patch tau@2.34 +rocm rocprofiler support

The `umea.se` mirror seems to have gone down (or at least is forbidden for now).

Revert the checksum changes in #47825; points at the official GNOME mirror
instead of the prior two places we were getting `gdk-pixbuf`.

Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>

.github/workflows/ci.yaml

@@ -9,6 +9,7 @@ on:
     branches:
       - develop
       - releases/**
+  merge_group:
 
 concurrency:
   group: ci-${{github.ref}}-${{github.event.pull_request.number || github.run_number}}
@@ -25,13 +26,17 @@ jobs:
       packages: ${{ steps.filter.outputs.packages }}
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-        if: ${{ github.event_name == 'push' }}
+        if: ${{ github.event_name == 'push' || github.event_name == 'merge_group' }}
         with:
           fetch-depth: 0
             # For pull requests it's not necessary to checkout the code
       - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36
         id: filter
         with:
+          # For merge group events, compare against the target branch (main)
+          base: ${{ github.event_name == 'merge_group' && github.event.merge_group.base_ref || '' }}
+          # For merge group events, use the merge group head ref
+          ref: ${{ github.event_name == 'merge_group' && github.event.merge_group.head_sha || github.ref }}
           # See https://github.com/dorny/paths-filter/issues/56 for the syntax used below
           # Don't run if we only modified packages in the
           # built-in repository or documentation
@@ -76,10 +81,11 @@ jobs:
 
   prechecks:
     needs: [ changes ]
-    uses: ./.github/workflows/valid-style.yml
+    uses: ./.github/workflows/prechecks.yml
     secrets: inherit
     with:
       with_coverage: ${{ needs.changes.outputs.core }}
+      with_packages: ${{ needs.changes.outputs.packages }}
 
   import-check:
     needs: [ changes ]
@@ -93,7 +99,7 @@ jobs:
     - name: Success
       run: |
         if [ "${{ needs.prechecks.result }}" == "failure" ] || [ "${{ needs.prechecks.result }}" == "canceled" ]; then
-          echo "Unit tests failed." 
+          echo "Unit tests failed."
           exit 1
         else
           exit 0
@@ -101,6 +107,7 @@ jobs:
 
   coverage:
     needs: [ unit-tests, prechecks ]
+    if: ${{ needs.changes.outputs.core }}
     uses: ./.github/workflows/coverage.yml
     secrets: inherit
 
@@ -113,10 +120,10 @@ jobs:
     - name: Status summary
       run: |
         if [ "${{ needs.unit-tests.result }}" == "failure" ] || [ "${{ needs.unit-tests.result }}" == "canceled" ]; then
-          echo "Unit tests failed." 
+          echo "Unit tests failed."
           exit 1
         elif [ "${{ needs.bootstrap.result }}" == "failure" ] || [ "${{ needs.bootstrap.result }}" == "canceled" ]; then
-          echo "Bootstrap tests failed." 
+          echo "Bootstrap tests failed."
           exit 1
         else
           exit 0

.github/workflows/import-check.yaml

@@ -39,7 +39,7 @@ jobs:
       uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
       with:
         repository: haampie/circular-import-fighter
-        ref: e38bcd0aa46368e30648b61b7f0d8c1ca68aadff
+        ref: 4cdb0bf15f04ab6b49041d5ef1bfd9644cce7f33
         path: circular-import-fighter
     - name: Install dependencies
       working-directory: circular-import-fighter

.github/workflows/prechecks.yml

@@ -1,4 +1,4 @@
-name: style
+name: prechecks
 
 on:
   workflow_call:
@@ -6,6 +6,9 @@ on:
       with_coverage:
         required: true
         type: string
+      with_packages:
+        required: true
+        type: string
 
 concurrency:
   group: style-${{github.ref}}-${{github.event.pull_request.number || github.run_number}}
@@ -30,6 +33,7 @@ jobs:
       run: vermin --backport importlib --backport argparse --violations --backport typing -t=3.6- -vvv lib/spack/spack/ lib/spack/llnl/ bin/
     - name: vermin (Repositories)
       run: vermin --backport importlib --backport argparse --violations --backport typing -t=3.6- -vvv var/spack/repos
+
   # Run style checks on the files that have been changed
   style:
     runs-on: ubuntu-latest
@@ -53,12 +57,25 @@ jobs:
     - name: Run style tests
       run: |
           share/spack/qa/run-style-tests
+
   audit:
     uses: ./.github/workflows/audit.yaml
     secrets: inherit
     with:
       with_coverage: ${{ inputs.with_coverage }}
       python_version: '3.13'
+
+  verify-checksums:
+    if: ${{ inputs.with_packages == 'true' }}
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29
+      with:
+        fetch-depth: 2
+    - name: Verify Added Checksums
+      run: |
+        bin/spack ci verify-versions HEAD^1 HEAD
+
   # Check that spack can bootstrap the development environment on Python 3.6 - RHEL8
   bootstrap-dev-rhel8:
     runs-on: ubuntu-latest

.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
-types-six==1.17.0.20241205
+flake8==7.1.2
+isort==6.0.1
+mypy==1.15.0
+types-six==1.17.0.20250304
 vermin==1.6.0

.gitignore

@@ -201,7 +201,6 @@ tramp
 
 # Org-mode
 .org-id-locations
-*_archive
 
 # flymake-mode
 *_flymake.*

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

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/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/config_yaml.rst

@@ -125,6 +125,8 @@ are stored in ``$spack/var/spack/cache``.  These are stored indefinitely
 by default. Can be purged with :ref:`spack clean --downloads
 <cmd-spack-clean>`.
 
+.. _Misc Cache:
+
 --------------------
 ``misc_cache``
 --------------------
@@ -334,3 +336,52 @@ create a new alias called ``inst`` that will always call ``install -v``:
 
    aliases:
      inst: install -v
+
+-------------------------------
+``concretization_cache:enable``
+-------------------------------
+
+When set to ``true``, Spack will utilize a cache of solver outputs from
+successful concretization runs. When enabled, Spack will check the concretization
+cache prior to running the solver. If a previous request to solve a given
+problem is present in the cache, Spack will load the concrete specs and other
+solver data from the cache rather than running the solver. Specs not previously
+concretized will be added to the cache on a successful solve. The cache additionally
+holds solver statistics, so commands like ``spack solve`` will still return information
+about the run that produced a given solver result.
+
+This cache is a subcache of the :ref:`Misc Cache` and as such will be cleaned when the Misc
+Cache is cleaned.
+
+When ``false`` or ommitted, all concretization requests will be performed from scatch
+
+----------------------------
+``concretization_cache:url``
+----------------------------
+
+Path to the location where Spack will root the concretization cache. Currently this only supports
+paths on the local filesystem.
+
+Default location is under the :ref:`Misc Cache` at: ``$misc_cache/concretization``
+
+------------------------------------
+``concretization_cache:entry_limit``
+------------------------------------
+
+Sets a limit on the number of concretization results that Spack will cache. The limit is evaluated
+after each concretization run; if Spack has stored more results than the limit allows, the
+oldest concretization results are pruned until 10% of the limit has been removed.
+
+Setting this value to 0 disables the automatic pruning. It is expected users will be
+responsible for maintaining this cache.
+
+-----------------------------------
+``concretization_cache:size_limit``
+-----------------------------------
+
+Sets a limit on the size of the concretization cache in bytes. The limit is evaluated
+after each concretization run; if Spack has stored more results than the limit allows, the
+oldest concretization results are pruned until 10% of the limit has been removed.
+
+Setting this value to 0 disables the automatic pruning. It is expected users will be
+responsible for maintaining this cache.

lib/spack/docs/configuration.rst

@@ -14,6 +14,7 @@ case you want to skip directly to specific docs:
 * :ref:`compilers.yaml <compiler-config>`
 * :ref:`concretizer.yaml <concretizer-options>`
 * :ref:`config.yaml <config-yaml>`
+* :ref:`include.yaml <include-yaml>`
 * :ref:`mirrors.yaml <mirrors>`
 * :ref:`modules.yaml <modules>`
 * :ref:`packages.yaml <packages-config>`

lib/spack/docs/environments.rst

@@ -457,6 +457,13 @@ developed package in the environment are concretized to match the
 version (and other constraints) passed as the spec argument to the
 ``spack develop`` command.
 
+When working deep in the graph it is often desirable to have multiple specs marked
+as ``develop`` so you don't have to restage and/or do full rebuilds each time you
+call ``spack install``.  The ``--recursive`` flag can be used in these scenarios
+to ensure that all the dependents of the initial spec you provide are also marked
+as develop specs.  The ``--recursive`` flag requires a pre-concretized environment
+so the graph can be traversed from the supplied spec all the way to the root specs.
+
 For packages with ``git`` attributes, git branches, tags, and commits can
 also be used as valid concrete versions (see :ref:`version-specifier`).
 This means that for a package ``foo``, ``spack develop foo@git.main`` will clone
@@ -670,24 +677,45 @@ This configuration sets the default compiler for all packages to
 Included configurations
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-Spack environments allow an ``include`` heading in their yaml
-schema. This heading pulls in external configuration files and applies
-them to the environment.
+Spack environments allow an ``include`` heading in their yaml schema.
+This heading pulls in external configuration files and applies them to
+the environment.
 
 .. code-block:: yaml
 
    spack:
      include:
-     - relative/path/to/config.yaml
+     - environment/relative/path/to/config.yaml
      - https://github.com/path/to/raw/config/compilers.yaml
      - /absolute/path/to/packages.yaml
+     - path: /path/to/$os/$target/environment
+       optional: true
+     - path: /path/to/os-specific/config-dir
+       when: os == "ventura"
+
+Included configuration files are required *unless* they are explicitly optional
+or the entry's condition evaluates to ``false``. Optional includes are specified
+with the ``optional`` clause and conditional with the ``when`` clause. (See
+:ref:`include-yaml` for more information on optional and conditional entries.)
+
+Files are listed using paths to individual files or directories containing them.
+Path entries may be absolute or relative to the environment or specified as 
+URLs. URLs to individual files need link to the **raw** form of the file's 
+contents (e.g., `GitHub
+<https://docs.github.com/en/repositories/working-with-files/using-files/viewing-and-understanding-files#viewing-or-copying-the-raw-file-content>`_ 
+or `GitLab
+<https://docs.gitlab.com/ee/api/repository_files.html#get-raw-file-from-repository>`_).
+Only the ``file``, ``ftp``, ``http`` and ``https`` protocols (or schemes) are
+supported. Spack-specific, environment and user path variables can be used.
+(See :ref:`config-file-variables` for more information.)
+
+.. warning::
+
+   Recursive includes are not currently processed in a breadth-first manner
+   so the value of a configuration option that is altered by multiple included
+   files may not be what you expect. This will be addressed in a future
+   update.
 
-Environments can include files or URLs. File paths can be relative or
-absolute. URLs include the path to the text for individual files or
-can be the path to a directory containing configuration files.
-Spack supports ``file``, ``http``, ``https`` and ``ftp`` protocols (or
-schemes). Spack-specific, environment and user path variables may be
-used in these paths. See :ref:`config-file-variables` for more information.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^
 Configuration precedence

lib/spack/docs/frequently_asked_questions.rst

@@ -30,7 +30,7 @@ than always choosing the latest versions or default variants.
 
 .. note::
 
-    As a rule of thumb: requirements + constraints > reuse > preferences > defaults.
+    As a rule of thumb: requirements + constraints > strong preferences > reuse > preferences > defaults.
 
 The following set of criteria (from lowest to highest precedence) explain
 common cases where concretization output may seem surprising at first.
@@ -56,7 +56,19 @@ common cases where concretization output may seem surprising at first.
       concretizer:
         reuse: dependencies  # other options are 'true' and 'false'
 
-3. :ref:`Package requirements <package-requirements>` configured in ``packages.yaml``,
+3. :ref:`Strong preferences <package-strong-preferences>` configured in ``packages.yaml``
+   are higher priority than reuse, and can be used to strongly prefer a specific version
+   or variant, without erroring out if it's not possible. Strong preferences are specified
+   as follows:
+
+   .. code-block:: yaml
+
+      packages:
+        foo:
+          prefer:
+          - "@1.1: ~mpi"
+
+4. :ref:`Package requirements <package-requirements>` configured in ``packages.yaml``,
    and constraints from the command line as well as ``package.py`` files override all
    of the above. Requirements are specified as follows:
 
@@ -66,6 +78,8 @@ common cases where concretization output may seem surprising at first.
         foo:
           require:
           - "@1.2: +mpi"
+          conflicts:
+          - "@1.4"
 
 Requirements and constraints restrict the set of possible solutions, while reuse
 behavior and preferences influence what an optimal solution looks like.

lib/spack/docs/include_yaml.rst

@@ -0,0 +1,51 @@
+.. Copyright Spack Project Developers. See COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _include-yaml:
+
+===============================
+Include Settings (include.yaml)
+===============================
+
+Spack allows you to include configuration files through ``include.yaml``.
+Using the ``include:`` heading results in pulling in external configuration
+information to be used by any Spack command.
+
+Included configuration files are required *unless* they are explicitly optional
+or the entry's condition evaluates to ``false``. Optional includes are specified
+with the ``optional`` clause and conditional with the ``when`` clause. For
+example,
+
+.. code-block:: yaml
+
+   include:
+   - /path/to/a/required/config.yaml
+   - path: /path/to/$os/$target/config
+     optional: true
+   - path: /path/to/os-specific/config-dir
+     when: os == "ventura"
+
+shows all three. The first entry, ``/path/to/a/required/config.yaml``,
+indicates that included ``config.yaml`` file is required (so must exist).
+Use of ``optional: true`` for ``/path/to/$os/$target/config`` means
+the path is only included if it exists. The condition ``os == "ventura"``
+in the ``when`` clause for ``/path/to/os-specific/config-dir`` means the
+path is only included when the operating system (``os``) is ``ventura``.
+
+The same conditions and variables in `Spec List References 
+<https://spack.readthedocs.io/en/latest/environments.html#spec-list-references>`_
+can be used for conditional activation in the ``when`` clauses.
+
+Included files can be specified by path or by their parent directory.
+Paths may be absolute, relative (to the configuration file including the path), 
+or specified as URLs. Only the ``file``, ``ftp``, ``http`` and ``https`` protocols (or
+schemes) are supported. Spack-specific, environment and user path variables
+can be used. (See :ref:`config-file-variables` for more information.)
+
+.. warning::
+
+   Recursive includes are not currently processed in a breadth-first manner
+   so the value of a configuration option that is altered by multiple included
+   files may not be what you expect. This will be addressed in a future
+   update.

lib/spack/docs/index.rst

@@ -71,6 +71,7 @@ or refer to the full manual below.
 
    configuration
    config_yaml
+   include_yaml
    packages_yaml
    build_settings
    environments

lib/spack/docs/packages_yaml.rst

@@ -486,6 +486,8 @@ present. For instance with a configuration like:
 
 you will use ``mvapich2~cuda %gcc`` as an ``mpi`` provider.
 
+.. _package-strong-preferences:
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Conflicts and strong preferences
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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

@@ -1,13 +1,13 @@
-sphinx==8.1.3
+sphinx==8.2.3
 sphinxcontrib-programoutput==0.18
 sphinx_design==0.6.1
 sphinx-rtd-theme==3.0.2
-python-levenshtein==0.26.1
+python-levenshtein==0.27.1
 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
+pytest==8.3.5
+isort==6.0.1
+black==25.1.0
+flake8==7.1.2
 mypy==1.11.1

lib/spack/llnl/util/filesystem.py

@@ -7,6 +7,7 @@
 import fnmatch
 import glob
 import hashlib
+import io
 import itertools
 import numbers
 import os
@@ -20,6 +21,7 @@
 from contextlib import contextmanager
 from itertools import accumulate
 from typing import (
+    IO,
     Callable,
     Deque,
     Dict,
@@ -2454,26 +2456,69 @@ class WindowsSimulatedRPath:
     and vis versa.
     """
 
-    def __init__(self, package, link_install_prefix=True):
+    def __init__(
+        self,
+        package,
+        base_modification_prefix: Optional[Union[str, pathlib.Path]] = None,
+        link_install_prefix: bool = True,
+    ):
         """
         Args:
             package (spack.package_base.PackageBase): Package requiring links
+            base_modification_prefix (str|pathlib.Path): Path representation indicating
+                the root directory in which to establish the simulated rpath, ie where the
+                symlinks that comprise the "rpath" behavior will be installed.
+
+                Note: This is a mutually exclusive option with `link_install_prefix` using
+                both is an error.
+
+                Default: None
             link_install_prefix (bool): Link against package's own install or stage root.
                 Packages that run their own executables during build and require rpaths to
-                the build directory during build time require this option. Default: install
+                the build directory during build time require this option.
+
+                Default: install
                 root
+
+                Note: This is a mutually exclusive option with `base_modification_prefix`, using
+                both is an error.
         """
         self.pkg = package
-        self._addl_rpaths = set()
+        self._addl_rpaths: set[str] = set()
+        if link_install_prefix and base_modification_prefix:
+            raise RuntimeError(
+                "Invalid combination of arguments given to WindowsSimulated RPath.\n"
+                "Select either `link_install_prefix` to create an install prefix rpath"
+                " or specify a `base_modification_prefix` for any other link type. "
+                "Specifying both arguments is invalid."
+            )
+        if not (link_install_prefix or base_modification_prefix):
+            raise RuntimeError(
+                "Insufficient arguments given to WindowsSimulatedRpath.\n"
+                "WindowsSimulatedRPath requires one of link_install_prefix"
+                " or base_modification_prefix to be specified."
+                " Neither was provided."
+            )
+
         self.link_install_prefix = link_install_prefix
-        self._additional_library_dependents = set()
+        if base_modification_prefix:
+            self.base_modification_prefix = pathlib.Path(base_modification_prefix)
+        else:
+            self.base_modification_prefix = pathlib.Path(self.pkg.prefix)
+        self._additional_library_dependents: set[pathlib.Path] = set()
+        if not self.link_install_prefix:
+            tty.debug(f"Generating rpath for non install context: {base_modification_prefix}")
 
     @property
     def library_dependents(self):
         """
         Set of directories where package binaries/libraries are located.
         """
-        return set([pathlib.Path(self.pkg.prefix.bin)]) | self._additional_library_dependents
+        base_pths = set()
+        if self.link_install_prefix:
+            base_pths.add(pathlib.Path(self.pkg.prefix.bin))
+        base_pths |= self._additional_library_dependents
+        return base_pths
 
     def add_library_dependent(self, *dest):
         """
@@ -2489,6 +2534,12 @@ def add_library_dependent(self, *dest):
                 new_pth = pathlib.Path(pth).parent
             else:
                 new_pth = pathlib.Path(pth)
+            path_is_in_prefix = new_pth.is_relative_to(self.base_modification_prefix)
+            if not path_is_in_prefix:
+                raise RuntimeError(
+                    f"Attempting to generate rpath symlink out of rpath context:\
+{str(self.base_modification_prefix)}"
+                )
             self._additional_library_dependents.add(new_pth)
 
     @property
@@ -2577,6 +2628,33 @@ def establish_link(self):
                 self._link(library, lib_dir)
 
 
+def make_package_test_rpath(pkg, test_dir: Union[str, pathlib.Path]):
+    """Establishes a temp Windows simulated rpath for the pkg in the testing directory
+    so an executable can test the libraries/executables with proper access
+    to dependent dlls
+
+    Note: this is a no-op on all other platforms besides Windows
+
+    Args:
+        pkg (spack.package_base.PackageBase): the package for which the rpath should be computed
+        test_dir: the testing directory in which we should construct an rpath
+    """
+    # link_install_prefix as false ensures we're not linking into the install prefix
+    mini_rpath = WindowsSimulatedRPath(pkg, link_install_prefix=False)
+    # add the testing directory as a location to install rpath symlinks
+    mini_rpath.add_library_dependent(test_dir)
+
+    # check for whether build_directory is available, if not
+    # assume the stage root is the build dir
+    build_dir_attr = getattr(pkg, "build_directory", None)
+    build_directory = build_dir_attr if build_dir_attr else pkg.stage.path
+    # add the build dir & build dir bin
+    mini_rpath.add_rpath(os.path.join(build_directory, "bin"))
+    mini_rpath.add_rpath(os.path.join(build_directory))
+    # construct rpath
+    mini_rpath.establish_link()
+
+
 @system_path_filter
 @memoized
 def can_access_dir(path):
@@ -2805,6 +2883,20 @@ def keep_modification_time(*filenames):
             os.utime(f, (os.path.getatime(f), mtime))
 
 
+@contextmanager
+def temporary_file_position(stream):
+    orig_pos = stream.tell()
+    yield
+    stream.seek(orig_pos)
+
+
+@contextmanager
+def current_file_position(stream: IO[str], loc: int, relative_to=io.SEEK_CUR):
+    with temporary_file_position(stream):
+        stream.seek(loc, relative_to)
+        yield
+
+
 @contextmanager
 def temporary_dir(
     suffix: Optional[str] = None, prefix: Optional[str] = None, dir: Optional[str] = None

lib/spack/llnl/util/lang.py

@@ -11,10 +11,11 @@
 import re
 import sys
 import traceback
+import types
 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"^\.#|~$"
@@ -707,14 +708,24 @@ def __init__(self, wrapped_object):
 
 
 class Singleton:
-    """Simple wrapper for lazily initialized singleton objects."""
+    """Wrapper for lazily initialized singleton objects."""
 
