Spack-Snake: A stack for python

Spack has the ability to provide a binary cache of python packages
for general use in the scientific and data analytics communities.
This PR is an effort to begin such a collection

lib/spack/docs/environments.rst

@@ -539,9 +539,7 @@ from the command line.
 
 You can also include an environment directly in the ``spack.yaml`` file. It
 involves adding the ``include_concrete`` heading in the yaml followed by the
-absolute path to the independent environments. Note, that you may use Spack
-config variables such as ``$spack`` or environment variables as long as the
-expression expands to an absolute path.
+absolute path to the independent environments.
 
 .. code-block:: yaml
 
@@ -551,7 +549,7 @@ expression expands to an absolute path.
          unify: true
      include_concrete:
      - /absolute/path/to/environment1
-     - $spack/../path/to/environment2
+     - /absolute/path/to/environment2
 
 
 Once the ``spack.yaml`` has been updated you must concretize the environment to

lib/spack/docs/packaging_guide.rst

@@ -497,7 +497,7 @@ extends Spack's ``Package`` class.  For example, here is
 .. code-block:: python
    :linenos:
 
-   from spack.package import *
+   from spack import *
 
    class Libelf(Package):
        """ ... description ... """
@@ -1089,7 +1089,7 @@ You've already seen the ``homepage`` and ``url`` package attributes:
 .. code-block:: python
    :linenos:
 
-   from spack.package import *
+   from spack import *
 
 
    class Mpich(Package):
@@ -6183,7 +6183,7 @@ running:
 
 .. code-block:: python
 
-   from spack.package import *
+   from spack import *
 
 This is already part of the boilerplate for packages created with
 ``spack create``.

lib/spack/spack/audit.py

@@ -350,7 +350,7 @@ def _ensure_no_folders_without_package_py(error_cls):
     for repository in spack.repo.PATH.repos:
         missing = []
         for entry in os.scandir(repository.packages_path):
-            if not entry.is_dir() or entry.name == "__pycache__":
+            if not entry.is_dir():
                 continue
             package_py = pathlib.Path(entry.path) / spack.repo.package_file_name
             if not package_py.exists():

lib/spack/spack/binary_distribution.py

@@ -717,11 +717,7 @@ def _read_specs_and_push_index(
         temp_dir: Location to write index.json and hash for pushing
     """
     for file in file_list:
-        try:
-            fetched_spec = spack.spec.Spec.from_dict(read_method(file))
-        except Exception as e:
-            tty.warn(f"Unable to fetch spec for manifest {file} due to: {e}")
-            continue
+        fetched_spec = spack.spec.Spec.from_dict(read_method(file))
         db.add(fetched_spec)
         db.mark(fetched_spec, "in_buildcache", True)
 
@@ -754,7 +750,6 @@ def file_read_method(manifest_path):
         cache_entry.destroy()
         return spec_dict
 
-    url_to_list = url_util.join(url, buildcache_relative_specs_url())
     sync_command_args = [
         "s3",
         "sync",
@@ -762,11 +757,11 @@ def file_read_method(manifest_path):
         "*",
         "--include",
         "*.spec.manifest.json",
-        url_to_list,
+        url,
         tmpspecsdir,
     ]
 
-    tty.debug(f"Using aws s3 sync to download manifests from {url_to_list} to {tmpspecsdir}")
+    tty.debug(f"Using aws s3 sync to download manifests from {url} to {tmpspecsdir}")
 
     try:
         aws(*sync_command_args, output=os.devnull, error=os.devnull)

lib/spack/spack/cmd/style.py

@@ -56,7 +56,7 @@ def is_package(f):
     """Whether flake8 should consider a file as a core file or a package.
 
     We run flake8 with different exceptions for the core and for
-    packages, since we allow `from spack.package import *` and poking globals
+    packages, since we allow `from spack import *` and poking globals
     into packages.
     """
     return f.startswith("var/spack/") and f.endswith("package.py")

lib/spack/spack/environment/environment.py

@@ -1049,11 +1049,7 @@ def add_view(name, values):
 
     def _process_concrete_includes(self):
         """Extract and load into memory included concrete spec data."""
-        _included_concrete_envs = self.manifest[TOP_LEVEL_KEY].get(included_concrete_name, [])
-        # Expand config and environment variables
-        self.included_concrete_envs = [
-            spack.util.path.canonicalize_path(_env) for _env in _included_concrete_envs
-        ]
+        self.included_concrete_envs = self.manifest[TOP_LEVEL_KEY].get(included_concrete_name, [])
 
         if self.included_concrete_envs:
             if os.path.exists(self.lock_path):

lib/spack/spack/main.py

@@ -550,6 +550,7 @@ def setup_main_options(args):
         spack.config.CONFIG.scopes["command_line"].sections["repos"] = syaml.syaml_dict(
             [(key, [spack.paths.mock_packages_path])]
         )
+        spack.repo.PATH = spack.repo.create(spack.config.CONFIG)
 
     # If the user asked for it, don't check ssl certs.
     if args.insecure:
@@ -560,8 +561,6 @@ def setup_main_options(args):
     for config_var in args.config_vars or []:
         spack.config.add(fullpath=config_var, scope="command_line")
 
-    spack.repo.enable_repo(spack.repo.create(spack.config.CONFIG))
-
     # On Windows10 console handling for ASCI/VT100 sequences is not
     # on by default. Turn on before we try to write to console
     # with color

lib/spack/spack/repo.py

@@ -91,8 +91,29 @@ class ReposFinder:
     Returns a loader based on the inspection of the current repository list.
     """
 
-    #: The current list of repositories.
-    repo_path: "RepoPath"
+    def __init__(self):
+        self._repo_init = _path
+        self._repo: Optional[RepoType] = None
+
+    @property
+    def current_repository(self):
+        if self._repo is None:
+            self._repo = self._repo_init()
+        return self._repo
+
+    @current_repository.setter
+    def current_repository(self, value):
+        self._repo = value
+
+    @contextlib.contextmanager
+    def switch_repo(self, substitute: "RepoType"):
+        """Switch the current repository list for the duration of the context manager."""
+        old = self._repo
+        try:
+            self._repo = substitute
+            yield
+        finally:
+            self._repo = old
 
     def find_spec(self, fullname, python_path, target=None):
         # "target" is not None only when calling importlib.reload()
@@ -113,11 +134,14 @@ def compute_loader(self, fullname: str):
         namespace, dot, module_name = fullname.rpartition(".")
 
         # If it's a module in some repo, or if it is the repo's namespace, let the repo handle it.
+        current_repo = self.current_repository
+        is_repo_path = isinstance(current_repo, RepoPath)
+        if is_repo_path:
+            repos = current_repo.repos
+        else:
+            repos = [current_repo]
 
-        if not hasattr(self, "repo_path"):
-            return None
-
-        for repo in self.repo_path.repos:
+        for repo in repos:
             # We are using the namespace of the repo and the repo contains the package
             if namespace == repo.full_namespace:
                 # With 2 nested conditionals we can call "repo.real_name" only once
@@ -132,7 +156,9 @@ def compute_loader(self, fullname: str):
 
         # No repo provides the namespace, but it is a valid prefix of
         # something in the RepoPath.
-        if self.repo_path.by_namespace.is_prefix(fullname[len(PKG_MODULE_PREFIX_V1) :]):
+        if is_repo_path and current_repo.by_namespace.is_prefix(
+            fullname[len(PKG_MODULE_PREFIX_V1) :]
+        ):
             return SpackNamespaceLoader()
 
         return None
@@ -232,8 +258,6 @@ def get_all_package_diffs(type: str, repo: "Repo", rev1="HEAD^1", rev2="HEAD") -
     changed: Set[str] = set()
     for path in lines:
         dir_name, _, _ = path.partition("/")
-        if not nm.valid_module_name(dir_name, repo.package_api):
-            continue
         pkg_name = nm.pkg_dir_to_pkg_name(dir_name, repo.package_api)
         if pkg_name not in added and pkg_name not in removed:
             changed.add(pkg_name)
@@ -638,6 +662,7 @@ def __init__(
                 if isinstance(repo, str):
                     assert cache is not None, "cache must hold a value, when repo is a string"
                     repo = Repo(repo, cache=cache, overrides=overrides)
+                repo.finder(self)
                 self.put_last(repo)
             except RepoError as e:
                 tty.warn(
@@ -647,20 +672,6 @@ def __init__(
                     f"    spack repo rm {repo}",
                 )
 
-    def enable(self) -> None:
-        """Set the relevant search paths for package module loading"""
-        REPOS_FINDER.repo_path = self
-        for p in reversed(self.python_paths()):
-            if p not in sys.path:
-                sys.path.insert(0, p)
-
-    def disable(self) -> None:
-        """Disable the search paths for package module loading"""
-        del REPOS_FINDER.repo_path
-        for p in self.python_paths():
-            if p in sys.path:
-                sys.path.remove(p)
-
     def ensure_unwrapped(self) -> "RepoPath":
         """Ensure we unwrap this object from any dynamic wrapper (like Singleton)"""
         return self
@@ -834,6 +845,9 @@ def python_paths(self) -> List[str]:
 
     def get_pkg_class(self, pkg_name: str) -> Type["spack.package_base.PackageBase"]:
         """Find a class for the spec's package and return the class object."""
+        for p in self.python_paths():
+            if p not in sys.path:
+                sys.path.insert(0, p)
         return self.repo_for_pkg(pkg_name).get_pkg_class(pkg_name)
 
     @autospec
@@ -1080,6 +1094,9 @@ def check(condition, msg):
         # Class attribute overrides by package name
         self.overrides = overrides or {}
 
+        # Optional reference to a RepoPath to influence module import from spack.pkg
+        self._finder: Optional[RepoPath] = None
+
         # Maps that goes from package name to corresponding file stat
         self._fast_package_checker: Optional[FastPackageChecker] = None
 
@@ -1091,6 +1108,9 @@ def check(condition, msg):
     def package_api_str(self) -> str:
         return f"v{self.package_api[0]}.{self.package_api[1]}"
 
+    def finder(self, value: RepoPath) -> None:
+        self._finder = value
+
     def real_name(self, import_name: str) -> Optional[str]:
         """Allow users to import Spack packages using Python identifiers.
 
@@ -1343,9 +1363,11 @@ def get_pkg_class(self, pkg_name: str) -> Type["spack.package_base.PackageBase"]
             fullname += ".package"
 
         class_name = nm.pkg_name_to_class_name(pkg_name)
-
+        if self.python_path and self.python_path not in sys.path:
+            sys.path.insert(0, self.python_path)
         try:
-            module = importlib.import_module(fullname)
+            with REPOS_FINDER.switch_repo(self._finder or self):
+                module = importlib.import_module(fullname)
         except ImportError as e:
             raise UnknownPackageError(fullname) from e
         except Exception as e:
@@ -1538,6 +1560,12 @@ def create_or_construct(
     return from_path(repo_yaml_dir)
 
 
+def _path(configuration=None):
+    """Get the singleton RepoPath instance for Spack."""
+    configuration = configuration or spack.config.CONFIG
+    return create(configuration=configuration)
+
+
 def create(configuration: spack.config.Configuration) -> RepoPath:
     """Create a RepoPath from a configuration object.
 
