packages/bazel/unix_cc_configure_fj-0.29.1.patch

+diff -Naur a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl
+--- a/tools/cpp/unix_cc_configure.bzl	1980-01-01 00:00:00.000000000 -0800
++++ b/tools/cpp/unix_cc_configure.bzl	2022-06-30 23:53:17.000000000 -0700
+@@ -379,7 +379,7 @@
+         "",
+         False,
+     ), ":")
+-    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 +468,6 @@
+                     # Security hardening requires optimization.
+                     # We need to undef it as some distributions now have it enabled by default.
+                     "-U_FORTIFY_SOURCE",
+-                    "-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/unix_cc_configure_fj-5.0.patch

+diff -Naur a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl
+--- a/tools/cpp/unix_cc_configure.bzl	1980-01-01 00:00:00.000000000 -0800
++++ b/tools/cpp/unix_cc_configure.bzl	2022-06-30 23:35:14.000000000 -0700
+@@ -417,10 +417,7 @@
+         bazel_linklibs,
+         False,
+     ), ":")
+-    gold_or_lld_linker_path = (
+-        _find_linker_path(repository_ctx, cc, "lld", is_clang) or
+-        _find_linker_path(repository_ctx, cc, "gold", is_clang)
+-    )
++    gold_or_lld_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
+@@ -531,7 +528,6 @@
+                     # Security hardening requires optimization.
+                     # We need to undef it as some distributions now have it enabled by default.
+                     "-U_FORTIFY_SOURCE",
+-                    "-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/unix_cc_configure_fj-5.2.patch

+diff -Naur a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl
+--- a/tools/cpp/unix_cc_configure.bzl	1980-01-01 00:00:00.000000000 -0800
++++ b/tools/cpp/unix_cc_configure.bzl	2022-06-30 23:58:26.945067883 -0700
+@@ -419,10 +419,7 @@
+         bazel_linklibs,
+         False,
+     ), ":")
+-    gold_or_lld_linker_path = (
+-        _find_linker_path(repository_ctx, cc, "lld", is_clang) or
+-        _find_linker_path(repository_ctx, cc, "gold", is_clang)
+-    )
++    gold_or_lld_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
+@@ -530,7 +527,6 @@
+             "%{cxx_builtin_include_directories}": get_starlark_list(builtin_include_directories),
+             "%{compile_flags}": get_starlark_list(
+                 [
+-                    "-fstack-protector",
+                     # All warnings are enabled. Maybe enable -Werror as well?
+                     "-Wall",
+                     # Enable a few more warnings that aren't part of -Wall.

packages/biobb-common/package.py

-# Copyright 2013-2021 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/tarball/v3.7.0"
-    git = 'https://github.com/bioexcel/biobb_common.git'
-
-    # FIXME: Add a list of GitHub accounts to
-    # notify when the package is updated.
-    # maintainers = ['github_user1', 'github_user2']
-
-    # Versions
-    version('3.7.0', branch='master')
-
-    # Dependencies
-    depends_on('py-setuptools')
-    depends_on('python@3.7:', 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-md/package.py

-from spack import *
-
-class BiobbMd(PythonPackage):
-    """Biobb_md is the Biobb module collection to perform molecular
-    dynamics simulations"""
-
-    # Homepage and download url
-    homepage = "https://github.com/bioexcel/biobb_md"
-    git = 'https://github.com/bioexcel/biobb_md.git'
-
-    # Versions
-    version('3.7.1', branch='master')
-
-    # Dependencies
-    depends_on('biobb-common')
-    depends_on('python@3.7:', type=('build', 'run'))
-    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/funniest1022/package.py

-from spack import *
-
-class Funniest1022(PythonPackage):
-    pypi = 'funniest1022/funniest1022-0.3.tar.gz'
-    maintainers = ['akarmas']
-    version('0.3', '248ec9320ad80dc4b05dca73e4deff78')
-    depends_on('python@3.8:', type=('build','run'))
-    depends_on('py-pandas', type=('build','run'))

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 {

packages/hxtorch/package.py

-# Copyright 2013-2022 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)
-from spack import *
 
