wrote test case backwards

* fix regression `apple-clang` vs `%apple-clang`
* use f-strings
* remove --verbose flag from LDFLAGS

.github/workflows/ci.yaml

@@ -81,6 +81,10 @@ 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

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

.github/workflows/import-check.yaml

@@ -0,0 +1,49 @@
+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

@@ -86,49 +86,6 @@ 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::
-    - '$spack/.staging'
+    - '$user_cache_path/stage'
   stage_name: '{name}-{version}-{hash:7}'

lib/spack/docs/build_settings.rst

@@ -34,6 +34,7 @@ an object, with the following keys:
 
 1. ``roots``: if ``true`` root specs are reused, if ``false`` only dependencies of root specs are reused
 2. ``from``: list of sources from which reused specs are taken
+3. ``namespaces``: list of namespaces from which to reuse specs, or the string ``"any"``.
 
 Each source in ``from`` is itself an object:
 
@@ -56,6 +57,7 @@ For instance, the following configuration:
    concretizer:
      reuse:
        roots: true
+       namespaces: [builtin]
        from:
        - type: local
          include:
@@ -63,7 +65,8 @@ For instance, the following configuration:
          - "%clang"
 
 tells the concretizer to reuse all specs compiled with either ``gcc`` or ``clang``, that are installed
-in the local store. Any spec from remote buildcaches is disregarded.
+in the local store. Any spec from remote buildcaches is disregarded. Any spec from a namespace other than
+Spack's builtin repo is disregarded.
 
 To reduce the boilerplate in configuration files, default values for the ``include`` and
 ``exclude`` options can be pushed up one level:

lib/spack/spack/build_systems/cmake.py

@@ -11,6 +11,7 @@
 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
@@ -458,19 +459,23 @@ def cmake(
     ) -> None:
         """Runs ``cmake`` in the build directory"""
 
-        # 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"
-        elif primary_generator == "Ninja":
-            configure_artifact = "ninja.build"
+        if spec.is_develop:
+            # skip cmake phase if it is an incremental develop build
 
-        if spec.is_develop and os.path.isfile(
-            os.path.join(self.build_directory, configure_artifact)
-        ):
-            return
+            # 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)
+            configure_artifact = "Makefile"
+            if 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
 
         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
+# flake8: noqa: F401, E402
 """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/relocate.py

@@ -236,22 +236,15 @@ 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/schema/concretizer.py

@@ -25,6 +25,12 @@
                             "roots": {"type": "boolean"},
                             "include": LIST_OF_SPECS,
                             "exclude": LIST_OF_SPECS,
+                            "namespaces": {
+                                "oneOf": [
+                                    {"type": "string", "enum": ["any"]},
+                                    {"type": "array", "items": {"type": "string"}},
+                                ]
+                            },
                             "from": {
                                 "type": "array",
                                 "items": {

lib/spack/spack/solver/asp.py

@@ -3986,6 +3986,7 @@ def __init__(self, configuration: spack.config.Configuration) -> None:
         self.configuration = configuration
         self.store = spack.store.create(configuration)
         self.reuse_strategy = ReuseStrategy.ROOTS
+        self.reuse_namespaces = "any"
 
         reuse_yaml = self.configuration.get("concretizer:reuse", False)
         self.reuse_sources = []
@@ -4016,6 +4017,7 @@ def __init__(self, configuration: spack.config.Configuration) -> None:
                 self.reuse_strategy = ReuseStrategy.ROOTS
             else:
                 self.reuse_strategy = ReuseStrategy.DEPENDENCIES
+            self.reuse_namespaces = reuse_yaml.get("namespaces", "any")
             default_include = reuse_yaml.get("include", [])
             default_exclude = reuse_yaml.get("exclude", [])
             default_sources = [{"type": "local"}, {"type": "buildcache"}]
@@ -4083,6 +4085,9 @@ def reusable_specs(self, specs: List[spack.spec.Spec]) -> List[spack.spec.Spec]:
         if self.reuse_strategy == ReuseStrategy.DEPENDENCIES:
             result = [spec for spec in result if not any(root in spec for root in specs)]
 
