344")
+ version("1.4.0", sha256="bd1ad564564a158ff62c290687f3db446038f9ac11a0bf6892712e3601af3bcd")
+
+ depends_on("python@2.7:2.8,3.5:", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
--
GitLab
From d09bfb473adeb754005f5a8114aca6b89aa54218 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Wed, 5 Mar 2025 16:47:26 +0000
Subject: [PATCH 50/80] feat(py-tblib): add version 2.0.0
---
packages/py-tblib/package.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/packages/py-tblib/package.py b/packages/py-tblib/package.py
index b76e9b84..f9f8511b 100644
--- a/packages/py-tblib/package.py
+++ b/packages/py-tblib/package.py
@@ -15,6 +15,9 @@ class PyTblib(PythonPackage):
license("BSD-2-Clause")
+ # begin EBRAINS (added): new version
+ version("2.0.0", sha256="a6df30f272c08bf8be66e0775fad862005d950a6b8449b94f7c788731d70ecd7")
+ # end EBRAINS
version("1.6.0", sha256="229bee3754cb5d98b4837dd5c4405e80cfab57cb9f93220410ad367f8b352344")
version("1.4.0", sha256="bd1ad564564a158ff62c290687f3db446038f9ac11a0bf6892712e3601af3bcd")
--
GitLab
From 615b2461648dfeb3fb389ce1a04abaa907214832 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Thu, 6 Mar 2025 18:06:54 +0000
Subject: [PATCH 51/80] fix(py-astropy): relax py-cython dependency version
range
see https://github.com/astropy/astropy/blob/v6.1.0/pyproject.toml#L128
---
packages/py-astropy/package.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/packages/py-astropy/package.py b/packages/py-astropy/package.py
index e780f21c..d62abe73 100644
--- a/packages/py-astropy/package.py
+++ b/packages/py-astropy/package.py
@@ -40,7 +40,9 @@ class PyAstropy(PythonPackage):
# TODO: probably fix, unrealistic
depends_on("py-cython@0.29.13:", type="build")
depends_on("py-cython@0.29.30", when="@5.1:6.0", type="build")
- depends_on("py-cython@3.0.0", when="@6.1.0:", type="build")
+ # begin EBRAINS (modified): relax dependency version constraint
+ depends_on("py-cython@3.0", when="@6:", type="build")
+ # end EBRAINS
# in newer pip versions --install-option does not exist
depends_on("py-pip@:23.0", type="build")
--
GitLab
From 5d459ce403ac413e379661cb115d5f0255dad668 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 23:14:08 +0000
Subject: [PATCH 52/80] feat(CI): update build env docker image
---
.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 858211ed..80b8a4d9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,7 +3,7 @@ stages:
- test
variables:
- BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/ebrains-spack-build-env/base:24.12
+ BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/ebrains-spack-build-env/base:devel
SPACK_PATH_GITLAB: /mnt/spack_v0.23.0
SYSTEMNAME: ebrainslab
GIT_SUBMODULE_STRATEGY: recursive
--
GitLab
From ca5bdd3ef09674a8f984c43e80cb9631a2b398f5 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 23:26:20 +0000
Subject: [PATCH 53/80] feat(CI): no need for spack-installed compiler on lab
image-based builds
---
install_spack_env.sh | 46 --------------------------------------------
1 file changed, 46 deletions(-)
diff --git a/install_spack_env.sh b/install_spack_env.sh
index 8de4f7df..31232625 100644
--- a/install_spack_env.sh
+++ b/install_spack_env.sh
@@ -79,52 +79,6 @@ if [[ ! $(spack mirror list | grep local_cache) ]]; then
spack mirror add local_cache ${SPACK_CACHE_BUILD}
fi
-# install platform compiler (extract version from packages.yaml)
-if [ $SYSTEMNAME == ebrainslab ]
-then
- EBRAINS_SPACK_COMPILER=$(grep 'compiler' $EBRAINS_REPO/site-config/$SYSTEMNAME/packages.yaml | awk -F'[][]' '{ print $2 }')
- spack compiler find
- spack load $EBRAINS_SPACK_COMPILER || {
- # dump dag to file
- spack spec -y $EBRAINS_SPACK_COMPILER arch=x86_64 > "/tmp/req_compiler.yaml"
- if [ -n "${OCI_CACHE_PREFIX}" ]; then
- # fetch missing sources (if packages not yet installed)
- python3 ${YASHCHIKI_HOME}/fetch_cached_sources.py \
- --local-cache=${SPACK_CACHE_SOURCE} \
- --remote-cache-type=oci \
- --remote-cache=${OCI_CACHE_PREFIX}/source_cache \
- --yashchiki-home=${YASHCHIKI_HOME} \
- /tmp/compiler_missing_paths_sources.dat /tmp/req_compiler.yaml
- # fetch missing build results (if packages not yet installed)
- python3 ${YASHCHIKI_HOME}/fetch_cached_buildresults.py \
- --local-cache=${SPACK_CACHE_BUILD}/build_cache \
- --remote-cache-type=oci \
- --remote-cache=${OCI_CACHE_PREFIX}/build_cache \
- --yashchiki-home=${YASHCHIKI_HOME} \
- /tmp/compiler_missing_paths_buildresults.dat /tmp/req_compiler.yaml
- fi
- spack install --no-check-signature -y -j$SPACK_JOBS $EBRAINS_SPACK_COMPILER arch=x86_64
- if [ -n "${OCI_CACHE_PREFIX}" ] && [ "${UPDATE_SPACK_OCI_CACHES:-false}" = "true" ]; then
- echo "Performing update of the source cache (for base compiler)"
- python3 ${YASHCHIKI_HOME}/update_cached_sources.py \
- --local-cache=${SPACK_CACHE_SOURCE} \
- --remote-cache-type=oci \
- --remote-cache=${OCI_CACHE_PREFIX}/source_cache \
- /tmp/compiler_missing_paths_sources.dat
- # push previously missing (but now installed) packages to the local cache
- spack buildcache create --unsigned ${SPACK_CACHE_BUILD} ${EBRAINS_SPACK_COMPILER} && ret=$? || ret=$?
- # upload packages from local to remote cache
- echo "Performing update of the build cache (for base compiler)"
- python3 ${YASHCHIKI_HOME}/update_cached_buildresults.py \
- --local-cache=${SPACK_CACHE_BUILD}/build_cache \
- --remote-cache-type=oci \
- --remote-cache=${OCI_CACHE_PREFIX}/build_cache \
- /tmp/compiler_missing_paths_buildresults.dat
- fi
- spack load $EBRAINS_SPACK_COMPILER
- }
-fi
-
spack compiler find
# create environment if it does not exist
--
GitLab
From a20260fdf5e0637144c24888cce288c547a36027 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 23:15:30 +0000
Subject: [PATCH 54/80] feat: update Spack to v0.23.1
---
.gitlab-ci.yml | 2 +-
README.md | 4 ++--
vendor/spack | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 80b8a4d9..17476bd7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,7 +4,7 @@ stages:
variables:
BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/ebrains-spack-build-env/base:devel
- SPACK_PATH_GITLAB: /mnt/spack_v0.23.0
+ SPACK_PATH_GITLAB: /mnt/spack_v0.23.1
SYSTEMNAME: ebrainslab
GIT_SUBMODULE_STRATEGY: recursive
GIT_CLEAN_FLAGS: -ffdxq
diff --git a/README.md b/README.md
index 36bce891..cc0ed81e 100644
--- a/README.md
+++ b/README.md
@@ -38,9 +38,9 @@ Clone this repository. You can use the `ebrains-yy-mm` branches to install the E
git clone --branch {branch-name} https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git
```
-Clone Spack. We currently use version v0.23.0:
+Clone Spack. We currently use version v0.23.1:
```
-git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.23.0 https://github.com/spack/spack
+git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.23.1 https://github.com/spack/spack
```
Activate Spack:
diff --git a/vendor/spack b/vendor/spack
index 65abf4d1..712b36d5 160000
--- a/vendor/spack
+++ b/vendor/spack
@@ -1 +1 @@
-Subproject commit 65abf4d14071280c6d4a183e20c0f6991ed49986
+Subproject commit 712b36d5963a179615bf72c48e90acff3cf4f6b9
--
GitLab
From 6125b2c7e95b9f44a66c583707911b7d1127b427 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 20:26:53 +0000
Subject: [PATCH 55/80] feat(python): copy package from upstream
---
.../python/cpython-windows-externals.patch | 28 +
packages/python/fj-rpath-3.1.patch | 13 +
packages/python/fj-rpath-3.9.patch | 11 +
packages/python/intel-3.7.patch | 38 +
packages/python/package.py | 1318 +++++++++++++++++
.../python/python-3.11-distutils-C++.patch | 257 ++++
.../python/python-3.7.2-distutils-C++.patch | 241 +++
.../python/python-3.7.3-distutils-C++.patch | 256 ++++
...ython-3.7.4+-distutils-C++-testsuite.patch | 138 ++
.../python/python-3.7.4+-distutils-C++.patch | 257 ++++
packages/python/rpath-non-gcc.patch | 15 +
packages/python/tkinter-3.10.patch | 11 +
packages/python/tkinter-3.11.patch | 25 +
packages/python/tkinter-3.7.patch | 17 +
packages/python/tkinter-3.8.patch | 12 +
15 files changed, 2637 insertions(+)
create mode 100644 packages/python/cpython-windows-externals.patch
create mode 100644 packages/python/fj-rpath-3.1.patch
create mode 100644 packages/python/fj-rpath-3.9.patch
create mode 100644 packages/python/intel-3.7.patch
create mode 100644 packages/python/package.py
create mode 100644 packages/python/python-3.11-distutils-C++.patch
create mode 100644 packages/python/python-3.7.2-distutils-C++.patch
create mode 100644 packages/python/python-3.7.3-distutils-C++.patch
create mode 100644 packages/python/python-3.7.4+-distutils-C++-testsuite.patch
create mode 100644 packages/python/python-3.7.4+-distutils-C++.patch
create mode 100644 packages/python/rpath-non-gcc.patch
create mode 100644 packages/python/tkinter-3.10.patch
create mode 100644 packages/python/tkinter-3.11.patch
create mode 100644 packages/python/tkinter-3.7.patch
create mode 100644 packages/python/tkinter-3.8.patch
diff --git a/packages/python/cpython-windows-externals.patch b/packages/python/cpython-windows-externals.patch
new file mode 100644
index 00000000..c3bcce98
--- /dev/null
+++ b/packages/python/cpython-windows-externals.patch
@@ -0,0 +1,28 @@
+diff --git a/PCbuild/get_externals.bat b/PCbuild/get_externals.bat
+index b5a44e3..52941c7 100644
+--- a/PCbuild/get_externals.bat
++++ b/PCbuild/get_externals.bat
+@@ -76,7 +76,7 @@ for %%e in (%libraries%) do (
+ echo.Fetching external binaries...
+
+ set binaries=
+-if NOT "%IncludeLibffi%"=="false" set binaries=%binaries% libffi
++if NOT "%IncludeLibffi%"=="false" set binaries=%binaries% libffi-3.3.0
+ if NOT "%IncludeSSL%"=="false" set binaries=%binaries% openssl-bin-1.1.1k-1
+ if NOT "%IncludeTkinter%"=="false" set binaries=%binaries% tcltk-8.6.9.0
+ if NOT "%IncludeSSLSrc%"=="false" set binaries=%binaries% nasm-2.11.06
+diff --git a/PCbuild/python.props b/PCbuild/python.props
+index 419d5eb..c66fb07 100644
+--- a/PCbuild/python.props
++++ b/PCbuild/python.props
+@@ -59,8 +59,8 @@
+ <sqlite3Dir>$(ExternalsDir)sqlite-3.35.5.0\</sqlite3Dir>
+ <bz2Dir>$(ExternalsDir)bzip2-1.0.6\</bz2Dir>
+ <lzmaDir>$(ExternalsDir)xz-5.2.2\</lzmaDir>
+- <libffiDir>$(ExternalsDir)libffi\</libffiDir>
+- <libffiOutDir>$(ExternalsDir)libffi\$(ArchName)\</libffiOutDir>
++ <libffiDir>$(ExternalsDir)libffi-3.3.0\</libffiDir>
++ <libffiOutDir>$(ExternalsDir)libffi-3.3.0\$(ArchName)\</libffiOutDir>
+ <libffiIncludeDir>$(libffiOutDir)include</libffiIncludeDir>
+ <opensslDir>$(ExternalsDir)openssl-1.1.1k\</opensslDir>
+ <opensslOutDir>$(ExternalsDir)openssl-bin-1.1.1k-1\$(ArchName)\</opensslOutDir>
diff --git a/packages/python/fj-rpath-3.1.patch b/packages/python/fj-rpath-3.1.patch
new file mode 100644
index 00000000..d25b58da
--- /dev/null
+++ b/packages/python/fj-rpath-3.1.patch
@@ -0,0 +1,13 @@
+--- a/Lib/distutils/unixccompiler.py 2009-05-09 21:55:12.000000000 +1000
++++ b/Lib/distutils/unixccompiler.py 2017-05-13 14:30:18.077518999 +1000
+@@ -215,7 +211,8 @@
+ return "-L" + dir
+
+ def _is_gcc(self, compiler_name):
+- return "gcc" in compiler_name or "g++" in compiler_name
++ return "gcc" in compiler_name or "g++" in compiler_name \
++ or "fcc" in compiler_name or "FCC" in compiler_name
+
+ def runtime_library_dir_option(self, dir):
+ # XXX Hackish, at the very least. See Python bug #445902:
+
diff --git a/packages/python/fj-rpath-3.9.patch b/packages/python/fj-rpath-3.9.patch
new file mode 100644
index 00000000..1542b367
--- /dev/null
+++ b/packages/python/fj-rpath-3.9.patch
@@ -0,0 +1,11 @@
+--- spack-src/Lib/distutils/unixccompiler.py.org 2022-01-31 14:42:34.000000000 +0900
++++ spack-src/Lib/distutils/unixccompiler.py 2022-01-31 14:43:19.000000000 +0900
+@@ -212,7 +212,7 @@
+
+ def _is_gcc(self, compiler_name):
+ # clang uses same syntax for rpath as gcc
+- return any(name in compiler_name for name in ("gcc", "g++", "clang"))
++ return any(name in compiler_name for name in ("gcc", "g++", "clang", "fcc", "FCC"))
+
+ def runtime_library_dir_option(self, dir):
+ # XXX Hackish, at the very least. See Python bug #445902:
diff --git a/packages/python/intel-3.7.patch b/packages/python/intel-3.7.patch
new file mode 100644
index 00000000..f2277624
--- /dev/null
+++ b/packages/python/intel-3.7.patch
@@ -0,0 +1,38 @@
+From 87ed388f41d761ddddc8447e5104569f2436c005 Mon Sep 17 00:00:00 2001
+From: Victor Stinner <vstinner@python.org>
+Date: Fri, 11 Oct 2019 15:13:51 +0200
+Subject: [PATCH] bpo-37415: Fix stdatomic.h header check for ICC compiler
+
+Fix stdatomic.h header check for ICC compiler: the ICC implementation
+lacks atomic_uintptr_t type which is needed by Python.
+
+Test:
+
+* atomic_int and atomic_uintptr_t types
+* atomic_load_explicit() and atomic_store_explicit()
+* memory_order_relaxed and memory_order_seq_cst constants
+
+But don't test ATOMIC_VAR_INIT(): it's not used in Python.
+---
+ configure | 7 +++++--
+ 1 file changed, 5 insertions(+), 2 deletions(-)
+
+diff --git a/configure b/configure
+index f1979c1b8124c..1b30a848a77e7 100755
+--- a/configure
++++ b/configure
+@@ -16734,9 +16722,12 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+
+
+ #include <stdatomic.h>
+- atomic_int value = ATOMIC_VAR_INIT(1);
++ atomic_int int_var;
++ atomic_uintptr_t uintptr_var;
+ int main() {
+- int loaded_value = atomic_load(&value);
++ atomic_store_explicit(&int_var, 5, memory_order_relaxed);
++ atomic_store_explicit(&uintptr_var, 0, memory_order_relaxed);
++ int loaded_value = atomic_load_explicit(&int_var, memory_order_seq_cst);
+ return 0;
+ }
+
diff --git a/packages/python/package.py b/packages/python/package.py
new file mode 100644
index 00000000..3bfdc240
--- /dev/null
+++ b/packages/python/package.py
@@ -0,0 +1,1318 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import glob
+import json
+import os
+import platform
+import re
+import subprocess
+import sys
+from shutil import copy
+from typing import Dict, List
+
+import llnl.util.tty as tty
+from llnl.util.lang import dedupe
+
+from spack.build_environment import dso_suffix, stat_suffix
+from spack.package import *
+from spack.util.prefix import Prefix
+
+
+def make_pyvenv_cfg(python_spec: "spack.spec.Spec", venv_prefix: str) -> str:
+ """Make a pyvenv_cfg file for a given (real) python command and venv prefix."""
+ python_cmd = python_spec.command.path
+ lines = [
+ # directory containing python command
+ f"home = {os.path.dirname(python_cmd)}",
+ # venv should not allow site packages from the real python to be loaded
+ "include-system-site-packages = false",
+ # version of the python command
+ f"version = {python_spec.version}",
+ # the path to the python command
+ f"executable = {python_cmd}",
+ # command "used" to create the pyvenv.cfg
+ f"command = {python_cmd} -m venv --without-pip {venv_prefix}",
+ ]
+
+ return "\n".join(lines) + "\n"
+
+
+class Python(Package):
+ """The Python programming language."""
+
+ homepage = "https://www.python.org/"
+ url = "https://www.python.org/ftp/python/3.8.0/Python-3.8.0.tgz"
+ list_url = "https://www.python.org/ftp/python/"
+ list_depth = 1
+ tags = ["windows"]
+
+ maintainers("skosukhin", "scheibelp")
+
+ phases = ["configure", "build", "install"]
+
+ #: phase
+ install_targets = ["install"]
+ build_targets: List[str] = []
+
+ license("0BSD")
+
+ version("3.13.0", sha256="12445c7b3db3126c41190bfdc1c8239c39c719404e844babbd015a1bc3fafcd4")
+ version("3.12.5", sha256="38dc4e2c261d49c661196066edbfb70fdb16be4a79cc8220c224dfeb5636d405")
+ version("3.12.4", sha256="01b3c1c082196f3b33168d344a9c85fb07bfe0e7ecfe77fee4443420d1ce2ad9")
+ version("3.12.3", sha256="a6b9459f45a6ebbbc1af44f5762623fa355a0c87208ed417628b379d762dddb0")
+ version("3.12.2", sha256="a7c4f6a9dc423d8c328003254ab0c9338b83037bd787d680826a5bf84308116e")
+ version("3.12.1", sha256="d01ec6a33bc10009b09c17da95cc2759af5a580a7316b3a446eb4190e13f97b2")
+ version("3.12.0", sha256="51412956d24a1ef7c97f1cb5f70e185c13e3de1f50d131c0aac6338080687afb")
+ version("3.11.9", sha256="e7de3240a8bc2b1e1ba5c81bf943f06861ff494b69fda990ce2722a504c6153d")
+ version("3.11.8", sha256="d3019a613b9e8761d260d9ebe3bd4df63976de30464e5c0189566e1ae3f61889")
+ version("3.11.7", sha256="068c05f82262e57641bd93458dfa883128858f5f4997aad7a36fd25b13b29209")
+ version("3.11.6", sha256="c049bf317e877cbf9fce8c3af902436774ecef5249a29d10984ca3a37f7f4736")
+ version("3.11.5", sha256="a12a0a013a30b846c786c010f2c19dd36b7298d888f7c4bd1581d90ce18b5e58")
+ version("3.11.4", sha256="85c37a265e5c9dd9f75b35f954e31fbfc10383162417285e30ad25cc073a0d63")
+ version("3.11.3", sha256="1a79f3df32265d9e6625f1a0b31c28eb1594df911403d11f3320ee1da1b3e048")
+ version("3.11.2", sha256="2411c74bda5bbcfcddaf4531f66d1adc73f247f529aee981b029513aefdbf849")
+ version("3.11.1", sha256="baed518e26b337d4d8105679caf68c5c32630d702614fc174e98cb95c46bdfa4")
+ version("3.11.0", sha256="64424e96e2457abbac899b90f9530985b51eef2905951febd935f0e73414caeb")
+ version("3.10.14", sha256="cefea32d3be89c02436711c95a45c7f8e880105514b78680c14fe76f5709a0f6")
+ version("3.10.13", sha256="698ec55234c1363bd813b460ed53b0f108877c7a133d48bde9a50a1eb57b7e65")
+ version("3.10.12", sha256="a43cd383f3999a6f4a7db2062b2fc9594fefa73e175b3aedafa295a51a7bb65c")
+ version("3.10.11", sha256="f3db31b668efa983508bd67b5712898aa4247899a346f2eb745734699ccd3859")
+ version("3.10.10", sha256="fba64559dde21ebdc953e4565e731573bb61159de8e4d4cedee70fb1196f610d")
+ version("3.10.9", sha256="4ccd7e46c8898f4c7862910a1703aa0e63525913a519abb2f55e26220a914d88")
+ version("3.10.8", sha256="f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a")
+ version("3.10.7", sha256="1b2e4e2df697c52d36731666979e648beeda5941d0f95740aafbf4163e5cc126")
+ version("3.10.6", sha256="848cb06a5caa85da5c45bd7a9221bb821e33fc2bdcba088c127c58fad44e6343")
+ version("3.10.5", sha256="18f57182a2de3b0be76dfc39fdcfd28156bb6dd23e5f08696f7492e9e3d0bf2d")
+ version("3.10.4", sha256="f3bcc65b1d5f1dc78675c746c98fcee823c038168fc629c5935b044d0911ad28")
+ version("3.10.3", sha256="5a3b029bad70ba2a019ebff08a65060a8b9b542ffc1a83c697f1449ecca9813b")
+ version("3.10.2", sha256="3c0ede893011319f9b0a56b44953a3d52c7abf9657c23fb4bc9ced93b86e9c97")
+ version("3.10.1", sha256="b76117670e7c5064344b9c138e141a377e686b9063f3a8a620ff674fa8ec90d3")
+ version("3.10.0", sha256="c4e0cbad57c90690cb813fb4663ef670b4d0f587d8171e2c42bd4c9245bd2758")
+ version("3.9.19", sha256="f5f9ec8088abca9e399c3b62fd8ef31dbd2e1472c0ccb35070d4d136821aaf71")
+ version("3.9.18", sha256="504ce8cfd59addc04c22f590377c6be454ae7406cb1ebf6f5a350149225a9354")
+ version("3.9.17", sha256="8ead58f669f7e19d777c3556b62fae29a81d7f06a7122ff9bc57f7dd82d7e014")
+ version("3.9.16", sha256="1ad539e9dbd2b42df714b69726e0693bc6b9d2d2c8e91c2e43204026605140c5")
+ version("3.9.15", sha256="48d1ccb29d5fbaf1fb8f912271d09f7450e426d4dfe95978ef6aaada70ece4d8")
+ version("3.9.14", sha256="9201836e2c16361b2b7408680502393737d44f227333fe2e5729c7d5f6041675")
+ version("3.9.13", sha256="829b0d26072a44689a6b0810f5b4a3933ee2a0b8a4bfc99d7c5893ffd4f97c44")
+ version("3.9.12", sha256="70e08462ebf265012bd2be88a63d2149d880c73e53f1712b7bbbe93750560ae8")
+ version("3.9.11", sha256="3442400072f582ac2f0df30895558f08883b416c8c7877ea55d40d00d8a93112")
+ version("3.9.10", sha256="1aa9c0702edbae8f6a2c95f70a49da8420aaa76b7889d3419c186bfc8c0e571e")
+ version("3.9.9", sha256="2cc7b67c1f3f66c571acc42479cdf691d8ed6b47bee12c9b68430413a17a44ea")
+ version("3.9.8", sha256="7447fb8bb270942d620dd24faa7814b1383b61fa99029a240025fd81c1db8283")
+ version("3.9.7", sha256="a838d3f9360d157040142b715db34f0218e535333696a5569dc6f854604eb9d1")
+ version("3.9.6", sha256="d0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866")
+ version("3.9.5", sha256="e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab")
+ version("3.9.4", sha256="66c4de16daa74a825cf9da9ddae1fe020b72c3854b73b1762011cc33f9e4592f")
+ version("3.9.3", sha256="3afeb61a45b5a2e6f1c0f621bd8cf925a4ff406099fdb3d8c97b993a5f43d048")
+ version("3.9.2", sha256="7899e8a6f7946748830d66739f2d8f2b30214dad956e56b9ba216b3de5581519")
+ version("3.9.1", sha256="29cb91ba038346da0bd9ab84a0a55a845d872c341a4da6879f462e94c741f117")
+ version("3.9.0", sha256="df796b2dc8ef085edae2597a41c1c0a63625ebd92487adaef2fed22b567873e8")
+ version("3.8.19", sha256="c7fa55a36e5c7a19ec37d8f90f60a2197548908c9ac8b31e7c0dbffdd470eeac")
+ version("3.8.18", sha256="7c5df68bab1be81a52dea0cc2e2705ea00553b67107a301188383d7b57320b16")
+ version("3.8.17", sha256="def428fa6cf61b66bcde72e3d9f7d07d33b2e4226f04f9d6fce8384c055113ae")
+ version("3.8.16", sha256="71ca9d935637ed2feb59e90a368361dc91eca472a90acb1d344a2e8178ccaf10")
+ version("3.8.15", sha256="924d46999df82aa2eaa1de5ca51d6800ffb56b4bf52486a28f40634e3362abc4")
+ version("3.8.14", sha256="41f959c480c59211feb55d5a28851a56c7e22d02ef91035606ebb21011723c31")
+ version("3.8.13", sha256="903b92d76354366b1d9c4434d0c81643345cef87c1600adfa36095d7b00eede4")
+ version("3.8.12", sha256="316aa33f3b7707d041e73f246efedb297a70898c4b91f127f66dc8d80c596f1a")
+ version("3.8.11", sha256="b77464ea80cec14581b86aeb7fb2ff02830e0abc7bcdc752b7b4bdfcd8f3e393")
+ version("3.8.10", sha256="b37ac74d2cbad2590e7cd0dd2b3826c29afe89a734090a87bf8c03c45066cb65")
+ version("3.8.9", sha256="9779ec1df000bf86914cdd40860b88da56c1e61db59d37784beca14a259ac9e9")
+ version("3.8.8", sha256="76c0763f048e4f9b861d24da76b7dd5c7a3ba7ec086f40caedeea359263276f7")
+ version("3.8.7", sha256="20e5a04262f0af2eb9c19240d7ec368f385788bba2d8dfba7e74b20bab4d2bac")
+ version("3.8.6", sha256="313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21")
+ version("3.8.5", sha256="015115023c382eb6ab83d512762fe3c5502fa0c6c52ffebc4831c4e1a06ffc49")
+ version("3.8.4", sha256="32c4d9817ef11793da4d0d95b3191c4db81d2e45544614e8449255ca9ae3cc18")
+ version("3.8.3", sha256="6af6d4d2e010f9655518d0fc6738c7ff7069f10a4d2fbd55509e467f092a8b90")
+ version("3.8.2", sha256="e634a7a74776c2b89516b2e013dda1728c89c8149b9863b8cea21946daf9d561")
+ version("3.8.1", sha256="c7cfa39a43b994621b245e029769e9126caa2a93571cee2e743b213cceac35fb")
+ version("3.8.0", sha256="f1069ad3cae8e7ec467aa98a6565a62a48ef196cb8f1455a245a08db5e1792df")
+ version(
+ "3.7.17",
+ sha256="fd50161bc2a04f4c22a0971ff0f3856d98b4bf294f89740a9f06b520aae63b49",
+ deprecated=True,
+ )
+ version(
+ "3.7.16",
+ sha256="0cf2da07fa464636755215415909e22eb1d058817af4824bc15af8390d05fb38",
+ deprecated=True,
+ )
+ version(
+ "3.7.15",
+ sha256="cf2993798ae8430f3af3a00d96d9fdf320719f4042f039380dca79967c25e436",
+ deprecated=True,
+ )
+ version(
+ "3.7.14",
+ sha256="82b2abf8978caa61a9011d166eede831b32de9cbebc0db8162900fa23437b709",
+ deprecated=True,
+ )
+ version(
+ "3.7.13",
+ sha256="e405417f50984bc5870c7e7a9f9aeb93e9d270f5ac67f667a0cd3a09439682b5",
+ deprecated=True,
+ )
+ version(
+ "3.7.12",
+ sha256="33b4daaf831be19219659466d12645f87ecec6eb21d4d9f9711018a7b66cce46",
+ deprecated=True,
+ )
+ version(
+ "3.7.11",
+ sha256="b4fba32182e16485d0a6022ba83c9251e6a1c14676ec243a9a07d3722cd4661a",
+ deprecated=True,
+ )
+ version(
+ "3.7.10",
+ sha256="c9649ad84dc3a434c8637df6963100b2e5608697f9ba56d82e3809e4148e0975",
+ deprecated=True,
+ )
+ version(
+ "3.7.9",
+ sha256="39b018bc7d8a165e59aa827d9ae45c45901739b0bbb13721e4f973f3521c166a",
+ deprecated=True,
+ )
+ version(
+ "3.7.8",
+ sha256="0e25835614dc221e3ecea5831b38fa90788b5389b99b675a751414c858789ab0",
+ deprecated=True,
+ )
+ version(
