Update py-numcodecs. (#45715)

* whizard: add a patch when using hepmc3 3.3.0 or newer

* whizard: comment with patch origin

---------

Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

.github/workflows/audit.yaml

@@ -29,7 +29,7 @@ jobs:
         shell: ${{ matrix.system.shell }}
     steps:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: ${{inputs.python_version}}
     - name: Install Python packages

.github/workflows/bootstrap.yml

@@ -63,7 +63,7 @@ jobs:
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
         with:
           python-version: "3.12"
       - name: Bootstrap clingo
@@ -128,7 +128,7 @@ jobs:
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
         with:
           python-version: |
             3.8

.github/workflows/build-containers.yml

@@ -87,7 +87,7 @@ jobs:
           fi
 
       - name: Upload Dockerfile
-        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a
+        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874
         with:
           name: dockerfiles_${{ matrix.dockerfile[0] }}
           path: dockerfiles
@@ -126,7 +126,7 @@ jobs:
     needs: deploy-images
     steps:
       - name: Merge Artifacts
-        uses: actions/upload-artifact/merge@834a144ee995460fba8ed112a2fc961b36a5ec5a
+        uses: actions/upload-artifact/merge@50769540e7f4bd5e21e526ee35c689e35e0d6874
         with:
           name: dockerfiles
           pattern: dockerfiles_*

.github/workflows/nightly-win-builds.yml

@@ -17,7 +17,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: 3.9
     - name: Install Python packages

.github/workflows/unit_tests.yaml

@@ -43,7 +43,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install System packages
@@ -91,7 +91,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: '3.11'
     - name: Install System packages
@@ -151,7 +151,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: '3.11'
     - name: Install System packages
@@ -188,7 +188,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Python packages
@@ -225,7 +225,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: 3.9
     - name: Install Python packages

.github/workflows/valid-style.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: '3.11'
         cache: 'pip'
@@ -38,7 +38,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: '3.11'
         cache: 'pip'

etc/spack/defaults/packages.yaml

@@ -72,3 +72,13 @@ packages:
     permissions:
       read: world
       write: user
+  cray-mpich:
+    buildable: false
+  cray-mvapich2:
+    buildable: false
+  fujitsu-mpi:
+    buildable: false
+  hpcx-mpi:
+    buildable: false
+  spectrum-mpi:
+    buildable: false

lib/spack/spack/build_systems/python.py

@@ -315,9 +315,9 @@ def get_external_python_for_prefix(self):
         )
 
         python_externals_detected = [
-            d.spec
-            for d in python_externals_detection.get("python", [])
-            if d.prefix == self.spec.external_path
+            spec
+            for spec in python_externals_detection.get("python", [])
+            if spec.external_path == self.spec.external_path
         ]
         if python_externals_detected:
             return python_externals_detected[0]

lib/spack/spack/compilers/__init__.py

@@ -273,24 +273,24 @@ def find_compilers(
 
     valid_compilers = {}
     for name, detected in detected_packages.items():
-        compilers = [x for x in detected if CompilerConfigFactory.from_external_spec(x.spec)]
+        compilers = [x for x in detected if CompilerConfigFactory.from_external_spec(x)]
         if not compilers:
             continue
         valid_compilers[name] = compilers
 
     def _has_fortran_compilers(x):
-        if "compilers" not in x.spec.extra_attributes:
+        if "compilers" not in x.extra_attributes:
             return False
 
-        return "fortran" in x.spec.extra_attributes["compilers"]
+        return "fortran" in x.extra_attributes["compilers"]
 
     if mixed_toolchain:
         gccs = [x for x in valid_compilers.get("gcc", []) if _has_fortran_compilers(x)]
         if gccs:
             best_gcc = sorted(
-                gccs, key=lambda x: spack.spec.parse_with_version_concrete(x.spec).version
+                gccs, key=lambda x: spack.spec.parse_with_version_concrete(x).version
             )[-1]
-            gfortran = best_gcc.spec.extra_attributes["compilers"]["fortran"]
+            gfortran = best_gcc.extra_attributes["compilers"]["fortran"]
             for name in ("llvm", "apple-clang"):
                 if name not in valid_compilers:
                     continue
@@ -298,11 +298,11 @@ def _has_fortran_compilers(x):
                 for candidate in candidates:
                     if _has_fortran_compilers(candidate):
                         continue
-                    candidate.spec.extra_attributes["compilers"]["fortran"] = gfortran
+                    candidate.extra_attributes["compilers"]["fortran"] = gfortran
 
     new_compilers = []
     for name, detected in valid_compilers.items():
-        for config in CompilerConfigFactory.from_specs([x.spec for x in detected]):
+        for config in CompilerConfigFactory.from_specs(detected):
             c = _compiler_from_config_entry(config["compiler"])
             if c in known_compilers:
                 continue

lib/spack/spack/detection/__init__.py

@@ -2,17 +2,11 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from .common import (
-    DetectedPackage,
-    executable_prefix,
-    set_virtuals_nonbuildable,
-    update_configuration,
-)
+from .common import executable_prefix, set_virtuals_nonbuildable, update_configuration
 from .path import by_path, executables_in_path
 from .test import detection_tests
 
 __all__ = [
-    "DetectedPackage",
     "by_path",
     "executables_in_path",
     "executable_prefix",

lib/spack/spack/detection/common.py

@@ -6,9 +6,9 @@
 function to update packages.yaml given a list of detected packages.
 
