packages/bazel/patch_for_fcc.patch

-diff --git a/src/main/cpp/blaze_util_posix.cc b/src/main/cpp/blaze_util_posix.cc
-index 87ba899180..1c967ee818 100644
---- a/src/main/cpp/blaze_util_posix.cc
-+++ b/src/main/cpp/blaze_util_posix.cc
-@@ -565,7 +565,8 @@ static int setlk(int fd, struct flock *lock) {
-   // Prefer OFD locks if available.  POSIX locks can be lost "accidentally"
-   // due to any close() on the lock file, and are not reliably preserved
-   // across execve() on Linux, which we need for --batch mode.
--  if (fcntl(fd, F_OFD_SETLK, lock) == 0) return 0;
-+  //if (fcntl(fd, F_OFD_SETLK, lock) == 0) return 0;
-+  if (fcntl(fd, F_SETLK, lock) == 0) return 0;
-   if (errno != EINVAL) {
-     if (errno != EACCES && errno != EAGAIN) {
-       BAZEL_DIE(blaze_exit_code::LOCAL_ENVIRONMENTAL_ERROR)
-diff --git a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl
-index ccb18a431a..0c5c8fd6f0 100644
---- a/tools/cpp/unix_cc_configure.bzl
-+++ b/tools/cpp/unix_cc_configure.bzl
-@@ -379,7 +379,8 @@ def configure_unix_toolchain(repository_ctx, cpu_value, overriden_tools):
-         "",
-         False,
-     ), ":")
--    gold_linker_path = _find_gold_linker_path(repository_ctx, cc)
-+    #gold_linker_path = _find_gold_linker_path(repository_ctx, cc)
-+    gold_linker_path = None
-     cc_path = repository_ctx.path(cc)
-     if not str(cc_path).startswith(str(repository_ctx.path(".")) + "/"):
-         # cc is outside the repository, set -B
-@@ -468,7 +469,7 @@ def configure_unix_toolchain(repository_ctx, cpu_value, overriden_tools):
-                     # Security hardening requires optimization.
-                     # We need to undef it as some distributions now have it enabled by default.
-                     "-U_FORTIFY_SOURCE",
--                    "-fstack-protector",
-+                    #"-fstack-protector",
-                     # All warnings are enabled. Maybe enable -Werror as well?
-                     "-Wall",
-                     # Enable a few more warnings that aren't part of -Wall.

packages/bazel/patch_for_fcc2.patch

---- 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
-@@ -185,7 +185,7 @@ public class BazelRuleClassProvider {
- 
-         Map<String, String> spackEnv = System.getenv();
-         for (String envName : spackEnv.keySet()) {
--          if (envName.startsWith("SPACK_")) {
-+          if ((envName.startsWith("SPACK_")) || (envName.equals("fcc_ENV")) || (envName.equals("FCC_ENV"))) {
-             env.put(envName, spackEnv.get(envName));
-           }
-         }