-    def __init__(self, factory):
+    def __init__(self, factory: Callable[[], object]):
         """Create a new singleton to be inited with the factory function.
 
+        Most factories will simply create the object to be initialized and
+        return it.
+
+        In some cases, e.g. when bootstrapping some global state, the singleton
+        may need to be initialized incrementally. If the factory returns a generator
+        instead of a regular object, the singleton will assign each result yielded by
+        the generator to the singleton instance. This allows methods called by
+        the factory in later stages to refer back to the singleton.
+
         Args:
-            factory (function): function taking no arguments that
-                creates the singleton instance.
+            factory (function): function taking no arguments that creates the
+                singleton instance.
+
         """
         self.factory = factory
         self._instance = None
@@ -722,7 +733,16 @@ def __init__(self, factory):
     @property
     def instance(self):
         if self._instance is None:
-            self._instance = self.factory()
+            instance = self.factory()
+
+            if isinstance(instance, types.GeneratorType):
+                # if it's a generator, assign every value
+                for value in instance:
+                    self._instance = value
+            else:
+                # if not, just assign the result like a normal singleton
+                self._instance = instance
+
         return self._instance
 
     def __getattr__(self, name):
@@ -1080,3 +1100,88 @@ 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)

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.

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

lib/spack/spack/__init__.py

@@ -13,6 +13,18 @@
 __version__ = "1.0.0.dev0"
 spack_version = __version__
 
+#: The current Package API version implemented by this version of Spack. The Package API defines
+#: the Python interface for packages as well as the layout of package repositories. The minor
+#: version is incremented when the package API is extended in a backwards-compatible way. The major
+#: version is incremented upon breaking changes. This version is changed independently from the
+#: Spack version.
+package_api_version = (1, 0)
+
+#: The minimum Package API version that this version of Spack is compatible with. This should
+#: always be a tuple of the form ``(major, 0)``, since compatibility with vX.Y implies
+#: compatibility with vX.0.
+min_package_api_version = (1, 0)
+
 
 def __try_int(v):
     try:
@@ -79,4 +91,6 @@ def get_short_version() -> str:
     "get_version",
     "get_spack_commit",
     "get_short_version",
+    "package_api_version",
+    "min_package_api_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

@@ -881,21 +881,6 @@ def get_rpath_deps(pkg: spack.package_base.PackageBase) -> List[spack.spec.Spec]
     return _get_rpath_deps_from_spec(pkg.spec, pkg.transitive_rpaths)
 
 
-def load_external_modules(pkg):
-    """Traverse a package's spec DAG and load any external modules.
-
-    Traverse a package's dependencies and load any external modules
-    associated with them.
-
-    Args:
-        pkg (spack.package_base.PackageBase): package to load deps for
-    """
-    for dep in list(pkg.spec.traverse()):
-        external_modules = dep.external_modules or []
-        for external_module in external_modules:
-            load_module(external_module)
-
-
 def setup_package(pkg, dirty, context: Context = Context.BUILD):
     """Execute all environment setup routines."""
     if context not in (Context.BUILD, Context.TEST):
@@ -946,7 +931,7 @@ def setup_package(pkg, dirty, context: Context = Context.BUILD):
         for mod in pkg.compiler.modules:
             load_module(mod)
 
-    load_external_modules(pkg)
+    load_external_modules(setup_context)
 
     # Make sure nothing's strange about the Spack environment.
     validate(env_mods, tty.warn)
@@ -1235,6 +1220,21 @@ def _make_runnable(self, dep: spack.spec.Spec, env: EnvironmentModifications):
                 env.prepend_path("PATH", bin_dir)
 
 
+def load_external_modules(context: SetupContext) -> None:
+    """Traverse a package's spec DAG and load any external modules.
+
+    Traverse a package's dependencies and load any external modules
+    associated with them.
+
+    Args:
+        context: A populated SetupContext object
+    """
+    for spec, _ in context.external:
+        external_modules = spec.external_modules or []
+        for external_module in external_modules:
+            load_module(external_module)
+
+
 def _setup_pkg_and_run(
     serialized_pkg: "spack.subprocess_context.PackageInstallContext",
     function: Callable,

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
 
@@ -277,17 +278,24 @@ def initconfig_hardware_entries(self):
             entries.append("# ROCm")
             entries.append("#------------------{0}\n".format("-" * 30))
 
-            # Explicitly setting HIP_ROOT_DIR may be a patch that is no longer necessary
-            entries.append(cmake_cache_path("HIP_ROOT_DIR", "{0}".format(spec["hip"].prefix)))
-            llvm_bin = spec["llvm-amdgpu"].prefix.bin
-            llvm_prefix = spec["llvm-amdgpu"].prefix
-            # Some ROCm systems seem to point to /<path>/rocm-<ver>/ and
-            # others point to /<path>/rocm-<ver>/llvm
-            if os.path.basename(os.path.normpath(llvm_prefix)) != "llvm":
-                llvm_bin = os.path.join(llvm_prefix, "llvm/bin/")
-            entries.append(
-                cmake_cache_filepath("CMAKE_HIP_COMPILER", os.path.join(llvm_bin, "clang++"))
-            )
+            if spec.satisfies("^blt@0.7:"):
+                rocm_root = os.path.dirname(spec["llvm-amdgpu"].prefix)
+                entries.append(cmake_cache_path("ROCM_PATH", rocm_root))
+            else:
+                # Explicitly setting HIP_ROOT_DIR may be a patch that is no longer necessary
+                entries.append(cmake_cache_path("HIP_ROOT_DIR", "{0}".format(spec["hip"].prefix)))
+                llvm_bin = spec["llvm-amdgpu"].prefix.bin
+                llvm_prefix = spec["llvm-amdgpu"].prefix
+                # Some ROCm systems seem to point to /<path>/rocm-<ver>/ and
+                # others point to /<path>/rocm-<ver>/llvm
+                if os.path.basename(os.path.normpath(llvm_prefix)) != "llvm":
+                    llvm_bin = os.path.join(llvm_prefix, "llvm/bin/")
+                entries.append(
+                    cmake_cache_filepath(
+                        "CMAKE_HIP_COMPILER", os.path.join(llvm_bin, "amdclang++")
+                    )
+                )
+
             archs = self.spec.variants["amdgpu_target"].value
             if archs[0] != "none":
                 arch_str = ";".join(archs)
@@ -371,6 +379,10 @@ 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/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

@@ -6,6 +6,7 @@
 import codecs
 import json
 import os
+import pathlib
 import re
 import shutil
 import stat
@@ -13,16 +14,16 @@
 import tempfile
 import zipfile
 from collections import namedtuple
-from typing import Callable, Dict, List, Set
+from typing import Callable, Dict, List, Set, Union
 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
 
 import spack
 import spack.binary_distribution as bindist
-import spack.builder
 import spack.concretize
 import spack.config as cfg
 import spack.environment as ev
@@ -32,6 +33,7 @@
 import spack.paths
 import spack.repo
 import spack.spec
+import spack.store
 import spack.util.git
 import spack.util.gpg as gpg_util
 import spack.util.spack_yaml as syaml
@@ -40,6 +42,7 @@
 from spack import traverse
 from spack.error import SpackError
 from spack.reporters.cdash import SPACK_CDASH_TIMEOUT
+from spack.version import GitVersion, StandardVersion
 
 from .common import (
     IS_WINDOWS,
@@ -78,11 +81,53 @@ def get_change_revisions():
     return None, None
 
 
+def get_added_versions(
+    checksums_version_dict: Dict[str, Union[StandardVersion, GitVersion]],
+    path: str,
+    from_ref: str = "HEAD~1",
+    to_ref: str = "HEAD",
+) -> List[Union[StandardVersion, GitVersion]]:
+    """Get a list of the versions added between `from_ref` and `to_ref`.
+    Args:
+       checksums_version_dict (Dict): all package versions keyed by known checksums.
+       path (str): path to the package.py
+       from_ref (str): oldest git ref, defaults to `HEAD~1`
+       to_ref (str): newer git ref, defaults to `HEAD`
+    Returns: list of versions added between refs
+    """
+    git_exe = spack.util.git.git(required=True)
+
+    # Gather git diff
+    diff_lines = git_exe("diff", from_ref, to_ref, "--", path, output=str).split("\n")
+
+    # Store added and removed versions
+    # Removed versions are tracked here to determine when versions are moved in a file
+    # and show up as both added and removed in a git diff.
+    added_checksums = set()
+    removed_checksums = set()
+
+    # Scrape diff for modified versions and prune added versions if they show up
+    # as also removed (which means they've actually just moved in the file and
+    # we shouldn't need to rechecksum them)
+    for checksum in checksums_version_dict.keys():
+        for line in diff_lines:
+            if checksum in line:
+                if line.startswith("+"):
+                    added_checksums.add(checksum)
+                if line.startswith("-"):
+                    removed_checksums.add(checksum)
+
+    return [checksums_version_dict[c] for c in added_checksums - removed_checksums]
+
+
 def get_stack_changed(env_path, rev1="HEAD^", rev2="HEAD"):
     """Given an environment manifest path and two revisions to compare, return
     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):
@@ -220,7 +265,7 @@ def rebuild_filter(s: spack.spec.Spec) -> RebuildDecision:
 
 def _format_pruning_message(spec: spack.spec.Spec, prune: bool, reasons: List[str]) -> str:
     reason_msg = ", ".join(reasons)
-    spec_fmt = "{name}{@version}{%compiler}{/hash:7}"
+    spec_fmt = "{name}{@version}{/hash:7}{%compiler}"
 
     if not prune:
         status = colorize("@*g{[x]}  ")
@@ -577,22 +622,25 @@ def copy_stage_logs_to_artifacts(job_spec: spack.spec.Spec, job_log_dir: str) ->
     tty.debug(f"job spec: {job_spec}")
 
     try:
-        pkg_cls = spack.repo.PATH.get_pkg_class(job_spec.name)
-        job_pkg = pkg_cls(job_spec)
-        tty.debug(f"job package: {job_pkg}")
-    except AssertionError:
-        msg = f"Cannot copy stage logs: job spec ({job_spec}) must be concrete"
-        tty.error(msg)
+        package_metadata_root = pathlib.Path(spack.store.STORE.layout.metadata_path(job_spec))
+    except spack.error.SpackError as e:
+        tty.error(f"Cannot copy logs: {str(e)}")
         return
 
-    stage_dir = job_pkg.stage.path
-    tty.debug(f"stage dir: {stage_dir}")
-    for file in [
-        job_pkg.log_path,
-        job_pkg.env_mods_path,
-        *spack.builder.create(job_pkg).archive_files,
-    ]:
-        copy_files_to_artifacts(file, job_log_dir)
+    # Get the package's archived files
+    archive_files = []
+    archive_root = package_metadata_root / "archived-files"
+    if archive_root.is_dir():
+        archive_files = [f for f in archive_root.rglob("*") if f.is_file()]
+    else:
+        msg = "Cannot copy package archived files: archived-files must be a directory"
+        tty.warn(msg)
+
+    build_log_zipped = package_metadata_root / "spack-build-out.txt.gz"
+    build_env_mods = package_metadata_root / "spack-build-env.txt"
+
+    for f in [build_log_zipped, build_env_mods, *archive_files]:
+        copy_files_to_artifacts(str(f), job_log_dir)
 
 
 def copy_test_logs_to_artifacts(test_stage, job_test_dir):
@@ -612,7 +660,7 @@ 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
 
@@ -620,6 +668,10 @@ 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}")
 
@@ -637,13 +689,25 @@ def download_and_extract_artifacts(url, work_dir):
         response = urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
         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
 
-    with zipfile.ZipFile(artifacts_zip_path) as zip_file:
-        zip_file.extractall(work_dir)
-
-    os.remove(artifacts_zip_path)
+    return artifact_root
 
 
 def get_spack_info():
@@ -757,7 +821,7 @@ 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:
@@ -771,8 +835,11 @@ 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:
@@ -834,6 +901,9 @@ 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)
 
@@ -894,17 +964,20 @@ 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:
@@ -979,6 +1052,8 @@ 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",
@@ -986,14 +1061,14 @@ 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/__init__.py

@@ -330,7 +330,7 @@ def ensure_single_spec_or_die(spec, matching_specs):
     if len(matching_specs) <= 1:
         return
 
-    format_string = "{name}{@version}{%compiler.name}{@compiler.version}{ arch=architecture}"
+    format_string = "{name}{@version}{ arch=architecture} {%compiler.name}{@compiler.version}"
     args = ["%s matches multiple packages." % spec, "Matching packages:"]
     args += [
         colorize("  @K{%s} " % s.dag_hash(7)) + s.cformat(format_string) for s in matching_specs
@@ -471,12 +471,11 @@ def get_arg(name, default=None):
         nfmt = "{fullname}" if namespaces else "{name}"
         ffmt = ""
         if full_compiler or flags:
-            ffmt += "{%compiler.name}"
+            ffmt += "{compiler_flags} {%compiler.name}"
             if full_compiler:
                 ffmt += "{@compiler.version}"
-            ffmt += " {compiler_flags}"
         vfmt = "{variants}" if variants else ""
-        format_string = nfmt + "{@version}" + ffmt + vfmt
+        format_string = nfmt + "{@version}" + vfmt + ffmt
 
     def fmt(s, depth=0):
         """Formatter function for all output specs"""

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

@@ -4,12 +4,15 @@
 
 import json
 import os
+import re
 import shutil
+import sys
+from typing import Dict
 from urllib.parse import urlparse, urlunparse
 
 import llnl.util.filesystem as fs
-import llnl.util.tty as tty
 import llnl.util.tty.color as clr
+from llnl.util import tty
 
 import spack.binary_distribution as bindist
 import spack.ci as spack_ci
@@ -18,12 +21,22 @@
 import spack.cmd.common.arguments
 import spack.config as cfg
 import spack.environment as ev
+import spack.error
+import spack.fetch_strategy
 import spack.hash_types as ht
 import spack.mirrors.mirror
+import spack.package_base
+import spack.paths
+import spack.repo
+import spack.spec
+import spack.stage
+import spack.util.executable
+import spack.util.git
 import spack.util.gpg as gpg_util
 import spack.util.timer as timer
 import spack.util.url as url_util
 import spack.util.web as web_util
+import spack.version
 
 description = "manage continuous integration pipelines"
 section = "build"
@@ -32,6 +45,7 @@
 SPACK_COMMAND = "spack"
 INSTALL_FAIL_CODE = 1
 FAILED_CREATE_BUILDCACHE_CODE = 100
+BUILTIN = re.compile(r"var\/spack\/repos\/builtin\/packages\/([^\/]+)\/package\.py")
 
 
 def deindent(desc):
@@ -176,6 +190,11 @@ 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"
@@ -186,6 +205,16 @@ def setup_parser(subparser):
 
     reproduce.set_defaults(func=ci_reproduce)
 
+    # Verify checksums inside of ci workflows
+    verify_versions = subparsers.add_parser(
+        "verify-versions",
+        description=deindent(ci_verify_versions.__doc__),
+        help=spack.cmd.first_line(ci_verify_versions.__doc__),
+    )
+    verify_versions.add_argument("from_ref", help="git ref from which start looking at changes")
+    verify_versions.add_argument("to_ref", help="git ref to end looking at changes")
+    verify_versions.set_defaults(func=ci_verify_versions)
+
 
 def ci_generate(args):
     """generate jobs file from a CI-aware spack file
@@ -422,7 +451,7 @@ def ci_rebuild(args):
 
     # Arguments when installing the root from sources
     deps_install_args = install_args + ["--only=dependencies"]
-    root_install_args = install_args + ["--keep-stage", "--only=package"]
+    root_install_args = install_args + ["--only=package"]
 
     if cdash_handler:
         # Add additional arguments to `spack install` for CDash reporting.
@@ -459,8 +488,7 @@ def ci_rebuild(args):
                 job_spec.to_dict(hash=ht.dag_hash),
             )
 
-    # We generated the "spack install ..." command to "--keep-stage", copy
-    # any logs from the staging directory to artifacts now
+    # Copy logs and archived files from the install metadata (.spack) directory to artifacts now
     spack_ci.copy_stage_logs_to_artifacts(job_spec, job_log_dir)
 