+ "3.7.7",
+ sha256="8c8be91cd2648a1a0c251f04ea0bb4c2a5570feb9c45eaaa2241c785585b475a",
+ deprecated=True,
+ )
+ version(
+ "3.7.6",
+ sha256="aeee681c235ad336af116f08ab6563361a0c81c537072c1b309d6e4050aa2114",
+ deprecated=True,
+ )
+ version(
+ "3.7.5",
+ sha256="8ecc681ea0600bbfb366f2b173f727b205bb825d93d2f0b286bc4e58d37693da",
+ deprecated=True,
+ )
+ version(
+ "3.7.4",
+ sha256="d63e63e14e6d29e17490abbe6f7d17afb3db182dbd801229f14e55f4157c4ba3",
+ deprecated=True,
+ )
+ version(
+ "3.7.3",
+ sha256="d62e3015f2f89c970ac52343976b406694931742fbde2fed8d1ce8ebb4e1f8ff",
+ deprecated=True,
+ )
+ version(
+ "3.7.2",
+ sha256="f09d83c773b9cc72421abba2c317e4e6e05d919f9bcf34468e192b6a6c8e328d",
+ deprecated=True,
+ )
+ version(
+ "3.7.1",
+ sha256="36c1b81ac29d0f8341f727ef40864d99d8206897be96be73dc34d4739c9c9f06",
+ deprecated=True,
+ )
+ version(
+ "3.7.0",
+ sha256="85bb9feb6863e04fb1700b018d9d42d1caac178559ffa453d7e6a436e259fd0d",
+ deprecated=True,
+ )
+
+ depends_on("c", type="build") # generated
+ depends_on("cxx", type="build") # generated
+
+ extendable = True
+
+ # Variants to avoid cyclical dependencies for concretizer
+ variant("libxml2", default=True, description="Use a gettext library build with libxml2")
+
+ variant(
+ "debug", default=False, description="debug build with extra checks (this is high overhead)"
+ )
+
+ variant("shared", default=True, description="Enable shared libraries")
+ variant("pic", default=True, description="Produce position-independent code (for shared libs)")
+ variant(
+ "optimizations",
+ default=False,
+ description="Enable expensive build-time optimizations, if available",
+ )
+ # See https://legacy.python.org/dev/peps/pep-0394/
+ variant(
+ "pythoncmd",
+ default=sys.platform != "win32",
+ description="Symlink 'python3' executable to 'python' (not PEP 394 compliant)",
+ )
+
+ # Optional Python modules
+ variant("readline", default=sys.platform != "win32", description="Build readline module")
+ variant("ssl", default=True, description="Build ssl module")
+ variant("sqlite3", default=True, description="Build sqlite3 module")
+ variant("dbm", default=True, description="Build dbm module")
+ variant("nis", default=False, description="Build nis module")
+ variant("zlib", default=True, description="Build zlib module")
+ variant("bz2", default=True, description="Build bz2 module")
+ variant("lzma", default=True, description="Build lzma module")
+ variant("pyexpat", default=True, description="Build pyexpat module")
+ variant("ctypes", default=True, description="Build ctypes module")
+ variant("tkinter", default=False, description="Build tkinter module")
+ variant("uuid", default=True, description="Build uuid module")
+ variant("tix", default=False, description="Build Tix module", when="+tkinter")
+ variant("crypt", default=True, description="Build crypt module", when="@:3.12 platform=linux")
+ variant("crypt", default=True, description="Build crypt module", when="@:3.12 platform=darwin")
+
+ if sys.platform != "win32":
+ depends_on("gmake", type="build")
+ depends_on("pkgconfig@0.9.0:", type="build")
+ depends_on("gettext +libxml2", when="+libxml2")
+ depends_on("gettext ~libxml2", when="~libxml2")
+
+ # Optional dependencies
+ # See detect_modules() in setup.py for details
+ depends_on("readline", when="+readline")
+ depends_on("ncurses", when="+readline")
+ depends_on("openssl", when="+ssl")
+ # https://docs.python.org/3/whatsnew/3.7.html#build-changes
+ depends_on("openssl@1.0.2:", when="+ssl")
+ # https://docs.python.org/3.10/whatsnew/3.10.html#build-changes
+ depends_on("openssl@1.1.1:", when="@3.10:+ssl")
+ depends_on("sqlite@3.0.8:", when="@:3.9+sqlite3")
+ # https://docs.python.org/3.10/whatsnew/3.10.html#build-changes
+ depends_on("sqlite@3.7.15:", when="@3.10:+sqlite3")
+ depends_on("gdbm", when="+dbm") # alternatively ndbm or berkeley-db
+ depends_on("libnsl", when="+nis")
+ depends_on("zlib-api", when="+zlib")
+ depends_on("bzip2", when="+bz2")
+ depends_on("xz libs=shared", when="+lzma")
+ depends_on("expat", when="+pyexpat")
+ depends_on("libffi", when="+ctypes")
+ # https://docs.python.org/3/whatsnew/3.11.html#build-changes
+ depends_on("tk@8.5.12:", when="@3.11: +tkinter")
+ depends_on("tk", when="+tkinter")
+ depends_on("tcl@8.5.12:", when="@3.11: +tkinter")
+ depends_on("tcl", when="+tkinter")
+ depends_on("uuid", when="+uuid")
+ depends_on("tix", when="+tix")
+ depends_on("libxcrypt", when="+crypt")
+
+ # Python needs to be patched to build extensions w/ mixed C/C++ code:
+ # https://github.com/NixOS/nixpkgs/pull/19585/files
+ # https://bugs.python.org/issue1222585
+ #
+ # NOTE: This patch puts Spack's default Python installation out of
+ # sync with standard Python installs. If you're using such an
+ # installation as an external and encountering build issues with mixed
+ # C/C++ modules, consider installing a Spack-managed Python with
+ # this patch instead. For more information, see:
+ # https://github.com/spack/spack/pull/16856
+ patch("python-3.7.2-distutils-C++.patch", when="@3.7.2")
+ patch("python-3.7.3-distutils-C++.patch", when="@3.7.3")
+ patch("python-3.7.4+-distutils-C++.patch", when="@3.7.4:3.10")
+ patch("python-3.7.4+-distutils-C++-testsuite.patch", when="@3.7.4:3.11")
+ patch("python-3.11-distutils-C++.patch", when="@3.11.0:3.11")
+ patch("cpython-windows-externals.patch", when="@:3.9.6 platform=windows")
+ patch("tkinter-3.7.patch", when="@3.7 platform=darwin")
+ # Patch the setup script to deny that tcl/x11 exists rather than allowing
+ # autodetection of (possibly broken) system components
+ patch("tkinter-3.8.patch", when="@3.8:3.9 ~tkinter")
+ patch("tkinter-3.10.patch", when="@3.10.0:3.10 ~tkinter")
+ patch("tkinter-3.11.patch", when="@3.11.0:3.11 ~tkinter")
+
+ # Ensure that distutils chooses correct compiler option for RPATH:
+ patch("rpath-non-gcc.patch", when="@:3.11")
+
+ # Ensure that distutils chooses correct compiler option for RPATH on fj:
+ patch("fj-rpath-3.1.patch", when="@:3.9.7,3.10.0 %fj")
+ patch("fj-rpath-3.9.patch", when="@3.9.8:3.9,3.10.1:3.11 %fj")
+
+ # Fixes build with the Intel compilers
+ # https://github.com/python/cpython/pull/16717
+ patch("intel-3.7.patch", when="@3.7.1:3.7.5 %intel")
+
+ # CPython tries to build an Objective-C file with GCC's C frontend
+ # https://github.com/spack/spack/pull/16222
+ # https://github.com/python/cpython/pull/13306
+ conflicts(
+ "%gcc platform=darwin",
+ msg="CPython does not compile with GCC on macOS yet, use clang. "
+ "See: https://github.com/python/cpython/pull/13306",
+ )
+ conflicts("%nvhpc")
+
+ # https://bugs.python.org/issue45405
+ conflicts("@:3.7.12,3.8.0:3.8.12,3.9.0:3.9.7,3.10.0", when="%apple-clang@13:")
+
+ # See https://github.com/python/cpython/issues/106424
+ # datetime.now(timezone.utc) segfaults
+ conflicts("@3.9:", when="%oneapi@2022.2.1:2023")
+
+ # Used to cache various attributes that are expensive to compute
+ _config_vars: Dict[str, Dict[str, str]] = {}
+
+ # An in-source build with --enable-optimizations fails for python@3.X
+ build_directory = "spack-build"
+
+ executables = [r"^python\d?$"]
+
+ @classmethod
+ def determine_version(cls, exe):
+ # Newer versions of Python support `--version`,
+ # but older versions only support `-V`
+ # Output looks like:
+ # Python 3.7.7
+ # On pre-production Ubuntu, this is also possible:
+ # Python 3.10.2+
+ output = Executable(exe)("-V", output=str, error=str)
+ match = re.search(r"Python\s+([A-Za-z0-9_.-]+)", output)
+ return match.group(1) if match else None
+
+ @classmethod
+ def determine_variants(cls, exes, version_str):
+ python = Executable(exes[0])
+
+ variants = ""
+ for exe in exes:
+ if os.path.basename(exe) == "python":
+ variants += "+pythoncmd"
+ break
+ else:
+ variants += "~pythoncmd"
+
+ for module in [
+ "readline",
+ "sqlite3",
+ "dbm",
+ "nis",
+ "zlib",
+ "bz2",
+ "lzma",
+ "ctypes",
+ "tkinter",
+ "uuid",
+ ]:
+ try:
+ python("-c", "import " + module, error=os.devnull)
+ variants += "+" + module
+ except ProcessError:
+ variants += "~" + module
+
+ # Some variants enable multiple modules
+ try:
+ python("-c", "import ssl", error=os.devnull)
+ python("-c", "import hashlib", error=os.devnull)
+ variants += "+ssl"
+ except ProcessError:
+ variants += "~ssl"
+
+ try:
+ python("-c", "import xml.parsers.expat", error=os.devnull)
+ python("-c", "import xml.etree.ElementTree", error=os.devnull)
+ variants += "+pyexpat"
+ except ProcessError:
+ variants += "~pyexpat"
+
+ # Some variant names do not match module names
+ if "+tkinter" in variants:
+ try:
+ python("-c", "import tkinter.tix", error=os.devnull)
+ variants += "+tix"
+ except ProcessError:
+ variants += "~tix"
+
+ # Some modules are platform-dependent
+ if sys.platform != "win32":
+ try:
+ python("-c", "import crypt", error=os.devnull)
+ variants += "+crypt"
+ except ProcessError:
+ variants += "~crypt"
+
+ return variants
+
+ def url_for_version(self, version):
+ url = "https://www.python.org/ftp/python/{0}/Python-{1}.tgz"
+ return url.format(re.split("[a-z]", str(version))[0], version)
+
+ def patch(self):
+ # NOTE: Python's default installation procedure makes it possible for a
+ # user's local configurations to change the Spack installation. In
+ # order to prevent this behavior for a full installation, we must
+ # modify the installation script so that it ignores user files.
+ ff = FileFilter("Makefile.pre.in")
+ ff.filter(
+ r"^(.*)setup\.py(.*)((build)|(install))(.*)$", r"\1setup.py\2 --no-user-cfg \3\6"
+ )
+
+ def setup_build_environment(self, env):
+ spec = self.spec
+
+ # TODO: Python has incomplete support for Python modules with mixed
+ # C/C++ source, and patches are required to enable building for these
+ # modules. All Python versions without a viable patch are installed
+ # with a warning message about this potentially erroneous behavior.
+ if not spec.satisfies("@3.7.2:"):
+ tty.warn(
+ (
+ 'Python v{0} does not have the C++ "distutils" patch; '
+ "errors may occur when installing Python modules w/ "
+ "mixed C/C++ source files."
+ ).format(self.version)
+ )
+
+ env.unset("PYTHONPATH")
+ env.unset("PYTHONHOME")
+
+ # avoid build error on fugaku
+ if spec.satisfies("@3.10.0 arch=linux-rhel8-a64fx"):
+ if spec.satisfies("%gcc") or spec.satisfies("%fj"):
+ env.unset("LC_ALL")
+
+ # https://github.com/python/cpython/issues/87275
+ if spec.satisfies("@:3.9.5 +optimizations %apple-clang"):
+ xcrun = Executable("/usr/bin/xcrun")
+ env.set("LLVM_AR", xcrun("-find", "ar", output=str).strip())
+
+ def flag_handler(self, name, flags):
+ # python 3.8 requires -fwrapv when compiled with intel
+ if self.spec.satisfies("@3.8: %intel"):
+ if name == "cflags":
+ flags.append("-fwrapv")
+
+ # Fix for following issues for python with aocc%3.2.0:
+ # https://github.com/spack/spack/issues/29115
+ # https://github.com/spack/spack/pull/28708
+ if self.spec.satisfies("%aocc@3.2.0"):
+ if name == "cflags":
+ flags.extend(["-mllvm", "-disable-indvar-simplify=true"])
+
+ # allow flags to be passed through compiler wrapper
+ return (flags, None, None)
+
+ @property
+ def plat_arch(self):
+ """
+ String referencing platform architecture
+ filtered through Python's Windows build file
+ architecture support map
+
+ Note: This function really only makes
+ sense to use on Windows, could be overridden to
+ cross compile however.
+ """
+
+ arch_map = {"AMD64": "x64", "x86": "Win32", "IA64": "Win32", "EM64T": "Win32"}
+ arch = platform.machine()
+ if arch in arch_map:
+ arch = arch_map[arch]
+ return arch
+
+ @property
+ def win_build_params(self):
+ """
+ Arguments must be passed to the Python build batch script
+ in order to configure it to spec and system.
+ A number of these toggle optional MSBuild Projects
+ directly corresponding to the python support of the same
+ name.
+ """
+ args = []
+ args.append("-p %s" % self.plat_arch)
+ if self.spec.satisfies("+debug"):
+ args.append("-d")
+ if self.spec.satisfies("~ctypes"):
+ args.append("--no-ctypes")
+ if self.spec.satisfies("~ssl"):
+ args.append("--no-ssl")
+ if self.spec.satisfies("~tkinter"):
+ args.append("--no-tkinter")
+ return args
+
+ def win_installer(self, prefix):
+ """
+ Python on Windows does not export an install target
+ so we must handcraft one here. This structure
+ directly mimics the install tree of the Python
+ Installer on Windows.
+
+ Parameters:
+ prefix (str): Install prefix for package
+ """
+ proj_root = self.stage.source_path
+ pcbuild_root = os.path.join(proj_root, "PCbuild")
+ build_root = os.path.join(pcbuild_root, platform.machine().lower())
+ include_dir = os.path.join(proj_root, "Include")
+ copy_tree(include_dir, prefix.include)
+ doc_dir = os.path.join(proj_root, "Doc")
+ copy_tree(doc_dir, prefix.Doc)
+ tools_dir = os.path.join(proj_root, "Tools")
+ copy_tree(tools_dir, prefix.Tools)
+ lib_dir = os.path.join(proj_root, "Lib")
+ copy_tree(lib_dir, prefix.Lib)
+ pyconfig = os.path.join(proj_root, "PC", "pyconfig.h")
+ copy(pyconfig, prefix.include)
+ shared_libraries = []
+ shared_libraries.extend(glob.glob("%s\\*.exe" % build_root))
+ shared_libraries.extend(glob.glob("%s\\*.dll" % build_root))
+ shared_libraries.extend(glob.glob("%s\\*.pyd" % build_root))
+ os.makedirs(prefix.DLLs)
+ for lib in shared_libraries:
+ file_name = os.path.basename(lib)
+ if (
+ file_name.endswith(".exe")
+ or (file_name.endswith(".dll") and "python" in file_name)
+ or "vcruntime" in file_name
+ ):
+ copy(lib, prefix)
+ else:
+ copy(lib, prefix.DLLs)
+ static_libraries = glob.glob("%s\\*.lib" % build_root)
+ os.makedirs(prefix.libs, exist_ok=True)
+ for lib in static_libraries:
+ copy(lib, prefix.libs)
+
+ def configure_args(self):
+ spec = self.spec
+ config_args = []
+ cflags = []
+
+ # setup.py needs to be able to read the CPPFLAGS and LDFLAGS
+ # as it scans for the library and headers to build
+ link_deps = spec.dependencies(deptype="link")
+
+ if link_deps:
+ # Header files are often included assuming they reside in a
+ # subdirectory of prefix.include, e.g. #include <openssl/ssl.h>,
+ # which is why we don't use HeaderList here. The header files of
+ # libffi reside in prefix.lib but the configure script of Python
+ # finds them using pkg-config.
+ cppflags = " ".join("-I" + spec[dep.name].prefix.include for dep in link_deps)
+
+ # Currently, the only way to get SpecBuildInterface wrappers of the
+ # dependencies (which we need to get their 'libs') is to get them
+ # using spec.__getitem__.
+ ldflags = " ".join(spec[dep.name].libs.search_flags for dep in link_deps)
+
+ config_args.extend(["CPPFLAGS=" + cppflags, "LDFLAGS=" + ldflags])
+
+ if "+optimizations" in spec:
+ config_args.append("--enable-optimizations")
+ # Prefer thin LTO for faster compilation times.
+ if "@3.11.0: %clang@3.9:" in spec or "@3.11.0: %apple-clang@8:" in spec:
+ config_args.append("--with-lto=thin")
+ else:
+ config_args.append("--with-lto")
+ config_args.append("--with-computed-gotos")
+
+ if spec.satisfies("@3.7 %intel"):
+ config_args.append("--with-icc={0}".format(spack_cc))
+
+ if "+debug" in spec:
+ config_args.append("--with-pydebug")
+ else:
+ config_args.append("--without-pydebug")
+
+ if "+shared" in spec:
+ config_args.append("--enable-shared")
+ else:
+ config_args.append("--disable-shared")
+
+ config_args.append("--without-ensurepip")
+
+ if "+pic" in spec:
+ cflags.append(self.compiler.cc_pic_flag)
+
+ if "+ssl" in spec:
+ config_args.append("--with-openssl={0}".format(spec["openssl"].prefix))
+
+ if "+dbm" in spec:
+ # Default order is ndbm:gdbm:bdb
+ config_args.append("--with-dbmliborder=gdbm")
+ else:
+ config_args.append("--with-dbmliborder=")
+
+ if "+pyexpat" in spec:
+ config_args.append("--with-system-expat")
+ else:
+ config_args.append("--without-system-expat")
+
+ if self.version < Version("3.12.0"):
+ if "+ctypes" in spec:
+ config_args.append("--with-system-ffi")
+ else:
+ config_args.append("--without-system-ffi")
+
+ if "+tkinter" in spec:
+ config_args.extend(
+ [
+ "--with-tcltk-includes=-I{0} -I{1}".format(
+ spec["tcl"].prefix.include, spec["tk"].prefix.include
+ ),
+ "--with-tcltk-libs={0} {1}".format(
+ spec["tcl"].libs.ld_flags, spec["tk"].libs.ld_flags
+ ),
+ ]
+ )
+
+ # https://docs.python.org/3.8/library/sqlite3.html#f1
+ if spec.satisfies("+sqlite3 ^sqlite+dynamic_extensions"):
+ config_args.append("--enable-loadable-sqlite-extensions")
+
+ if spec.satisfies("%oneapi"):
+ cflags.append("-fp-model=strict")
+
+ if cflags:
+ config_args.append("CFLAGS={0}".format(" ".join(cflags)))
+
+ if self.version >= Version("3.12.0") and sys.platform == "darwin":
+ config_args.append("CURSES_LIBS={0}".format(spec["ncurses"].libs.link_flags))
+
+ return config_args
+
+ def configure(self, spec, prefix):
+ """Runs configure with the arguments specified in
+ :meth:`~spack.build_systems.autotools.AutotoolsPackage.configure_args`
+ and an appropriately set prefix.
+ """
+ with working_dir(self.stage.source_path, create=True):
+ if sys.platform == "win32":
+ pass
+ else:
+ options = getattr(self, "configure_flag_args", [])
+ options += ["--prefix={0}".format(prefix)]
+ options += self.configure_args()
+ configure(*options)
+
+ def build(self, spec, prefix):
+ """Makes the build targets specified by
+ :py:attr:``~.AutotoolsPackage.build_targets``
+ """
+ # Windows builds use a batch script to drive
+ # configure and build in one step
+ with working_dir(self.stage.source_path):
+ if sys.platform == "win32":
+ pcbuild_root = os.path.join(self.stage.source_path, "PCbuild")
+ builder_cmd = os.path.join(pcbuild_root, "build.bat")
+ try:
+ subprocess.check_output( # novermin
+ " ".join([builder_cmd] + self.win_build_params), stderr=subprocess.STDOUT
+ )
+ except subprocess.CalledProcessError as e:
+ raise ProcessError(
+ "Process exited with status %d" % e.returncode,
+ long_message=e.output.decode("utf-8"),
+ )
+ else:
+ # See https://autotools.io/automake/silent.html
+ params = ["V=1"]
+ params += self.build_targets
+ make(*params)
+
+ def install(self, spec, prefix):
+ """Makes the install targets specified by
+ :py:attr:``~.AutotoolsPackage.install_targets``
+ """
+ with working_dir(self.stage.source_path):
+ if sys.platform == "win32":
+ self.win_installer(prefix)
+ else:
+ # See https://github.com/python/cpython/issues/102007
+ make(*self.install_targets, parallel=False)
+
+ @run_after("install")
+ def filter_compilers(self):
+ """Run after install to tell the configuration files and Makefiles
+ to use the compilers that Spack built the package with.
+
+ If this isn't done, they'll have CC and CXX set to Spack's generic
+ cc and c++. We want them to be bound to whatever compiler
+ they were built with."""
+ if sys.platform == "win32":
+ return
+ kwargs = {"ignore_absent": True, "backup": False, "string": True}
+
+ filenames = [self.get_sysconfigdata_name(), self.config_vars["makefile_filename"]]
+
+ filter_file(spack_cc, self.compiler.cc, *filenames, **kwargs)
+ if spack_cxx and self.compiler.cxx:
+ filter_file(spack_cxx, self.compiler.cxx, *filenames, **kwargs)
+
+ @run_after("install")
+ def symlink(self):
+ if sys.platform == "win32":
+ return
+ spec = self.spec
+ prefix = self.prefix
+
+ if spec.satisfies("+pythoncmd"):
+ os.symlink(os.path.join(prefix.bin, "python3"), os.path.join(prefix.bin, "python"))
+ os.symlink(
+ os.path.join(prefix.bin, "python3-config"),
+ os.path.join(prefix.bin, "python-config"),
+ )
+
+ @run_after("install")
+ def install_python_gdb(self):
+ # https://devguide.python.org/gdb/
+ src = os.path.join("Tools", "gdb", "libpython.py")
+ if os.path.exists(src):
+ install(src, self.command.path + "-gdb.py")
+
+ @run_after("install")
+ @on_package_attributes(run_tests=True)
+ def import_tests(self):
+ """Test that basic Python functionality works."""
+
+ spec = self.spec
+
+ with working_dir("spack-test", create=True):
+ # Ensure that readline module works
+ if "+readline" in spec:
+ self.command("-c", "import readline")
+
+ # Ensure that ssl module works
+ if "+ssl" in spec:
+ self.command("-c", "import ssl")
+ self.command("-c", "import hashlib")
+
+ # Ensure that sqlite3 module works
+ if "+sqlite3" in spec:
+ self.command("-c", "import sqlite3")
+
+ # Ensure that dbm module works
+ if "+dbm" in spec:
+ self.command("-c", "import dbm")
+
+ # Ensure that nis module works
+ if "+nis" in spec:
+ self.command("-c", "import nis")
+
+ # Ensure that zlib module works
+ if "+zlib" in spec:
+ self.command("-c", "import zlib")
+
+ # Ensure that bz2 module works
+ if "+bz2" in spec:
+ self.command("-c", "import bz2")
+
+ # Ensure that lzma module works
+ if "+lzma" in spec:
+ self.command("-c", "import lzma")
+
+ # Ensure that pyexpat module works
+ if "+pyexpat" in spec:
+ self.command("-c", "import xml.parsers.expat")
+ self.command("-c", "import xml.etree.ElementTree")
+
+ # Ensure that ctypes module works
+ if "+ctypes" in spec:
+ self.command("-c", "import ctypes")
+
+ # Ensure that tkinter module works
+ # https://wiki.python.org/moin/TkInter
+ if "+tkinter" in spec:
+ # Only works if ForwardX11Trusted is enabled, i.e. `ssh -Y`
+ if "DISPLAY" in env:
+ self.command("-c", "import tkinter; tkinter._test()")
+ else:
+ self.command("-c", "import tkinter")
+
+ # Ensure that uuid module works
+ if "+uuid" in spec:
+ self.command("-c", "import uuid")
+
+ # Ensure that tix module works
+ if "+tix" in spec:
+ self.command("-c", "import tkinter.tix")
+
+ # Ensure that crypt module works
+ if "+crypt" in spec:
+ self.command("-c", "import crypt")
+
+ # ========================================================================
+ # Set up environment to make install easy for python extensions.
+ # ========================================================================
+
+ @property
+ def command(self):
+ """Returns the Python command, which may vary depending
+ on the version of Python and how it was installed.
+
+ In general, Python 3 only comes with a ``python3`` command. However, some
+ package managers will symlink ``python`` to ``python3``, while others
+ may contain ``python3.11``, ``python3.10``, and ``python3.9`` in the
+ same directory.
+
+ Returns:
+ Executable: the Python command
+ """
+ # We need to be careful here. If the user is using an externally
+ # installed python, several different commands could be located
+ # in the same directory. Be as specific as possible. Search for:
+ #
+ # * python3.11
+ # * python3
+ # * python
+ #
+ # in that order if using python@3.11.0, for example.
+ suffixes = [self.spec.version.up_to(2), self.spec.version.up_to(1), ""]
+ file_extension = "" if sys.platform != "win32" else ".exe"
+ patterns = [f"python{ver}{file_extension}" for ver in suffixes]
+ root = self.prefix.bin if sys.platform != "win32" else self.prefix
+ path = find_first(root, files=patterns)
+
+ if path is not None:
+ return Executable(path)
+
+ else:
+ # Give a last try at rhel8 platform python
+ if self.spec.external and self.prefix == "/usr" and self.spec.satisfies("os=rhel8"):
+ path = os.path.join(self.prefix, "libexec", "platform-python")
+ if os.path.exists(path):
+ return Executable(path)
+
+ raise RuntimeError(
+ f"cannot to locate the '{self.name}' command in {root} or its subdirectories"
+ )
+
+ @property
+ def config_vars(self):
+ """Return a set of variable definitions associated with a Python installation.