+import os
+import unittest.mock
+import xml.etree.ElementTree as ET
 
-class Hxtorch(WafPackage):
+from spack.package import *
+from spack.util.environment import EnvironmentModifications
+import spack.build_environment
+
+import importlib
+build_brainscales = importlib.import_module("spack.pkg.ebrains-spack-builds.build_brainscales")
+
+
+class Hxtorch(build_brainscales.BuildBrainscales):
     """hxtorch --- a PyTorch-based toplevel for the BrainScaleS-2 neuromorphic hardware systems"""
 
     homepage = "https://github.com/electronicvisions/hxtorch"
-    # This repo provides a waf binary used for the build below
+    # This repo provides a custom waf binary used for the build below
     git      = "https://github.com/electronicvisions/pynn-brainscales.git"
 
-    version('2.0-rc6', branch='waf')
-
-    # PPU compiler dependencies
-    depends_on('oppulance@2.0:')
+    maintainers = ["emuller", "muffgaga"]
+
+    # newer versions are defined in the common base package
+    version('8.0-a5',         tag='hxtorch-8.0-a5')
+    version('8.0-a4',         tag='hxtorch-8.0-a4')
+    version('8.0-a3',         tag='hxtorch-8.0-a3')
+    version('8.0-a2',         tag='hxtorch-8.0-a2')
+    version('8.0-a1',         tag='hxtorch-8.0-a1')
+    version('7.0-rc1-fixup3', tag='hxtorch-7.0-rc1-fixup3')
+    version('7.0-rc1-fixup2', tag='hxtorch-7.0-rc1-fixup2')
+    version('7.0-rc1-fixup1', branch='waf')
+
+    deps_hxtorch_core = [
+        # compiler for the BrainScaleS-2 embedded processor ("PPU"); needed for
+        # building/linking, at runtime and for testing
+        # (BTW. modern oppulance dependency via BuildBrainscales)
+        ('oppulance@8.0-a5', { "when":'@8.0-a5', "type": ('build', 'link', 'run', 'test') } ),
+        ('oppulance@8.0-a4', { "when":'@8.0-a4', "type": ('build', 'link', 'run', 'test') } ),
+        ('oppulance@8.0-a3', { "when":'@8.0-a3', "type": ('build', 'link', 'run', 'test') } ),
+        ('oppulance@8.0-a2', { "when":'@8.0-a2', "type": ('build', 'link', 'run', 'test') } ),
+        ('oppulance@8.0-a1', { "when":'@8.0-a1', "type": ('build', 'link', 'run', 'test') } ),
+        ('oppulance@7.0-rc1-fixup3', { "when":'@7.0-rc1-fixup3', "type": ('build', 'link', 'run', 'test') } ),
+        ('oppulance@7.0-rc1-fixup2', { "when":'@7.0-rc1-fixup2', "type": ('build', 'link', 'run', 'test') } ),
+        ('oppulance@7.0-rc1-fixup1', { "when":'@7.0-rc1-fixup1', "type": ('build', 'link', 'run', 'test') } ),
+
+        # host software dependencies
+        ('bitsery', { "type": ('build', 'link', 'run', 'test') } ),
+        ('binutils+gold+ld+plugins', { "type": ('build', 'link', 'run') } ), # specialize
+        ('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-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
+        ('intel-tbb', { "type": ('build', 'link', 'run') } ), # ppu gdbserver
+        ('libelf', { "type": ('build', 'link', 'run') } ),
+        ('liblockfile', { "type": ('build', 'link', 'run') } ),
+        ('log4cxx@0.12.1:1.0', { "when": "@:8.0-a3", "type": ('build', 'link', 'run') } ),
+        ('log4cxx@1.1: +events_at_exit', { "when": "@8.0-a4:", "type": ('build', 'link', 'run') } ),
+        ('pkgconfig', { "type": ('build', 'link', 'run') } ),
+        ('psmisc', { "type": ('run', 'test') } ),
+        ('python@3.7.0:', { "type": ('build', 'link', 'run') } ), # BrainScaleS-2 only supports Python >= 3.7
+        ('py-h5py', { "type": ('build', 'link', 'run') } ), # PyNN tests need it
+        ('py-matplotlib', { "type": ('build', 'link', 'run') } ),
+        ('py-networkx', { "type": ('build', 'link', 'run') } ),
+        ('py-nose', { "type": ('build', 'link', 'run') } ),
+        ('py-numpy', { "type": ('build', 'link', 'run') } ),
+        ('py-pybind11', { "type": ('build', 'link', 'run') } ),
+        ('py-pybind11-stubgen', { "type": ('build', 'link', 'run') } ),
+        ('py-pycodestyle', { "type": ('build', 'link', 'run') } ),
+        ('py-pyelftools', { "type": ('build', 'link', 'run') } ),
+        ('py-pylint', { "type": ('build', 'link', 'run') } ),
+        ('py-pytest', { "type": ('build', 'link', 'run') } ),
+        ('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') } ),
+        ('yaml-cpp+shared', { "type": ('build', 'link', 'run') } ),
+    ]
+
+    for dep, dep_kw in deps_hxtorch_core:
+        depends_on(dep, **dep_kw)
 
