r-ptw: update dependencies

.github/workflows/ci.yaml

@@ -81,10 +81,6 @@ jobs:
     with:
       with_coverage: ${{ needs.changes.outputs.core }}
 
-  import-check:
-    needs: [ changes ]
-    uses: ./.github/workflows/import-check.yaml
-
   all-prechecks:
     needs: [ prechecks ]
     if: ${{ always() }}

.github/workflows/coverage.yml

@@ -33,4 +33,3 @@ jobs:
       with:
         verbose: true
         fail_ci_if_error: false
-        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/import-check.yaml

@@ -1,49 +0,0 @@
-name: import-check
-
-on:
-  workflow_call:
-
-jobs:
-  # Check we don't make the situation with circular imports worse
-  import-check:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: julia-actions/setup-julia@v2
-      with:
-        version: '1.10'
-    - uses: julia-actions/cache@v2
-
-    # PR: use the base of the PR as the old commit
-    - name: Checkout PR base commit
-      if: github.event_name == 'pull_request'
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        ref: ${{ github.event.pull_request.base.sha }}
-        path: old
-    # not a PR: use the previous commit as the old commit
-    - name: Checkout previous commit
-      if: github.event_name != 'pull_request'
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        fetch-depth: 2
-        path: old
-    - name: Checkout previous commit
-      if: github.event_name != 'pull_request'
-      run: git -C old reset --hard HEAD^
-
-    - name: Checkout new commit
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        path: new
-    - name: Install circular import checker
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        repository: haampie/circular-import-fighter
-        ref: e38bcd0aa46368e30648b61b7f0d8c1ca68aadff
-        path: circular-import-fighter
-    - name: Install dependencies
-      working-directory: circular-import-fighter
-      run: make -j dependencies
-    - name: Circular import check
-      working-directory: circular-import-fighter
-      run: make -j compare "SPACK_ROOT=../old ../new"

.github/workflows/valid-style.yml

@@ -86,6 +86,49 @@ jobs:
           spack -d bootstrap now --dev
           spack -d style -t black
           spack unit-test -V
+  # Check we don't make the situation with circular imports worse
+  import-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: julia-actions/setup-julia@v2
+      with:
+        version: '1.10'
+    - uses: julia-actions/cache@v2
+
+    # PR: use the base of the PR as the old commit
+    - name: Checkout PR base commit
+      if: github.event_name == 'pull_request'
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+      with:
+        ref: ${{ github.event.pull_request.base.sha }}
+        path: old
+    # not a PR: use the previous commit as the old commit
+    - name: Checkout previous commit
+      if: github.event_name != 'pull_request'
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+      with:
+        fetch-depth: 2
+        path: old
+    - name: Checkout previous commit
+      if: github.event_name != 'pull_request'
+      run: git -C old reset --hard HEAD^
+
+    - name: Checkout new commit
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+      with:
+        path: new
+    - name: Install circular import checker
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+      with:
+        repository: haampie/circular-import-fighter
+        ref: 38c5473f619493d060d813c72c80eac86b3d2aeb
+        path: circular-import-fighter
+    - name: Install dependencies
+      working-directory: circular-import-fighter
+      run: make -j dependencies
+    - name: Circular import check
+      working-directory: circular-import-fighter
+      run: make -j compare "SPACK_ROOT=../old ../new"
 
   # Further style checks from pylint
   pylint:

etc/spack/defaults/windows/config.yaml

@@ -1,5 +1,5 @@
 config:
   locks: false
   build_stage::
-    - '$user_cache_path/stage'
+    - '$spack/.staging'
   stage_name: '{name}-{version}-{hash:7}'

lib/spack/spack/audit.py

@@ -61,7 +61,6 @@ def _search_duplicate_compilers(error_cls):
 import spack.util.crypto
 import spack.util.spack_yaml as syaml
 import spack.variant
-import spack.version
 
 #: Map an audit tag to a list of callables implementing checks
 CALLBACKS = {}
@@ -1138,23 +1137,10 @@ def _ensure_variants_have_descriptions(pkgs, error_cls):
     return errors
 
 
-def _skip_version_audit(host_arch: spack.spec.ArchSpec, pkg_cls) -> bool:
-    """The version audit is skipped if a package defines skip_version_audit as True or if the
-    host architecture satisfies any of the archs in the list skip_version_audit."""
-    skip_conditions = getattr(pkg_cls, "skip_version_audit", False)
-    if type(skip_conditions) is bool:
-        return skip_conditions
-    for condition in skip_conditions:
-        if host_arch.satisfies(spack.spec.Spec(condition).architecture):
-            return True
-    return False
-
-
 @package_directives
 def _version_constraints_are_satisfiable_by_some_version_in_repo(pkgs, error_cls):
     """Report if version constraints used in directives are not satisfiable"""
     errors = []
-    host_architecture = spack.spec.ArchSpec.default_arch()
     for pkg_name in pkgs:
         pkg_cls = spack.repo.PATH.get_pkg_class(pkg_name)
         filename = spack.repo.PATH.filename_for_package_name(pkg_name)
@@ -1170,13 +1156,20 @@ def _version_constraints_are_satisfiable_by_some_version_in_repo(pkgs, error_cls
 
                 dependencies_to_check.append(dep.spec)
 
+        host_architecture = spack.spec.ArchSpec.default_arch()
         for s in dependencies_to_check:
             dependency_pkg_cls = None
             try:
                 dependency_pkg_cls = spack.repo.PATH.get_pkg_class(s.name)
                 # Some packages have hacks that might cause failures on some platform
                 # Allow to explicitly set conditions to skip version checks in that case
-                assert _skip_version_audit(host_architecture, dependency_pkg_cls) or any(
+                skip_conditions = getattr(dependency_pkg_cls, "skip_version_audit", [])
+                skip_version_check = False
+                for condition in skip_conditions:
+                    if host_architecture.satisfies(spack.spec.Spec(condition).architecture):
+                        skip_version_check = True
+                        break
+                assert skip_version_check or any(
                     v.intersects(s.versions) for v in list(dependency_pkg_cls.versions)
                 )
             except Exception:
@@ -1195,64 +1188,6 @@ def _version_constraints_are_satisfiable_by_some_version_in_repo(pkgs, error_cls
     return errors
 
 
-@package_directives
-def _when_conditions_are_satisfiable_by_some_version(pkgs, error_cls):
-    """Report if versions in when conditions used in directives are not satisfiable"""
-    errors = []
-    attrs = {
-        "conflicts": "conflicts",
-        "dependencies": "depends_on",
-        "licenses": "license",
-        "patches": "patch",
-        "provided_together": "provides",
-        "provided": "provides",
-        "requirements": "requires",
-        "resources": "resource",
-        "splice_specs": "can_splice",
-        "variants": "variant",
-    }
-    host_architecture = spack.spec.ArchSpec.default_arch()
-    for pkg_name in pkgs:
-        pkg_cls = spack.repo.PATH.get_pkg_class(pkg_name)
-        filename = spack.repo.PATH.filename_for_package_name(pkg_name)
-        if _skip_version_audit(host_architecture, pkg_cls):
-            continue
-        if not pkg_cls.versions:
-            continue
-        range = spack.version.VersionRange(
-            min(pkg_cls.versions), spack.version.StandardVersion.typemax()
-        )
-        details = []
-        for attr, directive in attrs.items():
-            if attr == "patches":
-                # Patches should strictly apply to some known version
-                unsatisfiable = [
-                    when
-                    for when in getattr(pkg_cls, attr)
-                    if not any(y.intersects(when.versions) for y in pkg_cls.versions)
-                ]
-            else:
-                # Other directives should just be in the range of min known version to infinity.
-                # The reason being sometimes people add depends_on("foo@1.1", when="@1.1") because
-                # it's copied, even though only 1.0 and 1.2 are registered in Spack. It's too
-                # annoying to complain about that.
-                unsatisfiable = [
-                    when for when in getattr(pkg_cls, attr) if not range.intersects(when.versions)
-                ]
-            details.extend(f'{directive}(..., when="{x}")' for x in unsatisfiable)
-
-        if details:
-            errors.append(
-                error_cls(
-                    summary=f"{filename}: when conditions are not satisfiable by "
-                    f"any known version of {pkg_cls.name}",
-                    details=details,
-                )
-            )
-
-    return errors
-
-
 def _analyze_variants_in_directive(pkg, constraint, directive, error_cls):
     errors = []
     variant_names = pkg.variant_names()

lib/spack/spack/build_systems/cmake.py

@@ -11,7 +11,6 @@
 from typing import Any, List, Optional, Tuple
 
 import llnl.util.filesystem as fs
-from llnl.util import tty
 from llnl.util.lang import stable_partition
 
 import spack.builder
@@ -459,23 +458,19 @@ def cmake(
     ) -> None:
         """Runs ``cmake`` in the build directory"""
 
-        if spec.is_develop:
-            # skip cmake phase if it is an incremental develop build
-
-            # Determine the files that will re-run CMake that are generated from a successful
-            # configure step based on state
-            primary_generator = _extract_primary_generator(self.generator)
+        # skip cmake phase if it is an incremental develop build
+        # These are the files that will re-run CMake that are generated from a successful
+        # configure step
+        primary_generator = _extract_primary_generator(self.generator)
+        if primary_generator == "Unix Makefiles":
             configure_artifact = "Makefile"
-            if primary_generator == "Ninja":
-                configure_artifact = "ninja.build"
+        elif primary_generator == "Ninja":
+            configure_artifact = "ninja.build"
 
-            if os.path.isfile(os.path.join(self.build_directory, configure_artifact)):
-                tty.msg(
-                    "Incremental build criteria satisfied."
-                    "Skipping CMake configure step. To force configuration run"
-                    f" `spack clean {pkg.name}`"
-                )
-                return
+        if spec.is_develop and os.path.isfile(
+            os.path.join(self.build_directory, configure_artifact)
+        ):
+            return
 
         options = self.std_cmake_args
         options += self.cmake_args()

lib/spack/spack/package.py

@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-# flake8: noqa: F401, E402
+# flake8: noqa: F401
 """spack.package defines the public API for Spack packages, by re-exporting useful symbols from
 other modules. Packages should import this module, instead of importing from spack.* directly
 to ensure forward compatibility with future versions of Spack."""

lib/spack/spack/package_base.py

@@ -2284,6 +2284,14 @@ def rpath_args(self):
 build_system_flags = PackageBase.build_system_flags
 
 
+def use_cray_compiler_names():
+    """Compiler names for builds that rely on cray compiler names."""
+    os.environ["CC"] = "cc"
+    os.environ["CXX"] = "CC"
+    os.environ["FC"] = "ftn"
+    os.environ["F77"] = "ftn"
+
+
 def possible_dependencies(
     *pkg_or_spec: Union[str, spack.spec.Spec, typing.Type[PackageBase]],
     transitive: bool = True,

lib/spack/spack/relocate.py

@@ -236,15 +236,22 @@ def relocate_elf_binaries(binaries: Iterable[str], prefix_to_prefix: Dict[str, s
             _set_elf_rpaths_and_interpreter(path, rpaths=rpaths, interpreter=interpreter)
 
 
+def _warn_if_link_cant_be_relocated(link: str, target: str):
+    if not os.path.isabs(target):
+        return
+    tty.warn(f'Symbolic link at "{link}" to "{target}" cannot be relocated')
+
+
 def relocate_links(links: Iterable[str], prefix_to_prefix: Dict[str, str]) -> None:
     """Relocate links to a new install prefix."""
     regex = re.compile("|".join(re.escape(p) for p in prefix_to_prefix.keys()))
     for link in links:
         old_target = readlink(link)
-        if not os.path.isabs(old_target):
-            continue
         match = regex.match(old_target)
+
+        # No match.
         if match is None:
+            _warn_if_link_cant_be_relocated(link, old_target)
             continue
 
         new_target = prefix_to_prefix[match.group()] + old_target[match.end() :]

lib/spack/spack/spec.py

@@ -1527,8 +1527,9 @@ def __init__(self, spec_like=None, *, external_path=None, external_modules=None)
         self._external_path = external_path
         self.external_modules = Spec._format_module_list(external_modules)
 
-        # This attribute is used to store custom information for external specs.
-        self.extra_attributes: dict = {}
+        # This attribute is used to store custom information for
+        # external specs. None signal that it was not set yet.
+        self.extra_attributes = None
 
         # This attribute holds the original build copy of the spec if it is
         # deployed differently than it was built. None signals that the spec
@@ -2350,10 +2351,15 @@ def to_node_dict(self, hash=ht.dag_hash):
             )
 
         if self.external:
+            if self.extra_attributes:
+                extra_attributes = syaml.sorted_dict(self.extra_attributes)
+            else:
+                extra_attributes = None
+
             d["external"] = {
                 "path": self.external_path,
-                "module": self.external_modules or None,
-                "extra_attributes": syaml.sorted_dict(self.extra_attributes),
+                "module": self.external_modules,
+                "extra_attributes": extra_attributes,
             }
 
         if not self._concrete:
@@ -3855,13 +3861,6 @@ def _cmp_iter(self):
         for item in self._cmp_node():
             yield item
 
-        # If there is ever a breaking change to hash computation, whether accidental or purposeful,
-        # two specs can be identical modulo DAG hash, depending on what time they were concretized
-        # From the perspective of many operation in Spack (database, build cache, etc) a different
-        # DAG hash means a different spec. Here we ensure that two otherwise identical specs, one
-        # serialized before the hash change and one after, are considered different.
-        yield self.dag_hash() if self.concrete else None
-
         # This needs to be in _cmp_iter so that no specs with different process hashes
         # are considered the same by `__hash__` or `__eq__`.
         #
@@ -4909,7 +4908,7 @@ def from_node_dict(cls, node):
                 spec.external_modules = node["external"]["module"]
                 if spec.external_modules is False:
                     spec.external_modules = None
-                spec.extra_attributes = node["external"].get("extra_attributes") or {}
+                spec.extra_attributes = node["external"].get("extra_attributes", {})
 
         # specs read in are concrete unless marked abstract
         if node.get("concrete", True):

lib/spack/spack/test/spec_semantics.py

@@ -1989,26 +1989,3 @@ def test_equality_discriminate_on_propagation(lhs, rhs):
 
 def test_comparison_multivalued_variants():
     assert Spec("x=a") < Spec("x=a,b") < Spec("x==a,b") < Spec("x==a,b,c")
-
-
-def test_comparison_after_breaking_hash_change():
-    # We simulate a breaking change in DAG hash computation in Spack. We have two specs that are
-    # entirely equal modulo DAG hash. When deserializing these specs, we don't want them to compare
-    # as equal, because DAG hash is used throughout in Spack to distinguish between specs
-    # (e.g. database, build caches, install dir).
-    s = Spec("example@=1.0")
-    s._mark_concrete(True)
-
-    # compute the dag hash and a change to it
-    dag_hash = s.dag_hash()
-    new_dag_hash = f"{'b' if dag_hash[0] == 'a' else 'a'}{dag_hash[1:]}"
-
-    before_breakage = s.to_dict()
-    after_breakage = s.to_dict()
-    after_breakage["spec"]["nodes"][0]["hash"] = new_dag_hash
-    assert before_breakage != after_breakage
-
-    x = Spec.from_dict(before_breakage)
-    y = Spec.from_dict(after_breakage)
-    assert x != y
-    assert len({x, y}) == 2

pyproject.toml

@@ -1,7 +1,6 @@
 [project]
 name="spack"
 description="The spack package manager"
-requires-python=">=3.6"
 dependencies=[
   "clingo",
   "setuptools",
@@ -68,42 +67,9 @@ features = [
   "ci",
 ]
 
-[tool.ruff]
-line-length = 99
-extend-include = ["bin/spack"]
-extend-exclude = ["lib/spack/external", "*.pyi"]
-
-[tool.ruff.format]
-skip-magic-trailing-comma = true
-
-[tool.ruff.lint]
-extend-select = ["I"]
-ignore = ["E731", "E203"]
-
-[tool.ruff.lint.isort]
-split-on-trailing-comma = false
-section-order = [
-    "future",
-    "standard-library",
-    "third-party",
-    "archspec",
-    "llnl",
-    "spack",
-    "first-party",
-    "local-folder",
-]
-
-[tool.ruff.lint.isort.sections]
-spack = ["spack"]
-archspec = ["archspec"]
-llnl = ["llnl"]
-
-[tool.ruff.lint.per-file-ignores]
-"var/spack/repos/*/package.py" = ["F403", "F405", "F811", "F821"]
-"*-ci-package.py" = ["F403", "F405", "F821"]
-
 [tool.black]
 line-length = 99
+target-version = ['py36', 'py37', 'py38', 'py39', 'py310']
 include = '(lib/spack|var/spack/repos)/.*\.pyi?$|bin/spack$'
 extend-exclude = 'lib/spack/external'
 skip_magic_trailing_comma = true

share/spack/gitlab/cloud_pipelines/stacks/aws-isc-aarch64/spack.yaml

@@ -0,0 +1,141 @@
+spack:
+  view: false
+  packages:
+    all:
+      providers:
+        blas:
+        - openblas
+        mkl:
+        - intel-oneapi-mkl
+        mpi:
+        - openmpi
+        - mpich
+      variants: +mpi
+    tbb:
+      require: intel-tbb
+    binutils:
+      variants: +ld +gold +headers +libiberty ~nls
+      version:
+      - 2.36.1
+    doxygen:
+      version:
+      - 1.8.20
+    elfutils:
+      variants: ~nls
+    hdf5:
+      variants: +fortran +hl +shared
+    libfabric:
+      variants: fabrics=efa,tcp,udp,sockets,verbs,shm,mrail,rxd,rxm
+    libunwind:
+      variants: +pic +xz
+    mesa:
+      variants: ~llvm
+    mpich:
+      variants: ~wrapperrpath netmod=ofi device=ch4
+    ncurses:
+      variants: +termlib
+    openblas:
+      variants: threads=openmp
+    openmpi:
+      variants: fabrics=ofi +legacylaunchers
+    openturns:
+      version:
+      - '1.18'
+    relion:
+      variants: ~mklfft
+#    texlive:
+#      version: [20210325]
+    trilinos:
+      variants: +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext
+        +ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu
+        +nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos
+        +teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
+    xz:
+      variants: +pic
+
+  definitions:
+
+  - compiler_specs:
+    - gcc@11
+    # Licensing OK?
+    # - intel-oneapi-compilers@2022.1
+    # - nvhpc
+
+  - app_specs:
+    - bwa
+# Depends on simde which requires newer compiler?
+    #- bowtie2
+    # Requires x86_64 specific ASM
+    #- cistem
+    - cromwell
+    - fastqc
+    - flux-sched
+    - flux-core
+    - flux-pmix
+    - gatk
+    - gromacs
+    - lammps
+    - wrf build_type=dm+sm
+    - mfem
+    - mpas-model ^parallelio+pnetcdf
+    - nextflow
+    - octave
+    - openfoam
+    - osu-micro-benchmarks
+    - parallel
+    # - paraview
+    - picard
+    - quantum-espresso
+    - raja
+# Depends on bowtie2 -> simde which requires newer compiler?
+    #- rsem
+    # Errors on texlive
+    #- rstudio
+    - salmon
+    - samtools
+    - seqtk
+    - snakemake
+    - star
+    # Requires gcc@9:
+    #- ufs-weather-model
+# requires LLVM which fails without constraint
+    #- visit
+
+  - lib_specs:
+    - openmpi fabrics=ofi
+    - openmpi fabrics=ofi +legacylaunchers
+    - openmpi fabrics=auto
+    - mpich
+    - libfabric
+
+  - compiler:
+    - '%gcc@7.3.1'
+
+  - target:
+    - target=aarch64
+
+
+  specs:
+
+  - matrix:
+    - - $app_specs
+    - - $compiler
+    - - $target
+
+  - matrix:
+    - - $lib_specs
+    - - $compiler
+    - - $target
+
+  - matrix:
+    - - $compiler_specs
+    - - $compiler
+    - - $target
+
+  ci:
+    pipeline-gen:
+    - build-job:
+        image: {name: ghcr.io/spack/e4s-amazonlinux-2:v2023-03-09, entrypoint: ['']}
+
+  cdash:
+    build-group: AWS Packages

share/spack/gitlab/cloud_pipelines/stacks/aws-isc/spack.yaml

@@ -0,0 +1,153 @@
+spack:
+  view: false
+  packages:
+    all:
+      providers:
+        blas:
+        - openblas
+        mkl:
+        - intel-oneapi-mkl
+        mpi:
+        - openmpi
+        - mpich
+      variants: +mpi
+    tbb:
+      require: intel-tbb
+    binutils:
+      variants: +ld +gold +headers +libiberty ~nls
+      version:
+      - 2.36.1
+    doxygen:
+      version:
+      - 1.8.20
+    elfutils:
+      variants: ~nls
+    hdf5:
+      variants: +fortran +hl +shared
+    libfabric:
+      variants: fabrics=efa,tcp,udp,sockets,verbs,shm,mrail,rxd,rxm
+    libunwind:
+      variants: +pic +xz
+    mesa:
+      variants: ~llvm
+    mpich:
+      variants: ~wrapperrpath netmod=ofi device=ch4
+    ncurses:
+      variants: +termlib
+    openblas:
+      variants: threads=openmp
+    openmpi:
+      variants: fabrics=ofi +legacylaunchers
+    openturns:
+      version:
+      - '1.18'
+    relion:
+      variants: ~mklfft
+#    texlive:
+#      version: [20210325]
+    trilinos:
+      variants: +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext
+        +ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu
+        +nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos
+        +teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
+    xz:
+      variants: +pic
+
+  definitions:
+
+  - compiler_specs:
+    - gcc@11
+    # Licensing OK?
+    # - intel-oneapi-compilers@2022.1
+    # - nvhpc
+
+  - cuda_specs:
+# Disabled for consistency with aarch64
+    #- relion +cuda cuda_arch=70
+    - raja +cuda cuda_arch=70
+    - mfem +cuda cuda_arch=70
+
+  - app_specs:
+    - bwa
+# Disabled for consistency with aarch64
+    #- bowtie2
+# Disabled for consistency with aarch64
+    #- cistem
+    - cromwell
+    - fastqc
+    - flux-sched
+    - flux-core
+    - flux-pmix
+    - gatk
+    - gromacs
+    - lammps
+    - wrf build_type=dm+sm
+    - mfem
+    - mpas-model ^parallelio+pnetcdf
+    - nextflow
+    - octave
+    - openfoam
+    - osu-micro-benchmarks
+    - parallel
+    # - paraview
+    - picard
+    - quantum-espresso
+# Build broken for gcc@7.3.1 x86_64_v4 (error: '_mm512_loadu_epi32' was not declared in this scope)
+    #- raja
+# Disabled for consistency with aarch64
+    #- rsem
+    # Errors on texlive
+    #- rstudio
+    - salmon
+    - samtools
+    - seqtk
+    - snakemake
+    - star
+    # Requires gcc@9:
+    #- ufs-weather-model
+# Disabled for consistency with aarch64
+    #- visit
+
+  - lib_specs:
+    - openmpi fabrics=ofi
+    - openmpi fabrics=ofi +legacylaunchers
+    - openmpi fabrics=auto
+    - mpich
+    - libfabric
+
+  - compiler:
+    - '%gcc@7.3.1'
+
+  - target:
+    - target=x86_64_v3
+
+
+  specs:
+
+  - matrix:
+    - - $cuda_specs
+    - - $compiler
+    - - $target
+
+  - matrix:
+    - - $app_specs
+    - - $compiler
+    - - $target
+
+  - matrix:
+    - - $lib_specs
+    - - $compiler
+    - - $target
+
+  - matrix:
+    - - $compiler_specs
+    - - $compiler
+    - - $target
+
+  ci:
+    pipeline-gen:
+    - build-job:
+        image: {name: ghcr.io/spack/e4s-amazonlinux-2:v2023-03-09, entrypoint: ['']}
+
+  cdash:
+    build-group: AWS Packages