+
+ Wrapper around various ``sysconfig`` functions. To see these variables on the
+ command line, run:
+
+ .. code-block:: console
+
+ $ python -m sysconfig
+
+ Returns:
+ dict: variable definitions
+ """
+ cmd = """
+import json
+from sysconfig import (
+ get_config_vars,
+ get_config_h_filename,
+ get_makefile_filename,
+ get_paths,
+)
+
+config = get_config_vars()
+config['config_h_filename'] = get_config_h_filename()
+config['makefile_filename'] = get_makefile_filename()
+config.update(get_paths())
+
+print(json.dumps(config))
+"""
+
+ dag_hash = self.spec.dag_hash()
+ lib_prefix = "lib" if sys.platform != "win32" else ""
+ if dag_hash not in self._config_vars:
+ # Default config vars
+ version = self.version.up_to(2)
+ if sys.platform == "win32":
+ version = str(version).split(".")[0]
+ config = {
+ # get_config_vars
+ "BINDIR": self.prefix.bin,
+ "CC": "cc",
+ "CONFINCLUDEPY": self.prefix.include.join("python{}").format(version),
+ "CXX": "c++",
+ "INCLUDEPY": self.prefix.include.join("python{}").format(version),
+ "LIBDEST": self.prefix.lib.join("python{}").format(version),
+ "LIBDIR": self.prefix.lib,
+ "LIBPL": self.prefix.lib.join("python{0}")
+ .join("config-{0}-{1}")
+ .format(version, sys.platform),
+ "LDLIBRARY": "{}python{}.{}".format(lib_prefix, version, dso_suffix),
+ "LIBRARY": "{}python{}.{}".format(lib_prefix, version, stat_suffix),
+ "LDSHARED": "cc",
+ "LDCXXSHARED": "c++",
+ "PYTHONFRAMEWORKPREFIX": "/System/Library/Frameworks",
+ "base": self.prefix,
+ "installed_base": self.prefix,
+ "installed_platbase": self.prefix,
+ "platbase": self.prefix,
+ "prefix": self.prefix,
+ # get_config_h_filename
+ "config_h_filename": self.prefix.include.join("python{}")
+ .join("pyconfig.h")
+ .format(version),
+ # get_makefile_filename
+ "makefile_filename": self.prefix.lib.join("python{0}")
+ .join("config-{0}-{1}")
+ .Makefile.format(version, sys.platform),
+ # get_paths
+ "data": self.prefix,
+ "include": self.prefix.include.join("python{}".format(version)),
+ "platinclude": self.prefix.include64.join("python{}".format(version)),
+ "platlib": self.prefix.lib64.join("python{}".format(version)).join(
+ "site-packages"
+ ),
+ "platstdlib": self.prefix.lib64.join("python{}".format(version)),
+ "purelib": self.prefix.lib.join("python{}".format(version)).join("site-packages"),
+ "scripts": self.prefix.bin,
+ "stdlib": self.prefix.lib.join("python{}".format(version)),
+ }
+
+ try:
+ config.update(json.loads(self.command("-c", cmd, output=str)))
+ except (ProcessError, RuntimeError):
+ pass
+ self._config_vars[dag_hash] = config
+ return self._config_vars[dag_hash]
+
+ def get_sysconfigdata_name(self):
+ """Return the full path name of the sysconfigdata file."""
+
+ libdest = self.config_vars["LIBDEST"]
+
+ cmd = "from sysconfig import _get_sysconfigdata_name; "
+ cmd += "print(_get_sysconfigdata_name())"
+ filename = self.command("-c", cmd, output=str).strip()
+ filename += ".py"
+
+ return join_path(libdest, filename)
+
+ @property
+ def home(self):
+ """Most of the time, ``PYTHONHOME`` is simply
+ ``spec['python'].prefix``. However, if the user is using an
+ externally installed python, it may be symlinked. For example,
+ Homebrew installs python in ``/usr/local/Cellar/python/2.7.12_2``
+ and symlinks it to ``/usr/local``. Users may not know the actual
+ installation directory and add ``/usr/local`` to their
+ ``packages.yaml`` unknowingly. Query the python executable to
+ determine exactly where it is installed.
+ """
+ return Prefix(self.config_vars["base"])
+
+ def find_library(self, library):
+ # Spack installs libraries into lib, except on openSUSE where it installs them
+ # into lib64. If the user is using an externally installed package, it may be
+ # in either lib or lib64, so we need to ask Python where its LIBDIR is.
+ libdir = self.config_vars["LIBDIR"]
+
+ # Debian and derivatives use a triplet subdir under /usr/lib, LIBPL can be used
+ # to get the Python library directory
+ libpldir = self.config_vars["LIBPL"]
+
+ # The system Python installation on macOS and Homebrew installations
+ # install libraries into a Frameworks directory
+ frameworkprefix = self.config_vars["PYTHONFRAMEWORKPREFIX"]
+
+ # Get the active Xcode environment's Framework location.
+ macos_developerdir = os.environ.get("DEVELOPER_DIR")
+ if macos_developerdir and os.path.exists(macos_developerdir):
+ macos_developerdir = os.path.join(macos_developerdir, "Library", "Frameworks")
+ else:
+ macos_developerdir = ""
+
+ # Windows libraries are installed directly to BINDIR
+ win_bin_dir = self.config_vars["BINDIR"]
+ win_root_dir = self.config_vars["prefix"]
+
+ directories = [
+ libdir,
+ libpldir,
+ frameworkprefix,
+ macos_developerdir,
+ win_bin_dir,
+ win_root_dir,
+ ]
+
+ if self.spec.satisfies("platform=windows"):
+ lib_dirs = ["libs"]
+ else:
+ # The Python shipped with Xcode command line tools isn't in any of these locations
+ lib_dirs = ["lib", "lib64"]
+
+ for subdir in lib_dirs:
+ directories.append(os.path.join(self.config_vars["base"], subdir))
+
+ directories = dedupe(directories)
+ for directory in directories:
+ path = os.path.join(directory, library)
+ if os.path.exists(path):
+ return LibraryList(path)
+
+ @property
+ def libs(self):
+ py_version = self.version.up_to(2)
+ if sys.platform == "win32":
+ py_version = str(py_version).replace(".", "")
+ lib_prefix = "lib" if sys.platform != "win32" else ""
+ # The values of LDLIBRARY and LIBRARY aren't reliable. Intel Python uses a
+ # static binary but installs shared libraries, so sysconfig reports
+ # libpythonX.Y.a but only libpythonX.Y.so exists. So we add our own paths, too.
+
+ # With framework python on macOS, self.config_vars["LDLIBRARY"] can point
+ # to a library that is not linkable because it does not have the required
+ # suffix of a shared library (it is called "Python" without extention).
+ # The linker then falls back to libPython.tbd in the default macOS
+ # software tree, which security settings prohibit to link against
+ # (your binary is not an allowed client of /path/to/libPython.tbd).
+ # To avoid this, we replace the entry in config_vars with a default value.
+ file_extension_shared = os.path.splitext(self.config_vars["LDLIBRARY"])[-1]
+ if file_extension_shared == "":
+ shared_libs = []
+ else:
+ shared_libs = [self.config_vars["LDLIBRARY"]]
+ shared_libs += ["{}python{}.{}".format(lib_prefix, py_version, dso_suffix)]
+ # Like LDLIBRARY for Python on Mac OS, LIBRARY may refer to an un-linkable object
+ file_extension_static = os.path.splitext(self.config_vars["LIBRARY"])[-1]
+ if file_extension_static == "":
+ static_libs = []
+ else:
+ static_libs = [self.config_vars["LIBRARY"]]
+ static_libs += ["{}python{}.{}".format(lib_prefix, py_version, stat_suffix)]
+
+ # The +shared variant isn't reliable, as `spack external find` currently can't
+ # detect it. If +shared, prefer the shared libraries, but check for static if
+ # those aren't found. Vice versa for ~shared.
+ if self.spec.satisfies("platform=windows"):
+ # Since we are searching for link libraries, on Windows search only for
+ # ".Lib" extensions by default as those represent import libraries for implict links.
+ candidates = static_libs
+ elif self.spec.satisfies("+shared"):
+ candidates = shared_libs + static_libs
+ else:
+ candidates = static_libs + shared_libs
+
+ for candidate in dedupe(candidates):
+ lib = self.find_library(candidate)
+ if lib:
+ return lib
+
+ raise spack.error.NoLibrariesError(
+ "Unable to find {} libraries with the following names:\n\n* ".format(self.name)
+ + "\n* ".join(candidates)
+ )
+
+ @property
+ def headers(self):
+ # Locations where pyconfig.h could be
+ # This varies by system, especially on macOS where the command line tools are
+ # installed in a very different directory from the system python interpreter.
+ py_version = str(self.version.up_to(2))
+ candidates = [
+ os.path.dirname(self.config_vars["config_h_filename"]),
+ self.config_vars["INCLUDEPY"],
+ self.config_vars["CONFINCLUDEPY"],
+ os.path.join(self.config_vars["base"], "include", py_version),
+ os.path.join(self.config_vars["base"], "Headers"),
+ ]
+ candidates = list(dedupe(candidates))
+
+ for directory in candidates:
+ headers = find_headers("pyconfig", directory)
+ if headers:
+ config_h = headers[0]
+ break
+ else:
+ raise spack.error.NoHeadersError(
+ "Unable to locate {} headers in any of these locations:\n\n* ".format(self.name)
+ + "\n* ".join(candidates)
+ )
+
+ headers.directories = [os.path.dirname(config_h)]
+ return headers
+
+ # https://docs.python.org/3/library/sysconfig.html#installation-paths
+ # https://discuss.python.org/t/understanding-site-packages-directories/12959
+ # https://github.com/pypa/pip/blob/22.1/src/pip/_internal/locations/__init__.py
+ # https://github.com/pypa/installer/pull/103
+
+ # NOTE: XCode Python's sysconfing module was incorrectly patched, and hard-codes
+ # everything to be installed in /Library/Python. Therefore, we need to use a
+ # fallback in the following methods. For more information, see:
+ # https://github.com/pypa/pip/blob/22.1/src/pip/_internal/locations/__init__.py#L486
+
+ @property
+ def platlib(self):
+ """Directory for site-specific, platform-specific files.
+
+ Exact directory depends on platform/OS/Python version. Examples include:
+
+ * ``lib/pythonX.Y/site-packages`` on most POSIX systems
+ * ``lib64/pythonX.Y/site-packages`` on RHEL/CentOS/Fedora with system Python
+ * ``lib/pythonX/dist-packages`` on Debian/Ubuntu with system Python
+ * ``lib/python/site-packages`` on macOS with framework Python
+ * ``Lib/site-packages`` on Windows
+
+ Returns:
+ str: platform-specific site-packages directory
+ """
+ prefix = self.config_vars["platbase"] + os.sep
+ path = self.config_vars["platlib"]
+ if path.startswith(prefix):
+ return path.replace(prefix, "")
+ return os.path.join("lib64", f"python{self.version.up_to(2)}", "site-packages")
+
+ @property
+ def purelib(self):
+ """Directory for site-specific, non-platform-specific files.
+
+ Exact directory depends on platform/OS/Python version. Examples include:
+
+ * ``lib/pythonX.Y/site-packages`` on most POSIX systems
+ * ``lib/pythonX/dist-packages`` on Debian/Ubuntu with system Python
+ * ``lib/python/site-packages`` on macOS with framework Python
+ * ``Lib/site-packages`` on Windows
+
+ Returns:
+ str: platform-independent site-packages directory
+ """
+ prefix = self.config_vars["base"] + os.sep
+ path = self.config_vars["purelib"]
+ if path.startswith(prefix):
+ return path.replace(prefix, "")
+ return os.path.join("lib", f"python{self.version.up_to(2)}", "site-packages")
+
+ @property
+ def include(self):
+ """Directory for non-platform-specific header files.
+
+ Exact directory depends on platform/Python version/ABI flags. Examples include:
+
+ * ``include/pythonX.Y`` on most POSIX systems
+ * ``include/pythonX.Yd`` for debug builds
+ * ``include/pythonX.Ym`` for malloc builds
+ * ``include/pythonX.Yu`` for wide unicode builds
+ * ``include`` on macOS with framework Python
+ * ``Include`` on Windows
+
+ Returns:
+ str: platform-independent header file directory
+ """
+ prefix = self.config_vars["installed_base"] + os.sep
+ path = self.config_vars["include"]
+ if path.startswith(prefix):
+ return path.replace(prefix, "")
+ return os.path.join("include", "python{}".format(self.version.up_to(2)))
+
+ def setup_dependent_build_environment(self, env, dependent_spec):
+ """Set PYTHONPATH to include the site-packages directory for the
+ extension and any other python extensions it depends on.
+ """
+ # We need to make sure that the extensions are compiled and linked with
+ # the Spack wrapper. Paths to the executables that are used for these
+ # operations are normally taken from the sysconfigdata file, which we
+ # modify after the installation (see method filter compilers). The
+ # modified file contains paths to the real compilers, not the wrappers.
+ # The values in the file, however, can be overridden with environment
+ # variables. The first variable, CC (CXX), which is used for
+ # compilation, is set by Spack for the dependent package by default.
+ # That is not 100% correct because the value for CC (CXX) in the
+ # sysconfigdata file often contains additional compiler flags (e.g.
+ # -pthread), which we lose by simply setting CC (CXX) to the path to the
+ # Spack wrapper. Moreover, the user might try to build an extension with
+ # a compiler that is different from the one that was used to build
+ # Python itself, which might have unexpected side effects. However, the
+ # experience shows that none of the above is a real issue and we will
+ # not try to change the default behaviour. Given that, we will simply
+ # try to modify LDSHARED (LDCXXSHARED), the second variable, which is
+ # used for linking, in a consistent manner.
+
+ for compile_var, link_var in [("CC", "LDSHARED"), ("CXX", "LDCXXSHARED")]:
+ # First, we get the values from the sysconfigdata:
+ config_compile = self.config_vars[compile_var]
+ config_link = self.config_vars[link_var]
+
+ # The dependent environment will have the compilation command set to
+ # the following:
+ new_compile = join_path(
+ spack.paths.build_env_path,
+ dependent_spec.package.compiler.link_paths[compile_var.lower()],
+ )
+
+ # Normally, the link command starts with the compilation command:
+ if config_link.startswith(config_compile):
+ new_link = new_compile + config_link[len(config_compile) :]
+ else:
+ # Otherwise, we try to replace the compiler command if it
+ # appears "in the middle" of the link command; to avoid
+ # mistaking some substring of a path for the compiler (e.g. to
+ # avoid replacing "gcc" in "-L/path/to/gcc/"), we require that
+ # the compiler command be surrounded by spaces. Note this may
+ # leave "config_link" unchanged if the compilation command does
+ # not appear in the link command at all, for example if "ld" is
+ # invoked directly (no change would be required in that case
+ # because Spack arranges for the Spack ld wrapper to be the
+ # first instance of "ld" in PATH).
+ new_link = config_link.replace(f" {config_compile} ", f" {new_compile} ")
+
+ # There is logic in the sysconfig module that is sensitive to the
+ # fact that LDSHARED is set in the environment, therefore we export
+ # the variable only if the new value is different from what we got
+ # from the sysconfigdata file:
+ if config_link != new_link and sys.platform != "win32":
+ env.set(link_var, new_link)
+
+ def setup_dependent_run_environment(self, env, dependent_spec):
+ """Set PYTHONPATH to include the site-packages directory for the
+ extension and any other python extensions it depends on.
+ """
+ if not dependent_spec.package.extends(self.spec) or dependent_spec.dependencies(
+ "python-venv"
+ ):
+ return
+
+ # Packages may be installed in platform-specific or platform-independent site-packages
+ # directories
+ for directory in {self.platlib, self.purelib}:
+ env.prepend_path("PYTHONPATH", os.path.join(dependent_spec.prefix, directory))
+
+ def setup_dependent_package(self, module, dependent_spec):
+ """Called before python modules' install() methods."""
+ module.python = self.command
+ module.python_include = join_path(dependent_spec.prefix, self.include)
+ module.python_platlib = join_path(dependent_spec.prefix, self.platlib)
+ module.python_purelib = join_path(dependent_spec.prefix, self.purelib)
+
+ def add_files_to_view(self, view, merge_map, skip_if_exists=True):
+ """Make the view a virtual environment if it isn't one already.
+
+ If `python-venv` is linked into the view, it will already be a virtual
+ environment. If not, then this is an older python that doesn't use the
+ python-venv support, or we may be using python packages that
+ use ``depends_on("python")`` but not ``extends("python")``.
+
+ We used to copy the python interpreter in, but we can get the same effect in a
+ simpler way by adding a ``pyvenv.cfg`` to the environment.
+
+ """
+ super().add_files_to_view(view, merge_map, skip_if_exists=skip_if_exists)
+
+ # location of python inside the view, where we will put the venv config
+ projection = view.get_projection_for_spec(self.spec)
+ pyvenv_cfg = os.path.join(projection, "pyvenv.cfg")
+ if os.path.lexists(pyvenv_cfg):
+ return
+
+ # don't put a pyvenv.cfg in a copy view
+ if view.link_type == "copy":
+ return
+
+ with open(pyvenv_cfg, "w") as cfg_file:
+ cfg_file.write(make_pyvenv_cfg(self.spec["python"], projection))
+
+ def test_hello_world(self):
+ """run simple hello world program"""
+ # do not use self.command because we are also testing the run env
+ python = self.spec["python"].command
+
+ msg = "hello world!"
+ out = python("-c", f'print("{msg}")', output=str.split, error=str.split)
+ assert msg in out
+
+ def test_import_executable(self):
+ """ensure import of installed executable works"""
+ python = self.spec["python"].command
+
+ out = python("-c", "import sys; print(sys.executable)", output=str.split, error=str.split)
+ assert self.spec.prefix in out
diff --git a/packages/python/python-3.11-distutils-C++.patch b/packages/python/python-3.11-distutils-C++.patch
new file mode 100644
index 00000000..335e06b9
--- /dev/null
+++ b/packages/python/python-3.11-distutils-C++.patch
@@ -0,0 +1,257 @@
+diff --git a/Lib/_osx_support.py b/Lib/_osx_support.py
+index aa66c8b9f4..71e6556bac 100644
+--- a/Lib/_osx_support.py
++++ b/Lib/_osx_support.py
+@@ -14,13 +14,13 @@
+ # configuration variables that may contain universal build flags,
+ # like "-arch" or "-isdkroot", that may need customization for
+ # the user environment
+-_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS', 'BASECFLAGS',
+- 'BLDSHARED', 'LDSHARED', 'CC', 'CXX',
+- 'PY_CFLAGS', 'PY_LDFLAGS', 'PY_CPPFLAGS',
+- 'PY_CORE_CFLAGS', 'PY_CORE_LDFLAGS')
++_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'CXXFLAGS', 'LDFLAGS', 'CPPFLAGS',
++ 'BASECFLAGS', 'BLDSHARED', 'LDSHARED', 'LDCXXSHARED',
++ 'CC', 'CXX', 'PY_CFLAGS', 'PY_LDFLAGS',
++ 'PY_CPPFLAGS', 'PY_CORE_LDFLAGS', 'PY_CORE_CFLAGS')
+
+ # configuration variables that may contain compiler calls
+-_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'CC', 'CXX')
++_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'LDCXXSHARED', 'CC', 'CXX')
+
+ # prefix added to original configuration variable names
+ _INITPRE = '_OSX_SUPPORT_INITIAL_'
+diff --git a/Lib/distutils/cygwinccompiler.py b/Lib/distutils/cygwinccompiler.py
+index 66c12dd358..dddb9fd2d4 100644
+--- a/Lib/distutils/cygwinccompiler.py
++++ b/Lib/distutils/cygwinccompiler.py
+@@ -123,8 +123,10 @@ def __init__(self, verbose=0, dry_run=0, force=0):
+ # dllwrap 2.10.90 is buggy
+ if self.ld_version >= "2.10.90":
+ self.linker_dll = "gcc"
++ self.linker_dll_cxx = "g++"
+ else:
+ self.linker_dll = "dllwrap"
++ self.linker_dll_cxx = "dllwrap"
+
+ # ld_version >= "2.13" support -shared so use it instead of
+ # -mdll -static
+@@ -138,9 +140,13 @@ def __init__(self, verbose=0, dry_run=0, force=0):
+ self.set_executables(compiler='gcc -mcygwin -O -Wall',
+ compiler_so='gcc -mcygwin -mdll -O -Wall',
+ compiler_cxx='g++ -mcygwin -O -Wall',
++ compiler_so_cxx='g++ -mcygwin -mdll -O -Wall',
+ linker_exe='gcc -mcygwin',
+ linker_so=('%s -mcygwin %s' %
+- (self.linker_dll, shared_option)))
++ (self.linker_dll, shared_option)),
++ linker_exe_cxx='g++ -mcygwin',
++ linker_so_cxx=('%s -mcygwin %s' %
++ (self.linker_dll_cxx, shared_option)))
+
+ # cygwin and mingw32 need different sets of libraries
+ if self.gcc_version == "2.91.57":
+@@ -164,8 +170,12 @@ def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+ raise CompileError(msg)
+ else: # for other files use the C-compiler
+ try:
+- self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+- extra_postargs)
++ if self.detect_language(src) == 'c++':
++ self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++ extra_postargs)
++ else:
++ self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++ extra_postargs)
+ except DistutilsExecError as msg:
+ raise CompileError(msg)
+
+@@ -300,9 +310,14 @@ def __init__(self, verbose=0, dry_run=0, force=0):
+ self.set_executables(compiler='gcc -O -Wall',
+ compiler_so='gcc -mdll -O -Wall',
+ compiler_cxx='g++ -O -Wall',
++ compiler_so_cxx='g++ -mdll -O -Wall',
+ linker_exe='gcc',
+ linker_so='%s %s %s'
+ % (self.linker_dll, shared_option,
++ entry_point),
++ linker_exe_cxx='g++',
++ linker_so_cxx='%s %s %s'
++ % (self.linker_dll_cxx, shared_option,
+ entry_point))
+ # Maybe we should also append -mthreads, but then the finished
+ # dlls need another dll (mingwm10.dll see Mingw32 docs)
+diff --git a/Lib/distutils/sysconfig.py b/Lib/distutils/sysconfig.py
+index 3414a761e7..f1af560cc1 100644
+--- a/Lib/distutils/sysconfig.py
++++ b/Lib/distutils/sysconfig.py
+@@ -216,9 +216,11 @@ def customize_compiler(compiler):
+ _osx_support.customize_compiler(_config_vars)
+ _config_vars['CUSTOMIZED_OSX_COMPILER'] = 'True'
+
+- (cc, cxx, cflags, ccshared, ldshared, shlib_suffix, ar, ar_flags) = \
+- get_config_vars('CC', 'CXX', 'CFLAGS',
+- 'CCSHARED', 'LDSHARED', 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++ (cc, cxx, cflags, ccshared, ldshared, ldcxxshared, shlib_suffix, ar, ar_flags) = \
++ get_config_vars('CC', 'CXX', 'CFLAGS', 'CCSHARED', 'LDSHARED', 'LDCXXSHARED',
++ 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++
++ cxxflags = cflags
+
+ if 'CC' in os.environ:
+ newcc = os.environ['CC']
+@@ -233,19 +235,27 @@ def customize_compiler(compiler):
+ cxx = os.environ['CXX']
+ if 'LDSHARED' in os.environ:
+ ldshared = os.environ['LDSHARED']
++ if 'LDCXXSHARED' in os.environ:
++ ldcxxshared = os.environ['LDCXXSHARED']
+ if 'CPP' in os.environ:
+ cpp = os.environ['CPP']
+ else:
+ cpp = cc + " -E" # not always
+ if 'LDFLAGS' in os.environ:
+ ldshared = ldshared + ' ' + os.environ['LDFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['LDFLAGS']
+ if 'CFLAGS' in os.environ:
+- cflags = cflags + ' ' + os.environ['CFLAGS']
++ cflags = os.environ['CFLAGS']
+ ldshared = ldshared + ' ' + os.environ['CFLAGS']
++ if 'CXXFLAGS' in os.environ:
++ cxxflags = os.environ['CXXFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['CXXFLAGS']
+ if 'CPPFLAGS' in os.environ:
+ cpp = cpp + ' ' + os.environ['CPPFLAGS']
+ cflags = cflags + ' ' + os.environ['CPPFLAGS']
++ cxxflags = cxxflags + ' ' + os.environ['CPPFLAGS']
+ ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['CPPFLAGS']
+ if 'AR' in os.environ:
+ ar = os.environ['AR']
+ if 'ARFLAGS' in os.environ:
+@@ -254,13 +264,17 @@ def customize_compiler(compiler):
+ archiver = ar + ' ' + ar_flags
+
+ cc_cmd = cc + ' ' + cflags
++ cxx_cmd = cxx + ' ' + cxxflags
+ compiler.set_executables(
+ preprocessor=cpp,
+ compiler=cc_cmd,
+ compiler_so=cc_cmd + ' ' + ccshared,
+- compiler_cxx=cxx,
++ compiler_cxx=cxx_cmd,
++ compiler_so_cxx=cxx_cmd + ' ' + ccshared,
+ linker_so=ldshared,
+ linker_exe=cc,
++ linker_so_cxx=ldcxxshared,
++ linker_exe_cxx=cxx,
+ archiver=archiver)
+
+ compiler.shared_lib_extension = shlib_suffix
+diff --git a/Lib/distutils/unixccompiler.py b/Lib/distutils/unixccompiler.py
+index d00c48981e..4a3d271fee 100644
+--- a/Lib/distutils/unixccompiler.py
++++ b/Lib/distutils/unixccompiler.py
+@@ -52,14 +52,17 @@ class UnixCCompiler(CCompiler):
+ # are pretty generic; they will probably have to be set by an outsider
+ # (eg. using information discovered by the sysconfig about building
+ # Python extensions).
+- executables = {'preprocessor' : None,
+- 'compiler' : ["cc"],
+- 'compiler_so' : ["cc"],
+- 'compiler_cxx' : ["cc"],
+- 'linker_so' : ["cc", "-shared"],
+- 'linker_exe' : ["cc"],
+- 'archiver' : ["ar", "-cr"],
+- 'ranlib' : None,
++ executables = {'preprocessor' : None,
++ 'compiler' : ["cc"],
++ 'compiler_so' : ["cc"],
++ 'compiler_cxx' : ["c++"],
++ 'compiler_so_cxx' : ["c++"],
++ 'linker_so' : ["cc", "-shared"],
++ 'linker_exe' : ["cc"],
++ 'linker_so_cxx' : ["c++", "-shared"],
++ 'linker_exe_cxx' : ["c++"],
++ 'archiver' : ["ar", "-cr"],
++ 'ranlib' : None,
+ }
+
+ if sys.platform[:6] == "darwin":
+@@ -110,12 +113,19 @@ def preprocess(self, source, output_file=None, macros=None,
+
+ def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+ compiler_so = self.compiler_so
++ compiler_so_cxx = self.compiler_so_cxx
+ if sys.platform == 'darwin':
+ compiler_so = _osx_support.compiler_fixup(compiler_so,
+ cc_args + extra_postargs)
++ compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx,
++ cc_args + extra_postargs)
+ try:
+- self.spawn(compiler_so + cc_args + [src, '-o', obj] +
+- extra_postargs)
++ if self.detect_language(src) == 'c++':
++ self.spawn(compiler_so_cxx + cc_args + [src, '-o', obj] +
++ extra_postargs)
++ else:
++ self.spawn(compiler_so + cc_args + [src, '-o', obj] +
++ extra_postargs)
+ except DistutilsExecError as msg:
+ raise CompileError(msg)
+
+@@ -173,30 +183,16 @@ def link(self, target_desc, objects,
+ ld_args.extend(extra_postargs)
+ self.mkpath(os.path.dirname(output_filename))
+ try:
+- if target_desc == CCompiler.EXECUTABLE:
+- linker = self.linker_exe[:]
++ if target_lang == "c++":
++ if target_desc == CCompiler.EXECUTABLE:
++ linker = self.linker_exe_cxx[:]
++ else:
++ linker = self.linker_so_cxx[:]
+ else:
+- linker = self.linker_so[:]
+- if target_lang == "c++" and self.compiler_cxx:
+- # skip over environment variable settings if /usr/bin/env
+- # is used to set up the linker's environment.