     # If the installation succeeded and we're running stand-alone tests for
@@ -608,7 +636,12 @@ 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,
     )
 
 
@@ -650,6 +683,159 @@ def _gitlab_artifacts_url(url: str) -> str:
     return urlunparse(parsed._replace(path="/".join(parts), fragment="", query=""))
 
 
+def validate_standard_versions(
+    pkg: spack.package_base.PackageBase, versions: spack.version.VersionList
+) -> bool:
+    """Get and test the checksum of a package version based on a tarball.
+    Args:
+      pkg spack.package_base.PackageBase: Spack package for which to validate a version checksum
+      versions spack.version.VersionList: list of package versions to validate
+    Returns: bool: result of the validation. True is valid and false is failed.
+    """
+    url_dict: Dict[spack.version.StandardVersion, str] = {}
+
+    for version in versions:
+        url = pkg.find_valid_url_for_version(version)
+        url_dict[version] = url
+
+    version_hashes = spack.stage.get_checksums_for_versions(
+        url_dict, pkg.name, fetch_options=pkg.fetch_options
+    )
+
+    valid_checksums = True
+    for version, sha in version_hashes.items():
+        if sha != pkg.versions[version]["sha256"]:
+            tty.error(
+                f"Invalid checksum found {pkg.name}@{version}\n"
+                f"    [package.py] {pkg.versions[version]['sha256']}\n"
+                f"    [Downloaded] {sha}"
+            )
+            valid_checksums = False
+            continue
+
+        tty.info(f"Validated {pkg.name}@{version} --> {sha}")
+
+    return valid_checksums
+
+
+def validate_git_versions(
+    pkg: spack.package_base.PackageBase, versions: spack.version.VersionList
+) -> bool:
+    """Get and test the commit and tag of a package version based on a git repository.
+    Args:
+      pkg spack.package_base.PackageBase: Spack package for which to validate a version
+      versions spack.version.VersionList: list of package versions to validate
+    Returns: bool: result of the validation. True is valid and false is failed.
+    """
+    valid_commit = True
+    for version in versions:
+        fetcher = spack.fetch_strategy.for_package_version(pkg, version)
+        with spack.stage.Stage(fetcher) as stage:
+            known_commit = pkg.versions[version]["commit"]
+            try:
+                stage.fetch()
+            except spack.error.FetchError:
+                tty.error(
+                    f"Invalid commit for {pkg.name}@{version}\n"
+                    f"    {known_commit} could not be checked out in the git repository."
+                )
+                valid_commit = False
+                continue
+
+            # Test if the specified tag matches the commit in the package.py
+            # We retrieve the commit associated with a tag and compare it to the
+            # commit that is located in the package.py file.
+            if "tag" in pkg.versions[version]:
+                tag = pkg.versions[version]["tag"]
+                try:
+                    with fs.working_dir(stage.source_path):
+                        found_commit = fetcher.git(
+                            "rev-list", "-n", "1", tag, output=str, error=str
+                        ).strip()
+                except spack.util.executable.ProcessError:
+                    tty.error(
+                        f"Invalid tag for {pkg.name}@{version}\n"
+                        f"    {tag} could not be found in the git repository."
+                    )
+                    valid_commit = False
+                    continue
+
+                if found_commit != known_commit:
+                    tty.error(
+                        f"Mismatched tag <-> commit found for {pkg.name}@{version}\n"
+                        f"    [package.py] {known_commit}\n"
+                        f"    [Downloaded] {found_commit}"
+                    )
+                    valid_commit = False
+                    continue
+
+            # If we have downloaded the repository, found the commit, and compared
+            # the tag (if specified) we can conclude that the version is pointing
+            # at what we would expect.
+            tty.info(f"Validated {pkg.name}@{version} --> {known_commit}")
+
+    return valid_commit
+
+
+def ci_verify_versions(args):
+    """validate version checksum & commits between git refs
+    This command takes a from_ref and to_ref arguments and
+    then parses the git diff between the two to determine which packages
+    have been modified verifies the new checksums inside of them.
+    """
+    with fs.working_dir(spack.paths.prefix):
+        # We use HEAD^1 explicitly on the merge commit created by
+        # GitHub Actions. However HEAD~1 is a safer default for the helper function.
+        files = spack.util.git.get_modified_files(from_ref=args.from_ref, to_ref=args.to_ref)
+
+    # Get a list of package names from the modified files.
+    pkgs = [(m.group(1), p) for p in files for m in [BUILTIN.search(p)] if m]
+
+    failed_version = False
+    for pkg_name, path in pkgs:
+        spec = spack.spec.Spec(pkg_name)
+        pkg = spack.repo.PATH.get_pkg_class(spec.name)(spec)
+
+        # Skip checking manual download packages and trust the maintainers
+        if pkg.manual_download:
+            tty.warn(f"Skipping manual download package: {pkg_name}")
+            continue
+
+        # Store versions checksums / commits for future loop
+        checksums_version_dict = {}
+        commits_version_dict = {}
+        for version in pkg.versions:
+            # If the package version defines a sha256 we'll use that as the high entropy
+            # string to detect which versions have been added between from_ref and to_ref
+            if "sha256" in pkg.versions[version]:
+                checksums_version_dict[pkg.versions[version]["sha256"]] = version
+
+            # If a package version instead defines a commit we'll use that as a
+            # high entropy string to detect new versions.
+            elif "commit" in pkg.versions[version]:
+                commits_version_dict[pkg.versions[version]["commit"]] = version
+
+            # TODO: enforce every version have a commit or a sha256 defined if not
+            # an infinite version (there are a lot of package's where this doesn't work yet.)
+
+        with fs.working_dir(spack.paths.prefix):
+            added_checksums = spack_ci.get_added_versions(
+                checksums_version_dict, path, from_ref=args.from_ref, to_ref=args.to_ref
+            )
+            added_commits = spack_ci.get_added_versions(
+                commits_version_dict, path, from_ref=args.from_ref, to_ref=args.to_ref
+            )
+
+        if added_checksums:
+            failed_version = not validate_standard_versions(pkg, added_checksums) or failed_version
+
+        if added_commits:
+            failed_version = not validate_git_versions(pkg, added_commits) or failed_version
+
+    if failed_version:
+        sys.exit(1)
+
+
 def ci(parser, args):
     if args.func:
         return args.func(args)

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/config.py

@@ -350,9 +350,12 @@ def _config_change(config_path, match_spec_str=None):
                 if spack.config.get(key_path, scope=scope):
                     ideal_scope_to_modify = scope
                     break
+            # If we find our key in a specific scope, that's the one we want
+            # to modify. Otherwise we use the default write scope.
+            write_scope = ideal_scope_to_modify or spack.config.default_modify_scope()
 
             update_path = f"{key_path}:[{str(spec)}]"
-            spack.config.add(update_path, scope=ideal_scope_to_modify)
+            spack.config.add(update_path, scope=write_scope)
     else:
         raise ValueError("'config change' can currently only change 'require' sections")
 

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"
@@ -55,7 +55,7 @@ def dependencies(parser, args):
         env = ev.active_environment()
         spec = spack.cmd.disambiguate_spec(specs[0], env)
 
-        format_string = "{name}{@version}{%compiler}{/hash:7}"
+        format_string = "{name}{@version}{/hash:7}{%compiler}"
         if sys.stdout.isatty():
             tty.msg("Dependencies of %s" % spec.format(format_string, color=True))
         deps = spack.store.STORE.db.installed_relatives(
@@ -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/dependents.py

@@ -93,7 +93,7 @@ def dependents(parser, args):
         env = ev.active_environment()
         spec = spack.cmd.disambiguate_spec(specs[0], env)
 
-        format_string = "{name}{@version}{%compiler}{/hash:7}"
+        format_string = "{name}{@version}{/hash:7}{%compiler}"
         if sys.stdout.isatty():
             tty.msg("Dependents of %s" % spec.cformat(format_string))
         deps = spack.store.STORE.db.installed_relatives(spec, "parents", args.transitive)

lib/spack/spack/cmd/develop.py

@@ -3,11 +3,13 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
 import shutil
+from typing import Optional
 
 import llnl.util.tty as tty
 
 import spack.cmd
 import spack.config
+import spack.environment
 import spack.fetch_strategy
 import spack.repo
 import spack.spec
@@ -31,37 +33,33 @@ def setup_parser(subparser):
         "--no-clone",
         action="store_false",
         dest="clone",
-        default=None,
         help="do not clone, the package already exists at the source path",
     )
     clone_group.add_argument(
         "--clone",
         action="store_true",
         dest="clone",
-        default=None,
-        help="clone the package even if the path already exists",
+        default=True,
+        help=(
+            "(default) clone the package unless the path already exists, "
+            "use --force to overwrite"
+        ),
     )
 
     subparser.add_argument(
         "-f", "--force", help="remove any files or directories that block cloning source code"
     )
 
+    subparser.add_argument(
+        "-r",
+        "--recursive",
+        action="store_true",
+        help="traverse nodes of the graph to mark everything up to the root as a develop spec",
+    )
+
     arguments.add_common_arguments(subparser, ["spec"])
 
 
-def _update_config(spec, path):
-    find_fn = lambda section: spec.name in section
-
-    entry = {"spec": str(spec)}
-    if path != spec.name:
-        entry["path"] = path
-
-    def change_fn(section):
-        section[spec.name] = entry
-
-    spack.config.change_or_add("develop", find_fn, change_fn)
-
-
 def _retrieve_develop_source(spec: spack.spec.Spec, abspath: str) -> None:
     # "steal" the source code via staging API. We ask for a stage
     # to be created, then copy it afterwards somewhere else. It would be
@@ -83,86 +81,159 @@ def _retrieve_develop_source(spec: spack.spec.Spec, abspath: str) -> None:
     package.stage.steal_source(abspath)
 
 
-def develop(parser, args):
-    # Note: we could put develop specs in any scope, but I assume
-    # users would only ever want to do this for either (a) an active
-    # env or (b) a specified config file (e.g. that is included by
-    # an environment)
-    # TODO: when https://github.com/spack/spack/pull/35307 is merged,
-    # an active env is not required if a scope is specified
-    env = spack.cmd.require_active_env(cmd_name="develop")
-    if not args.spec:
-        if args.clone is False:
-            raise SpackError("No spec provided to spack develop command")
+def assure_concrete_spec(env: spack.environment.Environment, spec: spack.spec.Spec):
+    version = spec.versions.concrete_range_as_version
+    if not version:
+        # first check environment for a matching concrete spec
+        matching_specs = env.all_matching_specs(spec)
+        if matching_specs:
+            version = matching_specs[0].version
+            test_spec = spack.spec.Spec(f"{spec}@{version}")
+            for m_spec in matching_specs:
+                if not m_spec.satisfies(test_spec):
+                    raise SpackError(
+                        f"{spec.name}: has multiple concrete instances in the graph that can't be"
+                        " satisified by a single develop spec. To use `spack develop` ensure one"
+                        " of the following:"
+                        f"\n a) {spec.name} nodes can satisfy the same develop spec (minimally "
+                        "this means they all share the same version)"
+                        f"\n b) Provide a concrete develop spec ({spec.name}@[version]) to clearly"
+                        " indicate what should be developed"
+                    )
+        else:
+            # look up the maximum version so infintiy versions are preferred for develop
+            version = max(spec.package_class.versions.keys())
+            tty.msg(f"Defaulting to highest version: {spec.name}@{version}")
+    spec.versions = spack.version.VersionList([version])
 
-        # download all dev specs
-        for name, entry in env.dev_specs.items():
-            path = entry.get("path", name)
-            abspath = spack.util.path.canonicalize_path(path, default_wd=env.path)
 
-            if os.path.exists(abspath):
-                msg = "Skipping developer download of %s" % entry["spec"]
-                msg += " because its path already exists."
-                tty.msg(msg)
-                continue
+def setup_src_code(spec: spack.spec.Spec, src_path: str, clone: bool = True, force: bool = False):
+    """
+    Handle checking, cloning or overwriting source code
+    """
+    assert spec.versions
 
-            # Both old syntax `spack develop pkg@x` and new syntax `spack develop pkg@=x`
-            # are currently supported.
-            spec = spack.spec.parse_with_version_concrete(entry["spec"])
-            _retrieve_develop_source(spec, abspath)
+    if clone:
+        _clone(spec, src_path, force)
 
-        if not env.dev_specs:
-            tty.warn("No develop specs to download")
-
-        return
-
-    specs = spack.cmd.parse_specs(args.spec)
-    if len(specs) > 1:
-        raise SpackError("spack develop requires at most one named spec")
-
-    spec = specs[0]
+    if not clone and not os.path.exists(src_path):
+        raise SpackError(f"Provided path {src_path} does not exist")
 
     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])
 
-    # If user does not specify --path, we choose to create a directory in the
-    # active environment's directory, named after the spec
-    path = args.path or spec.name
-    if not os.path.isabs(path):
-        abspath = spack.util.path.canonicalize_path(path, default_wd=env.path)
-    else:
-        abspath = path
 
-    # clone default: only if the path doesn't exist
-    clone = args.clone
-    if clone is None:
-        clone = not os.path.exists(abspath)
+def _update_config(spec, path):
+    find_fn = lambda section: spec.name in section
 
-    if not clone and not os.path.exists(abspath):
-        raise SpackError("Provided path %s does not exist" % abspath)
+    entry = {"spec": str(spec)}
+    if path and path != spec.name:
+        entry["path"] = path
 
-    if clone:
-        if os.path.exists(abspath):
-            if args.force:
-                shutil.rmtree(abspath)
-            else:
-                msg = "Path %s already exists and cannot be cloned to." % abspath
-                msg += " Use `spack develop -f` to overwrite."
-                raise SpackError(msg)
+    def change_fn(section):
+        section[spec.name] = entry
 
-        _retrieve_develop_source(spec, abspath)
+    spack.config.change_or_add("develop", find_fn, change_fn)
+
+
+def update_env(
+    env: spack.environment.Environment,
+    spec: spack.spec.Spec,
+    specified_path: Optional[str] = None,
+    build_dir: Optional[str] = None,
+):
+    """
+    Update the spack.yaml file with additions or changes from a develop call
+    """
+    tty.debug(f"Updating develop config for {env.name} transactionally")
+
+    if not specified_path:
+        dev_entry = env.dev_specs.get(spec.name)
+        if dev_entry:
+            specified_path = dev_entry.get("path", None)
 
-    tty.debug("Updating develop config for {0} transactionally".format(env.name))
     with env.write_transaction():
-        if args.build_directory is not None:
+        if build_dir is not None:
             spack.config.add(
-                "packages:{}:package_attributes:build_directory:{}".format(
-                    spec.name, args.build_directory
-                ),
+                f"packages:{spec.name}:package_attributes:build_directory:{build_dir}",
                 env.scope_name,
             )
-        _update_config(spec, path)
+        # add develop spec and update path
+        _update_config(spec, specified_path)
+
+
+def _clone(spec: spack.spec.Spec, abspath: str, force: bool = False):
+    if os.path.exists(abspath):
+        if force:
+            shutil.rmtree(abspath)
+        else:
+            msg = f"Skipping developer download of {spec.name}"
+            msg += f" because its path {abspath} already exists."
+            tty.msg(msg)
+            return
+
+    # cloning can take a while and it's nice to get a message for the longer clones
+    tty.msg(f"Cloning source code for {spec}")
+    _retrieve_develop_source(spec, abspath)
+
+
+def _abs_code_path(
+    env: spack.environment.Environment, spec: spack.spec.Spec, path: Optional[str] = None
+):
+    src_path = path if path else spec.name
+    return spack.util.path.canonicalize_path(src_path, default_wd=env.path)
+
+
+def _dev_spec_generator(args, env):
+    """
+    Generator function to loop over all the develop specs based on how the command is called
+    If no specs are supplied then loop over the develop specs listed in the environment.
+    """
+    if not args.spec:
+        if args.clone is False:
+            raise SpackError("No spec provided to spack develop command")
+
+        for name, entry in env.dev_specs.items():
+            path = entry.get("path", name)
+            abspath = spack.util.path.canonicalize_path(path, default_wd=env.path)
+            # Both old syntax `spack develop pkg@x` and new syntax `spack develop pkg@=x`
+            # are currently supported.
+            spec = spack.spec.parse_with_version_concrete(entry["spec"])
+            yield spec, abspath
+    else:
+        specs = spack.cmd.parse_specs(args.spec)
+        if (args.path or args.build_directory) and len(specs) > 1:
+            raise SpackError(
+                "spack develop requires at most one named spec when using the --path or"
+                " --build-directory arguments"
+            )
+
+        for spec in specs:
+            if args.recursive:
+                concrete_specs = env.all_matching_specs(spec)
+                if not concrete_specs:
+                    tty.warn(
+                        f"{spec.name} has no matching concrete specs in the environment and "
+                        "will be skipped. `spack develop --recursive` requires a concretized"
+                        " environment"
+                    )
+                else:
+                    for s in concrete_specs:
+                        for node_spec in s.traverse(direction="parents", root=True):
+                            tty.debug(f"Recursive develop for {node_spec.name}")
+                            yield node_spec, _abs_code_path(env, node_spec, args.path)
+            else:
+                yield spec, _abs_code_path(env, spec, args.path)
+
+
+def develop(parser, args):
+    env = spack.cmd.require_active_env(cmd_name="develop")
+
+    for spec, abspath in _dev_spec_generator(args, env):
+        assure_concrete_spec(env, spec)
+        setup_src_code(spec, abspath, clone=args.clone, force=args.force)
+        update_env(env, spec, args.path, args.build_directory)

lib/spack/spack/cmd/help.py

@@ -73,7 +73,7 @@
       boxlib @B{dim=2}                  boxlib built for 2 dimensions
       libdwarf @g{%intel} ^libelf@g{%gcc}
           libdwarf, built with intel compiler, linked to libelf built with gcc
-      mvapich2 @g{%gcc} @B{fabrics=psm,mrail,sock}
+      mvapich2 @B{fabrics=psm,mrail,sock} @g{%gcc}
           mvapich2, built with gcc compiler, with support for multiple fabrics
 """
 

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/modules/__init__.py

@@ -383,8 +383,10 @@ def modules_cmd(parser, args, module_type, callbacks=callbacks):
         query = " ".join(str(s) for s in args.constraint_specs)
         msg = f"the constraint '{query}' matches multiple packages:\n"
         for s in specs:
-            spec_fmt = "{hash:7} {name}{@version}{%compiler}"
-            spec_fmt += "{compiler_flags}{variants}{arch=architecture}"
+            spec_fmt = (
+                "{hash:7} {name}{@version}{compiler_flags}{variants}"
+                "{arch=architecture} {%compiler}"
+            )
             msg += "\t" + s.cformat(spec_fmt) + "\n"
         tty.die(msg, "In this context exactly *one* match is needed.")
 

