add test for incompatible version from specific package

Current location is within the Spack prefix, which causes builds to
pollute VCS with stage artifacts and generally inflates the Spack
install prefix.

This PR moves it to the user cache location now that we can
consistently support paths with spaces on Windows.

.github/workflows/build-containers.yml

@@ -40,17 +40,17 @@ jobs:
         # 1: Platforms to build for
         # 2: Base image (e.g. ubuntu:22.04)
         dockerfile: [[amazon-linux, 'linux/amd64,linux/arm64', 'amazonlinux:2'],
-                     [centos-stream9, 'linux/amd64,linux/arm64,linux/ppc64le', 'centos:stream9'],
-                     [leap15, 'linux/amd64,linux/arm64,linux/ppc64le', 'opensuse/leap:15'],
-                     [ubuntu-focal, 'linux/amd64,linux/arm64,linux/ppc64le', 'ubuntu:20.04'],
-                     [ubuntu-jammy, 'linux/amd64,linux/arm64,linux/ppc64le', 'ubuntu:22.04'],
-                     [ubuntu-noble, 'linux/amd64,linux/arm64,linux/ppc64le', 'ubuntu:24.04'],
-                     [almalinux8, 'linux/amd64,linux/arm64,linux/ppc64le', 'almalinux:8'],
-                     [almalinux9, 'linux/amd64,linux/arm64,linux/ppc64le', 'almalinux:9'],
+                     [centos-stream9, 'linux/amd64,linux/arm64', 'centos:stream9'],
+                     [leap15, 'linux/amd64,linux/arm64', 'opensuse/leap:15'],
+                     [ubuntu-focal, 'linux/amd64,linux/arm64', 'ubuntu:20.04'],
+                     [ubuntu-jammy, 'linux/amd64,linux/arm64', 'ubuntu:22.04'],
+                     [ubuntu-noble, 'linux/amd64,linux/arm64', 'ubuntu:24.04'],
+                     [almalinux8, 'linux/amd64,linux/arm64', 'almalinux:8'],
+                     [almalinux9, 'linux/amd64,linux/arm64', 'almalinux:9'],
                      [rockylinux8, 'linux/amd64,linux/arm64', 'rockylinux:8'],
                      [rockylinux9, 'linux/amd64,linux/arm64', 'rockylinux:9'],
-                     [fedora39, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:39'],
-                     [fedora40, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:40']]
+                     [fedora39, 'linux/amd64,linux/arm64', 'fedora:39'],
+                     [fedora40, 'linux/amd64,linux/arm64', 'fedora:40']]
     name: Build ${{ matrix.dockerfile[0] }}
     if: github.repository == 'spack/spack'
     steps:

.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

@@ -86,66 +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: ${{ github.event.pull_request.base.sha }}
-        path: old
-    # not a PR: use the previous commit as the old commit
-    - name: Checkout previous commit
-      if: github.event_name != 'pull_request'
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        fetch-depth: 2
-        path: old
-    - name: Checkout previous commit
-      if: github.event_name != 'pull_request'
-      run: git -C old reset --hard HEAD^
-
-    - name: Checkout new commit
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        path: new
-    - name: Install circular import checker
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        repository: haampie/circular-import-fighter
-        ref: b5d6ce9be35f602cca7d5a6aa0259fca10639cca
-        path: circular-import-fighter
-    - name: Install dependencies
-      working-directory: circular-import-fighter
-      run: make -j dependencies
-    - name: Problematic imports before
-      working-directory: circular-import-fighter
-      run: make SPACK_ROOT=../old SUFFIX=.old
-    - name: Problematic imports after
-      working-directory: circular-import-fighter
-      run: make SPACK_ROOT=../new SUFFIX=.new
-    - name: Compare import cycles
-      working-directory: circular-import-fighter
-      run: |
-        edges_before="$(head -n1 solution.old)"
-        edges_after="$(head -n1 solution.new)"
-        if [ "$edges_after" -gt "$edges_before" ]; then
-          printf '\033[1;31mImport check failed: %s imports need to be deleted, ' "$edges_after"
-          printf 'previously this was %s\033[0m\n'  "$edges_before"
-          printf 'Compare \033[1;97m"Problematic imports before"\033[0m and '
-          printf '\033[1;97m"Problematic imports after"\033[0m.\n'
-          exit 1
-        else
-          printf '\033[1;32mImport check passed: %s <= %s\033[0m\n' "$edges_after" "$edges_before"
-        fi
 
   # 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_systems/autotoolspackage.rst

@@ -272,9 +272,9 @@ often lists dependencies and the flags needed to locate them. The
 "environment variables" section lists environment variables that the
 build system uses to pass flags to the compiler and linker.
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-Addings flags to configure
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Adding flags to configure
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 For most of the flags you encounter, you will want a variant to
 optionally enable/disable them. You can then optionally pass these
@@ -285,7 +285,7 @@ function like so:
 
    def configure_args(self):
        args = []
-
+       ...
        if self.spec.satisfies("+mpi"):
            args.append("--enable-mpi")
        else:
@@ -299,7 +299,10 @@ Alternatively, you can use the :ref:`enable_or_disable  <autotools_enable_or_dis
 .. code-block:: python
 
    def configure_args(self):
-       return [self.enable_or_disable("mpi")]
+       args = []
+       ...
+       args.extend(self.enable_or_disable("mpi"))
+       return args
 
 
 Note that we are explicitly disabling MPI support if it is not
@@ -344,7 +347,14 @@ typically used to enable or disable some feature within the package.
        default=False,
        description="Memchecker support for debugging [degrades performance]"
    )
-   config_args.extend(self.enable_or_disable("memchecker"))
+   ...
+
+   def configure_args(self):
+       args = []
+       ...
+       args.extend(self.enable_or_disable("memchecker"))
+
+       return args
 
 In this example, specifying the variant ``+memchecker`` will generate
 the following configuration options:

lib/spack/docs/contribution_guide.rst

@@ -361,7 +361,6 @@ and the tags associated with the class of runners to build on.
     * ``.linux_neoverse_n1``
     * ``.linux_neoverse_v1``
     * ``.linux_neoverse_v2``
-    * ``.linux_power``
     * ``.linux_skylake``
     * ``.linux_x86_64``
     * ``.linux_x86_64_v4``

lib/spack/docs/environments.rst

@@ -112,6 +112,19 @@ the original but may concretize differently in the presence of different
 explicit or default configuration settings (e.g., a different version of
 Spack or for a different user account).
 
+Environments created from a manifest will copy any included configs
+from relative paths inside the environment. Relative paths from
+outside the environment will cause errors, and absolute paths will be
+kept absolute. For example, if ``spack.yaml`` includes:
+
+.. code-block:: yaml
+
+   spack:
+     include: [./config.yaml]
+
+then the created environment will have its own copy of the file
+``config.yaml`` copied from the location in the original environment.
+
 Create an environment from a ``spack.lock`` file using:
 
 .. code-block:: console
@@ -160,7 +173,7 @@ accepts.  If an environment already exists then spack will simply activate it
 and ignore the create-specific flags.
 
 .. code-block:: console
-   
+
    $ spack env activate --create -p myenv
    # ...
    # [creates if myenv does not exist yet]
@@ -424,8 +437,8 @@ Developing Packages in a Spack Environment
 
 The ``spack develop`` command allows one to develop Spack packages in
 an environment. It requires a spec containing a concrete version, and
-will configure Spack to install the package from local source. 
-If a version is not provided from the command line interface then spack 
+will configure Spack to install the package from local source.
+If a version is not provided from the command line interface then spack
 will automatically pick the highest version the package has defined.
 This means any infinity versions (``develop``, ``main``, ``stable``) will be
 preferred in this selection process.
@@ -435,9 +448,9 @@ set, and Spack will ensure the package and its dependents are rebuilt
 any time the environment is installed if the package's local source
 code has been modified. Spack's native implementation to check for modifications
 is to check if ``mtime`` is newer than the installation.
-A custom check can be created by overriding the ``detect_dev_src_change`` method 
-in your package class. This is particularly useful for projects using custom spack repo's 
-to drive development and want to optimize performance. 
+A custom check can be created by overriding the ``detect_dev_src_change`` method
+in your package class. This is particularly useful for projects using custom spack repo's
+to drive development and want to optimize performance.
 
 Spack ensures that all instances of a
 developed package in the environment are concretized to match the
@@ -453,7 +466,7 @@ Further development on ``foo`` can be tested by re-installing the environment,
 and eventually committed and pushed to the upstream git repo.
 
 If the package being developed supports out-of-source builds then users can use the
-``--build_directory`` flag to control the location and name of the build directory. 
+``--build_directory`` flag to control the location and name of the build directory.
 This is a shortcut to set the ``package_attributes:build_directory`` in the
 ``packages`` configuration (see :ref:`assigning-package-attributes`).
 The supplied location will become the build-directory for that package in all future builds.

lib/spack/llnl/util/filesystem.py

@@ -668,7 +668,7 @@ def copy(src, dest, _permissions=False):
         _permissions (bool): for internal use only
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* matches multiple files but *dest* is
             not a directory
     """
@@ -679,7 +679,7 @@ def copy(src, dest, _permissions=False):
 
     files = glob.glob(src)
     if not files:
-        raise IOError("No such file or directory: '{0}'".format(src))
+        raise OSError("No such file or directory: '{0}'".format(src))
     if len(files) > 1 and not os.path.isdir(dest):
         raise ValueError(
             "'{0}' matches multiple files but '{1}' is not a directory".format(src, dest)
@@ -710,7 +710,7 @@ def install(src, dest):
         dest (str): the destination file or directory
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* matches multiple files but *dest* is
             not a directory
     """
@@ -748,7 +748,7 @@ def copy_tree(
         _permissions (bool): for internal use only
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* is a parent directory of *dest*
     """
     if _permissions:
@@ -762,7 +762,7 @@ def copy_tree(
 
     files = glob.glob(src)
     if not files:
-        raise IOError("No such file or directory: '{0}'".format(src))
+        raise OSError("No such file or directory: '{0}'".format(src))
 
     # For Windows hard-links and junctions, the source path must exist to make a symlink. Add
     # all symlinks to this list while traversing the tree, then when finished, make all
@@ -843,7 +843,7 @@ def install_tree(src, dest, symlinks=True, ignore=None):
         ignore (typing.Callable): function indicating which files to ignore
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* is a parent directory of *dest*
     """
     copy_tree(src, dest, symlinks=symlinks, ignore=ignore, _permissions=True)

lib/spack/llnl/util/link_tree.py

@@ -308,7 +308,7 @@ class LinkTree:
 
     def __init__(self, source_root):
         if not os.path.exists(source_root):
-            raise IOError("No such file or directory: '%s'", source_root)
+            raise OSError("No such file or directory: '%s'", source_root)
 
         self._root = source_root
 

lib/spack/llnl/util/lock.py

@@ -391,7 +391,7 @@ def _poll_lock(self, op: int) -> bool:
 
             return True
 
-        except IOError as e:
+        except OSError as e:
             # EAGAIN and EACCES == locked by another process (so try again)
             if e.errno not in (errno.EAGAIN, errno.EACCES):
                 raise

lib/spack/llnl/util/tty/log.py

@@ -918,7 +918,7 @@ def _writer_daemon(
                         try:
                             if stdin_file.read(1) == "v":
                                 echo = not echo
-                        except IOError as e:
+                        except OSError as e:
                             # If SIGTTIN is ignored, the system gives EIO
                             # to let the caller know the read failed b/c it
                             # was in the bg. Ignore that too.
@@ -1013,7 +1013,7 @@ def wrapped(*args, **kwargs):
         while True:
             try:
                 return function(*args, **kwargs)
-            except IOError as e:
+            except OSError as e:
                 if e.errno == errno.EINTR:
                     continue
                 raise

lib/spack/spack/__init__.py

@@ -10,7 +10,7 @@
 import spack.util.git
 
 #: PEP440 canonical <major>.<minor>.<micro>.<devN> string
-__version__ = "0.24.0.dev0"
+__version__ = "1.0.0.dev0"
 spack_version = __version__
 
 

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
@@ -458,11 +459,23 @@ def cmake(
     ) -> None:
         """Runs ``cmake`` in the build directory"""
 
-        # skip cmake phase if it is an incremental develop build
-        if spec.is_develop and os.path.isfile(
-            os.path.join(self.build_directory, "CMakeCache.txt")
-        ):
-            return
+        if spec.is_develop:
+            # skip cmake phase if it is an incremental develop build
+
+            # Determine the files that will re-run CMake that are generated from a successful
+            # configure step based on state
+            primary_generator = _extract_primary_generator(self.generator)
+            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/build_systems/cuda.py

@@ -15,7 +15,7 @@ class CudaPackage(PackageBase):
     """Auxiliary class which contains CUDA variant, dependencies and conflicts
     and is meant to unify and facilitate its usage.
 
