vtk: relax seacas dependency

* Honor package-specified cmake_prefix_paths at runtime

* Add paths in the correct order and prune duplicates

* Normalize paths for windows' sake

.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: 4cdb0bf15f04ab6b49041d5ef1bfd9644cce7f33
+        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/requirements/style/requirements.txt

@@ -1,7 +1,7 @@
-black==24.10.0
+black==25.1.0
 clingo==5.7.1
-flake8==7.1.1
-isort==5.13.2
-mypy==1.11.2
+flake8==7.1.2
+isort==6.0.0
+mypy==1.15.0
 types-six==1.17.0.20241205
 vermin==1.6.0

.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/concretizer.yaml

@@ -43,6 +43,28 @@ concretizer:
     # (e.g. py-setuptools, cmake etc.)
     # "full" (experimental): allows separation of the entire build-tool stack (e.g. the entire "cmake" subDAG)
     strategy: minimal
+    # Maximum number of duplicates in a DAG, when using a strategy that allows duplicates. "default" is the
+    # number used if there isn't a more specific alternative
+    max_dupes:
+      default: 1
+      # Virtuals
+      c: 2
+      cxx: 2
+      fortran: 1
+      # Regular packages
+      cmake: 2
+      gmake: 2
+      python: 2
+      python-venv: 2
+      py-cython: 2
+      py-flit-core: 2
+      py-pip: 2
+      py-setuptools: 2
+      py-wheel: 2
+      xcb-proto: 2
+      # Compilers
+      gcc: 2
+      llvm: 2
   # Option to specify compatibility between operating systems for reuse of compilers and packages
   # Specified as a key: [list] where the key is the os that is being targeted, and the list contains the OS's
   # it can reuse. Note this is a directional compatibility so mutual compatibility between two OS's
@@ -63,3 +85,7 @@ concretizer:
   # Setting this to false yields unreproducible results, so we advise to use that value only
   # for debugging purposes (e.g. check which constraints can help Spack concretize faster).
   error_on_timeout: true
+
+  # Static analysis may reduce the concretization time by generating smaller ASP problems, in
+  # cases where there are requirements that prevent part of the search space to be explored.
+  static_analysis: false

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/basic_usage.rst

@@ -1761,19 +1761,24 @@ Verifying installations
 The ``spack verify`` command can be used to verify the validity of
 Spack-installed packages any time after installation.
 
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+``spack verify manifest``
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
 At installation time, Spack creates a manifest of every file in the
 installation prefix. For links, Spack tracks the mode, ownership, and
 destination. For directories, Spack tracks the mode, and
 ownership. For files, Spack tracks the mode, ownership, modification
-time, hash, and size. The Spack verify command will check, for every
-file in each package, whether any of those attributes have changed. It
-will also check for newly added files or deleted files from the
-installation prefix. Spack can either check all installed packages
+time, hash, and size. The ``spack verify manifest`` command will check,
+for every file in each package, whether any of those attributes have
+changed. It will also check for newly added files or deleted files from
+the installation prefix. Spack can either check all installed packages
 using the `-a,--all` or accept specs listed on the command line to
 verify.
 
-The ``spack verify`` command can also verify for individual files that
-they haven't been altered since installation time. If the given file
+The ``spack verify manifest`` command can also verify for individual files
+that they haven't been altered since installation time. If the given file
 is not in a Spack installation prefix, Spack will report that it is
 not owned by any package. To check individual files instead of specs,
 use the ``-f,--files`` option.
@@ -1788,6 +1793,22 @@ check only local packages (as opposed to those used transparently from
 ``upstream`` spack instances) and the ``-j,--json`` option to output
 machine-readable json data for any errors.
 
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+``spack verify libraries``
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``spack verify libraries`` command can be used to verify that packages
+do not have accidental system dependencies. This command scans the install
+prefixes of packages for executables and shared libraries, and resolves
+their needed libraries in their RPATHs. When needed libraries cannot be
+located, an error is reported. This typically indicates that a package
+was linked against a system library, instead of a library provided by
+a Spack package.
+
+This verification can also be enabled as a post-install hook by setting
+``config:shared_linking:missing_library_policy`` to ``error`` or ``warn``
+in :ref:`config.yaml <config-yaml>`.
+
 -----------------------
 Filesystem requirements
 -----------------------

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/conf.py

@@ -223,6 +223,10 @@ def setup(sphinx):
     ("py:class", "spack.compiler.CompilerCache"),
     # TypeVar that is not handled correctly
     ("py:class", "llnl.util.lang.T"),
+    ("py:class", "llnl.util.lang.KT"),
+    ("py:class", "llnl.util.lang.VT"),
+    ("py:obj", "llnl.util.lang.KT"),
+    ("py:obj", "llnl.util.lang.VT"),
 ]
 
 # The reST default role (used for this markup: `text`) to use for all documents.

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/docs/pipelines.rst

@@ -820,6 +820,69 @@ presence of a ``SPACK_CDASH_AUTH_TOKEN`` environment variable during the
 build group on CDash called "Release Testing" (that group will be created if
 it didn't already exist).
 
+.. _ci_artifacts:
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+CI Artifacts Directory Layout
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When running the CI build using the command ``spack ci rebuild`` a number of directories are created for
+storing data generated during the CI job. The default root directory for artifacts is ``job_scratch_root``.
+This can be overridden by passing the argument ``--artifacts-root`` to the ``spack ci generate`` command
+or by setting the ``SPACK_ARTIFACTS_ROOT`` environment variable in the build job scripts.
+
+The top level directories under the artifact root are ``concrete_environment``, ``logs``, ``reproduction``,
+``tests``, and ``user_data``. Spack does not restrict what is written to any of these directories nor does
+it require user specified files be written to any specific directory.
+
+------------------------
+``concrete_environment``
+------------------------
+
+The directory ``concrete_environment`` is used to communicate the ci generate processed ``spack.yaml`` and
+the concrete ``spack.lock`` for the CI environment.
+
+--------
+``logs``
+--------
+
+The directory ``logs`` contains the spack build log, ``spack-build-out.txt``, and the spack build environment
+modification file, ``spack-build-mod-env.txt``. Additionally all files specified by the packages ``Builder``
+property ``archive_files`` are also copied here (ie. ``CMakeCache.txt`` in ``CMakeBuilder``).
+
+----------------
+``reproduction``
+----------------
+
+The directory ``reproduction`` is used to store the files needed by the ``spack reproduce-build`` command.
+This includes ``repro.json``, copies of all of the files in ``concrete_environment``, the concrete spec
+JSON file for the current spec being built, and all of the files written in the artifacts root directory.
+
+The ``repro.json`` file is not versioned and is only designed to work with the version of spack CI was run with.
+An example of what a ``repro.json`` may look like is here.
+
+.. code:: json
+
+  {
+    "job_name": "adios2@2.9.2 /feaevuj %gcc@11.4.0 arch=linux-ubuntu20.04-x86_64_v3 E4S ROCm External",
+    "job_spec_json": "adios2.json",
+    "ci_project_dir": "/builds/spack/spack"
+  }
+
+---------
+``tests``
+---------
+
+The directory ``tests`` is used to store output from running ``spack test <job spec>``. This may or may not have
+data in it depending on the package that was built and the availability of tests.
+
+-------------
+``user_data``
+-------------
+
+The directory ``user_data`` is used to store everything else that shouldn't be copied to the ``reproduction`` direcotory.
+Users may use this to store additional logs or metrics or other types of files generated by the build job.
+
 -------------------------------------
 Using a custom spack in your pipeline
 -------------------------------------

lib/spack/docs/requirements.txt

@@ -1,4 +1,4 @@
-sphinx==8.1.3
+sphinx==8.2.1
 sphinxcontrib-programoutput==0.18
 sphinx_design==0.6.1
 sphinx-rtd-theme==3.0.2
@@ -7,7 +7,7 @@ docutils==0.21.2
 pygments==2.19.1
 urllib3==2.3.0
 pytest==8.3.4
-isort==5.13.2
-black==24.10.0
-flake8==7.1.1
+isort==6.0.0
+black==25.1.0
+flake8==7.1.2
 mypy==1.11.1

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/lang.py

@@ -14,7 +14,7 @@
 import typing
 import warnings
 from datetime import datetime, timedelta
-from typing import Callable, Dict, Iterable, List, Tuple, TypeVar
+from typing import Callable, Dict, Iterable, List, Mapping, Optional, Tuple, TypeVar
 
 # Ignore emacs backups when listing modules
 ignore_modules = r"^\.#|~$"
@@ -1080,3 +1080,88 @@ def __set__(self, instance, value):
 
     def factory(self, instance, owner):
         raise NotImplementedError("must be implemented by derived classes")
+
+
+KT = TypeVar("KT")
+VT = TypeVar("VT")
+
+
+class PriorityOrderedMapping(Mapping[KT, VT]):
+    """Mapping that iterates over key according to an integer priority. If the priority is
+    the same for two keys, insertion order is what matters.
+
+    The priority is set when the key/value pair is added. If not set, the highest current priority
+    is used.
+    """
+
+    _data: Dict[KT, VT]
+    _priorities: List[Tuple[int, KT]]
+
+    def __init__(self) -> None:
+        self._data = {}
+        # Tuple of (priority, key)
+        self._priorities = []
+
+    def __getitem__(self, key: KT) -> VT:
+        return self._data[key]
+
+    def __len__(self) -> int:
+        return len(self._data)
+
+    def __iter__(self):
+        yield from (key for _, key in self._priorities)
+
+    def __reversed__(self):
+        yield from (key for _, key in reversed(self._priorities))
+
+    def reversed_keys(self):
+        """Iterates over keys from the highest priority, to the lowest."""
+        return reversed(self)
+
+    def reversed_values(self):
+        """Iterates over values from the highest priority, to the lowest."""
+        yield from (self._data[key] for _, key in reversed(self._priorities))
+
+    def _highest_priority(self) -> int:
+        if not self._priorities:
+            return 0
+        result, _ = self._priorities[-1]
+        return result
+
+    def add(self, key: KT, *, value: VT, priority: Optional[int] = None) -> None:
+        """Adds a key/value pair to the mapping, with a specific priority.
+
+        If the priority is None, then it is assumed to be the highest priority value currently
+        in the container.
+
+        Raises:
+              ValueError: when the same priority is already in the mapping
+        """
+        if priority is None:
+            priority = self._highest_priority()
+
+        if key in self._data:
+            self.remove(key)
+
+        self._priorities.append((priority, key))
+        # We rely on sort being stable
+        self._priorities.sort(key=lambda x: x[0])
+        self._data[key] = value
+        assert len(self._data) == len(self._priorities)
+
+    def remove(self, key: KT) -> VT:
+        """Removes a key from the mapping.
+
+        Returns:
+            The value associated with the key being removed
+
+        Raises:
+            KeyError: if the key is not in the mapping
+        """
+        if key not in self._data:
+            raise KeyError(f"cannot find {key}")
+
+        popped_item = self._data.pop(key)
+        self._priorities = [(p, k) for p, k in self._priorities if k != key]
+        assert len(self._data) == len(self._priorities)
+        return popped_item

lib/spack/llnl/util/link_tree.py

@@ -41,6 +41,16 @@ def __init__(self, dst, src_a=None, src_b=None):
         self.src_a = src_a
         self.src_b = src_b
 
+    def __repr__(self) -> str:
+        return f"MergeConflict(dst={self.dst!r}, src_a={self.src_a!r}, src_b={self.src_b!r})"
+
+
+def _samefile(a: str, b: str):
+    try:
+        return os.path.samefile(a, b)
+    except OSError:
+        return False
+
 
 class SourceMergeVisitor(BaseDirectoryVisitor):
     """
@@ -50,9 +60,14 @@ class SourceMergeVisitor(BaseDirectoryVisitor):
     - A list of merge conflicts in dst/
     """
 
-    def __init__(self, ignore: Optional[Callable[[str], bool]] = None):
+    def __init__(
+        self, ignore: Optional[Callable[[str], bool]] = None, normalize_paths: bool = False
+    ):
         self.ignore = ignore if ignore is not None else lambda f: False
 
+        # On case-insensitive filesystems, normalize paths to detect duplications
+        self.normalize_paths = normalize_paths
+
         # When mapping <src root> to <dst root>/<projection>, we need to prepend the <projection>
         # bit to the relative path in the destination dir.
         self.projection: str = ""
@@ -71,10 +86,88 @@ def __init__(self, ignore: Optional[Callable[[str], bool]] = None):
         # and can run mkdir in order.
         self.directories: Dict[str, Tuple[str, str]] = {}
 
+        # If the visitor is configured to normalize paths, keep a map of
+        # normalized path to: original path, root directory + relative path
+        self._directories_normalized: Dict[str, Tuple[str, str, str]] = {}
+
         # Files to link. Maps dst_rel to (src_root, src_rel). This is an ordered dict, where files
         # are guaranteed to be grouped by src_root in the order they were visited.
         self.files: Dict[str, Tuple[str, str]] = {}
 
+        # If the visitor is configured to normalize paths, keep a map of
+        # normalized path to: original path, root directory + relative path
+        self._files_normalized: Dict[str, Tuple[str, str, str]] = {}
+
+    def _in_directories(self, proj_rel_path: str) -> bool:
+        """
+        Check if a path is already in the directory list
+        """
+        if self.normalize_paths:
+            return proj_rel_path.lower() in self._directories_normalized
+        else:
+            return proj_rel_path in self.directories
+
+    def _directory(self, proj_rel_path: str) -> Tuple[str, str, str]:
+        """
+        Get the directory that is mapped to a path
+        """
+        if self.normalize_paths:
+            return self._directories_normalized[proj_rel_path.lower()]
+        else:
+            return (proj_rel_path, *self.directories[proj_rel_path])
+
+    def _del_directory(self, proj_rel_path: str):
+        """
+        Remove a directory from the list of directories
+        """
+        del self.directories[proj_rel_path]
+        if self.normalize_paths:
+            del self._directories_normalized[proj_rel_path.lower()]
+
+    def _add_directory(self, proj_rel_path: str, root: str, rel_path: str):
+        """
+        Add a directory to the list of directories.
+        Also stores the normalized version for later lookups
+        """
+        self.directories[proj_rel_path] = (root, rel_path)
+        if self.normalize_paths:
+            self._directories_normalized[proj_rel_path.lower()] = (proj_rel_path, root, rel_path)
+
+    def _in_files(self, proj_rel_path: str) -> bool:
+        """
+        Check if a path is already in the files list
+        """
+        if self.normalize_paths:
+            return proj_rel_path.lower() in self._files_normalized
+        else:
+            return proj_rel_path in self.files
+
+    def _file(self, proj_rel_path: str) -> Tuple[str, str, str]:
+        """
+        Get the file that is mapped to a path
+        """
+        if self.normalize_paths:
+            return self._files_normalized[proj_rel_path.lower()]
+        else:
+            return (proj_rel_path, *self.files[proj_rel_path])
+
+    def _del_file(self, proj_rel_path: str):
+        """
+        Remove a file from the list of files
+        """
+        del self.files[proj_rel_path]
+        if self.normalize_paths:
+            del self._files_normalized[proj_rel_path.lower()]
+
+    def _add_file(self, proj_rel_path: str, root: str, rel_path: str):
+        """
+        Add a file to the list of files
+        Also stores the normalized version for later lookups
+        """
+        self.files[proj_rel_path] = (root, rel_path)
+        if self.normalize_paths:
+            self._files_normalized[proj_rel_path.lower()] = (proj_rel_path, root, rel_path)
+
     def before_visit_dir(self, root: str, rel_path: str, depth: int) -> bool:
         """
         Register a directory if dst / rel_path is not blocked by a file or ignored.
@@ -84,23 +177,28 @@ def before_visit_dir(self, root: str, rel_path: str, depth: int) -> bool:
         if self.ignore(rel_path):
             # Don't recurse when dir is ignored.
             return False
-        elif proj_rel_path in self.files:
-            # Can't create a dir where a file is.
-            src_a_root, src_a_relpath = self.files[proj_rel_path]
-            self.fatal_conflicts.append(
-                MergeConflict(
-                    dst=proj_rel_path,
-                    src_a=os.path.join(src_a_root, src_a_relpath),
-                    src_b=os.path.join(root, rel_path),
+        elif self._in_files(proj_rel_path):
+            # A file-dir conflict is fatal except if they're the same file (symlinked dir).
+            src_a = os.path.join(*self._file(proj_rel_path))
+            src_b = os.path.join(root, rel_path)
+
+            if not _samefile(src_a, src_b):
+                self.fatal_conflicts.append(
+                    MergeConflict(dst=proj_rel_path, src_a=src_a, src_b=src_b)
                 )
-            )
-            return False
-        elif proj_rel_path in self.directories:
+                return False
+
+            # Remove the link in favor of the dir.
+            existing_proj_rel_path, _, _ = self._file(proj_rel_path)
+            self._del_file(existing_proj_rel_path)
+            self._add_directory(proj_rel_path, root, rel_path)
+            return True
+        elif self._in_directories(proj_rel_path):
             # No new directory, carry on.
             return True
         else:
             # Register new directory.
-            self.directories[proj_rel_path] = (root, rel_path)
+            self._add_directory(proj_rel_path, root, rel_path)
             return True
 
     def before_visit_symlinked_dir(self, root: str, rel_path: str, depth: int) -> bool:
@@ -132,7 +230,7 @@ def before_visit_symlinked_dir(self, root: str, rel_path: str, depth: int) -> bo
         if handle_as_dir:
             return self.before_visit_dir(root, rel_path, depth)
 
-        self.visit_file(root, rel_path, depth)
+        self.visit_file(root, rel_path, depth, symlink=True)
         return False
 
     def visit_file(self, root: str, rel_path: str, depth: int, *, symlink: bool = False) -> None:
@@ -140,30 +238,23 @@ def visit_file(self, root: str, rel_path: str, depth: int, *, symlink: bool = Fa
 
         if self.ignore(rel_path):
             pass
-        elif proj_rel_path in self.directories:
-            # Can't create a file where a dir is; fatal error
-            self.fatal_conflicts.append(
-                MergeConflict(
-                    dst=proj_rel_path,
-                    src_a=os.path.join(*self.directories[proj_rel_path]),
-                    src_b=os.path.join(root, rel_path),
+        elif self._in_directories(proj_rel_path):
+            # Can't create a file where a dir is, unless they are the same file (symlinked dir),
+            # in which case we simply drop the symlink in favor of the actual dir.
+            src_a = os.path.join(*self._directory(proj_rel_path))
+            src_b = os.path.join(root, rel_path)
+            if not symlink or not _samefile(src_a, src_b):
+                self.fatal_conflicts.append(
+                    MergeConflict(dst=proj_rel_path, src_a=src_a, src_b=src_b)
                 )
-            )
-        elif proj_rel_path in self.files:
+        elif self._in_files(proj_rel_path):
             # When two files project to the same path, they conflict iff they are distinct.
             # If they are the same (i.e. one links to the other), register regular files rather
             # than symlinks. The reason is that in copy-type views, we need a copy of the actual
             # file, not the symlink.
-
-            src_a = os.path.join(*self.files[proj_rel_path])
+            src_a = os.path.join(*self._file(proj_rel_path))
             src_b = os.path.join(root, rel_path)
-
-            try:
-                samefile = os.path.samefile(src_a, src_b)
-            except OSError:
-                samefile = False
-
-            if not samefile:
+            if not _samefile(src_a, src_b):
                 # Distinct files produce a conflict.
                 self.file_conflicts.append(
                     MergeConflict(dst=proj_rel_path, src_a=src_a, src_b=src_b)
@@ -173,12 +264,12 @@ def visit_file(self, root: str, rel_path: str, depth: int, *, symlink: bool = Fa
             if not symlink:
                 # Remove the link in favor of the actual file. The del is necessary to maintain the
                 # order of the files dict, which is grouped by root.
-                del self.files[proj_rel_path]
-                self.files[proj_rel_path] = (root, rel_path)
-
+                existing_proj_rel_path, _, _ = self._file(proj_rel_path)
+                self._del_file(existing_proj_rel_path)
+                self._add_file(proj_rel_path, root, rel_path)
         else:
             # Otherwise register this file to be linked.
-            self.files[proj_rel_path] = (root, rel_path)
+            self._add_file(proj_rel_path, root, rel_path)
 
     def visit_symlinked_file(self, root: str, rel_path: str, depth: int) -> None:
         # Treat symlinked files as ordinary files (without "dereferencing")
@@ -197,11 +288,11 @@ def set_projection(self, projection: str) -> None:
         path = ""
         for part in self.projection.split(os.sep):
             path = os.path.join(path, part)
-            if path not in self.files:
-                self.directories[path] = ("<projection>", path)
+            if not self._in_files(path):
+                self._add_directory(path, "<projection>", path)
             else:
                 # Can't create a dir where a file is.
-                src_a_root, src_a_relpath = self.files[path]
+                _, src_a_root, src_a_relpath = self._file(path)
                 self.fatal_conflicts.append(
                     MergeConflict(
                         dst=path,
@@ -227,8 +318,8 @@ def __init__(self, source_merge_visitor: SourceMergeVisitor):
     def before_visit_dir(self, root: str, rel_path: str, depth: int) -> bool:
         # If destination dir is a file in a src dir, add a conflict,
         # and don't traverse deeper
-        if rel_path in self.src.files:
-            src_a_root, src_a_relpath = self.src.files[rel_path]
+        if self.src._in_files(rel_path):
+            _, src_a_root, src_a_relpath = self.src._file(rel_path)
             self.src.fatal_conflicts.append(
                 MergeConflict(
                     rel_path, os.path.join(src_a_root, src_a_relpath), os.path.join(root, rel_path)
@@ -238,8 +329,9 @@ def before_visit_dir(self, root: str, rel_path: str, depth: int) -> bool:
 
         # If destination dir was also a src dir, remove the mkdir
         # action, and traverse deeper.
-        if rel_path in self.src.directories:
-            del self.src.directories[rel_path]
+        if self.src._in_directories(rel_path):
+            existing_proj_rel_path, _, _ = self.src._directory(rel_path)
+            self.src._del_directory(existing_proj_rel_path)
             return True
 
         # If the destination dir does not appear in the src dir,
@@ -252,38 +344,24 @@ def before_visit_symlinked_dir(self, root: str, rel_path: str, depth: int) -> bo
         be seen as files; we should not accidentally merge
         source dir with a symlinked dest dir.
         """
-        # Always conflict
-        if rel_path in self.src.directories:
-            src_a_root, src_a_relpath = self.src.directories[rel_path]
-            self.src.fatal_conflicts.append(
-                MergeConflict(
-                    rel_path, os.path.join(src_a_root, src_a_relpath), os.path.join(root, rel_path)
-                )
-            )
 
-        if rel_path in self.src.files:
-            src_a_root, src_a_relpath = self.src.files[rel_path]
-            self.src.fatal_conflicts.append(
-                MergeConflict(
-                    rel_path, os.path.join(src_a_root, src_a_relpath), os.path.join(root, rel_path)
-                )
-            )
+        self.visit_file(root, rel_path, depth)
 
         # Never descend into symlinked target dirs.
         return False
 
     def visit_file(self, root: str, rel_path: str, depth: int) -> None:
         # Can't merge a file if target already exists
-        if rel_path in self.src.directories:
-            src_a_root, src_a_relpath = self.src.directories[rel_path]
+        if self.src._in_directories(rel_path):
+            _, src_a_root, src_a_relpath = self.src._directory(rel_path)
             self.src.fatal_conflicts.append(
                 MergeConflict(
                     rel_path, os.path.join(src_a_root, src_a_relpath), os.path.join(root, rel_path)
                 )
             )
 
-        elif rel_path in self.src.files:
-            src_a_root, src_a_relpath = self.src.files[rel_path]
+        elif self.src._in_files(rel_path):
+            _, src_a_root, src_a_relpath = self.src._file(rel_path)
             self.src.fatal_conflicts.append(
                 MergeConflict(
                     rel_path, os.path.join(src_a_root, src_a_relpath), os.path.join(root, rel_path)
@@ -308,7 +386,7 @@ 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

@@ -269,7 +269,7 @@ def __init__(
 
     @staticmethod
     def _poll_interval_generator(
-        _wait_times: Optional[Tuple[float, float, float]] = None
+        _wait_times: Optional[Tuple[float, float, float]] = None,
     ) -> Generator[float, None, None]:
         """This implements a backoff scheme for polling a contended resource
         by suggesting a succession of wait times between polls.
@@ -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

@@ -2,8 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-"""Utility classes for logging the output of blocks of code.
-"""
+"""Utility classes for logging the output of blocks of code."""
 import atexit
 import ctypes
 import errno
@@ -344,26 +343,6 @@ def close(self):
             self.file.close()
 
 
-@contextmanager
-def replace_environment(env):
-    """Replace the current environment (`os.environ`) with `env`.
-
-    If `env` is empty (or None), this unsets all current environment
-    variables.
-    """
-    env = env or {}
-    old_env = os.environ.copy()
-    try:
-        os.environ.clear()
-        for name, val in env.items():
-            os.environ[name] = val
-        yield
-    finally:
-        os.environ.clear()
-        for name, val in old_env.items():
-            os.environ[name] = val
-
-
 def log_output(*args, **kwargs):
     """Context manager that logs its output to a file.
 
