builtin: add missing commit= to git versions

Signed-off-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

.github/workflows/build-containers.yml

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

.github/workflows/ci.yaml

@@ -81,6 +81,10 @@ jobs:
     with:
       with_coverage: ${{ needs.changes.outputs.core }}
 
+  import-check:
+    needs: [ changes ]
+    uses: ./.github/workflows/import-check.yaml
+
   all-prechecks:
     needs: [ prechecks ]
     if: ${{ always() }}

.github/workflows/coverage.yml

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

.github/workflows/import-check.yaml

@@ -0,0 +1,49 @@
+name: import-check
+
+on:
+  workflow_call:
+
+jobs:
+  # Check we don't make the situation with circular imports worse
+  import-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: julia-actions/setup-julia@v2
+      with:
+        version: '1.10'
+    - uses: julia-actions/cache@v2
+
+    # PR: use the base of the PR as the old commit
+    - name: Checkout PR base commit
+      if: github.event_name == 'pull_request'
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+      with:
+        ref: ${{ github.event.pull_request.base.sha }}
+        path: old
+    # not a PR: use the previous commit as the old commit
+    - name: Checkout previous commit
+      if: github.event_name != 'pull_request'
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+      with:
+        fetch-depth: 2
+        path: old
+    - name: Checkout previous commit
+      if: github.event_name != 'pull_request'
+      run: git -C old reset --hard HEAD^
+
+    - name: Checkout new commit
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+      with:
+        path: new
+    - name: Install circular import checker
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
+      with:
+        repository: haampie/circular-import-fighter
+        ref: 4cdb0bf15f04ab6b49041d5ef1bfd9644cce7f33
+        path: circular-import-fighter
+    - name: Install dependencies
+      working-directory: circular-import-fighter
+      run: make -j dependencies
+    - name: Circular import check
+      working-directory: circular-import-fighter
+      run: make -j compare "SPACK_ROOT=../old ../new"

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

@@ -1,7 +1,7 @@
-black==24.10.0
+black==25.1.0
 clingo==5.7.1
-flake8==7.1.1
+flake8==7.1.2
-isort==5.13.2
+isort==6.0.1
-mypy==1.11.2
+mypy==1.15.0
-types-six==1.17.0.20241205
+types-six==1.17.0.20250304
 vermin==1.6.0

.github/workflows/valid-style.yml

@@ -86,66 +86,6 @@ jobs:
           spack -d bootstrap now --dev
           spack -d style -t black
           spack unit-test -V
-  # Check we don't make the situation with circular imports worse
-  import-check:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: julia-actions/setup-julia@v2
-      with:
-        version: '1.10'
-    - uses: julia-actions/cache@v2
-
-    # PR: use the base of the PR as the old commit
-    - name: Checkout PR base commit
-      if: github.event_name == 'pull_request'
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        ref: ${{ github.event.pull_request.base.sha }}
-        path: old
-    # not a PR: use the previous commit as the old commit
-    - name: Checkout previous commit
-      if: github.event_name != 'pull_request'
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        fetch-depth: 2
-        path: old
-    - name: Checkout previous commit
-      if: github.event_name != 'pull_request'
-      run: git -C old reset --hard HEAD^
-
-    - name: Checkout new commit
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        path: new
-    - name: Install circular import checker
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        repository: haampie/circular-import-fighter
-        ref: b5d6ce9be35f602cca7d5a6aa0259fca10639cca
-        path: circular-import-fighter
-    - name: Install dependencies
-      working-directory: circular-import-fighter
-      run: make -j dependencies
-    - name: Problematic imports before
-      working-directory: circular-import-fighter
-      run: make SPACK_ROOT=../old SUFFIX=.old
-    - name: Problematic imports after
-      working-directory: circular-import-fighter
-      run: make SPACK_ROOT=../new SUFFIX=.new
-    - name: Compare import cycles
-      working-directory: circular-import-fighter
-      run: |
-        edges_before="$(head -n1 solution.old)"
-        edges_after="$(head -n1 solution.new)"
-        if [ "$edges_after" -gt "$edges_before" ]; then
-          printf '\033[1;31mImport check failed: %s imports need to be deleted, ' "$edges_after"
-          printf 'previously this was %s\033[0m\n'  "$edges_before"
-          printf 'Compare \033[1;97m"Problematic imports before"\033[0m and '
-          printf '\033[1;97m"Problematic imports after"\033[0m.\n'
-          exit 1
-        else
-          printf '\033[1;32mImport check passed: %s <= %s\033[0m\n' "$edges_after" "$edges_before"
-        fi
 
   # Further style checks from pylint
   pylint:

.gitignore

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

bin/spack

@@ -25,7 +25,6 @@ exit 1
 # The code above runs this file with our preferred python interpreter.
 
 import os
-import os.path
 import sys
 
 min_python3 = (3, 6)

etc/spack/defaults/concretizer.yaml

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

etc/spack/defaults/packages.yaml

@@ -36,7 +36,7 @@ packages:
       go-or-gccgo-bootstrap: [go-bootstrap, gcc]
       iconv: [libiconv]
       ipp: [intel-oneapi-ipp]
-      java: [openjdk, jdk, ibm-java]
+      java: [openjdk, jdk]
       jpeg: [libjpeg-turbo, libjpeg]
       lapack: [openblas, amdlibflame]
       libc: [glibc, musl]
@@ -73,15 +73,27 @@ packages:
     permissions:
       read: world
       write: user
+  cray-fftw:
+    buildable: false
+  cray-libsci:
+    buildable: false
   cray-mpich:
     buildable: false
   cray-mvapich2:
     buildable: false
+  cray-pmi:
+    buildable: false
   egl:
     buildable: false
+  essl:
+    buildable: false
   fujitsu-mpi:
     buildable: false
+  fujitsu-ssl2:
+    buildable: false
   hpcx-mpi:
     buildable: false
+  mpt:
+    buildable: false
   spectrum-mpi:
     buildable: false

etc/spack/defaults/windows/config.yaml

@@ -1,5 +1,5 @@
 config:
   locks: false
   build_stage::
-    - '$spack/.staging'
+    - '$user_cache_path/stage'
   stage_name: '{name}-{version}-{hash:7}'

lib/spack/docs/basic_usage.rst

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

lib/spack/docs/bootstrapping.rst

@@ -170,7 +170,7 @@ bootstrapping.
    To register the mirror on the platform where it's supposed to be used run the following command(s):
      % spack bootstrap add --trust local-sources /opt/bootstrap/metadata/sources
      % spack bootstrap add --trust local-binaries /opt/bootstrap/metadata/binaries
-
+     % spack buildcache update-index /opt/bootstrap/bootstrap_cache
 
 This command needs to be run on a machine with internet access and the resulting folder
 has to be moved over to the air-gapped system. Once the local sources are added using the

lib/spack/docs/build_systems/autotoolspackage.rst

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

lib/spack/docs/build_systems/custompackage.rst

@@ -56,13 +56,13 @@ If you look at the ``perl`` package, you'll see:
 
 .. code-block:: python
 
-   phases = ["configure", "build", "install"]
+   phases = ("configure", "build", "install")
 
 Similarly, ``cmake`` defines:
 
 .. code-block:: python
 
-   phases = ["bootstrap", "build", "install"]
+   phases = ("bootstrap", "build", "install")
 
 If we look at the ``cmake`` example, this tells Spack's ``PackageBase``
 class to run the ``bootstrap``, ``build``, and ``install`` functions

lib/spack/docs/conf.py

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

lib/spack/docs/config_yaml.rst

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

lib/spack/docs/configuration.rst

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

lib/spack/docs/contribution_guide.rst

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

lib/spack/docs/environments.rst

@@ -112,6 +112,19 @@ the original but may concretize differently in the presence of different
 explicit or default configuration settings (e.g., a different version of
 Spack or for a different user account).
 
+Environments created from a manifest will copy any included configs
+from relative paths inside the environment. Relative paths from
+outside the environment will cause errors, and absolute paths will be
+kept absolute. For example, if ``spack.yaml`` includes:
+
+.. code-block:: yaml
+
+   spack:
+     include: [./config.yaml]
+
+then the created environment will have its own copy of the file
+``config.yaml`` copied from the location in the original environment.
+
 Create an environment from a ``spack.lock`` file using:
 
 .. code-block:: console
@@ -160,7 +173,7 @@ accepts.  If an environment already exists then spack will simply activate it
 and ignore the create-specific flags.
 
 .. code-block:: console
-   
+
    $ spack env activate --create -p myenv
    # ...
    # [creates if myenv does not exist yet]
@@ -424,8 +437,8 @@ Developing Packages in a Spack Environment
 
 The ``spack develop`` command allows one to develop Spack packages in
 an environment. It requires a spec containing a concrete version, and
-will configure Spack to install the package from local source. 
+will configure Spack to install the package from local source.
-If a version is not provided from the command line interface then spack 
+If a version is not provided from the command line interface then spack
 will automatically pick the highest version the package has defined.
 This means any infinity versions (``develop``, ``main``, ``stable``) will be
 preferred in this selection process.
@@ -435,9 +448,9 @@ set, and Spack will ensure the package and its dependents are rebuilt
 any time the environment is installed if the package's local source
 code has been modified. Spack's native implementation to check for modifications
 is to check if ``mtime`` is newer than the installation.
-A custom check can be created by overriding the ``detect_dev_src_change`` method 
+A custom check can be created by overriding the ``detect_dev_src_change`` method
-in your package class. This is particularly useful for projects using custom spack repo's 
+in your package class. This is particularly useful for projects using custom spack repo's
-to drive development and want to optimize performance. 
+to drive development and want to optimize performance.
 
 Spack ensures that all instances of a
 developed package in the environment are concretized to match the
@@ -453,7 +466,7 @@ Further development on ``foo`` can be tested by re-installing the environment,
 and eventually committed and pushed to the upstream git repo.
 
 If the package being developed supports out-of-source builds then users can use the
-``--build_directory`` flag to control the location and name of the build directory. 
+``--build_directory`` flag to control the location and name of the build directory.
 This is a shortcut to set the ``package_attributes:build_directory`` in the
 ``packages`` configuration (see :ref:`assigning-package-attributes`).
 The supplied location will become the build-directory for that package in all future builds.
@@ -657,24 +670,45 @@ This configuration sets the default compiler for all packages to
 Included configurations
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-Spack environments allow an ``include`` heading in their yaml
+Spack environments allow an ``include`` heading in their yaml schema.
-schema. This heading pulls in external configuration files and applies
+This heading pulls in external configuration files and applies them to
-them to the environment.
+the environment.
 
 .. code-block:: yaml
 
    spack:
      include:
-     - relative/path/to/config.yaml
+     - environment/relative/path/to/config.yaml
      - https://github.com/path/to/raw/config/compilers.yaml
      - /absolute/path/to/packages.yaml
+     - path: /path/to/$os/$target/environment
+       optional: true
+     - path: /path/to/os-specific/config-dir
+       when: os == "ventura"
+
+Included configuration files are required *unless* they are explicitly optional
+or the entry's condition evaluates to ``false``. Optional includes are specified
+with the ``optional`` clause and conditional with the ``when`` clause. (See
+:ref:`include-yaml` for more information on optional and conditional entries.)
+
+Files are listed using paths to individual files or directories containing them.
+Path entries may be absolute or relative to the environment or specified as 
+URLs. URLs to individual files need link to the **raw** form of the file's 
+contents (e.g., `GitHub
+<https://docs.github.com/en/repositories/working-with-files/using-files/viewing-and-understanding-files#viewing-or-copying-the-raw-file-content>`_ 
+or `GitLab
+<https://docs.gitlab.com/ee/api/repository_files.html#get-raw-file-from-repository>`_).
+Only the ``file``, ``ftp``, ``http`` and ``https`` protocols (or schemes) are
+supported. Spack-specific, environment and user path variables can be used.
+(See :ref:`config-file-variables` for more information.)
+
+.. warning::
+
+   Recursive includes are not currently processed in a breadth-first manner
+   so the value of a configuration option that is altered by multiple included
+   files may not be what you expect. This will be addressed in a future
+   update.
 
-Environments can include files or URLs. File paths can be relative or
-absolute. URLs include the path to the text for individual files or
-can be the path to a directory containing configuration files.
-Spack supports ``file``, ``http``, ``https`` and ``ftp`` protocols (or
-schemes). Spack-specific, environment and user path variables may be
-used in these paths. See :ref:`config-file-variables` for more information.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^
 Configuration precedence

lib/spack/docs/include_yaml.rst

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

lib/spack/docs/index.rst

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

lib/spack/docs/pipelines.rst

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

lib/spack/docs/requirements.txt

@@ -1,13 +1,13 @@
-sphinx==8.1.3
+sphinx==8.2.3
 sphinxcontrib-programoutput==0.18
 sphinx_design==0.6.1
 sphinx-rtd-theme==3.0.2
-python-levenshtein==0.26.1
+python-levenshtein==0.27.1
 docutils==0.21.2
 pygments==2.19.1
 urllib3==2.3.0
-pytest==8.3.4
+pytest==8.3.5
-isort==5.13.2
+isort==6.0.1
-black==24.10.0
+black==25.1.0
-flake8==7.1.1
+flake8==7.1.2
 mypy==1.11.1

lib/spack/llnl/url.py

@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """URL primitives that just require Python standard library."""
 import itertools
-import os.path
+import os
 import re
 from typing import Optional, Set, Tuple
 from urllib.parse import urlsplit, urlunsplit

lib/spack/llnl/util/filesystem.py

@@ -7,6 +7,7 @@
 import fnmatch
 import glob
 import hashlib
+import io
 import itertools
 import numbers
 import os
@@ -20,6 +21,7 @@
 from contextlib import contextmanager
 from itertools import accumulate
 from typing import (
+    IO,
     Callable,
     Deque,
     Dict,
@@ -668,7 +670,7 @@ def copy(src, dest, _permissions=False):
         _permissions (bool): for internal use only
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* matches multiple files but *dest* is
             not a directory
     """
@@ -679,7 +681,7 @@ def copy(src, dest, _permissions=False):
 
     files = glob.glob(src)
     if not files:
-        raise IOError("No such file or directory: '{0}'".format(src))
+        raise OSError("No such file or directory: '{0}'".format(src))
     if len(files) > 1 and not os.path.isdir(dest):
         raise ValueError(
             "'{0}' matches multiple files but '{1}' is not a directory".format(src, dest)
@@ -710,7 +712,7 @@ def install(src, dest):
         dest (str): the destination file or directory
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* matches multiple files but *dest* is
             not a directory
     """
@@ -748,7 +750,7 @@ def copy_tree(
         _permissions (bool): for internal use only
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* is a parent directory of *dest*
     """
     if _permissions:
@@ -762,7 +764,7 @@ def copy_tree(
 
     files = glob.glob(src)
     if not files:
-        raise IOError("No such file or directory: '{0}'".format(src))
+        raise OSError("No such file or directory: '{0}'".format(src))
 
     # For Windows hard-links and junctions, the source path must exist to make a symlink. Add
     # all symlinks to this list while traversing the tree, then when finished, make all
@@ -843,7 +845,7 @@ def install_tree(src, dest, symlinks=True, ignore=None):
         ignore (typing.Callable): function indicating which files to ignore
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* is a parent directory of *dest*
     """
     copy_tree(src, dest, symlinks=symlinks, ignore=ignore, _permissions=True)
@@ -1472,7 +1474,7 @@ def set_executable(path):
 def recursive_mtime_greater_than(path: str, time: float) -> bool:
     """Returns true if any file or dir recursively under `path` has mtime greater than `time`."""
     # use bfs order to increase likelihood of early return
-    queue: Deque[str] = collections.deque()
+    queue: Deque[str] = collections.deque([path])
 
     if os.stat(path).st_mtime > time:
         return True
@@ -2454,26 +2456,69 @@ class WindowsSimulatedRPath:
     and vis versa.
     """
 
-    def __init__(self, package, link_install_prefix=True):
+    def __init__(
+        self,
+        package,
+        base_modification_prefix: Optional[Union[str, pathlib.Path]] = None,
+        link_install_prefix: bool = True,
+    ):
         """
         Args:
             package (spack.package_base.PackageBase): Package requiring links
+            base_modification_prefix (str|pathlib.Path): Path representation indicating
+                the root directory in which to establish the simulated rpath, ie where the
+                symlinks that comprise the "rpath" behavior will be installed.
+
+                Note: This is a mutually exclusive option with `link_install_prefix` using
+                both is an error.
+
+                Default: None
             link_install_prefix (bool): Link against package's own install or stage root.
                 Packages that run their own executables during build and require rpaths to
-                the build directory during build time require this option. Default: install
+                the build directory during build time require this option.
+
+                Default: install
                 root
+
+                Note: This is a mutually exclusive option with `base_modification_prefix`, using
+                both is an error.
         """
         self.pkg = package
-        self._addl_rpaths = set()
+        self._addl_rpaths: set[str] = set()
+        if link_install_prefix and base_modification_prefix:
+            raise RuntimeError(
+                "Invalid combination of arguments given to WindowsSimulated RPath.\n"
+                "Select either `link_install_prefix` to create an install prefix rpath"
+                " or specify a `base_modification_prefix` for any other link type. "
+                "Specifying both arguments is invalid."
+            )
+        if not (link_install_prefix or base_modification_prefix):
+            raise RuntimeError(
+                "Insufficient arguments given to WindowsSimulatedRpath.\n"
+                "WindowsSimulatedRPath requires one of link_install_prefix"
+                " or base_modification_prefix to be specified."
+                " Neither was provided."
+            )
+
         self.link_install_prefix = link_install_prefix
-        self._additional_library_dependents = set()
+        if base_modification_prefix:
+            self.base_modification_prefix = pathlib.Path(base_modification_prefix)
+        else:
+            self.base_modification_prefix = pathlib.Path(self.pkg.prefix)
+        self._additional_library_dependents: set[pathlib.Path] = set()
+        if not self.link_install_prefix:
+            tty.debug(f"Generating rpath for non install context: {base_modification_prefix}")
 