@@ -1560,10 +1588,8 @@ def create(configuration: spack.config.Configuration) -> RepoPath:
     return RepoPath(*repo_dirs, cache=spack.caches.MISC_CACHE, overrides=overrides)
 
 
-#: Global package repository instance.
-PATH: RepoPath = llnl.util.lang.Singleton(
-    lambda: create(configuration=spack.config.CONFIG)
-)  # type: ignore[assignment]
+#: Singleton repo path instance
+PATH: RepoPath = llnl.util.lang.Singleton(_path)  # type: ignore
 
 # Add the finder to sys.meta_path
 REPOS_FINDER = ReposFinder()
@@ -1589,27 +1615,20 @@ def use_repositories(
     Returns:
         Corresponding RepoPath object
     """
+    global PATH
     paths = [getattr(x, "root", x) for x in paths_and_repos]
-    scope_name = f"use-repo-{uuid.uuid4()}"
+    scope_name = "use-repo-{}".format(uuid.uuid4())
     repos_key = "repos:" if override else "repos"
     spack.config.CONFIG.push_scope(
         spack.config.InternalConfigScope(name=scope_name, data={repos_key: paths})
     )
-    old_repo, new_repo = PATH, create(configuration=spack.config.CONFIG)
-    old_repo.disable()
-    enable_repo(new_repo)
+    PATH, saved = create(configuration=spack.config.CONFIG), PATH
     try:
-        yield new_repo
+        with REPOS_FINDER.switch_repo(PATH):  # type: ignore
+            yield PATH
     finally:
         spack.config.CONFIG.remove_scope(scope_name=scope_name)
-        enable_repo(old_repo)
-
-
-def enable_repo(repo_path: RepoPath) -> None:
-    """Set the global package repository and make them available in module search paths."""
-    global PATH
-    PATH = repo_path
-    PATH.enable()
+        PATH = saved
 
 
 class MockRepositoryBuilder:

lib/spack/spack/subprocess_context.py

@@ -106,7 +106,7 @@ def __init__(self):
 
     def restore(self):
         spack.config.CONFIG = self.config
-        spack.repo.enable_repo(spack.repo.create(self.config))
+        spack.repo.PATH = spack.repo.create(self.config)
         spack.platforms.host = self.platform
         spack.store.STORE = self.store
         self.test_patches.restore()
@@ -129,6 +129,7 @@ def restore(self):
 
 
 def store_patches():
+    global patches
     module_patches = list()
     class_patches = list()
     if not patches:

lib/spack/spack/test/cmd/ci.py

@@ -2028,12 +2028,13 @@ def test_ci_verify_versions_valid(
     tmpdir,
 ):
     repo, _, commits = mock_git_package_changes
-    with spack.repo.use_repositories(repo):
-        monkeypatch.setattr(spack.repo, "builtin_repo", lambda: repo)
+    spack.repo.PATH.put_first(repo)
 
-        out = ci_cmd("verify-versions", commits[-1], commits[-3])
-        assert "Validated diff-test@2.1.5" in out
-        assert "Validated diff-test@2.1.6" in out
+    monkeypatch.setattr(spack.repo, "builtin_repo", lambda: repo)
+
+    out = ci_cmd("verify-versions", commits[-1], commits[-3])
+    assert "Validated diff-test@2.1.5" in out
+    assert "Validated diff-test@2.1.6" in out
 
 
 def test_ci_verify_versions_standard_invalid(
@@ -2044,21 +2045,23 @@ def test_ci_verify_versions_standard_invalid(
     verify_git_versions_invalid,
 ):
     repo, _, commits = mock_git_package_changes
-    with spack.repo.use_repositories(repo):
-        monkeypatch.setattr(spack.repo, "builtin_repo", lambda: repo)
+    spack.repo.PATH.put_first(repo)
 
-        out = ci_cmd("verify-versions", commits[-1], commits[-3], fail_on_error=False)
-        assert "Invalid checksum found diff-test@2.1.5" in out
-        assert "Invalid commit for diff-test@2.1.6" in out
+    monkeypatch.setattr(spack.repo, "builtin_repo", lambda: repo)
+
+    out = ci_cmd("verify-versions", commits[-1], commits[-3], fail_on_error=False)
+    assert "Invalid checksum found diff-test@2.1.5" in out
+    assert "Invalid commit for diff-test@2.1.6" in out
 
 
 def test_ci_verify_versions_manual_package(monkeypatch, mock_packages, mock_git_package_changes):
     repo, _, commits = mock_git_package_changes
-    with spack.repo.use_repositories(repo):
-        monkeypatch.setattr(spack.repo, "builtin_repo", lambda: repo)
+    spack.repo.PATH.put_first(repo)
 
-        pkg_class = spack.spec.Spec("diff-test").package_class
-        monkeypatch.setattr(pkg_class, "manual_download", True)
+    monkeypatch.setattr(spack.repo, "builtin_repo", lambda: repo)
 
-        out = ci_cmd("verify-versions", commits[-1], commits[-2])
-        assert "Skipping manual download package: diff-test" in out
+    pkg_class = spack.spec.Spec("diff-test").package_class
+    monkeypatch.setattr(pkg_class, "manual_download", True)
+
+    out = ci_cmd("verify-versions", commits[-1], commits[-2])
+    assert "Skipping manual download package: diff-test" in out

lib/spack/spack/test/cmd/find.py

@@ -448,7 +448,7 @@ def test_find_loaded(database, working_env):
 
 
 @pytest.mark.regression("37712")
-def test_environment_with_version_range_in_compiler_doesnt_fail(tmp_path, mock_packages):
+def test_environment_with_version_range_in_compiler_doesnt_fail(tmp_path):
     """Tests that having an active environment with a root spec containing a compiler constrained
     by a version range (i.e. @X.Y rather the single version than @=X.Y) doesn't result in an error
     when invoking "spack find".

lib/spack/spack/test/repo.py

@@ -312,6 +312,7 @@ class TestRepoPath:
     def test_creation_from_string(self, mock_test_cache):
         repo = spack.repo.RepoPath(spack.paths.mock_packages_path, cache=mock_test_cache)
         assert len(repo.repos) == 1
+        assert repo.repos[0]._finder is repo
         assert repo.by_namespace["builtin.mock"] is repo.repos[0]
 
     def test_get_repo(self, mock_test_cache):

lib/spack/spack/test/spec_list.py

@@ -55,7 +55,6 @@ def parser_and_speclist():
     return parser, result
 
 
-@pytest.mark.usefixtures("mock_packages")
 class TestSpecList:
     @pytest.mark.regression("28749")
     @pytest.mark.parametrize(
@@ -84,8 +83,8 @@ class TestSpecList:
             ),
             # A constraint affects both the root and a dependency
             (
-                [{"matrix": [["version-test-root"], ["%gcc"], ["^version-test-pkg%gcc"]]}],
-                ["version-test-root%gcc ^version-test-pkg%gcc"],
+                [{"matrix": [["gromacs"], ["%gcc"], ["+plumed ^plumed%gcc"]]}],
+                ["gromacs+plumed%gcc ^plumed%gcc"],
             ),
         ],
     )
@@ -159,7 +158,7 @@ def test_spec_list_recursion_specs_as_constraints(self):
         assert result.specs == DEFAULT_SPECS
 
     @pytest.mark.regression("16841")
-    def test_spec_list_matrix_exclude(self):
+    def test_spec_list_matrix_exclude(self, mock_packages):
         parser = SpecListParser()
         result = parser.parse_user_specs(
             name="specs",
@@ -172,7 +171,7 @@ def test_spec_list_matrix_exclude(self):
         )
         assert len(result.specs) == 1
 
-    def test_spec_list_exclude_with_abstract_hashes(self, install_mockery):
+    def test_spec_list_exclude_with_abstract_hashes(self, mock_packages, install_mockery):
         # Put mpich in the database so it can be referred to by hash.
         mpich_1 = spack.concretize.concretize_one("mpich+debug")
         mpich_2 = spack.concretize.concretize_one("mpich~debug")

share/spack/gitlab/cloud_pipelines/stacks/radiuss/spack.yaml

@@ -5,17 +5,11 @@ spack:
       target: [ "x86_64_v3" ]
       require:
       - target=x86_64_v3
-      # prefer %gcc@7.5.0 but also allow %gcc@12
-      - one_of: ['%gcc@7.5.0', '%gcc@12']
+      - '%gcc@7.5.0'
 
       providers:
         mpi: [mvapich2]
 
-    mfem:
-      require:
-      # gcc@7.5.0 crashes when building mfem@4.8.0, so use gcc@12
-      - '%gcc@12'
-
   specs:
   - ascent  # ^conduit@0.6.0
   - axom

share/spack/gitlab/cloud_pipelines/stacks/spack-snake/spack.yaml

@@ -0,0 +1,44 @@
+spack:
+  view: false
+
+  concretizer:
+    reuse: false
+    unify: false
+    static_analysis: true
+
+  packages:
+    all:
+      require:
+      - "%gcc"
+      - target=x86_64_v3
+      variants: +mpi
+    c:
+      require: gcc
+    cxx:
+      require: gcc
+    fortran:
+      require: gcc
+    mpi:
+      require:
+      - openmpi
+    blas:
+      require:
+      - openblas
+    lapack:
+      require:
+      - openblas
+  specs:
+  - python
+  - py-numpy
+  - py-scipy
+  - py-matplotlib
+  - py-pip
+  - py-mpi4py
+
+  ci:
+    pipeline-gen:
+    - build-job:
+        image: ghcr.io/spack/spack/ubuntu22.04-runner-amd64-gcc-11.4:2024.03.01
+
+  cdash:
+    build-group: spack-snake

share/spack/qa/run-unit-tests

@@ -40,7 +40,9 @@ spack -p --lines 20 spec mpileaks%gcc
 $coverage_run $(which spack) bootstrap status --dev --optional
 
 # Check that we can import Spack packages directly as a first import
-$coverage_run $(which spack) python -c "from spack_repo.builtin.packages.mpileaks.package import Mpileaks"
+# TODO: this check is disabled, because sys.path is only updated once
+# spack.repo.PATH.get_pkg_class is called.
+# $coverage_run $(which spack) python -c "import spack.pkg.builtin.mpileaks; repr(spack.pkg.builtin.mpileaks.Mpileaks)"
 
 #-----------------------------------------------------------
 # Run unit tests with code coverage

var/spack/repos/spack_repo/builtin/__init__.py

@@ -1,3 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)

var/spack/repos/spack_repo/builtin/packages/__init__.py

@@ -1,3 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)

var/spack/repos/spack_repo/builtin/packages/amr_wind/package.py

@@ -20,12 +20,6 @@ class AmrWind(CMakePackage, CudaPackage, ROCmPackage):
     license("BSD-3-Clause")
 
     version("main", branch="main", submodules=True)
-    version(
-        "3.4.2", tag="v3.4.2", commit="ed475a0533dfacf1fdff0b707518ccf99040d9f9", submodules=True
-    )
-    version(
-        "3.4.1", tag="v3.4.1", commit="effe63ca9061e6d2bd5c5e84b690d29c0869f029", submodules=True
-    )
     version(
         "3.4.0", tag="v3.4.0", commit="38d1b9fd0b70aab4a01fd507f039750c2508bd1c", submodules=True
     )

var/spack/repos/spack_repo/builtin/packages/apache_tvm/package.py

@@ -13,15 +13,13 @@ class ApacheTvm(CMakePackage, CudaPackage):
     hardware backend."""
 