 Ideally, each detection method should be placed in a specific subpackage
-and implement at least a function that returns a list of DetectedPackage
-objects. The update in packages.yaml can then be done using the function
-provided here.
+and implement at least a function that returns a list of specs.
+
+The update in packages.yaml can then be done using the function provided here.
 
 The module also contains other functions that might be useful across different
 detection mechanisms.
@@ -17,9 +17,10 @@
 import itertools
 import os
 import os.path
+import pathlib
 import re
 import sys
-from typing import Dict, List, NamedTuple, Optional, Set, Tuple, Union
+from typing import Dict, List, Optional, Set, Tuple, Union
 
 import llnl.util.tty
 
@@ -30,27 +31,6 @@
 import spack.util.windows_registry
 
 
-class DetectedPackage(NamedTuple):
-    """Information on a package that has been detected."""
-
-    #: Spec that was detected
-    spec: spack.spec.Spec
-    #: Prefix of the spec
-    prefix: str
-
-    def __reduce__(self):
-        return DetectedPackage.restore, (str(self.spec), self.prefix, self.spec.extra_attributes)
-
-    @staticmethod
-    def restore(
-        spec_str: str, prefix: str, extra_attributes: Optional[Dict[str, str]]
-    ) -> "DetectedPackage":
-        spec = spack.spec.Spec.from_detection(
-            spec_str=spec_str, external_path=prefix, extra_attributes=extra_attributes
-        )
-        return DetectedPackage(spec=spec, prefix=prefix)
-
-
 def _externals_in_packages_yaml() -> Set[spack.spec.Spec]:
     """Returns all the specs mentioned as externals in packages.yaml"""
     packages_yaml = spack.config.get("packages")
@@ -65,7 +45,7 @@ def _externals_in_packages_yaml() -> Set[spack.spec.Spec]:
 
 
 def _pkg_config_dict(
-    external_pkg_entries: List[DetectedPackage],
+    external_pkg_entries: List["spack.spec.Spec"],
 ) -> Dict[str, Union[bool, List[Dict[str, ExternalEntryType]]]]:
     """Generate a package specific config dict according to the packages.yaml schema.
 
@@ -85,22 +65,19 @@ def _pkg_config_dict(
     pkg_dict = spack.util.spack_yaml.syaml_dict()
     pkg_dict["externals"] = []
     for e in external_pkg_entries:
-        if not _spec_is_valid(e.spec):
+        if not _spec_is_valid(e):
             continue
 
         external_items: List[Tuple[str, ExternalEntryType]] = [
-            ("spec", str(e.spec)),
-            ("prefix", e.prefix),
+            ("spec", str(e)),
+            ("prefix", pathlib.Path(e.external_path).as_posix()),
         ]
-        if e.spec.external_modules:
-            external_items.append(("modules", e.spec.external_modules))
+        if e.external_modules:
+            external_items.append(("modules", e.external_modules))
 
-        if e.spec.extra_attributes:
+        if e.extra_attributes:
             external_items.append(
-                (
-                    "extra_attributes",
-                    spack.util.spack_yaml.syaml_dict(e.spec.extra_attributes.items()),
-                )
+                ("extra_attributes", spack.util.spack_yaml.syaml_dict(e.extra_attributes.items()))
             )
 
         # external_items.extend(e.spec.extra_attributes.items())
@@ -221,33 +198,32 @@ def library_prefix(library_dir: str) -> str:
 
 
 def update_configuration(
-    detected_packages: Dict[str, List[DetectedPackage]],
+    detected_packages: Dict[str, List["spack.spec.Spec"]],
     scope: Optional[str] = None,
     buildable: bool = True,
 ) -> List[spack.spec.Spec]:
     """Add the packages passed as arguments to packages.yaml
 
     Args:
-        detected_packages: list of DetectedPackage objects to be added
+        detected_packages: list of specs to be added
         scope: configuration scope where to add the detected packages
         buildable: whether the detected packages are buildable or not
     """
     predefined_external_specs = _externals_in_packages_yaml()
     pkg_to_cfg, all_new_specs = {}, []
     for package_name, entries in detected_packages.items():
-        new_entries = [e for e in entries if (e.spec not in predefined_external_specs)]
+        new_entries = [s for s in entries if s not in predefined_external_specs]
 
         pkg_config = _pkg_config_dict(new_entries)
         external_entries = pkg_config.get("externals", [])
         assert not isinstance(external_entries, bool), "unexpected value for external entry"
 
-        all_new_specs.extend([x.spec for x in new_entries])
+        all_new_specs.extend(new_entries)
         if buildable is False:
             pkg_config["buildable"] = False
         pkg_to_cfg[package_name] = pkg_config
 
     pkgs_cfg = spack.config.get("packages", scope=scope)
-
     pkgs_cfg = spack.config.merge_yaml(pkgs_cfg, pkg_to_cfg)
     spack.config.set("packages", pkgs_cfg, scope=scope)
 

lib/spack/spack/detection/path.py

@@ -24,7 +24,6 @@
 import spack.util.ld_so_conf
 
 from .common import (
-    DetectedPackage,
     WindowsCompilerExternalPaths,
     WindowsKitExternalPaths,
     _convert_to_iterable,
@@ -229,7 +228,7 @@ def prefix_from_path(self, *, path: str) -> str:
 
     def detect_specs(
         self, *, pkg: Type["spack.package_base.PackageBase"], paths: List[str]
-    ) -> List[DetectedPackage]:
+    ) -> List["spack.spec.Spec"]:
         """Given a list of files matching the search patterns, returns a list of detected specs.
 