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

@@ -6,8 +6,9 @@
 import os
 import re
 import sys
-from itertools import zip_longest
-from typing import Dict, List, Optional
+import warnings
+from itertools import islice, zip_longest
+from typing import Callable, Dict, List, Optional
 
 import llnl.util.tty as tty
 import llnl.util.tty.color as color
@@ -16,6 +17,9 @@
 import spack.paths
 import spack.repo
 import spack.util.git
+import spack.util.spack_yaml
+from spack.spec_parser import SPEC_TOKENIZER, SpecTokens
+from spack.tokenize import Token
 from spack.util.executable import Executable, which
 
 description = "runs source code style checks on spack"
@@ -198,6 +202,13 @@ def setup_parser(subparser):
         action="append",
         help="specify tools to skip (choose from %s)" % ", ".join(tool_names),
     )
+    subparser.add_argument(
+        "--spec-strings",
+        action="store_true",
+        help="upgrade spec strings in Python, JSON and YAML files for compatibility with Spack "
+        "v1.0 and v0.x. Example: spack style --spec-strings $(git ls-files). Note: this flag "
+        "will be removed in Spack v1.0.",
+    )
 
     subparser.add_argument("files", nargs=argparse.REMAINDER, help="specific files to check")
 
@@ -423,7 +434,8 @@ 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 +450,7 @@ 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
@@ -506,7 +518,196 @@ def _bootstrap_dev_dependencies():
         spack.bootstrap.ensure_environment_dependencies()
 
 
+IS_PROBABLY_COMPILER = re.compile(r"%[a-zA-Z_][a-zA-Z0-9\-]")
+
+
+def _spec_str_reorder_compiler(idx: int, blocks: List[List[Token]]) -> None:
+    # only move the compiler to the back if it exists and is not already at the end
+    if not 0 <= idx < len(blocks) - 1:
+        return
+    # if there's only whitespace after the compiler, don't move it
+    if all(token.kind == SpecTokens.WS for block in blocks[idx + 1 :] for token in block):
+        return
+    # rotate left and always add at least one WS token between compiler and previous token
+    compiler_block = blocks.pop(idx)
+    if compiler_block[0].kind != SpecTokens.WS:
+        compiler_block.insert(0, Token(SpecTokens.WS, " "))
+    # delete the WS tokens from the new first block if it was at the very start, to prevent leading
+    # WS tokens.
+    while idx == 0 and blocks[0][0].kind == SpecTokens.WS:
+        blocks[0].pop(0)
+    blocks.append(compiler_block)
+
+
+def _spec_str_format(spec_str: str) -> Optional[str]:
+    """Given any string, try to parse as spec string, and rotate the compiler token to the end
+    of each spec instance. Returns the formatted string if it was changed, otherwise None."""
+    # We parse blocks of tokens that include leading whitespace, and move the compiler block to
+    # the end when we hit a dependency ^... or the end of a string.
+    # [@3.1][ +foo][ +bar][ %gcc@3.1][ +baz]
+    # [@3.1][ +foo][ +bar][ +baz][ %gcc@3.1]
+
+    current_block: List[Token] = []
+    blocks: List[List[Token]] = []
+    compiler_block_idx = -1
+    in_edge_attr = False
+
+    for token in SPEC_TOKENIZER.tokenize(spec_str):
+        if token.kind == SpecTokens.UNEXPECTED:
+            # parsing error, we cannot fix this string.
+            return None
+        elif token.kind in (SpecTokens.COMPILER, SpecTokens.COMPILER_AND_VERSION):
+            # multiple compilers are not supported in Spack v0.x, so early return
+            if compiler_block_idx != -1:
+                return None
+            current_block.append(token)
+            blocks.append(current_block)
+            current_block = []
+            compiler_block_idx = len(blocks) - 1
+        elif token.kind in (
+            SpecTokens.START_EDGE_PROPERTIES,
+            SpecTokens.DEPENDENCY,
+            SpecTokens.UNQUALIFIED_PACKAGE_NAME,
+            SpecTokens.FULLY_QUALIFIED_PACKAGE_NAME,
+        ):
+            _spec_str_reorder_compiler(compiler_block_idx, blocks)
+            compiler_block_idx = -1
+            if token.kind == SpecTokens.START_EDGE_PROPERTIES:
+                in_edge_attr = True
+            current_block.append(token)
+            blocks.append(current_block)
+            current_block = []
+        elif token.kind == SpecTokens.END_EDGE_PROPERTIES:
+            in_edge_attr = False
+            current_block.append(token)
+            blocks.append(current_block)
+            current_block = []
+        elif in_edge_attr:
+            current_block.append(token)
+        elif token.kind in (
+            SpecTokens.VERSION_HASH_PAIR,
+            SpecTokens.GIT_VERSION,
+            SpecTokens.VERSION,
+            SpecTokens.PROPAGATED_BOOL_VARIANT,
+            SpecTokens.BOOL_VARIANT,
+            SpecTokens.PROPAGATED_KEY_VALUE_PAIR,
+            SpecTokens.KEY_VALUE_PAIR,
+            SpecTokens.DAG_HASH,
+        ):
+            current_block.append(token)
+            blocks.append(current_block)
+            current_block = []
+        elif token.kind == SpecTokens.WS:
+            current_block.append(token)
+        else:
+            raise ValueError(f"unexpected token {token}")
+
+    if current_block:
+        blocks.append(current_block)
+    _spec_str_reorder_compiler(compiler_block_idx, blocks)
+
+    new_spec_str = "".join(token.value for block in blocks for token in block)
+    return new_spec_str if spec_str != new_spec_str else None
+
+
+SpecStrHandler = Callable[[str, int, int, str, str], None]
+
+
+def _spec_str_default_handler(path: str, line: int, col: int, old: str, new: str):
+    """A SpecStrHandler that prints formatted spec strings and their locations."""
+    print(f"{path}:{line}:{col}: `{old}` -> `{new}`")
+
+
+def _spec_str_fix_handler(path: str, line: int, col: int, old: str, new: str):
+    """A SpecStrHandler that updates formatted spec strings in files."""
+    with open(path, "r", encoding="utf-8") as f:
+        lines = f.readlines()
+    new_line = lines[line - 1].replace(old, new)
+    if new_line == lines[line - 1]:
+        tty.warn(f"{path}:{line}:{col}: could not apply fix: `{old}` -> `{new}`")
+        return
+    lines[line - 1] = new_line
+    print(f"{path}:{line}:{col}: fixed `{old}` -> `{new}`")
+    with open(path, "w", encoding="utf-8") as f:
+        f.writelines(lines)
+
+
+def _spec_str_ast(path: str, tree: ast.AST, handler: SpecStrHandler) -> None:
+    """Walk the AST of a Python file and apply handler to formatted spec strings."""
+    has_constant = sys.version_info >= (3, 8)
+    for node in ast.walk(tree):
+        if has_constant and isinstance(node, ast.Constant) and isinstance(node.value, str):
+            current_str = node.value
+        elif not has_constant and isinstance(node, ast.Str):
+            current_str = node.s
+        else:
+            continue
+        if not IS_PROBABLY_COMPILER.search(current_str):
+            continue
+        new = _spec_str_format(current_str)
+        if new is not None:
+            handler(path, node.lineno, node.col_offset, current_str, new)
+
+
+def _spec_str_json_and_yaml(path: str, data: dict, handler: SpecStrHandler) -> None:
+    """Walk a YAML or JSON data structure and apply handler to formatted spec strings."""
+    queue = [data]
+    seen = set()
+
+    while queue:
+        current = queue.pop(0)
+        if id(current) in seen:
+            continue
+        seen.add(id(current))
+        if isinstance(current, dict):
+            queue.extend(current.values())
+            queue.extend(current.keys())
+        elif isinstance(current, list):
+            queue.extend(current)
+        elif isinstance(current, str) and IS_PROBABLY_COMPILER.search(current):
+            new = _spec_str_format(current)
+            if new is not None:
+                mark = getattr(current, "_start_mark", None)
+                if mark:
+                    line, col = mark.line + 1, mark.column + 1
+                else:
+                    line, col = 0, 0
+                handler(path, line, col, current, new)
+
+
+def _check_spec_strings(
+    paths: List[str], handler: SpecStrHandler = _spec_str_default_handler
+) -> None:
+    """Open Python, JSON and YAML files, and format their string literals that look like spec
+    strings. A handler is called for each formatting, which can be used to print or apply fixes."""
+    for path in paths:
+        is_json_or_yaml = path.endswith(".json") or path.endswith(".yaml") or path.endswith(".yml")
+        is_python = path.endswith(".py")
+        if not is_json_or_yaml and not is_python:
+            continue
+
+        try:
+            with open(path, "r", encoding="utf-8") as f:
+                # skip files that are likely too large to be user code or config
+                if os.fstat(f.fileno()).st_size > 1024 * 1024:
+                    warnings.warn(f"skipping {path}: too large.")
+                    continue
+                if is_json_or_yaml:
+                    _spec_str_json_and_yaml(path, spack.util.spack_yaml.load_config(f), handler)
+                elif is_python:
+                    _spec_str_ast(path, ast.parse(f.read()), handler)
+        except (OSError, spack.util.spack_yaml.SpackYAMLError, SyntaxError, ValueError):
+            warnings.warn(f"skipping {path}")
+            continue
+
+
 def style(parser, args):
+    if args.spec_strings:
+        if not args.files:
+            tty.die("No files provided to check spec strings.")
+        handler = _spec_str_fix_handler if args.fix else _spec_str_default_handler
+        return _check_spec_strings(args.files, handler)
+
     # save initial working directory for relativizing paths later
     args.initial_working_dir = os.getcwd()
 

lib/spack/spack/cmd/test.py

@@ -252,7 +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

@@ -17,6 +17,7 @@
     pytest = None  # type: ignore
 
 import llnl.util.filesystem
+import llnl.util.tty as tty
 import llnl.util.tty.color as color
 from llnl.util.tty.colify import colify
 
@@ -216,7 +217,7 @@ 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
@@ -236,6 +237,12 @@ def unit_test(parser, args, unknown_args):
         pytest_root = spack.extensions.load_extension(args.extension)
 
     if args.numprocesses is not None and args.numprocesses > 1:
+        try:
+            import xdist  # noqa: F401
+        except ImportError:
+            tty.error("parallel unit-test requires pytest-xdist module")
+            return 1
+
         pytest_args.extend(
             [
                 "--dist",

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

@@ -32,9 +32,10 @@
 import copy
 import functools
 import os
+import os.path
 import re
 import sys
-from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union
+from typing import Any, Callable, Dict, Generator, List, NamedTuple, Optional, Tuple, Union
 
 import jsonschema
 
@@ -42,7 +43,6 @@
 
 import spack.error
 import spack.paths
-import spack.platforms
 import spack.schema
 import spack.schema.bootstrap
 import spack.schema.cdash
@@ -54,17 +54,20 @@
 import spack.schema.develop
 import spack.schema.env
 import spack.schema.env_vars
+import spack.schema.include
+import spack.schema.merged
 import spack.schema.mirrors
 import spack.schema.modules
 import spack.schema.packages
 import spack.schema.repos
 import spack.schema.upstreams
 import spack.schema.view
-
-# Hacked yaml for configuration files preserves line numbers.
+import spack.util.remote_file_cache as rfc_util
 import spack.util.spack_yaml as syaml
-import spack.util.web as web_util
 from spack.util.cpus import cpus_available
+from spack.util.spack_yaml import get_mark_from_yaml_data
+
+from .enums import ConfigScopePriority
 
 #: Dict from section names -> schema for that section
 SECTION_SCHEMAS: Dict[str, Any] = {
@@ -72,6 +75,7 @@
     "concretizer": spack.schema.concretizer.schema,
     "definitions": spack.schema.definitions.schema,
     "env_vars": spack.schema.env_vars.schema,
+    "include": spack.schema.include.schema,
     "view": spack.schema.view.schema,
     "develop": spack.schema.develop.schema,
     "mirrors": spack.schema.mirrors.schema,
@@ -119,6 +123,17 @@
 #: Type used for raw YAML configuration
 YamlConfigDict = Dict[str, Any]
 
+#: prefix for name of included configuration scopes
+INCLUDE_SCOPE_PREFIX = "include"
+
+#: safeguard for recursive includes -- maximum include depth
+MAX_RECURSIVE_INCLUDES = 100
+
+
+def _include_cache_location():
+    """Location to cache included configuration files."""
+    return os.path.join(spack.paths.user_cache_path, "includes")
+
 
 class ConfigScope:
     def __init__(self, name: str) -> None:
@@ -126,6 +141,25 @@ def __init__(self, name: str) -> None:
         self.writable = False
         self.sections = syaml.syaml_dict()
 
+        #: names of any included scopes
+        self._included_scopes: Optional[List["ConfigScope"]] = None
+
+    @property
+    def included_scopes(self) -> List["ConfigScope"]:
+        """Memoized list of included scopes, in the order they appear in this scope."""
+        if self._included_scopes is None:
+            self._included_scopes = []
+
+            includes = self.get_section("include")
+            if includes:
+                include_paths = [included_path(data) for data in includes["include"]]
+                for path in include_paths:
+                    included_scope = include_path_scope(path)
+                    if included_scope:
+                        self._included_scopes.append(included_scope)
+
+        return self._included_scopes
+
     def get_section_filename(self, section: str) -> str:
         raise NotImplementedError
 
@@ -408,26 +442,18 @@ 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 +461,59 @@ 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, _depth: int = 0
+    ) -> 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
+        """
+        # TODO: As a follow on to #48784, change this to create a graph of the
+        # TODO: includes AND ensure properly sorted such that the order included
+        # TODO: at the highest level is reflected in the value of an option that
+        # TODO: is set in multiple included files.
+        # before pushing the scope itself, push any included scopes recursively, at same priority
+        for included_scope in reversed(scope.included_scopes):
+            if _depth + 1 > MAX_RECURSIVE_INCLUDES:  # make sure we're not recursing endlessly
+                mark = ""
+                if hasattr(included_scope, "path") and syaml.marked(included_scope.path):
+                    mark = included_scope.path._start_mark  # type: ignore
+                raise RecursiveIncludeError(
+                    f"Maximum include recursion exceeded in {included_scope.name}", str(mark)
+                )
+
+            # record this inclusion so that remove_scope() can use it
+            self.push_scope(included_scope, priority=priority, _depth=_depth + 1)
+
+        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: REMOVE SCOPE]: {str(scope)}", level=2)
+        except KeyError as e:
+            tty.debug(f"[CONFIGURATION: REMOVE SCOPE]: {e}", level=2)
+            return None
+
+        # transitively remove included scopes
+        for included_scope in scope.included_scopes:
+            assert (
+                included_scope.name in self.scopes
+            ), f"Included scope '{included_scope.name}' was never added to configuration!"
+            self.remove_scope(included_scope.name)
+
         return scope
 
     @property
@@ -473,15 +522,13 @@ 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 +795,7 @@ 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 +809,7 @@ 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 +819,86 @@ 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."""
+    import spack.platforms  # circular dependency
+
     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)
+
+
+#: Class for the relevance of an optional path conditioned on a limited
+#: python code that evaluates to a boolean and or explicit specification
+#: as optional.
+class IncludePath(NamedTuple):
+    path: str
+    when: str
+    sha256: str
+    optional: bool
+
+
+def included_path(entry: Union[str, dict]) -> IncludePath:
+    """Convert the included path entry into an IncludePath.
+
+    Args:
+        entry: include configuration entry
+
+    Returns: converted entry, where an empty ``when`` means the path is
+        not conditionally included
+    """
+    if isinstance(entry, str):
+        return IncludePath(path=entry, sha256="", when="", optional=False)
+
+    path = entry["path"]
+    sha256 = entry.get("sha256", "")
+    when = entry.get("when", "")
+    optional = entry.get("optional", False)
+    return IncludePath(path=path, sha256=sha256, when=when, optional=optional)
+
+
+def include_path_scope(include: IncludePath) -> Optional[ConfigScope]:
+    """Instantiate an appropriate configuration scope for the given path.
+
+    Args:
+        include: optional include path
+
+    Returns: configuration scope
+
+    Raises:
+        ValueError: included path has an unsupported URL scheme, is required
+            but does not exist; configuration stage directory argument is missing
+        ConfigFileError: unable to access remote configuration file(s)
+    """
+    # circular dependencies
+    import spack.spec
+
+    if (not include.when) or spack.spec.eval_conditional(include.when):
+        config_path = rfc_util.local_path(include.path, include.sha256, _include_cache_location)
+        if not config_path:
+            raise ConfigFileError(f"Unable to fetch remote configuration from {include.path}")
+
+        if os.path.isdir(config_path):
+            # directories are treated as regular ConfigScopes
+            config_name = f"{INCLUDE_SCOPE_PREFIX}:{os.path.basename(config_path)}"
+            tty.debug(f"Creating DirectoryConfigScope {config_name} for '{config_path}'")
+            return DirectoryConfigScope(config_name, config_path)
+
+        if os.path.exists(config_path):
+            # files are assumed to be SingleFileScopes
+            config_name = f"{INCLUDE_SCOPE_PREFIX}:{config_path}"
+            tty.debug(f"Creating SingleFileScope {config_name} for '{config_path}'")
+            return SingleFileScope(config_name, config_path, spack.schema.merged.schema)
+
+        if not include.optional:
+            path = f" at ({config_path})" if config_path != include.path else ""
+            raise ValueError(f"Required path ({include.path}) does not exist{path}")
+
+    return None
 
 
 def config_paths_from_entry_points() -> List[Tuple[str, str]]:
@@ -806,18 +926,17 @@ def config_paths_from_entry_points() -> List[Tuple[str, str]]:
     return config_paths
 
 
-def create() -> Configuration:
+def create_incremental() -> Generator[Configuration, None, None]:
     """Singleton Configuration instance.
 