     homepage = "https://tvm.apache.org/"
+    url = "https://dlcdn.apache.org/tvm/tvm-v0.16.0/apache-tvm-src-v0.16.0.tar.gz"
 
     license("Apache-2.0", checked_by="alex391")
-    url = "https://github.com/apache/tvm/releases/download/v0.19.0/apache-tvm-src-v0.19.0.tar.gz"
 
-    version("0.19.0", sha256="13fd707eae37b9b2b77bccd39668764f61ae6824d50cd1ab8164df1c75565be1")
     version(
         "0.16.0",
         sha256="55e2629c39248ef3b1ee280e34a960182bd17bea7ae0d0fa132bbdaaf5aba1ac",
-        url="https://dlcdn.apache.org/tvm/tvm-v0.16.0/apache-tvm-src-v0.16.0.tar.gz",
         deprecated=True,
     )
 
@@ -30,16 +28,10 @@ class ApacheTvm(CMakePackage, CudaPackage):
     depends_on("c", type="build")
     depends_on("cxx", type="build")
     depends_on("cmake@3.18:", type="build")
-
-    depends_on("python@3.7:", type=("build", "run"))
-    conflicts("^python@3.9.0:", when="@:0.16")
-
+    depends_on("python@3.7:3.8", type=("build", "run"))
     depends_on("zlib-api", type=("link", "run"))
     depends_on("ncurses", type=("link", "run"))
-
-    depends_on("llvm@4:", type="build", when="+llvm")
-    conflicts("^llvm@19.0.0:", when="@:0.16+llvm")
-
+    depends_on("llvm@4:18.1.8", type="build", when="+llvm")
     depends_on("cuda@8:", when="+cuda")
 
     def cmake_args(self):

var/spack/repos/spack_repo/builtin/packages/cbtf_krell/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import spack.store
 from spack.package import *
 
 
@@ -40,6 +41,11 @@ class CbtfKrell(CMakePackage):
         description="The build type to build",
         values=("Debug", "Release", "RelWithDebInfo"),
     )
+    variant(
+        "crayfe",
+        default=False,
+        description="build only the FE tool using the runtime_dir to point to target build.",
+    )
 
     # Fix build errors with gcc >= 10
     patch(
@@ -141,6 +147,44 @@ def set_mpi_cmake_options(self, spec, cmake_options):
 
         cmake_options.extend(mpi_options)
 
+    def set_cray_login_node_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
+        # the appropriate Cray login node libraries
+
+        cray_login_node_options = []
+        rt_platform = "cray"
+        # How do we get the compute node (CNL) cbtf package
+        # install directory path. spec['cbtf'].prefix is the
+        # login node path for this build, as we are building
+        # the login node components with this spack invocation. We
+        # need these paths to be the ones created in the CNL
+        # spack invocation.
+        be_cbtf = spack.store.db.query_one("cbtf arch=cray-CNL-haswell")
+        be_cbtfk = spack.store.db.query_one("cbtf-krell arch=cray-CNL-haswell")
+        be_papi = spack.store.db.query_one("papi arch=cray-CNL-haswell")
+        be_boost = spack.store.db.query_one("boost arch=cray-CNL-haswell")
+        be_mont = spack.store.db.query_one("libmonitor arch=cray-CNL-haswell")
+        be_unw = spack.store.db.query_one("libunwind arch=cray-CNL-haswell")
+        be_xer = spack.store.db.query_one("xerces-c arch=cray-CNL-haswell")
+        be_dyn = spack.store.db.query_one("dyninst arch=cray-CNL-haswell")
+        be_mrnet = spack.store.db.query_one("mrnet arch=cray-CNL-haswell")
+
+        cray_login_node_options.append("-DCN_RUNTIME_PLATFORM=%s" % rt_platform)
+
+        # Use install directories as CMAKE args for the building
+        # of login cbtf-krell
+        cray_login_node_options.append("-DCBTF_CN_RUNTIME_DIR=%s" % be_cbtf.prefix)
+        cray_login_node_options.append("-DCBTF_KRELL_CN_RUNTIME_DIR=%s" % be_cbtfk.prefix)
+        cray_login_node_options.append("-DPAPI_CN_RUNTIME_DIR=%s" % be_papi.prefix)
+        cray_login_node_options.append("-DBOOST_CN_RUNTIME_DIR=%s" % be_boost.prefix)
+        cray_login_node_options.append("-DLIBMONITOR_CN_RUNTIME_DIR=%s" % be_mont.prefix)
+        cray_login_node_options.append("-DLIBUNWIND_CN_RUNTIME_DIR=%s" % be_unw.prefix)
+        cray_login_node_options.append("-DXERCESC_CN_RUNTIME_DIR=%s" % be_xer.prefix)
+        cray_login_node_options.append("-DDYNINST_CN_RUNTIME_DIR=%s" % be_dyn.prefix)
+        cray_login_node_options.append("-DMRNET_CN_RUNTIME_DIR=%s" % be_mrnet.prefix)
+
+        cmake_options.extend(cray_login_node_options)
+
     def cmake_args(self):
         spec = self.spec
 
@@ -174,6 +218,11 @@ def cmake_args(self):
         # Add any MPI implementations coming from variant settings
         self.set_mpi_cmake_options(spec, cmake_args)
 
+        if self.spec.satisfies("+crayfe"):
+            # We need to build target/compute node components/libraries first
+            # then pass those libraries to the cbtf-krell login node build
+            self.set_cray_login_node_cmake_options(spec, cmake_args)
+
         return cmake_args
 
     def setup_run_environment(self, env: EnvironmentModifications) -> None:

var/spack/repos/spack_repo/builtin/packages/conquest/package.py

@@ -87,8 +87,6 @@ def edit(self, spec, prefix):
         else:
             defs_file = FileFilter("./src/system.make")
 
-        defs_file.filter(".*FC=.*", f"FC={spec['mpi'].mpifc}")
-        defs_file.filter(".*F77=.*", f"F77={spec['mpi'].mpif77}")
         defs_file.filter(".*COMPFLAGS=.*", f"COMPFLAGS= {fflags}")
         defs_file.filter(".*LINKFLAGS=.*", f"LINKFLAGS= {ldflags}")
         defs_file.filter(".*BLAS=.*", f"BLAS= {lapack_ld} {blas_ld}")

var/spack/repos/spack_repo/builtin/packages/cryodrgn/package.py

@@ -15,26 +15,23 @@ class Cryodrgn(PythonPackage):
 
     license("GPL-3.0-only", checked_by="A-N-Other")
 
-    version("3.4.3", sha256="eadc41190d3c6abe983164db299ebb0d7340840281774eaaea1a12627a80dc10")
     version("2.3.0", sha256="9dd75967fddfa56d6b2fbfc56933c50c9fb994326112513f223e8296adbf0afc")
 
-    depends_on("python@3.9:3.11", type=("build", "run"), when="@3.4.3:")
-    depends_on("python@3.7:3.11", type=("build", "run"), when="@2.3.0")
+    depends_on("python@3.7:", type=("build", "run"))
 
     depends_on("py-setuptools@61:", type="build")
     depends_on("py-setuptools-scm@6.2:", type="build")
 
     depends_on("py-torch@1:", type=("build", "run"))
     depends_on("py-pandas@:1", type=("build", "run"))
-    depends_on("py-numpy@:1.26", type=("build", "run"))
-    depends_on("py-matplotlib@:3.6", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
     depends_on("py-pyyaml", type=("build", "run"))
     depends_on("py-scipy@1.3.1:", type=("build", "run"))
     depends_on("py-scikit-learn", type=("build", "run"))
     depends_on("py-seaborn@:0.11", type=("build", "run"))
     depends_on("py-cufflinks", type=("build", "run"))
     depends_on("py-jupyterlab", type=("build", "run"))
-    depends_on("py-notebook@:6", type=("build", "run"), when="@3.4.3:")
     depends_on("py-umap-learn", type=("build", "run"))
     depends_on("py-ipywidgets@:7", type=("build", "run"))
     depends_on("py-healpy", type=("build", "run"))

var/spack/repos/spack_repo/builtin/packages/dd4hep/package.py

@@ -25,7 +25,6 @@ class Dd4hep(CMakePackage):
     license("LGPL-3.0-or-later")
 
     version("master", branch="master")
-    version("1.32", sha256="8bde4eab9af9841e040447282ea7df3a16e4bcec587c3a1e32f41987da9b1b4d")
     version("1.31", sha256="9c06a1b4462fc1b51161404889c74b37350162d0b0ac2154db27e3f102670bd1")
     version("1.30", sha256="02de46151e945eff58cffd84b4b86d35051f4436608199c3efb4d2e1183889fe")
     version("1.29", sha256="435d25a7ef093d8bf660f288b5a89b98556b4c1c293c55b93bf641fb4cba77e9")

var/spack/repos/spack_repo/builtin/packages/fmt/package.py

@@ -17,7 +17,6 @@ class Fmt(CMakePackage):
 
     license("MIT")
 
-    version("11.2.0", sha256="203eb4e8aa0d746c62d8f903df58e0419e3751591bb53ff971096eaa0ebd4ec3")
     version("11.1.4", sha256="49b039601196e1a765e81c5c9a05a61ed3d33f23b3961323d7322e4fe213d3e6")
     version("11.1.3", sha256="7df2fd3426b18d552840c071c977dc891efe274051d2e7c47e2c83c3918ba6df")
     version("11.1.2", sha256="ef54df1d4ba28519e31bf179f6a4fb5851d684c328ca051ce5da1b52bf8b1641")

var/spack/repos/spack_repo/builtin/packages/glib/package.py

@@ -30,11 +30,7 @@ class Glib(MesonPackage):
     # Even minor versions are stable, odd minor versions are development, only add even numbers
     version("2.82.5", sha256="05c2031f9bdf6b5aba7a06ca84f0b4aced28b19bf1b50c6ab25cc675277cbc3f")
     version("2.82.2", sha256="ab45f5a323048b1659ee0fbda5cecd94b099ab3e4b9abf26ae06aeb3e781fd63")
-    version(
-        "2.78.3",
-        sha256="609801dd373796e515972bf95fc0b2daa44545481ee2f465c4f204d224b2bc21",
-        preferred=True,
-    )
+    version("2.78.3", sha256="609801dd373796e515972bf95fc0b2daa44545481ee2f465c4f204d224b2bc21")
     version("2.78.0", sha256="44eaab8b720877ce303c5540b657b126f12dc94972d9880b52959f43fb537b30")
     version("2.76.6", sha256="1136ae6987dcbb64e0be3197a80190520f7acab81e2bfb937dc85c11c8aa9f04")
     version("2.76.4", sha256="5a5a191c96836e166a7771f7ea6ca2b0069c603c7da3cba1cd38d1694a395dda")

var/spack/repos/spack_repo/builtin/packages/go/package.py

@@ -39,11 +39,9 @@ class Go(Package):
 
     license("BSD-3-Clause")
 
