unifyfs: new v2.0 release (#41851)

Add v2.0 release
Remove deprecated versions
Clean up dependencies for removed deprecated versions
Remove patches for removed deprecated versions

.github/workflows/audit.yaml

@@ -23,7 +23,7 @@ jobs:
         operating_system: ["ubuntu-latest", "macos-latest"]
     steps:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # @v2
       with:
         python-version: ${{inputs.python_version}}
     - name: Install Python packages

.github/workflows/bootstrap.yml

@@ -159,7 +159,7 @@ jobs:
           brew install cmake bison@2.7 tree
       - name: Checkout
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
-      - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # @v2
         with:
           python-version: "3.12"
       - name: Bootstrap clingo

.github/workflows/build-containers.yml

@@ -57,7 +57,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
 
-      - uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934
+      - uses: docker/metadata-action@9dc751fe249ad99385a2583ee0d084c400eee04e
         id: docker_meta
         with:
           images: |

.github/workflows/nightly-win-builds.yml

@@ -17,7 +17,7 @@ jobs:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
       with:
         python-version: 3.9
     - name: Install Python packages

.github/workflows/style/requirements.txt

@@ -1,7 +1,7 @@
-black==23.11.0
+black==23.12.1
 clingo==5.6.2
 flake8==6.1.0
-isort==5.12.0
-mypy==1.6.1
+isort==5.13.2
+mypy==1.8.0
 types-six==1.16.21.9
 vermin==1.6.0

.github/workflows/unit_tests.yaml

@@ -54,7 +54,7 @@ jobs:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # @v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install System packages
@@ -101,7 +101,7 @@ jobs:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # @v2
       with:
         python-version: '3.11'
     - name: Install System packages
@@ -159,7 +159,7 @@ jobs:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # @v2
       with:
         python-version: '3.11'
     - name: Install System packages
@@ -194,7 +194,7 @@ jobs:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # @v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Python packages

.github/workflows/valid-style.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
       with:
         python-version: '3.11'
         cache: 'pip'
@@ -38,7 +38,7 @@ jobs:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
       with:
         python-version: '3.11'
         cache: 'pip'

.github/workflows/windows_python.yml

@@ -18,7 +18,7 @@ jobs:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
       with:
         python-version: 3.9
     - name: Install Python packages
@@ -42,7 +42,7 @@ jobs:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
       with:
         python-version: 3.9
     - name: Install Python packages
@@ -66,7 +66,7 @@ jobs:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c
       with:
         python-version: 3.9
     - name: Install Python packages

CITATION.cff

@@ -31,13 +31,17 @@ type: software
 message: "If you are referencing Spack in a publication, please cite the paper below."
 title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
 abstract: >-
-  Large HPC centers spend considerable time supporting software for thousands of users, but the complexity of HPC software is quickly outpacing the capabilities of existing software management tools.
-  Scientific applications require specific versions of compilers, MPI, and other dependency libraries, so using a single, standard software stack is infeasible.
-  However, managing many configurations is difficult because the configuration space is combinatorial in size.
-  We introduce Spack, a tool used at Lawrence Livermore National Laboratory to manage this complexity.
-  Spack provides a novel, re- cursive specification syntax to invoke parametric builds of packages and dependencies.
-  It allows any number of builds to coexist on the same system, and it ensures that installed packages can find their dependencies, regardless of the environment.
-  We show through real-world use cases that Spack supports diverse and demanding applications, bringing order to HPC software chaos.
+  Large HPC centers spend considerable time supporting software for thousands of users, but the
+  complexity of HPC software is quickly outpacing the capabilities of existing software management
+  tools. Scientific applications require specific versions of compilers, MPI, and other dependency
+  libraries, so using a single, standard software stack is infeasible. However, managing many
+  configurations is difficult because the configuration space is combinatorial in size. We
+  introduce Spack, a tool used at Lawrence Livermore National Laboratory to manage this complexity.
+  Spack provides a novel, re- cursive specification syntax to invoke parametric builds of packages
+  and dependencies. It allows any number of builds to coexist on the same system, and it ensures
+  that installed packages can find their dependencies, regardless of the environment. We show
+  through real-world use cases that Spack supports diverse and demanding applications, bringing
+  order to HPC software chaos.
 preferred-citation:
   title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
   type: conference-paper
@@ -71,7 +75,7 @@ preferred-citation:
       type: doi
       value: 10.1145/2807591.2807623
     - description: "The DOE Document Release Number of the work"
-      type: other 
+      type: other
       value: "LLNL-CONF-669890"
 authors:
   - family-names: "Gamblin"

README.md

@@ -1,13 +1,34 @@
-# <img src="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo.svg" width="64" valign="middle" alt="Spack"/> Spack
+<div align="left">
 