     This constructs one instance associated with this module and returns
     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 = [
@@ -847,16 +966,29 @@ def create() -> Configuration:
 
     # add each scope and its platform-specific directory
     for name, path in configuration_paths:
-        cfg.push_scope(DirectoryConfigScope(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)
 
-        # Each scope can have per-platfom overrides in subdirectories
-        _add_platform_scope(cfg, name, path)
+        # yield the config incrementally so that each config level's init code can get
+        # data from the one below. This can be tricky, but it enables us to have a
+        # single unified config system.
+        #
+        # TODO: think about whether we want to restrict what types of config can be used
+        #     at each level. e.g., we may want to just more forcibly disallow remote
+        #     config (which uses ssl and other config options) for some of the scopes,
+        #     to make the bootstrap issues more explicit, even if allowing config scope
+        #     init to reference lower scopes is more flexible.
+        yield cfg
 
-    return cfg
+
+def create() -> Configuration:
+    """Create a configuration using create_incremental(), return the last yielded result."""
+    return list(create_incremental())[-1]
 
 
 #: This is the singleton configuration instance for Spack.
-CONFIG: Configuration = lang.Singleton(create)  # type: ignore
+CONFIG: Configuration = lang.Singleton(create_incremental)  # type: ignore
 
 
 def add_from_file(filename: str, scope: Optional[str] = None) -> None:
@@ -952,10 +1084,11 @@ def set(path: str, value: Any, scope: Optional[str] = None) -> None:
 
     Accepts the path syntax described in ``get()``.
     """
-    return CONFIG.set(path, value, scope)
+    result = CONFIG.set(path, value, scope)
+    return result
 
 
-def scopes() -> Dict[str, ConfigScope]:
+def scopes() -> lang.PriorityOrderedMapping[str, ConfigScope]:
     """Convenience function to get list of configuration scopes."""
     return CONFIG.scopes
 
@@ -1409,7 +1542,7 @@ 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 +1557,7 @@ 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
@@ -1435,137 +1568,44 @@ 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
-
-        # 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))
-
-    configuration = Configuration(*scopes)
-    return configuration
-
-
-def raw_github_gitlab_url(url: str) -> str:
-    """Transform a github URL to the raw form to avoid undesirable html.
+def create_from(*scopes_or_paths: Union[ScopeWithOptionalPriority, str]) -> Configuration:
+    """Creates a configuration object from the scopes passed in input.
 
     Args:
-        url: url to be converted to raw form
+        *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.
 
-    Returns:
-        Raw github/gitlab url or the original url
+    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)
+        ... )
     """
-    # Note we rely on GitHub to redirect the 'raw' URL returned here to the
-    # actual URL under https://raw.githubusercontent.com/ with '/blob'
-    # removed and or, '/blame' if needed.
-    if "github" in url or "gitlab" in url:
-        return url.replace("/blob/", "/raw/")
-
-    return url
-
-
-def collect_urls(base_url: str) -> list:
-    """Return a list of configuration URLs.
-
-    Arguments:
-        base_url: URL for a configuration (yaml) file or a directory
-            containing yaml file(s)
-
-    Returns:
-        List of configuration file(s) or empty list if none
-    """
-    if not base_url:
-        return []
-
-    extension = ".yaml"
-
-    if base_url.endswith(extension):
-        return [base_url]
-
-    # Collect configuration URLs if the base_url is a "directory".
-    _, links = web_util.spider(base_url, 0)
-    return [link for link in links if link.endswith(extension)]
-
-
-def fetch_remote_configs(url: str, dest_dir: str, skip_existing: bool = True) -> str:
-    """Retrieve configuration file(s) at the specified URL.
-
-    Arguments:
-        url: URL for a configuration (yaml) file or a directory containing
-            yaml file(s)
-        dest_dir: destination directory
-        skip_existing: Skip files that already exist in dest_dir if
-            ``True``; otherwise, replace those files
-
-    Returns:
-        Path to the corresponding file if URL is or contains a
-        single file and it is the only file in the destination directory or
-        the root (dest_dir) directory if multiple configuration files exist
-        or are retrieved.
-    """
-
-    def _fetch_file(url):
-        raw = raw_github_gitlab_url(url)
-        tty.debug(f"Reading config from url {raw}")
-        return web_util.fetch_url_text(raw, dest_dir=dest_dir)
-
-    if not url:
-        raise ConfigFileError("Cannot retrieve configuration without a URL")
-
-    # Return the local path to the cached configuration file OR to the
-    # directory containing the cached configuration files.
-    config_links = collect_urls(url)
-    existing_files = os.listdir(dest_dir) if os.path.isdir(dest_dir) else []
-
-    paths = []
-    for config_url in config_links:
-        basename = os.path.basename(config_url)
-        if skip_existing and basename in existing_files:
-            tty.warn(
-                f"Will not fetch configuration from {config_url} since a "
-                f"version already exists in {dest_dir}"
-            )
-            path = os.path.join(dest_dir, basename)
-        else:
-            path = _fetch_file(config_url)
-
-        if path:
-            paths.append(path)
-
-    if paths:
-        return dest_dir if len(paths) > 1 else paths[0]
-
-    raise ConfigFileError(f"Cannot retrieve configuration (yaml) from {url}")
-
-
-def get_mark_from_yaml_data(obj):
-    """Try to get ``spack.util.spack_yaml`` mark from YAML data.
-
-    We try the object, and if that fails we try its first member (if it's a container).
-
-    Returns:
-        mark if one is found, otherwise None.
-    """
-    # mark of object itelf
-    mark = getattr(obj, "_start_mark", None)
-    if mark:
-        return mark
-
-    # mark of first member if it is a container
-    if isinstance(obj, (list, dict)):
-        first_member = next(iter(obj), None)
-        if first_member:
-            mark = getattr(first_member, "_start_mark", None)
-
-    return mark
+    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 determine_number_of_jobs(
@@ -1672,3 +1712,7 @@ def get_path(path, data):
 
         # give up and return None if nothing worked
         return None
+
+
+class RecursiveIncludeError(spack.error.SpackError):
+    """Too many levels of recursive includes."""

lib/spack/spack/database.py

@@ -41,6 +41,8 @@
     Union,
 )
 
+import spack.repo
+
 try:
     import uuid
 
@@ -1124,7 +1126,7 @@ def _add(
             installation_time:
                 Date and time of installation
             allow_missing: if True, don't warn when installation is not found on on disk
-                This is useful when installing specs without build deps.
+                This is useful when installing specs without build/test deps.
         """
         if not spec.concrete:
             raise NonConcreteSpecAddError("Specs added to DB must be concrete.")
@@ -1144,10 +1146,8 @@ def _add(
                 edge.spec,
                 explicit=False,
                 installation_time=installation_time,
-                # allow missing build-only deps. This prevents excessive warnings when a spec is
-                # installed, and its build dep is missing a build dep; there's no need to install
-                # the build dep's build dep first, and there's no need to warn about it missing.
-                allow_missing=allow_missing or edge.depflag == dt.BUILD,
+                # allow missing build / test only deps
+                allow_missing=allow_missing or edge.depflag & (dt.BUILD | dt.TEST) == edge.depflag,
             )
 
         # Make sure the directory layout agrees whether the spec is installed
@@ -1556,7 +1556,12 @@ 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

@@ -7,6 +7,7 @@
 import collections
 import concurrent.futures
 import os
+import pathlib
 import re
 import sys
 import traceback
@@ -15,6 +16,7 @@
 
 import llnl.util.filesystem
 import llnl.util.lang
+import llnl.util.symlink
 import llnl.util.tty
 
 import spack.error
@@ -70,13 +72,21 @@ def dedupe_paths(paths: List[str]) -> List[str]:
     """Deduplicate paths based on inode and device number. In case the list contains first a
     symlink and then the directory it points to, the symlink is replaced with the directory path.
     This ensures that we pick for example ``/usr/bin`` over ``/bin`` if the latter is a symlink to
-    the former`."""
+    the former."""
     seen: Dict[Tuple[int, int], str] = {}
+
+    linked_parent_check = lambda x: any(
+        [llnl.util.symlink.islink(str(y)) for y in pathlib.Path(x).parents]
+    )
+
     for path in paths:
         identifier = file_identifier(path)
         if identifier not in seen:
             seen[identifier] = path
-        elif not os.path.islink(path):
+        # we also want to deprioritize paths if they contain a symlink in any parent
+        # (not just the basedir): e.g. oneapi has "latest/bin",
+        # where "latest" is a symlink to 2025.0"
+        elif not (llnl.util.symlink.islink(path) or linked_parent_check(path)):
             seen[identifier] = path
     return list(seen.values())
 
@@ -243,7 +253,7 @@ 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 +269,8 @@ 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 +317,10 @@ 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

@@ -462,8 +462,7 @@ def _execute_extends(pkg):
         if dep_spec.name == "python" and not pkg.name == "python-venv":
             _depends_on(pkg, spack.spec.Spec("python-venv"), when=when, type=("build", "run"))
 
-        # TODO: the values of the extendees dictionary are not used. Remove in next refactor.
-        pkg.extendees[dep_spec.name] = (dep_spec, None)
+        pkg.extendees[dep_spec.name] = (dep_spec, when_spec)
 
     return _execute_extends
 
@@ -568,7 +567,7 @@ 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/depfile.py

@@ -166,7 +166,7 @@ def __init__(
                 " ".join(self._install_target(s.safe_name()) for s in item.prereqs),
                 item.target.spec_hash(),
                 item.target.unsafe_format(
-                    "{name}{@version}{%compiler}{variants}{arch=architecture}"
+                    "{name}{@version}{variants}{ arch=architecture} {%compiler}"
                 ),
                 item.buildcache_flag,
             )

lib/spack/spack/environment/environment.py

@@ -10,8 +10,6 @@
 import re
 import shutil
 import stat
-import urllib.parse
-import urllib.request
 import warnings
 from typing import Any, Dict, Iterable, List, Optional, Sequence, Tuple, Union
 
@@ -32,7 +30,6 @@
 import spack.paths
 import spack.repo
 import spack.schema.env
-import spack.schema.merged
 import spack.spec
 import spack.spec_list
 import spack.store
@@ -43,7 +40,6 @@
 import spack.util.path
 import spack.util.spack_json as sjson
 import spack.util.spack_yaml as syaml
-import spack.util.url
 from spack import traverse
 from spack.installer import PackageInstaller
 from spack.schema.env import TOP_LEVEL_KEY
@@ -51,6 +47,8 @@
 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
@@ -387,6 +385,7 @@ def create_in_dir(
                 # dev paths in this environment to refer to their original
                 # locations.
                 _rewrite_relative_dev_paths_on_relocation(env, init_file_dir)
+                _rewrite_relative_repos_paths_on_relocation(env, init_file_dir)
 
     return env
 
@@ -403,8 +402,8 @@ def _rewrite_relative_dev_paths_on_relocation(env, init_file_dir):
             dev_path = substitute_path_variables(entry["path"])
             expanded_path = spack.util.path.canonicalize_path(dev_path, default_wd=init_file_dir)
 
-            # Skip if the expanded path is the same (e.g. when absolute)
-            if dev_path == expanded_path:
+            # Skip if the substituted and expanded path is the same (e.g. when absolute)
+            if entry["path"] == expanded_path:
                 continue
 
             tty.debug("Expanding develop path for {0} to {1}".format(name, expanded_path))
@@ -419,6 +418,34 @@ def _rewrite_relative_dev_paths_on_relocation(env, init_file_dir):
         env._re_read()
 
 
+def _rewrite_relative_repos_paths_on_relocation(env, init_file_dir):
+    """When initializing the environment from a manifest file and we plan
+    to store the environment in a different directory, we have to rewrite
+    relative repo paths to absolute ones and expand environment variables."""
+    with env:
+        repos_specs = spack.config.get("repos", default={}, scope=env.scope_name)
+        if not repos_specs:
+            return
+        for i, entry in enumerate(repos_specs):
+            repo_path = substitute_path_variables(entry)
+            expanded_path = spack.util.path.canonicalize_path(repo_path, default_wd=init_file_dir)
+
+            # Skip if the substituted and expanded path is the same (e.g. when absolute)
+            if entry == expanded_path:
+                continue
+
+            tty.debug("Expanding repo path for {0} to {1}".format(entry, expanded_path))
+
+            repos_specs[i] = expanded_path
+
+        spack.config.set("repos", repos_specs, scope=env.scope_name)
+
+        env.repos_specs = None
+        # If we changed the environment's spack.yaml scope, that will not be reflected
+        # in the manifest that we read
+        env._re_read()
+
+
 def environment_dir_from_name(name: str, exists_ok: bool = True) -> str:
     """Returns the directory associated with a named environment.
 
@@ -546,13 +573,6 @@ def _write_yaml(data, str_or_file):
     syaml.dump_config(data, str_or_file, default_flow_style=False)
 
 
-def _eval_conditional(string):
-    """Evaluate conditional definitions using restricted variable scope."""
-    valid_variables = spack.spec.get_host_environment()
-    valid_variables.update({"re": re, "env": os.environ})
-    return eval(string, valid_variables)
-
-
 def _is_dev_spec_and_has_changed(spec):
     """Check if the passed spec is a dev build and whether it has changed since the
     last installation"""
@@ -985,7 +1005,7 @@ def _process_definition(self, entry):
         """Process a single spec definition item."""
         when_string = entry.get("when")
         if when_string is not None:
-            when = _eval_conditional(when_string)
+            when = spack.spec.eval_conditional(when_string)
             assert len([x for x in entry if x != "when"]) == 1
         else:
             when = True
@@ -1108,11 +1128,6 @@ def user_specs(self):
 
     @property
     def dev_specs(self):
-        if not self._dev_specs:
-            self._dev_specs = self._read_dev_specs()
-        return self._dev_specs
-
-    def _read_dev_specs(self):
         dev_specs = {}
         dev_config = spack.config.get("develop", {})
         for name, entry in dev_config.items():
@@ -1530,9 +1545,6 @@ def _get_specs_to_concretize(
         return new_user_specs, kept_user_specs, specs_to_concretize
 
     def _concretize_together_where_possible(self, tests: bool = False) -> Sequence[SpecPair]:
-        # Avoid cyclic dependency
-        import spack.solver.asp
-
         # Exit early if the set of concretized specs is the set of user specs
         new_user_specs, _, specs_to_concretize = self._get_specs_to_concretize()
         if not new_user_specs:
@@ -2392,6 +2404,8 @@ def invalidate_repository_cache(self):
 
     def __enter__(self):
         self._previous_active = _active_environment
+        if self._previous_active:
+            deactivate()
         activate(self)
         return self
 
@@ -2641,20 +2655,23 @@ def _ensure_env_dir():
         # error handling for bad manifests is handled on other code paths
         return
 
+    # TODO: make this recursive
     includes = manifest[TOP_LEVEL_KEY].get("include", [])
     for include in includes:
-        if os.path.isabs(include):
+        included_path = spack.config.included_path(include)
+        path = included_path.path
+        if os.path.isabs(path):
             continue
 
-        abspath = pathlib.Path(os.path.normpath(environment_dir / include))
+        abspath = pathlib.Path(os.path.normpath(environment_dir / path))
         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}")
+            tty.debug(f"Will not copy relative include file from outside environment: {path}")
             continue
 
-        orig_abspath = os.path.normpath(envfile.parent / include)
+        orig_abspath = os.path.normpath(envfile.parent / path)
         if not os.path.exists(orig_abspath):
-            tty.warn(f"Included file does not exist; will not copy: '{include}'")
+            tty.warn(f"Included file does not exist; will not copy: '{path}'")
             continue
 
         fs.touchp(abspath)
@@ -2877,7 +2894,7 @@ def extract_name(_item):
                 continue
 
             condition_str = item.get("when", "True")
-            if not _eval_conditional(condition_str):
+            if not spack.spec.eval_conditional(condition_str):
                 continue
 
             yield idx, item
@@ -2938,127 +2955,20 @@ def __iter__(self):
     def __str__(self):
         return str(self.manifest_file)
 
-    @property
-    def included_config_scopes(self) -> List[spack.config.ConfigScope]:
-        """List of included configuration scopes from the manifest.
-
-        Scopes are listed in the YAML file in order from highest to
-        lowest precedence, so configuration from earlier scope will take
-        precedence over later ones.
-
-        This routine returns them in the order they should be pushed onto
-        the internal scope stack (so, in reverse, from lowest to highest).
-
-        Returns: Configuration scopes associated with the environment manifest
-
-        Raises:
-            SpackEnvironmentError: if the manifest includes a remote file but
-                no configuration stage directory has been identified
-        """
-        scopes: List[spack.config.ConfigScope] = []
-
-        # load config scopes added via 'include:', in reverse so that
-        # highest-precedence scopes are last.
-        includes = self[TOP_LEVEL_KEY].get("include", [])
-        missing = []
-        for i, config_path in enumerate(reversed(includes)):
-            # allow paths to contain spack config/environment variables, etc.
-            config_path = substitute_path_variables(config_path)
-            include_url = urllib.parse.urlparse(config_path)
-
-            # If scheme is not valid, config_path is not a url
-            # of a type Spack is generally aware
-            if spack.util.url.validate_scheme(include_url.scheme):
-                # Transform file:// URLs to direct includes.
-                if include_url.scheme == "file":
-                    config_path = urllib.request.url2pathname(include_url.path)
-
-                # Any other URL should be fetched.
-                elif include_url.scheme in ("http", "https", "ftp"):
-                    # Stage any remote configuration file(s)
-                    staged_configs = (
-                        os.listdir(self.config_stage_dir)
-                        if os.path.exists(self.config_stage_dir)
-                        else []
-                    )
-                    remote_path = urllib.request.url2pathname(include_url.path)
-                    basename = os.path.basename(remote_path)
-                    if basename in staged_configs:
-                        # Do NOT re-stage configuration files over existing
-                        # ones with the same name since there is a risk of
-                        # losing changes (e.g., from 'spack config update').
-                        tty.warn(
-                            "Will not re-stage configuration from {0} to avoid "
-                            "losing changes to the already staged file of the "
-                            "same name.".format(remote_path)
-                        )
-
-                        # Recognize the configuration stage directory
-                        # is flattened to ensure a single copy of each
-                        # configuration file.
-                        config_path = self.config_stage_dir
-                        if basename.endswith(".yaml"):
-                            config_path = os.path.join(config_path, basename)
-                    else:
-                        staged_path = spack.config.fetch_remote_configs(
-                            config_path, str(self.config_stage_dir), skip_existing=True
-                        )
-                        if not staged_path:
-                            raise SpackEnvironmentError(
-                                "Unable to fetch remote configuration {0}".format(config_path)
-                            )
-                        config_path = staged_path
-
-                elif include_url.scheme:
-                    raise ValueError(
-                        f"Unsupported URL scheme ({include_url.scheme}) for "
-                        f"environment include: {config_path}"
-                    )
-
-            # treat relative paths as relative to the environment
-            if not os.path.isabs(config_path):
-                config_path = os.path.join(self.manifest_dir, config_path)
-                config_path = os.path.normpath(os.path.realpath(config_path))
-
-            if os.path.isdir(config_path):
-                # directories are treated as regular ConfigScopes
-                config_name = f"env:{self.name}:{os.path.basename(config_path)}"
-                tty.debug(f"Creating DirectoryConfigScope {config_name} for '{config_path}'")
-                scopes.append(spack.config.DirectoryConfigScope(config_name, config_path))
-            elif os.path.exists(config_path):
-                # files are assumed to be SingleFileScopes
-                config_name = f"env:{self.name}:{config_path}"
-                tty.debug(f"Creating SingleFileScope {config_name} for '{config_path}'")
-                scopes.append(
-                    spack.config.SingleFileScope(
-                        config_name, config_path, spack.schema.merged.schema
-                    )
-                )
-            else:
-                missing.append(config_path)
-                continue
-
-        if missing:
-            msg = "Detected {0} missing include path(s):".format(len(missing))
-            msg += "\n   {0}".format("\n   ".join(missing))
-            raise spack.config.ConfigFileError(msg)
-
-        return scopes
-
     @property
     def env_config_scopes(self) -> List[spack.config.ConfigScope]:
         """A list of all configuration scopes for the environment manifest. On the first call this
         instantiates all the scopes, on subsequent calls it returns the cached list."""
         if self._config_scopes is not None:
             return self._config_scopes
+
         scopes: List[spack.config.ConfigScope] = [
-            *self.included_config_scopes,
             spack.config.SingleFileScope(
                 self.scope_name,
                 str(self.manifest_file),
                 spack.schema.env.schema,
                 yaml_path=[TOP_LEVEL_KEY],
-            ),
+            )
         ]
         ensure_no_disallowed_env_config_mods(scopes)
         self._config_scopes = scopes
@@ -3067,14 +2977,12 @@ 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/environment/shell.py