+        if self.reuse_namespaces != "any":
+            result = [spec for spec in result if spec.namespace in self.reuse_namespaces]
+
         return result
 
 

lib/spack/spack/spec.py

@@ -1527,9 +1527,8 @@ 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. None signal that it was not set yet.
-        self.extra_attributes = None
+        # This attribute is used to store custom information for external specs.
+        self.extra_attributes: dict = {}
 
         # This attribute holds the original build copy of the spec if it is
         # deployed differently than it was built. None signals that the spec
@@ -2351,15 +2350,10 @@ 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,
-                "extra_attributes": extra_attributes,
+                "module": self.external_modules or None,
+                "extra_attributes": syaml.sorted_dict(self.extra_attributes),
             }
 
         if not self._concrete:
@@ -3861,6 +3855,13 @@ 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__`.
         #
@@ -4908,7 +4909,7 @@ 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", {})
+                spec.extra_attributes = node["external"].get("extra_attributes") or {}
 
         # specs read in are concrete unless marked abstract
         if node.get("concrete", True):

lib/spack/spack/test/concretization/core.py

@@ -1460,6 +1460,35 @@ def test_no_reuse_when_variant_condition_does_not_hold(self, mutable_database, m
         new2 = spack.concretize.concretize_one("conditional-variant-pkg +two_whens")
         assert new2.satisfies("@2 +two_whens +version_based")
 
+    def test_reuse_by_namespace(self, mutable_database, mock_packages):
+        spack.config.set("concretizer:reuse", True)
+        # Set spack to prefer an older version when doing new builds, but prioritize reuse higher
+        spack.config.set("packages:libelf", {"version": ["0.8.10"]})
+
+        # Expected behavior is to reuse the libelf@0.8.13 from mutable database
+        # despite configured preference for older version
+        reuse = spack.concretize.concretize_one("libelf")
+        assert reuse.installed
+        assert reuse.satisfies("@0.8.13")
+
+        # Reuse is turned off, so preference will be respected
+        spack.config.set("concretizer:reuse", {"namespaces": []})
+        noreuse = spack.concretize.concretize_one("libelf")
+        assert not noreuse.installed
+        assert noreuse.satisfies("@0.8.10")
+
+        # Expected behavior same as first concretization
+        spack.config.set("concretizer:reuse", {"namespaces": ["builtin.mock"]})
+        noreuse = spack.concretize.concretize_one("libelf")
+        assert noreuse.installed
+        assert noreuse.satisfies("@0.8.13")
+
+        # Expected behavior same as second concretization
+        spack.config.set("concretizer:reuse", {"namespaces": ["foobar"]})
+        noreuse = spack.concretize.concretize_one("libelf")
+        assert not noreuse.installed
+        assert noreuse.satisfies("@0.8.10")
+
     def test_reuse_with_flags(self, mutable_database, mutable_config):
         spack.config.set("concretizer:reuse", True)
         spec = spack.concretize.concretize_one("pkg-a cflags=-g cxxflags=-g")

lib/spack/spack/test/spec_semantics.py

@@ -1989,3 +1989,26 @@ 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

@@ -1,6 +1,7 @@
 [project]
 name="spack"
 description="The spack package manager"
+requires-python=">=3.6"
 dependencies=[
   "clingo",
   "setuptools",
@@ -67,9 +68,42 @@ 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

@@ -1,141 +0,0 @@
-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

@@ -1,153 +0,0 @@
-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

@@ -13,29 +13,41 @@ 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 +analysis +dd4hep +edm4hep +examples +fatras +geant4 +hepmc3 +podio +pythia8 +python +tgeo cxxstd=20
+  - acts ~cuda
   #- agile  # fails on c++>11 compiler
   - alpgen
   - ampt
   - apfel +lhapdf +python
-  - celeritas +geant4 +hepmc3 +openmp +root +shared +vecgeom cxxstd=20
+  - celeritas ~cuda +openmp ~rocm +vecgeom
   - cepgen
   - cernlib +shared
   - collier
@@ -82,19 +94,28 @@ spack:
   - py-vector
   - pythia8 +evtgen +fastjet +hdf5 +hepmc +hepmc3 +lhapdf ~madgraph5amc +python +rivet ~root # pythia8 and root circularly depend
   - rivet hepmc=3
-  - 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
+  - root ~cuda
   - 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 +gdml +geant4 +root
+  - vecgeom ~cuda
   - 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 ^dyninst@10.0.0 ^elfutils@0.170
+spack -p --lines 20 spec mpileaks%gcc
 $coverage_run $(which spack) bootstrap status --dev --optional
 