@@ -447,7 +426,6 @@ def __init__(
         self.echo = echo
         self.debug = debug
         self.buffer = buffer
-        self.env = env  # the environment to use for _writer_daemon
         self.filter_fn = filter_fn
 
         self._active = False  # used to prevent re-entry
@@ -519,21 +497,20 @@ def __enter__(self):
                 # just don't forward input if this fails
                 pass
 
-            with replace_environment(self.env):
-                self.process = multiprocessing.Process(
-                    target=_writer_daemon,
-                    args=(
-                        input_fd,
-                        read_fd,
-                        self.write_fd,
-                        self.echo,
-                        self.log_file,
-                        child_pipe,
-                        self.filter_fn,
-                    ),
-                )
-                self.process.daemon = True  # must set before start()
-                self.process.start()
+            self.process = multiprocessing.Process(
+                target=_writer_daemon,
+                args=(
+                    input_fd,
+                    read_fd,
+                    self.write_fd,
+                    self.echo,
+                    self.log_file,
+                    child_pipe,
+                    self.filter_fn,
+                ),
+            )
+            self.process.daemon = True  # must set before start()
+            self.process.start()
 
         finally:
             if input_fd:
@@ -729,10 +706,7 @@ class winlog:
     Does not support the use of 'v' toggling as nixlog does.
     """
 
-    def __init__(
-        self, file_like=None, echo=False, debug=0, buffer=False, env=None, filter_fn=None
-    ):
-        self.env = env
+    def __init__(self, file_like=None, echo=False, debug=0, buffer=False, filter_fn=None):
         self.debug = debug
         self.echo = echo
         self.logfile = file_like
@@ -789,11 +763,10 @@ def background_reader(reader, echo_writer, _kill):
                     reader.close()
 
             self._active = True
-            with replace_environment(self.env):
-                self._thread = Thread(
-                    target=background_reader, args=(self.reader, self.echo_writer, self._kill)
-                )
-                self._thread.start()
+            self._thread = Thread(
+                target=background_reader, args=(self.reader, self.echo_writer, self._kill)
+            )
+            self._thread.start()
         return self
 
     def __exit__(self, exc_type, exc_val, exc_tb):
@@ -918,7 +891,7 @@ 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 +986,7 @@ 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/audit.py

@@ -1010,7 +1010,7 @@ def _issues_in_depends_on_directive(pkgs, error_cls):
             for dep_name, dep in deps_by_name.items():
 
                 def check_virtual_with_variants(spec, msg):
-                    if not spec.virtual or not spec.variants:
+                    if not spack.repo.PATH.is_virtual(spec.name) or not spec.variants:
                         return
                     error = error_cls(
                         f"{pkg_name}: {msg}",

lib/spack/spack/binary_distribution.py

@@ -923,7 +923,7 @@ class FileTypes:
     UNKNOWN = 2
 
 
-NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7F-\x9F]")
+NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7f-\x9f]")
 
 
 def file_type(f: IO[bytes]) -> int:
@@ -2529,10 +2529,10 @@ def install_root_node(
         allow_missing: when true, allows installing a node with missing dependencies
     """
     # Early termination
-    if spec.external or spec.virtual:
-        warnings.warn("Skipping external or virtual package {0}".format(spec.format()))
+    if spec.external or not spec.concrete:
+        warnings.warn("Skipping external or abstract spec {0}".format(spec.format()))
         return
-    elif spec.concrete and spec.installed and not force:
+    elif spec.installed and not force:
         warnings.warn("Package for spec {0} already installed.".format(spec.format()))
         return
 

lib/spack/spack/bootstrap/core.py

@@ -292,7 +292,12 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
 
         # Install the spec that should make the module importable
         with spack.config.override(self.mirror_scope):
-            PackageInstaller([concrete_spec.package], fail_fast=True).install()
+            PackageInstaller(
+                [concrete_spec.package],
+                fail_fast=True,
+                package_use_cache=False,
+                dependencies_use_cache=False,
+            ).install()
 
         if _try_import_from_store(module, query_spec=concrete_spec, query_info=info):
             self.last_search = info
@@ -362,6 +367,7 @@ def ensure_module_importable_or_raise(module: str, abstract_spec: Optional[str]
     for current_config in bootstrapping_sources():
         if not source_is_enabled(current_config):
             continue
+
         with exception_handler.forward(current_config["name"], Exception):
             if create_bootstrapper(current_config).try_import(module, abstract_spec):
                 return

lib/spack/spack/build_environment.py

@@ -1234,6 +1234,10 @@ def _make_runnable(self, dep: spack.spec.Spec, env: EnvironmentModifications):
             if os.path.isdir(bin_dir):
                 env.prepend_path("PATH", bin_dir)
 
+        for cp_dir in spack.build_systems.cmake.get_cmake_prefix_path(dep.package):
+            env.append_path("CMAKE_PREFIX_PATH", cp_dir)
+        env.prune_duplicate_paths("CMAKE_PREFIX_PATH")
+
 
 def _setup_pkg_and_run(
     serialized_pkg: "spack.subprocess_context.PackageInstallContext",

lib/spack/spack/build_systems/cached_cmake.py

@@ -12,6 +12,7 @@
 import spack.phase_callbacks
 import spack.spec
 import spack.util.prefix
+from spack.directives import depends_on
 
 from .cmake import CMakeBuilder, CMakePackage
 
@@ -371,6 +372,10 @@ class CachedCMakePackage(CMakePackage):
 
     CMakeBuilder = CachedCMakeBuilder
 
+    # These dependencies are assumed in the builder
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
+
     def flag_handler(self, name, flags):
         if name in ("cflags", "cxxflags", "cppflags", "fflags"):
             return None, None, None  # handled in the cmake cache

lib/spack/spack/build_systems/cargo.py

@@ -70,10 +70,16 @@ def build_directory(self):
         """Return the directory containing the main Cargo.toml."""
         return self.pkg.stage.source_path
 
+    @property
+    def std_build_args(self):
+        """Standard arguments for ``cargo build`` provided as a property for
+        convenience of package writers."""
+        return ["-j", str(self.pkg.module.make_jobs)]
+
     @property
     def build_args(self):
         """Arguments for ``cargo build``."""
-        return ["-j", str(self.pkg.module.make_jobs)]
+        return []
 
     @property
     def check_args(self):
@@ -88,7 +94,9 @@ def build(
     ) -> None:
         """Runs ``cargo install`` in the source directory"""
         with fs.working_dir(self.build_directory):
-            pkg.module.cargo("install", "--root", "out", "--path", ".", *self.build_args)
+            pkg.module.cargo(
+                "install", "--root", "out", "--path", ".", *self.std_build_args, *self.build_args
+            )
 
     def install(
         self, pkg: CargoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix

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/build_systems/meson.py

@@ -48,6 +48,9 @@ class MesonPackage(spack.package_base.PackageBase):
         variant("strip", default=False, description="Strip targets on install")
         depends_on("meson", type="build")
         depends_on("ninja", type="build")
+        # Meson uses pkg-config for dependency detection, and this dependency is
+        # often overlooked by packages that use meson as a build system.
+        depends_on("pkgconfig", type="build")
         # Python detection in meson requires distutils to be importable, but distutils no longer
         # exists in Python 3.12. In Spack, we can't use setuptools as distutils replacement,
         # because the distutils-precedence.pth startup file that setuptools ships with is not run

lib/spack/spack/build_systems/oneapi.py

@@ -142,7 +142,7 @@ def setup_run_environment(self, env):
            $ source {prefix}/{component}/{version}/env/vars.sh
         """
         # Only if environment modifications are desired (default is +envmods)
-        if "~envmods" not in self.spec:
+        if "+envmods" in self.spec:
             env.extend(
                 EnvironmentModifications.from_sourcing_file(
                     self.component_prefix.env.join("vars.sh"), *self.env_script_args

lib/spack/spack/ci/__init__.py

@@ -14,8 +14,9 @@
 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.path
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 from llnl.util.tty.color import cescape, colorize
@@ -62,6 +63,8 @@
 
 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
@@ -81,6 +84,9 @@ def get_stack_changed(env_path, rev1="HEAD^", rev2="HEAD"):
     whether or not the stack was changed.  Returns True if the environment
     manifest changed between the provided revisions (or additionally if the
     `.gitlab-ci.yml` file itself changed).  Returns False otherwise."""
+    # git returns posix paths always, normalize input to be comptaible
+    # with that
+    env_path = llnl.path.convert_to_posix_path(env_path)
     git = spack.util.git.git()
     if git:
         with fs.working_dir(spack.paths.prefix):
@@ -610,7 +616,7 @@ def copy_test_logs_to_artifacts(test_stage, job_test_dir):
     copy_files_to_artifacts(os.path.join(test_stage, "*", "*.txt"), job_test_dir)
 
 
-def download_and_extract_artifacts(url, work_dir):
+def download_and_extract_artifacts(url, work_dir) -> str:
     """Look for gitlab artifacts.zip at the given url, and attempt to download
         and extract the contents into the given work_dir
 
@@ -618,6 +624,10 @@ def download_and_extract_artifacts(url, work_dir):
 
         url (str): Complete url to artifacts.zip file
         work_dir (str): Path to destination where artifacts should be extracted
+
+    Output:
+
+        Artifacts root path relative to the archive root
     """
     tty.msg(f"Fetching artifacts from: {url}")
 
@@ -627,31 +637,33 @@ 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)
 
-    with open(artifacts_zip_path, "wb") as out_file:
-        shutil.copyfileobj(response, out_file)
+        with zipfile.ZipFile(artifacts_zip_path) as zip_file:
+            zip_file.extractall(work_dir)
+            # Get the artifact root
+            artifact_root = ""
+            for f in zip_file.filelist:
+                if "spack.lock" in f.filename:
+                    artifact_root = os.path.dirname(os.path.dirname(f.filename))
+                    break
+    except OSError as e:
+        raise SpackError(f"Error fetching artifacts: {e}")
+    finally:
+        try:
+            os.remove(artifacts_zip_path)
+        except FileNotFoundError:
+            # If the file doesn't exist we are already raising
+            pass
 
-    zip_file = zipfile.ZipFile(artifacts_zip_path)
-    zip_file.extractall(work_dir)
-    zip_file.close()
-
-    os.remove(artifacts_zip_path)
+    return artifact_root
 
 
 def get_spack_info():
@@ -765,7 +777,7 @@ def setup_spack_repro_version(repro_dir, checkout_commit, merge_commit=None):
     return True
 
 
-def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
+def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime, use_local_head):
     """Given a url to gitlab artifacts.zip from a failed 'spack ci rebuild' job,
     attempt to setup an environment in which the failure can be reproduced
     locally.  This entails the following:
@@ -779,8 +791,11 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     commands to run to reproduce the build once inside the container.
     """
     work_dir = os.path.realpath(work_dir)
+    if os.path.exists(work_dir) and os.listdir(work_dir):
+        raise SpackError(f"Cannot run reproducer in non-emptry working dir:\n  {work_dir}")
+
     platform_script_ext = "ps1" if IS_WINDOWS else "sh"
-    download_and_extract_artifacts(url, work_dir)
+    artifact_root = download_and_extract_artifacts(url, work_dir)
 
     gpg_path = None
     if gpg_url:
@@ -842,6 +857,9 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     with open(repro_file, encoding="utf-8") as fd:
         repro_details = json.load(fd)
 
+    spec_file = fs.find(work_dir, repro_details["job_spec_json"])[0]
+    reproducer_spec = spack.spec.Spec.from_specfile(spec_file)
+
     repro_dir = os.path.dirname(repro_file)
     rel_repro_dir = repro_dir.replace(work_dir, "").lstrip(os.path.sep)
 
@@ -902,17 +920,20 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     commit_regex = re.compile(r"commit\s+([^\s]+)")
     merge_commit_regex = re.compile(r"Merge\s+([^\s]+)\s+into\s+([^\s]+)")
 
-    # Try the more specific merge commit regex first
-    m = merge_commit_regex.search(spack_info)
-    if m:
-        # This was a merge commit and we captured the parents
-        commit_1 = m.group(1)
-        commit_2 = m.group(2)
+    if use_local_head:
+        commit_1 = "HEAD"
     else:
-        # Not a merge commit, just get the commit sha
-        m = commit_regex.search(spack_info)
+        # Try the more specific merge commit regex first
+        m = merge_commit_regex.search(spack_info)
         if m:
+            # This was a merge commit and we captured the parents
             commit_1 = m.group(1)
+            commit_2 = m.group(2)
+        else:
+            # Not a merge commit, just get the commit sha
+            m = commit_regex.search(spack_info)
+            if m:
+                commit_1 = m.group(1)
 
     setup_result = False
     if commit_1:
@@ -987,6 +1008,8 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
             "entrypoint", entrypoint_script, work_dir, run=False, exit_on_failure=False
         )
 
+        # Attempt to create a unique name for the reproducer container
+        container_suffix = "_" + reproducer_spec.dag_hash() if reproducer_spec else ""
         docker_command = [
             runtime,
             "run",
@@ -994,14 +1017,14 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
             "-t",
             "--rm",
             "--name",
-            "spack_reproducer",
+            f"spack_reproducer{container_suffix}",
             "-v",
             ":".join([work_dir, mounted_workdir, "Z"]),
             "-v",
             ":".join(
                 [
-                    os.path.join(work_dir, "jobs_scratch_dir"),
-                    os.path.join(mount_as_dir, "jobs_scratch_dir"),
+                    os.path.join(work_dir, artifact_root),
+                    os.path.join(mount_as_dir, artifact_root),
                     "Z",
                 ]
             ),

lib/spack/spack/cmd/checksum.py

@@ -4,7 +4,7 @@
 
 import re
 import sys
-from typing import Dict, Optional
+from typing import Dict, Optional, Tuple
 
 import llnl.string
 import llnl.util.lang
@@ -181,7 +181,11 @@ def checksum(parser, args):
     print()
 
     if args.add_to_package:
-        add_versions_to_package(pkg, version_lines, args.batch)
+        path = spack.repo.PATH.filename_for_package_name(pkg.name)
+        num_versions_added = add_versions_to_pkg(path, version_lines)
+        tty.msg(f"Added {num_versions_added} new versions to {pkg.name} in {path}")
+        if not args.batch and sys.stdin.isatty():
+            editor(path)
 
 
 def print_checksum_status(pkg: PackageBase, version_hashes: dict):
@@ -227,20 +231,9 @@ def print_checksum_status(pkg: PackageBase, version_hashes: dict):
         tty.die("Invalid checksums found.")
 
 
-def add_versions_to_package(pkg: PackageBase, version_lines: str, is_batch: bool):
-    """
-    Add checksumed versions to a package's instructions and open a user's
-    editor so they may double check the work of the function.
-
-    Args:
-        pkg (spack.package_base.PackageBase): A package class for a given package in Spack.
-        version_lines (str): A string of rendered version lines.
-
-    """
-    # Get filename and path for package
-    filename = spack.repo.PATH.filename_for_package_name(pkg.name)
+def _update_version_statements(package_src: str, version_lines: str) -> Tuple[int, str]:
+    """Returns a tuple of number of versions added and the package's modified contents."""
     num_versions_added = 0
-
     version_statement_re = re.compile(r"([\t ]+version\([^\)]*\))")
     version_re = re.compile(r'[\t ]+version\(\s*"([^"]+)"[^\)]*\)')
 
@@ -252,33 +245,34 @@ def add_versions_to_package(pkg: PackageBase, version_lines: str, is_batch: bool
         if match:
             new_versions.append((Version(match.group(1)), ver_line))
 
-    with open(filename, "r+", encoding="utf-8") as f:
-        contents = f.read()
-        split_contents = version_statement_re.split(contents)
+    split_contents = version_statement_re.split(package_src)
 
-        for i, subsection in enumerate(split_contents):
-            # If there are no more versions to add we should exit
-            if len(new_versions) <= 0:
-                break
+    for i, subsection in enumerate(split_contents):
+        # If there are no more versions to add we should exit
+        if len(new_versions) <= 0:
+            break
 
-            # Check if the section contains a version
-            contents_version = version_re.match(subsection)
-            if contents_version is not None:
-                parsed_version = Version(contents_version.group(1))
+        # Check if the section contains a version
+        contents_version = version_re.match(subsection)
+        if contents_version is not None:
+            parsed_version = Version(contents_version.group(1))
 
-                if parsed_version < new_versions[0][0]:
-                    split_contents[i:i] = [new_versions.pop(0)[1], " # FIXME", "\n"]
-                    num_versions_added += 1
+            if parsed_version < new_versions[0][0]:
+                split_contents[i:i] = [new_versions.pop(0)[1], "  # FIXME", "\n"]
+                num_versions_added += 1
 
-                elif parsed_version == new_versions[0][0]:
-                    new_versions.pop(0)
+            elif parsed_version == new_versions[0][0]:
+                new_versions.pop(0)
 
-        # Seek back to the start of the file so we can rewrite the file contents.
-        f.seek(0)
-        f.writelines("".join(split_contents))
+    return num_versions_added, "".join(split_contents)
 
-        tty.msg(f"Added {num_versions_added} new versions to {pkg.name}")
-        tty.msg(f"Open {filename} to review the additions.")
 
-    if sys.stdout.isatty() and not is_batch:
-        editor(filename)
+def add_versions_to_pkg(path: str, version_lines: str) -> int:
+    """Add new versions to a package.py file. Returns the number of versions added."""
+    with open(path, "r", encoding="utf-8") as f:
+        package_src = f.read()
+    num_versions_added, package_src = _update_version_statements(package_src, version_lines)
+    if num_versions_added > 0:
+        with open(path, "w", encoding="utf-8") as f:
+            f.write(package_src)
+    return num_versions_added

lib/spack/spack/cmd/ci.py

@@ -176,6 +176,11 @@ def setup_parser(subparser):
     reproduce.add_argument(
         "-s", "--autostart", help="Run docker reproducer automatically", action="store_true"
     )
+    reproduce.add_argument(
+        "--use-local-head",
+        help="Use the HEAD of the local Spack instead of reproducing a commit",
+        action="store_true",
+    )
     gpg_group = reproduce.add_mutually_exclusive_group(required=False)
     gpg_group.add_argument(
         "--gpg-file", help="Path to public GPG key for validating binary cache installs"
@@ -608,7 +613,12 @@ def ci_reproduce(args):
         gpg_key_url = None
 
     return spack_ci.reproduce_ci_job(
-        args.job_url, args.working_dir, args.autostart, gpg_key_url, args.runtime
+        args.job_url,
+        args.working_dir,
+        args.autostart,
+        gpg_key_url,
+        args.runtime,
+        args.use_local_head,
     )
 
 

lib/spack/spack/cmd/common/arguments.py

@@ -528,7 +528,6 @@ def __call__(self, parser, namespace, values, option_string):
         # the const from the constructor or a value from the CLI.
         # Note that this is only called if the argument is actually
         # specified on the command line.
-        spack.config.CONFIG.ensure_scope_ordering()
         spack.config.set(self.config_path, self.const, scope="command_line")
 
 

lib/spack/spack/cmd/debug.py

@@ -2,23 +2,11 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os
 import platform
-import re
-import sys
-from datetime import datetime
-from glob import glob
-
-import llnl.util.tty as tty
-from llnl.util.filesystem import working_dir
 
 import spack
-import spack.paths
 import spack.platforms
 import spack.spec
-import spack.store
-import spack.util.git
-from spack.util.executable import which
 
 description = "debugging commands for troubleshooting Spack"
 section = "developer"
@@ -27,63 +15,9 @@
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar="SUBCOMMAND", dest="debug_command")
-    sp.add_parser("create-db-tarball", help="create a tarball of Spack's installation metadata")
     sp.add_parser("report", help="print information useful for bug reports")
 
 
-def _debug_tarball_suffix():
-    now = datetime.now()
-    suffix = now.strftime("%Y-%m-%d-%H%M%S")
-
-    git = spack.util.git.git()
-    if not git:
-        return "nobranch-nogit-%s" % suffix
-
-    with working_dir(spack.paths.prefix):
-        if not os.path.isdir(".git"):
-            return "nobranch.nogit.%s" % suffix
-
-        # Get symbolic branch name and strip any special chars (mainly '/')
-        symbolic = git("rev-parse", "--abbrev-ref", "--short", "HEAD", output=str).strip()
-        symbolic = re.sub(r"[^\w.-]", "-", symbolic)
-
-        # Get the commit hash too.
-        commit = git("rev-parse", "--short", "HEAD", output=str).strip()
-
-        if symbolic == commit:
-            return "nobranch.%s.%s" % (commit, suffix)
-        else:
-            return "%s.%s.%s" % (symbolic, commit, suffix)
-
-
-def create_db_tarball(args):
-    tar = which("tar")
-    tarball_name = "spack-db.%s.tar.gz" % _debug_tarball_suffix()
-    tarball_path = os.path.abspath(tarball_name)
-
-    base = os.path.basename(str(spack.store.STORE.root))
-    transform_args = []
-    # Currently --transform and -s are not supported by Windows native tar
-    if "GNU" in tar("--version", output=str):
-        transform_args = ["--transform", "s/^%s/%s/" % (base, tarball_name)]
-    elif sys.platform != "win32":
-        transform_args = ["-s", "/^%s/%s/" % (base, tarball_name)]
-
-    wd = os.path.dirname(str(spack.store.STORE.root))
-    with working_dir(wd):
-        files = [spack.store.STORE.db._index_path]
-        files += glob("%s/*/*/*/.spack/spec.json" % base)
-        files += glob("%s/*/*/*/.spack/spec.yaml" % base)
-        files = [os.path.relpath(f) for f in files]
-
-        args = ["-czf", tarball_path]
-        args += transform_args
-        args += files
-        tar(*args)
-
-    tty.msg("Created %s" % tarball_name)
-
-
 def report(args):
     host_platform = spack.platforms.host()
     host_os = host_platform.default_operating_system()
@@ -95,5 +29,5 @@ def report(args):
 
 
 def debug(parser, args):
-    action = {"create-db-tarball": create_db_tarball, "report": report}
-    action[args.debug_command](args)
+    if args.debug_command == "report":
+        report(args)

lib/spack/spack/cmd/dependencies.py

@@ -9,9 +9,9 @@
 
 import spack.cmd
 import spack.environment as ev
-import spack.package_base
 import spack.store
 from spack.cmd.common import arguments
+from spack.solver.input_analysis import create_graph_analyzer
 
 description = "show dependencies of a package"
 section = "basic"
@@ -68,15 +68,17 @@ def dependencies(parser, args):
 
     else:
         spec = specs[0]
-        dependencies = spack.package_base.possible_dependencies(
+        dependencies, virtuals, _ = create_graph_analyzer().possible_dependencies(
             spec,
             transitive=args.transitive,
             expand_virtuals=args.expand_virtuals,
-            depflag=args.deptype,
+            allowed_deps=args.deptype,
         )
+        if not args.expand_virtuals:
+            dependencies.update(virtuals)
 
         if spec.name in dependencies:
-            del dependencies[spec.name]
+            dependencies.remove(spec.name)
 
         if dependencies:
             colify(sorted(dependencies))

lib/spack/spack/cmd/develop.py

@@ -125,7 +125,7 @@ def develop(parser, args):
     version = spec.versions.concrete_range_as_version
     if not version:
         # look up the maximum version so infintiy versions are preferred for develop
-        version = max(spec.package_class.versions.keys())
+        version = max(spack.repo.PATH.get_pkg_class(spec.fullname).versions.keys())
         tty.msg(f"Defaulting to highest version: {spec.name}@{version}")
     spec.versions = spack.version.VersionList([version])
 

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/mirror.py

@@ -545,7 +545,7 @@ def _not_license_excluded(self, x):
         package does not explicitly forbid redistributing source."""
         if self.private:
             return True
-        elif x.package_class.redistribute_source(x):
+        elif spack.repo.PATH.get_pkg_class(x.fullname).redistribute_source(x):
             return True
         else:
             tty.debug(

lib/spack/spack/cmd/providers.py

@@ -41,7 +41,11 @@ def providers(parser, args):
     specs = spack.cmd.parse_specs(args.virtual_package)
 
     # Check prerequisites
-    non_virtual = [str(s) for s in specs if not s.virtual or s.name not in valid_virtuals]
+    non_virtual = [
+        str(s)
+        for s in specs
+        if not spack.repo.PATH.is_virtual(s.name) or s.name not in valid_virtuals
+    ]
     if non_virtual:
         msg = "non-virtual specs cannot be part of the query "
         msg += "[{0}]\n".format(", ".join(non_virtual))

lib/spack/spack/cmd/style.py

@@ -6,7 +6,7 @@
 import os
 import re
 import sys
-from itertools import zip_longest
+from itertools import islice, zip_longest
 from typing import Dict, List, Optional
 
 import llnl.util.tty as tty
@@ -423,7 +423,8 @@ def _run_import_check(
             continue
 
         for m in is_abs_import.finditer(contents):
-            if contents.count(m.group(1)) == 1:
+            # Find at most two occurences: the first is the import itself, the second is its usage.
+            if len(list(islice(re.finditer(rf"{re.escape(m.group(1))}(?!\w)", contents), 2))) == 1:
                 to_remove.append(m.group(0))
                 exit_code = 1
                 print(f"{pretty_path}: redundant import: {m.group(1)}", file=out)
@@ -438,7 +439,7 @@ def _run_import_check(
             module = _module_part(root, m.group(0))
             if not module or module in to_add:
                 continue
-            if re.search(rf"import {re.escape(module)}\b(?!\.)", contents):
+            if re.search(rf"import {re.escape(module)}(?!\w|\.)", contents):
                 continue
             to_add.add(module)
             exit_code = 1

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)
 
@@ -253,7 +252,9 @@ def has_test_and_tags(pkg_class):
     hashes = env.all_hashes() if env else None
 
     specs = spack.store.STORE.db.query(hashes=hashes)
-    specs = list(filter(lambda s: has_test_and_tags(s.package_class), specs))
+    specs = list(
+        filter(lambda s: has_test_and_tags(spack.repo.PATH.get_pkg_class(s.fullname)), specs)
+    )
 
     spack.cmd.display_specs(specs, long=True)
 

lib/spack/spack/cmd/unit_test.py

@@ -216,7 +216,7 @@ def unit_test(parser, args, unknown_args):
     # Ensure clingo is available before switching to the
     # mock configuration used by unit tests
     with spack.bootstrap.ensure_bootstrap_configuration():
-        spack.bootstrap.ensure_core_dependencies()
+        spack.bootstrap.ensure_clingo_importable_or_raise()
         if pytest is None:
             spack.bootstrap.ensure_environment_dependencies()
             import pytest

lib/spack/spack/cmd/verify.py

@@ -2,35 +2,48 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import argparse
+import io
+from typing import List, Optional
 
 import llnl.util.tty as tty
+from llnl.string import plural
+from llnl.util.filesystem import visit_directory_tree
 
 import spack.cmd
 import spack.environment as ev
+import spack.spec
 import spack.store
 import spack.verify
+import spack.verify_libraries
+from spack.cmd.common import arguments
 
-description = "check that all spack packages are on disk as installed"
+description = "verify spack installations on disk"
 section = "admin"
 level = "long"
 
+MANIFEST_SUBPARSER: Optional[argparse.ArgumentParser] = None
 
-def setup_parser(subparser):
-    setup_parser.parser = subparser
 
-    subparser.add_argument(
+def setup_parser(subparser: argparse.ArgumentParser):
+    global MANIFEST_SUBPARSER
+    sp = subparser.add_subparsers(metavar="SUBCOMMAND", dest="verify_command")
+
+    MANIFEST_SUBPARSER = sp.add_parser(
+        "manifest", help=verify_manifest.__doc__, description=verify_manifest.__doc__
+    )
+    MANIFEST_SUBPARSER.add_argument(
         "-l", "--local", action="store_true", help="verify only locally installed packages"
     )
-    subparser.add_argument(
+    MANIFEST_SUBPARSER.add_argument(
         "-j", "--json", action="store_true", help="ouptut json-formatted errors"
     )
-    subparser.add_argument("-a", "--all", action="store_true", help="verify all packages")
-    subparser.add_argument(
+    MANIFEST_SUBPARSER.add_argument("-a", "--all", action="store_true", help="verify all packages")
+    MANIFEST_SUBPARSER.add_argument(
         "specs_or_files", nargs=argparse.REMAINDER, help="specs or files to verify"
     )
 
-    type = subparser.add_mutually_exclusive_group()
-    type.add_argument(
+    manifest_sp_type = MANIFEST_SUBPARSER.add_mutually_exclusive_group()
+    manifest_sp_type.add_argument(
         "-s",
         "--specs",
         action="store_const",
@@ -39,7 +52,7 @@ def setup_parser(subparser):
         default="specs",
         help="treat entries as specs (default)",
     )
-    type.add_argument(
+    manifest_sp_type.add_argument(
         "-f",
         "--files",
         action="store_const",
@@ -49,14 +62,67 @@ def setup_parser(subparser):
         help="treat entries as absolute filenames\n\ncannot be used with '-a'",
     )
 
+    libraries_subparser = sp.add_parser(
+        "libraries", help=verify_libraries.__doc__, description=verify_libraries.__doc__
+    )
+
+    arguments.add_common_arguments(libraries_subparser, ["constraint"])
+
 
 def verify(parser, args):
+    cmd = args.verify_command
+    if cmd == "libraries":
+        return verify_libraries(args)
+    elif cmd == "manifest":
+        return verify_manifest(args)
+    parser.error("invalid verify subcommand")
+
+
+def verify_libraries(args):
+    """verify that shared libraries of install packages can be located in rpaths (Linux only)"""
+    specs_from_db = [s for s in args.specs(installed=True) if not s.external]
+
+    tty.info(f"Checking {len(specs_from_db)} packages for shared library resolution")
+
+    errors = 0
+    for spec in specs_from_db:
+        try:
+            pkg = spec.package
+        except Exception:
+            tty.warn(f"Skipping {spec.cformat('{name}{@version}{/hash}')} due to missing package")
+        error_msg = _verify_libraries(spec, pkg.unresolved_libraries)
+        if error_msg is not None:
+            errors += 1
+            tty.error(error_msg)
+
+    if errors:
+        tty.error(f"Cannot resolve shared libraries in {plural(errors, 'package')}")
+        return 1
+
+
+def _verify_libraries(spec: spack.spec.Spec, unresolved_libraries: List[str]) -> Optional[str]:
+    """Go over the prefix of the installed spec and verify its shared libraries can be resolved."""
+    visitor = spack.verify_libraries.ResolveSharedElfLibDepsVisitor(
+        [*spack.verify_libraries.ALLOW_UNRESOLVED, *unresolved_libraries]
+    )
+    visit_directory_tree(spec.prefix, visitor)
+
+    if not visitor.problems:
+        return None
+
+    output = io.StringIO()
+    visitor.write(output, indent=4, brief=True)
+    message = output.getvalue().rstrip()
+    return f"{spec.cformat('{name}{@version}{/hash}')}: {spec.prefix}:\n{message}"
+
+
+def verify_manifest(args):
+    """verify that install directories have not been modified since installation"""
     local = args.local
 
     if args.type == "files":
         if args.all:
-            setup_parser.parser.print_help()
-            return 1
+            MANIFEST_SUBPARSER.error("cannot use --all with --files")
 
         for file in args.specs_or_files:
             results = spack.verify.check_file_manifest(file)
@@ -87,8 +153,7 @@ def verify(parser, args):
         env = ev.active_environment()
         specs = list(map(lambda x: spack.cmd.disambiguate_spec(x, env, local=local), spec_args))
     else:
-        setup_parser.parser.print_help()
-        return 1
+        MANIFEST_SUBPARSER.error("use --all or specify specs to verify")
 
     for spec in specs:
         tty.debug("Verifying package %s")

lib/spack/spack/concretize.py

@@ -220,7 +220,7 @@ def concretize_one(spec: Union[str, Spec], tests: TestsType = False) -> Spec:
     opt, i, answer = min(result.answers)
     name = spec.name
     # TODO: Consolidate this code with similar code in solve.py
-    if spec.virtual:
+    if spack.repo.PATH.is_virtual(spec.name):
         providers = [s.name for s in answer.values() if s.package.provides(name)]
         name = providers[0]
 

lib/spack/spack/config.py

@@ -66,6 +66,8 @@
 import spack.util.web as web_util
 from spack.util.cpus import cpus_available
 
+from .enums import ConfigScopePriority
+
 #: Dict from section names -> schema for that section
 SECTION_SCHEMAS: Dict[str, Any] = {
     "compilers": spack.schema.compilers.schema,
@@ -408,26 +410,18 @@ def _method(self, *args, **kwargs):
     return _method
 
 
-class Configuration:
-    """A full Spack configuration, from a hierarchy of config files.
+ScopeWithOptionalPriority = Union[ConfigScope, Tuple[int, ConfigScope]]
+ScopeWithPriority = Tuple[int, ConfigScope]
 
-    This class makes it easy to add a new scope on top of an existing one.
-    """
+
+class Configuration:
+    """A hierarchical configuration, merging a number of scopes at different priorities."""
 