packages/bazel/rename-gettid-functions-0.25.patch

-From d1d017390b799c59d6fdf7b8afa6136d218bdd61 Mon Sep 17 00:00:00 2001
-From: Benjamin Peterson <benjamin@dropbox.com>
-Date: Fri, 3 May 2019 08:11:00 -0700
-Subject: [PATCH] Rename gettid() functions.
-
-glibc 2.30 will declare its own gettid; see https://sourceware.org/git/?p=glibc.git;a=commit;h=1d0fc213824eaa2a8f8c4385daaa698ee8fb7c92. Rename the grpc versions to avoid naming conflicts.
----
- src/core/lib/gpr/log_linux.cc          | 4 ++--
- src/core/lib/gpr/log_posix.cc          | 4 ++--
- src/core/lib/iomgr/ev_epollex_linux.cc | 4 ++--
- 3 files changed, 6 insertions(+), 6 deletions(-)
-
-diff --git third_party/grpc/src/core/lib/gpr/log_linux.cc.orig src/core/lib/gpr/log_linux.cc
-index 561276f0c20..8b597b4cf2f 100644
---- third_party/grpc/src/core/lib/gpr/log_linux.cc.orig	2019-06-21 10:42:13.235611417 -0400
-+++ third_party/grpc/src/core/lib/gpr/log_linux.cc	2019-06-21 10:42:16.686608855 -0400
-@@ -40,7 +40,7 @@
- #include <time.h>
- #include <unistd.h>
- 
--static long gettid(void) { return syscall(__NR_gettid); }
-+static long sys_gettid(void) { return syscall(__NR_gettid); }
- 
- void gpr_log(const char* file, int line, gpr_log_severity severity,
-              const char* format, ...) {
-@@ -70,7 +70,7 @@ void gpr_default_log(gpr_log_func_args*
-   gpr_timespec now = gpr_now(GPR_CLOCK_REALTIME);
-   struct tm tm;
-   static __thread long tid = 0;
--  if (tid == 0) tid = gettid();
-+  if (tid == 0) tid = sys_gettid();
- 
-   timer = static_cast<time_t>(now.tv_sec);
-   final_slash = strrchr(args->file, '/');
-diff --git third_party/grpc/src/core/lib/gpr/log_posix.cc.orig src/core/lib/gpr/log_posix.cc
-index b6edc14ab6b..2f7c6ce3760 100644
---- third_party/grpc/src/core/lib/gpr/log_posix.cc.orig	2019-06-21 10:42:13.242611412 -0400
-+++ third_party/grpc/src/core/lib/gpr/log_posix.cc	2019-06-21 10:42:22.794604319 -0400
-@@ -30,7 +30,7 @@
- #include <string.h>
- #include <time.h>
- 
--static intptr_t gettid(void) { return (intptr_t)pthread_self(); }
-+static intptr_t sys_gettid(void) { return (intptr_t)pthread_self(); }
- 
- void gpr_log(const char* file, int line, gpr_log_severity severity,
-              const char* format, ...) {
-@@ -85,7 +85,7 @@ void gpr_default_log(gpr_log_func_args*
-   char* prefix;
-   gpr_asprintf(&prefix, "%s%s.%09d %7tu %s:%d]",
-                gpr_log_severity_string(args->severity), time_buffer,
--               (int)(now.tv_nsec), gettid(), display_file, args->line);
-+               (int)(now.tv_nsec), sys_gettid(), display_file, args->line);
- 
-   fprintf(stderr, "%-70s %s\n", prefix, args->message);
-   gpr_free(prefix);
-diff --git third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc.orig src/core/lib/iomgr/ev_epollex_linux.cc
-index 08116b3ab53..76f59844312 100644
---- third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc.orig	2019-06-21 10:42:13.247611408 -0400
-+++ third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc	2019-06-21 10:42:29.767599141 -0400
-@@ -1150,7 +1150,7 @@ static void end_worker(grpc_pollset* pol
- }
- 
- #ifndef NDEBUG
--static long gettid(void) { return syscall(__NR_gettid); }
-+static long sys_gettid(void) { return syscall(__NR_gettid); }
- #endif
- 
- /* pollset->mu lock must be held by the caller before calling this.
-@@ -1170,7 +1170,7 @@ static grpc_error* pollset_work(grpc_pol
- #define WORKER_PTR (&worker)
- #endif
- #ifndef NDEBUG
--  WORKER_PTR->originator = gettid();
-+  WORKER_PTR->originator = sys_gettid();
- #endif
-   if (grpc_polling_trace.enabled()) {
-     gpr_log(GPR_INFO,

packages/bazel/unix_cc_configure-0.10.patch

---- 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):

packages/bazel/unix_cc_configure-0.5.3.patch

---- 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."""