     @property
     def library_dependents(self):
         """
         Set of directories where package binaries/libraries are located.
         """
-        return set([pathlib.Path(self.pkg.prefix.bin)]) | self._additional_library_dependents
+        base_pths = set()
+        if self.link_install_prefix:
+            base_pths.add(pathlib.Path(self.pkg.prefix.bin))
+        base_pths |= self._additional_library_dependents
+        return base_pths
 
     def add_library_dependent(self, *dest):
         """
@@ -2489,6 +2534,12 @@ def add_library_dependent(self, *dest):
                 new_pth = pathlib.Path(pth).parent
             else:
                 new_pth = pathlib.Path(pth)
+            path_is_in_prefix = new_pth.is_relative_to(self.base_modification_prefix)
+            if not path_is_in_prefix:
+                raise RuntimeError(
+                    f"Attempting to generate rpath symlink out of rpath context:\
+{str(self.base_modification_prefix)}"
+                )
             self._additional_library_dependents.add(new_pth)
 
     @property
@@ -2577,6 +2628,33 @@ def establish_link(self):
                 self._link(library, lib_dir)
 
 
+def make_package_test_rpath(pkg, test_dir: Union[str, pathlib.Path]):
+    """Establishes a temp Windows simulated rpath for the pkg in the testing directory
+    so an executable can test the libraries/executables with proper access
+    to dependent dlls
+
+    Note: this is a no-op on all other platforms besides Windows
+
+    Args:
+        pkg (spack.package_base.PackageBase): the package for which the rpath should be computed
+        test_dir: the testing directory in which we should construct an rpath
+    """
+    # link_install_prefix as false ensures we're not linking into the install prefix
+    mini_rpath = WindowsSimulatedRPath(pkg, link_install_prefix=False)
+    # add the testing directory as a location to install rpath symlinks
+    mini_rpath.add_library_dependent(test_dir)
+
+    # check for whether build_directory is available, if not
+    # assume the stage root is the build dir
+    build_dir_attr = getattr(pkg, "build_directory", None)
+    build_directory = build_dir_attr if build_dir_attr else pkg.stage.path
+    # add the build dir & build dir bin
+    mini_rpath.add_rpath(os.path.join(build_directory, "bin"))
+    mini_rpath.add_rpath(os.path.join(build_directory))
+    # construct rpath
+    mini_rpath.establish_link()
+
+
 @system_path_filter
 @memoized
 def can_access_dir(path):
@@ -2805,6 +2883,20 @@ def keep_modification_time(*filenames):
             os.utime(f, (os.path.getatime(f), mtime))
 
 
+@contextmanager
+def temporary_file_position(stream):
+    orig_pos = stream.tell()
+    yield
+    stream.seek(orig_pos)
+
+
+@contextmanager
+def current_file_position(stream: IO[str], loc: int, relative_to=io.SEEK_CUR):
+    with temporary_file_position(stream):
+        stream.seek(loc, relative_to)
+        yield
+
+
 @contextmanager
 def temporary_dir(
     suffix: Optional[str] = None, prefix: Optional[str] = None, dir: Optional[str] = None

lib/spack/llnl/util/lang.py

@@ -11,10 +11,11 @@
 import re
 import sys
 import traceback
+import types
 import typing
 import warnings
 from datetime import datetime, timedelta
-from typing import Callable, Dict, Iterable, List, Tuple, TypeVar
+from typing import Callable, Dict, Iterable, List, Mapping, Optional, Tuple, TypeVar
 
 # Ignore emacs backups when listing modules
 ignore_modules = r"^\.#|~$"
@@ -707,14 +708,24 @@ def __init__(self, wrapped_object):
 
 
 class Singleton:
-    """Simple wrapper for lazily initialized singleton objects."""
+    """Wrapper for lazily initialized singleton objects."""
 
-    def __init__(self, factory):
+    def __init__(self, factory: Callable[[], object]):
         """Create a new singleton to be inited with the factory function.
 
+        Most factories will simply create the object to be initialized and
+        return it.
+
+        In some cases, e.g. when bootstrapping some global state, the singleton
+        may need to be initialized incrementally. If the factory returns a generator
+        instead of a regular object, the singleton will assign each result yielded by
+        the generator to the singleton instance. This allows methods called by
+        the factory in later stages to refer back to the singleton.
+
         Args:
-            factory (function): function taking no arguments that
+            factory (function): function taking no arguments that creates the
-                creates the singleton instance.
+                singleton instance.
+
         """
         self.factory = factory
         self._instance = None
@@ -722,7 +733,16 @@ def __init__(self, factory):
     @property
     def instance(self):
         if self._instance is None:
-            self._instance = self.factory()
+            instance = self.factory()
+
+            if isinstance(instance, types.GeneratorType):
+                # if it's a generator, assign every value
+                for value in instance:
+                    self._instance = value
+            else:
+                # if not, just assign the result like a normal singleton
+                self._instance = instance
+
         return self._instance
 
     def __getattr__(self, name):
@@ -1080,3 +1100,88 @@ def __set__(self, instance, value):
 
     def factory(self, instance, owner):
         raise NotImplementedError("must be implemented by derived classes")
+
+
+KT = TypeVar("KT")
+VT = TypeVar("VT")
+
+
+class PriorityOrderedMapping(Mapping[KT, VT]):
+    """Mapping that iterates over key according to an integer priority. If the priority is
+    the same for two keys, insertion order is what matters.
+
+    The priority is set when the key/value pair is added. If not set, the highest current priority
+    is used.
+    """
+
+    _data: Dict[KT, VT]
+    _priorities: List[Tuple[int, KT]]
+
+    def __init__(self) -> None:
+        self._data = {}
+        # Tuple of (priority, key)
+        self._priorities = []
+
+    def __getitem__(self, key: KT) -> VT:
+        return self._data[key]
+
+    def __len__(self) -> int:
+        return len(self._data)
+
+    def __iter__(self):
+        yield from (key for _, key in self._priorities)
+
+    def __reversed__(self):
+        yield from (key for _, key in reversed(self._priorities))
+
+    def reversed_keys(self):
+        """Iterates over keys from the highest priority, to the lowest."""
+        return reversed(self)
+
+    def reversed_values(self):
+        """Iterates over values from the highest priority, to the lowest."""
+        yield from (self._data[key] for _, key in reversed(self._priorities))
+
+    def _highest_priority(self) -> int:
+        if not self._priorities:
+            return 0
+        result, _ = self._priorities[-1]
+        return result
+
+    def add(self, key: KT, *, value: VT, priority: Optional[int] = None) -> None:
+        """Adds a key/value pair to the mapping, with a specific priority.
+
+        If the priority is None, then it is assumed to be the highest priority value currently
+        in the container.
+
+        Raises:
+              ValueError: when the same priority is already in the mapping
+        """
+        if priority is None:
+            priority = self._highest_priority()
+
+        if key in self._data:
+            self.remove(key)
+
+        self._priorities.append((priority, key))
+        # We rely on sort being stable
+        self._priorities.sort(key=lambda x: x[0])
+        self._data[key] = value
+        assert len(self._data) == len(self._priorities)
+
+    def remove(self, key: KT) -> VT:
+        """Removes a key from the mapping.
+
+        Returns:
+            The value associated with the key being removed
+
+        Raises:
+            KeyError: if the key is not in the mapping
+        """
+        if key not in self._data:
+            raise KeyError(f"cannot find {key}")
+
+        popped_item = self._data.pop(key)
+        self._priorities = [(p, k) for p, k in self._priorities if k != key]
+        assert len(self._data) == len(self._priorities)
+        return popped_item

lib/spack/llnl/util/link_tree.py

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

lib/spack/llnl/util/lock.py

@@ -269,7 +269,7 @@ def __init__(
 
     @staticmethod
     def _poll_interval_generator(
-        _wait_times: Optional[Tuple[float, float, float]] = None
+        _wait_times: Optional[Tuple[float, float, float]] = None,
     ) -> Generator[float, None, None]:
         """This implements a backoff scheme for polling a contended resource
         by suggesting a succession of wait times between polls.
@@ -391,7 +391,7 @@ def _poll_lock(self, op: int) -> bool:
 
             return True
 
-        except IOError as e:
+        except OSError as e:
             # EAGAIN and EACCES == locked by another process (so try again)
             if e.errno not in (errno.EAGAIN, errno.EACCES):
                 raise

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

@@ -2,8 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-"""Utility classes for logging the output of blocks of code.
+"""Utility classes for logging the output of blocks of code."""
-"""
 import atexit
 import ctypes
 import errno
@@ -344,26 +343,6 @@ def close(self):
             self.file.close()
 
 
-@contextmanager
-def replace_environment(env):
-    """Replace the current environment (`os.environ`) with `env`.
-
-    If `env` is empty (or None), this unsets all current environment
-    variables.
-    """
-    env = env or {}
-    old_env = os.environ.copy()
-    try:
-        os.environ.clear()
-        for name, val in env.items():
-            os.environ[name] = val
-        yield
-    finally:
-        os.environ.clear()
-        for name, val in old_env.items():
-            os.environ[name] = val
-
-
 def log_output(*args, **kwargs):
     """Context manager that logs its output to a file.
 
@@ -447,7 +426,6 @@ def __init__(
         self.echo = echo
         self.debug = debug
         self.buffer = buffer
-        self.env = env  # the environment to use for _writer_daemon
         self.filter_fn = filter_fn
 
         self._active = False  # used to prevent re-entry
@@ -519,21 +497,20 @@ def __enter__(self):
                 # just don't forward input if this fails
                 pass
 
-            with replace_environment(self.env):
+            self.process = multiprocessing.Process(
-                self.process = multiprocessing.Process(
+                target=_writer_daemon,
-                    target=_writer_daemon,
+                args=(
-                    args=(
+                    input_fd,
-                        input_fd,
+                    read_fd,
-                        read_fd,
+                    self.write_fd,
-                        self.write_fd,
+                    self.echo,
-                        self.echo,
+                    self.log_file,
-                        self.log_file,
+                    child_pipe,
-                        child_pipe,
+                    self.filter_fn,
-                        self.filter_fn,
+                ),
-                    ),
+            )
-                )
+            self.process.daemon = True  # must set before start()
-                self.process.daemon = True  # must set before start()
+            self.process.start()
-                self.process.start()
 
         finally:
             if input_fd:
@@ -729,10 +706,7 @@ class winlog:
     Does not support the use of 'v' toggling as nixlog does.
     """
 
-    def __init__(
+    def __init__(self, file_like=None, echo=False, debug=0, buffer=False, filter_fn=None):
-        self, file_like=None, echo=False, debug=0, buffer=False, env=None, filter_fn=None
-    ):
-        self.env = env
         self.debug = debug
         self.echo = echo
         self.logfile = file_like
@@ -789,11 +763,10 @@ def background_reader(reader, echo_writer, _kill):
                     reader.close()
 
             self._active = True
-            with replace_environment(self.env):
+            self._thread = Thread(
-                self._thread = Thread(
+                target=background_reader, args=(self.reader, self.echo_writer, self._kill)
-                    target=background_reader, args=(self.reader, self.echo_writer, self._kill)
+            )
-                )
+            self._thread.start()
-                self._thread.start()
         return self
 
     def __exit__(self, exc_type, exc_val, exc_tb):
@@ -918,7 +891,7 @@ def _writer_daemon(
                         try:
                             if stdin_file.read(1) == "v":
                                 echo = not echo
-                        except IOError as e:
+                        except OSError as e:
                             # If SIGTTIN is ignored, the system gives EIO
                             # to let the caller know the read failed b/c it
                             # was in the bg. Ignore that too.
@@ -1013,7 +986,7 @@ def wrapped(*args, **kwargs):
         while True:
             try:
                 return function(*args, **kwargs)
-            except IOError as e:
+            except OSError as e:
                 if e.errno == errno.EINTR:
                     continue
                 raise

lib/spack/spack/__init__.py

@@ -10,9 +10,21 @@
 import spack.util.git
 
 #: PEP440 canonical <major>.<minor>.<micro>.<devN> string
-__version__ = "0.24.0.dev0"
+__version__ = "1.0.0.dev0"
 spack_version = __version__
 
+#: The current Package API version implemented by this version of Spack. The Package API defines
+#: the Python interface for packages as well as the layout of package repositories. The minor
+#: version is incremented when the package API is extended in a backwards-compatible way. The major
+#: version is incremented upon breaking changes. This version is changed independently from the
+#: Spack version.
+package_api_version = (1, 0)
+
+#: The minimum Package API version that this version of Spack is compatible with. This should
+#: always be a tuple of the form ``(major, 0)``, since compatibility with vX.Y implies
+#: compatibility with vX.0.
+min_package_api_version = (1, 0)
+
 
 def __try_int(v):
     try:
@@ -79,4 +91,6 @@ def get_short_version() -> str:
     "get_version",
     "get_spack_commit",
     "get_short_version",
+    "package_api_version",
+    "min_package_api_version",
 ]

lib/spack/spack/audit.py

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

lib/spack/spack/binary_distribution.py

@@ -5,6 +5,7 @@
 import codecs
 import collections
 import concurrent.futures
+import contextlib
 import copy
 import hashlib
 import io
@@ -91,6 +92,9 @@
 CURRENT_BUILD_CACHE_LAYOUT_VERSION = 2
 
 
+INDEX_HASH_FILE = "index.json.hash"
+
+
 class BuildCacheDatabase(spack_db.Database):
     """A database for binary buildcaches.
 
@@ -502,7 +506,7 @@ def _fetch_and_cache_index(self, mirror_url, cache_entry={}):
         scheme = urllib.parse.urlparse(mirror_url).scheme
 
         if scheme != "oci" and not web_util.url_exists(
-            url_util.join(mirror_url, BUILD_CACHE_RELATIVE_PATH, "index.json")
+            url_util.join(mirror_url, BUILD_CACHE_RELATIVE_PATH, spack_db.INDEX_JSON_FILE)
         ):
             return False
 
@@ -704,7 +708,7 @@ 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")
+    index_json_path = os.path.join(temp_dir, spack_db.INDEX_JSON_FILE)
     with open(index_json_path, "w", encoding="utf-8") as f:
         db._write_to_file(f)
 
@@ -714,14 +718,14 @@ def _read_specs_and_push_index(
         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")
+    index_hash_path = os.path.join(temp_dir, INDEX_HASH_FILE)
     with open(index_hash_path, "w", encoding="utf-8") as f:
         f.write(index_hash)
 
     # Push the index itself
     web_util.push_to_url(
         index_json_path,
-        url_util.join(cache_prefix, "index.json"),
+        url_util.join(cache_prefix, spack_db.INDEX_JSON_FILE),
         keep_original=False,
         extra_args={"ContentType": "application/json", "CacheControl": "no-cache"},
     )
@@ -729,7 +733,7 @@ def _read_specs_and_push_index(
     # Push the hash
     web_util.push_to_url(
         index_hash_path,
-        url_util.join(cache_prefix, "index.json.hash"),
+        url_util.join(cache_prefix, INDEX_HASH_FILE),
         keep_original=False,
         extra_args={"ContentType": "text/plain", "CacheControl": "no-cache"},
     )
@@ -798,7 +802,7 @@ def url_read_method(url):
         try:
             _, _, spec_file = web_util.read_from_url(url)
             contents = codecs.getreader("utf-8")(spec_file).read()
-        except web_util.SpackWebError as e:
+        except (web_util.SpackWebError, OSError) as e:
             tty.error(f"Error reading specfile: {url}: {e}")
         return contents
 
@@ -919,7 +923,7 @@ class FileTypes:
     UNKNOWN = 2
 
 
-NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7F-\x9F]")
+NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7f-\x9f]")
 
 
 def file_type(f: IO[bytes]) -> int:
@@ -1785,7 +1789,7 @@ def _oci_update_index(
         db.mark(spec, "in_buildcache", True)
 
     # Create the index.json file
-    index_json_path = os.path.join(tmpdir, "index.json")
+    index_json_path = os.path.join(tmpdir, spack_db.INDEX_JSON_FILE)
     with open(index_json_path, "w", encoding="utf-8") as f:
         db._write_to_file(f)
 
@@ -2006,7 +2010,7 @@ def fetch_url_to_mirror(url):
 
                 # Download the config = spec.json and the relevant tarball
                 try:
-                    manifest = json.loads(response.read())
+                    manifest = json.load(response)
                     spec_digest = spack.oci.image.Digest.from_string(manifest["config"]["digest"])
                     tarball_digest = spack.oci.image.Digest.from_string(
                         manifest["layers"][-1]["digest"]
@@ -2267,6 +2271,24 @@ def relocate_package(spec: spack.spec.Spec) -> None:
             with fsys.edit_in_place_through_temporary_file(binary) as tmp_binary:
                 codesign("-fs-", tmp_binary)
 