@@ -8,6 +8,7 @@
 import llnl.util.tty as tty
 from llnl.util.tty.color import colorize
 
+import spack.config
 import spack.environment as ev
 import spack.repo
 import spack.schema.environment
@@ -158,7 +159,8 @@ def activate(
     # become PATH variables.
     #
 
-    env_vars_yaml = env.manifest.configuration.get("env_vars", None)
+    with env.manifest.use_config():
+        env_vars_yaml = spack.config.get("env_vars", None)
     if env_vars_yaml:
         env_mods.extend(spack.schema.environment.parse(env_vars_yaml))
 
@@ -195,7 +197,8 @@ def deactivate() -> EnvironmentModifications:
     if active is None:
         return env_mods
 
-    env_vars_yaml = active.manifest.configuration.get("env_vars", None)
+    with active.manifest.use_config():
+        env_vars_yaml = spack.config.get("env_vars", None)
     if env_vars_yaml:
         env_mods.extend(spack.schema.environment.parse(env_vars_yaml).reversed())
 

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.
@@ -642,7 +643,7 @@ def print_status(self, *specs, **kwargs):
                 specs.sort()
 
                 abbreviated = [
-                    s.cformat("{name}{@version}{%compiler}{compiler_flags}{variants}")
+                    s.cformat("{name}{@version}{compiler_flags}{variants}{%compiler}")
                     for s in specs
                 ]
 
@@ -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:
@@ -827,7 +831,7 @@ 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)
@@ -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):
@@ -482,7 +482,7 @@ class SimpleDAG(DotGraphBuilder):
     """Simple DOT graph, with nodes colored uniformly and edges without properties"""
 
     def node_entry(self, node):
-        format_option = "{name}{@version}{%compiler}{/hash:7}"
+        format_option = "{name}{@version}{/hash:7}{%compiler}"
         return node.dag_hash(), f'[label="{node.format(format_option)}"]'
 
     def edge_entry(self, edge):
@@ -515,7 +515,7 @@ def visit(self, edge):
         super().visit(edge)
 
     def node_entry(self, node):
-        node_str = node.format("{name}{@version}{%compiler}{/hash:7}")
+        node_str = node.format("{name}{@version}{/hash:7}{%compiler}")
         options = f'[label="{node_str}", group="build_dependencies", fillcolor="coral"]'
         if node.dag_hash() in self.main_unified_space:
             options = f'[label="{node_str}", group="main_psid"]'
@@ -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/hash_types.py

@@ -6,7 +6,7 @@
 import spack.deptypes as dt
 import spack.repo
 
-hashes = []
+HASHES = []
 
 
 class SpecHashDescriptor:
@@ -23,7 +23,7 @@ def __init__(self, depflag: dt.DepFlag, package_hash, name, override=None):
         self.depflag = depflag
         self.package_hash = package_hash
         self.name = name
-        hashes.append(self)
+        HASHES.append(self)
         # Allow spec hashes to have an alternate computation method
         self.override = override
 
@@ -43,13 +43,9 @@ def __repr__(self):
         )
 
 
-#: Spack's deployment hash. Includes all inputs that can affect how a package is built.
-dag_hash = SpecHashDescriptor(depflag=dt.BUILD | dt.LINK | dt.RUN, package_hash=True, name="hash")
-
-
-#: Hash descriptor used only to transfer a DAG, as is, across processes
-process_hash = SpecHashDescriptor(
-    depflag=dt.BUILD | dt.LINK | dt.RUN | dt.TEST, package_hash=True, name="process_hash"
+#: The DAG hash includes all inputs that can affect how a package is built.
+dag_hash = SpecHashDescriptor(
+    depflag=dt.BUILD | dt.LINK | dt.RUN | dt.TEST, package_hash=True, name="hash"
 )
 
 

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/install_test.py

@@ -21,7 +21,6 @@
 from llnl.util.lang import nullcontext
 from llnl.util.tty.color import colorize
 
-import spack.build_environment
 import spack.config
 import spack.error
 import spack.package_base
@@ -398,7 +397,7 @@ def stand_alone_tests(self, kwargs):
         Args:
             kwargs (dict): arguments to be used by the test process
         """
-        import spack.build_environment
+        import spack.build_environment  # avoid circular dependency
 
         spack.build_environment.start_build_process(self.pkg, test_process, kwargs)
 
@@ -463,6 +462,8 @@ def write_tested_status(self):
 
 @contextlib.contextmanager
 def test_part(pkg: Pb, test_name: str, purpose: str, work_dir: str = ".", verbose: bool = False):
+    import spack.build_environment  # avoid circular dependency
+
     wdir = "." if work_dir is None else work_dir
     tester = pkg.tester
     assert test_name and test_name.startswith(
@@ -566,7 +567,7 @@ 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 +624,7 @@ 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 +669,7 @@ 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/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
 
@@ -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/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"""
@@ -565,6 +564,12 @@ def __init__(self, configuration):
     def spec(self):
         return self.conf.spec
 
+    @tengine.context_property
+    def tags(self):
+        if not hasattr(self.spec.package, "tags"):
+            return []
+        return self.spec.package.tags
+
     @tengine.context_property
     def timestamp(self):
         return datetime.datetime.now()
@@ -775,10 +780,6 @@ 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 +817,10 @@ 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/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
@@ -49,6 +48,7 @@
 import spack.store
 import spack.url
 import spack.util.environment
+import spack.util.executable
 import spack.util.path
 import spack.util.web
 import spack.variant
@@ -126,9 +126,10 @@ def windows_establish_runtime_linkage(self):
         # Spack should in general not modify things it has not installed
         # we can reasonably expect externals to have their link interface properly established
         if sys.platform == "win32" and not self.spec.external:
-            self.win_rpath.add_library_dependent(*self.win_add_library_dependent())
-            self.win_rpath.add_rpath(*self.win_add_rpath())
-            self.win_rpath.establish_link()
+            win_rpath = fsys.WindowsSimulatedRPath(self)
+            win_rpath.add_library_dependent(*self.win_add_library_dependent())
+            win_rpath.add_rpath(*self.win_add_rpath())
+            win_rpath.establish_link()
 
 
 #: Registers which are the detectable packages, by repo and package name
@@ -710,19 +711,6 @@ 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.
@@ -756,7 +744,6 @@ def __init__(self, spec):
         # Set up timing variables
         self._fetch_time = 0.0
 
-        self.win_rpath = fsys.WindowsSimulatedRPath(self)
         super().__init__()
 
     def __getitem__(self, key: str) -> "PackageBase":
@@ -822,104 +809,6 @@ 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."""
@@ -1399,12 +1288,13 @@ def extendee_spec(self):
         if not self.extendees:
             return None
 
-        deps = []
-
         # If the extendee is in the spec's deps already, return that.
-        for dep in self.spec.traverse(deptype=("link", "run")):
-            if dep.name in self.extendees:
-                deps.append(dep)
+        deps = [
+            dep
+            for dep in self.spec.dependencies(deptype=("link", "run"))
+            for d, when in self.extendees.values()
+            if dep.satisfies(d) and self.spec.satisfies(when)
+        ]
 
         if deps:
             assert len(deps) == 1
@@ -1481,6 +1371,14 @@ def prefix(self):
     def home(self):
         return self.prefix
 
+    @property
+    def command(self) -> spack.util.executable.Executable:
+        """Returns the main executable for this package."""
+        path = os.path.join(self.home.bin, self.spec.name)
+        if fsys.is_exe(path):
+            return spack.util.executable.Executable(path)
+        raise RuntimeError(f"Unable to locate {self.spec.name} command in {self.home.bin}")
+
     @property  # type: ignore[misc]
     @memoized
     def compiler(self):
@@ -2284,47 +2182,6 @@ def rpath_args(self):
 build_system_flags = PackageBase.build_system_flags
 
 
-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/paths.py

@@ -108,6 +108,8 @@ def _get_user_cache_path():
 #: transient caches for Spack data (virtual cache, patch sha256 lookup, etc.)
 default_misc_cache_path = os.path.join(user_cache_path, "cache")
 
+#: concretization cache for Spack concretizations
+default_conc_cache_path = os.path.join(default_misc_cache_path, "concretization")
 
 # Below paths pull configuration from the host environment.
 #

lib/spack/spack/relocate.py

@@ -283,21 +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:
@@ -406,8 +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

@@ -32,6 +32,7 @@
 import llnl.util.tty as tty
 from llnl.util.filesystem import working_dir
 
+import spack
 import spack.caches
 import spack.config
 import spack.error
@@ -49,6 +50,8 @@
 #: Package modules are imported as spack.pkg.<repo-namespace>.<pkg-name>
 ROOT_PYTHON_NAMESPACE = "spack.pkg"
 
+_API_REGEX = re.compile(r"^v(\d+)\.(\d+)$")
+
 
 def python_package_for_repo(namespace):
     """Returns the full namespace of a repository, given its relative one
@@ -909,19 +912,52 @@ def __reduce__(self):
         return RepoPath.unmarshal, self.marshal()
 
 
+def _parse_package_api_version(
+    config: Dict[str, Any],
+    min_api: Tuple[int, int] = spack.min_package_api_version,
+    max_api: Tuple[int, int] = spack.package_api_version,
+) -> Tuple[int, int]:
+    api = config.get("api")
+    if api is None:
+        package_api = (1, 0)
+    else:
+        if not isinstance(api, str):
+            raise BadRepoError(f"Invalid Package API version '{api}'. Must be of the form vX.Y")
+        api_match = _API_REGEX.match(api)
+        if api_match is None:
+            raise BadRepoError(f"Invalid Package API version '{api}'. Must be of the form vX.Y")
+        package_api = (int(api_match.group(1)), int(api_match.group(2)))
+
+    if min_api <= package_api <= max_api:
+        return package_api
+
+    min_str = ".".join(str(i) for i in min_api)
+    max_str = ".".join(str(i) for i in max_api)
+    curr_str = ".".join(str(i) for i in package_api)
+    raise BadRepoError(
+        f"Package API v{curr_str} is not supported by this version of Spack ("
+        f"must be between v{min_str} and v{max_str})"
+    )
+
+
 class Repo:
     """Class representing a package repository in the filesystem.
 
-    Each package repository must have a top-level configuration file
-    called `repo.yaml`.
+    Each package repository must have a top-level configuration file called `repo.yaml`.
 
-    Currently, `repo.yaml` must define:
+    It contains the following keys:
 
     `namespace`:
         A Python namespace where the repository's packages should live.
 
     `subdirectory`:
         An optional subdirectory name where packages are placed
+
+    `api`:
+        A string of the form vX.Y that indicates the Package API version. The default is "v1.0".
+        For the repo to be compatible with the current version of Spack, the version must be
+        greater than or equal to :py:data:`spack.min_package_api_version` and less than or equal to
+        :py:data:`spack.package_api_version`.
     """
 
     def __init__(
@@ -958,7 +994,7 @@ def check(condition, msg):
             f"{os.path.join(root, repo_config_name)} must define a namespace.",
         )
 
-        self.namespace = config["namespace"]
+        self.namespace: str = config["namespace"]
         check(
             re.match(r"[a-zA-Z][a-zA-Z0-9_.]+", self.namespace),
             f"Invalid namespace '{self.namespace}' in repo '{self.root}'. "
@@ -971,12 +1007,14 @@ def check(condition, msg):
         # Keep name components around for checking prefixes.
         self._names = self.full_namespace.split(".")
 
-        packages_dir = config.get("subdirectory", packages_dir_name)
+        packages_dir: str = config.get("subdirectory", packages_dir_name)
         self.packages_path = os.path.join(self.root, packages_dir)
         check(
             os.path.isdir(self.packages_path), f"No directory '{packages_dir}' found in '{root}'"
         )
 
+        self.package_api = _parse_package_api_version(config)
+
         # Class attribute overrides by package name
         self.overrides = overrides or {}
 
@@ -1026,7 +1064,7 @@ def is_prefix(self, fullname: str) -> bool:
         parts = fullname.split(".")
         return self._names[: len(parts)] == parts
 
-    def _read_config(self) -> Dict[str, str]:
+    def _read_config(self) -> Dict[str, Any]:
         """Check for a YAML config file in this db's root directory."""
         try:
             with open(self.config_file, encoding="utf-8") as reponame_file:
@@ -1368,6 +1406,8 @@ def create_repo(root, namespace=None, subdir=packages_dir_name):
             config.write(f"  namespace: '{namespace}'\n")
             if subdir != packages_dir_name:
                 config.write(f"  subdirectory: '{subdir}'\n")
+            x, y = spack.package_api_version
+            config.write(f"  api: v{x}.{y}\n")
 
     except OSError as e:
         # try to clean up.

lib/spack/spack/reporters/cdash.py

@@ -177,7 +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

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/config.py

@@ -58,6 +58,15 @@
                     {"type": "string"},  # deprecated
                 ]
             },
+            "concretization_cache": {
+                "type": "object",
+                "properties": {
+                    "enable": {"type": "boolean"},
+                    "url": {"type": "string"},
+                    "entry_limit": {"type": "integer", "minimum": 0},
+                    "size_limit": {"type": "integer", "minimum": 0},
+                },
+            },
             "install_hash_length": {"type": "integer", "minimum": 1},
             "install_path_scheme": {"type": "string"},  # deprecated
             "build_stage": {

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/env.py

@@ -29,11 +29,7 @@
             # merged configuration scope schemas
             spack.schema.merged.properties,
             # extra environment schema properties
-            {
-                "include": {"type": "array", "default": [], "items": {"type": "string"}},
-                "specs": spec_list_schema,
-                "include_concrete": include_concrete,
-            },
+            {"specs": spec_list_schema, "include_concrete": include_concrete},
         ),
     }
 }

lib/spack/spack/schema/include.py

@@ -0,0 +1,41 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+"""Schema for include.yaml configuration file.
+
+.. literalinclude:: _spack_root/lib/spack/spack/schema/include.py
+   :lines: 12-
+"""
+from typing import Any, Dict
+
+#: Properties for inclusion in other schemas
+properties: Dict[str, Any] = {
+    "include": {
+        "type": "array",
+        "default": [],
+        "additionalProperties": False,
+        "items": {
+            "anyOf": [
+                {
+                    "type": "object",
+                    "properties": {
+                        "when": {"type": "string"},
+                        "path": {"type": "string"},
+                        "sha256": {"type": "string"},
+                        "optional": {"type": "boolean"},
+                    },
+                    "required": ["path"],
+                    "additionalProperties": False,
+                },
+                {"type": "string"},
+            ]
+        },
+    }
+}
+
+#: Full schema with metadata
+schema = {
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "title": "Spack include configuration file schema",
+    "properties": properties,
+}

lib/spack/spack/schema/merged.py

@@ -21,6 +21,7 @@
 import spack.schema.definitions
 import spack.schema.develop
 import spack.schema.env_vars
+import spack.schema.include
 import spack.schema.mirrors
 import spack.schema.modules
 import spack.schema.packages
@@ -40,6 +41,7 @@
     spack.schema.definitions.properties,
     spack.schema.develop.properties,
     spack.schema.env_vars.properties,
+    spack.schema.include.properties,
     spack.schema.mirrors.properties,
     spack.schema.modules.properties,
     spack.schema.packages.properties,
@@ -48,7 +50,6 @@
     spack.schema.view.properties,
 )
 
-
 #: Full schema with metadata
 schema = {
     "$schema": "http://json-schema.org/draft-07/schema#",

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/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.
 
 %-----------------------------------------------------------------------------
@@ -586,6 +597,13 @@ attr("virtual_on_edge", PackageNode, ProviderNode, Virtual)
 attr("virtual_on_incoming_edges", ProviderNode, Virtual)
   :- attr("virtual_on_edge", _, ProviderNode, Virtual).
 
+% This is needed to allow requirement on virtuals,
+% when a virtual root is requested
+attr("virtual_on_incoming_edges", ProviderNode, Virtual)
+  :- attr("virtual_root", node(min_dupe_id, Virtual)),
+     attr("root", ProviderNode),
+     provider(ProviderNode, node(min_dupe_id, Virtual)).
+
 % dependencies on virtuals also imply that the virtual is a virtual node
 1 { attr("virtual_node", node(0..X-1, Virtual)) : max_dupes(Virtual, X) }
   :- node_depends_on_virtual(PackageNode, Virtual).
@@ -942,12 +960,14 @@ error(100, "Cannot set variant '{0}' for package '{1}' because the variant condi
      build(node(ID, Package)).
 
 % at most one variant value for single-valued variants.
-error(100, "'{0}' required multiple values for single-valued variant '{1}'", Package, Variant)
+error(100, "'{0}' requires conflicting variant values 'Spec({1}={2})' and 'Spec({1}={3})'", Package, Variant, Value1, Value2)
   :- attr("node", node(ID, Package)),
      node_has_variant(node(ID, Package), Variant, _),
      variant_single_value(node(ID, Package), Variant),
-     build(node(ID, Package)),
-     2 { attr("variant_value", node(ID, Package), Variant, Value) }.
+     attr("variant_value", node(ID, Package), Variant, Value1),
+     attr("variant_value", node(ID, Package), Variant, Value2),
+     Value1 < Value2,
+     build(node(ID, Package)).
 
 error(100, "No valid value for variant '{1}' of package '{0}'", Package, Variant)
   :- attr("node", node(ID, Package)),

lib/spack/spack/solver/core.py

@@ -31,16 +31,19 @@ class AspObject:
     """Object representing a piece of ASP code."""
 