     # convert to typing.OrderedDict when we drop 3.6, or OrderedDict when we reach 3.9
-    scopes: Dict[str, ConfigScope]
+    scopes: lang.PriorityOrderedMapping[str, ConfigScope]
 
-    def __init__(self, *scopes: ConfigScope) -> None:
-        """Initialize a configuration with an initial list of scopes.
-
-        Args:
-            scopes: list of scopes to add to this
-                Configuration, ordered from lowest to highest precedence
-
-        """
-        self.scopes = collections.OrderedDict()
-        for scope in scopes:
-            self.push_scope(scope)
+    def __init__(self) -> None:
+        self.scopes = lang.PriorityOrderedMapping()
         self.format_updates: Dict[str, List[ConfigScope]] = collections.defaultdict(list)
 
     def ensure_unwrapped(self) -> "Configuration":
@@ -435,36 +429,31 @@ def ensure_unwrapped(self) -> "Configuration":
         return self
 
     def highest(self) -> ConfigScope:
-        """Scope with highest precedence"""
-        return next(reversed(self.scopes.values()))  # type: ignore
+        """Scope with the highest precedence"""
+        return next(self.scopes.reversed_values())  # type: ignore
 
     @_config_mutator
-    def ensure_scope_ordering(self):
-        """Ensure that scope order matches documented precedent"""
-        # FIXME: We also need to consider that custom configurations and other orderings
-        # may not be preserved correctly
-        if "command_line" in self.scopes:
-            # TODO (when dropping python 3.6): self.scopes.move_to_end
-            self.scopes["command_line"] = self.remove_scope("command_line")
+    def push_scope(self, scope: ConfigScope, priority: Optional[int] = None) -> None:
+        """Adds a scope to the Configuration, at a given priority.
 
-    @_config_mutator
-    def push_scope(self, scope: ConfigScope) -> None:
-        """Add a higher precedence scope to the Configuration."""
-        tty.debug(f"[CONFIGURATION: PUSH SCOPE]: {str(scope)}", level=2)
-        self.scopes[scope.name] = scope
+        If a priority is not given, it is assumed to be the current highest priority.
 
-    @_config_mutator
-    def pop_scope(self) -> ConfigScope:
-        """Remove the highest precedence scope and return it."""
-        name, scope = self.scopes.popitem(last=True)  # type: ignore[call-arg]
-        tty.debug(f"[CONFIGURATION: POP SCOPE]: {str(scope)}", level=2)
-        return scope
+        Args:
+            scope: scope to be added
+            priority: priority of the scope
+        """
+        tty.debug(f"[CONFIGURATION: PUSH SCOPE]: {str(scope)}, priority={priority}", level=2)
+        self.scopes.add(scope.name, value=scope, priority=priority)
 
     @_config_mutator
     def remove_scope(self, scope_name: str) -> Optional[ConfigScope]:
-        """Remove scope by name; has no effect when ``scope_name`` does not exist"""
-        scope = self.scopes.pop(scope_name, None)
-        tty.debug(f"[CONFIGURATION: POP SCOPE]: {str(scope)}", level=2)
+        """Removes a scope by name, and returns it. If the scope does not exist, returns None."""
+        try:
+            scope = self.scopes.remove(scope_name)
+            tty.debug(f"[CONFIGURATION: POP SCOPE]: {str(scope)}", level=2)
+        except KeyError as e:
+            tty.debug(f"[CONFIGURATION: POP SCOPE]: {e}", level=2)
+            return None
         return scope
 
     @property
@@ -473,15 +462,13 @@ def writable_scopes(self) -> Generator[ConfigScope, None, None]:
         return (s for s in self.scopes.values() if s.writable)
 
     def highest_precedence_scope(self) -> ConfigScope:
-        """Writable scope with highest precedence."""
-        return next(s for s in reversed(self.scopes.values()) if s.writable)  # type: ignore
+        """Writable scope with the highest precedence."""
+        return next(s for s in self.scopes.reversed_values() if s.writable)
 
     def highest_precedence_non_platform_scope(self) -> ConfigScope:
-        """Writable non-platform scope with highest precedence"""
+        """Writable non-platform scope with the highest precedence"""
         return next(
-            s
-            for s in reversed(self.scopes.values())  # type: ignore
-            if s.writable and not s.is_platform_dependent
+            s for s in self.scopes.reversed_values() if s.writable and not s.is_platform_dependent
         )
 
     def matching_scopes(self, reg_expr) -> List[ConfigScope]:
@@ -748,7 +735,7 @@ def override(
     """
     if isinstance(path_or_scope, ConfigScope):
         overrides = path_or_scope
-        CONFIG.push_scope(path_or_scope)
+        CONFIG.push_scope(path_or_scope, priority=None)
     else:
         base_name = _OVERRIDES_BASE_NAME
         # Ensure the new override gets a unique scope name
@@ -762,7 +749,7 @@ def override(
                 break
 
         overrides = InternalConfigScope(scope_name)
-        CONFIG.push_scope(overrides)
+        CONFIG.push_scope(overrides, priority=None)
         CONFIG.set(path_or_scope, value, scope=scope_name)
 
     try:
@@ -772,13 +759,15 @@ def override(
         assert scope is overrides
 
 
-def _add_platform_scope(cfg: Configuration, name: str, path: str, writable: bool = True) -> None:
+def _add_platform_scope(
+    cfg: Configuration, name: str, path: str, priority: ConfigScopePriority, writable: bool = True
+) -> None:
     """Add a platform-specific subdirectory for the current platform."""
     platform = spack.platforms.host().name
     scope = DirectoryConfigScope(
         f"{name}/{platform}", os.path.join(path, platform), writable=writable
     )
-    cfg.push_scope(scope)
+    cfg.push_scope(scope, priority=priority)
 
 
 def config_paths_from_entry_points() -> List[Tuple[str, str]]:
@@ -813,11 +802,10 @@ def create() -> Configuration:
     it. It is bundled inside a function so that configuration can be
     initialized lazily.
     """
-    cfg = Configuration()
-
     # first do the builtin, hardcoded defaults
-    builtin = InternalConfigScope("_builtin", CONFIG_DEFAULTS)
-    cfg.push_scope(builtin)
+    cfg = create_from(
+        (ConfigScopePriority.BUILTIN, InternalConfigScope("_builtin", CONFIG_DEFAULTS))
+    )
 
     # Builtin paths to configuration files in Spack
     configuration_paths = [
@@ -847,10 +835,9 @@ def create() -> Configuration:
 
     # add each scope and its platform-specific directory
     for name, path in configuration_paths:
-        cfg.push_scope(DirectoryConfigScope(name, path))
-
-        # Each scope can have per-platfom overrides in subdirectories
-        _add_platform_scope(cfg, name, path)
+        cfg.push_scope(DirectoryConfigScope(name, path), priority=ConfigScopePriority.CONFIG_FILES)
+        # Each scope can have per-platform overrides in subdirectories
+        _add_platform_scope(cfg, name, path, priority=ConfigScopePriority.CONFIG_FILES)
 
     return cfg
 
@@ -955,7 +942,7 @@ def set(path: str, value: Any, scope: Optional[str] = None) -> None:
     return CONFIG.set(path, value, scope)
 
 
-def scopes() -> Dict[str, ConfigScope]:
+def scopes() -> lang.PriorityOrderedMapping[str, ConfigScope]:
     """Convenience function to get list of configuration scopes."""
     return CONFIG.scopes
 
@@ -1409,7 +1396,7 @@ def ensure_latest_format_fn(section: str) -> Callable[[YamlConfigDict], bool]:
 
 @contextlib.contextmanager
 def use_configuration(
-    *scopes_or_paths: Union[ConfigScope, str]
+    *scopes_or_paths: Union[ScopeWithOptionalPriority, str]
 ) -> Generator[Configuration, None, None]:
     """Use the configuration scopes passed as arguments within the context manager.
 
@@ -1424,7 +1411,7 @@ def use_configuration(
     global CONFIG
 
     # Normalize input and construct a Configuration object
-    configuration = _config_from(scopes_or_paths)
+    configuration = create_from(*scopes_or_paths)
     CONFIG.clear_caches(), configuration.clear_caches()
 
     saved_config, CONFIG = CONFIG, configuration
@@ -1435,23 +1422,44 @@ def use_configuration(
         CONFIG = saved_config
 
 
+def _normalize_input(entry: Union[ScopeWithOptionalPriority, str]) -> ScopeWithPriority:
+    if isinstance(entry, tuple):
+        return entry
+
+    default_priority = ConfigScopePriority.CONFIG_FILES
+    if isinstance(entry, ConfigScope):
+        return default_priority, entry
+
+    # Otherwise we need to construct it
+    path = os.path.normpath(entry)
+    assert os.path.isdir(path), f'"{path}" must be a directory'
+    name = os.path.basename(path)
+    return default_priority, DirectoryConfigScope(name, path)
+
+
 @lang.memoized
-def _config_from(scopes_or_paths: List[Union[ConfigScope, str]]) -> Configuration:
-    scopes = []
-    for scope_or_path in scopes_or_paths:
-        # If we have a config scope we are already done
-        if isinstance(scope_or_path, ConfigScope):
-            scopes.append(scope_or_path)
-            continue
+def create_from(*scopes_or_paths: Union[ScopeWithOptionalPriority, str]) -> Configuration:
+    """Creates a configuration object from the scopes passed in input.
 
-        # Otherwise we need to construct it
-        path = os.path.normpath(scope_or_path)
-        assert os.path.isdir(path), f'"{path}" must be a directory'
-        name = os.path.basename(path)
-        scopes.append(DirectoryConfigScope(name, path))
+    Args:
+        *scopes_or_paths: either a tuple of (priority, ConfigScope), or a ConfigScope, or a string
+            If priority is not given, it is assumed to be ConfigScopePriority.CONFIG_FILES. If a
+            string is given, a DirectoryConfigScope is created from it.
 
-    configuration = Configuration(*scopes)
-    return configuration
+    Examples:
+
+        >>> builtin_scope = InternalConfigScope("_builtin", {"config": {"build_jobs": 1}})
+        >>> cl_scope = InternalConfigScope("command_line", {"config": {"build_jobs": 10}})
+        >>> cfg = create_from(
+        ...     (ConfigScopePriority.COMMAND_LINE, cl_scope),
+        ...     (ConfigScopePriority.BUILTIN, builtin_scope)
+        ... )
+    """
+    scopes_with_priority = [_normalize_input(x) for x in scopes_or_paths]
+    result = Configuration()
+    for priority, scope in scopes_with_priority:
+        result.push_scope(scope, priority=priority)
+    return result
 
 
 def raw_github_gitlab_url(url: str) -> str:

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/database.py

@@ -41,6 +41,8 @@
     Union,
 )
 
+import spack.repo
+
 try:
     import uuid
 
@@ -1556,7 +1558,12 @@ def _query(
         # If we did fine something, the query spec can't be virtual b/c we matched an actual
         # package installation, so skip the virtual check entirely. If we *didn't* find anything,
         # check all the deferred specs *if* the query is virtual.
-        if not results and query_spec is not None and deferred and query_spec.virtual:
+        if (
+            not results
+            and query_spec is not None
+            and deferred
+            and spack.repo.PATH.is_virtual(query_spec.name)
+        ):
             results = [spec for spec in deferred if spec.satisfies(query_spec)]
 
         return results

lib/spack/spack/detection/common.py

@@ -310,7 +310,7 @@ def find_windows_kit_roots() -> List[str]:
 
     @staticmethod
     def find_windows_kit_bin_paths(
-        kit_base: Union[Optional[str], Optional[list]] = None
+        kit_base: Union[Optional[str], Optional[list]] = None,
     ) -> List[str]:
         """Returns Windows kit bin directory per version"""
         kit_base = WindowsKitExternalPaths.find_windows_kit_roots() if not kit_base else kit_base
@@ -325,7 +325,7 @@ def find_windows_kit_bin_paths(
 
     @staticmethod
     def find_windows_kit_lib_paths(
-        kit_base: Union[Optional[str], Optional[list]] = None
+        kit_base: Union[Optional[str], Optional[list]] = None,
     ) -> List[str]:
         """Returns Windows kit lib directory per version"""
         kit_base = WindowsKitExternalPaths.find_windows_kit_roots() if not kit_base else kit_base

lib/spack/spack/detection/path.py

@@ -243,7 +243,7 @@ def prefix_from_path(self, *, path: str) -> str:
         raise NotImplementedError("must be implemented by derived classes")
 
     def detect_specs(
-        self, *, pkg: Type["spack.package_base.PackageBase"], paths: List[str]
+        self, *, pkg: Type["spack.package_base.PackageBase"], paths: Iterable[str]
     ) -> List["spack.spec.Spec"]:
         """Given a list of files matching the search patterns, returns a list of detected specs.
 
@@ -259,6 +259,8 @@ def detect_specs(
             )
             return []
 
+        from spack.repo import PATH as repo_path
+
         result = []
         for candidate_path, items_in_prefix in _group_by_prefix(
             llnl.util.lang.dedupe(paths)
@@ -305,7 +307,10 @@ def detect_specs(
 
                 resolved_specs[spec] = candidate_path
                 try:
-                    spec.validate_detection()
+                    # Validate the spec calling a package specific method
+                    pkg_cls = repo_path.get_pkg_class(spec.name)
+                    validate_fn = getattr(pkg_cls, "validate_detected_spec", lambda x, y: None)
+                    validate_fn(spec, spec.extra_attributes)
                 except Exception as e:
                     msg = (
                         f'"{spec}" has been detected on the system but will '

lib/spack/spack/directives.py

@@ -568,7 +568,7 @@ def patch(
     """
 
     def _execute_patch(
-        pkg_or_dep: Union[Type[spack.package_base.PackageBase], Dependency]
+        pkg_or_dep: Union[Type[spack.package_base.PackageBase], Dependency],
     ) -> None:
         pkg = pkg_or_dep.pkg if isinstance(pkg_or_dep, Dependency) else pkg_or_dep
 

lib/spack/spack/directory_layout.py

@@ -25,7 +25,7 @@
 }
 
 
-def _check_concrete(spec):
+def _check_concrete(spec: "spack.spec.Spec") -> None:
     """If the spec is not concrete, raise a ValueError"""
     if not spec.concrete:
         raise ValueError("Specs passed to a DirectoryLayout must be concrete!")
@@ -51,7 +51,7 @@ def specs_from_metadata_dirs(root: str) -> List["spack.spec.Spec"]:
         spec = _get_spec(prefix)
 
         if spec:
-            spec.prefix = prefix
+            spec.set_prefix(prefix)
             specs.append(spec)
             continue
 
@@ -84,7 +84,7 @@ class DirectoryLayout:
 
     def __init__(
         self,
-        root,
+        root: str,
         *,
         projections: Optional[Dict[str, str]] = None,
         hash_length: Optional[int] = None,
@@ -120,17 +120,17 @@ def __init__(
         self.manifest_file_name = "install_manifest.json"
 
     @property
-    def hidden_file_regexes(self):
+    def hidden_file_regexes(self) -> Tuple[str]:
         return ("^{0}$".format(re.escape(self.metadata_dir)),)
 
-    def relative_path_for_spec(self, spec):
+    def relative_path_for_spec(self, spec: "spack.spec.Spec") -> str:
         _check_concrete(spec)
 
         projection = spack.projections.get_projection(self.projections, spec)
         path = spec.format_path(projection)
         return str(Path(path))
 
-    def write_spec(self, spec, path):
+    def write_spec(self, spec: "spack.spec.Spec", path: str) -> None:
         """Write a spec out to a file."""
         _check_concrete(spec)
         with open(path, "w", encoding="utf-8") as f:
@@ -138,7 +138,7 @@ def write_spec(self, spec, path):
             # the full provenance, so it's availabe if we want it later
             spec.to_json(f, hash=ht.dag_hash)
 
-    def write_host_environment(self, spec):
+    def write_host_environment(self, spec: "spack.spec.Spec") -> None:
         """The host environment is a json file with os, kernel, and spack
         versioning. We use it in the case that an analysis later needs to
         easily access this information.
@@ -148,7 +148,7 @@ def write_host_environment(self, spec):
         with open(env_file, "w", encoding="utf-8") as fd:
             sjson.dump(environ, fd)
 
-    def read_spec(self, path):
+    def read_spec(self, path: str) -> "spack.spec.Spec":
         """Read the contents of a file and parse them as a spec"""
         try:
             with open(path, encoding="utf-8") as f:
@@ -159,26 +159,28 @@ def read_spec(self, path):
                     # Too late for conversion; spec_file_path() already called.
                     spec = spack.spec.Spec.from_yaml(f)
                 else:
-                    raise SpecReadError(
-                        "Did not recognize spec file extension:" " {0}".format(extension)
-                    )
+                    raise SpecReadError(f"Did not recognize spec file extension: {extension}")
         except Exception as e:
             if spack.config.get("config:debug"):
                 raise
-            raise SpecReadError("Unable to read file: %s" % path, "Cause: " + str(e))
+            raise SpecReadError(f"Unable to read file: {path}", f"Cause: {e}")
 
         # Specs read from actual installations are always concrete
         spec._mark_concrete()
         return spec
 
-    def spec_file_path(self, spec):
+    def spec_file_path(self, spec: "spack.spec.Spec") -> str:
         """Gets full path to spec file"""
         _check_concrete(spec)
         yaml_path = os.path.join(self.metadata_path(spec), self._spec_file_name_yaml)
         json_path = os.path.join(self.metadata_path(spec), self.spec_file_name)
         return yaml_path if os.path.exists(yaml_path) else json_path
 
-    def deprecated_file_path(self, deprecated_spec, deprecator_spec=None):
+    def deprecated_file_path(
+        self,
+        deprecated_spec: "spack.spec.Spec",
+        deprecator_spec: Optional["spack.spec.Spec"] = None,
+    ) -> str:
         """Gets full path to spec file for deprecated spec
 
         If the deprecator_spec is provided, use that. Otherwise, assume
@@ -212,16 +214,16 @@ def deprecated_file_path(self, deprecated_spec, deprecator_spec=None):
 
         return yaml_path if os.path.exists(yaml_path) else json_path
 
-    def metadata_path(self, spec):
+    def metadata_path(self, spec: "spack.spec.Spec") -> str:
         return os.path.join(spec.prefix, self.metadata_dir)
 
-    def env_metadata_path(self, spec):
+    def env_metadata_path(self, spec: "spack.spec.Spec") -> str:
         return os.path.join(self.metadata_path(spec), "install_environment.json")
 
-    def build_packages_path(self, spec):
+    def build_packages_path(self, spec: "spack.spec.Spec") -> str:
         return os.path.join(self.metadata_path(spec), self.packages_dir)
 
-    def create_install_directory(self, spec):
+    def create_install_directory(self, spec: "spack.spec.Spec") -> None:
         _check_concrete(spec)
 
         # Create install directory with properly configured permissions
@@ -239,7 +241,7 @@ def create_install_directory(self, spec):
 
         self.write_spec(spec, self.spec_file_path(spec))
 
-    def ensure_installed(self, spec):
+    def ensure_installed(self, spec: "spack.spec.Spec") -> None:
         """
         Throws InconsistentInstallDirectoryError if:
         1. spec prefix does not exist
@@ -266,7 +268,7 @@ def ensure_installed(self, spec):
                 "Spec file in %s does not match hash!" % spec_file_path
             )
 
-    def path_for_spec(self, spec):
+    def path_for_spec(self, spec: "spack.spec.Spec") -> str:
         """Return absolute path from the root to a directory for the spec."""
         _check_concrete(spec)
 
@@ -277,23 +279,13 @@ def path_for_spec(self, spec):
         assert not path.startswith(self.root)
         return os.path.join(self.root, path)
 
-    def remove_install_directory(self, spec, deprecated=False):
+    def remove_install_directory(self, spec: "spack.spec.Spec", deprecated: bool = False) -> None:
         """Removes a prefix and any empty parent directories from the root.
         Raised RemoveFailedError if something goes wrong.
         """
         path = self.path_for_spec(spec)
         assert path.startswith(self.root)
 
-        # Windows readonly files cannot be removed by Python
-        # directly, change permissions before attempting to remove
-        if sys.platform == "win32":
-            kwargs = {
-                "ignore_errors": False,
-                "onerror": fs.readonly_file_handler(ignore_errors=False),
-            }
-        else:
-            kwargs = {}  # the default value for ignore_errors is false
-
         if deprecated:
             if os.path.exists(path):
                 try:
@@ -304,7 +296,16 @@ def remove_install_directory(self, spec, deprecated=False):
                     raise RemoveFailedError(spec, path, e) from e
         elif os.path.exists(path):
             try:
-                shutil.rmtree(path, **kwargs)
+                if sys.platform == "win32":
+                    # Windows readonly files cannot be removed by Python
+                    # directly, change permissions before attempting to remove
+                    shutil.rmtree(
+                        path,
+                        ignore_errors=False,
+                        onerror=fs.readonly_file_handler(ignore_errors=False),
+                    )
+                else:
+                    shutil.rmtree(path)
             except OSError as e:
                 raise RemoveFailedError(spec, path, e) from e
 

lib/spack/spack/enums.py

@@ -12,3 +12,13 @@ class InstallRecordStatus(enum.Flag):
     DEPRECATED = enum.auto()
     MISSING = enum.auto()
     ANY = INSTALLED | DEPRECATED | MISSING
+
+
+class ConfigScopePriority(enum.IntEnum):
+    """Priorities of the different kind of config scopes used by Spack"""
+
+    BUILTIN = 0
+    CONFIG_FILES = 1
+    CUSTOM = 2
+    ENVIRONMENT = 3
+    COMMAND_LINE = 4

lib/spack/spack/environment/environment.py

@@ -51,6 +51,8 @@
 from spack.spec_list import SpecList
 from spack.util.path import substitute_path_variables
 
+from ..enums import ConfigScopePriority
+
 SpecPair = spack.concretize.SpecPair
 
 #: environment variable used to indicate the active environment
@@ -581,7 +583,7 @@ 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 +863,7 @@ 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)
@@ -2392,6 +2394,8 @@ def invalidate_repository_cache(self):
 
     def __enter__(self):
         self._previous_active = _active_environment
+        if self._previous_active:
+            deactivate()
         activate(self)
         return self
 
@@ -2554,7 +2558,7 @@ 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 +2638,32 @@ 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
@@ -3041,14 +3071,12 @@ def env_config_scopes(self) -> List[spack.config.ConfigScope]:
     def prepare_config_scope(self) -> None:
         """Add the manifest's scopes to the global configuration search path."""
         for scope in self.env_config_scopes:
-            spack.config.CONFIG.push_scope(scope)
-        spack.config.CONFIG.ensure_scope_ordering()
+            spack.config.CONFIG.push_scope(scope, priority=ConfigScopePriority.ENVIRONMENT)
 
     def deactivate_config_scope(self) -> None:
         """Remove any of the manifest's scopes from the global config path."""
         for scope in self.env_config_scopes:
             spack.config.CONFIG.remove_scope(scope.name)
-        spack.config.CONFIG.ensure_scope_ordering()
 
     @contextlib.contextmanager
     def use_config(self):

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

@@ -9,7 +9,8 @@
 import shutil
 import stat
 import sys
-from typing import Callable, Dict, Optional
+import tempfile
+from typing import Callable, Dict, List, Optional
 
 from typing_extensions import Literal
 
@@ -77,7 +78,7 @@ def view_copy(
 
     # Order of this dict is somewhat irrelevant
     prefix_to_projection = {
-        s.prefix: view.get_projection_for_spec(s)
+        str(s.prefix): view.get_projection_for_spec(s)
         for s in spec.traverse(root=True, order="breadth")
         if not s.external
     }
@@ -184,7 +185,7 @@ def __init__(
     def link(self, src: str, dst: str, spec: Optional[spack.spec.Spec] = None) -> None:
         self._link(src, dst, self, spec)
 
-    def add_specs(self, *specs, **kwargs):
+    def add_specs(self, *specs: spack.spec.Spec, **kwargs) -> None:
         """
         Add given specs to view.
 
@@ -199,19 +200,19 @@ def add_specs(self, *specs, **kwargs):
         """
         raise NotImplementedError
 
-    def add_standalone(self, spec):
+    def add_standalone(self, spec: spack.spec.Spec) -> bool:
         """
         Add (link) a standalone package into this view.
         """
         raise NotImplementedError
 
-    def check_added(self, spec):
+    def check_added(self, spec: spack.spec.Spec) -> bool:
         """
         Check if the given concrete spec is active in this view.
         """
         raise NotImplementedError
 
-    def remove_specs(self, *specs, **kwargs):
+    def remove_specs(self, *specs: spack.spec.Spec, **kwargs) -> None:
         """
         Removes given specs from view.
 