-    Maintainers: ax3l, Rombur, davidbeckingsale
+    Maintainers: ax3l, Rombur, davidbeckingsale, pauleonix
     """
 
     # https://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#gpu-feature-list
@@ -47,6 +47,12 @@ class CudaPackage(PackageBase):
         "89",
         "90",
         "90a",
+        "100",
+        "100a",
+        "101",
+        "101a",
+        "120",
+        "120a",
     )
 
     # FIXME: keep cuda and cuda_arch separate to make usage easier until
@@ -99,39 +105,56 @@ def compute_capabilities(arch_list: Iterable[str]) -> List[str]:
     # CUDA version vs Architecture
     # https://en.wikipedia.org/wiki/CUDA#GPUs_supported
     # https://docs.nvidia.com/cuda/cuda-toolkit-release-notes/index.html#deprecated-features
+    # Tesla support:
     depends_on("cuda@:6.0", when="cuda_arch=10")
     depends_on("cuda@:6.5", when="cuda_arch=11")
     depends_on("cuda@2.1:6.5", when="cuda_arch=12")
     depends_on("cuda@2.1:6.5", when="cuda_arch=13")
 
+    # Fermi support:
     depends_on("cuda@3.0:8.0", when="cuda_arch=20")
     depends_on("cuda@3.2:8.0", when="cuda_arch=21")
 
+    # Kepler support:
     depends_on("cuda@5.0:10.2", when="cuda_arch=30")
     depends_on("cuda@5.0:10.2", when="cuda_arch=32")
     depends_on("cuda@5.0:11.8", when="cuda_arch=35")
     depends_on("cuda@6.5:11.8", when="cuda_arch=37")
 
+    # Maxwell support:
     depends_on("cuda@6.0:", when="cuda_arch=50")
     depends_on("cuda@6.5:", when="cuda_arch=52")
     depends_on("cuda@6.5:", when="cuda_arch=53")
 
+    # Pascal support:
     depends_on("cuda@8.0:", when="cuda_arch=60")
     depends_on("cuda@8.0:", when="cuda_arch=61")
     depends_on("cuda@8.0:", when="cuda_arch=62")
 
+    # Volta support:
     depends_on("cuda@9.0:", when="cuda_arch=70")
+    # Turing support:
     depends_on("cuda@9.0:", when="cuda_arch=72")
     depends_on("cuda@10.0:", when="cuda_arch=75")
 
+    # Ampere support:
     depends_on("cuda@11.0:", when="cuda_arch=80")
     depends_on("cuda@11.1:", when="cuda_arch=86")
     depends_on("cuda@11.4:", when="cuda_arch=87")
+    # Ada support:
     depends_on("cuda@11.8:", when="cuda_arch=89")
 
+    # Hopper support:
     depends_on("cuda@12.0:", when="cuda_arch=90")
     depends_on("cuda@12.0:", when="cuda_arch=90a")
 
+    # Blackwell support:
+    depends_on("cuda@12.8:", when="cuda_arch=100")
+    depends_on("cuda@12.8:", when="cuda_arch=100a")
+    depends_on("cuda@12.8:", when="cuda_arch=101")
+    depends_on("cuda@12.8:", when="cuda_arch=101a")
+    depends_on("cuda@12.8:", when="cuda_arch=120")
+    depends_on("cuda@12.8:", when="cuda_arch=120a")
     # From the NVIDIA install guide we know of conflicts for particular
     # platforms (linux, darwin), architectures (x86, powerpc) and compilers
     # (gcc, clang). We don't restrict %gcc and %clang conflicts to
@@ -163,6 +186,7 @@ def compute_capabilities(arch_list: Iterable[str]) -> List[str]:
         conflicts("%gcc@12:", when="+cuda ^cuda@:11.8")
         conflicts("%gcc@13:", when="+cuda ^cuda@:12.3")
         conflicts("%gcc@14:", when="+cuda ^cuda@:12.6")
+        conflicts("%gcc@15:", when="+cuda ^cuda@:12.8")
         conflicts("%clang@12:", when="+cuda ^cuda@:11.4.0")
         conflicts("%clang@13:", when="+cuda ^cuda@:11.5")
         conflicts("%clang@14:", when="+cuda ^cuda@:11.7")
@@ -171,6 +195,7 @@ def compute_capabilities(arch_list: Iterable[str]) -> List[str]:
         conflicts("%clang@17:", when="+cuda ^cuda@:12.3")
         conflicts("%clang@18:", when="+cuda ^cuda@:12.5")
         conflicts("%clang@19:", when="+cuda ^cuda@:12.6")
+        conflicts("%clang@20:", when="+cuda ^cuda@:12.8")
 
         # https://gist.github.com/ax3l/9489132#gistcomment-3860114
         conflicts("%gcc@10", when="+cuda ^cuda@:11.4.0")

lib/spack/spack/ci/__init__.py

@@ -14,7 +14,7 @@
 import zipfile
 from collections import namedtuple
 from typing import Callable, Dict, List, Set
-from urllib.request import HTTPHandler, Request, build_opener
+from urllib.request import Request
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
@@ -62,6 +62,8 @@
 
 PushResult = namedtuple("PushResult", "success url")
 
+urlopen = web_util.urlopen  # alias for mocking in tests
+
 
 def get_change_revisions():
     """If this is a git repo get the revisions to use when checking
@@ -627,29 +629,19 @@ def download_and_extract_artifacts(url, work_dir):
     if token:
         headers["PRIVATE-TOKEN"] = token
 
-    opener = build_opener(HTTPHandler)
-
-    request = Request(url, headers=headers)
-    request.get_method = lambda: "GET"
-
-    response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
-    response_code = response.getcode()
-
-    if response_code != 200:
-        msg = f"Error response code ({response_code}) in reproduce_ci_job"
-        raise SpackError(msg)
-
+    request = Request(url, headers=headers, method="GET")
     artifacts_zip_path = os.path.join(work_dir, "artifacts.zip")
+    os.makedirs(work_dir, exist_ok=True)
 
-    if not os.path.exists(work_dir):
-        os.makedirs(work_dir)
+    try:
+        response = urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
+        with open(artifacts_zip_path, "wb") as out_file:
+            shutil.copyfileobj(response, out_file)
+    except OSError as e:
+        raise SpackError(f"Error fetching artifacts: {e}")
 
-    with open(artifacts_zip_path, "wb") as out_file:
-        shutil.copyfileobj(response, out_file)
-
-    zip_file = zipfile.ZipFile(artifacts_zip_path)
-    zip_file.extractall(work_dir)
-    zip_file.close()
+    with zipfile.ZipFile(artifacts_zip_path) as zip_file:
+        zip_file.extractall(work_dir)
 
     os.remove(artifacts_zip_path)
 

lib/spack/spack/cmd/external.py

@@ -110,10 +110,7 @@ def external_find(args):
             # Note that KeyboardInterrupt does not subclass Exception
             # (so CTRL-C will terminate the program as expected).
             skip_msg = "Skipping manifest and continuing with other external checks"
-            if (isinstance(e, IOError) or isinstance(e, OSError)) and e.errno in [
-                errno.EPERM,
-                errno.EACCES,
-            ]:
+            if isinstance(e, OSError) and e.errno in (errno.EPERM, errno.EACCES):
                 # The manifest file does not have sufficient permissions enabled:
                 # print a warning and keep going
                 tty.warn("Unable to read manifest due to insufficient permissions.", skip_msg)

lib/spack/spack/cmd/test.py

@@ -177,16 +177,15 @@ def test_run(args):
         matching = spack.store.STORE.db.query_local(spec, hashes=hashes, explicit=explicit)
         if spec and not matching:
             tty.warn("No {0}installed packages match spec {1}".format(explicit_str, spec))
-            """
-            TODO: Need to write out a log message and/or CDASH Testing
-              output that package not installed IF continue to process
-              these issues here.
 
-            if args.log_format:
-                # Proceed with the spec assuming the test process
-                # to ensure report package as skipped (e.g., for CI)
-                specs_to_test.append(spec)
-            """
+            # TODO: Need to write out a log message and/or CDASH Testing
+            #   output that package not installed IF continue to process
+            #   these issues here.
+
+            # if args.log_format:
+            #     # Proceed with the spec assuming the test process
+            #     # to ensure report package as skipped (e.g., for CI)
+            #     specs_to_test.append(spec)
 
         specs_to_test.extend(matching)
 

lib/spack/spack/container/__init__.py

@@ -57,7 +57,7 @@ def validate(configuration_file):
     # Set the default value of the concretization strategy to unify and
     # warn if the user explicitly set another value
     env_dict.setdefault("concretizer", {"unify": True})
-    if not env_dict["concretizer"]["unify"] is True:
+    if env_dict["concretizer"]["unify"] is not True:
         warnings.warn(
             '"concretizer:unify" is not set to "true", which means the '
             "generated image may contain different variants of the same "

lib/spack/spack/environment/environment.py

@@ -581,7 +581,7 @@ def _error_on_nonempty_view_dir(new_root):
     # Check if the target path lexists
     try:
         st = os.lstat(new_root)
-    except (IOError, OSError):
+    except OSError:
         return
 
     # Empty directories are fine
@@ -861,7 +861,7 @@ def regenerate(self, concrete_roots: List[Spec]) -> None:
         ):
             try:
                 shutil.rmtree(old_root)
-            except (IOError, OSError) as e:
+            except OSError as e:
                 msg = "Failed to remove old view at %s\n" % old_root
                 msg += str(e)
                 tty.warn(msg)
@@ -2554,7 +2554,7 @@ def is_latest_format(manifest):
     try:
         with open(manifest, encoding="utf-8") as f:
             data = syaml.load(f)
-    except (OSError, IOError):
+    except OSError:
         return True
     top_level_key = _top_level_key(data)
     changed = spack.schema.env.update(data[top_level_key])
@@ -2634,6 +2634,32 @@ def _ensure_env_dir():
 
     shutil.copy(envfile, target_manifest)
 
+    # Copy relative path includes that live inside the environment dir
+    try:
+        manifest = EnvironmentManifestFile(environment_dir)
+    except Exception:
+        # error handling for bad manifests is handled on other code paths
+        return
+
+    includes = manifest[TOP_LEVEL_KEY].get("include", [])
+    for include in includes:
+        if os.path.isabs(include):
+            continue
+
+        abspath = pathlib.Path(os.path.normpath(environment_dir / include))
+        common_path = pathlib.Path(os.path.commonpath([environment_dir, abspath]))
+        if common_path != environment_dir:
+            tty.debug(f"Will not copy relative include from outside environment: {include}")
+            continue
+
+        orig_abspath = os.path.normpath(envfile.parent / include)
+        if not os.path.exists(orig_abspath):
+            tty.warn(f"Included file does not exist; will not copy: '{include}'")
+            continue
+
+        fs.touchp(abspath)
+        shutil.copy(orig_abspath, abspath)
+
 
 class EnvironmentManifestFile(collections.abc.Mapping):
     """Manages the in-memory representation of a manifest file, and its synchronization

lib/spack/spack/extensions.py

@@ -187,7 +187,7 @@ def path_for_extension(target_name: str, *, paths: List[str]) -> str:
         if name == target_name:
             return path
     else:
-        raise IOError('extension "{0}" not found'.format(target_name))
+        raise OSError('extension "{0}" not found'.format(target_name))
 
 
 def get_module(cmd_name):

lib/spack/spack/filesystem_view.py

@@ -427,7 +427,7 @@ def needs_file(spec, file):
             try:
                 with open(manifest_file, "r", encoding="utf-8") as f:
                     manifest = s_json.load(f)
-            except (OSError, IOError):
+            except OSError:
                 # if we can't load it, assume it doesn't know about the file.
                 manifest = {}
             return test_path in manifest
@@ -831,7 +831,7 @@ def get_spec_from_file(filename):
     try:
         with open(filename, "r", encoding="utf-8") as f:
             return spack.spec.Spec.from_yaml(f)
-    except IOError:
+    except OSError:
         return None
 
 

lib/spack/spack/hooks/absolutify_elf_sonames.py

@@ -26,7 +26,7 @@ def is_shared_library_elf(filepath):
         with open(filepath, "rb") as f:
             elf = parse_elf(f, interpreter=True, dynamic_section=True)
             return elf.has_pt_dynamic and (elf.has_soname or not elf.has_pt_interp)
-    except (IOError, OSError, ElfParsingError):
+    except (OSError, ElfParsingError):
         return False
 