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

@@ -13,41 +13,29 @@ spack:
         mpi: [mpich]
         tbb: [intel-tbb]
       variants: +mpi
-    acts:
-      require: +analysis +dd4hep +edm4hep +examples +fatras +geant4 +hepmc3 +podio +pythia8 +python ~svg +tgeo cxxstd=20
-    celeritas:
-      require: +geant4 +hepmc3 +root +shared cxxstd=20
-    hip:
-      require: '@5.7.1 +rocm'
-    root:
-      require: +davix +dcache +examples +fftw +fits +fortran +gdml +graphviz +gsl +http +math +minuit +mlp +mysql +opengl +postgres +pythia8 +python +r +roofit +root7 +rpath ~shadow +spectrum +sqlite +ssl +tbb +threads +tmva +tmva-cpu +unuran +vc +vdt +veccore +webgui +x +xml +xrootd # cxxstd=20
-      # note: root cxxstd=20 not concretizable within sherpa
-    vecgeom:
-      require: +gdml +geant4 +root +shared cxxstd=20
 
     # Mark geant4 data as external to prevent wasting bandwidth on GB-scale files
     geant4-data:
-      buildable: false
       externals:
-      - spec: geant4-data@11.3.0
-        prefix: /usr
-      - spec: geant4-data@11.2.2
-        prefix: /usr
-      - spec: geant4-data@11.2.0
-        prefix: /usr
-      - spec: geant4-data@11.1.0
-        prefix: /usr
-      - spec: geant4-data@11.0.0
-        prefix: /usr
+        - spec: geant4-data@11.3.0
+          prefix: /usr
+        - spec: geant4-data@11.2.2
+          prefix: /usr
+        - spec: geant4-data@11.2.0
+          prefix: /usr
+        - spec: geant4-data@11.1.0
+          prefix: /usr
+        - spec: geant4-data@11.0.0
+          prefix: /usr
 
   specs:
   # CPU
-  - acts ~cuda
+  - acts +analysis +dd4hep +edm4hep +examples +fatras +geant4 +hepmc3 +podio +pythia8 +python +tgeo cxxstd=20
   #- agile  # fails on c++>11 compiler
   - alpgen
   - ampt
   - apfel +lhapdf +python
-  - celeritas ~cuda +openmp ~rocm +vecgeom
+  - celeritas +geant4 +hepmc3 +openmp +root +shared +vecgeom cxxstd=20
   - cepgen
   - cernlib +shared
   - collier
@@ -94,28 +82,19 @@ spack:
   - py-vector
   - pythia8 +evtgen +fastjet +hdf5 +hepmc +hepmc3 +lhapdf ~madgraph5amc +python +rivet ~root # pythia8 and root circularly depend
   - rivet hepmc=3
-  - root ~cuda
+  - root +davix +dcache +examples +fftw +fits +fortran +gdml +graphviz +gsl +http +math +minuit +mlp +mysql +opengl +postgres +pythia8 +python +r +roofit +root7 +rpath ~shadow +spectrum +sqlite +ssl +tbb +threads +tmva +unuran +vc +vdt +veccore +webgui +x +xml +xrootd
   - sherpa +analysis ~blackhat +gzip +hepmc3 +hepmc3root +lhapdf +lhole +openloops +pythia ~python ~recola ~rivet +root +ufo cxxstd=20
   - tauola +hepmc3 +lhapdf cxxstd=20
   - thepeg hepmc=3 ~rivet
-  - vecgeom ~cuda
+  - vecgeom +gdml +geant4 +root
   - whizard +fastjet +gosam hepmc=3 +lcio +lhapdf +openloops +openmp +pythia8
   - xrootd +davix +http +krb5 +python +readline +scitokens-cpp
   - yoda +root
 
-  # CUDA
-  #- acts +cuda +traccc cuda_arch=80
-  #- celeritas +cuda ~openmp +vecgeom cuda_arch=80
-  - root +cuda +cudnn +tmva-gpu
-  - vecgeom +cuda cuda_arch=80
-
-  # ROCm
-  - celeritas +rocm amdgpu_target=gfx90a ~openmp ~vecgeom  # only available with ORANGE
-
   ci:
     pipeline-gen:
     - build-job:
-        image: ghcr.io/spack/spack/ubuntu22.04-runner-amd64-gcc-11.4:2024.03.01
+        image: "ghcr.io/spack/spack/ubuntu22.04-runner-amd64-gcc-11.4:2024.03.01"
 
   cdash:
     build-group: HEP

share/spack/qa/run-unit-tests

@@ -36,7 +36,7 @@ bin/spack -h
 bin/spack help -a
 
 # Profile and print top 20 lines for a simple call to spack spec
-spack -p --lines 20 spec mpileaks%gcc
+spack -p --lines 20 spec mpileaks%gcc ^dyninst@10.0.0 ^elfutils@0.170
 $coverage_run $(which spack) bootstrap status --dev --optional
 
 # Check that we can import Spack packages directly as a first import

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

@@ -40,7 +40,6 @@ class Acts(CMakePackage, CudaPackage):
     # Supported Acts versions
     version("main", branch="main")
     version("master", branch="main", deprecated=True)  # For compatibility
-    version("39.0.0", commit="b055202e2fbdd509bc186eb4782714bc46f38f3f", submodules=True)
     version("38.2.0", commit="9cb8f4494656553fd9b85955938b79b2fac4c9b0", submodules=True)
     version("38.1.0", commit="8a20c88808f10bf4fcdfd7c6e077f23614c3ab90", submodules=True)
     version("38.0.0", commit="0a6b5155e29e3b755bf351b8a76067fff9b4214b", submodules=True)

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

@@ -4,6 +4,7 @@
 
 import os
 
+from spack.build_environment import optimization_flags
 from spack.package import *
 from spack.pkg.builtin.fftw import FftwBase
 
@@ -94,14 +95,14 @@ class Amdfftw(FftwBase):
     )
     variant(
         "amd-dynamic-dispatcher",
-        default=False,
+        default=True,
         when="@4.1: %aocc@4.1.0:",
         description="Single portable optimized library"
         " to execute on different x86 CPU architectures",
     )
     variant(
         "amd-dynamic-dispatcher",
-        default=False,
+        default=True,
         when="@3.2: %gcc",
         description="Single portable optimized library"
         " to execute on different x86 CPU architectures",
@@ -202,10 +203,11 @@ def configure(self, spec, prefix):
         if not self.compiler.f77 or not self.compiler.fc:
             options.append("--disable-fortran")
 
-        if "avx512" in spec.target:
-            options.append("CFLAGS=-mprefer-vector-width=512")
-        else:
-            options.append("CFLAGS=-mprefer-vector-width=256")
+        # Cross compilation is supported in amd-fftw by making use of target
+        # variable to set AMD_ARCH configure option.
+        # Spack user can not directly use AMD_ARCH for this purpose but should
+        # use target variable to set appropriate -march option in AMD_ARCH.
+        options.append(f"AMD_ARCH={optimization_flags(self.compiler, spec.target)}")
 
         # Specific SIMD support.
         # float and double precisions are supported

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

@@ -148,14 +148,6 @@ class Ascent(CMakePackage, CudaPackage):
     # https://github.com/Alpine-DAV/ascent/pull/1123
     patch("ascent-find-raja-pr1123.patch", when="@0.9.0")
 
-    # patch for fix typo in coord_type
-    # https://github.com/Alpine-DAV/ascent/pull/1408
-    patch(
-        "https://github.com/Alpine-DAV/ascent/pull/1408.patch?full_index=1",
-        when="@0.9.3 %oneapi@2025:",
-        sha256="7de7f51e57f3d743c39ad80d8783a4eb482be1def51eb2d3f9259246c661f164",
-    )
-
     ##########################################################################
     # package dependencies
     ###########################################################################
@@ -476,9 +468,6 @@ def hostconfig(self):
         if cflags:
             cfg.write(cmake_cache_entry("CMAKE_C_FLAGS", cflags))
         cxxflags = cppflags + " ".join(spec.compiler_flags["cxxflags"])
-        if spec.satisfies("%oneapi@2025:"):
-            cxxflags += "-Wno-error=missing-template-arg-list-after-template-kw "
-            cxxflags += "-Wno-missing-template-arg-list-after-template-kw"
         if cxxflags:
             cfg.write(cmake_cache_entry("CMAKE_CXX_FLAGS", cxxflags))
         fflags = " ".join(spec.compiler_flags["fflags"])

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

@@ -23,10 +23,6 @@ class Bash(AutotoolsPackage, GNUMirrorPackage):
 
     depends_on("c", type="build")  # generated
 
-    depends_on("autoconf", type="build")
-    depends_on("automake", type="build")
-    depends_on("libtool", type="build")
-
     depends_on("ncurses")
     depends_on("readline@8.2:", when="@5.2:")
     depends_on("readline@5.0:")

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

@@ -2,7 +2,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack.build_systems.cmake import CMakeBuilder
 from spack.package import *
 
 
@@ -82,22 +81,13 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("py-breathe", type="build", when="+doc")
     depends_on("py-sphinx", type="build", when="+doc")
 
-    with when("+cuda"):
-        depends_on("thrust")
-    with when("+rocm"):
-        depends_on("hiprand")
-        depends_on("rocprim")
-        depends_on("rocrand")
-        depends_on("rocthrust")
-
     for _std in _cxxstd_values:
         depends_on("geant4 cxxstd=" + _std, when="+geant4 cxxstd=" + _std)
         depends_on("root cxxstd=" + _std, when="+root cxxstd=" + _std)
         depends_on("vecgeom cxxstd=" + _std, when="+vecgeom cxxstd=" + _std)
 
-    depends_on("vecgeom +cuda cuda_arch=none", when="+vecgeom +cuda cuda_arch=none")
     for _arch in CudaPackage.cuda_arch_values:
-        depends_on(f"vecgeom +cuda cuda_arch={_arch}", when=f"+vecgeom +cuda cuda_arch={_arch}")
+        depends_on("vecgeom+cuda cuda_arch=" + _arch, when="+vecgeom +cuda cuda_arch=" + _arch)
 
     conflicts("+rocm", when="+cuda", msg="AMD and NVIDIA accelerators are incompatible")
     conflicts("+rocm", when="+vecgeom", msg="HIP support is only available with ORANGE")
@@ -121,7 +111,7 @@ def cmake_args(self):
             from_variant("CELERITAS_BUILD_DOCS", "doc"),
             define("CELERITAS_BUILD_DEMOS", False),
             define("CELERITAS_BUILD_TESTS", False),
-            from_variant("CELERITAS_USE_HIP", "rocm"),
+            from_variant("Celeritas_USE_HIP", "rocm"),
             define("CELERITAS_USE_MPI", False),
             define("CELERITAS_USE_Python", True),
         ]
@@ -129,22 +119,6 @@ def cmake_args(self):
         for pkg in ["CUDA", "Geant4", "HepMC3", "OpenMP", "ROOT", "SWIG", "VecGeom"]:
             args.append(from_variant("CELERITAS_USE_" + pkg, pkg.lower()))
 
-        if self.spec.satisfies("+cuda"):
-            args.append(CMakeBuilder.define_cuda_architectures(self))
-        if self.spec.satisfies("+rocm"):
-            args.append(CMakeBuilder.define_hip_architectures(self))
-            args.append(
-                define(
-                    "CMAKE_HIP_FLAGS",
-                    " ".join(
-                        [
-                            f"-I{self.spec[p].prefix.include}"
-                            for p in ["hiprand", "rocprim", "rocrand", "rocthrust"]
-                        ]
-                    ),
-                )
-            )
-
         if self.version < Version("0.5"):
             # JSON is required for 0.5 and later
             args.append(define("CELERITAS_USE_JSON", True))

var/spack/repos/builtin/packages/clingo-bootstrap/package.py

@@ -92,9 +92,9 @@ def pgo_train(self):
 
         # Set PGO training flags.
         generate_mods = EnvironmentModifications()
-        generate_mods.append_flags("CFLAGS", f"-fprofile-generate={reports}")
-        generate_mods.append_flags("CXXFLAGS", f"-fprofile-generate={reports}")
-        generate_mods.append_flags("LDFLAGS", f"-fprofile-generate={reports}")
+        generate_mods.append_flags("CFLAGS", "-fprofile-generate={}".format(reports))
+        generate_mods.append_flags("CXXFLAGS", "-fprofile-generate={}".format(reports))
+        generate_mods.append_flags("LDFLAGS", "-fprofile-generate={} --verbose".format(reports))
 
         with working_dir(self.build_directory, create=True):
             cmake(*cmake_options, sources, extra_env=generate_mods)
@@ -118,14 +118,14 @@ def pgo_train(self):
         # Clean the build dir.
         rmtree(self.build_directory, ignore_errors=True)
 
-        if self.spec.satisfies("%clang") or self.spec.satisfies("%apple-clang"):
+        if self.spec.satisfies("%clang") or self.spec.satisfies("apple-clang"):
             # merge reports
             use_report = join_path(reports, "merged.prof")
             raw_files = glob.glob(join_path(reports, "*.profraw"))
-            llvm_profdata("merge", f"--output={use_report}", *raw_files)
-            use_flag = f"-fprofile-instr-use={use_report}"
+            llvm_profdata("merge", "--output={}".format(use_report), *raw_files)
+            use_flag = "-fprofile-instr-use={}".format(use_report)
         else:
-            use_flag = f"-fprofile-use={reports}"
+            use_flag = "-fprofile-use={}".format(reports)
 
         # Set PGO use flags for next cmake phase.
         use_mods = EnvironmentModifications()

var/spack/repos/builtin/packages/code-server/package.py

@@ -12,11 +12,58 @@ class CodeServer(Package):
     homepage = "https://coder.com/docs/code-server/latest"
     url = "https://github.com/coder/code-server/releases/download/v4.4.0/code-server-4.4.0-linux-amd64.tar.gz"
 
-    version("4.96.4", sha256="b3f9025d00f2cdf61caf83945ef7225d4a3eb576c4c007e45868f45713e39c8e")
+    version("4.12.0", sha256="d50ee947c4144a6ff2656e664ecbb3f70b75168b8a6e8c3eef47787f3c240c26")
+    version("4.11.0", sha256="4eb233054941ec298caec6fc84dfba0a72c1bc5fadc0fe4896b10f3f4a291d51")
+    version("4.10.1", sha256="f34ce611a9c058982a5e9d200fdf009788e3a564e970b053f4145574bce21b09")
+    version("4.4.0", sha256="e3dd265acb18c2230c72d19bbce619ac5c1bd800ebb26e5e169c4d613069500d")
+    version("4.3.0", sha256="42c71e98de85270b164b023ef8eb0692cf7700c03081ba5a44eaca014a92eb57")
+    version("4.2.0", sha256="98be5bc43ac604c49ae11da259e318b581757a59a25edeee5cf55317ca589ec6")
+    version("4.1.0", sha256="f720b20d1f615b78f3a1be9b1614f3d99ed722b8da3047a4143dbe5835e52ce3")
+    version("4.0.2", sha256="68c11afa3288707a6880920013d8bac7404cd590eb4f63cac92979d0b0bf4fd1")
+    version("4.0.1", sha256="5fe6d26e9d19e685946f0f392d9c822e5303a800cac3ac54a6a2c26104d239fd")
+    version("3.12.0", sha256="d3ca41a55e36d73d80300702af2687e25d440cff6b613bb58a2c88d9b8a0a38f")
+    version("3.11.1", sha256="d34b0b79582196d59d44ac971aabb7f15cb05d837318b94f62470dc8475665e9")
+    version("3.11.0", sha256="dddb97f044ed615a4b8a526328fca6ad703b9c671a28a6090d84668a18755589")
+    version("3.10.2", sha256="47154a6b9e61a0313ba499dd5d948613a17841c2f580612f9721c31964622bf5")
+    version("3.10.1", sha256="18175624df78976488dbcc2a26f2582a71cef5ca0a419e691b1b70da0b27c7ef")
+    version("3.10.0", sha256="5dfce848747f3dd5074cba435cca6730ac99d6d3aa3f50e0a9bf222ad12d3e97")
+    version("3.9.3", sha256="eba42eaf868c2144795b1ac54929e3b252ae35403bf8553b3412a5ac4f365a41")
+    version("3.9.2", sha256="5dbda5ac598223006f72bcb700b133a752aabe4468ed8105806d1d69b5364408")
+    version("3.9.1", sha256="f2648a4387c5a5be8666fb82a7b8a58274c45b91942251ab337e202e078ae8a5")
+    version("3.9.0", sha256="229b0fb95d78a7f7ff0dd55bc151a7521fcd699af50151faf67f6c7ce51110f4")
+    version("3.8.1", sha256="130cf94e3921d0e2adfa33e875bf1aa81fd28548aac94fd31fbc589baa68d45f")
+    version("3.8.0", sha256="70b069f26b30c38cca5fa07b5f25db4d15976de80af3a644b9105d1b5e23e7d5")
+    version("3.7.4", sha256="01ca0e48df44df70cdf702644b013102024a5b30edf6c1fbb2e10b0310056382")
+    version("3.7.3", sha256="7a90f3171c9bc6f65266066e35cc34d48a032910c136ea21116d28f3d7214547")
+    version("3.7.2", sha256="c3054f214392b1b2eb4c77c57cb950ac5d733d349a426975e8bf32028e65a226")
+    version("3.7.1", sha256="bebd9e0c46e0fd4b4f295fd91fc2db135a694614db972095e9842bf7969f4cee")
+    version("3.7.0", sha256="5f8df8ed3924e8e594674d73fb50b00a06efa529f96a0495a5ee8c39c68f3ce1")
+    version("3.6.2", sha256="fd4ac7d61f3e1b2a5034f1706e409c77fad299adef0ede204828d8ecfe317e45")
+    version("3.6.1", sha256="bbe4ef9585e093b3521deb34a0820d2136172271862d6396df21c2e9a26c6374")
+    version("3.6.0", sha256="d1ae4f7263741e0551358d3ed77dad587b33b352d827623d4df25e98f9e21019")
+    version("3.5.0", sha256="90c19c84611becac4af1fb0bd5324ab30f9200769fa7914cd10ccb6b88c657bb")
+    version("3.4.1", sha256="afdb89f4dc7201c03cb35d4f8dc1ccb6060bd0da324a6789089de264d3406817")
+    version("3.4.0", sha256="918c28696b73b96dc9361977f93e788d5c8884b5d4a088d206f05d5b8bccb738")
+    version("3.3.1", sha256="57b9855b20f511e22776ee8a53d1ff30f864498814c4c0b0af3510f71d7a2969")
+    version("3.3.0", sha256="6ca5148a447b41753d5151c5a49a8af24122c7b0808609782aec454e66be4f2c")
+    version("3.2.0", sha256="a8157e8766d6a0e255c72db25e8677a57adb8d889d653e78750b4d26a6ff7400")
+    version("3.1.1", sha256="5dd922d28b2e351c146081849d987fb1e439ee7d53b941434b2eecb2a194da71")
+    version("3.1.0", sha256="5ef85c8f280ce781a176a8b77386b333efe892755a5c325a1782e4eac6016e59")
+    version("3.0.2", sha256="04367cfeb23991f3dc3f1ef8e3dfe5e9d683bb50c9e1fa69e3c21757facfd7ee")
 
     depends_on("c", type="build")  # generated
     depends_on("cxx", type="build")  # generated
 