packages/biobb-common/package.py

-# 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 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"
-    url      = "https://github.com/bioexcel/biobb_common/archive/refs/tags/v3.8.1.tar.gz"
-
-    maintainers = ['dbeltran']
-
-    # Versions
-    version('3.8.1', sha256='b6c939c1445ea2f8282e491e0414cc15f4934466ca24ecd77e24cef2e7df49e4')
-
-    # 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'))
-

packages/biobb-gromacs/package.py

-# 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 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"
-    url      = "https://github.com/bioexcel/biobb_gromacs/archive/refs/tags/v3.8.1.tar.gz"
-
-    maintainers = ['dbeltran']
-
-    # Versions
-    version('3.8.1', sha256='6da49b691b14a8bcf7ffca08c898fe9affd258ca2f8c7be4981df840a6907efa')
-
-    # Dependencies
-    depends_on('python@3.8:',type=('build', 'run'))
-    depends_on('biobb-common@3.8.1', type=('build', 'run'), when='@3.8.1')
-    depends_on('gromacs')

packages/build-brainscales/package.py

+# 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 unittest.mock
+import xml.etree.ElementTree as ET
+
+from spack.package import *
+from spack.util.environment import EnvironmentModifications
+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",
+        tag="ebrains-9.0-a9",
+        commit="41d2597bd6c1c20aee4d538c42c248195a133680",
+        submodules=True,
+    )
+    version(
+        "9.0-a8",
+        git="https://github.com/electronicvisions/releases-ebrains",
+        tag="ebrains-9.0-a8",
+        commit="44323be431da4b4b43890815f453c27207dee0b2",
+        submodules=True,
+    )
+    version(
+        "9.0-a7",
+        git="https://github.com/electronicvisions/releases-ebrains",
+        tag="ebrains-9.0-a7",
+        commit="2337adc6a33f907900d2b8be5d9f0b15872a200a",
+        submodules=True,
+    )
+    version(
+        "9.0-a6",
+        git="https://github.com/electronicvisions/releases-ebrains",
+        tag="ebrains-9.0-a6",
+        commit="e9b6746edb5e8465ae2848556b70e4edd555182e",
+        submodules=True,
+    )
+    version(
+        "9.0-a5",
+        git="https://github.com/electronicvisions/releases-ebrains",
+        tag="ebrains-9.0-a5",
+        commit="5fcb0682626d83c089e016aaf433e0938e921634",
+        submodules=True,
+    )
+    version(
+        "9.0-a4",
+        git="https://github.com/electronicvisions/releases-ebrains",
+        tag="ebrains-9.0-a4",
+        commit="8d5be2a23ac1eb0129bdf1f83fb0a1c5193c4c85",
+        submodules=True,
+    )
+
+    # common dependencies of BuildBrainscales-derived packages
+    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'))
+    depends_on('oppulance@9.0-a6', when='@9.0-a6', type=('build', 'link', 'run', 'test'))
+    depends_on('oppulance@9.0-a5', when='@9.0-a5', type=('build', 'link', 'run', 'test'))
+    depends_on('oppulance@9.0-a4', when='@9.0-a4', type=('build', 'link', 'run', 'test'))
+
+    # waf setup performs git clone and might query gerrit
+    depends_on('git', type=('build', 'link'))
+    depends_on('py-git-review', type=('build', 'link'))
+
+    # old BrainScaleS EBRAINS releases used `waf setup --project=X` to download
+    # sources of the dependent repositories
+    @when("@:8")
+    def do_fetch(self, mirror_only=False):
+        """Setup the project."""
+
+        self.stage.create()
+        self.stage.fetch(mirror_only)
+
+        # if fetcher didn't do anything, it's cached already
+        if not os.path.exists(self.stage.source_path):
+            return
+
+        with working_dir(self.stage.source_path):
+            python = which('python3')
+            if self.spec.satisfies('@:7'):
+                python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
+                    '--clone-depth=2',
+                    '--without-munge',
+                    '--without-hxcomm-hostarq',
+                    '--without-hxcomm-extoll',
+                    '--project=' + str(self.spec.name),