@@ -230,25 +231,25 @@ def remove_specs(self, *specs, **kwargs):
         """
         raise NotImplementedError
 
-    def remove_standalone(self, spec):
+    def remove_standalone(self, spec: spack.spec.Spec) -> None:
         """
         Remove (unlink) a standalone package from this view.
         """
         raise NotImplementedError
 
-    def get_projection_for_spec(self, spec):
+    def get_projection_for_spec(self, spec: spack.spec.Spec) -> str:
         """
         Get the projection in this view for a spec.
         """
         raise NotImplementedError
 
-    def get_all_specs(self):
+    def get_all_specs(self) -> List[spack.spec.Spec]:
         """
         Get all specs currently active in this view.
         """
         raise NotImplementedError
 
-    def get_spec(self, spec):
+    def get_spec(self, spec: spack.spec.Spec) -> Optional[spack.spec.Spec]:
         """
         Return the actual spec linked in this view (i.e. do not look it up
         in the database by name).
@@ -262,7 +263,7 @@ def get_spec(self, spec):
         """
         raise NotImplementedError
 
-    def print_status(self, *specs, **kwargs):
+    def print_status(self, *specs: spack.spec.Spec, **kwargs) -> None:
         """
         Print a short summary about the given specs, detailing whether..
             * ..they are active in the view.
@@ -427,7 +428,7 @@ 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
@@ -693,7 +694,7 @@ def _sanity_check_view_projection(self, specs):
                 raise ConflictingSpecsError(current_spec, conflicting_spec)
             seen[metadata_dir] = current_spec
 
-    def add_specs(self, *specs: spack.spec.Spec) -> None:
+    def add_specs(self, *specs, **kwargs) -> None:
         """Link a root-to-leaf topologically ordered list of specs into the view."""
         assert all((s.concrete for s in specs))
         if len(specs) == 0:
@@ -708,7 +709,10 @@ def add_specs(self, *specs: spack.spec.Spec) -> None:
         def skip_list(file):
             return os.path.basename(file) == spack.store.STORE.layout.metadata_dir
 
-        visitor = SourceMergeVisitor(ignore=skip_list)
+        # Determine if the root is on a case-insensitive filesystem
+        normalize_paths = is_folder_on_case_insensitive_filesystem(self._root)
+
+        visitor = SourceMergeVisitor(ignore=skip_list, normalize_paths=normalize_paths)
 
         # Gather all the directories to be made and files to be linked
         for spec in specs:
@@ -827,11 +831,11 @@ def get_projection_for_spec(self, spec):
 #####################
 # utility functions #
 #####################
-def get_spec_from_file(filename):
+def get_spec_from_file(filename) -> Optional[spack.spec.Spec]:
     try:
         with open(filename, "r", encoding="utf-8") as f:
             return spack.spec.Spec.from_yaml(f)
-    except IOError:
+    except OSError:
         return None
 
 
@@ -884,3 +888,8 @@ def get_dependencies(specs):
 
 class ConflictingProjectionsError(SpackError):
     """Raised when a view has a projections file and is given one manually."""
+
+
+def is_folder_on_case_insensitive_filesystem(path: str) -> bool:
+    with tempfile.NamedTemporaryFile(dir=path, prefix=".sentinel") as sentinel:
+        return os.path.exists(os.path.join(path, os.path.basename(sentinel.name).upper()))

lib/spack/spack/graph.py

@@ -42,10 +42,10 @@
 import llnl.util.tty.color
 
 import spack.deptypes as dt
-import spack.repo
 import spack.spec
 import spack.tengine
 import spack.traverse
+from spack.solver.input_analysis import create_graph_analyzer
 
 
 def find(seq, predicate):
@@ -537,10 +537,11 @@ def edge_entry(self, edge):
 
 def _static_edges(specs, depflag):
     for spec in specs:
-        pkg_cls = spack.repo.PATH.get_pkg_class(spec.name)
-        possible = pkg_cls.possible_dependencies(expand_virtuals=True, depflag=depflag)
+        *_, edges = create_graph_analyzer().possible_dependencies(
+            spec.name, expand_virtuals=True, allowed_deps=depflag
+        )
 
-        for parent_name, dependencies in possible.items():
+        for parent_name, dependencies in edges.items():
             for dependency_name in dependencies:
                 yield spack.spec.DependencySpec(
                     spack.spec.Spec(parent_name),

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/resolve_shared_libraries.py

@@ -2,198 +2,14 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import fnmatch
 import io
-import os
-import re
-from typing import Dict, List, Union
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import BaseDirectoryVisitor, visit_directory_tree
-from llnl.util.lang import stable_partition
+from llnl.util.filesystem import visit_directory_tree
 
 import spack.config
 import spack.error
-import spack.util.elf as elf
-
-#: Patterns for names of libraries that are allowed to be unresolved when *just* looking at RPATHs
-#: added by Spack. These are libraries outside of Spack's control, and assumed to be located in
-#: default search paths of the dynamic linker.
-ALLOW_UNRESOLVED = [
-    # kernel
-    "linux-vdso.so.*",
-    "libselinux.so.*",
-    # musl libc
-    "ld-musl-*.so.*",
-    # glibc
-    "ld-linux*.so.*",
-    "ld64.so.*",
-    "libanl.so.*",
-    "libc.so.*",
-    "libdl.so.*",
-    "libm.so.*",
-    "libmemusage.so.*",
-    "libmvec.so.*",
-    "libnsl.so.*",
-    "libnss_compat.so.*",
-    "libnss_db.so.*",
-    "libnss_dns.so.*",
-    "libnss_files.so.*",
-    "libnss_hesiod.so.*",
-    "libpcprofile.so.*",
-    "libpthread.so.*",
-    "libresolv.so.*",
-    "librt.so.*",
-    "libSegFault.so.*",
-    "libthread_db.so.*",
-    "libutil.so.*",
-    # gcc -- this is required even with gcc-runtime, because e.g. libstdc++ depends on libgcc_s,
-    # but the binaries we copy from the compiler don't have an $ORIGIN rpath.
-    "libasan.so.*",
-    "libatomic.so.*",
-    "libcc1.so.*",
-    "libgcc_s.so.*",
-    "libgfortran.so.*",
-    "libgomp.so.*",
-    "libitm.so.*",
-    "liblsan.so.*",
-    "libquadmath.so.*",
-    "libssp.so.*",
-    "libstdc++.so.*",
-    "libtsan.so.*",
-    "libubsan.so.*",
-    # systemd
-    "libudev.so.*",
-    # cuda driver
-    "libcuda.so.*",
-]
-
-
-def is_compatible(parent: elf.ElfFile, child: elf.ElfFile) -> bool:
-    return (
-        child.elf_hdr.e_type == elf.ELF_CONSTANTS.ET_DYN
-        and parent.is_little_endian == child.is_little_endian
-        and parent.is_64_bit == child.is_64_bit
-        and parent.elf_hdr.e_machine == child.elf_hdr.e_machine
-    )
-
-
-def candidate_matches(current_elf: elf.ElfFile, candidate_path: bytes) -> bool:
-    try:
-        with open(candidate_path, "rb") as g:
-            return is_compatible(current_elf, elf.parse_elf(g))
-    except (OSError, elf.ElfParsingError):
-        return False
-
-
-class Problem:
-    def __init__(
-        self, resolved: Dict[bytes, bytes], unresolved: List[bytes], relative_rpaths: List[bytes]
-    ) -> None:
-        self.resolved = resolved
-        self.unresolved = unresolved
-        self.relative_rpaths = relative_rpaths
-
-
-class ResolveSharedElfLibDepsVisitor(BaseDirectoryVisitor):
-    def __init__(self, allow_unresolved_patterns: List[str]) -> None:
-        self.problems: Dict[str, Problem] = {}
-        self._allow_unresolved_regex = re.compile(
-            "|".join(fnmatch.translate(x) for x in allow_unresolved_patterns)
-        )
-
-    def allow_unresolved(self, needed: bytes) -> bool:
-        try:
-            name = needed.decode("utf-8")
-        except UnicodeDecodeError:
-            return False
-        return bool(self._allow_unresolved_regex.match(name))
-
-    def visit_file(self, root: str, rel_path: str, depth: int) -> None:
-        # We work with byte strings for paths.
-        path = os.path.join(root, rel_path).encode("utf-8")
-
-        # For $ORIGIN interpolation: should not have trailing dir seperator.
-        origin = os.path.dirname(path)
-
-        # Retrieve the needed libs + rpaths.
-        try:
-            with open(path, "rb") as f:
-                parsed_elf = elf.parse_elf(f, interpreter=False, dynamic_section=True)
-        except (OSError, elf.ElfParsingError):
-            # Not dealing with an invalid ELF file.
-            return
-
-        # If there's no needed libs all is good
-        if not parsed_elf.has_needed:
-            return
-
-        # Get the needed libs and rpaths (notice: byte strings)
-        # Don't force an encoding cause paths are just a bag of bytes.
-        needed_libs = parsed_elf.dt_needed_strs
-
-        rpaths = parsed_elf.dt_rpath_str.split(b":") if parsed_elf.has_rpath else []
-
-        # We only interpolate $ORIGIN, not $LIB and $PLATFORM, they're not really
-        # supported in general. Also remove empty paths.
-        rpaths = [x.replace(b"$ORIGIN", origin) for x in rpaths if x]
-
-        # Do not allow relative rpaths (they are relative to the current working directory)
-        rpaths, relative_rpaths = stable_partition(rpaths, os.path.isabs)
-
-        # If there's a / in the needed lib, it's opened directly, otherwise it needs
-        # a search.
-        direct_libs, search_libs = stable_partition(needed_libs, lambda x: b"/" in x)
-
-        # Do not allow relative paths in direct libs (they are relative to the current working
-        # directory)
-        direct_libs, unresolved = stable_partition(direct_libs, os.path.isabs)
-
-        resolved: Dict[bytes, bytes] = {}
-
-        for lib in search_libs:
-            if self.allow_unresolved(lib):
-                continue
-            for rpath in rpaths:
-                candidate = os.path.join(rpath, lib)
-                if candidate_matches(parsed_elf, candidate):
-                    resolved[lib] = candidate
-                    break
-            else:
-                unresolved.append(lib)
-
-        # Check if directly opened libs are compatible
-        for lib in direct_libs:
-            if candidate_matches(parsed_elf, lib):
-                resolved[lib] = lib
-            else:
-                unresolved.append(lib)
-
-        if unresolved or relative_rpaths:
-            self.problems[rel_path] = Problem(resolved, unresolved, relative_rpaths)
-
-    def visit_symlinked_file(self, root: str, rel_path: str, depth: int) -> None:
-        pass
-
-    def before_visit_dir(self, root: str, rel_path: str, depth: int) -> bool:
-        # There can be binaries in .spack/test which shouldn't be checked.
-        if rel_path == ".spack":
-            return False
-        return True
-
-    def before_visit_symlinked_dir(self, root: str, rel_path: str, depth: int) -> bool:
-        return False
-
-
-class CannotLocateSharedLibraries(spack.error.SpackError):
-    pass
-
-
-def maybe_decode(byte_str: bytes) -> Union[str, bytes]:
-    try:
-        return byte_str.decode("utf-8")
-    except UnicodeDecodeError:
-        return byte_str
+import spack.verify_libraries
 
 
 def post_install(spec, explicit):
@@ -204,36 +20,23 @@ def post_install(spec, explicit):
     if policy == "ignore" or spec.external or spec.platform not in ("linux", "freebsd"):
         return
 
-    visitor = ResolveSharedElfLibDepsVisitor(
-        [*ALLOW_UNRESOLVED, *spec.package.unresolved_libraries]
+    visitor = spack.verify_libraries.ResolveSharedElfLibDepsVisitor(
+        [*spack.verify_libraries.ALLOW_UNRESOLVED, *spec.package.unresolved_libraries]
     )
     visit_directory_tree(spec.prefix, visitor)
 
-    # All good?
     if not visitor.problems:
         return
 
-    # For now just list the issues (print it in ldd style, except we don't recurse)
-    output = io.StringIO()
-    output.write("not all executables and libraries can resolve their dependencies:\n")
-    for path, problem in visitor.problems.items():
-        output.write(path)
-        output.write("\n")
-        for needed, full_path in problem.resolved.items():
-            output.write("        ")
-            if needed == full_path:
-                output.write(maybe_decode(needed))
-            else:
-                output.write(f"{maybe_decode(needed)} => {maybe_decode(full_path)}")
-            output.write("\n")
-        for not_found in problem.unresolved:
-            output.write(f"        {maybe_decode(not_found)} => not found\n")
-        for relative_rpath in problem.relative_rpaths:
-            output.write(f"        {maybe_decode(relative_rpath)} => relative rpath\n")
-
+    output = io.StringIO("not all executables and libraries can resolve their dependencies:\n")
+    visitor.write(output)
     message = output.getvalue().strip()
 
     if policy == "error":
         raise CannotLocateSharedLibraries(message)
 
     tty.warn(message)
+
+
+class CannotLocateSharedLibraries(spack.error.SpackError):
+    pass

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/install_test.py

@@ -566,7 +566,7 @@ def copy_test_files(pkg: Pb, test_spec: spack.spec.Spec):
 
     # copy test data into test stage data dir
     try:
-        pkg_cls = test_spec.package_class
+        pkg_cls = spack.repo.PATH.get_pkg_class(test_spec.fullname)
     except spack.repo.UnknownPackageError:
         tty.debug(f"{test_spec.name}: skipping test data copy since no package class found")
         return
@@ -623,7 +623,7 @@ def test_functions(
         vpkgs = virtuals(pkg)
         for vname in vpkgs:
             try:
-                classes.append((Spec(vname)).package_class)
+                classes.append(spack.repo.PATH.get_pkg_class(vname))
             except spack.repo.UnknownPackageError:
                 tty.debug(f"{vname}: virtual does not appear to have a package file")
 
@@ -668,7 +668,7 @@ def process_test_parts(pkg: Pb, test_specs: List[spack.spec.Spec], verbose: bool
 
             # grab test functions associated with the spec, which may be virtual
             try:
-                tests = test_functions(spec.package_class)
+                tests = test_functions(spack.repo.PATH.get_pkg_class(spec.fullname))
             except spack.repo.UnknownPackageError:
                 # Some virtuals don't have a package so we don't want to report
                 # them as not having tests when that isn't appropriate.

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):
@@ -2436,11 +2436,7 @@ def _real_install(self) -> None:
                     # DEBUGGING TIP - to debug this section, insert an IPython
                     # embed here, and run the sections below without log capture
                     log_contextmanager = log_output(
-                        log_file,
-                        self.echo,
-                        True,
-                        env=self.unmodified_env,
-                        filter_fn=self.filter_fn,
+                        log_file, self.echo, True, filter_fn=self.filter_fn
                     )
 
                     with log_contextmanager as logger:

lib/spack/spack/main.py

@@ -47,6 +47,8 @@
 import spack.util.environment
 import spack.util.lock
 
+from .enums import ConfigScopePriority
+
 #: names of profile statistics
 stat_names = pstats.Stats.sort_arg_dict_default
 
@@ -163,7 +165,7 @@ 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!
@@ -872,14 +874,19 @@ def add_command_line_scopes(
         scopes = ev.environment_path_scopes(name, path)
         if scopes is None:
             if os.path.isdir(path):  # directory with config files
-                cfg.push_scope(spack.config.DirectoryConfigScope(name, path, writable=False))
-                spack.config._add_platform_scope(cfg, name, path, writable=False)
+                cfg.push_scope(
+                    spack.config.DirectoryConfigScope(name, path, writable=False),
+                    priority=ConfigScopePriority.CUSTOM,
+                )
+                spack.config._add_platform_scope(
+                    cfg, name, path, priority=ConfigScopePriority.CUSTOM, writable=False
+                )
                 continue
             else:
                 raise spack.error.ConfigError(f"Invalid configuration scope: {path}")
 
         for scope in scopes:
-            cfg.push_scope(scope)
+            cfg.push_scope(scope, priority=ConfigScopePriority.CUSTOM)
 
 
 def _main(argv=None):
@@ -952,7 +959,9 @@ def _main(argv=None):
     # Push scopes from the command line last
     if args.config_scopes:
         add_command_line_scopes(spack.config.CONFIG, args.config_scopes)
-    spack.config.CONFIG.push_scope(spack.config.InternalConfigScope("command_line"))
+    spack.config.CONFIG.push_scope(
+        spack.config.InternalConfigScope("command_line"), priority=ConfigScopePriority.COMMAND_LINE
+    )
     setup_main_options(args)
 
     # ------------------------------------------------------------------------
@@ -998,6 +1007,7 @@ def finish_parse_and_run(parser, cmd_name, main_args, env_format_error):
     args, unknown = parser.parse_known_args(main_args.command)
     # we need to inherit verbose since the install command checks for it
     args.verbose = main_args.verbose
+    args.lines = main_args.lines
 
     # Now that we know what command this is and what its args are, determine
     # whether we can continue with a bad environment and raise if not.

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/modules/common.py

@@ -330,18 +330,17 @@ class BaseConfiguration:
     default_projections = {"all": "{name}/{version}-{compiler.name}-{compiler.version}"}
 
     def __init__(self, spec: spack.spec.Spec, module_set_name: str, explicit: bool) -> None:
-        # Module where type(self) is defined
-        m = inspect.getmodule(self)
-        assert m is not None  # make mypy happy
-        self.module = m
         # Spec for which we want to generate a module file
         self.spec = spec
         self.name = module_set_name
         self.explicit = explicit
-        # Dictionary of configuration options that should be applied
-        # to the spec
+        # Dictionary of configuration options that should be applied to the spec
         self.conf = merge_config_rules(self.module.configuration(self.name), self.spec)
 
+    @property
+    def module(self):
+        return inspect.getmodule(self)
+
     @property
     def projections(self):
         """Projection from specs to module names"""
@@ -775,10 +774,6 @@ def __init__(
     ) -> None:
         self.spec = spec
 
-        # This class is meant to be derived. Get the module of the
-        # actual writer.
-        self.module = inspect.getmodule(self)
-        assert self.module is not None  # make mypy happy
         m = self.module
 
         # Create the triplet of configuration/layout/context
@@ -816,6 +811,10 @@ def __init__(
             name = type(self).__name__
             raise ModulercHeaderNotDefined(msg.format(name))
 
+    @property
+    def module(self):
+        return inspect.getmodule(self)
+
     def _get_template(self):
         """Gets the template that will be rendered for this spec."""
         # Get templates and put them in the order of importance:

lib/spack/spack/modules/lmod.py

@@ -209,7 +209,7 @@ def provides(self):
         # All the other tokens in the hierarchy must be virtual dependencies
         for x in self.hierarchy_tokens:
             if self.spec.package.provides(x):
-                provides[x] = self.spec[x]
+                provides[x] = self.spec
         return provides
 
     @property

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

@@ -22,7 +22,6 @@
 import textwrap
 import time
 import traceback
-import typing
 from typing import Any, Callable, Dict, Iterable, List, Optional, Set, Tuple, Type, TypeVar, Union
 
 from typing_extensions import Literal
@@ -66,10 +65,6 @@
 ]
 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 +696,6 @@ 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
 
@@ -717,19 +709,6 @@ class PackageBase(WindowsRPath, PackageViewMixin, metaclass=PackageMeta):
     #: Do not include @ here in order not to unnecessarily ping the users.
     maintainers: List[str] = []
 
-    #: List of attributes to be excluded from a package's hash.
-    metadata_attrs = [
-        "homepage",
-        "url",
-        "urls",
-        "list_url",
-        "extendable",
-        "parallel",
-        "make_jobs",
-        "maintainers",
-        "tags",
-    ]
-
     #: Set to ``True`` to indicate the stand-alone test requires a compiler.
     #: It is used to ensure a compiler and build dependencies like 'cmake'
     #: are available to build a custom test code.
@@ -829,104 +808,6 @@ def get_variant(self, name: str) -> spack.variant.Variant:
         except StopIteration:
             raise ValueError(f"No variant '{name}' on spec: {self.spec}")
 
-    @classmethod
-    def possible_dependencies(
-        cls,
-        transitive: bool = True,
-        expand_virtuals: bool = True,
-        depflag: dt.DepFlag = dt.ALL,
-        visited: Optional[dict] = None,
-        missing: Optional[dict] = None,
-        virtuals: Optional[set] = None,
-    ) -> Dict[str, Set[str]]:
-        """Return dict of possible dependencies of this package.
-
-        Args:
-            transitive (bool or None): return all transitive dependencies if
-                True, only direct dependencies if False (default True)..
-            expand_virtuals (bool or None): expand virtual dependencies into
-                all possible implementations (default True)
-            depflag: dependency types to consider
-            visited (dict or None): dict of names of dependencies visited so
-                far, mapped to their immediate dependencies' names.
-            missing (dict or None): dict to populate with packages and their
-                *missing* dependencies.
-            virtuals (set): if provided, populate with virtuals seen so far.
-
-        Returns:
-            (dict): dictionary mapping dependency names to *their*
-                immediate dependencies
-
-        Each item in the returned dictionary maps a (potentially
-        transitive) dependency of this package to its possible
-        *immediate* dependencies. If ``expand_virtuals`` is ``False``,
-        virtual package names wil be inserted as keys mapped to empty
-        sets of dependencies.  Virtuals, if not expanded, are treated as
-        though they have no immediate dependencies.
-
-        Missing dependencies by default are ignored, but if a
-        missing dict is provided, it will be populated with package names
-        mapped to any dependencies they have that are in no
-        repositories. This is only populated if transitive is True.
-
-        Note: the returned dict *includes* the package itself.
-
-        """
-        visited = {} if visited is None else visited
-        missing = {} if missing is None else missing
-
-        visited.setdefault(cls.name, set())
-
-        for name, conditions in cls.dependencies_by_name(when=True).items():
-            # check whether this dependency could be of the type asked for
-            depflag_union = 0
-            for deplist in conditions.values():
-                for dep in deplist:
-                    depflag_union |= dep.depflag
-            if not (depflag & depflag_union):
-                continue
-
-            # expand virtuals if enabled, otherwise just stop at virtuals
-            if spack.repo.PATH.is_virtual(name):
-                if virtuals is not None:
-                    virtuals.add(name)
-                if expand_virtuals:
-                    providers = spack.repo.PATH.providers_for(name)
-                    dep_names = [spec.name for spec in providers]
-                else:
-                    visited.setdefault(cls.name, set()).add(name)
-                    visited.setdefault(name, set())
-                    continue
-            else:
-                dep_names = [name]
-
-            # add the dependency names to the visited dict
-            visited.setdefault(cls.name, set()).update(set(dep_names))
-
-            # recursively traverse dependencies
-            for dep_name in dep_names:
-                if dep_name in visited:
-                    continue
-
-                visited.setdefault(dep_name, set())
-
-                # skip the rest if not transitive
-                if not transitive:
-                    continue
-
-                try:
-                    dep_cls = spack.repo.PATH.get_pkg_class(dep_name)
-                except spack.repo.UnknownPackageError:
-                    # log unknown packages
-                    missing.setdefault(cls.name, set()).add(dep_name)
-                    continue
-
-                dep_cls.possible_dependencies(
-                    transitive, expand_virtuals, depflag, visited, missing, virtuals
-                )
-
-        return visited
-
     @classproperty
     def package_dir(cls):
         """Directory where the package.py file lives."""
@@ -2291,55 +2172,6 @@ def rpath_args(self):
 build_system_flags = PackageBase.build_system_flags
 
 
-def use_cray_compiler_names():
-    """Compiler names for builds that rely on cray compiler names."""
-    os.environ["CC"] = "cc"
-    os.environ["CXX"] = "CC"
-    os.environ["FC"] = "ftn"
-    os.environ["F77"] = "ftn"
-
-
-def possible_dependencies(
-    *pkg_or_spec: Union[str, spack.spec.Spec, typing.Type[PackageBase]],
-    transitive: bool = True,
-    expand_virtuals: bool = True,
-    depflag: dt.DepFlag = dt.ALL,
-    missing: Optional[dict] = None,
-    virtuals: Optional[set] = None,
-) -> Dict[str, Set[str]]:
-    """Get the possible dependencies of a number of packages.
-
-    See ``PackageBase.possible_dependencies`` for details.
-    """
-    packages = []
-    for pos in pkg_or_spec:
-        if isinstance(pos, PackageMeta) and issubclass(pos, PackageBase):
-            packages.append(pos)
-            continue
-
-        if not isinstance(pos, spack.spec.Spec):
-            pos = spack.spec.Spec(pos)
-
-        if spack.repo.PATH.is_virtual(pos.name):
-            packages.extend(p.package_class for p in spack.repo.PATH.providers_for(pos.name))
-            continue
-        else:
-            packages.append(pos.package_class)
-
-    visited: Dict[str, Set[str]] = {}
-    for pkg in packages:
-        pkg.possible_dependencies(
-            visited=visited,
-            transitive=transitive,
-            expand_virtuals=expand_virtuals,
-            depflag=depflag,
-            missing=missing,
-            virtuals=virtuals,
-        )
-
-    return visited
-
-
 def deprecated_version(pkg: PackageBase, version: Union[str, StandardVersion]) -> bool:
     """Return True iff the version is deprecated.
 

lib/spack/spack/patch.py

@@ -83,6 +83,7 @@ def __init__(
         level: int,
         working_dir: str,
         reverse: bool = False,
+        ordering_key: Optional[Tuple[str, int]] = None,
     ) -> None:
         """Initialize a new Patch instance.
 
@@ -92,6 +93,7 @@ def __init__(
             level: patch level
             working_dir: relative path *within* the stage to change to
             reverse: reverse the patch
+            ordering_key: key used to ensure patches are applied in a consistent order
         """
         # validate level (must be an integer >= 0)
         if not isinstance(level, int) or not level >= 0:
@@ -105,6 +107,13 @@ def __init__(
         self.working_dir = working_dir
         self.reverse = reverse
 
+        # The ordering key is passed when executing package.py directives, and is only relevant
+        # after a solve to build concrete specs with consistently ordered patches. For concrete
+        # specs read from a file, we add patches in the order of its patches variants and the
+        # ordering_key is irrelevant. In that case, use a default value so we don't need to branch
+        # on whether ordering_key is None where it's used, just to make static analysis happy.
+        self.ordering_key: Tuple[str, int] = ordering_key or ("", 0)
+
     def apply(self, stage: "spack.stage.Stage") -> None:
         """Apply a patch to source in a stage.
 