+- # This is needed on OSX. Note: this assumes that the
+- # normal and C++ compiler have the same environment
+- # settings.
+- i = 0
+- if os.path.basename(linker[0]) == "env":
+- i = 1
+- while '=' in linker[i]:
+- i += 1
+-
+- if os.path.basename(linker[i]) == 'ld_so_aix':
+- # AIX platforms prefix the compiler with the ld_so_aix
+- # script, so we need to adjust our linker index
+- offset = 1
++ if target_desc == CCompiler.EXECUTABLE:
++ linker = self.linker_exe[:]
+ else:
+- offset = 0
+-
+- linker[i+offset] = self.compiler_cxx[i]
++ linker = self.linker_so[:]
+
+ if sys.platform == 'darwin':
+ linker = _osx_support.compiler_fixup(linker, ld_args)
+diff --git a/Makefile.pre.in b/Makefile.pre.in
+index f803391346..090f14c46c 100644
+--- a/Makefile.pre.in
++++ b/Makefile.pre.in
+@@ -732,9 +732,9 @@ sharedmods: $(BUILDPYTHON) pybuilddir.txt @LIBMPDEC_INTERNAL@ @LIBEXPAT_INTERNAL
+ *\ -s*|s*) quiet="-q";; \
+ *) quiet="";; \
+ esac; \
+- echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++ echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ $(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build"; \
+- $(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++ $(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ $(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build
+
+
diff --git a/packages/python/python-3.7.2-distutils-C++.patch b/packages/python/python-3.7.2-distutils-C++.patch
new file mode 100644
index 00000000..5728fad6
--- /dev/null
+++ b/packages/python/python-3.7.2-distutils-C++.patch
@@ -0,0 +1,241 @@
+--- a/Lib/_osx_support.py
++++ b/Lib/_osx_support.py
+@@ -14,13 +14,13 @@ __all__ = [
+ # configuration variables that may contain universal build flags,
+ # like "-arch" or "-isdkroot", that may need customization for
+ # the user environment
+-_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS', 'BASECFLAGS',
+- 'BLDSHARED', 'LDSHARED', 'CC', 'CXX',
+- 'PY_CFLAGS', 'PY_LDFLAGS', 'PY_CPPFLAGS',
+- 'PY_CORE_CFLAGS', 'PY_CORE_LDFLAGS')
++_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'CXXFLAGS', 'LDFLAGS', 'CPPFLAGS',
++ 'BASECFLAGS', 'BLDSHARED', 'LDSHARED', 'LDCXXSHARED',
++ 'CC', 'CXX', 'PY_CFLAGS', 'PY_LDFLAGS',
++ 'PY_CPPFLAGS', 'PY_CORE_LDFLAGS', 'PY_CORE_CFLAGS')
+
+ # configuration variables that may contain compiler calls
+-_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'CC', 'CXX')
++_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'LDCXXSHARED', 'CC', 'CXX')
+
+ # prefix added to original configuration variable names
+ _INITPRE = '_OSX_SUPPORT_INITIAL_'
+--- a/Lib/distutils/cygwinccompiler.py
++++ b/Lib/distutils/cygwinccompiler.py
+@@ -125,8 +125,10 @@ class CygwinCCompiler(UnixCCompiler):
+ # dllwrap 2.10.90 is buggy
+ if self.ld_version >= "2.10.90":
+ self.linker_dll = "gcc"
++ self.linker_dll_cxx = "g++"
+ else:
+ self.linker_dll = "dllwrap"
++ self.linker_dll_cxx = "dllwrap"
+
+ # ld_version >= "2.13" support -shared so use it instead of
+ # -mdll -static
+@@ -140,9 +142,13 @@ class CygwinCCompiler(UnixCCompiler):
+ self.set_executables(compiler='gcc -mcygwin -O -Wall',
+ compiler_so='gcc -mcygwin -mdll -O -Wall',
+ compiler_cxx='g++ -mcygwin -O -Wall',
++ compiler_so_cxx='g++ -mcygwin -mdll -O -Wall',
+ linker_exe='gcc -mcygwin',
+ linker_so=('%s -mcygwin %s' %
+- (self.linker_dll, shared_option)))
++ (self.linker_dll, shared_option)),
++ linker_exe_cxx='g++ -mcygwin',
++ linker_so_cxx=('%s -mcygwin %s' %
++ (self.linker_dll_cxx, shared_option)))
+
+ # cygwin and mingw32 need different sets of libraries
+ if self.gcc_version == "2.91.57":
+@@ -166,8 +172,12 @@ class CygwinCCompiler(UnixCCompiler):
+ raise CompileError(msg)
+ else: # for other files use the C-compiler
+ try:
+- self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+- extra_postargs)
++ if self.detect_language(src) == 'c++':
++ self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++ extra_postargs)
++ else:
++ self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++ extra_postargs)
+ except DistutilsExecError as msg:
+ raise CompileError(msg)
+
+@@ -302,9 +312,14 @@ class Mingw32CCompiler(CygwinCCompiler):
+ self.set_executables(compiler='gcc -O -Wall',
+ compiler_so='gcc -mdll -O -Wall',
+ compiler_cxx='g++ -O -Wall',
++ compiler_so_cxx='g++ -mdll -O -Wall',
+ linker_exe='gcc',
+ linker_so='%s %s %s'
+ % (self.linker_dll, shared_option,
++ entry_point),
++ linker_exe_cxx='g++',
++ linker_so_cxx='%s %s %s'
++ % (self.linker_dll_cxx, shared_option,
+ entry_point))
+ # Maybe we should also append -mthreads, but then the finished
+ # dlls need another dll (mingwm10.dll see Mingw32 docs)
+--- a/Lib/distutils/sysconfig.py
++++ b/Lib/distutils/sysconfig.py
+@@ -170,9 +170,11 @@ def customize_compiler(compiler):
+ _osx_support.customize_compiler(_config_vars)
+ _config_vars['CUSTOMIZED_OSX_COMPILER'] = 'True'
+
+- (cc, cxx, opt, cflags, ccshared, ldshared, shlib_suffix, ar, ar_flags) = \
+- get_config_vars('CC', 'CXX', 'OPT', 'CFLAGS',
+- 'CCSHARED', 'LDSHARED', 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++ (cc, cxx, cflags, ccshared, ldshared, ldcxxshared, shlib_suffix, ar, ar_flags) = \
++ get_config_vars('CC', 'CXX', 'CFLAGS', 'CCSHARED', 'LDSHARED', 'LDCXXSHARED',
++ 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++
++ cxxflags = cflags
+
+ if 'CC' in os.environ:
+ newcc = os.environ['CC']
+@@ -187,19 +189,27 @@ def customize_compiler(compiler):
+ cxx = os.environ['CXX']
+ if 'LDSHARED' in os.environ:
+ ldshared = os.environ['LDSHARED']
++ if 'LDCXXSHARED' in os.environ:
++ ldcxxshared = os.environ['LDCXXSHARED']
+ if 'CPP' in os.environ:
+ cpp = os.environ['CPP']
+ else:
+ cpp = cc + " -E" # not always
+ if 'LDFLAGS' in os.environ:
+ ldshared = ldshared + ' ' + os.environ['LDFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['LDFLAGS']
+ if 'CFLAGS' in os.environ:
+- cflags = opt + ' ' + os.environ['CFLAGS']
++ cflags = os.environ['CFLAGS']
+ ldshared = ldshared + ' ' + os.environ['CFLAGS']
++ if 'CXXFLAGS' in os.environ:
++ cxxflags = os.environ['CXXFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['CXXFLAGS']
+ if 'CPPFLAGS' in os.environ:
+ cpp = cpp + ' ' + os.environ['CPPFLAGS']
+ cflags = cflags + ' ' + os.environ['CPPFLAGS']
++ cxxflags = cxxflags + ' ' + os.environ['CPPFLAGS']
+ ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['CPPFLAGS']
+ if 'AR' in os.environ:
+ ar = os.environ['AR']
+ if 'ARFLAGS' in os.environ:
+@@ -208,13 +218,17 @@ def customize_compiler(compiler):
+ archiver = ar + ' ' + ar_flags
+
+ cc_cmd = cc + ' ' + cflags
++ cxx_cmd = cxx + ' ' + cxxflags
+ compiler.set_executables(
+ preprocessor=cpp,
+ compiler=cc_cmd,
+ compiler_so=cc_cmd + ' ' + ccshared,
+- compiler_cxx=cxx,
++ compiler_cxx=cxx_cmd,
++ compiler_so_cxx=cxx_cmd + ' ' + ccshared,
+ linker_so=ldshared,
+ linker_exe=cc,
++ linker_so_cxx=ldcxxshared,
++ linker_exe_cxx=cxx,
+ archiver=archiver)
+
+ compiler.shared_lib_extension = shlib_suffix
+--- a/Lib/distutils/unixccompiler.py
++++ b/Lib/distutils/unixccompiler.py
+@@ -52,14 +52,17 @@ class UnixCCompiler(CCompiler):
+ # are pretty generic; they will probably have to be set by an outsider
+ # (eg. using information discovered by the sysconfig about building
+ # Python extensions).
+- executables = {'preprocessor' : None,
+- 'compiler' : ["cc"],
+- 'compiler_so' : ["cc"],
+- 'compiler_cxx' : ["cc"],
+- 'linker_so' : ["cc", "-shared"],
+- 'linker_exe' : ["cc"],
+- 'archiver' : ["ar", "-cr"],
+- 'ranlib' : None,
++ executables = {'preprocessor' : None,
++ 'compiler' : ["cc"],
++ 'compiler_so' : ["cc"],
++ 'compiler_cxx' : ["c++"],
++ 'compiler_so_cxx' : ["c++"],
++ 'linker_so' : ["cc", "-shared"],
++ 'linker_exe' : ["cc"],
++ 'linker_so_cxx' : ["c++", "-shared"],
++ 'linker_exe_cxx' : ["c++"],
++ 'archiver' : ["ar", "-cr"],
++ 'ranlib' : None,
+ }
+
+ if sys.platform[:6] == "darwin":
+@@ -110,12 +113,19 @@ class UnixCCompiler(CCompiler):
+
+ def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+ compiler_so = self.compiler_so
++ compiler_so_cxx = self.compiler_so_cxx
+ if sys.platform == 'darwin':
+ compiler_so = _osx_support.compiler_fixup(compiler_so,
+ cc_args + extra_postargs)
++ compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx,
++ cc_args + extra_postargs)
+ try:
+- self.spawn(compiler_so + cc_args + [src, '-o', obj] +
+- extra_postargs)
++ if self.detect_language(src) == 'c++':
++ self.spawn(compiler_so_cxx + cc_args + [src, '-o', obj] +
++ extra_postargs)
++ else:
++ self.spawn(compiler_so + cc_args + [src, '-o', obj] +
++ extra_postargs)
+ except DistutilsExecError as msg:
+ raise CompileError(msg)
+
+@@ -173,22 +183,16 @@ class UnixCCompiler(CCompiler):
+ ld_args.extend(extra_postargs)
+ self.mkpath(os.path.dirname(output_filename))
+ try:
+- if target_desc == CCompiler.EXECUTABLE:
+- linker = self.linker_exe[:]
++ if target_lang == "c++":
++ if target_desc == CCompiler.EXECUTABLE:
++ linker = self.linker_exe_cxx[:]
++ else:
++ linker = self.linker_so_cxx[:]
+ else:
+- linker = self.linker_so[:]
+- if target_lang == "c++" and self.compiler_cxx:
+- # skip over environment variable settings if /usr/bin/env
+- # is used to set up the linker's environment.
+- # This is needed on OSX. Note: this assumes that the
+- # normal and C++ compiler have the same environment
+- # settings.
+- i = 0
+- if os.path.basename(linker[0]) == "env":
+- i = 1
+- while '=' in linker[i]:
+- i += 1
+- linker[i] = self.compiler_cxx[i]
++ if target_desc == CCompiler.EXECUTABLE:
++ linker = self.linker_exe[:]
++ else:
++ linker = self.linker_so[:]
+
+ if sys.platform == 'darwin':
+ linker = _osx_support.compiler_fixup(linker, ld_args)
+--- a/Makefile.pre.in
++++ b/Makefile.pre.in
+@@ -584,10 +584,10 @@ sharedmods: $(BUILDPYTHON) pybuilddir.txt Modules/_math.o
+ *\ -s*|s*) quiet="-q";; \
+ *) quiet="";; \
+ esac; \
+- echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++ echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ _TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ $(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build"; \
+- $(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++ $(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ _TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ $(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build
+
diff --git a/packages/python/python-3.7.3-distutils-C++.patch b/packages/python/python-3.7.3-distutils-C++.patch
new file mode 100644
index 00000000..e29323bf
--- /dev/null
+++ b/packages/python/python-3.7.3-distutils-C++.patch
@@ -0,0 +1,256 @@
+diff --git a/Lib/_osx_support.py b/Lib/_osx_support.py
+index db6674e..ccbe09a 100644
+--- a/Lib/_osx_support.py
++++ b/Lib/_osx_support.py
+@@ -14,13 +14,13 @@ __all__ = [
+ # configuration variables that may contain universal build flags,
+ # like "-arch" or "-isdkroot", that may need customization for
+ # the user environment
+-_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS', 'BASECFLAGS',
+- 'BLDSHARED', 'LDSHARED', 'CC', 'CXX',
+- 'PY_CFLAGS', 'PY_LDFLAGS', 'PY_CPPFLAGS',
+- 'PY_CORE_CFLAGS', 'PY_CORE_LDFLAGS')
++_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'CXXFLAGS', 'LDFLAGS', 'CPPFLAGS',
++ 'BASECFLAGS', 'BLDSHARED', 'LDSHARED', 'LDCXXSHARED',
++ 'CC', 'CXX', 'PY_CFLAGS', 'PY_LDFLAGS',
++ 'PY_CPPFLAGS', 'PY_CORE_LDFLAGS', 'PY_CORE_CFLAGS')
+
+ # configuration variables that may contain compiler calls
+-_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'CC', 'CXX')
++_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'LDCXXSHARED', 'CC', 'CXX')
+
+ # prefix added to original configuration variable names
+ _INITPRE = '_OSX_SUPPORT_INITIAL_'
+diff --git a/Lib/distutils/cygwinccompiler.py b/Lib/distutils/cygwinccompiler.py
+index 6c5d777..640fa2d 100644
+--- a/Lib/distutils/cygwinccompiler.py
++++ b/Lib/distutils/cygwinccompiler.py
+@@ -125,8 +125,10 @@ class CygwinCCompiler(UnixCCompiler):
+ # dllwrap 2.10.90 is buggy
+ if self.ld_version >= "2.10.90":
+ self.linker_dll = "gcc"
++ self.linker_dll_cxx = "g++"
+ else:
+ self.linker_dll = "dllwrap"
++ self.linker_dll_cxx = "dllwrap"
+
+ # ld_version >= "2.13" support -shared so use it instead of
+ # -mdll -static
+@@ -140,9 +142,13 @@ class CygwinCCompiler(UnixCCompiler):
+ self.set_executables(compiler='gcc -mcygwin -O -Wall',
+ compiler_so='gcc -mcygwin -mdll -O -Wall',
+ compiler_cxx='g++ -mcygwin -O -Wall',
++ compiler_so_cxx='g++ -mcygwin -mdll -O -Wall',
+ linker_exe='gcc -mcygwin',
+ linker_so=('%s -mcygwin %s' %
+- (self.linker_dll, shared_option)))
++ (self.linker_dll, shared_option)),
++ linker_exe_cxx='g++ -mcygwin',
++ linker_so_cxx=('%s -mcygwin %s' %
++ (self.linker_dll_cxx, shared_option)))
+
+ # cygwin and mingw32 need different sets of libraries
+ if self.gcc_version == "2.91.57":
+@@ -166,8 +172,12 @@ class CygwinCCompiler(UnixCCompiler):
+ raise CompileError(msg)
+ else: # for other files use the C-compiler
+ try:
+- self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+- extra_postargs)
++ if self.detect_language(src) == 'c++':
++ self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++ extra_postargs)
++ else:
++ self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++ extra_postargs)
+ except DistutilsExecError as msg:
+ raise CompileError(msg)
+
+@@ -302,9 +312,14 @@ class Mingw32CCompiler(CygwinCCompiler):
+ self.set_executables(compiler='gcc -O -Wall',
+ compiler_so='gcc -mdll -O -Wall',
+ compiler_cxx='g++ -O -Wall',
++ compiler_so_cxx='g++ -mdll -O -Wall',
+ linker_exe='gcc',
+ linker_so='%s %s %s'
+ % (self.linker_dll, shared_option,
++ entry_point),
++ linker_exe_cxx='g++',
++ linker_so_cxx='%s %s %s'
++ % (self.linker_dll_cxx, shared_option,
+ entry_point))
+ # Maybe we should also append -mthreads, but then the finished
+ # dlls need another dll (mingwm10.dll see Mingw32 docs)
+diff --git a/Lib/distutils/sysconfig.py b/Lib/distutils/sysconfig.py
+index 83160f8..b735369 100644
+--- a/Lib/distutils/sysconfig.py
++++ b/Lib/distutils/sysconfig.py
+@@ -183,9 +183,11 @@ def customize_compiler(compiler):
+ _osx_support.customize_compiler(_config_vars)
+ _config_vars['CUSTOMIZED_OSX_COMPILER'] = 'True'
+
+- (cc, cxx, opt, cflags, ccshared, ldshared, shlib_suffix, ar, ar_flags) = \
++ (cc, cxx, opt, cflags, ccshared, ldshared, ldcxxshared, shlib_suffix, ar, ar_flags) = \
+ get_config_vars('CC', 'CXX', 'OPT', 'CFLAGS',
+- 'CCSHARED', 'LDSHARED', 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++ 'CCSHARED', 'LDSHARED', 'LDCXXSHARED', 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++
++ cxxflags = cflags
+
+ if 'CC' in os.environ:
+ newcc = os.environ['CC']
+@@ -200,19 +202,27 @@ def customize_compiler(compiler):
+ cxx = os.environ['CXX']
+ if 'LDSHARED' in os.environ:
+ ldshared = os.environ['LDSHARED']
++ if 'LDCXXSHARED' in os.environ:
++ ldcxxshared = os.environ['LDCXXSHARED']
+ if 'CPP' in os.environ:
+ cpp = os.environ['CPP']
+ else:
+ cpp = cc + " -E" # not always
+ if 'LDFLAGS' in os.environ:
+ ldshared = ldshared + ' ' + os.environ['LDFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['LDFLAGS']
+ if 'CFLAGS' in os.environ:
+ cflags = opt + ' ' + os.environ['CFLAGS']
+ ldshared = ldshared + ' ' + os.environ['CFLAGS']
++ if 'CXXFLAGS' in os.environ:
++ cxxflags = opt + ' ' + os.environ['CXXFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['CXXFLAGS']
+ if 'CPPFLAGS' in os.environ:
+ cpp = cpp + ' ' + os.environ['CPPFLAGS']
++ cxxflags = cxxflags + ' ' + os.environ['CPPFLAGS']
+ cflags = cflags + ' ' + os.environ['CPPFLAGS']
+ ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['CPPFLAGS']
+ if 'AR' in os.environ:
+ ar = os.environ['AR']
+ if 'ARFLAGS' in os.environ:
+@@ -221,13 +231,17 @@ def customize_compiler(compiler):
+ archiver = ar + ' ' + ar_flags
+
+ cc_cmd = cc + ' ' + cflags
++ cxx_cmd = cxx + ' ' + cxxflags
+ compiler.set_executables(
+ preprocessor=cpp,
+ compiler=cc_cmd,
+ compiler_so=cc_cmd + ' ' + ccshared,
+- compiler_cxx=cxx,
++ compiler_cxx=cxx_cmd,
++ compiler_so_cxx=cxx_cmd + ' ' + ccshared,
+ linker_so=ldshared,
+ linker_exe=cc,
++ linker_so_cxx=ldcxxshared,
++ linker_exe_cxx=cxx,
+ archiver=archiver)
+
+ compiler.shared_lib_extension = shlib_suffix
+diff --git a/Lib/distutils/unixccompiler.py b/Lib/distutils/unixccompiler.py
+index d10a78d..7e88781 100644
+--- a/Lib/distutils/unixccompiler.py
++++ b/Lib/distutils/unixccompiler.py
+@@ -52,14 +52,17 @@ class UnixCCompiler(CCompiler):
+ # are pretty generic; they will probably have to be set by an outsider
+ # (eg. using information discovered by the sysconfig about building
+ # Python extensions).
+- executables = {'preprocessor' : None,
+- 'compiler' : ["cc"],
+- 'compiler_so' : ["cc"],
+- 'compiler_cxx' : ["cc"],
+- 'linker_so' : ["cc", "-shared"],
+- 'linker_exe' : ["cc"],
+- 'archiver' : ["ar", "-cr"],
+- 'ranlib' : None,
++ executables = {'preprocessor' : None,
++ 'compiler' : ["cc"],
++ 'compiler_so' : ["cc"],
++ 'compiler_cxx' : ["c++"],
++ 'compiler_so_cxx' : ["c++"],
++ 'linker_so' : ["cc", "-shared"],
++ 'linker_exe' : ["cc"],
++ 'linker_so_cxx' : ["c++", "-shared"],
++ 'linker_exe_cxx' : ["c++"],
++ 'archiver' : ["ar", "-cr"],
++ 'ranlib' : None,
+ }
+
+ if sys.platform[:6] == "darwin":
+@@ -110,12 +113,19 @@ class UnixCCompiler(CCompiler):
+
+ def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+ compiler_so = self.compiler_so
++ compiler_so_cxx = self.compiler_so_cxx
+ if sys.platform == 'darwin':
+ compiler_so = _osx_support.compiler_fixup(compiler_so,
+ cc_args + extra_postargs)
++ compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx,
++ cc_args + extra_postargs)
+ try:
+- self.spawn(compiler_so + cc_args + [src, '-o', obj] +
+- extra_postargs)
++ if self.detect_language(src) == 'c++':
++ self.spawn(compiler_so_cxx + cc_args + [src, '-o', obj] +
++ extra_postargs)
++ else:
++ self.spawn(compiler_so + cc_args + [src, '-o', obj] +
++ extra_postargs)
+ except DistutilsExecError as msg:
+ raise CompileError(msg)
+
+@@ -173,30 +183,16 @@ class UnixCCompiler(CCompiler):
+ ld_args.extend(extra_postargs)
+ self.mkpath(os.path.dirname(output_filename))
+ try:
+- if target_desc == CCompiler.EXECUTABLE:
+- linker = self.linker_exe[:]
++ if target_lang == "c++":
++ if target_desc == CCompiler.EXECUTABLE:
++ linker = self.linker_exe_cxx[:]
++ else:
++ linker = self.linker_so_cxx[:]
+ else:
+- linker = self.linker_so[:]
+- if target_lang == "c++" and self.compiler_cxx:
+- # skip over environment variable settings if /usr/bin/env
+- # is used to set up the linker's environment.
+- # This is needed on OSX. Note: this assumes that the
+- # normal and C++ compiler have the same environment
+- # settings.
+- i = 0
+- if os.path.basename(linker[0]) == "env":
+- i = 1
+- while '=' in linker[i]:
+- i += 1
+-
+- if os.path.basename(linker[i]) == 'ld_so_aix':
+- # AIX platforms prefix the compiler with the ld_so_aix
+- # script, so we need to adjust our linker index
+- offset = 1
++ if target_desc == CCompiler.EXECUTABLE:
++ linker = self.linker_exe[:]
+ else:
+- offset = 0
+-
+- linker[i+offset] = self.compiler_cxx[i]
++ linker = self.linker_so[:]
+
+ if sys.platform == 'darwin':
+ linker = _osx_support.compiler_fixup(linker, ld_args)
+diff --git a/Makefile.pre.in b/Makefile.pre.in
+index 2d2e11f..8456e3f 100644
+--- a/Makefile.pre.in
++++ b/Makefile.pre.in
+@@ -615,10 +615,10 @@ sharedmods: $(BUILDPYTHON) pybuilddir.txt Modules/_math.o
+ *\ -s*|s*) quiet="-q";; \
+ *) quiet="";; \
+ esac; \
+- echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++ echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ _TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ $(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build"; \
+- $(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++ $(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ _TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ $(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build
+
diff --git a/packages/python/python-3.7.4+-distutils-C++-testsuite.patch b/packages/python/python-3.7.4+-distutils-C++-testsuite.patch
new file mode 100644
index 00000000..99361087
--- /dev/null
+++ b/packages/python/python-3.7.4+-distutils-C++-testsuite.patch
@@ -0,0 +1,138 @@
+This patch updates the distutils test suite for:
+var/spack/repos/builtin/packages/python/python-3.7.4+-distutils-C++.patch
+
+That patch fixes several shortcomings in the distutils C++ support,
+most prominently missing support for passing CXXFLAGS from the environment.
+
+Since it does not update the distutils testsuite, it causes the testsuite
+to fail, which this patch updates to pass.
+
+-----------------------------------------------------------------------------
+Spack changelog
+- Added patch header to aid understanding the patch and maintainance
+- Updated the distutils testsuite in Lib/distutils/tests/test_sysconfig.py
+
+-----------------------------------------------------------------------------
+Upstream status
+
+Upstream bug: https://bugs.python.org/issue1222585
+
+Status: Closed, wont fix, comment by Eric Araujo, Python Core Dev:
+"setuptools and other active build tools are the better target for this feature."
+https://bugs.python.org/issue1222585#msg379348
+
+But according to the last-but-oncomment, setuptools seems to be lacking there too.
+https://bugs.python.org/issue1222585#msg371840
+
+-----------------------------------------------------------------------------
+Description
+
+distutils has no support for CXXFLAGS, this patch adds it.
+
+Upstream distutils requires to pass all CXXFLAGS (C++-specific CFLAGS)
+as part of the CXX enviromnent variable instead.
+
+This patch:
+- adds CXXFLAGS support
+- adds LDCXXSHARED like LDSHARED
+- passes cflags to CXX like it passes them to CC.
+
+The distutils testsuite is updated accordingly to pass the tests.
+Since it passes, it is the authoritative info of the current effects of this patch.
+
+See the update of the distutils testsuite in Lib/distutils/tests/test_sysconfig.py
+below for details on the effect of this patch.