 
-def _id(thing: Any) -> Union[str, AspObject]:
+def _id(thing: Any) -> Union[str, int, AspObject]:
     """Quote string if needed for it to be a valid identifier."""
-    if isinstance(thing, AspObject):
+    if isinstance(thing, bool):
+        return f'"{thing}"'
+    elif isinstance(thing, (AspObject, int)):
         return thing
-    elif isinstance(thing, bool):
-        return f'"{str(thing)}"'
-    elif isinstance(thing, int):
-        return str(thing)
     else:
-        return f'"{str(thing)}"'
+        if isinstance(thing, str):
+            # escape characters that cannot be in clingo strings
+            thing = thing.replace("\\", r"\\")
+            thing = thing.replace("\n", r"\n")
+            thing = thing.replace('"', r"\"")
+        return f'"{thing}"'
 
 
 class AspVar(AspObject):
@@ -90,26 +93,9 @@ def __call__(self, *args: Any) -> "AspFunction":
         """
         return AspFunction(self.name, self.args + args)
 
-    def _argify(self, arg: Any) -> Any:
-        """Turn the argument into an appropriate clingo symbol"""
-        if isinstance(arg, bool):
-            return clingo().String(str(arg))
-        elif isinstance(arg, int):
-            return clingo().Number(arg)
-        elif isinstance(arg, AspFunction):
-            return clingo().Function(arg.name, [self._argify(x) for x in arg.args], positive=True)
-        elif isinstance(arg, AspVar):
-            return clingo().Variable(arg.name)
-        return clingo().String(str(arg))
-
-    def symbol(self):
-        """Return a clingo symbol for this function"""
-        return clingo().Function(
-            self.name, [self._argify(arg) for arg in self.args], positive=True
-        )
-
     def __str__(self) -> str:
-        return f"{self.name}({', '.join(str(_id(arg)) for arg in self.args)})"
+        args = f"({','.join(str(_id(arg)) for arg in self.args)})"
+        return f"{self.name}{args}"
 
     def __repr__(self) -> str:
         return str(self)

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/error_messages.lp

@@ -117,7 +117,7 @@ error(0, "Cannot find a valid provider for virtual {0}", Virtual, startcauses, C
      condition_holds(Cause, node(CID, TriggerPkg)).
 
 % At most one variant value for single-valued variants
-error(0, "'{0}' required multiple values for single-valued variant '{1}'\n    Requested 'Spec({1}={2})' and 'Spec({1}={3})'", Package, Variant, Value1, Value2, startcauses, Cause1, X, Cause2, X)
+error(0, "'{0}' requires conflicting variant values 'Spec({1}={2})' and 'Spec({1}={3})'", Package, Variant, Value1, Value2, startcauses, Cause1, X, Cause2, X)
   :- attr("node", node(X, Package)),
      node_has_variant(node(X, Package), Variant, VariantID),
      variant_single_value(node(X, Package), Variant),

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/solver/requirements.py

@@ -10,7 +10,7 @@
 import spack.error
 import spack.package_base
 import spack.spec
-from spack.config import get_mark_from_yaml_data
+from spack.util.spack_yaml import get_mark_from_yaml_data
 
 
 class RequirementKind(enum.Enum):
@@ -66,18 +66,29 @@ def rules_from_package_py(self, pkg: spack.package_base.PackageBase) -> List[Req
         return rules
 
     def rules_from_virtual(self, virtual_str: str) -> List[RequirementRule]:
-        requirements = self.config.get("packages", {}).get(virtual_str, {}).get("require", [])
-        return self._rules_from_requirements(
-            virtual_str, requirements, kind=RequirementKind.VIRTUAL
-        )
+        kind, requests = self._raw_yaml_data(virtual_str, section="require", virtual=True)
+        result = self._rules_from_requirements(virtual_str, requests, kind=kind)
+
+        kind, requests = self._raw_yaml_data(virtual_str, section="prefer", virtual=True)
+        result.extend(self._rules_from_preferences(virtual_str, preferences=requests, kind=kind))
+
+        kind, requests = self._raw_yaml_data(virtual_str, section="conflict", virtual=True)
+        result.extend(self._rules_from_conflicts(virtual_str, conflicts=requests, kind=kind))
+
+        return result
 
     def rules_from_require(self, pkg: spack.package_base.PackageBase) -> List[RequirementRule]:
-        kind, requirements = self._raw_yaml_data(pkg, section="require")
+        kind, requirements = self._raw_yaml_data(pkg.name, section="require")
         return self._rules_from_requirements(pkg.name, requirements, kind=kind)
 
     def rules_from_prefer(self, pkg: spack.package_base.PackageBase) -> List[RequirementRule]:
+        kind, preferences = self._raw_yaml_data(pkg.name, section="prefer")
+        return self._rules_from_preferences(pkg.name, preferences=preferences, kind=kind)
+
+    def _rules_from_preferences(
+        self, pkg_name: str, *, preferences, kind: RequirementKind
+    ) -> List[RequirementRule]:
         result = []
-        kind, preferences = self._raw_yaml_data(pkg, section="prefer")
         for item in preferences:
             spec, condition, message = self._parse_prefer_conflict_item(item)
             result.append(
@@ -86,7 +97,7 @@ def rules_from_prefer(self, pkg: spack.package_base.PackageBase) -> List[Require
                 # require:
                 # - any_of: [spec_str, "@:"]
                 RequirementRule(
-                    pkg_name=pkg.name,
+                    pkg_name=pkg_name,
                     policy="any_of",
                     requirements=[spec, spack.spec.Spec("@:")],
                     kind=kind,
@@ -97,8 +108,13 @@ def rules_from_prefer(self, pkg: spack.package_base.PackageBase) -> List[Require
         return result
 
     def rules_from_conflict(self, pkg: spack.package_base.PackageBase) -> List[RequirementRule]:
+        kind, conflicts = self._raw_yaml_data(pkg.name, section="conflict")
+        return self._rules_from_conflicts(pkg.name, conflicts=conflicts, kind=kind)
+
+    def _rules_from_conflicts(
+        self, pkg_name: str, *, conflicts, kind: RequirementKind
+    ) -> List[RequirementRule]:
         result = []
-        kind, conflicts = self._raw_yaml_data(pkg, section="conflict")
         for item in conflicts:
             spec, condition, message = self._parse_prefer_conflict_item(item)
             result.append(
@@ -107,7 +123,7 @@ def rules_from_conflict(self, pkg: spack.package_base.PackageBase) -> List[Requi
                 # require:
                 # - one_of: [spec_str, "@:"]
                 RequirementRule(
-                    pkg_name=pkg.name,
+                    pkg_name=pkg_name,
                     policy="one_of",
                     requirements=[spec, spack.spec.Spec("@:")],
                     kind=kind,
@@ -129,10 +145,14 @@ def _parse_prefer_conflict_item(self, item):
             message = item.get("message")
         return spec, condition, message
 
-    def _raw_yaml_data(self, pkg: spack.package_base.PackageBase, *, section: str):
+    def _raw_yaml_data(self, pkg_name: str, *, section: str, virtual: bool = False):
         config = self.config.get("packages")
-        data = config.get(pkg.name, {}).get(section, [])
+        data = config.get(pkg_name, {}).get(section, [])
         kind = RequirementKind.PACKAGE
+
+        if virtual:
+            return RequirementKind.VIRTUAL, data
+
         if not data:
             data = config.get("all", {}).get(section, [])
             kind = RequirementKind.DEFAULT
@@ -165,7 +185,8 @@ def _rules_from_requirements(
 
                 # validate specs from YAML first, and fail with line numbers if parsing fails.
                 constraints = [
-                    parse_spec_from_yaml_string(constraint) for constraint in constraints
+                    parse_spec_from_yaml_string(constraint, named=kind == RequirementKind.VIRTUAL)
+                    for constraint in constraints
                 ]
                 when_str = requirement.get("when")
                 when = parse_spec_from_yaml_string(when_str) if when_str else spack.spec.Spec()
@@ -203,7 +224,7 @@ def reject_requirement_constraint(
                 s.validate_or_raise()
             except spack.error.SpackError as e:
                 tty.debug(
-                    f"[SETUP] Rejecting the default '{constraint}' requirement "
+                    f"[{__name__}] Rejecting the default '{constraint}' requirement "
                     f"on '{pkg_name}': {str(e)}",
                     level=2,
                 )
@@ -211,21 +232,37 @@ def reject_requirement_constraint(
         return False
 
 
-def parse_spec_from_yaml_string(string: str) -> spack.spec.Spec:
+def parse_spec_from_yaml_string(string: str, *, named: bool = False) -> spack.spec.Spec:
     """Parse a spec from YAML and add file/line info to errors, if it's available.
 
     Parse a ``Spec`` from the supplied string, but also intercept any syntax errors and
     add file/line information for debugging using file/line annotations from the string.
 
-    Arguments:
+    Args:
         string: a string representing a ``Spec`` from config YAML.
-
+        named: if True, the spec must have a name
     """
     try:
-        return spack.spec.Spec(string)
+        result = spack.spec.Spec(string)
     except spack.error.SpecSyntaxError as e:
         mark = get_mark_from_yaml_data(string)
         if mark:
             msg = f"{mark.name}:{mark.line + 1}: {str(e)}"
             raise spack.error.SpecSyntaxError(msg) from e
         raise e
+
+    if named is True and not result.name:
+        msg = f"expected a named spec, but got '{string}' instead"
+        mark = get_mark_from_yaml_data(string)
+
+        # Add a hint in case it's dependencies
+        deps = result.dependencies()
+        if len(deps) == 1:
+            msg = f"{msg}. Did you mean '{deps[0]}'?"
+
+        if mark:
+            msg = f"{mark.name}:{mark.line + 1}: {msg}"
+
+        raise spack.error.SpackError(msg)
+
+    return result

lib/spack/spack/spec.py

@@ -52,6 +52,7 @@
 import enum
 import io
 import itertools
+import json
 import os
 import pathlib
 import platform
@@ -96,9 +97,7 @@
 import spack.spec_parser
 import spack.store
 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
@@ -175,15 +174,17 @@
 #:     Spec(Spec("string").format()) == Spec("string)"
 DEFAULT_FORMAT = (
     "{name}{@versions}"
-    "{%compiler.name}{@compiler.versions}{compiler_flags}"
+    "{compiler_flags}"
     "{variants}{ namespace=namespace_if_anonymous}{ arch=architecture}{/abstract_hash}"
+    " {%compiler.name}{@compiler.versions}"
 )
 
 #: Display format, which eliminates extra `@=` in the output, for readability.
 DISPLAY_FORMAT = (
     "{name}{@version}"
-    "{%compiler.name}{@compiler.version}{compiler_flags}"
+    "{compiler_flags}"
     "{variants}{ namespace=namespace_if_anonymous}{ arch=architecture}{/abstract_hash}"
+    " {%compiler.name}{@compiler.version}"
 )
 
 #: Regular expression to pull spec contents out of clearsigned signature
@@ -798,7 +799,7 @@ 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)))
@@ -1108,28 +1109,6 @@ def clear(self):
         self.edges.clear()
 
 
-def _command_default_handler(spec: "Spec"):
-    """Default handler when looking for the 'command' attribute.
-
-    Tries to search for ``spec.name`` in the ``spec.home.bin`` directory.
-
-    Parameters:
-        spec: spec that is being queried
-
-    Returns:
-        Executable: An executable of the command
-
-    Raises:
-        RuntimeError: If the command is not found
-    """
-    home = getattr(spec.package, "home")
-    path = os.path.join(home.bin, spec.name)
-
-    if fs.is_exe(path):
-        return spack.util.executable.Executable(path)
-    raise RuntimeError(f"Unable to locate {spec.name} command in {home.bin}")
-
-
 def _headers_default_handler(spec: "Spec"):
     """Default handler when looking for the 'headers' attribute.
 
@@ -1333,18 +1312,22 @@ class SpecBuildInterface(lang.ObjectWrapper):
     home = ForwardQueryToPackage("home", default_handler=None)
     headers = ForwardQueryToPackage("headers", default_handler=_headers_default_handler)
     libs = ForwardQueryToPackage("libs", default_handler=_libs_default_handler)
-    command = ForwardQueryToPackage(
-        "command", default_handler=_command_default_handler, _indirect=True
-    )
+    command = ForwardQueryToPackage("command", default_handler=None, _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
         )
@@ -1507,7 +1490,7 @@ def __init__(self, spec_like=None, *, external_path=None, external_modules=None)
         self.abstract_hash = None
 
         # initial values for all spec hash types
-        for h in ht.hashes:
+        for h in ht.HASHES:
             setattr(self, h.attr, None)
 
         # cache for spec's prefix, computed lazily by prefix property
@@ -1905,10 +1888,22 @@ 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
@@ -2088,32 +2083,34 @@ def long_spec(self):
     def short_spec(self):
         """Returns a version of the spec with the dependencies hashed
         instead of completely enumerated."""
-        spec_format = "{name}{@version}{%compiler.name}{@compiler.version}"
-        spec_format += "{variants}{ arch=architecture}{/hash:7}"
-        return self.format(spec_format)
+        return self.format(
+            "{name}{@version}{variants}{ arch=architecture}"
+            "{/hash:7}{%compiler.name}{@compiler.version}"
+        )
 
     @property
     def cshort_spec(self):
         """Returns an auto-colorized version of ``self.short_spec``."""
-        spec_format = "{name}{@version}{%compiler.name}{@compiler.version}"
-        spec_format += "{variants}{ arch=architecture}{/hash:7}"
-        return self.cformat(spec_format)
+        return self.cformat(
+            "{name}{@version}{variants}{ arch=architecture}"
+            "{/hash:7}{%compiler.name}{@compiler.version}"
+        )
 
     @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):
@@ -2127,7 +2124,9 @@ 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)
@@ -2174,30 +2173,16 @@ def package_hash(self):
     def dag_hash(self, length=None):
         """This is Spack's default hash, used to identify installations.
 
-        Same as the full hash (includes package hash and build/link/run deps).
-        Tells us when package files and any dependencies have changes.
-
         NOTE: Versions of Spack prior to 0.18 only included link and run deps.
+        NOTE: Versions of Spack prior to 1.0 only did not include test deps.
 
         """
         return self._cached_hash(ht.dag_hash, length)
 
-    def process_hash(self, length=None):
-        """Hash used to transfer specs among processes.
-
-        This hash includes build and test dependencies and is only used to
-        serialize a spec and pass it around among processes.
-        """
-        return self._cached_hash(ht.process_hash, length)
-
     def dag_hash_bit_prefix(self, bits):
         """Get the first <bits> bits of the DAG hash as an integer type."""
         return spack.util.hash.base32_prefix_bits(self.dag_hash(), bits)
 
-    def process_hash_bit_prefix(self, bits):
-        """Get the first <bits> bits of the DAG hash as an integer type."""
-        return spack.util.hash.base32_prefix_bits(self.process_hash(), bits)
-
     def _lookup_hash(self):
         """Lookup just one spec with an abstract hash, returning a spec from the the environment,
         store, or finally, binary caches."""
@@ -2688,7 +2673,7 @@ 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.
@@ -2717,7 +2702,7 @@ 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:
@@ -2740,7 +2725,7 @@ def from_dict(data):
         return spec
 
     @staticmethod
-    def from_yaml(stream):
+    def from_yaml(stream) -> "Spec":
         """Construct a spec from YAML.
 
         Args:
@@ -2750,7 +2735,7 @@ 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:
@@ -2760,7 +2745,7 @@ 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):
@@ -2808,24 +2793,6 @@ 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
@@ -2842,94 +2809,6 @@ 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.
@@ -3084,7 +2963,7 @@ 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.
@@ -3093,7 +2972,7 @@ 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)
 
@@ -3111,7 +2990,7 @@ 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
@@ -3328,7 +3207,9 @@ 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))
@@ -3336,8 +3217,8 @@ 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)
@@ -3407,12 +3288,20 @@ 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
@@ -3442,7 +3331,9 @@ 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)
@@ -3510,7 +3401,7 @@ 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:
@@ -3554,10 +3445,6 @@ 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.
@@ -3662,11 +3549,11 @@ def _dup(self, other: "Spec", deps: Union[bool, dt.DepTypes, dt.DepFlag] = True)
 
         if self._concrete:
             self._dunder_hash = other._dunder_hash
-            for h in ht.hashes:
+            for h in ht.HASHES:
                 setattr(self, h.attr, getattr(other, h.attr, None))
         else:
             self._dunder_hash = None
-            for h in ht.hashes:
+            for h in ht.HASHES:
                 setattr(self, h.attr, None)
 
         return changed
@@ -3747,30 +3634,23 @@ 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.
@@ -3786,8 +3666,11 @@ 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."""
@@ -3862,16 +3745,6 @@ def _cmp_iter(self):
         # 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__`.
-        #
-        # TODO: We should eventually unify the `_cmp_*` methods with `to_node_dict` so
-        # TODO: there aren't two sources of truth, but this needs some thought, since
-        # TODO: they exist for speed.  We should benchmark whether it's really worth
-        # TODO: having two types of hashing now that we use `json` instead of `yaml` for
-        # TODO: spec hashing.
-        yield self.process_hash() if self.concrete else None
-
         def deps():
             for dep in sorted(itertools.chain.from_iterable(self._dependencies.values())):
                 yield dep.spec.name
@@ -4525,7 +4398,7 @@ def clear_caches(self, ignore: Tuple[str, ...] = ()) -> None:
         """
         Clears all cached hashes in a Spec, while preserving other properties.
         """
-        for h in ht.hashes:
+        for h in ht.HASHES:
             if h.attr not in ignore:
                 if hasattr(self, h.attr):
                     setattr(self, h.attr, None)
@@ -4534,18 +4407,12 @@ def clear_caches(self, ignore: Tuple[str, ...] = ()) -> None:
                 setattr(self, attr, None)
 
     def __hash__(self):
-        # If the spec is concrete, we leverage the process hash and just use
-        # a 64-bit prefix of it. The process hash has the advantage that it's
-        # computed once per concrete spec, and it's saved -- so if we read
-        # concrete specs we don't need to recompute the whole hash. This is
-        # good for large, unchanging specs.
-        #
-        # We use the process hash instead of the DAG hash here because the DAG
-        # hash includes the package hash, which can cause infinite recursion,
-        # and which isn't defined unless the spec has a known package.
+        # If the spec is concrete, we leverage the dag hash and just use a 64-bit prefix of it.
+        # The dag hash has the advantage that it's computed once per concrete spec, and it's saved
+        # -- so if we read concrete specs we don't need to recompute the whole hash.
         if self.concrete:
             if not self._dunder_hash:
-                self._dunder_hash = self.process_hash_bit_prefix(64)
+                self._dunder_hash = self.dag_hash_bit_prefix(64)
             return self._dunder_hash
 
         # This is the normal hash for lazy_lexicographic_ordering. It's
@@ -4554,7 +4421,7 @@ def __hash__(self):
         return hash(lang.tuplify(self._cmp_iter))
 
     def __reduce__(self):
-        return Spec.from_dict, (self.to_dict(hash=ht.process_hash),)
+        return Spec.from_dict, (self.to_dict(hash=ht.dag_hash),)
 
     def attach_git_version_lookup(self):
         # Add a git lookup method for GitVersions
@@ -4697,17 +4564,6 @@ 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():
@@ -4765,14 +4621,14 @@ 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]
@@ -4834,31 +4690,51 @@ 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:
@@ -4867,7 +4743,7 @@ def from_node_dict(cls, node):
         spec = Spec()
 
         name, node = cls.name_and_data(node)
-        for h in ht.hashes:
+        for h in ht.HASHES:
             setattr(spec, h.attr, node.get(h.name, None))
 
         spec.name = name
@@ -5050,7 +4926,7 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
         """
         for dep_name, elt in deps.items():
             if isinstance(elt, dict):
-                for h in ht.hashes:
+                for h in ht.HASHES:
                     if h.name in elt:
                         dep_hash, deptypes = elt[h.name], elt["type"]
                         hash_type = h.name
@@ -5093,7 +4969,7 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
             dep_name = dep["name"]
             if isinstance(elt, dict):
                 # new format: elements of dependency spec are keyed.
-                for h in ht.hashes:
+                for h in ht.HASHES:
                     if h.name in elt:
                         dep_hash, deptypes, hash_type, virtuals = cls.extract_info_from_dep(elt, h)
                         break
@@ -5203,6 +5079,13 @@ def get_host_environment() -> Dict[str, Any]:
     }
 
 
+def eval_conditional(string):
+    """Evaluate conditional definitions using restricted variable scope."""
+    valid_variables = get_host_environment()
+    valid_variables.update({"re": re, "env": os.environ})
+    return eval(string, valid_variables)
+
+
 class SpecParseError(spack.error.SpecError):
     """Wrapper for ParseError for when we're parsing specs."""
 