+    def url_for_version(self, version):
+        if version <= Version("3.2.0"):
+            return "https://github.com/coder/code-server/releases/download/{0}/code-server-{0}-linux-x86_64.tar.gz".format(
+                version
+            )
+        else:
+            return "https://github.com/coder/code-server/releases/download/v{0}/code-server-{0}-linux-amd64.tar.gz".format(
+                version
+            )
+
     def install(self, spec, prefix):
         install_tree(".", prefix)
 

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

@@ -18,8 +18,7 @@ class Cpuinfo(CMakePackage):
     license("BSD-2-Clause")
 
     version("main", branch="main")
-    version("2024-09-26", commit="1e83a2fdd3102f65c6f1fb602c1b320486218a99")  # py-torch@2.6:
-    version("2024-09-06", commit="094fc30b9256f54dad5ad23bcbfb5de74781422f")  # py-torch@2.5.1
+    version("2024-09-06", commit="094fc30b9256f54dad5ad23bcbfb5de74781422f")  # py-torch@2.5.1:
     version("2024-08-30", commit="fa1c679da8d19e1d87f20175ae1ec10995cd3dd3")  # py-torch@2.5.0
     version("2023-11-04", commit="d6860c477c99f1fce9e28eb206891af3c0e1a1d7")  # py-torch@2.3:2.4
     version("2023-01-13", commit="6481e8bef08f606ddd627e4d3be89f64d62e1b8a")  # py-torch@2.1:2.2

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

@@ -25,7 +25,6 @@ class Dcap(AutotoolsPackage):
     depends_on("m4", type="build")
 
     depends_on("openssl")
-    depends_on("libxcrypt")
     depends_on("zlib-api")
 
     variant("plugins", default=True, description="Build plugins")

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

@@ -25,7 +25,6 @@ class Dd4hep(CMakePackage):
     license("LGPL-3.0-or-later")
 
     version("master", branch="master")
-    version("1.31", sha256="9c06a1b4462fc1b51161404889c74b37350162d0b0ac2154db27e3f102670bd1")
     version("1.30", sha256="02de46151e945eff58cffd84b4b86d35051f4436608199c3efb4d2e1183889fe")
     version("1.29", sha256="435d25a7ef093d8bf660f288b5a89b98556b4c1c293c55b93bf641fb4cba77e9")
     version("1.28", sha256="b28d671eda0154073873a044a384486e66f1f200065deca99537aa84f07328ad")
@@ -119,16 +118,13 @@ class Dd4hep(CMakePackage):
     depends_on("tbb", when="+tbb")
     depends_on("intel-tbb@:2020.3", when="+tbb @:1.23")
     depends_on("lcio", when="+lcio")
+    depends_on("edm4hep", when="+edm4hep")
+    depends_on("podio", when="+edm4hep")
+    depends_on("podio@:0.16.03", when="@:1.23 +edm4hep")
+    depends_on("podio@0.16:", when="@1.24: +edm4hep")
+    depends_on("podio@0.16.3:", when="@1.26: +edm4hep")
+    depends_on("podio@:0", when="@:1.29 +edm4hep")
     depends_on("py-pytest", type=("build", "test"))
-    with when("+edm4hep"):
-        depends_on("edm4hep")
-        depends_on("edm4hep@0.10.5:", when="@1.31:")
-        depends_on("podio")
-        depends_on("podio@:0.16.03", when="@:1.23")
-        depends_on("podio@:0", when="@:1.29")
-        depends_on("podio@0.16:", when="@1.24:")
-        depends_on("podio@0.16.3:", when="@1.26:")
-        depends_on("podio@0.16.7:", when="@1.31:")
 
     # See https://github.com/AIDASoft/DD4hep/pull/771 and https://github.com/AIDASoft/DD4hep/pull/876
     conflicts(

var/spack/repos/builtin/packages/dla-future-fortran/package.py

@@ -20,7 +20,6 @@ class DlaFutureFortran(CMakePackage):
     license("BSD-3-Clause")
 
     version("main", branch="main")
-    version("0.3.0", sha256="404ce0d2d3df9317764450158901fd6cb2198b37f5687e9616519100ad6e9ece")
     version("0.2.0", sha256="7fd3e1779c111b35f0d2701a024398b4f6e8dea4af523b6c8617d28c0b7ae61a")
     version("0.1.0", sha256="9fd8a105cbb2f3e1daf8a49910f98fce68ca0b954773dba98a91464cf2e7c1da")
 
@@ -37,7 +36,6 @@ class DlaFutureFortran(CMakePackage):
 
     depends_on("dla-future@0.4.1:0.5 +scalapack", when="@0.1.0")
     depends_on("dla-future@0.6.0: +scalapack", when="@0.2.0:")
-    depends_on("dla-future@0.7.3: +scalapack", when="@0.3:")
     depends_on("dla-future +shared", when="+shared")
 
     depends_on("mpi", when="+test")

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

@@ -33,30 +33,60 @@ class Dyninst(CMakePackage):
     version("10.2.1", sha256="8077c6c7a12577d2ffdcd07521c1eb1b7367da94d9a7ef10bf14053aeaae7ba1")
     version("10.2.0", sha256="4212b93bef4563c7de7dce4258e899bcde52315a571087e87fde9f8040123b43")
     version("10.1.0", sha256="4a121d70c1bb020408a7a697d74602e18250c3c85800f230566fcccd593c0129")
+    version("10.0.0", sha256="542fccf5c57c4fe784b1a9a9e3db01d40b16ad04e7174dc6f7eb23440485ba06")
+    version(
+        "9.3.2", tag="v9.3.2", commit="5d2ddacb273682daa014ae22f17f3575e05b411e", deprecated=True
+    )
+    version(
+        "9.3.0", tag="v9.3.0", commit="9b8e9c1f16d4616b827d2d36955604a8e3fb915c", deprecated=True
+    )
+    version(
+        "9.2.0", tag="v9.2.0", commit="3a6ad66df7294417cf61618acdcfcc0fecccb045", deprecated=True
+    )
+    version(
+        "9.1.0", tag="v9.1.0", commit="df6d090061bae7ff2ba5a6bd57bb2ecbf538ef7a", deprecated=True
+    )
+    version(
+        "8.2.1", tag="v8.2.1", commit="939afcbad1a8273636a3686a31b51dae4f1f0c11", deprecated=True
+    )
 
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
+    depends_on("c", type="build")  # generated
+    depends_on("cxx", type="build")  # generated
 
-    variant("openmp", default=True, description="Enable OpenMP support for ParseAPI ")
+    variant(
+        "openmp",
+        default=True,
+        description="Enable OpenMP support for ParseAPI " "(version 10.0.0 or later)",
+    )
 
     variant("static", default=False, description="Build static libraries")
 
     variant("stat_dysect", default=False, description="Patch for STAT's DySectAPI")
 
-    depends_on(
-        "boost+atomic+chrono+date_time+filesystem+system+thread+timer+container+random+exception"
+    boost_libs = (
+        "+atomic+chrono+date_time+filesystem+system+thread+timer+container+random+exception"
     )
-    depends_on("boost@1.61.0:", when="@10.1.0:")
-    depends_on("boost@1.67.0:", when="@11.0.0:")
-    depends_on("boost@1.70.0:", when="@12:12.3.0")
-    depends_on("boost@1.71.0:", when="@13:")
+
+    depends_on("boost@1.61.0:" + boost_libs, when="@10.1.0:")
+    depends_on("boost@1.61.0:1.69" + boost_libs, when="@:10.0")
+    depends_on("boost@1.67.0:" + boost_libs, when="@11.0.0:")
+    depends_on("boost@1.70.0:" + boost_libs, when="@12:12.3.0")
+    depends_on("boost@1.71.0:" + boost_libs, when="@13:")
 
     depends_on("libiberty+pic")
 
-    # Parallel DWARF parsing requires a thread-safe libdw
-    depends_on("elfutils", type="link")
+    # Dyninst uses elfutils starting with 9.3.0, and used libelf
+    # before that.
+    # NB: Parallel DWARF parsing in Dyninst 10.2.0 requires a thread-
+    #     safe libdw
     depends_on("elfutils@0.186:", type="link", when="@12.0.1:")
     depends_on("elfutils@0.178:", type="link", when="@10.2.0:")
+    depends_on("elfutils", type="link", when="@9.3.0:10.1")
+    depends_on("libelf", type="link", when="@:9.2")
+
+    # Dyninst uses libdw from elfutils starting with 10.0, and used
+    # libdwarf before that.
+    depends_on("libdwarf", when="@:9")
 
     with when("@:12.3.0"):
         # findtbb.cmake in the dynist repo does not work with recent tbb
@@ -65,16 +95,21 @@ class Dyninst(CMakePackage):
         conflicts("^intel-oneapi-tbb@2021.1:")
         conflicts("^intel-parallel-studio")
 
-    depends_on("tbb")
-    requires("^[virtuals=tbb] intel-tbb@2019.9:", when="@13.0.0:")
+    depends_on("intel-tbb@2019.9:", when="@13.0.0:")
+    depends_on("tbb@2018.6.0:", when="@10.0.0:12.3.0")
 
     with when("@13.0.0:"):
         depends_on("cmake@3.14.0:", type="build")
         conflicts("cmake@3.19.0")
 
     depends_on("cmake@3.4.0:", type="build", when="@10.1.0:")
+    depends_on("cmake@3.0.0:", type="build", when="@10.0.0:10.0")
+    depends_on("cmake@2.8:", type="build", when="@:9")
 
     patch("stat_dysect.patch", when="+stat_dysect")
+    patch("stackanalysis_h.patch", when="@9.2.0")
+    patch("v9.3.2-auto.patch", when="@9.3.2 %gcc@:4.7")
+    patch("tribool.patch", when="@9.3.0:10.0.0 ^boost@1.69:")
     patch(
         "missing_include_deque.patch",
         when="@10.0.0:12.2.0",
@@ -89,21 +124,92 @@ class Dyninst(CMakePackage):
     # Version 11.0 requires a C++11-compliant ABI
     conflicts("%gcc@:5", when="@11.0.0:")
 
+    # Versions 9.3.x used cotire, but have no knob to turn it off.
+    # Cotire has no real use for one-time builds and can break
+    # parallel builds with both static and shared libs.
+    @when("@9.3.0:9.3")
+    def patch(self):
+        filter_file("USE_COTIRE true", "USE_COTIRE false", "cmake/shared.cmake")
+
+    # New style cmake args, starting with 10.1.
+    @when("@10.1.0:")
     def cmake_args(self):
         spec = self.spec
+
         args = [
-            self.define("Boost_ROOT_DIR", spec["boost"].prefix),
-            self.define("ElfUtils_ROOT_DIR", spec["elfutils"].prefix),
-            self.define("LibIberty_ROOT_DIR", spec["libiberty"].prefix),
-            self.define("TBB_ROOT_DIR", spec["tbb"].prefix),
+            "-DBoost_ROOT_DIR=%s" % spec["boost"].prefix,
+            "-DElfUtils_ROOT_DIR=%s" % spec["elf"].prefix,
+            "-DLibIberty_ROOT_DIR=%s" % spec["libiberty"].prefix,
+            "-DTBB_ROOT_DIR=%s" % spec["tbb"].prefix,
             self.define("LibIberty_LIBRARIES", spec["libiberty"].libs),
-            self.define_from_variant("USE_OpenMP", "openmp"),
-            self.define_from_variant("ENABLE_STATIC_LIBS", "static"),
         ]
 
-        # Make sure Dyninst doesn't try to build its own dependencies outside of Spack
+        if spec.satisfies("+openmp"):
+            args.append("-DUSE_OpenMP=ON")
+        else:
+            args.append("-DUSE_OpenMP=OFF")
+
+        if spec.satisfies("+static"):
+            args.append("-DENABLE_STATIC_LIBS=YES")
+        else:
+            args.append("-DENABLE_STATIC_LIBS=NO")
+
+        # Make sure Dyninst doesn't try to build its own dependencies
+        # outside of Spack
         if spec.satisfies("@10.2.0:12.3.0"):
-            args.append(self.define("STERILE_BUILD", True))
+            args.append("-DSTERILE_BUILD=ON")
+
+        return args
+
+    # Old style cmake args, up through 10.0.
+    @when("@:10.0")
+    def cmake_args(self):
+        spec = self.spec
+
+        # Elf -- the directory containing libelf.h.
+        elf = spec["elf"].prefix
+        elf_include = os.path.dirname(find_headers("libelf", elf.include, recursive=True)[0])
+
+        # Dwarf -- the directory containing elfutils/libdw.h or
+        # libdwarf.h, and the path to libdw.so or libdwarf.so.
+        if spec.satisfies("@10.0.0:"):
+            dwarf_include = elf.include
+            dwarf_lib = find_libraries("libdw", elf, recursive=True)
+        else:
+            dwarf_include = spec["libdwarf"].prefix.include
+            dwarf_lib = spec["libdwarf"].libs
+
+        args = [
+            "-DPATH_BOOST=%s" % spec["boost"].prefix,
+            "-DIBERTY_LIBRARIES=%s" % spec["libiberty"].libs,
+            "-DLIBELF_INCLUDE_DIR=%s" % elf_include,
+            "-DLIBELF_LIBRARIES=%s" % spec["elf"].libs,
+            "-DLIBDWARF_INCLUDE_DIR=%s" % dwarf_include,
+            "-DLIBDWARF_LIBRARIES=%s" % dwarf_lib,
+        ]
+
+        # TBB include and lib directories, version 10.x or later.
+        if spec.satisfies("@10.0.0:"):
+            args.extend(
+                [
+                    "-DTBB_INCLUDE_DIRS=%s" % spec["tbb"].prefix.include,
+                    "-DTBB_LIBRARY=%s" % spec["tbb"].prefix.lib,
+                ]
+            )
+
+        # Openmp applies to version 10.x or later.
+        if spec.satisfies("@10.0.0:"):
+            if spec.satisfies("+openmp"):
+                args.append("-DUSE_OpenMP=ON")
+            else:
+                args.append("-DUSE_OpenMP=OFF")
+
+        # Static libs started with version 9.1.0.
+        if spec.satisfies("@9.1.0:"):
+            if spec.satisfies("+static"):
+                args.append("-DENABLE_STATIC_LIBS=1")
+            else:
+                args.append("-DENABLE_STATIC_LIBS=NO")
 
         return args
 

var/spack/repos/builtin/packages/dyninst/stackanalysis_h.patch

@@ -0,0 +1,11 @@
+--- a/dataflowAPI/h/stackanalysis.h	2016-06-29 14:54:14.000000000 -0700
++++ b/dataflowAPI/h/stackanalysis.h	2016-08-02 09:50:13.619079000 -0700
+@@ -331,7 +331,7 @@
+ 
+    // To build intervals, we must replay the effect of each instruction.
+    // To avoid sucking enormous time, we keep those transfer functions around...
+-   typedef std::map<ParseAPI::Block *, std::map<Offset, TransferFuncs>>
++   typedef std::map<ParseAPI::Block *, std::map<Offset, TransferFuncs> >
+       InstructionEffects;
+ 
+    DATAFLOW_EXPORT StackAnalysis();

var/spack/repos/builtin/packages/dyninst/tribool.patch

@@ -0,0 +1,34 @@
+Add explicit casts from boost::tribool to bool.  Starting with 1.69,
+tribool added 'explicit' to the conversion operator to bool, and this
+was breaking the build when using boost >= 1.69.
+
+Patch is from:  https://github.com/dyninst/dyninst/commit/54a2debd9
+
+
+diff --git a/dataflowAPI/rose/util/Message.C b/dataflowAPI/rose/util/Message.C
+index a8a66ad4c..5e276f97d 100644
+--- a/dataflowAPI/rose/util/Message.C
++++ b/dataflowAPI/rose/util/Message.C
+@@ -1123,7 +1123,7 @@ StreamBuf::bake() {
+         destination_->bakeDestinations(message_.properties(), baked_/*out*/);
+         anyUnbuffered_ = false;
+         for (BakedDestinations::const_iterator bi=baked_.begin(); bi!=baked_.end() && !anyUnbuffered_; ++bi)
+-            anyUnbuffered_ = !bi->second.isBuffered;
++            anyUnbuffered_ = static_cast<bool>(!bi->second.isBuffered);
+         isBaked_ = true;
+     }
+ }
+diff --git a/dataflowAPI/rose/util/Message.h b/dataflowAPI/rose/util/Message.h
+index 816f68d2e..03592cb97 100644
+--- a/dataflowAPI/rose/util/Message.h
++++ b/dataflowAPI/rose/util/Message.h
+@@ -386,7 +386,8 @@ struct SAWYER_EXPORT ColorSpec {
+     ColorSpec(AnsiColor fg, AnsiColor bg, bool bold): foreground(fg), background(bg), bold(bold) {}
+ 
+     /** Returns true if this object is in its default-constructed state. */
+-    bool isDefault() const { return COLOR_DEFAULT==foreground && COLOR_DEFAULT==background && !bold; }
++    bool isDefault() const { return COLOR_DEFAULT==foreground && COLOR_DEFAULT==background
++                                    && static_cast<bool>(!bold); }
+ };
+ 
+ /** Colors to use for each message importance.

var/spack/repos/builtin/packages/dyninst/v9.3.2-auto.patch

@@ -0,0 +1,73 @@
+Change some 'for (const auto& t: type)' usage to the older but
+equivalent 'for (auto t = type.begin(); ...)'.  This patch allows
+dyninst 9.3.2 to build with gcc 4.4 which doesn't support the newer
+syntax.
+
+
+diff --git a/dyninstAPI/src/BPatch.C b/dyninstAPI/src/BPatch.C
+index ebf7db0c4..49fe69f9a 100644
+--- a/dyninstAPI/src/BPatch.C
++++ b/dyninstAPI/src/BPatch.C
+@@ -166,16 +166,16 @@ BPatch::BPatch()
+     stdTypes = BPatch_typeCollection::getGlobalTypeCollection();
+     vector<Type *> *sTypes = Symtab::getAllstdTypes();
+     BPatch_type* type = NULL;
+-    for(const auto& t: *sTypes) {
+-        stdTypes->addType(type = new BPatch_type(t));
++    for(auto t = sTypes->begin(); t != sTypes->end(); ++t) {
++        stdTypes->addType(type = new BPatch_type(*t));
+         type->decrRefCount();
+     }
+     delete sTypes;
+ 
+     builtInTypes = new BPatch_builtInTypeCollection;
+     sTypes = Symtab::getAllbuiltInTypes();
+-    for(const auto& t: *sTypes) {
+-        builtInTypes->addBuiltInType(type = new BPatch_type(t));
++    for(auto t = sTypes->begin(); t != sTypes->end(); ++t) {
++        builtInTypes->addBuiltInType(type = new BPatch_type(*t));
+         type->decrRefCount();
+     }
+     delete sTypes;
+diff --git a/dyninstAPI/src/BPatch_collections.C b/dyninstAPI/src/BPatch_collections.C
+index f4e2986a3..129f8b74a 100644
+--- a/dyninstAPI/src/BPatch_collections.C
++++ b/dyninstAPI/src/BPatch_collections.C
+@@ -172,12 +172,12 @@ BPatch_typeCollection::~BPatch_typeCollection()
+     assert(refcount == 0 ||
+            refcount == 1);
+ 
+-    for(const auto& t: typesByName) {
+-        t.second->decrRefCount();
++    for(auto t = typesByName.begin(); t != typesByName.end(); ++t) {
++        t->second->decrRefCount();
+     }
+ 
+-    for(const auto& t: typesByID) {
+-        t.second->decrRefCount();
++    for(auto t = typesByID.begin(); t != typesByID.end(); ++t) {
++        t->second->decrRefCount();
+     }
+ }
+ 
+diff --git a/symtabAPI/src/Collections.C b/symtabAPI/src/Collections.C
+index 7431dd6bf..43c339f45 100644
+--- a/symtabAPI/src/Collections.C
++++ b/symtabAPI/src/Collections.C
+@@ -318,12 +318,12 @@ typeCollection::typeCollection() :
+ typeCollection::~typeCollection()
+ {
+     // delete all of the types
+-    for(const auto& t: typesByName) {
+-        t.second->decrRefCount();
++    for(auto t = typesByName.begin(); t != typesByName.end(); ++t) {
++        t->second->decrRefCount();
+     }
+ 
+-    for(const auto& t: typesByID) {
+-        t.second->decrRefCount();
++    for(auto t = typesByID.begin(); t != typesByID.end(); ++t) {
++        t->second->decrRefCount();
+     }
+ }
+ 

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

@@ -14,7 +14,7 @@ class Enzyme(CMakePackage):
     """
 
     homepage = "https://enzyme.mit.edu"
-    url = "https://github.com/wsmoses/Enzyme/archive/v0.0.172.tar.gz"
+    url = "https://github.com/wsmoses/Enzyme/archive/v0.0.15.tar.gz"
     list_url = "https://github.com/wsmoses/Enzyme/releases"
     git = "https://github.com/wsmoses/Enzyme"
 
@@ -23,7 +23,6 @@ class Enzyme(CMakePackage):
     root_cmakelists_dir = "enzyme"
 
     version("main", branch="main")
-    version("0.0.172", sha256="688200164787d543641cb446cff20f6a8e8b5c92bb7032ebe7f867efa67ceafb")
     version("0.0.135", sha256="49c798534faec7ba524a3ed053dd4352d690a44d3cad5a14915c9398dc9b175b")
     version("0.0.100", sha256="fbc53ec02adc0303ff200d7699afface2d9fbc7350664e6c6d4c527ef11c2e82")
     version("0.0.81", sha256="4c17d0c28f0572a3ab97a60f1e56bbc045ed5dd64c2daac53ae34371ca5e8b34")
@@ -43,8 +42,7 @@ class Enzyme(CMakePackage):
     depends_on("llvm@7:14", when="@0.0.48:0.0.68")
     depends_on("llvm@9:16", when="@0.0.69:0.0.79")
     depends_on("llvm@11:16", when="@0.0.80:0.0.99")
-    depends_on("llvm@11:19", when="@0.0.100:0.0.148")
-    depends_on("llvm@15:19", when="@0.0.149:")
+    depends_on("llvm@11:19", when="@0.0.100:")
     depends_on("cmake@3.13:", type="build")
 
     def cmake_args(self):