 

lib/spack/spack/hooks/sbang.py

@@ -166,7 +166,7 @@ def filter_shebangs_in_directory(directory, filenames=None):
         # Only look at executable, non-symlink files.
         try:
             st = os.lstat(path)
-        except (IOError, OSError):
+        except OSError:
             continue
 
         if stat.S_ISLNK(st.st_mode) or stat.S_ISDIR(st.st_mode) or not st.st_mode & is_exe:

lib/spack/spack/installer.py

@@ -814,7 +814,7 @@ def get_depflags(self, pkg: "spack.package_base.PackageBase") -> int:
         # Include build dependencies if pkg is going to be built from sources, or
         # if build deps are explicitly requested.
         if include_build_deps or not (
-            cache_only or pkg.spec.installed and not pkg.spec.dag_hash() in self.overwrite
+            cache_only or pkg.spec.installed and pkg.spec.dag_hash() not in self.overwrite
         ):
             depflag |= dt.BUILD
         if self.run_tests(pkg):

lib/spack/spack/main.py

@@ -163,7 +163,7 @@ def format_help_sections(self, level):
         # lazily add all commands to the parser when needed.
         add_all_commands(self)
 
-        """Print help on subcommands in neatly formatted sections."""
+        # Print help on subcommands in neatly formatted sections.
         formatter = self._get_formatter()
 
         # Create a list of subcommand actions. Argparse internals are nasty!

lib/spack/spack/mirrors/mirror.py

@@ -64,7 +64,7 @@ def from_local_path(path: str):
     @staticmethod
     def from_url(url: str):
         """Create an anonymous mirror by URL. This method validates the URL."""
-        if not urllib.parse.urlparse(url).scheme in supported_url_schemes:
+        if urllib.parse.urlparse(url).scheme not in supported_url_schemes:
             raise ValueError(
                 f'"{url}" is not a valid mirror URL. '
                 f"Scheme must be one of {supported_url_schemes}."

lib/spack/spack/oci/opener.py

@@ -383,6 +383,7 @@ def create_opener():
     """Create an opener that can handle OCI authentication."""
     opener = urllib.request.OpenerDirector()
     for handler in [
+        urllib.request.ProxyHandler(),
         urllib.request.UnknownHandler(),
         urllib.request.HTTPSHandler(context=spack.util.web.ssl_create_default_context()),
         spack.util.web.SpackHTTPDefaultErrorHandler(),

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."""
@@ -13,6 +13,17 @@
 # import most common types used in packages
 from typing import Dict, List, Optional
 
+
+class tty:
+    import llnl.util.tty as _tty
+
+    debug = _tty.debug
+    error = _tty.error
+    info = _tty.info
+    msg = _tty.msg
+    warn = _tty.warn
+
+
 from llnl.util.filesystem import (
     FileFilter,
     FileList,
@@ -49,7 +60,6 @@
 )
 from llnl.util.symlink import symlink
 
-# These props will be overridden when the build env is set up.
 from spack.build_environment import MakeExecutable
 from spack.build_systems.aspell_dict import AspellDictPackage
 from spack.build_systems.autotools import AutotoolsPackage
@@ -136,8 +146,10 @@
 )
 from spack.phase_callbacks import run_after, run_before
 from spack.spec import Spec
+from spack.util.environment import EnvironmentModifications
 from spack.util.executable import Executable, ProcessError, which, which_string
 from spack.util.filesystem import fix_darwin_install_name
+from spack.util.prefix import Prefix
 from spack.variant import any_combination_of, auto_or_any_combination_of, disjoint_sets
 from spack.version import Version, ver
 

lib/spack/spack/package_base.py

@@ -31,6 +31,7 @@
 import llnl.util.tty as tty
 from llnl.util.lang import classproperty, memoized
 
+import spack
 import spack.compilers
 import spack.config
 import spack.dependency
@@ -60,16 +61,13 @@
 from spack.util.package_hash import package_hash
 from spack.util.typing import SupportsRichComparison
 from spack.version import GitVersion, StandardVersion
+from spack.version import ver as version_from_str
 
 FLAG_HANDLER_RETURN_TYPE = Tuple[
     Optional[Iterable[str]], Optional[Iterable[str]], Optional[Iterable[str]]
 ]
 FLAG_HANDLER_TYPE = Callable[[str, Iterable[str]], FLAG_HANDLER_RETURN_TYPE]
 
-"""Allowed URL schemes for spack packages."""
-_ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
-
-
 #: Filename for the Spack build/install log.
 _spack_build_logfile = "spack-build-out.txt"
 
@@ -701,9 +699,6 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
     #: Verbosity level, preserved across installs.
     _verbose = None
 
-    #: index of patches by sha256 sum, built lazily
-    _patches_by_hash = None
-
     #: Package homepage where users can find more information about the package
     homepage: Optional[str] = None
 
@@ -738,10 +733,22 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
     #: TestSuite instance used to manage stand-alone tests for 1+ specs.
     test_suite: Optional[Any] = None
 
+    #: compatibility requirements with Spack
+    #: if value is ``None``, requirements from repo are still applied
+    required_spack_version = None
+
     def __init__(self, spec):
         # this determines how the package should be built.
         self.spec: spack.spec.Spec = spec
 
+        # is this package more restrictive in compatibility than the repo is
+        if self.required_spack_version:
+            spack_version = version_from_str(spack.spack_version)
+            required_version = version_from_str(self.required_spack_version)
+            if not spack_version.satisfies(required_version):
+                msg = f"Package {self.name} requires Spack version {self.required_spack_version}."
+                raise PackageError(msg)
+
         # Allow custom staging paths for packages
         self.path = None
 

lib/spack/spack/patch.py

@@ -6,7 +6,7 @@
 import os
 import pathlib
 import sys
-from typing import Any, Dict, Optional, Set, Tuple, Type, Union
+from typing import Any, Dict, Optional, Tuple, Type, Union
 
 import llnl.util.filesystem
 from llnl.url import allowed_archive
@@ -503,38 +503,36 @@ def patch_for_package(self, sha256: str, pkg: "spack.package_base.PackageBase")
         patch_dict["sha256"] = sha256
         return from_dict(patch_dict, repository=self.repository)
 
-    def update_packages(self, pkgs_fullname: Set[str]) -> None:
+    def update_package(self, pkg_fullname: str) -> None:
         """Update the patch cache.
 
         Args:
             pkg_fullname: package to update.
         """
         # remove this package from any patch entries that reference it.
-        if self.index:
-            empty = []
-            for sha256, package_to_patch in self.index.items():
-                remove = []
-                for fullname, patch_dict in package_to_patch.items():
-                    if patch_dict["owner"] in pkgs_fullname:
-                        remove.append(fullname)
+        empty = []
+        for sha256, package_to_patch in self.index.items():
+            remove = []
+            for fullname, patch_dict in package_to_patch.items():
+                if patch_dict["owner"] == pkg_fullname:
+                    remove.append(fullname)
 
-                for fullname in remove:
-                    package_to_patch.pop(fullname)
+            for fullname in remove:
+                package_to_patch.pop(fullname)
 
-                if not package_to_patch:
-                    empty.append(sha256)
+            if not package_to_patch:
+                empty.append(sha256)
 
-            # remove any entries that are now empty
-            for sha256 in empty:
-                del self.index[sha256]
+        # remove any entries that are now empty
+        for sha256 in empty:
+            del self.index[sha256]
 
         # update the index with per-package patch indexes
-        for pkg_fullname in pkgs_fullname:
-            pkg_cls = self.repository.get_pkg_class(pkg_fullname)
-            partial_index = self._index_patches(pkg_cls, self.repository)
-            for sha256, package_to_patch in partial_index.items():
-                p2p = self.index.setdefault(sha256, {})
-                p2p.update(package_to_patch)
+        pkg_cls = self.repository.get_pkg_class(pkg_fullname)
+        partial_index = self._index_patches(pkg_cls, self.repository)
+        for sha256, package_to_patch in partial_index.items():
+            p2p = self.index.setdefault(sha256, {})
+            p2p.update(package_to_patch)
 
     def update(self, other: "PatchCache") -> None:
         """Update this cache with the contents of another.

lib/spack/spack/provider_index.py

@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Classes and functions to manage providers of virtual dependencies"""
-from typing import Dict, Iterable, List, Optional, Set, Union
+from typing import Dict, List, Optional, Set
 
 import spack.error
 import spack.spec
@@ -26,7 +26,7 @@ class _IndexBase:
     #: Calling providers_for(spec) will find specs that provide a
     #: matching implementation of MPI. Derived class need to construct
     #: this attribute according to the semantics above.
-    providers: Dict[str, Dict["spack.spec.Spec", Set["spack.spec.Spec"]]]
+    providers: Dict[str, Dict[str, Set[str]]]
 
     def providers_for(self, virtual_spec):
         """Return a list of specs of all packages that provide virtual
@@ -99,56 +99,66 @@ def __init__(
         self.repository = repository
         self.restrict = restrict
         self.providers = {}
-        if specs:
-            self.update_packages(specs)
 
-    def update_packages(self, specs: Iterable[Union[str, "spack.spec.Spec"]]):
+        specs = specs or []
+        for spec in specs:
+            if not isinstance(spec, spack.spec.Spec):
+                spec = spack.spec.Spec(spec)
+
+            if self.repository.is_virtual_safe(spec.name):
+                continue
+
+            self.update(spec)
+
+    def update(self, spec):
         """Update the provider index with additional virtual specs.
 
         Args:
             spec: spec potentially providing additional virtual specs
         """
-        for spec in specs:
-            if not isinstance(spec, spack.spec.Spec):
-                spec = spack.spec.Spec(spec)
+        if not isinstance(spec, spack.spec.Spec):
+            spec = spack.spec.Spec(spec)
 
-            if not spec.name or self.repository.is_virtual_safe(spec.name):
-                # Only non-virtual packages with name can provide virtual specs.
-                continue
+        if not spec.name:
+            # Empty specs do not have a package
+            return
 
-            pkg_provided = self.repository.get_pkg_class(spec.name).provided
-            for provider_spec_readonly, provided_specs in pkg_provided.items():
-                for provided_spec in provided_specs:
-                    # TODO: fix this comment.
-                    # We want satisfaction other than flags
-                    provider_spec = provider_spec_readonly.copy()
-                    provider_spec.compiler_flags = spec.compiler_flags.copy()
+        msg = "cannot update an index passing the virtual spec '{}'".format(spec.name)
+        assert not self.repository.is_virtual_safe(spec.name), msg
 
-                    if spec.intersects(provider_spec, deps=False):
-                        provided_name = provided_spec.name
+        pkg_provided = self.repository.get_pkg_class(spec.name).provided
+        for provider_spec_readonly, provided_specs in pkg_provided.items():
+            for provided_spec in provided_specs:
+                # TODO: fix this comment.
+                # We want satisfaction other than flags
+                provider_spec = provider_spec_readonly.copy()
+                provider_spec.compiler_flags = spec.compiler_flags.copy()
 
-                        provider_map = self.providers.setdefault(provided_name, {})
-                        if provided_spec not in provider_map:
-                            provider_map[provided_spec] = set()
+                if spec.intersects(provider_spec, deps=False):
+                    provided_name = provided_spec.name
 
-                        if self.restrict:
-                            provider_set = provider_map[provided_spec]
+                    provider_map = self.providers.setdefault(provided_name, {})
+                    if provided_spec not in provider_map:
+                        provider_map[provided_spec] = set()
 
-                            # If this package existed in the index before,
-                            # need to take the old versions out, as they're
-                            # now more constrained.
-                            old = {s for s in provider_set if s.name == spec.name}
-                            provider_set.difference_update(old)
+                    if self.restrict:
+                        provider_set = provider_map[provided_spec]
 
-                            # Now add the new version.
-                            provider_set.add(spec)
+                        # If this package existed in the index before,
+                        # need to take the old versions out, as they're
+                        # now more constrained.
+                        old = set([s for s in provider_set if s.name == spec.name])
+                        provider_set.difference_update(old)
 
-                        else:
-                            # Before putting the spec in the map, constrain
-                            # it so that it provides what was asked for.
-                            constrained = spec.copy()
-                            constrained.constrain(provider_spec)
-                            provider_map[provided_spec].add(constrained)
+                        # Now add the new version.
+                        provider_set.add(spec)
+
+                    else:
+                        # Before putting the spec in the map, constrain
+                        # it so that it provides what was asked for.
+                        constrained = spec.copy()
+                        constrained.constrain(provider_spec)
+                        provider_map[provided_spec].add(constrained)
 
     def to_json(self, stream=None):
         """Dump a JSON representation of this object.
@@ -183,13 +193,14 @@ def merge(self, other):
 
                 spdict[provided_spec] = spdict[provided_spec].union(opdict[provided_spec])
 
-    def remove_providers(self, pkgs_fullname: Set[str]):
+    def remove_provider(self, pkg_name):
         """Remove a provider from the ProviderIndex."""
         empty_pkg_dict = []
         for pkg, pkg_dict in self.providers.items():
             empty_pset = []
             for provided, pset in pkg_dict.items():
-                pset.difference_update(pkgs_fullname)
+                same_name = set(p for p in pset if p.fullname == pkg_name)
+                pset.difference_update(same_name)
 
                 if not pset:
                     empty_pset.append(provided)

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/repo.py

@@ -32,6 +32,7 @@
 import llnl.util.tty as tty
 from llnl.util.filesystem import working_dir
 
+import spack
 import spack.caches
 import spack.config
 import spack.error
@@ -40,6 +41,7 @@
 import spack.spec
 import spack.tag
 import spack.tengine
+import spack.version
 import spack.util.file_cache
 import spack.util.git
 import spack.util.naming as nm
@@ -49,6 +51,11 @@
 #: Package modules are imported as spack.pkg.<repo-namespace>.<pkg-name>
 ROOT_PYTHON_NAMESPACE = "spack.pkg"
 
+_required_repo_version = "0:"
+
+#: Version of the repo interface that this version of Spack is compatible with
+required_repo_version = spack.version.ver(_required_repo_version)
+
 
 def python_package_for_repo(namespace):
     """Returns the full namespace of a repository, given its relative one
@@ -465,7 +472,7 @@ def read(self, stream):
         """Read this index from a provided file object."""
 