+    install_manifest = os.path.join(
+        spec.prefix,
+        spack.store.STORE.layout.metadata_dir,
+        spack.store.STORE.layout.manifest_file_name,
+    )
+    if not os.path.exists(install_manifest):
+        spec_id = spec.format("{name}/{hash:7}")
+        tty.warn("No manifest file in tarball for spec %s" % spec_id)
+
+    # overwrite old metadata with new
+    if spec.spliced:
+        # rewrite spec on disk
+        spack.store.STORE.layout.write_spec(spec, spack.store.STORE.layout.spec_file_path(spec))
+
+        # de-cache the install manifest
+        with contextlib.suppress(FileNotFoundError):
+            os.unlink(install_manifest)
+
 
 def _extract_inner_tarball(spec, filename, extract_to, signature_required: bool, remote_checksum):
     stagepath = os.path.dirname(filename)
@@ -2433,15 +2455,6 @@ def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
     except Exception as e:
         shutil.rmtree(spec.prefix, ignore_errors=True)
         raise e
-    else:
-        manifest_file = os.path.join(
-            spec.prefix,
-            spack.store.STORE.layout.metadata_dir,
-            spack.store.STORE.layout.manifest_file_name,
-        )
-        if not os.path.exists(manifest_file):
-            spec_id = spec.format("{name}/{hash:7}")
-            tty.warn("No manifest file in tarball for spec %s" % spec_id)
     finally:
         if tmpdir:
             shutil.rmtree(tmpdir, ignore_errors=True)
@@ -2516,10 +2529,10 @@ def install_root_node(
         allow_missing: when true, allows installing a node with missing dependencies
     """
     # Early termination
-    if spec.external or spec.virtual:
+    if spec.external or not spec.concrete:
-        warnings.warn("Skipping external or virtual package {0}".format(spec.format()))
+        warnings.warn("Skipping external or abstract spec {0}".format(spec.format()))
         return
-    elif spec.concrete and spec.installed and not force:
+    elif spec.installed and not force:
         warnings.warn("Package for spec {0} already installed.".format(spec.format()))
         return
 
@@ -2546,10 +2559,6 @@ def install_root_node(
         tty.msg('Installing "{0}" from a buildcache'.format(spec.format()))
         extract_tarball(spec, download_result, force)
         spec.package.windows_establish_runtime_linkage()
-        if spec.spliced:  # overwrite old metadata with new
-            spack.store.STORE.layout.write_spec(
-                spec, spack.store.STORE.layout.spec_file_path(spec)
-            )
         spack.hooks.post_install(spec, False)
         spack.store.STORE.db.add(spec, allow_missing=allow_missing)
 
@@ -2587,11 +2596,14 @@ def try_direct_fetch(spec, mirrors=None):
         )
         try:
             _, _, fs = web_util.read_from_url(buildcache_fetch_url_signed_json)
+            specfile_contents = codecs.getreader("utf-8")(fs).read()
             specfile_is_signed = True
-        except web_util.SpackWebError as e1:
+        except (web_util.SpackWebError, OSError) as e1:
             try:
                 _, _, fs = web_util.read_from_url(buildcache_fetch_url_json)
-            except web_util.SpackWebError as e2:
+                specfile_contents = codecs.getreader("utf-8")(fs).read()
+                specfile_is_signed = False
+            except (web_util.SpackWebError, OSError) as e2:
                 tty.debug(
                     f"Did not find {specfile_name} on {buildcache_fetch_url_signed_json}",
                     e1,
@@ -2601,7 +2613,6 @@ def try_direct_fetch(spec, mirrors=None):
                     f"Did not find {specfile_name} on {buildcache_fetch_url_json}", e2, level=2
                 )
                 continue
-        specfile_contents = codecs.getreader("utf-8")(fs).read()
 
         # read the spec from the build cache file. All specs in build caches
         # are concrete (as they are built) so we need to mark this spec
@@ -2695,8 +2706,9 @@ def get_keys(install=False, trust=False, force=False, mirrors=None):
 
         try:
             _, _, json_file = web_util.read_from_url(keys_index)
-            json_index = sjson.load(codecs.getreader("utf-8")(json_file))
+            json_index = sjson.load(json_file)
-        except web_util.SpackWebError as url_err:
+        except (web_util.SpackWebError, OSError, ValueError) as url_err:
+            # TODO: avoid repeated request
             if web_util.url_exists(keys_index):
                 tty.error(
                     f"Unable to find public keys in {url_util.format(fetch_url)},"
@@ -2943,14 +2955,14 @@ def __init__(self, url, local_hash, urlopen=web_util.urlopen):
 
     def get_remote_hash(self):
         # Failure to fetch index.json.hash is not fatal
-        url_index_hash = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, "index.json.hash")
+        url_index_hash = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, INDEX_HASH_FILE)
         try:
             response = self.urlopen(urllib.request.Request(url_index_hash, headers=self.headers))
-        except (TimeoutError, urllib.error.URLError):
+            remote_hash = response.read(64)
+        except OSError:
             return None
 
         # Validate the hash
-        remote_hash = response.read(64)
         if not re.match(rb"[a-f\d]{64}$", remote_hash):
             return None
         return remote_hash.decode("utf-8")
@@ -2964,17 +2976,17 @@ def conditional_fetch(self) -> FetchIndexResult:
             return FetchIndexResult(etag=None, hash=None, data=None, fresh=True)
 
         # Otherwise, download index.json
-        url_index = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, "index.json")
+        url_index = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, spack_db.INDEX_JSON_FILE)
 
         try:
             response = self.urlopen(urllib.request.Request(url_index, headers=self.headers))
-        except (TimeoutError, urllib.error.URLError) as e:
+        except OSError as e:
-            raise FetchIndexError("Could not fetch index from {}".format(url_index), e) from e
+            raise FetchIndexError(f"Could not fetch index from {url_index}", e) from e
 
         try:
             result = codecs.getreader("utf-8")(response).read()
-        except ValueError as e:
+        except (ValueError, OSError) as e:
-            raise FetchIndexError("Remote index {} is invalid".format(url_index), e) from e
+            raise FetchIndexError(f"Remote index {url_index} is invalid") from e
 
         computed_hash = compute_hash(result)
 
@@ -3008,7 +3020,7 @@ def __init__(self, url, etag, urlopen=web_util.urlopen):
 
     def conditional_fetch(self) -> FetchIndexResult:
         # Just do a conditional fetch immediately
-        url = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, "index.json")
+        url = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, spack_db.INDEX_JSON_FILE)
         headers = {"User-Agent": web_util.SPACK_USER_AGENT, "If-None-Match": f'"{self.etag}"'}
 
         try:
@@ -3018,12 +3030,12 @@ def conditional_fetch(self) -> FetchIndexResult:
                 # Not modified; that means fresh.
                 return FetchIndexResult(etag=None, hash=None, data=None, fresh=True)
             raise FetchIndexError(f"Could not fetch index {url}", e) from e
-        except (TimeoutError, urllib.error.URLError) as e:
+        except OSError as e:  # URLError, socket.timeout, etc.
             raise FetchIndexError(f"Could not fetch index {url}", e) from e
 
         try:
             result = codecs.getreader("utf-8")(response).read()
-        except ValueError as e:
+        except (ValueError, OSError) as e:
             raise FetchIndexError(f"Remote index {url} is invalid", e) from e
 
         headers = response.headers
@@ -3055,11 +3067,11 @@ def conditional_fetch(self) -> FetchIndexResult:
                     headers={"Accept": "application/vnd.oci.image.manifest.v1+json"},
                 )
             )
-        except (TimeoutError, urllib.error.URLError) as e:
+        except OSError as e:
             raise FetchIndexError(f"Could not fetch manifest from {url_manifest}", e) from e
 
         try:
-            manifest = json.loads(response.read())
+            manifest = json.load(response)
         except Exception as e:
             raise FetchIndexError(f"Remote index {url_manifest} is invalid", e) from e
 
@@ -3074,14 +3086,16 @@ def conditional_fetch(self) -> FetchIndexResult:
             return FetchIndexResult(etag=None, hash=None, data=None, fresh=True)
 
         # Otherwise fetch the blob / index.json
-        response = self.urlopen(
+        try:
-            urllib.request.Request(
+            response = self.urlopen(
-                url=self.ref.blob_url(index_digest),
+                urllib.request.Request(
-                headers={"Accept": "application/vnd.oci.image.layer.v1.tar+gzip"},
+                    url=self.ref.blob_url(index_digest),
+                    headers={"Accept": "application/vnd.oci.image.layer.v1.tar+gzip"},
+                )
             )
-        )
+            result = codecs.getreader("utf-8")(response).read()
-
+        except (OSError, ValueError) as e:
-        result = codecs.getreader("utf-8")(response).read()
+            raise FetchIndexError(f"Remote index {url_manifest} is invalid", e) from e
 
         # Make sure the blob we download has the advertised hash
         if compute_hash(result) != index_digest.digest:

lib/spack/spack/bootstrap/_common.py

@@ -5,7 +5,7 @@
 import fnmatch
 import glob
 import importlib
-import os.path
+import os
 import re
 import sys
 import sysconfig

lib/spack/spack/bootstrap/clingo.py

@@ -27,9 +27,9 @@
 class ClingoBootstrapConcretizer:
     def __init__(self, configuration):
         self.host_platform = spack.platforms.host()
-        self.host_os = self.host_platform.operating_system("frontend")
+        self.host_os = self.host_platform.default_operating_system()
         self.host_target = archspec.cpu.host().family
-        self.host_architecture = spack.spec.ArchSpec.frontend_arch()
+        self.host_architecture = spack.spec.ArchSpec.default_arch()
         self.host_architecture.target = str(self.host_target)
         self.host_compiler = self._valid_compiler_or_raise()
         self.host_python = self.python_external_spec()

lib/spack/spack/bootstrap/config.py

@@ -4,7 +4,7 @@
 """Manage configuration swapping for bootstrapping purposes"""
 
 import contextlib
-import os.path
+import os
 import sys
 from typing import Any, Dict, Generator, MutableSequence, Sequence
 
@@ -141,7 +141,7 @@ def _bootstrap_config_scopes() -> Sequence["spack.config.ConfigScope"]:
 
 
 def _add_compilers_if_missing() -> None:
-    arch = spack.spec.ArchSpec.frontend_arch()
+    arch = spack.spec.ArchSpec.default_arch()
     if not spack.compilers.compilers_for_arch(arch):
         spack.compilers.find_compilers()
 

lib/spack/spack/bootstrap/core.py

@@ -25,7 +25,6 @@
 import functools
 import json
 import os
-import os.path
 import sys
 import uuid
 from typing import Any, Callable, Dict, List, Optional, Tuple
@@ -46,6 +45,7 @@
 import spack.util.executable
 import spack.util.path
 import spack.util.spack_yaml
+import spack.util.url
 import spack.version
 from spack.installer import PackageInstaller
 
@@ -97,8 +97,12 @@ def __init__(self, conf: ConfigDictionary) -> None:
         self.name = conf["name"]
         self.metadata_dir = spack.util.path.canonicalize_path(conf["metadata"])
 
-        # Promote (relative) paths to file urls
+        # Check for relative paths, and turn them into absolute paths
-        self.url = spack.mirrors.mirror.Mirror(conf["info"]["url"]).fetch_url
+        # root is the metadata_dir
+        maybe_url = conf["info"]["url"]
+        if spack.util.url.is_path_instead_of_url(maybe_url) and not os.path.isabs(maybe_url):
+            maybe_url = os.path.join(self.metadata_dir, maybe_url)
+        self.url = spack.mirrors.mirror.Mirror(maybe_url).fetch_url
 
     @property
     def mirror_scope(self) -> spack.config.InternalConfigScope:
@@ -288,7 +292,12 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
 
         # Install the spec that should make the module importable
         with spack.config.override(self.mirror_scope):
-            PackageInstaller([concrete_spec.package], fail_fast=True).install()
+            PackageInstaller(
+                [concrete_spec.package],
+                fail_fast=True,
+                package_use_cache=False,
+                dependencies_use_cache=False,
+            ).install()
 
         if _try_import_from_store(module, query_spec=concrete_spec, query_info=info):
             self.last_search = info
@@ -358,6 +367,7 @@ def ensure_module_importable_or_raise(module: str, abstract_spec: Optional[str]
     for current_config in bootstrapping_sources():
         if not source_is_enabled(current_config):
             continue
+
         with exception_handler.forward(current_config["name"], Exception):
             if create_bootstrapper(current_config).try_import(module, abstract_spec):
                 return

lib/spack/spack/build_environment.py

@@ -301,11 +301,13 @@ def clean_environment():
     env.unset("CPLUS_INCLUDE_PATH")
     env.unset("OBJC_INCLUDE_PATH")
 
+    # prevent configure scripts from sourcing variables from config site file (AC_SITE_LOAD).
+    env.set("CONFIG_SITE", os.devnull)
     env.unset("CMAKE_PREFIX_PATH")
+
     env.unset("PYTHONPATH")
     env.unset("R_HOME")
     env.unset("R_ENVIRON")
-
     env.unset("LUA_PATH")
     env.unset("LUA_CPATH")
 

lib/spack/spack/build_systems/aspell_dict.py

@@ -6,7 +6,9 @@
 import llnl.util.filesystem as fs
 
 import spack.directives
+import spack.spec
 import spack.util.executable
+import spack.util.prefix
 
 from .autotools import AutotoolsBuilder, AutotoolsPackage
 
@@ -17,19 +19,18 @@ class AspellBuilder(AutotoolsBuilder):
     to the Aspell extensions.
     """
 
-    def configure(self, pkg, spec, prefix):
+    def configure(
+        self,
+        pkg: "AspellDictPackage",  # type: ignore[override]
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
+    ):
         aspell = spec["aspell"].prefix.bin.aspell
         prezip = spec["aspell"].prefix.bin.prezip
         destdir = prefix
 
-        sh = spack.util.executable.which("sh")
+        sh = spack.util.executable.Executable("/bin/sh")
-        sh(
+        sh("./configure", "--vars", f"ASPELL={aspell}", f"PREZIP={prezip}", f"DESTDIR={destdir}")
-            "./configure",
-            "--vars",
-            "ASPELL={0}".format(aspell),
-            "PREZIP={0}".format(prezip),
-            "DESTDIR={0}".format(destdir),
-        )
 
 
 # Aspell dictionaries install their bits into their prefix.lib

lib/spack/spack/build_systems/autotools.py

@@ -2,7 +2,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
-import os.path
 import stat
 import subprocess
 from typing import Callable, List, Optional, Set, Tuple, Union
@@ -534,7 +533,7 @@ def build_directory(self) -> str:
         return build_dir
 
     @spack.phase_callbacks.run_before("autoreconf")
-    def delete_configure_to_force_update(self) -> None:
+    def _delete_configure_to_force_update(self) -> None:
         if self.force_autoreconf:
             fs.force_remove(self.configure_abs_path)
 
@@ -547,7 +546,7 @@ def autoreconf_search_path_args(self) -> List[str]:
         return _autoreconf_search_path_args(self.spec)
 
     @spack.phase_callbacks.run_after("autoreconf")
-    def set_configure_or_die(self) -> None:
+    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.
 