@@ -202,9 +211,8 @@ def __init__(
             msg += "package %s.%s does not exist." % (pkg.namespace, pkg.name)
             raise ValueError(msg)
 
-        super().__init__(pkg, abs_path, level, working_dir, reverse)
+        super().__init__(pkg, abs_path, level, working_dir, reverse, ordering_key)
         self.path = abs_path
-        self.ordering_key = ordering_key
 
     @property
     def sha256(self) -> str:
@@ -266,13 +274,11 @@ def __init__(
             archive_sha256: sha256 sum of the *archive*, if the patch is compressed
                 (only required for compressed URL patches)
         """
-        super().__init__(pkg, url, level, working_dir, reverse)
+        super().__init__(pkg, url, level, working_dir, reverse, ordering_key)
 
         self.url = url
         self._stage: Optional["spack.stage.Stage"] = None
 
-        self.ordering_key = ordering_key
-
         if allowed_archive(self.url) and not archive_sha256:
             raise spack.error.PatchDirectiveError(
                 "Compressed patches require 'archive_sha256' "

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() :]
@@ -290,21 +283,21 @@ def relocate_text_bin(binaries: Iterable[str], prefix_to_prefix: PrefixToPrefix)
 def is_macho_magic(magic: bytes) -> bool:
     return (
         # In order of popularity: 64-bit mach-o le/be, 32-bit mach-o le/be.
-        magic.startswith(b"\xCF\xFA\xED\xFE")
-        or magic.startswith(b"\xFE\xED\xFA\xCF")
-        or magic.startswith(b"\xCE\xFA\xED\xFE")
-        or magic.startswith(b"\xFE\xED\xFA\xCE")
+        magic.startswith(b"\xcf\xfa\xed\xfe")
+        or magic.startswith(b"\xfe\xed\xfa\xcf")
+        or magic.startswith(b"\xce\xfa\xed\xfe")
+        or magic.startswith(b"\xfe\xed\xfa\xce")
         # universal binaries: 0xcafebabe be (most common?) or 0xbebafeca le (not sure if exists).
         # Here we need to disambiguate mach-o and JVM class files. In mach-o the next 4 bytes are
         # the number of binaries; in JVM class files it's the java version number. We assume there
         # are less than 10 binaries in a universal binary.
-        or (magic.startswith(b"\xCA\xFE\xBA\xBE") and int.from_bytes(magic[4:8], "big") < 10)
-        or (magic.startswith(b"\xBE\xBA\xFE\xCA") and int.from_bytes(magic[4:8], "little") < 10)
+        or (magic.startswith(b"\xca\xfe\xba\xbe") and int.from_bytes(magic[4:8], "big") < 10)
+        or (magic.startswith(b"\xbe\xba\xfe\xca") and int.from_bytes(magic[4:8], "little") < 10)
     )
 
 
 def is_elf_magic(magic: bytes) -> bool:
-    return magic.startswith(b"\x7FELF")
+    return magic.startswith(b"\x7fELF")
 
 
 def is_binary(filename: str) -> bool:
@@ -413,8 +406,8 @@ def fixup_macos_rpaths(spec):
     entries which makes it harder to adjust with ``install_name_tool
     -delete_rpath``.
     """
-    if spec.external or spec.virtual:
-        tty.warn("external or virtual package cannot be fixed up: {0!s}".format(spec))
+    if spec.external or not spec.concrete:
+        tty.warn("external/abstract spec cannot be fixed up: {0!s}".format(spec))
         return False
 
     if "platform=darwin" not in spec:

lib/spack/spack/repo.py

@@ -1041,7 +1041,7 @@ 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":
@@ -1369,7 +1369,7 @@ 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
@@ -176,7 +177,7 @@ def build_report_for_package(self, report_dir, package, duration):
         # something went wrong pre-cdash "configure" phase b/c we have an exception and only
         # "update" was encounterd.
         # dump the report in the configure line so teams can see what the issue is
-        if len(phases_encountered) == 1 and package["exception"]:
+        if len(phases_encountered) == 1 and package.get("exception"):
             # TODO this mapping is not ideal since these are pre-configure errors
             # we need to determine if a more appropriate cdash phase can be utilized
             # for now we will add a message to the log explaining this
@@ -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/schema/__init__.py

@@ -7,8 +7,7 @@
 import warnings
 
 import jsonschema
-
-import llnl.util.lang
+import jsonschema.validators
 
 from spack.error import SpecSyntaxError
 
@@ -18,59 +17,59 @@ class DeprecationMessage(typing.NamedTuple):
     error: bool
 
 
-# jsonschema is imported lazily as it is heavy to import
-# and increases the start-up time
-def _make_validator():
-    def _validate_spec(validator, is_spec, instance, schema):
-        """Check if the attributes on instance are valid specs."""
-        import spack.spec_parser
+def _validate_spec(validator, is_spec, instance, schema):
+    """Check if all additional keys are valid specs."""
+    import spack.spec_parser
 
-        if not validator.is_type(instance, "object"):
-            return
+    if not validator.is_type(instance, "object"):
+        return
 
-        for spec_str in instance:
-            try:
-                spack.spec_parser.parse(spec_str)
-            except SpecSyntaxError:
-                yield jsonschema.ValidationError(f"the key '{spec_str}' is not a valid spec")
+    properties = schema.get("properties") or {}
 
-    def _deprecated_properties(validator, deprecated, instance, schema):
-        if not (validator.is_type(instance, "object") or validator.is_type(instance, "array")):
-            return
-
-        if not deprecated:
-            return
-
-        deprecations = {
-            name: DeprecationMessage(message=x["message"], error=x["error"])
-            for x in deprecated
-            for name in x["names"]
-        }
-
-        # Get a list of the deprecated properties, return if there is none
-        issues = [entry for entry in instance if entry in deprecations]
-        if not issues:
-            return
-
-        # Process issues
-        errors = []
-        for name in issues:
-            msg = deprecations[name].message.format(name=name)
-            if deprecations[name].error:
-                errors.append(msg)
-            else:
-                warnings.warn(msg)
-
-        if errors:
-            yield jsonschema.ValidationError("\n".join(errors))
-
-    return jsonschema.validators.extend(
-        jsonschema.Draft7Validator,
-        {"validate_spec": _validate_spec, "deprecatedProperties": _deprecated_properties},
-    )
+    for spec_str in instance:
+        if spec_str in properties:
+            continue
+        try:
+            spack.spec_parser.parse(spec_str)
+        except SpecSyntaxError:
+            yield jsonschema.ValidationError(f"the key '{spec_str}' is not a valid spec")
 
 
-Validator = llnl.util.lang.Singleton(_make_validator)
+def _deprecated_properties(validator, deprecated, instance, schema):
+    if not (validator.is_type(instance, "object") or validator.is_type(instance, "array")):
+        return
+
+    if not deprecated:
+        return
+
+    deprecations = {
+        name: DeprecationMessage(message=x["message"], error=x["error"])
+        for x in deprecated
+        for name in x["names"]
+    }
+
+    # Get a list of the deprecated properties, return if there is none
+    issues = [entry for entry in instance if entry in deprecations]
+    if not issues:
+        return
+
+    # Process issues
+    errors = []
+    for name in issues:
+        msg = deprecations[name].message.format(name=name)
+        if deprecations[name].error:
+            errors.append(msg)
+        else:
+            warnings.warn(msg)
+
+    if errors:
+        yield jsonschema.ValidationError("\n".join(errors))
+
+
+Validator = jsonschema.validators.extend(
+    jsonschema.Draft7Validator,
+    {"additionalKeysAreSpecs": _validate_spec, "deprecatedProperties": _deprecated_properties},
+)
 
 
 def _append(string: str) -> bool:

lib/spack/spack/schema/concretizer.py

@@ -84,9 +84,14 @@
             "duplicates": {
                 "type": "object",
                 "properties": {
-                    "strategy": {"type": "string", "enum": ["none", "minimal", "full"]}
+                    "strategy": {"type": "string", "enum": ["none", "minimal", "full"]},
+                    "max_dupes": {
+                        "type": "object",
+                        "additional_properties": {"type": "integer", "minimum": 1},
+                    },
                 },
             },
+            "static_analysis": {"type": "boolean"},
             "timeout": {"type": "integer", "minimum": 0},
             "error_on_timeout": {"type": "boolean"},
             "os_compatible": {"type": "object", "additionalProperties": {"type": "array"}},

lib/spack/spack/schema/cray_manifest.py

@@ -3,12 +3,12 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 """Schema for Cray descriptive manifest: this describes a set of
-   installed packages on the system and also specifies dependency
-   relationships between them (so this provides more information than
-   external entries in packages configuration).
+installed packages on the system and also specifies dependency
+relationships between them (so this provides more information than
+external entries in packages configuration).
 
-   This does not specify a configuration - it is an input format
-   that is consumed and transformed into Spack DB records.
+This does not specify a configuration - it is an input format
+that is consumed and transformed into Spack DB records.
 """
 from typing import Any, Dict
 

lib/spack/spack/schema/modules.py

@@ -39,7 +39,7 @@
         "load": array_of_strings,
         "suffixes": {
             "type": "object",
-            "validate_spec": True,
+            "additionalKeysAreSpecs": True,
             "additionalProperties": {"type": "string"},  # key
         },
         "environment": spack.schema.environment.definition,
@@ -48,40 +48,44 @@
 
 projections_scheme = spack.schema.projections.properties["projections"]
 
-module_type_configuration: Dict = {
+common_props = {
+    "verbose": {"type": "boolean", "default": False},
+    "hash_length": {"type": "integer", "minimum": 0, "default": 7},
+    "include": array_of_strings,
+    "exclude": array_of_strings,
+    "exclude_implicits": {"type": "boolean", "default": False},
+    "defaults": array_of_strings,
+    "hide_implicits": {"type": "boolean", "default": False},
+    "naming_scheme": {"type": "string"},
+    "projections": projections_scheme,
+    "all": module_file_configuration,
+}
+
+tcl_configuration = {
     "type": "object",
     "default": {},
-    "validate_spec": True,
-    "properties": {
-        "verbose": {"type": "boolean", "default": False},
-        "hash_length": {"type": "integer", "minimum": 0, "default": 7},
-        "include": array_of_strings,
-        "exclude": array_of_strings,
-        "exclude_implicits": {"type": "boolean", "default": False},
-        "defaults": array_of_strings,
-        "hide_implicits": {"type": "boolean", "default": False},
-        "naming_scheme": {"type": "string"},
-        "projections": projections_scheme,
-        "all": module_file_configuration,
-    },
+    "additionalKeysAreSpecs": True,
+    "properties": {**common_props},
     "additionalProperties": module_file_configuration,
 }
 
-tcl_configuration = module_type_configuration.copy()
-
-lmod_configuration = module_type_configuration.copy()
-lmod_configuration["properties"].update(
-    {
+lmod_configuration = {
+    "type": "object",
+    "default": {},
+    "additionalKeysAreSpecs": True,
+    "properties": {
+        **common_props,
         "core_compilers": array_of_strings,
         "hierarchy": array_of_strings,
         "core_specs": array_of_strings,
         "filter_hierarchy_specs": {
             "type": "object",
-            "validate_spec": True,
+            "additionalKeysAreSpecs": True,
             "additionalProperties": array_of_strings,
         },
-    }
-)
+    },
+    "additionalProperties": module_file_configuration,
+}
 
 module_config_properties = {
     "use_view": {"anyOf": [{"type": "string"}, {"type": "boolean"}]},

lib/spack/spack/solver/asp.py

@@ -6,6 +6,7 @@
 import copy
 import enum
 import functools
+import io
 import itertools
 import os
 import pathlib
@@ -35,6 +36,7 @@
 import spack.error
 import spack.package_base
 import spack.package_prefs
+import spack.patch
 import spack.platforms
 import spack.repo
 import spack.solver.splicing
@@ -42,6 +44,7 @@
 import spack.store
 import spack.util.crypto
 import spack.util.libc
+import spack.util.module_cmd as md
 import spack.util.path
 import spack.util.timer
 import spack.variant as vt
@@ -62,7 +65,7 @@
     parse_files,
     parse_term,
 )
-from .counter import FullDuplicatesCounter, MinimalDuplicatesCounter, NoDuplicatesCounter
+from .input_analysis import create_counter, create_graph_analyzer
 from .requirements import RequirementKind, RequirementParser, RequirementRule
 from .version_order import concretization_version_order
 
@@ -73,17 +76,19 @@
 #: Enable the addition of a runtime node
 WITH_RUNTIME = sys.platform != "win32"
 
-#: Data class that contain configuration on what a
-#: clingo solve should output.
-#:
-#: Args:
-#:     timers (bool):  Print out coarse timers for different solve phases.
-#:     stats (bool): Whether to output Clingo's internal solver statistics.
-#:     out: Optional output stream for the generated ASP program.
-#:     setup_only (bool): if True, stop after setup and don't solve (default False).
-OutputConfiguration = collections.namedtuple(
-    "OutputConfiguration", ["timers", "stats", "out", "setup_only"]
-)
+
+class OutputConfiguration(NamedTuple):
+    """Data class that contains configuration on what a clingo solve should output."""
+
+    #: Print out coarse timers for different solve phases
+    timers: bool
+    #: Whether to output Clingo's internal solver statistics
+    stats: bool
+    #: Optional output stream for the generated ASP program
+    out: Optional[io.IOBase]
+    #: If True, stop after setup and don't solve
+    setup_only: bool
+
 
 #: Default output configuration for a solve
 DEFAULT_OUTPUT_CONFIGURATION = OutputConfiguration(
@@ -271,15 +276,6 @@ def remove_node(spec: spack.spec.Spec, facts: List[AspFunction]) -> List[AspFunc
     return list(filter(lambda x: x.args[0] not in ("node", "virtual_node"), facts))
 
 
-def _create_counter(specs: List[spack.spec.Spec], tests: bool):
-    strategy = spack.config.CONFIG.get("concretizer:duplicates:strategy", "none")
-    if strategy == "full":
-        return FullDuplicatesCounter(specs, tests=tests)
-    if strategy == "minimal":
-        return MinimalDuplicatesCounter(specs, tests=tests)
-    return NoDuplicatesCounter(specs, tests=tests)
-
-
 def all_libcs() -> Set[spack.spec.Spec]:
     """Return a set of all libc specs targeted by any configured compiler. If none, fall back to
     libc determined from the current Python process if dynamically linked."""
@@ -507,7 +503,7 @@ def _compute_specs_from_answer_set(self):
             # The specs must be unified to get here, so it is safe to associate any satisfying spec
             # with the input. Multiple inputs may be matched to the same concrete spec
             node = SpecBuilder.make_node(pkg=input_spec.name)
-            if input_spec.virtual:
+            if spack.repo.PATH.is_virtual(input_spec.name):
                 providers = [
                     spec.name for spec in answer.values() if spec.package.provides(input_spec.name)
                 ]
@@ -1121,6 +1117,8 @@ class SpackSolverSetup:
     """Class to set up and run a Spack concretization solve."""
 
     def __init__(self, tests: bool = False):
+        self.possible_graph = create_graph_analyzer()
+
         # these are all initialized in setup()
         self.gen: "ProblemInstanceBuilder" = ProblemInstanceBuilder()
         self.requirement_parser = RequirementParser(spack.config.CONFIG)
@@ -1660,13 +1658,16 @@ def track_dependencies(input_spec, requirements):
                     return requirements + [fn.attr("track_dependencies", input_spec.name)]
 
                 def dependency_holds(input_spec, requirements):
-                    return remove_node(input_spec, requirements) + [
+                    result = remove_node(input_spec, requirements) + [
                         fn.attr(
                             "dependency_holds", pkg.name, input_spec.name, dt.flag_to_string(t)
                         )
                         for t in dt.ALL_FLAGS
                         if t & depflag
                     ]
+                    if input_spec.name not in pkg.extendees:
+                        return result
+                    return result + [fn.attr("extends", pkg.name, input_spec.name)]
 
                 context = ConditionContext()
                 context.source = ConstraintOrigin.append_type_suffix(
@@ -2087,7 +2088,11 @@ def _spec_clauses(
         f: Union[Type[_Head], Type[_Body]] = _Body if body else _Head
 
         if spec.name:
-            clauses.append(f.node(spec.name) if not spec.virtual else f.virtual_node(spec.name))
+            clauses.append(
+                f.node(spec.name)
+                if not spack.repo.PATH.is_virtual(spec.name)
+                else f.virtual_node(spec.name)
+            )
         if spec.namespace:
             clauses.append(f.namespace(spec.name, spec.namespace))
 
@@ -2114,7 +2119,7 @@ def _spec_clauses(
 
             for value in variant.value_as_tuple:
                 # ensure that the value *can* be valid for the spec
-                if spec.name and not spec.concrete and not spec.virtual:
+                if spec.name and not spec.concrete and not spack.repo.PATH.is_virtual(spec.name):
                     variant_defs = vt.prevalidate_variant_value(
                         self.pkg_class(spec.name), variant, spec
                     )
@@ -2397,38 +2402,20 @@ def keyfun(os):
 
     def target_defaults(self, specs):
         """Add facts about targets and target compatibility."""
-        self.gen.h2("Default target")
-
-        platform = spack.platforms.host()
-        uarch = archspec.cpu.TARGETS.get(platform.default)
-
         self.gen.h2("Target compatibility")
 
-        # Construct the list of targets which are compatible with the host
-        candidate_targets = [uarch] + uarch.ancestors
-
-        # Get configuration options
-        granularity = spack.config.get("concretizer:targets:granularity")
-        host_compatible = spack.config.get("concretizer:targets:host_compatible")
-
-        # Add targets which are not compatible with the current host
-        if not host_compatible:
-            additional_targets_in_family = sorted(
-                [
-                    t
-                    for t in archspec.cpu.TARGETS.values()
-                    if (t.family.name == uarch.family.name and t not in candidate_targets)
-                ],
-                key=lambda x: len(x.ancestors),
-                reverse=True,
-            )
-            candidate_targets += additional_targets_in_family
-
-        # Check if we want only generic architecture
-        if granularity == "generic":
-            candidate_targets = [t for t in candidate_targets if t.vendor == "generic"]
-
         # Add targets explicitly requested from specs
+        candidate_targets = []
+        for x in self.possible_graph.candidate_targets():
+            if all(
+                self.possible_graph.unreachable(pkg_name=pkg_name, when_spec=f"target={x}")
+                for pkg_name in self.pkgs
+            ):
+                tty.debug(f"[{__name__}] excluding target={x}, cause no package can use it")
+                continue
+            candidate_targets.append(x)
+
+        host_compatible = spack.config.CONFIG.get("concretizer:targets:host_compatible")
         for spec in specs:
             if not spec.architecture or not spec.architecture.target:
                 continue
@@ -2444,6 +2431,8 @@ def target_defaults(self, specs):
                     if ancestor not in candidate_targets:
                         candidate_targets.append(ancestor)
 
+        platform = spack.platforms.host()
+        uarch = archspec.cpu.TARGETS.get(platform.default)
         best_targets = {uarch.family.name}
         for compiler_id, known_compiler in enumerate(self.possible_compilers):
             if not known_compiler.available:
@@ -2501,7 +2490,6 @@ def target_defaults(self, specs):
             self.gen.newline()
 
         self.default_targets = list(sorted(set(self.default_targets)))
-
         self.target_preferences()
 
     def virtual_providers(self):
@@ -2605,7 +2593,14 @@ def define_variant_values(self):
         # Tell the concretizer about possible values from specs seen in spec_clauses().
         # We might want to order these facts by pkg and name if we are debugging.
         for pkg_name, variant_def_id, value in self.variant_values_from_specs:
-            vid = self.variant_ids_by_def_id[variant_def_id]
+            try:
+                vid = self.variant_ids_by_def_id[variant_def_id]
+            except KeyError:
+                tty.debug(
+                    f"[{__name__}] cannot retrieve id of the {value} variant from {pkg_name}"
+                )
+                continue
+
             self.gen.fact(fn.pkg_fact(pkg_name, fn.variant_possible_value(vid, value)))
 
     def register_concrete_spec(self, spec, possible):
@@ -2676,7 +2671,7 @@ def setup(
         """
         check_packages_exist(specs)
 
-        node_counter = _create_counter(specs, tests=self.tests)
+        node_counter = create_counter(specs, tests=self.tests, possible_graph=self.possible_graph)
         self.possible_virtuals = node_counter.possible_virtuals()
         self.pkgs = node_counter.possible_dependencies()
         self.libcs = sorted(all_libcs())  # type: ignore[type-var]
@@ -2684,7 +2679,9 @@ def setup(
         # Fail if we already know an unreachable node is requested
         for spec in specs:
             missing_deps = [
-                str(d) for d in spec.traverse() if d.name not in self.pkgs and not d.virtual
+                str(d)
+                for d in spec.traverse()
+                if d.name not in self.pkgs and not spack.repo.PATH.is_virtual(d.name)
             ]
             if missing_deps:
                 raise spack.spec.InvalidDependencyError(spec.name, missing_deps)
@@ -2901,7 +2898,11 @@ def literal_specs(self, specs):
                     pkg_name = clause.args[1]
                     self.gen.fact(fn.mentioned_in_literal(trigger_id, root_name, pkg_name))
 
-            requirements.append(fn.attr("virtual_root" if spec.virtual else "root", spec.name))
+            requirements.append(
+                fn.attr(
+                    "virtual_root" if spack.repo.PATH.is_virtual(spec.name) else "root", spec.name
+                )
+            )
             cache[imposed_spec_key] = (effect_id, requirements)
             self.gen.fact(fn.pkg_fact(spec.name, fn.condition_effect(condition_id, effect_id)))
 
@@ -3489,7 +3490,7 @@ def external_spec_selected(self, node, idx):
         self._specs[node].extra_attributes = spec_info.get("extra_attributes", {})
 
         # If this is an extension, update the dependencies to include the extendee
-        package = self._specs[node].package_class(self._specs[node])
+        package = spack.repo.PATH.get_pkg_class(self._specs[node].fullname)(self._specs[node])
         extendee_spec = package.extendee_spec
 
         if extendee_spec:
@@ -3706,11 +3707,11 @@ def build_specs(self, function_tuples):
         roots = [spec.root for spec in self._specs.values()]
         roots = dict((id(r), r) for r in roots)
         for root in roots.values():
-            spack.spec.Spec.inject_patches_variant(root)
+            _inject_patches_variant(root)
 
         # Add external paths to specs with just external modules
         for s in self._specs.values():
-            spack.spec.Spec.ensure_external_path_if_external(s)
+            _ensure_external_path_if_external(s)
 
         for s in self._specs.values():
             _develop_specs_from_env(s, ev.active_environment())
@@ -3782,6 +3783,92 @@ def execute_explicit_splices(self):
         return specs
 
 
+def _inject_patches_variant(root: spack.spec.Spec) -> None:
+    # This dictionary will store object IDs rather than Specs as keys
+    # since the Spec __hash__ will change as patches are added to them
+    spec_to_patches: Dict[int, Set[spack.patch.Patch]] = {}
+    for s in root.traverse():
+        # After concretizing, assign namespaces to anything left.
+        # Note that this doesn't count as a "change".  The repository
+        # configuration is constant throughout a spack run, and
+        # normalize and concretize evaluate Packages using Repo.get(),
+        # which respects precedence.  So, a namespace assignment isn't
+        # changing how a package name would have been interpreted and
+        # we can do it as late as possible to allow as much
+        # compatibility across repositories as possible.
+        if s.namespace is None:
+            s.namespace = spack.repo.PATH.repo_for_pkg(s.name).namespace
+
+        if s.concrete:
+            continue
+
+        # Add any patches from the package to the spec.
+        node_patches = {
+            patch
+            for cond, patch_list in spack.repo.PATH.get_pkg_class(s.fullname).patches.items()
+            if s.satisfies(cond)
+            for patch in patch_list
+        }
+        if node_patches:
+            spec_to_patches[id(s)] = node_patches
+
+    # Also record all patches required on dependencies by depends_on(..., patch=...)
+    for dspec in root.traverse_edges(deptype=dt.ALL, cover="edges", root=False):
+        if dspec.spec.concrete:
+            continue
+
+        pkg_deps = spack.repo.PATH.get_pkg_class(dspec.parent.fullname).dependencies
+
+        edge_patches: List[spack.patch.Patch] = []
+        for cond, deps_by_name in pkg_deps.items():
+            if not dspec.parent.satisfies(cond):
+                continue
+
+            dependency = deps_by_name.get(dspec.spec.name)
+            if not dependency:
+                continue
+
+            for pcond, patch_list in dependency.patches.items():
+                if dspec.spec.satisfies(pcond):
+                    edge_patches.extend(patch_list)
+
+        if edge_patches:
+            spec_to_patches.setdefault(id(dspec.spec), set()).update(edge_patches)
+
+    for spec in root.traverse():
+        if id(spec) not in spec_to_patches:
+            continue
+
+        patches = list(spec_to_patches[id(spec)])
+        variant: vt.MultiValuedVariant = spec.variants.setdefault(
+            "patches", vt.MultiValuedVariant("patches", ())
+        )
+        variant.value = tuple(p.sha256 for p in patches)
+        # FIXME: Monkey patches variant to store patches order
+        ordered_hashes = [(*p.ordering_key, p.sha256) for p in patches if p.ordering_key]
+        ordered_hashes.sort()
+        tty.debug(
+            f"Ordered hashes [{spec.name}]: "
+            + ", ".join("/".join(str(e) for e in t) for t in ordered_hashes)
+        )
+        setattr(
+            variant, "_patches_in_order_of_appearance", [sha256 for _, _, sha256 in ordered_hashes]
+        )
+
+
+def _ensure_external_path_if_external(spec: spack.spec.Spec) -> None:
+    if not spec.external_modules or spec.external_path:
+        return
+
+    # Get the path from the module the package can override the default
+    # (this is mostly needed for Cray)
+    pkg_cls = spack.repo.PATH.get_pkg_class(spec.name)
+    package = pkg_cls(spec)
+    spec.external_path = getattr(package, "external_prefix", None) or md.path_from_modules(
+        spec.external_modules
+    )
+
+
 def _develop_specs_from_env(spec, env):
     dev_info = env.dev_specs.get(spec.name, {}) if env else {}
     if not dev_info:
@@ -4102,10 +4189,10 @@ def _check_input_and_extract_concrete_specs(specs):
         reusable = []
         for root in specs:
             for s in root.traverse():
-                if s.virtual:
-                    continue
                 if s.concrete:
                     reusable.append(s)
+                elif spack.repo.PATH.is_virtual(s.name):
+                    continue
                 spack.spec.Spec.ensure_valid_variants(s)
         return reusable
 

lib/spack/spack/solver/concretize.lp

@@ -265,6 +265,7 @@ error(100, "Cannot select a single version for virtual '{0}'", Virtual)
 % If we select a deprecated version, mark the package as deprecated
 attr("deprecated", node(ID, Package), Version) :-
      attr("version", node(ID, Package), Version),
+     not external(node(ID, Package)),
      pkg_fact(Package, deprecated_version(Version)).
 
 error(100, "Package '{0}' needs the deprecated version '{1}', and this is not allowed", Package, Version)
@@ -523,6 +524,16 @@ error(10, "'{0}' is not a valid dependency for any package in the DAG", Package)
   :- attr("node", node(ID, Package)),
      not needed(node(ID, Package)).
 
+
+% Extensions depending on each other must all extend the same node (e.g. all Python packages
+% depending on each other must depend on the same Python interpreter)
+error(100, "{0} and {1} must depend on the same {2}", ExtensionParent, ExtensionChild, ExtendeePackage)
+  :- depends_on(ExtensionParent, ExtensionChild),
+     attr("extends", ExtensionParent, ExtendeePackage),
+     depends_on(ExtensionParent, node(X, ExtendeePackage)),
+     depends_on(ExtensionChild,  node(Y, ExtendeePackage)),
+     X != Y.
+
 #defined dependency_type/2.
 