         Args:
@@ -295,16 +294,16 @@ def detect_specs(
                     warnings.warn(msg)
                     continue
 
-                if spec.external_path:
-                    prefix = spec.external_path
+                if not spec.external_path:
+                    spec.external_path = prefix
 
-                result.append(DetectedPackage(spec=spec, prefix=prefix))
+                result.append(spec)
 
         return result
 
     def find(
         self, *, pkg_name: str, repository, initial_guess: Optional[List[str]] = None
-    ) -> List[DetectedPackage]:
+    ) -> List["spack.spec.Spec"]:
         """For a given package, returns a list of detected specs.
 
         Args:
@@ -388,7 +387,7 @@ def by_path(
     *,
     path_hints: Optional[List[str]] = None,
     max_workers: Optional[int] = None,
-) -> Dict[str, List[DetectedPackage]]:
+) -> Dict[str, List["spack.spec.Spec"]]:
     """Return the list of packages that have been detected on the system, keyed by
     unqualified package name.
 

lib/spack/spack/detection/test.py

@@ -68,7 +68,7 @@ def execute(self) -> List[spack.spec.Spec]:
         with self._mock_layout() as path_hints:
             entries = by_path([self.test.pkg_name], path_hints=path_hints)
             _, unqualified_name = spack.repo.partition_package_name(self.test.pkg_name)
-            specs = set(x.spec for x in entries[unqualified_name])
+            specs = set(entries[unqualified_name])
         return list(specs)
 
     @contextlib.contextmanager

lib/spack/spack/test/cmd/external.py

@@ -44,7 +44,7 @@ def test_find_external_single_package(mock_executable):
 
     assert len(specs_by_package) == 1 and "cmake" in specs_by_package
     detected_spec = specs_by_package["cmake"]
-    assert len(detected_spec) == 1 and detected_spec[0].spec == Spec("cmake@1.foo")
+    assert len(detected_spec) == 1 and detected_spec[0] == Spec("cmake@1.foo")
 
 
 def test_find_external_two_instances_same_package(mock_executable):
@@ -61,10 +61,10 @@ def test_find_external_two_instances_same_package(mock_executable):
     )
 
     assert len(detected_specs) == 2
-    spec_to_path = {e.spec: e.prefix for e in detected_specs}
+    spec_to_path = {s: s.external_path for s in detected_specs}
     assert spec_to_path[Spec("cmake@1.foo")] == (
         spack.detection.executable_prefix(str(cmake1.parent))
-    )
+    ), spec_to_path
     assert spec_to_path[Spec("cmake@3.17.2")] == (
         spack.detection.executable_prefix(str(cmake2.parent))
     )
@@ -72,12 +72,8 @@ def test_find_external_two_instances_same_package(mock_executable):
 
 def test_find_external_update_config(mutable_config):
     entries = [
-        spack.detection.DetectedPackage(
-            Spec.from_detection("cmake@1.foo", external_path="/x/y1/"), "/x/y1/"
-        ),
-        spack.detection.DetectedPackage(
-            Spec.from_detection("cmake@3.17.2", external_path="/x/y2/"), "/x/y2/"
-        ),
+        Spec.from_detection("cmake@1.foo", external_path="/x/y1"),
+        Spec.from_detection("cmake@3.17.2", external_path="/x/y2"),
     ]
     pkg_to_entries = {"cmake": entries}
 
@@ -88,8 +84,8 @@ def test_find_external_update_config(mutable_config):
     cmake_cfg = pkgs_cfg["cmake"]
     cmake_externals = cmake_cfg["externals"]
 
-    assert {"spec": "cmake@1.foo", "prefix": "/x/y1/"} in cmake_externals
-    assert {"spec": "cmake@3.17.2", "prefix": "/x/y2/"} in cmake_externals
+    assert {"spec": "cmake@1.foo", "prefix": "/x/y1"} in cmake_externals
+    assert {"spec": "cmake@3.17.2", "prefix": "/x/y2"} in cmake_externals
 
 
 def test_get_executables(working_env, mock_executable):
@@ -229,19 +225,15 @@ def test_find_external_merge(mutable_config, mutable_mock_repo, tmp_path):
     """Checks that 'spack find external' doesn't overwrite an existing spec in packages.yaml."""
     pkgs_cfg_init = {
         "find-externals1": {
-            "externals": [{"spec": "find-externals1@1.1", "prefix": "/preexisting-prefix/"}],
+            "externals": [{"spec": "find-externals1@1.1", "prefix": "/preexisting-prefix"}],
             "buildable": False,
         }
     }
 
     mutable_config.update_config("packages", pkgs_cfg_init)
     entries = [
-        spack.detection.DetectedPackage(
-            Spec.from_detection("find-externals1@1.1", external_path="/x/y1/"), "/x/y1/"
-        ),
-        spack.detection.DetectedPackage(
-            Spec.from_detection("find-externals1@1.2", external_path="/x/y2/"), "/x/y2/"
-        ),
+        Spec.from_detection("find-externals1@1.1", external_path="/x/y1"),
+        Spec.from_detection("find-externals1@1.2", external_path="/x/y2"),
     ]
     pkg_to_entries = {"find-externals1": entries}
     scope = spack.config.default_modify_scope("packages")
@@ -251,8 +243,8 @@ def test_find_external_merge(mutable_config, mutable_mock_repo, tmp_path):
     pkg_cfg = pkgs_cfg["find-externals1"]
     pkg_externals = pkg_cfg["externals"]
 