     @abc.abstractmethod
-    def update(self, pkgs_fullname: Set[str]):
+    def update(self, pkg_fullname):
         """Update the index in memory with information about a package."""
 
     @abc.abstractmethod
@@ -482,8 +489,8 @@ def _create(self):
     def read(self, stream):
         self.index = spack.tag.TagIndex.from_json(stream, self.repository)
 
-    def update(self, pkgs_fullname: Set[str]):
-        self.index.update_packages({p.split(".")[-1] for p in pkgs_fullname})
+    def update(self, pkg_fullname):
+        self.index.update_package(pkg_fullname.split(".")[-1])
 
     def write(self, stream):
         self.index.to_json(stream)
@@ -498,14 +505,15 @@ def _create(self):
     def read(self, stream):
         self.index = spack.provider_index.ProviderIndex.from_json(stream, self.repository)
 
-    def update(self, pkgs_fullname: Set[str]):
+    def update(self, pkg_fullname):
+        name = pkg_fullname.split(".")[-1]
         is_virtual = (
-            lambda name: not self.repository.exists(name)
-            or self.repository.get_pkg_class(name).virtual
+            not self.repository.exists(name) or self.repository.get_pkg_class(name).virtual
         )
-        non_virtual_pkgs_fullname = {p for p in pkgs_fullname if not is_virtual(p.split(".")[-1])}
-        self.index.remove_providers(non_virtual_pkgs_fullname)
-        self.index.update_packages(non_virtual_pkgs_fullname)
+        if is_virtual:
+            return
+        self.index.remove_provider(pkg_fullname)
+        self.index.update(pkg_fullname)
 
     def write(self, stream):
         self.index.to_json(stream)
@@ -530,8 +538,8 @@ def read(self, stream):
     def write(self, stream):
         self.index.to_json(stream)
 
-    def update(self, pkgs_fullname: Set[str]):
-        self.index.update_packages(pkgs_fullname)
+    def update(self, pkg_fullname):
+        self.index.update_package(pkg_fullname)
 
 
 class RepoIndex:
@@ -621,7 +629,9 @@ def _build_index(self, name: str, indexer: Indexer):
                 if new_index_mtime != index_mtime:
                     needs_update = self.checker.modified_since(new_index_mtime)
 
-                indexer.update({f"{self.namespace}.{pkg_name}" for pkg_name in needs_update})
+                for pkg_name in needs_update:
+                    indexer.update(f"{self.namespace}.{pkg_name}")
+
                 indexer.write(new)
 
         return indexer.index
@@ -948,7 +958,7 @@ def check(condition, msg):
         self.config_file = os.path.join(self.root, repo_config_name)
         check(os.path.isfile(self.config_file), f"No {repo_config_name} found in '{root}'")
 
-        # Read configuration and validate namespace
+        # Read configuration and validate
         config = self._read_config()
         check(
             "namespace" in config,
@@ -962,6 +972,19 @@ def check(condition, msg):
             "Namespaces must be valid python identifiers separated by '.'",
         )
 
+        required_version = spack.version.ver(config.get("required_spack_version", ":"))
+        spack_version = spack.version.ver(spack.spack_version)
+        check(
+            spack_version.satisfies(required_version),
+            f"Repo {self.namespace} requires Spack version {required_version}",
+        )
+
+        repo_version = spack.version.ver(config.get("version", "0"))
+        check(
+            repo_version.satisfies(required_repo_version),
+            f"Spack requires repo version {required_repo_version}",
+        )
+
         # Set up 'full_namespace' to include the super-namespace
         self.full_namespace = python_package_for_repo(self.namespace)
 
@@ -1038,7 +1061,7 @@ def _read_config(self) -> Dict[str, str]:
 
                 return yaml_data["repo"]
 
-        except IOError:
+        except OSError:
             tty.die(f"Error reading {self.config_file} when opening {self.root}")
 
     def get(self, spec: "spack.spec.Spec") -> "spack.package_base.PackageBase":
@@ -1366,7 +1389,7 @@ def create_repo(root, namespace=None, subdir=packages_dir_name):
             if subdir != packages_dir_name:
                 config.write(f"  subdirectory: '{subdir}'\n")
 
-    except (IOError, OSError) as e:
+    except OSError as e:
         # try to clean up.
         if existed:
             shutil.rmtree(config_path, ignore_errors=True)

lib/spack/spack/reporters/cdash.py

@@ -1,6 +1,7 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import codecs
 import collections
 import hashlib
 import os
@@ -13,7 +14,7 @@
 import xml.sax.saxutils
 from typing import Dict, Optional
 from urllib.parse import urlencode
-from urllib.request import HTTPSHandler, Request, build_opener
+from urllib.request import Request
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import working_dir
@@ -24,10 +25,10 @@
 import spack.spec
 import spack.tengine
 import spack.util.git
+import spack.util.web as web_util
 from spack.error import SpackError
 from spack.util.crypto import checksum
 from spack.util.log_parse import parse_log_events
-from spack.util.web import ssl_create_default_context
 
 from .base import Reporter
 from .extract import extract_test_parts
@@ -433,7 +434,6 @@ def upload(self, filename):
         # Compute md5 checksum for the contents of this file.
         md5sum = checksum(hashlib.md5, filename, block_size=8192)
 
-        opener = build_opener(HTTPSHandler(context=ssl_create_default_context()))
         with open(filename, "rb") as f:
             params_dict = {
                 "build": self.buildname,
@@ -443,26 +443,21 @@ def upload(self, filename):
             }
             encoded_params = urlencode(params_dict)
             url = "{0}&{1}".format(self.cdash_upload_url, encoded_params)
-            request = Request(url, data=f)
+            request = Request(url, data=f, method="PUT")
             request.add_header("Content-Type", "text/xml")
             request.add_header("Content-Length", os.path.getsize(filename))
             if self.authtoken:
                 request.add_header("Authorization", "Bearer {0}".format(self.authtoken))
             try:
-                # By default, urllib2 only support GET and POST.
-                # CDash expects this file to be uploaded via PUT.
-                request.get_method = lambda: "PUT"
-                response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
+                response = web_util.urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
                 if self.current_package_name not in self.buildIds:
-                    resp_value = response.read()
-                    if isinstance(resp_value, bytes):
-                        resp_value = resp_value.decode("utf-8")
+                    resp_value = codecs.getreader("utf-8")(response).read()
                     match = self.buildid_regexp.search(resp_value)
                     if match:
                         buildid = match.group(1)
                         self.buildIds[self.current_package_name] = buildid
             except Exception as e:
-                print("Upload to CDash failed: {0}".format(e))
+                print(f"Upload to CDash failed: {e}")
 
     def finalize_report(self):
         if self.buildIds:

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__`.
         #
@@ -4726,7 +4727,10 @@ def __str__(self):
         bool_keys = []
         kv_keys = []
         for key in sorted_keys:
-            bool_keys.append(key) if isinstance(self[key].value, bool) else kv_keys.append(key)
+            if isinstance(self[key].value, bool):
+                bool_keys.append(key)
+            else:
+                kv_keys.append(key)
 
         # add spaces before and after key/value variants.
         string = io.StringIO()
@@ -4905,7 +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/tag.py

@@ -5,7 +5,6 @@
 import collections
 import copy
 from collections.abc import Mapping
-from typing import Set
 
 import spack.error
 import spack.repo
@@ -111,20 +110,23 @@ def merge(self, other):
             spkgs, opkgs = self.tags[tag], other.tags[tag]
             self.tags[tag] = sorted(list(set(spkgs + opkgs)))
 
-    def update_packages(self, pkg_names: Set[str]):
-        """Updates a package in the tag index."""
+    def update_package(self, pkg_name):
+        """Updates a package in the tag index.
+
+        Args:
+            pkg_name (str): name of the package to be removed from the index
+        """
+        pkg_cls = self.repository.get_pkg_class(pkg_name)
+
         # Remove the package from the list of packages, if present
         for pkg_list in self._tag_dict.values():
-            if pkg_names.isdisjoint(pkg_list):
-                continue
-            pkg_list[:] = [pkg for pkg in pkg_list if pkg not in pkg_names]
+            if pkg_name in pkg_list:
+                pkg_list.remove(pkg_name)
 
         # Add it again under the appropriate tags
-        for pkg_name in pkg_names:
-            pkg_cls = self.repository.get_pkg_class(pkg_name)
-            for tag in getattr(pkg_cls, "tags", []):
-                tag = tag.lower()
-                self._tag_dict[tag].append(pkg_cls.name)
+        for tag in getattr(pkg_cls, "tags", []):
+            tag = tag.lower()
+            self._tag_dict[tag].append(pkg_cls.name)
 
 
 class TagIndexError(spack.error.SpackError):

lib/spack/spack/test/ci.py

@@ -1,8 +1,10 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import io
 import os
 import subprocess
+from urllib.error import HTTPError
 
 import pytest
 
@@ -15,6 +17,7 @@
 import spack.paths as spack_paths
 import spack.repo as repo
 import spack.util.git
+from spack.test.conftest import MockHTTPResponse
 
 pytestmark = [pytest.mark.usefixtures("mock_packages")]
 
@@ -162,38 +165,8 @@ def test_import_signing_key(mock_gnupghome):
     ci.import_signing_key(signing_key)
 
 
-class FakeWebResponder:
-    def __init__(self, response_code=200, content_to_read=[]):
-        self._resp_code = response_code
-        self._content = content_to_read
-        self._read = [False for c in content_to_read]
-
-    def open(self, request, data=None, timeout=object()):
-        return self
-
-    def getcode(self):
-        return self._resp_code
-
-    def read(self, length=None):
-        if len(self._content) <= 0:
-            return None
-
-        if not self._read[-1]:
-            return_content = self._content[-1]
-            if length:
-                self._read[-1] = True
-            else:
-                self._read.pop()
-                self._content.pop()
-            return return_content
-
-        self._read.pop()
-        self._content.pop()
-        return None
-
-
-def test_download_and_extract_artifacts(tmpdir, monkeypatch, working_env):
-    os.environ.update({"GITLAB_PRIVATE_TOKEN": "faketoken"})
+def test_download_and_extract_artifacts(tmpdir, monkeypatch):
+    monkeypatch.setenv("GITLAB_PRIVATE_TOKEN", "faketoken")
 
     url = "https://www.nosuchurlexists.itsfake/artifacts.zip"
     working_dir = os.path.join(tmpdir.strpath, "repro")
@@ -201,10 +174,13 @@ def test_download_and_extract_artifacts(tmpdir, monkeypatch, working_env):
         spack_paths.test_path, "data", "ci", "gitlab", "artifacts.zip"
     )
 
-    with open(test_artifacts_path, "rb") as fd:
-        fake_responder = FakeWebResponder(content_to_read=[fd.read()])
+    def _urlopen_OK(*args, **kwargs):
+        with open(test_artifacts_path, "rb") as f:
+            return MockHTTPResponse(
+                "200", "OK", {"Content-Type": "application/zip"}, io.BytesIO(f.read())
+            )
 
-    monkeypatch.setattr(ci, "build_opener", lambda handler: fake_responder)
+    monkeypatch.setattr(ci, "urlopen", _urlopen_OK)
 
     ci.download_and_extract_artifacts(url, working_dir)
 
@@ -214,7 +190,11 @@ def test_download_and_extract_artifacts(tmpdir, monkeypatch, working_env):
     found_install = fs.find(working_dir, "install.sh")
     assert len(found_install) == 1
 
-    fake_responder._resp_code = 400
+    def _urlopen_500(*args, **kwargs):
+        raise HTTPError(url, 500, "Internal Server Error", {}, None)
+
+    monkeypatch.setattr(ci, "urlopen", _urlopen_500)
+
     with pytest.raises(spack.error.SpackError):
         ci.download_and_extract_artifacts(url, working_dir)
 
@@ -328,16 +308,14 @@ def test_get_spec_filter_list(mutable_mock_env_path, mutable_mock_repo):
     e1.add("hypre")
     e1.concretize()
 
-    """
-    Concretizing the above environment results in the following graphs:
+    # Concretizing the above environment results in the following graphs:
 