 # Check that we can import Spack packages directly as a first import

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

@@ -40,6 +40,7 @@ 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

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

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

@@ -23,6 +23,10 @@ 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

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack.build_systems.cmake import CMakeBuilder
 from spack.package import *
 
 
@@ -81,13 +82,22 @@ 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("vecgeom+cuda cuda_arch=" + _arch, when="+vecgeom +cuda cuda_arch=" + _arch)
+        depends_on(f"vecgeom +cuda cuda_arch={_arch}", when=f"+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")
@@ -111,7 +121,7 @@ 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),
         ]
@@ -119,6 +129,22 @@ 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", "-fprofile-generate={}".format(reports))
-        generate_mods.append_flags("CXXFLAGS", "-fprofile-generate={}".format(reports))
-        generate_mods.append_flags("LDFLAGS", "-fprofile-generate={} --verbose".format(reports))
+        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}")
 
         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", "--output={}".format(use_report), *raw_files)
-            use_flag = "-fprofile-instr-use={}".format(use_report)
+            llvm_profdata("merge", f"--output={use_report}", *raw_files)
+            use_flag = f"-fprofile-instr-use={use_report}"
         else:
-            use_flag = "-fprofile-use={}".format(reports)
+            use_flag = f"-fprofile-use={reports}"
 
         # Set PGO use flags for next cmake phase.
         use_mods = EnvironmentModifications()

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

@@ -12,58 +12,11 @@ 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("4.12.0", 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")
+    version("4.96.4", sha256="b3f9025d00f2cdf61caf83945ef7225d4a3eb576c4c007e45868f45713e39c8e")
 
     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

@@ -18,7 +18,8 @@ class Cpuinfo(CMakePackage):
     license("BSD-2-Clause")
 
     version("main", branch="main")
-    version("2024-09-06", commit="094fc30b9256f54dad5ad23bcbfb5de74781422f")  # py-torch@2.5.1:
+    version("2024-09-26", commit="1e83a2fdd3102f65c6f1fb602c1b320486218a99")  # py-torch@2.6:
+    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

@@ -25,6 +25,7 @@ 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

@@ -25,6 +25,7 @@ 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")
@@ -118,13 +119,16 @@ 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

@@ -20,6 +20,7 @@ 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")
 
@@ -36,6 +37,7 @@ 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

@@ -33,60 +33,30 @@ 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")  # generated
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
-    variant(
-        "openmp",
-        default=True,
-        description="Enable OpenMP support for ParseAPI " "(version 10.0.0 or later)",
-    )
+    variant("openmp", default=True, description="Enable OpenMP support for ParseAPI ")
 
     variant("static", default=False, description="Build static libraries")
 
     variant("stat_dysect", default=False, description="Patch for STAT's DySectAPI")
 
-    boost_libs = (
-        "+atomic+chrono+date_time+filesystem+system+thread+timer+container+random+exception"
+    depends_on(
+        "boost+atomic+chrono+date_time+filesystem+system+thread+timer+container+random+exception"
     )
-
-    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("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("libiberty+pic")
 
-    # 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
+    # Parallel DWARF parsing requires a thread-safe libdw
+    depends_on("elfutils", type="link")
     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
@@ -95,21 +65,16 @@ class Dyninst(CMakePackage):
         conflicts("^intel-oneapi-tbb@2021.1:")
         conflicts("^intel-parallel-studio")
 
