petsc: fix compilers listed in pkgconfig/petsc.pc (#48201)

* petsc: fix compilers listed in pkgconfig/petsc.pc

* Also fix reconfigure*.py

.github/workflows/audit.yaml

@@ -66,7 +66,7 @@ jobs:
           ./share/spack/qa/validate_last_exit.ps1
           spack -d audit externals
           ./share/spack/qa/validate_last_exit.ps1
-    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
       if: ${{ inputs.with_coverage == 'true' && runner.os != 'Windows' }}
       with:
         name: coverage-audits-${{ matrix.system.os }}

.github/workflows/bootstrap.yml

@@ -161,11 +161,7 @@ jobs:
           source share/spack/setup-env.sh
           spack -d gpg list
           tree $HOME/.spack/bootstrap/store/
-      - name: Bootstrap File
-        run: |
-          source share/spack/setup-env.sh
-          spack -d python share/spack/qa/bootstrap-file.py
-          tree $HOME/.spack/bootstrap/store/
+
 
   windows:
     runs-on: "windows-latest"
@@ -196,9 +192,3 @@ jobs:
           spack -d gpg list
           ./share/spack/qa/validate_last_exit.ps1
           tree $env:userprofile/.spack/bootstrap/store/
-      - name: Bootstrap File
-        run: |
-          ./share/spack/setup-env.ps1
-          spack -d python share/spack/qa/bootstrap-file.py
-          ./share/spack/qa/validate_last_exit.ps1
-          tree $env:userprofile/.spack/bootstrap/store/

.github/workflows/build-containers.yml

@@ -57,7 +57,13 @@ jobs:
       - name: Checkout
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
 
-      - uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81
+      - name: Determine latest release tag
+        id: latest
+        run: |
+          git fetch --quiet --tags
+          echo "tag=$(git tag --list --sort=-v:refname | grep -E '^v[0-9]+\.[0-9]+\.[0-9]+$' | head -n 1)" | tee -a $GITHUB_OUTPUT
+
+      - uses: docker/metadata-action@369eb591f429131d6889c46b94e711f089e6ca96
         id: docker_meta
         with:
           images: |
@@ -71,6 +77,7 @@ jobs:
               type=semver,pattern={{major}}
               type=ref,event=branch
               type=ref,event=pr
+              type=raw,value=latest,enable=${{ github.ref == format('refs/tags/{0}', steps.latest.outputs.tag) }}
 
       - name: Generate the Dockerfile
         env:
@@ -87,7 +94,7 @@ jobs:
           fi
 
       - name: Upload Dockerfile
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+        uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
         with:
           name: dockerfiles_${{ matrix.dockerfile[0] }}
           path: dockerfiles
@@ -96,7 +103,7 @@ jobs:
         uses: docker/setup-qemu-action@49b3bc8e6bdd4a60e6116a5414239cba5943d3cf
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@c47758b77c9736f4b2ef4073d4d51994fabfe349
+        uses: docker/setup-buildx-action@6524bf65af31da8d45b59e8c27de4bd072b392f5
 
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567
@@ -113,7 +120,7 @@ jobs:
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build & Deploy ${{ matrix.dockerfile[0] }}
-        uses: docker/build-push-action@4f58ea79222b3b9dc2c8bbdd6debcef730109a75
+        uses: docker/build-push-action@48aba3b46d1b1fec4febb7c5d0c644b249a11355
         with:
           context: dockerfiles/${{ matrix.dockerfile[0] }}
           platforms: ${{ matrix.dockerfile[1] }}
@@ -126,7 +133,7 @@ jobs:
     needs: deploy-images
     steps:
       - name: Merge Artifacts
-        uses: actions/upload-artifact/merge@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+        uses: actions/upload-artifact/merge@6f51ac03b9356f520e9adb1b1b7802705f340c2b
         with:
           name: dockerfiles
           pattern: dockerfiles_*

.github/workflows/coverage.yml

@@ -29,6 +29,7 @@ jobs:
     - run: coverage xml
 
     - name: "Upload coverage report to CodeCov"
-      uses: codecov/codecov-action@b9fd7d16f6d7d1b5d2bec1a2887e65ceed900238
+      uses: codecov/codecov-action@05f5a9cfad807516dbbef9929c4a42df3eb78766
       with:
         verbose: true
+        fail_ci_if_error: false

.github/workflows/requirements/style/requirements.txt

@@ -3,5 +3,5 @@ clingo==5.7.1
 flake8==7.1.1
 isort==5.13.2
 mypy==1.8.0
-types-six==1.16.21.20241105
+types-six==1.17.0.20241205
 vermin==1.6.0

.github/workflows/unit_tests.yaml

@@ -15,17 +15,17 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         on_develop:
         - ${{ github.ref == 'refs/heads/develop' }}
         include:
         - python-version: '3.6'
           os: ubuntu-20.04
           on_develop: ${{ github.ref == 'refs/heads/develop' }}
-        exclude:
         - python-version: '3.7'
-          os: ubuntu-latest
-          on_develop: false
+          os: ubuntu-22.04
+          on_develop: ${{ github.ref == 'refs/heads/develop' }}
+        exclude:
         - python-version: '3.8'
           os: ubuntu-latest
           on_develop: false
@@ -52,7 +52,13 @@ jobs:
           # Needed for unit tests
           sudo apt-get -y install \
               coreutils cvs gfortran graphviz gnupg2 mercurial ninja-build \
-              cmake bison libbison-dev kcov
+              cmake bison libbison-dev subversion
+    # On ubuntu 24.04, kcov was removed. It may come back in some future Ubuntu
+    - name: Set up Homebrew
+      id: set-up-homebrew
+      uses: Homebrew/actions/setup-homebrew@40e9946c182a64b3db1bf51be0dcb915f7802aa9
+    - name: Install kcov with brew
+      run: "brew install kcov"
     - name: Install Python packages
       run: |
           pip install --upgrade pip setuptools pytest pytest-xdist pytest-cov
@@ -80,7 +86,7 @@ jobs:
           UNIT_TEST_COVERAGE: ${{ matrix.python-version == '3.11' }}
       run: |
           share/spack/qa/run-unit-tests
-    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
       with:
         name: coverage-${{ matrix.os }}-python${{ matrix.python-version }}
         path: coverage
@@ -99,7 +105,13 @@ jobs:
       run: |
           sudo apt-get -y update
           # Needed for shell tests
-          sudo apt-get install -y coreutils kcov csh zsh tcsh fish dash bash
+          sudo apt-get install -y coreutils csh zsh tcsh fish dash bash subversion
+    # On ubuntu 24.04, kcov was removed. It may come back in some future Ubuntu
+    - name: Set up Homebrew
+      id: set-up-homebrew
+      uses: Homebrew/actions/setup-homebrew@40e9946c182a64b3db1bf51be0dcb915f7802aa9
+    - name: Install kcov with brew
+      run: "brew install kcov"
     - name: Install Python packages
       run: |
           pip install --upgrade pip setuptools pytest coverage[toml] pytest-xdist
@@ -113,7 +125,7 @@ jobs:
           COVERAGE: true
       run: |
           share/spack/qa/run-shell-tests
-    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
       with:
         name: coverage-shell
         path: coverage
@@ -128,13 +140,13 @@ jobs:
     - name: Install dependencies
       run: |
           dnf install -y \
-              bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
+              bzip2 curl gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
               make patch tcl unzip which xz
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
     - name: Setup repo and non-root user
       run: |
           git --version
-          git config --global --add safe.directory /__w/spack/spack
+          git config --global --add safe.directory '*'
           git fetch --unshallow
           . .github/workflows/bin/setup_git.sh
           useradd spack-test
@@ -175,7 +187,7 @@ jobs:
         spack bootstrap status
         spack solve zlib
         spack unit-test --verbose --cov --cov-config=pyproject.toml --cov-report=xml:coverage.xml lib/spack/spack/test/concretization/core.py
-    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
       with:
         name: coverage-clingo-cffi
         path: coverage
@@ -213,7 +225,7 @@ jobs:
         $(which spack) solve zlib
         common_args=(--dist loadfile --tx '4*popen//python=./bin/spack-tmpconfig python -u ./bin/spack python' -x)
         $(which spack) unit-test --verbose --cov --cov-config=pyproject.toml --cov-report=xml:coverage.xml "${common_args[@]}"
-    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
       with:
         name: coverage-${{ matrix.os }}-python${{ matrix.python-version }}
         path: coverage
@@ -244,7 +256,7 @@ jobs:
       run: |
         spack unit-test -x --verbose --cov --cov-config=pyproject.toml
         ./share/spack/qa/validate_last_exit.ps1
-    - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
+    - uses: actions/upload-artifact@6f51ac03b9356f520e9adb1b1b7802705f340c2b
       with:
         name: coverage-windows
         path: coverage

.github/workflows/valid-style.yml

@@ -13,8 +13,7 @@ concurrency:
 
 
 jobs:
-  # Validate that the code can be run on all the Python versions
-  # supported by Spack
+  # Validate that the code can be run on all the Python versions supported by Spack
   validate:
     runs-on: ubuntu-latest
     steps:
@@ -74,7 +73,7 @@ jobs:
       - name: Setup repo and non-root user
         run: |
           git --version
-          git config --global --add safe.directory /__w/spack/spack
+          git config --global --add safe.directory '*'
           git fetch --unshallow
           . .github/workflows/bin/setup_git.sh
           useradd spack-test
@@ -87,6 +86,7 @@ jobs:
           spack -d bootstrap now --dev
           spack -d style -t black
           spack unit-test -V
+  # Check we don't make the situation with circular imports worse
   import-check:
     runs-on: ubuntu-latest
     steps:
@@ -121,28 +121,46 @@ jobs:
       uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
       with:
         repository: haampie/circular-import-fighter
-        ref: 9f60f51bc7134e0be73f27623f1b0357d1718427
+        ref: b5d6ce9be35f602cca7d5a6aa0259fca10639cca
         path: circular-import-fighter
     - name: Install dependencies
       working-directory: circular-import-fighter
       run: make -j dependencies
-    - name: Import cycles before
+    - name: Problematic imports before
       working-directory: circular-import-fighter
-      run: make SPACK_ROOT=../old && cp solution solution.old
-    - name: Import cycles after
+      run: make SPACK_ROOT=../old SUFFIX=.old
+    - name: Problematic imports after
       working-directory: circular-import-fighter
-      run: make clean-graph && make SPACK_ROOT=../new && cp solution solution.new
+      run: make SPACK_ROOT=../new SUFFIX=.new
     - name: Compare import cycles
       working-directory: circular-import-fighter
       run: |
-        edges_before="$(grep -oP 'edges to delete: \K\d+' solution.old)"
-        edges_after="$(grep -oP 'edges to delete: \K\d+' solution.new)"
+        edges_before="$(head -n1 solution.old)"
+        edges_after="$(head -n1 solution.new)"
         if [ "$edges_after" -gt "$edges_before" ]; then
           printf '\033[1;31mImport check failed: %s imports need to be deleted, ' "$edges_after"
           printf 'previously this was %s\033[0m\n'  "$edges_before"
-          printf 'Compare \033[1;97m"Import cycles before"\033[0m and '
-          printf '\033[1;97m"Import cycles after"\033[0m to see problematic imports.\n'
+          printf 'Compare \033[1;97m"Problematic imports before"\033[0m and '
+          printf '\033[1;97m"Problematic imports after"\033[0m.\n'
           exit 1
         else
           printf '\033[1;32mImport check passed: %s <= %s\033[0m\n' "$edges_after" "$edges_before"
         fi
+
+  # Further style checks from pylint
+  pylint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
+        with:
+          python-version: '3.13'
+          cache: 'pip'
+      - name: Install Python packages
+        run: |
+          pip install --upgrade pip setuptools pylint
+      - name: Pylint (Spack Core)
+        run: |
+          pylint -j 4 --disable=all --enable=unspecified-encoding --ignore-paths=lib/spack/external lib

COPYRIGHT

@@ -102,6 +102,6 @@ PackageName: sbang
 PackageHomePage: https://github.com/spack/sbang
 PackageLicenseDeclared: Apache-2.0 OR MIT
 
-PackageName: six
-PackageHomePage: https://pypi.python.org/pypi/six
-PackageLicenseDeclared: MIT
+PackageName: typing_extensions
+PackageHomePage: https://pypi.org/project/typing-extensions/
+PackageLicenseDeclared: Python-2.0

README.md

@@ -70,7 +70,7 @@ Tutorial
 ----------------
 
 We maintain a
-[**hands-on tutorial**](https://spack.readthedocs.io/en/latest/tutorial.html).
+[**hands-on tutorial**](https://spack-tutorial.readthedocs.io/).
 It covers basic to advanced usage, packaging, developer features, and large HPC
 deployments.  You can do all of the exercises on your own laptop using a
 Docker container.

etc/spack/defaults/concretizer.yaml

@@ -55,3 +55,11 @@ concretizer:
   splice:
     explicit: []
     automatic: false
+  # Maximum time, in seconds, allowed for the 'solve' phase. If set to 0, there is no time limit.
+  timeout: 0
+  # If set to true, exceeding the timeout will always result in a concretization error. If false,
+  # the best (suboptimal) model computed before the timeout is used.
+  #
+  # 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

etc/spack/defaults/config.yaml

@@ -194,6 +194,12 @@ config:
     # executables with many dependencies, in particular on slow filesystems.
     bind: false
 
+    # Controls the handling of missing dynamic libraries after installation.
+    # Options are ignore (default), warn, or error. If set to error, the
+    # installation fails if installed binaries reference dynamic libraries that
+    # are not found in their specified rpaths.
+    missing_library_policy: ignore
+
 
   # Set to 'false' to allow installation on filesystems that doesn't allow setgid bit
   # manipulation by unprivileged user (e.g. AFS)

etc/spack/defaults/packages.yaml

@@ -76,6 +76,8 @@ packages:
     buildable: false
   cray-mvapich2:
     buildable: false
+  egl:
+    buildable: false
   fujitsu-mpi:
     buildable: false
   hpcx-mpi:

lib/spack/docs/binary_caches.rst

@@ -265,25 +265,30 @@ infrastructure, or to cache Spack built binaries in Github Actions and
 GitLab CI.
 
 To get started, configure an OCI mirror using ``oci://`` as the scheme,
-and optionally specify a username and password (or personal access token):
+and optionally specify variables that hold the username and password (or
+personal access token) for the registry:
 
 .. code-block:: console
 
-    $ spack mirror add --oci-username username --oci-password password my_registry oci://example.com/my_image
+    $ spack mirror add --oci-username-variable REGISTRY_USER \
+                       --oci-password-variable REGISTRY_TOKEN \
+                       my_registry oci://example.com/my_image
 
 Spack follows the naming conventions of Docker, with Dockerhub as the default
 registry. To use Dockerhub, you can omit the registry domain:
 
 .. code-block:: console
 
-    $ spack mirror add --oci-username username --oci-password password my_registry oci://username/my_image
+    $ spack mirror add ... my_registry oci://username/my_image
 
 From here, you can use the mirror as any other build cache:
 
 .. code-block:: console
 
+    $ export REGISTRY_USER=...
+    $ export REGISTRY_TOKEN=...
     $ spack buildcache push my_registry <specs...>  # push to the registry
-    $ spack install <specs...> # install from the registry
+    $ spack install <specs...>  # or install from the registry
 
 A unique feature of buildcaches on top of OCI registries is that it's incredibly
 easy to generate get a runnable container image with the binaries installed. This

lib/spack/docs/build_systems/qmakepackage.rst

@@ -25,6 +25,14 @@ QMake does not appear to have a standardized way of specifying
 the installation directory, so you may have to set environment
 variables or edit ``*.pro`` files to get things working properly.
 
+QMake packages will depend on the virtual ``qmake`` package which
+is provided by multiple versions of Qt: ``qt`` provides Qt up to
+Qt5, and ``qt-base`` provides Qt from version Qt6 onwards. This
+split was motivated by the desire to split the single Qt package
+into its components to allow for more fine-grained installation.
+To depend on a specific version, refer to the documentation on
+:ref:`virtual-dependencies`.
+
 ^^^^^^
 Phases
 ^^^^^^

lib/spack/docs/conf.py

@@ -210,7 +210,7 @@ def setup(sphinx):
     # Spack classes that are private and we don't want to expose
     ("py:class", "spack.provider_index._IndexBase"),
     ("py:class", "spack.repo._PrependFileLoader"),
-    ("py:class", "spack.build_systems._checks.BaseBuilder"),
+    ("py:class", "spack.build_systems._checks.BuilderWithDefaults"),
     # Spack classes that intersphinx is unable to resolve
     ("py:class", "spack.version.StandardVersion"),
     ("py:class", "spack.spec.DependencySpec"),

lib/spack/docs/containers.rst

@@ -38,9 +38,11 @@ just have to configure and OCI registry and run ``spack buildcache push``.
    spack -e . install
 
    # Configure the registry
-   spack -e . mirror add --oci-username ... --oci-password ... container-registry oci://example.com/name/image
+   spack -e . mirror add --oci-username-variable REGISTRY_USER \
+                         --oci-password-variable REGISTRY_TOKEN \
+                        container-registry oci://example.com/name/image
 
-   # Push the image
+   # Push the image (do set REGISTRY_USER and REGISTRY_TOKEN)
    spack -e . buildcache push --update-index --base-image ubuntu:22.04 --tag my_env container-registry
 
 The resulting container image can then be run as follows:

lib/spack/docs/developer_guide.rst

@@ -178,8 +178,8 @@ Spec-related modules
   Contains :class:`~spack.spec.Spec`. Also implements most of the logic for concretization
   of specs.
 
-:mod:`spack.parser`
-  Contains :class:`~spack.parser.SpecParser` and functions related to parsing specs.
+:mod:`spack.spec_parser`
+  Contains :class:`~spack.spec_parser.SpecParser` and functions related to parsing specs.
 
 :mod:`spack.version`
   Implements a simple :class:`~spack.version.Version` class with simple

lib/spack/docs/environments.rst

@@ -1042,7 +1042,7 @@ file snippet we define a view named ``mpis``, rooted at
 ``/path/to/view`` in which all projections use the package name,
 version, and compiler name to determine the path for a given
 package. This view selects all packages that depend on MPI, and
-excludes those built with the PGI compiler at version 18.5.
+excludes those built with the GCC compiler at version 18.5.
 The root specs with their (transitive) link and run type dependencies
 will be put in the view due to the  ``link: all`` option,
 and the files in the view will be symlinks to the spack install
@@ -1056,7 +1056,7 @@ directories.
        mpis:
          root: /path/to/view
          select: [^mpi]
-         exclude: ['%pgi@18.5']
+         exclude: ['%gcc@18.5']
          projections:
            all: '{name}/{version}-{compiler.name}'
          link: all

lib/spack/docs/getting_started.rst

@@ -35,7 +35,7 @@ A build matrix showing which packages are working on which systems is shown belo
       .. code-block:: console
 
          apt update
-         apt install bzip2 ca-certificates file g++ gcc gfortran git gzip lsb-release patch python3 tar unzip xz-utils zstd
+         apt install bzip2 ca-certificates g++ gcc gfortran git gzip lsb-release patch python3 tar unzip xz-utils zstd
 
    .. tab-item:: RHEL
 
@@ -148,20 +148,22 @@ The first time you concretize a spec, Spack will bootstrap automatically:
    --------------------------------
    zlib@1.2.13%gcc@9.4.0+optimize+pic+shared build_system=makefile arch=linux-ubuntu20.04-icelake
 
+The default bootstrap behavior is to use pre-built binaries. You can verify the
+active bootstrap repositories with:
+
+.. command-output:: spack bootstrap list
+
 If for security concerns you cannot bootstrap ``clingo`` from pre-built
 binaries, you have to disable fetching the binaries we generated with Github Actions.
 
 .. code-block:: console
 
-   $ spack bootstrap disable github-actions-v0.4
-   ==> "github-actions-v0.4" is now disabled and will not be used for bootstrapping
-   $ spack bootstrap disable github-actions-v0.3
-   ==> "github-actions-v0.3" is now disabled and will not be used for bootstrapping
-
-You can verify that the new settings are effective with:
-
-.. command-output:: spack bootstrap list
+   $ spack bootstrap disable github-actions-v0.6
+   ==> "github-actions-v0.6" is now disabled and will not be used for bootstrapping
+   $ spack bootstrap disable github-actions-v0.5
+   ==> "github-actions-v0.5" is now disabled and will not be used for bootstrapping
 
+You can verify that the new settings are effective with ``spack bootstrap list``.
 
 .. note::
 
@@ -283,10 +285,6 @@ compilers`` or ``spack compiler list``:
        intel@14.0.1  intel@13.0.1  intel@12.1.2  intel@10.1
    -- clang -------------------------------------------------------
        clang@3.4  clang@3.3  clang@3.2  clang@3.1
-   -- pgi ---------------------------------------------------------
-       pgi@14.3-0   pgi@13.2-0  pgi@12.1-0   pgi@10.9-0  pgi@8.0-1
-       pgi@13.10-0  pgi@13.1-1  pgi@11.10-0  pgi@10.2-0  pgi@7.1-3
-       pgi@13.6-0   pgi@12.8-0  pgi@11.1-0   pgi@9.0-4   pgi@7.0-6
 
 Any of these compilers can be used to build Spack packages.  More on
 how this is done is in :ref:`sec-specs`.
@@ -806,65 +804,6 @@ flags to the ``icc`` command:
            spec: intel@15.0.24.4.9.3
 
 
-^^^
-PGI
-^^^
-
-PGI comes with two sets of compilers for C++ and Fortran,
-distinguishable by their names.  "Old" compilers:
-
-.. code-block:: yaml
-
-    cc:  /soft/pgi/15.10/linux86-64/15.10/bin/pgcc
-    cxx: /soft/pgi/15.10/linux86-64/15.10/bin/pgCC
-    f77: /soft/pgi/15.10/linux86-64/15.10/bin/pgf77
-    fc:  /soft/pgi/15.10/linux86-64/15.10/bin/pgf90
-
-"New" compilers:
-
-.. code-block:: yaml
-
-    cc:  /soft/pgi/15.10/linux86-64/15.10/bin/pgcc
-    cxx: /soft/pgi/15.10/linux86-64/15.10/bin/pgc++
-    f77: /soft/pgi/15.10/linux86-64/15.10/bin/pgfortran
-    fc:  /soft/pgi/15.10/linux86-64/15.10/bin/pgfortran
-
-Older installations of PGI contains just the old compilers; whereas
-newer installations contain the old and the new.  The new compiler is
-considered preferable, as some packages
-(``hdf``) will not build with the old compiler.
-
-When auto-detecting a PGI compiler, there are cases where Spack will
-find the old compilers, when you really want it to find the new
-compilers.  It is best to check this ``compilers.yaml``; and if the old
-compilers are being used, change ``pgf77`` and ``pgf90`` to
-``pgfortran``.
-
-Other issues:
-
-* There are reports that some packages will not build with PGI,
-  including ``libpciaccess`` and ``openssl``.  A workaround is to
-  build these packages with another compiler and then use them as
-  dependencies for PGI-build packages.  For example:
-
-  .. code-block:: console
-
-     $ spack install openmpi%pgi ^libpciaccess%gcc
-
-
-* PGI requires a license to use; see :ref:`licensed-compilers` for more
-  information on installation.
-
-.. note::
-
-   It is believed the problem with HDF 4 is that everything is
-   compiled with the ``F77`` compiler, but at some point some Fortran
-   90 code slipped in there. So compilers that can handle both FORTRAN
-   77 and Fortran 90 (``gfortran``, ``pgfortran``, etc) are fine.  But
-   compilers specific to one or the other (``pgf77``, ``pgf90``) won't
-   work.
-
-
 ^^^
 NAG
 ^^^
@@ -1389,6 +1328,7 @@ Required:
 * Microsoft Visual Studio
 * Python
 * Git
+* 7z
 
 Optional:
 * Intel Fortran (needed for some packages)
@@ -1454,6 +1394,13 @@ as the project providing Git support on Windows. This is additionally the recomm
 for installing Git on Windows, a link to which can be found above. Spack requires the
 utilities vendored by this project.
 
+"""
+7zip
+"""
+
+A tool for extracting ``.xz`` files is required for extracting source tarballs. The latest 7zip
+can be located at https://sourceforge.net/projects/sevenzip/.
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Step 2: Install and setup Spack
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

lib/spack/docs/packaging_guide.rst

@@ -1928,71 +1928,29 @@ to the empty list.
 String. A URL pointing to license setup instructions for the software.
 Defaults to the empty string.
 
-For example, let's take a look at the package for the PGI compilers.
+For example, let's take a look at the Arm Forge package.
 
 .. code-block:: python
 
    # Licensing
    license_required = True
-   license_comment  = "#"
-   license_files    = ["license.dat"]
-   license_vars     = ["PGROUPD_LICENSE_FILE", "LM_LICENSE_FILE"]
-   license_url      = "http://www.pgroup.com/doc/pgiinstall.pdf"
+   license_comment = "#"
+   license_files = ["licences/Licence"]
+   license_vars = [
+       "ALLINEA_LICENSE_DIR",
+       "ALLINEA_LICENCE_DIR",
+       "ALLINEA_LICENSE_FILE",
+       "ALLINEA_LICENCE_FILE",
+   ]
+   license_url = "https://developer.arm.com/documentation/101169/latest/Use-Arm-Licence-Server"
 
-As you can see, PGI requires a license. Its license manager, FlexNet, uses
-the ``#`` symbol to denote a comment. It expects the license file to be
-named ``license.dat`` and to be located directly in the installation prefix.
-If you would like the installation file to be located elsewhere, simply set
-``PGROUPD_LICENSE_FILE`` or ``LM_LICENSE_FILE`` after installation. For
-further instructions on installation and licensing, see the URL provided.
+Arm Forge requires a license. Its license manager uses the ``#`` symbol to denote a comment.
+It expects the license file to be named ``License`` and to be located in a ``licenses`` directory
+in the installation prefix.
 
-Let's walk through a sample PGI installation to see exactly what Spack is
-and isn't capable of. Since PGI does not provide a download URL, it must
-be downloaded manually. It can either be added to a mirror or located in
-the current directory when ``spack install pgi`` is run. See :ref:`mirrors`
-for instructions on setting up a mirror.
-
-After running ``spack install pgi``, the first thing that will happen is
-Spack will create a global license file located at
-``$SPACK_ROOT/etc/spack/licenses/pgi/license.dat``. It will then open up the
-file using :ref:`your favorite editor <controlling-the-editor>`. It will look like
-this:
-
-.. code-block:: sh
-
-   # A license is required to use pgi.
-   #
-   # The recommended solution is to store your license key in this global
-   # license file. After installation, the following symlink(s) will be
-   # added to point to this file (relative to the installation prefix):
-   #
-   #   license.dat
-   #
-   # Alternatively, use one of the following environment variable(s):
-   #
-   #   PGROUPD_LICENSE_FILE
-   #   LM_LICENSE_FILE
-   #
-   # If you choose to store your license in a non-standard location, you may
-   # set one of these variable(s) to the full pathname to the license file, or
-   # port@host if you store your license keys on a dedicated license server.
-   # You will likely want to set this variable in a module file so that it
-   # gets loaded every time someone tries to use pgi.
-   #
-   # For further information on how to acquire a license, please refer to:
-   #
-   #   http://www.pgroup.com/doc/pgiinstall.pdf
-   #
-   # You may enter your license below.
-
-You can add your license directly to this file, or tell FlexNet to use a
-license stored on a separate license server. Here is an example that
-points to a license server called licman1:
-
-.. code-block:: none
-
-   SERVER licman1.mcs.anl.gov 00163eb7fba5 27200
-   USE_SERVER
+If you would like the installation file to be located elsewhere, simply set ``ALLINEA_LICENSE_DIR`` or
+one of the other license variables after installation. For further instructions on installation and
+licensing, see the URL provided.
 
 If your package requires the license to install, you can reference the
 location of this global license using ``self.global_license_file``.
@@ -2967,9 +2925,9 @@ make sense during the build phase may not be needed at runtime, and vice versa.
 it makes sense to let a dependency set the environment variables for its dependents. To allow all
 this, Spack provides four different methods that can be overridden in a package:
 
-1. :meth:`setup_build_environment <spack.builder.Builder.setup_build_environment>`
+1. :meth:`setup_build_environment <spack.builder.BaseBuilder.setup_build_environment>`
 2. :meth:`setup_run_environment <spack.package_base.PackageBase.setup_run_environment>`
-3. :meth:`setup_dependent_build_environment <spack.builder.Builder.setup_dependent_build_environment>`
+3. :meth:`setup_dependent_build_environment <spack.builder.BaseBuilder.setup_dependent_build_environment>`
 4. :meth:`setup_dependent_run_environment <spack.package_base.PackageBase.setup_dependent_run_environment>`
 
 The Qt package, for instance, uses this call:
@@ -5179,7 +5137,7 @@ other checks.
      - Not applicable
    * - :ref:`PythonPackage <pythonpackage>`
      - Not applicable
-     - ``test`` (module imports)
+     - ``test_imports`` (module imports)
    * - :ref:`QMakePackage <qmakepackage>`
      - ``check`` (``make check``)
      - Not applicable
@@ -5188,7 +5146,7 @@ other checks.
      - Not applicable
    * - :ref:`SIPPackage <sippackage>`
      - Not applicable
-     - ``test`` (module imports)
+     - ``test_imports`` (module imports)
    * - :ref:`WafPackage <wafpackage>`
      - ``build_test`` (must be overridden)
      - ``install_test`` (must be overridden)

lib/spack/docs/requirements.txt

@@ -1,12 +1,12 @@
 sphinx==8.1.3
-sphinxcontrib-programoutput==0.17
+sphinxcontrib-programoutput==0.18
 sphinx_design==0.6.1
-sphinx-rtd-theme==3.0.1
+sphinx-rtd-theme==3.0.2
 python-levenshtein==0.26.1
 docutils==0.21.2
 pygments==2.18.0
-urllib3==2.2.3
-pytest==8.3.3
+urllib3==2.3.0
+pytest==8.3.4
 isort==5.13.2
 black==24.10.0
 flake8==7.1.1

lib/spack/docs/tables/system_prerequisites.csv

@@ -8,7 +8,6 @@ unzip, , , Compress/Decompress archives
 bzip2, , , Compress/Decompress archives
 xz, , , Compress/Decompress archives
 zstd, , Optional, Compress/Decompress archives
-file, , , Create/Use Buildcaches
 lsb-release, , , Linux: identify operating system version
 gnupg2, , , Sign/Verify Buildcaches
 git, , , Manage Software Repositories

lib/spack/external/_vendoring/typing_extensions.LICENSE

@@ -0,0 +1,254 @@
+A. HISTORY OF THE SOFTWARE
+==========================
+
+Python was created in the early 1990s by Guido van Rossum at Stichting
+Mathematisch Centrum (CWI, see http://www.cwi.nl) in the Netherlands
+as a successor of a language called ABC.  Guido remains Python's
+principal author, although it includes many contributions from others.
+
+In 1995, Guido continued his work on Python at the Corporation for
+National Research Initiatives (CNRI, see http://www.cnri.reston.va.us)
+in Reston, Virginia where he released several versions of the
+software.
+
+In May 2000, Guido and the Python core development team moved to
+BeOpen.com to form the BeOpen PythonLabs team.  In October of the same
+year, the PythonLabs team moved to Digital Creations (now Zope
+Corporation, see http://www.zope.com).  In 2001, the Python Software
+Foundation (PSF, see http://www.python.org/psf/) was formed, a
+non-profit organization created specifically to own Python-related
+Intellectual Property.  Zope Corporation is a sponsoring member of
+the PSF.
+
+All Python releases are Open Source (see http://www.opensource.org for
+the Open Source Definition).  Historically, most, but not all, Python
+releases have also been GPL-compatible; the table below summarizes
+the various releases.
+
+    Release         Derived     Year        Owner       GPL-
+                    from                                compatible? (1)
+
+    0.9.0 thru 1.2              1991-1995   CWI         yes
+    1.3 thru 1.5.2  1.2         1995-1999   CNRI        yes
+    1.6             1.5.2       2000        CNRI        no
+    2.0             1.6         2000        BeOpen.com  no
+    1.6.1           1.6         2001        CNRI        yes (2)
+    2.1             2.0+1.6.1   2001        PSF         no
+    2.0.1           2.0+1.6.1   2001        PSF         yes
+    2.1.1           2.1+2.0.1   2001        PSF         yes
+    2.1.2           2.1.1       2002        PSF         yes
+    2.1.3           2.1.2       2002        PSF         yes
+    2.2 and above   2.1.1       2001-now    PSF         yes
+
+Footnotes:
+
+(1) GPL-compatible doesn't mean that we're distributing Python under
+    the GPL.  All Python licenses, unlike the GPL, let you distribute
+    a modified version without making your changes open source.  The
+    GPL-compatible licenses make it possible to combine Python with
+    other software that is released under the GPL; the others don't.
+
+(2) According to Richard Stallman, 1.6.1 is not GPL-compatible,
+    because its license has a choice of law clause.  According to
+    CNRI, however, Stallman's lawyer has told CNRI's lawyer that 1.6.1
+    is "not incompatible" with the GPL.
+
+Thanks to the many outside volunteers who have worked under Guido's
+direction to make these releases possible.
+
+
+B. TERMS AND CONDITIONS FOR ACCESSING OR OTHERWISE USING PYTHON
+===============================================================
+
+PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2
+--------------------------------------------
+
+1. This LICENSE AGREEMENT is between the Python Software Foundation
+("PSF"), and the Individual or Organization ("Licensee") accessing and
+otherwise using this software ("Python") in source or binary form and
+its associated documentation.
+
+2. Subject to the terms and conditions of this License Agreement, PSF hereby
+grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce,
+analyze, test, perform and/or display publicly, prepare derivative works,
+distribute, and otherwise use Python alone or in any derivative version,
+provided, however, that PSF's License Agreement and PSF's notice of copyright,
+i.e., "Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
+2011, 2012, 2013, 2014 Python Software Foundation; All Rights Reserved" are
+retained in Python alone or in any derivative version prepared by Licensee.
+
+3. In the event Licensee prepares a derivative work that is based on
+or incorporates Python or any part thereof, and wants to make
+the derivative work available to others as provided herein, then
+Licensee hereby agrees to include in any such work a brief summary of
+the changes made to Python.
+
+4. PSF is making Python available to Licensee on an "AS IS"
+basis.  PSF MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
+IMPLIED.  BY WAY OF EXAMPLE, BUT NOT LIMITATION, PSF MAKES NO AND
+DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON WILL NOT
+INFRINGE ANY THIRD PARTY RIGHTS.
+
+5. PSF SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
+FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
+A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON,
+OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+
+6. This License Agreement will automatically terminate upon a material
+breach of its terms and conditions.
+
+7. Nothing in this License Agreement shall be deemed to create any
+relationship of agency, partnership, or joint venture between PSF and
+Licensee.  This License Agreement does not grant permission to use PSF
+trademarks or trade name in a trademark sense to endorse or promote
+products or services of Licensee, or any third party.
+
+8. By copying, installing or otherwise using Python, Licensee
+agrees to be bound by the terms and conditions of this License
+Agreement.
+
+
+BEOPEN.COM LICENSE AGREEMENT FOR PYTHON 2.0
+-------------------------------------------
+
+BEOPEN PYTHON OPEN SOURCE LICENSE AGREEMENT VERSION 1
+
+1. This LICENSE AGREEMENT is between BeOpen.com ("BeOpen"), having an
+office at 160 Saratoga Avenue, Santa Clara, CA 95051, and the
+Individual or Organization ("Licensee") accessing and otherwise using
+this software in source or binary form and its associated
+documentation ("the Software").
+
+2. Subject to the terms and conditions of this BeOpen Python License
+Agreement, BeOpen hereby grants Licensee a non-exclusive,
+royalty-free, world-wide license to reproduce, analyze, test, perform
+and/or display publicly, prepare derivative works, distribute, and
+otherwise use the Software alone or in any derivative version,
+provided, however, that the BeOpen Python License is retained in the
+Software, alone or in any derivative version prepared by Licensee.
+
+3. BeOpen is making the Software available to Licensee on an "AS IS"
+basis.  BEOPEN MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
+IMPLIED.  BY WAY OF EXAMPLE, BUT NOT LIMITATION, BEOPEN MAKES NO AND
+DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE WILL NOT
+INFRINGE ANY THIRD PARTY RIGHTS.
+
+4. BEOPEN SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF THE
+SOFTWARE FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS
+AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THE SOFTWARE, OR ANY
+DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+
+5. This License Agreement will automatically terminate upon a material
+breach of its terms and conditions.
+
+6. This License Agreement shall be governed by and interpreted in all
+respects by the law of the State of California, excluding conflict of
+law provisions.  Nothing in this License Agreement shall be deemed to
+create any relationship of agency, partnership, or joint venture
+between BeOpen and Licensee.  This License Agreement does not grant
+permission to use BeOpen trademarks or trade names in a trademark
+sense to endorse or promote products or services of Licensee, or any
+third party.  As an exception, the "BeOpen Python" logos available at
+http://www.pythonlabs.com/logos.html may be used according to the
+permissions granted on that web page.
+
+7. By copying, installing or otherwise using the software, Licensee
+agrees to be bound by the terms and conditions of this License
+Agreement.
+
+
+CNRI LICENSE AGREEMENT FOR PYTHON 1.6.1
+---------------------------------------
+
+1. This LICENSE AGREEMENT is between the Corporation for National
+Research Initiatives, having an office at 1895 Preston White Drive,
+Reston, VA 20191 ("CNRI"), and the Individual or Organization
+("Licensee") accessing and otherwise using Python 1.6.1 software in
+source or binary form and its associated documentation.
+
+2. Subject to the terms and conditions of this License Agreement, CNRI
+hereby grants Licensee a nonexclusive, royalty-free, world-wide
+license to reproduce, analyze, test, perform and/or display publicly,
+prepare derivative works, distribute, and otherwise use Python 1.6.1
+alone or in any derivative version, provided, however, that CNRI's
+License Agreement and CNRI's notice of copyright, i.e., "Copyright (c)
+1995-2001 Corporation for National Research Initiatives; All Rights
+Reserved" are retained in Python 1.6.1 alone or in any derivative
+version prepared by Licensee.  Alternately, in lieu of CNRI's License
+Agreement, Licensee may substitute the following text (omitting the
+quotes): "Python 1.6.1 is made available subject to the terms and
+conditions in CNRI's License Agreement.  This Agreement together with
+Python 1.6.1 may be located on the Internet using the following
+unique, persistent identifier (known as a handle): 1895.22/1013.  This
+Agreement may also be obtained from a proxy server on the Internet
+using the following URL: http://hdl.handle.net/1895.22/1013".
+
+3. In the event Licensee prepares a derivative work that is based on
+or incorporates Python 1.6.1 or any part thereof, and wants to make
+the derivative work available to others as provided herein, then
+Licensee hereby agrees to include in any such work a brief summary of
+the changes made to Python 1.6.1.
+
+4. CNRI is making Python 1.6.1 available to Licensee on an "AS IS"
+basis.  CNRI MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
+IMPLIED.  BY WAY OF EXAMPLE, BUT NOT LIMITATION, CNRI MAKES NO AND
+DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF PYTHON 1.6.1 WILL NOT
+INFRINGE ANY THIRD PARTY RIGHTS.
+
+5. CNRI SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON
+1.6.1 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS
+A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON 1.6.1,
+OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+
+6. This License Agreement will automatically terminate upon a material
+breach of its terms and conditions.
+
+7. This License Agreement shall be governed by the federal
+intellectual property law of the United States, including without
+limitation the federal copyright law, and, to the extent such
+U.S. federal law does not apply, by the law of the Commonwealth of
+Virginia, excluding Virginia's conflict of law provisions.
+Notwithstanding the foregoing, with regard to derivative works based
+on Python 1.6.1 that incorporate non-separable material that was
+previously distributed under the GNU General Public License (GPL), the
+law of the Commonwealth of Virginia shall govern this License
+Agreement only as to issues arising under or with respect to
+Paragraphs 4, 5, and 7 of this License Agreement.  Nothing in this
+License Agreement shall be deemed to create any relationship of
+agency, partnership, or joint venture between CNRI and Licensee.  This
+License Agreement does not grant permission to use CNRI trademarks or
+trade name in a trademark sense to endorse or promote products or
+services of Licensee, or any third party.
+
+8. By clicking on the "ACCEPT" button where indicated, or by copying,
+installing or otherwise using Python 1.6.1, Licensee agrees to be
+bound by the terms and conditions of this License Agreement.
+
+        ACCEPT
+
+
+CWI LICENSE AGREEMENT FOR PYTHON 0.9.0 THROUGH 1.2
+--------------------------------------------------
+
+Copyright (c) 1991 - 1995, Stichting Mathematisch Centrum Amsterdam,
+The Netherlands.  All rights reserved.
+
+Permission to use, copy, modify, and distribute this software and its
+documentation for any purpose and without fee is hereby granted,
+provided that the above copyright notice appear in all copies and that
+both that copyright notice and this permission notice appear in
+supporting documentation, and that the name of Stichting Mathematisch
+Centrum or CWI not be used in advertising or publicity pertaining to
+distribution of the software without specific, written prior
+permission.
+
+STICHTING MATHEMATISCH CENTRUM DISCLAIMS ALL WARRANTIES WITH REGARD TO
+THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS, IN NO EVENT SHALL STICHTING MATHEMATISCH CENTRUM BE LIABLE
+FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT
+OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

lib/spack/external/_vendoring/typing_extensions.pyi

@@ -0,0 +1 @@
+from typing_extensions import *

lib/spack/external/vendor.txt

@@ -8,3 +8,4 @@ six==1.16.0
 macholib==1.16.2
   altgraph==0.17.3
 ruamel.yaml==0.17.21
+typing_extensions==4.1.1

lib/spack/llnl/path.py

@@ -66,7 +66,7 @@ def _is_url(path_or_url: str) -> bool:
     return result
 
 
-def system_path_filter(_func=None, arg_slice: Optional[slice] = None):
+def _system_path_filter(_func=None, arg_slice: Optional[slice] = None):
     """Filters function arguments to account for platform path separators.
     Optional slicing range can be specified to select specific arguments
 
@@ -100,6 +100,16 @@ def path_filter_caller(*args, **kwargs):
     return holder_func
 
 
+def _noop_decorator(_func=None, arg_slice: Optional[slice] = None):
+    return _func if _func else lambda x: x
+
+
+if sys.platform == "win32":
+    system_path_filter = _system_path_filter
+else:
+    system_path_filter = _noop_decorator
+
+
 def sanitize_win_longpath(path: str) -> str:
     """Strip Windows extended path prefix from strings
     Returns sanitized string.

lib/spack/llnl/util/filesystem.py

@@ -24,6 +24,7 @@
     Callable,
     Deque,
     Dict,
+    Generator,
     Iterable,
     List,
     Match,
@@ -300,35 +301,32 @@ def filter_file(
     ignore_absent: bool = False,
     start_at: Optional[str] = None,
     stop_at: Optional[str] = None,
+    encoding: Optional[str] = "utf-8",
 ) -> None:
     r"""Like sed, but uses python regular expressions.
 