-    assert {"spec": "find-externals1@1.1", "prefix": "/preexisting-prefix/"} in pkg_externals
-    assert {"spec": "find-externals1@1.2", "prefix": "/x/y2/"} in pkg_externals
+    assert {"spec": "find-externals1@1.1", "prefix": "/preexisting-prefix"} in pkg_externals
+    assert {"spec": "find-externals1@1.2", "prefix": "/x/y2"} in pkg_externals
 
 
 def test_list_detectable_packages(mutable_config, mutable_mock_repo):
@@ -278,7 +270,7 @@ def _determine_variants(cls, exes, version_str):
 
     assert len(detected_specs) == 1
 
-    gcc = detected_specs[0].spec
+    gcc = detected_specs[0]
     assert gcc.name == "gcc"
     assert gcc.external_path == os.path.sep + os.path.join("opt", "gcc", "bin")
 

lib/spack/spack/test/concretize.py

@@ -2109,11 +2109,13 @@ def test_external_python_extension_find_dependency_from_detection(self, monkeypa
         """Test that python extensions have access to a python dependency
 
         when python isn't otherwise in the DAG"""
-        python_spec = Spec("python@=detected")
         prefix = os.path.sep + "fake"
+        python_spec = Spec.from_detection("python@=detected", external_path=prefix)
 
         def find_fake_python(classes, path_hints):
-            return {"python": [spack.detection.DetectedPackage(python_spec, prefix=path_hints[0])]}
+            return {
+                "python": [Spec.from_detection("python@=detected", external_path=path_hints[0])]
+            }
 
         monkeypatch.setattr(spack.detection, "by_path", find_fake_python)
         external_conf = {
@@ -2128,7 +2130,8 @@ def find_fake_python(classes, path_hints):
 
         assert "python" in spec["py-extension1"]
         assert spec["python"].prefix == prefix
-        assert spec["python"] == python_spec
+        assert spec["python"].external
+        assert spec["python"].satisfies(python_spec)
 
     def test_external_python_extension_find_unified_python(self):
         """Test that python extensions use the same python as other specs in unified env"""

lib/spack/spack/test/detection.py

@@ -11,11 +11,7 @@
 def test_detection_update_config(mutable_config):
     # mock detected package
     detected_packages = collections.defaultdict(list)
-    detected_packages["cmake"] = [
-        spack.detection.common.DetectedPackage(
-            spec=spack.spec.Spec("cmake@3.27.5"), prefix="/usr/bin"
-        )
-    ]
+    detected_packages["cmake"] = [spack.spec.Spec("cmake@3.27.5", external_path="/usr/bin")]
 
     # update config for new package
     spack.detection.common.update_configuration(detected_packages)

var/spack/repos/builtin/packages/boost/package.py

@@ -462,24 +462,24 @@ def flag_handler(self, name, flags):
 
     def determine_toolset(self, spec):
         toolsets = {
-            "g++": "gcc",
-            "icpc": "intel",
-            "icpx": "intel",
-            "clang++": "clang",
-            "armclang++": "clang",
-            "xlc++": "xlcpp",
-            "xlc++_r": "xlcpp",
-            "pgc++": "pgi",
-            "nvc++": "pgi",
-            "FCC": "clang",
+            "%gcc": "gcc",
+            "%intel": "intel",
+            "%oneapi": "intel",
+            "%clang": "clang",
+            "%arm": "clang",
+            "%xl": "xlcpp",
+            "%xl_r": "xlcpp",
+            "%pgi": "pgi",
+            "%nvhpc": "pgi",
+            "%fj": "clang",
         }
 
         if spec.satisfies("@1.47:"):
-            toolsets["icpc"] += "-linux"
-            toolsets["icpx"] += "-linux"
+            toolsets["%intel"] += "-linux"
+            toolsets["%oneapi"] += "-linux"
 
         for cc, toolset in toolsets.items():
-            if cc in self.compiler.cxx_names:
+            if self.spec.satisfies(cc):
                 return toolset
 
         # fallback to gcc if no toolset found

var/spack/repos/builtin/packages/casacore/package.py

@@ -18,9 +18,12 @@ class Casacore(CMakePackage):
 
     license("LGPL-2.0-only")
 
