packages/bazel/gcc11_2.patch

+diff --git a/third_party/ijar/zlib_client.h b/third_party/ijar/zlib_client.h
+index c4b051e0100c..0a917ff0a99a 100644
+--- a/third_party/ijar/zlib_client.h
++++ b/third_party/ijar/zlib_client.h
+@@ -16,7 +16,9 @@
+ #define THIRD_PARTY_IJAR_ZLIB_CLIENT_H_
+ 
+ #include <limits.h>
++
+ #include <limits>
++#include <stdexcept>
+ 
+ #include "third_party/ijar/common.h"
+ 

packages/bazel/gcc11_3.patch

+diff --git a/third_party/ijar/mapped_file_unix.cc b/third_party/ijar/mapped_file_unix.cc
+index 6e3a90871844..65179e3290ec 100644
+--- a/third_party/ijar/mapped_file_unix.cc
++++ b/third_party/ijar/mapped_file_unix.cc
+@@ -15,10 +15,11 @@
+ #include <errno.h>
+ #include <fcntl.h>
+ #include <stdio.h>
+-#include <unistd.h>
+ #include <sys/mman.h>
++#include <unistd.h>
+ 
+ #include <algorithm>
++#include <limits>
+ 
+ #include "third_party/ijar/mapped_file.h"
+ 

packages/bazel/gcc11_4.patch

+--- a/third_party/grpc/grpc_1.33.1.patch
++++ b/third_party/grpc/grpc_1.33.1.patch
+@@ -58,6 +58,14 @@ index 09fcad95a2..9b737e5deb 100644
+      )
+  
+      native.bind(
++@@ -245,6 +245,7 @@ def grpc_deps():
++                 "https://storage.googleapis.com/grpc-bazel-mirror/github.com/abseil/abseil-cpp/archive/df3ea785d8c30a9503321a3d35ee7d35808f190d.tar.gz",
++                 "https://github.com/abseil/abseil-cpp/archive/df3ea785d8c30a9503321a3d35ee7d35808f190d.tar.gz",
++             ],
+++            patches = ["@com_github_grpc_grpc//:third_party/abseil-cpp/absl.patch"],
++         )
++
++     if "bazel_toolchains" not in native.existing_rules():
+ diff --git a/bazel/grpc_extra_deps.bzl b/bazel/grpc_extra_deps.bzl
+ index 4c1dfad2e8..f63c54ddef 100644
+ --- a/bazel/grpc_extra_deps.bzl
+@@ -120,3 +128,25 @@ index c047f0c515..7c24fbc617 100644
+          ":windows": "@com_github_grpc_grpc//third_party/cares:config_windows/ares_config.h",
+          ":android": "@com_github_grpc_grpc//third_party/cares:config_android/ares_config.h",
+          "//conditions:default": "@com_github_grpc_grpc//third_party/cares:config_linux/ares_config.h",
++
++--- /dev/null
+++++ b/third_party/abseil-cpp/absl.patch
++@@ -0,0 +1,18 @@
+++0e2c62da1dcaf6529abab952bdcc96c6de2d9506 by Abseil Team <absl-team@google.com>:
+++
+++Add missing <limits> include
+++
+++PiperOrigin-RevId: 339054753
+++
+++--
+++
+++--- absl/synchronization/internal/graphcycles.cc
++++++ absl/synchronization/internal/graphcycles.cc
+++@@ -37,6 +37,7 @@
+++ 
+++ #include <algorithm>
+++ #include <array>
++++#include <limits>
+++ #include "absl/base/internal/hide_ptr.h"
+++ #include "absl/base/internal/raw_logging.h"
+++ #include "absl/base/internal/spinlock.h"
+