-    depends_on("intel-tbb@2019.9:", when="@13.0.0:")
-    depends_on("tbb@2018.6.0:", when="@10.0.0:12.3.0")
+    depends_on("tbb")
+    requires("^[virtuals=tbb] intel-tbb@2019.9:", when="@13.0.0:")
 
     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",
@@ -124,92 +89,21 @@ 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 = [
-            "-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("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),
             self.define("LibIberty_LIBRARIES", spec["libiberty"].libs),
+            self.define_from_variant("USE_OpenMP", "openmp"),
+            self.define_from_variant("ENABLE_STATIC_LIBS", "static"),
         ]
 
-        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
+        # 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("-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")
+            args.append(self.define("STERILE_BUILD", True))
 
         return args
 

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

@@ -1,11 +0,0 @@
---- 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

@@ -1,34 +0,0 @@
-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

@@ -1,73 +0,0 @@
-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/v0.0.15.tar.gz"
+    url = "https://github.com/wsmoses/Enzyme/archive/v0.0.172.tar.gz"
     list_url = "https://github.com/wsmoses/Enzyme/releases"
     git = "https://github.com/wsmoses/Enzyme"
 
@@ -23,6 +23,7 @@ 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")
@@ -42,7 +43,8 @@ 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:")
+    depends_on("llvm@11:19", when="@0.0.100:0.0.148")
+    depends_on("llvm@15:19", when="@0.0.149:")
     depends_on("cmake@3.13:", type="build")
 
     def cmake_args(self):

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

@@ -20,12 +20,16 @@ class Flecsi(CMakePackage, CudaPackage, ROCmPackage):
 
     tags = ["e4s"]
 
-    version("develop", branch="develop", deprecated=True)
+    version("2.3.1", tag="v2.3.1", commit="6c04b9b21790533e457764bd7f8f26757db1552f")
     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")
-    version("2.0.0", tag="v2.0.0", commit="5ceebadf75d1c98999ea9e9446926722d061ec22")
+    version(
+        "2.1.0", tag="v2.1.0", commit="533df139c267e2a93c268dfe68f9aec55de11cf0", deprecated=True
+    )
+    version(
+        "2.0.0", tag="v2.0.0", commit="5ceebadf75d1c98999ea9e9446926722d061ec22", deprecated=True
+    )
 
     variant(
         "backend",
@@ -46,8 +50,8 @@ class Flecsi(CMakePackage, CudaPackage, ROCmPackage):
         description="Set Caliper Profiling Detail",
         multi=False,
     )
-    variant("kokkos", default=False, description="Enable Kokkos Support")
-    variant("openmp", default=False, description="Enable OpenMP Support")
+    variant("kokkos", default=False, description="Enable Kokkos Support", when="@:2.3.1")
+    variant("openmp", default=False, description="Enable OpenMP Support", when="@:2.3.1")
 
     depends_on("c", type="build")
     depends_on("cxx", type="build")
@@ -69,18 +73,22 @@ 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 +cuda +cuda_constexpr +cuda_lambda", when="+kokkos +cuda")
+    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 +rocm", when="+kokkos +rocm")
     depends_on("kokkos +openmp", when="+kokkos +openmp")
-    depends_on("legion@cr-20210122", when="backend=legion @2.0:2.2.1")
+    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-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 +openmp")
-    depends_on("legion+cuda", when="backend=legion +cuda")
-    depends_on("legion+rocm", when="backend=legion +rocm")
+    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("hdf5@1.10.7:", when="backend=legion +hdf5")
     depends_on("hpx@1.10.0: cxxstd=17 malloc=system", when="backend=hpx")
     depends_on("mpi")
@@ -97,11 +105,13 @@ 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}"
@@ -130,13 +140,13 @@ def cmake_args(self):
                 self.define_from_variant("ENABLE_DOCUMENTATION", "doc"),
             ]
 
-            if self.spec.satisfies("+rocm"):
+            if self.spec.satisfies("^kokkos +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

@@ -18,6 +18,8 @@ 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"
@@ -64,6 +66,13 @@ 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
@@ -131,6 +140,7 @@ 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