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

@@ -20,16 +20,12 @@ class Flecsi(CMakePackage, CudaPackage, ROCmPackage):
 
     tags = ["e4s"]
 
-    version("2.3.1", tag="v2.3.1", commit="6c04b9b21790533e457764bd7f8f26757db1552f")
+    version("develop", branch="develop", deprecated=True)
     version("2.3.0", tag="v2.3.0", commit="90bc8267fceb02060e54646f73b45d4252aef491")
     version("2.2.1", tag="v2.2.1", commit="84b5b232aebab40610f57387778db80f6c8c84c5")
     version("2.2.0", tag="v2.2.0", commit="dd531ac16c5df124d76e385c6ebe9b9589c2d3ad")
-    version(
-        "2.1.0", tag="v2.1.0", commit="533df139c267e2a93c268dfe68f9aec55de11cf0", deprecated=True
-    )
-    version(
-        "2.0.0", tag="v2.0.0", commit="5ceebadf75d1c98999ea9e9446926722d061ec22", deprecated=True
-    )
+    version("2.1.0", tag="v2.1.0", commit="533df139c267e2a93c268dfe68f9aec55de11cf0")
+    version("2.0.0", tag="v2.0.0", commit="5ceebadf75d1c98999ea9e9446926722d061ec22")
 
     variant(
         "backend",
@@ -50,8 +46,8 @@ class Flecsi(CMakePackage, CudaPackage, ROCmPackage):
         description="Set Caliper Profiling Detail",
         multi=False,
     )
-    variant("kokkos", default=False, description="Enable Kokkos Support", when="@:2.3.1")
-    variant("openmp", default=False, description="Enable OpenMP Support", when="@:2.3.1")
+    variant("kokkos", default=False, description="Enable Kokkos Support")
+    variant("openmp", default=False, description="Enable OpenMP Support")
 
     depends_on("c", type="build")
     depends_on("cxx", type="build")
@@ -73,22 +69,18 @@ class Flecsi(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("boost@1.79.0:", when="@2.2:")
     depends_on("kokkos@3.2.00:", when="+kokkos")
     depends_on("kokkos@3.7:", when="+kokkos @2.3:")
-    depends_on("kokkos@3.7:", when="@2.4:")
-    depends_on("kokkos +cuda", when="+kokkos +cuda")
-    requires("^kokkos +cuda_constexpr +cuda_lambda", when="^kokkos +cuda")
+    depends_on("kokkos +cuda +cuda_constexpr +cuda_lambda", when="+kokkos +cuda")
     depends_on("kokkos +rocm", when="+kokkos +rocm")
     depends_on("kokkos +openmp", when="+kokkos +openmp")
-    requires("+openmp", when="@:2.3.1 ^kokkos +openmp")
-    depends_on("legion@cr-20210122", when="backend=legion @2.0:2.1.0")
+    depends_on("legion@cr-20210122", when="backend=legion @2.0:2.2.1")
     depends_on("legion@cr-20230307", when="backend=legion @2.2.0:2.2.1")
     depends_on("legion@24.03.0:", when="backend=legion @2.2.2:")
-    depends_on("legion@24.09.0:", when="backend=legion @2.3.1:")
     depends_on("legion+shared", when="backend=legion +shared")
     depends_on("legion+hdf5", when="backend=legion +hdf5")
-    depends_on("legion+kokkos", when="backend=legion ^kokkos")
-    depends_on("legion+openmp", when="backend=legion ^kokkos+openmp")
-    depends_on("legion+cuda", when="backend=legion ^kokkos+cuda")
-    depends_on("legion+rocm", when="backend=legion ^kokkos+rocm")
+    depends_on("legion+kokkos", when="backend=legion +kokkos")
+    depends_on("legion+openmp", when="backend=legion +openmp")
+    depends_on("legion+cuda", when="backend=legion +cuda")
+    depends_on("legion+rocm", when="backend=legion +rocm")
     depends_on("hdf5@1.10.7:", when="backend=legion +hdf5")
     depends_on("hpx@1.10.0: cxxstd=17 malloc=system", when="backend=hpx")
     depends_on("mpi")
@@ -105,13 +97,11 @@ class Flecsi(CMakePackage, CudaPackage, ROCmPackage):
 
     # Propagate cuda_arch requirement to dependencies
     for _flag in CudaPackage.cuda_arch_values:
-        requires(f"+cuda cuda_arch={_flag}", when=f"^kokkos +cuda cuda_arch={_flag}")
         depends_on(f"kokkos cuda_arch={_flag}", when=f"+cuda+kokkos cuda_arch={_flag}")
         depends_on(f"legion cuda_arch={_flag}", when=f"backend=legion +cuda cuda_arch={_flag}")
 
     # Propagate amdgpu_target requirement to dependencies
     for _flag in ROCmPackage.amdgpu_targets:
-        requires(f"+rocm amdgpu_target={_flag}", when=f"^kokkos +rocm amdgpu_target={_flag}")
         depends_on(f"kokkos amdgpu_target={_flag}", when=f"+kokkos +rocm amdgpu_target={_flag}")
         depends_on(
             f"legion amdgpu_target={_flag}", when=f"backend=legion +rocm amdgpu_target={_flag}"
@@ -140,13 +130,13 @@ def cmake_args(self):
                 self.define_from_variant("ENABLE_DOCUMENTATION", "doc"),
             ]
 
-            if self.spec.satisfies("^kokkos +rocm"):
+            if self.spec.satisfies("+rocm"):
                 options.append(self.define("CMAKE_CXX_COMPILER", self.spec["hip"].hipcc))
                 options.append(self.define("CMAKE_C_COMPILER", self.spec["hip"].hipcc))
                 if self.spec.satisfies("backend=legion"):
                     # CMake pulled in via find_package(Legion) won't work without this
                     options.append(self.define("HIP_PATH", "{0}/hip".format(spec["hip"].prefix)))
-            elif self.spec.satisfies("^kokkos"):
+            elif self.spec.satisfies("+kokkos"):
                 options.append(self.define("CMAKE_CXX_COMPILER", self.spec["kokkos"].kokkos_cxx))
         else:
             # kept for supporing version prior to 2.2

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

@@ -18,8 +18,6 @@ class Fms(CMakePackage):
     license("LGPL-3.0-or-later")
 
     maintainers("AlexanderRichert-NOAA", "Hang-Lei-NOAA", "edwardhartnett", "rem1776", "climbfuji")
-    version("2025.01", sha256="19997ef5468a06c60c1e7af3a56ab7f8a33da814a30827293ca34df5bd888d6f")
-    version("2024.03", sha256="4c1e6bdfafcfec19a4a1c08770c313ab3135d47ec8319f6b07f24d2589caf44d")
     version("2024.02", sha256="47e5740bb066f5eb032e1de163eb762c7258880a2932f4cc4e34e769e0cc2b0e")
     version(
         "2024.01.01", sha256="41c8686bad2b1aed76275e35cbe1af855f7dfce9b6d8907744ea2e8174758f6a"
@@ -66,13 +64,6 @@ class Fms(CMakePackage):
         when="@2023.03",
     )
 
-    variant(
-        "portable_kinds",
-        description="Use iso_c_binding variable kinds",
-        when="@2025.01:",
-        default=False,
-    )
-
     variant("shared", description="Build shared libraries", when="@2024.02:", default=False)
     # What the following patch is providing is available in version 2024.03
     # and newer so it is only needed to 2024.02
@@ -140,7 +131,6 @@ def cmake_args(self):
             self.define_from_variant("OPENMP"),
             self.define_from_variant("ENABLE_QUAD_PRECISION", "quad_precision"),
             self.define_from_variant("SHARED_LIBS", "shared"),
-            self.define_from_variant("PORTABLE_KINDS", "portable_kinds"),
             self.define_from_variant("WITH_YAML", "yaml"),
             self.define_from_variant("CONSTANTS"),
             self.define_from_variant("LARGEFILE", "large_file"),

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

@@ -23,7 +23,6 @@ class Harfbuzz(MesonPackage, AutotoolsPackage):
 
     license("MIT")
 
-    version("10.2.0", sha256="620e3468faec2ea8685d32c46a58469b850ef63040b3565cde05959825b48227")
     version("10.1.0", sha256="6ce3520f2d089a33cef0fc48321334b8e0b72141f6a763719aaaecd2779ecb82")
     version("10.0.1", sha256="b2cb13bd351904cb9038f907dc0dee0ae07127061242fe3556b2795c4e9748fc")
     version("10.0.0", sha256="c2dfe016ad833a5043ecc6579043f04e8e6d50064e02ad449bb466e6431e3e04")

var/spack/repos/builtin/packages/hip-tests/package.py

@@ -1,177 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-
-import os
-
-import spack.build_systems.cmake
-from spack.package import *
-
-
-class HipTests(CMakePackage):
-    """This repository provides unit tests for HIP implementation."""
-
-    homepage = "https://github.com/ROCm/hip-tests"
-    url = "https://github.com/ROCm/hip-tests/archive/refs/tags/rocm-6.1.2.tar.gz"
-    git = "https://github.com/ROCm/hip-tests.git"
-    tags = ["rocm"]
-
-    maintainers("srekolam", "renjithravindrankannath", "afzpatel")
-
-    version("6.3.1", sha256="0fc1cf4f46f2bbef377d65803d86c2489b01b598c468070c79c5114a661f07c6")
-    version("6.3.0", sha256="8081d4ab1a43ffa1cebd646668d83008b799ab98c14daf7b455922355a439c8a")
-    version("6.2.4", sha256="1478b49583d09cb3a96e26ec3bf8dc5ff3e3ec72fa133bb6d7768595d825051e")
-    version("6.2.1", sha256="90fcf0169889533b882d289f9cb8a7baf9bd46a3ce36752b915083931dc839f1")
-    version("6.2.0", sha256="314837dbac78be71844ceb959476470c484fdcd4fb622ff8de9277783e0fcf1c")
-    version("6.1.2", sha256="5b14e4a30d8d8fb56c43e262009646ba9188eac1c8ff882d9a606a4bec69b56b")
-    version("6.1.1", sha256="10c96ee72adf4580056292ab17cfd858a2fd7bc07abeb41c6780bd147b47f7af")
-    version("6.1.0", sha256="cf3a6a7c43116032d933cc3bc88bfc4b17a4ee1513c978e751755ca11a5ed381")
-
-    depends_on("c", type="build")  # generated
-    depends_on("cxx", type="build")  # generated
-    depends_on("cmake", type="run")
-
-    for ver in ["6.1.0", "6.1.1", "6.1.2", "6.2.0", "6.2.1", "6.2.4", "6.3.0", "6.3.1"]:
-        depends_on(f"rocm-cmake@{ver}:", type="build", when=f"@{ver}")
-        depends_on(f"hip@{ver}", when=f"@{ver}")
-        depends_on(f"rocm-core@{ver}", when=f"@{ver}")
-        depends_on(f"rocminfo@{ver}", when=f"@{ver}")
-        depends_on(f"hipify-clang@{ver}", when=f"@{ver}")
-        depends_on(f"llvm-amdgpu@{ver}", when=f"@{ver}")
-
-    root_cmakelists_dir = "catch"
-
-    def patch(self):
-        filter_file(
-            "${ROCM_PATH}/bin/rocm_agent_enumerator",
-            f"{self.spec['rocminfo'].prefix}/bin/rocm_agent_enumerator",
-            "catch/CMakeLists.txt",
-            string=True,
-        )
-        filter_file(
-            "/opt/rocm/bin/rocm_agent_enumerator",
-            f"{self.spec['rocminfo'].prefix}/bin/rocm_agent_enumerator",
-            "catch/hipTestMain/hip_test_context.cc",
-            string=True,
-        )
-        filter_file(
-            "${HIP_PATH}/llvm",
-            self.spec["llvm-amdgpu"].prefix,
-            "samples/2_Cookbook/17_llvm_ir_to_executable/CMakeLists.txt",
-            "samples/2_Cookbook/16_assembly_to_executable/CMakeLists.txt",
-            string=True,
-        )
-        filter_file(
-            "${ROCM_PATH}/llvm",
-            self.spec["llvm-amdgpu"].prefix,
-            "catch/CMakeLists.txt",
-            "samples/2_Cookbook/16_assembly_to_executable/CMakeLists.txt",
-            "samples/2_Cookbook/21_cmake_hip_cxx_clang/CMakeLists.txt",
-            "samples/2_Cookbook/18_cmake_hip_device/CMakeLists.txt",
-            "samples/2_Cookbook/17_llvm_ir_to_executable/CMakeLists.txt",
-            "samples/2_Cookbook/23_cmake_hiprtc/CMakeLists.txt",
-            "samples/2_Cookbook/22_cmake_hip_lang/CMakeLists.txt",
-            "samples/2_Cookbook/19_cmake_lang/CMakeLists.txt",
-            string=True,
-        )
-        filter_file(
-            "${CMAKE_PREFIX_PATH}/bin/hipify-perl",
-            f"{self.spec['hipify-clang'].prefix.bin}/hipify-perl",
-            "samples/0_Intro/square/CMakeLists.txt",
-            string=True,
-        )
-
-    def setup_build_environment(self, env):
-        env.set("CXX", self.spec["hip"].hipcc)
-
-    def cmake_args(self):
-        args = [
-            self.define("HIP_PLATFORM", "amd"),
-            self.define("HIP_PATH", self.spec["hip"].prefix),
-            self.define("ROCM_PATH", self.spec["hip"].prefix),
-        ]
-        if self.spec.satisfies("^cmake@3.21.0:3.21.2"):
-            args.append(self.define("__skip_rocmclang", "ON"))
-        return args
-
-    def build(self, spec, prefix):
-        with working_dir(self.build_directory):
-            make("build_tests")
-
-    @run_after("install")
-    def cache_test_sources(self):
-        """Copy the tests source files after the package is installed to an
-        install test subdirectory for use during `spack test run`."""
-        cache_extra_test_sources(self, "samples")
-
-    def test_samples(self):
-        """build and run all hip samples"""
-        sample_test_binaries = [
-            "0_Intro/bit_extract/bit_extract",
-            "0_Intro/module_api/launchKernelHcc.hip.out",
-            "0_Intro/module_api/runKernel.hip.out",
-            "0_Intro/module_api/defaultDriver.hip.out",
-            "0_Intro/module_api_global/runKernel1.hip.out",
-            "0_Intro/square/square",
-            "1_Utils/hipDispatchLatency/hipDispatchEnqueueRateMT",
-            "1_Utils/hipDispatchLatency/hipDispatchLatency",
-            "1_Utils/hipInfo/hipInfo",
-            "2_Cookbook/0_MatrixTranspose/MatrixTranspose",
-            "2_Cookbook/1_hipEvent/hipEvent",
-            "2_Cookbook/3_shared_memory/sharedMemory",
-            "2_Cookbook/4_shfl/shfl",
-            "2_Cookbook/5_2dshfl/2dshfl",
-            "2_Cookbook/6_dynamic_shared/dynamic_shared",
-            "2_Cookbook/8_peer2peer/peer2peer",
-            "2_Cookbook/9_unroll/unroll",
-            "2_Cookbook/10_inline_asm/inline_asm",
-            "2_Cookbook/11_texture_driver/texture2dDrv",
-            "2_Cookbook/12_cmake_hip_add_executable/MatrixTranspose1",
-            "2_Cookbook/13_occupancy/occupancy",
-            "2_Cookbook/14_gpu_arch/gpuarch",
-            "2_Cookbook/15_static_library/device_functions/test_device_static",
-            "2_Cookbook/15_static_library/host_functions/test_opt_static",
-            "2_Cookbook/16_assembly_to_executable/square_asm.out",
-            "2_Cookbook/17_llvm_ir_to_executable/square_ir.out",
-            "2_Cookbook/18_cmake_hip_device/test_cpp",
-            "2_Cookbook/19_cmake_lang/test_cpp1",
-            "2_Cookbook/19_cmake_lang/test_fortran",
-            "2_Cookbook/21_cmake_hip_cxx_clang/square1",
-            "2_Cookbook/22_cmake_hip_lang/square2",
-            "2_Cookbook/23_cmake_hiprtc/test",
-        ]
-
-        test_dir = join_path(self.test_suite.current_test_cache_dir, "samples")
-        prefix_paths = ";".join(spack.build_systems.cmake.get_cmake_prefix_path(self))
-        clang_cpp_path = join_path(self.spec["llvm-amdgpu"].prefix, "bin", "clang++")
-        clang_path = join_path(self.spec["llvm-amdgpu"].prefix, "bin", "clang")
-        cc_options = [
-            f"-DCMAKE_MODULE_PATH={self.spec['hip'].prefix.lib.cmake.hip}",
-            f"-DCMAKE_PREFIX_PATH={prefix_paths}",
-            f"-DCMAKE_CXX_COMPILER={clang_cpp_path}",
-            f"-DCMAKE_C_COMPILER={clang_path}",
-            f"-DHIP_HIPCC_EXECUTABLE={self.spec['hip'].prefix.bin}/hipcc",
-            f"-DCMAKE_HIP_COMPILER_ROCM={clang_cpp_path}",
-            ".",
-        ]
-
-        cmake = which(self.spec["cmake"].prefix.bin.cmake)
-        with working_dir(test_dir, create=True):
-            cmake(*cc_options)
-            make("build_samples")
-            for binary_path in sample_test_binaries:
-                # binaries need to run in their directories
-                bin_dir, binary = os.path.split(binary_path)
-                with working_dir(bin_dir, create=True):
-                    with test_part(
-                        self,
-                        "test_sample_{0}".format(binary),
-                        purpose="configure, build and run test: {0}".format(binary),
-                    ):
-                        exe = Executable(binary)
-                        if binary == "hipDispatchEnqueueRateMT":
-                            options = ["16", "0"]
-                        else:
-                            options = []
-                        exe(*options)

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

@@ -5,6 +5,7 @@
 import os
 import re
 
+import spack.build_environment
 from spack.hooks.sbang import filter_shebang
 from spack.package import *
 
@@ -324,6 +325,33 @@ class Hip(CMakePackage):
             when=f"@{d_version} +cuda",
         )
 
+    # Add hiptests sources thru the below
+    for d_version, d_shasum in [
+        ("6.3.1", "0fc1cf4f46f2bbef377d65803d86c2489b01b598c468070c79c5114a661f07c6"),
+        ("6.3.0", "8081d4ab1a43ffa1cebd646668d83008b799ab98c14daf7b455922355a439c8a"),
+        ("6.2.4", "1478b49583d09cb3a96e26ec3bf8dc5ff3e3ec72fa133bb6d7768595d825051e"),
+        ("6.2.1", "90fcf0169889533b882d289f9cb8a7baf9bd46a3ce36752b915083931dc839f1"),
+        ("6.2.0", "314837dbac78be71844ceb959476470c484fdcd4fb622ff8de9277783e0fcf1c"),
+        ("6.1.2", "5b14e4a30d8d8fb56c43e262009646ba9188eac1c8ff882d9a606a4bec69b56b"),
+        ("6.1.1", "10c96ee72adf4580056292ab17cfd858a2fd7bc07abeb41c6780bd147b47f7af"),
+        ("6.1.0", "cf3a6a7c43116032d933cc3bc88bfc4b17a4ee1513c978e751755ca11a5ed381"),
+        ("6.0.2", "740ca064f4909c20d83226a63c2f164f7555783ec5f5f70be5bc23d3587ad829"),
+        ("6.0.0", "e8f92a0f5d1f6093ca1fb24ff1b7140128900fcdc6e9f01f153d6907e5c2d807"),
+        ("5.7.1", "28fbdf49f405adfee903bc0f05a43ac392c55b34c514c3582dfb7d6d67e79985"),
+        ("5.7.0", "b1dae3cfc715e71dce92ac1da94265a9398944c76cee85ffab8f0c93665a48d6"),
+        ("5.6.1", "5b3002ddfafda162329e4d9e6ac1200eeb48ff08e666b342aa8aeca30750f48b"),
+        ("5.6.0", "8cf4509bf9c0747dab8ed8fec1365a9156792034b517207a0b2d63270429fd2e"),
+    ]:
+        resource(
+            name="hip-tests",
+            url=f"https://github.com/ROCm/hip-tests/archive/refs/tags/rocm-{d_version}.tar.gz",
+            sha256=d_shasum,
+            expand=True,
+            destination="",
+            placement="hip-tests",
+            when=f"@{d_version}",
+        )
+
     # Improve compilation without git repo and remove compiler rt linkage
     # for host and correction in CMake target path variable and
     # correcting the CMake path variable.
@@ -645,3 +673,69 @@ def cmake_args(self):
         if self.spec.satisfies("@6.0:"):
             args.append(self.define("HIPCC_BIN_DIR", self.spec["hipcc"].prefix.bin))
         return args
+
+    test_src_dir_old = "samples"
+    test_src_dir = "hip-tests/samples"
+
+    @run_after("install")
+    def install_samples(self):
+        if self.spec.satisfies("@5.6.0:"):
+            install_tree(self.test_src_dir, self.spec.prefix.share.samples)
+
+    @run_after("install")
+    def cache_test_sources(self):
+        """Copy the tests source files after the package is installed to an
+        install test subdirectory for use during `spack test run`."""
+        if self.spec.satisfies("@5.1:5.5"):
+            cache_extra_test_sources(self, [self.test_src_dir_old])
+        elif self.spec.satisfies("@5.6:"):
+            cache_extra_test_sources(self, [self.test_src_dir])
+
+    def test_samples(self):
+        """build and run all hip samples"""
+        if self.spec.satisfies("@5.1:5.5"):
+            test_dir = join_path(self.test_suite.current_test_cache_dir, self.test_src_dir_old)
+        elif self.spec.satisfies("@5.6:"):
+            test_dir = join_path(self.test_suite.current_test_cache_dir, self.test_src_dir)
+        prefixes = ";".join(spack.build_environment.get_cmake_prefix_path(self))
+        cc_options = ["-DCMAKE_PREFIX_PATH=" + prefixes, ".."]
+
+        amdclang_path = join_path(self.spec["llvm-amdgpu"].prefix, "bin", "amdclang++")
+        os.environ["CXX"] = amdclang_path
+        os.environ["FC"] = "/usr/bin/gfortran"
+
+        cmake = which(self.spec["cmake"].prefix.bin.cmake)
+
+        for root, dirs, files in os.walk(test_dir):
+            dirs.sort()
+            if "CMakeLists.txt" in files or "Makefile" in files:
+                with working_dir(root, create=True):
+                    head, test_name = os.path.split(root)
+                    with test_part(
+                        self,
+                        "test_sample_{0}".format(test_name),
+                        purpose="configure, build and run test: {0}".format(test_name),
+                    ):
+                        if "CMakeLists.txt" in files:
+                            print("Configuring  test " + test_name)
+                            os.mkdir("build")
+                            os.chdir("build")
+                            cmake(*cc_options)
+
+                        print("Building test " + test_name)
+                        make(parallel=False)
+                        # iterate through the files in dir to find the newly built binary
+                        for file in os.listdir("."):
+                            if (
+                                file not in files
+                                and os.path.isfile(file)
+                                and os.access(file, os.X_OK)
+                                and not file.endswith(".o")
+                            ):
+                                print("Executing test binary: " + file)
+                                exe = which(file)
+                                if file == "hipDispatchEnqueueRateMT":
+                                    options = ["16", "0"]
+                                else:
+                                    options = []
+                                exe(*options)

var/spack/repos/builtin/packages/icu4c/package.py

@@ -72,7 +72,7 @@ def url_for_version(self, version):
         return url.format(version.dashed, version.underscored)
 
     def flag_handler(self, name, flags):
-        if name == "cxxflags" and not self.spec.platform == "windows":
+        if name == "cxxflags":
             # Control of the C++ Standard is via adding the required "-std"
             # flag to CXXFLAGS in env
             flags.append(getattr(self.compiler, f"cxx{self.spec.variants['cxxstd'].value}_flag"))
@@ -125,7 +125,7 @@ def msbuild_args(self):
     @property
     def build_directory(self):
         solution_path = pathlib.Path(self.pkg.stage.source_path)
-        if self.spec.satisfies("@:67"):
+        if self.spec.satsifies("@:67"):
             solution_path = solution_path / "icu"
         solution_path = solution_path / "source" / "allinone"
         return str(solution_path)