 %-----------------------------------------------------------------------------

lib/spack/spack/solver/counter.py

@@ -1,179 +0,0 @@
-# Copyright Spack Project Developers. See COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import collections
-from typing import List, Set
-
-from llnl.util import lang
-
-import spack.deptypes as dt
-import spack.package_base
-import spack.repo
-import spack.spec
-
-PossibleDependencies = Set[str]
-
-
-class Counter:
-    """Computes the possible packages and the maximum number of duplicates
-    allowed for each of them.
-
-    Args:
-        specs: abstract specs to concretize
-        tests: if True, add test dependencies to the list of possible packages
-    """
-
-    def __init__(self, specs: List["spack.spec.Spec"], tests: bool) -> None:
-        runtime_pkgs = spack.repo.PATH.packages_with_tags("runtime")
-        runtime_virtuals = set()
-        for x in runtime_pkgs:
-            pkg_class = spack.repo.PATH.get_pkg_class(x)
-            runtime_virtuals.update(pkg_class.provided_virtual_names())
-
-        self.specs = specs + [spack.spec.Spec(x) for x in runtime_pkgs]
-
-        self.link_run_types: dt.DepFlag = dt.LINK | dt.RUN | dt.TEST
-        self.all_types: dt.DepFlag = dt.ALL
-        if not tests:
-            self.link_run_types = dt.LINK | dt.RUN
-            self.all_types = dt.LINK | dt.RUN | dt.BUILD
-
-        self._possible_dependencies: PossibleDependencies = set()
-        self._possible_virtuals: Set[str] = (
-            set(x.name for x in specs if x.virtual) | runtime_virtuals
-        )
-
-    def possible_dependencies(self) -> PossibleDependencies:
-        """Returns the list of possible dependencies"""
-        self.ensure_cache_values()
-        return self._possible_dependencies
-
-    def possible_virtuals(self) -> Set[str]:
-        """Returns the list of possible virtuals"""
-        self.ensure_cache_values()
-        return self._possible_virtuals
-
-    def ensure_cache_values(self) -> None:
-        """Ensure the cache values have been computed"""
-        if self._possible_dependencies:
-            return
-        self._compute_cache_values()
-
-    def possible_packages_facts(self, gen: "spack.solver.asp.PyclingoDriver", fn) -> None:
-        """Emit facts associated with the possible packages"""
-        raise NotImplementedError("must be implemented by derived classes")
-
-    def _compute_cache_values(self):
-        raise NotImplementedError("must be implemented by derived classes")
-
-
-class NoDuplicatesCounter(Counter):
-    def _compute_cache_values(self):
-        result = spack.package_base.possible_dependencies(
-            *self.specs, virtuals=self._possible_virtuals, depflag=self.all_types
-        )
-        self._possible_dependencies = set(result)
-
-    def possible_packages_facts(self, gen, fn):
-        gen.h2("Maximum number of nodes (packages)")
-        for package_name in sorted(self.possible_dependencies()):
-            gen.fact(fn.max_dupes(package_name, 1))
-        gen.newline()
-        gen.h2("Maximum number of nodes (virtual packages)")
-        for package_name in sorted(self.possible_virtuals()):
-            gen.fact(fn.max_dupes(package_name, 1))
-        gen.newline()
-        gen.h2("Possible package in link-run subDAG")
-        for name in sorted(self.possible_dependencies()):
-            gen.fact(fn.possible_in_link_run(name))
-        gen.newline()
-
-
-class MinimalDuplicatesCounter(NoDuplicatesCounter):
-    def __init__(self, specs, tests):
-        super().__init__(specs, tests)
-        self._link_run: PossibleDependencies = set()
-        self._direct_build: PossibleDependencies = set()
-        self._total_build: PossibleDependencies = set()
-        self._link_run_virtuals: Set[str] = set()
-
-    def _compute_cache_values(self):
-        self._link_run = set(
-            spack.package_base.possible_dependencies(
-                *self.specs, virtuals=self._possible_virtuals, depflag=self.link_run_types
-            )
-        )
-        self._link_run_virtuals.update(self._possible_virtuals)
-        for x in self._link_run:
-            build_dependencies = spack.repo.PATH.get_pkg_class(x).dependencies_of_type(dt.BUILD)
-            virtuals, reals = lang.stable_partition(
-                build_dependencies, spack.repo.PATH.is_virtual_safe
-            )
-
-            self._possible_virtuals.update(virtuals)
-            for virtual_dep in virtuals:
-                providers = spack.repo.PATH.providers_for(virtual_dep)
-                self._direct_build.update(str(x) for x in providers)
-
-            self._direct_build.update(reals)
-
-        self._total_build = set(
-            spack.package_base.possible_dependencies(
-                *self._direct_build, virtuals=self._possible_virtuals, depflag=self.all_types
-            )
-        )
-        self._possible_dependencies = set(self._link_run) | set(self._total_build)
-
-    def possible_packages_facts(self, gen, fn):
-        build_tools = spack.repo.PATH.packages_with_tags("build-tools")
-        gen.h2("Packages with at most a single node")
-        for package_name in sorted(self.possible_dependencies() - build_tools):
-            gen.fact(fn.max_dupes(package_name, 1))
-        gen.newline()
-
-        gen.h2("Packages with at multiple possible nodes (build-tools)")
-        for package_name in sorted(self.possible_dependencies() & build_tools):
-            gen.fact(fn.max_dupes(package_name, 2))
-            gen.fact(fn.multiple_unification_sets(package_name))
-        gen.newline()
-
-        gen.h2("Maximum number of nodes (virtual packages)")
-        for package_name in sorted(self.possible_virtuals()):
-            gen.fact(fn.max_dupes(package_name, 1))
-        gen.newline()
-
-        gen.h2("Possible package in link-run subDAG")
-        for name in sorted(self._link_run):
-            gen.fact(fn.possible_in_link_run(name))
-        gen.newline()
-
-
-class FullDuplicatesCounter(MinimalDuplicatesCounter):
-    def possible_packages_facts(self, gen, fn):
-        build_tools = spack.repo.PATH.packages_with_tags("build-tools")
-        counter = collections.Counter(
-            list(self._link_run) + list(self._total_build) + list(self._direct_build)
-        )
-        gen.h2("Maximum number of nodes")
-        for pkg, count in sorted(counter.items(), key=lambda x: (x[1], x[0])):
-            count = min(count, 2)
-            gen.fact(fn.max_dupes(pkg, count))
-        gen.newline()
-
-        gen.h2("Build unification sets ")
-        for name in sorted(self.possible_dependencies() & build_tools):
-            gen.fact(fn.multiple_unification_sets(name))
-        gen.newline()
-
-        gen.h2("Possible package in link-run subDAG")
-        for name in sorted(self._link_run):
-            gen.fact(fn.possible_in_link_run(name))
-        gen.newline()
-
-        counter = collections.Counter(
-            list(self._link_run_virtuals) + list(self._possible_virtuals)
-        )
-        gen.h2("Maximum number of virtual nodes")
-        for pkg, count in sorted(counter.items(), key=lambda x: (x[1], x[0])):
-            gen.fact(fn.max_dupes(pkg, count))
-        gen.newline()

lib/spack/spack/solver/input_analysis.py

@@ -0,0 +1,539 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+"""Classes to analyze the input of a solve, and provide information to set up the ASP problem"""
+import collections
+from typing import Dict, List, NamedTuple, Set, Tuple, Union
+
+import archspec.cpu
+
+from llnl.util import lang, tty
+
+import spack.binary_distribution
+import spack.config
+import spack.deptypes as dt
+import spack.platforms
+import spack.repo
+import spack.spec
+import spack.store
+from spack.error import SpackError
+
+RUNTIME_TAG = "runtime"
+
+
+class PossibleGraph(NamedTuple):
+    real_pkgs: Set[str]
+    virtuals: Set[str]
+    edges: Dict[str, Set[str]]
+
+
+class PossibleDependencyGraph:
+    """Returns information needed to set up an ASP problem"""
+
+    def unreachable(self, *, pkg_name: str, when_spec: spack.spec.Spec) -> bool:
+        """Returns true if the context can determine that the condition cannot ever
+        be met on pkg_name.
+        """
+        raise NotImplementedError
+
+    def candidate_targets(self) -> List[archspec.cpu.Microarchitecture]:
+        """Returns a list of targets that are candidate for concretization"""
+        raise NotImplementedError
+
+    def possible_dependencies(
+        self,
+        *specs: Union[spack.spec.Spec, str],
+        allowed_deps: dt.DepFlag,
+        transitive: bool = True,
+        strict_depflag: bool = False,
+        expand_virtuals: bool = True,
+    ) -> PossibleGraph:
+        """Returns the set of possible dependencies, and the set of possible virtuals.
+
+        Both sets always include runtime packages, which may be injected by compilers.
+
+        Args:
+            transitive: return transitive dependencies if True, only direct dependencies if False
+            allowed_deps: dependency types to consider
+            strict_depflag: if True, only the specific dep type is considered, if False any
+                deptype that intersects with allowed deptype is considered
+            expand_virtuals: expand virtual dependencies into all possible implementations
+        """
+        raise NotImplementedError
+
+
+class NoStaticAnalysis(PossibleDependencyGraph):
+    """Implementation that tries to minimize the setup time (i.e. defaults to give fast
+    answers), rather than trying to reduce the ASP problem size with more complex analysis.
+    """
+
+    def __init__(self, *, configuration: spack.config.Configuration, repo: spack.repo.RepoPath):
+        self.configuration = configuration
+        self.repo = repo
+        self.runtime_pkgs = set(self.repo.packages_with_tags(RUNTIME_TAG))
+        self.runtime_virtuals = set()
+        self._platform_condition = spack.spec.Spec(
+            f"platform={spack.platforms.host()} target={archspec.cpu.host().family}:"
+        )
+        for x in self.runtime_pkgs:
+            pkg_class = self.repo.get_pkg_class(x)
+            self.runtime_virtuals.update(pkg_class.provided_virtual_names())
+
+        try:
+            self.libc_pkgs = [x.name for x in self.providers_for("libc")]
+        except spack.repo.UnknownPackageError:
+            self.libc_pkgs = []
+
+    def is_virtual(self, name: str) -> bool:
+        return self.repo.is_virtual(name)
+
+    @lang.memoized
+    def is_allowed_on_this_platform(self, *, pkg_name: str) -> bool:
+        """Returns true if a package is allowed on the current host"""
+        pkg_cls = self.repo.get_pkg_class(pkg_name)
+        for when_spec, conditions in pkg_cls.requirements.items():
+            if not when_spec.intersects(self._platform_condition):
+                continue
+            for requirements, _, _ in conditions:
+                if not any(x.intersects(self._platform_condition) for x in requirements):
+                    tty.debug(f"[{__name__}] {pkg_name} is not for this platform")
+                    return False
+        return True
+
+    def providers_for(self, virtual_str: str) -> List[spack.spec.Spec]:
+        """Returns a list of possible providers for the virtual string in input."""
+        return self.repo.providers_for(virtual_str)
+
+    def can_be_installed(self, *, pkg_name) -> bool:
+        """Returns True if a package can be installed, False otherwise."""
+        return True
+
+    def unreachable(self, *, pkg_name: str, when_spec: spack.spec.Spec) -> bool:
+        """Returns true if the context can determine that the condition cannot ever
+        be met on pkg_name.
+        """
+        return False
+
+    def candidate_targets(self) -> List[archspec.cpu.Microarchitecture]:
+        """Returns a list of targets that are candidate for concretization"""
+        platform = spack.platforms.host()
+        default_target = archspec.cpu.TARGETS[platform.default]
+
+        # Construct the list of targets which are compatible with the host
+        candidate_targets = [default_target] + default_target.ancestors
+        granularity = self.configuration.get("concretizer:targets:granularity")
+        host_compatible = self.configuration.get("concretizer:targets:host_compatible")
+
+        # Add targets which are not compatible with the current host
+        if not host_compatible:
+            additional_targets_in_family = sorted(
+                [
+                    t
+                    for t in archspec.cpu.TARGETS.values()
+                    if (t.family.name == default_target.family.name and t not in candidate_targets)
+                ],
+                key=lambda x: len(x.ancestors),
+                reverse=True,
+            )
+            candidate_targets += additional_targets_in_family
+
+        # Check if we want only generic architecture
+        if granularity == "generic":
+            candidate_targets = [t for t in candidate_targets if t.vendor == "generic"]
+
+        return candidate_targets
+
+    def possible_dependencies(
+        self,
+        *specs: Union[spack.spec.Spec, str],
+        allowed_deps: dt.DepFlag,
+        transitive: bool = True,
+        strict_depflag: bool = False,
+        expand_virtuals: bool = True,
+    ) -> PossibleGraph:
+        stack = [x for x in self._package_list(specs)]
+        virtuals: Set[str] = set()
+        edges: Dict[str, Set[str]] = {}
+
+        while stack:
+            pkg_name = stack.pop()
+
+            if pkg_name in edges:
+                continue
+
+            edges[pkg_name] = set()
+
+            # Since libc is not buildable, there is no need to extend the
+            # search space with libc dependencies.
+            if pkg_name in self.libc_pkgs:
+                continue
+
+            pkg_cls = self.repo.get_pkg_class(pkg_name=pkg_name)
+            for name, conditions in pkg_cls.dependencies_by_name(when=True).items():
+                if all(self.unreachable(pkg_name=pkg_name, when_spec=x) for x in conditions):
+                    tty.debug(
+                        f"[{__name__}] Not adding {name} as a dep of {pkg_name}, because "
+                        f"conditions cannot be met"
+                    )
+                    continue
+
+                if not self._has_deptypes(
+                    conditions, allowed_deps=allowed_deps, strict=strict_depflag
+                ):
+                    continue
+
+                if name in virtuals:
+                    continue
+
+                dep_names = set()
+                if self.is_virtual(name):
+                    virtuals.add(name)
+                    if expand_virtuals:
+                        providers = self.providers_for(name)
+                        dep_names = {spec.name for spec in providers}
+                else:
+                    dep_names = {name}
+
+                edges[pkg_name].update(dep_names)
+
+                if not transitive:
+                    continue
+
+                for dep_name in dep_names:
+                    if dep_name in edges:
+                        continue
+
+                    if not self._is_possible(pkg_name=dep_name):
+                        continue
+
+                    stack.append(dep_name)
+
+        real_packages = set(edges)
+        if not transitive:
+            # We exit early, so add children from the edges information
+            for root, children in edges.items():
+                real_packages.update(x for x in children if self._is_possible(pkg_name=x))
+
+        virtuals.update(self.runtime_virtuals)
+        real_packages = real_packages | self.runtime_pkgs
+        return PossibleGraph(real_pkgs=real_packages, virtuals=virtuals, edges=edges)
+
+    def _package_list(self, specs: Tuple[Union[spack.spec.Spec, str], ...]) -> List[str]:
+        stack = []
+        for current_spec in specs:
+            if isinstance(current_spec, str):
+                current_spec = spack.spec.Spec(current_spec)
+
+            if self.repo.is_virtual(current_spec.name):
+                stack.extend([p.name for p in self.providers_for(current_spec.name)])
+                continue
+
+            stack.append(current_spec.name)
+        return sorted(set(stack))
+
+    def _has_deptypes(self, dependencies, *, allowed_deps: dt.DepFlag, strict: bool) -> bool:
+        if strict is True:
+            return any(
+                dep.depflag == allowed_deps for deplist in dependencies.values() for dep in deplist
+            )
+        return any(
+            dep.depflag & allowed_deps for deplist in dependencies.values() for dep in deplist
+        )
+
+    def _is_possible(self, *, pkg_name):
+        try:
+            return self.is_allowed_on_this_platform(pkg_name=pkg_name) and self.can_be_installed(
+                pkg_name=pkg_name
+            )
+        except spack.repo.UnknownPackageError:
+            return False
+
+
+class StaticAnalysis(NoStaticAnalysis):
+    """Performs some static analysis of the configuration, store, etc. to provide more precise
+    answers on whether some packages can be installed, or used as a provider.
+
+    It increases the setup time, but might decrease the grounding and solve time considerably,
+    especially when requirements restrict the possible choices for providers.
+    """
+
+    def __init__(
+        self,
+        *,
+        configuration: spack.config.Configuration,
+        repo: spack.repo.RepoPath,
+        store: spack.store.Store,
+        binary_index: spack.binary_distribution.BinaryCacheIndex,
+    ):
+        super().__init__(configuration=configuration, repo=repo)
+        self.store = store
+        self.binary_index = binary_index
+
+    @lang.memoized
+    def providers_for(self, virtual_str: str) -> List[spack.spec.Spec]:
+        candidates = super().providers_for(virtual_str)
+        result = []
+        for spec in candidates:
+            if not self._is_provider_candidate(pkg_name=spec.name, virtual=virtual_str):
+                continue
+            result.append(spec)
+        return result
+
+    @lang.memoized
+    def buildcache_specs(self) -> List[spack.spec.Spec]:
+        self.binary_index.update()
+        return self.binary_index.get_all_built_specs()
+
+    @lang.memoized
+    def can_be_installed(self, *, pkg_name) -> bool:
+        if self.configuration.get(f"packages:{pkg_name}:buildable", True):
+            return True
+
+        if self.configuration.get(f"packages:{pkg_name}:externals", []):
+            return True
+
+        reuse = self.configuration.get("concretizer:reuse")
+        if reuse is not False and self.store.db.query(pkg_name):
+            return True
+
+        if reuse is not False and any(x.name == pkg_name for x in self.buildcache_specs()):
+            return True
+
+        tty.debug(f"[{__name__}] {pkg_name} cannot be installed")
+        return False
+
+    @lang.memoized
+    def _is_provider_candidate(self, *, pkg_name: str, virtual: str) -> bool:
+        if not self.is_allowed_on_this_platform(pkg_name=pkg_name):
+            return False
+
+        if not self.can_be_installed(pkg_name=pkg_name):
+            return False
+
+        virtual_spec = spack.spec.Spec(virtual)
+        if self.unreachable(pkg_name=virtual_spec.name, when_spec=pkg_name):
+            tty.debug(f"[{__name__}] {pkg_name} cannot be a provider for {virtual}")
+            return False
+
+        return True
+
+    @lang.memoized
+    def unreachable(self, *, pkg_name: str, when_spec: spack.spec.Spec) -> bool:
+        """Returns true if the context can determine that the condition cannot ever
+        be met on pkg_name.
+        """
+        candidates = self.configuration.get(f"packages:{pkg_name}:require", [])
+        if not candidates and pkg_name != "all":
+            return self.unreachable(pkg_name="all", when_spec=when_spec)
+
+        if not candidates:
+            return False
+
+        if isinstance(candidates, str):
+            candidates = [candidates]
+
+        union_requirement = spack.spec.Spec()
+        for c in candidates:
+            if not isinstance(c, str):
+                continue
+            try:
+                union_requirement.constrain(c)
+            except SpackError:
+                # Less optimized, but shouldn't fail
+                pass
+
+        if not union_requirement.intersects(when_spec):
+            return True
+
+        return False
+
+
+def create_graph_analyzer() -> PossibleDependencyGraph:
+    static_analysis = spack.config.CONFIG.get("concretizer:static_analysis", False)
+    if static_analysis:
+        return StaticAnalysis(
+            configuration=spack.config.CONFIG,
+            repo=spack.repo.PATH,
+            store=spack.store.STORE,
+            binary_index=spack.binary_distribution.BINARY_INDEX,
+        )
+    return NoStaticAnalysis(configuration=spack.config.CONFIG, repo=spack.repo.PATH)
+
+
+class Counter:
+    """Computes the possible packages and the maximum number of duplicates
+    allowed for each of them.
+
+    Args:
+        specs: abstract specs to concretize
+        tests: if True, add test dependencies to the list of possible packages
+    """
+
+    def __init__(
+        self, specs: List["spack.spec.Spec"], tests: bool, possible_graph: PossibleDependencyGraph
+    ) -> None:
+        self.possible_graph = possible_graph
+        self.specs = specs
+        self.link_run_types: dt.DepFlag = dt.LINK | dt.RUN | dt.TEST
+        self.all_types: dt.DepFlag = dt.ALL
+        if not tests:
+            self.link_run_types = dt.LINK | dt.RUN
+            self.all_types = dt.LINK | dt.RUN | dt.BUILD
+
+        self._possible_dependencies: Set[str] = set()
+        self._possible_virtuals: Set[str] = {
+            x.name for x in specs if spack.repo.PATH.is_virtual(x.name)
+        }
+
+    def possible_dependencies(self) -> Set[str]:
+        """Returns the list of possible dependencies"""
+        self.ensure_cache_values()
+        return self._possible_dependencies
+
+    def possible_virtuals(self) -> Set[str]:
+        """Returns the list of possible virtuals"""
+        self.ensure_cache_values()
+        return self._possible_virtuals
+
+    def ensure_cache_values(self) -> None:
+        """Ensure the cache values have been computed"""
+        if self._possible_dependencies:
+            return
+        self._compute_cache_values()
+
+    def possible_packages_facts(self, gen: "spack.solver.asp.ProblemInstanceBuilder", fn) -> None:
+        """Emit facts associated with the possible packages"""
+        raise NotImplementedError("must be implemented by derived classes")
+
+    def _compute_cache_values(self) -> None:
+        raise NotImplementedError("must be implemented by derived classes")
+
+
+class NoDuplicatesCounter(Counter):
+    def _compute_cache_values(self) -> None:
+        self._possible_dependencies, virtuals, _ = self.possible_graph.possible_dependencies(
+            *self.specs, allowed_deps=self.all_types
+        )
+        self._possible_virtuals.update(virtuals)
+
+    def possible_packages_facts(self, gen: "spack.solver.asp.ProblemInstanceBuilder", fn) -> None:
+        gen.h2("Maximum number of nodes (packages)")
+        for package_name in sorted(self.possible_dependencies()):
+            gen.fact(fn.max_dupes(package_name, 1))
+        gen.newline()
+        gen.h2("Maximum number of nodes (virtual packages)")
+        for package_name in sorted(self.possible_virtuals()):
+            gen.fact(fn.max_dupes(package_name, 1))
+        gen.newline()
+        gen.h2("Possible package in link-run subDAG")
+        for name in sorted(self.possible_dependencies()):
+            gen.fact(fn.possible_in_link_run(name))
+        gen.newline()
+
+
+class MinimalDuplicatesCounter(NoDuplicatesCounter):
+    def __init__(
+        self, specs: List["spack.spec.Spec"], tests: bool, possible_graph: PossibleDependencyGraph
+    ) -> None:
+        super().__init__(specs, tests, possible_graph)
+        self._link_run: Set[str] = set()
+        self._direct_build: Set[str] = set()
+        self._total_build: Set[str] = set()
+        self._link_run_virtuals: Set[str] = set()
+
+    def _compute_cache_values(self) -> None:
+        self._link_run, virtuals, _ = self.possible_graph.possible_dependencies(
+            *self.specs, allowed_deps=self.link_run_types
+        )
+        self._possible_virtuals.update(virtuals)
+        self._link_run_virtuals.update(virtuals)
+        for x in self._link_run:
+            reals, virtuals, _ = self.possible_graph.possible_dependencies(
+                x, allowed_deps=dt.BUILD, transitive=False, strict_depflag=True
+            )
+            self._possible_virtuals.update(virtuals)
+            self._direct_build.update(reals)
+
+        self._total_build, virtuals, _ = self.possible_graph.possible_dependencies(
+            *self._direct_build, allowed_deps=self.all_types
+        )
+        self._possible_virtuals.update(virtuals)
+        self._possible_dependencies = set(self._link_run) | set(self._total_build)
+
+    def possible_packages_facts(self, gen, fn):
+        build_tools = spack.repo.PATH.packages_with_tags("build-tools")
+        gen.h2("Packages with at most a single node")
+        for package_name in sorted(self.possible_dependencies() - build_tools):
+            gen.fact(fn.max_dupes(package_name, 1))
+        gen.newline()
+
+        gen.h2("Packages with at multiple possible nodes (build-tools)")
+        default = spack.config.CONFIG.get("concretizer:duplicates:max_dupes:default", 2)
+        for package_name in sorted(self.possible_dependencies() & build_tools):
+            max_dupes = spack.config.CONFIG.get(
+                f"concretizer:duplicates:max_dupes:{package_name}", default
+            )
+            gen.fact(fn.max_dupes(package_name, max_dupes))
+            if max_dupes > 1:
+                gen.fact(fn.multiple_unification_sets(package_name))
+        gen.newline()
+
+        gen.h2("Maximum number of nodes (link-run virtuals)")
+        for package_name in sorted(self._link_run_virtuals):
+            gen.fact(fn.max_dupes(package_name, 1))
+        gen.newline()
+
+        gen.h2("Maximum number of nodes (other virtuals)")
+        for package_name in sorted(self.possible_virtuals() - self._link_run_virtuals):
+            max_dupes = spack.config.CONFIG.get(
+                f"concretizer:duplicates:max_dupes:{package_name}", default
+            )
+            gen.fact(fn.max_dupes(package_name, max_dupes))
+        gen.newline()
+
+        gen.h2("Possible package in link-run subDAG")
+        for name in sorted(self._link_run):
+            gen.fact(fn.possible_in_link_run(name))
+        gen.newline()
+
+
+class FullDuplicatesCounter(MinimalDuplicatesCounter):
+    def possible_packages_facts(self, gen, fn):
+        build_tools = spack.repo.PATH.packages_with_tags("build-tools")
+        counter = collections.Counter(
+            list(self._link_run) + list(self._total_build) + list(self._direct_build)
+        )
+        gen.h2("Maximum number of nodes")
+        for pkg, count in sorted(counter.items(), key=lambda x: (x[1], x[0])):
+            count = min(count, 2)
+            gen.fact(fn.max_dupes(pkg, count))
+        gen.newline()
+
+        gen.h2("Build unification sets ")
+        for name in sorted(self.possible_dependencies() & build_tools):
+            gen.fact(fn.multiple_unification_sets(name))
+        gen.newline()
+
+        gen.h2("Possible package in link-run subDAG")
+        for name in sorted(self._link_run):
+            gen.fact(fn.possible_in_link_run(name))
+        gen.newline()
+
+        counter = collections.Counter(
+            list(self._link_run_virtuals) + list(self._possible_virtuals)
+        )
+        gen.h2("Maximum number of virtual nodes")
+        for pkg, count in sorted(counter.items(), key=lambda x: (x[1], x[0])):
+            gen.fact(fn.max_dupes(pkg, count))
+        gen.newline()
+
+
+def create_counter(
+    specs: List[spack.spec.Spec], tests: bool, possible_graph: PossibleDependencyGraph
+) -> Counter:
+    strategy = spack.config.CONFIG.get("concretizer:duplicates:strategy", "none")
+    if strategy == "full":
+        return FullDuplicatesCounter(specs, tests=tests, possible_graph=possible_graph)
+    if strategy == "minimal":
+        return MinimalDuplicatesCounter(specs, tests=tests, possible_graph=possible_graph)
+    return NoDuplicatesCounter(specs, tests=tests, possible_graph=possible_graph)

lib/spack/spack/spec.py

@@ -52,6 +52,7 @@
 import enum
 import io
 import itertools
+import json
 import os
 import pathlib
 import platform
@@ -98,7 +99,6 @@
 import spack.traverse
 import spack.util.executable
 import spack.util.hash
-import spack.util.module_cmd as md
 import spack.util.prefix
 import spack.util.spack_json as sjson
 import spack.util.spack_yaml as syaml
@@ -798,7 +798,7 @@ def update_deptypes(self, depflag: dt.DepFlag) -> bool:
         self.depflag = new
         return True
 
-    def update_virtuals(self, virtuals: Tuple[str, ...]) -> bool:
+    def update_virtuals(self, virtuals: Iterable[str]) -> bool:
         """Update the list of provided virtuals"""
         old = self.virtuals
         self.virtuals = tuple(sorted(set(virtuals).union(self.virtuals)))
@@ -1337,14 +1337,20 @@ class SpecBuildInterface(lang.ObjectWrapper):
         "command", default_handler=_command_default_handler, _indirect=True
     )
 
-    def __init__(self, spec: "Spec", name: str, query_parameters: List[str], _parent: "Spec"):
+    def __init__(
+        self,
+        spec: "Spec",
+        name: str,
+        query_parameters: List[str],
+        _parent: "Spec",
+        is_virtual: bool,
+    ):
         super().__init__(spec)
         # Adding new attributes goes after super() call since the ObjectWrapper
         # resets __dict__ to behave like the passed object
         original_spec = getattr(spec, "wrapped_obj", spec)
         self.wrapped_obj = original_spec
-        self.token = original_spec, name, query_parameters, _parent
-        is_virtual = spack.repo.PATH.is_virtual(name)
+        self.token = original_spec, name, query_parameters, _parent, is_virtual
         self.last_query = QueryState(
             name=name, extra_parameters=query_parameters, isvirtual=is_virtual
         )
@@ -1527,9 +1533,8 @@ 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
@@ -1906,10 +1911,22 @@ def package_class(self):
         """Internal package call gets only the class object for a package.
         Use this to just get package metadata.
         """
+        warnings.warn(
+            "`Spec.package_class` is deprecated and will be removed in version 1.0.0. Use "
+            "`spack.repo.PATH.get_pkg_class(spec.fullname) instead.",
+            category=spack.error.SpackAPIWarning,
+            stacklevel=2,
+        )
         return spack.repo.PATH.get_pkg_class(self.fullname)
 
     @property
     def virtual(self):
+        warnings.warn(
+            "`Spec.virtual` is deprecated and will be removed in version 1.0.0. Use "
+            "`spack.repo.PATH.is_virtual(spec.name)` instead.",
+            category=spack.error.SpackAPIWarning,
+            stacklevel=2,
+        )
         return spack.repo.PATH.is_virtual(self.name)
 
     @property
@@ -2101,20 +2118,20 @@ def cshort_spec(self):
         return self.cformat(spec_format)
 
     @property
-    def prefix(self):
+    def prefix(self) -> spack.util.prefix.Prefix:
         if not self._concrete:
-            raise spack.error.SpecError("Spec is not concrete: " + str(self))
+            raise spack.error.SpecError(f"Spec is not concrete: {self}")
 
         if self._prefix is None:
-            upstream, record = spack.store.STORE.db.query_by_spec_hash(self.dag_hash())
+            _, record = spack.store.STORE.db.query_by_spec_hash(self.dag_hash())
             if record and record.path:
-                self.prefix = record.path
+                self.set_prefix(record.path)
             else:
-                self.prefix = spack.store.STORE.layout.path_for_spec(self)
+                self.set_prefix(spack.store.STORE.layout.path_for_spec(self))
+        assert self._prefix is not None
         return self._prefix
 
-    @prefix.setter
-    def prefix(self, value):
+    def set_prefix(self, value: str) -> None:
         self._prefix = spack.util.prefix.Prefix(llnl.path.convert_to_platform_path(value))
 
     def spec_hash(self, hash):
@@ -2128,7 +2145,9 @@ def spec_hash(self, hash):
         if hash.override is not None:
             return hash.override(self)
         node_dict = self.to_node_dict(hash=hash)
-        json_text = sjson.dump(node_dict)
+        json_text = json.dumps(
+            node_dict, ensure_ascii=True, indent=None, separators=(",", ":"), sort_keys=False
+        )
         # This implements "frankenhashes", preserving the last 7 characters of the
         # original hash when splicing so that we can avoid relocation issues
         out = spack.util.hash.b32_hash(json_text)
@@ -2351,15 +2370,10 @@ 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:
@@ -2694,7 +2708,7 @@ def name_and_dependency_types(s: str) -> Tuple[str, dt.DepFlag]:
                 return name, depflag
 
             def spec_and_dependency_types(
-                s: Union[Spec, Tuple[Spec, str]]
+                s: Union[Spec, Tuple[Spec, str]],
             ) -> Tuple[Spec, dt.DepFlag]:
                 """Given a non-string key in the literal, extracts the spec
                 and its dependency types.
@@ -2723,7 +2737,7 @@ def spec_and_dependency_types(
         return spec_builder(spec_dict)
 
     @staticmethod
-    def from_dict(data):
+    def from_dict(data) -> "Spec":
         """Construct a spec from JSON/YAML.
 