@@ -571,10 +570,7 @@ def configure_args(self) -> List[str]:
         return []
 
     def autoreconf(
-        self,
+        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Not needed usually, configure should be already there"""
 
@@ -603,10 +599,7 @@ def autoreconf(
             self.pkg.module.autoreconf(*autoreconf_args)
 
     def configure(
-        self,
+        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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.
@@ -619,10 +612,7 @@ def configure(
             pkg.module.configure(*options)
 
     def build(
-        self,
+        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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
@@ -632,10 +622,7 @@ def build(
             pkg.module.make(*params)
 
     def install(
-        self,
+        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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):
@@ -832,7 +819,7 @@ def installcheck(self) -> None:
             self.pkg._if_make_target_execute("installcheck")
 
     @spack.phase_callbacks.run_after("install")
-    def remove_libtool_archives(self) -> None:
+    def _remove_libtool_archives(self) -> None:
         """Remove all .la files in prefix sub-folders if the package sets
         ``install_libtool_archives`` to be False.
         """

lib/spack/spack/build_systems/cached_cmake.py

@@ -10,6 +10,9 @@
 import llnl.util.tty as tty
 
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
+from spack.directives import depends_on
 
 from .cmake import CMakeBuilder, CMakePackage
 
@@ -330,7 +333,9 @@ def initconfig_package_entries(self):
         """This method is to be overwritten by the package"""
         return []
 
-    def initconfig(self, pkg, spec, prefix):
+    def initconfig(
+        self, pkg: "CachedCMakePackage", spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         cache_entries = (
             self.std_initconfig_entries()
             + self.initconfig_compiler_entries()
@@ -367,6 +372,10 @@ class CachedCMakePackage(CMakePackage):
 
     CMakeBuilder = CachedCMakeBuilder
 
+    # These dependencies are assumed in the builder
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
+
     def flag_handler(self, name, flags):
         if name in ("cflags", "cxxflags", "cppflags", "fflags"):
             return None, None, None  # handled in the cmake cache

lib/spack/spack/build_systems/cargo.py

@@ -7,6 +7,8 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, depends_on
 from spack.multimethod import when
 
@@ -68,10 +70,16 @@ def build_directory(self):
         """Return the directory containing the main Cargo.toml."""
         return self.pkg.stage.source_path
 
+    @property
+    def std_build_args(self):
+        """Standard arguments for ``cargo build`` provided as a property for
+        convenience of package writers."""
+        return ["-j", str(self.pkg.module.make_jobs)]
+
     @property
     def build_args(self):
         """Arguments for ``cargo build``."""
-        return ["-j", str(self.pkg.module.make_jobs)]
+        return []
 
     @property
     def check_args(self):
@@ -81,12 +89,18 @@ def check_args(self):
     def setup_build_environment(self, env):
         env.set("CARGO_HOME", self.stage.path)
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: CargoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Runs ``cargo install`` in the source directory"""
         with fs.working_dir(self.build_directory):
-            pkg.module.cargo("install", "--root", "out", "--path", ".", *self.build_args)
+            pkg.module.cargo(
+                "install", "--root", "out", "--path", ".", *self.std_build_args, *self.build_args
+            )
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: CargoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Copy build files into package prefix."""
         with fs.working_dir(self.build_directory):
             fs.install_tree("out", prefix)

lib/spack/spack/build_systems/cmake.py

@@ -11,6 +11,7 @@
 from typing import Any, List, Optional, Tuple
 
 import llnl.util.filesystem as fs
+from llnl.util import tty
 from llnl.util.lang import stable_partition
 
 import spack.builder
@@ -454,18 +455,27 @@ def cmake_args(self) -> List[str]:
         return []
 
     def cmake(
-        self,
+        self, pkg: CMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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
+        if spec.is_develop:
-        if spec.is_develop and os.path.isfile(
+            # skip cmake phase if it is an incremental develop build
-            os.path.join(self.build_directory, "CMakeCache.txt")
+
-        ):
+            # Determine the files that will re-run CMake that are generated from a successful
-            return
+            # configure step based on state
+            primary_generator = _extract_primary_generator(self.generator)
+            configure_artifact = "Makefile"
+            if primary_generator == "Ninja":
+                configure_artifact = "ninja.build"
+
+            if os.path.isfile(os.path.join(self.build_directory, configure_artifact)):
+                tty.msg(
+                    "Incremental build criteria satisfied."
+                    "Skipping CMake configure step. To force configuration run"
+                    f" `spack clean {pkg.name}`"
+                )
+                return
 
         options = self.std_cmake_args
         options += self.cmake_args()
@@ -474,10 +484,7 @@ def cmake(
             pkg.module.cmake(*options)
 
     def build(
-        self,
+        self, pkg: CMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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):
@@ -488,10 +495,7 @@ def build(
                 pkg.module.ninja(*self.build_targets)
 
     def install(
-        self,
+        self, pkg: CMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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):

lib/spack/spack/build_systems/cuda.py

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

lib/spack/spack/build_systems/generic.py

@@ -7,6 +7,8 @@
 import spack.directives
 import spack.package_base
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 
 from ._checks import BuilderWithDefaults, apply_macos_rpath_fixups, execute_install_time_tests
 
@@ -48,3 +50,8 @@ class GenericBuilder(BuilderWithDefaults):
 
     # unconditionally perform any post-install phase tests
     spack.phase_callbacks.run_after("install")(execute_install_time_tests)
+
+    def install(
+        self, pkg: Package, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
+        raise NotImplementedError

lib/spack/spack/build_systems/go.py

@@ -7,7 +7,9 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
-from spack.directives import build_system, extends
+import spack.spec
+import spack.util.prefix
+from spack.directives import build_system, depends_on
 from spack.multimethod import when
 
 from ._checks import BuilderWithDefaults, execute_install_time_tests
@@ -26,9 +28,7 @@ class GoPackage(spack.package_base.PackageBase):
     build_system("go")
 
     with when("build_system=go"):
-        # TODO: this seems like it should be depends_on, see
+        depends_on("go", type="build")
-        # setup_dependent_build_environment in go for why I kept it like this
-        extends("go@1.14:", type="build")
 
 
 @spack.builder.builder("go")
@@ -71,6 +71,7 @@ class GoBuilder(BuilderWithDefaults):
     def setup_build_environment(self, env):
         env.set("GO111MODULE", "on")
         env.set("GOTOOLCHAIN", "local")
+        env.set("GOPATH", fs.join_path(self.pkg.stage.path, "go"))
 
     @property
     def build_directory(self):
@@ -81,19 +82,31 @@ def build_directory(self):
     def build_args(self):
         """Arguments for ``go build``."""
         # Pass ldflags -s = --strip-all and -w = --no-warnings by default
-        return ["-modcacherw", "-ldflags", "-s -w", "-o", f"{self.pkg.name}"]
+        return [
+            "-p",
+            str(self.pkg.module.make_jobs),
+            "-modcacherw",
+            "-ldflags",
+            "-s -w",
+            "-o",
+            f"{self.pkg.name}",
+        ]
 
     @property
     def check_args(self):
         """Argument for ``go test`` during check phase"""
         return []
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: GoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Runs ``go build`` in the source directory"""
         with fs.working_dir(self.build_directory):
             pkg.module.go("build", *self.build_args)
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: GoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Install built binaries into prefix bin."""
         with fs.working_dir(self.build_directory):
             fs.mkdirp(prefix.bin)

lib/spack/spack/build_systems/lua.py

@@ -7,7 +7,9 @@
 
 import spack.builder
 import spack.package_base
+import spack.spec
 import spack.util.executable
+import spack.util.prefix
 from spack.directives import build_system, depends_on, extends
 from spack.multimethod import when
 
@@ -55,7 +57,9 @@ class LuaBuilder(spack.builder.Builder):
     #: Names associated with package attributes in the old build-system format
     legacy_attributes = ()
 
-    def unpack(self, pkg, spec, prefix):
+    def unpack(
+        self, pkg: LuaPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         if os.path.splitext(pkg.stage.archive_file)[1] == ".rock":
             directory = pkg.luarocks("unpack", pkg.stage.archive_file, output=str)
             dirlines = directory.split("\n")
@@ -66,15 +70,16 @@ def unpack(self, pkg, spec, prefix):
     def _generate_tree_line(name, prefix):
         return """{{ name = "{name}", root = "{prefix}" }};""".format(name=name, prefix=prefix)
 
-    def generate_luarocks_config(self, pkg, spec, prefix):
+    def generate_luarocks_config(
+        self, pkg: LuaPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         spec = self.pkg.spec
         table_entries = []
         for d in spec.traverse(deptype=("build", "run")):
             if d.package.extends(self.pkg.extendee_spec):
                 table_entries.append(self._generate_tree_line(d.name, d.prefix))
 
-        path = self._luarocks_config_path()
+        with open(self._luarocks_config_path(), "w", encoding="utf-8") as config:
-        with open(path, "w", encoding="utf-8") as config:
             config.write(
                 """
                 deps_mode="all"
@@ -85,23 +90,26 @@ def generate_luarocks_config(self, pkg, spec, prefix):
                     "\n".join(table_entries)
                 )
             )
-        return path
 
-    def preprocess(self, pkg, spec, prefix):
+    def preprocess(
+        self, pkg: LuaPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Override this to preprocess source before building with luarocks"""
         pass
 
     def luarocks_args(self):
         return []
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: LuaPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         rock = "."
         specs = find(".", "*.rockspec", recursive=False)
         if specs:
             rock = specs[0]
         rocks_args = self.luarocks_args()
         rocks_args.append(rock)
-        self.pkg.luarocks("--tree=" + prefix, "make", *rocks_args)
+        pkg.luarocks("--tree=" + prefix, "make", *rocks_args)
 
     def _luarocks_config_path(self):
         return os.path.join(self.pkg.stage.source_path, "spack_luarocks.lua")

lib/spack/spack/build_systems/makefile.py

@@ -98,29 +98,20 @@ def build_directory(self) -> str:
         return self.pkg.stage.source_path
 
     def edit(
-        self,
+        self, pkg: MakefilePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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,
+        self, pkg: MakefilePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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,
+        self, pkg: MakefilePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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):

lib/spack/spack/build_systems/maven.py

@@ -5,6 +5,8 @@
 
 import spack.builder
 import spack.package_base
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, depends_on
 from spack.multimethod import when
 from spack.util.executable import which
@@ -58,16 +60,20 @@ def build_args(self):
         """List of args to pass to build phase."""
         return []
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: MavenPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Compile code and package into a JAR file."""
         with fs.working_dir(self.build_directory):
-            mvn = which("mvn")
+            mvn = which("mvn", required=True)
             if self.pkg.run_tests:
                 mvn("verify", *self.build_args())
             else:
                 mvn("package", "-DskipTests", *self.build_args())
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: MavenPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Copy to installation prefix."""
         with fs.working_dir(self.build_directory):
             fs.install_tree(".", prefix)

lib/spack/spack/build_systems/meson.py

@@ -48,6 +48,9 @@ class MesonPackage(spack.package_base.PackageBase):
         variant("strip", default=False, description="Strip targets on install")
         depends_on("meson", type="build")
         depends_on("ninja", type="build")
+        # Meson uses pkg-config for dependency detection, and this dependency is
+        # often overlooked by packages that use meson as a build system.
+        depends_on("pkgconfig", type="build")
         # Python detection in meson requires distutils to be importable, but distutils no longer
         # exists in Python 3.12. In Spack, we can't use setuptools as distutils replacement,
         # because the distutils-precedence.pth startup file that setuptools ships with is not run
@@ -188,10 +191,7 @@ def meson_args(self) -> List[str]:
         return []
 
     def meson(
-        self,
+        self, pkg: MesonPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Run ``meson`` in the build directory"""
         options = []
@@ -204,10 +204,7 @@ def meson(
             pkg.module.meson(*options)
 
     def build(
-        self,
+        self, pkg: MesonPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Make the build targets"""
         options = ["-v"]
@@ -216,10 +213,7 @@ def build(
             pkg.module.ninja(*options)
 
     def install(
-        self,
+        self, pkg: MesonPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-        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):

lib/spack/spack/build_systems/msbuild.py

@@ -7,6 +7,8 @@
 
 import spack.builder
 import spack.package_base
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, conflicts
 
 from ._checks import BuilderWithDefaults
@@ -99,7 +101,9 @@ def msbuild_install_args(self):
         as `msbuild_args` by default."""
         return self.msbuild_args()
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: MSBuildPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Run "msbuild" on the build targets specified by the builder."""
         with fs.working_dir(self.build_directory):
             pkg.module.msbuild(
@@ -108,7 +112,9 @@ def build(self, pkg, spec, prefix):
                 self.define_targets(*self.build_targets),
             )
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: MSBuildPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Run "msbuild" on the install targets specified by the builder.
         This is INSTALL by default"""
         with fs.working_dir(self.build_directory):

lib/spack/spack/build_systems/nmake.py

@@ -7,6 +7,8 @@
 
 import spack.builder
 import spack.package_base
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, conflicts
 
 from ._checks import BuilderWithDefaults
@@ -123,7 +125,9 @@ def nmake_install_args(self):
         Individual packages should override to specify NMake args to command line"""
         return []
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: NMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Run "nmake" on the build targets specified by the builder."""
         opts = self.std_nmake_args
         opts += self.nmake_args()
@@ -132,7 +136,9 @@ def build(self, pkg, spec, prefix):
         with fs.working_dir(self.build_directory):
             pkg.module.nmake(*opts, *self.build_targets, ignore_quotes=self.ignore_quotes)
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: NMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Run "nmake" on the install targets specified by the builder.
         This is INSTALL by default"""
         opts = self.std_nmake_args

lib/spack/spack/build_systems/octave.py

@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import spack.builder
 import spack.package_base
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, extends
 from spack.multimethod import when
 
@@ -42,7 +44,9 @@ class OctaveBuilder(BuilderWithDefaults):
     #: Names associated with package attributes in the old build-system format
     legacy_attributes = ()
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: OctavePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Install the package from the archive file"""
         pkg.module.octave(
             "--quiet",

lib/spack/spack/build_systems/oneapi.py

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

lib/spack/spack/build_systems/perl.py

@@ -10,6 +10,8 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, depends_on, extends
 from spack.install_test import SkipTest, test_part
 from spack.multimethod import when
@@ -149,7 +151,9 @@ def configure_args(self):
         """
         return []
 
-    def configure(self, pkg, spec, prefix):
+    def configure(
+        self, pkg: PerlPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Run Makefile.PL or Build.PL with arguments consisting of
         an appropriate installation base directory followed by the
         list returned by :py:meth:`~.PerlBuilder.configure_args`.
@@ -173,7 +177,9 @@ def fix_shebang(self):
             repl = "#!/usr/bin/env perl"
             filter_file(pattern, repl, "Build", backup=False)
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: PerlPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Builds a Perl package."""
         self.build_executable()
 
@@ -184,6 +190,8 @@ def check(self):
         """Runs built-in tests of a Perl package."""
         self.build_executable("test")
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: PerlPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Installs a Perl package."""
         self.build_executable("install")

lib/spack/spack/build_systems/python.py

@@ -28,6 +28,7 @@
 import spack.repo
 import spack.spec
 import spack.store
+import spack.util.prefix
 from spack.directives import build_system, depends_on, extends
 from spack.error import NoHeadersError, NoLibrariesError
 from spack.install_test import test_part
@@ -263,16 +264,17 @@ def update_external_dependencies(self, extendee_spec=None):
                     # Ensure architecture information is present
                     if not python.architecture:
                         host_platform = spack.platforms.host()
-                        host_os = host_platform.operating_system("default_os")
+                        host_os = host_platform.default_operating_system()
-                        host_target = host_platform.target("default_target")
+                        host_target = host_platform.default_target()
                         python.architecture = spack.spec.ArchSpec(
                             (str(host_platform), str(host_os), str(host_target))
                         )
                     else:
                         if not python.architecture.platform:
                             python.architecture.platform = spack.platforms.host()
+                        platform = spack.platforms.by_name(python.architecture.platform)
                         if not python.architecture.os:
-                            python.architecture.os = "default_os"
+                            python.architecture.os = platform.default_operating_system()
                         if not python.architecture.target:
                             python.architecture.target = archspec.cpu.host().family.name
 

lib/spack/spack/build_systems/qmake.py

@@ -6,6 +6,8 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, depends_on
 
 from ._checks import BuilderWithDefaults, execute_build_time_tests
@@ -62,17 +64,23 @@ def qmake_args(self):
         """List of arguments passed to qmake."""
         return []
 
-    def qmake(self, pkg, spec, prefix):
+    def qmake(
+        self, pkg: QMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Run ``qmake`` to configure the project and generate a Makefile."""
         with working_dir(self.build_directory):
             pkg.module.qmake(*self.qmake_args())
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: QMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Make the build targets"""
         with working_dir(self.build_directory):
             pkg.module.make()
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: QMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Make the install targets"""
         with working_dir(self.build_directory):
             pkg.module.make("install")

lib/spack/spack/build_systems/racket.py

@@ -9,6 +9,8 @@
 import llnl.util.tty as tty
 
 import spack.builder
+import spack.spec
+import spack.util.prefix
 from spack.build_environment import SPACK_NO_PARALLEL_MAKE
 from spack.config import determine_number_of_jobs
 from spack.directives import build_system, extends, maintainers
@@ -74,18 +76,22 @@ def build_directory(self):
             ret = os.path.join(ret, self.subdirectory)
         return ret
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: RacketPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Install everything from build directory."""
         raco = Executable("raco")
         with fs.working_dir(self.build_directory):
-            parallel = self.pkg.parallel and (not env_flag(SPACK_NO_PARALLEL_MAKE))
+            parallel = pkg.parallel and (not env_flag(SPACK_NO_PARALLEL_MAKE))
+            name = pkg.racket_name
+            assert name is not None, "Racket package name is not set"
             args = [
                 "pkg",
                 "install",
                 "-t",
                 "dir",
                 "-n",
-                self.pkg.racket_name,
+                name,
                 "--deps",
                 "fail",
                 "--ignore-implies",
@@ -101,8 +107,7 @@ def install(self, pkg, spec, prefix):
             except ProcessError:
                 args.insert(-2, "--skip-installed")
                 raco(*args)
-                msg = (
+                tty.warn(
-                    "Racket package {0} was already installed, uninstalling via "
+                    f"Racket package {name} was already installed, uninstalling via "
                     "Spack may make someone unhappy!"
                 )
-                tty.warn(msg.format(self.pkg.racket_name))

lib/spack/spack/build_systems/ruby.py

@@ -5,6 +5,8 @@
 
 import spack.builder
 import spack.package_base
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, extends, maintainers
 
 from ._checks import BuilderWithDefaults
@@ -42,7 +44,9 @@ class RubyBuilder(BuilderWithDefaults):
     #: Names associated with package attributes in the old build-system format
     legacy_attributes = ()
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: RubyPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Build a Ruby gem."""
 
         # ruby-rake provides both rake.gemspec and Rakefile, but only
@@ -58,7 +62,9 @@ def build(self, pkg, spec, prefix):
             # Some Ruby packages only ship `*.gem` files, so nothing to build
             pass
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: RubyPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Install a Ruby gem.
 