-    version("1.24.3", sha256="229c08b600b1446798109fae1f569228102c8473caba8104b6418cb5bc032878")
     version("1.24.2", sha256="9dc77ffadc16d837a1bf32d99c624cb4df0647cee7b119edd9e7b1bcc05f2e00")
     version("1.24.1", sha256="8244ebf46c65607db10222b5806aeb31c1fcf8979c1b6b12f60c677e9a3c0656")
     version("1.24.0", sha256="d14120614acb29d12bcab72bd689f257eb4be9e0b6f88a8fb7e41ac65f8556e5")
-    version("1.23.9", sha256="08f6419547563ed9e7037d12b9c8909677c72f75f62ef85887ed9dbf49b8d2dd")
     version("1.23.8", sha256="0ca1f1e37ea255e3ce283af3f4e628502fb444587da987a5bb96d6c6f15930d4")
     version("1.23.7", sha256="7cfabd46b73eb4c26b19d69515dd043d7183a6559acccd5cfdb25eb6b266a458")
     version("1.23.6", sha256="039c5b04e65279daceee8a6f71e70bd05cf5b801782b6f77c6e19e2ed0511222")

var/spack/repos/spack_repo/builtin/packages/hpx/package.py

@@ -66,7 +66,7 @@ class Hpx(CMakePackage, CudaPackage, ROCmPackage):
         values=lambda x: isinstance(x, str) and (x.isdigit() or x == "auto"),
     )
 
-    instrumentation_values = ("google_perftools", "papi", "valgrind", "thread_debug")
+    instrumentation_values = ("apex", "google_perftools", "papi", "valgrind", "thread_debug")
     variant(
         "instrumentation",
         values=any_combination_of(*instrumentation_values),
@@ -93,11 +93,10 @@ class Hpx(CMakePackage, CudaPackage, ROCmPackage):
     variant("examples", default=False, description="Build examples")
     variant("async_mpi", default=False, description="Enable MPI Futures.")
     variant("async_cuda", default=False, description="Enable CUDA Futures.")
-    variant("apex", default=False, description="Enable APEX support")
 
     # Build dependencies
     depends_on("cxx", type="build")
-    depends_on("apex", when="+apex")
+
     depends_on("python", type=("build", "test", "run"))
     depends_on("git", type="build")
     depends_on("cmake", type="build")
@@ -123,6 +122,7 @@ class Hpx(CMakePackage, CudaPackage, ROCmPackage):
 
     depends_on("cuda", when="+async_cuda")
 
+    depends_on("otf2", when="instrumentation=apex")
     depends_on("gperftools", when="instrumentation=google_perftools")
     depends_on("papi", when="instrumentation=papi")
     depends_on("valgrind", when="instrumentation=valgrind")
@@ -155,7 +155,6 @@ class Hpx(CMakePackage, CudaPackage, ROCmPackage):
 
     # Restrictions for 1.5.x
     conflicts("cxxstd=11", when="@1.5:")
-    depends_on("apex@2.3:", when="@1.5")
 
     # Restrictions for 1.2.X
     with when("@:1.2.1"):
@@ -212,6 +211,8 @@ class Hpx(CMakePackage, CudaPackage, ROCmPackage):
     conflicts("~generic_coroutines", when="target=aarch64:", msg=_msg_generic_coroutines_target)
     conflicts("~generic_coroutines", when="target=arm:", msg=_msg_generic_coroutines_target)
 
+    # Patches APEX
+    patch("git_external.patch", when="@1.3.0 instrumentation=apex")
     patch("mimalloc_no_version_requirement.patch", when="@:1.8.0 malloc=mimalloc")
 
     def url_for_version(self, version):
@@ -241,7 +242,6 @@ def cmake_args(self):
             self.define_from_variant("HPX_WITH_EXAMPLES", "examples"),
             self.define_from_variant("HPX_WITH_ASYNC_MPI", "async_mpi"),
             self.define_from_variant("HPX_WITH_ASYNC_CUDA", "async_cuda"),
-            self.define_from_variant("HPX_WITH_APEX", "apex"),
             self.define("HPX_WITH_TESTS", self.run_tests),
             self.define("HPX_WITH_NETWORKING", "networking=none" not in spec),
             self.define("HPX_WITH_PARCELPORT_TCP", spec.satisfies("networking=tcp")),
@@ -278,4 +278,14 @@ def cmake_args(self):
                 self.define("HPX_WITH_LOGGING", True),
             ]
 
+        if spec.satisfies("instrumentation=apex"):
+            args += [
+                self.define("APEX_WITH_OTF2", True),
+                self.define("OTF2_ROOT", spec["otf2"].prefix),
+            ]
+
+            # it seems like there was a bug in the default version of APEX in 1.5.x
+            if spec.satisfies("@1.5"):
+                args += [self.define("HPX_WITH_APEX_TAG", "v2.3.0")]
+
         return args

var/spack/repos/spack_repo/builtin/packages/icon/package.py

@@ -14,16 +14,11 @@ class Icon(AutotoolsPackage):
 
     homepage = "https://www.icon-model.org"
     url = "https://gitlab.dkrz.de/icon/icon-model/-/archive/icon-2024.01-public/icon-model-icon-2024.01-public.tar.gz"
-    git = "https://gitlab.dkrz.de/icon/icon-model.git"
-    submodules = True
 
     maintainers("skosukhin", "Try2Code")
 
     license("BSD-3-Clause", checked_by="skosukhin")
 
-    version(
-        "2025.04", tag="icon-2025.04-public", commit="1be2ca66ea0de149971d2e77e88a9f11c764bd22"
-    )
     version("2024.10", sha256="5c461c783eb577c97accd632b18140c3da91c1853d836ca2385f376532e9bad1")
     version("2024.07", sha256="f53043ba1b36b8c19d0d2617ab601c3b9138b90f8ff8ca6db0fd079665eb5efa")
     version("2024.01-1", sha256="3e57608b7e1e3cf2f4cb318cfe2fdb39678bd53ca093955d99570bd6d7544184")
@@ -100,9 +95,10 @@ class Icon(AutotoolsPackage):
     # Optimization Features:
     variant("mixed-precision", default=False, description="Enable mixed-precision dynamical core")
 
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
-    depends_on("fortran", type="build")
+    depends_on("c", type="build")  # generated
+    depends_on("cxx", type="build")  # generated
+    depends_on("fortran", type="build")  # generated
+
     depends_on("python", type="build")
     depends_on("perl", type="build")
     depends_on("cmake@3.18:", type="build")
@@ -209,13 +205,11 @@ def configure_args(self):
                 "-arch=sm_{0}".format(self.nvidia_targets[gpu]),
                 "-ccbin={0}".format(spack_cxx),
             ]
+            flags["ICON_LDFLAGS"].extend(self.compiler.stdcxx_libs)
             libs += self.spec["cuda"].libs
         else:
             args.append("--disable-gpu")
 
-        if gpu in self.nvidia_targets or "+comin" in self.spec:
-            flags["ICON_LDFLAGS"].extend(self.compiler.stdcxx_libs)
-
         if self.compiler.name == "gcc":
             flags["CFLAGS"].append("-g")
             flags["ICON_CFLAGS"].append("-O3")

var/spack/repos/spack_repo/builtin/packages/jsonnet/package.py

@@ -3,77 +3,41 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
-import spack.build_systems.python
-from spack.build_systems import cmake, makefile
+from spack.build_systems.python import PythonPipBuilder
 from spack.package import *
 
 
-class Jsonnet(MakefilePackage, CMakePackage):
+class Jsonnet(MakefilePackage):
     """A data templating language for app and tool developers based on JSON"""
 
     homepage = "https://jsonnet.org/"
     git = "https://github.com/google/jsonnet.git"
     url = "https://github.com/google/jsonnet/archive/refs/tags/v0.18.0.tar.gz"
 
-    maintainers("greenc-FNAL", "gartung", "jcpunk", "marcmengel", "marcpaterno")
+    maintainers("jcpunk")
 
     license("Apache-2.0")
 
     version("master", branch="master")
-    version("0.21.0", sha256="a12ebca72e43e7061ffe4ef910e572b95edd7778a543d6bf85f6355bd290300e")
-    version("0.20.0", sha256="77bd269073807731f6b11ff8d7c03e9065aafb8e4d038935deb388325e52511b")
-    version("0.19.1", sha256="f5a20f2dc98fdebd5d42a45365f52fa59a7e6b174e43970fea4f9718a914e887")
     version("0.18.0", sha256="85c240c4740f0c788c4d49f9c9c0942f5a2d1c2ae58b2c71068107bc80a3ced4")
     version("0.17.0", sha256="076b52edf888c01097010ad4299e3b2e7a72b60a41abbc65af364af1ed3c8dbe")
 
-    variant("python", default=False, description="Provide Python bindings for jsonnet")
-
-    build_system("makefile", conditional("cmake", when="@0.21.0:"), default="makefile")
-
     conflicts("%gcc@:5.4.99", when="@0.18.0:")
 
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
-
-    with when("build_system=cmake"):
-        depends_on("nlohmann-json@3.6.1:")
+    depends_on("c", type="build")  # generated
+    depends_on("cxx", type="build")  # generated
 
+    variant("python", default=False, description="Provide Python bindings for jsonnet")
     extends("python", when="+python")
     depends_on("py-setuptools", type=("build",), when="+python")
     depends_on("py-pip", type=("build",), when="+python")
     depends_on("py-wheel", type=("build",), when="+python")
 
-
-class MakefileBuilder(makefile.MakefileBuilder):
-
     @property
     def install_targets(self):
         return ["PREFIX={0}".format(self.prefix), "install"]
 
     @run_after("install")
     def python_install(self):
-        if self.pkg.spec.satisfies("+python"):
-            pip(
-                *spack.build_systems.python.PythonPipBuilder.std_args(self.pkg),
-                f"--prefix={self.pkg.prefix}",
-                ".",
-            )
-
-
-class CMakeBuilder(cmake.CMakeBuilder):
-
-    def cmake_args(self):
-        return [
-            self.define("USE_SYSTEM_JSON", True),
-            self.define("BUILD_SHARED_BINARIES", True),
-            self.define("BUILD_TESTS", self.pkg.run_tests),
-        ]
-
-    @run_after("install")
-    def python_install(self):
-        if self.pkg.spec.satisfies("+python"):
-            pip(
-                *spack.build_systems.python.PythonPipBuilder.std_args(self.pkg),
-                f"--prefix={self.pkg.prefix}",
-                ".",
-            )
+        if "+python" in self.spec:
+            pip(*PythonPipBuilder.std_args(self), f"--prefix={self.prefix}", ".")

var/spack/repos/spack_repo/builtin/packages/lemon/package.py

@@ -22,8 +22,7 @@ class Lemon(CMakePackage):
     # soplex not mentioned in docs but shown in cmakecache
     # variant("soplex", default=False, description="Enable SOPLEX solver backend") #TODO
 