+    version("3.6.1", sha256="480d3340fa17e9ba67f18efbaff4bbb272a01d1f400d2295c0b6c86eb7abcf82")
+    version("3.6.0", sha256="c88075aa73c2139b323b71a7f5d56cec5a6a0de649efd11e2d00ca033be5a0d7")
     version("3.5.0", sha256="63f1c8eff932b0fcbd38c598a5811e6e5397b72835b637d6f426105a183b3f91")
     version("3.4.0", sha256="31f02ad2e26f29bab4a47a2a69e049d7bc511084a0b8263360e6157356f92ae1")
     version("3.3.0", sha256="3a714644b908ef6e81489b792cc9b80f6d8267a275e15d38a42a6a5137d39d3d")
+    version("3.2.1", sha256="f87ce81d2b42ec5401cff8317baeeb9a3b408b716bb791ef252ad97af6e235ad")
     version("3.2.0", sha256="ae5d3786cb6dfdd7ebc5eecc0c724ff02bbf6929720bc23be43a027978e79a5f")
     version("3.1.2", sha256="ac94f4246412eb45d503f1019cabe2bb04e3861e1f3254b832d9b1164ea5f281")
     version("3.1.1", sha256="85d2b17d856592fb206b17e0a344a29330650a4269c80b87f8abb3eaf3dadad4")
@@ -28,9 +31,9 @@ class Casacore(CMakePackage):
     version("3.0.0", sha256="6f0e68fd77b5c96299f7583a03a53a90980ec347bff9dfb4c0abb0e2933e6bcb")
     version("2.4.1", sha256="58eccc875053b2c6fe44fe53b6463030ef169597ec29926936f18d27b5087d63")
 
-    depends_on("c", type="build")  # generated
-    depends_on("cxx", type="build")  # generated
-    depends_on("fortran", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
+    depends_on("fortran", type="build")
 
     depends_on("cmake@3.7.1:", type="build")
 
@@ -63,15 +66,18 @@ class Casacore(CMakePackage):
     depends_on("fftw@3.0.0: precision=float,double", when="~fftpack")
     depends_on("sofa-c", type="test")
     depends_on("hdf5", when="+hdf5")
-    depends_on("adios2+mpi", when="+adios2")
+    depends_on("adios2@2.6.0:", when="+adios2")
+    depends_on("adios2+mpi", when="+adios2+mpi")
+    depends_on("adios2~mpi", when="+adios2~mpi")
     depends_on("mpi", when="+mpi")
-    depends_on("python@2.6:", when="+python")
+    depends_on("python@2.6:", when="@:3.5.0 +python")
+    depends_on("python@3:", when="@3.6.0: +python")
     depends_on("boost +python", when="+python")
     depends_on("boost +system +filesystem", when="+dysco")
-    depends_on("py-numpy", when="+python")
+    depends_on("py-numpy@:1", when="@:3.6.0 +python")
+    depends_on("py-numpy", when="@3.6.1: +python")
     depends_on("gsl", when="+dysco")
 
-    conflicts("~mpi", when="+adios2")
     conflicts("+tablelocking", when="+mpi")
     conflicts("~threads", when="+openmp")
 
@@ -97,19 +103,27 @@ def cmake_args(self):
         # FFTPack can be selected.
         if spec.satisfies("@3.4.0:"):
             if spec.satisfies("+fftpack"):
-                args.append("-DBUILD_FFTPACK_DEPRECATED=YES")
+                args.append(self.define("BUILD_FFTPACK_DEPRECATED", True))
         else:
             args.append(self.define("USE_FFTW3", spec.satisfies("~fftpack")))
 
         # Python2 and Python3 binding
         if spec.satisfies("~python"):
-            args.extend(["-DBUILD_PYTHON=NO", "-DBUILD_PYTHON3=NO"])
+            args.extend([self.define("BUILD_PYTHON", False), self.define("BUILD_PYTHON3", False)])
         elif spec.satisfies("^python@3.0.0:"):
-            args.extend(["-DBUILD_PYTHON=NO", "-DBUILD_PYTHON3=YES"])
+            args.extend([self.define("BUILD_PYTHON", False), self.define("BUILD_PYTHON3", True)])
         else:
-            args.extend(["-DBUILD_PYTHON=YES", "-DBUILD_PYTHON3=NO"])
+            args.extend([self.define("BUILD_PYTHON", True), self.define("BUILD_PYTHON3", False)])
+        if spec.satisfies("@3.6.0:"):
+            args.append(self.define("USE_PCH", True))
+
+        # tests won't pass unless measures data are installed, which
+        # we don't do in this package, and for which we don't yet
+        # provide any way of specifying at build time
+        #
+        # args.append(self.define('BUILD_TESTING', self.run_tests))
+        args.append(self.define("BUILD_TESTING", False))
 
-        args.append("-DBUILD_TESTING=OFF")
         return args
 
     def patch(self):

var/spack/repos/builtin/packages/cray-mpich/package.py

@@ -32,6 +32,8 @@ class CrayMpich(Package):
     depends_on("cray-pmi")
     depends_on("libfabric")
 
+    requires("platform=linux", msg="Cray MPICH is only available on Cray")
+
     # cray-mpich 8.1.7: features MPI compiler wrappers
     variant("wrappers", default=True, when="@8.1.7:", description="enable MPI wrappers")
 

var/spack/repos/builtin/packages/cray-mvapich2/package.py

@@ -26,6 +26,8 @@ class CrayMvapich2(Package):
 
     provides("mpi@3")
 
+    requires("platform=linux", msg="Cray MVAPICH2 is only available on Cray")
+
     def setup_run_environment(self, env):
         if spack_cc is None:
             return

var/spack/repos/builtin/packages/doctest/package.py

@@ -0,0 +1,25 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class Doctest(CMakePackage):
+    """The fastest feature-rich C++11/14/17/20/23 single-header testing framework"""
+
+    homepage = "https://github.com/doctest/doctest"
+    url = "https://github.com/doctest/doctest/archive/refs/tags/v2.4.11.tar.gz"
+
+    license("MIT", checked_by="pranav-sivaraman")
+
+    version("2.4.11", sha256="632ed2c05a7f53fa961381497bf8069093f0d6628c5f26286161fbd32a560186")
+
+    depends_on("cxx", type="build")
+    depends_on("cmake@3:", type="build")
+
+    def cmake_args(self):
+        args = [self.define("DOCTEST_WITH_TESTS", self.run_tests)]
+        return args

var/spack/repos/builtin/packages/fujitsu-mpi/package.py

@@ -22,6 +22,8 @@ class FujitsuMpi(Package):
         msg="currently only supports Fujitsu, Clang, or GCC compilers",
     )
 