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

@@ -23,7 +23,6 @@ class Justbuild(Package):
     license("Apache-2.0")
 
     version("master", branch="master")
-    version("1.4.3", tag="v1.4.3", commit="dfbfdc230805a7c92baa7e49d82edc2816e00511")
     version("1.4.2", tag="v1.4.2", commit="7fd5d41bc219acf0d15da5dfc75d8dd4a6c53ba3")
     version("1.4.1", tag="v1.4.1", commit="2dc306f510c7ba0661d95bd75305f7deb5eb54b2")
     version("1.4.0", tag="v1.4.0", commit="562bddf70175a602f896397f41ee5f5e07e834eb")

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

@@ -20,7 +20,6 @@ class Lcio(CMakePackage):
     license("BSD-3-Clause")
 
     version("master", branch="master")
-    version("2.22.4", sha256="5d60eeb4df8611059f4bc839ac098f5d7e3608a662591e9cbae48aed07995514")
     version("2.22.3", sha256="5b9715786c5e953f8854881c5d0c4a48030a5491f1701232b82e960ac7980162")
     version("2.22.2", sha256="e5ad9690af85160ef52dd407fc0995451b4293f3aee415a8ea8a950de63d87a1")
     version("2.22.1", sha256="4bc3d2c83af7b1c65d6736dd14ee82f41af7ce9bfc7cfe779c5f47417e8dc326")

var/spack/repos/builtin/packages/libgcrypt/o_flag_munging-1.10.patch

@@ -1,39 +0,0 @@
-From 7cea256ef1a6017e722bdfd5b7381fa90580d55a Mon Sep 17 00:00:00 2001
-From: "simit.ghane" <simit.ghane@lge.com>
-Date: Tue, 7 May 2024 14:09:03 +0530
-Subject: [PATCH] fix o_flag_munging
-
----
- cipher/Makefile.am | 2 +-
- random/Makefile.am | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/cipher/Makefile.am b/cipher/Makefile.am
-index c3d642b2..04bf25e9 100644
---- a/cipher/Makefile.am
-+++ b/cipher/Makefile.am
-@@ -153,7 +153,7 @@ gost-s-box: gost-s-box.c
- 
- 
- if ENABLE_O_FLAG_MUNGING
--o_flag_munging = sed -e 's/-O\([2-9sgz][2-9sgz]*\)/-O1/' -e 's/-Ofast/-O1/g'
-+o_flag_munging = sed -e 's/[[:blank:]]-O\([2-9sgz][2-9sgz]*\)/ -O1 /g' -e 's/[[:blank:]]-Ofast/ -O1 /g'
- else
- o_flag_munging = cat
- endif
-diff --git a/random/Makefile.am b/random/Makefile.am
-index 0c935a05..a42e4306 100644
---- a/random/Makefile.am
-+++ b/random/Makefile.am
-@@ -56,7 +56,7 @@ jitterentropy-base.c jitterentropy.h jitterentropy-base-user.h
- 
- # The rndjent module needs to be compiled without optimization.  */
- if ENABLE_O_FLAG_MUNGING
--o_flag_munging = sed -e 's/-O\([1-9sgz][1-9sgz]*\)/-O0/g' -e 's/-Ofast/-O0/g'
-+o_flag_munging = sed -e 's/[[:blank:]]-O\([1-9sgz][1-9sgz]*\)/ -O0 /g' -e 's/[[:blank:]]-Ofast/ -O0 /g'
- else
- o_flag_munging = cat
- endif
--- 
-2.43.0
-

var/spack/repos/builtin/packages/libgcrypt/o_flag_munging-1.11.patch

@@ -1,50 +0,0 @@
-From 9c11f1e12a6ddbd49b5fd38c94e6a004f8da6e29 Mon Sep 17 00:00:00 2001
-From: "simit.ghane" <simit.ghane@lge.com>
-Date: Tue, 11 Jun 2024 07:22:28 +0530
-Subject: [PATCH] random:cipher: handle substitution in sed command
-
-* cipher/Makefile.am (o_flag_munging): Add 'g' flag for first sed
-expression.
-* random/Makefile.am (o_flag_munging): Likewise.
---
-
-It was there earlier and accidentally removed from
-Makefile.am of cipher and random
-
-Signed-off-by: simit.ghane <simit.ghane@lge.com>
-[jk: add changelog to commit message]
-Signed-off-by: Jussi Kivilinna <jussi.kivilinna@iki.fi>
----
- cipher/Makefile.am | 2 +-
- random/Makefile.am | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/cipher/Makefile.am b/cipher/Makefile.am
-index ea9014cc..149c9f21 100644
---- a/cipher/Makefile.am
-+++ b/cipher/Makefile.am
-@@ -169,7 +169,7 @@ gost-s-box$(EXEEXT_FOR_BUILD): gost-s-box.c
- 
- 
- if ENABLE_O_FLAG_MUNGING
--o_flag_munging = sed -e 's/[[:blank:]]-O\([2-9sgz][2-9sgz]*\)/ -O1 /' -e 's/[[:blank:]]-Ofast/ -O1 /g'
-+o_flag_munging = sed -e 's/[[:blank:]]-O\([2-9sgz][2-9sgz]*\)/ -O1 /g' -e 's/[[:blank:]]-Ofast/ -O1 /g'
- else
- o_flag_munging = cat
- endif
-diff --git a/random/Makefile.am b/random/Makefile.am
-index c7100ef8..a42e4306 100644
---- a/random/Makefile.am
-+++ b/random/Makefile.am
-@@ -56,7 +56,7 @@ jitterentropy-base.c jitterentropy.h jitterentropy-base-user.h
- 
- # The rndjent module needs to be compiled without optimization.  */
- if ENABLE_O_FLAG_MUNGING
--o_flag_munging = sed -e 's/[[:blank:]]-O\([1-9sgz][1-9sgz]*\)/ -O0 /' -e 's/[[:blank:]]-Ofast/ -O0 /g'
-+o_flag_munging = sed -e 's/[[:blank:]]-O\([1-9sgz][1-9sgz]*\)/ -O0 /g' -e 's/[[:blank:]]-Ofast/ -O0 /g'
- else
- o_flag_munging = cat
- endif
--- 
-2.43.0
-

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

@@ -17,26 +17,26 @@ class Libgcrypt(AutotoolsPackage):
 
     version("1.11.0", sha256="09120c9867ce7f2081d6aaa1775386b98c2f2f246135761aae47d81f58685b9c")
     version("1.10.3", sha256="8b0870897ac5ac67ded568dcfadf45969cfa8a6beb0fd60af2a9eadc2a3272aa")
+    version("1.10.2", sha256="3b9c02a004b68c256add99701de00b383accccf37177e0d6c58289664cce0c03")
+    version("1.10.1", sha256="ef14ae546b0084cd84259f61a55e07a38c3b53afc0f546bffcef2f01baffe9de")
+    version("1.10.0", sha256="6a00f5c05caa4c4acc120c46b63857da0d4ff61dc4b4b03933fa8d46013fae81")
 
+    # End of life: 2024-03-31
     with default_args(deprecated=True):
-        version(
-            "1.10.2", sha256="3b9c02a004b68c256add99701de00b383accccf37177e0d6c58289664cce0c03"
-        )
-        version(
-            "1.10.1", sha256="ef14ae546b0084cd84259f61a55e07a38c3b53afc0f546bffcef2f01baffe9de"
-        )
-        version(
-            "1.10.0", sha256="6a00f5c05caa4c4acc120c46b63857da0d4ff61dc4b4b03933fa8d46013fae81"
-        )
-        # End of life: 2024-12-31 (LTS)
-        version("1.8.9", sha256="2bda4790aa5f0895d3407cf7bf6bd7727fd992f25a45a63d92fef10767fa3769")
-        version("1.8.7", sha256="03b70f028299561b7034b8966d7dd77ef16ed139c43440925fe8782561974748")
-        version("1.8.6", sha256="0cba2700617b99fc33864a0c16b1fa7fdf9781d9ed3509f5d767178e5fd7b975")
-        version("1.8.5", sha256="3b4a2a94cb637eff5bdebbcaf46f4d95c4f25206f459809339cdada0eb577ac3")
-        version("1.8.4", sha256="f638143a0672628fde0cad745e9b14deb85dffb175709cacc1f4fe24b93f2227")
-        version("1.8.1", sha256="7a2875f8b1ae0301732e878c0cca2c9664ff09ef71408f085c50e332656a78b3")
+        version("1.9.4", sha256="ea849c83a72454e3ed4267697e8ca03390aee972ab421e7df69dfe42b65caaf7")
+        version("1.9.3", sha256="97ebe4f94e2f7e35b752194ce15a0f3c66324e0ff6af26659bbfb5ff2ec328fd")
+        version("1.9.2", sha256="b2c10d091513b271e47177274607b1ffba3d95b188bbfa8797f948aec9053c5a")
+        version("1.9.1", sha256="c5a67a8b9b2bd370fb415ed1ee31c7172e5683076493cf4a3678a0fbdf0265d9")
 
-    depends_on("c", type="build")
+    # End of life: 2024-12-31 (LTS)
+    version("1.8.9", sha256="2bda4790aa5f0895d3407cf7bf6bd7727fd992f25a45a63d92fef10767fa3769")
+    version("1.8.7", sha256="03b70f028299561b7034b8966d7dd77ef16ed139c43440925fe8782561974748")
+    version("1.8.6", sha256="0cba2700617b99fc33864a0c16b1fa7fdf9781d9ed3509f5d767178e5fd7b975")
+    version("1.8.5", sha256="3b4a2a94cb637eff5bdebbcaf46f4d95c4f25206f459809339cdada0eb577ac3")
+    version("1.8.4", sha256="f638143a0672628fde0cad745e9b14deb85dffb175709cacc1f4fe24b93f2227")
+    version("1.8.1", sha256="7a2875f8b1ae0301732e878c0cca2c9664ff09ef71408f085c50e332656a78b3")
+
+    depends_on("c", type="build")  # generated
 
     depends_on("libgpg-error@1.25:")
     depends_on("libgpg-error@1.27:", when="@1.9:")
@@ -58,9 +58,6 @@ def flag_handler(self, name, flags):
     # https://git.gnupg.org/cgi-bin/gitweb.cgi?p=libgcrypt.git;a=commit;h=b42116d6067a5233f72e5598032d4b396bb8eaac
     patch("conditional_avx512.patch", when="@1.11.0")
 
-    patch("o_flag_munging-1.10.patch", when="@1.10")
-    patch("o_flag_munging-1.11.patch", when="@1.11")
-
     def check(self):
         # Without this hack, `make check` fails on macOS when SIP is enabled
         # https://bugs.gnupg.org/gnupg/issue2056

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

@@ -15,7 +15,6 @@ class Libice(AutotoolsPackage, XorgPackage):
 
     maintainers("wdconinc")
 
-    version("1.1.2", sha256="1da62f732f8679c20045708a29372b82dff9e7eceee543ed488b845002b3b0ff")
     version("1.1.1", sha256="04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210")
     version("1.1.0", sha256="7a735ec530d7a437955747eabac06bbc0b695da77fd1b4d1df3b0a483d823875")
     version("1.0.10", sha256="1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d")

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

@@ -15,7 +15,6 @@ class Libsm(AutotoolsPackage, XorgPackage):
 
     maintainers("wdconinc")
 
-    version("1.2.5", sha256="a11c3d23b60dce0c13256a8ce9478c1ea330719c0747b5adfbce60571198fa57")
     version("1.2.4", sha256="51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15")
     version("1.2.3", sha256="1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320")
     version("1.2.2", sha256="14bb7c669ce2b8ff712fbdbf48120e3742a77edcd5e025d6b3325ed30cf120f4")

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

@@ -730,19 +730,6 @@ class Llvm(CMakePackage, CudaPackage, LlvmDetection, CompilerPackage):
 
     patch("sanitizer-platform-limits-posix-xdr-macos.patch", when="@10:14 platform=darwin")
 
-    # https://github.com/spack/spack/issues/48865
-    patch(
-        "https://github.com/llvm/llvm-project/commit/f4be5ed6a3fef0b2b0c60b29e1c0638926638d28.patch?full_index=1",
-        sha256="51740996bbc01a5049fa859134ad44ffc9514da212cc7d9a445c8d16d6cc867e",
-        when="@15",
-    )
-    # https://github.com/spack/spack/issues/48865
-    patch(
-        "https://github.com/llvm/llvm-project/commit/73e15b5edb4fa4a77e68c299a6e3b21e610d351f.patch?full_index=1",
-        sha256="b540ef6e3728d7881d95775a163314fac6e2f9207f5d5e8b79c8c73c73ba4dc3",
-        when="@15:16",
-    )
-
     @when("@14:17")
     def patch(self):
         # https://github.com/llvm/llvm-project/pull/69458

var/spack/repos/builtin/packages/mummer4/48bit_index.patch

@@ -1,10 +0,0 @@
---- include/mummer/48bit_index.hpp	2020-10-01 01:47:50.000000000 +0100
-+++ include/mummer/48bit_index.hpp.patched	2023-06-09 12:07:09.949856479 +0100
-@@ -6,6 +6,7 @@
- #endif
- 
-+#include <cstdint>
- #include "48bit_iterator.hpp"
- 
- template<typename IDX>
- struct fortyeight_index {

var/spack/repos/builtin/packages/mummer4/package.py

@@ -25,6 +25,3 @@ class Mummer4(AutotoolsPackage):
     depends_on("perl@5.6.0:", type=("build", "run"))
     depends_on("awk", type="run")
     depends_on("sed", type="run")
-
-    # Adds missing inclusion of <cstdint>
-    patch("48bit_index.patch", level=0, when="%gcc@13:")

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

@@ -1,97 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class Nnn(MakefilePackage):
-    """nnn (n³) is a full-featured terminal file manager.
-    It's tiny, nearly 0-config and incredibly fast."""
-
-    homepage = "https://github.com/jarun/nnn"
-    url = "https://github.com/jarun/nnn/archive/refs/tags/v5.0.tar.gz"
-
-    maintainers("fthaler")
-
-    license("BSD-2-Clause", checked_by="fthaler")
-
-    version("5.0", sha256="31e8fd85f3dd7ab2bf0525c3c0926269a1e6d35a5343a6714315642370d8605a")
-
-    depends_on("binutils", type="build")
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
-    depends_on("pkgconfig", type="build")
-
-    depends_on("coreutils")
-    depends_on("file")
-    depends_on("git", when="+gitstatus")
-    depends_on("ncurses")
-    depends_on("pcre", when="+pcre")
-    depends_on("readline", when="+readline")
-    depends_on("sed")
-    depends_on("tar")
-    depends_on("zip")
-
-    variant("mouse", default=True, description="Enable mouse support")
-    variant(
-        "pcre",
-        default=False,
-        description="Use Perl Compatible Regular Expressions (default is POSIX)",
-    )
-    variant("readline", default=True, description="Compile with readline")
-    variant(
-        "icons",
-        values=("none", "emoji", "nerd", "icons-in-terminal"),
-        default="emoji",
-        description="Choose the icons to use "
-        "(see https://github.com/jarun/nnn/wiki/Advanced-use-cases#file-icons)",
-    )
-
-    variant("colemak", default=False, description="Key bindings for Colemak keyboard layout")
-    variant("gitstatus", default=True, description="Add git status column to the detail view")
-    variant("namefirst", default=False, description="Print filenames first in the detail view")
-    variant(
-        "restorepreview",
-        default=False,
-        description="Add pipe to close and restore preview-tui for internal undetached edits",
-    )
-
-    def setup_build_environment(self, env):
-        spec = self.spec
-        env.set("PREFIX", self.prefix)
-        if "+pcre" in spec:
-            env.append_flags("CPPFLAGS", spec["pcre"].headers.include_flags)
-            env.append_flags("LDFLAGS", spec["pcre"].libs.ld_flags)
-
-    @property
-    def build_targets(self):
-        spec = self.spec
-        targets = []
-        if "~mouse" in spec:
-            targets.append("O_NOMOUSE=1")
-        if "+pcre" in spec:
-            targets.append("O_PCRE=1")
-        if "~readline" in spec:
-            targets.append("O_NORL=1")
-
-        if "icons=emoji" in spec:
-            targets.append("O_EMOJI=1")
-        elif "icons=nerd" in spec:
-            targets.append("O_NERD=1")
-        elif "icons=icons-in-terminal" in spec:
-            targets.append("O_ICONS=1")
-
-        if "+colemak" in spec:
-            targets.append("O_COLEMAK=1")
-        if "+gitstatus" in spec:
-            targets.append("O_GITSTATUS=1")
-        if "+namefirst" in spec:
-            targets.append("O_NAMEFIRST=1")
-        if "+restorepreview" in spec:
-            targets.append("O_RESTOREPREVIEW=1")
-        return targets
-
-    @property
-    def install_targets(self):
-        return self.build_targets + ["strip", "install"]

var/spack/repos/builtin/packages/nvpl-blas/package.py

@@ -21,7 +21,6 @@ class NvplBlas(Package):
 
     license("UNKNOWN")
 
-    version("0.4.0.1", sha256="6655898327ed36afd0242719075447058c3c89640b5b9bbfeb5af4dd5c101174")
     version("0.3.0", sha256="b51cb199a440c1e8673d3d845d395950c9a9020d4e83af2655eb96c23c6ec90d")
     version("0.2.0.1", sha256="ba29f6a9d3831b6ae5c9265b4d124c13b9b9e0faea025359b02b41ad230975c2")
     version("0.1.0", sha256="4ccc894593cbcbfaa1a4f3c54505982691971667acf191c9ab0f4252a37c8063")

var/spack/repos/builtin/packages/nvpl-lapack/package.py

@@ -21,7 +21,6 @@ class NvplLapack(Package):
 
     license("UNKNOWN")
 