         Args:
@@ -2746,7 +2760,7 @@ def from_dict(data):
         return spec
 
     @staticmethod
-    def from_yaml(stream):
+    def from_yaml(stream) -> "Spec":
         """Construct a spec from YAML.
 
         Args:
@@ -2756,7 +2770,7 @@ def from_yaml(stream):
         return Spec.from_dict(data)
 
     @staticmethod
-    def from_json(stream):
+    def from_json(stream) -> "Spec":
         """Construct a spec from JSON.
 
         Args:
@@ -2766,7 +2780,7 @@ def from_json(stream):
             data = sjson.load(stream)
             return Spec.from_dict(data)
         except Exception as e:
-            raise sjson.SpackJSONError("error parsing JSON spec:", str(e)) from e
+            raise sjson.SpackJSONError("error parsing JSON spec:", e) from e
 
     @staticmethod
     def extract_json_from_clearsig(data):
@@ -2814,24 +2828,6 @@ def from_detection(
         s.extra_attributes = extra_attributes
         return s
 
-    def validate_detection(self):
-        """Validate the detection of an external spec.
-
-        This method is used as part of Spack's detection protocol, and is
-        not meant for client code use.
-        """
-        # Assert that _extra_attributes is a Mapping and not None,
-        # which likely means the spec was created with Spec.from_detection
-        msg = 'cannot validate "{0}" since it was not created ' "using Spec.from_detection".format(
-            self
-        )
-        assert isinstance(self.extra_attributes, collections.abc.Mapping), msg
-
-        # Validate the spec calling a package specific method
-        pkg_cls = spack.repo.PATH.get_pkg_class(self.name)
-        validate_fn = getattr(pkg_cls, "validate_detected_spec", lambda x, y: None)
-        validate_fn(self, self.extra_attributes)
-
     def _patches_assigned(self):
         """Whether patches have been assigned to this spec by the concretizer."""
         # FIXME: _patches_in_order_of_appearance is attached after concretization
@@ -2848,94 +2844,6 @@ def _patches_assigned(self):
 
         return True
 
-    @staticmethod
-    def inject_patches_variant(root):
-        # This dictionary will store object IDs rather than Specs as keys
-        # since the Spec __hash__ will change as patches are added to them
-        spec_to_patches = {}
-        for s in root.traverse():
-            # After concretizing, assign namespaces to anything left.
-            # Note that this doesn't count as a "change".  The repository
-            # configuration is constant throughout a spack run, and
-            # normalize and concretize evaluate Packages using Repo.get(),
-            # which respects precedence.  So, a namespace assignment isn't
-            # changing how a package name would have been interpreted and
-            # we can do it as late as possible to allow as much
-            # compatibility across repositories as possible.
-            if s.namespace is None:
-                s.namespace = spack.repo.PATH.repo_for_pkg(s.name).namespace
-
-            if s.concrete:
-                continue
-
-            # Add any patches from the package to the spec.
-            patches = set()
-            for cond, patch_list in s.package_class.patches.items():
-                if s.satisfies(cond):
-                    for patch in patch_list:
-                        patches.add(patch)
-            if patches:
-                spec_to_patches[id(s)] = patches
-
-        # Also record all patches required on dependencies by
-        # depends_on(..., patch=...)
-        for dspec in root.traverse_edges(deptype=all, cover="edges", root=False):
-            if dspec.spec.concrete:
-                continue
-
-            pkg_deps = dspec.parent.package_class.dependencies
-
-            patches = []
-            for cond, deps_by_name in pkg_deps.items():
-                if not dspec.parent.satisfies(cond):
-                    continue
-
-                dependency = deps_by_name.get(dspec.spec.name)
-                if not dependency:
-                    continue
-
-                for pcond, patch_list in dependency.patches.items():
-                    if dspec.spec.satisfies(pcond):
-                        patches.extend(patch_list)
-
-            if patches:
-                all_patches = spec_to_patches.setdefault(id(dspec.spec), set())
-                for patch in patches:
-                    all_patches.add(patch)
-
-        for spec in root.traverse():
-            if id(spec) not in spec_to_patches:
-                continue
-
-            patches = list(lang.dedupe(spec_to_patches[id(spec)]))
-            mvar = spec.variants.setdefault("patches", vt.MultiValuedVariant("patches", ()))
-            mvar.value = tuple(p.sha256 for p in patches)
-            # FIXME: Monkey patches mvar to store patches order
-            full_order_keys = list(tuple(p.ordering_key) + (p.sha256,) for p in patches)
-            ordered_hashes = sorted(full_order_keys)
-            tty.debug(
-                "Ordered hashes [{0}]: ".format(spec.name)
-                + ", ".join("/".join(str(e) for e in t) for t in ordered_hashes)
-            )
-            mvar._patches_in_order_of_appearance = list(t[-1] for t in ordered_hashes)
-
-    @staticmethod
-    def ensure_external_path_if_external(external_spec):
-        if external_spec.external_modules and not external_spec.external_path:
-            compiler = spack.compilers.compiler_for_spec(
-                external_spec.compiler, external_spec.architecture
-            )
-            for mod in compiler.modules:
-                md.load_module(mod)
-
-            # Get the path from the module the package can override the default
-            # (this is mostly needed for Cray)
-            pkg_cls = spack.repo.PATH.get_pkg_class(external_spec.name)
-            package = pkg_cls(external_spec)
-            external_spec.external_path = getattr(
-                package, "external_prefix", md.path_from_modules(external_spec.external_modules)
-            )
-
     @staticmethod
     def ensure_no_deprecated(root):
         """Raise if a deprecated spec is in the dag.
@@ -3090,7 +2998,7 @@ def validate_or_raise(self):
         # FIXME: raise just the first one encountered
         for spec in self.traverse():
             # raise an UnknownPackageError if the spec's package isn't real.
-            if (not spec.virtual) and spec.name:
+            if spec.name and not spack.repo.PATH.is_virtual(spec.name):
                 spack.repo.PATH.get_pkg_class(spec.fullname)
 
             # validate compiler in addition to the package name.
@@ -3099,7 +3007,7 @@ def validate_or_raise(self):
                     raise UnsupportedCompilerError(spec.compiler.name)
 
             # Ensure correctness of variants (if the spec is not virtual)
-            if not spec.virtual:
+            if not spack.repo.PATH.is_virtual(spec.name):
                 Spec.ensure_valid_variants(spec)
                 substitute_abstract_variants(spec)
 
@@ -3117,7 +3025,7 @@ def ensure_valid_variants(spec):
         if spec.concrete:
             return
 
-        pkg_cls = spec.package_class
+        pkg_cls = spack.repo.PATH.get_pkg_class(spec.fullname)
         pkg_variants = pkg_cls.variant_names()
         # reserved names are variants that may be set on any package
         # but are not necessarily recorded by the package's class
@@ -3334,7 +3242,9 @@ def intersects(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
 
         # If the names are different, we need to consider virtuals
         if self.name != other.name and self.name and other.name:
-            if self.virtual and other.virtual:
+            self_virtual = spack.repo.PATH.is_virtual(self.name)
+            other_virtual = spack.repo.PATH.is_virtual(other.name)
+            if self_virtual and other_virtual:
                 # Two virtual specs intersect only if there are providers for both
                 lhs = spack.repo.PATH.providers_for(str(self))
                 rhs = spack.repo.PATH.providers_for(str(other))
@@ -3342,8 +3252,8 @@ def intersects(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
                 return bool(intersection)
 
             # A provider can satisfy a virtual dependency.
-            elif self.virtual or other.virtual:
-                virtual_spec, non_virtual_spec = (self, other) if self.virtual else (other, self)
+            elif self_virtual or other_virtual:
+                virtual_spec, non_virtual_spec = (self, other) if self_virtual else (other, self)
                 try:
                     # Here we might get an abstract spec
                     pkg_cls = spack.repo.PATH.get_pkg_class(non_virtual_spec.fullname)
@@ -3413,12 +3323,20 @@ def _intersects_dependencies(self, other):
         # These two loops handle cases where there is an overly restrictive
         # vpkg in one spec for a provider in the other (e.g., mpi@3: is not
         # compatible with mpich2)
-        for spec in self.virtual_dependencies():
-            if spec.name in other_index and not other_index.providers_for(spec):
+        for spec in self.traverse():
+            if (
+                spack.repo.PATH.is_virtual(spec.name)
+                and spec.name in other_index
+                and not other_index.providers_for(spec)
+            ):
                 return False
 
-        for spec in other.virtual_dependencies():
-            if spec.name in self_index and not self_index.providers_for(spec):
+        for spec in other.traverse():
+            if (
+                spack.repo.PATH.is_virtual(spec.name)
+                and spec.name in self_index
+                and not self_index.providers_for(spec)
+            ):
                 return False
 
         return True
@@ -3448,7 +3366,9 @@ def satisfies(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
         # If the names are different, we need to consider virtuals
         if self.name != other.name and self.name and other.name:
             # A concrete provider can satisfy a virtual dependency.
-            if not self.virtual and other.virtual:
+            if not spack.repo.PATH.is_virtual(self.name) and spack.repo.PATH.is_virtual(
+                other.name
+            ):
                 try:
                     # Here we might get an abstract spec
                     pkg_cls = spack.repo.PATH.get_pkg_class(self.fullname)
@@ -3516,7 +3436,7 @@ def satisfies(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
         lhs_edges: Dict[str, Set[DependencySpec]] = collections.defaultdict(set)
         for rhs_edge in other.traverse_edges(root=False, cover="edges"):
             # If we are checking for ^mpi we need to verify if there is any edge
-            if rhs_edge.spec.virtual:
+            if spack.repo.PATH.is_virtual(rhs_edge.spec.name):
                 rhs_edge.update_virtuals(virtuals=(rhs_edge.spec.name,))
 
             if not rhs_edge.virtuals:
@@ -3560,10 +3480,6 @@ def satisfies(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
             for rhs in other.traverse(root=False)
         )
 
-    def virtual_dependencies(self):
-        """Return list of any virtual deps in this spec."""
-        return [spec for spec in self.traverse() if spec.virtual]
-
     @property  # type: ignore[misc] # decorated prop not supported in mypy
     def patches(self):
         """Return patch objects for any patch sha256 sums on this Spec.
@@ -3753,30 +3669,23 @@ def __getitem__(self, name: str):
             csv = query_parameters.pop().strip()
             query_parameters = re.split(r"\s*,\s*", csv)
 
-        order = lambda: itertools.chain(
-            self.traverse_edges(deptype=dt.LINK, order="breadth", cover="edges"),
-            self.edges_to_dependencies(depflag=dt.BUILD | dt.RUN | dt.TEST),
-            self.traverse_edges(deptype=dt.ALL, order="breadth", cover="edges"),
+        # Consider all direct dependencies and transitive runtime dependencies
+        order = itertools.chain(
+            self.edges_to_dependencies(depflag=dt.ALL),
+            self.traverse_edges(deptype=dt.LINK | dt.RUN, order="breadth", cover="edges"),
         )
 
-        # Consider runtime dependencies and direct build/test deps before transitive dependencies,
-        # and prefer matches closest to the root.
         try:
-            child: Spec = next(
-                e.spec
-                for e in itertools.chain(
-                    (e for e in order() if e.spec.name == name or name in e.virtuals),
-                    # for historical reasons
-                    (e for e in order() if e.spec.concrete and e.spec.package.provides(name)),
-                )
-            )
-        except StopIteration:
-            raise KeyError(f"No spec with name {name} in {self}")
+            edge = next((e for e in order if e.spec.name == name or name in e.virtuals))
+        except StopIteration as e:
+            raise KeyError(f"No spec with name {name} in {self}") from e
 
         if self._concrete:
-            return SpecBuildInterface(child, name, query_parameters, _parent=self)
+            return SpecBuildInterface(
+                edge.spec, name, query_parameters, _parent=self, is_virtual=name in edge.virtuals
+            )
 
-        return child
+        return edge.spec
 
     def __contains__(self, spec):
         """True if this spec or some dependency satisfies the spec.
@@ -3792,8 +3701,11 @@ def __contains__(self, spec):
         # if anonymous or same name, we only have to look at the root
         if not spec.name or spec.name == self.name:
             return self.satisfies(spec)
-        else:
-            return any(s.satisfies(spec) for s in self.traverse(root=False))
+        try:
+            dep = self[spec.name]
+        except KeyError:
+            return False
+        return dep.satisfies(spec)
 
     def eq_dag(self, other, deptypes=True, vs=None, vo=None):
         """True if the full dependency DAGs of specs are equal."""
@@ -3861,6 +3773,13 @@ 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__`.
         #
@@ -4696,17 +4615,6 @@ def constrain(self, other: "VariantMap") -> bool:
 
         return changed
 
-    @property
-    def concrete(self):
-        """Returns True if the spec is concrete in terms of variants.
-
-        Returns:
-            bool: True or False
-        """
-        return self.spec._concrete or all(
-            v in self for v in self.spec.package_class.variant_names()
-        )
-
     def copy(self) -> "VariantMap":
         clone = VariantMap(self.spec)
         for name, variant in self.items():
@@ -4726,7 +4634,10 @@ 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()
@@ -4761,14 +4672,14 @@ def substitute_abstract_variants(spec: Spec):
         elif name in vt.reserved_names:
             continue
 
-        variant_defs = spec.package_class.variant_definitions(name)
+        variant_defs = spack.repo.PATH.get_pkg_class(spec.fullname).variant_definitions(name)
         valid_defs = []
         for when, vdef in variant_defs:
             if when.intersects(spec):
                 valid_defs.append(vdef)
 
         if not valid_defs:
-            if name not in spec.package_class.variant_names():
+            if name not in spack.repo.PATH.get_pkg_class(spec.fullname).variant_names():
                 unknown.append(name)
             else:
                 whens = [str(when) for when, _ in variant_defs]
@@ -4830,31 +4741,51 @@ def merge_abstract_anonymous_specs(*abstract_specs: Spec):
     return merged_spec
 
 
-def reconstruct_virtuals_on_edges(spec):
-    """Reconstruct virtuals on edges. Used to read from old DB and reindex.
+def reconstruct_virtuals_on_edges(spec: Spec) -> None:
+    """Reconstruct virtuals on edges. Used to read from old DB and reindex."""
+    virtuals_needed: Dict[str, Set[str]] = {}
+    virtuals_provided: Dict[str, Set[str]] = {}
+    for edge in spec.traverse_edges(cover="edges", root=False):
+        parent_key = edge.parent.dag_hash()
+        if parent_key not in virtuals_needed:
+            # Construct which virtuals are needed by parent
+            virtuals_needed[parent_key] = set()
+            try:
+                parent_pkg = edge.parent.package
+            except Exception as e:
+                warnings.warn(
+                    f"cannot reconstruct virtual dependencies on {edge.parent.name}: {e}"
+                )
+                continue
 
-    Args:
-        spec: spec on which we want to reconstruct virtuals
-    """
-    # Collect all possible virtuals
-    possible_virtuals = set()
-    for node in spec.traverse():
-        try:
-            possible_virtuals.update({x for x in node.package.dependencies if Spec(x).virtual})
-        except Exception as e:
-            warnings.warn(f"cannot reconstruct virtual dependencies on package {node.name}: {e}")
+            virtuals_needed[parent_key].update(
+                name
+                for name, when_deps in parent_pkg.dependencies_by_name(when=True).items()
+                if spack.repo.PATH.is_virtual(name)
+                and any(edge.parent.satisfies(x) for x in when_deps)
+            )
+
+        if not virtuals_needed[parent_key]:
             continue
 
-    # Assume all incoming edges to provider are marked with virtuals=
-    for vspec in possible_virtuals:
-        try:
-            provider = spec[vspec]
-        except KeyError:
-            # Virtual not in the DAG
+        child_key = edge.spec.dag_hash()
+        if child_key not in virtuals_provided:
+            virtuals_provided[child_key] = set()
+            try:
+                child_pkg = edge.spec.package
+            except Exception as e:
+                warnings.warn(
+                    f"cannot reconstruct virtual dependencies on {edge.parent.name}: {e}"
+                )
+                continue
+            virtuals_provided[child_key].update(x.name for x in child_pkg.virtuals_provided)
+
+        if not virtuals_provided[child_key]:
             continue
 
-        for edge in provider.edges_from_dependents():
-            edge.update_virtuals([vspec])
+        virtuals_to_add = virtuals_needed[parent_key] & virtuals_provided[child_key]
+        if virtuals_to_add:
+            edge.update_virtuals(virtuals_to_add)
 
 
 class SpecfileReaderBase:
@@ -4905,7 +4836,7 @@ def from_node_dict(cls, node):
                 spec.external_modules = node["external"]["module"]
                 if spec.external_modules is False:
                     spec.external_modules = None
-                spec.extra_attributes = node["external"].get("extra_attributes", {})
+                spec.extra_attributes = node["external"].get("extra_attributes") or {}
 
         # specs read in are concrete unless marked abstract
         if node.get("concrete", True):

lib/spack/spack/test/abi_splicing.py

@@ -1,7 +1,7 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-""" Test ABI-based splicing of dependencies """
+"""Test ABI-based splicing of dependencies"""
 
 from typing import List
 

lib/spack/spack/test/build_environment.py

@@ -388,7 +388,7 @@ def test_wrapper_variables(
     root = spack.concretize.concretize_one("dt-diamond")
 
     for s in root.traverse():
-        s.prefix = "/{0}-prefix/".format(s.name)
+        s.set_prefix(f"/{s.name}-prefix/")
 
     dep_pkg = root["dt-diamond-left"].package
     dep_lib_paths = ["/test/path/to/ex1.so", "/test/path/to/subdir/ex2.so"]
@@ -396,7 +396,7 @@ def test_wrapper_variables(
     dep_libs = LibraryList(dep_lib_paths)
 
     dep2_pkg = root["dt-diamond-right"].package
-    dep2_pkg.spec.prefix = str(installation_dir_with_headers)
+    dep2_pkg.spec.set_prefix(str(installation_dir_with_headers))
 
     setattr(dep_pkg, "libs", dep_libs)
     try:
@@ -542,7 +542,7 @@ def test_build_jobs_sequential_is_sequential():
         spack.config.determine_number_of_jobs(
             parallel=False,
             max_cpus=8,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("command_line", {"config": {"build_jobs": 8}}),
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 8}}),
             ),
@@ -556,7 +556,7 @@ def test_build_jobs_command_line_overrides():
         spack.config.determine_number_of_jobs(
             parallel=True,
             max_cpus=1,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("command_line", {"config": {"build_jobs": 10}}),
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 1}}),
             ),
@@ -567,7 +567,7 @@ def test_build_jobs_command_line_overrides():
         spack.config.determine_number_of_jobs(
             parallel=True,
             max_cpus=100,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("command_line", {"config": {"build_jobs": 10}}),
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 100}}),
             ),
@@ -581,7 +581,7 @@ def test_build_jobs_defaults():
         spack.config.determine_number_of_jobs(
             parallel=True,
             max_cpus=10,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 1}})
             ),
         )
@@ -591,7 +591,7 @@ def test_build_jobs_defaults():
         spack.config.determine_number_of_jobs(
             parallel=True,
             max_cpus=10,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 100}})
             ),
         )

lib/spack/spack/test/build_systems.py

@@ -403,8 +403,8 @@ def test_autoreconf_search_path_args_multiple(default_mock_concretization, tmpdi
     aclocal_fst = str(tmpdir.mkdir("fst").mkdir("share").mkdir("aclocal"))
     aclocal_snd = str(tmpdir.mkdir("snd").mkdir("share").mkdir("aclocal"))
     build_dep_one, build_dep_two = spec.dependencies(deptype="build")
-    build_dep_one.prefix = str(tmpdir.join("fst"))
-    build_dep_two.prefix = str(tmpdir.join("snd"))
+    build_dep_one.set_prefix(str(tmpdir.join("fst")))
+    build_dep_two.set_prefix(str(tmpdir.join("snd")))
     assert spack.build_systems.autotools._autoreconf_search_path_args(spec) == [
         "-I",
         aclocal_fst,
@@ -422,8 +422,8 @@ def test_autoreconf_search_path_args_skip_automake(default_mock_concretization,
     aclocal_snd = str(tmpdir.mkdir("snd").mkdir("share").mkdir("aclocal"))
     build_dep_one, build_dep_two = spec.dependencies(deptype="build")
     build_dep_one.name = "automake"
-    build_dep_one.prefix = str(tmpdir.join("fst"))
-    build_dep_two.prefix = str(tmpdir.join("snd"))
+    build_dep_one.set_prefix(str(tmpdir.join("fst")))
+    build_dep_two.set_prefix(str(tmpdir.join("snd")))
     assert spack.build_systems.autotools._autoreconf_search_path_args(spec) == ["-I", aclocal_snd]
 
 
@@ -434,7 +434,7 @@ def test_autoreconf_search_path_args_external_order(default_mock_concretization,
     aclocal_snd = str(tmpdir.mkdir("snd").mkdir("share").mkdir("aclocal"))
     build_dep_one, build_dep_two = spec.dependencies(deptype="build")
     build_dep_one.external_path = str(tmpdir.join("fst"))
-    build_dep_two.prefix = str(tmpdir.join("snd"))
+    build_dep_two.set_prefix(str(tmpdir.join("snd")))
     assert spack.build_systems.autotools._autoreconf_search_path_args(spec) == [
         "-I",
         aclocal_snd,
@@ -447,8 +447,8 @@ def test_autoreconf_search_path_skip_nonexisting(default_mock_concretization, tm
     """Skip -I flags for non-existing directories"""
     spec = default_mock_concretization("dttop")
     build_dep_one, build_dep_two = spec.dependencies(deptype="build")
-    build_dep_one.prefix = str(tmpdir.join("fst"))
-    build_dep_two.prefix = str(tmpdir.join("snd"))
+    build_dep_one.set_prefix(str(tmpdir.join("fst")))
+    build_dep_two.set_prefix(str(tmpdir.join("snd")))
     assert spack.build_systems.autotools._autoreconf_search_path_args(spec) == []
 
 

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/build_env.py

@@ -12,7 +12,7 @@
 build_env = SpackCommand("build-env")
 
 
-@pytest.mark.parametrize("pkg", [("zlib",), ("zlib", "--")])
+@pytest.mark.parametrize("pkg", [("pkg-c",), ("pkg-c", "--")])
 @pytest.mark.usefixtures("config", "mock_packages", "working_env")
 def test_it_just_runs(pkg):
     build_env(*pkg)
@@ -38,7 +38,7 @@ def test_build_env_requires_a_spec(args):
 @pytest.mark.usefixtures("config", "mock_packages", "working_env")
 def test_dump(shell_as, shell, tmpdir):
     with tmpdir.as_cwd():
-        build_env("--dump", _out_file, "zlib")
+        build_env("--dump", _out_file, "pkg-c")
         with open(_out_file, encoding="utf-8") as f:
             if shell == "pwsh":
                 assert any(line.startswith("$Env:PATH") for line in f.readlines())
@@ -51,7 +51,7 @@ def test_dump(shell_as, shell, tmpdir):
 @pytest.mark.usefixtures("config", "mock_packages", "working_env")
 def test_pickle(tmpdir):
     with tmpdir.as_cwd():
-        build_env("--pickle", _out_file, "zlib")
+        build_env("--pickle", _out_file, "pkg-c")
         environment = pickle.load(open(_out_file, "rb"))
         assert isinstance(environment, dict)
         assert "PATH" in environment

lib/spack/spack/test/cmd/buildcache.py

@@ -148,7 +148,7 @@ def test_update_key_index(
     s = spack.concretize.concretize_one("libdwarf")
 
     # Install a package
-    install(s.name)
+    install("--fake", s.name)
 
     # Put installed package in the buildcache, which, because we're signing
     # it, should result in the public key getting pushed to the buildcache
@@ -178,7 +178,7 @@ def test_buildcache_autopush(tmp_path, install_mockery, mock_fetch):
     s = spack.concretize.concretize_one("libdwarf")
 
     # Install and generate build cache index
-    PackageInstaller([s.package], explicit=True).install()
+    PackageInstaller([s.package], fake=True, explicit=True).install()
 
     metadata_file = spack.binary_distribution.tarball_name(s, ".spec.json")
 
@@ -220,7 +220,7 @@ def verify_mirror_contents():
 
     # Install a package and put it in the buildcache
     s = spack.concretize.concretize_one(out_env_pkg)
-    install(s.name)
+    install("--fake", s.name)
     buildcache("push", "-u", "-f", src_mirror_url, s.name)
 
     env("create", "test")

lib/spack/spack/test/cmd/checksum.py

@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import argparse
+import pathlib
 
 import pytest
 
@@ -22,7 +23,15 @@
 
 
 @pytest.fixture
-def can_fetch_versions(monkeypatch):
+def no_add(monkeypatch):
+    def add_versions_to_pkg(pkg, version_lines, open_in_editor):
+        raise AssertionError("Should not be called")
+
+    monkeypatch.setattr(spack.cmd.checksum, "add_versions_to_pkg", add_versions_to_pkg)
+
+
+@pytest.fixture
+def can_fetch_versions(monkeypatch, no_add):
     """Fake successful version detection."""
 
     def fetch_remote_versions(pkg, concurrency):
@@ -45,7 +54,7 @@ def url_exists(url, curl=None):
 
 
 @pytest.fixture
-def cannot_fetch_versions(monkeypatch):
+def cannot_fetch_versions(monkeypatch, no_add):
     """Fake unsuccessful version detection."""
 
     def fetch_remote_versions(pkg, concurrency):
@@ -88,7 +97,6 @@ def test_checksum_args(arguments, expected):
         (["--batch", "preferred-test"], "version of preferred-test"),
         (["--latest", "preferred-test"], "Found 1 version"),
         (["--preferred", "preferred-test"], "Found 1 version"),
-        (["--add-to-package", "preferred-test"], "Added 0 new versions to"),
         (["--verify", "preferred-test"], "Verified 1 of 1"),
         (["--verify", "zlib", "1.2.13"], "1.2.13  [-] No previous checksum"),
     ],
@@ -271,15 +279,12 @@ def test_checksum_interactive_unrecognized_command():
     assert interactive_version_filter(v.copy(), input=input) == v
 