-    # host software dependencies
-    depends_on('bitsery', type=('build', 'link', 'run'))
-    depends_on('binutils+gold+ld+plugins', type=('build', 'link', 'run')) # specialize
-    depends_on('boost@1.69.0: +graph+icu+mpi+python+numpy+coroutine+context cxxstd=17', type=('build', 'link', 'run')) # specialize boost (non-clingo, type=('build', 'link', 'run'))
-    depends_on('cereal', type=('build', 'link', 'run'))
-    depends_on('cppcheck', type=('build', 'link', 'run'))
-    depends_on('doxygen+graphviz', type=('build', 'link', 'run'))
-    depends_on('genpybind@ebrains', type=('build', 'link', 'run'))
-    depends_on('gflags', type=('build', 'link', 'run'))
-    depends_on('googletest@1.11.0: +gmock', type=('build', 'link', 'run')) # variadic templates needed
-    depends_on('intel-tbb', type=('build', 'link', 'run'))  # ppu gdbserver
-    depends_on('libelf', type=('build', 'link', 'run'))
-    depends_on('liblockfile', type=('build', 'link', 'run'))
-    depends_on('llvm', type=('build', 'link', 'run'))
-    depends_on('log4cxx', type=('build', 'link', 'run'))
-    depends_on('pkg-config', type=('build', 'link', 'run'))
-    depends_on('python@3.7.0:', type=('build', 'link', 'run')) # BrainScaleS(-2, type=('build', 'link', 'run')) only supports Python >= 3.7
-    depends_on('py-h5py', type=('build', 'link', 'run')) # PyNN tests need it
-    depends_on('py-matplotlib', type=('build', 'link', 'run'))
-    depends_on('py-nose', type=('build', 'link', 'run'))
-    depends_on('py-numpy', type=('build', 'link', 'run'))
-    depends_on('py-pybind11', type=('build', 'link', 'run'))
-    depends_on('py-pybind11-stubgen', type=('build', 'link', 'run'))
-    depends_on('py-pycodestyle', type=('build', 'link', 'run'))
-    depends_on('py-pyelftools', type=('build', 'link', 'run'))
-    depends_on('py-pylint', type=('build', 'link', 'run'))
-    depends_on('py-torch', type=('build', 'link', 'run'))
-    depends_on('py-pyyaml', type=('build', 'link', 'run'))
-    depends_on('py-scipy', type=('build', 'link', 'run'))
-    depends_on('py-sqlalchemy', type=('build', 'link', 'run'))
-    depends_on('util-linux', type=('build', 'link', 'run'))
-    depends_on('yaml-cpp+shared', type=('build', 'link', 'run'))
     extends('python')
 