-    Filters every line of each file through regex and replaces the file
-    with a filtered version.  Preserves mode of filtered files.
+    Filters every line of each file through regex and replaces the file with a filtered version.
+    Preserves mode of filtered files.
 
-    As with re.sub, ``repl`` can be either a string or a callable.
-    If it is a callable, it is passed the match object and should
-    return a suitable replacement string.  If it is a string, it
-    can contain ``\1``, ``\2``, etc. to represent back-substitution
-    as sed would allow.
+    As with re.sub, ``repl`` can be either a string or a callable. If it is a callable, it is
+    passed the match object and should return a suitable replacement string.  If it is a string, it
+    can contain ``\1``, ``\2``, etc. to represent back-substitution as sed would allow.
 
     Args:
-        regex (str): The regular expression to search for
-        repl (str): The string to replace matches with
-        *filenames: One or more files to search and replace
-        string (bool): Treat regex as a plain string. Default it False
-        backup (bool): Make backup file(s) suffixed with ``~``. Default is False
-        ignore_absent (bool): Ignore any files that don't exist.
-            Default is False
-        start_at (str): Marker used to start applying the replacements. If a
-            text line matches this marker filtering is started at the next line.
-            All contents before the marker and the marker itself are copied
-            verbatim. Default is to start filtering from the first line of the
-            file.
-        stop_at (str): Marker used to stop scanning the file further. If a text
-            line matches this marker filtering is stopped and the rest of the
-            file is copied verbatim. Default is to filter until the end of the
-            file.
+        regex: The regular expression to search for
+        repl: The string to replace matches with
+        *filenames: One or more files to search and replace string: Treat regex as a plain string.
+            Default it False backup: Make backup file(s) suffixed with ``~``. Default is False
+        ignore_absent: Ignore any files that don't exist. Default is False
+        start_at: Marker used to start applying the replacements. If a text line matches this
+            marker filtering is started at the next line. All contents before the marker and the
+            marker itself are copied verbatim. Default is to start filtering from the first line of
+            the file.
+        stop_at: Marker used to stop scanning the file further. If a text line matches this marker
+            filtering is stopped and the rest of the file is copied verbatim. Default is to filter
+            until the end of the file.
+        encoding: The encoding to use when reading and writing the files. Default is None, which
+            uses the system's default encoding.
     """
     # Allow strings to use \1, \2, etc. for replacement, like sed
     if not callable(repl):
@@ -344,72 +342,56 @@ def groupid_to_group(x):
 
     if string:
         regex = re.escape(regex)
-    for filename in path_to_os_path(*filenames):
-        msg = 'FILTER FILE: {0} [replacing "{1}"]'
-        tty.debug(msg.format(filename, regex))
-
-        backup_filename = filename + "~"
-        tmp_filename = filename + ".spack~"
-
-        if ignore_absent and not os.path.exists(filename):
-            msg = 'FILTER FILE: file "{0}" not found. Skipping to next file.'
-            tty.debug(msg.format(filename))
+    regex_compiled = re.compile(regex)
+    for path in path_to_os_path(*filenames):
+        if ignore_absent and not os.path.exists(path):
+            tty.debug(f'FILTER FILE: file "{path}" not found. Skipping to next file.')
             continue
+        else:
+            tty.debug(f'FILTER FILE: {path} [replacing "{regex}"]')
 
-        # Create backup file. Don't overwrite an existing backup
-        # file in case this file is being filtered multiple times.
-        if not os.path.exists(backup_filename):
-            shutil.copy(filename, backup_filename)
+        fd, temp_path = tempfile.mkstemp(
+            prefix=f"{os.path.basename(path)}.", dir=os.path.dirname(path)
+        )
+        os.close(fd)
 
-        # Create a temporary file to read from. We cannot use backup_filename
-        # in case filter_file is invoked multiple times on the same file.
-        shutil.copy(filename, tmp_filename)
+        shutil.copy(path, temp_path)
+        errored = False
 
         try:
-            # Open as a text file and filter until the end of the file is
-            # reached, or we found a marker in the line if it was specified
-            #
-            # To avoid translating line endings (\n to \r\n and vice-versa)
-            # we force os.open to ignore translations and use the line endings
-            # the file comes with
-            with open(tmp_filename, mode="r", errors="surrogateescape", newline="") as input_file:
-                with open(filename, mode="w", errors="surrogateescape", newline="") as output_file:
-                    do_filtering = start_at is None
-                    # Using iter and readline is a workaround needed not to
-                    # disable input_file.tell(), which will happen if we call
-                    # input_file.next() implicitly via the for loop
-                    for line in iter(input_file.readline, ""):
-                        if stop_at is not None:
-                            current_position = input_file.tell()
+            # Open as a text file and filter until the end of the file is reached, or we found a
+            # marker in the line if it was specified. To avoid translating line endings (\n to
+            # \r\n and vice-versa) use newline="".
+            with open(
+                temp_path, mode="r", errors="surrogateescape", newline="", encoding=encoding
+            ) as input_file, open(
+                path, mode="w", errors="surrogateescape", newline="", encoding=encoding
+            ) as output_file:
+                if start_at is None and stop_at is None:  # common case, avoids branching in loop
+                    for line in input_file:
+                        output_file.write(re.sub(regex_compiled, repl, line))
+                else:
+                    # state is -1 before start_at; 0 between; 1 after stop_at
+                    state = 0 if start_at is None else -1
+                    for line in input_file:
+                        if state == 0:
                             if stop_at == line.strip():
-                                output_file.write(line)
-                                break
-                        if do_filtering:
-                            filtered_line = re.sub(regex, repl, line)
-                            output_file.write(filtered_line)
-                        else:
-                            do_filtering = start_at == line.strip()
-                            output_file.write(line)
-                    else:
-                        current_position = None
-
-            # If we stopped filtering at some point, reopen the file in
-            # binary mode and copy verbatim the remaining part
-            if current_position and stop_at:
-                with open(tmp_filename, mode="rb") as input_binary_buffer:
-                    input_binary_buffer.seek(current_position)
-                    with open(filename, mode="ab") as output_binary_buffer:
-                        output_binary_buffer.writelines(input_binary_buffer.readlines())
+                                state = 1
+                            else:
+                                line = re.sub(regex_compiled, repl, line)
+                        elif state == -1 and start_at == line.strip():
+                            state = 0
+                        output_file.write(line)
 
         except BaseException:
-            # clean up the original file on failure.
-            shutil.move(backup_filename, filename)
+            # restore the original file
+            os.rename(temp_path, path)
+            errored = True
             raise
 
         finally:
-            os.remove(tmp_filename)
-            if not backup and os.path.exists(backup_filename):
-                os.remove(backup_filename)
+            if not errored and not backup:
+                os.unlink(temp_path)
 
 
 class FileFilter:
@@ -1114,12 +1096,12 @@ def hash_directory(directory, ignore=[]):
 
 @contextmanager
 @system_path_filter
-def write_tmp_and_move(filename):
+def write_tmp_and_move(filename: str, *, encoding: Optional[str] = None):
     """Write to a temporary file, then move into place."""
     dirname = os.path.dirname(filename)
     basename = os.path.basename(filename)
     tmp = os.path.join(dirname, ".%s.tmp" % basename)
-    with open(tmp, "w") as f:
+    with open(tmp, "w", encoding=encoding) as f:
         yield f
     shutil.move(tmp, filename)
 
@@ -2772,22 +2754,6 @@ def prefixes(path):
     return paths
 
 
-@system_path_filter
-def md5sum(file):
-    """Compute the MD5 sum of a file.
-
-    Args:
-        file (str): file to be checksummed
-
-    Returns:
-        MD5 sum of the file's content
-    """
-    md5 = hashlib.md5()
-    with open(file, "rb") as f:
-        md5.update(f.read())
-    return md5.digest()
-
-
 @system_path_filter
 def remove_directory_contents(dir):
     """Remove all contents of a directory."""
@@ -2838,6 +2804,25 @@ def temporary_dir(
         remove_directory_contents(tmp_dir)
 
 
+@contextmanager
+def edit_in_place_through_temporary_file(file_path: str) -> Generator[str, None, None]:
+    """Context manager for modifying ``file_path`` in place, preserving its inode and hardlinks,
+    for functions or external tools that do not support in-place editing. Notice that this function
+    is unsafe in that it works with paths instead of a file descriptors, but this is by design,
+    since we assume the call site will create a new inode at the same path."""
+    tmp_fd, tmp_path = tempfile.mkstemp(
+        dir=os.path.dirname(file_path), prefix=f"{os.path.basename(file_path)}."
+    )
+    # windows cannot replace a file with open fds, so close since the call site needs to replace.
+    os.close(tmp_fd)
+    try:
+        shutil.copyfile(file_path, tmp_path, follow_symlinks=True)
+        yield tmp_path
+        shutil.copyfile(tmp_path, file_path, follow_symlinks=True)
+    finally:
+        os.unlink(tmp_path)
+
+
 def filesummary(path, print_bytes=16) -> Tuple[int, bytes]:
     """Create a small summary of the given file. Does not error
     when file does not exist.

lib/spack/llnl/util/lang.py

@@ -863,8 +863,10 @@ def elide_list(line_list: List[str], max_num: int = 10) -> List[str]:
 
 if sys.version_info >= (3, 9):
     PatternStr = re.Pattern[str]
+    PatternBytes = re.Pattern[bytes]
 else:
     PatternStr = typing.Pattern[str]
+    PatternBytes = typing.Pattern[bytes]
 
 
 def fnmatch_translate_multiple(named_patterns: Dict[str, str]) -> str:

lib/spack/llnl/util/lock.py

@@ -96,8 +96,8 @@ def get_fh(self, path: str) -> IO:
         Arguments:
           path: path to lock file we want a filehandle for
         """
-        # Open writable files as 'r+' so we can upgrade to write later
-        os_mode, fh_mode = (os.O_RDWR | os.O_CREAT), "r+"
+        # Open writable files as rb+ so we can upgrade to write later
+        os_mode, fh_mode = (os.O_RDWR | os.O_CREAT), "rb+"
 
         pid = os.getpid()
         open_file = None  # OpenFile object, if there is one
@@ -124,7 +124,7 @@ def get_fh(self, path: str) -> IO:
                 # we know path exists but not if it's writable. If it's read-only,
                 # only open the file for reading (and fail if we're trying to get
                 # an exclusive (write) lock on it)
-                os_mode, fh_mode = os.O_RDONLY, "r"
+                os_mode, fh_mode = os.O_RDONLY, "rb"
 
             fd = os.open(path, os_mode)
             fh = os.fdopen(fd, fh_mode)
@@ -243,7 +243,7 @@ def __init__(
                 helpful for distinguishing between different Spack locks.
         """
         self.path = path
-        self._file: Optional[IO] = None
+        self._file: Optional[IO[bytes]] = None
         self._reads = 0
         self._writes = 0
 
@@ -329,9 +329,9 @@ def _lock(self, op: int, timeout: Optional[float] = None) -> Tuple[float, int]:
             self._ensure_parent_directory()
             self._file = FILE_TRACKER.get_fh(self.path)
 
-        if LockType.to_module(op) == fcntl.LOCK_EX and self._file.mode == "r":
+        if LockType.to_module(op) == fcntl.LOCK_EX and self._file.mode == "rb":
             # Attempt to upgrade to write lock w/a read-only file.
-            # If the file were writable, we'd have opened it 'r+'
+            # If the file were writable, we'd have opened it rb+
             raise LockROFileError(self.path)
 
         self._log_debug(
@@ -426,7 +426,7 @@ def _read_log_debug_data(self) -> None:
 
         line = self._file.read()
         if line:
-            pid, host = line.strip().split(",")
+            pid, host = line.decode("utf-8").strip().split(",")
             _, _, pid = pid.rpartition("=")
             _, _, self.host = host.rpartition("=")
             self.pid = int(pid)
@@ -442,7 +442,7 @@ def _write_log_debug_data(self) -> None:
 
         # write pid, host to disk to sync over FS
         self._file.seek(0)
-        self._file.write("pid=%s,host=%s" % (self.pid, self.host))
+        self._file.write(f"pid={self.pid},host={self.host}".encode("utf-8"))
         self._file.truncate()
         self._file.flush()
         os.fsync(self._file.fileno())

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

@@ -161,7 +161,7 @@ def _err_check(result, func, args):
             )
             # Use conout$ here to handle a redirectired stdout/get active console associated
             # with spack
-            with open(r"\\.\CONOUT$", "w") as conout:
+            with open(r"\\.\CONOUT$", "w", encoding="utf-8") as conout:
                 # Link above would use kernel32.GetStdHandle(-11) however this would not handle
                 # a redirected stdout appropriately, so we always refer to the current CONSOLE out
                 # which is defined as conout$ on Windows.

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

@@ -762,7 +762,7 @@ def __enter__(self):
             self.reader = open(self.logfile, mode="rb+")
 
             # Dup stdout so we can still write to it after redirection
-            self.echo_writer = open(os.dup(sys.stdout.fileno()), "w")
+            self.echo_writer = open(os.dup(sys.stdout.fileno()), "w", encoding=sys.stdout.encoding)
             # Redirect stdout and stderr to write to logfile
             self.stderr.redirect_stream(self.writer.fileno())
             self.stdout.redirect_stream(self.writer.fileno())
@@ -879,10 +879,13 @@ def _writer_daemon(
     write_fd.close()
 
     # 1. Use line buffering (3rd param = 1) since Python 3 has a bug
-    # that prevents unbuffered text I/O.
-    # 2. Python 3.x before 3.7 does not open with UTF-8 encoding by default
+    #    that prevents unbuffered text I/O. [needs citation]
+    # 2. Enforce a UTF-8 interpretation of build process output with errors replaced by '?'.
+    #    The downside is that the log file will not contain the exact output of the build process.
     # 3. closefd=False because Connection has "ownership"
-    read_file = os.fdopen(read_fd.fileno(), "r", 1, encoding="utf-8", closefd=False)
+    read_file = os.fdopen(
+        read_fd.fileno(), "r", 1, encoding="utf-8", errors="replace", closefd=False
+    )
 
     if stdin_fd:
         stdin_file = os.fdopen(stdin_fd.fileno(), closefd=False)
@@ -928,11 +931,7 @@ def _writer_daemon(
                     try:
                         while line_count < 100:
                             # Handle output from the calling process.
-                            try:
-                                line = _retry(read_file.readline)()
-                            except UnicodeDecodeError:
-                                # installs like --test=root gpgme produce non-UTF8 logs
-                                line = "<line lost: output was not encoded as UTF-8>\n"
+                            line = _retry(read_file.readline)()
 
                             if not line:
                                 return
@@ -946,6 +945,13 @@ def _writer_daemon(
                                 output_line = clean_line
                                 if filter_fn:
                                     output_line = filter_fn(clean_line)
+                                enc = sys.stdout.encoding
+                                if enc != "utf-8":
+                                    # On Python 3.6 and 3.7-3.14 with non-{utf-8,C} locale stdout
+                                    # may not be able to handle utf-8 output. We do an inefficient
+                                    # dance of re-encoding with errors replaced, so stdout.write
+                                    # does not raise.
+                                    output_line = output_line.encode(enc, "replace").decode(enc)
                                 sys.stdout.write(output_line)
 
                             # Stripped output to log file.

lib/spack/spack/__init__.py

@@ -11,7 +11,7 @@
 import spack.util.git
 
 #: PEP440 canonical <major>.<minor>.<micro>.<devN> string
-__version__ = "0.23.0.dev0"
+__version__ = "0.24.0.dev0"
 spack_version = __version__
 
 

lib/spack/spack/audit.py

@@ -571,8 +571,13 @@ def _search_for_deprecated_package_methods(pkgs, error_cls):
 @package_properties
 def _ensure_all_package_names_are_lowercase(pkgs, error_cls):
     """Ensure package names are lowercase and consistent"""
+    reserved_names = ("all",)
     badname_regex, errors = re.compile(r"[_A-Z]"), []
     for pkg_name in pkgs:
+        if pkg_name in reserved_names:
+            error_msg = f"The name '{pkg_name}' is reserved, and cannot be used for packages"
+            errors.append(error_cls(error_msg, []))
+
         if badname_regex.search(pkg_name):
             error_msg = f"Package name '{pkg_name}' should be lowercase and must not contain '_'"
             errors.append(error_cls(error_msg, []))
@@ -651,7 +656,7 @@ def _ensure_docstring_and_no_fixme(pkgs, error_cls):
     for pkg_name in pkgs:
         details = []
         filename = spack.repo.PATH.filename_for_package_name(pkg_name)
-        with open(filename, "r") as package_file:
+        with open(filename, "r", encoding="utf-8") as package_file:
             for i, line in enumerate(package_file):
                 pattern = next((r for r in fixme_regexes if r.search(line)), None)
                 if pattern:
@@ -688,19 +693,19 @@ def invalid_sha256_digest(fetcher):
                     return h, True
             return None, False
 
-        error_msg = "Package '{}' does not use sha256 checksum".format(pkg_name)
+        error_msg = f"Package '{pkg_name}' does not use sha256 checksum"
         details = []
         for v, args in pkg.versions.items():
             fetcher = spack.fetch_strategy.for_package_version(pkg, v)
             digest, is_bad = invalid_sha256_digest(fetcher)
             if is_bad:
-                details.append("{}@{} uses {}".format(pkg_name, v, digest))
+                details.append(f"{pkg_name}@{v} uses {digest}")
 
         for _, resources in pkg.resources.items():
             for resource in resources:
                 digest, is_bad = invalid_sha256_digest(resource.fetcher)
                 if is_bad:
-                    details.append("Resource in '{}' uses {}".format(pkg_name, digest))
+                    details.append(f"Resource in '{pkg_name}' uses {digest}")
         if details:
             errors.append(error_cls(error_msg, details))
 
@@ -804,7 +809,7 @@ def _uses_deprecated_globals(pkgs, error_cls):
             continue
 
         file = spack.repo.PATH.filename_for_package_name(pkg_name)
-        tree = ast.parse(open(file).read())
+        tree = ast.parse(open(file, "rb").read())
         visitor = DeprecatedMagicGlobals(("std_cmake_args", "std_meson_args", "std_pip_args"))
         visitor.visit(tree)
         if visitor.references_to_globals:
@@ -1004,20 +1009,6 @@ def _issues_in_depends_on_directive(pkgs, error_cls):
 
         for when, deps_by_name in pkg_cls.dependencies.items():
             for dep_name, dep in deps_by_name.items():
-                # Check if there are nested dependencies declared. We don't want directives like:
-                #
-                #     depends_on('foo+bar ^fee+baz')
-                #
-                # but we'd like to have two dependencies listed instead.
-                nested_dependencies = dep.spec.dependencies()
-                if nested_dependencies:
-                    summary = f"{pkg_name}: nested dependency declaration '{dep.spec}'"
-                    ndir = len(nested_dependencies) + 1
-                    details = [
-                        f"split depends_on('{dep.spec}', when='{when}') into {ndir} directives",
-                        f"in {filename}",
-                    ]
-                    errors.append(error_cls(summary=summary, details=details))
 
                 def check_virtual_with_variants(spec, msg):
                     if not spec.virtual or not spec.variants:

lib/spack/spack/binary_distribution.py

@@ -24,13 +24,12 @@
 import urllib.request
 import warnings
 from contextlib import closing
-from typing import Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
+from typing import IO, Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
 
 import llnl.util.filesystem as fsys
 import llnl.util.lang
 import llnl.util.tty as tty
-from llnl.util.filesystem import BaseDirectoryVisitor, mkdirp, visit_directory_tree
-from llnl.util.symlink import readlink
+from llnl.util.filesystem import mkdirp
 
 import spack.caches
 import spack.config as config
@@ -40,7 +39,7 @@
 import spack.hash_types as ht
 import spack.hooks
 import spack.hooks.sbang
-import spack.mirror
+import spack.mirrors.mirror
 import spack.oci.image
 import spack.oci.oci
 import spack.oci.opener
@@ -54,7 +53,6 @@
 import spack.util.archive
 import spack.util.crypto
 import spack.util.file_cache as file_cache
-import spack.util.filesystem as ssys
 import spack.util.gpg
 import spack.util.parallel
 import spack.util.path
@@ -69,10 +67,8 @@
     Digest,
     ImageReference,
     default_config,
-    default_index_tag,
     default_manifest,
-    default_tag,
-    tag_is_spec,
+    ensure_valid_tag,
 )
 from spack.oci.oci import (
     copy_missing_layers_with_retry,
@@ -83,10 +79,11 @@
 )
 from spack.package_prefs import get_package_dir_permissions, get_package_group
 from spack.relocate_text import utf8_paths_to_single_binary_regex
-from spack.spec import Spec
 from spack.stage import Stage
 from spack.util.executable import which
 
+from .enums import InstallRecordStatus
+
 BUILD_CACHE_RELATIVE_PATH = "build_cache"
 BUILD_CACHE_KEYS_RELATIVE_PATH = "_pgp"
 
@@ -252,7 +249,7 @@ def _associate_built_specs_with_mirror(self, cache_key, mirror_url):
 
             spec_list = [
                 s
-                for s in db.query_local(installed=any)
+                for s in db.query_local(installed=InstallRecordStatus.ANY)
                 if s.external or db.query_local_by_spec_hash(s.dag_hash()).in_buildcache
             ]
 
@@ -367,7 +364,7 @@ def update(self, with_cooldown=False):
         on disk under ``_index_cache_root``)."""
         self._init_local_index_cache()
         configured_mirror_urls = [
-            m.fetch_url for m in spack.mirror.MirrorCollection(binary=True).values()
+            m.fetch_url for m in spack.mirrors.mirror.MirrorCollection(binary=True).values()
         ]
         items_to_remove = []
         spec_cache_clear_needed = False
@@ -584,133 +581,15 @@ def buildinfo_file_name(prefix):
 
 def read_buildinfo_file(prefix):
     """Read buildinfo file"""
-    with open(buildinfo_file_name(prefix), "r") as f:
+    with open(buildinfo_file_name(prefix), "r", encoding="utf-8") as f:
         return syaml.load(f)
 
 
-class BuildManifestVisitor(BaseDirectoryVisitor):
-    """Visitor that collects a list of files and symlinks
-    that can be checked for need of relocation. It knows how
-    to dedupe hardlinks and deal with symlinks to files and
-    directories."""
-
-    def __init__(self):
-        # Save unique identifiers of hardlinks to avoid relocating them multiple times
-        self.visited = set()
-
-        # Lists of files we will check
-        self.files = []
-        self.symlinks = []
-
-    def seen_before(self, root, rel_path):
-        stat_result = os.lstat(os.path.join(root, rel_path))
-        if stat_result.st_nlink == 1:
-            return False
-        identifier = (stat_result.st_dev, stat_result.st_ino)
-        if identifier in self.visited:
-            return True
-        else:
-            self.visited.add(identifier)
-            return False
-
-    def visit_file(self, root, rel_path, depth):
-        if self.seen_before(root, rel_path):
-            return
-        self.files.append(rel_path)
-
-    def visit_symlinked_file(self, root, rel_path, depth):
-        # Note: symlinks *can* be hardlinked, but it is unclear if
-        # symlinks can be relinked in-place (preserving inode).
-        # Therefore, we do *not* de-dupe hardlinked symlinks.
-        self.symlinks.append(rel_path)
-
-    def before_visit_dir(self, root, rel_path, depth):
-        return os.path.basename(rel_path) not in (".spack", "man")
-
-    def before_visit_symlinked_dir(self, root, rel_path, depth):
-        # Treat symlinked directories simply as symlinks.
-        self.visit_symlinked_file(root, rel_path, depth)
-        # Never recurse into symlinked directories.
-        return False
-
-
-def file_matches(path, regex):
-    with open(path, "rb") as f:
-        contents = f.read()
-    return bool(regex.search(contents))
-
-
-def get_buildfile_manifest(spec):
-    """
-    Return a data structure with information about a build, including
-    text_to_relocate, binary_to_relocate, binary_to_relocate_fullpath
-    link_to_relocate, and other, which means it doesn't fit any of previous
-    checks (and should not be relocated). We exclude docs (man) and
-    metadata (.spack). This can be used to find a particular kind of file
-    in spack, or to generate the build metadata.
-    """
-    data = {
-        "text_to_relocate": [],
-        "binary_to_relocate": [],
-        "link_to_relocate": [],
-        "other": [],
-        "binary_to_relocate_fullpath": [],
-        "hardlinks_deduped": True,
-    }
-
-    # Guard against filesystem footguns of hardlinks and symlinks by using
-    # a visitor to retrieve a list of files and symlinks, so we don't have
-    # to worry about hardlinks of symlinked dirs and what not.
-    visitor = BuildManifestVisitor()
-    root = spec.prefix
-    visit_directory_tree(root, visitor)
-
-    # Collect a list of prefixes for this package and it's dependencies, Spack will
-    # look for them to decide if text file needs to be relocated or not
-    prefixes = [d.prefix for d in spec.traverse(root=True, deptype="all") if not d.external]
-    prefixes.append(spack.hooks.sbang.sbang_install_path())
-    prefixes.append(str(spack.store.STORE.layout.root))
-
-    # Create a giant regex that matches all prefixes
-    regex = utf8_paths_to_single_binary_regex(prefixes)
-
-    # Symlinks.
-
-    # Obvious bugs:
-    #   1. relative links are not relocated.
-    #   2. paths are used as strings.
-    for rel_path in visitor.symlinks:
-        abs_path = os.path.join(root, rel_path)
-        link = readlink(abs_path)
-        if os.path.isabs(link) and link.startswith(spack.store.STORE.layout.root):
-            data["link_to_relocate"].append(rel_path)
-
-    # Non-symlinks.
-    for rel_path in visitor.files:
-        abs_path = os.path.join(root, rel_path)
-        m_type, m_subtype = ssys.mime_type(abs_path)
-
-        if relocate.needs_binary_relocation(m_type, m_subtype):
-            # Why is this branch not part of needs_binary_relocation? :(
-            if (
-                (
-                    m_subtype in ("x-executable", "x-sharedlib", "x-pie-executable")
-                    and sys.platform != "darwin"
-                )
-                or (m_subtype in ("x-mach-binary") and sys.platform == "darwin")
-                or (not rel_path.endswith(".o"))
-            ):
-                data["binary_to_relocate"].append(rel_path)
-                data["binary_to_relocate_fullpath"].append(abs_path)
-                continue
-
-        elif relocate.needs_text_relocation(m_type, m_subtype) and file_matches(abs_path, regex):
-            data["text_to_relocate"].append(rel_path)
-            continue
-
-        data["other"].append(abs_path)
-
-    return data
+def file_matches(f: IO[bytes], regex: llnl.util.lang.PatternBytes) -> bool:
+    try:
+        return bool(regex.search(f.read()))
+    finally:
+        f.seek(0)
 
 
 def deps_to_relocate(spec):
@@ -743,17 +622,15 @@ def deps_to_relocate(spec):
 
 def get_buildinfo_dict(spec):
     """Create metadata for a tarball"""
-    manifest = get_buildfile_manifest(spec)
-
     return {
         "sbang_install_path": spack.hooks.sbang.sbang_install_path(),
         "buildpath": spack.store.STORE.layout.root,
         "spackprefix": spack.paths.prefix,
         "relative_prefix": os.path.relpath(spec.prefix, spack.store.STORE.layout.root),
-        "relocate_textfiles": manifest["text_to_relocate"],
-        "relocate_binaries": manifest["binary_to_relocate"],
-        "relocate_links": manifest["link_to_relocate"],
-        "hardlinks_deduped": manifest["hardlinks_deduped"],
+        # "relocate_textfiles": [],
+        # "relocate_binaries": [],
+        # "relocate_links": [],
+        "hardlinks_deduped": True,
         "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in deps_to_relocate(spec)},
     }
 
@@ -825,10 +702,10 @@ def _read_specs_and_push_index(
         contents = read_method(file)
         # Need full spec.json name or this gets confused with index.json.
         if file.endswith(".json.sig"):
-            specfile_json = Spec.extract_json_from_clearsig(contents)
-            fetched_spec = Spec.from_dict(specfile_json)
+            specfile_json = spack.spec.Spec.extract_json_from_clearsig(contents)
+            fetched_spec = spack.spec.Spec.from_dict(specfile_json)
         elif file.endswith(".json"):
-            fetched_spec = Spec.from_json(contents)
+            fetched_spec = spack.spec.Spec.from_json(contents)
         else:
             continue
 
@@ -838,17 +715,17 @@ def _read_specs_and_push_index(
     # Now generate the index, compute its hash, and push the two files to
     # the mirror.
     index_json_path = os.path.join(temp_dir, "index.json")
-    with open(index_json_path, "w") as f:
+    with open(index_json_path, "w", encoding="utf-8") as f:
         db._write_to_file(f)
 
     # Read the index back in and compute its hash
-    with open(index_json_path) as f:
+    with open(index_json_path, encoding="utf-8") as f:
         index_string = f.read()
         index_hash = compute_hash(index_string)
 
     # Write the hash out to a local file
     index_hash_path = os.path.join(temp_dir, "index.json.hash")
-    with open(index_hash_path, "w") as f:
+    with open(index_hash_path, "w", encoding="utf-8") as f:
         f.write(index_hash)
 
     # Push the index itself
@@ -882,7 +759,7 @@ def _specs_from_cache_aws_cli(cache_prefix):
     aws = which("aws")
 
     def file_read_method(file_path):
-        with open(file_path) as fd:
+        with open(file_path, encoding="utf-8") as fd:
             return fd.read()
 
     tmpspecsdir = tempfile.mkdtemp()
@@ -1027,7 +904,7 @@ def generate_key_index(key_prefix: str, tmpdir: str) -> None:
     target = os.path.join(tmpdir, "index.json")
 
     index = {"keys": dict((fingerprint, {}) for fingerprint in sorted(set(fingerprints)))}
-    with open(target, "w") as f:
+    with open(target, "w", encoding="utf-8") as f:
         sjson.dump(index, f)
 
     try:
@@ -1043,7 +920,55 @@ def generate_key_index(key_prefix: str, tmpdir: str) -> None:
         ) from e
 
 
-def tarfile_of_spec_prefix(tar: tarfile.TarFile, prefix: str) -> None:
+class FileTypes:
+    BINARY = 0
+    TEXT = 1
+    UNKNOWN = 2
+
+
+NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7F-\x9F]")
+
+
+def file_type(f: IO[bytes]) -> int:
+    try:
+        # first check if this is an ELF or mach-o binary.
+        magic = f.read(8)
+        if len(magic) < 8:
+            return FileTypes.UNKNOWN
+        elif relocate.is_elf_magic(magic) or relocate.is_macho_magic(magic):
+            return FileTypes.BINARY
+
+        f.seek(0)
+
+        # Then try utf-8, which has a fast exponential decay in false positive rate with file size.
+        # Use chunked reads for fast early exit.
+        f_txt = io.TextIOWrapper(f, encoding="utf-8", errors="strict")
+        try:
+            while f_txt.read(1024):
+                pass
+            return FileTypes.TEXT
+        except UnicodeError:
+            f_txt.seek(0)
+            pass
+        finally:
+            f_txt.detach()
+        # Finally try iso-8859-1 heuristically. In Python, all possible 256 byte values are valid.
+        # We classify it as text if it does not contain any control characters / null bytes.
+        data = f.read(1024)
+        while data:
+            if NOT_ISO8859_1_TEXT.search(data):
+                break
+            data = f.read(1024)
+        else:
+            return FileTypes.TEXT
+        return FileTypes.UNKNOWN
+    finally:
+        f.seek(0)
+
+
+def tarfile_of_spec_prefix(
+    tar: tarfile.TarFile, prefix: str, prefixes_to_relocate: List[str]
+) -> dict:
     """Create a tarfile of an install prefix of a spec. Skips existing buildinfo file.
 