@@ -5361,8 +5244,10 @@ def __init__(self, spec):
 
 class AmbiguousHashError(spack.error.SpecError):
     def __init__(self, msg, *specs):
-        spec_fmt = "{namespace}.{name}{@version}{%compiler}{compiler_flags}"
-        spec_fmt += "{variants}{ arch=architecture}{/hash:7}"
+        spec_fmt = (
+            "{namespace}.{name}{@version}{compiler_flags}{variants}"
+            "{ arch=architecture}{/hash:7}{%compiler}"
+        )
         specs_str = "\n  " + "\n  ".join(spec.format(spec_fmt) for spec in specs)
         super().__init__(msg + specs_str)
 

lib/spack/spack/spec_parser.py

@@ -60,13 +60,17 @@
 import pathlib
 import re
 import sys
-from typing import Iterator, List, Optional
+import traceback
+import warnings
+from typing import Iterator, List, Optional, Tuple
 
 from llnl.util.tty import color
 
 import spack.deptypes
 import spack.error
+import spack.paths
 import spack.spec
+import spack.util.spack_yaml
 import spack.version
 from spack.tokenize import Token, TokenBase, Tokenizer
 
@@ -204,6 +208,32 @@ def __init__(self, tokens: List[Token], text: str):
         super().__init__(message)
 
 
+def _warn_about_variant_after_compiler(literal_str: str, issues: List[str]):
+    """Issue a warning if variant or other token is preceded by a compiler token. The warning is
+    only issued if it's actionable: either we know the config file it originates from, or we have
+    call site that's not internal to Spack."""
+    ignore = [spack.paths.lib_path, spack.paths.bin_path]
+    mark = spack.util.spack_yaml.get_mark_from_yaml_data(literal_str)
+    issue_str = ", ".join(issues)
+    error = f"{issue_str} in `{literal_str}`"
+
+    # warning from config file
+    if mark:
+        warnings.warn(f"{mark.name}:{mark.line + 1}: {error}")
+        return
+
+    # warning from hopefully package.py
+    for frame in reversed(traceback.extract_stack()):
+        if frame.lineno and not any(frame.filename.startswith(path) for path in ignore):
+            warnings.warn_explicit(
+                error,
+                category=spack.error.SpackAPIWarning,
+                filename=frame.filename,
+                lineno=frame.lineno,
+            )
+            return
+
+
 class SpecParser:
     """Parse text into specs"""
 
@@ -242,26 +272,31 @@ def add_dependency(dep, **edge_properties):
                 raise SpecParsingError(str(e), self.ctx.current_token, self.literal_str) from e
 
         initial_spec = initial_spec or spack.spec.Spec()
-        root_spec = SpecNodeParser(self.ctx, self.literal_str).parse(initial_spec)
+        root_spec, parser_warnings = SpecNodeParser(self.ctx, self.literal_str).parse(initial_spec)
         while True:
             if self.ctx.accept(SpecTokens.START_EDGE_PROPERTIES):
                 edge_properties = EdgeAttributeParser(self.ctx, self.literal_str).parse()
                 edge_properties.setdefault("depflag", 0)
                 edge_properties.setdefault("virtuals", ())
-                dependency = self._parse_node(root_spec)
+                dependency, warnings = self._parse_node(root_spec)
+                parser_warnings.extend(warnings)
                 add_dependency(dependency, **edge_properties)
 
             elif self.ctx.accept(SpecTokens.DEPENDENCY):
-                dependency = self._parse_node(root_spec)
+                dependency, warnings = self._parse_node(root_spec)
+                parser_warnings.extend(warnings)
                 add_dependency(dependency, depflag=0, virtuals=())
 
             else:
                 break
 
+        if parser_warnings:
+            _warn_about_variant_after_compiler(self.literal_str, parser_warnings)
+
         return root_spec
 
     def _parse_node(self, root_spec):
-        dependency = SpecNodeParser(self.ctx, self.literal_str).parse()
+        dependency, parser_warnings = SpecNodeParser(self.ctx, self.literal_str).parse()
         if dependency is None:
             msg = (
                 "the dependency sigil and any optional edge attributes must be followed by a "
@@ -270,7 +305,7 @@ def _parse_node(self, root_spec):
             raise SpecParsingError(msg, self.ctx.current_token, self.literal_str)
         if root_spec.concrete:
             raise spack.spec.RedundantSpecError(root_spec, "^" + str(dependency))
-        return dependency
+        return dependency, parser_warnings
 
     def all_specs(self) -> List["spack.spec.Spec"]:
         """Return all the specs that remain to be parsed"""
@@ -290,7 +325,7 @@ def __init__(self, ctx, literal_str):
 
     def parse(
         self, initial_spec: Optional["spack.spec.Spec"] = None
-    ) -> Optional["spack.spec.Spec"]:
+    ) -> Tuple["spack.spec.Spec", List[str]]:
         """Parse a single spec node from a stream of tokens
 
         Args:
@@ -299,12 +334,15 @@ def parse(
         Return
             The object passed as argument
         """
-        if not self.ctx.next_token or self.ctx.expect(SpecTokens.DEPENDENCY):
-            return initial_spec
+        parser_warnings: List[str] = []
+        last_compiler = None
 
         if initial_spec is None:
             initial_spec = spack.spec.Spec()
 
+        if not self.ctx.next_token or self.ctx.expect(SpecTokens.DEPENDENCY):
+            return initial_spec, parser_warnings
+
         # If we start with a package name we have a named spec, we cannot
         # accept another package name afterwards in a node
         if self.ctx.accept(SpecTokens.UNQUALIFIED_PACKAGE_NAME):
@@ -318,7 +356,7 @@ def parse(
             initial_spec.namespace = namespace
 
         elif self.ctx.accept(SpecTokens.FILENAME):
-            return FileParser(self.ctx).parse(initial_spec)
+            return FileParser(self.ctx).parse(initial_spec), parser_warnings
 
         def raise_parsing_error(string: str, cause: Optional[Exception] = None):
             """Raise a spec parsing error with token context."""
@@ -331,6 +369,12 @@ def add_flag(name: str, value: str, propagate: bool):
             except Exception as e:
                 raise_parsing_error(str(e), e)
 
+        def warn_if_after_compiler(token: str):
+            """Register a warning for %compiler followed by +variant that will in the future apply
+            to the compiler instead of the current root."""
+            if last_compiler:
+                parser_warnings.append(f"`{token}` should go before `{last_compiler}`")
+
         while True:
             if self.ctx.accept(SpecTokens.COMPILER):
                 if self.has_compiler:
@@ -339,6 +383,7 @@ def add_flag(name: str, value: str, propagate: bool):
                 compiler_name = self.ctx.current_token.value[1:]
                 initial_spec.compiler = spack.spec.CompilerSpec(compiler_name.strip(), ":")
                 self.has_compiler = True
+                last_compiler = self.ctx.current_token.value
 
             elif self.ctx.accept(SpecTokens.COMPILER_AND_VERSION):
                 if self.has_compiler:
@@ -349,6 +394,7 @@ def add_flag(name: str, value: str, propagate: bool):
                     compiler_name.strip(), compiler_version
                 )
                 self.has_compiler = True
+                last_compiler = self.ctx.current_token.value
 
             elif (
                 self.ctx.accept(SpecTokens.VERSION_HASH_PAIR)
@@ -363,14 +409,17 @@ def add_flag(name: str, value: str, propagate: bool):
                 )
                 initial_spec.attach_git_version_lookup()
                 self.has_version = True
+                warn_if_after_compiler(self.ctx.current_token.value)
 
             elif self.ctx.accept(SpecTokens.BOOL_VARIANT):
                 variant_value = self.ctx.current_token.value[0] == "+"
                 add_flag(self.ctx.current_token.value[1:].strip(), variant_value, propagate=False)
+                warn_if_after_compiler(self.ctx.current_token.value)
 
             elif self.ctx.accept(SpecTokens.PROPAGATED_BOOL_VARIANT):
                 variant_value = self.ctx.current_token.value[0:2] == "++"
                 add_flag(self.ctx.current_token.value[2:].strip(), variant_value, propagate=True)
+                warn_if_after_compiler(self.ctx.current_token.value)
 
             elif self.ctx.accept(SpecTokens.KEY_VALUE_PAIR):
                 match = SPLIT_KVP.match(self.ctx.current_token.value)
@@ -378,6 +427,7 @@ def add_flag(name: str, value: str, propagate: bool):
 
                 name, _, value = match.groups()
                 add_flag(name, strip_quotes_and_unescape(value), propagate=False)
+                warn_if_after_compiler(self.ctx.current_token.value)
 
             elif self.ctx.accept(SpecTokens.PROPAGATED_KEY_VALUE_PAIR):
                 match = SPLIT_KVP.match(self.ctx.current_token.value)
@@ -385,17 +435,19 @@ def add_flag(name: str, value: str, propagate: bool):
 
                 name, _, value = match.groups()
                 add_flag(name, strip_quotes_and_unescape(value), propagate=True)
+                warn_if_after_compiler(self.ctx.current_token.value)
 
             elif self.ctx.expect(SpecTokens.DAG_HASH):
                 if initial_spec.abstract_hash:
                     break
                 self.ctx.accept(SpecTokens.DAG_HASH)
                 initial_spec.abstract_hash = self.ctx.current_token.value[1:]
+                warn_if_after_compiler(self.ctx.current_token.value)
 
             else:
                 break
 
-        return initial_spec
+        return initial_spec, parser_warnings
 
 
 class FileParser:
@@ -485,23 +537,18 @@ def parse_one_or_raise(
         text (str): text to be parsed
         initial_spec: buffer where to parse the spec. If None a new one will be created.
     """
-    stripped_text = text.strip()
-    parser = SpecParser(stripped_text)
+    parser = SpecParser(text)
     result = parser.next_spec(initial_spec)
-    last_token = parser.ctx.current_token
+    next_token = parser.ctx.next_token
 
-    if last_token is not None and last_token.end != len(stripped_text):
-        message = "a single spec was requested, but parsed more than one:"
-        message += f"\n{text}"
-        if last_token is not None:
-            underline = f"\n{' ' * last_token.end}{'^' * (len(text) - last_token.end)}"
-            message += color.colorize(f"@*r{{{underline}}}")
+    if next_token:
+        message = f"expected a single spec, but got more:\n{text}"
+        underline = f"\n{' ' * next_token.start}{'^' * len(next_token.value)}"
+        message += color.colorize(f"@*r{{{underline}}}")
         raise ValueError(message)
 
     if result is None:
-        message = "a single spec was requested, but none was parsed:"
-        message += f"\n{text}"
-        raise ValueError(message)
+        raise ValueError("expected a single spec, but got none")
 
     return result
 

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/architecture.py

@@ -129,7 +129,7 @@ def test_satisfy_strict_constraint_when_not_concrete(architecture_tuple, constra
 )
 def test_concretize_target_ranges(root_target_range, dep_target_range, result, monkeypatch):
     spec = Spec(
-        f"pkg-a %gcc@10 foobar=bar target={root_target_range} ^pkg-b target={dep_target_range}"
+        f"pkg-a foobar=bar target={root_target_range} %gcc@10 ^pkg-b target={dep_target_range}"
     )
     with spack.concretize.disable_compiler_existence_check():
         spec = spack.concretize.concretize_one(spec)

lib/spack/spack/test/bindist.py

@@ -200,7 +200,11 @@ def dummy_prefix(tmpdir):
 @pytest.mark.requires_executables(*required_executables)
 @pytest.mark.maybeslow
 @pytest.mark.usefixtures(
-    "default_config", "cache_directory", "install_dir_default_layout", "temporary_mirror"
+    "default_config",
+    "cache_directory",
+    "install_dir_default_layout",
+    "temporary_mirror",
+    "mutable_mock_env_path",
 )
 def test_default_rpaths_create_install_default_layout(temporary_mirror_dir):
     """
@@ -272,7 +276,11 @@ def test_default_rpaths_install_nondefault_layout(temporary_mirror_dir):
 @pytest.mark.maybeslow
 @pytest.mark.nomockstage
 @pytest.mark.usefixtures(
-    "default_config", "cache_directory", "install_dir_default_layout", "temporary_mirror"
+    "default_config",
+    "cache_directory",
+    "install_dir_default_layout",
+    "temporary_mirror",
+    "mutable_mock_env_path",
 )
 def test_relative_rpaths_install_default_layout(temporary_mirror_dir):
     """
@@ -569,7 +577,6 @@ def test_FetchCacheError_only_accepts_lists_of_errors():
 def test_FetchCacheError_pretty_printing_multiple():
     e = bindist.FetchCacheError([RuntimeError("Oops!"), TypeError("Trouble!")])
     str_e = str(e)
-    print("'" + str_e + "'")
     assert "Multiple errors" in str_e
     assert "Error 1: RuntimeError: Oops!" in str_e
     assert "Error 2: TypeError: Trouble!" in str_e
@@ -1133,7 +1140,7 @@ def test_get_valid_spec_file_no_json(tmp_path, filename):
 
 def test_download_tarball_with_unsupported_layout_fails(tmp_path, mutable_config, capsys):
     layout_version = bindist.CURRENT_BUILD_CACHE_LAYOUT_VERSION + 1
-    spec = Spec("gmake@4.4.1%gcc@13.1.0 arch=linux-ubuntu23.04-zen2")
+    spec = Spec("gmake@4.4.1 arch=linux-ubuntu23.04-zen2 %gcc@13.1.0")
     spec._mark_concrete()
     spec_dict = spec.to_dict()
     spec_dict["buildcache_layout_version"] = layout_version

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/cc.py

@@ -210,7 +210,6 @@ def check_args_contents(cc, args, must_contain, must_not_contain):
     """
     with set_env(SPACK_TEST_COMMAND="dump-args"):
         cc_modified_args = cc(*args, output=str).strip().split("\n")
-        print(cc_modified_args)
         for a in must_contain:
             assert a in cc_modified_args
         for a in must_not_contain:

lib/spack/spack/test/ci.py

@@ -18,6 +18,7 @@
 import spack.repo as repo
 import spack.util.git
 from spack.test.conftest import MockHTTPResponse
+from spack.version import Version
 
 pytestmark = [pytest.mark.usefixtures("mock_packages")]
 
@@ -30,6 +31,43 @@ def repro_dir(tmp_path):
         yield result
 
 
+def test_get_added_versions_new_checksum(mock_git_package_changes):
+    repo_path, filename, commits = mock_git_package_changes
+
+    checksum_versions = {
+        "3f6576971397b379d4205ae5451ff5a68edf6c103b2f03c4188ed7075fbb5f04": Version("2.1.5"),
+        "a0293475e6a44a3f6c045229fe50f69dc0eebc62a42405a51f19d46a5541e77a": Version("2.1.4"),
+        "6c0853bb27738b811f2b4d4af095323c3d5ce36ceed6b50e5f773204fb8f7200": Version("2.0.7"),
+        "86993903527d9b12fc543335c19c1d33a93797b3d4d37648b5addae83679ecd8": Version("2.0.0"),
+    }
+
+    with fs.working_dir(str(repo_path)):
+        added_versions = ci.get_added_versions(
+            checksum_versions, filename, from_ref=commits[-1], to_ref=commits[-2]
+        )
+        assert len(added_versions) == 1
+        assert added_versions[0] == Version("2.1.5")
+
+
+def test_get_added_versions_new_commit(mock_git_package_changes):
+    repo_path, filename, commits = mock_git_package_changes
+
+    checksum_versions = {
+        "74253725f884e2424a0dd8ae3f69896d5377f325": Version("2.1.6"),
+        "3f6576971397b379d4205ae5451ff5a68edf6c103b2f03c4188ed7075fbb5f04": Version("2.1.5"),
+        "a0293475e6a44a3f6c045229fe50f69dc0eebc62a42405a51f19d46a5541e77a": Version("2.1.4"),
+        "6c0853bb27738b811f2b4d4af095323c3d5ce36ceed6b50e5f773204fb8f7200": Version("2.0.7"),
+        "86993903527d9b12fc543335c19c1d33a93797b3d4d37648b5addae83679ecd8": Version("2.0.0"),
+    }
+
+    with fs.working_dir(str(repo_path)):
+        added_versions = ci.get_added_versions(
+            checksum_versions, filename, from_ref=commits[2], to_ref=commits[1]
+        )
+        assert len(added_versions) == 1
+        assert added_versions[0] == Version("2.1.6")
+
+
 def test_pipeline_dag(config, tmpdir):
     r"""Test creation, pruning, and traversal of PipelineDAG using the
     following package dependency graph:
@@ -347,7 +385,6 @@ def test_get_spec_filter_list(mutable_mock_env_path, mutable_mock_repo):
     for key, val in expectations.items():
         affected_specs = ci.get_spec_filter_list(e1, touched, dependent_traverse_depth=key)
         affected_pkg_names = set([s.name for s in affected_specs])
-        print(f"{key}: {affected_pkg_names}")
         assert affected_pkg_names == val
 
 

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")
 
@@ -214,13 +214,11 @@ def verify_mirror_contents():
             if in_env_pkg in p:
                 found_pkg = True
 
-        if not found_pkg:
-            print("Expected to find {0} in {1}".format(in_env_pkg, dest_mirror_dir))
-            assert False
+        assert found_pkg, f"Expected to find {in_env_pkg} in {dest_mirror_dir}"
 
     # 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")