         The ruby package sets ``GEM_HOME`` to tell gem where to install to."""

lib/spack/spack/build_systems/scons.py

@@ -4,6 +4,8 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, depends_on
 
 from ._checks import BuilderWithDefaults, execute_build_time_tests
@@ -59,7 +61,9 @@ def build_args(self, spec, prefix):
         """Arguments to pass to build."""
         return []
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: SConsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Build the package."""
         pkg.module.scons(*self.build_args(spec, prefix))
 
@@ -67,7 +71,9 @@ def install_args(self, spec, prefix):
         """Arguments to pass to install."""
         return []
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: SConsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Install the package."""
         pkg.module.scons("install", *self.install_args(spec, prefix))
 

lib/spack/spack/build_systems/sip.py

@@ -11,6 +11,8 @@
 import spack.install_test
 import spack.package_base
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, depends_on, extends
 from spack.multimethod import when
 from spack.util.executable import Executable
@@ -41,6 +43,7 @@ class SIPPackage(spack.package_base.PackageBase):
     with when("build_system=sip"):
         extends("python", type=("build", "link", "run"))
         depends_on("py-sip", type="build")
+        depends_on("gmake", type="build")
 
     @property
     def import_modules(self):
@@ -130,7 +133,9 @@ class SIPBuilder(BuilderWithDefaults):
 
     build_directory = "build"
 
-    def configure(self, pkg, spec, prefix):
+    def configure(
+        self, pkg: SIPPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Configure the package."""
 
         # https://www.riverbankcomputing.com/static/Docs/sip/command_line_tools.html
@@ -148,7 +153,9 @@ def configure_args(self):
         """Arguments to pass to configure."""
         return []
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: SIPPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Build the package."""
         args = self.build_args()
 
@@ -159,7 +166,9 @@ def build_args(self):
         """Arguments to pass to build."""
         return []
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: SIPPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Install the package."""
         args = self.install_args()
 

lib/spack/spack/build_systems/waf.py

@@ -6,6 +6,8 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, depends_on
 
 from ._checks import BuilderWithDefaults, execute_build_time_tests, execute_install_time_tests
@@ -97,7 +99,9 @@ def waf(self, *args, **kwargs):
         with working_dir(self.build_directory):
             self.python("waf", "-j{0}".format(jobs), *args, **kwargs)
 
-    def configure(self, pkg, spec, prefix):
+    def configure(
+        self, pkg: WafPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Configures the project."""
         args = ["--prefix={0}".format(self.pkg.prefix)]
         args += self.configure_args()
@@ -108,7 +112,9 @@ def configure_args(self):
         """Arguments to pass to configure."""
         return []
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: WafPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Executes the build."""
         args = self.build_args()
 
@@ -118,7 +124,9 @@ def build_args(self):
         """Arguments to pass to build."""
         return []
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: WafPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Installs the targets on the system."""
         args = self.install_args()
 

lib/spack/spack/ci/__init__.py

@@ -14,9 +14,9 @@
 import zipfile
 from collections import namedtuple
 from typing import Callable, Dict, List, Set
-from urllib.error import HTTPError, URLError
+from urllib.request import Request
-from urllib.request import HTTPHandler, Request, build_opener
 
+import llnl.path
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 from llnl.util.tty.color import cescape, colorize
@@ -63,6 +63,8 @@
 
 PushResult = namedtuple("PushResult", "success url")
 
+urlopen = web_util.urlopen  # alias for mocking in tests
+
 
 def get_change_revisions():
     """If this is a git repo get the revisions to use when checking
@@ -82,6 +84,9 @@ def get_stack_changed(env_path, rev1="HEAD^", rev2="HEAD"):
     whether or not the stack was changed.  Returns True if the environment
     manifest changed between the provided revisions (or additionally if the
     `.gitlab-ci.yml` file itself changed).  Returns False otherwise."""
+    # git returns posix paths always, normalize input to be comptaible
+    # with that
+    env_path = llnl.path.convert_to_posix_path(env_path)
     git = spack.util.git.git()
     if git:
         with fs.working_dir(spack.paths.prefix):
@@ -472,12 +477,9 @@ def generate_pipeline(env: ev.Environment, args) -> None:
     # Use all unpruned specs to populate the build group for this set
     cdash_config = cfg.get("cdash")
     if options.cdash_handler and options.cdash_handler.auth_token:
-        try:
+        options.cdash_handler.populate_buildgroup(
-            options.cdash_handler.populate_buildgroup(
+            [options.cdash_handler.build_name(s) for s in pipeline_specs]
-                [options.cdash_handler.build_name(s) for s in pipeline_specs]
+        )
-            )
-        except (SpackError, HTTPError, URLError, TimeoutError) as err:
-            tty.warn(f"Problem populating buildgroup: {err}")
     elif cdash_config:
         # warn only if there was actually a CDash configuration.
         tty.warn("Unable to populate buildgroup without CDash credentials")
@@ -614,7 +616,7 @@ def copy_test_logs_to_artifacts(test_stage, job_test_dir):
     copy_files_to_artifacts(os.path.join(test_stage, "*", "*.txt"), job_test_dir)
 
 
-def download_and_extract_artifacts(url, work_dir):
+def download_and_extract_artifacts(url, work_dir) -> str:
     """Look for gitlab artifacts.zip at the given url, and attempt to download
         and extract the contents into the given work_dir
 
@@ -622,6 +624,10 @@ def download_and_extract_artifacts(url, work_dir):
 
         url (str): Complete url to artifacts.zip file
         work_dir (str): Path to destination where artifacts should be extracted
+
+    Output:
+
+        Artifacts root path relative to the archive root
     """
     tty.msg(f"Fetching artifacts from: {url}")
 
@@ -631,31 +637,33 @@ def download_and_extract_artifacts(url, work_dir):
     if token:
         headers["PRIVATE-TOKEN"] = token
 
-    opener = build_opener(HTTPHandler)
+    request = Request(url, headers=headers, method="GET")
-
-    request = Request(url, headers=headers)
-    request.get_method = lambda: "GET"
-
-    response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
-    response_code = response.getcode()
-
-    if response_code != 200:
-        msg = f"Error response code ({response_code}) in reproduce_ci_job"
-        raise SpackError(msg)
-
     artifacts_zip_path = os.path.join(work_dir, "artifacts.zip")
+    os.makedirs(work_dir, exist_ok=True)
 
-    if not os.path.exists(work_dir):
+    try:
-        os.makedirs(work_dir)
+        response = urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
+        with open(artifacts_zip_path, "wb") as out_file:
+            shutil.copyfileobj(response, out_file)
 
-    with open(artifacts_zip_path, "wb") as out_file:
+        with zipfile.ZipFile(artifacts_zip_path) as zip_file:
-        shutil.copyfileobj(response, out_file)
+            zip_file.extractall(work_dir)
+            # Get the artifact root
+            artifact_root = ""
+            for f in zip_file.filelist:
+                if "spack.lock" in f.filename:
+                    artifact_root = os.path.dirname(os.path.dirname(f.filename))
+                    break
+    except OSError as e:
+        raise SpackError(f"Error fetching artifacts: {e}")
+    finally:
+        try:
+            os.remove(artifacts_zip_path)
+        except FileNotFoundError:
+            # If the file doesn't exist we are already raising
+            pass
 
-    zip_file = zipfile.ZipFile(artifacts_zip_path)
+    return artifact_root
-    zip_file.extractall(work_dir)
-    zip_file.close()
-
-    os.remove(artifacts_zip_path)
 
 
 def get_spack_info():
@@ -769,7 +777,7 @@ def setup_spack_repro_version(repro_dir, checkout_commit, merge_commit=None):
     return True
 
 
-def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
+def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime, use_local_head):
     """Given a url to gitlab artifacts.zip from a failed 'spack ci rebuild' job,
     attempt to setup an environment in which the failure can be reproduced
     locally.  This entails the following:
@@ -783,8 +791,11 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     commands to run to reproduce the build once inside the container.
     """
     work_dir = os.path.realpath(work_dir)
+    if os.path.exists(work_dir) and os.listdir(work_dir):
+        raise SpackError(f"Cannot run reproducer in non-emptry working dir:\n  {work_dir}")
+
     platform_script_ext = "ps1" if IS_WINDOWS else "sh"
-    download_and_extract_artifacts(url, work_dir)
+    artifact_root = download_and_extract_artifacts(url, work_dir)
 
     gpg_path = None
     if gpg_url:
@@ -846,6 +857,9 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     with open(repro_file, encoding="utf-8") as fd:
         repro_details = json.load(fd)
 
+    spec_file = fs.find(work_dir, repro_details["job_spec_json"])[0]
+    reproducer_spec = spack.spec.Spec.from_specfile(spec_file)
+
     repro_dir = os.path.dirname(repro_file)
     rel_repro_dir = repro_dir.replace(work_dir, "").lstrip(os.path.sep)
 
@@ -906,17 +920,20 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     commit_regex = re.compile(r"commit\s+([^\s]+)")
     merge_commit_regex = re.compile(r"Merge\s+([^\s]+)\s+into\s+([^\s]+)")
 
-    # Try the more specific merge commit regex first
+    if use_local_head:
-    m = merge_commit_regex.search(spack_info)
+        commit_1 = "HEAD"
-    if m:
-        # This was a merge commit and we captured the parents
-        commit_1 = m.group(1)
-        commit_2 = m.group(2)
     else:
-        # Not a merge commit, just get the commit sha
+        # Try the more specific merge commit regex first
-        m = commit_regex.search(spack_info)
+        m = merge_commit_regex.search(spack_info)
         if m:
+            # This was a merge commit and we captured the parents
             commit_1 = m.group(1)
+            commit_2 = m.group(2)
+        else:
+            # Not a merge commit, just get the commit sha
+            m = commit_regex.search(spack_info)
+            if m:
+                commit_1 = m.group(1)
 
     setup_result = False
     if commit_1:
@@ -991,6 +1008,8 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
             "entrypoint", entrypoint_script, work_dir, run=False, exit_on_failure=False
         )
 
+        # Attempt to create a unique name for the reproducer container
+        container_suffix = "_" + reproducer_spec.dag_hash() if reproducer_spec else ""
         docker_command = [
             runtime,
             "run",
@@ -998,14 +1017,14 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
             "-t",
             "--rm",
             "--name",
-            "spack_reproducer",
+            f"spack_reproducer{container_suffix}",
             "-v",
             ":".join([work_dir, mounted_workdir, "Z"]),
             "-v",
             ":".join(
                 [
-                    os.path.join(work_dir, "jobs_scratch_dir"),
+                    os.path.join(work_dir, artifact_root),
-                    os.path.join(mount_as_dir, "jobs_scratch_dir"),
+                    os.path.join(mount_as_dir, artifact_root),
                     "Z",
                 ]
             ),

lib/spack/spack/ci/common.py

@@ -1,23 +1,21 @@
 # Copyright Spack Project Developers. See 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
+from urllib.request import Request
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
-from llnl.util.lang import Singleton, memoized
+from llnl.util.lang import memoized
 
 import spack.binary_distribution as bindist
 import spack.config as cfg
@@ -35,32 +33,11 @@
 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)
+
+# this exists purely for testing purposes
+_urlopen = web_util.urlopen
 
 
 def copy_files_to_artifacts(src, artifacts_dir):
@@ -279,26 +256,25 @@ def copy_test_results(self, source, dest):
         reports = fs.join_path(source, "*_Test*.xml")
         copy_files_to_artifacts(reports, dest)
 
-    def create_buildgroup(self, opener, headers, url, group_name, group_type):
+    def create_buildgroup(self, 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)
+        try:
-        response_code = response.getcode()
+            response_text = _urlopen(request, timeout=SPACK_CDASH_TIMEOUT).read()
-
+        except OSError as e:
-        if response_code not in [200, 201]:
+            tty.warn(f"Failed to create CDash buildgroup: {e}")
-            msg = f"Creating buildgroup failed (response code = {response_code})"
-            tty.warn(msg)
             return None
 
-        response_text = response.read()
+        try:
-        response_json = json.loads(response_text)
+            response_json = json.loads(response_text)
-        build_group_id = response_json["id"]
+            return response_json["id"]
-
+        except (json.JSONDecodeError, KeyError) as e:
-        return build_group_id
+            tty.warn(f"Failed to parse CDash response: {e}")
+            return None
 
     def populate_buildgroup(self, job_names):
         url = f"{self.url}/api/v1/buildgroup.php"
@@ -308,16 +284,11 @@ def populate_buildgroup(self, job_names):
             "Content-Type": "application/json",
         }
 
-        opener = build_opener(HTTPHandler)
+        parent_group_id = self.create_buildgroup(headers, url, self.build_group, "Daily")
-
+        group_id = self.create_buildgroup(headers, url, f"Latest {self.build_group}", "Latest")
-        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(f"Failed to create or retrieve buildgroups for {self.build_group}")
-            tty.warn(msg)
             return
 
         data = {
@@ -329,15 +300,12 @@ def populate_buildgroup(self, job_names):
 
         enc_data = json.dumps(data).encode("utf-8")
 
-        request = Request(url, data=enc_data, headers=headers)
+        request = Request(url, data=enc_data, headers=headers, method="PUT")
-        request.get_method = lambda: "PUT"
 
-        response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
+        try:
-        response_code = response.getcode()
+            _urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
-
+        except OSError as e:
-        if response_code != 200:
+            tty.warn(f"Failed to populate CDash buildgroup: {e}")
-            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
@@ -735,9 +703,6 @@ def _apply_section(dest, src):
                 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", [])
@@ -771,19 +736,15 @@ def job_query(job):
                         endpoint_url._replace(query=query).geturl(), headers=header, method="GET"
                     )
                     try:
-                        response = _dyn_mapping_urlopener(
+                        response = _urlopen(request)
-                            request, verify_ssl=verify_ssl, timeout=timeout
+                        config = json.load(response)
-                        )
                     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"Failed to fetch dynamic mapping for query:\n\t{query}: {e}")
-                        tty.warn(f"{e}")
                         continue
 
-                    config = json.load(codecs.getreader("utf-8")(response))
-
                     # Strip ignore keys
                     if ignored:
                         for key in ignored:

lib/spack/spack/cmd/arch.py

@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import collections
+import warnings
 
 import archspec.cpu
 
@@ -51,10 +52,10 @@ def setup_parser(subparser):
         "-t", "--target", action="store_true", default=False, help="print only the target"
     )
     parts2.add_argument(
-        "-f", "--frontend", action="store_true", default=False, help="print frontend"
+        "-f", "--frontend", action="store_true", default=False, help="print frontend (DEPRECATED)"
     )
     parts2.add_argument(
-        "-b", "--backend", action="store_true", default=False, help="print backend"
+        "-b", "--backend", action="store_true", default=False, help="print backend (DEPRECATED)"
     )
 
 
@@ -98,15 +99,14 @@ def arch(parser, args):
         display_targets(archspec.cpu.TARGETS)
         return
 
-    os_args, target_args = "default_os", "default_target"
     if args.frontend:
-        os_args, target_args = "frontend", "frontend"
+        warnings.warn("the argument --frontend is deprecated, and will be removed in Spack v1.0")
     elif args.backend:
-        os_args, target_args = "backend", "backend"
+        warnings.warn("the argument --backend is deprecated, and will be removed in Spack v1.0")
 
     host_platform = spack.platforms.host()
-    host_os = host_platform.operating_system(os_args)
+    host_os = host_platform.default_operating_system()
-    host_target = host_platform.target(target_args)
+    host_target = host_platform.default_target()
     if args.family:
         host_target = host_target.family
     elif args.generic:

lib/spack/spack/cmd/bootstrap.py

@@ -1,7 +1,7 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import os.path
+import os
 import shutil
 import sys
 import tempfile
@@ -436,6 +436,7 @@ def write_metadata(subdir, metadata):
         shutil.copy(spack.util.path.canonicalize_path(GNUPG_JSON), abs_directory)
         shutil.copy(spack.util.path.canonicalize_path(PATCHELF_JSON), abs_directory)
         instructions += cmd.format("local-binaries", rel_directory)
+        instructions += "  % spack buildcache update-index <final-path>/bootstrap_cache\n"
     print(instructions)
 
 

lib/spack/spack/cmd/checksum.py

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

lib/spack/spack/cmd/ci.py

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

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

@@ -4,7 +4,7 @@
 
 
 import argparse
-import os.path
+import os
 import textwrap
 
 from llnl.util.lang import stable_partition
@@ -528,7 +528,6 @@ def __call__(self, parser, namespace, values, option_string):
         # the const from the constructor or a value from the CLI.
         # Note that this is only called if the argument is actually
         # specified on the command line.
-        spack.config.CONFIG.ensure_scope_ordering()
         spack.config.set(self.config_path, self.const, scope="command_line")
 
 

lib/spack/spack/cmd/config.py

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

lib/spack/spack/cmd/containerize.py

@@ -2,7 +2,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
-import os.path
 
 import llnl.util.tty
 

lib/spack/spack/cmd/debug.py

@@ -2,23 +2,11 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os
 import platform
-import re
-import sys
-from datetime import datetime
-from glob import glob
-
-import llnl.util.tty as tty
-from llnl.util.filesystem import working_dir
 
 import spack
-import spack.paths
 import spack.platforms
 import spack.spec
-import spack.store
-import spack.util.git
-from spack.util.executable import which
 
 description = "debugging commands for troubleshooting Spack"
 section = "developer"
@@ -27,67 +15,13 @@
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar="SUBCOMMAND", dest="debug_command")
-    sp.add_parser("create-db-tarball", help="create a tarball of Spack's installation metadata")
     sp.add_parser("report", help="print information useful for bug reports")
 