-    version("0.3.0", sha256="41cc18fc52f6869747b4185a96e34de93a53eb9d6aa95aab07082958055161b0")
     version("0.2.3.1", sha256="25927df133c5486fd71d5976c93917c96e62275a78dffc354bcaf1b022f56f8e")
     version("0.2.2.1", sha256="cdfbf69517a044e99e3e6231c8b2f4e845fd0de57775ccad6b4b0b4fe7e91e84")
     version("0.2.0.1", sha256="7054f775b18916ee662c94ad7682ace53debbe8ee36fa926000fe412961edb0b")

var/spack/repos/builtin/packages/nwchem/oneapi2025.patch

@@ -1,36 +0,0 @@
-diff -ruN spack-src/src/config/makefile.h spack-src-patched/src/config/makefile.h
---- spack-src/src/config/makefile.h	2024-08-28 02:30:22.000000000 +0000
-+++ spack-src-patched/src/config/makefile.h	2025-02-07 16:03:07.315882016 +0000
-@@ -2364,15 +2364,14 @@
- 		    _GOTAVX2 := $(shell cat /proc/cpuinfo | grep fma | tail -n 1 | awk ' /fma/  {print "Y"}')
- 		    _GOTAVX512F := $(shell cat /proc/cpuinfo | grep avx512f | tail -n 1 | awk ' /avx512f/  {print "Y"}')
-                 endif
--		_IFCE := $(shell ifort -V  2>&1 |head -1 |awk ' /64/ {print "Y";exit};')
--		_IFCV7 := $(shell ifort -v  2>&1|grep "Version "|head -n 1|awk ' /7./  {print "Y";exit}')
--		_IFCV11 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 11) {print "Y";exit}}')
--		_IFCV12 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 12) {print "Y";exit}}')
--		_IFCV14 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 14) {print "Y";exit}}')
--		_IFCV15ORNEWER := $(shell ifort -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 15) {print "Y";exit}}')
--	       _IFCV17 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 17) {print "Y";exit}}')
--	       _IFCV18 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 18) {print "Y";exit}}')
--
-+                _IFCE := $(shell $(FC) -V  2>&1 |head -1 |awk ' /64/ {print "Y";exit};')
-+		_IFCV7 := $(shell $(FC) -v  2>&1|grep "Version "|head -n 1|awk ' /7./  {print "Y";exit}')
-+		_IFCV11 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 11) {print "Y";exit}}')
-+		_IFCV12 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 12) {print "Y";exit}}')
-+		_IFCV14 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 14) {print "Y";exit}}')
-+		_IFCV15ORNEWER := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 15) {print "Y";exit}}')
-+	        _IFCV17 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 17) {print "Y";exit}}')
-+	        _IFCV18 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 18) {print "Y";exit}}')
- #               Intel EM64T is required
-                 ifneq ($(_IFCE),Y)
-                     defineFCE:
-@@ -2406,7 +2405,7 @@
- #               CPP=fpp -P
- #
-                 ifeq ($(_IFCV15ORNEWER), Y)
--		 IFORTVER := $(shell ifort -v 2>&1|cut -d " " -f 3)
-+                 IFORTVER := $(shell $(FC) -v 2>&1|cut -d " " -f 3)
- #                ifeq ($(IFORTVER),2021.7.0)
- #                   $(info     )
- #                   $(info     ifort 2021.7.0 not validated)

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

@@ -13,14 +13,11 @@ class Nwchem(Package):
 
     homepage = "https://nwchemgit.github.io"
     url = "https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem-7.2.0-release.revision-d0d141fd-srconly.2023-03-10.tar.bz2"
-    git = "https://github.com/nwchemgit/nwchem.git"
 
     tags = ["ecp", "ecp-apps"]
 
     maintainers("jeffhammond")
 
-    version("master", branch="master")
-
     version(
         "7.2.3",
         sha256="8cb4ec065215bc0316d8e01f67f1674a572f7d0f565c52e4a327975c04ddb6eb",
@@ -72,9 +69,6 @@ class Nwchem(Package):
         "elpa", default=False, description="Enable optimised diagonalisation routines from ELPA"
     )
 
-    # https://github.com/nwchemgit/nwchem/pull/1034
-    patch("oneapi2025.patch", when="@7.2.3 %oneapi@2025:")
-
     # This patch is for the modification of the build system (e.g. compiler flags) and
     # Fortran syntax to enable the compilation with Fujitsu compilers. The modification
     # will be merged to the next release of NWChem (see https://github.com/nwchemgit/nwchem/issues/347

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

@@ -1,62 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class Openturbine(CMakePackage, CudaPackage, ROCmPackage):
-    """An open-source wind turbine structural dynamics simulation code."""
-
-    license("MIT License", checked_by="ddement")
-
-    homepage = "https://www.exascaleproject.org/research-project/exawind/"
-    url = "https://github.com/Exawind/openturbine.git"
-    git = "https://github.com/Exawind/openturbine.git"
-
-    maintainers("faisal-bhuiyan", "ddement", "deslaughter")
-
-    version("main", branch="main")
-
-    variant("tests", default=False, description="Build OpenTurbine Test Suite")
-    variant("openmp", default=False, description="Build OpenTurbine with OpenMP support")
-    variant("vtk", default=False, description="Enable VTK")
-    variant("adi", default=False, description="Build the OpenFAST ADI external project")
-    variant("rosco", default=False, description="Build the ROSCO controller external project")
-
-    depends_on("cxx", type="build")
-    depends_on("yaml-cpp")
-    depends_on("kokkos-kernels+blas+lapack")
-    depends_on("trilinos+amesos2")
-
-    depends_on("kokkos-kernels@4.3:")
-    depends_on("trilinos@16:")
-
-    depends_on("kokkos-kernels+cuda+cublas+cusparse+cusolver", when="+cuda")
-    depends_on("kokkos-kernels+rocblas+rocsparse+rocsolver", when="+rocm")
-    depends_on("kokkos-kernels+openmp", when="+openmp")
-    depends_on("trilinos+cuda+basker", when="+cuda")
-    depends_on("trilinos+rocm+basker", when="+rocm")
-    depends_on("trilinos+openmp+basker", when="+openmp")
-    depends_on("kokkos-kernels~cuda", when="~cuda")
-    depends_on("kokkos-kernels~openmp", when="~openmp")
-    depends_on("trilinos~cuda", when="~cuda")
-    depends_on("trilinos~rocm", when="~rocm")
-    depends_on("trilinos~openmp", when="~openmp")
-
-    depends_on("googletest", when="+tests")
-
-    depends_on("vtk", when="+vtk")
-
-    depends_on("fortran", type="build", when="+adi")
-
-    depends_on("fortran", type="build", when="+rosco")
-
-    def cmake_args(self):
-        options = [
-            self.define_from_variant("OpenTurbine_ENABLE_TESTS", "tests"),
-            self.define_from_variant("OpenTurbine_ENABLE_VTK", "vtk"),
-            self.define_from_variant("OpenTurbine_BUILD_OPENFAST_ADI", "adi"),
-            self.define_from_variant("OpenTurbine_BUILD_ROSCO_CONTROLLER", "rosco"),
-        ]
-        return options

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

@@ -1,34 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class Pfind(Package):
-    """
-    The tool provides parallel access to a single directory. However, this
-    feature depends on the distribution of the "cookie" returned by telldir().
-    Depending on the system, it may work.
-    """
-
-    homepage = "https://github.com/VI4IO/pfind"
-    git = "https://github.com/VI4IO/pfind.git"
-
-    version("main", branch="master")
-
-    depends_on("mpi")
-
-    def setup_build_environment(self, env):
-        env.set("CC", self.spec["mpi"].mpicc, force=True)
-        env.set("CXX", self.spec["mpi"].mpicxx, force=True)
-
-    def install(self, spec, prefix):
-
-        for installer_path in ["./prepare.sh", "./compile.sh"]:
-            set_executable(installer_path)
-            installer = Executable(installer_path)
-            installer()
-
-        mkdirp(prefix.bin)
-        install("pfind", prefix.bin)

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

@@ -18,7 +18,6 @@ class Pika(CMakePackage, CudaPackage, ROCmPackage):
 
     license("BSL-1.0")
 
-    version("0.32.0", sha256="19217e3eecff30a7038f5712b6e161db09f12d7077550e8f66add74b3e524d29")
     version("0.31.0", sha256="bdbd8e36afb367cc2c7172e5a819c756e4ee20e74dfdec4905f2e84bf097eb7c")
     version("0.30.1", sha256="b0f3689a3edd30f8d674e19b5134fc5013813f843c45797c1015163e51989ac0")
     version("0.30.0", sha256="1798bf7de2505bc707bf95716fda8de5630b2e2ae54a6c4ef59f9931394d31cc")

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

@@ -31,7 +31,7 @@ class PyArch(PythonPackage):
     # "numpy>=2.0.0rc1,<3" ???
     # https://github.com/bashtage/arch/blob/9ced09e2566c0ebcad962d2441b1e79e2aaa7c9f/requirements.txt#L1
     # numpy>=1.22.3 ???
-    depends_on("py-numpy@1.22.3:", type=("build", "run"))
+    depends_on("py-numpy@1.22.3", type=("build", "run"))
 
     depends_on("py-scipy@1.8:", type="run")
     depends_on("py-pandas@1.4:", type="run")

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

@@ -1,37 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from spack.package import *
-
-
-class PyElevation(PythonPackage):
-    """
-    Python script to download global terrain digital elevation models,
-    SRTM 30m DEM and SRTM 90m DEM.
-    """
-
-    homepage = "http://elevation.bopen.eu/"
-    pypi = "elevation/elevation-1.1.3.tar.gz"
-
-    maintainers("Chrismarsh")
-
-    license("Apache-2.0", checked_by="Chrismarsh")
-
-    version("1.1.3", sha256="be27446562e7964f7d8fa78c4829dbbb8ac43df405ad09be8c49633adb8f4877")
-
-    depends_on("py-setuptools@42:", type="build")
-    depends_on("py-setuptools-scm@3.4: +toml", type="build")
-    depends_on("py-setuptools-scm-git-archive", type="build")
-    depends_on("py-click", type="build")
-
-    depends_on("py-fasteners")
-    depends_on("py-rasterio")
-    depends_on("py-fiona")
-    depends_on("py-appdirs")
-
-    # listed in
-    # https://github.com/bopen/elevation/blob/1.1.3/README.rst
-    depends_on("curl")
-    depends_on("unzip")
-    depends_on("gzip")
-    depends_on("gdal+python")

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

@@ -14,7 +14,6 @@ class PyLlvmlite(PythonPackage):
 
     license("BSD-2-Clause")
 
-    version("0.44.0", sha256="07667d66a5d150abed9157ab6c0b9393c9356f229784a4385c02f99e94fc94d4")
     version("0.43.0", sha256="ae2b5b5c3ef67354824fb75517c8db5fbe93bc02cd9671f3c62271626bc041d5")
     version("0.42.0", sha256="f92b09243c0cc3f457da8b983f67bd8e1295d0f5b3746c7a1861d7a99403854a")
     version("0.41.1", sha256="f19f767a018e6ec89608e1f6b13348fa2fcde657151137cb64e56d48598a92db")
@@ -52,8 +51,7 @@ class PyLlvmlite(PythonPackage):
     depends_on("python@:3.8", when="@0.31:0.35", type=("build", "run"))
 
     # https://github.com/numba/llvmlite#compatibility
-    depends_on("llvm@15", when="@0.44:")
-    depends_on("llvm@14", when="@0.41:0.43")
+    depends_on("llvm@14", when="@0.41:")
     depends_on("llvm@11:14", when="@0.40")
     depends_on("llvm@11", when="@0.37:0.39")
     for t in [
@@ -68,7 +66,6 @@ class PyLlvmlite(PythonPackage):
         "x86_64:",
     ]:
         depends_on("llvm@10.0", when=f"@0.34:0.36 target={t}")
-
     depends_on("llvm@9.0", when="@0.34:0.36 target=aarch64:")
     depends_on("llvm@9.0", when="@0.33")
     depends_on("llvm@7.0:7.1,8.0", when="@0.29:0.32")

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

@@ -17,7 +17,6 @@ class PyMaturin(PythonPackage):
 
     license("Apache-2.0")
 
-    version("1.8.2", sha256="e31abc70f6f93285d6e63d2f4459c079c94c259dd757370482d2d4ceb9ec1fa0")
     version("1.6.0", sha256="b955025c24c8babc808db49e0ff90db8b4b1320dcc16b14eb26132841737230d")
     version("1.5.1", sha256="3dd834ece80edb866af18cbd4635e0ecac40139c726428d5f1849ae154b26dca")
     version("1.4.0", sha256="ed12e1768094a7adeafc3a74ebdb8dc2201fa64c4e7e31f14cfc70378bf93790")
@@ -43,5 +42,4 @@ class PyMaturin(PythonPackage):
     # May be an accidental dependency, remove in the future
     # https://git.alpinelinux.org/aports/commit/?id=7ad298b467403b96a6b97d050170e367f147a75f
     # https://patchwork.yoctoproject.org/project/oe-core/patch/8803dc101b641c948805cab9e5784c38f43b0e51.1702791173.git.tim.orling@konsulko.com/
-    # This seems to still be an issue for others
-    depends_on("bzip2")
+    depends_on("bzip2", when="platform=darwin")

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

@@ -16,7 +16,6 @@ class PyNumba(PythonPackage):
 
     license("BSD-2-Clause")
 
-    version("0.61.0", sha256="888d2e89b8160899e19591467e8fdd4970e07606e1fbc248f239c89818d5f925")
     version("0.60.0", sha256="5df6158e5584eece5fc83294b949fd30b9f1125df7708862205217e068aabf16")
     version("0.59.1", sha256="76f69132b96028d2774ed20415e8c528a34e3299a40581bae178f0994a2f370b")
     version("0.58.1", sha256="487ded0633efccd9ca3a46364b40006dbdaca0f95e99b8b83e778d1195ebcbaa")
@@ -47,9 +46,6 @@ class PyNumba(PythonPackage):
 
     variant("tbb", default=False, description="Build with Intel Threading Building Blocks")
 
-    # Be careful that the bounds given in setup.py are exclusive on the upper bound
-    # i.e., [min, max)
-    depends_on("python@3.10:3.13", when="@0.61:", type=("build", "run"))
     depends_on("python@3.9:3.12", when="@0.59:", type=("build", "run"))
     depends_on("python@3.8:3.11", when="@0.57:0.58", type=("build", "run"))
     depends_on("python@3.7:3.10", when="@0.55:0.56", type=("build", "run"))
@@ -57,7 +53,7 @@ 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"))
-    depends_on("py-numpy@2.0:2.2", when="@0.60:", type=("build", "run"))
+    depends_on("py-numpy@2.0", 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"))
@@ -67,7 +63,6 @@ class PyNumba(PythonPackage):
     depends_on("py-numpy@1.17:1.20", when="@0.54", type=("build", "run"))
     depends_on("py-numpy@1.15:1.20", when="@0.48:0.53", type=("build", "run"))
     depends_on("py-setuptools", type=("build", "run"))
-    depends_on("py-llvmlite@0.44", when="@0.61", type=("build", "run"))
     depends_on("py-llvmlite@0.43", when="@0.60", type=("build", "run"))
     depends_on("py-llvmlite@0.42", when="@0.59", type=("build", "run"))
     depends_on("py-llvmlite@0.41", when="@0.58", type=("build", "run"))

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

@@ -13,11 +13,8 @@ class PyPatsy(PythonPackage):
     homepage = "https://github.com/pydata/patsy"
     pypi = "patsy/patsy-0.5.2.tar.gz"
 
-    maintainers("climbfuji")
-
     license("PSF-2.0")
 
-    version("0.5.4", sha256="7dabc527597308de0e8f188faa20af7e06a89bdaa306756dfc7783693ea16af4")
     version("0.5.3", sha256="bdc18001875e319bc91c812c1eb6a10be4bb13cb81eb763f466179dca3b67277")
     version("0.5.2", sha256="5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d")
     version("0.5.1", sha256="f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991")

var/spack/repos/builtin/packages/py-pybind11/package.py

@@ -26,7 +26,6 @@ class PyPybind11(CMakePackage, PythonExtension):
     maintainers("ax3l")
 
     version("master", branch="master")
-    version("2.13.6", sha256="e08cb87f4773da97fa7b5f035de8763abc656d87d5773e62f6da0587d1f0ec20")
     version("2.13.5", sha256="b1e209c42b3a9ed74da3e0b25a4f4cd478d89d5efbb48f04b277df427faf6252")
     version("2.13.4", sha256="efc901aa0aab439a3fea6efeaf930b5a349fb06394bf845c64ce15a9cf8f0240")
     version("2.13.3", sha256="6e7a84ec241544f2f5e30c7a82c09c81f0541dd14e9d9ef61051e07105f9c445")

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

@@ -20,7 +20,6 @@ class PyShapely(PythonPackage):
     license("BSD-3-Clause")
 
     version("main", branch="main")
-    version("2.0.7", sha256="28fe2997aab9a9dc026dc6a355d04e85841546b2a5d232ed953e3321ab958ee5")
     version("2.0.6", sha256="997f6159b1484059ec239cacaa53467fd8b5564dabe186cd84ac2944663b0bf6")
     version("2.0.5", sha256="bff2366bc786bfa6cb353d6b47d0443c570c32776612e527ee47b6df63fcfe32")
     version("2.0.4", sha256="5dc736127fac70009b8d309a0eeb74f3e08979e530cf7017f2f507ef62e6cfb8")

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

@@ -15,11 +15,8 @@ class PyStatsmodels(PythonPackage):
     pypi = "statsmodels/statsmodels-0.8.0.tar.gz"
     git = "https://github.com/statsmodels/statsmodels.git"
 
-    maintainers("climbfuji")
-
     license("BSD-3-Clause")
 
-    version("0.14.1", sha256="2260efdc1ef89f39c670a0bd8151b1d0843567781bcafec6cda0534eb47a94f6")
     version("0.14.0", sha256="6875c7d689e966d948f15eb816ab5616f4928706b180cf470fd5907ab6f647a4")
     version("0.13.5", sha256="593526acae1c0fda0ea6c48439f67c3943094c542fe769f8b90fe9e6c6cc4871")
     version("0.13.2", sha256="77dc292c9939c036a476f1770f9d08976b05437daa229928da73231147cde7d4")
@@ -36,44 +33,37 @@ class PyStatsmodels(PythonPackage):
     depends_on("python@3.8:", when="@0.14:", type=("build", "link", "run"))
     depends_on("python", type=("build", "link", "run"))
 
-    depends_on("py-setuptools@69.0.2:", when="@0.14.1: ^python@3.12:", type="build")
-    depends_on("py-setuptools@63.4.3:", when="@0.14.1:", type="build")
     depends_on("py-setuptools@59.2:", when="@0.13.3:", type="build")
     depends_on("py-setuptools@0.6c5:", type="build")
 
     # pyproject.toml
-    depends_on("py-cython@0.29.33:3", when="@0.14.1", type="build")
-    depends_on("py-cython@0.29.26:2", when="@0.14.0", type="build")
+    depends_on("py-cython@0.29.26:2", when="@0.14:", type="build")
     depends_on("py-cython@0.29.32:2", when="@0.13.5:0.13", type="build")
-    depends_on("py-cython@0.29.22:2", when="@0.13:0.13.4", type="build")
-    depends_on("py-cython@0.29.14:2", when="@0.12", type="build")
-    depends_on("py-cython@0.29:2", when="@:0.11", type="build")
-    depends_on("py-setuptools-scm+toml@8", when="@0.14.1:", type="build")
-    depends_on("py-setuptools-scm+toml@7.0", when="@0.13.3:0.14.0", type="build")
+    depends_on("py-cython@0.29.22:2", when="@0.13:", type="build")
+    depends_on("py-cython@0.29.14:2", when="@0.12:", type="build")
+    depends_on("py-cython@0.29:2", type="build")
+    depends_on("py-setuptools-scm+toml@7.0", when="@0.13.3:", type="build")
 
     # patsy@0.5.1 works around a Python change
     #    https://github.com/statsmodels/statsmodels/issues/5343 and
     #    https://github.com/pydata/patsy/pull/131
 