     Args:
@@ -1059,6 +984,33 @@ def tarfile_of_spec_prefix(tar: tarfile.TarFile, prefix: str) -> None:
     except OSError:
         skip = lambda entry: False
 
+    binary_regex = utf8_paths_to_single_binary_regex(prefixes_to_relocate)
+
+    relocate_binaries = []
+    relocate_links = []
+    relocate_textfiles = []
+
+    # use callbacks to add files and symlinks, so we can register which files need relocation upon
+    # extraction.
+    def add_file(tar: tarfile.TarFile, info: tarfile.TarInfo, path: str):
+        with open(path, "rb") as f:
+            relpath = os.path.relpath(path, prefix)
+            # no need to relocate anything in the .spack directory
+            if relpath.split(os.sep, 1)[0] == ".spack":
+                tar.addfile(info, f)
+                return
+            f_type = file_type(f)
+            if f_type == FileTypes.BINARY:
+                relocate_binaries.append(os.path.relpath(path, prefix))
+            elif f_type == FileTypes.TEXT and file_matches(f, binary_regex):
+                relocate_textfiles.append(os.path.relpath(path, prefix))
+            tar.addfile(info, f)
+
+    def add_symlink(tar: tarfile.TarFile, info: tarfile.TarInfo, path: str):
+        if os.path.isabs(info.linkname) and binary_regex.match(info.linkname.encode("utf-8")):
+            relocate_links.append(os.path.relpath(path, prefix))
+        tar.addfile(info)
+
     spack.util.archive.reproducible_tarfile_from_prefix(
         tar,
         prefix,
@@ -1066,29 +1018,51 @@ def tarfile_of_spec_prefix(tar: tarfile.TarFile, prefix: str) -> None:
         # used in runtimes like AWS lambda.
         include_parent_directories=True,
         skip=skip,
+        add_file=add_file,
+        add_symlink=add_symlink,
+    )
+
+    return {
+        "relocate_binaries": relocate_binaries,
+        "relocate_links": relocate_links,
+        "relocate_textfiles": relocate_textfiles,
+    }
+
+
+def create_tarball(spec: spack.spec.Spec, tarfile_path: str) -> Tuple[str, str]:
+    """Create a tarball of a spec and return the checksums of the compressed tarfile and the
+    uncompressed tarfile."""
+    return _do_create_tarball(
+        tarfile_path,
+        spec.prefix,
+        buildinfo=get_buildinfo_dict(spec),
+        prefixes_to_relocate=prefixes_to_relocate(spec),
     )
 
 
-def _do_create_tarball(tarfile_path: str, binaries_dir: str, buildinfo: dict):
+def _do_create_tarball(
+    tarfile_path: str, prefix: str, buildinfo: dict, prefixes_to_relocate: List[str]
+) -> Tuple[str, str]:
     with spack.util.archive.gzip_compressed_tarfile(tarfile_path) as (
         tar,
-        inner_checksum,
-        outer_checksum,
+        tar_gz_checksum,
+        tar_checksum,
     ):
         # Tarball the install prefix
-        tarfile_of_spec_prefix(tar, binaries_dir)
+        files_to_relocate = tarfile_of_spec_prefix(tar, prefix, prefixes_to_relocate)
+        buildinfo.update(files_to_relocate)
 
         # Serialize buildinfo for the tarball
         bstring = syaml.dump(buildinfo, default_flow_style=True).encode("utf-8")
         tarinfo = tarfile.TarInfo(
-            name=spack.util.archive.default_path_to_name(buildinfo_file_name(binaries_dir))
+            name=spack.util.archive.default_path_to_name(buildinfo_file_name(prefix))
         )
         tarinfo.type = tarfile.REGTYPE
         tarinfo.size = len(bstring)
         tarinfo.mode = 0o644
         tar.addfile(tarinfo, io.BytesIO(bstring))
 
-    return inner_checksum.hexdigest(), outer_checksum.hexdigest()
+    return tar_gz_checksum.hexdigest(), tar_checksum.hexdigest()
 
 
 class ExistsInBuildcache(NamedTuple):
@@ -1098,7 +1072,7 @@ class ExistsInBuildcache(NamedTuple):
 
 
 class BuildcacheFiles:
-    def __init__(self, spec: Spec, local: str, remote: str):
+    def __init__(self, spec: spack.spec.Spec, local: str, remote: str):
         """
         Args:
             spec: The spec whose tarball and specfile are being managed.
@@ -1128,7 +1102,7 @@ def local_tarball(self) -> str:
         return os.path.join(self.local, f"{self.spec.dag_hash()}.tar.gz")
 
 
-def _exists_in_buildcache(spec: Spec, tmpdir: str, out_url: str) -> ExistsInBuildcache:
+def _exists_in_buildcache(spec: spack.spec.Spec, tmpdir: str, out_url: str) -> ExistsInBuildcache:
     """returns a tuple of bools (signed, unsigned, tarball) indicating whether specfiles/tarballs
     exist in the buildcache"""
     files = BuildcacheFiles(spec, tmpdir, out_url)
@@ -1138,12 +1112,23 @@ def _exists_in_buildcache(spec: Spec, tmpdir: str, out_url: str) -> ExistsInBuil
     return ExistsInBuildcache(signed, unsigned, tarball)
 
 
+def prefixes_to_relocate(spec):
+    prefixes = [s.prefix for s in deps_to_relocate(spec)]
+    prefixes.append(spack.hooks.sbang.sbang_install_path())
+    prefixes.append(str(spack.store.STORE.layout.root))
+    return prefixes
+
+
 def _url_upload_tarball_and_specfile(
-    spec: Spec, tmpdir: str, out_url: str, exists: ExistsInBuildcache, signing_key: Optional[str]
+    spec: spack.spec.Spec,
+    tmpdir: str,
+    out_url: str,
+    exists: ExistsInBuildcache,
+    signing_key: Optional[str],
 ):
     files = BuildcacheFiles(spec, tmpdir, out_url)
     tarball = files.local_tarball()
-    checksum, _ = _do_create_tarball(tarball, spec.prefix, get_buildinfo_dict(spec))
+    checksum, _ = create_tarball(spec, tarball)
     spec_dict = spec.to_dict(hash=ht.dag_hash)
     spec_dict["buildcache_layout_version"] = CURRENT_BUILD_CACHE_LAYOUT_VERSION
     spec_dict["binary_cache_checksum"] = {"hash_algorithm": "sha256", "hash": checksum}
@@ -1157,7 +1142,7 @@ def _url_upload_tarball_and_specfile(
     web_util.push_to_url(tarball, files.remote_tarball(), keep_original=False)
 
     specfile = files.local_specfile()
-    with open(specfile, "w") as f:
+    with open(specfile, "w", encoding="utf-8") as f:
         # Note: when using gpg clear sign, we need to avoid long lines (19995 chars).
         # If lines are longer, they are truncated without error. Thanks GPG!
         # So, here we still add newlines, but no indent, so save on file size and
@@ -1174,7 +1159,7 @@ def _url_upload_tarball_and_specfile(
 
 
 class Uploader:
-    def __init__(self, mirror: spack.mirror.Mirror, force: bool, update_index: bool):
+    def __init__(self, mirror: spack.mirrors.mirror.Mirror, force: bool, update_index: bool):
         self.mirror = mirror
         self.force = force
         self.update_index = update_index
@@ -1222,7 +1207,7 @@ def tag(self, tag: str, roots: List[spack.spec.Spec]):
 class OCIUploader(Uploader):
     def __init__(
         self,
-        mirror: spack.mirror.Mirror,
+        mirror: spack.mirrors.mirror.Mirror,
         force: bool,
         update_index: bool,
         base_image: Optional[str],
@@ -1271,7 +1256,7 @@ def tag(self, tag: str, roots: List[spack.spec.Spec]):
 class URLUploader(Uploader):
     def __init__(
         self,
-        mirror: spack.mirror.Mirror,
+        mirror: spack.mirrors.mirror.Mirror,
         force: bool,
         update_index: bool,
         signing_key: Optional[str],
@@ -1295,7 +1280,7 @@ def push(
 
 
 def make_uploader(
-    mirror: spack.mirror.Mirror,
+    mirror: spack.mirrors.mirror.Mirror,
     force: bool = False,
     update_index: bool = False,
     signing_key: Optional[str] = None,
@@ -1312,7 +1297,7 @@ def make_uploader(
         )
 
 
-def _format_spec(spec: Spec) -> str:
+def _format_spec(spec: spack.spec.Spec) -> str:
     return spec.cformat("{name}{@version}{/hash:7}")
 
 
@@ -1335,7 +1320,7 @@ def _progress(self):
             return f"[{self.n:{digits}}/{self.total}] "
         return ""
 
-    def start(self, spec: Spec, running: bool) -> None:
+    def start(self, spec: spack.spec.Spec, running: bool) -> None:
         self.n += 1
         self.running = running
         self.pre = self._progress()
@@ -1354,18 +1339,18 @@ def fail(self) -> None:
 
 
 def _url_push(
-    specs: List[Spec],
+    specs: List[spack.spec.Spec],
     out_url: str,
     signing_key: Optional[str],
     force: bool,
     update_index: bool,
     tmpdir: str,
     executor: concurrent.futures.Executor,
-) -> Tuple[List[Spec], List[Tuple[Spec, BaseException]]]:
+) -> Tuple[List[spack.spec.Spec], List[Tuple[spack.spec.Spec, BaseException]]]:
     """Pushes to the provided build cache, and returns a list of skipped specs that were already
     present (when force=False), and a list of errors. Does not raise on error."""
-    skipped: List[Spec] = []
-    errors: List[Tuple[Spec, BaseException]] = []
+    skipped: List[spack.spec.Spec] = []
+    errors: List[Tuple[spack.spec.Spec, BaseException]] = []
 
     exists_futures = [
         executor.submit(_exists_in_buildcache, spec, tmpdir, out_url) for spec in specs
@@ -1438,7 +1423,7 @@ def _url_push(
     return skipped, errors
 
 
-def _oci_upload_success_msg(spec: Spec, digest: Digest, size: int, elapsed: float):
+def _oci_upload_success_msg(spec: spack.spec.Spec, digest: Digest, size: int, elapsed: float):
     elapsed = max(elapsed, 0.001)  # guard against division by zero
     return (
         f"Pushed {_format_spec(spec)}: {digest} ({elapsed:.2f}s, "
@@ -1467,13 +1452,11 @@ def _oci_push_pkg_blob(
     filename = os.path.join(tmpdir, f"{spec.dag_hash()}.tar.gz")
 
     # Create an oci.image.layer aka tarball of the package
-    compressed_tarfile_checksum, tarfile_checksum = _do_create_tarball(
-        filename, spec.prefix, get_buildinfo_dict(spec)
-    )
+    tar_gz_checksum, tar_checksum = create_tarball(spec, filename)
 
     blob = spack.oci.oci.Blob(
-        Digest.from_sha256(compressed_tarfile_checksum),
-        Digest.from_sha256(tarfile_checksum),
+        Digest.from_sha256(tar_gz_checksum),
+        Digest.from_sha256(tar_checksum),
         os.path.getsize(filename),
     )
 
@@ -1524,7 +1507,7 @@ def _oci_put_manifest(
 ):
     architecture = _oci_archspec_to_gooarch(specs[0])
 
-    expected_blobs: List[Spec] = [
+    expected_blobs: List[spack.spec.Spec] = [
         s
         for s in traverse.traverse_nodes(specs, order="topo", deptype=("link", "run"), root=True)
         if not s.external
@@ -1568,7 +1551,7 @@ def _oci_put_manifest(
 
     config_file = os.path.join(tmpdir, f"{specs[0].dag_hash()}.config.json")
 
-    with open(config_file, "w") as f:
+    with open(config_file, "w", encoding="utf-8") as f:
         json.dump(config, f, separators=(",", ":"))
 
     config_file_checksum = Digest.from_sha256(
@@ -1638,19 +1621,33 @@ def _oci_update_base_images(
         )
 
 
+def _oci_default_tag(spec: spack.spec.Spec) -> str:
+    """Return a valid, default image tag for a spec."""
+    return ensure_valid_tag(f"{spec.name}-{spec.version}-{spec.dag_hash()}.spack")
+
+
+#: Default OCI index tag
+default_index_tag = "index.spack"
+
+
+def tag_is_spec(tag: str) -> bool:
+    """Check if a tag is likely a Spec"""
+    return tag.endswith(".spack") and tag != default_index_tag
+
+
 def _oci_push(
     *,
     target_image: ImageReference,
     base_image: Optional[ImageReference],
-    installed_specs_with_deps: List[Spec],
+    installed_specs_with_deps: List[spack.spec.Spec],
     tmpdir: str,
     executor: concurrent.futures.Executor,
     force: bool = False,
 ) -> Tuple[
-    List[Spec],
+    List[spack.spec.Spec],
     Dict[str, Tuple[dict, dict]],
     Dict[str, spack.oci.oci.Blob],
-    List[Tuple[Spec, BaseException]],
+    List[Tuple[spack.spec.Spec, BaseException]],
 ]:
     # Spec dag hash -> blob
     checksums: Dict[str, spack.oci.oci.Blob] = {}
@@ -1659,13 +1656,15 @@ def _oci_push(
     base_images: Dict[str, Tuple[dict, dict]] = {}
 
     # Specs not uploaded because they already exist
-    skipped: List[Spec] = []
+    skipped: List[spack.spec.Spec] = []
 
     if not force:
         tty.info("Checking for existing specs in the buildcache")
         blobs_to_upload = []
 
-        tags_to_check = (target_image.with_tag(default_tag(s)) for s in installed_specs_with_deps)
+        tags_to_check = (
+            target_image.with_tag(_oci_default_tag(s)) for s in installed_specs_with_deps
+        )
         available_blobs = executor.map(_oci_get_blob_info, tags_to_check)
 
         for spec, maybe_blob in zip(installed_specs_with_deps, available_blobs):
@@ -1693,8 +1692,8 @@ def _oci_push(
         executor.submit(_oci_push_pkg_blob, target_image, spec, tmpdir) for spec in blobs_to_upload
     ]
 
-    manifests_to_upload: List[Spec] = []
-    errors: List[Tuple[Spec, BaseException]] = []
+    manifests_to_upload: List[spack.spec.Spec] = []
+    errors: List[Tuple[spack.spec.Spec, BaseException]] = []
 
     # And update the spec to blob mapping for successful uploads
     for spec, blob_future in zip(blobs_to_upload, blob_futures):
@@ -1720,7 +1719,7 @@ def _oci_push(
             base_image_cache=base_images,
         )
 
-    def extra_config(spec: Spec):
+    def extra_config(spec: spack.spec.Spec):
         spec_dict = spec.to_dict(hash=ht.dag_hash)
         spec_dict["buildcache_layout_version"] = CURRENT_BUILD_CACHE_LAYOUT_VERSION
         spec_dict["binary_cache_checksum"] = {
@@ -1736,7 +1735,7 @@ def extra_config(spec: Spec):
             _oci_put_manifest,
             base_images,
             checksums,
-            target_image.with_tag(default_tag(spec)),
+            target_image.with_tag(_oci_default_tag(spec)),
             tmpdir,
             extra_config(spec),
             {"org.opencontainers.image.description": spec.format()},
@@ -1753,7 +1752,7 @@ def extra_config(spec: Spec):
         manifest_progress.start(spec, manifest_future.running())
         if error is None:
             manifest_progress.ok(
-                f"Tagged {_format_spec(spec)} as {target_image.with_tag(default_tag(spec))}"
+                f"Tagged {_format_spec(spec)} as {target_image.with_tag(_oci_default_tag(spec))}"
             )
         else:
             manifest_progress.fail()
@@ -1788,13 +1787,13 @@ def _oci_update_index(
     db = BuildCacheDatabase(db_root_dir)
 
     for spec_dict in spec_dicts:
-        spec = Spec.from_dict(spec_dict)
+        spec = spack.spec.Spec.from_dict(spec_dict)
         db.add(spec)
         db.mark(spec, "in_buildcache", True)
 
     # Create the index.json file
     index_json_path = os.path.join(tmpdir, "index.json")
-    with open(index_json_path, "w") as f:
+    with open(index_json_path, "w", encoding="utf-8") as f:
         db._write_to_file(f)
 
     # Create an empty config.json file
@@ -1903,7 +1902,7 @@ def _get_valid_spec_file(path: str, max_supported_layout: int) -> Tuple[Dict, in
     try:
         as_string = binary_content.decode("utf-8")
         if path.endswith(".json.sig"):
-            spec_dict = Spec.extract_json_from_clearsig(as_string)
+            spec_dict = spack.spec.Spec.extract_json_from_clearsig(as_string)
         else:
             spec_dict = json.loads(as_string)
     except Exception as e:
@@ -1951,9 +1950,9 @@ def download_tarball(spec, unsigned: Optional[bool] = False, mirrors_for_spec=No
            "signature_verified": "true-if-binary-pkg-was-already-verified"
        }
     """
-    configured_mirrors: Iterable[spack.mirror.Mirror] = spack.mirror.MirrorCollection(
-        binary=True
-    ).values()
+    configured_mirrors: Iterable[spack.mirrors.mirror.Mirror] = (
+        spack.mirrors.mirror.MirrorCollection(binary=True).values()
+    )
     if not configured_mirrors:
         tty.die("Please add a spack mirror to allow download of pre-compiled packages.")
 
@@ -1978,7 +1977,7 @@ def fetch_url_to_mirror(url):
         for mirror in configured_mirrors:
             if mirror.fetch_url == url:
                 return mirror
-        return spack.mirror.Mirror(url)
+        return spack.mirrors.mirror.Mirror(url)
 
     mirrors = [fetch_url_to_mirror(url) for url in mirror_urls]
 
@@ -1999,7 +1998,7 @@ def fetch_url_to_mirror(url):
             if fetch_url.startswith("oci://"):
                 ref = spack.oci.image.ImageReference.from_string(
                     fetch_url[len("oci://") :]
-                ).with_tag(spack.oci.image.default_tag(spec))
+                ).with_tag(_oci_default_tag(spec))
 
                 # Fetch the manifest
                 try:
@@ -2243,7 +2242,8 @@ def relocate_package(spec):
             ]
             if analogs:
                 # Prefer same-name analogs and prefer higher versions
-                # This matches the preferences in Spec.splice, so we will find same node
+                # This matches the preferences in spack.spec.Spec.splice, so we
+                # will find same node
                 analog = max(analogs, key=lambda a: (a.name == s.name, a.version))
 
         lookup_dag_hash = analog.dag_hash()
@@ -2332,7 +2332,9 @@ def is_backup_file(file):
             if not codesign:
                 return
             for binary in changed_files:
-                codesign("-fs-", binary)
+                # preserve the original inode by running codesign on a copy
+                with fsys.edit_in_place_through_temporary_file(binary) as tmp_binary:
+                    codesign("-fs-", tmp_binary)
 
     # If we are installing back to the same location
     # relocate the sbang location if the spack directory changed
@@ -2413,6 +2415,14 @@ def _tar_strip_component(tar: tarfile.TarFile, prefix: str):
         yield m
 
 
+def extract_buildcache_tarball(tarfile_path: str, destination: str) -> None:
+    with closing(tarfile.open(tarfile_path, "r")) as tar:
+        # Remove common prefix from tarball entries and directly extract them to the install dir.
+        tar.extractall(
+            path=destination, members=_tar_strip_component(tar, prefix=_ensure_common_prefix(tar))
+        )
+
+
 def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
     """
     extract binary tarball for given package into install area
@@ -2482,12 +2492,7 @@ def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
                 tarfile_path, size, contents, "sha256", expected, local_checksum
             )
     try:
-        with closing(tarfile.open(tarfile_path, "r")) as tar:
-            # Remove install prefix from tarfil to extract directly into spec.prefix
-            tar.extractall(
-                path=spec.prefix,
-                members=_tar_strip_component(tar, prefix=_ensure_common_prefix(tar)),
-            )
+        extract_buildcache_tarball(tarfile_path, destination=spec.prefix)
     except Exception:
         shutil.rmtree(spec.prefix, ignore_errors=True)
         _delete_staged_downloads(download_result)
@@ -2646,7 +2651,7 @@ def try_direct_fetch(spec, mirrors=None):
     specfile_is_signed = False
     found_specs = []
 
-    binary_mirrors = spack.mirror.MirrorCollection(mirrors=mirrors, binary=True).values()
+    binary_mirrors = spack.mirrors.mirror.MirrorCollection(mirrors=mirrors, binary=True).values()
 
     for mirror in binary_mirrors:
         buildcache_fetch_url_json = url_util.join(
@@ -2677,10 +2682,10 @@ def try_direct_fetch(spec, mirrors=None):
         # are concrete (as they are built) so we need to mark this spec
         # concrete on read-in.
         if specfile_is_signed:
-            specfile_json = Spec.extract_json_from_clearsig(specfile_contents)
-            fetched_spec = Spec.from_dict(specfile_json)
+            specfile_json = spack.spec.Spec.extract_json_from_clearsig(specfile_contents)
+            fetched_spec = spack.spec.Spec.from_dict(specfile_json)
         else:
-            fetched_spec = Spec.from_json(specfile_contents)
+            fetched_spec = spack.spec.Spec.from_json(specfile_contents)
         fetched_spec._mark_concrete()
 
         found_specs.append({"mirror_url": mirror.fetch_url, "spec": fetched_spec})
@@ -2707,7 +2712,7 @@ def get_mirrors_for_spec(spec=None, mirrors_to_check=None, index_only=False):
     if spec is None:
         return []
 
-    if not spack.mirror.MirrorCollection(mirrors=mirrors_to_check, binary=True):
+    if not spack.mirrors.mirror.MirrorCollection(mirrors=mirrors_to_check, binary=True):
         tty.debug("No Spack mirrors are currently configured")
         return {}
 
@@ -2746,7 +2751,7 @@ def clear_spec_cache():
 
 def get_keys(install=False, trust=False, force=False, mirrors=None):
     """Get pgp public keys available on mirror with suffix .pub"""
-    mirror_collection = mirrors or spack.mirror.MirrorCollection(binary=True)
+    mirror_collection = mirrors or spack.mirrors.mirror.MirrorCollection(binary=True)
 
     if not mirror_collection:
         tty.die("Please add a spack mirror to allow " + "download of build caches.")
@@ -2801,7 +2806,7 @@ def get_keys(install=False, trust=False, force=False, mirrors=None):
 
 
 def _url_push_keys(
-    *mirrors: Union[spack.mirror.Mirror, str],
+    *mirrors: Union[spack.mirrors.mirror.Mirror, str],
     keys: List[str],
     tmpdir: str,
     update_index: bool = False,
@@ -2868,7 +2873,7 @@ def check_specs_against_mirrors(mirrors, specs, output_file=None):
 
     """
     rebuilds = {}
-    for mirror in spack.mirror.MirrorCollection(mirrors, binary=True).values():
+    for mirror in spack.mirrors.mirror.MirrorCollection(mirrors, binary=True).values():
         tty.debug("Checking for built specs at {0}".format(mirror.fetch_url))
 
         rebuild_list = []
@@ -2885,7 +2890,7 @@ def check_specs_against_mirrors(mirrors, specs, output_file=None):
             }
 
     if output_file:
-        with open(output_file, "w") as outf:
+        with open(output_file, "w", encoding="utf-8") as outf:
             outf.write(json.dumps(rebuilds))
 
     return 1 if rebuilds else 0
@@ -2912,7 +2917,7 @@ def _download_buildcache_entry(mirror_root, descriptions):
 
 
 def download_buildcache_entry(file_descriptions, mirror_url=None):
-    if not mirror_url and not spack.mirror.MirrorCollection(binary=True):
+    if not mirror_url and not spack.mirrors.mirror.MirrorCollection(binary=True):
         tty.die(
             "Please provide or add a spack mirror to allow " + "download of buildcache entries."
         )
@@ -2921,7 +2926,7 @@ def download_buildcache_entry(file_descriptions, mirror_url=None):
         mirror_root = os.path.join(mirror_url, BUILD_CACHE_RELATIVE_PATH)
         return _download_buildcache_entry(mirror_root, file_descriptions)
 
-    for mirror in spack.mirror.MirrorCollection(binary=True).values():
+    for mirror in spack.mirrors.mirror.MirrorCollection(binary=True).values():
         mirror_root = os.path.join(mirror.fetch_url, BUILD_CACHE_RELATIVE_PATH)
 
         if _download_buildcache_entry(mirror_root, file_descriptions):
@@ -2979,7 +2984,7 @@ def __init__(self, all_architectures):
 
         self.possible_specs = specs
 
-    def __call__(self, spec: Spec, **kwargs):
+    def __call__(self, spec: spack.spec.Spec, **kwargs):
         """
         Args:
             spec: The spec being searched for
@@ -3117,7 +3122,7 @@ def __init__(self, url: str, local_hash, urlopen=None) -> None:
 
     def conditional_fetch(self) -> FetchIndexResult:
         """Download an index from an OCI registry type mirror."""
-        url_manifest = self.ref.with_tag(spack.oci.image.default_index_tag).manifest_url()
+        url_manifest = self.ref.with_tag(default_index_tag).manifest_url()
         try:
             response = self.urlopen(
                 urllib.request.Request(

lib/spack/spack/bootstrap/__init__.py

@@ -9,7 +9,6 @@
     all_core_root_specs,
     ensure_clingo_importable_or_raise,
     ensure_core_dependencies,
-    ensure_file_in_path_or_raise,
     ensure_gpg_in_path_or_raise,
     ensure_patchelf_in_path_or_raise,
 )
@@ -20,7 +19,6 @@
     "is_bootstrapping",
     "ensure_bootstrap_configuration",
     "ensure_core_dependencies",
-    "ensure_file_in_path_or_raise",
     "ensure_gpg_in_path_or_raise",
     "ensure_clingo_importable_or_raise",
     "ensure_patchelf_in_path_or_raise",

lib/spack/spack/bootstrap/core.py

@@ -37,7 +37,7 @@
 import spack.binary_distribution
 import spack.config
 import spack.detection
-import spack.mirror
+import spack.mirrors.mirror
 import spack.platforms
 import spack.spec
 import spack.store
@@ -91,7 +91,7 @@ def __init__(self, conf: ConfigDictionary) -> None:
         self.metadata_dir = spack.util.path.canonicalize_path(conf["metadata"])
 
         # Promote (relative) paths to file urls
-        self.url = spack.mirror.Mirror(conf["info"]["url"]).fetch_url
+        self.url = spack.mirrors.mirror.Mirror(conf["info"]["url"]).fetch_url
 
     @property
     def mirror_scope(self) -> spack.config.InternalConfigScope:
@@ -481,19 +481,6 @@ def ensure_gpg_in_path_or_raise() -> None:
     )
 
 
-def file_root_spec() -> str:
-    """Return the root spec used to bootstrap file"""
-    root_spec_name = "win-file" if IS_WINDOWS else "file"
-    return _root_spec(root_spec_name)
-
-
-def ensure_file_in_path_or_raise() -> None:
-    """Ensure file is in the PATH or raise"""
-    return ensure_executables_in_path_or_raise(
-        executables=["file"], abstract_spec=file_root_spec()
-    )
-
-
 def patchelf_root_spec() -> str:
     """Return the root spec used to bootstrap patchelf"""
     # 0.13.1 is the last version not to require C++17.
@@ -577,15 +564,13 @@ def ensure_core_dependencies() -> None:
     """Ensure the presence of all the core dependencies."""
     if sys.platform.lower() == "linux":
         ensure_patchelf_in_path_or_raise()
-    elif sys.platform == "win32":
-        ensure_file_in_path_or_raise()
     ensure_gpg_in_path_or_raise()
     ensure_clingo_importable_or_raise()
 
 
 def all_core_root_specs() -> List[str]:
     """Return a list of all the core root specs that may be used to bootstrap Spack"""
-    return [clingo_root_spec(), gnupg_root_spec(), patchelf_root_spec(), file_root_spec()]
+    return [clingo_root_spec(), gnupg_root_spec(), patchelf_root_spec()]
 
 
 def bootstrapping_sources(scope: Optional[str] = None):

lib/spack/spack/bootstrap/status.py

@@ -3,8 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Query the status of bootstrapping on this machine"""
-import platform
-from typing import List, Optional, Sequence, Tuple, Union
+import sys
+from typing import Dict, List, Optional, Sequence, Tuple, Union
 
 import spack.util.executable
 
@@ -72,7 +72,7 @@ def _core_requirements() -> List[RequiredResponseType]:
         "bzip2": _missing("bzip2", "required to compress/decompress code archives"),
         "git": _missing("git", "required to fetch/manage git repositories"),
     }
-    if platform.system().lower() == "linux":
+    if sys.platform == "linux":
         _core_system_exes["xz"] = _missing("xz", "required to compress/decompress code archives")
 
     # Executables that are not bootstrapped yet
@@ -87,17 +87,16 @@ def _core_requirements() -> List[RequiredResponseType]:
 
 
 def _buildcache_requirements() -> List[RequiredResponseType]:
-    _buildcache_exes = {
-        "file": _missing("file", "required to analyze files for buildcaches", system_only=False),
-        ("gpg2", "gpg"): _missing("gpg2", "required to sign/verify buildcaches", False),
+    _buildcache_exes: Dict[ExecutablesType, str] = {
+        ("gpg2", "gpg"): _missing("gpg2", "required to sign/verify buildcaches", False)
     }
-    if platform.system().lower() == "darwin":
+    if sys.platform == "darwin":
         _buildcache_exes["otool"] = _missing("otool", "required to relocate binaries")
 
     # Executables that are not bootstrapped yet
     result = [_required_system_executable(exe, msg) for exe, msg in _buildcache_exes.items()]
 
-    if platform.system().lower() == "linux":
+    if sys.platform == "linux":
         result.append(
             _required_executable(
                 "patchelf",

lib/spack/spack/build_environment.py

@@ -56,7 +56,6 @@
 from llnl.util.symlink import symlink
 from llnl.util.tty.color import cescape, colorize
 
-import spack.build_systems._checks
 import spack.build_systems.cmake
 import spack.build_systems.meson
 import spack.build_systems.python
@@ -883,6 +882,9 @@ def __init__(self, *roots: spack.spec.Spec, context: Context):
         elif context == Context.RUN:
             self.root_depflag = dt.RUN | dt.LINK
 
+    def accept(self, item):
+        return True
+
     def neighbors(self, item):
         spec = item.edge.spec
         if spec.dag_hash() in self.root_hashes:
@@ -920,19 +922,19 @@ def effective_deptypes(
     a flag specifying in what way they do so. The list is ordered topologically
     from root to leaf, meaning that environment modifications should be applied
     in reverse so that dependents override dependencies, not the other way around."""
-    visitor = traverse.TopoVisitor(
-        EnvironmentVisitor(*specs, context=context),
-        key=lambda x: x.dag_hash(),
+    topo_sorted_edges = traverse.traverse_topo_edges_generator(
+        traverse.with_artificial_edges(specs),
+        visitor=EnvironmentVisitor(*specs, context=context),
+        key=traverse.by_dag_hash,
         root=True,
         all_edges=True,
     )
-    traverse.traverse_depth_first_with_visitor(traverse.with_artificial_edges(specs), visitor)
 
     # Dictionary with "no mode" as default value, so it's easy to write modes[x] |= flag.
     use_modes = defaultdict(lambda: UseMode(0))
     nodes_with_type = []
 
-    for edge in visitor.edges:
+    for edge in topo_sorted_edges:
         parent, child, depflag = edge.parent, edge.spec, edge.depflag
 
         # Mark the starting point
@@ -1375,7 +1377,7 @@ def exitcode_msg(p):
     return child_result
 
 
-CONTEXT_BASES = (spack.package_base.PackageBase, spack.build_systems._checks.BaseBuilder)
+CONTEXT_BASES = (spack.package_base.PackageBase, spack.builder.Builder)
 
 
 def get_package_context(traceback, context=3):
@@ -1424,27 +1426,20 @@ def make_stack(tb, stack=None):
     # We found obj, the Package implementation we care about.
     # Point out the location in the install method where we failed.
     filename = inspect.getfile(frame.f_code)
-    lineno = frame.f_lineno
-    if os.path.basename(filename) == "package.py":
-        # subtract 1 because we inject a magic import at the top of package files.
-        # TODO: get rid of the magic import.
-        lineno -= 1
-
-    lines = ["{0}:{1:d}, in {2}:".format(filename, lineno, frame.f_code.co_name)]
+    lines = [f"{filename}:{frame.f_lineno}, in {frame.f_code.co_name}:"]
 
     # Build a message showing context in the install method.
     sourcelines, start = inspect.getsourcelines(frame)
 
     # Calculate lineno of the error relative to the start of the function.
-    fun_lineno = lineno - start
+    fun_lineno = frame.f_lineno - start
     start_ctx = max(0, fun_lineno - context)
     sourcelines = sourcelines[start_ctx : fun_lineno + context + 1]
 
     for i, line in enumerate(sourcelines):
         is_error = start_ctx + i == fun_lineno
-        mark = ">> " if is_error else "   "
         # Add start to get lineno relative to start of file, not function.
-        marked = "  {0}{1:-6d}{2}".format(mark, start + start_ctx + i, line.rstrip())
+        marked = f"  {'>> ' if is_error else '   '}{start + start_ctx + i:-6d}{line.rstrip()}"
         if is_error:
             marked = colorize("@R{%s}" % cescape(marked))
         lines.append(marked)

lib/spack/spack/build_systems/_checks.py

@@ -9,6 +9,7 @@
 
 import spack.builder
 import spack.error
+import spack.phase_callbacks
 import spack.relocate
 import spack.spec
 import spack.store
@@ -63,7 +64,7 @@ def apply_macos_rpath_fixups(builder: spack.builder.Builder):
 
 
 def ensure_build_dependencies_or_raise(
-    spec: spack.spec.Spec, dependencies: List[spack.spec.Spec], error_msg: str
+    spec: spack.spec.Spec, dependencies: List[str], error_msg: str
 ):
     """Ensure that some build dependencies are present in the concrete spec.
 
@@ -71,7 +72,7 @@ def ensure_build_dependencies_or_raise(
 
     Args:
         spec: concrete spec to be checked.
-        dependencies: list of abstract specs to be satisfied
+        dependencies: list of package names of required build dependencies
         error_msg: brief error message to be prepended to a longer description
 
     Raises:
@@ -127,8 +128,8 @@ def execute_install_time_tests(builder: spack.builder.Builder):
     builder.pkg.tester.phase_tests(builder, "install", builder.install_time_test_callbacks)
 
 
-class BaseBuilder(spack.builder.Builder):
-    """Base class for builders to register common checks"""
+class BuilderWithDefaults(spack.builder.Builder):
+    """Base class for all specific builders with common callbacks registered."""
 
     # Check that self.prefix is there after installation
-    spack.builder.run_after("install")(sanity_check_prefix)
+    spack.phase_callbacks.run_after("install")(sanity_check_prefix)

lib/spack/spack/build_systems/autotools.py

@@ -6,7 +6,7 @@
 import os.path
 import stat
 import subprocess
-from typing import List
+from typing import Callable, List, Optional, Set, Tuple, Union
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
@@ -15,6 +15,9 @@
 import spack.builder
 import spack.error
 import spack.package_base
+import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, conflicts, depends_on
 from spack.multimethod import when
 from spack.operating_systems.mac_os import macos_version
@@ -22,7 +25,7 @@
 from spack.version import Version
 
 from ._checks import (
-    BaseBuilder,
+    BuilderWithDefaults,
     apply_macos_rpath_fixups,
     ensure_build_dependencies_or_raise,
     execute_build_time_tests,
@@ -69,14 +72,14 @@ def flags_to_build_system_args(self, flags):
     # Legacy methods (used by too many packages to change them,
     # need to forward to the builder)
     def enable_or_disable(self, *args, **kwargs):
-        return self.builder.enable_or_disable(*args, **kwargs)
+        return spack.builder.create(self).enable_or_disable(*args, **kwargs)
 
     def with_or_without(self, *args, **kwargs):
-        return self.builder.with_or_without(*args, **kwargs)
+        return spack.builder.create(self).with_or_without(*args, **kwargs)
 
 
 @spack.builder.builder("autotools")
-class AutotoolsBuilder(BaseBuilder):
+class AutotoolsBuilder(BuilderWithDefaults):
     """The autotools builder encodes the default way of installing software built
     with autotools. It has four phases that can be overridden, if need be:
 
@@ -157,7 +160,7 @@ class AutotoolsBuilder(BaseBuilder):
     install_libtool_archives = False
 
     @property
-    def patch_config_files(self):
+    def patch_config_files(self) -> bool:
         """Whether to update old ``config.guess`` and ``config.sub`` files
         distributed with the tarball.
 
@@ -177,23 +180,20 @@ def patch_config_files(self):
         )
 
     @property
-    def _removed_la_files_log(self):
+    def _removed_la_files_log(self) -> str:
         """File containing the list of removed libtool archives"""
-        build_dir = self.build_directory
-        if not os.path.isabs(self.build_directory):
-            build_dir = os.path.join(self.pkg.stage.path, build_dir)
-        return os.path.join(build_dir, "removed_la_files.txt")
+        return os.path.join(self.build_directory, "removed_la_files.txt")
 
     @property
-    def archive_files(self):
+    def archive_files(self) -> List[str]:
         """Files to archive for packages based on autotools"""
         files = [os.path.join(self.build_directory, "config.log")]
         if not self.install_libtool_archives:
             files.append(self._removed_la_files_log)
         return files
 
-    @spack.builder.run_after("autoreconf")
-    def _do_patch_config_files(self):
+    @spack.phase_callbacks.run_after("autoreconf")
+    def _do_patch_config_files(self) -> None:
         """Some packages ship with older config.guess/config.sub files and need to
         have these updated when installed on a newer architecture.
 