@@ -23,6 +23,7 @@ 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

@@ -0,0 +1,177 @@
+# 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

@@ -5,7 +5,6 @@
 import os
 import re
 
-import spack.build_environment
 from spack.hooks.sbang import filter_shebang
 from spack.package import *
 
@@ -325,33 +324,6 @@ 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.
@@ -673,69 +645,3 @@ 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":
+        if name == "cxxflags" and not self.spec.platform == "windows":
             # 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.satsifies("@:67"):
+        if self.spec.satisfies("@:67"):
             solution_path = solution_path / "icu"
         solution_path = solution_path / "source" / "allinone"
         return str(solution_path)

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

@@ -23,6 +23,7 @@ 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

@@ -20,6 +20,7 @@ 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/libice/package.py

@@ -15,6 +15,7 @@ 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

@@ -15,6 +15,7 @@ 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

@@ -730,6 +730,19 @@ 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

@@ -0,0 +1,10 @@
+--- 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

@@ -25,3 +25,6 @@ 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

@@ -0,0 +1,97 @@
+# 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

@@ -21,6 +21,7 @@ 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

@@ -21,6 +21,7 @@ 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/openturbine/package.py

@@ -0,0 +1,62 @@
+# 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

@@ -0,0 +1,34 @@
+# 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

@@ -18,6 +18,7 @@ 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

@@ -0,0 +1,37 @@
+# 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

@@ -14,6 +14,7 @@ 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")
@@ -51,7 +52,8 @@ 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@14", when="@0.41:")
+    depends_on("llvm@15", when="@0.44:")
+    depends_on("llvm@14", when="@0.41:0.43")
     depends_on("llvm@11:14", when="@0.40")
     depends_on("llvm@11", when="@0.37:0.39")
     for t in [
@@ -66,6 +68,7 @@ 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

@@ -17,6 +17,7 @@ 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")
@@ -42,4 +43,5 @@ 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/
-    depends_on("bzip2", when="platform=darwin")
+    # This seems to still be an issue for others
+    depends_on("bzip2")

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

@@ -16,6 +16,7 @@ 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")
@@ -46,6 +47,9 @@ 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"))
@@ -53,7 +57,7 @@ class PyNumba(PythonPackage):
     depends_on("python@3.6:3.9", when="@0.53", type=("build", "run"))
     depends_on("python@3.6:3.8", when="@0.52", type=("build", "run"))
     depends_on("python@3.6:3.8", when="@0.48:0.51", type=("build", "run"))
-    depends_on("py-numpy@2.0", when="@0.60:", type=("build", "run"))
+    depends_on("py-numpy@2.0:2.2", when="@0.60:", type=("build", "run"))
     depends_on("py-numpy@1.22:1.26", when="@0.58.1:0.59", type=("build", "run"))
     depends_on("py-numpy@1.21:1.25", when="@0.58.0", type=("build", "run"))
     depends_on("py-numpy@1.21:1.24", when="@0.57", type=("build", "run"))
@@ -63,6 +67,7 @@ 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

@@ -13,8 +13,11 @@ 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

@@ -26,6 +26,7 @@ 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

@@ -20,6 +20,7 @@ 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

@@ -15,8 +15,11 @@ 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")
@@ -33,37 +36,44 @@ 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@0.29.26:2", when="@0.14:", type="build")
+    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@0.29.32:2", when="@0.13.5:0.13", 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")
+    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")
 
     # 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@1.18:", when="@0.14:", type=("build", "link", "run"))
+    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@1.17:", 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")
+    conflicts("^py-scipy@1.9.2", when="@:0.14.1")
     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

@@ -17,13 +17,17 @@ class PyTorchNvidiaApex(PythonPackage, CudaPackage):
     license("BSD-3-Clause")
 
     version("master", branch="master")
-    version("24.04.01", sha256="065bc5c0146ee579d5db2b38ca3949da4dc799b871961a2c9eb19e18892166ce")
+    version(
+        "24.04.01",
+        sha256="065bc5c0146ee579d5db2b38ca3949da4dc799b871961a2c9eb19e18892166ce",
+        preferred=True,
+    )
     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")
+    version("2020-10-19", commit="8a1ed9e8d35dfad26fb973996319965e4224dcdd", deprecated=True)
 
     depends_on("c", type="build")
     depends_on("cxx", type="build")
@@ -75,6 +79,17 @@ 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