-    mpileaks -> mpich (provides mpi virtual dep of mpileaks)
-             -> callpath -> dyninst -> libelf
-                                    -> libdwarf -> libelf
-                         -> mpich (provides mpi dep of callpath)
+    # mpileaks -> mpich (provides mpi virtual dep of mpileaks)
+    #          -> callpath -> dyninst -> libelf
+    #                                 -> libdwarf -> libelf
+    #                      -> mpich (provides mpi dep of callpath)
 
-    hypre -> openblas-with-lapack (provides lapack and blas virtual deps of hypre)
-    """
+    # hypre -> openblas-with-lapack (provides lapack and blas virtual deps of hypre)
 
     touched = ["libdwarf"]
 

lib/spack/spack/test/cmd/env.py

@@ -1038,6 +1038,58 @@ def test_init_from_yaml(environment_from_manifest):
     assert not e2.specs_by_hash
 
 
+def test_init_from_yaml_relative_includes(tmp_path):
+    files = [
+        "relative_copied/packages.yaml",
+        "./relative_copied/compilers.yaml",
+        "repos.yaml",
+        "./config.yaml",
+    ]
+
+    manifest = f"""
+spack:
+  specs: []
+  include: {files}
+"""
+
+    e1_path = tmp_path / "e1"
+    e1_manifest = e1_path / "spack.yaml"
+    fs.mkdirp(e1_path)
+    with open(e1_manifest, "w", encoding="utf-8") as f:
+        f.write(manifest)
+
+    for f in files:
+        fs.touchp(e1_path / f)
+
+    e2 = _env_create("test2", init_file=e1_manifest)
+
+    for f in files:
+        assert os.path.exists(os.path.join(e2.path, f))
+
+
+def test_init_from_yaml_relative_includes_outside_env(tmp_path):
+    files = ["../outside_env_not_copied/repos.yaml"]
+
+    manifest = f"""
+spack:
+  specs: []
+  include: {files}
+"""
+
+    # subdir to ensure parent of environment dir is not shared
+    e1_path = tmp_path / "e1_subdir" / "e1"
+    e1_manifest = e1_path / "spack.yaml"
+    fs.mkdirp(e1_path)
+    with open(e1_manifest, "w", encoding="utf-8") as f:
+        f.write(manifest)
+
+    for f in files:
+        fs.touchp(e1_path / f)
+
+    with pytest.raises(spack.config.ConfigFileError, match="Detected 1 missing include"):
+        _ = _env_create("test2", init_file=e1_manifest)
+
+
 def test_env_view_external_prefix(tmp_path, mutable_database, mock_packages):
     fake_prefix = tmp_path / "a-prefix"
     fake_bin = fake_prefix / "bin"

lib/spack/spack/test/cmd/gc.py

@@ -139,7 +139,7 @@ def test_gc_except_specific_environments(mutable_database, mutable_mock_env_path
 def test_gc_except_nonexisting_dir_env(mutable_database, mutable_mock_env_path, tmpdir):
     output = gc("-ye", tmpdir.strpath, fail_on_error=False)
     assert "No such environment" in output
-    gc.returncode == 1
+    assert gc.returncode == 1
 
 
 @pytest.mark.db

lib/spack/spack/test/cmd/load.py

@@ -26,9 +26,9 @@ def test_manpath_trailing_colon(
         else ("--sh", "export %s=%s", ";")
     )
 
-    """Test that the commands generated by load add the MANPATH prefix
-    inspections. Also test that Spack correctly preserves the default/existing
-    manpath search path via a trailing colon"""
+    # Test that the commands generated by load add the MANPATH prefix
+    # inspections. Also test that Spack correctly preserves the default/existing
+    # manpath search path via a trailing colon
     install("mpileaks")
 
     sh_out = load(shell, "mpileaks")
@@ -81,7 +81,9 @@ def extract_value(output, variable):
 
         # Finally, do we list them in topo order?
         for i, pkg in enumerate(pkgs):
-            set(s.name for s in mpileaks_spec[pkg].traverse(direction="parents")) in set(pkgs[:i])
+            assert {s.name for s in mpileaks_spec[pkg].traverse(direction="parents")}.issubset(
+                pkgs[: i + 1]
+            )
 
         # Lastly, do we keep track that mpileaks was loaded?
         assert (

lib/spack/spack/test/concretization/flag_mixing.py

@@ -1,17 +1,6 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import pathlib
-
-import pytest
-
-import spack.concretize
-import spack.config
-import spack.environment as ev
-import spack.paths
-import spack.repo
-import spack.spec
-import spack.util.spack_yaml as syaml
 
 """
 These tests include the following package DAGs:
@@ -42,6 +31,18 @@
 y
 """
 
+import pathlib
+
+import pytest
+
+import spack.concretize
+import spack.config
+import spack.environment as ev
+import spack.paths
+import spack.repo
+import spack.spec
+import spack.util.spack_yaml as syaml
+
 
 @pytest.fixture
 def test_repo(mutable_config, monkeypatch, mock_stage):

lib/spack/spack/test/concretization/requirements.py

@@ -182,7 +182,7 @@ def test_requirement_adds_version_satisfies(
 
     # Sanity check: early version of T does not include U
     s0 = spack.concretize.concretize_one("t@2.0")
-    assert not ("u" in s0)
+    assert "u" not in s0
 
     conf_str = """\
 packages:

lib/spack/spack/test/install.py

@@ -458,7 +458,7 @@ def test_log_install_without_build_files(install_mockery):
     spec = spack.concretize.concretize_one("trivial-install-test-package")
 
     # Attempt installing log without the build log file
-    with pytest.raises(IOError, match="No such file or directory"):
+    with pytest.raises(OSError, match="No such file or directory"):
         spack.installer.log(spec.package)
 
 

lib/spack/spack/test/installer.py

@@ -470,7 +470,7 @@ def _repoerr(repo, name):
 
     # The call to install_tree will raise the exception since not mocking
     # creation of dependency package files within *install* directories.
-    with pytest.raises(IOError, match=path if sys.platform != "win32" else ""):
+    with pytest.raises(OSError, match=path if sys.platform != "win32" else ""):
         inst.dump_packages(spec, path)
 
     # Now try the error path, which requires the mock directory structure

lib/spack/spack/test/llnl/util/filesystem.py

@@ -82,7 +82,7 @@ def test_non_existing_src(self, stage):
         """Test using a non-existing source."""
 
         with fs.working_dir(str(stage)):
-            with pytest.raises(IOError, match="No such file or directory"):
+            with pytest.raises(OSError, match="No such file or directory"):
                 fs.copy("source/none", "dest")
 
     def test_multiple_src_file_dest(self, stage):
@@ -139,7 +139,7 @@ def test_non_existing_src(self, stage):
         """Test using a non-existing source."""
 
         with fs.working_dir(str(stage)):
-            with pytest.raises(IOError, match="No such file or directory"):
+            with pytest.raises(OSError, match="No such file or directory"):
                 fs.install("source/none", "dest")
 
     def test_multiple_src_file_dest(self, stage):
@@ -220,7 +220,7 @@ def test_non_existing_src(self, stage):
         """Test using a non-existing source."""
 
         with fs.working_dir(str(stage)):
-            with pytest.raises(IOError, match="No such file or directory"):
+            with pytest.raises(OSError, match="No such file or directory"):
                 fs.copy_tree("source/none", "dest")
 
     def test_parent_dir(self, stage):
@@ -301,7 +301,7 @@ def test_non_existing_src(self, stage):
         """Test using a non-existing source."""
 
         with fs.working_dir(str(stage)):
-            with pytest.raises(IOError, match="No such file or directory"):
+            with pytest.raises(OSError, match="No such file or directory"):
                 fs.install_tree("source/none", "dest")
 
     def test_parent_dir(self, stage):

lib/spack/spack/test/llnl/util/lock.py

@@ -93,28 +93,26 @@
     pass
 
 
-"""This is a list of filesystem locations to test locks in.  Paths are
-expanded so that %u is replaced with the current username. '~' is also
-legal and will be expanded to the user's home directory.
-
-Tests are skipped for directories that don't exist, so you'll need to
-update this with the locations of NFS, Lustre, and other mounts on your
-system.
-"""
+#: This is a list of filesystem locations to test locks in.  Paths are
+#: expanded so that %u is replaced with the current username. '~' is also
+#: legal and will be expanded to the user's home directory.
+#:
+#: Tests are skipped for directories that don't exist, so you'll need to
+#: update this with the locations of NFS, Lustre, and other mounts on your
+#: system.
 locations = [
     tempfile.gettempdir(),
     os.path.join("/nfs/tmp2/", getpass.getuser()),
     os.path.join("/p/lscratch*/", getpass.getuser()),
 ]
 
-"""This is the longest a failed multiproc test will take.
-Barriers will time out and raise an exception after this interval.
-In MPI mode, barriers don't time out (they hang).  See mpi_multiproc_test.
-"""
+#: This is the longest a failed multiproc test will take.
+#: Barriers will time out and raise an exception after this interval.
+#: In MPI mode, barriers don't time out (they hang).  See mpi_multiproc_test.
 barrier_timeout = 5
 
-"""This is the lock timeout for expected failures.
-This may need to be higher for some filesystems."""
+#: This is the lock timeout for expected failures.
+#: This may need to be higher for some filesystems.
 lock_fail_timeout = 0.1
 
 
@@ -286,9 +284,8 @@ def wait(self):
     comm.Barrier()  # barrier after each MPI test.
 
 
-"""``multiproc_test()`` should be called by tests below.
-``multiproc_test()`` will work for either MPI runs or for local runs.
-"""
+#: ``multiproc_test()`` should be called by tests below.
+#: ``multiproc_test()`` will work for either MPI runs or for local runs.
 multiproc_test = mpi_multiproc_test if mpi else local_multiproc_test
 
 
@@ -1339,7 +1336,7 @@ def test_poll_lock_exception(tmpdir, monkeypatch, err_num, err_msg):
     """Test poll lock exception handling."""
 
     def _lockf(fd, cmd, len, start, whence):
-        raise IOError(err_num, err_msg)
+        raise OSError(err_num, err_msg)
 
     with tmpdir.as_cwd():
         lockfile = "lockfile"
@@ -1351,7 +1348,7 @@ def _lockf(fd, cmd, len, start, whence):
         if err_num in [errno.EAGAIN, errno.EACCES]:
             assert not lock._poll_lock(fcntl.LOCK_EX)
         else:
-            with pytest.raises(IOError, match=err_msg):
+            with pytest.raises(OSError, match=err_msg):
                 lock._poll_lock(fcntl.LOCK_EX)
 
         monkeypatch.undo()

lib/spack/spack/test/modules/tcl.py

@@ -238,10 +238,7 @@ def test_exclude(self, modulefile_content, module_configuration, host_architectu
 
         assert len([x for x in content if "module load " in x]) == 1
 
-        # Catch "Exception" to avoid using FileNotFoundError on Python 3
-        # and IOError on Python 2 or common bases like EnvironmentError
-        # which are not officially documented
-        with pytest.raises(Exception):
+        with pytest.raises(FileNotFoundError):
             modulefile_content(f"callpath target={host_architecture_str}")
 
         content = modulefile_content(f"zmpi target={host_architecture_str}")

lib/spack/spack/test/repo.py

@@ -38,6 +38,27 @@ def extra_repo(tmp_path_factory, request):
     return spack.repo.Repo(str(repo_dir), cache=repo_cache), request.param
 
 
+@pytest.fixture(scope="function")
+def versioned_repo(tmp_path_factory, request):
+    def _execute(spack_version, repo_version):
+        repo_namespace = "extra_test_repo"
+        repo_dir = tmp_path_factory.mktemp(repo_namespace)
+        cache_dir = tmp_path_factory.mktemp("cache")
+        (repo_dir / "packages").mkdir(parents=True, exist_ok=True)
+        (repo_dir / "repo.yaml").write_text(
+            f"""
+repo:
+  namespace: extra_test_repo
+  required_spack_version: '{spack_version}'
+  version: '{repo_version}'
+"""
+        )
+        repo_cache = spack.util.file_cache.FileCache(str(cache_dir))
+        return spack.repo.Repo(str(repo_dir), cache=repo_cache)
+
+    return _execute
+
+
 def test_repo_getpkg(mutable_mock_repo):
     mutable_mock_repo.get_pkg_class("pkg-a")
     mutable_mock_repo.get_pkg_class("builtin.mock.pkg-a")
@@ -303,3 +324,24 @@ def test_get_repo(self, mock_test_cache):
         # foo is not there, raise
         with pytest.raises(spack.repo.UnknownNamespaceError):
             repo.get_repo("foo")
+
+
+def test_incompatible_repo(versioned_repo):
+    with pytest.raises(spack.repo.BadRepoError, match="requires Spack version"):
+        # test added after Spack passed version 0.22
+        versioned_repo(":0.22", ":")
+
+    with pytest.raises(spack.repo.BadRepoError, match="requires repo version"):
+        # ":a" < "0", and all Spack versions require at least "0:"
+        versioned_repo(":", ":a")
+
+
+def test_incompatible_package_version(mock_packages, monkeypatch):
+    spec = spack.concretize.concretize_one("pkg-a")
+    package = spack.repo.PATH.get(spec)
+
+    pkg_class = spec.package_class
+    monkeypatch.setattr(pkg_class, "required_spack_version", ":0.22")
+
+    with pytest.raises(spack.error.PackageError, match="requires Spack version"):
+        _ = spack.repo.PATH.get(spec)

lib/spack/spack/test/reporters.py

@@ -132,7 +132,8 @@ def test_reporters_extract_skipped(state):
     parts = spack.reporters.extract.extract_test_parts("fake", outputs)
 
     assert len(parts) == 1
-    parts[0]["completed"] == expected
+
+    assert parts[0]["completed"] == spack.reporters.extract.completed["skipped"]
 
 
 def test_reporters_skip_new():

lib/spack/spack/test/sbang.py

@@ -198,7 +198,7 @@ def script_dir(sbang_line):
     ],
 )
 def test_shebang_interpreter_regex(shebang, interpreter):
-    sbang.get_interpreter(shebang) == interpreter
+    assert sbang.get_interpreter(shebang) == interpreter
 
 
 def test_shebang_handling(script_dir, sbang_line):

lib/spack/spack/test/spec_dag.py

@@ -428,31 +428,29 @@ def test_copy_through_spec_build_interface(self):
         c2 = s["mpileaks"]["mpileaks"].copy()
         assert c0 == c1 == c2 == s
 