@@ -294,7 +294,7 @@ def runs_ok(script_abs_path):
    and set the prefix to the directory containing the `config.guess` and
    `config.sub` files.
 """
-            raise spack.error.InstallError(msg.format(", ".join(to_be_found), self.name))
+            raise spack.error.InstallError(msg.format(", ".join(to_be_found), self.pkg.name))
 
         # Copy the good files over the bad ones
         for abs_path in to_be_patched:
@@ -304,8 +304,8 @@ def runs_ok(script_abs_path):
             fs.copy(substitutes[name], abs_path)
             os.chmod(abs_path, mode)
 
-    @spack.builder.run_before("configure")
-    def _patch_usr_bin_file(self):
+    @spack.phase_callbacks.run_before("configure")
+    def _patch_usr_bin_file(self) -> None:
         """On NixOS file is not available in /usr/bin/file. Patch configure
         scripts to use file from path."""
 
@@ -316,8 +316,8 @@ def _patch_usr_bin_file(self):
             with fs.keep_modification_time(*x.filenames):
                 x.filter(regex="/usr/bin/file", repl="file", string=True)
 
-    @spack.builder.run_before("configure")
-    def _set_autotools_environment_variables(self):
+    @spack.phase_callbacks.run_before("configure")
+    def _set_autotools_environment_variables(self) -> None:
         """Many autotools builds use a version of mknod.m4 that fails when
         running as root unless FORCE_UNSAFE_CONFIGURE is set to 1.
 
@@ -330,8 +330,8 @@ def _set_autotools_environment_variables(self):
         """
         os.environ["FORCE_UNSAFE_CONFIGURE"] = "1"
 
-    @spack.builder.run_before("configure")
-    def _do_patch_libtool_configure(self):
+    @spack.phase_callbacks.run_before("configure")
+    def _do_patch_libtool_configure(self) -> None:
         """Patch bugs that propagate from libtool macros into "configure" and
         further into "libtool". Note that patches that can be fixed by patching
         "libtool" directly should be implemented in the _do_patch_libtool method
@@ -358,8 +358,8 @@ def _do_patch_libtool_configure(self):
             # Support Libtool 2.4.2 and older:
             x.filter(regex=r'^(\s*test \$p = "-R")(; then\s*)$', repl=r'\1 || test x-l = x"$p"\2')
 
-    @spack.builder.run_after("configure")
-    def _do_patch_libtool(self):
+    @spack.phase_callbacks.run_after("configure")
+    def _do_patch_libtool(self) -> None:
         """If configure generates a "libtool" script that does not correctly
         detect the compiler (and patch_libtool is set), patch in the correct
         values for libtool variables.
@@ -507,27 +507,69 @@ def _do_patch_libtool(self):
             )
 
     @property
-    def configure_directory(self):
+    def configure_directory(self) -> str:
         """Return the directory where 'configure' resides."""
         return self.pkg.stage.source_path
 
     @property
-    def configure_abs_path(self):
+    def configure_abs_path(self) -> str:
         # Absolute path to configure
         configure_abs_path = os.path.join(os.path.abspath(self.configure_directory), "configure")
         return configure_abs_path
 
     @property
-    def build_directory(self):
+    def build_directory(self) -> str:
         """Override to provide another place to build the package"""
-        return self.configure_directory
+        # Handle the case where the configure directory is set to a non-absolute path
+        # Non-absolute paths are always relative to the staging source path
+        build_dir = self.configure_directory
+        if not os.path.isabs(build_dir):
+            build_dir = os.path.join(self.pkg.stage.source_path, build_dir)
+        return build_dir
 
-    @spack.builder.run_before("autoreconf")
-    def delete_configure_to_force_update(self):
+    @spack.phase_callbacks.run_before("autoreconf")
+    def delete_configure_to_force_update(self) -> None:
         if self.force_autoreconf:
             fs.force_remove(self.configure_abs_path)
 
-    def autoreconf(self, pkg, spec, prefix):
+    @property
+    def autoreconf_search_path_args(self) -> List[str]:
+        """Search path includes for autoreconf. Add an -I flag for all `aclocal` dirs
+        of build deps, skips the default path of automake, move external include
+        flags to the back, since they might pull in unrelated m4 files shadowing
+        spack dependencies."""
+        return _autoreconf_search_path_args(self.spec)
+
+    @spack.phase_callbacks.run_after("autoreconf")
+    def set_configure_or_die(self) -> None:
+        """Ensure the presence of a "configure" script, or raise. If the "configure"
+        is found, a module level attribute is set.
+
+        Raises:
+             RuntimeError: if the "configure" script is not found
+        """
+        # Check if the "configure" script is there. If not raise a RuntimeError.
+        if not os.path.exists(self.configure_abs_path):
+            msg = "configure script not found in {0}"
+            raise RuntimeError(msg.format(self.configure_directory))
+
+        # Monkey-patch the configure script in the corresponding module
+        globals_for_pkg = spack.build_environment.ModuleChangePropagator(self.pkg)
+        globals_for_pkg.configure = Executable(self.configure_abs_path)
+        globals_for_pkg.propagate_changes_to_mro()
+
+    def configure_args(self) -> List[str]:
+        """Return the list of all the arguments that must be passed to configure,
+        except ``--prefix`` which will be pre-pended to the list.
+        """
+        return []
+
+    def autoreconf(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Not needed usually, configure should be already there"""
 
         # If configure exists nothing needs to be done
@@ -554,39 +596,12 @@ def autoreconf(self, pkg, spec, prefix):
             autoreconf_args += self.autoreconf_extra_args
             self.pkg.module.autoreconf(*autoreconf_args)
 
-    @property
-    def autoreconf_search_path_args(self):
-        """Search path includes for autoreconf. Add an -I flag for all `aclocal` dirs
-        of build deps, skips the default path of automake, move external include
-        flags to the back, since they might pull in unrelated m4 files shadowing
-        spack dependencies."""
-        return _autoreconf_search_path_args(self.spec)
-
-    @spack.builder.run_after("autoreconf")
-    def set_configure_or_die(self):
-        """Ensure the presence of a "configure" script, or raise. If the "configure"
-        is found, a module level attribute is set.
-
-        Raises:
-             RuntimeError: if the "configure" script is not found
-        """
-        # Check if the "configure" script is there. If not raise a RuntimeError.
-        if not os.path.exists(self.configure_abs_path):
-            msg = "configure script not found in {0}"
-            raise RuntimeError(msg.format(self.configure_directory))
-
-        # Monkey-patch the configure script in the corresponding module
-        globals_for_pkg = spack.build_environment.ModuleChangePropagator(self.pkg)
-        globals_for_pkg.configure = Executable(self.configure_abs_path)
-        globals_for_pkg.propagate_changes_to_mro()
-
-    def configure_args(self):
-        """Return the list of all the arguments that must be passed to configure,
-        except ``--prefix`` which will be pre-pended to the list.
-        """
-        return []
-
-    def configure(self, pkg, spec, prefix):
+    def configure(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Run "configure", with the arguments specified by the builder and an
         appropriately set prefix.
         """
@@ -597,7 +612,12 @@ def configure(self, pkg, spec, prefix):
         with fs.working_dir(self.build_directory, create=True):
             pkg.module.configure(*options)
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Run "make" on the build targets specified by the builder."""
         # See https://autotools.io/automake/silent.html
         params = ["V=1"]
@@ -605,41 +625,49 @@ def build(self, pkg, spec, prefix):
         with fs.working_dir(self.build_directory):
             pkg.module.make(*params)
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Run "make" on the install targets specified by the builder."""
         with fs.working_dir(self.build_directory):
             pkg.module.make(*self.install_targets)
 
-    spack.builder.run_after("build")(execute_build_time_tests)
+    spack.phase_callbacks.run_after("build")(execute_build_time_tests)
 
-    def check(self):
+    def check(self) -> None:
         """Run "make" on the ``test`` and ``check`` targets, if found."""
         with fs.working_dir(self.build_directory):
             self.pkg._if_make_target_execute("test")
             self.pkg._if_make_target_execute("check")
 
     def _activate_or_not(
-        self, name, activation_word, deactivation_word, activation_value=None, variant=None
-    ):
+        self,
+        name: str,
+        activation_word: str,
+        deactivation_word: str,
+        activation_value: Optional[Union[Callable, str]] = None,
+        variant=None,
+    ) -> List[str]:
         """This function contain the current implementation details of
         :meth:`~spack.build_systems.autotools.AutotoolsBuilder.with_or_without` and
         :meth:`~spack.build_systems.autotools.AutotoolsBuilder.enable_or_disable`.
 
         Args:
-            name (str): name of the option that is being activated or not
-            activation_word (str): the default activation word ('with' in the
-                case of ``with_or_without``)
-            deactivation_word (str): the default deactivation word ('without'
-                in the case of ``with_or_without``)
-            activation_value (typing.Callable): callable that accepts a single
-                value. This value is either one of the allowed values for a
-                multi-valued variant or the name of a bool-valued variant.
+            name: name of the option that is being activated or not
+            activation_word: the default activation word ('with' in the case of
+                ``with_or_without``)
+            deactivation_word: the default deactivation word ('without' in the case of
+                ``with_or_without``)
+            activation_value: callable that accepts a single value. This value is either one of the
+                allowed values for a multi-valued variant or the name of a bool-valued variant.
                 Returns the parameter to be used when the value is activated.
 
-                The special value 'prefix' can also be assigned and will return
+                The special value "prefix" can also be assigned and will return
                 ``spec[name].prefix`` as activation parameter.
-            variant (str): name of the variant that is being processed
-                           (if different from option name)
+            variant: name of the variant that is being processed (if different from option name)
 
         Examples:
 
@@ -647,19 +675,19 @@ def _activate_or_not(
 
             .. code-block:: python
 
-                variant('foo', values=('x', 'y'), description='')
-                variant('bar', default=True, description='')
-                variant('ba_z', default=True, description='')
+                variant("foo", values=("x", "y"), description=")
+                variant("bar", default=True, description=")
+                variant("ba_z", default=True, description=")
 
             calling this function like:
 
             .. code-block:: python
 
                 _activate_or_not(
-                    'foo', 'with', 'without', activation_value='prefix'
+                    "foo", "with", "without", activation_value="prefix"
                 )
-                _activate_or_not('bar', 'with', 'without')
-                _activate_or_not('ba-z', 'with', 'without', variant='ba_z')
+                _activate_or_not("bar", "with", "without")
+                _activate_or_not("ba-z", "with", "without", variant="ba_z")
 
             will generate the following configuration options:
 
@@ -679,8 +707,8 @@ def _activate_or_not(
         Raises:
             KeyError: if name is not among known variants
         """
-        spec = self.pkg.spec
-        args = []
+        spec: spack.spec.Spec = self.pkg.spec
+        args: List[str] = []
 
         if activation_value == "prefix":
             activation_value = lambda x: spec[x].prefix
@@ -698,7 +726,7 @@ def _activate_or_not(
         # Create a list of pairs. Each pair includes a configuration
         # option and whether or not that option is activated
         vdef = self.pkg.get_variant(variant)
-        if set(vdef.values) == set((True, False)):
+        if set(vdef.values) == set((True, False)):  # type: ignore
             # BoolValuedVariant carry information about a single option.
             # Nonetheless, for uniformity of treatment we'll package them
             # in an iterable of one element.
@@ -709,14 +737,12 @@ def _activate_or_not(
             # package's build system. It excludes values which have special
             # meanings and do not correspond to features (e.g. "none")
             feature_values = getattr(vdef.values, "feature_values", None) or vdef.values
-            options = [(value, f"{variant}={value}" in spec) for value in feature_values]
+            options = [(v, f"{variant}={v}" in spec) for v in feature_values]  # type: ignore
 
         # For each allowed value in the list of values
         for option_value, activated in options:
             # Search for an override in the package for this value
-            override_name = "{0}_or_{1}_{2}".format(
-                activation_word, deactivation_word, option_value
-            )
+            override_name = f"{activation_word}_or_{deactivation_word}_{option_value}"
             line_generator = getattr(self, override_name, None) or getattr(
                 self.pkg, override_name, None
             )
@@ -725,19 +751,24 @@ def _activate_or_not(
 
                 def _default_generator(is_activated):
                     if is_activated:
-                        line = "--{0}-{1}".format(activation_word, option_value)
+                        line = f"--{activation_word}-{option_value}"
                         if activation_value is not None and activation_value(
                             option_value
                         ):  # NOQA=ignore=E501
-                            line += "={0}".format(activation_value(option_value))
+                            line = f"{line}={activation_value(option_value)}"
                         return line
-                    return "--{0}-{1}".format(deactivation_word, option_value)
+                    return f"--{deactivation_word}-{option_value}"
 
                 line_generator = _default_generator
             args.append(line_generator(activated))
         return args
 
-    def with_or_without(self, name, activation_value=None, variant=None):
+    def with_or_without(
+        self,
+        name: str,
+        activation_value: Optional[Union[Callable, str]] = None,
+        variant: Optional[str] = None,
+    ) -> List[str]:
         """Inspects a variant and returns the arguments that activate
         or deactivate the selected feature(s) for the configure options.
 
@@ -752,12 +783,11 @@ def with_or_without(self, name, activation_value=None, variant=None):
         ``variant=value`` is in the spec.
 
         Args:
-            name (str): name of a valid multi-valued variant
-            activation_value (typing.Callable): callable that accepts a single
-                value and returns the parameter to be used leading to an entry
-                of the type ``--with-{name}={parameter}``.
+            name: name of a valid multi-valued variant
+            activation_value: callable that accepts a single value and returns the parameter to be
+                used leading to an entry of the type ``--with-{name}={parameter}``.
 
-                The special value 'prefix' can also be assigned and will return
+                The special value "prefix" can also be assigned and will return
                 ``spec[name].prefix`` as activation parameter.
 
         Returns:
@@ -765,18 +795,22 @@ def with_or_without(self, name, activation_value=None, variant=None):
         """
         return self._activate_or_not(name, "with", "without", activation_value, variant)
 
-    def enable_or_disable(self, name, activation_value=None, variant=None):
+    def enable_or_disable(
+        self,
+        name: str,
+        activation_value: Optional[Union[Callable, str]] = None,
+        variant: Optional[str] = None,
+    ) -> List[str]:
         """Same as
         :meth:`~spack.build_systems.autotools.AutotoolsBuilder.with_or_without`
         but substitute ``with`` with ``enable`` and ``without`` with ``disable``.
 
         Args:
-            name (str): name of a valid multi-valued variant
-            activation_value (typing.Callable): if present accepts a single value
-                and returns the parameter to be used leading to an entry of the
-                type ``--enable-{name}={parameter}``
+            name: name of a valid multi-valued variant
+            activation_value: if present accepts a single value and returns the parameter to be
+                used leading to an entry of the type ``--enable-{name}={parameter}``
 
-                The special value 'prefix' can also be assigned and will return
+                The special value "prefix" can also be assigned and will return
                 ``spec[name].prefix`` as activation parameter.
 
         Returns:
@@ -784,15 +818,15 @@ def enable_or_disable(self, name, activation_value=None, variant=None):
         """
         return self._activate_or_not(name, "enable", "disable", activation_value, variant)
 
-    spack.builder.run_after("install")(execute_install_time_tests)
+    spack.phase_callbacks.run_after("install")(execute_install_time_tests)
 
-    def installcheck(self):
+    def installcheck(self) -> None:
         """Run "make" on the ``installcheck`` target, if found."""
         with fs.working_dir(self.build_directory):
             self.pkg._if_make_target_execute("installcheck")
 
-    @spack.builder.run_after("install")
-    def remove_libtool_archives(self):
+    @spack.phase_callbacks.run_after("install")
+    def remove_libtool_archives(self) -> None:
         """Remove all .la files in prefix sub-folders if the package sets
         ``install_libtool_archives`` to be False.
         """
@@ -804,7 +838,7 @@ def remove_libtool_archives(self):
         libtool_files = fs.find(str(self.pkg.prefix), "*.la", recursive=True)
         with fs.safe_remove(*libtool_files):
             fs.mkdirp(os.path.dirname(self._removed_la_files_log))
-            with open(self._removed_la_files_log, mode="w") as f:
+            with open(self._removed_la_files_log, mode="w", encoding="utf-8") as f:
                 f.write("\n".join(libtool_files))
 
     def setup_build_environment(self, env):
@@ -814,12 +848,13 @@ def setup_build_environment(self, env):
             env.set("MACOSX_DEPLOYMENT_TARGET", "10.16")
 
     # On macOS, force rpaths for shared library IDs and remove duplicate rpaths
-    spack.builder.run_after("install", when="platform=darwin")(apply_macos_rpath_fixups)
+    spack.phase_callbacks.run_after("install", when="platform=darwin")(apply_macos_rpath_fixups)
 
 
-def _autoreconf_search_path_args(spec):
-    dirs_seen = set()
-    flags_spack, flags_external = [], []
+def _autoreconf_search_path_args(spec: spack.spec.Spec) -> List[str]:
+    dirs_seen: Set[Tuple[int, int]] = set()
+    flags_spack: List[str] = []
+    flags_external: List[str] = []
 
     # We don't want to add an include flag for automake's default search path.
     for automake in spec.dependencies(name="automake", deptype="build"):

lib/spack/spack/build_systems/cached_cmake.py

@@ -10,7 +10,7 @@
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 
-import spack.builder
+import spack.phase_callbacks
 
 from .cmake import CMakeBuilder, CMakePackage
 
@@ -192,7 +192,10 @@ def initconfig_mpi_entries(self):
 
         entries.append(cmake_cache_path("MPI_C_COMPILER", spec["mpi"].mpicc))
         entries.append(cmake_cache_path("MPI_CXX_COMPILER", spec["mpi"].mpicxx))
-        entries.append(cmake_cache_path("MPI_Fortran_COMPILER", spec["mpi"].mpifc))
+
+        # not all MPIs have Fortran wrappers
+        if hasattr(spec["mpi"], "mpifc"):
+            entries.append(cmake_cache_path("MPI_Fortran_COMPILER", spec["mpi"].mpifc))
 
         # Check for slurm
         using_slurm = False
@@ -321,7 +324,7 @@ def initconfig(self, pkg, spec, prefix):
             + self.initconfig_package_entries()
         )
 
-        with open(self.cache_name, "w") as f:
+        with open(self.cache_name, "w", encoding="utf-8") as f:
             for entry in cache_entries:
                 f.write("%s\n" % entry)
             f.write("\n")
@@ -332,7 +335,7 @@ def std_cmake_args(self):
         args.extend(["-C", self.cache_path])
         return args
 
-    @spack.builder.run_after("install")
+    @spack.phase_callbacks.run_after("install")
     def install_cmake_cache(self):
         fs.mkdirp(self.pkg.spec.prefix.share.cmake)
         fs.install(self.cache_path, self.pkg.spec.prefix.share.cmake)

lib/spack/spack/build_systems/cargo.py

@@ -7,10 +7,11 @@
 
 import spack.builder
 import spack.package_base
+import spack.phase_callbacks
 from spack.directives import build_system, depends_on
 from spack.multimethod import when
 
-from ._checks import BaseBuilder, execute_install_time_tests
+from ._checks import BuilderWithDefaults, execute_install_time_tests
 
 
 class CargoPackage(spack.package_base.PackageBase):
@@ -27,7 +28,7 @@ class CargoPackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("cargo")
-class CargoBuilder(BaseBuilder):
+class CargoBuilder(BuilderWithDefaults):
     """The Cargo builder encodes the most common way of building software with
     a rust Cargo.toml file. It has two phases that can be overridden, if need be:
 
@@ -77,7 +78,7 @@ def install(self, pkg, spec, prefix):
         with fs.working_dir(self.build_directory):
             fs.install_tree("out", prefix)
 
-    spack.builder.run_after("install")(execute_install_time_tests)
+    spack.phase_callbacks.run_after("install")(execute_install_time_tests)
 
     def check(self):
         """Run "cargo test"."""

lib/spack/spack/build_systems/cmake.py

@@ -9,7 +9,7 @@
 import re
 import sys
 from itertools import chain
-from typing import List, Optional, Set, Tuple
+from typing import Any, List, Optional, Tuple
 
 import llnl.util.filesystem as fs
 from llnl.util.lang import stable_partition
@@ -18,11 +18,15 @@
 import spack.deptypes as dt
 import spack.error
 import spack.package_base
+import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
+from spack import traverse
 from spack.directives import build_system, conflicts, depends_on, variant
 from spack.multimethod import when
 from spack.util.environment import filter_system_paths
 
-from ._checks import BaseBuilder, execute_build_time_tests
+from ._checks import BuilderWithDefaults, execute_build_time_tests
 
 # Regex to extract the primary generator from the CMake generator
 # string.
@@ -48,9 +52,9 @@ def _maybe_set_python_hints(pkg: spack.package_base.PackageBase, args: List[str]
     python_executable = pkg.spec["python"].command.path
     args.extend(
         [
-            CMakeBuilder.define("PYTHON_EXECUTABLE", python_executable),
-            CMakeBuilder.define("Python_EXECUTABLE", python_executable),
-            CMakeBuilder.define("Python3_EXECUTABLE", python_executable),
+            define("PYTHON_EXECUTABLE", python_executable),
+            define("Python_EXECUTABLE", python_executable),
+            define("Python3_EXECUTABLE", python_executable),
         ]
     )
 
@@ -85,7 +89,7 @@ def _conditional_cmake_defaults(pkg: spack.package_base.PackageBase, args: List[
         ipo = False
 
     if cmake.satisfies("@3.9:"):
-        args.append(CMakeBuilder.define("CMAKE_INTERPROCEDURAL_OPTIMIZATION", ipo))
+        args.append(define("CMAKE_INTERPROCEDURAL_OPTIMIZATION", ipo))
 
     # Disable Package Registry: export(PACKAGE) may put files in the user's home directory, and
     # find_package may search there. This is not what we want.
@@ -93,30 +97,36 @@ def _conditional_cmake_defaults(pkg: spack.package_base.PackageBase, args: List[
     # Do not populate CMake User Package Registry
     if cmake.satisfies("@3.15:"):
         # see https://cmake.org/cmake/help/latest/policy/CMP0090.html
-        args.append(CMakeBuilder.define("CMAKE_POLICY_DEFAULT_CMP0090", "NEW"))
+        args.append(define("CMAKE_POLICY_DEFAULT_CMP0090", "NEW"))
     elif cmake.satisfies("@3.1:"):
         # see https://cmake.org/cmake/help/latest/variable/CMAKE_EXPORT_NO_PACKAGE_REGISTRY.html
-        args.append(CMakeBuilder.define("CMAKE_EXPORT_NO_PACKAGE_REGISTRY", True))
+        args.append(define("CMAKE_EXPORT_NO_PACKAGE_REGISTRY", True))
 
     # Do not use CMake User/System Package Registry
     # https://cmake.org/cmake/help/latest/manual/cmake-packages.7.html#disabling-the-package-registry
     if cmake.satisfies("@3.16:"):
-        args.append(CMakeBuilder.define("CMAKE_FIND_USE_PACKAGE_REGISTRY", False))
+        args.append(define("CMAKE_FIND_USE_PACKAGE_REGISTRY", False))
     elif cmake.satisfies("@3.1:3.15"):
-        args.append(CMakeBuilder.define("CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY", False))
-        args.append(CMakeBuilder.define("CMAKE_FIND_PACKAGE_NO_SYSTEM_PACKAGE_REGISTRY", False))
+        args.append(define("CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY", False))
+        args.append(define("CMAKE_FIND_PACKAGE_NO_SYSTEM_PACKAGE_REGISTRY", False))
 
     # Export a compilation database if supported.
     if _supports_compilation_databases(pkg):
-        args.append(CMakeBuilder.define("CMAKE_EXPORT_COMPILE_COMMANDS", True))
+        args.append(define("CMAKE_EXPORT_COMPILE_COMMANDS", True))
 
     # Enable MACOSX_RPATH by default when cmake_minimum_required < 3
     # https://cmake.org/cmake/help/latest/policy/CMP0042.html
     if pkg.spec.satisfies("platform=darwin") and cmake.satisfies("@3:"):
-        args.append(CMakeBuilder.define("CMAKE_POLICY_DEFAULT_CMP0042", "NEW"))
+        args.append(define("CMAKE_POLICY_DEFAULT_CMP0042", "NEW"))
+
+    # Disable find package's config mode for versions of Boost that
+    # didn't provide it. See https://github.com/spack/spack/issues/20169
+    # and https://cmake.org/cmake/help/latest/module/FindBoost.html
+    if pkg.spec.satisfies("^boost@:1.69.0"):
+        args.append(define("Boost_NO_BOOST_CMAKE", True))
 
 
-def generator(*names: str, default: Optional[str] = None):
+def generator(*names: str, default: Optional[str] = None) -> None:
     """The build system generator to use.
 
     See ``cmake --help`` for a list of valid generators.
@@ -157,15 +167,18 @@ def _values(x):
 def get_cmake_prefix_path(pkg: spack.package_base.PackageBase) -> List[str]:
     """Obtain the CMAKE_PREFIX_PATH entries for a package, based on the cmake_prefix_path package
     attribute of direct build/test and transitive link dependencies."""
-    # Add direct build/test deps
-    selected: Set[str] = {s.dag_hash() for s in pkg.spec.dependencies(deptype=dt.BUILD | dt.TEST)}
-    # Add transitive link deps
-    selected.update(s.dag_hash() for s in pkg.spec.traverse(root=False, deptype=dt.LINK))
-    # Separate out externals so they do not shadow Spack prefixes
-    externals, spack_built = stable_partition(
-        (s for s in pkg.spec.traverse(root=False, order="topo") if s.dag_hash() in selected),
-        lambda x: x.external,
+    edges = traverse.traverse_topo_edges_generator(
+        traverse.with_artificial_edges([pkg.spec]),
+        visitor=traverse.MixedDepthVisitor(
+            direct=dt.BUILD | dt.TEST, transitive=dt.LINK, key=traverse.by_dag_hash
+        ),
+        key=traverse.by_dag_hash,
+        root=False,
+        all_edges=False,  # cover all nodes, not all edges
     )
+    ordered_specs = [edge.spec for edge in edges]
+    # Separate out externals so they do not shadow Spack prefixes
+    externals, spack_built = stable_partition((s for s in ordered_specs), lambda x: x.external)
 
     return filter_system_paths(
         path for spec in chain(spack_built, externals) for path in spec.package.cmake_prefix_paths
@@ -263,15 +276,15 @@ def flags_to_build_system_args(self, flags):
 
     # Legacy methods (used by too many packages to change them,
     # need to forward to the builder)
-    def define(self, *args, **kwargs):
-        return self.builder.define(*args, **kwargs)
+    def define(self, cmake_var: str, value: Any) -> str:
+        return define(cmake_var, value)
 
-    def define_from_variant(self, *args, **kwargs):
-        return self.builder.define_from_variant(*args, **kwargs)
+    def define_from_variant(self, cmake_var: str, variant: Optional[str] = None) -> str:
+        return define_from_variant(self, cmake_var, variant)
 
 
 @spack.builder.builder("cmake")
-class CMakeBuilder(BaseBuilder):
+class CMakeBuilder(BuilderWithDefaults):
     """The cmake builder encodes the default way of building software with CMake. IT
     has three phases that can be overridden:
 
@@ -321,15 +334,15 @@ class CMakeBuilder(BaseBuilder):
     build_time_test_callbacks = ["check"]
 
     @property
-    def archive_files(self):
+    def archive_files(self) -> List[str]:
         """Files to archive for packages based on CMake"""
         files = [os.path.join(self.build_directory, "CMakeCache.txt")]
-        if _supports_compilation_databases(self):
+        if _supports_compilation_databases(self.pkg):
             files.append(os.path.join(self.build_directory, "compile_commands.json"))
         return files
 
     @property
-    def root_cmakelists_dir(self):
+    def root_cmakelists_dir(self) -> str:
         """The relative path to the directory containing CMakeLists.txt
 
         This path is relative to the root of the extracted tarball,
@@ -338,16 +351,17 @@ def root_cmakelists_dir(self):
         return self.pkg.stage.source_path
 
     @property
-    def generator(self):
+    def generator(self) -> str:
         if self.spec.satisfies("generator=make"):
             return "Unix Makefiles"
         if self.spec.satisfies("generator=ninja"):
             return "Ninja"
-        msg = f'{self.spec.format()} has an unsupported value for the "generator" variant'
-        raise ValueError(msg)
+        raise ValueError(
+            f'{self.spec.format()} has an unsupported value for the "generator" variant'
+        )
 
     @property
-    def std_cmake_args(self):
+    def std_cmake_args(self) -> List[str]:
         """Standard cmake arguments provided as a property for
         convenience of package writers
         """
@@ -356,7 +370,9 @@ def std_cmake_args(self):
         return args
 
     @staticmethod
-    def std_args(pkg, generator=None):
+    def std_args(
+        pkg: spack.package_base.PackageBase, generator: Optional[str] = None
+    ) -> List[str]:
         """Computes the standard cmake arguments for a generic package"""
         default_generator = "Ninja" if sys.platform == "win32" else "Unix Makefiles"
         generator = generator or default_generator
@@ -373,7 +389,6 @@ def std_args(pkg, generator=None):
         except KeyError:
             build_type = "RelWithDebInfo"
 
-        define = CMakeBuilder.define
         args = [
             "-G",
             generator,
@@ -405,152 +420,31 @@ def std_args(pkg, generator=None):
         return args
 
     @staticmethod
-    def define_cuda_architectures(pkg):
-        """Returns the str ``-DCMAKE_CUDA_ARCHITECTURES:STRING=(expanded cuda_arch)``.
-
-        ``cuda_arch`` is variant composed of a list of target CUDA architectures and
-        it is declared in the cuda package.
-
-        This method is no-op for cmake<3.18 and when ``cuda_arch`` variant is not set.
-
-        """
-        cmake_flag = str()
-        if "cuda_arch" in pkg.spec.variants and pkg.spec.satisfies("^cmake@3.18:"):
-            cmake_flag = CMakeBuilder.define(
-                "CMAKE_CUDA_ARCHITECTURES", pkg.spec.variants["cuda_arch"].value
-            )
-
-        return cmake_flag
+    def define_cuda_architectures(pkg: spack.package_base.PackageBase) -> str:
+        return define_cuda_architectures(pkg)
 
     @staticmethod
-    def define_hip_architectures(pkg):
-        """Returns the str ``-DCMAKE_HIP_ARCHITECTURES:STRING=(expanded amdgpu_target)``.
-
-        ``amdgpu_target`` is variant composed of a list of the target HIP
-        architectures and it is declared in the rocm package.
-
-        This method is no-op for cmake<3.18 and when ``amdgpu_target`` variant is
-        not set.
-
-        """
-        cmake_flag = str()
-        if "amdgpu_target" in pkg.spec.variants and pkg.spec.satisfies("^cmake@3.21:"):
-            cmake_flag = CMakeBuilder.define(
-                "CMAKE_HIP_ARCHITECTURES", pkg.spec.variants["amdgpu_target"].value
-            )
-
-        return cmake_flag
+    def define_hip_architectures(pkg: spack.package_base.PackageBase) -> str:
+        return define_hip_architectures(pkg)
 
     @staticmethod
-    def define(cmake_var, value):
-        """Return a CMake command line argument that defines a variable.
+    def define(cmake_var: str, value: Any) -> str:
+        return define(cmake_var, value)
 
-        The resulting argument will convert boolean values to OFF/ON
-        and lists/tuples to CMake semicolon-separated string lists. All other
-        values will be interpreted as strings.
-
-        Examples:
-
-            .. code-block:: python
-
-                [define('BUILD_SHARED_LIBS', True),
-                 define('CMAKE_CXX_STANDARD', 14),
-                 define('swr', ['avx', 'avx2'])]
-
-            will generate the following configuration options:
-
-            .. code-block:: console
-
-                ["-DBUILD_SHARED_LIBS:BOOL=ON",
-                 "-DCMAKE_CXX_STANDARD:STRING=14",
-                 "-DSWR:STRING=avx;avx2]
-
-        """
-        # Create a list of pairs. Each pair includes a configuration
-        # option and whether or not that option is activated
-        if isinstance(value, bool):
-            kind = "BOOL"
-            value = "ON" if value else "OFF"
-        else:
-            kind = "STRING"
-            if isinstance(value, collections.abc.Sequence) and not isinstance(value, str):
-                value = ";".join(str(v) for v in value)
-            else:
-                value = str(value)
-
-        return "".join(["-D", cmake_var, ":", kind, "=", value])
-
-    def define_from_variant(self, cmake_var, variant=None):
-        """Return a CMake command line argument from the given variant's value.
-
-        The optional ``variant`` argument defaults to the lower-case transform
-        of ``cmake_var``.
-
-        This utility function is similar to
-        :meth:`~spack.build_systems.autotools.AutotoolsBuilder.with_or_without`.
-
-        Examples:
-
-            Given a package with:
-
-            .. code-block:: python
-
-                variant('cxxstd', default='11', values=('11', '14'),
-                        multi=False, description='')
-                variant('shared', default=True, description='')
-                variant('swr', values=any_combination_of('avx', 'avx2'),
-                        description='')
-
-            calling this function like:
-
-            .. code-block:: python
-
-                [self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
-                 self.define_from_variant('CMAKE_CXX_STANDARD', 'cxxstd'),
-                 self.define_from_variant('SWR')]
-
-            will generate the following configuration options:
-
-            .. code-block:: console
-
-                ["-DBUILD_SHARED_LIBS:BOOL=ON",
-                 "-DCMAKE_CXX_STANDARD:STRING=14",
-                 "-DSWR:STRING=avx;avx2]
-
-            for ``<spec-name> cxxstd=14 +shared swr=avx,avx2``
-
-        Note: if the provided variant is conditional, and the condition is not met,
-                this function returns an empty string. CMake discards empty strings
-                provided on the command line.
-        """
-
-        if variant is None:
-            variant = cmake_var.lower()
-
-        if not self.pkg.has_variant(variant):
-            raise KeyError('"{0}" is not a variant of "{1}"'.format(variant, self.pkg.name))
-
-        if variant not in self.pkg.spec.variants:
-            return ""
-
-        value = self.pkg.spec.variants[variant].value
-        if isinstance(value, (tuple, list)):
-            # Sort multi-valued variants for reproducibility
-            value = sorted(value)
-
-        return self.define(cmake_var, value)
+    def define_from_variant(self, cmake_var: str, variant: Optional[str] = None) -> str:
+        return define_from_variant(self.pkg, cmake_var, variant)
 
     @property
-    def build_dirname(self):
+    def build_dirname(self) -> str:
         """Directory name to use when building the package."""
-        return "spack-build-%s" % self.pkg.spec.dag_hash(7)
+        return f"spack-build-{self.pkg.spec.dag_hash(7)}"
 
     @property
-    def build_directory(self):
+    def build_directory(self) -> str:
         """Full-path to the directory to use when building the package."""
         return os.path.join(self.pkg.stage.path, self.build_dirname)
 
-    def cmake_args(self):
+    def cmake_args(self) -> List[str]:
         """List of all the arguments that must be passed to cmake, except:
 
             * CMAKE_INSTALL_PREFIX
@@ -560,7 +454,12 @@ def cmake_args(self):
         """
         return []
 
-    def cmake(self, pkg, spec, prefix):
+    def cmake(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Runs ``cmake`` in the build directory"""
 
         # skip cmake phase if it is an incremental develop build
@@ -575,7 +474,12 @@ def cmake(self, pkg, spec, prefix):
         with fs.working_dir(self.build_directory, create=True):
             pkg.module.cmake(*options)
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Make the build targets"""
         with fs.working_dir(self.build_directory):
             if self.generator == "Unix Makefiles":
@@ -584,7 +488,12 @@ def build(self, pkg, spec, prefix):
                 self.build_targets.append("-v")
                 pkg.module.ninja(*self.build_targets)
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Make the install targets"""
         with fs.working_dir(self.build_directory):
             if self.generator == "Unix Makefiles":
@@ -592,9 +501,9 @@ def install(self, pkg, spec, prefix):
             elif self.generator == "Ninja":
                 pkg.module.ninja(*self.install_targets)
 
-    spack.builder.run_after("build")(execute_build_time_tests)
+    spack.phase_callbacks.run_after("build")(execute_build_time_tests)
 