@@ -24,6 +24,7 @@ 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")
@@ -164,17 +165,18 @@ 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@1.16.6:")
+        depends_on("py-numpy")
         # https://github.com/pytorch/pytorch/issues/107302
         depends_on("py-numpy@:1", when="@:2.2")
         depends_on("py-pyyaml")
@@ -188,15 +190,18 @@ 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@2024-02-29", when="@2.3:+xnnpack")
+    # 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@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@2024-09-06", when="@2.5.1:")
+    depends_on("cpuinfo@2024-09-26", when="@2.6:")
+    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")
@@ -216,7 +221,8 @@ 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@1.16.0", when="@2.3:")
+    # depends_on("onnx@1.17.0", when="@2.6:")
+    # depends_on("onnx@1.16.0", when="@2.3:2.5")
     # 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")
@@ -242,7 +248,8 @@ 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@2.13.5:", when="@2.5:")
+        depends_on("py-pybind11@2.13.6:", when="@2.6:")
+        depends_on("py-pybind11@2.13.5:", when="@2.5")
         depends_on("py-pybind11@2.12.0:", 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")
@@ -309,6 +316,14 @@ 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",
@@ -343,6 +358,9 @@ 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")
@@ -672,6 +690,7 @@ 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

@@ -0,0 +1,34 @@
+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

@@ -17,6 +17,7 @@ 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")
@@ -66,7 +67,8 @@ class PyTorchaudio(PythonPackage):
 
     with default_args(type=("build", "link", "run")):
         # Based on PyPI wheel availability
-        depends_on("python@3.9:3.12", when="@2.5:")
+        depends_on("python@3.9:3.13", when="@2.6:")
+        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")
@@ -74,6 +76,7 @@ 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")
@@ -126,7 +129,7 @@ class PyTorchaudio(PythonPackage):
     patch(
         "https://github.com/pytorch/audio/pull/3811.patch?full_index=1",
         sha256="34dce3403abb03f62827e8a1efcdb2bf7742477a01f155ebb9c7fefe9588b132",
-        when="@2.2:",
+        when="@2.2:2.5",
     )
     conflicts("^cuda@12.5:", when="@:2.1")
 

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

@@ -18,6 +18,7 @@ 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")
@@ -85,8 +86,6 @@ 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"))
@@ -97,8 +96,8 @@ class PyTorchvision(PythonPackage):
 
     with default_args(type=("build", "link", "run")):
         # Based on PyPI wheel availability
-        depends_on("python@3.9:3.13", when="@0.20:")
-        depends_on("python@3.8:3.12", when="@0.17:0.19")
+        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@3.8:3.11", 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")
@@ -106,6 +105,7 @@ 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")
@@ -156,8 +156,6 @@ 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")
@@ -214,7 +212,7 @@ 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", "heic", "avif", "nvjpeg", "video_codec", "ffmpeg"]
+        extensions = ["png", "jpeg", "webp", "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

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

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

@@ -13,9 +13,6 @@ 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

@@ -13,9 +13,6 @@ 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

@@ -14,9 +14,6 @@ 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

@@ -13,9 +13,6 @@ 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

@@ -13,9 +13,6 @@ 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

@@ -13,9 +13,6 @@ 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

@@ -16,9 +16,6 @@ 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

@@ -21,9 +21,6 @@ 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

@@ -15,9 +15,6 @@ 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

@@ -20,9 +20,6 @@ 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

@@ -15,9 +15,6 @@ 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

@@ -19,9 +19,6 @@ 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

@@ -14,9 +14,6 @@ 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")
@@ -30,7 +27,6 @@ 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

@@ -13,9 +13,6 @@ 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

@@ -13,9 +13,6 @@ 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

@@ -14,9 +14,6 @@ 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

@@ -14,9 +14,6 @@ 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

@@ -14,7 +14,6 @@ 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

@@ -15,9 +15,6 @@ 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

@@ -14,9 +14,6 @@ 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")
@@ -31,6 +28,5 @@ 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