+
+diff --git a/Lib/distutils/tests/test_sysconfig.py b/Lib/distutils/tests/test_sysconfig.py
+index db6674e..ccbe09a 100644
+--- a/Lib/distutils/tests/test_sysconfig.py
++++ b/Lib/distutils/tests/test_sysconfig.py
+@@ -89,8 +89,10 @@
+ 'CXX': 'sc_cxx',
+ 'ARFLAGS': '--sc-arflags',
+ 'CFLAGS': '--sc-cflags',
++ 'CXXFLAGS': '--sc-cxxflags',
+ 'CCSHARED': '--sc-ccshared',
+ 'LDSHARED': 'sc_ldshared',
++ 'LDCXXSHARED': 'sc_ldshared_cxx',
+ 'SHLIB_SUFFIX': 'sc_shutil_suffix',
+
+ # On macOS, disable _osx_support.customize_compiler()
+@@ -114,11 +116,13 @@
+ os.environ['AR'] = 'env_ar'
+ os.environ['CC'] = 'env_cc'
+ os.environ['CPP'] = 'env_cpp'
+- os.environ['CXX'] = 'env_cxx --env-cxx-flags'
++ os.environ['CXX'] = 'env_cxx'
+ os.environ['LDSHARED'] = 'env_ldshared'
++ os.environ['LDCXXSHARED'] = 'env_ldshared_cxx'
+ os.environ['LDFLAGS'] = '--env-ldflags'
+ os.environ['ARFLAGS'] = '--env-arflags'
+ os.environ['CFLAGS'] = '--env-cflags'
++ os.environ['CXXFLAGS'] = '--env-cxxflags'
+ os.environ['CPPFLAGS'] = '--env-cppflags'
+
+ comp = self.customize_compiler()
+@@ -128,16 +132,24 @@
+ 'env_cpp --env-cppflags')
+ self.assertEqual(comp.exes['compiler'],
+ 'env_cc --sc-cflags --env-cflags --env-cppflags')
++ self.assertEqual(comp.exes['compiler_cxx'],
++ 'env_cxx --sc-cflags --env-cxxflags --env-cppflags')
+ self.assertEqual(comp.exes['compiler_so'],
+ ('env_cc --sc-cflags '
+ '--env-cflags ''--env-cppflags --sc-ccshared'))
+- self.assertEqual(comp.exes['compiler_cxx'],
+- 'env_cxx --env-cxx-flags')
++ self.assertEqual(comp.exes['compiler_so_cxx'],
++ ('env_cxx --sc-cflags '
++ '--env-cxxflags ''--env-cppflags --sc-ccshared'))
+ self.assertEqual(comp.exes['linker_exe'],
+ 'env_cc')
++ self.assertEqual(comp.exes['linker_exe_cxx'],
++ 'env_cxx')
+ self.assertEqual(comp.exes['linker_so'],
+ ('env_ldshared --env-ldflags --env-cflags'
+ ' --env-cppflags'))
++ self.assertEqual(comp.exes['linker_so_cxx'],
++ ('env_ldshared_cxx --env-ldflags --env-cxxflags'
++ ' --env-cppflags'))
+ self.assertEqual(comp.shared_lib_extension, 'sc_shutil_suffix')
+
+ del os.environ['AR']
+@@ -145,9 +157,11 @@
+ del os.environ['CPP']
+ del os.environ['CXX']
+ del os.environ['LDSHARED']
++ del os.environ['LDCXXSHARED']
+ del os.environ['LDFLAGS']
+ del os.environ['ARFLAGS']
+ del os.environ['CFLAGS']
++ del os.environ['CXXFLAGS']
+ del os.environ['CPPFLAGS']
+
+ comp = self.customize_compiler()
+@@ -157,14 +171,21 @@
+ 'sc_cc -E')
+ self.assertEqual(comp.exes['compiler'],
+ 'sc_cc --sc-cflags')
++ # TODO: Likely this sould get --sc-cxxflags instead:
++ self.assertEqual(comp.exes['compiler_cxx'],
++ 'sc_cxx --sc-cflags')
+ self.assertEqual(comp.exes['compiler_so'],
+ 'sc_cc --sc-cflags --sc-ccshared')
+- self.assertEqual(comp.exes['compiler_cxx'],
+- 'sc_cxx')
++ self.assertEqual(comp.exes['compiler_so_cxx'],
++ 'sc_cxx --sc-cflags --sc-ccshared')
+ self.assertEqual(comp.exes['linker_exe'],
+ 'sc_cc')
++ self.assertEqual(comp.exes['linker_exe_cxx'],
++ 'sc_cxx')
+ self.assertEqual(comp.exes['linker_so'],
+ 'sc_ldshared')
++ self.assertEqual(comp.exes['linker_so_cxx'],
++ 'sc_ldshared_cxx')
+ self.assertEqual(comp.shared_lib_extension, 'sc_shutil_suffix')
+
+ def test_parse_makefile_base(self):
diff --git a/packages/python/python-3.7.4+-distutils-C++.patch b/packages/python/python-3.7.4+-distutils-C++.patch
new file mode 100644
index 00000000..02daf0a1
--- /dev/null
+++ b/packages/python/python-3.7.4+-distutils-C++.patch
@@ -0,0 +1,257 @@
+diff --git a/Lib/_osx_support.py b/Lib/_osx_support.py
+index db6674e..ccbe09a 100644
+--- a/Lib/_osx_support.py
++++ b/Lib/_osx_support.py
+@@ -14,13 +14,13 @@ __all__ = [
+ # configuration variables that may contain universal build flags,
+ # like "-arch" or "-isdkroot", that may need customization for
+ # the user environment
+-_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'LDFLAGS', 'CPPFLAGS', 'BASECFLAGS',
+- 'BLDSHARED', 'LDSHARED', 'CC', 'CXX',
+- 'PY_CFLAGS', 'PY_LDFLAGS', 'PY_CPPFLAGS',
+- 'PY_CORE_CFLAGS', 'PY_CORE_LDFLAGS')
++_UNIVERSAL_CONFIG_VARS = ('CFLAGS', 'CXXFLAGS', 'LDFLAGS', 'CPPFLAGS',
++ 'BASECFLAGS', 'BLDSHARED', 'LDSHARED', 'LDCXXSHARED',
++ 'CC', 'CXX', 'PY_CFLAGS', 'PY_LDFLAGS',
++ 'PY_CPPFLAGS', 'PY_CORE_LDFLAGS', 'PY_CORE_CFLAGS')
+
+ # configuration variables that may contain compiler calls
+-_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'CC', 'CXX')
++_COMPILER_CONFIG_VARS = ('BLDSHARED', 'LDSHARED', 'LDCXXSHARED', 'CC', 'CXX')
+
+ # prefix added to original configuration variable names
+ _INITPRE = '_OSX_SUPPORT_INITIAL_'
+diff --git a/Lib/distutils/cygwinccompiler.py b/Lib/distutils/cygwinccompiler.py
+index 6c5d777..640fa2d 100644
+--- a/Lib/distutils/cygwinccompiler.py
++++ b/Lib/distutils/cygwinccompiler.py
+@@ -125,8 +125,10 @@ class CygwinCCompiler(UnixCCompiler):
+ # dllwrap 2.10.90 is buggy
+ if self.ld_version >= "2.10.90":
+ self.linker_dll = "gcc"
++ self.linker_dll_cxx = "g++"
+ else:
+ self.linker_dll = "dllwrap"
++ self.linker_dll_cxx = "dllwrap"
+
+ # ld_version >= "2.13" support -shared so use it instead of
+ # -mdll -static
+@@ -140,9 +142,13 @@ class CygwinCCompiler(UnixCCompiler):
+ self.set_executables(compiler='gcc -mcygwin -O -Wall',
+ compiler_so='gcc -mcygwin -mdll -O -Wall',
+ compiler_cxx='g++ -mcygwin -O -Wall',
++ compiler_so_cxx='g++ -mcygwin -mdll -O -Wall',
+ linker_exe='gcc -mcygwin',
+ linker_so=('%s -mcygwin %s' %
+- (self.linker_dll, shared_option)))
++ (self.linker_dll, shared_option)),
++ linker_exe_cxx='g++ -mcygwin',
++ linker_so_cxx=('%s -mcygwin %s' %
++ (self.linker_dll_cxx, shared_option)))
+
+ # cygwin and mingw32 need different sets of libraries
+ if self.gcc_version == "2.91.57":
+@@ -166,8 +172,12 @@ class CygwinCCompiler(UnixCCompiler):
+ raise CompileError(msg)
+ else: # for other files use the C-compiler
+ try:
+- self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+- extra_postargs)
++ if self.detect_language(src) == 'c++':
++ self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++ extra_postargs)
++ else:
++ self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++ extra_postargs)
+ except DistutilsExecError as msg:
+ raise CompileError(msg)
+
+@@ -302,9 +312,14 @@ class Mingw32CCompiler(CygwinCCompiler):
+ self.set_executables(compiler='gcc -O -Wall',
+ compiler_so='gcc -mdll -O -Wall',
+ compiler_cxx='g++ -O -Wall',
++ compiler_so_cxx='g++ -mdll -O -Wall',
+ linker_exe='gcc',
+ linker_so='%s %s %s'
+ % (self.linker_dll, shared_option,
++ entry_point),
++ linker_exe_cxx='g++',
++ linker_so_cxx='%s %s %s'
++ % (self.linker_dll_cxx, shared_option,
+ entry_point))
+ # Maybe we should also append -mthreads, but then the finished
+ # dlls need another dll (mingwm10.dll see Mingw32 docs)
+diff --git a/Lib/distutils/sysconfig.py b/Lib/distutils/sysconfig.py
+index 0a034ee..ecf4759 100644
+--- a/Lib/distutils/sysconfig.py
++++ b/Lib/distutils/sysconfig.py
+@@ -188,9 +188,11 @@ def customize_compiler(compiler):
+ _osx_support.customize_compiler(_config_vars)
+ _config_vars['CUSTOMIZED_OSX_COMPILER'] = 'True'
+
+- (cc, cxx, cflags, ccshared, ldshared, shlib_suffix, ar, ar_flags) = \
+- get_config_vars('CC', 'CXX', 'CFLAGS',
+- 'CCSHARED', 'LDSHARED', 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++ (cc, cxx, cflags, ccshared, ldshared, ldcxxshared, shlib_suffix, ar, ar_flags) = \
++ get_config_vars('CC', 'CXX', 'CFLAGS', 'CCSHARED', 'LDSHARED', 'LDCXXSHARED',
++ 'SHLIB_SUFFIX', 'AR', 'ARFLAGS')
++
++ cxxflags = cflags
+
+ if 'CC' in os.environ:
+ newcc = os.environ['CC']
+@@ -205,19 +207,27 @@ def customize_compiler(compiler):
+ cxx = os.environ['CXX']
+ if 'LDSHARED' in os.environ:
+ ldshared = os.environ['LDSHARED']
++ if 'LDCXXSHARED' in os.environ:
++ ldcxxshared = os.environ['LDCXXSHARED']
+ if 'CPP' in os.environ:
+ cpp = os.environ['CPP']
+ else:
+ cpp = cc + " -E" # not always
+ if 'LDFLAGS' in os.environ:
+ ldshared = ldshared + ' ' + os.environ['LDFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['LDFLAGS']
+ if 'CFLAGS' in os.environ:
+ cflags = cflags + ' ' + os.environ['CFLAGS']
+ ldshared = ldshared + ' ' + os.environ['CFLAGS']
++ if 'CXXFLAGS' in os.environ:
++ cxxflags = cxxflags + ' ' + os.environ['CXXFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['CXXFLAGS']
+ if 'CPPFLAGS' in os.environ:
+ cpp = cpp + ' ' + os.environ['CPPFLAGS']
+ cflags = cflags + ' ' + os.environ['CPPFLAGS']
++ cxxflags = cxxflags + ' ' + os.environ['CPPFLAGS']
+ ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
++ ldcxxshared = ldcxxshared + ' ' + os.environ['CPPFLAGS']
+ if 'AR' in os.environ:
+ ar = os.environ['AR']
+ if 'ARFLAGS' in os.environ:
+@@ -226,13 +236,17 @@ def customize_compiler(compiler):
+ archiver = ar + ' ' + ar_flags
+
+ cc_cmd = cc + ' ' + cflags
++ cxx_cmd = cxx + ' ' + cxxflags
+ compiler.set_executables(
+ preprocessor=cpp,
+ compiler=cc_cmd,
+ compiler_so=cc_cmd + ' ' + ccshared,
+- compiler_cxx=cxx,
++ compiler_cxx=cxx_cmd,
++ compiler_so_cxx=cxx_cmd + ' ' + ccshared,
+ linker_so=ldshared,
+ linker_exe=cc,
++ linker_so_cxx=ldcxxshared,
++ linker_exe_cxx=cxx,
+ archiver=archiver)
+
+ compiler.shared_lib_extension = shlib_suffix
+diff --git a/Lib/distutils/unixccompiler.py b/Lib/distutils/unixccompiler.py
+index d10a78d..7e88781 100644
+--- a/Lib/distutils/unixccompiler.py
++++ b/Lib/distutils/unixccompiler.py
+@@ -52,14 +52,17 @@ class UnixCCompiler(CCompiler):
+ # are pretty generic; they will probably have to be set by an outsider
+ # (eg. using information discovered by the sysconfig about building
+ # Python extensions).
+- executables = {'preprocessor' : None,
+- 'compiler' : ["cc"],
+- 'compiler_so' : ["cc"],
+- 'compiler_cxx' : ["cc"],
+- 'linker_so' : ["cc", "-shared"],
+- 'linker_exe' : ["cc"],
+- 'archiver' : ["ar", "-cr"],
+- 'ranlib' : None,
++ executables = {'preprocessor' : None,
++ 'compiler' : ["cc"],
++ 'compiler_so' : ["cc"],
++ 'compiler_cxx' : ["c++"],
++ 'compiler_so_cxx' : ["c++"],
++ 'linker_so' : ["cc", "-shared"],
++ 'linker_exe' : ["cc"],
++ 'linker_so_cxx' : ["c++", "-shared"],
++ 'linker_exe_cxx' : ["c++"],
++ 'archiver' : ["ar", "-cr"],
++ 'ranlib' : None,
+ }
+
+ if sys.platform[:6] == "darwin":
+@@ -110,12 +113,19 @@ class UnixCCompiler(CCompiler):
+
+ def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
+ compiler_so = self.compiler_so
++ compiler_so_cxx = self.compiler_so_cxx
+ if sys.platform == 'darwin':
+ compiler_so = _osx_support.compiler_fixup(compiler_so,
+ cc_args + extra_postargs)
++ compiler_so_cxx = _osx_support.compiler_fixup(compiler_so_cxx,
++ cc_args + extra_postargs)
+ try:
+- self.spawn(compiler_so + cc_args + [src, '-o', obj] +
+- extra_postargs)
++ if self.detect_language(src) == 'c++':
++ self.spawn(compiler_so_cxx + cc_args + [src, '-o', obj] +
++ extra_postargs)
++ else:
++ self.spawn(compiler_so + cc_args + [src, '-o', obj] +
++ extra_postargs)
+ except DistutilsExecError as msg:
+ raise CompileError(msg)
+
+@@ -173,30 +183,16 @@ class UnixCCompiler(CCompiler):
+ ld_args.extend(extra_postargs)
+ self.mkpath(os.path.dirname(output_filename))
+ try:
+- if target_desc == CCompiler.EXECUTABLE:
+- linker = self.linker_exe[:]
++ if target_lang == "c++":
++ if target_desc == CCompiler.EXECUTABLE:
++ linker = self.linker_exe_cxx[:]
++ else:
++ linker = self.linker_so_cxx[:]
+ else:
+- linker = self.linker_so[:]
+- if target_lang == "c++" and self.compiler_cxx:
+- # skip over environment variable settings if /usr/bin/env
+- # is used to set up the linker's environment.
+- # This is needed on OSX. Note: this assumes that the
+- # normal and C++ compiler have the same environment
+- # settings.
+- i = 0
+- if os.path.basename(linker[0]) == "env":
+- i = 1
+- while '=' in linker[i]:
+- i += 1
+-
+- if os.path.basename(linker[i]) == 'ld_so_aix':
+- # AIX platforms prefix the compiler with the ld_so_aix
+- # script, so we need to adjust our linker index
+- offset = 1
++ if target_desc == CCompiler.EXECUTABLE:
++ linker = self.linker_exe[:]
+ else:
+- offset = 0
+-
+- linker[i+offset] = self.compiler_cxx[i]
++ linker = self.linker_so[:]
+
+ if sys.platform == 'darwin':
+ linker = _osx_support.compiler_fixup(linker, ld_args)
+diff --git a/Makefile.pre.in b/Makefile.pre.in
+index 35ca1a8..cfa79df 100644
+--- a/Makefile.pre.in
++++ b/Makefile.pre.in
+@@ -618,10 +618,10 @@ sharedmods: $(BUILDPYTHON) pybuilddir.txt Modules/_math.o
+ *\ -s*|s*) quiet="-q";; \
+ *) quiet="";; \
+ esac; \
+- echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++ echo "$(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ _TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ $(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build"; \
+- $(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' OPT='$(OPT)' \
++ $(RUNSHARED) CC='$(CC)' LDSHARED='$(BLDSHARED)' CFLAGS='$(PY_CFLAGS)' \
+ _TCLTK_INCLUDES='$(TCLTK_INCLUDES)' _TCLTK_LIBS='$(TCLTK_LIBS)' \
+ $(PYTHON_FOR_BUILD) $(srcdir)/setup.py $$quiet build
+
diff --git a/packages/python/rpath-non-gcc.patch b/packages/python/rpath-non-gcc.patch
new file mode 100644
index 00000000..f203bbba
--- /dev/null
+++ b/packages/python/rpath-non-gcc.patch
@@ -0,0 +1,15 @@
+--- a/Lib/distutils/unixccompiler.py 2009-05-09 21:55:12.000000000 +1000
++++ b/Lib/distutils/unixccompiler.py 2017-05-13 14:30:18.077518999 +1000
+@@ -299,10 +299,8 @@
+ else:
+ return "-Wl,-R" + dir
+ else:
+- # No idea how --enable-new-dtags would be passed on to
+- # ld if this system was using GNU ld. Don't know if a
+- # system like this even exists.
+- return "-R" + dir
++ # Patched by spack to use gcc syntax by default:
++ return "-Wl,-R" + dir
+
+ def library_option(self, lib):
+ return "-l" + lib
diff --git a/packages/python/tkinter-3.10.patch b/packages/python/tkinter-3.10.patch
new file mode 100644
index 00000000..e06be826
--- /dev/null
+++ b/packages/python/tkinter-3.10.patch
@@ -0,0 +1,11 @@
+--- a/setup.py 2021-12-06 12:23:39.000000000 -0600
++++ b/setup.py 2021-12-14 10:30:33.000000000 -0600
+@@ -2099,6 +2099,8 @@
+ #
+ # Detection stops at the first successful method.
+
++ return False
++
+ # Check for Tcl and Tk at the locations indicated by _TCLTK_INCLUDES
+ # and _TCLTK_LIBS environment variables.
+ if self.detect_tkinter_fromenv():
diff --git a/packages/python/tkinter-3.11.patch b/packages/python/tkinter-3.11.patch
new file mode 100644
index 00000000..fe2d54bd
--- /dev/null
+++ b/packages/python/tkinter-3.11.patch
@@ -0,0 +1,25 @@
+From a49e95e44961a0b6703ef9cb577d2ae5334c4a62 Mon Sep 17 00:00:00 2001
+From: Harmen Stoppels <harmenstoppels@gmail.com>
+Date: Thu, 3 Nov 2022 13:54:00 +0100
+Subject: [PATCH] disable tkinter explicitly
+
+---
+ setup.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index 15d0d45..642adb3 100644
+--- a/setup.py
++++ b/setup.py
+@@ -1358,7 +1358,7 @@ class PyBuildExt(build_ext):
+ self.detect_decimal()
+ self.detect_ctypes()
+ self.detect_multiprocessing()
+- self.detect_tkinter()
++ # self.detect_tkinter()
+ self.detect_uuid()
+
+ # Uncomment the next line if you want to play with xxmodule.c
+--
+2.38.1
+
diff --git a/packages/python/tkinter-3.7.patch b/packages/python/tkinter-3.7.patch
new file mode 100644
index 00000000..87e19018
--- /dev/null
+++ b/packages/python/tkinter-3.7.patch
@@ -0,0 +1,17 @@
+diff -Naur a/setup.py b/setup.py
+--- a/setup.py 2019-01-13 18:59:14.000000000 -0600
++++ b/setup.py 2019-01-13 19:00:31.000000000 -0600
+@@ -1787,13 +1787,6 @@
+ if self.detect_tkinter_explicitly():
+ return
+
+- # Rather than complicate the code below, detecting and building
+- # AquaTk is a separate method. Only one Tkinter will be built on
+- # Darwin - either AquaTk, if it is found, or X11 based Tk.
+- if (host_platform == 'darwin' and
+- self.detect_tkinter_darwin(inc_dirs, lib_dirs)):
+- return
+-
+ # Assume we haven't found any of the libraries or include files
+ # The versions with dots are used on Unix, and the versions without
+ # dots on Windows, for detection by cygwin.
diff --git a/packages/python/tkinter-3.8.patch b/packages/python/tkinter-3.8.patch
new file mode 100644
index 00000000..a1fc5729
--- /dev/null
+++ b/packages/python/tkinter-3.8.patch
@@ -0,0 +1,12 @@
+diff -Naur a/setup.py b/setup.py
+--- a/setup.py.orig 2021-09-29 21:28:23.000000000 -0400
++++ a/setup.py 2021-09-29 21:28:44.000000000 -0400
+@@ -1826,6 +1826,8 @@
+ def detect_tkinter(self):
+ # The _tkinter module.
+
++ return False
++
+ # Check whether --with-tcltk-includes and --with-tcltk-libs were
+ # configured or passed into the make target. If so, use these values
+ # to build tkinter and bypass the searches for Tcl and TK in standard
--
GitLab
From ba0d0c4ed2b905dd2167150e105301790e011948 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 20:30:33 +0000
Subject: [PATCH 56/80] fix(python): fix lib(n)curses detection
from https://github.com/spack/spack/pull/35092
fixes https://github.com/spack/spack/issues/34872
---
packages/python/curses.patch | 13 +++++++++++++
packages/python/package.py | 6 ++++++
2 files changed, 19 insertions(+)
create mode 100644 packages/python/curses.patch
diff --git a/packages/python/curses.patch b/packages/python/curses.patch
new file mode 100644
index 00000000..b83ec60e
--- /dev/null
+++ b/packages/python/curses.patch
@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index 85a2b26357..8c83b9f175 100644
+--- a/setup.py
++++ b/setup.py
+@@ -1088,7 +1088,7 @@ def detect_readline_curses(self):
+ if ret == 0:
+ with open(tmpfile) as fp:
+ for ln in fp:
+- if 'curses' in ln:
++ if 'libcurses' in ln or 'libncurses' in ln:
+ readline_termcap_library = re.sub(
+ r'.*lib(n?cursesw?)\.so.*', r'\1', ln
+ ).rstrip()
diff --git a/packages/python/package.py b/packages/python/package.py
index 3bfdc240..85ba69c0 100644
--- a/packages/python/package.py
+++ b/packages/python/package.py
@@ -333,6 +333,12 @@ class Python(Package):
# https://github.com/python/cpython/pull/16717
patch("intel-3.7.patch", when="@3.7.1:3.7.5 %intel")
+ # begin EBRAINS (added)
+ # Fix curses/readline detection logic to not be triggered by path name
+ # https://github.com/spack/spack/issues/34872
+ patch("curses.patch", when="@:3.11")
+ # end EBRAINS
+
# CPython tries to build an Objective-C file with GCC's C frontend
# https://github.com/spack/spack/pull/16222
# https://github.com/python/cpython/pull/13306
--
GitLab
From a13d18ae9953349b0e2d303f3cc4b595882828fc Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 22:47:19 +0000
Subject: [PATCH 57/80] feat(python): add version 3.11.10
---
packages/python/package.py | 3 +++
1 file changed, 3 insertions(+)
diff --git a/packages/python/package.py b/packages/python/package.py
index 85ba69c0..6b9add7e 100644
--- a/packages/python/package.py
+++ b/packages/python/package.py
@@ -66,6 +66,9 @@ class Python(Package):
version("3.12.2", sha256="a7c4f6a9dc423d8c328003254ab0c9338b83037bd787d680826a5bf84308116e")
version("3.12.1", sha256="d01ec6a33bc10009b09c17da95cc2759af5a580a7316b3a446eb4190e13f97b2")
version("3.12.0", sha256="51412956d24a1ef7c97f1cb5f70e185c13e3de1f50d131c0aac6338080687afb")
+ # begin EBRAINS (added): add version
+ version("3.11.10", sha256="92f2faf242681bfa406d53a51e17d42c5373affe23a130cd9697e132ef574706")
+ # end EBRAINS
version("3.11.9", sha256="e7de3240a8bc2b1e1ba5c81bf943f06861ff494b69fda990ce2722a504c6153d")
version("3.11.8", sha256="d3019a613b9e8761d260d9ebe3bd4df63976de30464e5c0189566e1ae3f61889")
version("3.11.7", sha256="068c05f82262e57641bd93458dfa883128858f5f4997aad7a36fd25b13b29209")
--
GitLab
From 94dbb0dcb4c690738af79ea0ff53fe1e4b50b224 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 4 Mar 2025 23:21:35 +0000
Subject: [PATCH 58/80] feat(ebrainslab): make gcc and python versions more
specific
---
site-config/ebrainslab/packages.yaml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/site-config/ebrainslab/packages.yaml b/site-config/ebrainslab/packages.yaml
index 44e6777d..90978f93 100644
--- a/site-config/ebrainslab/packages.yaml
+++ b/site-config/ebrainslab/packages.yaml
@@ -2,10 +2,10 @@ packages:
all:
# collab-specific settings
target: [x86_64]
- compiler: [gcc@13]
+ compiler: [gcc@13.3.0]
python:
# collab-specific settings
- require: "@3.11"
+ require: "@3.11.10"
r:
# EM: +X fixes build for collab
require: "@4.3.3+X"
--
GitLab
From b59780fbd3c05d8088633fce6fcd8186dca1b7f1 Mon Sep 17 00:00:00 2001
From: Abolfazl Ziaeemehr <abolfazl.ziaee-mehr@univ-amu.fr>
Date: Fri, 7 Mar 2025 18:20:13 +0100
Subject: [PATCH 59/80] fix(py-vbi): add version 0.1.3
---
packages/py-vbi/fix-install.patch | 12 ------------
packages/py-vbi/package.py | 7 ++++---
2 files changed, 4 insertions(+), 15 deletions(-)
delete mode 100644 packages/py-vbi/fix-install.patch
diff --git a/packages/py-vbi/fix-install.patch b/packages/py-vbi/fix-install.patch
deleted file mode 100644
index d84cceb0..00000000
--- a/packages/py-vbi/fix-install.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/pyproject.toml b/pyproject.toml
-index debc24e..2e0500b 100644
---- a/pyproject.toml
-+++ b/pyproject.toml
-@@ -58,7 +58,6 @@ path = "vbi/_version.py"
-
-
- [tool.setuptools]
--packages = ["vbi"]
- include-package-data = true
-
- [tool.setuptools.package-data]
diff --git a/packages/py-vbi/package.py b/packages/py-vbi/package.py
index 138893c5..0ac988a2 100644
--- a/packages/py-vbi/package.py
+++ b/packages/py-vbi/package.py
@@ -6,16 +6,16 @@
from spack import *
-class PyVbi(PythonPackage):
+class PyVbi(PythonPackage, CudaPackage):
homepage = "https://vbi.readthedocs.io/latest/"
git = "https://github.com/ins-amu/vbi"
url = "https://github.com/ins-amu/vbi/archive/refs/tags/v0.1.3.tar.gz"
- version("0.1.3", "54fa2062f44c9ec8219fae3c13c52a4bd17141b5467b982987673de0662c5255")
+ version("0.1.3", "8ccccf2bf0def2bf97f4706b8597c4cb3ac5f0cf2ac5f08566e22cd6273c1163")
version("0.1.2", "6ccfeeec718be62a480002a8370130a3e3344955186f99ecbb15b646b68210d6")
+
- patch('fix-install.patch')
depends_on("python@3.8:", type=("build","run"))
depends_on("py-setuptools", type="build")
@@ -37,6 +37,7 @@ class PyVbi(PythonPackage):
depends_on("py-scikit-learn", type=("build", "run"))
depends_on("py-pycatch22", type=("build", "run"))
depends_on("py-pytest", type="test")
+ depends_on("py-cupy", type=("build", "run"), when="+cuda")
@run_after("install")
@on_package_attributes(run_tests=True)
--
GitLab
From 431ef1ea26ed436e64947fec7c4e882d0501733e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Tue, 18 Feb 2025 19:31:45 +0100
Subject: [PATCH 60/80] fix(BSS2): build %gcc@13.3
---
packages/build-brainscales/package.py | 8 ++++++++
packages/hxtorch/package.py | 3 +++
packages/oppulance/package.py | 7 +++++++
packages/pynn-brainscales/package.py | 3 +++
packages/wf-brainscales2-demos/package.py | 1 +
spack.yaml | 8 ++++----
6 files changed, 26 insertions(+), 4 deletions(-)
diff --git a/packages/build-brainscales/package.py b/packages/build-brainscales/package.py
index 6ea4a370..cec40a9c 100644
--- a/packages/build-brainscales/package.py
+++ b/packages/build-brainscales/package.py
@@ -15,6 +15,13 @@ import spack.build_environment
class BuildBrainscales(WafPackage):
"""Common stuff for BrainScaleS packages..."""