-    def check(self):
+    def check(self) -> None:
         """Search the CMake-generated files for the targets ``test`` and ``check``,
         and runs them if found.
         """
@@ -605,3 +514,133 @@ def check(self):
             elif self.generator == "Ninja":
                 self.pkg._if_ninja_target_execute("test", jobs_env="CTEST_PARALLEL_LEVEL")
                 self.pkg._if_ninja_target_execute("check")
+
+
+def define(cmake_var: str, value: Any) -> str:
+    """Return a CMake command line argument that defines a variable.
+
+    The resulting argument will convert boolean values to OFF/ON and lists/tuples to CMake
+    semicolon-separated string lists. All other values will be interpreted as strings.
+
+    Examples:
+
+        .. code-block:: python
+
+            [define("BUILD_SHARED_LIBS", True),
+                define("CMAKE_CXX_STANDARD", 14),
+                define("swr", ["avx", "avx2"])]
+
+        will generate the following configuration options:
+
+        .. code-block:: console
+
+            ["-DBUILD_SHARED_LIBS:BOOL=ON",
+                "-DCMAKE_CXX_STANDARD:STRING=14",
+                "-DSWR:STRING=avx;avx2]
+
+    """
+    # Create a list of pairs. Each pair includes a configuration
+    # option and whether or not that option is activated
+    if isinstance(value, bool):
+        kind = "BOOL"
+        value = "ON" if value else "OFF"
+    else:
+        kind = "STRING"
+        if isinstance(value, collections.abc.Sequence) and not isinstance(value, str):
+            value = ";".join(str(v) for v in value)
+        else:
+            value = str(value)
+
+    return "".join(["-D", cmake_var, ":", kind, "=", value])
+
+
+def define_from_variant(
+    pkg: spack.package_base.PackageBase, cmake_var: str, variant: Optional[str] = None
+) -> str:
+    """Return a CMake command line argument from the given variant's value.
+
+    The optional ``variant`` argument defaults to the lower-case transform
+    of ``cmake_var``.
+
+    Examples:
+
+        Given a package with:
+
+        .. code-block:: python
+
+            variant("cxxstd", default="11", values=("11", "14"),
+                    multi=False, description="")
+            variant("shared", default=True, description="")
+            variant("swr", values=any_combination_of("avx", "avx2"),
+                    description="")
+
+        calling this function like:
+
+        .. code-block:: python
+
+            [
+                self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
+                self.define_from_variant("CMAKE_CXX_STANDARD", "cxxstd"),
+                self.define_from_variant("SWR"),
+            ]
+
+        will generate the following configuration options:
+
+        .. code-block:: console
+
+            [
+                "-DBUILD_SHARED_LIBS:BOOL=ON",
+                "-DCMAKE_CXX_STANDARD:STRING=14",
+                "-DSWR:STRING=avx;avx2",
+            ]
+
+        for ``<spec-name> cxxstd=14 +shared swr=avx,avx2``
+
+    Note: if the provided variant is conditional, and the condition is not met, this function
+        returns an empty string. CMake discards empty strings provided on the command line.
+    """
+    if variant is None:
+        variant = cmake_var.lower()
+
+    if not pkg.has_variant(variant):
+        raise KeyError('"{0}" is not a variant of "{1}"'.format(variant, pkg.name))
+
+    if variant not in pkg.spec.variants:
+        return ""
+
+    value = pkg.spec.variants[variant].value
+    if isinstance(value, (tuple, list)):
+        # Sort multi-valued variants for reproducibility
+        value = sorted(value)
+
+    return define(cmake_var, value)
+
+
+def define_hip_architectures(pkg: spack.package_base.PackageBase) -> str:
+    """Returns the str ``-DCMAKE_HIP_ARCHITECTURES:STRING=(expanded amdgpu_target)``.
+
+    ``amdgpu_target`` is variant composed of a list of the target HIP
+    architectures and it is declared in the rocm package.
+
+    This method is no-op for cmake<3.18 and when ``amdgpu_target`` variant is
+    not set.
+
+    """
+    if "amdgpu_target" in pkg.spec.variants and pkg.spec.satisfies("^cmake@3.21:"):
+        return define("CMAKE_HIP_ARCHITECTURES", pkg.spec.variants["amdgpu_target"].value)
+
+    return ""
+
+
+def define_cuda_architectures(pkg: spack.package_base.PackageBase) -> str:
+    """Returns the str ``-DCMAKE_CUDA_ARCHITECTURES:STRING=(expanded cuda_arch)``.
+
+    ``cuda_arch`` is variant composed of a list of target CUDA architectures and
+    it is declared in the cuda package.
+
+    This method is no-op for cmake<3.18 and when ``cuda_arch`` variant is not set.
+
+    """
+    if "cuda_arch" in pkg.spec.variants and pkg.spec.satisfies("^cmake@3.18:"):
+        return define("CMAKE_CUDA_ARCHITECTURES", pkg.spec.variants["cuda_arch"].value)
+    return ""

lib/spack/spack/build_systems/cuda.py

@@ -180,13 +180,6 @@ def compute_capabilities(arch_list: Iterable[str]) -> List[str]:
         conflicts("%gcc@7:", when="+cuda ^cuda@:9.1 target=x86_64:")
         conflicts("%gcc@8:", when="+cuda ^cuda@:10.0.130 target=x86_64:")
         conflicts("%gcc@9:", when="+cuda ^cuda@:10.2.89 target=x86_64:")
-        conflicts("%pgi@:14.8", when="+cuda ^cuda@:7.0.27 target=x86_64:")
-        conflicts("%pgi@:15.3,15.5:", when="+cuda ^cuda@7.5 target=x86_64:")
-        conflicts("%pgi@:16.2,16.0:16.3", when="+cuda ^cuda@8 target=x86_64:")
-        conflicts("%pgi@:15,18:", when="+cuda ^cuda@9.0:9.1 target=x86_64:")
-        conflicts("%pgi@:16,19:", when="+cuda ^cuda@9.2.88:10.0 target=x86_64:")
-        conflicts("%pgi@:17,20:", when="+cuda ^cuda@10.1.105:10.2.89 target=x86_64:")
-        conflicts("%pgi@:17,21:", when="+cuda ^cuda@11.0.2:11.1.0 target=x86_64:")
         conflicts("%clang@:3.4", when="+cuda ^cuda@:7.5 target=x86_64:")
         conflicts("%clang@:3.7,4:", when="+cuda ^cuda@8.0:9.0 target=x86_64:")
         conflicts("%clang@:3.7,4.1:", when="+cuda ^cuda@9.1 target=x86_64:")
@@ -212,9 +205,6 @@ def compute_capabilities(arch_list: Iterable[str]) -> List[str]:
         conflicts("%gcc@8:", when="+cuda ^cuda@:10.0.130 target=ppc64le:")
         conflicts("%gcc@9:", when="+cuda ^cuda@:10.1.243 target=ppc64le:")
         # officially, CUDA 11.0.2 only supports the system GCC 8.3 on ppc64le
-        conflicts("%pgi", when="+cuda ^cuda@:8 target=ppc64le:")
-        conflicts("%pgi@:16", when="+cuda ^cuda@:9.1.185 target=ppc64le:")
-        conflicts("%pgi@:17", when="+cuda ^cuda@:10 target=ppc64le:")
         conflicts("%clang@4:", when="+cuda ^cuda@:9.0.176 target=ppc64le:")
         conflicts("%clang@5:", when="+cuda ^cuda@:9.1 target=ppc64le:")
         conflicts("%clang@6:", when="+cuda ^cuda@:9.2 target=ppc64le:")

lib/spack/spack/build_systems/generic.py

@@ -7,8 +7,9 @@
 import spack.builder
 import spack.directives
 import spack.package_base
+import spack.phase_callbacks
 
-from ._checks import BaseBuilder, apply_macos_rpath_fixups, execute_install_time_tests
+from ._checks import BuilderWithDefaults, apply_macos_rpath_fixups, execute_install_time_tests
 
 
 class Package(spack.package_base.PackageBase):
@@ -26,7 +27,7 @@ class Package(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("generic")
-class GenericBuilder(BaseBuilder):
+class GenericBuilder(BuilderWithDefaults):
     """A builder for a generic build system, that require packagers
     to implement an "install" phase.
     """
@@ -44,7 +45,7 @@ class GenericBuilder(BaseBuilder):
     install_time_test_callbacks = []
 
     # On macOS, force rpaths for shared library IDs and remove duplicate rpaths
-    spack.builder.run_after("install", when="platform=darwin")(apply_macos_rpath_fixups)
+    spack.phase_callbacks.run_after("install", when="platform=darwin")(apply_macos_rpath_fixups)
 
     # unconditionally perform any post-install phase tests
-    spack.builder.run_after("install")(execute_install_time_tests)
+    spack.phase_callbacks.run_after("install")(execute_install_time_tests)

lib/spack/spack/build_systems/go.py

@@ -7,10 +7,11 @@
 
 import spack.builder
 import spack.package_base
+import spack.phase_callbacks
 from spack.directives import build_system, extends
 from spack.multimethod import when
 
-from ._checks import BaseBuilder, execute_install_time_tests
+from ._checks import BuilderWithDefaults, execute_install_time_tests
 
 
 class GoPackage(spack.package_base.PackageBase):
@@ -32,7 +33,7 @@ class GoPackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("go")
-class GoBuilder(BaseBuilder):
+class GoBuilder(BuilderWithDefaults):
     """The Go builder encodes the most common way of building software with
     a golang go.mod file. It has two phases that can be overridden, if need be:
 
@@ -99,7 +100,7 @@ def install(self, pkg, spec, prefix):
             fs.mkdirp(prefix.bin)
             fs.install(pkg.name, prefix.bin)
 
-    spack.builder.run_after("install")(execute_install_time_tests)
+    spack.phase_callbacks.run_after("install")(execute_install_time_tests)
 
     def check(self):
         """Run ``go test .`` in the source directory"""

lib/spack/spack/build_systems/intel.py

@@ -22,8 +22,8 @@
     install,
 )
 
-import spack.builder
 import spack.error
+import spack.phase_callbacks
 from spack.build_environment import dso_suffix
 from spack.error import InstallError
 from spack.util.environment import EnvironmentModifications
@@ -1153,7 +1153,7 @@ def _determine_license_type(self):
             # The file will have been created upon self.license_required AND
             # self.license_files having been populated, so the "if" is usually
             # true by the time the present function runs; ../hooks/licensing.py
-            with open(f) as fh:
+            with open(f, encoding="utf-8") as fh:
                 if re.search(r"^[ \t]*[^" + self.license_comment + "\n]", fh.read(), re.MULTILINE):
                     license_type = {
                         "ACTIVATION_TYPE": "license_file",
@@ -1163,7 +1163,7 @@ def _determine_license_type(self):
         debug_print(license_type)
         return license_type
 
-    @spack.builder.run_before("install")
+    @spack.phase_callbacks.run_before("install")
     def configure(self):
         """Generates the silent.cfg file to pass to installer.sh.
 
@@ -1185,7 +1185,7 @@ def configure(self):
         # our configuration accordingly. We can do this because the tokens are
         # quite long and specific.
 
-        validator_code = open("pset/check.awk", "r").read()
+        validator_code = open("pset/check.awk", "r", encoding="utf-8").read()
         # Let's go a little further and distill the tokens (plus some noise).
         tokenlike_words = set(re.findall(r"[A-Z_]{4,}", validator_code))
 
@@ -1222,7 +1222,7 @@ def configure(self):
             config_draft.update(self._determine_license_type)
 
         # Write sorted *by token* so the file looks less like a hash dump.
-        f = open("silent.cfg", "w")
+        f = open("silent.cfg", "w", encoding="utf-8")
         for token, value in sorted(config_draft.items()):
             if token in tokenlike_words:
                 f.write("%s=%s\n" % (token, value))
@@ -1250,7 +1250,7 @@ def install(self, spec, prefix):
         for f in glob.glob("%s/intel*log" % tmpdir):
             install(f, dst)
 
-    @spack.builder.run_after("install")
+    @spack.phase_callbacks.run_after("install")
     def validate_install(self):
         # Sometimes the installer exits with an error but doesn't pass a
         # non-zero exit code to spack. Check for the existence of a 'bin'
@@ -1258,7 +1258,7 @@ def validate_install(self):
         if not os.path.exists(self.prefix.bin):
             raise InstallError("The installer has failed to install anything.")
 
-    @spack.builder.run_after("install")
+    @spack.phase_callbacks.run_after("install")
     def configure_rpath(self):
         if "+rpath" not in self.spec:
             return
@@ -1273,10 +1273,10 @@ def configure_rpath(self):
                 raise InstallError("Cannot find compiler command to configure rpath:\n\t" + f)
 
             compiler_cfg = os.path.abspath(f + ".cfg")
-            with open(compiler_cfg, "w") as fh:
+            with open(compiler_cfg, "w", encoding="utf-8") as fh:
                 fh.write("-Xlinker -rpath={0}\n".format(compilers_lib_dir))
 
-    @spack.builder.run_after("install")
+    @spack.phase_callbacks.run_after("install")
     def configure_auto_dispatch(self):
         if self._has_compilers:
             if "auto_dispatch=none" in self.spec:
@@ -1297,10 +1297,10 @@ def configure_auto_dispatch(self):
                         ad.append(x)
 
                 compiler_cfg = os.path.abspath(f + ".cfg")
-                with open(compiler_cfg, "a") as fh:
+                with open(compiler_cfg, "a", encoding="utf-8") as fh:
                     fh.write("-ax{0}\n".format(",".join(ad)))
 
-    @spack.builder.run_after("install")
+    @spack.phase_callbacks.run_after("install")
     def filter_compiler_wrappers(self):
         if ("+mpi" in self.spec or self.provides("mpi")) and "~newdtags" in self.spec:
             bin_dir = self.component_bin_dir("mpi")
@@ -1308,7 +1308,7 @@ def filter_compiler_wrappers(self):
                 f = os.path.join(bin_dir, f)
                 filter_file("-Xlinker --enable-new-dtags", " ", f, string=True)
 
-    @spack.builder.run_after("install")
+    @spack.phase_callbacks.run_after("install")
     def uninstall_ism(self):
         # The "Intel(R) Software Improvement Program" [ahem] gets installed,
         # apparently regardless of PHONEHOME_SEND_USAGE_DATA.
@@ -1340,7 +1340,7 @@ def base_lib_dir(self):
         debug_print(d)
         return d
 
-    @spack.builder.run_after("install")
+    @spack.phase_callbacks.run_after("install")
     def modify_LLVMgold_rpath(self):
         """Add libimf.so and other required libraries to the RUNPATH of LLVMgold.so.
 

lib/spack/spack/build_systems/lua.py

@@ -75,7 +75,7 @@ def generate_luarocks_config(self, pkg, spec, prefix):
                 table_entries.append(self._generate_tree_line(d.name, d.prefix))
 
         path = self._luarocks_config_path()
-        with open(path, "w") as config:
+        with open(path, "w", encoding="utf-8") as config:
             config.write(
                 """
                 deps_mode="all"

lib/spack/spack/build_systems/makefile.py

@@ -8,11 +8,14 @@
 
 import spack.builder
 import spack.package_base
+import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, conflicts, depends_on
 from spack.multimethod import when
 
 from ._checks import (
-    BaseBuilder,
+    BuilderWithDefaults,
     apply_macos_rpath_fixups,
     execute_build_time_tests,
     execute_install_time_tests,
@@ -36,7 +39,7 @@ class MakefilePackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("makefile")
-class MakefileBuilder(BaseBuilder):
+class MakefileBuilder(BuilderWithDefaults):
     """The Makefile builder encodes the most common way of building software with
     Makefiles. It has three phases that can be overridden, if need be:
 
@@ -91,35 +94,50 @@ class MakefileBuilder(BaseBuilder):
     install_time_test_callbacks = ["installcheck"]
 
     @property
-    def build_directory(self):
+    def build_directory(self) -> str:
         """Return the directory containing the main Makefile."""
         return self.pkg.stage.source_path
 
-    def edit(self, pkg, spec, prefix):
+    def edit(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Edit the Makefile before calling make. The default is a no-op."""
         pass
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Run "make" on the build targets specified by the builder."""
         with fs.working_dir(self.build_directory):
             pkg.module.make(*self.build_targets)
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Run "make" on the install targets specified by the builder."""
         with fs.working_dir(self.build_directory):
             pkg.module.make(*self.install_targets)
 
-    spack.builder.run_after("build")(execute_build_time_tests)
+    spack.phase_callbacks.run_after("build")(execute_build_time_tests)
 
-    def check(self):
+    def check(self) -> None:
         """Run "make" on the ``test`` and ``check`` targets, if found."""
         with fs.working_dir(self.build_directory):
             self.pkg._if_make_target_execute("test")
             self.pkg._if_make_target_execute("check")
 
-    spack.builder.run_after("install")(execute_install_time_tests)
+    spack.phase_callbacks.run_after("install")(execute_install_time_tests)
 
-    def installcheck(self):
+    def installcheck(self) -> None:
         """Searches the Makefile for an ``installcheck`` target
         and runs it if found.
         """
@@ -127,4 +145,4 @@ def installcheck(self):
             self.pkg._if_make_target_execute("installcheck")
 
     # On macOS, force rpaths for shared library IDs and remove duplicate rpaths
-    spack.builder.run_after("install", when="platform=darwin")(apply_macos_rpath_fixups)
+    spack.phase_callbacks.run_after("install", when="platform=darwin")(apply_macos_rpath_fixups)

lib/spack/spack/build_systems/maven.py

@@ -10,7 +10,7 @@
 from spack.multimethod import when
 from spack.util.executable import which
 
-from ._checks import BaseBuilder
+from ._checks import BuilderWithDefaults
 
 
 class MavenPackage(spack.package_base.PackageBase):
@@ -34,7 +34,7 @@ class MavenPackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("maven")
-class MavenBuilder(BaseBuilder):
+class MavenBuilder(BuilderWithDefaults):
     """The Maven builder encodes the default way to build software with Maven.
     It has two phases that can be overridden, if need be:
 

lib/spack/spack/build_systems/meson.py

@@ -9,10 +9,13 @@
 
 import spack.builder
 import spack.package_base
+import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, conflicts, depends_on, variant
 from spack.multimethod import when
 
-from ._checks import BaseBuilder, execute_build_time_tests
+from ._checks import BuilderWithDefaults, execute_build_time_tests
 
 
 class MesonPackage(spack.package_base.PackageBase):
@@ -62,7 +65,7 @@ def flags_to_build_system_args(self, flags):
 
 
 @spack.builder.builder("meson")
-class MesonBuilder(BaseBuilder):
+class MesonBuilder(BuilderWithDefaults):
     """The Meson builder encodes the default way to build software with Meson.
     The builder has three phases that can be overridden, if need be:
 
@@ -112,7 +115,7 @@ def archive_files(self):
         return [os.path.join(self.build_directory, "meson-logs", "meson-log.txt")]
 
     @property
-    def root_mesonlists_dir(self):
+    def root_mesonlists_dir(self) -> str:
         """Relative path to the directory containing meson.build
 
         This path is relative to the root of the extracted tarball,
@@ -121,7 +124,7 @@ def root_mesonlists_dir(self):
         return self.pkg.stage.source_path
 
     @property
-    def std_meson_args(self):
+    def std_meson_args(self) -> List[str]:
         """Standard meson arguments provided as a property for convenience
         of package writers.
         """
@@ -132,7 +135,7 @@ def std_meson_args(self):
         return std_meson_args
 
     @staticmethod
-    def std_args(pkg):
+    def std_args(pkg) -> List[str]:
         """Standard meson arguments for a generic package."""
         try:
             build_type = pkg.spec.variants["buildtype"].value
@@ -172,7 +175,7 @@ def build_directory(self):
         """Directory to use when building the package."""
         return os.path.join(self.pkg.stage.path, self.build_dirname)
 
-    def meson_args(self):
+    def meson_args(self) -> List[str]:
         """List of arguments that must be passed to meson, except:
 
         * ``--prefix``
@@ -185,7 +188,12 @@ def meson_args(self):
         """
         return []
 
-    def meson(self, pkg, spec, prefix):
+    def meson(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Run ``meson`` in the build directory"""
         options = []
         if self.spec["meson"].satisfies("@0.64:"):
@@ -196,21 +204,31 @@ def meson(self, pkg, spec, prefix):
         with fs.working_dir(self.build_directory, create=True):
             pkg.module.meson(*options)
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Make the build targets"""
         options = ["-v"]
         options += self.build_targets
         with fs.working_dir(self.build_directory):
             pkg.module.ninja(*options)
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ) -> None:
         """Make the install targets"""
         with fs.working_dir(self.build_directory):
             pkg.module.ninja(*self.install_targets)
 
-    spack.builder.run_after("build")(execute_build_time_tests)
+    spack.phase_callbacks.run_after("build")(execute_build_time_tests)
 
-    def check(self):
+    def check(self) -> None:
         """Search Meson-generated files for the target ``test`` and run it if found."""
         with fs.working_dir(self.build_directory):
             self.pkg._if_ninja_target_execute("test")

lib/spack/spack/build_systems/msbuild.py

@@ -10,7 +10,7 @@
 import spack.package_base
 from spack.directives import build_system, conflicts
 
-from ._checks import BaseBuilder
+from ._checks import BuilderWithDefaults
 
 
 class MSBuildPackage(spack.package_base.PackageBase):
@@ -26,7 +26,7 @@ class MSBuildPackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("msbuild")
-class MSBuildBuilder(BaseBuilder):
+class MSBuildBuilder(BuilderWithDefaults):
     """The MSBuild builder encodes the most common way of building software with
     Mircosoft's MSBuild tool. It has two phases that can be overridden, if need be:
 

lib/spack/spack/build_systems/nmake.py

@@ -10,7 +10,7 @@
 import spack.package_base
 from spack.directives import build_system, conflicts
 
-from ._checks import BaseBuilder
+from ._checks import BuilderWithDefaults
 
 
 class NMakePackage(spack.package_base.PackageBase):
@@ -26,7 +26,7 @@ class NMakePackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("nmake")
-class NMakeBuilder(BaseBuilder):
+class NMakeBuilder(BuilderWithDefaults):
     """The NMake builder encodes the most common way of building software with
     Mircosoft's NMake tool. It has two phases that can be overridden, if need be:
 

lib/spack/spack/build_systems/octave.py

@@ -7,7 +7,7 @@
 from spack.directives import build_system, extends
 from spack.multimethod import when
 
-from ._checks import BaseBuilder
+from ._checks import BuilderWithDefaults
 
 
 class OctavePackage(spack.package_base.PackageBase):
@@ -29,7 +29,7 @@ class OctavePackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("octave")
-class OctaveBuilder(BaseBuilder):
+class OctaveBuilder(BuilderWithDefaults):
     """The octave builder provides the following phases that can be overridden:
 
     1. :py:meth:`~.OctaveBuilder.install`

lib/spack/spack/build_systems/oneapi.py

@@ -32,6 +32,9 @@ class IntelOneApiPackage(Package):
     # organization (e.g. University/Company).
     redistribute(source=False, binary=False)
 
+    # contains precompiled binaries without rpaths
+    unresolved_libraries = ["*"]
+
     for c in [
         "target=ppc64:",
         "target=ppc64le:",
@@ -255,7 +258,7 @@ def libs(self):
         return find_libraries("*", root=self.component_prefix.lib, recursive=not self.v2_layout)
 
 
-class IntelOneApiLibraryPackageWithSdk(IntelOneApiPackage):
+class IntelOneApiLibraryPackageWithSdk(IntelOneApiLibraryPackage):
     """Base class for Intel oneAPI library packages with SDK components.
 
     Contains some convenient default implementations for libraries

lib/spack/spack/build_systems/perl.py

@@ -10,11 +10,12 @@
 
 import spack.builder
 import spack.package_base
+import spack.phase_callbacks
 from spack.directives import build_system, extends
 from spack.install_test import SkipTest, test_part
 from spack.util.executable import Executable
 
-from ._checks import BaseBuilder, execute_build_time_tests
+from ._checks import BuilderWithDefaults, execute_build_time_tests
 
 
 class PerlPackage(spack.package_base.PackageBase):
@@ -84,7 +85,7 @@ def test_use(self):
 
 
 @spack.builder.builder("perl")
-class PerlBuilder(BaseBuilder):
+class PerlBuilder(BuilderWithDefaults):
     """The perl builder provides four phases that can be overridden, if required:
 
         1. :py:meth:`~.PerlBuilder.configure`
@@ -163,7 +164,7 @@ def configure(self, pkg, spec, prefix):
     # Build.PL may be too long causing the build to fail. Patching the shebang
     # does not happen until after install so set '/usr/bin/env perl' here in
     # the Build script.
-    @spack.builder.run_after("configure")
+    @spack.phase_callbacks.run_after("configure")
     def fix_shebang(self):
         if self.build_method == "Build.PL":
             pattern = "#!{0}".format(self.spec["perl"].command.path)
@@ -175,7 +176,7 @@ def build(self, pkg, spec, prefix):
         self.build_executable()
 
     # Ensure that tests run after build (if requested):
-    spack.builder.run_after("build")(execute_build_time_tests)
+    spack.phase_callbacks.run_after("build")(execute_build_time_tests)
 
     def check(self):
         """Runs built-in tests of a Perl package."""

lib/spack/spack/build_systems/python.py

@@ -24,6 +24,7 @@
 import spack.detection
 import spack.multimethod
 import spack.package_base
+import spack.phase_callbacks
 import spack.platforms
 import spack.repo
 import spack.spec
@@ -34,7 +35,7 @@
 from spack.spec import Spec
 from spack.util.prefix import Prefix
 
-from ._checks import BaseBuilder, execute_install_time_tests
+from ._checks import BuilderWithDefaults, execute_install_time_tests
 
 
 def _flatten_dict(dictionary: Mapping[str, object]) -> Iterable[str]:
@@ -374,7 +375,7 @@ def list_url(cls) -> Optional[str]:  # type: ignore[override]
         return None
 
     @property
-    def python_spec(self):
+    def python_spec(self) -> Spec:
         """Get python-venv if it exists or python otherwise."""
         python, *_ = self.spec.dependencies("python-venv") or self.spec.dependencies("python")
         return python
@@ -425,7 +426,7 @@ def libs(self) -> LibraryList:
 
 
 @spack.builder.builder("python_pip")
-class PythonPipBuilder(BaseBuilder):
+class PythonPipBuilder(BuilderWithDefaults):
     phases = ("install",)
 
     #: Names associated with package methods in the old build-system format
@@ -543,4 +544,4 @@ def install(self, pkg: PythonPackage, spec: Spec, prefix: Prefix) -> None:
         with fs.working_dir(self.build_directory):
             pip(*args)
 
-    spack.builder.run_after("install")(execute_install_time_tests)
+    spack.phase_callbacks.run_after("install")(execute_install_time_tests)

lib/spack/spack/build_systems/qmake.py

@@ -6,9 +6,10 @@
 
 import spack.builder
 import spack.package_base
+import spack.phase_callbacks
 from spack.directives import build_system, depends_on
 
-from ._checks import BaseBuilder, execute_build_time_tests
+from ._checks import BuilderWithDefaults, execute_build_time_tests
 
 
 class QMakePackage(spack.package_base.PackageBase):
@@ -30,7 +31,7 @@ class QMakePackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("qmake")
-class QMakeBuilder(BaseBuilder):
+class QMakeBuilder(BuilderWithDefaults):
     """The qmake builder provides three phases that can be overridden:
 
     1. :py:meth:`~.QMakeBuilder.qmake`
@@ -81,4 +82,4 @@ def check(self):
         with working_dir(self.build_directory):
             self.pkg._if_make_target_execute("check")
 
-    spack.builder.run_after("build")(execute_build_time_tests)
+    spack.phase_callbacks.run_after("build")(execute_build_time_tests)

lib/spack/spack/build_systems/ruby.py

@@ -8,7 +8,7 @@
 import spack.package_base
 from spack.directives import build_system, extends, maintainers
 
-from ._checks import BaseBuilder
+from ._checks import BuilderWithDefaults
 
 
 class RubyPackage(spack.package_base.PackageBase):
@@ -28,7 +28,7 @@ class RubyPackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("ruby")
-class RubyBuilder(BaseBuilder):
+class RubyBuilder(BuilderWithDefaults):
     """The Ruby builder provides two phases that can be overridden if required:
 
     #. :py:meth:`~.RubyBuilder.build`

lib/spack/spack/build_systems/scons.py

@@ -4,9 +4,10 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import spack.builder
 import spack.package_base
+import spack.phase_callbacks
 from spack.directives import build_system, depends_on
 
-from ._checks import BaseBuilder, execute_build_time_tests
+from ._checks import BuilderWithDefaults, execute_build_time_tests
 
 
 class SConsPackage(spack.package_base.PackageBase):
@@ -28,7 +29,7 @@ class SConsPackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("scons")
-class SConsBuilder(BaseBuilder):
+class SConsBuilder(BuilderWithDefaults):
     """The Scons builder provides the following phases that can be overridden:
 
     1. :py:meth:`~.SConsBuilder.build`
@@ -79,4 +80,4 @@ def build_test(self):
         """
         pass
 
-    spack.builder.run_after("build")(execute_build_time_tests)
+    spack.phase_callbacks.run_after("build")(execute_build_time_tests)

lib/spack/spack/build_systems/sip.py

@@ -11,11 +11,12 @@
 import spack.builder
 import spack.install_test
 import spack.package_base
+import spack.phase_callbacks
 from spack.directives import build_system, depends_on, extends
 from spack.multimethod import when
 from spack.util.executable import Executable
 
-from ._checks import BaseBuilder, execute_install_time_tests
+from ._checks import BuilderWithDefaults, execute_install_time_tests
 
 
 class SIPPackage(spack.package_base.PackageBase):
@@ -103,7 +104,7 @@ def test_imports(self):
 
 
 @spack.builder.builder("sip")
-class SIPBuilder(BaseBuilder):
+class SIPBuilder(BuilderWithDefaults):
     """The SIP builder provides the following phases that can be overridden:
 
     * configure
@@ -170,4 +171,4 @@ def install_args(self):
         """Arguments to pass to install."""
         return []
 
-    spack.builder.run_after("install")(execute_install_time_tests)
+    spack.phase_callbacks.run_after("install")(execute_install_time_tests)

lib/spack/spack/build_systems/waf.py

@@ -6,9 +6,10 @@
 
 import spack.builder
 import spack.package_base
+import spack.phase_callbacks
 from spack.directives import build_system, depends_on
 
-from ._checks import BaseBuilder, execute_build_time_tests, execute_install_time_tests
+from ._checks import BuilderWithDefaults, execute_build_time_tests, execute_install_time_tests
 
 
 class WafPackage(spack.package_base.PackageBase):
@@ -30,7 +31,7 @@ class WafPackage(spack.package_base.PackageBase):
 
 
 @spack.builder.builder("waf")
-class WafBuilder(BaseBuilder):
+class WafBuilder(BuilderWithDefaults):
     """The WAF builder provides the following phases that can be overridden:
 
     * configure
@@ -136,7 +137,7 @@ def build_test(self):
         """
         pass
 
-    spack.builder.run_after("build")(execute_build_time_tests)
+    spack.phase_callbacks.run_after("build")(execute_build_time_tests)
 
     def install_test(self):
         """Run unit tests after install.
@@ -146,4 +147,4 @@ def install_test(self):
         """
         pass
 
-    spack.builder.run_after("install")(execute_install_time_tests)
+    spack.phase_callbacks.run_after("install")(execute_install_time_tests)

lib/spack/spack/builder.py

@@ -6,44 +6,30 @@
 import collections.abc
 import copy
 import functools
-from typing import List, Optional, Tuple
-
-from llnl.util import lang
+from typing import Dict, List, Optional, Tuple, Type
 
 import spack.error
 import spack.multimethod
+import spack.package_base
+import spack.phase_callbacks
 import spack.repo
+import spack.spec
+import spack.util.environment
 
 #: Builder classes, as registered by the "builder" decorator
-BUILDER_CLS = {}
-
-#: An object of this kind is a shared global state used to collect callbacks during
-#: class definition time, and is flushed when the class object is created at the end
-#: of the class definition
-#:
-#: Args:
-#:    attribute_name (str): name of the attribute that will be attached to the builder
-#:    callbacks (list): container used to temporarily aggregate the callbacks
-CallbackTemporaryStage = collections.namedtuple(
-    "CallbackTemporaryStage", ["attribute_name", "callbacks"]
-)
-
-#: Shared global state to aggregate "@run_before" callbacks
-_RUN_BEFORE = CallbackTemporaryStage(attribute_name="run_before_callbacks", callbacks=[])
-#: Shared global state to aggregate "@run_after" callbacks
-_RUN_AFTER = CallbackTemporaryStage(attribute_name="run_after_callbacks", callbacks=[])
+BUILDER_CLS: Dict[str, Type["Builder"]] = {}
 
 #: Map id(pkg) to a builder, to avoid creating multiple
 #: builders for the same package object.
-_BUILDERS = {}
+_BUILDERS: Dict[int, "Builder"] = {}
 
 
-def builder(build_system_name):
+def builder(build_system_name: str):
     """Class decorator used to register the default builder
     for a given build-system.
 
     Args:
-        build_system_name (str): name of the build-system
+        build_system_name: name of the build-system
     """
 
     def _decorator(cls):
@@ -54,13 +40,9 @@ def _decorator(cls):
     return _decorator
 
 
-def create(pkg):
-    """Given a package object with an associated concrete spec,
-    return the builder object that can install it.
-
-    Args:
-         pkg (spack.package_base.PackageBase): package for which we want the builder
-    """
+def create(pkg: spack.package_base.PackageBase) -> "Builder":
+    """Given a package object with an associated concrete spec, return the builder object that can
+    install it."""
     if id(pkg) not in _BUILDERS:
         _BUILDERS[id(pkg)] = _create(pkg)
     return _BUILDERS[id(pkg)]
@@ -75,7 +57,7 @@ def __call__(self, spec, prefix):
         return self.phase_fn(self.builder.pkg, spec, prefix)
 
 
-def get_builder_class(pkg, name: str) -> Optional[type]:
+def get_builder_class(pkg, name: str) -> Optional[Type["Builder"]]:
     """Return the builder class if a package module defines it."""
     cls = getattr(pkg.module, name, None)
     if cls and cls.__module__.startswith(spack.repo.ROOT_PYTHON_NAMESPACE):
@@ -83,7 +65,7 @@ def get_builder_class(pkg, name: str) -> Optional[type]:
     return None
 
 
-def _create(pkg):
+def _create(pkg: spack.package_base.PackageBase) -> "Builder":
     """Return a new builder object for the package object being passed as argument.
 
     The function inspects the build-system used by the package object and try to:
@@ -103,7 +85,7 @@ class hierarchy (look at AspellDictPackage for an example of that)
     to look for build-related methods in the ``*Package``.
 
     Args:
-        pkg (spack.package_base.PackageBase): package object for which we need a builder
+        pkg: package object for which we need a builder
     """
     package_buildsystem = buildsystem_name(pkg)
     default_builder_cls = BUILDER_CLS[package_buildsystem]
@@ -168,8 +150,8 @@ def __forward(self, *args, **kwargs):
     # with the same name is defined in the Package, it will override this definition
     # (when _ForwardToBaseBuilder is initialized)
     for method_name in (
-        base_cls.phases
-        + base_cls.legacy_methods
+        base_cls.phases  # type: ignore
+        + base_cls.legacy_methods  # type: ignore
         + getattr(base_cls, "legacy_long_methods", tuple())
         + ("setup_build_environment", "setup_dependent_build_environment")
     ):
@@ -181,14 +163,14 @@ def __forward(self):
 
         return __forward
 
-    for attribute_name in base_cls.legacy_attributes:
+    for attribute_name in base_cls.legacy_attributes:  # type: ignore
         setattr(
             _ForwardToBaseBuilder,
             attribute_name,
             property(forward_property_to_getattr(attribute_name)),
         )
 
-    class Adapter(base_cls, metaclass=_PackageAdapterMeta):
+    class Adapter(base_cls, metaclass=_PackageAdapterMeta):  # type: ignore
         def __init__(self, pkg):
             # Deal with custom phases in packages here
             if hasattr(pkg, "phases"):
@@ -213,99 +195,18 @@ def setup_dependent_build_environment(self, env, dependent_spec):
     return Adapter(pkg)
 
 
-def buildsystem_name(pkg):
+def buildsystem_name(pkg: spack.package_base.PackageBase) -> str:
     """Given a package object with an associated concrete spec,
-    return the name of its build system.
-
-    Args:
-         pkg (spack.package_base.PackageBase): package for which we want
-            the build system name
-    """
+    return the name of its build system."""
     try:
         return pkg.spec.variants["build_system"].value
     except KeyError:
         # We are reading an old spec without the build_system variant
-        return pkg.legacy_buildsystem
-
-
-class PhaseCallbacksMeta(type):
-    """Permit to register arbitrary functions during class definition and run them
-    later, before or after a given install phase.
-
-    Each method decorated with ``run_before`` or ``run_after`` gets temporarily
-    stored in a global shared state when a class being defined is parsed by the Python
-    interpreter. At class definition time that temporary storage gets flushed and a list
-    of callbacks is attached to the class being defined.
-    """
-
-    def __new__(mcs, name, bases, attr_dict):
-        for temporary_stage in (_RUN_BEFORE, _RUN_AFTER):
-            staged_callbacks = temporary_stage.callbacks
-
-            # Here we have an adapter from an old-style package. This means there is no
-            # hierarchy of builders, and every callback that had to be combined between
-            # *Package and *Builder has been combined already by _PackageAdapterMeta
-            if name == "Adapter":
-                continue
-
-            # If we are here we have callbacks. To get a complete list, we accumulate all the
-            # callbacks from base classes, we deduplicate them, then prepend what we have
-            # registered here.
-            #
-            # The order should be:
-            # 1. Callbacks are registered in order within the same class
-            # 2. Callbacks defined in derived classes precede those defined in base
-            #    classes
-            callbacks_from_base = []
-            for base in bases:
-                current_callbacks = getattr(base, temporary_stage.attribute_name, None)
-                if not current_callbacks:
-                    continue
-                callbacks_from_base.extend(current_callbacks)
-            callbacks_from_base = list(lang.dedupe(callbacks_from_base))
-            # Set the callbacks in this class and flush the temporary stage
-            attr_dict[temporary_stage.attribute_name] = staged_callbacks[:] + callbacks_from_base
-            del temporary_stage.callbacks[:]
-
-        return super(PhaseCallbacksMeta, mcs).__new__(mcs, name, bases, attr_dict)
-
-    @staticmethod
-    def run_after(phase, when=None):
-        """Decorator to register a function for running after a given phase.
-
-        Args:
-            phase (str): phase after which the function must run.
-            when (str): condition under which the function is run (if None, it is always run).
-        """
-
-        def _decorator(fn):
-            key = (phase, when)
-            item = (key, fn)
-            _RUN_AFTER.callbacks.append(item)
-            return fn
-
-        return _decorator
-
-    @staticmethod
-    def run_before(phase, when=None):
-        """Decorator to register a function for running before a given phase.
-
-        Args:
-           phase (str): phase before which the function must run.
-           when (str): condition under which the function is run (if None, it is always run).
-        """
-
-        def _decorator(fn):
-            key = (phase, when)
-            item = (key, fn)
-            _RUN_BEFORE.callbacks.append(item)
-            return fn
-
-        return _decorator
+        return pkg.legacy_buildsystem  # type: ignore
 
 
 class BuilderMeta(
-    PhaseCallbacksMeta,
+    spack.phase_callbacks.PhaseCallbacksMeta,
     spack.multimethod.MultiMethodMeta,
     type(collections.abc.Sequence),  # type: ignore
 ):
@@ -400,8 +301,12 @@ def __new__(mcs, name, bases, attr_dict):
             )
 
         combine_callbacks = _PackageAdapterMeta.combine_callbacks
-        attr_dict[_RUN_BEFORE.attribute_name] = combine_callbacks(_RUN_BEFORE.attribute_name)
-        attr_dict[_RUN_AFTER.attribute_name] = combine_callbacks(_RUN_AFTER.attribute_name)
+        attr_dict[spack.phase_callbacks._RUN_BEFORE.attribute_name] = combine_callbacks(
+            spack.phase_callbacks._RUN_BEFORE.attribute_name
+        )
+        attr_dict[spack.phase_callbacks._RUN_AFTER.attribute_name] = combine_callbacks(
+            spack.phase_callbacks._RUN_AFTER.attribute_name
+        )
 
         return super(_PackageAdapterMeta, mcs).__new__(mcs, name, bases, attr_dict)
 
@@ -421,8 +326,8 @@ def __init__(self, name, builder):
         self.name = name
         self.builder = builder
         self.phase_fn = self._select_phase_fn()
-        self.run_before = self._make_callbacks(_RUN_BEFORE.attribute_name)
-        self.run_after = self._make_callbacks(_RUN_AFTER.attribute_name)
+        self.run_before = self._make_callbacks(spack.phase_callbacks._RUN_BEFORE.attribute_name)
+        self.run_after = self._make_callbacks(spack.phase_callbacks._RUN_AFTER.attribute_name)
 
     def _make_callbacks(self, callbacks_attribute):
         result = []
@@ -483,15 +388,103 @@ def copy(self):
         return copy.deepcopy(self)
 
 
-class Builder(collections.abc.Sequence, metaclass=BuilderMeta):
-    """A builder is a class that, given a package object (i.e. associated with
-    concrete spec), knows how to install it.
+class BaseBuilder(metaclass=BuilderMeta):
+    """An interface for builders, without any phases defined. This class is exposed in the package
+    API, so that packagers can create a single class to define ``setup_build_environment`` and
+    ``@run_before`` and ``@run_after`` callbacks that can be shared among different builders.
 