@@ -13,8 +13,6 @@ 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

@@ -16,9 +16,6 @@ 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

@@ -14,7 +14,6 @@ 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

@@ -17,9 +17,6 @@ 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

@@ -13,9 +13,6 @@ 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

@@ -12,9 +12,6 @@ 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

@@ -13,9 +13,6 @@ 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")

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

@@ -16,9 +16,6 @@ class RAims(RPackage):
 
     bioc = "AIMS"
 
-    version("1.38.0", commit="b7d238e6573f1921a4f255f9c7cd673a31482c1c")
-    version("1.36.0", commit="8c8f6120501a37595034c1c1759ccfb751e995e1")
-    version("1.34.0", commit="61910444b05ce6e438467177202a93046c700e32")
     version("1.32.0", commit="019415a6362e805465d43c157606e1774aed9e51")
     version("1.30.0", commit="2ab61159c5aa0902cc33fc1502f7853b66912cce")
     version("1.28.0", commit="84608df638b5694c08158ed77ad2c8a64c4e594b")

var/spack/repos/builtin/packages/r-aldex2/package.py

@@ -24,9 +24,6 @@ class RAldex2(RPackage):
 
     license("GPL-3.0-only")
 
-    version("1.38.0", commit="701515c185aa747e53c863afbb3730a9a331e242")
-    version("1.36.0", commit="c7a4c4bfc66baba750ef58163193f6b53830cf9b")
-    version("1.34.0", commit="eda12f9208ed90e9e2c2d6a47415a5c73c107e4b")
     version("1.32.0", commit="ba32b9a9b6a8f42906ea094318f00116f15e42eb")
     version("1.30.0", commit="cb6670515a8722f9cfedac12a8c2747a5298ee46")
     version("1.28.1", commit="f8d8ba6d2439bff75ab80f5466c9a047c31ed0a6")

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

@@ -13,9 +13,6 @@ class RAllelicimbalance(RPackage):
 
     bioc = "AllelicImbalance"
 
-    version("1.44.0", commit="c46bcc17963050a7fd01a23615de796fd3e8bd4b")
-    version("1.42.0", commit="4dc686c08a02d051ba1d8e82c909c2c751dc5613")
-    version("1.40.0", commit="e3fc91108af4816a237b588b23cc40133f6eee30")
     version("1.38.0", commit="75a3b0fefe635a0892eae338d0fdd4a9e091f957")
     version("1.36.0", commit="cb4910c1fd58cc4272c21251a8f120990e1aa431")
     version("1.34.0", commit="290708ccc4ceae1fbb9e9257cb254916449d389b")

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

@@ -18,7 +18,6 @@ class RAlsace(RPackage):
     bioc = "alsace"
 
     version("1.30.0", commit="d0e09b283da2b4869d5d6e6801399676246bc5bc")
-    version("1.28.0", commit="03344a1f12a5c86e61a8d69b68d9d16c3ed07561")
     version("1.26.0", commit="40a76404acb1466723a78a55d87c67eec3e6f306")
     version("1.20.0", commit="47f1cf8daafc864e5e3418009f349ce85d6b0389")
     version("1.18.0", commit="c9fc43c7b441de43b14ef1be69926c4c4a566191")

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

@@ -12,9 +12,6 @@ class RAltcdfenvs(RPackage):
 
     bioc = "altcdfenvs"
 
-    version("2.68.0", commit="53038c86c7c743272e00a71b5fcb4252b068cf13")
-    version("2.66.0", commit="34a3f5bc0b36543e20de6dd2035db3776677e8e2")
-    version("2.64.0", commit="86cec42b52c7b2450ae6dbc7b0ab73a98c32fc3b")
     version("2.62.0", commit="aedf0e9f98639d60b327e50957e504cf24b64bbb")
     version("2.60.0", commit="0bc0b4493b8e9fe2eb47fb8e9377123ce8f472bb")
     version("2.58.0", commit="08255a777ffa1e1414d3dd3062d95bfdd3dfd47c")