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
+    depends_on("cxx", type="build")  # generated
 
     depends_on("glpk", when="+glpk")
     depends_on("cplex", when="+ilog")

var/spack/repos/spack_repo/builtin/packages/libmng/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import spack.build_systems
 import spack.build_systems.autotools
 import spack.build_systems.cmake
 from spack.package import *

var/spack/repos/spack_repo/builtin/packages/libuv/package.py

@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import sys
 
+import spack.build_systems
 import spack.build_systems.autotools
 from spack.package import *
 

var/spack/repos/spack_repo/builtin/packages/llvm/package.py

@@ -1212,7 +1212,6 @@ def cmake_args(self):
                 [
                     define("LLVM_ENABLE_RUNTIMES", runtimes),
                     define("RUNTIMES_CMAKE_ARGS", runtime_cmake_args),
-                    define("LIBCXXABI_USE_LLVM_UNWINDER", not spec.satisfies("libunwind=none")),
                 ]
             )
 

var/spack/repos/spack_repo/builtin/packages/mesa/package.py

@@ -22,12 +22,10 @@ class Mesa(MesonPackage):
 
     version("main", branch="main")
     version(
-        "25.0.5",
-        sha256="c0d245dea0aa4b49f74b3d474b16542e4a8799791cd33d676c69f650ad4378d0",
+        "23.3.6",
+        sha256="cd3d6c60121dea73abbae99d399dc2facaecde1a8c6bd647e6d85410ff4b577b",
         preferred=True,
     )
-    version("24.3.4", sha256="e641ae27191d387599219694560d221b7feaa91c900bcec46bf444218ed66025")
-    version("23.3.6", sha256="cd3d6c60121dea73abbae99d399dc2facaecde1a8c6bd647e6d85410ff4b577b")
     version("23.3.3", sha256="518307c0057fa3cee8b58df78be431d4df5aafa7edc60d09278b2d7a0a80f3b4")
     version("23.2.1", sha256="64de0616fc2d801f929ab1ac2a4f16b3e2783c4309a724c8a259b20df8bbc1cc")
     version("23.1.9", sha256="295ba27c28146ed09214e8ce79afa1659edf9d142decc3c91f804552d64f7510")
@@ -68,7 +66,6 @@ class Mesa(MesonPackage):
     depends_on("python@:3.11", when="@:23.2", type="build")
     depends_on("py-packaging", type="build", when="^python@3.12:")
     depends_on("py-mako@0.8.0:", type="build")
-    depends_on("py-pyyaml", when="@24.2:", type="build")
     depends_on("unwind")
     depends_on("expat")
     depends_on("zlib-api")
@@ -129,9 +126,6 @@ class Mesa(MesonPackage):
         depends_on("libxt")
         depends_on("xrandr")
         depends_on("glproto@1.4.14:")
-        # In @24.3:, "libxshmfence@1.1:" is needed when:
-        # (with_dri_platform == 'drm') or (with_any_vk), see mesa's meson.build.
-        depends_on("libxshmfence@1.1:", when="@24.3:")
 
     # version specific issue
     # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=96130
@@ -204,6 +198,7 @@ def meson_args(self):
         args = [
             "-Dvulkan-drivers=",
             "-Dgallium-vdpau=disabled",
+            "-Dgallium-omx=disabled",
             "-Dgallium-va=disabled",
             "-Dgallium-xa=disabled",
             "-Dgallium-nine=false",
@@ -214,9 +209,6 @@ def meson_args(self):
         # gallium-xvmc was removed in @main and @2.23:
         if self.spec.satisfies("@:22.2"):
             args.append("-Dgallium-xvmc=disabled")
-        # the option 'gallium-omx' is present in @24.2.4 and removed in @main
-        if spec.satisfies("@:24.2.4"):
-            args.append("-Dgallium-omx=disabled")
 
         args_platforms = []
         args_gallium_drivers = ["swrast"]
@@ -255,14 +247,10 @@ def meson_args(self):
 
         if "+egl" in spec:
             num_frontends += 1
-            args.extend(["-Degl=enabled", "-Dgbm=enabled"])
-            if spec.satisfies("@:24.2.4"):
-                args.extend(["-Ddri3=enabled"])
+            args.extend(["-Degl=enabled", "-Dgbm=enabled", "-Ddri3=enabled"])
             args_platforms.append("surfaceless")
         else:
-            args.extend(["-Degl=disabled", "-Dgbm=disabled"])
-            if spec.satisfies("@:24.2.4"):
-                args.extend(["-Ddri3=disabled"])
+            args.extend(["-Degl=disabled", "-Dgbm=disabled", "-Ddri3=disabled"])
 
         args.append(opt_bool("+opengl" in spec, "opengl"))
         args.append(opt_enable("+opengles" in spec, "gles1"))

var/spack/repos/spack_repo/builtin/packages/mfem/mfem-4.8-nvcc-c++17.patch

@@ -1,129 +0,0 @@
-diff --git a/miniapps/dpg/convection-diffusion.cpp b/miniapps/dpg/convection-diffusion.cpp
-index 7659e52745..170f8f1c5e 100644
---- a/miniapps/dpg/convection-diffusion.cpp
-+++ b/miniapps/dpg/convection-diffusion.cpp
-@@ -79,7 +79,7 @@ enum prob_type
- };
- 
- prob_type prob;
--Vector beta;
-+Vector beta_glob;
- real_t epsilon;
- 
- real_t exact_u(const Vector & X);
-@@ -120,7 +120,7 @@ int main(int argc, char *argv[])
-                   "Theta parameter for AMR");
-    args.AddOption(&iprob, "-prob", "--problem", "Problem case"
-                   " 0: manufactured, 1: Erickson-Johnson ");
--   args.AddOption(&beta, "-beta", "--beta",
-+   args.AddOption(&beta_glob, "-beta", "--beta",
-                   "Vector Coefficient beta");
-    args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                   "--no-static-condensation", "Enable static condensation.");
-@@ -147,11 +147,11 @@ int main(int argc, char *argv[])
-    int dim = mesh.Dimension();
-    MFEM_VERIFY(dim > 1, "Dimension = 1 is not supported in this example");
- 
--   if (beta.Size() == 0)
-+   if (beta_glob.Size() == 0)
-    {
--      beta.SetSize(dim);
--      beta = 0.0;
--      beta[0] = 1.;
-+      beta_glob.SetSize(dim);
-+      beta_glob = 0.0;
-+      beta_glob[0] = 1.;
-    }
- 
-    args.PrintOptions(std::cout);
-@@ -199,10 +199,10 @@ int main(int argc, char *argv[])
-    ConstantCoefficient eps2(1/(epsilon*epsilon));
- 
-    ConstantCoefficient negeps(-epsilon);
--   VectorConstantCoefficient betacoeff(beta);
--   Vector negbeta = beta; negbeta.Neg();
--   DenseMatrix bbt(beta.Size());
--   MultVVt(beta, bbt);
-+   VectorConstantCoefficient betacoeff(beta_glob);
-+   Vector negbeta = beta_glob; negbeta.Neg();
-+   DenseMatrix bbt(beta_glob.Size());
-+   MultVVt(beta_glob, bbt);
-    MatrixConstantCoefficient bbtcoeff(bbt);
-    VectorConstantCoefficient negbetacoeff(negbeta);
- 
-@@ -598,7 +598,7 @@ void exact_hatf(const Vector & X, Vector & hatf)
-    hatf.SetSize(X.Size());
-    for (int i = 0; i<hatf.Size(); i++)
-    {
--      hatf[i] = beta[i] * u - sigma[i];
-+      hatf[i] = beta_glob[i] * u - sigma[i];
-    }
- }
- 
-@@ -612,7 +612,7 @@ real_t f_exact(const Vector & X)
-    real_t s = 0;
-    for (int i = 0; i<du.Size(); i++)
-    {
--      s += beta[i] * du[i];
-+      s += beta_glob[i] * du[i];
-    }
-    return -epsilon * d2u + s;
- }
-diff --git a/miniapps/dpg/pconvection-diffusion.cpp b/miniapps/dpg/pconvection-diffusion.cpp
-index 64d75d8d10..062f07d0f1 100644
---- a/miniapps/dpg/pconvection-diffusion.cpp
-+++ b/miniapps/dpg/pconvection-diffusion.cpp
-@@ -91,7 +91,7 @@ static const char *enum_str[] =
- };
- 
- prob_type prob;
--Vector beta;
-+Vector beta_glob;
- real_t epsilon;
- 
- real_t exact_u(const Vector & X);
-@@ -141,7 +141,7 @@ int main(int argc, char *argv[])
-                   "Theta parameter for AMR");
-    args.AddOption(&iprob, "-prob", "--problem", "Problem case"
-                   " 0: lshape, 1: General");
--   args.AddOption(&beta, "-beta", "--beta",
-+   args.AddOption(&beta_glob, "-beta", "--beta",
-                   "Vector Coefficient beta");
-    args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                   "--no-static-condensation", "Enable static condensation.");
-@@ -181,19 +181,19 @@ int main(int argc, char *argv[])
-       case sinusoidal:
-       case EJ:
-       {
--         if (beta.Size() == 0)
-+         if (beta_glob.Size() == 0)
-          {
--            beta.SetSize(dim);
--            beta = 0.0;
--            beta[0] = 1.;
-+            beta_glob.SetSize(dim);
-+            beta_glob = 0.0;
-+            beta_glob[0] = 1.;
-          }
-          break;
-       }
-       case bdr_layer:
-       {
--         beta.SetSize(dim);
--         beta[0] = 1.;
--         beta[1] = 2.;
-+         beta_glob.SetSize(dim);
-+         beta_glob[0] = 1.;
-+         beta_glob[1] = 2.;
-          exact_known = false;
-       }
-       break;
-@@ -846,7 +846,7 @@ void beta_function(const Vector & X, Vector & beta_val)
-    }
-    else
-    {
--      beta_val = beta;
-+      beta_val = beta_glob;
-    }
- }
- 

var/spack/repos/spack_repo/builtin/packages/mfem/package.py

@@ -49,13 +49,6 @@ class Mfem(Package, CudaPackage, ROCmPackage):
     # other version.
     version("develop", branch="master")
 