-[![Unit Tests](https://github.com/spack/spack/workflows/linux%20tests/badge.svg)](https://github.com/spack/spack/actions)
-[![Bootstrapping](https://github.com/spack/spack/actions/workflows/bootstrap.yml/badge.svg)](https://github.com/spack/spack/actions/workflows/bootstrap.yml)
-[![codecov](https://codecov.io/gh/spack/spack/branch/develop/graph/badge.svg)](https://codecov.io/gh/spack/spack)
-[![Containers](https://github.com/spack/spack/actions/workflows/build-containers.yml/badge.svg)](https://github.com/spack/spack/actions/workflows/build-containers.yml)
-[![Read the Docs](https://readthedocs.org/projects/spack/badge/?version=latest)](https://spack.readthedocs.io)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![Slack](https://slack.spack.io/badge.svg)](https://slack.spack.io)
-[![Matrix](https://img.shields.io/matrix/spack-space%3Amatrix.org?label=Matrix)](https://matrix.to/#/#spack-space:matrix.org)
+<h2>
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo-white-text.svg" width="250">
+  <source media="(prefers-color-scheme: light)" srcset="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo-text.svg" width="250">
+  <img alt="Spack" src="https://cdn.rawgit.com/spack/spack/develop/share/spack/logo/spack-logo-text.svg" width="250">
+</picture>
+
+<br>
+<br clear="all">
+
+<a href="https://github.com/spack/spack/actions/workflows/ci.yml"><img src="https://github.com/spack/spack/workflows/ci/badge.svg" alt="CI Status"></a>
+<a href="https://github.com/spack/spack/actions/workflows/bootstrapping.yml"><img src="https://github.com/spack/spack/actions/workflows/bootstrap.yml/badge.svg" alt="Bootstrap Status"></a>
+<a href="https://github.com/spack/spack/actions/workflows/build-containers.yml"><img src="https://github.com/spack/spack/actions/workflows/build-containers.yml/badge.svg" alt="Containers Status"></a>
+<a href="https://spack.readthedocs.io"><img src="https://readthedocs.org/projects/spack/badge/?version=latest" alt="Documentation Status"></a>
+<a href="https://codecov.io/gh/spack/spack"><img src="https://codecov.io/gh/spack/spack/branch/develop/graph/badge.svg" alt="Code coverage"/></a>
+<a href="https://slack.spack.io"><img src="https://slack.spack.io/badge.svg" alt="Slack"/></a>
+<a href="https://matrix.to/#/#spack-space:matrix.org"><img src="https://img.shields.io/matrix/spack-space%3Amatrix.org?label=matrix" alt="Matrix"/></a>
+
+</h2>
+
+**[Getting Started] &nbsp; • &nbsp; [Config] &nbsp; • &nbsp; [Community] &nbsp; • &nbsp; [Contributing] &nbsp; • &nbsp; [Packaging Guide]**
+
+[Getting Started]: https://spack.readthedocs.io/en/latest/getting_started.html
+[Config]: https://spack.readthedocs.io/en/latest/configuration.html
+[Community]: #community
+[Contributing]: https://spack.readthedocs.io/en/latest/contribution_guide.html
+[Packaging Guide]: https://spack.readthedocs.io/en/latest/packaging_guide.html
+
+</div>
 
 Spack is a multi-platform package manager that builds and installs
 multiple versions and configurations of software. It works on Linux,
@@ -66,10 +87,11 @@ Resources:
 * **Matrix space**: [#spack-space:matrix.org](https://matrix.to/#/#spack-space:matrix.org):
   [bridged](https://github.com/matrix-org/matrix-appservice-slack#matrix-appservice-slack) to Slack.
 * [**Github Discussions**](https://github.com/spack/spack/discussions):
-  not just for discussions, but also Q&A.
-* **Mailing list**: [groups.google.com/d/forum/spack](https://groups.google.com/d/forum/spack)
+  for Q&A and discussions. Note the pinned discussions for announcements.
 * **Twitter**: [@spackpm](https://twitter.com/spackpm). Be sure to
   `@mention` us!
+* **Mailing list**: [groups.google.com/d/forum/spack](https://groups.google.com/d/forum/spack):
+  only for announcements. Please use other venues for discussions.
 
 Contributing
 ------------------------

lib/spack/docs/binary_caches.rst

@@ -153,7 +153,43 @@ keyring, and trusting all downloaded keys.
 List of popular build caches
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-* `Extreme-scale Scientific Software Stack (E4S) <https://e4s-project.github.io/>`_: `build cache <https://oaciss.uoregon.edu/e4s/inventory.html>`_
+* `Extreme-scale Scientific Software Stack (E4S) <https://e4s-project.github.io/>`_: `build cache <https://oaciss.uoregon.edu/e4s/inventory.html>`_'
+
+-------------------
+Build cache signing
+-------------------
+
+By default, Spack will add a cryptographic signature to each package pushed to
+a build cache, and verifies the signature when installing from a build cache.
+
+Keys for signing can be managed with the :ref:`spack gpg <cmd-spack-gpg>` command,
+as well as ``spack buildcache keys`` as mentioned above.
+
+You can disable signing when pushing with ``spack buildcache push --unsigned``,
+and disable verification when installing from any build cache with
+``spack install --no-check-signature``.
+
+Alternatively, signing and verification can be enabled or disabled on a per build cache
+basis:
+
+.. code-block:: console
+
+    $ spack mirror add --signed <name> <url>  # enable signing and verification
+    $ spack mirror add --unsigned <name> <url>  # disable signing and verification
+
+    $ spack mirror set --signed <name>  # enable signing and verification for an existing mirror
+    $ spack mirror set --unsigned <name>  # disable signing and verification for an existing mirror
+
+Or you can directly edit the ``mirrors.yaml`` configuration file:
+
+.. code-block:: yaml
+
+    mirrors:
+      <name>:
+        url: <url>
+        signed: false # disable signing and verification
+
+See also :ref:`mirrors`.
 
 ----------
 Relocation
@@ -251,87 +287,13 @@ To significantly speed up Spack in GitHub Actions, binaries can be cached in
 GitHub Packages. This service is an OCI registry that can be linked to a GitHub
 repository.
 