-    """
-    Here is the graph with deptypes labeled (assume all packages have a 'dt'
-    prefix). Arrows are marked with the deptypes ('b' for 'build', 'l' for
-    'link', 'r' for 'run').
+    # Here is the graph with deptypes labeled (assume all packages have a 'dt'
+    # prefix). Arrows are marked with the deptypes ('b' for 'build', 'l' for
+    # 'link', 'r' for 'run').
 
-        use -bl-> top
+    #     use -bl-> top
 
-        top -b->  build1
-        top -bl-> link1
-        top -r->  run1
+    #     top -b->  build1
+    #     top -bl-> link1
+    #     top -r->  run1
 
-        build1 -b->  build2
-        build1 -bl-> link2
-        build1 -r->  run2
+    #     build1 -b->  build2
+    #     build1 -bl-> link2
+    #     build1 -r->  run2
 
-        link1 -bl-> link3
+    #     link1 -bl-> link3
 
-        run1 -bl-> link5
-        run1 -r->  run3
+    #     run1 -bl-> link5
+    #     run1 -r->  run3
 
-        link3 -b->  build2
-        link3 -bl-> link4
+    #     link3 -b->  build2
+    #     link3 -bl-> link4
 
-        run3 -b-> build3
-    """
+    #     run3 -b-> build3
 
     @pytest.mark.parametrize(
         "spec_str,deptypes,expected",

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

lib/spack/spack/test/stage.py

@@ -125,7 +125,7 @@ def check_expand_archive(stage, stage_name, expected_file_list):
 
         assert os.path.isfile(fn)
         with open(fn, encoding="utf-8") as _file:
-            _file.read() == contents
+            assert _file.read() == contents
 
 
 def check_fetch(stage, stage_name):

lib/spack/spack/test/tag.py

@@ -154,6 +154,7 @@ def test_tag_no_tags(mock_packages):
 def test_tag_update_package(mock_packages):
     mock_index = mock_packages.tag_index
     index = spack.tag.TagIndex(repository=mock_packages)
-    index.update_packages(set(spack.repo.all_package_names()))
+    for name in spack.repo.all_package_names():
+        index.update_package(name)
 
     ensure_tags_results_equal(mock_index.tags, index.tags)

lib/spack/spack/test/util/compression.py

@@ -20,12 +20,7 @@
 
 datadir = os.path.join(spack_root, "lib", "spack", "spack", "test", "data", "compression")
 
-ext_archive = {}
-[
-    ext_archive.update({ext: ".".join(["Foo", ext])})
-    for ext in llnl.url.ALLOWED_ARCHIVE_TYPES
-    if "TAR" not in ext
-]
+ext_archive = {ext: f"Foo.{ext}" for ext in llnl.url.ALLOWED_ARCHIVE_TYPES if "TAR" not in ext}
 # Spack does not use Python native handling for tarballs or zip
 # Don't test tarballs or zip in native test
 native_archive_list = [

lib/spack/spack/test/util/editor.py

@@ -204,13 +204,13 @@ def test_no_editor():
     def assert_exec(exe, args):
         assert False
 
-    with pytest.raises(EnvironmentError, match=r"No text editor found.*"):
+    with pytest.raises(OSError, match=r"No text editor found.*"):
         ed.editor("/path/to/file", exec_fn=assert_exec)
 
     def assert_exec(exe, args):
         return False
 
-    with pytest.raises(EnvironmentError, match=r"No text editor found.*"):
+    with pytest.raises(OSError, match=r"No text editor found.*"):
         ed.editor("/path/to/file", exec_fn=assert_exec)
 
 
@@ -220,5 +220,5 @@ def test_exec_fn_executable(editor_var, good_exe, bad_exe):
     assert ed.editor(exec_fn=ed.executable)
 
     os.environ[editor_var] = bad_exe
-    with pytest.raises(EnvironmentError, match=r"No text editor found.*"):
+    with pytest.raises(OSError, match=r"No text editor found.*"):
         ed.editor(exec_fn=ed.executable)

lib/spack/spack/util/editor.py

@@ -9,7 +9,7 @@
 defined by the EDITOR environment variable if VISUAL is not set or the
 specified editor fails (e.g. no DISPLAY for a graphical editor). If
 neither variable is set, we fall back to one of several common editors,
-raising an EnvironmentError if we are unable to find one.
+raising an OSError if we are unable to find one.
 """
 import os
 import shlex
@@ -141,7 +141,7 @@ def try_env_var(var):
         return True
 
     # Fail if nothing could be found
-    raise EnvironmentError(
+    raise OSError(
         "No text editor found! Please set the VISUAL and/or EDITOR "
         "environment variable(s) to your preferred text editor."
     )

lib/spack/spack/util/ld_so_conf.py

@@ -46,7 +46,7 @@ def _process_ld_so_conf_queue(queue):
         try:
             with open(p, "rb") as f:
                 lines = f.readlines()
-        except (IOError, OSError):
+        except OSError:
             continue
 
         for line in lines:
@@ -132,7 +132,7 @@ def host_dynamic_linker_search_paths():
 
             if os.path.exists(possible_conf):
                 conf_file = possible_conf
-    except (IOError, OSError, elf_utils.ElfParsingError):
+    except (OSError, elf_utils.ElfParsingError):
         pass
 
     # Note: ld_so_conf doesn't error if the file does not exist.

lib/spack/spack/util/spack_yaml.py

@@ -436,8 +436,8 @@ def _dump_annotated(handler, data, stream=None):
     width = max(clen(a) for a in _ANNOTATIONS)
     formats = ["%%-%ds  %%s\n" % (width + cextra(a)) for a in _ANNOTATIONS]
 
-    for f, a, l in zip(formats, _ANNOTATIONS, lines):
-        stream.write(f % (a, l))
+    for fmt, annotation, line in zip(formats, _ANNOTATIONS, lines):
+        stream.write(fmt % (annotation, line))
 
     if getvalue:
         return getvalue()

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/.gitlab-ci.yml

@@ -59,11 +59,6 @@ default:
     SPACK_TARGET_PLATFORM: "linux"
     SPACK_TARGET_ARCH: "aarch64"
 
-.linux_power:
-  variables:
-    SPACK_TARGET_PLATFORM: "linux"
-    SPACK_TARGET_ARCH: "ppc64le"
-
 .win64-msvc2019:
   variables:
     SPACK_TARGET_PLATFORM: "win64"
@@ -352,35 +347,6 @@ e4s-oneapi-build:
     - artifacts: True
       job: e4s-oneapi-generate
 
-########################################
-# E4S on Power
-########################################
-.e4s-power-generate-tags-and-image:
-  image: { "name": "ghcr.io/spack/ubuntu20.04-runner-ppc64-gcc-11.4:2023.08.01", "entrypoint": [""] }
-  tags: ["spack", "public", "large", "ppc64le"]
-
-.e4s-power:
-  extends: [".linux_power"]
-  variables:
-    SPACK_CI_STACK_NAME: e4s-power
-
-e4s-power-generate:
-  extends: [ ".e4s-power", ".generate-x86_64", ".e4s-power-generate-tags-and-image"]
-  variables:
-    # Override concretization pool for metal runners
-    SPACK_CONCRETIZE_JOBS: 16
-
-e4s-power-build:
-  extends: [ ".e4s-power", ".build" ]
-  trigger:
-    include:
-      - artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
-        job: e4s-power-generate
-    strategy: depend
-  needs:
-    - artifacts: True
-      job: e4s-power-generate
-
 #########################################
 # Build tests for different build-systems
 #########################################
@@ -573,57 +539,6 @@ data-vis-sdk-build:
     - artifacts: True
       job: data-vis-sdk-generate
 
-########################################
-# AWS ISC Applications (x86_64)
-########################################
-
-# Call this AFTER .*-generate
-.aws-isc-overrides:
-  # This controls image for generate step; build step is controlled by spack.yaml
-  # Note that generator emits OS info for build so these should be the same.
-  image: { "name": "ghcr.io/spack/e4s-amazonlinux-2:v2023-03-09", "entrypoint": [""] }
-
-.aws-isc:
-  extends: [ ".linux_x86_64_v3" ]
-  variables:
-    SPACK_CI_STACK_NAME: aws-isc
-
-aws-isc-generate:
-  extends: [ ".aws-isc", ".generate-x86_64", ".aws-isc-overrides", ".tags-x86_64_v4" ]
-
-aws-isc-build:
-  extends: [ ".aws-isc", ".build" ]
-  trigger:
-    include:
-      - artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
-        job: aws-isc-generate
-    strategy: depend
-  needs:
-    - artifacts: True
-      job: aws-isc-generate
-
-# Parallel Pipeline for aarch64 (reuses override image, but generates and builds on aarch64)
-
-.aws-isc-aarch64:
-  extends: [ ".linux_aarch64" ]
-  variables:
-    SPACK_CI_STACK_NAME: aws-isc-aarch64
-
-aws-isc-aarch64-generate:
-  extends: [ ".aws-isc-aarch64", ".generate-aarch64", ".aws-isc-overrides" ]
-
-aws-isc-aarch64-build:
-  extends: [ ".aws-isc-aarch64", ".build" ]
-  trigger:
-    include:
-      - artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
-        job: aws-isc-aarch64-generate
-    strategy: depend
-  needs:
-    - artifacts: True
-      job: aws-isc-aarch64-generate
-
-
 ########################################
 # Spack Tutorial
 ########################################

share/spack/gitlab/cloud_pipelines/configs/linux/ppc64le/ci.yaml

@@ -1,22 +0,0 @@
-ci:
-  pipeline-gen:
-  - build-job:
-      tags: ["ppc64le"]
-      # Power runners overrides the default script
-      # - don't download make
-      # - no intermediate keys
-      script::
-      - uname -a || true
-      - grep -E 'vendor|model name' /proc/cpuinfo 2>/dev/null | sort -u || head -n10 /proc/cpuinfo 2>/dev/null || true
-      - nproc
-      - . "./share/spack/setup-env.sh"
-      - spack --version
-      - spack arch
-      - cd ${SPACK_CONCRETE_ENV_DIR}
-      - spack env activate --without-view .
-      - if [ -n "$SPACK_BUILD_JOBS" ]; then spack config add "config:build_jobs:$SPACK_BUILD_JOBS"; fi
-      - spack config add "config:install_tree:projections:${SPACK_JOB_SPEC_PKG_NAME}:'morepadding/{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}'"
-      - mkdir -p ${SPACK_ARTIFACTS_ROOT}/user_data
-      - if [[ -r /mnt/key/e4s.gpg ]]; then spack gpg trust /mnt/key/e4s.gpg; fi
-      - if [[ -r /mnt/key/spack_public_key.gpg ]]; then spack gpg trust /mnt/key/spack_public_key.gpg; fi
-      - spack --color=always --backtrace ci rebuild > >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_out.txt) 2> >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_err.txt >&2)

share/spack/gitlab/cloud_pipelines/configs/linux/ppc64le/concretizer.yaml

@@ -1,3 +0,0 @@
-concretizer:
-  targets:
-    granularity: generic

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@11.2
-    # 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@11.2
-    # 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/e4s-power/spack.yaml