+                    '--release-branch=ebrains-' + str(self.spec.version)
+                )
+            else:
+                python('./waf', 'setup', '--repo-db-url=https://github.com/electronicvisions/projects',
+                    '--clone-depth=2',
+                    '--without-munge',
+                    '--without-hxcomm-hostarq',
+                    '--project=' + str(self.spec.name),
+                    '--release-branch=ebrains-' + str(self.spec.version)
+                )
+
+
+        # 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):
+            self.stage.cache_local()
+
+    # new BrainScaleS EBRAINS releases use git submodules to download sources;
+    # we still need to keep the `.git/` folders of the submodules in the source cache though
+    @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(BuildBrainscales, self).do_fetch(mirror_only)
+
+    def _setup_common_env(self, env):
+        # grenade needs to find some libraries for the JIT-compilation of
+        # programs for BrainScaleS-2's embedded processor.
+        ppu_include_dirs = []
+        ppu_dep_names = ['bitsery', 'boost', 'cereal']
+        for ppu_dep_name in ppu_dep_names:
+            dep = self.spec[ppu_dep_name]
+            dep_include_dirs = set(dep.headers.directories)
+            ppu_include_dirs.extend(list(dep_include_dirs))
+        for dir in reversed(ppu_include_dirs):
+            env.prepend_path("C_INCLUDE_PATH", dir)
+            env.prepend_path("CPLUS_INCLUDE_PATH", dir)
+
+    def setup_build_environment(self, env):
+        my_envmod = EnvironmentModifications(env)
+        spack.build_environment.set_wrapper_variables(self, my_envmod)
+        my_env = {}
+        my_envmod.apply_modifications(my_env)
+
+        def get_path(env, name):
+            path = env.get(name, "").strip()
+            if path:
+                return path.split(os.pathsep)
+            return []
+
+        # 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)
+                env.prepend_path("LD_LIBRARY_PATH", dir)
+        for dir in reversed(self.compiler.implicit_rpaths()):
+            env.prepend_path("LIBRARY_PATH", dir)
+            # technically this is probably not needed for the non-configure steps
+            env.prepend_path("LD_LIBRARY_PATH", dir)
+
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        self._setup_common_env(env)
+
+    def setup_run_environment(self, env):
+        self._setup_common_env(env)
+
+    def setup_dependent_run_environment(self, env, dependent_spec):
+        self._setup_common_env(env)
+
+    # override configure step as we perform a project setup first
+    def configure(self, spec, prefix):
+        """Configure the project."""
+
+        args = ['--prefix={0}'.format(self.prefix)]
+        args += self.configure_args()
+
+        if spec.version >= Version("9"):
+            self.waf('setup', '--directory=' + str(spec.name), '--repo-db-url=https://github.com/electronicvisions/projects')
+        self.waf('configure', '--build-profile=release', '--disable-doxygen', *args)
+
+    def build_args(self):
+        args = ['--keep', '--test-execnone', '-v']
+        return args
+
+    def build_test(self):
+        self.builder.waf('build', '--test-execall')
+        copy_tree('build/test_results', join_path(self.prefix, '.build'))
+        copy_tree('build/test_results', join_path(self.stage.path, ".install_time_tests"))
+        # propagate failures from junit output to spack
+        tree = ET.parse('build/test_results/summary.xml')
+        for testsuite in tree.getroot():
+            for testcase in testsuite:
+                if (testcase.get('name').startswith("pycodestyle") or
+                    testcase.get('name').startswith("pylint")):
+                    continue
+                for elem in testcase:
+                    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')))
+
+    def install_args(self):
+        args = ['--test-execnone']
+        return args