-A typical workflow is to include a ``spack.yaml`` environment in your repository
-that specifies the packages to install, the target architecture, and the build
-cache to use under ``mirrors``:
-
-.. code-block:: yaml
-
-    spack:
-      specs:
-      - python@3.11
-      config:
-        install_tree:
-          root: /opt/spack
-          padded_length: 128
-      packages:
-        all:
-          require: target=x86_64_v2
-      mirrors:
-        local-buildcache: oci://ghcr.io/<organization>/<repository>
-
-A GitHub action can then be used to install the packages and push them to the
-build cache:
-
-.. code-block:: yaml
-
-    name: Install Spack packages
-
-    on: push
-
-    env:
-      SPACK_COLOR: always
-
-    jobs:
-      example:
-        runs-on: ubuntu-22.04
-        permissions:
-          packages: write
-        steps:
-        - name: Checkout
-          uses: actions/checkout@v3
-
-        - name: Checkout Spack
-          uses: actions/checkout@v3
-          with:
-            repository: spack/spack
-            path: spack
-
-        - name: Setup Spack
-          run: echo "$PWD/spack/bin" >> "$GITHUB_PATH"
-
-        - name: Concretize
-          run: spack -e . concretize
-
-        - name: Install
-          run: spack -e . install --no-check-signature
-
-        - name: Run tests
-            run: ./my_view/bin/python3 -c 'print("hello world")'
-
-        - name: Push to buildcache
-          run: |
-            spack -e . mirror set --oci-username ${{ github.actor }} --oci-password "${{ secrets.GITHUB_TOKEN }}" local-buildcache
-            spack -e . buildcache push --base-image ubuntu:22.04 --unsigned --update-index local-buildcache
-          if: ${{ !cancelled() }}
-
-The first time this action runs, it will build the packages from source and
-push them to the build cache. Subsequent runs will pull the binaries from the
-build cache. The concretizer will ensure that prebuilt binaries are favored
-over source builds.
-
-The build cache entries appear in the GitHub Packages section of your repository,
-and contain instructions for pulling and running them with ``docker`` or ``podman``.
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Using Spack's public build cache for GitHub Actions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 Spack offers a public build cache for GitHub Actions with a set of common packages,
 which lets you get started quickly. See the following resources for more information:
 
-* `spack/github-actions-buildcache <https://github.com/spack/github-actions-buildcache>`_
+* `spack/setup-spack <https://github.com/spack/setup-spack>`_ for setting up Spack in GitHub
+  Actions
+* `spack/github-actions-buildcache <https://github.com/spack/github-actions-buildcache>`_ for
+  more details on the public build cache
 
 .. _cmd-spack-buildcache:
 

lib/spack/docs/build_systems/cmakepackage.rst

@@ -82,7 +82,7 @@ class already contains:
 
 .. code-block:: python
 
-   depends_on('cmake', type='build')
+   depends_on("cmake", type="build")
 
 
 If you need to specify a particular version requirement, you can
@@ -90,7 +90,7 @@ override this in your package:
 
 .. code-block:: python
 
-   depends_on('cmake@2.8.12:', type='build')
+   depends_on("cmake@2.8.12:", type="build")
 
 
 ^^^^^^^^^^^^^^^^^^^
@@ -137,10 +137,10 @@ and without the :meth:`~spack.build_systems.cmake.CMakeBuilder.define` and
 
    def cmake_args(self):
        args = [
-           '-DWHATEVER:STRING=somevalue',
-           self.define('ENABLE_BROKEN_FEATURE', False),
-           self.define_from_variant('DETECT_HDF5', 'hdf5'),
-           self.define_from_variant('THREADS'), # True if +threads
+           "-DWHATEVER:STRING=somevalue",
+           self.define("ENABLE_BROKEN_FEATURE", False),
+           self.define_from_variant("DETECT_HDF5", "hdf5"),
+           self.define_from_variant("THREADS"), # True if +threads
        ]
 
        return args
@@ -151,10 +151,10 @@ and CMake simply ignores the empty command line argument. For example the follow
 
 .. code-block:: python
 
-   variant('example', default=True, when='@2.0:')
+   variant("example", default=True, when="@2.0:")
 
    def cmake_args(self):
-      return [self.define_from_variant('EXAMPLE', 'example')]
+      return [self.define_from_variant("EXAMPLE", "example")]
 
 will generate ``'cmake' '-DEXAMPLE=ON' ...`` when `@2.0: +example` is met, but will
 result in ``'cmake' '' ...`` when the spec version is below ``2.0``.
@@ -193,9 +193,9 @@ a variant to control this:
 
 .. code-block:: python
 
-   variant('build_type', default='RelWithDebInfo',
-           description='CMake build type',
-           values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'))
+   variant("build_type", default="RelWithDebInfo",
+           description="CMake build type",
+           values=("Debug", "Release", "RelWithDebInfo", "MinSizeRel"))
 
 However, not every CMake package accepts all four of these options.
 Grep the ``CMakeLists.txt`` file to see if the default values are
@@ -205,9 +205,9 @@ package overrides the default variant with:
 
 .. code-block:: python
 
-   variant('build_type', default='DebugRelease',
-           description='The build type to build',
-           values=('Debug', 'Release', 'DebugRelease'))
+   variant("build_type", default="DebugRelease",
+           description="The build type to build",
+           values=("Debug", "Release", "DebugRelease"))
 
 For more information on ``CMAKE_BUILD_TYPE``, see:
 https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html
@@ -250,7 +250,7 @@ generator is Ninja. To switch to the Ninja generator, simply add:
 
 .. code-block:: python
 
-   generator = 'Ninja'
+   generator = "Ninja"
 