-    The builder behaves like a sequence, and when iterated over return the
-    "phases" of the installation in the correct order.
+    Example:
 
-    Args:
-        pkg (spack.package_base.PackageBase): package object to be built
+    .. code-block:: python
+
+       class AnyBuilder(BaseBuilder):
+           @run_after("install")
+           def fixup_install(self):
+                # do something after the package is installed
+                pass
+
+           def setup_build_environment(self, env):
+                env.set("MY_ENV_VAR", "my_value")
+
+        class CMakeBuilder(cmake.CMakeBuilder, AnyBuilder):
+            pass
+
+        class AutotoolsBuilder(autotools.AutotoolsBuilder, AnyBuilder):
+            pass
+    """
+
+    def __init__(self, pkg: spack.package_base.PackageBase) -> None:
+        self.pkg = pkg
+
+    @property
+    def spec(self) -> spack.spec.Spec:
+        return self.pkg.spec
+
+    @property
+    def stage(self):
+        return self.pkg.stage
+
+    @property
+    def prefix(self):
+        return self.pkg.prefix
+
+    def setup_build_environment(
+        self, env: spack.util.environment.EnvironmentModifications
+    ) -> None:
+        """Sets up the build environment for a package.
+
+        This method will be called before the current package prefix exists in
+        Spack's store.
+
+        Args:
+            env: environment modifications to be applied when the package is built. Package authors
+                can call methods on it to alter the build environment.
+        """
+        if not hasattr(super(), "setup_build_environment"):
+            return
+        super().setup_build_environment(env)  # type: ignore
+
+    def setup_dependent_build_environment(
+        self, env: spack.util.environment.EnvironmentModifications, dependent_spec: spack.spec.Spec
+    ) -> None:
+        """Sets up the build environment of a package that depends on this one.
+
+        This is similar to ``setup_build_environment``, but it is used to modify the build
+        environment of a package that *depends* on this one.
+
+        This gives packages the ability to set environment variables for the build of the
+        dependent, which can be useful to provide search hints for headers or libraries if they are
+        not in standard locations.
+
+        This method will be called before the dependent package prefix exists in Spack's store.
+
+        Args:
+            env: environment modifications to be applied when the dependent package is built.
+                Package authors can call methods on it to alter the build environment.
+
+            dependent_spec: the spec of the dependent package about to be built. This allows the
+                extendee (self) to query the dependent's state. Note that *this* package's spec is
+                available as ``self.spec``
+        """
+        if not hasattr(super(), "setup_dependent_build_environment"):
+            return
+        super().setup_dependent_build_environment(env, dependent_spec)  # type: ignore
+
+    def __repr__(self):
+        fmt = "{name}{/hash:7}"
+        return f"{self.__class__.__name__}({self.spec.format(fmt)})"
+
+    def __str__(self):
+        fmt = "{name}{/hash:7}"
+        return f'"{self.__class__.__name__}" builder for "{self.spec.format(fmt)}"'
+
+
+class Builder(BaseBuilder, collections.abc.Sequence):
+    """A builder is a class that, given a package object (i.e. associated with concrete spec),
+    knows how to install it.
+
+    The builder behaves like a sequence, and when iterated over return the "phases" of the
+    installation in the correct order.
     """
 
     #: Sequence of phases. Must be defined in derived classes
@@ -506,95 +499,22 @@ class Builder(collections.abc.Sequence, metaclass=BuilderMeta):
     build_time_test_callbacks: List[str]
     install_time_test_callbacks: List[str]
 
-    #: List of glob expressions. Each expression must either be
-    #: absolute or relative to the package source path.
-    #: Matching artifacts found at the end of the build process will be
-    #: copied in the same directory tree as _spack_build_logfile and
-    #: _spack_build_envfile.
-    archive_files: List[str] = []
+    #: List of glob expressions. Each expression must either be absolute or relative to the package
+    #: source path. Matching artifacts found at the end of the build process will be copied in the
+    #: same directory tree as _spack_build_logfile and _spack_build_envfile.
+    @property
+    def archive_files(self) -> List[str]:
+        return []
 
-    def __init__(self, pkg):
-        self.pkg = pkg
+    def __init__(self, pkg: spack.package_base.PackageBase) -> None:
+        super().__init__(pkg)
         self.callbacks = {}
         for phase in self.phases:
             self.callbacks[phase] = InstallationPhase(phase, self)
 
-    @property
-    def spec(self):
-        return self.pkg.spec
-
-    @property
-    def stage(self):
-        return self.pkg.stage
-
-    @property
-    def prefix(self):
-        return self.pkg.prefix
-
-    def setup_build_environment(self, env):
-        """Sets up the build environment for a package.
-
-        This method will be called before the current package prefix exists in
-        Spack's store.
-
-        Args:
-            env (spack.util.environment.EnvironmentModifications): environment
-                modifications to be applied when the package is built. Package authors
-                can call methods on it to alter the build environment.
-        """
-        if not hasattr(super(), "setup_build_environment"):
-            return
-        super().setup_build_environment(env)
-
-    def setup_dependent_build_environment(self, env, dependent_spec):
-        """Sets up the build environment of packages that depend on this one.
-
-        This is similar to ``setup_build_environment``, but it is used to
-        modify the build environments of packages that *depend* on this one.
-
-        This gives packages like Python and others that follow the extension
-        model a way to implement common environment or compile-time settings
-        for dependencies.
-
-        This method will be called before the dependent package prefix exists
-        in Spack's store.
-
-        Examples:
-            1. Installing python modules generally requires ``PYTHONPATH``
-            to point to the ``lib/pythonX.Y/site-packages`` directory in the
-            module's install prefix. This method could be used to set that
-            variable.
-
-        Args:
-            env (spack.util.environment.EnvironmentModifications): environment
-                modifications to be applied when the dependent package is built.
-                Package authors can call methods on it to alter the build environment.
-
-            dependent_spec (spack.spec.Spec): the spec of the dependent package
-                about to be built. This allows the extendee (self) to query
-                the dependent's state. Note that *this* package's spec is
-                available as ``self.spec``
-        """
-        if not hasattr(super(), "setup_dependent_build_environment"):
-            return
-        super().setup_dependent_build_environment(env, dependent_spec)
-
     def __getitem__(self, idx):
         key = self.phases[idx]
         return self.callbacks[key]
 
     def __len__(self):
         return len(self.phases)
-
-    def __repr__(self):
-        msg = "{0}({1})"
-        return msg.format(type(self).__name__, self.pkg.spec.format("{name}/{hash:7}"))
-
-    def __str__(self):
-        msg = '"{0}" builder for "{1}"'
-        return msg.format(type(self).build_system, self.pkg.spec.format("{name}/{hash:7}"))
-
-
-# Export these names as standalone to be used in packages
-run_after = PhaseCallbacksMeta.run_after
-run_before = PhaseCallbacksMeta.run_before

lib/spack/spack/ci/README.md

@@ -0,0 +1,41 @@
+# Spack CI generators
+
+This document describes how the ci module can be extended to provide novel
+ci generators.  The module currently has only a single generator for gitlab.
+The unit-tests for the ci module define a small custom generator for testing
+purposes as well.
+
+The process of generating a pipeline involves creating a ci-enabled spack
+environment, activating it, and running `spack ci generate`, possibly with
+arguments describing things like where the output should be written.
+
+Internally pipeline generation is broken into two components: general and
+ci platform specific.
+
+## General pipeline functionality
+
+General pipeline functionality includes building a pipeline graph (really,
+a forest), pruning it in a variety of ways, and gathering attributes for all
+the generated spec build jobs from the spack configuration.
+
+All of the above functionality is defined in the `__init__.py` of the top-level
+ci module, and should be roughly the same for pipelines generated for any
+platform.
+
+## CI platform specific functionality
+
+Functionality specific to CI platforms (e.g. gitlab, gha, etc.) should be
+defined in a dedicated module.  In order to define a generator for a new
+platform, there are only a few requirements:
+
+1. add a file under `ci` in which you define a generator method decorated with
+the `@generator` attribute. .
+
+1. import it from `lib/spack/spack/ci/__init__.py`, so that your new generator
+is registered.
+
+1. the generator method must take as arguments PipelineDag, SpackCIConfig,
+and PipelineOptions objects, in that order.
+
+1. the generator method must produce an output file containing the
+generated pipeline.

lib/spack/spack/ci/common.py

@@ -0,0 +1,825 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import codecs
+import copy
+import json
+import os
+import re
+import ssl
+import sys
+import time
+from collections import deque
+from enum import Enum
+from typing import Dict, Generator, List, Optional, Set, Tuple
+from urllib.parse import quote, urlencode, urlparse
+from urllib.request import HTTPHandler, HTTPSHandler, Request, build_opener
+
+import llnl.util.filesystem as fs
+import llnl.util.tty as tty
+from llnl.util.lang import Singleton, memoized
+
+import spack.binary_distribution as bindist
+import spack.config as cfg
+import spack.deptypes as dt
+import spack.environment as ev
+import spack.error
+import spack.mirrors.mirror
+import spack.schema
+import spack.spec
+import spack.util.spack_yaml as syaml
+import spack.util.url as url_util
+import spack.util.web as web_util
+from spack import traverse
+from spack.reporters import CDash, CDashConfiguration
+from spack.reporters.cdash import SPACK_CDASH_TIMEOUT
+from spack.reporters.cdash import build_stamp as cdash_build_stamp
+
+
+def _urlopen():
+    error_handler = web_util.SpackHTTPDefaultErrorHandler()
+
+    # One opener with HTTPS ssl enabled
+    with_ssl = build_opener(
+        HTTPHandler(), HTTPSHandler(context=web_util.ssl_create_default_context()), error_handler
+    )
+
+    # One opener with HTTPS ssl disabled
+    without_ssl = build_opener(
+        HTTPHandler(), HTTPSHandler(context=ssl._create_unverified_context()), error_handler
+    )
+
+    # And dynamically dispatch based on the config:verify_ssl.
+    def dispatch_open(fullurl, data=None, timeout=None, verify_ssl=True):
+        opener = with_ssl if verify_ssl else without_ssl
+        timeout = timeout or cfg.get("config:connect_timeout", 1)
+        return opener.open(fullurl, data, timeout)
+
+    return dispatch_open
+
+
+IS_WINDOWS = sys.platform == "win32"
+SPACK_RESERVED_TAGS = ["public", "protected", "notary"]
+_dyn_mapping_urlopener = Singleton(_urlopen)
+
+
+def copy_files_to_artifacts(src, artifacts_dir):
+    """
+    Copy file(s) to the given artifacts directory
+
+    Parameters:
+        src (str): the glob-friendly path expression for the file(s) to copy
+        artifacts_dir (str): the destination directory
+    """
+    try:
+        fs.copy(src, artifacts_dir)
+    except Exception as err:
+        msg = (
+            f"Unable to copy files ({src}) to artifacts {artifacts_dir} due to "
+            f"exception: {str(err)}"
+        )
+        tty.warn(msg)
+
+
+def win_quote(quote_str: str) -> str:
+    if IS_WINDOWS:
+        quote_str = f'"{quote_str}"'
+    return quote_str
+
+
+def _spec_matches(spec, match_string):
+    return spec.intersects(match_string)
+
+
+def _noop(x):
+    return x
+
+
+def unpack_script(script_section, op=_noop):
+    script = []
+    for cmd in script_section:
+        if isinstance(cmd, list):
+            for subcmd in cmd:
+                script.append(op(subcmd))
+        else:
+            script.append(op(cmd))
+
+    return script
+
+
+def ensure_expected_target_path(path: str) -> str:
+    """Returns passed paths with all Windows path separators exchanged
+    for posix separators
+
+    TODO (johnwparent): Refactor config + cli read/write to deal only in posix style paths
+    """
+    if path:
+        return path.replace("\\", "/")
+    return path
+
+
+def update_env_scopes(
+    env: ev.Environment,
+    cli_scopes: List[str],
+    output_file: str,
+    transform_windows_paths: bool = False,
+) -> None:
+    """Add any config scopes from cli_scopes which aren't already included in the
+    environment, by reading the yaml, adding the missing includes, and writing the
+    updated yaml back to the same location.
+    """
+    with open(env.manifest_path, "r", encoding="utf-8") as env_fd:
+        env_yaml_root = syaml.load(env_fd)
+
+    # Add config scopes to environment
+    env_includes = env_yaml_root["spack"].get("include", [])
+    include_scopes: List[str] = []
+    for scope in cli_scopes:
+        if scope not in include_scopes and scope not in env_includes:
+            include_scopes.insert(0, scope)
+    env_includes.extend(include_scopes)
+    env_yaml_root["spack"]["include"] = [
+        ensure_expected_target_path(i) if transform_windows_paths else i for i in env_includes
+    ]
+
+    with open(output_file, "w", encoding="utf-8") as fd:
+        syaml.dump_config(env_yaml_root, fd, default_flow_style=False)
+
+
+def write_pipeline_manifest(specs, src_prefix, dest_prefix, output_file):
+    """Write out the file describing specs that should be copied"""
+    buildcache_copies = {}
+
+    for release_spec in specs:
+        release_spec_dag_hash = release_spec.dag_hash()
+        # TODO: This assumes signed version of the spec
+        buildcache_copies[release_spec_dag_hash] = [
+            {
+                "src": url_util.join(
+                    src_prefix,
+                    bindist.build_cache_relative_path(),
+                    bindist.tarball_name(release_spec, ".spec.json.sig"),
+                ),
+                "dest": url_util.join(
+                    dest_prefix,
+                    bindist.build_cache_relative_path(),
+                    bindist.tarball_name(release_spec, ".spec.json.sig"),
+                ),
+            },
+            {
+                "src": url_util.join(
+                    src_prefix,
+                    bindist.build_cache_relative_path(),
+                    bindist.tarball_path_name(release_spec, ".spack"),
+                ),
+                "dest": url_util.join(
+                    dest_prefix,
+                    bindist.build_cache_relative_path(),
+                    bindist.tarball_path_name(release_spec, ".spack"),
+                ),
+            },
+        ]
+
+    target_dir = os.path.dirname(output_file)
+
+    if not os.path.exists(target_dir):
+        os.makedirs(target_dir)
+
+    with open(output_file, "w", encoding="utf-8") as fd:
+        fd.write(json.dumps(buildcache_copies))
+
+
+class CDashHandler:
+    """
+    Class for managing CDash data and processing.
+    """
+
+    def __init__(self, ci_cdash):
+        # start with the gitlab ci configuration
+        self.url = ci_cdash.get("url")
+        self.build_group = ci_cdash.get("build-group")
+        self.project = ci_cdash.get("project")
+        self.site = ci_cdash.get("site")
+
+        # grab the authorization token when available
+        self.auth_token = os.environ.get("SPACK_CDASH_AUTH_TOKEN")
+        if self.auth_token:
+            tty.verbose("Using CDash auth token from environment")
+
+        # append runner description to the site if available
+        runner = os.environ.get("CI_RUNNER_DESCRIPTION")
+        if runner:
+            self.site += f" ({runner})"
+
+    def args(self):
+        return [
+            "--cdash-upload-url",
+            win_quote(self.upload_url),
+            "--cdash-build",
+            win_quote(self.build_name()),
+            "--cdash-site",
+            win_quote(self.site),
+            "--cdash-buildstamp",
+            win_quote(self.build_stamp),
+        ]
+
+    def build_name(self, spec: Optional[spack.spec.Spec] = None) -> Optional[str]:
+        """Returns the CDash build name.
+
+        A name will be generated if the `spec` is provided,
+        otherwise, the value will be retrieved from the environment
+        through the `SPACK_CDASH_BUILD_NAME` variable.
+
+        Returns: (str) given spec's CDash build name."""
+        if spec:
+            build_name = f"{spec.name}@{spec.version}%{spec.compiler} \
+hash={spec.dag_hash()} arch={spec.architecture} ({self.build_group})"
+            tty.debug(f"Generated CDash build name ({build_name}) from the {spec.name}")
+            return build_name
+
+        env_build_name = os.environ.get("SPACK_CDASH_BUILD_NAME")
+        tty.debug(f"Using CDash build name ({env_build_name}) from the environment")
+        return env_build_name
+
+    @property  # type: ignore
+    def build_stamp(self):
+        """Returns the CDash build stamp.
+
+        The one defined by SPACK_CDASH_BUILD_STAMP environment variable
+        is preferred due to the representation of timestamps; otherwise,
+        one will be built.
+
+        Returns: (str) current CDash build stamp"""
+        build_stamp = os.environ.get("SPACK_CDASH_BUILD_STAMP")
+        if build_stamp:
+            tty.debug(f"Using build stamp ({build_stamp}) from the environment")
+            return build_stamp
+
+        build_stamp = cdash_build_stamp(self.build_group, time.time())
+        tty.debug(f"Generated new build stamp ({build_stamp})")
+        return build_stamp
+
+    @property  # type: ignore
+    @memoized
+    def project_enc(self):
+        tty.debug(f"Encoding project ({type(self.project)}): {self.project})")
+        encode = urlencode({"project": self.project})
+        index = encode.find("=") + 1
+        return encode[index:]
+
+    @property
+    def upload_url(self):
+        url_format = f"{self.url}/submit.php?project={self.project_enc}"
+        return url_format
+
+    def copy_test_results(self, source, dest):
+        """Copy test results to artifacts directory."""
+        reports = fs.join_path(source, "*_Test*.xml")
+        copy_files_to_artifacts(reports, dest)
+
+    def create_buildgroup(self, opener, headers, url, group_name, group_type):
+        data = {"newbuildgroup": group_name, "project": self.project, "type": group_type}
+
+        enc_data = json.dumps(data).encode("utf-8")
+
+        request = Request(url, data=enc_data, headers=headers)
+
+        response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
+        response_code = response.getcode()
+
+        if response_code not in [200, 201]:
+            msg = f"Creating buildgroup failed (response code = {response_code})"
+            tty.warn(msg)
+            return None
+
+        response_text = response.read()
+        response_json = json.loads(response_text)
+        build_group_id = response_json["id"]
+
+        return build_group_id
+
+    def populate_buildgroup(self, job_names):
+        url = f"{self.url}/api/v1/buildgroup.php"
+
+        headers = {
+            "Authorization": f"Bearer {self.auth_token}",
+            "Content-Type": "application/json",
+        }
+
+        opener = build_opener(HTTPHandler)
+
+        parent_group_id = self.create_buildgroup(opener, headers, url, self.build_group, "Daily")
+        group_id = self.create_buildgroup(
+            opener, headers, url, f"Latest {self.build_group}", "Latest"
+        )
+
+        if not parent_group_id or not group_id:
+            msg = f"Failed to create or retrieve buildgroups for {self.build_group}"
+            tty.warn(msg)
+            return
+
+        data = {
+            "dynamiclist": [
+                {"match": name, "parentgroupid": parent_group_id, "site": self.site}
+                for name in job_names
+            ]
+        }
+
+        enc_data = json.dumps(data).encode("utf-8")
+
+        request = Request(url, data=enc_data, headers=headers)
+        request.get_method = lambda: "PUT"
+
+        response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
+        response_code = response.getcode()
+
+        if response_code != 200:
+            msg = f"Error response code ({response_code}) in populate_buildgroup"
+            tty.warn(msg)
+
+    def report_skipped(self, spec: spack.spec.Spec, report_dir: str, reason: Optional[str]):
+        """Explicitly report skipping testing of a spec (e.g., it's CI
+        configuration identifies it as known to have broken tests or
+        the CI installation failed).
+
+        Args:
+            spec: spec being tested
+            report_dir: directory where the report will be written
+            reason: reason the test is being skipped
+        """
+        configuration = CDashConfiguration(
+            upload_url=self.upload_url,
+            packages=[spec.name],
+            build=self.build_name(),
+            site=self.site,
+            buildstamp=self.build_stamp,
+            track=None,
+        )
+        reporter = CDash(configuration=configuration)
+        reporter.test_skipped_report(report_dir, spec, reason)
+
+
+class PipelineType(Enum):
+    COPY_ONLY = 1
+    spack_copy_only = 1
+    PROTECTED_BRANCH = 2
+    spack_protected_branch = 2
+    PULL_REQUEST = 3
+    spack_pull_request = 3
+
+
+class PipelineOptions:
+    """A container for all pipeline options that can be specified (whether
+    via cli, config/yaml, or environment variables)"""
+
+    def __init__(
+        self,
+        env: ev.Environment,
+        buildcache_destination: spack.mirrors.mirror.Mirror,
+        artifacts_root: str = "jobs_scratch_dir",
+        print_summary: bool = True,
+        output_file: Optional[str] = None,
+        check_index_only: bool = False,
+        broken_specs_url: Optional[str] = None,
+        rebuild_index: bool = True,
+        untouched_pruning_dependent_depth: Optional[int] = None,
+        prune_untouched: bool = False,
+        prune_up_to_date: bool = True,
+        prune_external: bool = True,
+        stack_name: Optional[str] = None,
+        pipeline_type: Optional[PipelineType] = None,
+        require_signing: bool = False,
+        cdash_handler: Optional["CDashHandler"] = None,
+    ):
+        """
+        Args:
+            env: Active spack environment
+            buildcache_destination: The mirror where built binaries should be pushed
+            artifacts_root: Path to location where artifacts should be stored
+            print_summary: Print a summary of the scheduled pipeline
+            output_file: Path where output file should be written
+            check_index_only: Only fetch the index or fetch all spec files
+            broken_specs_url: URL where broken specs (on develop) should be reported
+            rebuild_index: Generate a job to rebuild mirror index after rebuilds
+            untouched_pruning_dependent_depth: How many parents to traverse from changed pkg specs
+            prune_untouched: Prune jobs for specs that were unchanged in git history
+            prune_up_to_date: Prune specs from pipeline if binary exists on the mirror
+            prune_external: Prune specs from pipeline if they are external
+            stack_name: Name of spack stack
+            pipeline_type: Type of pipeline running (optional)
+            require_signing: Require buildcache to be signed (fail w/out signing key)
+            cdash_handler: Object for communicating build information with CDash
+        """
+        self.env = env
+        self.buildcache_destination = buildcache_destination
+        self.artifacts_root = artifacts_root
+        self.print_summary = print_summary
+        self.output_file = output_file
+        self.check_index_only = check_index_only
+        self.broken_specs_url = broken_specs_url
+        self.rebuild_index = rebuild_index
+        self.untouched_pruning_dependent_depth = untouched_pruning_dependent_depth
+        self.prune_untouched = prune_untouched
+        self.prune_up_to_date = prune_up_to_date
+        self.prune_external = prune_external
+        self.stack_name = stack_name
+        self.pipeline_type = pipeline_type
+        self.require_signing = require_signing
+        self.cdash_handler = cdash_handler
+
+
+class PipelineNode:
+    spec: spack.spec.Spec
+    parents: Set[str]
+    children: Set[str]
+
+    def __init__(self, spec: spack.spec.Spec):
+        self.spec = spec
+        self.parents = set()
+        self.children = set()
+
+    @property
+    def key(self):
+        """Return key of the stored spec"""
+        return PipelineDag.key(self.spec)
+
+
+class PipelineDag:
+    """Turn a list of specs into a simple directed graph, that doesn't keep track
+    of edge types."""
+
+    @classmethod
+    def key(cls, spec: spack.spec.Spec) -> str:
+        return spec.dag_hash()
+
+    def __init__(self, specs: List[spack.spec.Spec]) -> None:
+        # Build dictionary of nodes
+        self.nodes: Dict[str, PipelineNode] = {
+            PipelineDag.key(s): PipelineNode(s)
+            for s in traverse.traverse_nodes(specs, deptype=dt.ALL_TYPES, root=True)
+        }
+
+        # Create edges
+        for edge in traverse.traverse_edges(
+            specs, deptype=dt.ALL_TYPES, root=False, cover="edges"
+        ):
+            parent_key = PipelineDag.key(edge.parent)
+            child_key = PipelineDag.key(edge.spec)
+
+            self.nodes[parent_key].children.add(child_key)
+            self.nodes[child_key].parents.add(parent_key)
+
+    def prune(self, node_key: str):
+        """Remove a node from the graph, and reconnect its parents and children"""
+        node = self.nodes[node_key]
+        for parent in node.parents:
+            self.nodes[parent].children.remove(node_key)
+            self.nodes[parent].children |= node.children
+        for child in node.children:
+            self.nodes[child].parents.remove(node_key)
+            self.nodes[child].parents |= node.parents
+        del self.nodes[node_key]
+
+    def traverse_nodes(
+        self, direction: str = "children"
+    ) -> Generator[Tuple[int, PipelineNode], None, None]:
+        """Yields (depth, node) from the pipeline graph.  Traversal is topologically
+        ordered from the roots if ``direction`` is ``children``, or from the leaves
+        if ``direction`` is ``parents``. The yielded depth is the length of the
+        longest path from the starting point to the yielded node."""
+        if direction == "children":
+            get_in_edges = lambda node: node.parents
+            get_out_edges = lambda node: node.children
+        else:
+            get_in_edges = lambda node: node.children
+            get_out_edges = lambda node: node.parents
+
+        sort_key = lambda k: self.nodes[k].spec.name
+
+        out_edges = {k: sorted(get_out_edges(n), key=sort_key) for k, n in self.nodes.items()}
+        num_in_edges = {k: len(get_in_edges(n)) for k, n in self.nodes.items()}
+
+        # Populate a queue with all the nodes that have no incoming edges
+        nodes = deque(
+            sorted(
+                [(0, key) for key in self.nodes.keys() if num_in_edges[key] == 0],
+                key=lambda item: item[1],
+            )
+        )
+
+        while nodes:
+            # Remove the next node, n, from the queue and yield it
+            depth, n_key = nodes.pop()
+            yield (depth, self.nodes[n_key])
+
+            # Remove an in-edge from every node, m, pointed to by an
+            # out-edge from n.  If any of those nodes are left with
+            # 0 remaining in-edges, add them to the queue.
+            for m in out_edges[n_key]:
+                num_in_edges[m] -= 1
+                if num_in_edges[m] == 0:
+                    nodes.appendleft((depth + 1, m))
+
+    def get_dependencies(self, node: PipelineNode) -> List[PipelineNode]:
+        """Returns a list of nodes corresponding to the direct dependencies
+        of the given node."""
+        return [self.nodes[k] for k in node.children]
+
+
+class SpackCIConfig:
+    """Spack CI object used to generate intermediate representation
+    used by the CI generator(s).
+    """
+
+    def __init__(self, ci_config):
+        """Given the information from the ci section of the config
+        and the staged jobs, set up meta data needed for generating Spack
+        CI IR.
+        """
+
+        self.ci_config = ci_config
+        self.named_jobs = ["any", "build", "copy", "cleanup", "noop", "reindex", "signing"]
+
+        self.ir = {
+            "jobs": {},
+            "rebuild-index": self.ci_config.get("rebuild-index", True),
+            "broken-specs-url": self.ci_config.get("broken-specs-url", None),
+            "broken-tests-packages": self.ci_config.get("broken-tests-packages", []),
+            "target": self.ci_config.get("target", "gitlab"),
+        }
+        jobs = self.ir["jobs"]
+
+        for name in self.named_jobs:
+            # Skip the special named jobs
+            if name not in ["any", "build"]:
+                jobs[name] = self.__init_job("")
+
+    def __init_job(self, release_spec):
+        """Initialize job object"""
+        job_object = {"spec": release_spec, "attributes": {}}
+        if release_spec:
+            job_vars = job_object["attributes"].setdefault("variables", {})
+            job_vars["SPACK_JOB_SPEC_DAG_HASH"] = release_spec.dag_hash()
+            job_vars["SPACK_JOB_SPEC_PKG_NAME"] = release_spec.name
+            job_vars["SPACK_JOB_SPEC_PKG_VERSION"] = release_spec.format("{version}")
+            job_vars["SPACK_JOB_SPEC_COMPILER_NAME"] = release_spec.format("{compiler.name}")
+            job_vars["SPACK_JOB_SPEC_COMPILER_VERSION"] = release_spec.format("{compiler.version}")
+            job_vars["SPACK_JOB_SPEC_ARCH"] = release_spec.format("{architecture}")
+            job_vars["SPACK_JOB_SPEC_VARIANTS"] = release_spec.format("{variants}")
+
+        return job_object
+
+    def __is_named(self, section):
+        """Check if a pipeline-gen configuration section is for a named job,
+        and if so return the name otherwise return none.
+        """
+        for _name in self.named_jobs:
+            keys = [f"{_name}-job", f"{_name}-job-remove"]
+            if any([key for key in keys if key in section]):
+                return _name
+
+        return None
+
+    @staticmethod
+    def __job_name(name, suffix=""):
+        """Compute the name of a named job with appropriate suffix.
+        Valid suffixes are either '-remove' or empty string or None
+        """
+        assert isinstance(name, str)
+
+        jname = name
+        if suffix:
+            jname = f"{name}-job{suffix}"
+        else:
+            jname = f"{name}-job"
+
+        return jname
+
+    def __apply_submapping(self, dest, spec, section):
+        """Apply submapping setion to the IR dict"""
+        matched = False
+        only_first = section.get("match_behavior", "first") == "first"
+
+        for match_attrs in reversed(section["submapping"]):
+            attrs = cfg.InternalConfigScope._process_dict_keyname_overrides(match_attrs)
+            for match_string in match_attrs["match"]:
+                if _spec_matches(spec, match_string):
+                    matched = True
+                    if "build-job-remove" in match_attrs:
+                        spack.config.remove_yaml(dest, attrs["build-job-remove"])
+                    if "build-job" in match_attrs:
+                        spack.schema.merge_yaml(dest, attrs["build-job"])
+                    break
+            if matched and only_first:
+                break
+
+        return dest
+
+    # Create jobs for all the pipeline specs
+    def init_pipeline_jobs(self, pipeline: PipelineDag):
+        for _, node in pipeline.traverse_nodes():
+            dag_hash = node.spec.dag_hash()
+            self.ir["jobs"][dag_hash] = self.__init_job(node.spec)
+
+    # Generate IR from the configs
+    def generate_ir(self):
+        """Generate the IR from the Spack CI configurations."""
+
+        jobs = self.ir["jobs"]
+
+        # Implicit job defaults
+        defaults = [
+            {
+                "build-job": {
+                    "script": [
+                        "cd {env_dir}",
+                        "spack env activate --without-view .",
+                        "spack ci rebuild",
+                    ]
+                }
+            },
+            {"noop-job": {"script": ['echo "All specs already up to date, nothing to rebuild."']}},
+        ]
+
+        # Job overrides
+        overrides = [
+            # Reindex script
+            {
+                "reindex-job": {
+                    "script:": ["spack buildcache update-index --keys {index_target_mirror}"]
+                }
+            },
+            # Cleanup script
+            {
+                "cleanup-job": {
+                    "script:": ["spack -d mirror destroy {mirror_prefix}/$CI_PIPELINE_ID"]
+                }
+            },
+            # Add signing job tags
+            {"signing-job": {"tags": ["aws", "protected", "notary"]}},
+            # Remove reserved tags
+            {"any-job-remove": {"tags": SPACK_RESERVED_TAGS}},
+        ]
+
+        pipeline_gen = overrides + self.ci_config.get("pipeline-gen", []) + defaults
+
+        for section in reversed(pipeline_gen):
+            name = self.__is_named(section)
+            has_submapping = "submapping" in section
+            has_dynmapping = "dynamic-mapping" in section
+            section = cfg.InternalConfigScope._process_dict_keyname_overrides(section)
+
+            if name:
+                remove_job_name = self.__job_name(name, suffix="-remove")
+                merge_job_name = self.__job_name(name)
+                do_remove = remove_job_name in section
+                do_merge = merge_job_name in section
+
+                def _apply_section(dest, src):
+                    if do_remove:
+                        dest = spack.config.remove_yaml(dest, src[remove_job_name])
+                    if do_merge:
+                        dest = copy.copy(spack.schema.merge_yaml(dest, src[merge_job_name]))
+
+                if name == "build":
+                    # Apply attributes to all build jobs
+                    for _, job in jobs.items():
+                        if job["spec"]:
+                            _apply_section(job["attributes"], section)
+                elif name == "any":
+                    # Apply section attributes too all jobs
+                    for _, job in jobs.items():
+                        _apply_section(job["attributes"], section)
+                else:
+                    # Create a signing job if there is script and the job hasn't
+                    # been initialized yet
+                    if name == "signing" and name not in jobs:
+                        if "signing-job" in section:
+                            if "script" not in section["signing-job"]:
+                                continue
+                            else:
+                                jobs[name] = self.__init_job("")
+                    # Apply attributes to named job
+                    _apply_section(jobs[name]["attributes"], section)
+
+            elif has_submapping:
+                # Apply section jobs with specs to match
+                for _, job in jobs.items():
+                    if job["spec"]:
+                        job["attributes"] = self.__apply_submapping(
+                            job["attributes"], job["spec"], section
+                        )
+            elif has_dynmapping:
+                mapping = section["dynamic-mapping"]
+
+                dynmap_name = mapping.get("name")
+
+                # Check if this section should be skipped
+                dynmap_skip = os.environ.get("SPACK_CI_SKIP_DYNAMIC_MAPPING")
+                if dynmap_name and dynmap_skip:
+                    if re.match(dynmap_skip, dynmap_name):
+                        continue
+
+                # Get the endpoint
+                endpoint = mapping["endpoint"]
+                endpoint_url = urlparse(endpoint)
+
+                # Configure the request header
+                header = {"User-Agent": web_util.SPACK_USER_AGENT}
+                header.update(mapping.get("header", {}))
+
+                # Expand header environment variables
+                # ie. if tokens are passed
+                for value in header.values():
+                    value = os.path.expandvars(value)
+
+                verify_ssl = mapping.get("verify_ssl", spack.config.get("config:verify_ssl", True))
+                timeout = mapping.get("timeout", spack.config.get("config:connect_timeout", 1))
+
+                required = mapping.get("require", [])
+                allowed = mapping.get("allow", [])
+                ignored = mapping.get("ignore", [])
+
+                # required keys are implicitly allowed
+                allowed = sorted(set(allowed + required))
+                ignored = sorted(set(ignored))
+                required = sorted(set(required))
+
+                # Make sure required things are not also ignored
+                assert not any([ikey in required for ikey in ignored])
+
+                def job_query(job):
+                    job_vars = job["attributes"]["variables"]
+                    query = (
+                        "{SPACK_JOB_SPEC_PKG_NAME}@{SPACK_JOB_SPEC_PKG_VERSION}"
+                        # The preceding spaces are required (ref. https://github.com/spack/spack-gantry/blob/develop/docs/api.md#allocation)
+                        " {SPACK_JOB_SPEC_VARIANTS}"
+                        " arch={SPACK_JOB_SPEC_ARCH}"
+                        "%{SPACK_JOB_SPEC_COMPILER_NAME}@{SPACK_JOB_SPEC_COMPILER_VERSION}"
+                    ).format_map(job_vars)
+                    return f"spec={quote(query)}"
+
+                for job in jobs.values():
+                    if not job["spec"]:
+                        continue
+
+                    # Create request for this job
+                    query = job_query(job)
+                    request = Request(
+                        endpoint_url._replace(query=query).geturl(), headers=header, method="GET"
+                    )
+                    try:
+                        response = _dyn_mapping_urlopener(
+                            request, verify_ssl=verify_ssl, timeout=timeout
+                        )
+                    except Exception as e:
+                        # For now just ignore any errors from dynamic mapping and continue
+                        # This is still experimental, and failures should not stop CI
+                        # from running normally
+                        tty.warn(f"Failed to fetch dynamic mapping for query:\n\t{query}")
+                        tty.warn(f"{e}")
+                        continue
+
+                    config = json.load(codecs.getreader("utf-8")(response))
+
+                    # Strip ignore keys
+                    if ignored:
+                        for key in ignored:
+                            if key in config:
+                                config.pop(key)
+
+                    # Only keep allowed keys
+                    clean_config = {}
+                    if allowed:
+                        for key in allowed:
+                            if key in config:
+                                clean_config[key] = config[key]
+                    else:
+                        clean_config = config
+
+                    # Verify all of the required keys are present
+                    if required:
+                        missing_keys = []
+                        for key in required:
+                            if key not in clean_config.keys():
+                                missing_keys.append(key)
+
+                        if missing_keys:
+                            tty.warn(f"Response missing required keys: {missing_keys}")
+
+                    if clean_config:
+                        job["attributes"] = spack.schema.merge_yaml(
+                            job.get("attributes", {}), clean_config
+                        )
+
+        for _, job in jobs.items():
+            if job["spec"]:
+                job["spec"] = job["spec"].name
+
+        return self.ir
+
+
+class SpackCIError(spack.error.SpackError):
+    def __init__(self, msg):
+        super().__init__(msg)