packages/clb-nb-utils/package.py

-from spack import *
+# 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 *
 
 # Usage
 # from clb_nb_utils import oauth

packages/fmt/fmt-attributes-cpp11_4.1.0.patch

-diff --git a/fmt/format.h b/fmt/format.h
-index 561a9e0..9faf5ca 100644
---- a/fmt/format.h
-+++ b/fmt/format.h
-@@ -153,7 +153,7 @@ typedef __int64          intmax_t;
- # define FMT_HAS_CPP_ATTRIBUTE(x) 0
- #endif
- 
--#if FMT_HAS_CPP_ATTRIBUTE(maybe_unused)
-+#if FMT_HAS_CPP_ATTRIBUTE(maybe_unused) && __cplusplus >= 201103L
- # define FMT_HAS_CXX17_ATTRIBUTE_MAYBE_UNUSED
- // VC++ 1910 support /std: option and that will set _MSVC_LANG macro
- // Clang with Microsoft CodeGen doesn't define _MSVC_LANG macro

packages/fmt/fmt-no-export-cpp11flag_3.0.0.patch

-diff --git a/fmt/CMakeLists.txt b/fmt/CMakeLists.txt
-index c0ef02e..1634924 100644
---- a/fmt/CMakeLists.txt
-+++ b/fmt/CMakeLists.txt
-@@ -14,8 +14,6 @@ if (FMT_CPPFORMAT)
-   add_library(cppformat ${FMT_SOURCES} ${FMT_HEADERS})
- endif ()
- 
--# Starting with cmake 3.1 the CXX_STANDARD property can be used instead.
--target_compile_options(fmt PUBLIC ${CPP11_FLAG})
- if (FMT_PEDANTIC)
-   target_compile_options(fmt PRIVATE ${PEDANTIC_COMPILE_FLAGS})
- endif ()

packages/fmt/fmt-use-cmake-cxx-standard_3.0.0.patch

-diff --git a/support/cmake/cxx11.cmake b/support/cmake/cxx11.cmake
-index 31ea106..8581b9a 100644
---- a/support/cmake/cxx11.cmake
-+++ b/support/cmake/cxx11.cmake
-@@ -37,6 +37,10 @@ if (FMT_USE_CPP11)
-   endif ()
- endif ()
- 
-+if (CMAKE_CXX_STANDARD)
-+  set(CPP11_FLAG )
-+endif ()
-+
- set(CMAKE_REQUIRED_FLAGS ${CPP11_FLAG})
- 
- # Check if variadic templates are working and not affected by GCC bug 39653:

packages/fmt/package.py

-# this package was adapted from the spack v0.19.0 upstream because the version
-# needed for arbor 0.8 was not available on the current spack version
-
-# Copyright 2013-2022 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 Fmt(CMakePackage):
-    """fmt (formerly cppformat) is an open-source formatting library.
-    It can be used as a safe alternative to printf or as a fast alternative
-    to C++ IOStreams."""
-
-    homepage = "https://fmt.dev/"
-    url = "https://github.com/fmtlib/fmt/releases/download/7.1.3/fmt-7.1.3.zip"
-    maintainers = ["msimberg"]
-    
-    version("9.1.0", sha256="cceb4cb9366e18a5742128cb3524ce5f50e88b476f1e54737a47ffdf4df4c996")
-    version("9.0.0", sha256="fc96dd2d2fdf2bded630787adba892c23cb9e35c6fd3273c136b0c57d4651ad6")
-    version("8.1.1", sha256="23778bad8edba12d76e4075da06db591f3b0e3c6c04928ced4a7282ca3400e5d")
-    version("8.1.0", sha256="d8e9f093b2241c3a9fc3895e23231ef9de00c762cfa0a9c65e4748755bc352ae")
-    version("8.0.1", sha256="a627a56eab9554fc1e5dd9a623d0768583b3a383ff70a4312ba68f94c9d415bf")
-    version("7.1.3", sha256="5d98c504d0205f912e22449ecdea776b78ce0bb096927334f80781e720084c9f")
-    version("7.1.2", sha256="4d6968ab7c01e95cc76df136755703defb985105a117b83057e4fd5d53680ea7")
-    version("7.1.0", sha256="308af4e36ee3ab527b51014a2a5d862682c84f5d16f7a597aea34c84853cbcb0")
-    version("6.1.2", sha256="63650f3c39a96371f5810c4e41d6f9b0bb10305064e6faf201cbafe297ea30e8")
-    version("5.3.0", sha256="4c0741e10183f75d7d6f730b8708a99b329b2f942dad5a9da3385ab92bb4a15c")
-    version("5.2.1", sha256="43894ab8fe561fc9e523a8024efc23018431fa86b95d45b06dbe6ddb29ffb6cd")
-    version("5.2.0", sha256="c016db7f825bce487a7929e1edb747b9902a2935057af6512cad3df3a080a027")
-    version("5.1.0", sha256="77ef9fea638dc846e484409fbc1ea710bb9bcea042e7b35b8805041bf7655ad5")
-    version("5.0.0", sha256="8dd58daf13e7e8adca99f8725ef3ae598f9c97efda7d6d8d4c49db5047879097")
-    version("4.1.0", sha256="9d49bf02ceb9d0eec51144b203b63b77e69d3798bb402fb82e7d0bdb06c79eeb")
-    version("4.0.0", sha256="10a9f184d4d66f135093a08396d3b0a0ebe8d97b79f8b3ddb8559f75fe4fcbc3")
-    version("3.0.2", sha256="51407b62a202b29d1a9c0eb5ecd4095d30031aea65407c42c25cb10cb5c59ad4")
-    version("3.0.1", sha256="4c9af0dc919a8ae7022b44e1a03c435e42d65c866f44667d8d920d342b098550")
-    version("3.0.0", sha256="1b050b66fa31b74f1d75a14f15e99e728ab79572f176a53b2f8ad7c201c30ceb")
-
-    variant(
-        "cxxstd",
-        default="11",
-        values=("98", "11", "14", "17"),
-        multi=False,
-        description="Use the specified C++ standard when building",
-    )
-    variant("shared", default=False, description="Build shared library")
-    variant("pic", default=True, description="Build position-independent code")
-
-    depends_on("cmake@3.1.0:", type="build")
-
-    # Supported compilers/standards are detailed here:
-    # http://fmtlib.net/latest/index.html#portability
-    conflicts("%gcc@:4.3", when="@5:")
-    conflicts("%llvm@:2.8", when="@5:")
-    # 5 and above require C++11
-    conflicts("cxxstd=98", when="@5:")
-    # 5.0.0 enables C++14 auto return types in C++11 mode
-    conflicts("cxxstd=11", when="@5.0.0")
-    # 4.1 fails with C++17 (https://github.com/fmtlib/fmt/issues/722)
-    conflicts("cxxstd=17", when="@4.1.0")
-    # edg based compilers have issues with fmt 9.0.0 and C++17 standard
-    # (https://github.com/fmtlib/fmt/issues/3028)
-    conflicts("cxxstd=17", when="@9.0.0%intel")
-    conflicts("cxxstd=17", when="@9.0.0%nvhpc")
-
-    # Use CMAKE_CXX_STANDARD to define C++ flag, as in later versions
-    patch("fmt-use-cmake-cxx-standard_3.0.0.patch", when="@3.0.0")
-
-    # Remove hardcoding of "-std=c++11/0x" in INTERFACE_COMPILE_OPTIONS
-    patch("fmt-no-export-cpp11flag_3.0.0.patch", when="@3.0.0:3.0.1")
-
-    # Only allow [[attributes]] on C++11 and higher
-    patch("fmt-attributes-cpp11_4.1.0.patch", when="@4.1.0")
-
-    # Fix compilation with hipcc/dpcpp: https://github.com/fmtlib/fmt/issues/3005
-    patch(
-        "https://github.com/fmtlib/fmt/commit/0b0f7cfbfcebd021c910078003d413354bd843e2.patch?full_index=1",
-        sha256="08fb707bf8b4fc890d6eed29217ead666558cbae38f9249e22ddb82212f0eb4a",
-        when="@9.0.0:9.1.0",
-    )
-
-    def cmake_args(self):
-        spec = self.spec
-        args = []
-
-        if self.spec.satisfies("+shared"):
-            args.append("-DBUILD_SHARED_LIBS=ON")
-
-        if "+pic" in spec:
-            args.extend(
-                [
-                    "-DCMAKE_C_FLAGS={0}".format(self.compiler.cc_pic_flag),
-                    "-DCMAKE_CXX_FLAGS={0}".format(self.compiler.cxx_pic_flag),
-                ]
-            )
-
-        args.append("-DCMAKE_CXX_STANDARD={0}".format(spec.variants["cxxstd"].value))
-        # Require standard at configure time to guarantee the
-        # compiler supports the selected standard.
-        args.append("-DCMAKE_CXX_STANDARD_REQUIRED=ON")
-
-        # When cxxstd is 98, must disable FMT_USE_CPP11
-        if "cxxstd=98" in spec:
-            args.append("-DFMT_USE_CPP11=OFF")
-
-        # Can't build docs without doxygen+python+virtualenv
-        # and call to build "doc" target
-        args.append("-DFMT_DOC=OFF")
-
-        return args
-