-    version(
-        "4.8.0",
-        sha256="49bd2a076b0d87863092cb55f8524b5292d9afb2e48c19f80222ada367819016",
-        url="https://bit.ly/mfem-4-8",
-        extension="tar.gz",
-    )
-
     version(
         "4.7.0",
         sha256="5e889493f5f79848f7b2d16afaae307c59880ac2a7ff2315551c60ca54717751",
@@ -289,7 +282,7 @@ class Mfem(Package, CudaPackage, ROCmPackage):
 
     depends_on("mpi", when="+mpi")
     depends_on("hipsparse", when="@4.4.0:+rocm")
-    depends_on("hipblas", when="@4.8.0:+rocm")
+    depends_on("hipblas", when="@4.4.0:+rocm")
 
     with when("+mpi"):
         depends_on("hypre")
@@ -339,7 +332,6 @@ class Mfem(Package, CudaPackage, ROCmPackage):
     depends_on("gslib~mpi~mpiio", when="+gslib~mpi")
     depends_on("gslib@1.0.5:1.0.6", when="@:4.2+gslib")
     depends_on("gslib@1.0.7:", when="@4.3.0:+gslib")
-    depends_on("gslib@1.0.9:", when="@4.8.0:+gslib")
     depends_on("suite-sparse", when="+suite-sparse")
     depends_on("superlu-dist", when="+superlu-dist")
     # If superlu-dist is built with +cuda, propagate cuda_arch
@@ -394,10 +386,8 @@ class Mfem(Package, CudaPackage, ROCmPackage):
     depends_on("conduit@0.3.1:,master:", when="+conduit")
     depends_on("conduit+mpi", when="+conduit+mpi")
     depends_on("libfms@0.2.0:", when="+fms")
-    depends_on("ginkgo@1.4.0:1.8", when="@:4.7+ginkgo")
-    depends_on("ginkgo@1.9.0:", when="@4.8:+ginkgo")
+    depends_on("ginkgo@1.4.0:", when="+ginkgo")
     conflicts("cxxstd=11", when="^ginkgo")
-    conflicts("cxxstd=14", when="^ginkgo@1.9:")
     for sm_ in CudaPackage.cuda_arch_values:
         depends_on(
             "ginkgo+cuda cuda_arch={0}".format(sm_), when="+ginkgo+cuda cuda_arch={0}".format(sm_)
@@ -523,7 +513,6 @@ class Mfem(Package, CudaPackage, ROCmPackage):
     )
     patch("mfem-4.7.patch", when="@4.7.0")
     patch("mfem-4.7-sundials-7.patch", when="@4.7.0+sundials ^sundials@7:")
-    patch("mfem-4.8-nvcc-c++17.patch", when="@4.8.0+cuda")
 
     phases = ["configure", "build", "install"]
 
@@ -580,7 +569,7 @@ def find_optional_library(name, prefix):
                 mfem_mpiexec = "jsrun"
                 mfem_mpiexec_np = "-p"
         elif "FLUX_EXEC_PATH" in os.environ:
-            mfem_mpiexec = "flux run -x -N 1"
+            mfem_mpiexec = "flux run"
             mfem_mpiexec_np = "-n"
         elif "PBS_JOBID" in os.environ:
             mfem_mpiexec = "mpiexec"
@@ -647,13 +636,11 @@ def find_optional_library(name, prefix):
             cxxstd = "14"
         if self.spec.satisfies("^sundials@6.4.0:"):
             cxxstd = "14"
+        if self.spec.satisfies("^ginkgo"):
+            cxxstd = "14"
         # When rocPRIM is used (e.g. by PETSc + ROCm) we need C++14:
         if self.spec.satisfies("^rocprim@5.5.0:"):
             cxxstd = "14"
-        if self.spec.satisfies("^ginkgo@1.4.0:1.8"):
-            cxxstd = "14"
-        if self.spec.satisfies("^ginkgo@1.9.0:"):
-            cxxstd = "17"
         cxxstd_req = spec.variants["cxxstd"].value
         if cxxstd_req != "auto":
             # Constraints for valid standard level should be imposed during
@@ -722,7 +709,7 @@ def find_optional_library(name, prefix):
 
             hypre_gpu_libs = ""
             if "+cuda" in hypre:
-                hypre_gpu_libs = " -lcusolver -lcusparse -lcurand -lcublas"
+                hypre_gpu_libs = " -lcusparse -lcurand -lcublas"
             elif "+rocm" in hypre:
                 hypre_rocm_libs = LibraryList([])
                 if "^rocsparse" in hypre:
@@ -862,7 +849,7 @@ def find_optional_library(name, prefix):
             ]
 
         if "+pumi" in spec:
-            pumi_libs_names = [
+            pumi_libs = [
                 "pumi",
                 "crv",
                 "ma",
@@ -876,11 +863,6 @@ def find_optional_library(name, prefix):
                 "apf_zoltan",
                 "spr",
             ]
-            pumi_libs_names = ["lib" + name for name in pumi_libs_names]
-            pumi = spec["pumi"]
-            pumi_libs = find_libraries(
-                pumi_libs_names, pumi.prefix, shared=("+shared" in pumi), recursive=True
-            )
             pumi_dep_zoltan = ""
             pumi_dep_parmetis = ""
             if "+zoltan" in spec["pumi"]:
@@ -892,7 +874,11 @@ def find_optional_library(name, prefix):
             options += [
                 "PUMI_OPT=-I%s" % spec["pumi"].prefix.include,
                 "PUMI_LIB=%s %s %s"
-                % (ld_flags_from_library_list(pumi_libs), pumi_dep_zoltan, pumi_dep_parmetis),
+                % (
+                    ld_flags_from_dirs([spec["pumi"].prefix.lib], pumi_libs),
+                    pumi_dep_zoltan,
+                    pumi_dep_parmetis,
+                ),
             ]
 
         if "+gslib" in spec:
@@ -1001,10 +987,9 @@ def find_optional_library(name, prefix):
             if "^rocprim" in spec and not spec["hip"].external:
                 # rocthrust [via petsc+rocm] has a dependency on rocprim
                 hip_headers += spec["rocprim"].headers
-            if "^hipblas" in spec:  # hipblas is needed @4.8.0:+rocm
-                # note: superlu-dist+rocm needs the hipblas header path too
+            if "^hipblas" in spec:
                 hipblas = spec["hipblas"]
-                hip_headers += self.all_headers(hipblas)
+                hip_headers += hipblas.headers
                 hip_libs += hipblas.libs
             if "%cce" in spec:
                 # We assume the proper Cray CCE module (cce) is loaded:
@@ -1028,22 +1013,6 @@ def find_optional_library(name, prefix):
                 hip_libs += find_libraries(craylibs, craylibs_path)
                 craylibs_path2 = join_path(craylibs_path, "../../../cce-clang", proc, "lib")
                 hip_libs += find_libraries("libunwind", craylibs_path2)
-            elif spec.satisfies("%rocmcc ^cray-mpich"):
-                # The AMD version of cray-mpich, libmpi_amd.so, needs the rpath
-                # to libflang.so (also needed for libpgmath.so and others).
-                rocmcc_bin_dir = os.path.dirname(env["SPACK_CXX"])
-                rocmcc_prefix = os.path.dirname(rocmcc_bin_dir)
-                rocmcc_libflang = find_libraries(
-                    "libflang", join_path(rocmcc_prefix, "lib/llvm/lib"), recursive=False
-                )
-                hip_libs += rocmcc_libflang
-            if spec.satisfies("^cray-mpich"):
-                # The cray-mpich library, libmpi_*.so, needs the rpath to
-                # libpmi.so.0 and libpmi2.so.0 if that path is not configured
-                # properly on system level.
-                libpmi_lib = find_libraries("libpmi", "/opt/cray/pe/lib64")
-                if libpmi_lib:
-                    hip_libs += libpmi_lib
 
             if hip_headers:
                 options += ["HIP_OPT=%s" % hip_headers.cpp_flags]
@@ -1408,12 +1377,3 @@ def ld_flags_from_dirs(self, pkg_dirs_list, pkg_libs_list):
         flags += ["-L%s" % dir for dir in pkg_dirs_list if not self.is_sys_lib_path(dir)]
         flags += ["-l%s" % lib for lib in pkg_libs_list]
         return " ".join(flags)
-
-    def all_headers(self, root_spec):
-        all_hdrs = HeaderList([])
-        for dep in root_spec.traverse(deptype="link"):
-            try:
-                all_hdrs += root_spec[dep.name].headers
-            except NoHeadersError:
-                pass
-        return all_hdrs

var/spack/repos/spack_repo/builtin/packages/mpilander/package.py

@@ -38,8 +38,6 @@ class Mpilander(CMakePackage):
     conflicts("%apple-clang@:7.4")
     conflicts("%intel@:16")
 
-    conflicts("platform=windows")
-
     def cmake_args(self):
         args = [
             # tests and examples

var/spack/repos/spack_repo/builtin/packages/musica/package.py

@@ -40,7 +40,6 @@ class Musica(CMakePackage):
     depends_on("cxx", type="build")
     depends_on("fortran", type="build")
     depends_on("mpi", when="+mpi")
-    depends_on("netcdf-fortran", when="+tuvx")
 
     def cmake_args(self):
         args = [

var/spack/repos/spack_repo/builtin/packages/openspeedshop/package.py

@@ -4,6 +4,7 @@
 
 import os
 
+import spack.store
 from spack.package import *
 
 from ..boost.package import Boost
@@ -37,6 +38,11 @@ class Openspeedshop(CMakePackage):
     variant(
         "runtime", default=False, description="build only the runtime libraries and collectors."
     )
+    variant(
+        "crayfe",
+        default=False,
+        description="build only the FE tool using the runtime_dir to point to target build.",
+    )
     variant("cuda", default=False, description="build with cuda packages included.")
 
     variant(
@@ -117,6 +123,11 @@ class Openspeedshop(CMakePackage):
     depends_on("cbtf-krell@develop", when="@develop", type=("build", "link", "run"))
     depends_on("cbtf-krell@1.9.3:9999", when="@2.4.0:9999", type=("build", "link", "run"))
 
+    depends_on("cbtf-krell@develop+crayfe", when="@develop+crayfe", type=("build", "link", "run"))
+    depends_on(
+        "cbtf-krell@1.9.3:9999+crayfe", when="@2.4.0:9999+crayfe", type=("build", "link", "run")
+    )
+
     depends_on("cbtf-krell@develop+mpich2", when="@develop+mpich2", type=("build", "link", "run"))
     depends_on(
         "cbtf-krell@1.9.3:9999+mpich2", when="@2.4.0:9999+mpich2", type=("build", "link", "run")
@@ -153,6 +164,29 @@ class Openspeedshop(CMakePackage):
 
     build_directory = "build_openspeedshop"
 
+    def set_cray_login_node_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
+        # Cray login node libraries
+
+        cray_login_node_options = []
+        rt_platform = "cray"
+
+        # How do we get the compute node (CNL) cbtf package install
+        # directory path?
+        # spec['cbtf'].prefix is the login node value for this build, as
+        # we only get here when building the login node components and
+        # that is all that is known to spack.
+        store = spack.store
+        be_ck = store.db.query_one("cbtf-krell arch=cray-CNL-haswell")
+
+        # Equivalent to install-tool cmake arg:
+        # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+        #               % <base dir>/cbtf_v2.4.0.release/compute)
+        cray_login_node_options.append("-DCBTF_KRELL_CN_RUNTIME_DIR=%s" % be_ck.prefix)
+        cray_login_node_options.append("-DRUNTIME_PLATFORM=%s" % rt_platform)
+
+        cmake_options.extend(cray_login_node_options)
+
     def cmake_args(self):
         spec = self.spec
 
@@ -206,6 +240,13 @@ def cmake_args(self):
             if spec.satisfies("+cuda"):
                 cmake_args.extend(["-DCBTF_ARGONAVIS_DIR=%s" % spec["cbtf-argonavis"].prefix])
 
+            if spec.satisfies("+crayfe"):
+                # We need to build target/compute node
+                # components/libraries first then pass
+                # those libraries to the openspeedshop
+                # login node build
+                self.set_cray_login_node_cmake_options(spec, cmake_args)
+
         return cmake_args
 
     def set_defaultbase_cmake_options(self, spec, cmake_options):

var/spack/repos/spack_repo/builtin/packages/openspeedshop_utils/package.py

@@ -4,6 +4,7 @@
 
 import os
 
+import spack.store
 from spack.package import *
 
 from ..boost.package import Boost
@@ -40,6 +41,11 @@ class OpenspeedshopUtils(CMakePackage):
     variant(
         "runtime", default=False, description="build only the runtime libraries and collectors."
     )
+    variant(
+        "crayfe",
+        default=False,
+        description="build only the FE tool using the runtime_dir to point to target build.",
+    )
     variant("cuda", default=False, description="build with cuda packages included.")
 