-    def setup_build_environment(self, env):
-        """waf needs to find headers and libraries by itself (mostly `boost`
-        tool, but also `gtest`); it also needs to run executables during
-        configuration."""
-
-        include = []
-        for dep in self.spec.traverse(deptype='build'):
-            query = self.spec[dep.name]
-            try:
-                include.extend(query.headers.directories)
-                print('headers:', query.headers.directories, "\n")
-            except:
-                pass
-
-        library = []
-        for dep in self.spec.traverse(deptype=('link', 'run')):
-            query = self.spec[dep.name]
-            try:
-                library.extend(query.libs.directories)
-                print('libs:', query.libs.directories, "\n")
-            except:
-                pass
-
-        path = []
-        for dep in self.spec.traverse(deptype=('build', 'link', 'run')):
-            query = self.spec[dep.name]
-            try:
-                path.append(query.prefix.bin)
-                print('bin:', query.prefix.bin, "\n")
-            except:
-                pass
-
-        # llvm might be built with ~shared_libs but still builds shared libs
-        if not any('llvm' in lib for lib in library):
-            library.append(self.spec['llvm'].prefix.lib)
-
-        env.set('CPATH', ':'.join(include))
-        env.set('C_INCLUDE_PATH', ':'.join(include))
-        env.set('CPLUS_INCLUDE_PATH', ':'.join(include))
-        env.set('LIBRARY_PATH', ':'.join(library))
-        env.set('LD_LIBRARY_PATH', ':'.join(library))
-        env.prepend_path('PATH', ':'.join(path))
-
-    def setup_run_environment(self, env):
-        env.prepend_path('PYTHONPATH', self.prefix.lib)
-
-    # override configure step as we perform a project setup first
-    def configure(self, spec, prefix):
-        """Setup and configure the project."""
-
-        self.waf('setup', '--repo-db-url=https://github.com/electronicvisions/projects', '--without-munge',
-            '--project=hxtorch@ebrains-' + str(spec.version),
-            '--project=haldls@ebrains-' + str(spec.version),
-            '--project=grenade@ebrains-' + str(spec.version),
-            '--project=code-format@ebrains-' + str(spec.version),
-            '--project=logger@ebrains-' + str(spec.version),
-            '--project=halco@ebrains-' + str(spec.version),
-            '--project=hate@ebrains-' + str(spec.version),
-            '--project=fisch@ebrains-' + str(spec.version),
-            '--project=ztl@ebrains-' + str(spec.version),
-            '--project=hxcomm@ebrains-' + str(spec.version),
-            '--project=rant@ebrains-' + str(spec.version),
-            '--project=pywrap@ebrains-' + str(spec.version),
-            '--project=lib-boost-patches@ebrains-' + str(spec.version),
-            '--project=sctrltp@ebrains-' + str(spec.version),
-            '--project=hwdb@ebrains-' + str(spec.version),
-            '--project=visions-slurm@ebrains-' + str(spec.version),
-            '--project=flange@ebrains-' + str(spec.version),
-            '--project=lib-rcf@ebrains-' + str(spec.version),
-            '--project=bss-hw-params@ebrains-' + str(spec.version),
-            '--project=libnux@ebrains-' + str(spec.version)
-         )
-
-        args = ['--prefix={0}'.format(self.prefix)]
-        args += self.configure_args()
-
-        self.waf('configure', *args)
+    # some versions of dependencies are broken
+    conflicts("boost@1.86.0") # sha1 digest changed length, but boost::compute didn't adapt
 
-    def build_args(self):
-        args = ['--keep', '--test-execnone', '-v']
+    patch("include-SparseTensorUtils.patch", when="@:8.0-a5")
 
-        return args
+    def install_test(self):
+        with working_dir('spack-test', create=True):
+            old_pythonpath = os.environ.get('PYTHONPATH', '')
+            os.environ['PYTHONPATH'] = ':'.join([str(self.prefix.lib), old_pythonpath])
+            bash = which("bash")
+            # ignore segfaults for now (exit code 139)
+            bash('-c', '(python -c "import hxtorch; print(hxtorch.__file__)" || ( test $? -eq 139 && echo "segfault")) || exit $?')

packages/inja/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 Inja(CMakePackage):
+    """Inja is a template engine for modern C++, loosely inspired by jinja for
+    python."""
+
+    homepage = "https://github.com/pantor/inja"
+    url      = "https://github.com/pantor/inja/archive/refs/tags/v3.3.0.tar.gz"
+
+    version('3.3.0', sha256='e628d994762dcdaa9a97f63a9b8b73d9af51af0ffa5acea6bdbba0aceaf8ee25')
+
+    depends_on('nlohmann-json@3.8.0:')
+
+    def cmake_args(self):
+        args = [
+            '-DINJA_USE_EMBEDDED_JSON:BOOL=OFF',
+            '-DINJA_BUILD_TESTS:BOOL=OFF',
+            '-DBUILD_BENCHMARK:BOOL=OFF',
+            '-DCOVERALLS:BOOL=OFF',
+        ]
+        return args