+ version(
+ "9.0-a9",
+ git="https://github.com/electronicvisions/releases-ebrains",
+ tag="ebrains-9.0-a9",
+ commit="5951428b7598ff9478fa834d7e991e3ff94709ee",
+ submodules=True,
+ )
version(
"9.0-a8",
git="https://github.com/electronicvisions/releases-ebrains",
@@ -52,6 +59,7 @@ class BuildBrainscales(WafPackage):
)
# common dependencies of BuildBrainscales-derived packages
+ depends_on('oppulance@9.0-a9', when='@9.0-a9', type=('build', 'link', 'run', 'test'))
depends_on('oppulance@9.0-a8', when='@9.0-a8', type=('build', 'link', 'run', 'test'))
depends_on('oppulance@9.0-a7', when='@9.0-a7', type=('build', 'link', 'run', 'test'))
depends_on('oppulance@9.0-a6', when='@9.0-a6', type=('build', 'link', 'run', 'test'))
diff --git a/packages/hxtorch/package.py b/packages/hxtorch/package.py
index 437a6886..ef237ceb 100644
--- a/packages/hxtorch/package.py
+++ b/packages/hxtorch/package.py
@@ -90,6 +90,9 @@ class Hxtorch(build_brainscales.BuildBrainscales):
extends('python')
+ # some versions of dependencies are broken
+ conflicts("boost@1.86.0") # sha1 digest changed length, but boost::compute didn't adapt
+
patch("include-SparseTensorUtils.patch", when="@:8.0-a5")
def install_test(self):
diff --git a/packages/oppulance/package.py b/packages/oppulance/package.py
index 2249a8b4..55d6b04e 100644
--- a/packages/oppulance/package.py
+++ b/packages/oppulance/package.py
@@ -21,6 +21,13 @@ class Oppulance(Package):
depends_on('wget')
depends_on('gmp')
+ version(
+ "9.0-a9",
+ git="https://github.com/electronicvisions/releases-ebrains",
+ tag="ebrains-9.0-a9",
+ commit="5951428b7598ff9478fa834d7e991e3ff94709ee",
+ submodules=True,
+ )
version(
"9.0-a8",
git="https://github.com/electronicvisions/releases-ebrains",
diff --git a/packages/pynn-brainscales/package.py b/packages/pynn-brainscales/package.py
index 13d850f7..3e68558d 100644
--- a/packages/pynn-brainscales/package.py
+++ b/packages/pynn-brainscales/package.py
@@ -82,6 +82,9 @@ class PynnBrainscales(build_brainscales.BuildBrainscales):
depends_on('yaml-cpp+shared', type=('build', 'link', 'run'))
extends('python')
+ # some versions of dependencies are broken
+ conflicts("boost@1.86.0") # sha1 digest changed length, but boost::compute didn't adapt
+
def install_test(self):
with working_dir('spack-test', create=True):
old_pythonpath = os.environ.get('PYTHONPATH', '')
diff --git a/packages/wf-brainscales2-demos/package.py b/packages/wf-brainscales2-demos/package.py
index 9226c76a..1dc5b24b 100644
--- a/packages/wf-brainscales2-demos/package.py
+++ b/packages/wf-brainscales2-demos/package.py
@@ -16,6 +16,7 @@ class WfBrainscales2Demos(Package):
maintainers = ["emuller", "muffgaga"]
# ECM: we probably should build the ipynb file in this package
+ version("9.0-a9", tag="jupyter-notebooks-9.0-a9")
version("9.0-a8", tag="jupyter-notebooks-9.0-a8")
version("9.0-a7", tag="jupyter-notebooks-9.0-a7")
version("9.0-a6", tag="jupyter-notebooks-9.0-a6")
diff --git a/spack.yaml b/spack.yaml
index 274a55d1..c6d455fd 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -12,10 +12,10 @@ spack:
- py-biobb-model@4.1.0
- py-biobb-structure-checking@3.13.4
- py-biobb-structure-utils@4.1.0
- - hxtorch@9.0-a8
+ - hxtorch@9.0-a9
- nest@3.8 +sonata
- neuron@8.2.3 +mpi
- - jaxsnn@9.0-a8
+ - jaxsnn@9.0-a9
- py-bluepyefe@2.3.6
- py-bluepymm@0.8.7
- py-bluepyopt@1.14.11
@@ -62,14 +62,14 @@ spack:
- py-tvb-ext-xircuits@1.1.0
- py-viziphant@0.4.0
- py-vbi
- - pynn-brainscales@9.0-a8
+ - pynn-brainscales@9.0-a9
- r-rgsl@0.1.1
- r-sbtabvfgen@0.1
- r-uqsa@2.2
- sda@7.3.3d
# Workflows (meta-packages)
- wf-biobb
- - wf-brainscales2-demos@9.0-a8
+ - wf-brainscales2-demos@9.0-a9
- wf-bsb@4.4 +nest +neuron
- wf-protein-association-rates@0.1
- wf-multi-area-model@1.2.0
--
GitLab
From d5bb12658deaf53b06fbed167bdb31a5512a842d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Wed, 26 Feb 2025 13:14:55 +0100
Subject: [PATCH 61/80] fix(genpybind): build on llvm@15
---
packages/genpybind/package.py | 1 +
packages/hxtorch/package.py | 2 +-
packages/pynn-brainscales/package.py | 2 +-
3 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/packages/genpybind/package.py b/packages/genpybind/package.py
index f5398139..012d2e5b 100644
--- a/packages/genpybind/package.py
+++ b/packages/genpybind/package.py
@@ -21,6 +21,7 @@ class Genpybind(WafPackage):
version('develop', branch='develop')
version('visions', branch='master', git='https://github.com/electronicvisions/genpybind')
+ version('ebrains-llvm15', tag='ebrains-9.0-a9', git='https://github.com/electronicvisions/genpybind')
version('ebrains', tag='ebrains_release-1-rc1', git='https://github.com/electronicvisions/genpybind')
depends_on(
diff --git a/packages/hxtorch/package.py b/packages/hxtorch/package.py
index ef237ceb..d4a5ea66 100644
--- a/packages/hxtorch/package.py
+++ b/packages/hxtorch/package.py
@@ -53,7 +53,7 @@ class Hxtorch(build_brainscales.BuildBrainscales):
('boost@1.69.0: +graph+icu+mpi+numpy+coroutine+context+filesystem+python+serialization+system+thread+program_options cxxstd=17', { "type": ('build', 'link', 'run', 'test') } ),
('cereal', { "type": ('build', 'link', 'run', 'test') } ),
('cppcheck', { "type": ('build', 'link', 'run') } ),
- ('genpybind@ebrains', { "type": ('build', 'link') } ),
+ ('genpybind@ebrains-llvm15', { "type": ('build', 'link') } ),
('gflags', { "type": ('build', 'link', 'run') } ),
('googletest@1.11.0:+gmock', { "type": ('build', 'link', 'run') } ), # variadic templates needed
('inja', { "type": ('build', 'link', 'run', 'test') } ),# template engine for PPU source jit generation
diff --git a/packages/pynn-brainscales/package.py b/packages/pynn-brainscales/package.py
index 3e68558d..e0836671 100644
--- a/packages/pynn-brainscales/package.py
+++ b/packages/pynn-brainscales/package.py
@@ -51,7 +51,7 @@ class PynnBrainscales(build_brainscales.BuildBrainscales):
depends_on('boost@1.69.0: +graph+icu+mpi+numpy+coroutine+context+filesystem+python+serialization+system+thread+program_options cxxstd=17', type=('build', 'link', 'run', 'test'))
depends_on('cereal', type=('build', 'link', 'run', 'test'))
depends_on('cppcheck', type=('build', 'link', 'run'))
- depends_on('genpybind@ebrains', type=('build', 'link'))
+ depends_on('genpybind@ebrains-llvm15', type=('build', 'link'))
depends_on('gflags', type=('build', 'link', 'run'))
depends_on('googletest@1.11.0:+gmock', type=('build', 'link', 'run')) # variadic templates needed
depends_on('inja', type=('build', 'link', 'run', 'test')) # template engine for PPU source jit generation
--
GitLab
From 4497875b0b58425c0832c8e56497054cf0d0d317 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Wed, 26 Feb 2025 17:43:37 +0100
Subject: [PATCH 62/80] fix(BSS2): build of python wrapper w/ llvm@15
---
packages/build-brainscales/package.py | 2 +-
packages/oppulance/package.py | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/packages/build-brainscales/package.py b/packages/build-brainscales/package.py
index cec40a9c..d1ab34f9 100644
--- a/packages/build-brainscales/package.py
+++ b/packages/build-brainscales/package.py
@@ -19,7 +19,7 @@ class BuildBrainscales(WafPackage):
"9.0-a9",
git="https://github.com/electronicvisions/releases-ebrains",
tag="ebrains-9.0-a9",
- commit="5951428b7598ff9478fa834d7e991e3ff94709ee",
+ commit="41d2597bd6c1c20aee4d538c42c248195a133680",
submodules=True,
)
version(
diff --git a/packages/oppulance/package.py b/packages/oppulance/package.py
index 55d6b04e..7df3c70f 100644
--- a/packages/oppulance/package.py
+++ b/packages/oppulance/package.py
@@ -25,7 +25,7 @@ class Oppulance(Package):
"9.0-a9",
git="https://github.com/electronicvisions/releases-ebrains",
tag="ebrains-9.0-a9",
- commit="5951428b7598ff9478fa834d7e991e3ff94709ee",
+ commit="41d2597bd6c1c20aee4d538c42c248195a133680",
submodules=True,
)
version(
--
GitLab
From fef3489ef38befa24e3ce5071adef4ef3ae5bfe7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Thu, 27 Feb 2025 15:01:49 +0100
Subject: [PATCH 63/80] fix(llvm): backport patches for clang's Python bindings
---
.../llvm15-clang-python-missing-kinds.patch | 238 ++++++++++++++++++
packages/llvm/package.py | 16 ++
2 files changed, 254 insertions(+)
create mode 100644 packages/llvm/llvm15-clang-python-missing-kinds.patch
diff --git a/packages/llvm/llvm15-clang-python-missing-kinds.patch b/packages/llvm/llvm15-clang-python-missing-kinds.patch
new file mode 100644
index 00000000..d45dc630
--- /dev/null
+++ b/packages/llvm/llvm15-clang-python-missing-kinds.patch
@@ -0,0 +1,238 @@
+From eb264d825beb048c6e673ddaf5aca069511fcfb3 Mon Sep 17 00:00:00 2001
+From: ykiko <ykikoykikoykiko@gmail.com>
+Date: Mon, 18 Mar 2024 22:13:10 +0800
+Subject: [PATCH] Add some missing Kinds to libclang python bindings (#85571)
+
+Add some Kinds existing in Index.h but missing in cindex.py.
+---
+ clang/bindings/python/clang/cindex.py | 173 +++++++++++++++++++++++++-
+ clang/docs/ReleaseNotes.rst | 2 +
+ clang/include/clang-c/Index.h | 2 +-
+ 3 files changed, 175 insertions(+), 2 deletions(-)
+
+diff --git a/clang/bindings/python/clang/cindex.py b/clang/bindings/python/clang/cindex.py
+index 44a34ca196274..302d99dccd77b 100644
+--- a/clang/bindings/python/clang/cindex.py
++++ b/clang/bindings/python/clang/cindex.py
+@@ -1091,6 +1091,29 @@ def __repr__(self):
+ # Represents an @available(...) check.
+ CursorKind.OBJC_AVAILABILITY_CHECK_EXPR = CursorKind(148)
+
++# Fixed point literal.
++CursorKind.FIXED_POINT_LITERAL = CursorKind(149)
++
++# OpenMP 5.0 [2.1.4, Array Shaping].
++CursorKind.OMP_ARRAY_SHAPING_EXPR = CursorKind(150)
++
++# OpenMP 5.0 [2.1.6 Iterators].
++CursorKind.OMP_ITERATOR_EXPR = CursorKind(151)
++
++# OpenCL's addrspace_cast<> expression.
++CursorKind.CXX_ADDRSPACE_CAST_EXPR = CursorKind(152)
++
++# Expression that references a C++20 concept.
++CursorKind.CONCEPT_SPECIALIZATION_EXPR = CursorKind(153)
++
++# Expression that references a C++20 requires expression.
++CursorKind.REQUIRES_EXPR = CursorKind(154)
++
++# Expression that references a C++20 parenthesized list aggregate initializer.
++CursorKind.CXX_PAREN_LIST_INIT_EXPR = CursorKind(155)
++
++# Represents a C++26 pack indexing expression.
++CursorKind.PACK_INDEXING_EXPR = CursorKind(156)
+
+ # A statement whose specific kind is not exposed via this interface.
+ #
+@@ -1312,6 +1335,114 @@ def __repr__(self):
+ # OpenMP teams distribute directive.
+ CursorKind.OMP_TEAMS_DISTRIBUTE_DIRECTIVE = CursorKind(271)
+
++# OpenMP teams distribute simd directive.
++CursorKind.OMP_TEAMS_DISTRIBUTE_DIRECTIVE = CursorKind(272)
++
++# OpenMP teams distribute parallel for simd directive.
++CursorKind.OMP_TEAMS_DISTRIBUTE_PARALLEL_FOR_SIMD_DIRECTIVE = CursorKind(273)
++
++# OpenMP teams distribute parallel for directive.
++CursorKind.OMP_TEAMS_DISTRIBUTE_PARALLEL_FOR_DIRECTIVE = CursorKind(274)
++
++# OpenMP target teams directive.
++CursorKind.OMP_TARGET_TEAMS_DIRECTIVE = CursorKind(275)
++
++# OpenMP target teams distribute directive.
++CursorKind.OMP_TARGET_TEAMS_DISTRIBUTE_DIRECTIVE = CursorKind(276)
++
++# OpenMP target teams distribute parallel for directive.
++CursorKind.OMP_TARGET_TEAMS_DISTRIBUTE_PARALLEL_FOR_DIRECTIVE = CursorKind(277)
++
++# OpenMP target teams distribute parallel for simd directive.
++CursorKind.OMP_TARGET_TEAMS_DISTRIBUTE_PARALLEL_FOR_SIMD_DIRECTIVE = CursorKind(278)
++
++# OpenMP target teams distribute simd directive.
++CursorKind.OMP_TARGET_TEAMS_DISTRIBUTE_SIMD_DIRECTIVE = CursorKind(279)
++
++# C++2a std::bit_cast expression.
++CursorKind.BUILTIN_BIT_CAST_EXPR = CursorKind(280)
++
++# OpenMP master taskloop directive.
++CursorKind.OMP_MASTER_TASK_LOOP_DIRECTIVE = CursorKind(281)
++
++# OpenMP parallel master taskloop directive.
++CursorKind.OMP_PARALLEL_MASTER_TASK_LOOP_DIRECTIVE = CursorKind(282)
++
++# OpenMP master taskloop simd directive.
++CursorKind.OMP_MASTER_TASK_LOOP_SIMD_DIRECTIVE = CursorKind(283)
++
++# OpenMP parallel master taskloop simd directive.
++CursorKind.OMP_PARALLEL_MASTER_TASK_LOOP_SIMD_DIRECTIVE = CursorKind(284)
++
++# OpenMP parallel master directive.
++CursorKind.OMP_PARALLEL_MASTER_DIRECTIVE = CursorKind(285)
++
++# OpenMP depobj directive.
++CursorKind.OMP_DEPOBJ_DIRECTIVE = CursorKind(286)
++
++# OpenMP scan directive.
++CursorKind.OMP_SCAN_DIRECTIVE = CursorKind(287)
++
++# OpenMP tile directive.
++CursorKind.OMP_TILE_DIRECTIVE = CursorKind(288)
++
++# OpenMP canonical loop.
++CursorKind.OMP_CANONICAL_LOOP = CursorKind(289)
++
++# OpenMP interop directive.
++CursorKind.OMP_INTEROP_DIRECTIVE = CursorKind(290)
++
++# OpenMP dispatch directive.
++CursorKind.OMP_DISPATCH_DIRECTIVE = CursorKind(291)
++
++# OpenMP masked directive.
++CursorKind.OMP_MASKED_DIRECTIVE = CursorKind(292)
++
++# OpenMP unroll directive.
++CursorKind.OMP_UNROLL_DIRECTIVE = CursorKind(293)
++
++# OpenMP metadirective directive.
++CursorKind.OMP_META_DIRECTIVE = CursorKind(294)
++
++# OpenMP loop directive.
++CursorKind.OMP_GENERIC_LOOP_DIRECTIVE = CursorKind(295)
++
++# OpenMP teams loop directive.
++CursorKind.OMP_TEAMS_GENERIC_LOOP_DIRECTIVE = CursorKind(296)
++
++# OpenMP target teams loop directive.
++CursorKind.OMP_TARGET_TEAMS_GENERIC_LOOP_DIRECTIVE = CursorKind(297)
++
++# OpenMP parallel loop directive.
++CursorKind.OMP_PARALLEL_GENERIC_LOOP_DIRECTIVE = CursorKind(298)
++
++# OpenMP target parallel loop directive.
++CursorKind.OMP_TARGET_PARALLEL_GENERIC_LOOP_DIRECTIVE = CursorKind(299)
++
++# OpenMP parallel masked directive.
++CursorKind.OMP_PARALLEL_MASKED_DIRECTIVE = CursorKind(300)
++
++# OpenMP masked taskloop directive.
++CursorKind.OMP_MASKED_TASK_LOOP_DIRECTIVE = CursorKind(301)
++
++# OpenMP masked taskloop simd directive.
++CursorKind.OMP_MASKED_TASK_LOOP_SIMD_DIRECTIVE = CursorKind(302)
++
++# OpenMP parallel masked taskloop directive.
++CursorKind.OMP_PARALLEL_MASKED_TASK_LOOP_DIRECTIVE = CursorKind(303)
++
++# OpenMP parallel masked taskloop simd directive.
++CursorKind.OMP_PARALLEL_MASKED_TASK_LOOP_SIMD_DIRECTIVE = CursorKind(304)
++
++# OpenMP error directive.
++CursorKind.OMP_ERROR_DIRECTIVE = CursorKind(305)
++
++# OpenMP scope directive.
++CursorKind.OMP_SCOPE_DIRECTIVE = CursorKind(306)
++
++# OpenACC Compute Construct.
++CursorKind.OPEN_ACC_COMPUTE_DIRECTIVE = CursorKind(320)
++
+ ###
+ # Other Kinds
+
+@@ -1349,6 +1480,24 @@ def __repr__(self):
+
+ CursorKind.DLLEXPORT_ATTR = CursorKind(418)
+ CursorKind.DLLIMPORT_ATTR = CursorKind(419)
++CursorKind.NS_RETURNS_RETAINED = CursorKind(420)
++CursorKind.NS_RETURNS_NOT_RETAINED = CursorKind(421)
++CursorKind.NS_RETURNS_AUTORELEASED = CursorKind(422)
++CursorKind.NS_CONSUMES_SELF = CursorKind(423)
++CursorKind.NS_CONSUMED = CursorKind(424)
++CursorKind.OBJC_EXCEPTION = CursorKind(425)
++CursorKind.OBJC_NSOBJECT = CursorKind(426)
++CursorKind.OBJC_INDEPENDENT_CLASS = CursorKind(427)
++CursorKind.OBJC_PRECISE_LIFETIME = CursorKind(428)
++CursorKind.OBJC_RETURNS_INNER_POINTER = CursorKind(429)
++CursorKind.OBJC_REQUIRES_SUPER = CursorKind(430)
++CursorKind.OBJC_ROOT_CLASS = CursorKind(431)
++CursorKind.OBJC_SUBCLASSING_RESTRICTED = CursorKind(432)
++CursorKind.OBJC_EXPLICIT_PROTOCOL_IMPL = CursorKind(433)
++CursorKind.OBJC_DESIGNATED_INITIALIZER = CursorKind(434)
++CursorKind.OBJC_RUNTIME_VISIBLE = CursorKind(435)
++CursorKind.OBJC_BOXABLE = CursorKind(436)
++CursorKind.FLAG_ENUM = CursorKind(437)
+ CursorKind.CONVERGENT_ATTR = CursorKind(438)
+ CursorKind.WARN_UNUSED_ATTR = CursorKind(439)
+ CursorKind.WARN_UNUSED_RESULT_ATTR = CursorKind(440)
+@@ -1395,6 +1544,11 @@ class TemplateArgumentKind(BaseEnumeration):
+ TemplateArgumentKind.DECLARATION = TemplateArgumentKind(2)
+ TemplateArgumentKind.NULLPTR = TemplateArgumentKind(3)
+ TemplateArgumentKind.INTEGRAL = TemplateArgumentKind(4)
++TemplateArgumentKind.TEMPLATE = TemplateArgumentKind(5)
++TemplateArgumentKind.TEMPLATE_EXPANSION = TemplateArgumentKind(6)
++TemplateArgumentKind.EXPRESSION = TemplateArgumentKind(7)
++TemplateArgumentKind.PACK = TemplateArgumentKind(8)
++TemplateArgumentKind.INVALID = TemplateArgumentKind(9)
+
+ ### Exception Specification Kinds ###
+ class ExceptionSpecificationKind(BaseEnumeration):
+@@ -2240,8 +2394,26 @@ def __repr__(self):
+ TypeKind.OCLQUEUE = TypeKind(159)
+ TypeKind.OCLRESERVEID = TypeKind(160)
+
++TypeKind.OBJCOBJECT = TypeKind(161)
++TypeKind.OBJCCLASS = TypeKind(162)
++TypeKind.ATTRIBUTED = TypeKind(163)
++
++TypeKind.OCLINTELSUBGROUPAVCMCEPAYLOAD = TypeKind(164)
++TypeKind.OCLINTELSUBGROUPAVCIMEPAYLOAD = TypeKind(165)
++TypeKind.OCLINTELSUBGROUPAVCREFPAYLOAD = TypeKind(166)
++TypeKind.OCLINTELSUBGROUPAVCSICPAYLOAD = TypeKind(167)
++TypeKind.OCLINTELSUBGROUPAVCMCERESULT = TypeKind(168)
++TypeKind.OCLINTELSUBGROUPAVCIMERESULT = TypeKind(169)
++TypeKind.OCLINTELSUBGROUPAVCREFRESULT = TypeKind(170)
++TypeKind.OCLINTELSUBGROUPAVCSICRESULT = TypeKind(171)
++TypeKind.OCLINTELSUBGROUPAVCIMERESULTSINGLEREFERENCESTREAMOUT = TypeKind(172)
++TypeKind.OCLINTELSUBGROUPAVCIMERESULTSDUALREFERENCESTREAMOUT = TypeKind(173)
++TypeKind.OCLINTELSUBGROUPAVCIMERESULTSSINGLEREFERENCESTREAMIN = TypeKind(174)
++TypeKind.OCLINTELSUBGROUPAVCIMEDUALREFERENCESTREAMIN = TypeKind(175)
++
+ TypeKind.EXTVECTOR = TypeKind(176)
+ TypeKind.ATOMIC = TypeKind(177)
++TypeKind.BTFTAGATTRIBUTED = TypeKind(178)
+
+ class RefQualifierKind(BaseEnumeration):
+ """Describes a specific ref-qualifier of a type."""
+diff --git a/clang/include/clang-c/Index.h b/clang/include/clang-c/Index.h
+index 3f3620609b6dd..60db3cf0966c0 100644
+--- a/clang/include/clang-c/Index.h
++++ b/clang/include/clang-c/Index.h
+@@ -1675,7 +1675,7 @@ enum CXCursorKind {
+ CXCursor_ConceptSpecializationExpr = 153,
+
+ /**
+- * Expression that references a C++20 concept.
++ * Expression that references a C++20 requires expression.