+    requires("platform=linux")
+
     def install(self, spec, prefix):
         raise InstallError("Fujitsu MPI is not installable; it is vendor supplied")
 

var/spack/repos/builtin/packages/gfsio/package.py

@@ -19,12 +19,15 @@ class Gfsio(CMakePackage):
     maintainers("AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett")
 
     version("develop", branch="develop")
+    version("1.4.2", sha256="1e92ba60c603a8d3019b2aa8134fb3a69e078b2d9398990638576d6c5aea4beb")
     version("1.4.1", sha256="eab106302f520600decc4f9665d7c6a55e7b4901fab6d9ef40f29702b89b69b1")
 
     depends_on("fortran", type="build")
 
     depends_on("pfunit", type="test")
 
+    conflicts("%oneapi", when="@:1.4.1", msg="Requires @1.4.2: for Intel oneAPI")
+
     def cmake_args(self):
         args = [self.define("ENABLE_TESTS", self.run_tests)]
         return args

var/spack/repos/builtin/packages/gromacs/package.py

@@ -253,15 +253,15 @@ class Gromacs(CMakePackage, CudaPackage):
     # see https://github.com/spack/spack/releases/tag/v0.20.0
 
     plumed_patches = {
-        "=2023": "2.9.0",
-        "2022.5": "2.8.2:2.9.0",
+        "=2023": "2.9.1",
+        "2022.5": "2.8.2:2.9.1",
         "2022.3": "2.8.1",
-        "2021.7": "2.8.2:2.9.0",
+        "2021.7": "2.8.2:2.9.1",
         "2021.6": "2.8.1",
         "2021.5": "2.7.5:2.7.6",
         "2021.4": "2.7.3:2.8.0",
         "=2021": "2.7.1:2.7.2",
-        "2020.7": "2.8.1:2.9.0",
+        "2020.7": "2.8.1:2.9.1",
         "2020.6": "2.7.2:2.8.0",
         "2020.5": "2.7.1",
         "2020.4": "2.6.2:2.7.0",

var/spack/repos/builtin/packages/hpcx-mpi/package.py

@@ -19,8 +19,10 @@ class HpcxMpi(Package):
 
     provides("mpi")
 
+    requires("platform=linux")
+
     def install(self, spec, prefix):
-        raise InstallError("HPC-X MPI is not buildable, it is for external " "specs only.")
+        raise InstallError("HPC-X MPI is not buildable, it is for external specs only.")
 
     def setup_dependent_package(self, module, dependent_spec):
         # This works for AOCC (AMD), Intel and GNU.

var/spack/repos/builtin/packages/landsfcutil/package.py

@@ -19,12 +19,15 @@ class Landsfcutil(CMakePackage):
     maintainers("edwardhartnett", "AlexanderRichert-NOAA", "Hang-Lei-NOAA")
 
     version("develop", branch="develop")
+    version("2.4.2", sha256="ac0ee4edaab3d273d9a6acffea8aa8a5b363366c3ade3e32539c057e84e4fa73")
     version("2.4.1", sha256="831c5005a480eabe9a8542b4deec838c2650f6966863ea2711cc0cc5db51ca14")
 
     depends_on("fortran", type="build")
 
     depends_on("pfunit", type="test")
 
+    conflicts("%oneapi", when="@:2.4.1", msg="Requires @2.4.2: for Intel oneAPI")
+
     def cmake_args(self):
         args = [self.define("ENABLE_TESTS", self.run_tests)]
         return args

var/spack/repos/builtin/packages/msmpi/package.py

@@ -33,6 +33,8 @@ class Msmpi(Package):
 
     patch("ifort_compat.patch")
 
+    requires("platform=windows")
+
     @classmethod
     def determine_version(cls, exe):
         # MSMPI is typically MS only, don't detect on other platforms

var/spack/repos/builtin/packages/plumed/package.py

@@ -32,6 +32,7 @@ class Plumed(AutotoolsPackage):
 
     version("master", branch="master")
 
+    version("2.9.1", sha256="e24563ad1eb657611918e0c978d9c5212340f128b4f1aa5efbd439a0b2e91b58")
     version("2.9.0", sha256="612d2387416b5f82dd8545709921440370e144fd46cef633654cf0ee43bac5f8")
 
     version("2.8.3", sha256="e98da486e252cdf290b0b5b2f3f021409ea0d2d775ab609a6ad68fc1ab143a3b")

var/spack/repos/builtin/packages/podio/package.py

@@ -99,6 +99,13 @@ class Podio(CMakePackage):
 
     conflicts("+rntuple", when="@:0.16", msg="rntuple support requires at least podio@0.17")
 