packages/bazel/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 re
+
+from spack.package import *
+
+
+class Bazel(Package):
+    """Bazel is an open-source build and test tool similar to Make, Maven, and
+    Gradle. It uses a human-readable, high-level build language. Bazel supports
+    projects in multiple languages and builds outputs for multiple platforms.
+    Bazel supports large codebases across multiple repositories, and large
+    numbers of users."""
+
+    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")
+    version("5.4.0", sha256="a1c62d9bcb4e03106ddf0b7bd96196ba246e1c9b7a935daf8d9beda8bbdcb8a1")
+    version("5.3.2", sha256="3880ad919592d1e3e40c506f13b32cd0a2e26f129d87cb6ba170f1801d7d7b82")
+    version("5.3.1", sha256="18486e7152ca26b26585e9b2a6f49f332b116310d3b7e5b70583f1f1f24bb8ae")
+    version("5.3.0", sha256="ee801491ff0ec3a562422322a033c9afe8809b64199e4a94c7433d4e14e6b921")
+    version("5.2.0", sha256="820a94dbb14071ed6d8c266cf0c080ecb265a5eea65307579489c4662c2d582a")
+    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")
+    version("4.2.0", sha256="74814b63920aaee47dbbbee7082e5c4317e4eebaf07e03c5fb5626e1716f1034")
+    version("4.1.0", sha256="f377d755c96a50f6bd2f423562598d822f43356783330a0b780ad442864d6eeb")
+    version("4.0.0", sha256="d350f80e70654932db252db380d2ec0144a00e86f8d9f2b4c799ffdb48e9cdd1")
+    version("3.7.2", sha256="de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1")
+    version("3.7.1", sha256="c9244e5905df6b0190113e26082c72d58b56b1b0dec66d076f083ce4089b0307")
+    version("3.7.0", sha256="63873623917c756d1be49ff4d5fc23049736180e6b9a7d5236c6f204eddae3cc")
+    version("3.6.0", sha256="3a18f24febb5203f11b0985b27e120ac623058d1d5ca79cd6df992e67d57240a")
+    version("3.5.1", sha256="67eae714578b22d24192b0eb3a2d35b07578bbd57a33c50f1e74f8acd6378b3c")
+    version("3.5.0", sha256="334429059cf82e222ca8a9d9dbbd26f8e1eb308613463c2b8655dd4201b127ec")
+    version("3.4.1", sha256="27af1f11c8f23436915925b25cf6e1fb07fccf2d2a193a307c93437c60f63ba8")
+    version("3.4.0", sha256="7583abf8905ba9dd5394294e815e8873635ac4e5067e63392e8a33b397e450d8")
+    version("3.3.1", sha256="e0f1f43c65c4e0a38522b37e81f6129d8a1f7cd3d8884847be306544a7492747")
+    version("3.3.0", sha256="05a03960de09d5775839c5766ad8a0a30f261feaba5fa53ce3e49168d1eee826")
+    version("3.2.0", sha256="44ec129436f6de45f2230e14100104919443a1364c2491f5601666b358738bfa")
+    version("3.1.0", sha256="d7f40d0cac95a06cea6cb5b7f7769085257caebc3ee84269dd9298da760d5615")
+    version("3.0.0", sha256="530f5132e0a50da7ebb0ed08d9b6f1ddfd0d7d9b5d0beb2df5d687a4c8daf6b3")
+    version("2.2.0", sha256="9379878a834d105a47a87d3d7b981852dd9f64bc16620eacd564b48533e169a7")
+    version("2.1.1", sha256="83f67f28f4e47ff69043307d1791c9bffe83949e84165d49058b84eded932647")
+    version("2.1.0", sha256="3371cd9050989173a3b27364668328653a65653a50a85c320adc53953b4d5f46")
+    version("2.0.1", sha256="a863ed9e6fc420fbd92e63a12fe1a5b9be1a7a36f11f61f1fdc582c813bbe543")
+    version("2.0.0", sha256="724da3c656f68e787a86ebb9844773aa1c2e3a873cc39462a8f1b336153d6cbb")
+
+    variant(
+        "nodepfail",
+        default=True,
+        description="Disable failing dependency checks due to injected absolute paths - "
+        "required for most builds using bazel with spack",
+    )
+
+    # begin EBRAINS (added): to provide ld via GCC_HOST_COMPILER_PREFIX
+    depends_on("binutils", type=("build"))
+    # end EBRAINS
+
+    # https://bazel.build/install/compile-source#bootstrap-unix-prereq
+    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("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")
+
+    # Inject include paths
+    patch("unix_cc_configure-3.0.patch", when="@3:")
+    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="@:5.3")
+    # end EBRAINS
+
+    # Disable dependency search
+    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="@:4.2.3,5:6.1.1")
+
+    # https://github.com/bazelbuild/bazel/issues/17958
+    patch(
+        "https://github.com/bazelbuild/bazel/commit/43dadb275b3f9690242bf2d94a0757c721d231a9.patch?full_index=1",
+        sha256="af73a49006baa05475b1b79dad83e1e014ebfe22f38aa55774f9a465404aed54",
+        when="@5.0:5.4.0,6.0",
+    )
+
+    # Fix build with Fujitsu compiler
+    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="@: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")
+
+    # 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="@: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("@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
+
+    # begin EBRAINS (added)
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        env.prepend_path("GCC_HOST_COMPILER_PREFIX", self.spec['binutils'].prefix.bin)
+    # end EBRAINS
+
+    def setup_build_environment(self, env):
+        # fix the broken linking (on power9)
+        # https://github.com/bazelbuild/bazel/issues/10327
+        env.set("BAZEL_LINKOPTS", "")
+        env.set("BAZEL_LINKLIBS", "-lstdc++")
+
+        # .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):
+        bash = which("bash")
+        bash("./compile.sh")
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install("output/bazel", prefix.bin)
+
+    @run_after("install")
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+        # https://github.com/Homebrew/homebrew-core/blob/master/Formula/bazel.rb
+
+        # Bazel does not work properly on NFS, switch to /tmp
+        with working_dir("/tmp/spack/bazel/spack-test", create=True):
+            touch("WORKSPACE")
+
+            with open("ProjectRunner.java", "w") as f:
+                f.write(
+                    """\
+public class ProjectRunner {
+    public static void main(String args[]) {
+        System.out.println("Hi!");
+    }
+}"""
+                )
+
+            with open("BUILD", "w") as f:
+                f.write(
+                    """\
+java_binary(
+    name = "bazel-test",
+    srcs = glob(["*.java"]),
+    main_class = "ProjectRunner",
+)"""
+                )
+
+            # Spack's logs don't handle colored output well
+            bazel = Executable(self.spec["bazel"].command.path)
+            bazel(
+                "--output_user_root=/tmp/spack/bazel/spack-test",
+                "build",
+                "--color=no",
+                f"--jobs={make_jobs}",
+                "//:bazel-test",
+            )
+
+            exe = Executable("bazel-bin/bazel-test")
+            assert exe(output=str) == "Hi!\n"
+
+    def setup_dependent_package(self, module, dependent_spec):
+        module.bazel = Executable(self.spec["bazel"].command.path)
+
+    @property
+    def parallel(self):
+        return not self.spec.satisfies("%fj")