 
-def test_checksum_versions(mock_packages, can_fetch_versions):
+def test_checksum_versions(mock_packages, can_fetch_versions, monkeypatch):
     pkg_cls = spack.repo.PATH.get_pkg_class("zlib")
     versions = [str(v) for v in pkg_cls.versions]
     output = spack_checksum("zlib", *versions)
     assert "Found 3 versions" in output
     assert "version(" in output
-    output = spack_checksum("--add-to-package", "zlib", *versions)
-    assert "Found 3 versions" in output
-    assert "Added 0 new versions to" in output
 
 
 def test_checksum_missing_version(mock_packages, cannot_fetch_versions):
@@ -287,7 +292,6 @@ def test_checksum_missing_version(mock_packages, cannot_fetch_versions):
     assert "Could not find any remote versions" in output
     output = spack_checksum("--add-to-package", "preferred-test", "99.99.99", fail_on_error=False)
     assert "Could not find any remote versions" in output
-    assert "Added 1 new versions to" not in output
 
 
 def test_checksum_deprecated_version(mock_packages, can_fetch_versions):
@@ -297,8 +301,6 @@ def test_checksum_deprecated_version(mock_packages, can_fetch_versions):
         "--add-to-package", "deprecated-versions", "1.1.0", fail_on_error=False
     )
     assert "Version 1.1.0 is deprecated" in output
-    # TODO alecbcs: broken assertion.
-    # assert "Added 0 new versions to" not in output
 
 
 def test_checksum_url(mock_packages, config):
@@ -337,3 +339,52 @@ def test_checksum_manual_download_fails(mock_packages, monkeypatch):
     monkeypatch.setattr(spack.package_base.PackageBase, "download_instr", error)
     with pytest.raises(ManualDownloadRequiredError, match=error):
         spack_checksum(name, *versions)
+
+
+def test_upate_package_contents(tmp_path: pathlib.Path):
+    """Test that the package.py file is updated with the new versions."""
+    pkg_path = tmp_path / "package.py"
+    pkg_path.write_text(
+        """\
+from spack.package import *
+
+class Zlib(Package):
+    homepage = "http://zlib.net"
+    url = "http://zlib.net/fossils/zlib-1.2.11.tar.gz"
+
+    version("1.2.11", sha256="c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1")
+    version("1.2.8", sha256="36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d")
+    version("1.2.3", sha256="1795c7d067a43174113fdf03447532f373e1c6c57c08d61d9e4e9be5e244b05e")
+    variant("pic", default=True, description="test")
+
+    def install(self, spec, prefix):
+        make("install")
+"""
+    )
+    version_lines = """\
+    version("1.2.13", sha256="abcdef1234567890abcdef1234567890abcdef1234567890abcdef1234567890")
+    version("1.2.5", sha256="abcdef1234567890abcdef1234567890abcdef1234567890abcdef1234567890")
+    version("1.2.3", sha256="1795c7d067a43174113fdf03447532f373e1c6c57c08d61d9e4e9be5e244b05e")
+"""
+    # two new versions are added
+    assert spack.cmd.checksum.add_versions_to_pkg(str(pkg_path), version_lines) == 2
+    assert (
+        pkg_path.read_text()
+        == """\
+from spack.package import *
+
+class Zlib(Package):
+    homepage = "http://zlib.net"
+    url = "http://zlib.net/fossils/zlib-1.2.11.tar.gz"
+
+    version("1.2.13", sha256="abcdef1234567890abcdef1234567890abcdef1234567890abcdef1234567890")  # FIXME
+    version("1.2.11", sha256="c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1")
+    version("1.2.8", sha256="36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d")
+    version("1.2.5", sha256="abcdef1234567890abcdef1234567890abcdef1234567890abcdef1234567890")  # FIXME
+    version("1.2.3", sha256="1795c7d067a43174113fdf03447532f373e1c6c57c08d61d9e4e9be5e244b05e")
+    variant("pic", default=True, description="test")
+
+    def install(self, spec, prefix):
+        make("install")
+"""
+    )

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

@@ -28,6 +28,7 @@
 from spack.ci.generator_registry import generator
 from spack.cmd.ci import FAILED_CREATE_BUILDCACHE_CODE
 from spack.database import INDEX_JSON_FILE
+from spack.error import SpackError
 from spack.schema.buildcache_spec import schema as specfile_schema
 from spack.schema.database_index import schema as db_idx_schema
 from spack.spec import Spec
@@ -170,7 +171,9 @@ def test_ci_generate_with_env(ci_generate_test, tmp_path, mock_binary_index):
     url: https://my.fake.cdash
     project: Not used
     site: Nothing
-"""
+""",
+        "--artifacts-root",
+        str(tmp_path / "my_artifacts_root"),
     )
     yaml_contents = syaml.load(outputfile.read_text())
 
@@ -192,7 +195,7 @@ def test_ci_generate_with_env(ci_generate_test, tmp_path, mock_binary_index):
 
     assert "variables" in yaml_contents
     assert "SPACK_ARTIFACTS_ROOT" in yaml_contents["variables"]
-    assert yaml_contents["variables"]["SPACK_ARTIFACTS_ROOT"] == "jobs_scratch_dir"
+    assert yaml_contents["variables"]["SPACK_ARTIFACTS_ROOT"] == "my_artifacts_root"
 
 
 def test_ci_generate_with_env_missing_section(ci_generate_test, tmp_path, mock_binary_index):
@@ -1062,7 +1065,7 @@ def test_ci_rebuild_index(
             with open(tmp_path / "spec.json", "w", encoding="utf-8") as f:
                 f.write(concrete_spec.to_json(hash=ht.dag_hash))
 
-            install_cmd("--add", "-f", str(tmp_path / "spec.json"))
+            install_cmd("--fake", "--add", "-f", str(tmp_path / "spec.json"))
             buildcache_cmd("push", "-u", "-f", mirror_url, "callpath")
             ci_cmd("rebuild-index")
 
@@ -1322,44 +1325,50 @@ def test_ci_reproduce(
         env.concretize()
         env.write()
 
-        repro_dir.mkdir()
+    def fake_download_and_extract_artifacts(url, work_dir, merge_commit_test=True):
+        with working_dir(tmp_path), ev.Environment(".") as env:
+            if not os.path.exists(repro_dir):
+                repro_dir.mkdir()
 
-        job_spec = env.concrete_roots()[0]
-        with open(repro_dir / "archivefiles.json", "w", encoding="utf-8") as f:
-            f.write(job_spec.to_json(hash=ht.dag_hash))
+            job_spec = env.concrete_roots()[0]
+            with open(repro_dir / "archivefiles.json", "w", encoding="utf-8") as f:
+                f.write(job_spec.to_json(hash=ht.dag_hash))
+                artifacts_root = repro_dir / "jobs_scratch_dir"
+                pipeline_path = artifacts_root / "pipeline.yml"
 
-        artifacts_root = repro_dir / "scratch_dir"
-        pipeline_path = artifacts_root / "pipeline.yml"
-
-        ci_cmd(
-            "generate",
-            "--output-file",
-            str(pipeline_path),
-            "--artifacts-root",
-            str(artifacts_root),
-        )
-
-        job_name = gitlab_generator.get_job_name(job_spec)
-
-        with open(repro_dir / "repro.json", "w", encoding="utf-8") as f:
-            f.write(
-                json.dumps(
-                    {
-                        "job_name": job_name,
-                        "job_spec_json": "archivefiles.json",
-                        "ci_project_dir": str(repro_dir),
-                    }
+                ci_cmd(
+                    "generate",
+                    "--output-file",
+                    str(pipeline_path),
+                    "--artifacts-root",
+                    str(artifacts_root),
                 )
-            )
 
-        with open(repro_dir / "install.sh", "w", encoding="utf-8") as f:
-            f.write("#!/bin/sh\n\n#fake install\nspack install blah\n")
+                job_name = gitlab_generator.get_job_name(job_spec)
 
-        with open(repro_dir / "spack_info.txt", "w", encoding="utf-8") as f:
-            f.write(f"\nMerge {last_two_git_commits[1]} into {last_two_git_commits[0]}\n\n")
+                with open(repro_dir / "repro.json", "w", encoding="utf-8") as f:
+                    f.write(
+                        json.dumps(
+                            {
+                                "job_name": job_name,
+                                "job_spec_json": "archivefiles.json",
+                                "ci_project_dir": str(repro_dir),
+                            }
+                        )
+                    )
 
-    def fake_download_and_extract_artifacts(url, work_dir):
-        pass
+                with open(repro_dir / "install.sh", "w", encoding="utf-8") as f:
+                    f.write("#!/bin/sh\n\n#fake install\nspack install blah\n")
+
+                with open(repro_dir / "spack_info.txt", "w", encoding="utf-8") as f:
+                    if merge_commit_test:
+                        f.write(
+                            f"\nMerge {last_two_git_commits[1]} into {last_two_git_commits[0]}\n\n"
+                        )
+                    else:
+                        f.write(f"\ncommit {last_two_git_commits[1]}\n\n")
+
+            return "jobs_scratch_dir"
 
     monkeypatch.setattr(ci, "download_and_extract_artifacts", fake_download_and_extract_artifacts)
     rep_out = ci_cmd(
@@ -1375,6 +1384,64 @@ def fake_download_and_extract_artifacts(url, work_dir):
     # Make sure we tell the user where it is when not in interactive mode
     assert f"$ {repro_dir}/start.sh" in rep_out
 
+    # Ensure the correct commits are used
+    assert f"checkout_commit: {last_two_git_commits[0]}" in rep_out
+    assert f"merge_commit: {last_two_git_commits[1]}" in rep_out
+
+    # Test re-running in dirty working dir
+    with pytest.raises(SpackError, match=f"{repro_dir}"):
+        rep_out = ci_cmd(
+            "reproduce-build",
+            "https://example.com/api/v1/projects/1/jobs/2/artifacts",
+            "--working-dir",
+            str(repro_dir),
+            output=str,
+        )
+
+    # Cleanup between  tests
+    shutil.rmtree(repro_dir)
+
+    # Test --use-local-head
+    rep_out = ci_cmd(
+        "reproduce-build",
+        "https://example.com/api/v1/projects/1/jobs/2/artifacts",
+        "--use-local-head",
+        "--working-dir",
+        str(repro_dir),
+        output=str,
+    )
+
+    # Make sure we are checkout out the HEAD commit without a merge commit
+    assert "checkout_commit: HEAD" in rep_out
+    assert "merge_commit: None" in rep_out
+
+    # Test the case where the spack_info.txt is not a merge commit
+    monkeypatch.setattr(
+        ci,
+        "download_and_extract_artifacts",
+        lambda url, wd: fake_download_and_extract_artifacts(url, wd, False),
+    )
+
+    # Cleanup between  tests
+    shutil.rmtree(repro_dir)
+
+    rep_out = ci_cmd(
+        "reproduce-build",
+        "https://example.com/api/v1/projects/1/jobs/2/artifacts",
+        "--working-dir",
+        str(repro_dir),
+        output=str,
+    )
+    # Make sure the script was generated
+    assert (repro_dir / "start.sh").exists()
+
+    # Make sure we tell the user where it is when not in interactive mode
+    assert f"$ {repro_dir}/start.sh" in rep_out
+
+    # Ensure the correct commit is used (different than HEAD)
+    assert f"checkout_commit: {last_two_git_commits[1]}" in rep_out
+    assert "merge_commit: None" in rep_out
+
 
 @pytest.mark.parametrize(
     "url_in,url_out",

lib/spack/spack/test/cmd/config.py

@@ -335,7 +335,7 @@ def test_config_add_override_leaf_from_file(mutable_empty_config, tmpdir):
 
 
 def test_config_add_update_dict_from_file(mutable_empty_config, tmpdir):
-    config("add", "packages:all:compiler:[gcc]")
+    config("add", "packages:all:require:['%gcc']")
 
     # contents to add to file
     contents = """spack:
@@ -357,7 +357,7 @@ def test_config_add_update_dict_from_file(mutable_empty_config, tmpdir):
     expected = """packages:
   all:
     target: [x86_64]
-    compiler: [gcc]
+    require: ['%gcc']
 """
 
     assert expected == output
@@ -606,7 +606,6 @@ def test_config_prefer_upstream(
     packages = syaml.load(open(cfg_file, encoding="utf-8"))["packages"]
 
     # Make sure only the non-default variants are set.
-    assert packages["all"] == {"compiler": ["gcc@=10.2.1"]}
     assert packages["boost"] == {"variants": "+debug +graph", "version": ["1.63.0"]}
     assert packages["dependency-install"] == {"version": ["2.0"]}
     # Ensure that neither variant gets listed for hdf5, since they conflict

lib/spack/spack/test/cmd/debug.py

@@ -2,52 +2,16 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os
 import platform
 
-import pytest
-
 import spack
 import spack.platforms
 import spack.spec
-from spack.database import INDEX_JSON_FILE
 from spack.main import SpackCommand
-from spack.util.executable import which
 
 debug = SpackCommand("debug")
 
 
-@pytest.mark.db
-def test_create_db_tarball(tmpdir, database):
-    with tmpdir.as_cwd():
-        debug("create-db-tarball")
-
-        # get the first non-dotfile to avoid coverage files in the directory
-        files = os.listdir(os.getcwd())
-        tarball_name = next(
-            f for f in files if not f.startswith(".") and not f.startswith("tests")
-        )
-
-        # debug command made an archive
-        assert os.path.exists(tarball_name)
-
-        # print contents of archive
-        tar = which("tar")
-        contents = tar("tzf", tarball_name, output=str)
-
-        # DB file is included
-        assert INDEX_JSON_FILE in contents
-
-        # specfiles from all installs are included
-        for spec in database.query():
-            # externals won't have a specfile
-            if spec.external:
-                continue
-
-            spec_suffix = "%s/.spack/spec.json" % spec.dag_hash()
-            assert spec_suffix in contents
-
-
 def test_report():
     out = debug("report")
     host_platform = spack.platforms.host()

lib/spack/spack/test/cmd/dependencies.py

@@ -24,32 +24,24 @@
 mpi_deps = ["fake"]
 
 
-def test_direct_dependencies(mock_packages):
-    out = dependencies("mpileaks")
-    actual = set(re.split(r"\s+", out.strip()))
-    expected = set(["callpath"] + mpis)
-    assert expected == actual
-
-
-def test_transitive_dependencies(mock_packages):
-    out = dependencies("--transitive", "mpileaks")
-    actual = set(re.split(r"\s+", out.strip()))
-    expected = set(["callpath", "dyninst", "libdwarf", "libelf"] + mpis + mpi_deps)
-    assert expected == actual
-
-
-def test_transitive_dependencies_with_deptypes(mock_packages):
-    out = dependencies("--transitive", "--deptype=link,run", "dtbuild1")
-    deps = set(re.split(r"\s+", out.strip()))
-    assert set(["dtlink2", "dtrun2"]) == deps
-
-    out = dependencies("--transitive", "--deptype=build", "dtbuild1")
-    deps = set(re.split(r"\s+", out.strip()))
-    assert set(["dtbuild2", "dtlink2"]) == deps
-
-    out = dependencies("--transitive", "--deptype=link", "dtbuild1")
-    deps = set(re.split(r"\s+", out.strip()))
-    assert set(["dtlink2"]) == deps
+@pytest.mark.parametrize(
+    "cli_args,expected",
+    [
+        (["mpileaks"], set(["callpath"] + mpis)),
+        (
+            ["--transitive", "mpileaks"],
+            set(["callpath", "dyninst", "libdwarf", "libelf"] + mpis + mpi_deps),
+        ),
+        (["--transitive", "--deptype=link,run", "dtbuild1"], {"dtlink2", "dtrun2"}),
+        (["--transitive", "--deptype=build", "dtbuild1"], {"dtbuild2", "dtlink2"}),
+        (["--transitive", "--deptype=link", "dtbuild1"], {"dtlink2"}),
+    ],
+)
+def test_direct_dependencies(cli_args, expected, mock_runtimes):
+    out = dependencies(*cli_args)
+    result = set(re.split(r"\s+", out.strip()))
+    expected.update(mock_runtimes)
+    assert expected == result
 
 
 @pytest.mark.db

lib/spack/spack/test/cmd/deprecate.py

@@ -17,16 +17,16 @@
 
 
 def test_deprecate(mock_packages, mock_archive, mock_fetch, install_mockery):
-    install("libelf@0.8.13")
-    install("libelf@0.8.10")
+    install("--fake", "libelf@0.8.13")
+    install("--fake", "libelf@0.8.10")
 
-    all_installed = spack.store.STORE.db.query()
+    all_installed = spack.store.STORE.db.query("libelf")
     assert len(all_installed) == 2
 
     deprecate("-y", "libelf@0.8.10", "libelf@0.8.13")
 
-    non_deprecated = spack.store.STORE.db.query()
-    all_available = spack.store.STORE.db.query(installed=InstallRecordStatus.ANY)
+    non_deprecated = spack.store.STORE.db.query("libelf")
+    all_available = spack.store.STORE.db.query("libelf", installed=InstallRecordStatus.ANY)
     assert all_available == all_installed
     assert non_deprecated == spack.store.STORE.db.query("libelf@0.8.13")
 
@@ -39,24 +39,24 @@ def test_deprecate_fails_no_such_package(mock_packages, mock_archive, mock_fetch
     output = deprecate("-y", "libelf@0.8.10", "libelf@0.8.13", fail_on_error=False)
     assert "Spec 'libelf@0.8.10' matches no installed packages" in output
 
-    install("libelf@0.8.10")
+    install("--fake", "libelf@0.8.10")
 
     output = deprecate("-y", "libelf@0.8.10", "libelf@0.8.13", fail_on_error=False)
     assert "Spec 'libelf@0.8.13' matches no installed packages" in output
 
 
-def test_deprecate_install(mock_packages, mock_archive, mock_fetch, install_mockery):
-    """Tests that the ```-i`` option allows us to deprecate in favor of a spec
-    that is not yet installed."""
-    install("libelf@0.8.10")
-
-    to_deprecate = spack.store.STORE.db.query()
+def test_deprecate_install(mock_packages, mock_archive, mock_fetch, install_mockery, monkeypatch):
+    """Tests that the -i option allows us to deprecate in favor of a spec
+    that is not yet installed.
+    """
+    install("--fake", "libelf@0.8.10")
+    to_deprecate = spack.store.STORE.db.query("libelf")
     assert len(to_deprecate) == 1
 
     deprecate("-y", "-i", "libelf@0.8.10", "libelf@0.8.13")
 
-    non_deprecated = spack.store.STORE.db.query()
-    deprecated = spack.store.STORE.db.query(installed=InstallRecordStatus.DEPRECATED)
+    non_deprecated = spack.store.STORE.db.query("libelf")
+    deprecated = spack.store.STORE.db.query("libelf", installed=InstallRecordStatus.DEPRECATED)
     assert deprecated == to_deprecate
     assert len(non_deprecated) == 1
     assert non_deprecated[0].satisfies("libelf@0.8.13")
@@ -64,8 +64,8 @@ def test_deprecate_install(mock_packages, mock_archive, mock_fetch, install_mock
 
 def test_deprecate_deps(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Test that the deprecate command deprecates all dependencies properly."""
-    install("libdwarf@20130729 ^libelf@0.8.13")
-    install("libdwarf@20130207 ^libelf@0.8.10")
+    install("--fake", "libdwarf@20130729 ^libelf@0.8.13")
+    install("--fake", "libdwarf@20130207 ^libelf@0.8.10")
 
     new_spec = spack.concretize.concretize_one("libdwarf@20130729^libelf@0.8.13")
     old_spec = spack.concretize.concretize_one("libdwarf@20130207^libelf@0.8.10")
@@ -81,14 +81,14 @@ def test_deprecate_deps(mock_packages, mock_archive, mock_fetch, install_mockery
     assert all_available == all_installed
     assert sorted(all_available) == sorted(deprecated + non_deprecated)
 
-    assert sorted(non_deprecated) == sorted(list(new_spec.traverse()))
-    assert sorted(deprecated) == sorted(list(old_spec.traverse()))
+    assert sorted(non_deprecated) == sorted(new_spec.traverse())
+    assert sorted(deprecated) == sorted([old_spec, old_spec["libelf"]])
 
 
 def test_uninstall_deprecated(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Tests that we can still uninstall deprecated packages."""
-    install("libelf@0.8.13")
-    install("libelf@0.8.10")
+    install("--fake", "libelf@0.8.13")
+    install("--fake", "libelf@0.8.10")
 
     deprecate("-y", "libelf@0.8.10", "libelf@0.8.13")
 
@@ -104,9 +104,9 @@ def test_uninstall_deprecated(mock_packages, mock_archive, mock_fetch, install_m
 
 def test_deprecate_already_deprecated(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Tests that we can re-deprecate a spec to change its deprecator."""
-    install("libelf@0.8.13")
-    install("libelf@0.8.12")
-    install("libelf@0.8.10")
+    install("--fake", "libelf@0.8.13")
+    install("--fake", "libelf@0.8.12")
+    install("--fake", "libelf@0.8.10")
 
     deprecated_spec = spack.concretize.concretize_one("libelf@0.8.10")
 
@@ -117,8 +117,8 @@ def test_deprecate_already_deprecated(mock_packages, mock_archive, mock_fetch, i
 
     deprecate("-y", "libelf@0.8.10", "libelf@0.8.13")
 
-    non_deprecated = spack.store.STORE.db.query()
-    all_available = spack.store.STORE.db.query(installed=InstallRecordStatus.ANY)
+    non_deprecated = spack.store.STORE.db.query("libelf")
+    all_available = spack.store.STORE.db.query("libelf", installed=InstallRecordStatus.ANY)
     assert len(non_deprecated) == 2
     assert len(all_available) == 3
 
@@ -129,9 +129,9 @@ def test_deprecate_already_deprecated(mock_packages, mock_archive, mock_fetch, i
 def test_deprecate_deprecator(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Tests that when a deprecator spec is deprecated, its deprecatee specs
     are updated to point to the new deprecator."""
-    install("libelf@0.8.13")
-    install("libelf@0.8.12")
-    install("libelf@0.8.10")
+    install("--fake", "libelf@0.8.13")
+    install("--fake", "libelf@0.8.12")
+    install("--fake", "libelf@0.8.10")
 
     first_deprecated_spec = spack.concretize.concretize_one("libelf@0.8.10")
     second_deprecated_spec = spack.concretize.concretize_one("libelf@0.8.12")
@@ -144,8 +144,8 @@ def test_deprecate_deprecator(mock_packages, mock_archive, mock_fetch, install_m
 
     deprecate("-y", "libelf@0.8.12", "libelf@0.8.13")
 
-    non_deprecated = spack.store.STORE.db.query()
-    all_available = spack.store.STORE.db.query(installed=InstallRecordStatus.ANY)
+    non_deprecated = spack.store.STORE.db.query("libelf")
+    all_available = spack.store.STORE.db.query("libelf", installed=InstallRecordStatus.ANY)
     assert len(non_deprecated) == 1
     assert len(all_available) == 3
 
@@ -158,8 +158,8 @@ def test_deprecate_deprecator(mock_packages, mock_archive, mock_fetch, install_m
 def test_concretize_deprecated(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Tests that the concretizer throws an error if we concretize to a
     deprecated spec"""
-    install("libelf@0.8.13")
-    install("libelf@0.8.10")
+    install("--fake", "libelf@0.8.13")
+    install("--fake", "libelf@0.8.10")
 
     deprecate("-y", "libelf@0.8.10", "libelf@0.8.13")
 

lib/spack/spack/test/cmd/dev_build.py

@@ -127,16 +127,15 @@ def test_dev_build_before_until(tmpdir, install_mockery):
         assert not_installed in out
 
 
-def print_spack_cc(*args):
-    # Eat arguments and print environment variable to test
-    print(os.environ.get("CC", ""))
+def _print_spack_short_spec(*args):
+    print(f"SPACK_SHORT_SPEC={os.environ['SPACK_SHORT_SPEC']}")
 
 
 def test_dev_build_drop_in(tmpdir, mock_packages, monkeypatch, install_mockery, working_env):
-    monkeypatch.setattr(os, "execvp", print_spack_cc)
+    monkeypatch.setattr(os, "execvp", _print_spack_short_spec)
     with tmpdir.as_cwd():
         output = dev_build("-b", "edit", "--drop-in", "sh", "dev-build-test-install@0.0.0")
-        assert os.path.join("lib", "spack", "env") in output
+        assert "SPACK_SHORT_SPEC=dev-build-test-install@0.0.0" in output
 
 
 def test_dev_build_fails_already_installed(tmpdir, install_mockery):

lib/spack/spack/test/cmd/diff.py

@@ -194,7 +194,7 @@ def test_diff_cmd(install_mockery, mock_fetch, mock_archive, mock_packages):
 
 def test_load_first(install_mockery, mock_fetch, mock_archive, mock_packages):
     """Test with and without the --first option"""
-    install_cmd("mpileaks")
+    install_cmd("--fake", "mpileaks")
 
     # Only one version of mpileaks will work
     diff_cmd("mpileaks", "mpileaks")

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"
@@ -1698,7 +1750,10 @@ def check_stage(spec):
         spec = spack.concretize.concretize_one(spec)
         for dep in spec.traverse():
             stage_name = f"{stage_prefix}{dep.name}-{dep.version}-{dep.dag_hash()}"
-            assert os.path.isdir(os.path.join(root, stage_name))
+            if dep.external:
+                assert not os.path.exists(os.path.join(root, stage_name))
+            else:
+                assert os.path.isdir(os.path.join(root, stage_name))
 
     check_stage("mpileaks")
     check_stage("zmpi")
@@ -3023,11 +3078,10 @@ def test_stack_view_activate_from_default(
         assert "FOOBAR=mpileaks" in shell
 
 
-def test_envvar_set_in_activate(tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery):
-    filename = str(tmpdir.join("spack.yaml"))
-    with open(filename, "w", encoding="utf-8") as f:
-        f.write(
-            """\
+def test_envvar_set_in_activate(tmp_path, mock_packages, install_mockery):
+    spack_yaml = tmp_path / "spack.yaml"
+    spack_yaml.write_text(
+        """
 spack:
   specs:
     - cmake%gcc
@@ -3035,21 +3089,21 @@ def test_envvar_set_in_activate(tmpdir, mock_fetch, mock_packages, mock_archive,
     set:
       ENVAR_SET_IN_ENV_LOAD: "True"
 """
-        )
-    with tmpdir.as_cwd():
-        env("create", "test", "./spack.yaml")
-        with ev.read("test"):
-            install()
+    )
 
-        test_env = ev.read("test")
-        output = env("activate", "--sh", "test")
+    env("create", "test", str(spack_yaml))
+    with ev.read("test"):
+        install("--fake")
 
-        assert "ENVAR_SET_IN_ENV_LOAD=True" in output
+    test_env = ev.read("test")
+    output = env("activate", "--sh", "test")
 
-        with test_env:
-            with spack.util.environment.set_env(ENVAR_SET_IN_ENV_LOAD="True"):
-                output = env("deactivate", "--sh")
-                assert "unset ENVAR_SET_IN_ENV_LOAD" in output
+    assert "ENVAR_SET_IN_ENV_LOAD=True" in output
+
+    with test_env:
+        with spack.util.environment.set_env(ENVAR_SET_IN_ENV_LOAD="True"):
+            output = env("deactivate", "--sh")
+            assert "unset ENVAR_SET_IN_ENV_LOAD" in output
 
 
 def test_stack_view_no_activate_without_default(

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

@@ -233,21 +233,27 @@ def test_display_json_deps(database, capsys):
 @pytest.mark.db
 def test_find_format(database, config):
     output = find("--format", "{name}-{^mpi.name}", "mpileaks")
-    assert set(output.strip().split("\n")) == set(
-        ["mpileaks-zmpi", "mpileaks-mpich", "mpileaks-mpich2"]
-    )
+    assert set(output.strip().split("\n")) == {
+        "mpileaks-zmpi",
+        "mpileaks-mpich",
+        "mpileaks-mpich2",
+    }
 
     output = find("--format", "{name}-{version}-{compiler.name}-{^mpi.name}", "mpileaks")
     assert "installed package" not in output
-    assert set(output.strip().split("\n")) == set(
-        ["mpileaks-2.3-gcc-zmpi", "mpileaks-2.3-gcc-mpich", "mpileaks-2.3-gcc-mpich2"]
-    )
+    assert set(output.strip().split("\n")) == {
+        "mpileaks-2.3-gcc-zmpi",
+        "mpileaks-2.3-gcc-mpich",
+        "mpileaks-2.3-gcc-mpich2",
+    }
 
     output = find("--format", "{name}-{^mpi.name}-{hash:7}", "mpileaks")
     elements = output.strip().split("\n")
-    assert set(e[:-7] for e in elements) == set(
-        ["mpileaks-zmpi-", "mpileaks-mpich-", "mpileaks-mpich2-"]
-    )
+    assert set(e[:-7] for e in elements) == {
+        "mpileaks-zmpi-",
+        "mpileaks-mpich-",
+        "mpileaks-mpich2-",
+    }
 
     # hashes are in base32
     for e in elements:
@@ -348,7 +354,7 @@ def test_find_prefix_in_env(
     """Test `find` formats requiring concrete specs work in environments."""
     env("create", "test")
     with ev.read("test"):
-        install("--add", "mpileaks")
+        install("--fake", "--add", "mpileaks")
         find("-p")
         find("-l")
         find("-L")

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