+    # See https://github.com/AIDASoft/podio/pull/600
+    patch(
+        "https://github.com/AIDASoft/podio/commit/0222a077aaff817b21a46a590af0f8329dd27d67.patch?full_index=1",
+        when="@0.17:0.99",
+        sha256="9e42e0995634f2afdd358cd19383e882dc9143cce1b6afb0d2c4a1ec9add6e15",
+    )
+
     # See https://github.com/AIDASoft/podio/pull/599 that landed after 0.99
     extends("python", when="@1.0:")
 

var/spack/repos/builtin/packages/py-jsonlines/package.py

@@ -0,0 +1,21 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyJsonlines(PythonPackage):
+    """Library with helpers for the jsonlines file format"""
+
+    homepage = "https://github.com/wbolster/jsonlines"
+    pypi = "jsonlines/jsonlines-4.0.0.tar.gz"
+
+    license("BSD-3-Clause", checked_by="alex391")
+
+    version("4.0.0", sha256="0c6d2c09117550c089995247f605ae4cf77dd1533041d366351f6f298822ea74")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-attrs@19.2.0:", type=("build", "run"))

var/spack/repos/builtin/packages/py-numcodecs/package.py

@@ -24,6 +24,9 @@ class PyNumcodecs(PythonPackage):
 
     version("main", branch="main", submodules=True)
     version("master", branch="main", submodules=True, deprecated=True)
+    version("0.13.0", sha256="ba4fac7036ea5a078c7afe1d4dffeb9685080d42f19c9c16b12dad866703aa2e")
+    version("0.12.1", sha256="05d91a433733e7eef268d7e80ec226a0232da244289614a8f3826901aec1098e")
+    version("0.12.0", sha256="6388e5f4e94d18a7165fbd1c9d3637673b74157cff8bc644005f9e2a4c717d6e")
     version("0.11.0", sha256="6c058b321de84a1729299b0eae4d652b2e48ea1ca7f9df0da65cb13470e635eb")
     version("0.7.3", sha256="022b12ad83eb623ec53f154859d49f6ec43b15c36052fa864eaf2d9ee786dd85")
     version("0.6.4", sha256="ef4843d5db4d074e607e9b85156835c10d006afc10e175bda62ff5412fca6e4d")
@@ -32,7 +35,8 @@ class PyNumcodecs(PythonPackage):
 
     variant("msgpack", default=False, description="Codec to encode data as msgpacked bytes.")
 
-    depends_on("python@3.8:", when="@0.11:", type=("build", "link", "run"))
+    depends_on("python@3.10:", when="@0.13:", type=("build", "link", "run"))
+    depends_on("python@3.8:", when="@0.11:0.12", type=("build", "link", "run"))
     depends_on("python@3.6:3", when="@0.7:0.10", type=("build", "link", "run"))
     depends_on("py-setuptools@64:", when="@0.11:", type="build")
     depends_on("py-setuptools@18.1:", type="build")

var/spack/repos/builtin/packages/py-ops/package.py

@@ -0,0 +1,24 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyOps(PythonPackage):
+    """The Python library behind great charms"""
+
+    homepage = "https://github.com/canonical/operator"
+    pypi = "ops/ops-1.4.0.tar.gz"
+
+    license("Apache-2.0", checked_by="qwertos")
+
+    version("2.16.0", sha256="c4405185744c82589fca4752a76cd7eabd667cf2d3f07d2700b82777186b8de9")
+    version("1.4.0", sha256="6bb7c8d8cd3eb1da99469564e37a04f9677205c4c07ef97167e0b93a17ccb59a")
+
+    depends_on("python@3.8:", when="@2.16:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-pyyaml@6", when="@2.16:", type=("build", "run"))
+    depends_on("py-websocket-client@1", when="@2.16:", type=("build", "run"))

var/spack/repos/builtin/packages/seacas/package.py

@@ -231,7 +231,9 @@ class Seacas(CMakePackage):
     depends_on("cmake@3.17:", when="@:2023-05-30", type="build")
     depends_on("mpi", when="+mpi")
     depends_on("zlib-api", when="+zlib")
-    depends_on("parallel")
+    depends_on("parallel", when="platform=linux", type="run")
+    depends_on("parallel", when="platform=darwin", type="run")
+    depends_on("parallel", when="platform=freebsd", type="run")
     depends_on("trilinos~exodus+mpi+pamgen", when="+mpi+pamgen")
     depends_on("trilinos~exodus~mpi+pamgen", when="~mpi+pamgen")
     # Always depends on netcdf-c
@@ -487,3 +489,9 @@ def cmake_args(self):
             options.append(define("CMAKE_INSTALL_NAME_DIR", self.prefix.lib))
 
         return options
+
+    @run_after("install")
+    def symlink_parallel(self):
+        if not self.spec.dependencies("parallel"):
+            return
+        symlink(self.spec["parallel"].prefix.bin.parallel, self.prefix.bin.parallel)

var/spack/repos/builtin/packages/sfcio/package.py

@@ -19,12 +19,15 @@ class Sfcio(CMakePackage):
     maintainers("AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett")
 
     version("develop", branch="develop")
+    version("1.4.2", sha256="bfde52320b836886a766ff8d0d6707b8a533c903b947f8b49250c544aaccaaac")
     version("1.4.1", sha256="d9f900cf18ec1a839b4128c069b1336317ffc682086283443354896746b89c59")
 
     depends_on("fortran", type="build")
 
     depends_on("pfunit", type="test")
 