packages/jaxsnn/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 {

packages/jaxsnn/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
+
+import importlib
+build_brainscales = importlib.import_module("spack.pkg.ebrains-spack-builds.build_brainscales")
+hxtorch = importlib.import_module("spack.pkg.ebrains-spack-builds.hxtorch")
+
+
+class Jaxsnn(build_brainscales.BuildBrainscales):
+    """jaxsnn is an event-based approach to machine-learning-inspired training
+    and simulation of SNNs, including support for the BrainScaleS-2
+    neuromorphic backend."""
+
+    homepage = "https://github.com/electronicvisions/jaxsnn"
+    # This repo provides a custom waf binary used for the build below
+    git      = "https://github.com/electronicvisions/pynn-brainscales.git"
+
+    maintainers = ["emuller", "muffgaga"]
+
+    # newer versions are defined in the common base package
+    version('8.0-a5', tag='jaxsnn-8.0-a5')
+    version('8.0-a4', tag='jaxsnn-8.0-a4')
+    version('8.0-a3', tag='jaxsnn-8.0-a3')
+    version('8.0-a2', tag='jaxsnn-8.0-a2')
+    version('8.0-a1', tag='jaxsnn-8.0-a1')
+
+    # dependencies inherited from hxtorch.core
+    for dep, dep_kw in hxtorch.Hxtorch.deps_hxtorch_core:
+        depends_on(dep, **dep_kw)
+
+    # main dependencies w/o hxtorch.core dependencies (those come via hxtorch above)
+    depends_on('py-jax@0.4.13:', type=('build', 'link', 'run'))
+    depends_on('py-matplotlib', type=('build', 'link', 'run'))
+    depends_on('py-optax', type=('build', 'link', 'run'))
+    depends_on('py-tree-math', type=('build', 'link', 'run'))
+    extends('python')
+
+    patch("include-SparseTensorUtils.patch", when="@:8.0-a5")
+
+    def install_test(self):
+        with working_dir('spack-test', create=True):
+            old_pythonpath = os.environ.get('PYTHONPATH', '')
+            os.environ['PYTHONPATH'] = ':'.join([str(self.prefix.lib), old_pythonpath])
+            bash = which("bash")
+            # ignore segfaults for now (exit code 139)
+            bash('-c', '(python -c "import jaxsnn; print(jaxsnn.__file__)" || ( test $? -eq 139 && echo "segfault")) || exit $?')

packages/libvips/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 Libvips(AutotoolsPackage):
+    """libvips is a demand-driven, horizontally threaded image processing
+    library. Compared to similar libraries, libvips runs quickly and uses
+    little memory."""
+
+    homepage = "https://libvips.github.io/libvips/"
+    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")
+
+    variant("tiff", default=False, description="Enable TIFF support")
+
+    variant("png", default=False, description="Enable pngfile support")
+
+    variant("poppler", default=False, description="Enable PDF rendering via poppler")
+
+    # TODO: Add more variants!
+
+    depends_on("pkgconfig", type="build")
+    depends_on("glib")
+    depends_on("expat")
+
+    depends_on("fftw", when="+fftw")
+    depends_on("libjpeg", when="+jpeg")
+    depends_on("libtiff", when="+tiff")
+    depends_on("libpng", when="+png")
+    depends_on("poppler +glib", when="+poppler")
+
+    # begin EBRAINS (added): to fix build errors
+    depends_on("gobject-introspection")
+    depends_on("cfitsio")
+    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}"

packages/libxcb/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 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/"
+    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",
+        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", 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")
+    # end EBRAINS
+    depends_on("pkgconfig", type="build")
+    depends_on("util-macros", type="build")
+
+    def configure_args(self):
+        config_args = []
+
+        # -Werror flags are not properly interpreted by the NVIDIA compiler
+        if self.spec.satisfies("%nvhpc@:20.11"):
+            config_args.append("--disable-selective-werror")
+
+        return config_args
+
+    def patch(self):
+        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