 
 ``CMakePackage`` defaults to "Unix Makefiles". If you switch to the
@@ -258,7 +258,7 @@ Ninja generator, make sure to add:
 
 .. code-block:: python
 
-   depends_on('ninja', type='build')
+   depends_on("ninja", type="build")
 
 to the package as well. Aside from that, you shouldn't need to do
 anything else. Spack will automatically detect that you are using
@@ -288,7 +288,7 @@ like so:
 
 .. code-block:: python
 
-   root_cmakelists_dir = 'src'
+   root_cmakelists_dir = "src"
 
 
 Note that this path is relative to the root of the extracted tarball,
@@ -304,7 +304,7 @@ different sub-directory, simply override ``build_directory`` like so:
 
 .. code-block:: python
 
-   build_directory = 'my-build'
+   build_directory = "my-build"
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 Build and install targets
@@ -324,8 +324,8 @@ library or build the documentation, you can add these like so:
 
 .. code-block:: python
 
-   build_targets = ['all', 'docs']
-   install_targets = ['install', 'docs']
+   build_targets = ["all", "docs"]
+   install_targets = ["install", "docs"]
 
 ^^^^^^^
 Testing

lib/spack/docs/build_systems/intelpackage.rst

@@ -90,7 +90,7 @@ and optimizers do require a paid license.  In Spack, they are packaged as:
     TODO: Confirm and possible change(!) the scope of MPI components (runtime
     vs. devel) in current (and previous?) *cluster/professional/composer*
     editions, i.e., presence in downloads, possibly subject to license
-    coverage(!); see `disussion in PR #4300
+    coverage(!); see `discussion in PR #4300
     <https://github.com/spack/spack/pull/4300#issuecomment-305582898>`_.  [NB:
     An "mpi" subdirectory is not indicative of the full MPI SDK being present
     (i.e., ``mpicc``, ..., and header files).  The directory may just as well
@@ -934,9 +934,9 @@ a *virtual* ``mkl`` package is declared in Spack.
   .. code-block:: python
 
      # Examples for absolute and conditional dependencies:
-     depends_on('mkl')
-     depends_on('mkl', when='+mkl')
-     depends_on('mkl', when='fftw=mkl')
+     depends_on("mkl")
+     depends_on("mkl", when="+mkl")
+     depends_on("mkl", when="fftw=mkl")
 
   The ``MKLROOT`` environment variable (part of the documented API) will be set
   during all stages of client package installation, and is available to both
@@ -972,8 +972,8 @@ a *virtual* ``mkl`` package is declared in Spack.
       def configure_args(self):
           args = []
           ...
-          args.append('--with-blas=%s' % self.spec['blas'].libs.ld_flags)
-          args.append('--with-lapack=%s' % self.spec['lapack'].libs.ld_flags)
+          args.append("--with-blas=%s" % self.spec["blas"].libs.ld_flags)
+          args.append("--with-lapack=%s" % self.spec["lapack"].libs.ld_flags)
           ...
 
   .. tip::
@@ -989,13 +989,13 @@ a *virtual* ``mkl`` package is declared in Spack.
 
   .. code-block:: python
 
-    self.spec['blas'].headers.include_flags
+    self.spec["blas"].headers.include_flags
 
   and to generate linker options (``-L<dir> -llibname ...``), use the same as above,
 
   .. code-block:: python
 
-    self.spec['blas'].libs.ld_flags
+    self.spec["blas"].libs.ld_flags
 
   See
   :ref:`MakefilePackage <makefilepackage>`

lib/spack/docs/build_systems/luapackage.rst

@@ -88,7 +88,7 @@ override the ``luarocks_args`` method like so:
 .. code-block:: python
 
     def luarocks_args(self):
-        return ['flag1', 'flag2']
+        return ["flag1", "flag2"]
 
 One common use of this is to override warnings or flags for newer compilers, as in:
 

lib/spack/docs/build_systems/mavenpackage.rst

@@ -48,8 +48,8 @@ class automatically adds the following dependencies:
 
 .. code-block:: python
 
-   depends_on('java', type=('build', 'run'))
-   depends_on('maven', type='build')
+   depends_on("java", type=("build", "run"))
+   depends_on("maven", type="build")
 
 
 In the ``pom.xml`` file, you may see sections like:
@@ -72,8 +72,8 @@ should add:
 
 .. code-block:: python
 
-   depends_on('java@7:', type='build')
-   depends_on('maven@3.5.4:', type='build')
+   depends_on("java@7:", type="build")
+   depends_on("maven@3.5.4:", type="build")
 
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -88,9 +88,9 @@ the build phase. For example:
 
    def build_args(self):
        return [
-           '-Pdist,native',
-           '-Dtar',
-           '-Dmaven.javadoc.skip=true'
+           "-Pdist,native",
+           "-Dtar",
+           "-Dmaven.javadoc.skip=true"
        ]
 
 

lib/spack/docs/build_systems/mesonpackage.rst

@@ -86,8 +86,8 @@ the ``MesonPackage`` base class already contains:
 
 .. code-block:: python
 
-   depends_on('meson', type='build')
-   depends_on('ninja', type='build')
+   depends_on("meson", type="build")
+   depends_on("ninja", type="build")
 
 
 If you need to specify a particular version requirement, you can
@@ -95,8 +95,8 @@ override this in your package:
 
 .. code-block:: python
 
-   depends_on('meson@0.43.0:', type='build')
-   depends_on('ninja', type='build')
+   depends_on("meson@0.43.0:", type="build")
+   depends_on("ninja", type="build")
 