+    conflicts("%oneapi", when="@:1.4.1", msg="Requires @1.4.2: for Intel oneAPI")
+
     def cmake_args(self):
         args = [self.define("ENABLE_TESTS", self.run_tests)]
         return args

var/spack/repos/builtin/packages/sigio/package.py

@@ -19,10 +19,13 @@ class Sigio(CMakePackage):
     maintainers("AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett")
 
     version("develop", branch="develop")
+    version("2.3.3", sha256="2b4a04be3be10f222d0ff47f973f65a03b8b5521dcad8e8866f3bfe4e8dfafab")
     version("2.3.2", sha256="333f3cf3a97f97103cbafcafc2ad89b24faa55b1332a98adc1637855e8a5b613")
 
     depends_on("fortran", type="build")
 
+    conflicts("%oneapi", when="@:2.3.2", msg="Requires @2.3.3: for Intel OneAPI")
+
     def cmake_args(self):
         args = [self.define("ENABLE_TESTS", self.run_tests)]
         return args

var/spack/repos/builtin/packages/spectrum-mpi/package.py

@@ -20,7 +20,7 @@ class SpectrumMpi(BundlePackage):
 
     provides("mpi")
 
-    conflicts("platform=windows")
+    requires("platform=linux")
 
     executables = ["^ompi_info$"]
 

var/spack/repos/builtin/packages/unzip/package.py

@@ -22,6 +22,7 @@ class Unzip(MakefilePackage):
     # clang and oneapi need this patch, likely others
     # There is no problem with it on gcc, so make it a catch all
     patch("configure-cflags.patch")
+    patch("strip.patch")
 
     def get_make_args(self):
         make_args = ["-f", join_path("unix", "Makefile")]
@@ -31,7 +32,7 @@ def get_make_args(self):
         cflags.append("-Wno-error=implicit-int")
         cflags.append("-DLARGE_FILE_SUPPORT")
 
-        make_args.append(f"LOC=\"{' '.join(cflags)}\"")
+        make_args.append(f"LOC={' '.join(cflags)}")
         return make_args
 
     @property

var/spack/repos/builtin/packages/unzip/strip.patch

@@ -0,0 +1,11 @@
+--- spack-src/unix/configure	2024-08-23 14:21:34.822163922 +0200
++++ spack-src/unix/configure.patched	2024-08-23 14:27:24.862640828 +0200
+@@ -17,7 +17,7 @@
+ IZ_BZIP2=${3}
+ CFLAGS="${CFLAGS} -I. -DUNIX"
+ LFLAGS1=""
+-LFLAGS2="-s"
++LFLAGS2="-Wl,-s"
+ LN="ln -s"
+ 
+ CFLAGS_OPT=''

var/spack/repos/builtin/packages/vtk/package.py

@@ -142,6 +142,10 @@ class Vtk(CMakePackage):
     # a patch with the same name is also applied to paraview
     # the two patches are the same but for the path to the files they patch
     patch("vtk_alias_hdf5.patch", when="@9:")
+    # VTK 9.0 on Windows uses dll instead of lib for hdf5-hl target, which fails linking. Can't
+    # be fixed by bumping CMake lower bound, because VTK vendors FindHDF5.cmake. Various other
+    # patches to FindHDF5.cmake are missing, so add conflict instead of a series of patches.
+    conflicts("@9.0 platform=windows")
     depends_on("libxt", when="^[virtuals=gl] glx platform=linux")
 
     # VTK will need Qt5OpenGL, and qt needs '-opengl' for that

var/spack/repos/builtin/packages/whizard/hepmc3.3.0.patch

@@ -0,0 +1,25 @@
+--- a/src/hepmc/HepMC3Wrap.cpp	2024-08-21 20:16:15.770305323 +0200
++++ b/src/hepmc/HepMC3Wrap.cpp	2024-08-21 20:16:28.463638884 +0200
+@@ -161,7 +162,7 @@
+ }
+ 
+ extern "C" void gen_event_add_vertex( GenEvent* evt, GenVertex* v ) {
+-  evt->add_vertex( v );
++  evt->add_vertex( GenVertexPtr(v) );
+ }
+ 
+ extern "C" void gen_event_set_signal_process_vertex
+@@ -237,11 +238,11 @@
+ }
+ 
+ extern "C" void gen_vertex_add_particle_in( GenVertex* v, GenParticle* p ) {
+-  v->add_particle_in( p );
++  v->add_particle_in( GenParticlePtr(p) );
+ }
+ 
+ extern "C" void gen_vertex_add_particle_out( GenVertex* v, GenParticle* p ) {
+-  v->add_particle_out( p );
++  v->add_particle_out( GenParticlePtr(p) );
+ }
+ 
+ extern "C" bool gen_vertex_is_valid( GenVertex* v ) {

var/spack/repos/builtin/packages/whizard/package.py

@@ -92,6 +92,9 @@ class Whizard(AutotoolsPackage):
     # that happens, this needs to be adapted with a when clause
     patch("parallel_build_fix.patch", when="@3:3.1.3")
     patch("parallel_build_fix_2.8.patch", when="@2.8")
+
+    # Subset of https://gitlab.tp.nt.uni-siegen.de/whizard/public/-/commit/f6048e4
+    patch("hepmc3.3.0.patch", when="@3:3.1.4^hepmc3@3.3.0:")
     # Make sure that the patch actually has an effect by running autoreconf
     force_autoreconf = True
     # Which then requires the following build dependencies