@@ -1,271 +0,0 @@
-spack:
-  view: false
-
-  concretizer:
-    reuse: false
-    unify: false
-
-  packages:
-    all:
-      require: "%gcc@9.4.0 target=ppc64le"
-      compiler: [gcc@9.4.0]
-      providers:
-        blas: [openblas]
-        mpi: [mpich]
-      variants: +mpi cuda_arch=70
-    binutils:
-      variants: +ld +gold +headers +libiberty ~nls
-    hdf5:
-      variants: +fortran +hl +shared
-    libfabric:
-      variants: fabrics=sockets,tcp,udp,rxm
-    openblas:
-      variants: threads=openmp
-    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
-    mpi:
-      require: mpich
-    mpich:
-      require: '~wrapperrpath ~hwloc %gcc@9.4.0 target=ppc64le'
-    ncurses:
-      require: '@6.3 +termlib %gcc@9.4.0 target=ppc64le'
-    faodel:
-      require: "~tcmalloc %gcc@9.4.0 target=ppc64le"
-    tbb:
-      require: intel-tbb
-    vtk-m:
-      require: "+examples %gcc@9.4.0 target=ppc64le"
-    cuda:
-      require: "@11.4.4 %gcc@9.4.0 target=ppc64le"
-    paraview:
-      require: "+examples %gcc@9.4.0 target=ppc64le"
-
-
-  specs:
-  # CPU
-  - adios
-  - alquimia
-  - aml
-  - amrex
-  - arborx
-  - argobots
-  - axom
-  - bolt
-  - boost
-  - bricks
-  - butterflypack
-  - cabana
-  - caliper
-  - chai
-  - chapel ~rocm ~cuda
-  - charliecloud
-  - conduit
-  - cp2k +mpi
-  - datatransferkit
-  - drishti
-  - dxt-explorer
-  - dyninst
-  - exaworks
-  - fftx
-  - flecsi
-  - flit
-  - flux-core
-  - fortrilinos
-  - gasnet
-  - ginkgo
-  - globalarrays
-  - gmp
-  - gotcha
-  - gptune
-  - gromacs +cp2k ^cp2k +mpi build_system=cmake
-  - h5bench
-  - hdf5-vol-async
-  - hdf5-vol-cache
-  - hdf5-vol-log
-  - heffte +fftw
-  - hpctoolkit
-  - hpx networking=mpi
-  - hypre
-  - kokkos +openmp
-  - kokkos-kernels +openmp
-  - laghos
-  - lammps
-  - lbann
-  - legion
-  - libnrm
-  - libquo
-  - libunwind
-  - loki
-  - mercury
-  - metall
-  - mfem
-  - mgard +serial +openmp +timing +unstructured ~cuda
-  - mpark-variant
-  - mpifileutils ~xattr
-  - nccmp
-  - nco
-  - netlib-scalapack
-  - nrm
-  - nvhpc
-  - nwchem
-  - omega-h
-  - openfoam
-  - openmpi
-  - openpmd-api
-  - papi
-  - papyrus
-  - paraview ~cuda ~rocm
-  - parsec ~cuda
-  - pdt
-  - petsc
-  - plasma
-  - plumed
-  - precice
-  - pruners-ninja
-  - pumi
-  - py-amrex
-  - py-h5py
-  - py-jupyterhub
-  - py-libensemble
-  - py-petsc4py
-  - qthreads scheduler=distrib
-  - quantum-espresso
-  - raja
-  - rempi
-  - scr
-  - slate ~cuda
-  - slepc
-  - stc
-  - strumpack ~slate
-  - sundials
-  - superlu
-  - superlu-dist
-  - swig@4.0.2-fortran
-  - sz3
-  - tasmanian
-  - tau +mpi +python                       # +syscall fails: https://github.com/spack/spack/pull/40830#issuecomment-1790799772; tau: has issue with `spack env depfile` build
-  - trilinos +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
-  - turbine
-  - umap
-  - umpire
-  - upcxx
-  - wannier90
-  - warpx +python
-  - wps
-  - wrf
-  - xyce +mpi +shared +pymi +pymi_static_tpls
-  # INCLUDED IN ECP DAV CPU
-  - adios2
-  - ascent
-  - darshan-runtime
-  - darshan-util
-  - faodel
-  - hdf5
-  - libcatalyst
-  - parallel-netcdf
-  - py-cinemasci
-  - sz
-  - unifyfs
-  - veloc
-  # - visit                                 # libext, libxkbfile, libxrender, libxt, silo (https://github.com/spack/spack/issues/39538), cairo
-  - vtk-m
-  - zfp
-  # - ecp-data-vis-sdk ~cuda ~rocm +adios2 +ascent +cinema +darshan +faodel +hdf5 ~paraview +pnetcdf +sz +unifyfs +veloc ~visit +vtkm +zfp # +visit: libext, libxkbfile, libxrender, libxt, silo (https://github.com/spack/spack/issues/39538), cairo
-  # --
-  # - dealii                                # fltk: https://github.com/spack/spack/issues/38791
-  # - geopm-runtime                         # cairo: *** No autoreconf found, please install it ***
-  # - glvis                                 # glvis: https://github.com/spack/spack/issues/42839
-  # - libpressio +bitgrooming +bzip2 ~cuda ~cusz +fpzip +hdf5 +libdistributed +lua +openmp +python +sz +sz3 +unix +zfp # py-numcodecs: gcc: error: unrecognized command line option '-mno-sse2'; did you mean '-mno-isel'? gcc: error: unrecognized command line option '-mno-avx2'
-  # - phist +mpi                            # ghost@develop: gcc-9: error: unrecognized command line option '-march=native'; did you mean '-mcpu=native'?
-  # - variorum                              # variorum: https://github.com/spack/spack/issues/38786
-
-  # PYTHON PACKAGES
-  - opencv +python3
-  - py-jax
-  - py-jupyterlab
-  - py-matplotlib
-  - py-mpi4py
-  - py-notebook
-  - py-numba
-  - py-numpy
-  - py-openai
-  - py-pandas
-  - py-plotly
-  - py-pooch
-  - py-pytest
-  - py-scikit-learn
-  - py-scipy
-  - py-seaborn
-  # - py-horovod        # py-torch, py-tensorflow
-  # - py-tensorflow     # error
-  # - py-torch          # error
-
-  # CUDA NOARCH
-  - bricks +cuda
-  - cabana +cuda ^kokkos +wrapper +cuda_lambda +cuda cuda_arch=70
-  - flux-core +cuda
-  - hpctoolkit +cuda
-  - papi +cuda
-  - tau +mpi +cuda
-  # --
-  # - legion +cuda                          # legion: needs NVIDIA driver
-
-  # CUDA 70
-  - amrex +cuda cuda_arch=70
-  - arborx +cuda cuda_arch=70 ^kokkos +wrapper
-  - caliper +cuda cuda_arch=70
-  - chai +cuda cuda_arch=70 ^umpire ~shared
-  - ecp-data-vis-sdk ~rocm +adios2 ~ascent +hdf5 +vtkm +zfp ~paraview +cuda cuda_arch=70
-  - exago +mpi +python +raja +hiop ~rocm +cuda cuda_arch=70 ~ipopt ^hiop@1.0.0 ~sparse +mpi +raja ~rocm +cuda cuda_arch=70 #^raja@0.14.0
-  - flecsi +cuda cuda_arch=70
-  - ginkgo +cuda cuda_arch=70
-  - gromacs +cuda cuda_arch=70
-  - heffte +cuda cuda_arch=70
-  - hpx +cuda cuda_arch=70
-  - hypre +cuda cuda_arch=70
-  - kokkos +wrapper +cuda cuda_arch=70
-  - kokkos-kernels +cuda cuda_arch=70 ^kokkos +wrapper +cuda cuda_arch=70
-  - magma +cuda cuda_arch=70
-  - mfem +cuda cuda_arch=70
-  - mgard +serial +openmp +timing +unstructured +cuda cuda_arch=70
-  - omega-h +cuda cuda_arch=70
-  - parsec +cuda cuda_arch=70
-  - petsc +cuda cuda_arch=70
-  - raja +cuda cuda_arch=70
-  - slate +cuda cuda_arch=70
-  - slepc +cuda cuda_arch=70
-  - strumpack ~slate +cuda cuda_arch=70
-  - sundials +cuda cuda_arch=70
-  - superlu-dist +cuda cuda_arch=70
-  - tasmanian +cuda cuda_arch=70
-  - umpire ~shared +cuda cuda_arch=70
-  # INCLUDED IN ECP DAV CUDA
-  - adios2 +cuda cuda_arch=70
-  # - ascent +cuda cuda_arch=70             # ascent: https://github.com/spack/spack/issues/38045
-  - paraview +cuda cuda_arch=70
-  - vtk-m +cuda cuda_arch=70
-  - zfp +cuda cuda_arch=70
-  # --
-  # - axom +cuda cuda_arch=70               # axom: https://github.com/spack/spack/issues/29520
-  # - cp2k +mpi +cuda cuda_arch=70          # dbcsr
-  # - cusz +cuda cuda_arch=70               # cusz: https://github.com/spack/spack/issues/38787
-  # - dealii +cuda cuda_arch=70             # fltk: https://github.com/spack/spack/issues/38791
-  # - lammps +cuda cuda_arch=70             # lammps: needs NVIDIA driver
-  # - lbann +cuda cuda_arch=70              # lbann: https://github.com/spack/spack/issues/38788
-  # - libpressio +bitgrooming +bzip2 +fpzip +hdf5 +libdistributed +lua +openmp +python +sz +sz3 +unix +zfp +json +remote +netcdf +cusz +mgard +cuda cuda_arch=70 ^cusz +cuda cuda_arch=70 # depends_on("cuda@11.7.1:", when="+cuda")
-  # - py-torch +cuda cuda_arch=70           # skipped
-  # - trilinos +cuda cuda_arch=70           # trilinos: https://github.com/trilinos/Trilinos/issues/11630
-  # - upcxx +cuda cuda_arch=70              # upcxx: needs NVIDIA driver
-
-  ci:
-    pipeline-gen:
-    - build-job:
-        image: ghcr.io/spack/ubuntu20.04-runner-ppc64-gcc-11.4:2023.08.01
-
-  cdash:
-    build-group: E4S Power

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
-  - sherpa +analysis ~blackhat +gzip +hepmc3 +hepmc3root +lhapdf +lhole +openloops +pythia ~python ~recola ~rivet +root +ufo
+  - 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/gitlab/cloud_pipelines/stacks/tutorial/spack.yaml

@@ -18,7 +18,7 @@ spack:
         - hdf5+hl+mpi ^mpich
         - trilinos
         - trilinos +hdf5 ^hdf5+hl+mpi ^mpich
-        - gcc@12.3.0
+        - gcc@12
         - mpileaks
         - lmod@8.7.18
         - environment-modules

var/spack/repos/builtin.mock/repo.yaml

@@ -1,2 +1,4 @@
 repo:
   namespace: builtin.mock
+  version: 0
+  required_spack_version: '0.23:1.0.0.dev0'

var/spack/repos/builtin/packages/7zip/package.py

@@ -100,10 +100,8 @@ def install(self, spec, prefix):
                 for ext in exts:
                     glob_str = os.path.join(pth, ext)
                     files = glob.glob(glob_str)
-                    [
+                    for x in files:
                         shutil.copy(
                             os.path.join(self._7z_src_dir, x),
                             os.path.join(prefix, os.path.basename(x)),
                         )
-                        for x in files
-                    ]

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

@@ -179,7 +179,7 @@ def configure_args(self):
             if spec.satisfies("@:8"):
                 oapp("--with-dft-flavor=atompaw+libxc")
             else:
-                "--without-wannier90",
+                oapp("--without-wannier90")
 
         if spec.satisfies("+mpi"):
             oapp(f"CC={spec['mpi'].mpicc}")

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

@@ -32,7 +32,7 @@ def edit(self, spec, prefix):
         # Dictionary mapping: compiler-name : ACE config-label
         supported = {"intel": "_icc", "gcc": ""}
 
-        if not (self.compiler.name in supported):
+        if self.compiler.name not in supported:
             raise Exception(
                 "compiler " + self.compiler.name + " not supported in ace spack-package"
             )

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/additivefoam/package.py

@@ -5,11 +5,8 @@
 import inspect
 import os
 
-import llnl.util.tty as tty
-
 import spack.pkg.builtin.openfoam as openfoam
 from spack.package import *
-from spack.version import Version
 
 
 class Additivefoam(Package):

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/amdlibflame/package.py

@@ -202,8 +202,8 @@ def configure_args(self):
             args.append("--enable-void-return-complex")
 
         if spec.satisfies("@3.0:3.1 %aocc"):
-            """To enabled Fortran to C calling convention for
-            complex types when compiling with aocc flang"""
+            # To enable Fortran to C calling convention for complex types when compiling with
+            # aocc flang
             args.append("--enable-f2c-dotc")
 
         if spec.satisfies("@3.0.1: +ilp64"):