+ */
+ CXCursor_RequiresExpr = 154,
+
diff --git a/packages/llvm/package.py b/packages/llvm/package.py
index b437b0ee..a0b9bd0e 100644
--- a/packages/llvm/package.py
+++ b/packages/llvm/package.py
@@ -548,6 +548,22 @@ class Llvm(CMakePackage, CudaPackage, LlvmDetection, CompilerPackage):
sha256="c6ca6b925f150e8644ce756023797b7f94c9619c62507231f979edab1c09af78",
when="@6:13",
)
+
+ # begin EBRAINS
+ # add missing concept declaration CursorKind to clang's Python bindings
+ patch(
+ "https://github.com/llvm/llvm-project/commit/8b322895207c34b434698954dc67404e0bbf8d8e.patch?full_index=1",
+ sha256="173050a7f08c01bbc18d1145f455cac827754d0436befc2afd1add86e884fac0",
+ when="@15:16",
+ )
+ # Add some Kinds existing in Index.h but missing in cindex.py (dropped release note changes)
+ patch(
+ # based on https://github.com/llvm/llvm-project/commit/eb264d825beb048c6e673ddaf5aca069511fcfb3.patch?full_index=1
+ "llvm15-clang-python-missing-kinds.patch",
+ when="@15:18",
+ )
+ # end EBRAINS
+
# fix building of older versions of llvm with newer versions of glibc
for compiler_rt_as in ["project", "runtime"]:
with when("compiler-rt={0}".format(compiler_rt_as)):
--
GitLab
From f53dab33c030369ba3723abb8e2326843d1c6a57 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Thu, 6 Mar 2025 09:01:28 +0100
Subject: [PATCH 64/80] fix: small bug in install script
---
install_spack_env.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/install_spack_env.sh b/install_spack_env.sh
index 31232625..a0ed1f67 100644
--- a/install_spack_env.sh
+++ b/install_spack_env.sh
@@ -130,7 +130,7 @@ spack-python -c "exit(not len(spack.environment.active_environment().uninstalled
else
echo "Updating of the source cache disabled."
fi
- if [ $ret -ne 0 ]; then
+ if [ "$ret" -ne 0 ]; then
(exit $ret)
fi
)
--
GitLab
From 429fc858aed713a5dcb086c89f4eb0563fe44aaf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Thu, 6 Mar 2025 09:01:40 +0100
Subject: [PATCH 65/80] fix(BSS2): cache content when downloading oppulance
first
---
packages/oppulance/package.py | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/packages/oppulance/package.py b/packages/oppulance/package.py
index 7df3c70f..7e0d22b6 100644
--- a/packages/oppulance/package.py
+++ b/packages/oppulance/package.py
@@ -4,6 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
+import unittest.mock
class Oppulance(Package):
@@ -137,6 +138,15 @@ class Oppulance(Package):
expand=False,
)
+ # see build-brainscales package for a description; we need to duplicate
+ # here, as the cache content is shared between the two repositories
+ @when("@9:")
+ def do_fetch(self, mirror_only=False):
+ # in the configure step, we need access to all archived .git folders
+ def custom_archive(self, destination):
+ super(spack.fetch_strategy.GitFetchStrategy, self).archive(destination)
+ with unittest.mock.patch('spack.fetch_strategy.GitFetchStrategy.archive', new=custom_archive):
+ super().do_fetch(mirror_only)
def install(self, spec, prefix):
ln = which('ln')
--
GitLab
From 366d5d56ee5ee18f884e649ff9674c145a730918 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Sat, 8 Mar 2025 10:08:31 +0100
Subject: [PATCH 66/80] fix(BSS2): ignore test fails because of missing
catchsegv
---
packages/build-brainscales/package.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/packages/build-brainscales/package.py b/packages/build-brainscales/package.py
index d1ab34f9..2419107c 100644
--- a/packages/build-brainscales/package.py
+++ b/packages/build-brainscales/package.py
@@ -208,6 +208,7 @@ class BuildBrainscales(WafPackage):
if (elem.tag == 'failure') and not (
elem.get('message').startswith("pylint:") or
elem.get('message').startswith("pycodestyle:") or
+ "catchsegv: not found" in elem.get('message') or
("OK" in elem.get('message') and "Segmentation fault" in elem.get('message'))):
raise RuntimeError("Failed test found: {}".format(testcase.get('name')))
--
GitLab
From 4ad76adb2ab36d449761ef20b362d1f2b210194e Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Mon, 10 Mar 2025 17:38:37 +0000
Subject: [PATCH 67/80] feat(apbs): relax python dependency version range
---
packages/apbs/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/apbs/package.py b/packages/apbs/package.py
index 63025099..f7f45c6e 100644
--- a/packages/apbs/package.py
+++ b/packages/apbs/package.py
@@ -40,7 +40,7 @@ class Apbs(CMakePackage):
depends_on('arpack-ng', type=('build', 'run'))
depends_on('suite-sparse', type=('build', 'run'))
depends_on('maloc', type=('build', 'run'))
- depends_on('python@3.8:3.10', type=('build', 'run'))
+ depends_on('python@3.8:3.11', type=('build', 'run'))
def cmake_args(self):
# Min and max Python versions need to be set as variables to pass tests.
--
GitLab
From ef9a764384ac97e9ea1bf2f55f7707bb7a9a401e Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Mon, 10 Mar 2025 17:41:03 +0000
Subject: [PATCH 68/80] feat(py-pdb2pqr): relax py-docutils dependency version
range
---
packages/py-pdb2pqr/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/py-pdb2pqr/package.py b/packages/py-pdb2pqr/package.py
index 9e3a72e8..1e87023a 100644
--- a/packages/py-pdb2pqr/package.py
+++ b/packages/py-pdb2pqr/package.py
@@ -28,7 +28,7 @@ class PyPdb2pqr(PythonPackage):
depends_on('python@3.8:', type=('build','run'))
depends_on('py-setuptools', type=('build'))
- depends_on('py-docutils@:0.18', type=('build','run'))
+ depends_on('py-docutils', type=('build','run'))
depends_on('py-mmcif-pdbx@1.1.2:', type=('build','run'))
depends_on('py-numpy', type=('build','run'))
depends_on('py-propka@3.2:', type=('build','run'))
--
GitLab
From a9c6db5fbc21e0cfde8423398e75afc61f5affde Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Mon, 10 Mar 2025 17:39:56 +0000
Subject: [PATCH 69/80] feat(py-biobb): add version 4.1.0
---
packages/py-biobb-analysis/package.py | 15 ++-------------
packages/py-biobb-chemistry/package.py | 15 ++-------------
spack.yaml | 4 ++--
3 files changed, 6 insertions(+), 28 deletions(-)
diff --git a/packages/py-biobb-analysis/package.py b/packages/py-biobb-analysis/package.py
index 799d4c36..9c580af0 100644
--- a/packages/py-biobb-analysis/package.py
+++ b/packages/py-biobb-analysis/package.py
@@ -12,14 +12,13 @@ class PyBiobbAnalysis(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_analysis"
git = 'https://github.com/bioexcel/biobb_analysis.git'
- url = 'https://github.com/bioexcel/biobb_analysis/archive/refs/tags/v4.0.1.tar.gz'
+ url = 'https://github.com/bioexcel/biobb_analysis/archive/refs/tags/v4.1.0.tar.gz'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
- version('master', branch='master')
- version('4.0.1', sha256='3d7190d0cae6af42b2e7c0ecf073930a609b699ef311e8b74afc1634958e09b0')
+ version('4.1.0', sha256='fecbb7ffa0e38f732fcc613adc7f1656e3c65af519a072269dabc244681f1791')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
@@ -27,16 +26,6 @@ class PyBiobbAnalysis(PythonPackage):
depends_on('gromacs')
depends_on('ambertools')
- # Patching to enable python 3.10 (not official, might not be stable)
- def patch(self):
- filter_file(" python_requires='>=3.7,<3.10',", " python_requires='>=3.7,<3.11',", "setup.py")
- filter_file(
- "'Programming Language :: Python :: 3.9'",
- "'Programming Language :: Python :: 3.9',\r\n "
- "'Programming Language :: Python :: 3.10'",
- "setup.py",
- )
-
# Test
@run_after('install')
@on_package_attributes(run_tests=True)
diff --git a/packages/py-biobb-chemistry/package.py b/packages/py-biobb-chemistry/package.py
index 6ec163b6..c30b8092 100644
--- a/packages/py-biobb-chemistry/package.py
+++ b/packages/py-biobb-chemistry/package.py
@@ -12,14 +12,13 @@ class PyBiobbChemistry(PythonPackage):
# Homepage and download url
homepage = "https://github.com/bioexcel/biobb_chemistry"
git = 'https://github.com/bioexcel/biobb_chemistry.git'
- url = 'https://github.com/bioexcel/biobb_chemistry/archive/refs/tags/v4.0.0.tar.gz'
+ url = 'https://github.com/bioexcel/biobb_chemistry/archive/refs/tags/v4.1.0.tar.gz'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
- version('master', branch='master')
- version('4.0.0', sha256='40f65b4a93dff24e19995265e41fd6821f5ac2f35199d938f1d00fa035883e64')
+ version('4.1.0', sha256='8d04943bbfcd83eb4d5d3247949cf035977fd097d5014a39354b0502e1cd16c8')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
@@ -28,16 +27,6 @@ class PyBiobbChemistry(PythonPackage):
depends_on('ambertools')
depends_on('acpype')
- # Patching to enable python 3.10 (not official, might not be stable)
- def patch(self):
- filter_file(" python_requires='>=3.7,<3.10',", " python_requires='>=3.7,<3.11',", "setup.py")
- filter_file(
- "'Programming Language :: Python :: 3.9'",
- "'Programming Language :: Python :: 3.9',\r\n "
- "'Programming Language :: Python :: 3.10'",
- "setup.py",
- )
-
# Test
@run_after('install')
@on_package_attributes(run_tests=True)
diff --git a/spack.yaml b/spack.yaml
index c6d455fd..9d86fd2f 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -4,8 +4,8 @@ spack:
specs:
# EBRAINS tools
- arbor@0.10.0 +python +mpi
- - py-biobb-analysis@4.0.1
- - py-biobb-chemistry@4.0.0
+ - py-biobb-analysis@4.1.0
+ - py-biobb-chemistry@4.1.0
- py-biobb-common@4.1.0
- py-biobb-gromacs@4.1.1
- py-biobb-io@4.1.0
--
GitLab
From 0cc20acdd73ce2461740fa0b01ebb7da7632811d Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Mon, 10 Mar 2025 17:43:53 +0000
Subject: [PATCH 70/80] feat(ambertools): copy package from upstream
---
packages/ambertools/package.py | 88 ++++++++++++++++++++++++++++++++++
1 file changed, 88 insertions(+)
create mode 100644 packages/ambertools/package.py
diff --git a/packages/ambertools/package.py b/packages/ambertools/package.py
new file mode 100644
index 00000000..f680b43c
--- /dev/null
+++ b/packages/ambertools/package.py
@@ -0,0 +1,88 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Ambertools(CMakePackage):
+ """AmberTools is a free, useful standalone package and a prerequisite
+ for installing Amber itself. The AmberTools suite is free of charge,
+ and its components are mostly released under the GNU General Public
+ License (GPL). A few components are included that are in the public
+ domain or which have other, open-source, licenses. The libsander and
+ libpbsa libraries use the LGPL license."""
+
+ homepage = "https://ambermd.org/AmberTools.php"
+ url = "https://ambermd.org/downloads/AmberTools22jlmrcc.tar.bz2"
+
+ maintainers("d-beltran")
+
+ version("22jlmrcc", sha256="1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121")
+
+ depends_on("flex", type="build")
+ depends_on("bison", type="build")
+ depends_on("tcsh", type="build")
+ depends_on("zlib", type=("build", "run"))
+ depends_on("bzip2", type=("build", "run"))
+ depends_on("blas", type=("build", "run"))
+ depends_on("lapack", type=("build", "run"))
+ depends_on("arpack-ng", type=("build", "run"))
+ depends_on("netcdf-c", type=("build", "run"))
+ depends_on("netcdf-fortran", type=("build", "run"))
+ depends_on("fftw", type=("build", "run"))
+ depends_on("readline", type=("build", "run"))
+ depends_on("netlib-xblas~plain_blas", type=("build", "run"))
+ # Specific variants needed for boost according to build logs
+ depends_on(
+ "boost+thread+system+program_options+iostreams+regex+timer+chrono+filesystem+graph",
+ type=("build", "run"),
+ )
+ # Python dependencies
+ depends_on("python@3.8:3.10 +tkinter", type=("build", "run"))
+ depends_on("py-setuptools", type="build")
+ depends_on("py-numpy", type=("build", "run"))
+ depends_on("py-matplotlib", type=("build", "run"))
+ depends_on("py-scipy", type=("build", "run"))
+
+ def cmake_args(self):
+ # Translated from ambertools build/run_cmake script
+ # We also add the TRUST_SYSTEM_LIBS argument mentioned in the ambertools guide
+ # https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Guide-to-Options
+ args = [
+ self.define("COMPILER", "GNU"),
+ self.define("MPI", False),
+ self.define("CUDA", False),
+ self.define("INSTALL_TESTS", True),
+ self.define("DOWNLOAD_MINICONDA", False),
+ self.define("TRUST_SYSTEM_LIBS", True),
+ # This is to avoid the x11 (X11_Xext_LIB) error
+ # It is equivalent to the "-noX11" flag accoridng to the docs:
+ # https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
+ self.define("BUILD_GUI", False),
+ ]
+ return args
+
+ def setup_run_environment(self, env):
+ env.set("AMBER_PREFIX", self.prefix)
+ env.set("AMBERHOME", self.prefix)
+
+ def setup_build_environment(self, env):
+ env.set("AMBER_PREFIX", self.prefix)
+ env.set("AMBERHOME", self.prefix)
+
+ @run_after("install")
+ @on_package_attributes(run_tests=True)
+ def check_install(self):
+ make("test.serial")
+
+ # Temporarily copy netcdf.h header file to netcdf-fortran/include to pass the Ambertools
+ # cmake check (quickest fix, will probably cause problems, needs to change)
+ @run_before("cmake")
+ def fix_check(self):
+ cp = Executable("cp")
+ cp(
+ self.spec["netcdf-c"].headers.directories[0] + "/netcdf.h",
+ self.spec["netcdf-fortran"].headers.directories[0],
+ )
--
GitLab
From 2cb260e64969b24b653aad73b9a4fbe7697a48c1 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Mon, 10 Mar 2025 17:45:39 +0000
Subject: [PATCH 71/80] feat(ambertools): add version 23
---
packages/ambertools/package.py | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/packages/ambertools/package.py b/packages/ambertools/package.py
index f680b43c..abe7df7d 100644
--- a/packages/ambertools/package.py
+++ b/packages/ambertools/package.py
@@ -19,6 +19,9 @@ class Ambertools(CMakePackage):
maintainers("d-beltran")
+ # begin EBRAINS (added): add version
+ version("23_rc6", sha256="debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d")
+ # end EBRAINS
version("22jlmrcc", sha256="1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121")
depends_on("flex", type="build")
@@ -40,7 +43,10 @@ class Ambertools(CMakePackage):
type=("build", "run"),
)
# Python dependencies
- depends_on("python@3.8:3.10 +tkinter", type=("build", "run"))
+ # begin EBRAINS (modified): add version
+ depends_on("python@3.8:3.10 +tkinter", type=("build", "run"), when="@22jlmrcc")
+ depends_on("python@3.8: +tkinter", type=("build", "run"), when="@23_rc6")
+ # end EBRAINS
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
--
GitLab
From 3681ab01f457ab98ffdcad66f5db27b7fbeead3d Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 11 Mar 2025 00:28:55 +0000
Subject: [PATCH 72/80] feat(sbml): add version 5.20.4
---
packages/sbml/package.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/packages/sbml/package.py b/packages/sbml/package.py
index f54fbb6b..7b40ffd5 100644
--- a/packages/sbml/package.py
+++ b/packages/sbml/package.py
@@ -17,6 +17,7 @@ class Sbml(CMakePackage):
license("LGPL-2.1-or-later")
# begin EBRAINS (added): add version
+ version("5.20.4", sha256="02c225d3513e1f5d6e3c0168456f568e67f006eddaab82f09b4bdf0d53d2050e", url="https://github.com/sbmlteam/libsbml/archive/refs/tags/v5.20.4.tar.gz")
version("5.19.0", sha256="a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547")
# end EBRAINS
version("5.18.0", sha256="6c01be2306ec0c9656b59cb082eb7b90176c39506dd0f912b02e08298a553360")
--
GitLab
From a26393e12b6cf8949fb5cdb8e4e8690cdd58c001 Mon Sep 17 00:00:00 2001
From: Adrian Ciu <adrian.ciu@codemart.ro>
Date: Tue, 11 Mar 2025 02:05:22 +0100
Subject: [PATCH 73/80] feat: import spack.package explicitly in all packages
---
packages/acpype/package.py | 2 +-
packages/apbs/package.py | 2 +-
packages/build-brainscales/package.py | 2 +-
packages/clb-nb-utils/package.py | 2 +-
packages/genpybind/package.py | 2 +-
packages/hxtorch/package.py | 2 +-
packages/inja/package.py | 2 +-
packages/jaxsnn/package.py | 2 +-
packages/nest/package.py | 2 +-
packages/oppulance/package.py | 2 +-
packages/psmisc/package.py | 2 +-
packages/py-annarchy/package.py | 2 +-
packages/py-bct/package.py | 2 +-
packages/py-biobb-analysis/package.py | 2 +-
packages/py-biobb-chemistry/package.py | 2 +-
packages/py-cerebstats/package.py | 2 +-
packages/py-cerebunit/package.py | 2 +-
packages/py-clang-format/package.py | 2 +-
packages/py-cons/package.py | 2 +-
packages/py-dicthash/package.py | 2 +-
packages/py-etuples/package.py | 2 +-
packages/py-flask-restx/package.py | 2 +-
packages/py-formencode/package.py | 3 +--
packages/py-frites/package.py | 2 +-
packages/py-hbp-archive/package.py | 2 +-
packages/py-hbp-neuromorphic-platform/package.py | 2 +-
packages/py-hippounit/package.py | 2 +-
packages/py-junitparser/package.py | 2 +-
packages/py-lems/package.py | 2 +-
packages/py-lfpy/package.py | 2 +-
packages/py-lfpykit/package.py | 2 +-
packages/py-libneuroml/package.py | 2 +-
packages/py-logical-unification/package.py | 2 +-
packages/py-mini-kanren/package.py | 2 +-
packages/py-mmcif-pdbx/package.py | 2 +-
packages/py-morphounit/package.py | 2 +-
packages/py-nameparser/package.py | 2 +-
packages/py-neo/package.py | 2 +-
packages/py-nested-dict/package.py | 2 +-
packages/py-nestml/package.py | 2 +-
packages/py-nflows/package.py | 2 +-
packages/py-nnmt/package.py | 2 +-
packages/py-odetoolbox/package.py | 2 +-
packages/py-pdb2pqr/package.py | 2 +-
packages/py-propka/package.py | 2 +-
packages/py-pyaescrypt/package.py | 2 +-
packages/py-pycatch22/package.py | 2 +-
packages/py-pyknos/package.py | 2 +-
packages/py-pymc/package.py | 2 +-
packages/py-pynn/package.py | 2 +-
packages/py-pyspike/package.py | 2 +-
packages/py-pyswarms/package.py | 2 +-
packages/py-pytensor/package.py | 2 +-
packages/py-python-keycloak/package.py | 2 +-
packages/py-pyunicore/package.py | 2 +-
packages/py-quantities-scidash/package.py | 2 +-
packages/py-quantities/package.py | 2 +-
packages/py-sbi/package.py | 2 +-
packages/py-sciunit/package.py | 2 +-
packages/py-snudda/package.py | 2 +-
packages/py-tvb-contrib/package.py | 2 +-
packages/py-tvb-data/package.py | 2 +-
packages/py-tvb-ext-bucket/package.py | 2 +-
packages/py-tvb-framework/package.py | 2 +-
packages/py-tvb-gdist/package.py | 2 +-
packages/py-tvb-library/package.py | 2 +-
packages/py-tvb-multiscale/package.py | 2 +-
packages/py-tvb-storage/package.py | 2 +-
packages/py-tvb-widgets/package.py | 2 +-
packages/py-umnn/package.py | 2 +-
packages/py-vbi/package.py | 2 +-
packages/py-viziphant/package.py | 2 +-
packages/py-zuko/package.py | 2 +-
packages/pynn-brainscales/package.py | 2 +-
packages/sda/package.py | 2 +-
packages/wf-biobb/package.py | 2 +-
packages/wf-brainscales2-demos/package.py | 2 +-
packages/wf-bsb/package.py | 2 +-
packages/wf-custom-python/package.py | 2 +-
packages/wf-human-multi-area-model/package.py | 2 +-
packages/wf-multi-area-model/package.py | 2 +-
packages/wf-protein-association-rates/package.py | 2 +-
packages/wf-uq-akar4/package.py | 2 +-
83 files changed, 83 insertions(+), 84 deletions(-)
diff --git a/packages/acpype/package.py b/packages/acpype/package.py
index cff6bc8e..c6382b76 100644
--- a/packages/acpype/package.py
+++ b/packages/acpype/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class Acpype(PythonPackage):
"""A tool based in Python to use Antechamber to generate topologies for chemical
diff --git a/packages/apbs/package.py b/packages/apbs/package.py
index f7f45c6e..bbfac340 100644
--- a/packages/apbs/package.py
+++ b/packages/apbs/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class Apbs(CMakePackage):
diff --git a/packages/build-brainscales/package.py b/packages/build-brainscales/package.py
index 2419107c..327501d1 100644
--- a/packages/build-brainscales/package.py
+++ b/packages/build-brainscales/package.py
@@ -7,7 +7,7 @@ import os
import unittest.mock
import xml.etree.ElementTree as ET
-from spack import *
+from spack.package import *
from spack.util.environment import EnvironmentModifications
import spack.build_environment
diff --git a/packages/clb-nb-utils/package.py b/packages/clb-nb-utils/package.py
index d75ae48c..40660252 100644
--- a/packages/clb-nb-utils/package.py
+++ b/packages/clb-nb-utils/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
# Usage
# from clb_nb_utils import oauth
diff --git a/packages/genpybind/package.py b/packages/genpybind/package.py
index 012d2e5b..bca2c483 100644
--- a/packages/genpybind/package.py
+++ b/packages/genpybind/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class Genpybind(WafPackage):
diff --git a/packages/hxtorch/package.py b/packages/hxtorch/package.py
index d4a5ea66..7d3a26bf 100644
--- a/packages/hxtorch/package.py
+++ b/packages/hxtorch/package.py
@@ -7,7 +7,7 @@ import os
import unittest.mock
import xml.etree.ElementTree as ET
-from spack import *
+from spack.package import *
from spack.util.environment import EnvironmentModifications
import spack.build_environment
diff --git a/packages/inja/package.py b/packages/inja/package.py
index f8f653e4..47a20743 100644
--- a/packages/inja/package.py
+++ b/packages/inja/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class Inja(CMakePackage):
diff --git a/packages/jaxsnn/package.py b/packages/jaxsnn/package.py
index b2b33296..8cca2481 100644
--- a/packages/jaxsnn/package.py
+++ b/packages/jaxsnn/package.py
@@ -7,7 +7,7 @@ import os
import unittest.mock
import xml.etree.ElementTree as ET
-from spack import *
+from spack.package import *
from spack.util.environment import EnvironmentModifications
import spack.build_environment
diff --git a/packages/nest/package.py b/packages/nest/package.py
index e97b81c8..d8e127da 100644
--- a/packages/nest/package.py
+++ b/packages/nest/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
import re
diff --git a/packages/oppulance/package.py b/packages/oppulance/package.py
index 7e0d22b6..7dc37d0a 100644
--- a/packages/oppulance/package.py
+++ b/packages/oppulance/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
import unittest.mock
diff --git a/packages/psmisc/package.py b/packages/psmisc/package.py
index f1a67530..4b727f19 100644
--- a/packages/psmisc/package.py
+++ b/packages/psmisc/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class Psmisc(AutotoolsPackage):
diff --git a/packages/py-annarchy/package.py b/packages/py-annarchy/package.py
index 4368d1e0..9fb9cab9 100644
--- a/packages/py-annarchy/package.py
+++ b/packages/py-annarchy/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyAnnarchy(PythonPackage):
diff --git a/packages/py-bct/package.py b/packages/py-bct/package.py
index bfa61d91..97ecec1b 100644
--- a/packages/py-bct/package.py
+++ b/packages/py-bct/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyBct(PythonPackage):
diff --git a/packages/py-biobb-analysis/package.py b/packages/py-biobb-analysis/package.py
index 9c580af0..79ce6edc 100644
--- a/packages/py-biobb-analysis/package.py
+++ b/packages/py-biobb-analysis/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyBiobbAnalysis(PythonPackage):
"""Biobb_analysis is the Biobb module collection to perform analysis
diff --git a/packages/py-biobb-chemistry/package.py b/packages/py-biobb-chemistry/package.py
index c30b8092..969a5058 100644
--- a/packages/py-biobb-chemistry/package.py
+++ b/packages/py-biobb-chemistry/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyBiobbChemistry(PythonPackage):
"""Biobb_chemistry is the Biobb module collection to perform chemistry
diff --git a/packages/py-cerebstats/package.py b/packages/py-cerebstats/package.py
index 5b1d3865..5c3a6f8a 100644
--- a/packages/py-cerebstats/package.py
+++ b/packages/py-cerebstats/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyCerebstats(PythonPackage):
diff --git a/packages/py-cerebunit/package.py b/packages/py-cerebunit/package.py
index d4a70054..62e29223 100644
--- a/packages/py-cerebunit/package.py
+++ b/packages/py-cerebunit/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyCerebunit(PythonPackage):
diff --git a/packages/py-clang-format/package.py b/packages/py-clang-format/package.py
index 7be2c021..19d74273 100644
--- a/packages/py-clang-format/package.py
+++ b/packages/py-clang-format/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyClangFormat(PythonPackage):
diff --git a/packages/py-cons/package.py b/packages/py-cons/package.py
index 77b2e1ab..e114b5b5 100644
--- a/packages/py-cons/package.py
+++ b/packages/py-cons/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyCons(PythonPackage):
diff --git a/packages/py-dicthash/package.py b/packages/py-dicthash/package.py
index 2fd2daf0..55ae9198 100644
--- a/packages/py-dicthash/package.py
+++ b/packages/py-dicthash/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyDicthash(PythonPackage):
diff --git a/packages/py-etuples/package.py b/packages/py-etuples/package.py
index d3462437..d8cca9f6 100644
--- a/packages/py-etuples/package.py
+++ b/packages/py-etuples/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyEtuples(PythonPackage):
diff --git a/packages/py-flask-restx/package.py b/packages/py-flask-restx/package.py
index 171f1039..7f9c45ec 100644
--- a/packages/py-flask-restx/package.py
+++ b/packages/py-flask-restx/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyFlaskRestx(PythonPackage):
diff --git a/packages/py-formencode/package.py b/packages/py-formencode/package.py
index f78e0e63..56c94e3d 100644
--- a/packages/py-formencode/package.py
+++ b/packages/py-formencode/package.py
@@ -3,8 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
-
+from spack.package import *
class PyFormencode(PythonPackage):
"""
diff --git a/packages/py-frites/package.py b/packages/py-frites/package.py
index 67c8f204..59aaca93 100644
--- a/packages/py-frites/package.py
+++ b/packages/py-frites/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyFrites(PythonPackage):
diff --git a/packages/py-hbp-archive/package.py b/packages/py-hbp-archive/package.py
index 580ec106..6f9921b0 100644
--- a/packages/py-hbp-archive/package.py
+++ b/packages/py-hbp-archive/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyHbpArchive(PythonPackage):
diff --git a/packages/py-hbp-neuromorphic-platform/package.py b/packages/py-hbp-neuromorphic-platform/package.py
index 06502497..3308957b 100644
--- a/packages/py-hbp-neuromorphic-platform/package.py
+++ b/packages/py-hbp-neuromorphic-platform/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyHbpNeuromorphicPlatform(PythonPackage):
diff --git a/packages/py-hippounit/package.py b/packages/py-hippounit/package.py
index 0317272c..0a6c294f 100644
--- a/packages/py-hippounit/package.py
+++ b/packages/py-hippounit/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyHippounit(PythonPackage):
diff --git a/packages/py-junitparser/package.py b/packages/py-junitparser/package.py
index 5f93f3e2..b794a44c 100644
--- a/packages/py-junitparser/package.py
+++ b/packages/py-junitparser/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyJunitparser(PythonPackage):
diff --git a/packages/py-lems/package.py b/packages/py-lems/package.py
index 456c8676..ff0173af 100644
--- a/packages/py-lems/package.py
+++ b/packages/py-lems/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyLems(PythonPackage):
diff --git a/packages/py-lfpy/package.py b/packages/py-lfpy/package.py
index bc3a1ee4..27cba28b 100644
--- a/packages/py-lfpy/package.py
+++ b/packages/py-lfpy/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyLfpy(PythonPackage):
diff --git a/packages/py-lfpykit/package.py b/packages/py-lfpykit/package.py
index 3768a8c4..ccabc623 100644
--- a/packages/py-lfpykit/package.py
+++ b/packages/py-lfpykit/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyLfpykit(PythonPackage):
diff --git a/packages/py-libneuroml/package.py b/packages/py-libneuroml/package.py
index d660b23e..babb2b21 100644
--- a/packages/py-libneuroml/package.py
+++ b/packages/py-libneuroml/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyLibneuroml(PythonPackage):
diff --git a/packages/py-logical-unification/package.py b/packages/py-logical-unification/package.py
index 7ba1620e..e4c453c1 100644
--- a/packages/py-logical-unification/package.py
+++ b/packages/py-logical-unification/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyLogicalUnification(PythonPackage):
diff --git a/packages/py-mini-kanren/package.py b/packages/py-mini-kanren/package.py
index 2d24eb02..d777ee61 100644
--- a/packages/py-mini-kanren/package.py
+++ b/packages/py-mini-kanren/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyMiniKanren(PythonPackage):
diff --git a/packages/py-mmcif-pdbx/package.py b/packages/py-mmcif-pdbx/package.py
index 02daf8fc..25dfc8ed 100644
--- a/packages/py-mmcif-pdbx/package.py
+++ b/packages/py-mmcif-pdbx/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyMmcifPdbx(PythonPackage):
diff --git a/packages/py-morphounit/package.py b/packages/py-morphounit/package.py
index 3884482e..382a6d49 100644
--- a/packages/py-morphounit/package.py
+++ b/packages/py-morphounit/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyMorphounit(PythonPackage):
diff --git a/packages/py-nameparser/package.py b/packages/py-nameparser/package.py
index a3e3eb71..f4eb768b 100644
--- a/packages/py-nameparser/package.py
+++ b/packages/py-nameparser/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyNameparser(PythonPackage):
diff --git a/packages/py-neo/package.py b/packages/py-neo/package.py
index 90054098..3ce2a9bc 100644
--- a/packages/py-neo/package.py
+++ b/packages/py-neo/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyNeo(PythonPackage):
diff --git a/packages/py-nested-dict/package.py b/packages/py-nested-dict/package.py
index 5fc5ff00..96e9b79b 100644
--- a/packages/py-nested-dict/package.py
+++ b/packages/py-nested-dict/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyNestedDict(PythonPackage):
diff --git a/packages/py-nestml/package.py b/packages/py-nestml/package.py
index a5ea9b1b..d3437f3b 100644
--- a/packages/py-nestml/package.py
+++ b/packages/py-nestml/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyNestml(PythonPackage):
diff --git a/packages/py-nflows/package.py b/packages/py-nflows/package.py
index 72f82caf..b6c32ffe 100644
--- a/packages/py-nflows/package.py
+++ b/packages/py-nflows/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyNflows(PythonPackage):
"""It is a comprehensive collection of normalizing flows using PyTorch."""