     variant(
@@ -111,6 +117,11 @@ class OpenspeedshopUtils(CMakePackage):
     depends_on("cbtf-krell@develop", when="@develop", type=("build", "link", "run"))
     depends_on("cbtf-krell@1.9.3:9999", when="@2.4.0:9999", type=("build", "link", "run"))
 
+    depends_on("cbtf-krell@develop+crayfe", when="@develop+crayfe", type=("build", "link", "run"))
+    depends_on(
+        "cbtf-krell@1.9.3:9999+crayfe", when="@2.4.0:9999+crayfe", type=("build", "link", "run")
+    )
+
     depends_on("cbtf-krell@develop+mpich2", when="@develop+mpich2", type=("build", "link", "run"))
     depends_on(
         "cbtf-krell@1.9.3:9999+mpich2", when="@2.4.0:9999+mpich2", type=("build", "link", "run")
@@ -147,6 +158,28 @@ class OpenspeedshopUtils(CMakePackage):
 
     build_directory = "build_openspeedshop"
 
+    def set_cray_login_node_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
+        # Cray login node libraries
+
+        cray_login_node_options = []
+        rt_platform = "cray"
+
+        # How do we get the compute node (CNL) cbtf package install
+        # directory path?
+        # spec['cbtf'].prefix is the login node value for this build, as
+        # we only get here when building the login node components and
+        # that is all that is known to spack.
+        be_ck = spack.store.db.query_one("cbtf-krell arch=cray-CNL-haswell")
+
+        # Equivalent to install-tool cmake arg:
+        # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+        #               % <base dir>/cbtf_v2.4.0elease/compute)
+        cray_login_node_options.append("-DCBTF_KRELL_CN_RUNTIME_DIR=%s" % be_ck.prefix)
+        cray_login_node_options.append("-DRUNTIME_PLATFORM=%s" % rt_platform)
+
+        cmake_options.extend(cray_login_node_options)
+
     def cmake_args(self):
         # Appends base options to cmake_args
         spec = self.spec
@@ -187,6 +220,13 @@ def cmake_args(self):
                 ]
             )
 
+            if spec.satisfies("+crayfe"):
+                # We need to build target/compute node
+                # components/libraries first then pass
+                # those libraries to the openspeedshop
+                # login node build
+                self.set_cray_login_node_cmake_options(spec, cmake_args)
+
         cmake_args.extend(["-DBUILD_QT3_GUI=FALSE"])
 
         return cmake_args

var/spack/repos/spack_repo/builtin/packages/paraconf/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *
 
 

var/spack/repos/spack_repo/builtin/packages/parsec/package.py

@@ -26,7 +26,6 @@ class Parsec(CMakePackage, CudaPackage):
     license("BSD-3-Clause-Open-MPI")
 
     version("master", branch="master")
-    version("4.0.2411", sha256="3f5750565b9f673626284dd0ba835dadea3633577fee50ac217baf43a335f2ef")
     version("3.0.2209", sha256="67d383d076991484cb2a265f56420abdea7cc1f329c63ac65a3e96fbfb6cc295")
     version("3.0.2012", sha256="7a8403ca67305738f3974cbc7a51b64c4ec353ae9170f2468262a9a52035eff6")
     version(
@@ -60,8 +59,6 @@ class Parsec(CMakePackage, CudaPackage):
     # TODO: Spack does not handle cross-compilation atm
     # variant('xcompile', default=False, description='Cross compile')
 
-    depends_on("c", type="build")
-
     depends_on("cmake@3.18:", type="build")
     depends_on("python", type="build")
     depends_on("flex", type="build")

var/spack/repos/spack_repo/builtin/packages/pdi/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.hooks.sbang import sbang_shebang_line
 from spack.package import *
 

var/spack/repos/spack_repo/builtin/packages/pdiplugin_decl_hdf5/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *
 
 from ..pdi.package import Pdi

var/spack/repos/spack_repo/builtin/packages/pdiplugin_decl_netcdf/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *
 
 from ..pdi.package import Pdi

var/spack/repos/spack_repo/builtin/packages/pdiplugin_mpi/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *
 
 from ..pdi.package import Pdi

var/spack/repos/spack_repo/builtin/packages/pdiplugin_pycall/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *
 
 from ..pdi.package import Pdi

var/spack/repos/spack_repo/builtin/packages/pdiplugin_serialize/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *
 
 from ..pdi.package import Pdi

var/spack/repos/spack_repo/builtin/packages/pdiplugin_set_value/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *
 
 from ..pdi.package import Pdi

var/spack/repos/spack_repo/builtin/packages/pdiplugin_trace/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *
 
 from ..pdi.package import Pdi

var/spack/repos/spack_repo/builtin/packages/pdiplugin_user_code/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *
 
 from ..pdi.package import Pdi

var/spack/repos/spack_repo/builtin/packages/petsc/package.py

@@ -264,9 +264,6 @@ class Petsc(Package, CudaPackage, ROCmPackage):
     variant("hwloc", default=False, description="Activates support for hwloc")
     variant("kokkos", default=False, description="Activates support for kokkos and kokkos-kernels")
     variant("fortran", default=True, description="Activates fortran support")
-    variant(
-        "fortran-bindings", default=True, when="+fortran", description="Activates fortran bindings"
-    )
 
     with when("+rocm"):
         # https://github.com/spack/spack/issues/37416
@@ -502,8 +499,6 @@ def mpi_dependent_options(self):
             ]
             if "+fortran" in self.spec:
                 compiler_opts.append("--with-fc=%s" % os.environ["FC"])
-                fb = "1" if self.spec.satisfies("+fortran-bindings") else "0"
-                compiler_opts.append(f"--with-fortran-bindings={fb}")
             else:
                 compiler_opts.append("--with-fc=0")
         else:
@@ -513,8 +508,6 @@ def mpi_dependent_options(self):
             ]
             if "+fortran" in self.spec:
                 compiler_opts.append("--with-fc=%s" % self.spec["mpi"].mpifc)
-                fb = "1" if self.spec.satisfies("+fortran-bindings") else "0"
-                compiler_opts.append(f"--with-fortran-bindings={fb}")
             else:
                 compiler_opts.append("--with-fc=0")
             if self.spec.satisfies("%intel"):

var/spack/repos/spack_repo/builtin/packages/py_hepstats/package.py

@@ -1,43 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyHepstats(PythonPackage):
-    """hepstats is a library for statistical inference aiming
-    to cover the needs in High Energy Physics.
-    It is part of the Scikit-HEP project.
-    """
-
-    homepage = "https://github.com/scikit-hep/hepstats"
-    pypi = "hepstats/hepstats-0.8.1.tar.gz"
-    maintainers("jonas-eschle")
-
-    license("BSD-3-Clause", checked_by="jonas-eschle")
-
-    tags = ["likelihood", "statistics", "inference", "fitting", "hep"]
-
-    version("0.9.2", sha256="cf929871d45e338492eef585faaaa23eff93b200b4787d6b6181dc81f2607be7")
-    version("0.8.1", sha256="ebb890496d7aebbf1d717de15d073be31d6775065308a4e0f263ed4051992b3f")
-
-    depends_on("python@3.9:", type=("build", "run"), when="@0.8:")
-    # Build system changed from setuptools to hatch with v0.9.0
-    depends_on("py-setuptools@42:", type="build", when="@:0.8.1")
-    depends_on("py-setuptools-scm@3.4:+toml", type="build", when="@:0.8.1")
-    depends_on("py-hatchling", type="build", when="@0.9.0:")
-    depends_on("py-hatch-vcs", type="build", when="@0.9.0:")
-
-    variant("zfit", default=False, description="Allows to use improved tools from zfit.")
-
-    with default_args(type=("build", "run")):
-        depends_on("py-pandas")
-        depends_on("py-numpy")
-        depends_on("py-asdf")
-        depends_on("py-scipy")
-        depends_on("py-tqdm")
-        depends_on("py-uhi")
-
-        with when("+zfit"):
-            depends_on("py-zfit@0.20:", when="@0.8:")

var/spack/repos/spack_repo/builtin/packages/py_numba/package.py

@@ -16,7 +16,6 @@ class PyNumba(PythonPackage):
 
     license("BSD-2-Clause")
 
-    version("0.61.2", sha256="8750ee147940a6637b80ecf7f95062185ad8726c8c28a2295b8ec1160a196f7d")
     version("0.61.0", sha256="888d2e89b8160899e19591467e8fdd4970e07606e1fbc248f239c89818d5f925")
     version("0.60.0", sha256="5df6158e5584eece5fc83294b949fd30b9f1125df7708862205217e068aabf16")
     version("0.59.1", sha256="76f69132b96028d2774ed20415e8c528a34e3299a40581bae178f0994a2f370b")
@@ -58,13 +57,7 @@ class PyNumba(PythonPackage):
     depends_on("python@3.6:3.9", when="@0.53", type=("build", "run"))
     depends_on("python@3.6:3.8", when="@0.52", type=("build", "run"))
     depends_on("python@3.6:3.8", when="@0.48:0.51", type=("build", "run"))
-
-    # max_numpy_run_version in setup.py is a non inclusive upper bound
-    # min_numpy_run_version < min_numpy_build_version and these ranges use
-    # min_numpy_build_version
-    depends_on("py-numpy@2.0:2.2", when="@0.61.2", type=("build", "run"))
-    depends_on("py-numpy@2.0:2.1", when="@0.61.0", type=("build", "run"))
-    depends_on("py-numpy@2.0", when="@0.60", type=("build", "run"))
+    depends_on("py-numpy@2.0:2.2", when="@0.60:", type=("build", "run"))
     depends_on("py-numpy@1.22:1.26", when="@0.58.1:0.59", type=("build", "run"))
     depends_on("py-numpy@1.21:1.25", when="@0.58.0", type=("build", "run"))
     depends_on("py-numpy@1.21:1.24", when="@0.57", type=("build", "run"))

var/spack/repos/spack_repo/builtin/packages/qjson/package.py

@@ -16,8 +16,7 @@ class Qjson(CMakePackage):
 
     version("0.9.0", sha256="e812617477f3c2bb990561767a4cd8b1d3803a52018d4878da302529552610d4")
 
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
+    depends_on("cxx", type="build")  # generated
 
     depends_on("qt")
 

var/spack/repos/spack_repo/builtin/packages/qtkeychain/package.py

@@ -15,8 +15,7 @@ class Qtkeychain(CMakePackage):
 
     version("0.9.1", sha256="9c2762d9d0759a65cdb80106d547db83c6e9fdea66f1973c6e9014f867c6f28e")
 