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

@@ -25,6 +25,7 @@ class Amrex(CMakePackage, CudaPackage, ROCmPackage):
     license("BSD-3-Clause")
 
     version("develop", branch="development")
+    version("25.02", sha256="2680a5a9afba04e211cd48d27799c5a25abbb36c6c3d2b6c13cd4757c7176b23")
     version("25.01", sha256="29eb35cf67d66b0fd0654282454c210abfadf27fcff8478b256e3196f237c74f")
     version("24.12", sha256="ca4b41ac73fabb9cf3600b530c9823eb3625f337d9b7b9699c1089e81c67fc67")
     version("24.11", sha256="31cc37b39f15e02252875815f6066046fc56a479bf459362b9889b0d6a202df6")
@@ -360,7 +361,7 @@ def cmake_args(self):
             args.append("-DAMReX_GPU_BACKEND=SYCL")
             # SYCL GPU backend only supported with Intel's oneAPI or DPC++ compilers
             sycl_compatible_compilers = ["icpx"]
-            if not (os.path.basename(self.compiler.cxx) in sycl_compatible_compilers):
+            if os.path.basename(self.compiler.cxx) not in sycl_compatible_compilers:
                 raise InstallError(
                     "AMReX's SYCL GPU Backend requires the oneAPI CXX (icpx) compiler."
                 )

var/spack/repos/builtin/packages/anaconda3/package.py

@@ -6,7 +6,6 @@
 from os.path import split
 
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 
 class Anaconda3(Package):

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

@@ -2,7 +2,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from llnl.util import tty
 
 from spack.package import *
 from spack.pkg.builtin.llvm import LlvmDetection

var/spack/repos/builtin/packages/aocl-da/package.py

@@ -5,7 +5,6 @@
 import os
 
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 
 class AoclDa(CMakePackage):

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

@@ -6,8 +6,6 @@
 import os
 import socket
 
-import llnl.util.tty as tty
-
 from spack.build_systems.cmake import CMakeBuilder
 from spack.package import *
 

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

@@ -3,8 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
-import llnl.util.tty as tty
-
 from spack.package import *
 from spack.util.environment import set_env
 

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

@@ -9,8 +9,6 @@
 import sys
 from os import environ as env
 
-import llnl.util.tty as tty
-
 from spack.package import *
 
 

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/bcl2fastq2/package.py

@@ -5,8 +5,6 @@
 import glob
 import os
 
-import llnl.util.tty as tty
-
 from spack.package import *
 from spack.pkg.builtin.boost import Boost
 

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

@@ -118,7 +118,7 @@ class Berkeleygw(MakefilePackage):
     def edit(self, spec, prefix):
         # archive is a tar file, despite the .gz expension
         tar = which("tar")
-        tar("-x", "-f", self.stage.archive_file, "--strip-components=1")
+        tar("-x", "-o", "-f", self.stage.archive_file, "--strip-components=1")
 
         # get generic arch.mk template
         if spec.satisfies("+mpi"):

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

@@ -160,8 +160,11 @@ class Binutils(AutotoolsPackage, GNUMirrorPackage):
 
     with when("platform=darwin"):
         conflicts("+gold", msg="Binutils cannot build linkers on macOS")
+        # 2.41 doesn't seem to have any problems.
         conflicts(
-            "libs=shared", when="@2.37:2.40", msg="https://github.com/spack/spack/issues/35817"
+            "libs=shared",
+            when="@2.37:2.40,2.42:",
+            msg="https://github.com/spack/spack/issues/35817",
         )
 
     conflicts(

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

@@ -4,8 +4,6 @@
 
 import os
 
-import llnl.util.tty as tty
-
 from spack.package import *
 from spack.package_test import compare_output
 from spack.pkg.builtin.boost import Boost

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

@@ -19,6 +19,11 @@ class Cdo(AutotoolsPackage):
 
     maintainers("skosukhin", "Try2Code")
 
+    version(
+        "2.5.0",
+        sha256="e865c05c1b52fd76b80e33421554db81b38b75210820bdc40e8690f4552f68e2",
+        url="https://code.mpimet.mpg.de/attachments/download/29786/cdo-2.5.0.tar.gz",
+    )
     version(
         "2.4.4",
         sha256="49f50bd18dacd585e9518cfd4f55548f692426edfb3b27ddcd1c653eab53d063",

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/charmpp/package.py

@@ -276,7 +276,7 @@ def charmarch(self):
     #            build-target=LIBS backend={0}'.format(b))
 
     def install(self, spec, prefix):
-        if not ("backend=mpi" in self.spec) or not ("backend=netlrts" in self.spec):
+        if "backend=mpi" not in self.spec or "backend=netlrts" not in self.spec:
             if self.spec.satisfies("+pthreads"):
                 raise InstallError(
                     "The pthreads option is only available on the Netlrts and MPI network layers."
@@ -396,7 +396,7 @@ def install(self, spec, prefix):
                         copy(filepath, tmppath)
                         os.remove(filepath)
                         os.rename(tmppath, filepath)
-                    except (IOError, OSError):
+                    except OSError:
                         pass
 
         tmp_path = join_path(builddir, "tmp")

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

@@ -8,7 +8,6 @@
 import spack.user_environment
 from spack.package import *
 from spack.pkg.builtin.clingo import Clingo
-from spack.util.environment import EnvironmentModifications
 
 
 class ClingoBootstrap(Clingo):

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

@@ -30,11 +30,13 @@ class Cmake(Package):
     license("BSD-3-Clause")
 
     version("master", branch="master")
+    version("3.31.5", sha256="66fb53a145648be56b46fa9e8ccade3a4d0dfc92e401e52ce76bdad1fea43d27")
     version("3.31.4", sha256="a6130bfe75f5ba5c73e672e34359f7c0a1931521957e8393a5c2922c8b0f7f25")
     version("3.31.3", sha256="fac45bc6d410b49b3113ab866074888d6c9e9dc81a141874446eb239ac38cb87")
     version("3.31.2", sha256="42abb3f48f37dbd739cdfeb19d3712db0c5935ed5c2aef6c340f9ae9114238a2")
     version("3.31.1", sha256="c4fc2a9bd0cd5f899ccb2fb81ec422e175090bc0de5d90e906dd453b53065719")
     version("3.31.0", sha256="300b71db6d69dcc1ab7c5aae61cbc1aa2778a3e00cbd918bc720203e311468c3")
+    version("3.30.7", sha256="470e44d9c7caa3bd869ef953071b84f565b5d378d0a9eccbbbcd72031f21b9de")
     version("3.30.6", sha256="a7aa25cdd8545156fe0fec95ebbd53cb2b5173a8717e227f6e8a755185c168cf")
     version("3.30.5", sha256="9f55e1a40508f2f29b7e065fa08c29f82c402fa0402da839fffe64a25755a86d")
     version("3.30.4", sha256="c759c97274f1e7aaaafcb1f0d261f9de9bf3a5d6ecb7e2df616324a46fe704b2")

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/conda4aarch64/package.py

@@ -3,7 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 
 class Conda4aarch64(Package):

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

@@ -8,8 +8,6 @@
 import socket
 from os import environ as env
 
-import llnl.util.tty as tty
-
 from spack.package import *
 
 

var/spack/repos/builtin/packages/cp2k/package.py

@@ -38,10 +38,11 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
     git = "https://github.com/cp2k/cp2k.git"
     list_url = "https://github.com/cp2k/cp2k/releases"
 
-    maintainers("dev-zero", "mtaillefumier")
+    maintainers("dev-zero", "mtaillefumier", "RMeli", "abussy")
 
     license("GPL-2.0-or-later")
 
+    version("2025.1", sha256="65c8ad5488897b0f995919b9fa77f2aba4b61677ba1e3c19bb093d5c08a8ce1d")
     version("2024.3", sha256="a6eeee773b6b1fb417def576e4049a89a08a0ed5feffcd7f0b33c7d7b48f19ba")
     version("2024.2", sha256="cc3e56c971dee9e89b705a1103765aba57bf41ad39a11c89d3de04c8b8cdf473")
     version("2024.1", sha256="a7abf149a278dfd5283dc592a2c4ae803b37d040df25d62a5e35af5c4557668f")
@@ -115,7 +116,9 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
     )
     variant("pytorch", default=False, description="Enable libtorch support")
     variant("quip", default=False, description="Enable quip support")
+    variant("dftd4", when="@2024.2:", default=False, description="Enable DFT-D4 support")
     variant("mpi_f08", default=False, description="Use MPI F08 module")
+    variant("smeagol", default=False, description="Enable libsmeagol support", when="@2025.2:")
 
     variant(
         "enable_regtests",
@@ -156,6 +159,7 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
     )
 
     depends_on("python@3", type="build")
+    depends_on("pkgconfig", type="build", when="build_system=cmake")
 
     depends_on("blas")
     depends_on("lapack")
@@ -193,13 +197,14 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
             )
 
     with when("+libxc"):
-        depends_on("pkgconfig", type="build", when="@7.0:")
+        depends_on("pkgconfig", type="build", when="@7.0: ^libxc@:6")
         depends_on("libxc@4.0.3:4", when="@7.0:8.1")
         depends_on("libxc@5.1.3:5.1", when="@8.2:8")
         depends_on("libxc@5.1.7:5.1", when="@9:2022.2")
         depends_on("libxc@6.1:", when="@2023.1:")
         depends_on("libxc@6.2:", when="@2023.2:")
         depends_on("libxc@:6", when="@:2024.3")
+        depends_on("libxc@7 build_system=cmake", when="@2025.2:")
 
     with when("+spla"):
         depends_on("spla+cuda+fortran", when="+cuda")
@@ -260,6 +265,8 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
         depends_on("plumed+mpi", when="+mpi")
         depends_on("plumed~mpi", when="~mpi")
 
+    depends_on("libsmeagol", when="+smeagol")
+
     # while we link statically against PEXSI, its own deps may be linked in
     # dynamically, therefore can't set this as pure build-type dependency.
     depends_on("pexsi+fortran@0.10.0:", when="+pexsi")
@@ -290,6 +297,8 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
 
     depends_on("spglib", when="+spglib")
 
+    depends_on("dftd4@3.6.0: build_system=cmake", when="+dftd4")
+
     with when("build_system=cmake"):
         depends_on("cmake@3.22:", type="build")
 
@@ -621,6 +630,18 @@ def edit(self, pkg, spec, prefix):
             ldflags += [spglib.search_flags]
             libs.append(spglib.ld_flags)
 
+        if spec.satisfies("+dftd4"):
+            cppflags += ["-D__DFTD4"]
+            dftd4 = spec["dftd4"].libs
+            ldflags += [dftd4.search_flags]
+            libs.append(dftd4.ld_flags)
+
+        if spec.satisfies("+smeagol"):
+            cppflags += ["-D__SMEAGOL"]
+            smeagol = spec["libsmeagol"].libs
+            ldflags += [smeagol.search_flags]
+            libs.append(smeagol.ld_flags)
+
         cc = spack_cc if "~mpi" in spec else spec["mpi"].mpicc
         cxx = spack_cxx if "~mpi" in spec else spec["mpi"].mpicxx
         fc = spack_fc if "~mpi" in spec else spec["mpi"].mpifc
@@ -763,8 +784,8 @@ def edit(self, pkg, spec, prefix):
                     "Point environment variable LIBSMM_PATH to "
                     "the absolute path of the libsmm.a file"
                 )
-            except IOError:
-                raise IOError(
+            except OSError:
+                raise OSError(
                     "The file LIBSMM_PATH pointed to does not "
                     "exist. Note that it must be absolute path."
                 )
@@ -994,7 +1015,9 @@ def cmake_args(self):
             self.define_from_variant("CP2K_USE_VORI", "libvori"),
             self.define_from_variant("CP2K_USE_SPLA", "spla"),
             self.define_from_variant("CP2K_USE_QUIP", "quip"),
+            self.define_from_variant("CP2K_USE_DFTD4", "dftd4"),
             self.define_from_variant("CP2K_USE_MPI_F08", "mpi_f08"),
+            self.define_from_variant("CP2K_USE_LIBSMEAGOL", "smeagol"),
         ]
 
         # we force the use elpa openmp threading support. might need to be revisited though

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

@@ -15,6 +15,7 @@ class Cppgsl(CMakePackage):
     license("MIT")
 
     version("main", branch="main")
+    version("4.1.0", sha256="0a227fc9c8e0bf25115f401b9a46c2a68cd28f299d24ab195284eb3f1d7794bd")
     version("4.0.0", sha256="f0e32cb10654fea91ad56bde89170d78cfbf4363ee0b01d8f097de2ba49f6ce9")
     version("3.1.0", sha256="d3234d7f94cea4389e3ca70619b82e8fb4c2f33bb3a070799f1e18eef500a083")
     version("2.1.0", sha256="ef73814657b073e1be86c8f7353718771bf4149b482b6cb54f99e79b23ff899d")
@@ -32,6 +33,7 @@ class Cppgsl(CMakePackage):
     )
 
     depends_on("cmake@3.1.3:", type="build")
+    depends_on("cmake@3.14:", type="build", when="@4.1:")
 
     def cmake_args(self):
         return [