diff --git a/packages/py-nnmt/package.py b/packages/py-nnmt/package.py
index 7b722a7f..c605bd72 100644
--- a/packages/py-nnmt/package.py
+++ b/packages/py-nnmt/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyNnmt(PythonPackage):
diff --git a/packages/py-odetoolbox/package.py b/packages/py-odetoolbox/package.py
index 3ebd6e68..c5ccc459 100644
--- a/packages/py-odetoolbox/package.py
+++ b/packages/py-odetoolbox/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyOdetoolbox(PythonPackage):
diff --git a/packages/py-pdb2pqr/package.py b/packages/py-pdb2pqr/package.py
index 1e87023a..b737eb38 100644
--- a/packages/py-pdb2pqr/package.py
+++ b/packages/py-pdb2pqr/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPdb2pqr(PythonPackage):
diff --git a/packages/py-propka/package.py b/packages/py-propka/package.py
index edb466b4..b75a09b3 100644
--- a/packages/py-propka/package.py
+++ b/packages/py-propka/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPropka(PythonPackage):
diff --git a/packages/py-pyaescrypt/package.py b/packages/py-pyaescrypt/package.py
index d0b38eb1..ab15e7f7 100644
--- a/packages/py-pyaescrypt/package.py
+++ b/packages/py-pyaescrypt/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPyaescrypt(PythonPackage):
diff --git a/packages/py-pycatch22/package.py b/packages/py-pycatch22/package.py
index 68c4be09..6707282e 100644
--- a/packages/py-pycatch22/package.py
+++ b/packages/py-pycatch22/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPycatch22(PythonPackage):
diff --git a/packages/py-pyknos/package.py b/packages/py-pyknos/package.py
index e9449a6d..151fd077 100644
--- a/packages/py-pyknos/package.py
+++ b/packages/py-pyknos/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPyknos(PythonPackage):
diff --git a/packages/py-pymc/package.py b/packages/py-pymc/package.py
index b7dc999f..453829ab 100644
--- a/packages/py-pymc/package.py
+++ b/packages/py-pymc/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPymc(PythonPackage):
diff --git a/packages/py-pynn/package.py b/packages/py-pynn/package.py
index f75382bc..73df7c20 100644
--- a/packages/py-pynn/package.py
+++ b/packages/py-pynn/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPynn(PythonPackage):
diff --git a/packages/py-pyspike/package.py b/packages/py-pyspike/package.py
index ddf17e7e..c0ce25b6 100644
--- a/packages/py-pyspike/package.py
+++ b/packages/py-pyspike/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPyspike(PythonPackage):
diff --git a/packages/py-pyswarms/package.py b/packages/py-pyswarms/package.py
index 60c85b39..f9d94540 100644
--- a/packages/py-pyswarms/package.py
+++ b/packages/py-pyswarms/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPyswarms(PythonPackage):
diff --git a/packages/py-pytensor/package.py b/packages/py-pytensor/package.py
index 4c045393..b47935f4 100644
--- a/packages/py-pytensor/package.py
+++ b/packages/py-pytensor/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPytensor(PythonPackage):
"""Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving
diff --git a/packages/py-python-keycloak/package.py b/packages/py-python-keycloak/package.py
index 44c4d562..b7f3d7cc 100644
--- a/packages/py-python-keycloak/package.py
+++ b/packages/py-python-keycloak/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPythonKeycloak(PythonPackage):
"""python-keycloak is a Python package providing access to the Keycloak API"""
diff --git a/packages/py-pyunicore/package.py b/packages/py-pyunicore/package.py
index 1d6b71b3..0eb54988 100644
--- a/packages/py-pyunicore/package.py
+++ b/packages/py-pyunicore/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyPyunicore(PythonPackage):
diff --git a/packages/py-quantities-scidash/package.py b/packages/py-quantities-scidash/package.py
index 08fcee32..f075e7fa 100644
--- a/packages/py-quantities-scidash/package.py
+++ b/packages/py-quantities-scidash/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyQuantitiesScidash(PythonPackage):
diff --git a/packages/py-quantities/package.py b/packages/py-quantities/package.py
index ffe38173..e5d14e95 100644
--- a/packages/py-quantities/package.py
+++ b/packages/py-quantities/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyQuantities(PythonPackage):
diff --git a/packages/py-sbi/package.py b/packages/py-sbi/package.py
index a560cd93..5e1c50df 100644
--- a/packages/py-sbi/package.py
+++ b/packages/py-sbi/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PySbi(PythonPackage):
diff --git a/packages/py-sciunit/package.py b/packages/py-sciunit/package.py
index 5684040b..ca8cf891 100644
--- a/packages/py-sciunit/package.py
+++ b/packages/py-sciunit/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PySciunit(PythonPackage):
diff --git a/packages/py-snudda/package.py b/packages/py-snudda/package.py
index 621df60f..f8458a3f 100644
--- a/packages/py-snudda/package.py
+++ b/packages/py-snudda/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PySnudda(PythonPackage):
diff --git a/packages/py-tvb-contrib/package.py b/packages/py-tvb-contrib/package.py
index 8f940f0c..7a136a1a 100644
--- a/packages/py-tvb-contrib/package.py
+++ b/packages/py-tvb-contrib/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyTvbContrib(PythonPackage):
diff --git a/packages/py-tvb-data/package.py b/packages/py-tvb-data/package.py
index 1e5e9353..abe486cd 100644
--- a/packages/py-tvb-data/package.py
+++ b/packages/py-tvb-data/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyTvbData(PythonPackage):
diff --git a/packages/py-tvb-ext-bucket/package.py b/packages/py-tvb-ext-bucket/package.py
index 3d5e7c2b..29fdae03 100644
--- a/packages/py-tvb-ext-bucket/package.py
+++ b/packages/py-tvb-ext-bucket/package.py
@@ -1,4 +1,4 @@
-from spack import *
+from spack.package import *
class PyTvbExtBucket(PythonPackage):
diff --git a/packages/py-tvb-framework/package.py b/packages/py-tvb-framework/package.py
index fb1ebc2f..12c01e6a 100644
--- a/packages/py-tvb-framework/package.py
+++ b/packages/py-tvb-framework/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyTvbFramework(PythonPackage):
diff --git a/packages/py-tvb-gdist/package.py b/packages/py-tvb-gdist/package.py
index 34f70127..38cfa771 100644
--- a/packages/py-tvb-gdist/package.py
+++ b/packages/py-tvb-gdist/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyTvbGdist(PythonPackage):
diff --git a/packages/py-tvb-library/package.py b/packages/py-tvb-library/package.py
index c624a102..8386fb5a 100644
--- a/packages/py-tvb-library/package.py
+++ b/packages/py-tvb-library/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyTvbLibrary(PythonPackage):
diff --git a/packages/py-tvb-multiscale/package.py b/packages/py-tvb-multiscale/package.py
index b57b8f03..176f5532 100644
--- a/packages/py-tvb-multiscale/package.py
+++ b/packages/py-tvb-multiscale/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyTvbMultiscale(PythonPackage):
diff --git a/packages/py-tvb-storage/package.py b/packages/py-tvb-storage/package.py
index d25e7690..4c6f89ad 100644
--- a/packages/py-tvb-storage/package.py
+++ b/packages/py-tvb-storage/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyTvbStorage(PythonPackage):
diff --git a/packages/py-tvb-widgets/package.py b/packages/py-tvb-widgets/package.py
index 855ac583..07dd8cf1 100644
--- a/packages/py-tvb-widgets/package.py
+++ b/packages/py-tvb-widgets/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyTvbWidgets(PythonPackage):
diff --git a/packages/py-umnn/package.py b/packages/py-umnn/package.py
index 545b1ec0..6cc01282 100644
--- a/packages/py-umnn/package.py
+++ b/packages/py-umnn/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyUmnn(PythonPackage):
diff --git a/packages/py-vbi/package.py b/packages/py-vbi/package.py
index 0ac988a2..9c4258de 100644
--- a/packages/py-vbi/package.py
+++ b/packages/py-vbi/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyVbi(PythonPackage, CudaPackage):
diff --git a/packages/py-viziphant/package.py b/packages/py-viziphant/package.py
index 22281cb4..8f409f9c 100644
--- a/packages/py-viziphant/package.py
+++ b/packages/py-viziphant/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyViziphant(PythonPackage):
diff --git a/packages/py-zuko/package.py b/packages/py-zuko/package.py
index 9c222273..5e712df7 100644
--- a/packages/py-zuko/package.py
+++ b/packages/py-zuko/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class PyZuko(PythonPackage):
diff --git a/packages/pynn-brainscales/package.py b/packages/pynn-brainscales/package.py
index e0836671..2a4a0a10 100644
--- a/packages/pynn-brainscales/package.py
+++ b/packages/pynn-brainscales/package.py
@@ -7,7 +7,7 @@ import os
import unittest.mock
import xml.etree.ElementTree as ET
-from spack import *
+from spack.package import *
from spack.util.environment import EnvironmentModifications
import spack.build_environment
diff --git a/packages/sda/package.py b/packages/sda/package.py
index 77f19f54..3fb569c5 100644
--- a/packages/sda/package.py
+++ b/packages/sda/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class Sda(MakefilePackage):
diff --git a/packages/wf-biobb/package.py b/packages/wf-biobb/package.py
index 28ff7c41..61d14695 100644
--- a/packages/wf-biobb/package.py
+++ b/packages/wf-biobb/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class WfBiobb(BundlePackage):
diff --git a/packages/wf-brainscales2-demos/package.py b/packages/wf-brainscales2-demos/package.py
index 1dc5b24b..02592a1d 100644
--- a/packages/wf-brainscales2-demos/package.py
+++ b/packages/wf-brainscales2-demos/package.py
@@ -4,7 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from glob import glob
-from spack import *
+from spack.package import *
import os
diff --git a/packages/wf-bsb/package.py b/packages/wf-bsb/package.py
index 2e843818..37ec15a7 100644
--- a/packages/wf-bsb/package.py
+++ b/packages/wf-bsb/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class WfBsb(BundlePackage):
diff --git a/packages/wf-custom-python/package.py b/packages/wf-custom-python/package.py
index 84ebe4cc..6fae2ed1 100644
--- a/packages/wf-custom-python/package.py
+++ b/packages/wf-custom-python/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class WfCustomPython(BundlePackage):
diff --git a/packages/wf-human-multi-area-model/package.py b/packages/wf-human-multi-area-model/package.py
index 5bcefe0d..d5246fc8 100644
--- a/packages/wf-human-multi-area-model/package.py
+++ b/packages/wf-human-multi-area-model/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class WfHumanMultiAreaModel(Package):
diff --git a/packages/wf-multi-area-model/package.py b/packages/wf-multi-area-model/package.py
index 51d59bb3..fa4828a0 100644
--- a/packages/wf-multi-area-model/package.py
+++ b/packages/wf-multi-area-model/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class WfMultiAreaModel(Package):
diff --git a/packages/wf-protein-association-rates/package.py b/packages/wf-protein-association-rates/package.py
index b20c409a..3d13eb8d 100644
--- a/packages/wf-protein-association-rates/package.py
+++ b/packages/wf-protein-association-rates/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class WfProteinAssociationRates(BundlePackage):
diff --git a/packages/wf-uq-akar4/package.py b/packages/wf-uq-akar4/package.py
index 10c3fb8f..5e819976 100644
--- a/packages/wf-uq-akar4/package.py
+++ b/packages/wf-uq-akar4/package.py
@@ -3,7 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack import *
+from spack.package import *
class WfUqAkar4(BundlePackage):
--
GitLab
From 11bd19f35b06131d3f8526cd13944910c949be89 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Fri, 7 Mar 2025 14:07:12 +0100
Subject: [PATCH 74/80] feat(BSS2): update packages (end-of-July 2024 -> "now")
---
packages/build-brainscales/package.py | 8 ++++++++
packages/genpybind/package.py | 1 +
packages/oppulance/package.py | 7 +++++++
packages/wf-brainscales2-demos/package.py | 1 +
spack.yaml | 8 ++++----
5 files changed, 21 insertions(+), 4 deletions(-)
diff --git a/packages/build-brainscales/package.py b/packages/build-brainscales/package.py
index 327501d1..9d78d8ce 100644
--- a/packages/build-brainscales/package.py
+++ b/packages/build-brainscales/package.py
@@ -15,6 +15,13 @@ import spack.build_environment
class BuildBrainscales(WafPackage):
"""Common stuff for BrainScaleS packages..."""
+ version(
+ "10.0-a1",
+ git="https://github.com/electronicvisions/releases-ebrains",
+ tag="ebrains-10.0-a1",
+ commit="d9bd675b446be8f313972aef2d6657ffbbb91ed2",
+ submodules=True,
+ )
version(
"9.0-a9",
git="https://github.com/electronicvisions/releases-ebrains",
@@ -59,6 +66,7 @@ class BuildBrainscales(WafPackage):
)
# common dependencies of BuildBrainscales-derived packages
+ depends_on('oppulance@10.0-a1', when='@10.0-a1', type=('build', 'link', 'run', 'test'))
depends_on('oppulance@9.0-a9', when='@9.0-a9', type=('build', 'link', 'run', 'test'))
depends_on('oppulance@9.0-a8', when='@9.0-a8', type=('build', 'link', 'run', 'test'))
depends_on('oppulance@9.0-a7', when='@9.0-a7', type=('build', 'link', 'run', 'test'))
diff --git a/packages/genpybind/package.py b/packages/genpybind/package.py
index bca2c483..79e1d7e8 100644
--- a/packages/genpybind/package.py
+++ b/packages/genpybind/package.py
@@ -21,6 +21,7 @@ class Genpybind(WafPackage):
version('develop', branch='develop')
version('visions', branch='master', git='https://github.com/electronicvisions/genpybind')
+ # good for ebrains-10.0 too…
version('ebrains-llvm15', tag='ebrains-9.0-a9', git='https://github.com/electronicvisions/genpybind')
version('ebrains', tag='ebrains_release-1-rc1', git='https://github.com/electronicvisions/genpybind')
diff --git a/packages/oppulance/package.py b/packages/oppulance/package.py
index 7dc37d0a..ede72e35 100644
--- a/packages/oppulance/package.py
+++ b/packages/oppulance/package.py
@@ -22,6 +22,13 @@ class Oppulance(Package):
depends_on('wget')
depends_on('gmp')
+ version(
+ "10.0-a1",
+ git="https://github.com/electronicvisions/releases-ebrains",
+ tag="ebrains-10.0-a1",
+ commit="d9bd675b446be8f313972aef2d6657ffbbb91ed2",
+ submodules=True,
+ )
version(
"9.0-a9",
git="https://github.com/electronicvisions/releases-ebrains",
diff --git a/packages/wf-brainscales2-demos/package.py b/packages/wf-brainscales2-demos/package.py
index 02592a1d..e98423a2 100644
--- a/packages/wf-brainscales2-demos/package.py
+++ b/packages/wf-brainscales2-demos/package.py
@@ -16,6 +16,7 @@ class WfBrainscales2Demos(Package):
maintainers = ["emuller", "muffgaga"]
# ECM: we probably should build the ipynb file in this package
+ version("10.0-a1", tag="jupyter-notebooks-10.0-a1")
version("9.0-a9", tag="jupyter-notebooks-9.0-a9")
version("9.0-a8", tag="jupyter-notebooks-9.0-a8")
version("9.0-a7", tag="jupyter-notebooks-9.0-a7")
diff --git a/spack.yaml b/spack.yaml
index 9d86fd2f..beaf68f9 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -12,10 +12,10 @@ spack:
- py-biobb-model@4.1.0
- py-biobb-structure-checking@3.13.4
- py-biobb-structure-utils@4.1.0
- - hxtorch@9.0-a9
+ - hxtorch@10.0-a1
- nest@3.8 +sonata
- neuron@8.2.3 +mpi
- - jaxsnn@9.0-a9
+ - jaxsnn@10.0-a1
- py-bluepyefe@2.3.6
- py-bluepymm@0.8.7
- py-bluepyopt@1.14.11
@@ -62,14 +62,14 @@ spack:
- py-tvb-ext-xircuits@1.1.0
- py-viziphant@0.4.0
- py-vbi
- - pynn-brainscales@9.0-a9
+ - pynn-brainscales@10.0-a1
- r-rgsl@0.1.1
- r-sbtabvfgen@0.1
- r-uqsa@2.2
- sda@7.3.3d
# Workflows (meta-packages)
- wf-biobb
- - wf-brainscales2-demos@9.0-a9
+ - wf-brainscales2-demos@10.0-a1
- wf-bsb@4.4 +nest +neuron
- wf-protein-association-rates@0.1
- wf-multi-area-model@1.2.0
--
GitLab
From 7aa466477e4eb779707347ed77277dc15c66befc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Sat, 8 Mar 2025 09:56:13 +0100
Subject: [PATCH 75/80] fix(BSS2): use old oppulance (unchanged in code)
---
packages/build-brainscales/package.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/packages/build-brainscales/package.py b/packages/build-brainscales/package.py
index 9d78d8ce..f679dab0 100644
--- a/packages/build-brainscales/package.py
+++ b/packages/build-brainscales/package.py
@@ -66,7 +66,7 @@ class BuildBrainscales(WafPackage):
)
# common dependencies of BuildBrainscales-derived packages
- depends_on('oppulance@10.0-a1', when='@10.0-a1', type=('build', 'link', 'run', 'test'))
+ depends_on('oppulance@9.0-a9', when='@10.0-a1', type=('build', 'link', 'run', 'test')) # keep the old one for now
depends_on('oppulance@9.0-a9', when='@9.0-a9', type=('build', 'link', 'run', 'test'))
depends_on('oppulance@9.0-a8', when='@9.0-a8', type=('build', 'link', 'run', 'test'))
depends_on('oppulance@9.0-a7', when='@9.0-a7', type=('build', 'link', 'run', 'test'))
--
GitLab
From 830af90825cf2b7859ebeaff6919cf891fc6d6d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eric=20M=C3=BCller?= <mueller@kip.uni-heidelberg.de>
Date: Mon, 10 Mar 2025 15:12:30 +0100
Subject: [PATCH 76/80] fix(BSS2(hxtorch)): add missing dependency on
py-quantities
---
packages/hxtorch/package.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/packages/hxtorch/package.py b/packages/hxtorch/package.py
index 7d3a26bf..a74813aa 100644
--- a/packages/hxtorch/package.py
+++ b/packages/hxtorch/package.py
@@ -79,6 +79,7 @@ class Hxtorch(build_brainscales.BuildBrainscales):
('py-torch@1.9.1:', { "type": ('build', 'link', 'run', 'test') } ),
('py-torchvision', { "type": ('run') } ), # for demos
('py-pyyaml', { "type": ('build', 'link', 'run') } ),
+ ('py-quantities@0.12.1:', { "type": ('build', 'link', 'run') } ), # PyNN-like interfacing of things?
('py-scipy', { "type": ('build', 'link', 'run') } ),
('py-sqlalchemy', { "type": ('build', 'link', 'run') } ),
('util-linux', { "type": ('build', 'link', 'run') } ),
--
GitLab
From 88ea272fa8ea4241d3623e249bf5f59f4042cf85 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 11 Mar 2025 06:35:08 +0000
Subject: [PATCH 77/80] feat(glfw): copy package from upstream
---
packages/glfw/package.py | 53 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
create mode 100644 packages/glfw/package.py
diff --git a/packages/glfw/package.py b/packages/glfw/package.py
new file mode 100644
index 00000000..ba005f77
--- /dev/null
+++ b/packages/glfw/package.py
@@ -0,0 +1,53 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Glfw(CMakePackage):
+ """GLFW is an Open Source, multi-platform library for
+ OpenGL, OpenGL ES and Vulkan development on the desktop. It
+ provides a simple API for creating windows, contexts and
+ surfaces, receiving input and events."""
+
+ homepage = "https://www.glfw.org/"
+ url = "https://github.com/glfw/glfw/archive/3.3.2.tar.gz"
+
+ license("Zlib")
+
+ version("3.3.8", sha256="f30f42e05f11e5fc62483e513b0488d5bceeab7d9c5da0ffe2252ad81816c713")
+ version("3.3.2", sha256="98768e12e615fbe9f3386f5bbfeb91b5a3b45a8c4c77159cef06b1f6ff749537")
+ version("3.3.1", sha256="6bca16e69361798817a4b62a5239a77253c29577fcd5d52ae8b85096e514177f")
+ version("3.3", sha256="81bf5fde487676a8af55cb317830703086bb534c53968d71936e7b48ee5a0f3e")
+ version("3.2.1", sha256="e10f0de1384d75e6fc210c53e91843f6110d6c4f3afbfb588130713c2f9d8fe8")
+ version("3.2", sha256="cb3aab46757981a39ae108e5207a1ecc4378e68949433a2b040ce2e17d8f6aa6")
+ version("3.1.2", sha256="6ac642087682aaf7f8397761a41a99042b2c656498217a1c63ba9706d1eef122")
+ version("3.1.1", sha256="4de311ec9bf43bfdc8423ddf93b91dc54dc73dcfbedfb0991b6fbb3a9baf245f")
+ version("3.1", sha256="2140f4c532e7ce4c84cb7e4c419d0979d5954fa1ce204b7646491bd2cc5bf308")
+ version("3.0.4", sha256="a4e7c57db2086803de4fc853bd472ff8b6d2639b9aa16e6ac6b19ffb53958caf")
+ version("3.0.3", sha256="7a182047ba6b1fdcda778b79aac249bb2328b6d141188cb5df29560715d01693")
+
+ depends_on("c", type="build") # generated
+
+ variant("doc", default=False, description="Build documentation")
+ variant("shared", default=False, description="Builds a shared version of the library")
+
+ # dependencies
+ depends_on("doxygen", type="build", when="+doc")
+
+ # linux only dependencies
+ depends_on("libxrandr", when="platform=linux")
+ depends_on("libxinerama", when="platform=linux")
+ depends_on("libxcursor", when="platform=linux")
+ depends_on("libxdamage", when="platform=linux")
+ depends_on("libxft", when="platform=linux")
+ depends_on("libxi", when="platform=linux")
+ depends_on("libxmu", when="platform=linux")
+ depends_on("freetype", when="platform=linux")
+ depends_on("fontconfig", when="platform=linux")
+ depends_on("pkgconfig", type="build", when="platform=linux")
+
+ def cmake_args(self):
+ return [self.define_from_variant("BUILD_SHARED_LIBS", "shared")]
--
GitLab
From aaeb83ce0c81ddeb15a4951a9da3c2ee7befafe6 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 11 Mar 2025 07:29:28 +0000
Subject: [PATCH 78/80] feat(glfw): add version 3.4
---
packages/glfw/package.py | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/packages/glfw/package.py b/packages/glfw/package.py
index ba005f77..ab81c753 100644
--- a/packages/glfw/package.py
+++ b/packages/glfw/package.py
@@ -17,6 +17,9 @@ class Glfw(CMakePackage):
license("Zlib")
+ # begin EBRAINS (added): new version
+ version("3.4", sha256="c038d34200234d071fae9345bc455e4a8f2f544ab60150765d7704e08f3dac01")
+ # end EBRAINS
version("3.3.8", sha256="f30f42e05f11e5fc62483e513b0488d5bceeab7d9c5da0ffe2252ad81816c713")
version("3.3.2", sha256="98768e12e615fbe9f3386f5bbfeb91b5a3b45a8c4c77159cef06b1f6ff749537")
version("3.3.1", sha256="6bca16e69361798817a4b62a5239a77253c29577fcd5d52ae8b85096e514177f")
@@ -49,5 +52,10 @@ class Glfw(CMakePackage):
depends_on("fontconfig", when="platform=linux")
depends_on("pkgconfig", type="build", when="platform=linux")
+ # begin EBRAINS (added): missing dependency
+ depends_on("wayland", when="platform=linux")
+ depends_on("libxkbcommon", when="platform=linux")
+ # end EBRAINS
+
def cmake_args(self):
return [self.define_from_variant("BUILD_SHARED_LIBS", "shared")]
--
GitLab
From e6ab62d07c1d7e7b7141a103f0664a74c6d7d23a Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 11 Mar 2025 07:30:14 +0000
Subject: [PATCH 79/80] feat(open3d): add version 0.19.0
---
packages/open3d/package.py | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/packages/open3d/package.py b/packages/open3d/package.py
index c1faaa0b..3deedf47 100644
--- a/packages/open3d/package.py
+++ b/packages/open3d/package.py
@@ -20,6 +20,9 @@ class Open3d(CMakePackage, CudaPackage):
license("MIT")
# begin EBRAINS (added): add version
+ version(
+ "0.19.0", tag="v0.19.0", commit="1e7b17438687a0b0c1e5a7187321ac7044afe275", submodules=True
+ )
version(
"0.18.0", tag="v0.18.0", commit="0f06a149c4fb9406fd3e432a5cb0c024f38e2f0e", submodules=True
)
@@ -66,12 +69,13 @@ class Open3d(CMakePackage, CudaPackage):
depends_on("assimp", when="@0.15:")
depends_on("jsoncpp", when="@0.15:")
depends_on("msgpack-c", when="@0.15:")
- # depends_on("tbb", when="@0.15:")
+ depends_on("tbb", when="@0.15:")
depends_on("cppzmq", when="@0.15:")
depends_on("curl", when="@0.17:")
depends_on("openssl", when="@0.17:")
# depends_on("vtk", when="@0.17:")
- depends_on("embree@:3", when="@0.18:")
+ depends_on("embree@:3", when="@0.18")
+ depends_on("embree@4:", when="@0.19:")
# end EBRAINS
extends("python", when="+python", type=("build", "link", "run"))
@@ -157,7 +161,7 @@ class Open3d(CMakePackage, CudaPackage):
args.append(self.define("USE_SYSTEM_JSONCPP", True))
args.append(self.define("USE_SYSTEM_MSGPACK", True))
args.append(self.define("USE_SYSTEM_NANOFLANN", True))
- # args.append(self.define("USE_SYSTEM_TBB", True))
+ args.append(self.define("USE_SYSTEM_TBB", True))
args.append(self.define("USE_SYSTEM_ZEROMQ", True))
if self.spec.satisfies("@0.17:"):
args.append(self.define("USE_SYSTEM_CURL", True))
@@ -204,3 +208,4 @@ class Open3d(CMakePackage, CudaPackage):
with working_dir("spack-test"):
python = which(python.path)
python("-c", "import open3d")
+
--
GitLab
From b8293048a5da7fef5adf21f225063999816c7438 Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Tue, 11 Mar 2025 13:45:12 +0000
Subject: [PATCH 80/80] feat(CI): increase number of jobs
---
.gitlab-ci.yml | 2 +-
create_job.sh | 8 ++++----
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 17476bd7..e8524909 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -274,7 +274,7 @@ sync-gitlab-spack-instance:
image: $BUILD_ENV_DOCKER_IMAGE
variables:
SPACK_REPO_PATH: $SPACK_PATH_GITLAB/ebrains-spack-builds
- SPACK_JOBS: 4
+ SPACK_JOBS: 16
OCI_CACHE_PREFIX: ""
UPDATE_SPACK_OCI_CACHES: false
script:
diff --git a/create_job.sh b/create_job.sh
index 60958e3b..56d80c8f 100644
--- a/create_job.sh
+++ b/create_job.sh
@@ -36,11 +36,11 @@ spec:
imagePullPolicy: Always
resources:
limits:
- cpu: '6'
- memory: '18Gi'
+ cpu: '8'
+ memory: '32Gi'
requests:
cpu: '4'
- memory: '12Gi'
+ memory: '20Gi'
volumeMounts:
- name: sharedbin
mountPath: /srv
@@ -99,7 +99,7 @@ spec:
- name: EBRAINS_REPO_PATH
value: $INSTALLATION_ROOT/ebrains-spack-builds
- name: SPACK_JOBS
- value: '4'
+ value: '6'
volumes:
- name: sharedbin
persistentVolumeClaim:
--
GitLab