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
+    depends_on("cxx", type="build")  # generated
 
     depends_on("qt+dbus")
     depends_on("libsecret")

var/spack/repos/spack_repo/builtin/packages/raja/package.py

@@ -195,7 +195,6 @@ class Raja(CachedCMakePackage, CudaPackage, ROCmPackage):
     )
     variant("omptarget", default=False, description="Build OpenMP on target device support")
     variant("sycl", default=False, description="Build sycl backend")
-    variant("gpu-profiling", default=False, description="Enable GPU profiling")
 
     variant("plugins", default=False, description="Enable runtime plugins")
     variant("examples", default=True, description="Build examples.")
@@ -268,10 +267,6 @@ class Raja(CachedCMakePackage, CudaPackage, ROCmPackage):
         for sm_ in CudaPackage.cuda_arch_values:
             depends_on("camp +cuda cuda_arch={0}".format(sm_), when="cuda_arch={0}".format(sm_))
 
-    conflicts("+gpu-profiling", when="~cuda~rocm", msg="GPU profiling requires CUDA or ROCm")
-    conflicts("+gpu-profiling +cuda", when="@:2022.02.99")
-    conflicts("+gpu-profiling +rocm", when="@:2022.02.99")
-
     conflicts("+omptarget +rocm")
     conflicts("+sycl +omptarget")
     conflicts("+sycl +rocm")
@@ -328,7 +323,11 @@ def initconfig_hardware_entries(self):
         entries.append("#------------------{0}\n".format("-" * 30))
 
         entries.append(cmake_cache_option("ENABLE_OPENMP", spec.satisfies("+openmp")))
-        entries.append(cmake_cache_option("ENABLE_CUDA", spec.satisfies("+cuda")))
+
+        if spec.satisfies("+cuda"):
+            entries.append(cmake_cache_option("ENABLE_CUDA", True))
+        else:
+            entries.append(cmake_cache_option("ENABLE_CUDA", False))
 
         if spec.satisfies("+rocm"):
             entries.append(cmake_cache_option("ENABLE_HIP", True))
@@ -377,12 +376,6 @@ def initconfig_package_entries(self):
         )
 
         entries.append(cmake_cache_option("RAJA_ENABLE_SYCL", spec.satisfies("+sycl")))
-        entries.append(
-            cmake_cache_option("RAJA_ENABLE_NV_TOOLS_EXT", spec.satisfies("+gpu-profiling +cuda"))
-        )
-        entries.append(
-            cmake_cache_option("RAJA_ENABLE_ROCTX", spec.satisfies("+gpu-profiling +rocm"))
-        )
 
         if spec.satisfies("+lowopttest"):
             entries.append(cmake_cache_string("CMAKE_CXX_FLAGS_RELEASE", "-O1"))

var/spack/repos/spack_repo/builtin/packages/sccache/package.py

@@ -5,6 +5,7 @@
 import os
 import re
 
+import spack.build_systems
 import spack.build_systems.cargo
 from spack.package import *
 

var/spack/repos/spack_repo/builtin/packages/seissol/package.py

@@ -41,10 +41,6 @@ class Seissol(CMakePackage, CudaPackage, ROCmPackage):
 
     maintainers("Thomas-Ulrich", "davschneller", "vikaskurapati")
 
-    depends_on("cxx", type="build")
-    depends_on("c", type="build")
-    depends_on("fortran", type="build", when="equations=poroelastic")
-
     variant("asagi", default=True, description="Use ASAGI for material input")
     variant(
         "convergence_order",
@@ -210,10 +206,8 @@ class Seissol(CMakePackage, CudaPackage, ROCmPackage):
 
     depends_on("asagi +mpi +mpi3", when="+asagi")
 
-    depends_on("asagi@:1.0.1", when="@:1.3.1 +asagi")
-
-    depends_on("easi ~asagi jit=lua", when="~asagi")
-    depends_on("easi +asagi jit=lua", when="+asagi")
+    depends_on("easi ~asagi jit=impalajit,lua", when="~asagi")
+    depends_on("easi +asagi jit=impalajit,lua", when="+asagi")
 
     depends_on("intel-oneapi-mkl threads=none", when="gemm_tools_list=MKL")
     depends_on("blis threads=none", when="gemm_tools_list=BLIS")
@@ -256,6 +250,7 @@ def cmake_args(self):
             self.define_from_variant("EQUATIONS", "equations"),
             self.define_from_variant("NETCDF", "netcdf"),
         ]
+
         gemm_tools_list = ",".join(self.spec.variants["gemm_tools_list"].value)
         args.append(f"-DGEMM_TOOLS_LIST={gemm_tools_list}")
 
@@ -366,7 +361,7 @@ def cmake_args(self):
 
         args.append(f"-DHOST_ARCH={hostarch}")
 
-        args.append(self.define("Python3_EXECUTABLE", self.spec["python"].command.path))
+        args.append(self.define("PYTHON_EXECUTABLE", self.spec["python"].command.path))
 
         return args
 

var/spack/repos/spack_repo/builtin/packages/singularity_eos/package.py

@@ -4,6 +4,7 @@
 
 import os
 
+import spack
 from spack.package import *
 
 
@@ -114,7 +115,9 @@ class SingularityEos(CMakePackage, CudaPackage):
     # specfic specs when using GPU/cuda offloading
     depends_on("kokkos +wrapper+cuda_lambda", when="+cuda+kokkos")
 
-    depends_on("kokkos-kernels ~shared", when="+kokkos-kernels")
+    # fix for older spacks
+    if Version(spack.spack_version) >= Version("0.17"):
+        depends_on("kokkos-kernels ~shared", when="+kokkos-kernels")
 
     for _flag in list(CudaPackage.cuda_arch_values):
         depends_on("kokkos cuda_arch=" + _flag, when="+cuda+kokkos cuda_arch=" + _flag)

var/spack/repos/spack_repo/builtin/packages/spectrum_mpi/package.py

@@ -132,13 +132,10 @@ def setup_dependent_build_environment(
             env.set("MPIF90", os.path.join(self.prefix.bin, "mpif90"))
 
         dependent_module = dependent_spec.package.module
-        if dependent_spec.satisfies("^c"):
-            env.set("OMPI_CC", dependent_module.spack_cc)
-        if dependent_spec.satisfies("^cxx"):
-            env.set("OMPI_CXX", dependent_module.spack_cxx)
-        if dependent_spec.satisfies("^fortran"):
-            env.set("OMPI_FC", dependent_module.spack_fc)
-            env.set("OMPI_F77", dependent_module.spack_f77)
+        env.set("OMPI_CC", dependent_module.spack_cc)
+        env.set("OMPI_CXX", dependent_module.spack_cxx)
+        env.set("OMPI_FC", dependent_module.spack_fc)
+        env.set("OMPI_F77", dependent_module.spack_f77)
         env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib)
 
     def setup_run_environment(self, env: EnvironmentModifications) -> None:

var/spack/repos/spack_repo/builtin/packages/sundials/package.py

@@ -405,7 +405,7 @@ def cmake_args(self):
         if "+rocm" in spec:
             args.extend(
                 [
-                    define("CMAKE_C_COMPILER", spec["llvm-amdgpu"].prefix.bin.amdclang),
+                    define("CMAKE_C_COMPILER", spec["llvm-amdgpu"].prefix.bin.clang),
                     define("CMAKE_CXX_COMPILER", spec["hip"].hipcc),
                     define("HIP_PATH", spec["hip"].prefix),
                     define("HIP_CLANG_INCLUDE_PATH", spec["llvm-amdgpu"].prefix.include),

var/spack/repos/spack_repo/builtin/packages/trivy/package.py

@@ -15,12 +15,9 @@ class Trivy(GoPackage):
 
     license("Apache-2.0", checked_by="RobertMaaskant")
 
-    version("0.62.1", sha256="1b8000f08876dd02203021414581275daa69db00fab731351dbcf2a008ebe82a")
-    version("0.62.0", sha256="2b0b4df4bbfebde00a14a0616f5013db4cbba0f021a780a7e3b717a2c2978493")
     version("0.61.1", sha256="f6ad43e008c008d67842c9e2b4af80c2e96854db8009fba48fc37b4f9b15f59b")
     version("0.61.0", sha256="1e97b1b67a4c3aee9c567534e60355033a58ce43a3705bdf198d7449d53b6979")
 
-    depends_on("go@1.24.2:", type="build", when="@0.62:")
     depends_on("go@1.24:", type="build")
 
     build_directory = "cmd/trivy"

var/spack/repos/spack_repo/builtin/packages/yaml_cpp/package.py

@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack.package import *
+from spack.spec import ConflictsInSpecError
 
 from ..boost.package import Boost
 
@@ -56,12 +57,20 @@ def flag_handler(self, name, flags):
         # the user can add arbitrary strings to the flags. Here we can at least
         # fail early.
         # We'll include cppflags in case users mistakenly put c++ flags there.
-        if (
-            name in ("cxxflags", "cppflags")
-            and self.spec.satisfies("+tests")
-            and "-stdlib=libc++" in flags
-        ):
-            raise InstallError(yaml_cpp_tests_libcxx_error_msg)
+        spec = self.spec
+        if name in ("cxxflags", "cppflags") and spec.satisfies("+tests"):
+            if "-stdlib=libc++" in flags:
+                raise ConflictsInSpecError(
+                    spec,
+                    [
+                        (
+                            spec,
+                            spec.compiler_flags[name],
+                            spec.variants["tests"],
+                            yaml_cpp_tests_libcxx_error_msg,
+                        )
+                    ],
+                )
         return (flags, None, None)
 
     def cmake_args(self):

var/spack/repos/spack_repo/builtin/packages/yosys/package.py

@@ -28,7 +28,6 @@ class Yosys(MakefilePackage):
 
     version("master", branch="master")
 
-    version("0.53", commit="53c22ab7c0ced80861c7536c5dae682c30fb5834", submodules=True)
     version("0.52", commit="fee39a3284c90249e1d9684cf6944ffbbcbb8f90", submodules=True)
     version("0.51", commit="c4b5190229616f7ebf8197f43990b4429de3e420", submodules=True)
     version("0.50", commit="b5170e1394f602c607e75bdbb1a2b637118f2086", submodules=True)

var/spack/repos/spack_repo/builtin/packages/yq/package.py

@@ -16,7 +16,6 @@ class Yq(GoPackage):
 
     license("MIT", checked_by="teaguesterling")
 
-    version("4.45.2", sha256="7ae8f8a4acc78dba5ab3a4bb004d390bbf6fe1cd1fc5746ff7db19f8e627b84f")
     version("4.45.1", sha256="074a21a002c32a1db3850064ad1fc420083d037951c8102adecfea6c5fd96427")
     version("4.44.6", sha256="c0acef928168e5fdb26cd7e8320eddde822f30cf1942817f3f6b854dd721653f")
     version("4.44.5", sha256="1505367f4a6c0c4f3b91c6197ffed4112d29ef97c48d0b5e66530cfa851d3f0e")
@@ -27,6 +26,5 @@ class Yq(GoPackage):
     version("4.35.2", sha256="8b17d710c56f764e9beff06d7a7b1c77d87c4ba4219ce4ce67e7ee29670f4f13")
 
     # from go.mod
-    depends_on("go@1.23:", type="build", when="@4.45.2:")
     depends_on("go@1.21:", type="build", when="@4.40:")
     depends_on("go@1.20:", type="build", when="@4.31:")

var/spack/repos/spack_repo/builtin/packages/zpp/package.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
 from spack.package import *