 
 ^^^^^^^^^^^^^^^^^^^
@@ -121,7 +121,7 @@ override the ``meson_args`` method like so:
 .. code-block:: python
 
    def meson_args(self):
-       return ['--warnlevel=3']
+       return ["--warnlevel=3"]
 
 
 This method can be used to pass flags as well as variables.

lib/spack/docs/build_systems/perlpackage.rst

@@ -118,7 +118,7 @@ so ``PerlPackage`` contains:
 
 .. code-block:: python
 
-   extends('perl')
+   extends("perl")
 
 
 If your package requires a specific version of Perl, you should
@@ -132,14 +132,14 @@ properly. If your package uses ``Makefile.PL`` to build, add:
 
 .. code-block:: python
 
-   depends_on('perl-extutils-makemaker', type='build')
+   depends_on("perl-extutils-makemaker", type="build")
 
 
 If your package uses ``Build.PL`` to build, add:
 
 .. code-block:: python
 
-   depends_on('perl-module-build', type='build')
+   depends_on("perl-module-build", type="build")
 
 
 ^^^^^^^^^^^^^^^^^
@@ -165,11 +165,11 @@ arguments to ``Makefile.PL`` or ``Build.PL`` by overriding
 .. code-block:: python
 
    def configure_args(self):
-       expat = self.spec['expat'].prefix
+       expat = self.spec["expat"].prefix
 
        return [
-           'EXPATLIBPATH={0}'.format(expat.lib),
-           'EXPATINCPATH={0}'.format(expat.include),
+           "EXPATLIBPATH={0}".format(expat.lib),
+           "EXPATINCPATH={0}".format(expat.include),
        ]
 
 

lib/spack/docs/build_systems/qmakepackage.rst

@@ -83,7 +83,7 @@ base class already contains:
 
 .. code-block:: python
 
-   depends_on('qt', type='build')
+   depends_on("qt", type="build")
 
 
 If you want to specify a particular version requirement, or need to
@@ -91,7 +91,7 @@ link to the ``qt`` libraries, you can override this in your package:
 
 .. code-block:: python
 
-   depends_on('qt@5.6.0:')
+   depends_on("qt@5.6.0:")
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 Passing arguments to qmake
@@ -103,7 +103,7 @@ override the ``qmake_args`` method like so:
 .. code-block:: python
 
    def qmake_args(self):
-       return ['-recursive']
+       return ["-recursive"]
 
 
 This method can be used to pass flags as well as variables.
@@ -118,7 +118,7 @@ sub-directory by adding the following to the package:
 
 .. code-block:: python
 
-   build_directory = 'src'
+   build_directory = "src"
 
 
 ^^^^^^^^^^^^^^^^^^^^^^

lib/spack/docs/build_systems/rpackage.rst

@@ -163,28 +163,28 @@ attributes that can be used to set ``homepage``, ``url``, ``list_url``, and
 
 .. code-block:: python
 
-   cran = 'caret'
+   cran = "caret"
 
 is equivalent to:
 
 .. code-block:: python
 
-   homepage = 'https://cloud.r-project.org/package=caret'
-   url      = 'https://cloud.r-project.org/src/contrib/caret_6.0-86.tar.gz'
-   list_url = 'https://cloud.r-project.org/src/contrib/Archive/caret'
+   homepage = "https://cloud.r-project.org/package=caret"
+   url      = "https://cloud.r-project.org/src/contrib/caret_6.0-86.tar.gz"
+   list_url = "https://cloud.r-project.org/src/contrib/Archive/caret"
 
 Likewise, the following ``bioc`` attribute:
 
 .. code-block:: python
 
-   bioc = 'BiocVersion'
+   bioc = "BiocVersion"
 
 is equivalent to:
 
 .. code-block:: python
 
-   homepage = 'https://bioconductor.org/packages/BiocVersion/'
-   git      = 'https://git.bioconductor.org/packages/BiocVersion'
+   homepage = "https://bioconductor.org/packages/BiocVersion/"
+   git      = "https://git.bioconductor.org/packages/BiocVersion"
 
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -200,7 +200,7 @@ base class contains:
 
 .. code-block:: python
 
-   extends('r')
+   extends("r")
 
 
 Take a close look at the homepage for ``caret``. If you look at the
@@ -209,7 +209,7 @@ You should add this to your package like so:
 
 .. code-block:: python
 
-   depends_on('r@3.2.0:', type=('build', 'run'))
+   depends_on("r@3.2.0:", type=("build", "run"))
 
 
 ^^^^^^^^^^^^^^
@@ -227,7 +227,7 @@ and list all of their dependencies in the following sections:
 * LinkingTo
 
 As far as Spack is concerned, all 3 of these dependency types
-correspond to ``type=('build', 'run')``, so you don't have to worry
+correspond to ``type=("build", "run")``, so you don't have to worry
 about the details. If you are curious what they mean,
 https://github.com/spack/spack/issues/2951 has a pretty good summary:
 
@@ -330,7 +330,7 @@ the dependency:
 
 .. code-block:: python
 
-   depends_on('r-lattice@0.20:', type=('build', 'run'))
+   depends_on("r-lattice@0.20:", type=("build", "run"))
 
 
 ^^^^^^^^^^^^^^^^^^
@@ -361,20 +361,20 @@ like so:
 .. code-block:: python
 
    def configure_args(self):
-       mpi_name = self.spec['mpi'].name
+       mpi_name = self.spec["mpi"].name
 