     # requirements.txt
-    depends_on("py-numpy@1.22.3:1", when="@0.14.1:", type=("build", "link", "run"))
-    depends_on("py-numpy@1.18:1", when="@0.14:", type=("build", "link", "run"))
+    depends_on("py-numpy@1.18:", when="@0.14:", type=("build", "link", "run"))
     depends_on("py-numpy@1.17:", when="@0.13:", type=("build", "link", "run"))
     depends_on("py-numpy@1.15:", when="@0.12.1:", type=("build", "link", "run"))
     depends_on("py-numpy@1.11:", when="@0.10.1:", type=("build", "link", "run"))
     # https://github.com/statsmodels/statsmodels/issues/9194
     depends_on("py-numpy@:1", when="@:0.14.1", type=("build", "link", "run"))
     depends_on("py-scipy@1.4:", when="@0.13.5:", type=("build", "run"))
-    conflicts("^py-scipy@1.9.2", when="@:0.14.1")
+    conflicts("^py-scipy@1.9.2")
     depends_on("py-scipy@1.3:", when="@0.13:", type=("build", "run"))
     depends_on("py-scipy@1.2:", when="@0.12:", type=("build", "run"))
     depends_on("py-scipy@0.18:", when="@0.10.1:", type=("build", "run"))
     depends_on("py-pandas@1:", when="@0.14:", type=("build", "run"))
-    conflicts("^py-scipy@2.1.0", when="@:0.14.1")
     depends_on("py-pandas@0.25:", when="@0.13:", type=("build", "run"))
     depends_on("py-pandas@0.23:", when="@0.12:", type=("build", "run"))
     depends_on("py-pandas@0.19:", when="@0.10.1:", type=("build", "run"))
-    depends_on("py-patsy@0.5.4:", when="@0.14.1:", type=("build", "run"))
     depends_on("py-patsy@0.5.2:", when="@0.13:", type=("build", "run"))
     depends_on("py-patsy@0.5.1:", when="@0.12:", type=("build", "run"))
     depends_on("py-patsy@0.4:", when="@0.10.1:", type=("build", "run"))

var/spack/repos/builtin/packages/py-torch-nvidia-apex/package.py

@@ -17,17 +17,13 @@ class PyTorchNvidiaApex(PythonPackage, CudaPackage):
     license("BSD-3-Clause")
 
     version("master", branch="master")
-    version(
-        "24.04.01",
-        sha256="065bc5c0146ee579d5db2b38ca3949da4dc799b871961a2c9eb19e18892166ce",
-        preferred=True,
-    )
+    version("24.04.01", sha256="065bc5c0146ee579d5db2b38ca3949da4dc799b871961a2c9eb19e18892166ce")
     version("23.08", tag="23.08")
     version("23.07", tag="23.07")
     version("23.06", tag="23.06")
     version("23.05", tag="23.05")
     version("22.03", tag="22.03")
-    version("2020-10-19", commit="8a1ed9e8d35dfad26fb973996319965e4224dcdd", deprecated=True)
+    version("2020-10-19", commit="8a1ed9e8d35dfad26fb973996319965e4224dcdd")
 
     depends_on("c", type="build")
     depends_on("cxx", type="build")
@@ -79,17 +75,6 @@ class PyTorchNvidiaApex(PythonPackage, CudaPackage):
     # https://github.com/NVIDIA/apex/issues/1498
     # https://github.com/NVIDIA/apex/pull/1499
     patch("1499.patch", when="@2020-10-19")
-    patch(
-        "https://github.com/NVIDIA/apex/pull/1879.patch?full_index=1",
-        sha256="8e2e21aa883d93e6c0ea0fecb812c8de906b2e77bcffeeb716adabd1dd76650e",
-        when="@23.05:2019",
-    )
-
-    patch(
-        "https://github.com/NVIDIA/apex/pull/1855.patch?full_index=1",
-        sha256="8481b1234a9ce1e8bef4e57a259d8528107761e1843777489e815ec3727397fd",
-        when="@:24.10",
-    )
 
     conflicts(
         "cuda_arch=none",

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

@@ -24,7 +24,6 @@ class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
     maintainers("adamjstewart")
 
     version("main", branch="main")
-    version("2.6.0", tag="v2.6.0", commit="1eba9b3aa3c43f86f4a2c807ac8e12c4a7767340")
     version("2.5.1", tag="v2.5.1", commit="a8d6afb511a69687bbb2b7e88a3cf67917e1697e")
     version("2.5.0", tag="v2.5.0", commit="32f585d9346e316e554c8d9bf7548af9f62141fc")
     version("2.4.1", tag="v2.4.1", commit="ee1b6804381c57161c477caa380a840a84167676")
@@ -165,18 +164,17 @@ class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
     with default_args(type=("build", "run")):
         # setup.py
         depends_on("py-filelock", when="@2:")
-        depends_on("py-typing-extensions@4.10:", when="@2.6:")
         depends_on("py-typing-extensions@4.8:", when="@2.2:")
         depends_on("py-typing-extensions@3.6.2.1:", when="@1.7:")
-        depends_on("py-setuptools")
         depends_on("py-sympy", when="@2:")
         depends_on("py-networkx", when="@2:")
         depends_on("py-jinja2", when="@2:")
         depends_on("py-fsspec", when="@2.1:")
 
         # pyproject.toml
+        depends_on("py-setuptools")
         depends_on("py-astunparse", when="@1.13:")
-        depends_on("py-numpy")
+        depends_on("py-numpy@1.16.6:")
         # https://github.com/pytorch/pytorch/issues/107302
         depends_on("py-numpy@:1", when="@:2.2")
         depends_on("py-pyyaml")
@@ -190,18 +188,15 @@ class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
     # Third party dependencies
     depends_on("fp16@2020-05-14", when="@1.6:")
     depends_on("fxdiv@2020-04-17", when="@1.6:")
-    depends_on("nvtx@3.1.0", when="@2.6:")
     # https://github.com/pytorch/pytorch/issues/60332
-    # depends_on("xnnpack@2024-11-08", when="@2.6:+xnnpack")
-    # depends_on("xnnpack@2024-02-29", when="@2.3:2.5+xnnpack")
+    # depends_on("xnnpack@2024-02-29", when="@2.3:+xnnpack")
     # depends_on("xnnpack@2022-12-21", when="@2.0:2.2+xnnpack")
     # depends_on("xnnpack@2022-02-16", when="@1.12:1+xnnpack")
     # depends_on("xnnpack@2021-06-21", when="@1.10:1.11+xnnpack")
     # depends_on("xnnpack@2021-02-22", when="@1.8:1.9+xnnpack")
     # depends_on("xnnpack@2020-03-23", when="@1.6:1.7+xnnpack")
     depends_on("benchmark", when="@1.6:+test")
-    depends_on("cpuinfo@2024-09-26", when="@2.6:")
-    depends_on("cpuinfo@2024-09-06", when="@2.5.1")
+    depends_on("cpuinfo@2024-09-06", when="@2.5.1:")
     depends_on("cpuinfo@2024-08-30", when="@2.5.0")
     depends_on("cpuinfo@2023-11-04", when="@2.3:2.4")
     depends_on("cpuinfo@2023-01-13", when="@2.1:2.2")
@@ -221,8 +216,7 @@ class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
     depends_on("gloo+libuv", when="@1.6: platform=darwin")
     depends_on("nccl", when="+nccl+cuda")
     # https://github.com/pytorch/pytorch/issues/60331
-    # depends_on("onnx@1.17.0", when="@2.6:")
-    # depends_on("onnx@1.16.0", when="@2.3:2.5")
+    # depends_on("onnx@1.16.0", when="@2.3:")
     # depends_on("onnx@1.15.0", when="@2.2")
     # depends_on("onnx@1.14.1", when="@2.1")
     # depends_on("onnx@1.13.1", when="@2.0")
@@ -248,8 +242,7 @@ class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
     depends_on("pthreadpool@2020-10-05", when="@1.8")
     depends_on("pthreadpool@2020-06-15", when="@1.6:1.7")
     with default_args(type=("build", "link", "run")):
-        depends_on("py-pybind11@2.13.6:", when="@2.6:")
-        depends_on("py-pybind11@2.13.5:", when="@2.5")
+        depends_on("py-pybind11@2.13.5:", when="@2.5:")
         depends_on("py-pybind11@2.12.0:", when="@2.3:2.4")
         depends_on("py-pybind11@2.11.0:", when="@2.1:2.2")
         depends_on("py-pybind11@2.10.1:", when="@2.0")
@@ -316,14 +309,6 @@ class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
 
     conflicts("%gcc@:9.3", when="@2.2:", msg="C++17 support required")
 
-    # https://github.com/pytorch/pytorch/issues/146239
-    patch(
-        "https://github.com/pytorch/pytorch/pull/140275.patch?full_index=1",
-        sha256="65f56305a27d47d7065711d1131c6ac1611fabcb55b129c27ed6beabe4b94fe0",
-        when="@2.6:",
-        reverse=True,
-    )
-
     # https://github.com/pytorch/pytorch/issues/90448
     patch(
         "https://github.com/pytorch/pytorch/pull/97270.patch?full_index=1",
@@ -358,9 +343,6 @@ class PyTorch(PythonPackage, CudaPackage, ROCmPackage):
     # https://github.com/pytorch/pytorch/pull/35607
     # https://github.com/pytorch/pytorch/pull/37865
     patch("xnnpack.patch", when="@1.5")
-    # https://github.com/pytorch/pytorch/issues/141083
-    # https://github.com/google/XNNPACK/commit/5f23827e66cca435fa400b6e221892ac95af0079
-    patch("xnnpack2.patch", when="@2.6", working_dir="third_party/XNNPACK")
 
     # Fixes build error when ROCm is enabled for pytorch-1.5 release
     patch("rocm.patch", when="@1.5+rocm")
@@ -690,7 +672,6 @@ def enable_or_disable(variant, keyword="USE", var=None):
         env.set("USE_SYSTEM_FXDIV", "ON")
         env.set("USE_SYSTEM_GLOO", "ON")
         env.set("USE_SYSTEM_NCCL", "ON")
-        env.set("USE_SYSTEM_NVTX", "ON")
         # https://github.com/pytorch/pytorch/issues/60331
         # env.set("USE_SYSTEM_ONNX", "ON")
         env.set("USE_SYSTEM_PSIMD", "ON")

var/spack/repos/builtin/packages/py-torch/xnnpack2.patch

@@ -1,34 +0,0 @@
-diff --git a/src/reference/unary-elementwise.cc b/src/reference/unary-elementwise.cc
-index bd95ded6c..da892d8be 100644
---- a/src/reference/unary-elementwise.cc
-+++ b/src/reference/unary-elementwise.cc
-@@ -127,6 +127,16 @@ struct ConvertOp {
-   }
- };
- 
-+#ifdef XNN_HAVE_FLOAT16
-+template <>
-+struct ConvertOp<xnn_bfloat16, _Float16> {
-+  explicit ConvertOp(const xnn_unary_uparams*) {}
-+  _Float16 operator()(xnn_bfloat16 x) const {
-+    return static_cast<_Float16>(static_cast<float>(x));
-+  }
-+};
-+#endif
-+
- template <typename TIn, typename TOut>
- const xnn_unary_elementwise_config* get_convert_config(
-     std::true_type /*input_quantized*/, std::true_type /*output_quantized*/) {
-diff --git a/src/xnnpack/simd/s16-neon.h b/src/xnnpack/simd/s16-neon.h
-index 4e8ebcfbd..e8392f4e9 100644
---- a/src/xnnpack/simd/s16-neon.h
-+++ b/src/xnnpack/simd/s16-neon.h
-@@ -70,7 +70,7 @@ static XNN_INLINE void xnn_store_tail_s16(int16_t* output, xnn_simd_s16_t v,
-     v_low = vget_high_s16(v);
-   }
-   if (num_elements & 2) {
--    vst1_lane_s32((void*) output, vreinterpret_s32_s16(v_low), 0);
-+    vst1_lane_s32((int32_t*) output, vreinterpret_s32_s16(v_low), 0);
-     output += 2;
-     v_low = vext_s16(v_low, v_low, 2);
-   }

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

@@ -17,7 +17,6 @@ class PyTorchaudio(PythonPackage):
     maintainers("adamjstewart")
 
     version("main", branch="main")
-    version("2.6.0", tag="v2.6.0", commit="d8831425203385077a03c1d92cfbbe3bf2106008")
     version("2.5.1", tag="v2.5.1", commit="1661daf10599ca8889f092ec37814fabbe202bb0")
     version("2.5.0", tag="v2.5.0", commit="56bc006d56a0d4960de6a1e0b6340cba4eda05cd")
     version("2.4.1", tag="v2.4.1", commit="e8cbe17769796ce963fbc71b8990f1474774e6d2")
@@ -67,8 +66,7 @@ class PyTorchaudio(PythonPackage):
 
     with default_args(type=("build", "link", "run")):
         # Based on PyPI wheel availability
-        depends_on("python@3.9:3.13", when="@2.6:")
-        depends_on("python@3.9:3.12", when="@2.5")
+        depends_on("python@3.9:3.12", when="@2.5:")
         depends_on("python@3.8:3.12", when="@2.2:2.4")
         depends_on("python@3.8:3.11", when="@2.0:2.1")
         depends_on("python@:3.10", when="@0.12:0")
@@ -76,7 +74,6 @@ class PyTorchaudio(PythonPackage):
         depends_on("python@:3.8", when="@:0.7.0")
 
         depends_on("py-torch@main", when="@main")
-        depends_on("py-torch@2.6.0", when="@2.6.0")
         depends_on("py-torch@2.5.1", when="@2.5.1")
         depends_on("py-torch@2.5.0", when="@2.5.0")
         depends_on("py-torch@2.4.1", when="@2.4.1")
@@ -129,7 +126,7 @@ class PyTorchaudio(PythonPackage):
     patch(
         "https://github.com/pytorch/audio/pull/3811.patch?full_index=1",
         sha256="34dce3403abb03f62827e8a1efcdb2bf7742477a01f155ebb9c7fefe9588b132",
-        when="@2.2:2.5",
+        when="@2.2:",
     )
     conflicts("^cuda@12.5:", when="@:2.1")
 

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

@@ -18,7 +18,6 @@ class PyTorchvision(PythonPackage):
     license("BSD-3-Clause")
 
     version("main", branch="main")
-    version("0.21.0", sha256="0a4a967bbb7f9810f792cd0289a07fb98c8fb5d1303fae8b63e3a6b05d720058")
     version("0.20.1", sha256="7e08c7f56e2c89859310e53d898f72bccc4987cd83e08cfd6303513da15a9e71")
     version("0.20.0", sha256="b59d9896c5c957c6db0018754bbd17d079c5102b82b9be0b438553b40a7b6029")
     version("0.19.1", sha256="083e75c467285595ec3eb3c7aa8493c19e53d7eb42f13046fb56a07c8897e5a8")
@@ -86,6 +85,8 @@ class PyTorchvision(PythonPackage):
     variant("png", default=True, description=desc.format("PNG"))
     variant("jpeg", default=True, description=desc.format("JPEG"))
     variant("webp", default=False, description=desc.format("WEBP"), when="@0.20:")
+    variant("heic", default=False, description=desc.format("HEIC"), when="@0.20:")
+    variant("avif", default=False, description=desc.format("AVIF"), when="@0.20:")
     variant("nvjpeg", default=False, description=desc.format("NVJPEG"))
     variant("video_codec", default=False, description=desc.format("video_codec"))
     variant("ffmpeg", default=False, description=desc.format("FFMPEG"))
@@ -96,8 +97,8 @@ class PyTorchvision(PythonPackage):
 
     with default_args(type=("build", "link", "run")):
         # Based on PyPI wheel availability
-        depends_on("python@3.9:3.13", when="@0.21:")
-        depends_on("python@3.8:3.12", when="@0.17:0.20")
+        depends_on("python@3.9:3.13", when="@0.20:")
+        depends_on("python@3.8:3.12", when="@0.17:0.19")
         depends_on("python@3.8:3.11", when="@0.15:0.16")
         depends_on("python@:3.10", when="@0.12:0.14")
         depends_on("python@:3.9", when="@0.8.2:0.11")
@@ -105,7 +106,6 @@ class PyTorchvision(PythonPackage):
 
         # https://github.com/pytorch/vision#installation
         depends_on("py-torch@main", when="@main")
-        depends_on("py-torch@2.6.0", when="@0.21.0")
         depends_on("py-torch@2.5.1", when="@0.20.1")
         depends_on("py-torch@2.5.0", when="@0.20.0")
         depends_on("py-torch@2.4.1", when="@0.19.1")
@@ -156,6 +156,8 @@ class PyTorchvision(PythonPackage):
     depends_on("libpng@1.6:", when="+png")
     depends_on("jpeg", when="+jpeg")
     depends_on("libwebp", when="+webp")
+    depends_on("libheif", when="+heic")
+    depends_on("libavif", when="+avif")
     depends_on("cuda", when="+nvjpeg")
     depends_on("cuda", when="+video_codec")
     depends_on("ffmpeg@3.1:", when="+ffmpeg")
@@ -212,7 +214,7 @@ def setup_build_environment(self, env):
         for gpu in ["cuda", "mps"]:
             env.set(f"FORCE_{gpu.upper()}", int(f"+{gpu}" in self.spec["py-torch"]))
 
-        extensions = ["png", "jpeg", "webp", "nvjpeg", "video_codec", "ffmpeg"]
+        extensions = ["png", "jpeg", "webp", "heic", "avif", "nvjpeg", "video_codec", "ffmpeg"]
         for extension in extensions:
             env.set(f"TORCHVISION_USE_{extension.upper()}", int(f"+{extension}" in self.spec))
 

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

@@ -13,7 +13,6 @@ class PyXesmf(PythonPackage):
 
     license("MIT")
 
-    version("0.8.8", sha256="8588f83007ce7011379991f516be3691df6fb30486741f0e1c33aa962056ea33")
     version("0.8.4", sha256="c5a2c4b3e8dbbc9fccd5772a940f9067d68e824215ef87ba222b06718c4eeb56")
 
     with default_args(type="build"):
@@ -22,9 +21,9 @@ class PyXesmf(PythonPackage):
 
     with default_args(type=("build", "run")):
         depends_on("py-cf-xarray@0.5.1:")
-
-        # esmf +python is only handled correctly in spack for 8.4+
-        depends_on("esmf@8.4.0: +python")
+        # TODO: add optional dependency
+        # https://github.com/esmf-org/esmf/tree/develop/src/addon/esmpy
+        # depends_on("py-esmpy@8:")
         depends_on("py-numba@0.55.2:")
         depends_on("py-numpy@1.16:")
         depends_on("py-shapely")

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

@@ -57,21 +57,15 @@ class Python(Package):
 
     license("0BSD")
 
-    version("3.13.2", sha256="b8d79530e3b7c96a5cb2d40d431ddb512af4a563e863728d8713039aa50203f9")
     version("3.13.1", sha256="1513925a9f255ef0793dbf2f78bb4533c9f184bdd0ad19763fd7f47a400a7c55")
     version("3.13.0", sha256="12445c7b3db3126c41190bfdc1c8239c39c719404e844babbd015a1bc3fafcd4")
-    version("3.12.9", sha256="45313e4c5f0e8acdec9580161d565cf5fea578e3eabf25df7cc6355bf4afa1ee")
     version("3.12.8", sha256="5978435c479a376648cb02854df3b892ace9ed7d32b1fead652712bee9d03a45")
-    version("3.12.7", sha256="73ac8fe780227bf371add8373c3079f42a0dc62deff8d612cd15a618082ab623")
-    version("3.12.6", sha256="85a4c1be906d20e5c5a69f2466b00da769c221d6a684acfd3a514dbf5bf10a66")
     version("3.12.5", sha256="38dc4e2c261d49c661196066edbfb70fdb16be4a79cc8220c224dfeb5636d405")
     version("3.12.4", sha256="01b3c1c082196f3b33168d344a9c85fb07bfe0e7ecfe77fee4443420d1ce2ad9")
     version("3.12.3", sha256="a6b9459f45a6ebbbc1af44f5762623fa355a0c87208ed417628b379d762dddb0")
     version("3.12.2", sha256="a7c4f6a9dc423d8c328003254ab0c9338b83037bd787d680826a5bf84308116e")
     version("3.12.1", sha256="d01ec6a33bc10009b09c17da95cc2759af5a580a7316b3a446eb4190e13f97b2")
     version("3.12.0", sha256="51412956d24a1ef7c97f1cb5f70e185c13e3de1f50d131c0aac6338080687afb")
-    version("3.11.11", sha256="883bddee3c92fcb91cf9c09c5343196953cbb9ced826213545849693970868ed")
-    version("3.11.10", sha256="92f2faf242681bfa406d53a51e17d42c5373affe23a130cd9697e132ef574706")
     version("3.11.9", sha256="e7de3240a8bc2b1e1ba5c81bf943f06861ff494b69fda990ce2722a504c6153d")
     version("3.11.8", sha256="d3019a613b9e8761d260d9ebe3bd4df63976de30464e5c0189566e1ae3f61889")
     version("3.11.7", sha256="068c05f82262e57641bd93458dfa883128858f5f4997aad7a36fd25b13b29209")
@@ -82,8 +76,6 @@ class Python(Package):
     version("3.11.2", sha256="2411c74bda5bbcfcddaf4531f66d1adc73f247f529aee981b029513aefdbf849")
     version("3.11.1", sha256="baed518e26b337d4d8105679caf68c5c32630d702614fc174e98cb95c46bdfa4")
     version("3.11.0", sha256="64424e96e2457abbac899b90f9530985b51eef2905951febd935f0e73414caeb")
-    version("3.10.16", sha256="f2e22ed965a93cfeb642378ed6e6cdbc127682664b24123679f3d013fafe9cd0")
-    version("3.10.15", sha256="a27864e5ba2a4474f8f6c58ab92ff52767ac8b66f1646923355a53fe3ef15074")
     version("3.10.14", sha256="cefea32d3be89c02436711c95a45c7f8e880105514b78680c14fe76f5709a0f6")
     version("3.10.13", sha256="698ec55234c1363bd813b460ed53b0f108877c7a133d48bde9a50a1eb57b7e65")
     version("3.10.12", sha256="a43cd383f3999a6f4a7db2062b2fc9594fefa73e175b3aedafa295a51a7bb65c")
@@ -99,8 +91,6 @@ class Python(Package):
     version("3.10.2", sha256="3c0ede893011319f9b0a56b44953a3d52c7abf9657c23fb4bc9ced93b86e9c97")
     version("3.10.1", sha256="b76117670e7c5064344b9c138e141a377e686b9063f3a8a620ff674fa8ec90d3")
     version("3.10.0", sha256="c4e0cbad57c90690cb813fb4663ef670b4d0f587d8171e2c42bd4c9245bd2758")
-    version("3.9.21", sha256="667c3ba2ca98d39ead1162f6548c3475768582e2ff89e0821d25eb956ac09944")
-    version("3.9.20", sha256="1e71f006222666e0a39f5a47be8221415c22c4dd8f25334cc41aee260b3d379e")
     version("3.9.19", sha256="f5f9ec8088abca9e399c3b62fd8ef31dbd2e1472c0ccb35070d4d136821aaf71")
     version("3.9.18", sha256="504ce8cfd59addc04c22f590377c6be454ae7406cb1ebf6f5a350149225a9354")
     version("3.9.17", sha256="8ead58f669f7e19d777c3556b62fae29a81d7f06a7122ff9bc57f7dd82d7e014")
@@ -122,9 +112,6 @@ class Python(Package):
     version("3.9.1", sha256="29cb91ba038346da0bd9ab84a0a55a845d872c341a4da6879f462e94c741f117")
     version("3.9.0", sha256="df796b2dc8ef085edae2597a41c1c0a63625ebd92487adaef2fed22b567873e8")
     with default_args(deprecated=True):
-        version(
-            "3.8.20", sha256="9f2d5962c2583e67ef75924cd56d0c1af78bf45ec57035cf8a2cc09f74f4bf78"
-        )
         version(
             "3.8.19", sha256="c7fa55a36e5c7a19ec37d8f90f60a2197548908c9ac8b31e7c0dbffdd470eeac"
         )
@@ -172,8 +159,8 @@ class Python(Package):
             "3.6.15", sha256="54570b7e339e2cfd72b29c7e2fdb47c0b7b18b7412e61de5b463fc087c13b043"
         )
 