packages/bazel/unix_cc_configure-0.15.patch

+--- a/tools/cpp/unix_cc_configure.bzl
++++ b/tools/cpp/unix_cc_configure.bzl
+@@ -145,11 +145,18 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, lang_flag, additional_fl
+     else:
+         inc_dirs = result.stderr[index1 + 1:index2].strip()
+ 
+-    return [
++    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_compiler_option_supported(repository_ctx, cc, option):
+     """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
+     result = repository_ctx.execute([

packages/bazel/unix_cc_configure-3.0.patch

+diff --git a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl
+index 5feb10b76a..cde0b8f8f1 100644
+--- a/tools/cpp/unix_cc_configure.bzl
++++ b/tools/cpp/unix_cc_configure.bzl
+@@ -151,8 +151,14 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, lang_flag, additional_fl
+         ).stdout.strip() + "/share"
+         inc_directories.append(_prepare_include_path(repository_ctx, resource_dir))
+ 
++    env = repository_ctx.os.environ
++    if "SPACK_INCLUDE_DIRS" in env:
++        for path in env["SPACK_INCLUDE_DIRS"].split(":"):
++            inc_directories.append(path)
++
+     return inc_directories
+ 
++
+ def _is_compiler_option_supported(repository_ctx, cc, option):
+     """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
+     result = repository_ctx.execute([

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/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

+# 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
+# oauth.get_token()
+class ClbNbUtils(PythonPackage):
+    url      = 'https://github.com/HumanBrainProject/clb-nb-utils/archive/refs/heads/master.zip'
+    maintainers = ['akarmas']
+    version('0.1.0','aa079ed0a8c4806db4657a6e7b534f4d')
+    depends_on('python@3.8:', type=('build','run'))
+    depends_on('py-setuptools', type=('build','run'))
+    depends_on('py-requests', type=('build','run'))

packages/genpybind/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 Genpybind(WafPackage):
+    """Autogeneration of Python bindings from manually annotated C++ headers"""
+
+    homepage = "https://github.com/kljohann/genpybind"
+    url      = "https://github.com/kljohann/genpybind/archive/v0.1.0.tar.gz"
+    git      = "https://github.com/kljohann/genpybind.git"
+
+    version('0.2.1', sha256='e4d993f0c65cb5cf635cec7df899cbd91af1f0bd8a3626f33e9e0925f5383384')
+    version('0.2.0', sha256='9d1e9d026a9e355e282aca549a2af108bedcc5bc59ba0b76a6072f88e4c0be4c')
+    version('0.1.1-pre', commit="9d06a3ad4b6b917c8fcc07261a97b13a3079bcba")
+    version('0.1.0', sha256='f25cb2b3180103cb96c42fb8d37be8b1f06b7721f6aa08841d5ae16361896407')
+    version('master', branch='master')
+    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'))
+    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()
+
+        if self.spec.satisfies("@visions") or self.spec.satisfies("@ebrains"):
+            # currently only our HEAD supports the rename
+            # TODO: adapt once the change is upstream
+            args.append("--genpybind-disable-tests")
+        else:
+            args.append("--disable-tests")
+        return 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 2013-2024 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")
+
+
+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 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='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)
+
+    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):
+        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}"