        # The type of MPI. Supported values are:
        # OPENMPI, LAM, MPICH, MPICH2, or CRAY
-       if mpi_name == 'openmpi':
-           Rmpi_type = 'OPENMPI'
-       elif mpi_name == 'mpich':
-           Rmpi_type = 'MPICH2'
+       if mpi_name == "openmpi":
+           Rmpi_type = "OPENMPI"
+       elif mpi_name == "mpich":
+           Rmpi_type = "MPICH2"
        else:
-           raise InstallError('Unsupported MPI type')
+           raise InstallError("Unsupported MPI type")
 
        return [
-           '--with-Rmpi-type={0}'.format(Rmpi_type),
-           '--with-mpi={0}'.format(spec['mpi'].prefix),
+           "--with-Rmpi-type={0}".format(Rmpi_type),
+           "--with-mpi={0}".format(spec["mpi"].prefix),
        ]
 
 

lib/spack/docs/build_systems/rubypackage.rst

@@ -84,8 +84,8 @@ The ``*.gemspec`` file may contain something like:
 
 .. code-block:: ruby
 
-   summary = 'An implementation of the AsciiDoc text processor and publishing toolchain'
-   description = 'A fast, open source text processor and publishing toolchain for converting AsciiDoc content to HTML 5, DocBook 5, and other formats.'
+   summary = "An implementation of the AsciiDoc text processor and publishing toolchain"
+   description = "A fast, open source text processor and publishing toolchain for converting AsciiDoc content to HTML 5, DocBook 5, and other formats."
 
 
 Either of these can be used for the description of the Spack package.
@@ -98,7 +98,7 @@ The ``*.gemspec`` file may contain something like:
 
 .. code-block:: ruby
 
-   homepage = 'https://asciidoctor.org'
+   homepage = "https://asciidoctor.org"
 
 
 This should be used as the official homepage of the Spack package.
@@ -112,21 +112,21 @@ the base class contains:
 
 .. code-block:: python
 
-   extends('ruby')
+   extends("ruby")
 
 
 The ``*.gemspec`` file may contain something like:
 
 .. code-block:: ruby
 
-   required_ruby_version = '>= 2.3.0'
+   required_ruby_version = ">= 2.3.0"
 
 
 This can be added to the Spack package using:
 
 .. code-block:: python
 
-   depends_on('ruby@2.3.0:', type=('build', 'run'))
+   depends_on("ruby@2.3.0:", type=("build", "run"))
 
 
 ^^^^^^^^^^^^^^^^^

lib/spack/docs/build_systems/sippackage.rst

@@ -124,7 +124,7 @@ are wrong, you can provide the names yourself by overriding
 
 .. code-block:: python
 
-   import_modules = ['PyQt5']
+   import_modules = ["PyQt5"]
 
 
 These tests often catch missing dependencies and non-RPATHed

lib/spack/docs/build_systems/wafpackage.rst

@@ -63,8 +63,8 @@ run package-specific unit tests.
 .. code-block:: python
 
    def installtest(self):
-       with working_dir('test'):
-           pytest = which('py.test')
+       with working_dir("test"):
+           pytest = which("py.test")
            pytest()
 
 
@@ -93,7 +93,7 @@ the following dependency automatically:
 
 .. code-block:: python
 
-   depends_on('python@2.5:', type='build')
+   depends_on("python@2.5:", type="build")
 
 
 Waf only supports Python 2.5 and up.
@@ -113,7 +113,7 @@ phase, you can use:
        args = []
 
        if self.run_tests:
-           args.append('--test')
+           args.append("--test")
 
        return args
 

lib/spack/docs/containers.rst

@@ -9,34 +9,96 @@
 Container Images
 ================
 
-Spack :ref:`environments` are a great tool to create container images, but
-preparing one that is suitable for production requires some more boilerplate
-than just:
+Spack :ref:`environments` can easily be turned into container images. This page
+outlines two ways in which this can be done:
+
+1. By installing the environment on the host system, and copying the installations
+   into the container image. This approach does not require any tools like Docker
+   or Singularity to be installed.
+2. By generating a Docker or Singularity recipe that can be used to build the
+   container image. In this approach, Spack builds the software inside the
+   container runtime, not on the host system.
+
+The first approach is easiest if you already have an installed environment,
+the second approach gives more control over the container image.
+
+---------------------------
+From existing installations
+---------------------------
+
+If you already have a Spack environment installed on your system, you can
+share the binaries as an OCI compatible container image. To get started you
+just have to configure and OCI registry and run ``spack buildcache push``.
+
+.. code-block:: console
+  
+   # Create and install an environment in the current directory
+   spack env create -d .
+   spack -e . add pkg-a pkg-b
+   spack -e . install
+
+   # Configure the registry
+   spack -e . mirror add --oci-username ... --oci-password ... container-registry oci://example.com/name/image
+
+   # Push the image
+   spack -e . buildcache push --update-index --base-image ubuntu:22.04 --tag my_env container-registry
+
+The resulting container image can then be run as follows:
+
+.. code-block:: console
+
+   $ docker run -it example.com/name/image:my_env
+
+The image generated by Spack consists of the specified base image with each package from the
+environment as a separate layer on top. The image is minimal by construction, it only contains the
+environment roots and its runtime dependencies.
+
+.. note::
+
+  When using registries like GHCR and Docker Hub, the ``--oci-password`` flag is not
+  the password for your account, but a personal access token you need to generate separately.
+
+The specified ``--base-image`` should have a libc that is compatible with the host system.
+For example if your host system is Ubuntu 20.04, you can use ``ubuntu:20.04``, ``ubuntu:22.04``
+or newer: the libc in the container image must be at least the version of the host system,
+assuming ABI compatibility. It is also perfectly fine to use a completely different
+Linux distribution as long as the libc is compatible.
+
+For convenience, Spack also turns the OCI registry into a :ref:`build cache <binary_caches_oci>`,
+so that future ``spack install`` of the environment will simply pull the binaries from the
+registry instead of doing source builds. The flag ``--update-index`` is needed to make Spack
+take the build cache into account when concretizing.
+
+.. note::
+
+  When generating container images in CI, the approach above is recommended when CI jobs
+  already run in a sandboxed environment. You can simply use ``spack`` directly
+  in the CI job and push the resulting image to a registry. Subsequent CI jobs should
+  run faster because Spack can install from the same registry instead of rebuilding from
+  sources.
+
+---------------------------------------------
+Generating recipes for Docker and Singularity
+---------------------------------------------
+
+Apart from copying existing installations into container images, Spack can also
+generate recipes for container images. This is useful if you want to run Spack
+itself in a sandboxed environment instead of on the host system.
+
+Since recipes need a little bit more boilerplate than
 