 
-def _debug_tarball_suffix():
-    now = datetime.now()
-    suffix = now.strftime("%Y-%m-%d-%H%M%S")
-
-    git = spack.util.git.git()
-    if not git:
-        return "nobranch-nogit-%s" % suffix
-
-    with working_dir(spack.paths.prefix):
-        if not os.path.isdir(".git"):
-            return "nobranch.nogit.%s" % suffix
-
-        # Get symbolic branch name and strip any special chars (mainly '/')
-        symbolic = git("rev-parse", "--abbrev-ref", "--short", "HEAD", output=str).strip()
-        symbolic = re.sub(r"[^\w.-]", "-", symbolic)
-
-        # Get the commit hash too.
-        commit = git("rev-parse", "--short", "HEAD", output=str).strip()
-
-        if symbolic == commit:
-            return "nobranch.%s.%s" % (commit, suffix)
-        else:
-            return "%s.%s.%s" % (symbolic, commit, suffix)
-
-
-def create_db_tarball(args):
-    tar = which("tar")
-    tarball_name = "spack-db.%s.tar.gz" % _debug_tarball_suffix()
-    tarball_path = os.path.abspath(tarball_name)
-
-    base = os.path.basename(str(spack.store.STORE.root))
-    transform_args = []
-    # Currently --transform and -s are not supported by Windows native tar
-    if "GNU" in tar("--version", output=str):
-        transform_args = ["--transform", "s/^%s/%s/" % (base, tarball_name)]
-    elif sys.platform != "win32":
-        transform_args = ["-s", "/^%s/%s/" % (base, tarball_name)]
-
-    wd = os.path.dirname(str(spack.store.STORE.root))
-    with working_dir(wd):
-        files = [spack.store.STORE.db._index_path]
-        files += glob("%s/*/*/*/.spack/spec.json" % base)
-        files += glob("%s/*/*/*/.spack/spec.yaml" % base)
-        files = [os.path.relpath(f) for f in files]
-
-        args = ["-czf", tarball_path]
-        args += transform_args
-        args += files
-        tar(*args)
-
-    tty.msg("Created %s" % tarball_name)
-
-
 def report(args):
     host_platform = spack.platforms.host()
-    host_os = host_platform.operating_system("frontend")
+    host_os = host_platform.default_operating_system()
-    host_target = host_platform.target("frontend")
+    host_target = host_platform.default_target()
     architecture = spack.spec.ArchSpec((str(host_platform), str(host_os), str(host_target)))
     print("* **Spack:**", spack.get_version())
     print("* **Python:**", platform.python_version())
@@ -95,5 +29,5 @@ def report(args):
 
 
 def debug(parser, args):
-    action = {"create-db-tarball": create_db_tarball, "report": report}
+    if args.debug_command == "report":
-    action[args.debug_command](args)
+        report(args)

lib/spack/spack/cmd/dependencies.py

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

lib/spack/spack/cmd/develop.py

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

lib/spack/spack/cmd/external.py

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

lib/spack/spack/cmd/help.py

@@ -54,10 +54,6 @@
       @m{target=target}                 specific <target> processor
       @m{arch=platform-os-target}       shortcut for all three above
 
-    cross-compiling:
-      @m{os=backend} or @m{os=be}           build for compute node (backend)
-      @m{os=frontend} or @m{os=fe}          build for login node (frontend)
-
     dependencies:
       ^dependency [constraints]     specify constraints on dependencies
       ^@K{/hash}                        build with a specific installed

lib/spack/spack/cmd/mirror.py

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

lib/spack/spack/cmd/modules/__init__.py

@@ -5,7 +5,7 @@
 """Implementation details of the ``spack module`` command."""
 
 import collections
-import os.path
+import os
 import shutil
 import sys
 

lib/spack/spack/cmd/providers.py

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

lib/spack/spack/cmd/style.py

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

lib/spack/spack/cmd/test.py

@@ -177,16 +177,15 @@ def test_run(args):
         matching = spack.store.STORE.db.query_local(spec, hashes=hashes, explicit=explicit)
         if spec and not matching:
             tty.warn("No {0}installed packages match spec {1}".format(explicit_str, spec))
-            """
-            TODO: Need to write out a log message and/or CDASH Testing
-              output that package not installed IF continue to process
-              these issues here.
 
-            if args.log_format:
+            # TODO: Need to write out a log message and/or CDASH Testing
-                # Proceed with the spec assuming the test process
+            #   output that package not installed IF continue to process
-                # to ensure report package as skipped (e.g., for CI)
+            #   these issues here.
-                specs_to_test.append(spec)
+
-            """
+            # if args.log_format:
+            #     # Proceed with the spec assuming the test process
+            #     # to ensure report package as skipped (e.g., for CI)
+            #     specs_to_test.append(spec)
 
         specs_to_test.extend(matching)
 
@@ -253,7 +252,9 @@ def has_test_and_tags(pkg_class):
     hashes = env.all_hashes() if env else None
 
     specs = spack.store.STORE.db.query(hashes=hashes)
-    specs = list(filter(lambda s: has_test_and_tags(s.package_class), specs))
+    specs = list(
+        filter(lambda s: has_test_and_tags(spack.repo.PATH.get_pkg_class(s.fullname)), specs)
+    )
 
     spack.cmd.display_specs(specs, long=True)
 

lib/spack/spack/cmd/tutorial.py

@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os.path
+import os
 import shutil
 
 import llnl.util.tty as tty

lib/spack/spack/cmd/unit_test.py

@@ -5,7 +5,7 @@
 import argparse
 import collections
 import io
-import os.path
+import os
 import re
 import sys
 
@@ -216,7 +216,7 @@ def unit_test(parser, args, unknown_args):
     # Ensure clingo is available before switching to the
     # mock configuration used by unit tests
     with spack.bootstrap.ensure_bootstrap_configuration():
-        spack.bootstrap.ensure_core_dependencies()
+        spack.bootstrap.ensure_clingo_importable_or_raise()
         if pytest is None:
             spack.bootstrap.ensure_environment_dependencies()
             import pytest

lib/spack/spack/cmd/verify.py

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

lib/spack/spack/compilers/__init__.py

@@ -801,17 +801,17 @@ def _extract_compiler_paths(spec: "spack.spec.Spec") -> Optional[Dict[str, str]]
     def _extract_os_and_target(spec: "spack.spec.Spec"):
         if not spec.architecture:
             host_platform = spack.platforms.host()
-            operating_system = host_platform.operating_system("default_os")
+            operating_system = host_platform.default_operating_system()
-            target = host_platform.target("default_target")
+            target = host_platform.default_target()
         else:
             target = spec.architecture.target
             if not target:
-                target = spack.platforms.host().target("default_target")
+                target = spack.platforms.host().default_target()
 
             operating_system = spec.os
             if not operating_system:
                 host_platform = spack.platforms.host()
-                operating_system = host_platform.operating_system("default_os")
+                operating_system = host_platform.default_operating_system()
         return operating_system, target
 
 

lib/spack/spack/concretize.py

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

lib/spack/spack/config.py

@@ -32,9 +32,10 @@
 import copy
 import functools
 import os
+import os.path
 import re
 import sys
-from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union
+from typing import Any, Callable, Dict, Generator, List, NamedTuple, Optional, Tuple, Union
 
 import jsonschema
 
@@ -42,7 +43,6 @@
 
 import spack.error
 import spack.paths
-import spack.platforms
 import spack.schema
 import spack.schema.bootstrap
 import spack.schema.cdash
@@ -53,23 +53,28 @@
 import spack.schema.definitions
 import spack.schema.develop
 import spack.schema.env
+import spack.schema.env_vars
+import spack.schema.include
+import spack.schema.merged
 import spack.schema.mirrors
 import spack.schema.modules
 import spack.schema.packages
 import spack.schema.repos
 import spack.schema.upstreams
 import spack.schema.view
-
+import spack.util.remote_file_cache as rfc_util
-# Hacked yaml for configuration files preserves line numbers.
 import spack.util.spack_yaml as syaml
-import spack.util.web as web_util
 from spack.util.cpus import cpus_available
 
+from .enums import ConfigScopePriority
+
 #: Dict from section names -> schema for that section
 SECTION_SCHEMAS: Dict[str, Any] = {
     "compilers": spack.schema.compilers.schema,
     "concretizer": spack.schema.concretizer.schema,
     "definitions": spack.schema.definitions.schema,
+    "env_vars": spack.schema.env_vars.schema,
+    "include": spack.schema.include.schema,
     "view": spack.schema.view.schema,
     "develop": spack.schema.develop.schema,
     "mirrors": spack.schema.mirrors.schema,
@@ -117,6 +122,17 @@
 #: Type used for raw YAML configuration
 YamlConfigDict = Dict[str, Any]
 
+#: prefix for name of included configuration scopes
+INCLUDE_SCOPE_PREFIX = "include"
+
+#: safeguard for recursive includes -- maximum include depth
+MAX_RECURSIVE_INCLUDES = 100
+
+
+def _include_cache_location():
+    """Location to cache included configuration files."""
+    return os.path.join(spack.paths.user_cache_path, "includes")
+
 
 class ConfigScope:
     def __init__(self, name: str) -> None:
@@ -124,6 +140,9 @@ def __init__(self, name: str) -> None:
         self.writable = False
         self.sections = syaml.syaml_dict()
 
+        #: names of any included scopes
+        self.included_scopes: List[str] = []
+
     def get_section_filename(self, section: str) -> str:
         raise NotImplementedError
 
@@ -406,26 +425,18 @@ def _method(self, *args, **kwargs):
     return _method
 
 
-class Configuration:
+ScopeWithOptionalPriority = Union[ConfigScope, Tuple[int, ConfigScope]]
-    """A full Spack configuration, from a hierarchy of config files.
+ScopeWithPriority = Tuple[int, ConfigScope]
 
-    This class makes it easy to add a new scope on top of an existing one.
+
-    """
+class Configuration:
+    """A hierarchical configuration, merging a number of scopes at different priorities."""
 
     # convert to typing.OrderedDict when we drop 3.6, or OrderedDict when we reach 3.9
-    scopes: Dict[str, ConfigScope]
+    scopes: lang.PriorityOrderedMapping[str, ConfigScope]
 
-    def __init__(self, *scopes: ConfigScope) -> None:
+    def __init__(self) -> None:
-        """Initialize a configuration with an initial list of scopes.
+        self.scopes = lang.PriorityOrderedMapping()
-
-        Args:
-            scopes: list of scopes to add to this
-                Configuration, ordered from lowest to highest precedence
-
-        """
-        self.scopes = collections.OrderedDict()
-        for scope in scopes:
-            self.push_scope(scope)
         self.format_updates: Dict[str, List[ConfigScope]] = collections.defaultdict(list)
 
     def ensure_unwrapped(self) -> "Configuration":
@@ -433,36 +444,64 @@ def ensure_unwrapped(self) -> "Configuration":
         return self
 
     def highest(self) -> ConfigScope:
-        """Scope with highest precedence"""
+        """Scope with the highest precedence"""
-        return next(reversed(self.scopes.values()))  # type: ignore
+        return next(self.scopes.reversed_values())  # type: ignore
 
     @_config_mutator
-    def ensure_scope_ordering(self):
+    def push_scope(
-        """Ensure that scope order matches documented precedent"""
+        self, scope: ConfigScope, priority: Optional[int] = None, _depth: int = 0
-        # FIXME: We also need to consider that custom configurations and other orderings
+    ) -> None:
-        # may not be preserved correctly
+        """Adds a scope to the Configuration, at a given priority.
-        if "command_line" in self.scopes:
-            # TODO (when dropping python 3.6): self.scopes.move_to_end
-            self.scopes["command_line"] = self.remove_scope("command_line")
 
-    @_config_mutator
+        If a priority is not given, it is assumed to be the current highest priority.
-    def push_scope(self, scope: ConfigScope) -> None:
-        """Add a higher precedence scope to the Configuration."""
-        tty.debug(f"[CONFIGURATION: PUSH SCOPE]: {str(scope)}", level=2)
-        self.scopes[scope.name] = scope
 
-    @_config_mutator
+        Args:
-    def pop_scope(self) -> ConfigScope:
+            scope: scope to be added
-        """Remove the highest precedence scope and return it."""
+            priority: priority of the scope
-        name, scope = self.scopes.popitem(last=True)  # type: ignore[call-arg]
+        """
-        tty.debug(f"[CONFIGURATION: POP SCOPE]: {str(scope)}", level=2)
+        tty.debug(f"[CONFIGURATION: PUSH SCOPE]: {str(scope)}, priority={priority}", level=2)
-        return scope
+
+        # TODO: As a follow on to #48784, change this to create a graph of the
+        # TODO: includes AND ensure properly sorted such that the order included
+        # TODO: at the highest level is reflected in the value of an option that
+        # TODO: is set in multiple included files.
+        # before pushing the scope itself, push any included scopes recursively, at same priority
+        includes = scope.get_section("include")
+        if includes:
+            include_paths = [included_path(data) for data in includes["include"]]
+            for path in reversed(include_paths):
+                included_scope = include_path_scope(path)
+                if not included_scope:
+                    continue
+
+                if _depth + 1 > MAX_RECURSIVE_INCLUDES:  # make sure we're not recursing endlessly
+                    mark = path.path._start_mark if syaml.marked(path.path) else ""  # type: ignore
+                    raise RecursiveIncludeError(
+                        f"Maximum include recursion exceeded in {path.path}", str(mark)
+                    )
+
+                # record this inclusion so that remove_scope() can use it
+                scope.included_scopes.append(included_scope.name)
+                self.push_scope(included_scope, priority=priority, _depth=_depth + 1)
+
+        self.scopes.add(scope.name, value=scope, priority=priority)
 
     @_config_mutator
     def remove_scope(self, scope_name: str) -> Optional[ConfigScope]:
-        """Remove scope by name; has no effect when ``scope_name`` does not exist"""
+        """Removes a scope by name, and returns it. If the scope does not exist, returns None."""
-        scope = self.scopes.pop(scope_name, None)
+        try:
-        tty.debug(f"[CONFIGURATION: POP SCOPE]: {str(scope)}", level=2)
+            scope = self.scopes.remove(scope_name)
+            tty.debug(f"[CONFIGURATION: REMOVE SCOPE]: {str(scope)}", level=2)
+        except KeyError as e:
+            tty.debug(f"[CONFIGURATION: REMOVE SCOPE]: {e}", level=2)
+            return None
+
+        # transitively remove included scopes
+        for inc in scope.included_scopes:
+            assert inc in self.scopes, f"Included scope '{inc}' was never added to configuration!"
+            self.remove_scope(inc)
+        scope.included_scopes.clear()  # clean up includes for bookkeeping
+
         return scope
 