packages/genpybind/package.py

-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
 
 
 class Genpybind(WafPackage):
@@ -40,16 +21,24 @@ 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')
 
     depends_on(
             'llvm+clang+python+visionary@5.0.0:',
-        type=('build', 'link', 'run'))
+        type=('build', 'link'))
     depends_on('binutils', type='build')
     depends_on('python@2.7:', type=('build', 'run'))
 
     extends('python')
 
+    patch('v0.2.1-python3.10.patch', when='@:0.2.1 ^python@3.10:')
+
+    # llvm-config needs to be found at build time of packages using genpybind
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        env.prepend_path("PATH", self.spec["llvm"].prefix.bin)
+
     def configure_args(self):
         args = super(Genpybind, self).configure_args()
 

packages/genpybind/v0.2.1-python3.10.patch

+diff --git a/genpybind/annotations.py b/genpybind/annotations.py
+index 1dfd1f4..871ef4d 100644
+--- a/genpybind/annotations.py
++++ b/genpybind/annotations.py
+@@ -3,7 +3,7 @@
+ from __future__ import unicode_literals
+ 
+ import ast
+-import collections
++from collections.abc import Sequence
+ 
+ from clang.cindex import CursorKind
+ 
+@@ -25,7 +25,7 @@ LOZENGE = u"◊"
+ SPECIAL_NAMES = {"true": True, "false": False, "default": None, "none": None}
+ 
+ 
+-class Annotations(collections.Sequence):
++class Annotations(Sequence):
+     def __init__(self, annotations=None):
+         # type: (Union[None, Text, Iterable[Text]]) -> None
+         self._annotations = []  # type: List[AnnotationT]
+diff --git a/genpybind/registry.py b/genpybind/registry.py
+index 4f66ace..75ba7a9 100644
+--- a/genpybind/registry.py
++++ b/genpybind/registry.py
+@@ -1,6 +1,6 @@
+ from __future__ import unicode_literals
+ 
+-import collections
++from collections.abc import Mapping
+ import re
+ 
+ from clang import cindex
+@@ -16,7 +16,7 @@ if False:  # pylint: disable=using-constant-test
+ RE_NON_IDENTIFIER = re.compile(r"[^a-zA-Z0-9_]+")
+ 
+ 
+-class Registry(collections.Mapping):
++class Registry(Mapping):
+     def __init__(self, tags=None):
+         # type: (Optional[Iterable[Text]]) -> None
+         self._declarations = {}  # type: Dict[Text, Optional[Declaration]]

packages/glfw/package.py

+# 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")
+
+    # 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")
+    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")
+
+    # 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")]

packages/hxtorch/include-SparseTensorUtils.patch

+diff --git a/src/hxtorch/spiking/types.cpp b/src/hxtorch/spiking/types.cpp
+index aaf670f..39322c8 100644
+--- a/hxtorch/src/hxtorch/spiking/types.cpp
++++ b/hxtorch/src/hxtorch/spiking/types.cpp
+@@ -2,7 +2,12 @@
+ #include "grenade/vx/common/time.h"
+ #include "hxtorch/spiking/detail/to_dense.h"
+ #include <ATen/Functions.h>
++#if __has_include(<ATen/native/SparseTensorUtils.h>)
++// moved in py-torch@2.1
++#include <ATen/native/SparseTensorUtils.h>
++#else
+ #include <ATen/SparseTensorUtils.h>
++#endif
+ #include <log4cxx/logger.h>
+ 
+ namespace hxtorch::spiking {