lib/spack/spack/ci/generator_registry.py

@@ -0,0 +1,36 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+# Holds all known formatters
+"""Generators that support writing out pipelines for various CI platforms,
+using a common pipeline graph definition.
+"""
+import spack.error
+
+_generators = {}
+
+
+def generator(name):
+    """Decorator to register a pipeline generator method.
+    A generator method should take PipelineDag, SpackCIConfig, and
+    PipelineOptions arguments, and should produce a pipeline file.
+    """
+
+    def _decorator(generate_method):
+        _generators[name] = generate_method
+        return generate_method
+
+    return _decorator
+
+
+def get_generator(name):
+    try:
+        return _generators[name]
+    except KeyError:
+        raise UnknownGeneratorException(name)
+
+
+class UnknownGeneratorException(spack.error.SpackError):
+    def __init__(self, generator_name):
+        super().__init__(f"No registered generator for {generator_name}")

lib/spack/spack/ci/gitlab.py

@@ -0,0 +1,416 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import copy
+import os
+import shutil
+from typing import List, Optional
+
+import ruamel.yaml
+
+import llnl.util.tty as tty
+
+import spack
+import spack.binary_distribution as bindist
+import spack.config as cfg
+import spack.mirrors.mirror
+import spack.schema
+import spack.spec
+import spack.util.spack_yaml as syaml
+
+from .common import (
+    SPACK_RESERVED_TAGS,
+    PipelineDag,
+    PipelineOptions,
+    PipelineType,
+    SpackCIConfig,
+    SpackCIError,
+    ensure_expected_target_path,
+    unpack_script,
+    update_env_scopes,
+    write_pipeline_manifest,
+)
+from .generator_registry import generator
+
+# See https://docs.gitlab.com/ee/ci/yaml/#retry for descriptions of conditions
+JOB_RETRY_CONDITIONS = [
+    # "always",
+    "unknown_failure",
+    "script_failure",
+    "api_failure",
+    "stuck_or_timeout_failure",
+    "runner_system_failure",
+    "runner_unsupported",
+    "stale_schedule",
+    # "job_execution_timeout",
+    "archived_failure",
+    "unmet_prerequisites",
+    "scheduler_failure",
+    "data_integrity_failure",
+]
+JOB_NAME_FORMAT = "{name}{@version} {/hash}"
+
+
+def _remove_reserved_tags(tags):
+    """Convenience function to strip reserved tags from jobs"""
+    return [tag for tag in tags if tag not in SPACK_RESERVED_TAGS]
+
+
+def get_job_name(spec: spack.spec.Spec, build_group: Optional[str] = None) -> str:
+    """Given a spec and possibly a build group, return the job name. If the
+    resulting name is longer than 255 characters, it will be truncated.
+
+    Arguments:
+        spec: Spec job will build
+        build_group: Name of build group this job belongs to (a CDash notion)
+
+    Returns: The job name
+    """
+    job_name = spec.format(JOB_NAME_FORMAT)
+
+    if build_group:
+        job_name = f"{job_name} {build_group}"
+
+    return job_name[:255]
+
+
+def maybe_generate_manifest(pipeline: PipelineDag, options: PipelineOptions, manifest_path):
+    # TODO: Consider including only hashes of rebuilt specs in the manifest,
+    # instead of full source and destination urls.  Also, consider renaming
+    # the variable that controls whether or not to write the manifest from
+    # "SPACK_COPY_BUILDCACHE" to "SPACK_WRITE_PIPELINE_MANIFEST" or similar.
+    spack_buildcache_copy = os.environ.get("SPACK_COPY_BUILDCACHE", None)
+    if spack_buildcache_copy:
+        buildcache_copy_src_prefix = options.buildcache_destination.fetch_url
+        buildcache_copy_dest_prefix = spack_buildcache_copy
+
+        if options.pipeline_type == PipelineType.COPY_ONLY:
+            manifest_specs = [s for s in options.env.all_specs() if not s.external]
+        else:
+            manifest_specs = [n.spec for _, n in pipeline.traverse_nodes(direction="children")]
+
+        write_pipeline_manifest(
+            manifest_specs, buildcache_copy_src_prefix, buildcache_copy_dest_prefix, manifest_path
+        )
+
+
+@generator("gitlab")
+def generate_gitlab_yaml(pipeline: PipelineDag, spack_ci: SpackCIConfig, options: PipelineOptions):
+    """Given a pipeline graph, job attributes, and pipeline options,
+    write a pipeline that can be consumed by GitLab to the given output file.
+
+    Arguments:
+        pipeline: An already pruned graph of jobs representing all the specs to build
+        spack_ci: An object containing the configured attributes of all jobs in the pipeline
+        options: An object containing all the pipeline options gathered from yaml, env, etc...
+    """
+    ci_project_dir = os.environ.get("CI_PROJECT_DIR") or os.getcwd()
+    generate_job_name = os.environ.get("CI_JOB_NAME", "job-does-not-exist")
+    generate_pipeline_id = os.environ.get("CI_PIPELINE_ID", "pipeline-does-not-exist")
+    artifacts_root = options.artifacts_root
+    if artifacts_root.startswith(ci_project_dir):
+        artifacts_root = os.path.relpath(artifacts_root, ci_project_dir)
+    pipeline_artifacts_dir = os.path.join(ci_project_dir, artifacts_root)
+    output_file = options.output_file
+
+    if not output_file:
+        output_file = os.path.abspath(".gitlab-ci.yml")
+    else:
+        output_file_path = os.path.abspath(output_file)
+        gen_ci_dir = os.path.dirname(output_file_path)
+        if not os.path.exists(gen_ci_dir):
+            os.makedirs(gen_ci_dir)
+
+    spack_ci_ir = spack_ci.generate_ir()
+
+    concrete_env_dir = os.path.join(pipeline_artifacts_dir, "concrete_environment")
+
+    # Now that we've added the mirrors we know about, they should be properly
+    # reflected in the environment manifest file, so copy that into the
+    # concrete environment directory, along with the spack.lock file.
+    if not os.path.exists(concrete_env_dir):
+        os.makedirs(concrete_env_dir)
+    shutil.copyfile(options.env.manifest_path, os.path.join(concrete_env_dir, "spack.yaml"))
+    shutil.copyfile(options.env.lock_path, os.path.join(concrete_env_dir, "spack.lock"))
+
+    update_env_scopes(
+        options.env,
+        [
+            os.path.relpath(s.path, concrete_env_dir)
+            for s in cfg.scopes().values()
+            if not s.writable
+            and isinstance(s, (cfg.DirectoryConfigScope))
+            and os.path.exists(s.path)
+        ],
+        os.path.join(concrete_env_dir, "spack.yaml"),
+        # Here transforming windows paths is only required in the special case
+        # of copy_only_pipelines, a unique scenario where the generate job and
+        # child pipelines are run on different platforms. To make this compatible
+        # w/ Windows, we cannot write Windows style path separators that will be
+        # consumed on by the Posix copy job runner.
+        #
+        # TODO (johnwparent): Refactor config + cli read/write to deal only in
+        # posix style paths
+        transform_windows_paths=(options.pipeline_type == PipelineType.COPY_ONLY),
+    )
+
+    job_log_dir = os.path.join(pipeline_artifacts_dir, "logs")
+    job_repro_dir = os.path.join(pipeline_artifacts_dir, "reproduction")
+    job_test_dir = os.path.join(pipeline_artifacts_dir, "tests")
+    user_artifacts_dir = os.path.join(pipeline_artifacts_dir, "user_data")
+
+    # We communicate relative paths to the downstream jobs to avoid issues in
+    # situations where the CI_PROJECT_DIR varies between the pipeline
+    # generation job and the rebuild jobs.  This can happen when gitlab
+    # checks out the project into a runner-specific directory, for example,
+    # and different runners are picked for generate and rebuild jobs.
+
+    rel_concrete_env_dir = os.path.relpath(concrete_env_dir, ci_project_dir)
+    rel_job_log_dir = os.path.relpath(job_log_dir, ci_project_dir)
+    rel_job_repro_dir = os.path.relpath(job_repro_dir, ci_project_dir)
+    rel_job_test_dir = os.path.relpath(job_test_dir, ci_project_dir)
+    rel_user_artifacts_dir = os.path.relpath(user_artifacts_dir, ci_project_dir)
+
+    def main_script_replacements(cmd):
+        return cmd.replace("{env_dir}", rel_concrete_env_dir)
+
+    output_object = {}
+    job_id = 0
+    stage_id = 0
+    stages: List[List] = []
+    stage_names = []
+
+    max_length_needs = 0
+    max_needs_job = ""
+
+    if not options.pipeline_type == PipelineType.COPY_ONLY:
+        for level, node in pipeline.traverse_nodes(direction="parents"):
+            stage_id = level
+            if len(stages) == stage_id:
+                stages.append([])
+            stages[stage_id].append(node.spec)
+            stage_name = f"stage-{level}"
+
+            if stage_name not in stage_names:
+                stage_names.append(stage_name)
+
+            release_spec = node.spec
+            release_spec_dag_hash = release_spec.dag_hash()
+
+            job_object = spack_ci_ir["jobs"][release_spec_dag_hash]["attributes"]
+
+            if not job_object:
+                tty.warn(f"No match found for {release_spec}, skipping it")
+                continue
+
+            if options.pipeline_type is not None:
+                # For spack pipelines "public" and "protected" are reserved tags
+                job_object["tags"] = _remove_reserved_tags(job_object.get("tags", []))
+                if options.pipeline_type == PipelineType.PROTECTED_BRANCH:
+                    job_object["tags"].extend(["protected"])
+                elif options.pipeline_type == PipelineType.PULL_REQUEST:
+                    job_object["tags"].extend(["public"])
+
+            if "script" not in job_object:
+                raise AttributeError
+
+            job_object["script"] = unpack_script(job_object["script"], op=main_script_replacements)
+
+            if "before_script" in job_object:
+                job_object["before_script"] = unpack_script(job_object["before_script"])
+
+            if "after_script" in job_object:
+                job_object["after_script"] = unpack_script(job_object["after_script"])
+
+            build_group = options.cdash_handler.build_group if options.cdash_handler else None
+            job_name = get_job_name(release_spec, build_group)
+
+            dep_nodes = pipeline.get_dependencies(node)
+            job_object["needs"] = [
+                {"job": get_job_name(dep_node.spec, build_group), "artifacts": False}
+                for dep_node in dep_nodes
+            ]
+
+            job_object["needs"].append(
+                {"job": generate_job_name, "pipeline": f"{generate_pipeline_id}"}
+            )
+
+            job_vars = job_object["variables"]
+
+            # Let downstream jobs know whether the spec needed rebuilding, regardless
+            # whether DAG pruning was enabled or not.
+            already_built = bindist.get_mirrors_for_spec(spec=release_spec, index_only=True)
+            job_vars["SPACK_SPEC_NEEDS_REBUILD"] = "False" if already_built else "True"
+
+            if options.cdash_handler:
+                build_name = options.cdash_handler.build_name(release_spec)
+                job_vars["SPACK_CDASH_BUILD_NAME"] = build_name
+                build_stamp = options.cdash_handler.build_stamp
+                job_vars["SPACK_CDASH_BUILD_STAMP"] = build_stamp
+
+            job_object["artifacts"] = spack.schema.merge_yaml(
+                job_object.get("artifacts", {}),
+                {
+                    "when": "always",
+                    "paths": [
+                        rel_job_log_dir,
+                        rel_job_repro_dir,
+                        rel_job_test_dir,
+                        rel_user_artifacts_dir,
+                    ],
+                },
+            )
+
+            job_object["stage"] = stage_name
+            job_object["retry"] = {"max": 2, "when": JOB_RETRY_CONDITIONS}
+            job_object["interruptible"] = True
+
+            length_needs = len(job_object["needs"])
+            if length_needs > max_length_needs:
+                max_length_needs = length_needs
+                max_needs_job = job_name
+
+            output_object[job_name] = job_object
+            job_id += 1
+
+        tty.debug(f"{job_id} build jobs generated in {stage_id} stages")
+
+    if job_id > 0:
+        tty.debug(f"The max_needs_job is {max_needs_job}, with {max_length_needs} needs")
+
+    service_job_retries = {
+        "max": 2,
+        "when": ["runner_system_failure", "stuck_or_timeout_failure", "script_failure"],
+    }
+
+    # In some cases, pipeline generation should write a manifest.  Currently
+    # the only purpose is to specify a list of sources and destinations for
+    # everything that should be copied.
+    distinguish_stack = options.stack_name if options.stack_name else "rebuilt"
+    manifest_path = os.path.join(
+        pipeline_artifacts_dir, "specs_to_copy", f"copy_{distinguish_stack}_specs.json"
+    )
+    maybe_generate_manifest(pipeline, options, manifest_path)
+
+    if options.pipeline_type == PipelineType.COPY_ONLY:
+        stage_names.append("copy")
+        sync_job = copy.deepcopy(spack_ci_ir["jobs"]["copy"]["attributes"])
+        sync_job["stage"] = "copy"
+        sync_job["needs"] = [{"job": generate_job_name, "pipeline": f"{generate_pipeline_id}"}]
+
+        if "variables" not in sync_job:
+            sync_job["variables"] = {}
+
+        sync_job["variables"][
+            "SPACK_COPY_ONLY_DESTINATION"
+        ] = options.buildcache_destination.fetch_url
+
+        pipeline_mirrors = spack.mirrors.mirror.MirrorCollection(binary=True)
+        if "buildcache-source" not in pipeline_mirrors:
+            raise SpackCIError("Copy-only pipelines require a mirror named 'buildcache-source'")
+
+        buildcache_source = pipeline_mirrors["buildcache-source"].fetch_url
+        sync_job["variables"]["SPACK_BUILDCACHE_SOURCE"] = buildcache_source
+        sync_job["dependencies"] = []
+
+        output_object["copy"] = sync_job
+        job_id += 1
+
+    if job_id > 0:
+        if (
+            "script" in spack_ci_ir["jobs"]["signing"]["attributes"]
+            and options.pipeline_type == PipelineType.PROTECTED_BRANCH
+        ):
+            # External signing: generate a job to check and sign binary pkgs
+            stage_names.append("stage-sign-pkgs")
+            signing_job = spack_ci_ir["jobs"]["signing"]["attributes"]
+
+            signing_job["script"] = unpack_script(signing_job["script"])
+
+            signing_job["stage"] = "stage-sign-pkgs"
+            signing_job["when"] = "always"
+            signing_job["retry"] = {"max": 2, "when": ["always"]}
+            signing_job["interruptible"] = True
+            if "variables" not in signing_job:
+                signing_job["variables"] = {}
+            signing_job["variables"][
+                "SPACK_BUILDCACHE_DESTINATION"
+            ] = options.buildcache_destination.push_url
+            signing_job["dependencies"] = []
+
+            output_object["sign-pkgs"] = signing_job
+
+        if options.rebuild_index:
+            # Add a final job to regenerate the index
+            stage_names.append("stage-rebuild-index")
+            final_job = spack_ci_ir["jobs"]["reindex"]["attributes"]
+
+            final_job["stage"] = "stage-rebuild-index"
+            target_mirror = options.buildcache_destination.push_url
+            final_job["script"] = unpack_script(
+                final_job["script"],
+                op=lambda cmd: cmd.replace("{index_target_mirror}", target_mirror),
+            )
+
+            final_job["when"] = "always"
+            final_job["retry"] = service_job_retries
+            final_job["interruptible"] = True
+            final_job["dependencies"] = []
+
+            output_object["rebuild-index"] = final_job
+
+        output_object["stages"] = stage_names
+
+        # Capture the version of Spack used to generate the pipeline, that can be
+        # passed to `git checkout` for version consistency. If we aren't in a Git
+        # repository, presume we are a Spack release and use the Git tag instead.
+        spack_version = spack.get_version()
+        version_to_clone = spack.get_spack_commit() or f"v{spack.spack_version}"
+
+        rebuild_everything = not options.prune_up_to_date and not options.prune_untouched
+
+        output_object["variables"] = {
+            "SPACK_ARTIFACTS_ROOT": artifacts_root,
+            "SPACK_CONCRETE_ENV_DIR": rel_concrete_env_dir,
+            "SPACK_VERSION": spack_version,
+            "SPACK_CHECKOUT_VERSION": version_to_clone,
+            "SPACK_JOB_LOG_DIR": rel_job_log_dir,
+            "SPACK_JOB_REPRO_DIR": rel_job_repro_dir,
+            "SPACK_JOB_TEST_DIR": rel_job_test_dir,
+            "SPACK_PIPELINE_TYPE": options.pipeline_type.name if options.pipeline_type else "None",
+            "SPACK_CI_STACK_NAME": os.environ.get("SPACK_CI_STACK_NAME", "None"),
+            "SPACK_REBUILD_CHECK_UP_TO_DATE": str(options.prune_up_to_date),
+            "SPACK_REBUILD_EVERYTHING": str(rebuild_everything),
+            "SPACK_REQUIRE_SIGNING": str(options.require_signing),
+        }
+
+        if options.stack_name:
+            output_object["variables"]["SPACK_CI_STACK_NAME"] = options.stack_name
+
+        output_vars = output_object["variables"]
+        for item, val in output_vars.items():
+            output_vars[item] = ensure_expected_target_path(val)
+
+    else:
+        # No jobs were generated
+        noop_job = spack_ci_ir["jobs"]["noop"]["attributes"]
+        # If this job fails ignore the status and carry on
+        noop_job["retry"] = 0
+        noop_job["allow_failure"] = True
+
+        tty.debug("No specs to rebuild, generating no-op job")
+        output_object = {"no-specs-to-rebuild": noop_job}
+
+    # Ensure the child pipeline always runs
+    output_object["workflow"] = {"rules": [{"when": "always"}]}
+
+    sorted_output = {}
+    for output_key, output_value in sorted(output_object.items()):
+        sorted_output[output_key] = output_value
+
+    # Minimize yaml output size through use of anchors
+    syaml.anchorify(sorted_output)
+
+    with open(output_file, "w", encoding="utf-8") as f:
+        ruamel.yaml.YAML().dump(sorted_output, f)

lib/spack/spack/cmd/__init__.py

@@ -4,12 +4,13 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import argparse
+import difflib
 import importlib
 import os
 import re
 import sys
 from collections import Counter
-from typing import List, Union
+from typing import List, Optional, Union
 
 import llnl.string
 import llnl.util.tty as tty
@@ -23,15 +24,18 @@
 import spack.environment as ev
 import spack.error
 import spack.extensions
-import spack.parser
 import spack.paths
+import spack.repo
 import spack.spec
+import spack.spec_parser
 import spack.store
 import spack.traverse as traverse
 import spack.user_environment as uenv
 import spack.util.spack_json as sjson
 import spack.util.spack_yaml as syaml
 
+from ..enums import InstallRecordStatus
+
 # cmd has a submodule called "list" so preserve the python list module
 python_list = list
 
@@ -122,6 +126,8 @@ def get_module(cmd_name):
         tty.debug("Imported {0} from built-in commands".format(pname))
     except ImportError:
         module = spack.extensions.get_module(cmd_name)
+        if not module:
+            raise CommandNotFoundError(cmd_name)
 
     attr_setdefault(module, SETUP_PARSER, lambda *args: None)  # null-op
     attr_setdefault(module, DESCRIPTION, "")
@@ -157,12 +163,12 @@ def quote_kvp(string: str) -> str:
     or ``name==``, and we assume the rest of the argument is the value. This covers the
     common cases of passign flags, e.g., ``cflags="-O2 -g"`` on the command line.
     """
-    match = spack.parser.SPLIT_KVP.match(string)
+    match = spack.spec_parser.SPLIT_KVP.match(string)
     if not match:
         return string
 
     key, delim, value = match.groups()
-    return f"{key}{delim}{spack.parser.quote_if_needed(value)}"
+    return f"{key}{delim}{spack.spec_parser.quote_if_needed(value)}"
 
 
 def parse_specs(
@@ -174,7 +180,7 @@ def parse_specs(
     args = [args] if isinstance(args, str) else args
     arg_string = " ".join([quote_kvp(arg) for arg in args])
 
-    specs = spack.parser.parse(arg_string)
+    specs = spack.spec_parser.parse(arg_string)
     if not concretize:
         return specs
 
@@ -266,39 +272,48 @@ def matching_specs_from_env(specs):
     return _concretize_spec_pairs(spec_pairs + additional_concrete_specs)[: len(spec_pairs)]
 
 
-def disambiguate_spec(spec, env, local=False, installed=True, first=False):
+def disambiguate_spec(
+    spec: spack.spec.Spec,
+    env: Optional[ev.Environment],
+    local: bool = False,
+    installed: Union[bool, InstallRecordStatus] = True,
+    first: bool = False,
+) -> spack.spec.Spec:
     """Given a spec, figure out which installed package it refers to.
 
-    Arguments:
-        spec (spack.spec.Spec): a spec to disambiguate
-        env (spack.environment.Environment): a spack environment,
-            if one is active, or None if no environment is active
-        local (bool): do not search chained spack instances
-        installed (bool or spack.database.InstallStatus or typing.Iterable):
-            install status argument passed to database query.
-            See ``spack.database.Database._query`` for details.
+    Args:
+        spec: a spec to disambiguate
+        env: a spack environment, if one is active, or None if no environment is active
+        local: do not search chained spack instances
+        installed: install status argument passed to database query.
+        first: returns the first matching spec, even if more than one match is found
     """
     hashes = env.all_hashes() if env else None
     return disambiguate_spec_from_hashes(spec, hashes, local, installed, first)
 
 
-def disambiguate_spec_from_hashes(spec, hashes, local=False, installed=True, first=False):
+def disambiguate_spec_from_hashes(
+    spec: spack.spec.Spec,
+    hashes: List[str],
+    local: bool = False,
+    installed: Union[bool, InstallRecordStatus] = True,
+    first: bool = False,
+) -> spack.spec.Spec:
     """Given a spec and a list of hashes, get concrete spec the spec refers to.
 
     Arguments:
-        spec (spack.spec.Spec): a spec to disambiguate
-        hashes (typing.Iterable): a set of hashes of specs among which to disambiguate
-        local (bool): do not search chained spack instances
-        installed (bool or spack.database.InstallStatus or typing.Iterable):
-            install status argument passed to database query.
-            See ``spack.database.Database._query`` for details.
+        spec: a spec to disambiguate
+        hashes: a set of hashes of specs among which to disambiguate
+        local: if True, do not search chained spack instances
+        installed: install status argument passed to database query.
+        first: returns the first matching spec, even if more than one match is found
     """
     if local:
         matching_specs = spack.store.STORE.db.query_local(spec, hashes=hashes, installed=installed)
     else:
         matching_specs = spack.store.STORE.db.query(spec, hashes=hashes, installed=installed)
     if not matching_specs:
-        tty.die("Spec '%s' matches no installed packages." % spec)
+        tty.die(f"Spec '{spec}' matches no installed packages.")
 
     elif first:
         return matching_specs[0]
@@ -679,3 +694,24 @@ def find_environment(args):
 def first_line(docstring):
     """Return the first line of the docstring."""
     return docstring.split("\n")[0]
+
+
+class CommandNotFoundError(spack.error.SpackError):
+    """Exception class thrown when a requested command is not recognized as
+    such.
+    """
+
+    def __init__(self, cmd_name):
+        msg = (
+            f"{cmd_name} is not a recognized Spack command or extension command; "
+            "check with `spack commands`."
+        )
+        long_msg = None
+
+        similar = difflib.get_close_matches(cmd_name, all_commands())
+
+        if 1 <= len(similar) <= 5:
+            long_msg = "\nDid you mean one of the following commands?\n  "
+            long_msg += "\n  ".join(similar)
+
+        super().__init__(msg, long_msg)

lib/spack/spack/cmd/bootstrap.py

@@ -16,7 +16,7 @@
 import spack.bootstrap.config
 import spack.bootstrap.core
 import spack.config
-import spack.mirror
+import spack.mirrors.utils
 import spack.spec
 import spack.stage
 import spack.util.path
@@ -29,7 +29,7 @@
 
 
 # Tarball to be downloaded if binary packages are requested in a local mirror
-BINARY_TARBALL = "https://github.com/spack/spack-bootstrap-mirrors/releases/download/v0.4/bootstrap-buildcache.tar.gz"
+BINARY_TARBALL = "https://github.com/spack/spack-bootstrap-mirrors/releases/download/v0.6/bootstrap-buildcache.tar.gz"
 
 #: Subdirectory where to create the mirror
 LOCAL_MIRROR_DIR = "bootstrap_cache"
@@ -51,9 +51,9 @@
     },
 }
 
-CLINGO_JSON = "$spack/share/spack/bootstrap/github-actions-v0.4/clingo.json"
-GNUPG_JSON = "$spack/share/spack/bootstrap/github-actions-v0.4/gnupg.json"
-PATCHELF_JSON = "$spack/share/spack/bootstrap/github-actions-v0.4/patchelf.json"
+CLINGO_JSON = "$spack/share/spack/bootstrap/github-actions-v0.6/clingo.json"
+GNUPG_JSON = "$spack/share/spack/bootstrap/github-actions-v0.6/gnupg.json"
+PATCHELF_JSON = "$spack/share/spack/bootstrap/github-actions-v0.6/patchelf.json"
 
 # Metadata for a generated source mirror
 SOURCE_METADATA = {
@@ -400,7 +400,7 @@ def _mirror(args):
         llnl.util.tty.set_msg_enabled(False)
         spec = spack.spec.Spec(spec_str).concretized()
         for node in spec.traverse():
-            spack.mirror.create(mirror_dir, [node])
+            spack.mirrors.utils.create(mirror_dir, [node])
         llnl.util.tty.set_msg_enabled(True)
 
     if args.binary_packages:
@@ -419,7 +419,7 @@ def write_metadata(subdir, metadata):
         metadata_rel_dir = os.path.join("metadata", subdir)
         metadata_yaml = os.path.join(args.root_dir, metadata_rel_dir, "metadata.yaml")
         llnl.util.filesystem.mkdirp(os.path.dirname(metadata_yaml))
-        with open(metadata_yaml, mode="w") as f:
+        with open(metadata_yaml, mode="w", encoding="utf-8") as f:
             spack.util.spack_yaml.dump(metadata, stream=f)
         return os.path.dirname(metadata_yaml), metadata_rel_dir
 

lib/spack/spack/cmd/buildcache.py

@@ -21,7 +21,7 @@
 import spack.deptypes as dt
 import spack.environment as ev
 import spack.error
-import spack.mirror
+import spack.mirrors.mirror
 import spack.oci.oci
 import spack.spec
 import spack.stage
@@ -34,6 +34,8 @@
 from spack.cmd.common import arguments
 from spack.spec import Spec, save_dependency_specfiles
 
+from ..enums import InstallRecordStatus
+
 description = "create, download and install binary packages"
 section = "packaging"
 level = "long"
@@ -308,7 +310,10 @@ def setup_parser(subparser: argparse.ArgumentParser):
 
 def _matching_specs(specs: List[Spec]) -> List[Spec]:
     """Disambiguate specs and return a list of matching specs"""
-    return [spack.cmd.disambiguate_spec(s, ev.active_environment(), installed=any) for s in specs]
+    return [
+        spack.cmd.disambiguate_spec(s, ev.active_environment(), installed=InstallRecordStatus.ANY)
+        for s in specs
+    ]
 
 
 def _format_spec(spec: Spec) -> str:
@@ -387,7 +392,7 @@ def push_fn(args):
         roots = spack.cmd.require_active_env(cmd_name="buildcache push").concrete_roots()
 
     mirror = args.mirror
-    assert isinstance(mirror, spack.mirror.Mirror)
+    assert isinstance(mirror, spack.mirrors.mirror.Mirror)
 
     push_url = mirror.push_url
 
@@ -726,7 +731,7 @@ def manifest_copy(manifest_file_list, dest_mirror=None):
     deduped_manifest = {}
 
     for manifest_path in manifest_file_list:
-        with open(manifest_path) as fd:
+        with open(manifest_path, encoding="utf-8") as fd:
             manifest = json.loads(fd.read())
             for spec_hash, copy_list in manifest.items():
                 # Last duplicate hash wins
@@ -745,7 +750,7 @@ def manifest_copy(manifest_file_list, dest_mirror=None):
             copy_buildcache_file(copy_file["src"], dest)
 
 
-def update_index(mirror: spack.mirror.Mirror, update_keys=False):
+def update_index(mirror: spack.mirrors.mirror.Mirror, update_keys=False):
     # Special case OCI images for now.
     try:
         image_ref = spack.oci.oci.image_from_mirror(mirror)

lib/spack/spack/cmd/checksum.py

@@ -253,7 +253,7 @@ 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+") as f:
+    with open(filename, "r+", encoding="utf-8") as f:
         contents = f.read()
         split_contents = version_statement_re.split(contents)
 

lib/spack/spack/cmd/ci.py

@@ -6,7 +6,6 @@
 import json
 import os
 import shutil
-import warnings
 from urllib.parse import urlparse, urlunparse
 
 import llnl.util.filesystem as fs
@@ -17,10 +16,11 @@
 import spack.ci as spack_ci
 import spack.cmd
 import spack.cmd.buildcache as buildcache
+import spack.cmd.common.arguments
 import spack.config as cfg
 import spack.environment as ev
 import spack.hash_types as ht
-import spack.mirror
+import spack.mirrors.mirror
 import spack.util.gpg as gpg_util
 import spack.util.timer as timer
 import spack.util.url as url_util
@@ -62,22 +62,8 @@ def setup_parser(subparser):
         "path to the file where generated jobs file should be written. "
         "default is .gitlab-ci.yml in the root of the repository",
     )
-    generate.add_argument(
-        "--optimize",
-        action="store_true",
-        default=False,
-        help="(DEPRECATED) optimize the gitlab yaml file for size\n\n"
-        "run the generated document through a series of optimization passes "
-        "designed to reduce the size of the generated file",
-    )
-    generate.add_argument(
-        "--dependencies",
-        action="store_true",
-        default=False,
-        help="(DEPRECATED) disable DAG scheduling (use 'plain' dependencies)",
-    )
-    prune_group = generate.add_mutually_exclusive_group()
-    prune_group.add_argument(
+    prune_dag_group = generate.add_mutually_exclusive_group()
+    prune_dag_group.add_argument(
         "--prune-dag",
         action="store_true",
         dest="prune_dag",
@@ -85,7 +71,7 @@ def setup_parser(subparser):
         help="skip up-to-date specs\n\n"
         "do not generate jobs for specs that are up-to-date on the mirror",
     )
-    prune_group.add_argument(
+    prune_dag_group.add_argument(
         "--no-prune-dag",
         action="store_false",
         dest="prune_dag",
@@ -93,6 +79,23 @@ def setup_parser(subparser):
         help="process up-to-date specs\n\n"
         "generate jobs for specs even when they are up-to-date on the mirror",
     )
+    prune_ext_group = generate.add_mutually_exclusive_group()
+    prune_ext_group.add_argument(
+        "--prune-externals",
+        action="store_true",
+        dest="prune_externals",
+        default=True,
+        help="skip external specs\n\n"
+        "do not generate jobs for specs that are marked as external",
+    )
+    prune_ext_group.add_argument(
+        "--no-prune-externals",
+        action="store_false",
+        dest="prune_externals",
+        default=True,
+        help="process external specs\n\n"
+        "generate jobs for specs even when they are marked as external",
+    )
     generate.add_argument(
         "--check-index-only",
         action="store_true",
@@ -108,14 +111,18 @@ def setup_parser(subparser):
     )
     generate.add_argument(
         "--artifacts-root",
-        default=None,
+        default="jobs_scratch_dir",
         help="path to the root of the artifacts directory\n\n"
-        "if provided, concrete environment files (spack.yaml, spack.lock) will be generated under "
-        "this directory. their location will be passed to generated child jobs through the "
-        "SPACK_CONCRETE_ENVIRONMENT_PATH variable",
+        "The spack ci module assumes it will normally be run from within your project "
+        "directory, wherever that is checked out to run your ci.  The artifacts root directory "
+        "should specifiy a name that can safely be used for artifacts within your project "
+        "directory.",
     )
     generate.set_defaults(func=ci_generate)
 
+    spack.cmd.common.arguments.add_concretizer_args(generate)
+    spack.cmd.common.arguments.add_common_arguments(generate, ["jobs"])
+
     # Rebuild the buildcache index associated with the mirror in the
     # active, gitlab-enabled environment.
     index = subparsers.add_parser(
@@ -145,6 +152,7 @@ def setup_parser(subparser):
         help="stop stand-alone tests after the first failure",
     )
     rebuild.set_defaults(func=ci_rebuild)
+    spack.cmd.common.arguments.add_common_arguments(rebuild, ["jobs"])
 
     # Facilitate reproduction of a failed CI build job
     reproduce = subparsers.add_parser(
@@ -187,42 +195,8 @@ def ci_generate(args):
     before invoking this command. the value must be the CDash authorization token needed to create
     a build group and register all generated jobs under it
     """
-    if args.optimize:
-        warnings.warn(
-            "The --optimize option has been deprecated, and currently has no effect. "
-            "It will be removed in Spack v0.24."
-        )
-
-    if args.dependencies:
-        warnings.warn(
-            "The --dependencies option has been deprecated, and currently has no effect. "
-            "It will be removed in Spack v0.24."
-        )
-
     env = spack.cmd.require_active_env(cmd_name="ci generate")
-
-    output_file = args.output_file
-    prune_dag = args.prune_dag
-    index_only = args.index_only
-    artifacts_root = args.artifacts_root
-
-    if not output_file:
-        output_file = os.path.abspath(".gitlab-ci.yml")
-    else:
-        output_file_path = os.path.abspath(output_file)
-        gen_ci_dir = os.path.dirname(output_file_path)
-        if not os.path.exists(gen_ci_dir):
-            os.makedirs(gen_ci_dir)
-
-    # Generate the jobs
-    spack_ci.generate_gitlab_ci_yaml(
-        env,
-        True,
-        output_file,
-        prune_dag=prune_dag,
-        check_index_only=index_only,
-        artifacts_root=artifacts_root,
-    )
+    spack_ci.generate_pipeline(env, args)
 
 
 def ci_reindex(args):
@@ -240,7 +214,7 @@ def ci_reindex(args):
     ci_mirrors = yaml_root["mirrors"]
     mirror_urls = [url for url in ci_mirrors.values()]
     remote_mirror_url = mirror_urls[0]
-    mirror = spack.mirror.Mirror(remote_mirror_url)
+    mirror = spack.mirrors.mirror.Mirror(remote_mirror_url)
 
     buildcache.update_index(mirror, update_keys=True)
 
@@ -328,7 +302,7 @@ def ci_rebuild(args):
 
     full_rebuild = True if rebuild_everything and rebuild_everything.lower() == "true" else False
 
-    pipeline_mirrors = spack.mirror.MirrorCollection(binary=True)
+    pipeline_mirrors = spack.mirrors.mirror.MirrorCollection(binary=True)
     buildcache_destination = None
     if "buildcache-destination" not in pipeline_mirrors:
         tty.die("spack ci rebuild requires a mirror named 'buildcache-destination")
@@ -387,7 +361,7 @@ def ci_rebuild(args):
     # Write this job's spec json into the reproduction directory, and it will
     # also be used in the generated "spack install" command to install the spec
     tty.debug("job concrete spec path: {0}".format(job_spec_json_path))
-    with open(job_spec_json_path, "w") as fd:
+    with open(job_spec_json_path, "w", encoding="utf-8") as fd:
         fd.write(job_spec.to_json(hash=ht.dag_hash))
 
     # Write some other details to aid in reproduction into an artifact
@@ -397,7 +371,7 @@ def ci_rebuild(args):
         "job_spec_json": job_spec_json_file,
         "ci_project_dir": ci_project_dir,
     }
-    with open(repro_file, "w") as fd:
+    with open(repro_file, "w", encoding="utf-8") as fd:
         fd.write(json.dumps(repro_details))
 
     # Write information about spack into an artifact in the repro dir
@@ -433,14 +407,19 @@ def ci_rebuild(args):
     if not config["verify_ssl"]:
         spack_cmd.append("-k")
 
-    install_args = [f'--use-buildcache={spack_ci.win_quote("package:never,dependencies:only")}']
+    install_args = [
+        f'--use-buildcache={spack_ci.common.win_quote("package:never,dependencies:only")}'
+    ]
 
     can_verify = spack_ci.can_verify_binaries()
     verify_binaries = can_verify and spack_is_pr_pipeline is False
     if not verify_binaries:
         install_args.append("--no-check-signature")
 