     @property
@@ -471,15 +510,13 @@ def writable_scopes(self) -> Generator[ConfigScope, None, None]:
         return (s for s in self.scopes.values() if s.writable)
 
     def highest_precedence_scope(self) -> ConfigScope:
-        """Writable scope with highest precedence."""
+        """Writable scope with the highest precedence."""
-        return next(s for s in reversed(self.scopes.values()) if s.writable)  # type: ignore
+        return next(s for s in self.scopes.reversed_values() if s.writable)
 
     def highest_precedence_non_platform_scope(self) -> ConfigScope:
-        """Writable non-platform scope with highest precedence"""
+        """Writable non-platform scope with the highest precedence"""
         return next(
-            s
+            s for s in self.scopes.reversed_values() if s.writable and not s.is_platform_dependent
-            for s in reversed(self.scopes.values())  # type: ignore
-            if s.writable and not s.is_platform_dependent
         )
 
     def matching_scopes(self, reg_expr) -> List[ConfigScope]:
@@ -746,7 +783,7 @@ def override(
     """
     if isinstance(path_or_scope, ConfigScope):
         overrides = path_or_scope
-        CONFIG.push_scope(path_or_scope)
+        CONFIG.push_scope(path_or_scope, priority=None)
     else:
         base_name = _OVERRIDES_BASE_NAME
         # Ensure the new override gets a unique scope name
@@ -760,7 +797,7 @@ def override(
                 break
 
         overrides = InternalConfigScope(scope_name)
-        CONFIG.push_scope(overrides)
+        CONFIG.push_scope(overrides, priority=None)
         CONFIG.set(path_or_scope, value, scope=scope_name)
 
     try:
@@ -770,13 +807,86 @@ def override(
         assert scope is overrides
 
 
-def _add_platform_scope(cfg: Configuration, name: str, path: str, writable: bool = True) -> None:
+def _add_platform_scope(
+    cfg: Configuration, name: str, path: str, priority: ConfigScopePriority, writable: bool = True
+) -> None:
     """Add a platform-specific subdirectory for the current platform."""
+    import spack.platforms  # circular dependency
+
     platform = spack.platforms.host().name
     scope = DirectoryConfigScope(
         f"{name}/{platform}", os.path.join(path, platform), writable=writable
     )
-    cfg.push_scope(scope)
+    cfg.push_scope(scope, priority=priority)
+
+
+#: Class for the relevance of an optional path conditioned on a limited
+#: python code that evaluates to a boolean and or explicit specification
+#: as optional.
+class IncludePath(NamedTuple):
+    path: str
+    when: str
+    sha256: str
+    optional: bool
+
+
+def included_path(entry: Union[str, dict]) -> IncludePath:
+    """Convert the included path entry into an IncludePath.
+
+    Args:
+        entry: include configuration entry
+
+    Returns: converted entry, where an empty ``when`` means the path is
+        not conditionally included
+    """
+    if isinstance(entry, str):
+        return IncludePath(path=entry, sha256="", when="", optional=False)
+
+    path = entry["path"]
+    sha256 = entry.get("sha256", "")
+    when = entry.get("when", "")
+    optional = entry.get("optional", False)
+    return IncludePath(path=path, sha256=sha256, when=when, optional=optional)
+
+
+def include_path_scope(include: IncludePath) -> Optional[ConfigScope]:
+    """Instantiate an appropriate configuration scope for the given path.
+
+    Args:
+        include: optional include path
+
+    Returns: configuration scope
+
+    Raises:
+        ValueError: included path has an unsupported URL scheme, is required
+            but does not exist; configuration stage directory argument is missing
+        ConfigFileError: unable to access remote configuration file(s)
+    """
+    # circular dependencies
+    import spack.spec
+
+    if (not include.when) or spack.spec.eval_conditional(include.when):
+        config_path = rfc_util.local_path(include.path, include.sha256, _include_cache_location)
+        if not config_path:
+            raise ConfigFileError(f"Unable to fetch remote configuration from {include.path}")
+
+        if os.path.isdir(config_path):
+            # directories are treated as regular ConfigScopes
+            config_name = f"{INCLUDE_SCOPE_PREFIX}:{os.path.basename(config_path)}"
+            tty.debug(f"Creating DirectoryConfigScope {config_name} for '{config_path}'")
+            return DirectoryConfigScope(config_name, config_path)
+
+        if os.path.exists(config_path):
+            # files are assumed to be SingleFileScopes
+            config_name = f"{INCLUDE_SCOPE_PREFIX}:{config_path}"
+            tty.debug(f"Creating SingleFileScope {config_name} for '{config_path}'")
+            return SingleFileScope(config_name, config_path, spack.schema.merged.schema)
+
+        if not include.optional:
+            path = f" at ({config_path})" if config_path != include.path else ""
+            raise ValueError(f"Required path ({include.path}) does not exist{path}")
+
+    return None
 
 
 def config_paths_from_entry_points() -> List[Tuple[str, str]]:
@@ -804,18 +914,17 @@ def config_paths_from_entry_points() -> List[Tuple[str, str]]:
     return config_paths
 
 
-def create() -> Configuration:
+def create_incremental() -> Generator[Configuration, None, None]:
     """Singleton Configuration instance.
 
     This constructs one instance associated with this module and returns
     it. It is bundled inside a function so that configuration can be
     initialized lazily.
     """
-    cfg = Configuration()
-
     # first do the builtin, hardcoded defaults
-    builtin = InternalConfigScope("_builtin", CONFIG_DEFAULTS)
+    cfg = create_from(
-    cfg.push_scope(builtin)
+        (ConfigScopePriority.BUILTIN, InternalConfigScope("_builtin", CONFIG_DEFAULTS))
+    )
 
     # Builtin paths to configuration files in Spack
     configuration_paths = [
@@ -845,16 +954,29 @@ def create() -> Configuration:
 
     # add each scope and its platform-specific directory
     for name, path in configuration_paths:
-        cfg.push_scope(DirectoryConfigScope(name, path))
+        cfg.push_scope(DirectoryConfigScope(name, path), priority=ConfigScopePriority.CONFIG_FILES)
+        # Each scope can have per-platform overrides in subdirectories
+        _add_platform_scope(cfg, name, path, priority=ConfigScopePriority.CONFIG_FILES)
 
-        # Each scope can have per-platfom overrides in subdirectories
+        # yield the config incrementally so that each config level's init code can get
-        _add_platform_scope(cfg, name, path)
+        # data from the one below. This can be tricky, but it enables us to have a
+        # single unified config system.
+        #
+        # TODO: think about whether we want to restrict what types of config can be used
+        #     at each level. e.g., we may want to just more forcibly disallow remote
+        #     config (which uses ssl and other config options) for some of the scopes,
+        #     to make the bootstrap issues more explicit, even if allowing config scope
+        #     init to reference lower scopes is more flexible.
+        yield cfg
 
-    return cfg
+
+def create() -> Configuration:
+    """Create a configuration using create_incremental(), return the last yielded result."""
+    return list(create_incremental())[-1]
 
 
 #: This is the singleton configuration instance for Spack.
-CONFIG: Configuration = lang.Singleton(create)  # type: ignore
+CONFIG: Configuration = lang.Singleton(create_incremental)  # type: ignore
 
 
 def add_from_file(filename: str, scope: Optional[str] = None) -> None:
@@ -950,10 +1072,11 @@ def set(path: str, value: Any, scope: Optional[str] = None) -> None:
 
     Accepts the path syntax described in ``get()``.
     """
-    return CONFIG.set(path, value, scope)
+    result = CONFIG.set(path, value, scope)
+    return result
 
 
-def scopes() -> Dict[str, ConfigScope]:
+def scopes() -> lang.PriorityOrderedMapping[str, ConfigScope]:
     """Convenience function to get list of configuration scopes."""
     return CONFIG.scopes
 
@@ -1407,7 +1530,7 @@ def ensure_latest_format_fn(section: str) -> Callable[[YamlConfigDict], bool]:
 
 @contextlib.contextmanager
 def use_configuration(
-    *scopes_or_paths: Union[ConfigScope, str]
+    *scopes_or_paths: Union[ScopeWithOptionalPriority, str]
 ) -> Generator[Configuration, None, None]:
     """Use the configuration scopes passed as arguments within the context manager.
 
@@ -1422,7 +1545,7 @@ def use_configuration(
     global CONFIG
 
     # Normalize input and construct a Configuration object
-    configuration = _config_from(scopes_or_paths)
+    configuration = create_from(*scopes_or_paths)
     CONFIG.clear_caches(), configuration.clear_caches()
 
     saved_config, CONFIG = CONFIG, configuration
@@ -1433,115 +1556,44 @@ def use_configuration(
         CONFIG = saved_config
 
 
+def _normalize_input(entry: Union[ScopeWithOptionalPriority, str]) -> ScopeWithPriority:
+    if isinstance(entry, tuple):
+        return entry
+
+    default_priority = ConfigScopePriority.CONFIG_FILES
+    if isinstance(entry, ConfigScope):
+        return default_priority, entry
+
+    # Otherwise we need to construct it
+    path = os.path.normpath(entry)
+    assert os.path.isdir(path), f'"{path}" must be a directory'
+    name = os.path.basename(path)
+    return default_priority, DirectoryConfigScope(name, path)
+
+
 @lang.memoized
-def _config_from(scopes_or_paths: List[Union[ConfigScope, str]]) -> Configuration:
+def create_from(*scopes_or_paths: Union[ScopeWithOptionalPriority, str]) -> Configuration:
-    scopes = []
+    """Creates a configuration object from the scopes passed in input.
-    for scope_or_path in scopes_or_paths:
-        # If we have a config scope we are already done
-        if isinstance(scope_or_path, ConfigScope):
-            scopes.append(scope_or_path)
-            continue
-
-        # Otherwise we need to construct it
-        path = os.path.normpath(scope_or_path)
-        assert os.path.isdir(path), f'"{path}" must be a directory'
-        name = os.path.basename(path)
-        scopes.append(DirectoryConfigScope(name, path))
-
-    configuration = Configuration(*scopes)
-    return configuration
-
-
-def raw_github_gitlab_url(url: str) -> str:
-    """Transform a github URL to the raw form to avoid undesirable html.
 
     Args:
-        url: url to be converted to raw form
+        *scopes_or_paths: either a tuple of (priority, ConfigScope), or a ConfigScope, or a string
+            If priority is not given, it is assumed to be ConfigScopePriority.CONFIG_FILES. If a
+            string is given, a DirectoryConfigScope is created from it.
 
-    Returns:
+    Examples:
-        Raw github/gitlab url or the original url
+
+        >>> builtin_scope = InternalConfigScope("_builtin", {"config": {"build_jobs": 1}})
+        >>> cl_scope = InternalConfigScope("command_line", {"config": {"build_jobs": 10}})
+        >>> cfg = create_from(
+        ...     (ConfigScopePriority.COMMAND_LINE, cl_scope),
+        ...     (ConfigScopePriority.BUILTIN, builtin_scope)
+        ... )
     """
-    # Note we rely on GitHub to redirect the 'raw' URL returned here to the
+    scopes_with_priority = [_normalize_input(x) for x in scopes_or_paths]
-    # actual URL under https://raw.githubusercontent.com/ with '/blob'
+    result = Configuration()
-    # removed and or, '/blame' if needed.
+    for priority, scope in scopes_with_priority:
-    if "github" in url or "gitlab" in url:
+        result.push_scope(scope, priority=priority)
-        return url.replace("/blob/", "/raw/")
+    return result
-
-    return url
-
-
-def collect_urls(base_url: str) -> list:
-    """Return a list of configuration URLs.
-
-    Arguments:
-        base_url: URL for a configuration (yaml) file or a directory
-            containing yaml file(s)
-
-    Returns:
-        List of configuration file(s) or empty list if none
-    """
-    if not base_url:
-        return []
-
-    extension = ".yaml"
-
-    if base_url.endswith(extension):
-        return [base_url]
-
-    # Collect configuration URLs if the base_url is a "directory".
-    _, links = web_util.spider(base_url, 0)
-    return [link for link in links if link.endswith(extension)]
-
-
-def fetch_remote_configs(url: str, dest_dir: str, skip_existing: bool = True) -> str:
-    """Retrieve configuration file(s) at the specified URL.
-
-    Arguments:
-        url: URL for a configuration (yaml) file or a directory containing
-            yaml file(s)
-        dest_dir: destination directory
-        skip_existing: Skip files that already exist in dest_dir if
-            ``True``; otherwise, replace those files
-
-    Returns:
-        Path to the corresponding file if URL is or contains a
-        single file and it is the only file in the destination directory or
-        the root (dest_dir) directory if multiple configuration files exist
-        or are retrieved.
-    """
-
-    def _fetch_file(url):
-        raw = raw_github_gitlab_url(url)
-        tty.debug(f"Reading config from url {raw}")
-        return web_util.fetch_url_text(raw, dest_dir=dest_dir)
-
-    if not url:
-        raise ConfigFileError("Cannot retrieve configuration without a URL")
-
-    # Return the local path to the cached configuration file OR to the
-    # directory containing the cached configuration files.
-    config_links = collect_urls(url)
-    existing_files = os.listdir(dest_dir) if os.path.isdir(dest_dir) else []
-
-    paths = []
-    for config_url in config_links:
-        basename = os.path.basename(config_url)
-        if skip_existing and basename in existing_files:
-            tty.warn(
-                f"Will not fetch configuration from {config_url} since a "
-                f"version already exists in {dest_dir}"
-            )
-            path = os.path.join(dest_dir, basename)
-        else:
-            path = _fetch_file(config_url)
-
-        if path:
-            paths.append(path)
-
-    if paths:
-        return dest_dir if len(paths) > 1 else paths[0]
-
-    raise ConfigFileError(f"Cannot retrieve configuration (yaml) from {url}")
 
 
 def get_mark_from_yaml_data(obj):
@@ -1670,3 +1722,7 @@ def get_path(path, data):
 
         # give up and return None if nothing worked
         return None
+
+
+class RecursiveIncludeError(spack.error.SpackError):
+    """Too many levels of recursive includes."""

lib/spack/spack/container/__init__.py

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

lib/spack/spack/container/images.py

@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Manages the details on the images used in the various stages."""
 import json
-import os.path
+import os
 import shlex
 import sys
 

lib/spack/spack/database.py

@@ -41,6 +41,8 @@
     Union,
 )
 
+import spack.repo
+
 try:
     import uuid
 
@@ -123,6 +125,15 @@
     "deprecated_for",
 )
 
+#: File where the database is written
+INDEX_JSON_FILE = "index.json"
+
+# Verifier file to check last modification of the DB
+_INDEX_VERIFIER_FILE = "index_verifier"
+
+# Lockfile for the database
+_LOCK_FILE = "lock"
+
 
 @llnl.util.lang.memoized
 def _getfqdn():
@@ -260,7 +271,7 @@ class ForbiddenLockError(SpackError):
 
 class ForbiddenLock:
     def __getattr__(self, name):
-        raise ForbiddenLockError("Cannot access attribute '{0}' of lock".format(name))
+        raise ForbiddenLockError(f"Cannot access attribute '{name}' of lock")
 
     def __reduce__(self):
         return ForbiddenLock, tuple()
@@ -589,9 +600,9 @@ def __init__(
         self.layout = layout
 
         # Set up layout of database files within the db dir
-        self._index_path = self.database_directory / "index.json"
+        self._index_path = self.database_directory / INDEX_JSON_FILE
-        self._verifier_path = self.database_directory / "index_verifier"
+        self._verifier_path = self.database_directory / _INDEX_VERIFIER_FILE
-        self._lock_path = self.database_directory / "lock"
+        self._lock_path = self.database_directory / _LOCK_FILE
 
         self.is_upstream = is_upstream
         self.last_seen_verifier = ""
@@ -606,7 +617,7 @@ def __init__(
 
         # initialize rest of state.
         self.db_lock_timeout = lock_cfg.database_timeout
-        tty.debug("DATABASE LOCK TIMEOUT: {0}s".format(str(self.db_lock_timeout)))
+        tty.debug(f"DATABASE LOCK TIMEOUT: {str(self.db_lock_timeout)}s")
 
         self.lock: Union[ForbiddenLock, lk.Lock]
         if self.is_upstream:
@@ -1090,7 +1101,7 @@ def _read(self):
                 self._state_is_inconsistent = False
             return
         elif self.is_upstream:
-            tty.warn("upstream not found: {0}".format(self._index_path))
+            tty.warn(f"upstream not found: {self._index_path}")
 
     def _add(
         self,
@@ -1547,7 +1558,12 @@ def _query(
         # If we did fine something, the query spec can't be virtual b/c we matched an actual
         # package installation, so skip the virtual check entirely. If we *didn't* find anything,
         # check all the deferred specs *if* the query is virtual.
-        if not results and query_spec is not None and deferred and query_spec.virtual:
+        if (
+            not results
+            and query_spec is not None
+            and deferred
+            and spack.repo.PATH.is_virtual(query_spec.name)
+        ):
             results = [spec for spec in deferred if spec.satisfies(query_spec)]
 
         return results

lib/spack/spack/detection/common.py

@@ -15,7 +15,6 @@
 import glob
 import itertools
 import os
-import os.path
 import pathlib
 import re
 import sys
@@ -311,7 +310,7 @@ def find_windows_kit_roots() -> List[str]:
 
     @staticmethod
     def find_windows_kit_bin_paths(
-        kit_base: Union[Optional[str], Optional[list]] = None
+        kit_base: Union[Optional[str], Optional[list]] = None,
     ) -> List[str]:
         """Returns Windows kit bin directory per version"""
         kit_base = WindowsKitExternalPaths.find_windows_kit_roots() if not kit_base else kit_base
@@ -326,7 +325,7 @@ def find_windows_kit_bin_paths(
 
     @staticmethod
     def find_windows_kit_lib_paths(
-        kit_base: Union[Optional[str], Optional[list]] = None
+        kit_base: Union[Optional[str], Optional[list]] = None,
     ) -> List[str]:
         """Returns Windows kit lib directory per version"""
         kit_base = WindowsKitExternalPaths.find_windows_kit_roots() if not kit_base else kit_base

lib/spack/spack/detection/path.py

@@ -7,7 +7,6 @@
 import collections
 import concurrent.futures
 import os
-import os.path
 import re
 import sys
 import traceback
@@ -244,7 +243,7 @@ def prefix_from_path(self, *, path: str) -> str:
         raise NotImplementedError("must be implemented by derived classes")
 
     def detect_specs(
-        self, *, pkg: Type["spack.package_base.PackageBase"], paths: List[str]
+        self, *, pkg: Type["spack.package_base.PackageBase"], paths: Iterable[str]
     ) -> List["spack.spec.Spec"]:
         """Given a list of files matching the search patterns, returns a list of detected specs.
 