 .. code-block:: docker
 
    COPY spack.yaml /environment
    RUN spack -e /environment install
 
-Additional actions may be needed to minimize the size of the
-container, or to update the system software that is installed in the base
-image, or to set up a proper entrypoint to run the image. These tasks are
-usually both necessary and repetitive, so Spack comes with a command
-to generate recipes for container images starting from a ``spack.yaml``.
+Spack provides a command to generate customizable recipes for container images. Customizations
+include minimizing the size of the image, installing packages in the base image using the system
+package manager, and setting up a proper entrypoint to run the image.
 
-.. seealso::
-
-  This page is a reference for generating recipes to build container images.
-  It means that your environment is built from scratch inside the container
-  runtime.
-
-  Since v0.21, Spack can also create container images from existing package installations
-  on your host system. See :ref:`binary_caches_oci` for more information on
-  that topic.
-
---------------------
+~~~~~~~~~~~~~~~~~~~~
 A Quick Introduction
---------------------
+~~~~~~~~~~~~~~~~~~~~
 
 Consider having a Spack environment like the following:
 
@@ -47,8 +109,8 @@ Consider having a Spack environment like the following:
      - gromacs+mpi
      - mpich
 
-Producing a ``Dockerfile`` from it is as simple as moving to the directory
-where the ``spack.yaml`` file is stored and giving the following command:
+Producing a ``Dockerfile`` from it is as simple as changing directories to
+where the ``spack.yaml`` file is stored and running the following command:
 
 .. code-block:: console
 
@@ -114,9 +176,9 @@ configuration are discussed in details in the sections below.
 
 .. _container_spack_images:
 
---------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 Spack Images on Docker Hub
---------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Docker images with Spack preinstalled and ready to be used are
 built when a release is tagged, or nightly on ``develop``. The images
@@ -186,9 +248,9 @@ by Spack use them as default base images for their ``build`` stage,
 even though handles to use custom base images provided by users are
 available to accommodate complex use cases.
 
----------------------------------
-Creating Images From Environments
----------------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Configuring the Container Recipe
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Any Spack Environment can be used for the automatic generation of container
 recipes. Sensible defaults are provided for things like the base image or the
@@ -229,18 +291,18 @@ under the ``container`` attribute of environments:
 
 A detailed description of the options available can be found in the :ref:`container_config_options` section.
 
--------------------
+~~~~~~~~~~~~~~~~~~~
 Setting Base Images
--------------------
+~~~~~~~~~~~~~~~~~~~
 
 The ``images`` subsection is used to select both the image where
 Spack builds the software and the image where the built software
 is installed. This attribute can be set in different ways and
 which one to use depends on the use case at hand.
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+""""""""""""""""""""""""""""""""""""""""
 Use Official Spack Images From Dockerhub
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+""""""""""""""""""""""""""""""""""""""""
 
 To generate a recipe that uses an official Docker image from the
 Spack organization to build the software and the corresponding official OS image
@@ -445,9 +507,9 @@ responsibility to ensure that:
 Therefore we don't recommend its use in cases that can be otherwise
 covered by the simplified mode shown first.
 
-----------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Singularity Definition Files
-----------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 In addition to producing recipes in ``Dockerfile`` format Spack can produce
 Singularity Definition Files by just changing the value of the ``format``
@@ -468,9 +530,9 @@ attribute:
 The minimum version of Singularity required to build a SIF (Singularity Image Format)
 image from the recipes generated by Spack is ``3.5.3``.
 
-------------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Extending the Jinja2 Templates
-------------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The Dockerfile and the Singularity definition file that Spack can generate are based on
 a few Jinja2 templates that are rendered according to the environment being containerized.
@@ -591,9 +653,9 @@ The recipe that gets generated contains the two extra instruction that we added
 
 .. _container_config_options:
 
------------------------
+~~~~~~~~~~~~~~~~~~~~~~~
 Configuration Reference
------------------------
+~~~~~~~~~~~~~~~~~~~~~~~
 
 The tables below describe all the configuration options that are currently supported
 to customize the generation of container recipes:
@@ -690,13 +752,13 @@ to customize the generation of container recipes:
      - Description string
      - No
 
---------------
+~~~~~~~~~~~~~~
 Best Practices
---------------
+~~~~~~~~~~~~~~
 
-^^^
+"""
 MPI
-^^^
+"""
 Due to the dependency on Fortran for OpenMPI, which is the spack default
 implementation, consider adding ``gfortran`` to the ``apt-get install`` list.
 