-    slash_hash = spack_ci.win_quote("/" + job_spec.dag_hash())
+    if args.jobs:
+        install_args.append(f"-j{args.jobs}")
+
+    slash_hash = spack_ci.common.win_quote("/" + job_spec.dag_hash())
 
     # Arguments when installing the root from sources
     deps_install_args = install_args + ["--only=dependencies"]
@@ -605,7 +584,7 @@ def ci_rebuild(args):
 
     rebuild_timer.stop()
     try:
-        with open("install_timers.json", "w") as timelog:
+        with open("install_timers.json", "w", encoding="utf-8") as timelog:
             extra_attributes = {"name": ".ci-rebuild"}
             rebuild_timer.write_json(timelog, extra_attributes=extra_attributes)
     except Exception as e:

lib/spack/spack/cmd/commands.py

@@ -743,7 +743,7 @@ def rst(args: Namespace, out: IO) -> None:
     # extract cross-refs of the form `_cmd-spack-<cmd>:` from rst files
     documented_commands: Set[str] = set()
     for filename in args.rst_files:
-        with open(filename) as f:
+        with open(filename, encoding="utf-8") as f:
             for line in f:
                 match = re.match(r"\.\. _cmd-(spack-.*):", line)
                 if match:
@@ -815,7 +815,7 @@ def prepend_header(args: Namespace, out: IO) -> None:
     if not args.header:
         return
 
-    with open(args.header) as header:
+    with open(args.header, encoding="utf-8") as header:
         out.write(header.read())
 
 
@@ -836,7 +836,7 @@ def _commands(parser: ArgumentParser, args: Namespace) -> None:
 
     if args.update:
         tty.msg(f"Updating file: {args.update}")
-        with open(args.update, "w") as f:
+        with open(args.update, "w", encoding="utf-8") as f:
             prepend_header(args, f)
             formatter(args, f)
 

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

@@ -14,7 +14,8 @@
 import spack.config
 import spack.deptypes as dt
 import spack.environment as ev
-import spack.mirror
+import spack.mirrors.mirror
+import spack.mirrors.utils
 import spack.reporters
 import spack.spec
 import spack.store
@@ -168,7 +169,7 @@ def installed_specs(args):
             else:
                 packages = []
                 for file in args.specfiles:
-                    with open(file, "r") as f:
+                    with open(file, "r", encoding="utf-8") as f:
                         s = spack.spec.Spec.from_yaml(f)
                         packages.append(s.format())
             return packages
@@ -528,6 +529,7 @@ 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")
 
 
@@ -689,31 +691,31 @@ def mirror_name_or_url(m):
 
     # If there's a \ or / in the name, it's interpreted as a path or url.
     if "/" in m or "\\" in m or m in (".", ".."):
-        return spack.mirror.Mirror(m)
+        return spack.mirrors.mirror.Mirror(m)
 
     # Otherwise, the named mirror is required to exist.
     try:
-        return spack.mirror.require_mirror_name(m)
+        return spack.mirrors.utils.require_mirror_name(m)
     except ValueError as e:
         raise argparse.ArgumentTypeError(f"{e}. Did you mean {os.path.join('.', m)}?") from e
 
 
 def mirror_url(url):
     try:
-        return spack.mirror.Mirror.from_url(url)
+        return spack.mirrors.mirror.Mirror.from_url(url)
     except ValueError as e:
         raise argparse.ArgumentTypeError(str(e)) from e
 
 
 def mirror_directory(path):
     try:
-        return spack.mirror.Mirror.from_local_path(path)
+        return spack.mirrors.mirror.Mirror.from_local_path(path)
     except ValueError as e:
         raise argparse.ArgumentTypeError(str(e)) from e
 
 
 def mirror_name(name):
     try:
-        return spack.mirror.require_mirror_name(name)
+        return spack.mirrors.utils.require_mirror_name(name)
     except ValueError as e:
         raise argparse.ArgumentTypeError(str(e)) from e

lib/spack/spack/cmd/config.py

@@ -14,6 +14,7 @@
 import spack.config
 import spack.environment as ev
 import spack.error
+import spack.schema
 import spack.schema.env
 import spack.spec
 import spack.store
@@ -566,7 +567,7 @@ def config_prefer_upstream(args):
 
     # Simply write the config to the specified file.
     existing = spack.config.get("packages", scope=scope)
-    new = spack.config.merge_yaml(existing, pkgs)
+    new = spack.schema.merge_yaml(existing, pkgs)
     spack.config.set("packages", new, scope)
     config_file = spack.config.CONFIG.get_config_filename(scope, section)
 

lib/spack/spack/cmd/create.py

@@ -110,7 +110,7 @@ def write(self, pkg_path):
         all_deps.append(self.dependencies)
 
         # Write out a template for the file
-        with open(pkg_path, "w") as pkg_file:
+        with open(pkg_path, "w", encoding="utf-8") as pkg_file:
             pkg_file.write(
                 package_template.format(
                     name=self.name,

lib/spack/spack/cmd/deprecate.py

@@ -23,9 +23,10 @@
 import spack.installer
 import spack.store
 from spack.cmd.common import arguments
-from spack.database import InstallStatuses
 from spack.error import SpackError
 
+from ..enums import InstallRecordStatus
+
 description = "replace one package with another via symlinks"
 section = "admin"
 level = "long"
@@ -95,8 +96,12 @@ def deprecate(parser, args):
     if len(specs) != 2:
         raise SpackError("spack deprecate requires exactly two specs")
 
-    install_query = [InstallStatuses.INSTALLED, InstallStatuses.DEPRECATED]
-    deprecate = spack.cmd.disambiguate_spec(specs[0], env, local=True, installed=install_query)
+    deprecate = spack.cmd.disambiguate_spec(
+        specs[0],
+        env,
+        local=True,
+        installed=(InstallRecordStatus.INSTALLED | InstallRecordStatus.DEPRECATED),
+    )
 
     if args.install:
         deprecator = specs[1].concretized()

lib/spack/spack/cmd/edit.py

@@ -76,7 +76,7 @@ def locate_package(name: str, repo: spack.repo.Repo) -> str:
     path = repo.filename_for_package_name(name)
 
     try:
-        with open(path, "r"):
+        with open(path, "r", encoding="utf-8"):
             return path
     except OSError as e:
         if e.errno == errno.ENOENT:
@@ -93,7 +93,7 @@ def locate_file(name: str, path: str) -> str:
 
     # Try to open direct match.
     try:
-        with open(file_path, "r"):
+        with open(file_path, "r", encoding="utf-8"):
             return file_path
     except OSError as e:
         if e.errno != errno.ENOENT:

lib/spack/spack/cmd/env.py

@@ -865,7 +865,7 @@ def env_loads(args):
     args.recurse_dependencies = False
 
     loads_file = fs.join_path(env.path, "loads")
-    with open(loads_file, "w") as f:
+    with open(loads_file, "w", encoding="utf-8") as f:
         specs = env._get_environment_specs(recurse_dependencies=recurse_dependencies)
 
         spack.cmd.modules.loads(module_type, specs, args, f)
@@ -1053,7 +1053,7 @@ def env_depfile(args):
 
     # Finally write to stdout/file.
     if args.output:
-        with open(args.output, "w") as f:
+        with open(args.output, "w", encoding="utf-8") as f:
             f.write(makefile)
     else:
         sys.stdout.write(makefile)

lib/spack/spack/cmd/find.py

@@ -17,7 +17,8 @@
 import spack.spec
 import spack.store
 from spack.cmd.common import arguments
-from spack.database import InstallStatuses
+
+from ..enums import InstallRecordStatus
 
 description = "list and search installed packages"
 section = "basic"
@@ -137,21 +138,22 @@ def setup_parser(subparser):
     subparser.add_argument(
         "--loaded", action="store_true", help="show only packages loaded in the user environment"
     )
-    subparser.add_argument(
+    only_missing_or_deprecated = subparser.add_mutually_exclusive_group()
+    only_missing_or_deprecated.add_argument(
         "-M",
         "--only-missing",
         action="store_true",
         dest="only_missing",
         help="show only missing dependencies",
     )
+    only_missing_or_deprecated.add_argument(
+        "--only-deprecated", action="store_true", help="show only deprecated packages"
+    )
     subparser.add_argument(
         "--deprecated",
         action="store_true",
         help="show deprecated packages as well as installed specs",
     )
-    subparser.add_argument(
-        "--only-deprecated", action="store_true", help="show only deprecated packages"
-    )
     subparser.add_argument(
         "--install-tree",
         action="store",
@@ -165,14 +167,23 @@ def setup_parser(subparser):
 
 
 def query_arguments(args):
-    # Set up query arguments.
-    installed = []
-    if not (args.only_missing or args.only_deprecated):
-        installed.append(InstallStatuses.INSTALLED)
-    if (args.deprecated or args.only_deprecated) and not args.only_missing:
-        installed.append(InstallStatuses.DEPRECATED)
-    if (args.missing or args.only_missing) and not args.only_deprecated:
-        installed.append(InstallStatuses.MISSING)
+    if args.only_missing and (args.deprecated or args.missing):
+        raise RuntimeError("cannot use --only-missing with --deprecated, or --missing")
+
+    if args.only_deprecated and (args.deprecated or args.missing):
+        raise RuntimeError("cannot use --only-deprecated with --deprecated, or --missing")
+
+    installed = InstallRecordStatus.INSTALLED
+    if args.only_missing:
+        installed = InstallRecordStatus.MISSING
+    elif args.only_deprecated:
+        installed = InstallRecordStatus.DEPRECATED
+
+    if args.missing:
+        installed |= InstallRecordStatus.MISSING
+
+    if args.deprecated:
+        installed |= InstallRecordStatus.DEPRECATED
 
     predicate_fn = None
     if args.unknown:

lib/spack/spack/cmd/gpg.py

@@ -8,7 +8,7 @@
 import tempfile
 
 import spack.binary_distribution
-import spack.mirror
+import spack.mirrors.mirror
 import spack.paths
 import spack.stage
 import spack.util.gpg
@@ -217,11 +217,11 @@ def gpg_publish(args):
     mirror = None
     if args.directory:
         url = spack.util.url.path_to_file_url(args.directory)
-        mirror = spack.mirror.Mirror(url, url)
+        mirror = spack.mirrors.mirror.Mirror(url, url)
     elif args.mirror_name:
-        mirror = spack.mirror.MirrorCollection(binary=True).lookup(args.mirror_name)
+        mirror = spack.mirrors.mirror.MirrorCollection(binary=True).lookup(args.mirror_name)
     elif args.mirror_url:
-        mirror = spack.mirror.Mirror(args.mirror_url, args.mirror_url)
+        mirror = spack.mirrors.mirror.Mirror(args.mirror_url, args.mirror_url)
 
     with tempfile.TemporaryDirectory(dir=spack.stage.get_stage_root()) as tmpdir:
         spack.binary_distribution._url_push_keys(

lib/spack/spack/cmd/help.py

@@ -78,8 +78,8 @@
       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{%pgi} @B{fabrics=psm,mrail,sock}
-          mvapich2, built with pgi compiler, with support for multiple fabrics
+      mvapich2 @g{%gcc} @B{fabrics=psm,mrail,sock}
+          mvapich2, built with gcc compiler, with support for multiple fabrics
 """
 
 

lib/spack/spack/cmd/info.py

@@ -11,6 +11,7 @@
 import llnl.util.tty.color as color
 from llnl.util.tty.colify import colify
 
+import spack.builder
 import spack.deptypes as dt
 import spack.fetch_strategy as fs
 import spack.install_test
@@ -202,11 +203,13 @@ def print_namespace(pkg, args):
 def print_phases(pkg, args):
     """output installation phases"""
 
-    if hasattr(pkg.builder, "phases") and pkg.builder.phases:
+    builder = spack.builder.create(pkg)
+
+    if hasattr(builder, "phases") and builder.phases:
         color.cprint("")
         color.cprint(section_title("Installation Phases:"))
         phase_str = ""
-        for phase in pkg.builder.phases:
+        for phase in builder.phases:
             phase_str += "    {0}".format(phase)
         color.cprint(phase_str)
 

lib/spack/spack/cmd/install.py

@@ -291,7 +291,7 @@ def _dump_log_on_error(e: InstallError):
         tty.error("'spack install' created no log.")
     else:
         sys.stderr.write("Full build log:\n")
-        with open(e.pkg.log_path, errors="replace") as log:
+        with open(e.pkg.log_path, errors="replace", encoding="utf-8") as log:
             shutil.copyfileobj(log, sys.stderr)
 
 
@@ -445,7 +445,7 @@ def concrete_specs_from_file(args):
     """Return the list of concrete specs read from files."""
     result = []
     for file in args.specfiles:
-        with open(file, "r") as f:
+        with open(file, "r", encoding="utf-8") as f:
             if file.endswith("yaml") or file.endswith("yml"):
                 s = spack.spec.Spec.from_yaml(f)
             else:

lib/spack/spack/cmd/license.py

@@ -191,7 +191,7 @@ def verify(args):
 
     for relpath in _licensed_files(args):
         path = os.path.join(args.root, relpath)
-        with open(path) as f:
+        with open(path, encoding="utf-8") as f:
             lines = [line for line in f][:license_lines]
 
         error = _check_license(lines, path)

lib/spack/spack/cmd/list.py

@@ -340,7 +340,7 @@ def list(parser, args):
                 return
 
         tty.msg("Updating file: %s" % args.update)
-        with open(args.update, "w") as f:
+        with open(args.update, "w", encoding="utf-8") as f:
             formatter(sorted_packages, f)
 
     elif args.count:

lib/spack/spack/cmd/make_installer.py

@@ -31,7 +31,7 @@ def line_to_rtf(str):
         return str.replace("\n", "\\par")
 
     contents = ""
-    with open(file_path, "r+") as f:
+    with open(file_path, "r+", encoding="utf-8") as f:
         for line in f.readlines():
             contents += line_to_rtf(line)
     return rtf_header.format(contents)
@@ -93,7 +93,7 @@ def make_installer(parser, args):
         rtf_spack_license = txt_to_rtf(spack_license)
         spack_license = posixpath.join(source_dir, "LICENSE.rtf")
 
-        with open(spack_license, "w") as rtf_license:
+        with open(spack_license, "w", encoding="utf-8") as rtf_license:
             written = rtf_license.write(rtf_spack_license)
             if written == 0:
                 raise RuntimeError("Failed to generate properly formatted license file")

lib/spack/spack/cmd/mark.py

@@ -10,7 +10,8 @@
 import spack.cmd
 import spack.store
 from spack.cmd.common import arguments
-from spack.database import InstallStatuses
+
+from ..enums import InstallRecordStatus
 
 description = "mark packages as explicitly or implicitly installed"
 section = "admin"
@@ -67,8 +68,7 @@ def find_matching_specs(specs, allow_multiple_matches=False):
     has_errors = False
 
     for spec in specs:
-        install_query = [InstallStatuses.INSTALLED]
-        matching = spack.store.STORE.db.query_local(spec, installed=install_query)
+        matching = spack.store.STORE.db.query_local(spec, installed=InstallRecordStatus.INSTALLED)
         # For each spec provided, make sure it refers to only one package.
         # Fail and ask user to be unambiguous if it doesn't
         if not allow_multiple_matches and len(matching) > 1:

lib/spack/spack/cmd/mirror.py

@@ -14,7 +14,8 @@
 import spack.concretize
 import spack.config
 import spack.environment as ev
-import spack.mirror
+import spack.mirrors.mirror
+import spack.mirrors.utils
 import spack.repo
 import spack.spec
 import spack.util.web as web_util
@@ -365,15 +366,15 @@ def mirror_add(args):
             connection["autopush"] = args.autopush
         if args.signed is not None:
             connection["signed"] = args.signed
-        mirror = spack.mirror.Mirror(connection, name=args.name)
+        mirror = spack.mirrors.mirror.Mirror(connection, name=args.name)
     else:
-        mirror = spack.mirror.Mirror(args.url, name=args.name)
-    spack.mirror.add(mirror, args.scope)
+        mirror = spack.mirrors.mirror.Mirror(args.url, name=args.name)
+    spack.mirrors.utils.add(mirror, args.scope)
 
 
 def mirror_remove(args):
     """remove a mirror by name"""
-    spack.mirror.remove(args.name, args.scope)
+    spack.mirrors.utils.remove(args.name, args.scope)
 
 
 def _configure_mirror(args):
@@ -382,7 +383,7 @@ def _configure_mirror(args):
     if args.name not in mirrors:
         tty.die(f"No mirror found with name {args.name}.")
 
-    entry = spack.mirror.Mirror(mirrors[args.name], args.name)
+    entry = spack.mirrors.mirror.Mirror(mirrors[args.name], args.name)
     direction = "fetch" if args.fetch else "push" if args.push else None
     changes = {}
     if args.url:
@@ -449,7 +450,7 @@ def mirror_set_url(args):
 def mirror_list(args):
     """print out available mirrors to the console"""
 
-    mirrors = spack.mirror.MirrorCollection(scope=args.scope)
+    mirrors = spack.mirrors.mirror.MirrorCollection(scope=args.scope)
     if not mirrors:
         tty.msg("No mirrors configured.")
         return
@@ -467,7 +468,7 @@ def specs_from_text_file(filename, concretize=False):
         concretize (bool): if True concretize the specs before returning
             the list.
     """
-    with open(filename, "r") as f:
+    with open(filename, "r", encoding="utf-8") as f:
         specs_in_file = f.readlines()
         specs_in_file = [s.strip() for s in specs_in_file]
     return spack.cmd.parse_specs(" ".join(specs_in_file), concretize=concretize)
@@ -489,9 +490,9 @@ def concrete_specs_from_user(args):
 
 def extend_with_additional_versions(specs, num_versions):
     if num_versions == "all":
-        mirror_specs = spack.mirror.get_all_versions(specs)
+        mirror_specs = spack.mirrors.utils.get_all_versions(specs)
     else:
-        mirror_specs = spack.mirror.get_matching_versions(specs, num_versions=num_versions)
+        mirror_specs = spack.mirrors.utils.get_matching_versions(specs, num_versions=num_versions)
     mirror_specs = [x.concretized() for x in mirror_specs]
     return mirror_specs
 
@@ -570,7 +571,7 @@ def concrete_specs_from_environment():
 
 def all_specs_with_all_versions():
     specs = [spack.spec.Spec(n) for n in spack.repo.all_package_names()]
-    mirror_specs = spack.mirror.get_all_versions(specs)
+    mirror_specs = spack.mirrors.utils.get_all_versions(specs)
     mirror_specs.sort(key=lambda s: (s.name, s.version))
     return mirror_specs
 
@@ -659,19 +660,21 @@ def _specs_and_action(args):
 
 
 def create_mirror_for_all_specs(mirror_specs, path, skip_unstable_versions):
-    mirror_cache, mirror_stats = spack.mirror.mirror_cache_and_stats(
+    mirror_cache, mirror_stats = spack.mirrors.utils.mirror_cache_and_stats(
         path, skip_unstable_versions=skip_unstable_versions
     )
     for candidate in mirror_specs:
         pkg_cls = spack.repo.PATH.get_pkg_class(candidate.name)
         pkg_obj = pkg_cls(spack.spec.Spec(candidate))
         mirror_stats.next_spec(pkg_obj.spec)
-        spack.mirror.create_mirror_from_package_object(pkg_obj, mirror_cache, mirror_stats)
+        spack.mirrors.utils.create_mirror_from_package_object(pkg_obj, mirror_cache, mirror_stats)
     process_mirror_stats(*mirror_stats.stats())
 
 
 def create_mirror_for_individual_specs(mirror_specs, path, skip_unstable_versions):
-    present, mirrored, error = spack.mirror.create(path, mirror_specs, skip_unstable_versions)
+    present, mirrored, error = spack.mirrors.utils.create(
+        path, mirror_specs, skip_unstable_versions
+    )
     tty.msg("Summary for mirror in {}".format(path))
     process_mirror_stats(present, mirrored, error)
 
@@ -681,7 +684,7 @@ def mirror_destroy(args):
     mirror_url = None
 
     if args.mirror_name:
-        result = spack.mirror.MirrorCollection().lookup(args.mirror_name)
+        result = spack.mirrors.mirror.MirrorCollection().lookup(args.mirror_name)
         mirror_url = result.push_url
     elif args.mirror_url:
         mirror_url = args.mirror_url

lib/spack/spack/cmd/modules/lmod.py

@@ -8,6 +8,7 @@
 import spack.cmd.common.arguments
 import spack.cmd.modules
 import spack.config
+import spack.modules
 import spack.modules.lmod
 
 

lib/spack/spack/cmd/modules/tcl.py

@@ -7,6 +7,7 @@
 import spack.cmd.common.arguments
 import spack.cmd.modules
 import spack.config
+import spack.modules
 import spack.modules.tcl
 
 

lib/spack/spack/cmd/pkg.py

@@ -150,7 +150,7 @@ def pkg_source(args):
         content = ph.canonical_source(spec)
     else:
         message = "Source for %s:" % filename
-        with open(filename) as f:
+        with open(filename, encoding="utf-8") as f:
             content = f.read()
 
     if sys.stdout.isatty():

lib/spack/spack/cmd/python.py

@@ -94,7 +94,7 @@ def ipython_interpreter(args):
     if "PYTHONSTARTUP" in os.environ:
         startup_file = os.environ["PYTHONSTARTUP"]
         if os.path.isfile(startup_file):
-            with open(startup_file) as startup:
+            with open(startup_file, encoding="utf-8") as startup:
                 exec(startup.read())
 
     # IPython can also support running a script OR command, not both
@@ -126,7 +126,7 @@ def python_interpreter(args):
         if "PYTHONSTARTUP" in os.environ:
             startup_file = os.environ["PYTHONSTARTUP"]
             if os.path.isfile(startup_file):
-                with open(startup_file) as startup:
+                with open(startup_file, encoding="utf-8") as startup:
                     console.runsource(startup.read(), startup_file, "exec")
         if args.python_command:
             propagate_exceptions_from(console)

lib/spack/spack/cmd/spec.py

@@ -82,14 +82,6 @@ def spec(parser, args):
     if args.namespaces:
         fmt = "{namespace}." + fmt
 
-    tree_kwargs = {
-        "cover": args.cover,
-        "format": fmt,
-        "hashlen": None if args.very_long else 7,
-        "show_types": args.types,
-        "status_fn": install_status_fn if args.install_status else None,
-    }
-
     # use a read transaction if we are getting install status for every
     # spec in the DAG.  This avoids repeatedly querying the DB.
     tree_context = lang.nullcontext
@@ -99,46 +91,35 @@ def spec(parser, args):
     env = ev.active_environment()
 
     if args.specs:
-        input_specs = spack.cmd.parse_specs(args.specs)
-        concretized_specs = spack.cmd.parse_specs(args.specs, concretize=True)
-        specs = list(zip(input_specs, concretized_specs))
+        concrete_specs = spack.cmd.parse_specs(args.specs, concretize=True)
     elif env:
         env.concretize()
-        specs = env.concretized_specs()
-
-        if not args.format:
-            # environments are printed together in a combined tree() invocation,
-            # except when using --yaml or --json, which we print spec by spec below.
-            tree_kwargs["key"] = spack.traverse.by_dag_hash
-            tree_kwargs["hashes"] = args.long or args.very_long
-            print(spack.spec.tree([concrete for _, concrete in specs], **tree_kwargs))
-            return
+        concrete_specs = env.concrete_roots()
     else:
         tty.die("spack spec requires at least one spec or an active environment")
 
-    for input, output in specs:
-        # With --yaml or --json, just print the raw specs to output
-        if args.format:
+    # With --yaml, --json, or --format, just print the raw specs to output
+    if args.format:
+        for spec in concrete_specs:
             if args.format == "yaml":
                 # use write because to_yaml already has a newline.
-                sys.stdout.write(output.to_yaml(hash=ht.dag_hash))
+                sys.stdout.write(spec.to_yaml(hash=ht.dag_hash))
             elif args.format == "json":
-                print(output.to_json(hash=ht.dag_hash))
+                print(spec.to_json(hash=ht.dag_hash))
             else:
-                print(output.format(args.format))
-            continue
+                print(spec.format(args.format))
+        return
 
-        with tree_context():
-            # Only show the headers for input specs that are not concrete to avoid
-            # repeated output. This happens because parse_specs outputs concrete
-            # specs for `/hash` inputs.
-            if not input.concrete:
-                tree_kwargs["hashes"] = False  # Always False for input spec
-                print("Input spec")
-                print("--------------------------------")
-                print(input.tree(**tree_kwargs))
-                print("Concretized")
-                print("--------------------------------")
-
-            tree_kwargs["hashes"] = args.long or args.very_long
-            print(output.tree(**tree_kwargs))
+    with tree_context():
+        print(
+            spack.spec.tree(
+                concrete_specs,
+                cover=args.cover,
+                format=fmt,
+                hashlen=None if args.very_long else 7,
+                show_types=args.types,
+                status_fn=install_status_fn if args.install_status else None,
+                hashes=args.long or args.very_long,
+                key=spack.traverse.by_dag_hash,
+            )
+        )

lib/spack/spack/cmd/stage.py

@@ -19,11 +19,48 @@
 level = "long"
 
 
+class StageFilter:
+    """
+    Encapsulation of reasons to skip staging
+    """
+
+    def __init__(self, exclusions, skip_installed):
+        """
+        :param exclusions: A list of specs to skip if satisfied.
+        :param skip_installed: A boolean indicating whether to skip already installed specs.
+        """
+        self.exclusions = exclusions
+        self.skip_installed = skip_installed
+
+    def __call__(self, spec):
+        """filter action, true means spec should be filtered"""
+        if spec.external:
+            return True
+
+        if self.skip_installed and spec.installed:
+            return True
+
+        if any(spec.satisfies(exclude) for exclude in self.exclusions):
+            return True
+
+        return False
+
+
 def setup_parser(subparser):
     arguments.add_common_arguments(subparser, ["no_checksum", "specs"])
     subparser.add_argument(
         "-p", "--path", dest="path", help="path to stage package, does not add to spack tree"
     )
+    subparser.add_argument(
+        "-e",
+        "--exclude",
+        action="append",
+        default=[],
+        help="exclude packages that satisfy the specified specs",
+    )
+    subparser.add_argument(
+        "-s", "--skip-installed", action="store_true", help="dont restage already installed specs"
+    )
     arguments.add_concretizer_args(subparser)
 
 
@@ -31,11 +68,14 @@ def stage(parser, args):
     if args.no_checksum:
         spack.config.set("config:checksum", False, scope="command_line")
 
+    exclusion_specs = spack.cmd.parse_specs(args.exclude, concretize=False)
+    filter = StageFilter(exclusion_specs, args.skip_installed)
+
     if not args.specs:
         env = ev.active_environment()
         if not env:
             tty.die("`spack stage` requires a spec or an active environment")
-        return _stage_env(env)
+        return _stage_env(env, filter)
 
     specs = spack.cmd.parse_specs(args.specs, concretize=False)
 
@@ -49,6 +89,11 @@ def stage(parser, args):
 
     specs = spack.cmd.matching_specs_from_env(specs)
     for spec in specs:
+        spec = spack.cmd.matching_spec_from_env(spec)
+
+        if filter(spec):
+            continue
+
         pkg = spec.package
 
         if custom_path:
@@ -57,9 +102,13 @@ def stage(parser, args):
         _stage(pkg)
 
 
-def _stage_env(env: ev.Environment):
+def _stage_env(env: ev.Environment, filter):
     tty.msg(f"Staging specs from environment {env.name}")
     for spec in spack.traverse.traverse_nodes(env.concrete_roots()):
+
+        if filter(spec):
+            continue
+
         _stage(spec.package)
 
 

lib/spack/spack/cmd/style.py

@@ -3,18 +3,21 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import argparse
+import ast
 import os
 import re
 import sys
 from itertools import zip_longest
+from typing import Dict, List, Optional
 
 import llnl.util.tty as tty
 import llnl.util.tty.color as color
 from llnl.util.filesystem import working_dir
 
 import spack.paths
+import spack.repo
 import spack.util.git
-from spack.util.executable import which
+from spack.util.executable import Executable, which
 
 description = "runs source code style checks on spack"
 section = "developer"
@@ -36,10 +39,7 @@ def grouper(iterable, n, fillvalue=None):
 #: double-check the results of other tools (if, e.g., --fix was provided)
 #: The list maps an executable name to a method to ensure the tool is
 #: bootstrapped or present in the environment.
-tool_names = ["isort", "black", "flake8", "mypy"]
-
-#: tools we run in spack style
-tools = {}
+tool_names = ["import", "isort", "black", "flake8", "mypy"]
 
 #: warnings to ignore in mypy
 mypy_ignores = [
@@ -61,14 +61,28 @@ def is_package(f):
 
 #: decorator for adding tools to the list
 class tool:
-    def __init__(self, name, required=False):
+    def __init__(self, name: str, required: bool = False, external: bool = True) -> None:
         self.name = name
+        self.external = external
         self.required = required
 
     def __call__(self, fun):
-        tools[self.name] = (fun, self.required)
+        self.fun = fun
+        tools[self.name] = self
         return fun
 
+    @property
+    def installed(self) -> bool:
+        return bool(which(self.name)) if self.external else True
+
+    @property
+    def executable(self) -> Optional[Executable]:
+        return which(self.name) if self.external else None
+
+
+#: tools we run in spack style
+tools: Dict[str, tool] = {}
+
 
 def changed_files(base="develop", untracked=True, all_files=False, root=None):
     """Get list of changed files in the Spack repository.
@@ -176,22 +190,22 @@ def setup_parser(subparser):
         "-t",
         "--tool",
         action="append",
-        help="specify which tools to run (default: %s)" % ",".join(tool_names),
+        help="specify which tools to run (default: %s)" % ", ".join(tool_names),
     )
     tool_group.add_argument(
         "-s",
         "--skip",
         metavar="TOOL",
         action="append",
-        help="specify tools to skip (choose from %s)" % ",".join(tool_names),
+        help="specify tools to skip (choose from %s)" % ", ".join(tool_names),
     )
 
     subparser.add_argument("files", nargs=argparse.REMAINDER, help="specific files to check")
 
 
-def cwd_relative(path, args):
+def cwd_relative(path, root, initial_working_dir):
     """Translate prefix-relative path to current working directory-relative."""
-    return os.path.relpath(os.path.join(args.root, path), args.initial_working_dir)
+    return os.path.relpath(os.path.join(root, path), initial_working_dir)
 
 
 def rewrite_and_print_output(
@@ -201,7 +215,10 @@ def rewrite_and_print_output(
 
     # print results relative to current working directory
     def translate(match):
-        return replacement.format(cwd_relative(match.group(1), args), *list(match.groups()[1:]))
+        return replacement.format(
+            cwd_relative(match.group(1), args.root, args.initial_working_dir),
+            *list(match.groups()[1:]),
+        )
 
     for line in output.split("\n"):
         if not line:
@@ -220,7 +237,7 @@ def print_style_header(file_list, args, tools_to_run):
     # translate modified paths to cwd_relative if needed
     paths = [filename.strip() for filename in file_list]
     if not args.root_relative:
-        paths = [cwd_relative(filename, args) for filename in paths]
+        paths = [cwd_relative(filename, args.root, args.initial_working_dir) for filename in paths]
 
     tty.msg("Modified files", *paths)
     sys.stdout.flush()
@@ -306,8 +323,6 @@ def process_files(file_list, is_args):
             rewrite_and_print_output(output, args, pat, replacement)
 
     packages_isort_args = (
-        "--rm",
-        "spack",
         "--rm",
         "spack.pkgkit",
         "--rm",
@@ -352,17 +367,137 @@ def run_black(black_cmd, file_list, args):
     return returncode
 
 
+def _module_part(root: str, expr: str):
+    parts = expr.split(".")
+    # spack.pkg is for repositories, don't try to resolve it here.
+    if ".".join(parts[:2]) == spack.repo.ROOT_PYTHON_NAMESPACE:
+        return None
+    while parts:
+        f1 = os.path.join(root, "lib", "spack", *parts) + ".py"
+        f2 = os.path.join(root, "lib", "spack", *parts, "__init__.py")
+
+        if (
+            os.path.exists(f1)
+            # ensure case sensitive match
+            and f"{parts[-1]}.py" in os.listdir(os.path.dirname(f1))
+            or os.path.exists(f2)
+        ):
+            return ".".join(parts)
+        parts.pop()
+    return None
+
+
+def _run_import_check(
+    file_list: List[str],
+    *,
+    fix: bool,
+    root_relative: bool,
+    root=spack.paths.prefix,
+    working_dir=spack.paths.prefix,
+    out=sys.stdout,
+):
+    if sys.version_info < (3, 9):
+        print("import check requires Python 3.9 or later")
+        return 0
+
+    is_use = re.compile(r"(?<!from )(?<!import )(?:llnl|spack)\.[a-zA-Z0-9_\.]+")
+
+    # redundant imports followed by a `# comment` are ignored, cause there can be legimitate reason
+    # to import a module: execute module scope init code, or to deal with circular imports.
+    is_abs_import = re.compile(r"^import ((?:llnl|spack)\.[a-zA-Z0-9_\.]+)$", re.MULTILINE)
+
+    exit_code = 0
+
+    for file in file_list:
+        to_add = set()
+        to_remove = []
+
+        pretty_path = file if root_relative else cwd_relative(file, root, working_dir)
+
+        try:
+            with open(file, "r", encoding="utf-8") as f:
+                contents = f.read()
+            parsed = ast.parse(contents)
+        except Exception:
+            exit_code = 1
+            print(f"{pretty_path}: could not parse", file=out)
+            continue
+
+        for m in is_abs_import.finditer(contents):
+            if contents.count(m.group(1)) == 1:
+                to_remove.append(m.group(0))
+                exit_code = 1
+                print(f"{pretty_path}: redundant import: {m.group(1)}", file=out)
+
+        # Clear all strings to avoid matching comments/strings etc.
+        for node in ast.walk(parsed):
+            if isinstance(node, ast.Constant) and isinstance(node.value, str):
+                node.value = ""
+
+        filtered_contents = ast.unparse(parsed)  # novermin
+        for m in is_use.finditer(filtered_contents):
+            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):
+                continue
+            to_add.add(module)
+            exit_code = 1
+            print(f"{pretty_path}: missing import: {module} ({m.group(0)})", file=out)
+
+        if not fix or not to_add and not to_remove:
+            continue
+
+        with open(file, "r", encoding="utf-8") as f:
+            lines = f.readlines()
+
+        if to_add:
+            # insert missing imports before the first import, delegate ordering to isort
+            for node in parsed.body:
+                if isinstance(node, (ast.Import, ast.ImportFrom)):
+                    first_line = node.lineno
+                    break
+            else:
+                print(f"{pretty_path}: could not fix", file=out)
+                continue
+            lines.insert(first_line, "\n".join(f"import {x}" for x in to_add) + "\n")
+
+        new_contents = "".join(lines)
+
+        # remove redundant imports
+        for statement in to_remove:
+            new_contents = new_contents.replace(f"{statement}\n", "")
+
+        with open(file, "w", encoding="utf-8") as f:
+            f.write(new_contents)
+
+    return exit_code
+
+
+@tool("import", external=False)
+def run_import_check(import_check_cmd, file_list, args):
+    exit_code = _run_import_check(
+        file_list,
+        fix=args.fix,
+        root_relative=args.root_relative,
+        root=args.root,
+        working_dir=args.initial_working_dir,
+    )
+    print_tool_result("import", exit_code)
+    return exit_code
+
+
 def validate_toolset(arg_value):
     """Validate --tool and --skip arguments (sets of optionally comma-separated tools)."""
     tools = set(",".join(arg_value).split(","))  # allow args like 'isort,flake8'
     for tool in tools:
         if tool not in tool_names:
-            tty.die("Invaild tool: '%s'" % tool, "Choose from: %s" % ", ".join(tool_names))
+            tty.die("Invalid tool: '%s'" % tool, "Choose from: %s" % ", ".join(tool_names))
     return tools
 
 
-def missing_tools(tools_to_run):
-    return [t for t in tools_to_run if which(t) is None]
+def missing_tools(tools_to_run: List[str]) -> List[str]:
+    return [t for t in tools_to_run if not tools[t].installed]
 
 
 def _bootstrap_dev_dependencies():
@@ -417,9 +552,9 @@ def prefix_relative(path):
 
         print_style_header(file_list, args, tools_to_run)
         for tool_name in tools_to_run:
-            run_function, required = tools[tool_name]
+            tool = tools[tool_name]
             print_tool_header(tool_name)
-            return_code |= run_function(which(tool_name), file_list, args)
+            return_code |= tool.fun(tool.executable, file_list, args)
 
     if return_code == 0:
         tty.msg(color.colorize("@*{spack style checks were clean}"))

lib/spack/spack/cmd/test.py

@@ -346,7 +346,7 @@ def _report_suite_results(test_suite, args, constraints):
         tty.msg("{0} for test suite '{1}'{2}:".format(results_desc, test_suite.name, matching))
 
         results = {}
-        with open(test_suite.results_file, "r") as f:
+        with open(test_suite.results_file, "r", encoding="utf-8") as f:
             for line in f:
                 pkg_id, status = line.split()
                 results[pkg_id] = status
@@ -371,7 +371,7 @@ def _report_suite_results(test_suite, args, constraints):
                     spec = test_specs[pkg_id]
                     log_file = test_suite.log_file_for_spec(spec)
                     if os.path.isfile(log_file):
-                        with open(log_file, "r") as f:
+                        with open(log_file, "r", encoding="utf-8") as f:
                             msg += "\n{0}".format("".join(f.readlines()))
                 tty.msg(msg)