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
+    depends_on("c", type="build")  # generated
+    depends_on("cxx", type="build")  # generated
 
     extendable = True
 

var/spack/repos/builtin/packages/r-a4/package.py

@@ -13,6 +13,9 @@ class RA4(RPackage):
 
     bioc = "a4"
 
+    version("1.54.0", commit="56cb1bc42bc4994e42071af04dcb75ebc0b24437")
+    version("1.52.0", commit="1270e4dd069313355c941c0470cf79352dc55b7f")
+    version("1.50.1", commit="3dba5687e0d029febfadbafcdcca5e54a4341a5b")
     version("1.48.0", commit="89ef9f4afdde5270acecc7c65be3752b71237eba")
     version("1.46.0", commit="1b8f1300025fb0940e7f24cff7ffec9fca02d0e4")
     version("1.44.0", commit="5b0fc5a9971d8f3688ad1f88a4f5ee1498e91633")

var/spack/repos/builtin/packages/r-a4base/package.py

@@ -13,6 +13,9 @@ class RA4base(RPackage):
 
     bioc = "a4Base"
 
+    version("1.54.0", commit="e45169b98e872087736bddbbc213fcd1951ed8ce")
+    version("1.52.0", commit="7312ef9ce99a61742a8c684739ae3e96b4733c02")
+    version("1.50.0", commit="26439bbad1e79464154cc5eb6adbcc69b3a231a0")
     version("1.48.0", commit="26d5793de3163091125feeed1de82e5406777b60")
     version("1.46.0", commit="be70ae723bb6031cdf9540d62dc6113761074e88")
     version("1.44.0", commit="9ae69e03118c7b14df0e6c9e3b25362b09f25bbe")

var/spack/repos/builtin/packages/r-a4classif/package.py

@@ -14,6 +14,9 @@ class RA4classif(RPackage):
 
     bioc = "a4Classif"
 
+    version("1.54.0", commit="9540e623465e1b67f1f2dc1cb566f47b76952a16")
+    version("1.52.0", commit="0366c84be3eddd933ed36acc07bd57b1fea4ae4a")
+    version("1.50.0", commit="1a416537c532a37a46a2719aa591e244cca6e779")
     version("1.48.0", commit="1e2ff90d5af6332beac630395a7494c8fd30aff4")
     version("1.46.0", commit="96794183a76ab7da7a1863ccd421640254447af5")
     version("1.44.0", commit="df0fce781f9bc480a1159d958c9a63c314a9ed01")

var/spack/repos/builtin/packages/r-a4core/package.py

@@ -13,6 +13,9 @@ class RA4core(RPackage):
 
     bioc = "a4Core"
 
+    version("1.54.0", commit="247927f7b6fdec427fac10291eeb4ebe8d5cb279")
+    version("1.52.0", commit="13a748dc52233ee90f6ff8f957ecba0b2b0d94d2")
+    version("1.50.0", commit="efe662190be692270d9bbb2c5e00baf46b23a442")
     version("1.48.0", commit="3dd09f0a662745fcfd3fee7048301f3524e8ac5c")
     version("1.46.0", commit="8999fe146be6d04ae36c725d2b6324a6ce8ceb83")
     version("1.44.0", commit="61a7f3a51a41af615bfd4c22984e4c4a82874e8c")

var/spack/repos/builtin/packages/r-a4preproc/package.py

@@ -13,6 +13,9 @@ class RA4preproc(RPackage):
 
     bioc = "a4Preproc"
 
+    version("1.54.0", commit="8b1a156f988e90f2cc8e4c6a17d4ac6452a46ce3")
+    version("1.52.0", commit="cfc6b6f66815c8d812144266298cab96a3c6c9b2")
+    version("1.50.0", commit="7f02ff9d1b65409c110ca2b695dceba6231c06cf")
     version("1.48.0", commit="d3bf8b82d7cabd2ef77253bb9a741dcde3ca3a41")
     version("1.46.0", commit="8463958692c73fd655a6dfec39ea99c915513719")
     version("1.44.0", commit="252381265b96b83803a93e0c2014dd6b0574e57f")

var/spack/repos/builtin/packages/r-a4reporting/package.py

@@ -13,6 +13,9 @@ class RA4reporting(RPackage):
 
     bioc = "a4Reporting"
 
+    version("1.54.0", commit="87a5a7498541f9fec60983c78d0ade920266e4d9")
+    version("1.52.0", commit="ce1eea6021b3e829ced7dcef8bf42440344ea8cf")
+    version("1.50.0", commit="5facc73ff067e1c1fa0e07d20e4151bcefad9b36")
     version("1.48.0", commit="de8c4b76f6b7ef502d77d55289df0d64fe70447c")
     version("1.46.0", commit="00b82d25bef4d518ae92f615d3a6f7931c0618dc")
     version("1.44.0", commit="bfe83507daf53e2e327474ea3012f0dc920efac1")

var/spack/repos/builtin/packages/r-absseq/package.py

@@ -16,6 +16,9 @@ class RAbsseq(RPackage):
 
     bioc = "ABSSeq"
 
+    version("1.60.0", commit="39efc102aaf3f65155be949ea0e2b4fae112d969")
+    version("1.58.0", commit="05f507feb439ca16983c24de32fcbd784476be40")
+    version("1.56.0", commit="60fbebd28c1be53f1d991b46eed5925a27c30f72")
     version("1.54.0", commit="5e7de8c2a6532073012660f22243c9f7a5568ef6")
     version("1.52.0", commit="07038c047775e17d5d29909927d2143efb63e9cb")
     version("1.50.0", commit="4f384d04ebaae6ea0b56e5cff9a9dcdcb6c8afb0")

var/spack/repos/builtin/packages/r-acde/package.py

@@ -21,6 +21,9 @@ class RAcde(RPackage):
 
     bioc = "acde"
 
+    version("1.36.0", commit="d779819cf0900a11ce15bd6a80ff794c4b6430a1")
+    version("1.34.0", commit="e99a19bb1d0c95a574b37376e3471f7dca12b1a3")
+    version("1.32.0", commit="1f7d0ce5c9c8666a73934bc4c0ec4a3e0db30ec6")
     version("1.30.0", commit="4c16b9fd6c91a433bf1345252e022571c4983cb5")
     version("1.28.0", commit="0edccca7be2475fa2ae3b3c36d0d64924c37b3c0")
     version("1.26.0", commit="dfef9a435062e948efd5eda22942a0d500baa992")

var/spack/repos/builtin/packages/r-acgh/package.py

@@ -15,6 +15,9 @@ class RAcgh(RPackage):
 
     bioc = "aCGH"
 
+    version("1.84.0", commit="e992a615337d0d2b4c4d369fa9b33f5f3a32ed1c")
+    version("1.82.0", commit="617c195db8de204f147370dcf1624df2ea48dff4")
+    version("1.80.0", commit="5ec9dd3644069574dd2ffd81c9ca0ac5d86e3d21")
     version("1.78.0", commit="75df3a4839af66ce177d1bbc3cec4ac03c21dc8e")
     version("1.76.0", commit="c6068522854ed0b1c3feb006619ef25590f70ad6")
     version("1.74.0", commit="e7ba380af0da138788eb6c86f5dbe453269c0810")

var/spack/repos/builtin/packages/r-acme/package.py

@@ -20,6 +20,9 @@ class RAcme(RPackage):
 
     bioc = "ACME"
 
+    version("2.62.0", commit="f631445a51969d2f11ed1698e8ad7fc4cee1fbf6")
+    version("2.60.0", commit="7a1f0e4c6e89d68a3887fba157374892f9dd2c8d")
+    version("2.58.0", commit="1b192d9040fd42346790d900bf02f6b4c7313696")
     version("2.56.0", commit="083af1249e67db11fd471babe67b146eb9c1700c")
     version("2.54.0", commit="8d39d9d6623adf427f5eba308790e1de01213870")
     version("2.52.0", commit="14a97c722d0201654af9e583e7e462b458c28a77")

var/spack/repos/builtin/packages/r-adsplit/package.py

@@ -15,6 +15,9 @@ class RAdsplit(RPackage):
 
     bioc = "adSplit"
 
+    version("1.76.0", commit="3bfef6d1d8a4e11632aeeadf25a00801564d5949")
+    version("1.74.0", commit="3df3361641cc343e106525e33bfcea675ec05e3a")
+    version("1.72.0", commit="194ddb23b683bc8633c9522456acc49c85b369b5")
     version("1.70.0", commit="a08a994215a459b856eae051c778e2b9144f52d9")
     version("1.68.0", commit="705977b5e1cb7dd69793cc673fa215baaba42af5")
     version("1.66.0", commit="64580a6f7a9bc6b16334267c90df48fbb839cc16")

var/spack/repos/builtin/packages/r-affxparser/package.py

@@ -19,6 +19,9 @@ class RAffxparser(RPackage):
 
     bioc = "affxparser"
 
+    version("1.78.0", commit="fab9ee2c921c61e84245601eb19d2b7c5c3acc3e")
+    version("1.76.0", commit="4f86ff876074195c1de2f4b36d74d98409b7055a")
+    version("1.74.0", commit="cada520ac224840d0de93d05c8924ad2006d77c3")
     version("1.72.0", commit="6e976af32f77835143f6b4e0c01c6016dc1b331c")
     version("1.70.0", commit="28f94cd3477e9500942be89cbcb5cad1bbb369fe")
     version("1.68.1", commit="821a01a2df18115a3b7864b3f45418255b7123eb")

var/spack/repos/builtin/packages/r-affy/package.py

@@ -14,6 +14,9 @@ class RAffy(RPackage):
 
     bioc = "affy"
 
+    version("1.84.0", commit="1174adf7e83ee46603189397cd557044802cda01")
+    version("1.82.0", commit="fb130de33532f6d15fe99ba02ff35cce07922308")
+    version("1.80.0", commit="a0d64dfdadfff1a1d7a4c39ba73e843e5e3fc6da")
     version("1.78.0", commit="cc7eac358b6e10ee86a7a93d2e436758f6fbd9b5")
     version("1.76.0", commit="3bb309388d5d6402c356d4a5270ee83c5b88942f")
     version("1.74.0", commit="2266c4a46eda7e5b64f7f3e17e8b61e7b85579ff")
@@ -27,6 +30,7 @@ class RAffy(RPackage):
 
     depends_on("c", type="build")  # generated
 
+    depends_on("r@2.8.0:", type=("build", "run"))
     depends_on("r@2.8.0:4.0", type=("build", "run"), when="@:1.68.0")
     depends_on("r-biocgenerics@0.1.12:", type=("build", "run"))
     depends_on("r-biobase@2.5.5:", type=("build", "run"))

var/spack/repos/builtin/packages/r-affycomp/package.py

@@ -13,6 +13,9 @@ class RAffycomp(RPackage):
 
     bioc = "affycomp"
 
+    version("1.82.0", commit="646461c2af419067de1d95691ca27e2ace50a436")
+    version("1.80.0", commit="2b69f9c6ec9f7c90287e254ba5bb9d658ce5820f")
+    version("1.78.0", commit="65cc8f00be57876705853adf0670b05a4ed6bf12")
     version("1.76.0", commit="8bfc628de26a739c5e0cb47aa22bfda7c8d0a922")
     version("1.74.0", commit="1160d6395f23085456938ba2bd38fb45597fc92f")
     version("1.72.0", commit="c52baea98b80abd4a99380ac9d4b68ef91869d40")

var/spack/repos/builtin/packages/r-affycontam/package.py

@@ -13,6 +13,9 @@ class RAffycontam(RPackage):
 
     bioc = "affyContam"
 
+    version("1.64.0", commit="c7cf836b166f981f9d87bf38cb2d8e2a6ab1bf6b")
+    version("1.62.0", commit="b0ced2ce1dff00e6eab4f0e091cebd6994298588")
+    version("1.60.0", commit="f2e21b7d4d700e135ae3bd0fa3531e001a7aa950")
     version("1.58.0", commit="5e91d79d7653a4f484b62eae7fd7e908de8cb9b6")
     version("1.56.0", commit="e2b8a4fba1648255eadce954a848f2dd8e22bcb3")
     version("1.54.0", commit="c5208b48b8881983ff53a4713244327e8ad13b78")

var/spack/repos/builtin/packages/r-affycoretools/package.py

@@ -14,6 +14,9 @@ class RAffycoretools(RPackage):
 
     bioc = "affycoretools"
 
+    version("1.78.0", commit="2eb1cc5d748832ecd4f8e610397b43c88099ccd4")
+    version("1.76.0", commit="4733a16c9629a62c5dc6fb3fef3a6e6def049a02")
+    version("1.74.0", commit="c04ad6fe6a8809b769bdff4cefb6d47a23e7a891")
     version("1.72.0", commit="229ae09efc1a66e64ea395019c32d16387bf81ac")
     version("1.70.0", commit="f09a788aa83e1e052a7c5f148a451a99fe9c9c96")
     version("1.68.1", commit="69546b1fe5edd71eca130d53d33f0fb0fcf62c97")

var/spack/repos/builtin/packages/r-affydata/package.py

@@ -14,6 +14,9 @@ class RAffydata(RPackage):
 
     bioc = "affydata"
 
+    version("1.54.0", commit="b3765c212d7721c189cd7326c18c4141b5227da0")
+    version("1.52.0", commit="54b35381b1b13161e0d0ef10627efc26ed8dc0c5")
+    version("1.50.0", commit="203e040f737bdeb65d8cd2123dc76036f23e4e3a")
     version("1.48.0", commit="037b86c86c114761ff1bcca64ab4e0bcd68063d3")
     version("1.46.0", commit="870745b886df9f1fbbd6130d266c0ef96f3afa66")
     version("1.44.0", commit="f18304a356cee8cd7297bab362b13c40e50439df")

var/spack/repos/builtin/packages/r-affyexpress/package.py

@@ -14,6 +14,7 @@ class RAffyexpress(RPackage):
 
     bioc = "AffyExpress"
 
+    version("1.58.0", commit="3b0f72dc19d923a87cc462673d933e58760a9cc9")
     version("1.56.0", commit="e07085833de2bbf81537410cad526d39f8a82478")
     version("1.50.0", commit="8b98703b63396df9692afb0e15b594658125cc96")
     version("1.48.0", commit="dbaed516b7529ef4f7588aafaf3c5f1d53a9bb92")

var/spack/repos/builtin/packages/r-affyilm/package.py

@@ -15,6 +15,9 @@ class RAffyilm(RPackage):
 
     bioc = "affyILM"
 
+    version("1.58.0", commit="0ceee74b89a9e2dcd8793371cb37e60a9c9a79da")
+    version("1.56.0", commit="ee6044051fce374b0c7ec858e5d300bba28cfafa")
+    version("1.54.0", commit="4586915a1be400f54e37506ebc1ddffb91480e89")
     version("1.52.0", commit="08ed8c60921ba1b9e04fa90e156eef1a3c899d15")
     version("1.50.0", commit="185cd8e4712a3378ce7a156d4940224bbb2c4122")
     version("1.48.0", commit="4603a4c4d6c2330a8a56a7bb657dc56c51a9393a")

var/spack/repos/builtin/packages/r-affyio/package.py

@@ -14,6 +14,9 @@ class RAffyio(RPackage):
 
     bioc = "affyio"
 
+    version("1.76.0", commit="ed8b074ada05f3b3eeba3032b1214179e3034a42")
+    version("1.74.0", commit="1d0948e7a76a00da985b9fdd38d36fa0ca85c2af")
+    version("1.72.0", commit="2f97a7e3710e44886b0b732d1c0dbb3165e9b84c")
     version("1.70.0", commit="95560567e27088863c64e868a8e5069fc725b8d7")
     version("1.68.0", commit="33080c5eeb14c0ca40f0d231706af4e0c2c1ef8b")
     version("1.66.0", commit="3a0b90704fc46cddd99a72b985a6bdb348f69b50")
@@ -28,5 +31,6 @@ class RAffyio(RPackage):
     depends_on("c", type="build")  # generated
 
     depends_on("r@2.6.0:", type=("build", "run"))
-    depends_on("r-zlibbioc", type=("build", "run"))
     depends_on("zlib-api")
+
+    depends_on("r-zlibbioc", type=("build", "run"), when="@:1.77.0")

var/spack/repos/builtin/packages/r-affypdnn/package.py

@@ -13,6 +13,8 @@ class RAffypdnn(RPackage):
 
     bioc = "affypdnn"
 
+    version("1.62.0", commit="22a6e97303bd60c8b365b51c38e4312d5b7ee995")
+    version("1.60.0", commit="9f8998fa4405fbbaea6f7a7eb6d3c1b29c3f5e09")
     version("1.58.0", commit="83d8b6b0d9606845bd77dbf7164dd5b160f32ccf")
     version("1.56.0", commit="5fd9c5265fb895a1f646cf72e8d5169669d979f2")
     version("1.54.0", commit="ea971b1b9cc443695a6614bef92e8e116ee87d55")

var/spack/repos/builtin/packages/r-affyplm/package.py

@@ -16,6 +16,9 @@ class RAffyplm(RPackage):
 
     bioc = "affyPLM"
 
+    version("1.82.0", commit="16d738761d115c14f72a083266e501edb72ce548")
+    version("1.80.0", commit="b0584edcaba058d5cfb06d64e22a4859c7d15b60")
+    version("1.78.0", commit="1fa54e253098269e93b3e8f88bc592041b855334")
     version("1.76.0", commit="45557df5a32f56aa5240439737c5718738fb4c27")
     version("1.74.0", commit="5f76ef92e69deabc19c5395eaec4adb85c66b63d")
     version("1.72.0", commit="394c0a8e213f188d0b1d01e20516df8bf1bc5c09")

var/spack/repos/builtin/packages/r-affyqcreport/package.py

@@ -14,6 +14,7 @@ class RAffyqcreport(RPackage):
 
     bioc = "affyQCReport"
 
+    version("1.70.0", commit="9e49c8c376d8b1d79981628920e5adc238bddeca")
     version("1.68.0", commit="34b42a16f87a90a595146f4a1802ed04f6bfccca")
     version("1.62.0", commit="92d4124b688b90a6a9b8a21ab9d13d92b368cee4")
     version("1.60.0", commit="d0c15b1c56fc1caf6f114877ea6c1b8483a0dcfa")

var/spack/repos/builtin/packages/r-affyrnadegradation/package.py

@@ -17,6 +17,9 @@ class RAffyrnadegradation(RPackage):
 
     bioc = "AffyRNADegradation"
 
+    version("1.52.0", commit="14b087a0fbe2796398ceaebe6232553bce90a2f1")
+    version("1.50.0", commit="2be3cbcdb710b069e82610c123c73a4cc4651a30")
+    version("1.48.0", commit="dfc274be6d53250bc516c9772022c771706c7545")
     version("1.46.0", commit="431ae61c9b3809829697ef71672c57171d93311e")
     version("1.44.0", commit="63881f41fc67cc7322b189446dcffb4e1060e303")
     version("1.42.0", commit="5775f41f538b3c8ee4d07d38cec1b49c548cebe6")

var/spack/repos/builtin/packages/r-agdex/package.py

@@ -13,6 +13,9 @@ class RAgdex(RPackage):
 
     bioc = "AGDEX"
 
+    version("1.54.0", commit="0dc73a6f55bf53ddea0689df48dc72d4983faf87")
+    version("1.52.0", commit="69fe01a6ce7045afe612daea363365b6deaeaed7")
+    version("1.50.0", commit="5b2ecdae7bbafee5c48de5b7181a55bda95143ba")
     version("1.48.0", commit="917920b397493b0ea40093044ebe36fff7c389ad")
     version("1.46.0", commit="d7c38e8bdcaa7b0261117c605e7f61e2b07e8316")
     version("1.44.0", commit="9d3eb90eaf7bf093c7fa73facb3df89506a85185")

var/spack/repos/builtin/packages/r-agilp/package.py

@@ -12,6 +12,9 @@ class RAgilp(RPackage):
 
     bioc = "agilp"
 
+    version("3.38.0", commit="5ed3359c61678afed7709bd3795702b9e94f46f3")
+    version("3.36.0", commit="204ae1003390b0b4efa5aa7d43f96c256e59fc9e")
+    version("3.34.0", commit="12c94ca5c5c1b6bc909571c1bee897a6268d9e39")
     version("3.32.0", commit="8291f7b7c1b6167952568f51593116afc6d0fc27")
     version("3.30.0", commit="a2c898dc901ccdda4b8582caff079ab20b1bfc28")
     version("3.28.0", commit="2c6dfccc76473b5bef13b75fa59adf46b3381f55")

var/spack/repos/builtin/packages/r-agimicrorna/package.py

@@ -13,6 +13,9 @@ class RAgimicrorna(RPackage):
 
     bioc = "AgiMicroRna"
 
+    version("2.56.0", commit="5e277127c2557b8cff752d3fca9f3a41b373d497")
+    version("2.54.0", commit="2c8850f9b62308a3932d74548689b24741347bab")
+    version("2.52.0", commit="73e65fb29170d1bee3b849f82a25ae7da3c6cd3b")
     version("2.50.0", commit="a812b0f4f215b093ca685889b65de60c6701b695")
     version("2.48.0", commit="4c163b1b730150a3a60a3815bd8c08fa04d71fc1")
     version("2.46.0", commit="8c6d73e1c3f1f9cc019bdb219b19e6179bb1efe4")