@@ -260,6 +259,8 @@ def detect_specs(
             )
             return []
 
+        from spack.repo import PATH as repo_path
+
         result = []
         for candidate_path, items_in_prefix in _group_by_prefix(
             llnl.util.lang.dedupe(paths)
@@ -306,7 +307,10 @@ def detect_specs(
 
                 resolved_specs[spec] = candidate_path
                 try:
-                    spec.validate_detection()
+                    # Validate the spec calling a package specific method
+                    pkg_cls = repo_path.get_pkg_class(spec.name)
+                    validate_fn = getattr(pkg_cls, "validate_detected_spec", lambda x, y: None)
+                    validate_fn(spec, spec.extra_attributes)
                 except Exception as e:
                     msg = (
                         f'"{spec}" has been detected on the system but will '

lib/spack/spack/directives.py

@@ -32,7 +32,7 @@ class OpenMpi(Package):
 """
 import collections
 import collections.abc
-import os.path
+import os
 import re
 from typing import Any, Callable, List, Optional, Tuple, Type, Union
 
@@ -568,7 +568,7 @@ def patch(
     """
 
     def _execute_patch(
-        pkg_or_dep: Union[Type[spack.package_base.PackageBase], Dependency]
+        pkg_or_dep: Union[Type[spack.package_base.PackageBase], Dependency],
     ) -> None:
         pkg = pkg_or_dep.pkg if isinstance(pkg_or_dep, Dependency) else pkg_or_dep
 

lib/spack/spack/directory_layout.py

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

lib/spack/spack/enums.py

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

lib/spack/spack/environment/environment.py

@@ -10,8 +10,6 @@
 import re
 import shutil
 import stat
-import urllib.parse
-import urllib.request
 import warnings
 from typing import Any, Dict, Iterable, List, Optional, Sequence, Tuple, Union
 
@@ -32,7 +30,6 @@
 import spack.paths
 import spack.repo
 import spack.schema.env
-import spack.schema.merged
 import spack.spec
 import spack.spec_list
 import spack.store
@@ -43,7 +40,6 @@
 import spack.util.path
 import spack.util.spack_json as sjson
 import spack.util.spack_yaml as syaml
-import spack.util.url
 from spack import traverse
 from spack.installer import PackageInstaller
 from spack.schema.env import TOP_LEVEL_KEY
@@ -51,6 +47,8 @@
 from spack.spec_list import SpecList
 from spack.util.path import substitute_path_variables
 
+from ..enums import ConfigScopePriority
+
 SpecPair = spack.concretize.SpecPair
 
 #: environment variable used to indicate the active environment
@@ -387,6 +385,7 @@ def create_in_dir(
                 # dev paths in this environment to refer to their original
                 # locations.
                 _rewrite_relative_dev_paths_on_relocation(env, init_file_dir)
+                _rewrite_relative_repos_paths_on_relocation(env, init_file_dir)
 
     return env
 
@@ -403,8 +402,8 @@ def _rewrite_relative_dev_paths_on_relocation(env, init_file_dir):
             dev_path = substitute_path_variables(entry["path"])
             expanded_path = spack.util.path.canonicalize_path(dev_path, default_wd=init_file_dir)
 
-            # Skip if the expanded path is the same (e.g. when absolute)
+            # Skip if the substituted and expanded path is the same (e.g. when absolute)
-            if dev_path == expanded_path:
+            if entry["path"] == expanded_path:
                 continue
 
             tty.debug("Expanding develop path for {0} to {1}".format(name, expanded_path))
@@ -419,6 +418,34 @@ def _rewrite_relative_dev_paths_on_relocation(env, init_file_dir):
         env._re_read()
 
 
+def _rewrite_relative_repos_paths_on_relocation(env, init_file_dir):
+    """When initializing the environment from a manifest file and we plan
+    to store the environment in a different directory, we have to rewrite
+    relative repo paths to absolute ones and expand environment variables."""
+    with env:
+        repos_specs = spack.config.get("repos", default={}, scope=env.scope_name)
+        if not repos_specs:
+            return
+        for i, entry in enumerate(repos_specs):
+            repo_path = substitute_path_variables(entry)
+            expanded_path = spack.util.path.canonicalize_path(repo_path, default_wd=init_file_dir)
+
+            # Skip if the substituted and expanded path is the same (e.g. when absolute)
+            if entry == expanded_path:
+                continue
+
+            tty.debug("Expanding repo path for {0} to {1}".format(entry, expanded_path))
+
+            repos_specs[i] = expanded_path
+
+        spack.config.set("repos", repos_specs, scope=env.scope_name)
+
+        env.repos_specs = None
+        # If we changed the environment's spack.yaml scope, that will not be reflected
+        # in the manifest that we read
+        env._re_read()
+
+
 def environment_dir_from_name(name: str, exists_ok: bool = True) -> str:
     """Returns the directory associated with a named environment.
 
@@ -546,13 +573,6 @@ def _write_yaml(data, str_or_file):
     syaml.dump_config(data, str_or_file, default_flow_style=False)
 
 
-def _eval_conditional(string):
-    """Evaluate conditional definitions using restricted variable scope."""
-    valid_variables = spack.spec.get_host_environment()
-    valid_variables.update({"re": re, "env": os.environ})
-    return eval(string, valid_variables)
-
-
 def _is_dev_spec_and_has_changed(spec):
     """Check if the passed spec is a dev build and whether it has changed since the
     last installation"""
@@ -581,7 +601,7 @@ def _error_on_nonempty_view_dir(new_root):
     # Check if the target path lexists
     try:
         st = os.lstat(new_root)
-    except (IOError, OSError):
+    except OSError:
         return
 
     # Empty directories are fine
@@ -861,7 +881,7 @@ def regenerate(self, concrete_roots: List[Spec]) -> None:
         ):
             try:
                 shutil.rmtree(old_root)
-            except (IOError, OSError) as e:
+            except OSError as e:
                 msg = "Failed to remove old view at %s\n" % old_root
                 msg += str(e)
                 tty.warn(msg)
@@ -985,7 +1005,7 @@ def _process_definition(self, entry):
         """Process a single spec definition item."""
         when_string = entry.get("when")
         if when_string is not None:
-            when = _eval_conditional(when_string)
+            when = spack.spec.eval_conditional(when_string)
             assert len([x for x in entry if x != "when"]) == 1
         else:
             when = True
@@ -1530,9 +1550,6 @@ def _get_specs_to_concretize(
         return new_user_specs, kept_user_specs, specs_to_concretize
 
     def _concretize_together_where_possible(self, tests: bool = False) -> Sequence[SpecPair]:
-        # Avoid cyclic dependency
-        import spack.solver.asp
-
         # Exit early if the set of concretized specs is the set of user specs
         new_user_specs, _, specs_to_concretize = self._get_specs_to_concretize()
         if not new_user_specs:
@@ -2392,6 +2409,8 @@ def invalidate_repository_cache(self):
 
     def __enter__(self):
         self._previous_active = _active_environment
+        if self._previous_active:
+            deactivate()
         activate(self)
         return self
 
@@ -2554,7 +2573,7 @@ def is_latest_format(manifest):
     try:
         with open(manifest, encoding="utf-8") as f:
             data = syaml.load(f)
-    except (OSError, IOError):
+    except OSError:
         return True
     top_level_key = _top_level_key(data)
     changed = spack.schema.env.update(data[top_level_key])
@@ -2634,6 +2653,35 @@ def _ensure_env_dir():
 
     shutil.copy(envfile, target_manifest)
 
+    # Copy relative path includes that live inside the environment dir
+    try:
+        manifest = EnvironmentManifestFile(environment_dir)
+    except Exception:
+        # error handling for bad manifests is handled on other code paths
+        return
+
+    # TODO: make this recursive
+    includes = manifest[TOP_LEVEL_KEY].get("include", [])
+    for include in includes:
+        included_path = spack.config.included_path(include)
+        path = included_path.path
+        if os.path.isabs(path):
+            continue
+
+        abspath = pathlib.Path(os.path.normpath(environment_dir / path))
+        common_path = pathlib.Path(os.path.commonpath([environment_dir, abspath]))
+        if common_path != environment_dir:
+            tty.debug(f"Will not copy relative include file from outside environment: {path}")
+            continue
+
+        orig_abspath = os.path.normpath(envfile.parent / path)
+        if not os.path.exists(orig_abspath):
+            tty.warn(f"Included file does not exist; will not copy: '{path}'")
+            continue
+
+        fs.touchp(abspath)
+        shutil.copy(orig_abspath, abspath)
+
 
 class EnvironmentManifestFile(collections.abc.Mapping):
     """Manages the in-memory representation of a manifest file, and its synchronization
@@ -2851,7 +2899,7 @@ def extract_name(_item):
                 continue
 
             condition_str = item.get("when", "True")
-            if not _eval_conditional(condition_str):
+            if not spack.spec.eval_conditional(condition_str):
                 continue
 
             yield idx, item
@@ -2912,127 +2960,20 @@ def __iter__(self):
     def __str__(self):
         return str(self.manifest_file)
 
-    @property
-    def included_config_scopes(self) -> List[spack.config.ConfigScope]:
-        """List of included configuration scopes from the manifest.
-
-        Scopes are listed in the YAML file in order from highest to
-        lowest precedence, so configuration from earlier scope will take
-        precedence over later ones.
-
-        This routine returns them in the order they should be pushed onto
-        the internal scope stack (so, in reverse, from lowest to highest).
-
-        Returns: Configuration scopes associated with the environment manifest
-
-        Raises:
-            SpackEnvironmentError: if the manifest includes a remote file but
-                no configuration stage directory has been identified
-        """
-        scopes: List[spack.config.ConfigScope] = []
-
-        # load config scopes added via 'include:', in reverse so that
-        # highest-precedence scopes are last.
-        includes = self[TOP_LEVEL_KEY].get("include", [])
-        missing = []
-        for i, config_path in enumerate(reversed(includes)):
-            # allow paths to contain spack config/environment variables, etc.
-            config_path = substitute_path_variables(config_path)
-            include_url = urllib.parse.urlparse(config_path)
-
-            # If scheme is not valid, config_path is not a url
-            # of a type Spack is generally aware
-            if spack.util.url.validate_scheme(include_url.scheme):
-                # Transform file:// URLs to direct includes.
-                if include_url.scheme == "file":
-                    config_path = urllib.request.url2pathname(include_url.path)
-
-                # Any other URL should be fetched.
-                elif include_url.scheme in ("http", "https", "ftp"):
-                    # Stage any remote configuration file(s)
-                    staged_configs = (
-                        os.listdir(self.config_stage_dir)
-                        if os.path.exists(self.config_stage_dir)
-                        else []
-                    )
-                    remote_path = urllib.request.url2pathname(include_url.path)
-                    basename = os.path.basename(remote_path)
-                    if basename in staged_configs:
-                        # Do NOT re-stage configuration files over existing
-                        # ones with the same name since there is a risk of
-                        # losing changes (e.g., from 'spack config update').
-                        tty.warn(
-                            "Will not re-stage configuration from {0} to avoid "
-                            "losing changes to the already staged file of the "
-                            "same name.".format(remote_path)
-                        )
-
-                        # Recognize the configuration stage directory
-                        # is flattened to ensure a single copy of each
-                        # configuration file.
-                        config_path = self.config_stage_dir
-                        if basename.endswith(".yaml"):
-                            config_path = os.path.join(config_path, basename)
-                    else:
-                        staged_path = spack.config.fetch_remote_configs(
-                            config_path, str(self.config_stage_dir), skip_existing=True
-                        )
-                        if not staged_path:
-                            raise SpackEnvironmentError(
-                                "Unable to fetch remote configuration {0}".format(config_path)
-                            )
-                        config_path = staged_path
-
-                elif include_url.scheme:
-                    raise ValueError(
-                        f"Unsupported URL scheme ({include_url.scheme}) for "
-                        f"environment include: {config_path}"
-                    )
-
-            # treat relative paths as relative to the environment
-            if not os.path.isabs(config_path):
-                config_path = os.path.join(self.manifest_dir, config_path)
-                config_path = os.path.normpath(os.path.realpath(config_path))
-
-            if os.path.isdir(config_path):
-                # directories are treated as regular ConfigScopes
-                config_name = f"env:{self.name}:{os.path.basename(config_path)}"
-                tty.debug(f"Creating DirectoryConfigScope {config_name} for '{config_path}'")
-                scopes.append(spack.config.DirectoryConfigScope(config_name, config_path))
-            elif os.path.exists(config_path):
-                # files are assumed to be SingleFileScopes
-                config_name = f"env:{self.name}:{config_path}"
-                tty.debug(f"Creating SingleFileScope {config_name} for '{config_path}'")
-                scopes.append(
-                    spack.config.SingleFileScope(
-                        config_name, config_path, spack.schema.merged.schema
-                    )
-                )
-            else:
-                missing.append(config_path)
-                continue
-
-        if missing:
-            msg = "Detected {0} missing include path(s):".format(len(missing))
-            msg += "\n   {0}".format("\n   ".join(missing))
-            raise spack.config.ConfigFileError(msg)
-
-        return scopes
-
     @property
     def env_config_scopes(self) -> List[spack.config.ConfigScope]:
         """A list of all configuration scopes for the environment manifest. On the first call this
         instantiates all the scopes, on subsequent calls it returns the cached list."""
         if self._config_scopes is not None:
             return self._config_scopes
+
         scopes: List[spack.config.ConfigScope] = [
-            *self.included_config_scopes,
             spack.config.SingleFileScope(
                 self.scope_name,
                 str(self.manifest_file),
                 spack.schema.env.schema,
                 yaml_path=[TOP_LEVEL_KEY],
-            ),
+            )
         ]
         ensure_no_disallowed_env_config_mods(scopes)
         self._config_scopes = scopes
@@ -3041,14 +2982,12 @@ def env_config_scopes(self) -> List[spack.config.ConfigScope]:
     def prepare_config_scope(self) -> None:
         """Add the manifest's scopes to the global configuration search path."""
         for scope in self.env_config_scopes:
-            spack.config.CONFIG.push_scope(scope)
+            spack.config.CONFIG.push_scope(scope, priority=ConfigScopePriority.ENVIRONMENT)
-        spack.config.CONFIG.ensure_scope_ordering()
 
     def deactivate_config_scope(self) -> None:
         """Remove any of the manifest's scopes from the global config path."""
         for scope in self.env_config_scopes:
             spack.config.CONFIG.remove_scope(scope.name)
-        spack.config.CONFIG.ensure_scope_ordering()
 
     @contextlib.contextmanager
     def use_config(self):

lib/spack/spack/environment/shell.py

@@ -10,6 +10,7 @@
 
 import spack.environment as ev
 import spack.repo
+import spack.schema.environment
 import spack.store
 from spack.util.environment import EnvironmentModifications
 
@@ -156,6 +157,11 @@ def activate(
     # MANPATH, PYTHONPATH, etc. All variables that end in PATH (case-sensitive)
     # become PATH variables.
     #
+
+    env_vars_yaml = env.manifest.configuration.get("env_vars", None)
+    if env_vars_yaml:
+        env_mods.extend(spack.schema.environment.parse(env_vars_yaml))
+
     try:
         if view and env.has_view(view):
             with spack.store.STORE.db.read_transaction():
@@ -189,6 +195,10 @@ def deactivate() -> EnvironmentModifications:
     if active is None:
         return env_mods
 
+    env_vars_yaml = active.manifest.configuration.get("env_vars", None)
+    if env_vars_yaml:
+        env_mods.extend(spack.schema.environment.parse(env_vars_yaml).reversed())
+
     active_view = os.getenv(ev.spack_env_view_var)
 
     if active_view and active.has_view(active_view):

lib/spack/spack/extensions.py

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

lib/spack/spack/fetch_strategy.py

@@ -25,7 +25,6 @@
 import functools
 import http.client
 import os
-import os.path
 import re
 import shutil
 import urllib.error
@@ -321,9 +320,15 @@ def _fetch_urllib(self, url):
 
         request = urllib.request.Request(url, headers={"User-Agent": web_util.SPACK_USER_AGENT})
 
+        if os.path.lexists(save_file):
+            os.remove(save_file)
+
         try:
             response = web_util.urlopen(request)
-        except (TimeoutError, urllib.error.URLError) as e:
+            tty.msg(f"Fetching {url}")
+            with open(save_file, "wb") as f:
+                shutil.copyfileobj(response, f)
+        except OSError as e:
             # clean up archive on failure.
             if self.archive_file:
                 os.remove(self.archive_file)
@@ -331,14 +336,6 @@ def _fetch_urllib(self, url):
                 os.remove(save_file)
             raise FailedDownloadError(e) from e
 
-        tty.msg(f"Fetching {url}")
-
-        if os.path.lexists(save_file):
-            os.remove(save_file)
-
-        with open(save_file, "wb") as f:
-            shutil.copyfileobj(response, f)
-
         # Save the redirected URL for error messages. Sometimes we're redirected to an arbitrary
         # mirror that is broken, leading to spurious download failures. In that case it's helpful
         # for users to know which URL was actually fetched.
@@ -535,11 +532,16 @@ def __init__(self, *, url: str, checksum: Optional[str] = None, **kwargs):
     @_needs_stage
     def fetch(self):
         file = self.stage.save_filename
-        tty.msg(f"Fetching {self.url}")
+
+        if os.path.lexists(file):
+            os.remove(file)
 
         try:
             response = self._urlopen(self.url)
-        except (TimeoutError, urllib.error.URLError) as e:
+            tty.msg(f"Fetching {self.url}")
+            with open(file, "wb") as f:
+                shutil.copyfileobj(response, f)
+        except OSError as e:
             # clean up archive on failure.
             if self.archive_file:
                 os.remove(self.archive_file)
@@ -547,12 +549,6 @@ def fetch(self):
                 os.remove(file)
             raise FailedDownloadError(e) from e
 
-        if os.path.lexists(file):
-            os.remove(file)
-
-        with open(file, "wb") as f:
-            shutil.copyfileobj(response, f)
-
 
 class VCSFetchStrategy(FetchStrategy):
     """Superclass for version control system fetch strategies.

lib/spack/spack/filesystem_view.py

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