@@ -707,9 +769,9 @@ For execution on HPC clusters, it can be helpful to import the docker
 image into Singularity in order to start a program with an *external*
 MPI. Otherwise, also add ``openssh-server`` to the ``apt-get install`` list.
 
-^^^^
+""""
 CUDA
-^^^^
+""""
 Starting from CUDA 9.0, Nvidia provides minimal CUDA images based on
 Ubuntu. Please see `their instructions <https://hub.docker.com/r/nvidia/cuda/>`_.
 Avoid double-installing CUDA by adding, e.g.
@@ -728,9 +790,9 @@ to your ``spack.yaml``.
 Users will either need ``nvidia-docker`` or e.g. Singularity to *execute*
 device kernels.
 
-^^^^^^^^^^^^^^^^^^^^^^^^^
+"""""""""""""""""""""""""
 Docker on Windows and OSX
-^^^^^^^^^^^^^^^^^^^^^^^^^
+"""""""""""""""""""""""""
 
 On Mac OS and Windows, docker runs on a hypervisor that is not allocated much
 memory by default, and some spack packages may fail to build due to lack of

lib/spack/docs/extensions.rst

@@ -9,46 +9,42 @@
 Custom Extensions
 =================
 
-*Spack extensions* permit you to extend Spack capabilities by deploying your
+*Spack extensions* allow you to extend Spack capabilities by deploying your
 own custom commands or logic in an arbitrary location on your filesystem.
 This might be extremely useful e.g. to develop and maintain a command whose purpose is
 too specific to be considered for reintegration into the mainline or to
 evolve a command through its early stages before starting a discussion to merge
 it upstream.
+
 From Spack's point of view an extension is any path in your filesystem which
-respects a prescribed naming and layout for files:
+respects the following naming and layout for files:
 
 .. code-block:: console
 
   spack-scripting/ # The top level directory must match the format 'spack-{extension_name}'
   ├── pytest.ini # Optional file if the extension ships its own tests
   ├── scripting # Folder that may contain modules that are needed for the extension commands
-  │   └── cmd # Folder containing extension commands
-  │       └── filter.py # A new command that will be available
-  ├── tests # Tests for this extension
+  │   ├── cmd # Folder containing extension commands
+  │   │   └── filter.py # A new command that will be available
+  │   └── functions.py # Module with internal details
+  └── tests # Tests for this extension
   │   ├── conftest.py
   │   └── test_filter.py
   └── templates # Templates that may be needed by the extension
 
-In the example above the extension named *scripting* adds an additional command (``filter``)
-and unit tests to verify its behavior. The code for this example can be
-obtained by cloning the corresponding git repository:
+In the example above, the extension is named *scripting*. It adds an additional command
+(``spack filter``) and unit tests to verify its behavior.
 
-.. TODO: write an ad-hoc "hello world" extension and make it part of the spack organization
+The extension can import any core Spack module in its implementation. When loaded by
+the ``spack`` command, the extension itself is imported as a Python package in the
+``spack.extensions`` namespace. In the example above, since the extension is named
+"scripting", the corresponding Python module is ``spack.extensions.scripting``.
+
+The code for this example extension can be obtained by cloning the corresponding git repository:
 
 .. code-block:: console
 
-   $ cd ~/
-   $ mkdir tmp && cd tmp
-   $ git clone https://github.com/alalazo/spack-scripting.git
-   Cloning into 'spack-scripting'...
-   remote: Counting objects: 11, done.
-   remote: Compressing objects: 100% (7/7), done.
-   remote: Total 11 (delta 0), reused 11 (delta 0), pack-reused 0
-   Receiving objects: 100% (11/11), done.
-
-As you can see by inspecting the sources, Python modules that are part of the extension
-can import any core Spack module.
+   $ git -C /tmp clone https://github.com/spack/spack-scripting.git
 
 ---------------------------------
 Configure Spack to Use Extensions
@@ -61,7 +57,7 @@ paths to ``config.yaml``. In the case of our example this means ensuring that:
 
    config:
      extensions:
-     - ~/tmp/spack-scripting
+     - /tmp/spack-scripting
 
 is part of your configuration file. Once this is setup any command that the extension provides
 will be available from the command line:
@@ -86,37 +82,32 @@ will be available from the command line:
      --implicit       select specs that are not installed or were installed implicitly
      --output OUTPUT  where to dump the result
 
-The corresponding unit tests can be run giving the appropriate options
-to ``spack unit-test``:
+The corresponding unit tests can be run giving the appropriate options to ``spack unit-test``:
 
 .. code-block:: console
 
    $ spack unit-test --extension=scripting
-
-   ============================================================== test session starts ===============================================================
-   platform linux2 -- Python 2.7.15rc1, pytest-3.2.5, py-1.4.34, pluggy-0.4.0
-   rootdir: /home/mculpo/tmp/spack-scripting, inifile: pytest.ini
+   ========================================== test session starts ===========================================
+   platform linux -- Python 3.11.5, pytest-7.4.3, pluggy-1.3.0
+   rootdir: /home/culpo/github/spack-scripting
+   configfile: pytest.ini
+   testpaths: tests
+   plugins: xdist-3.5.0
    collected 5 items
 
-   tests/test_filter.py ...XX
-   ============================================================ short test summary info =============================================================
-   XPASS tests/test_filter.py::test_filtering_specs[flags3-specs3-expected3]
-   XPASS tests/test_filter.py::test_filtering_specs[flags4-specs4-expected4]
+   tests/test_filter.py .....                                                                         [100%]
 
-   =========================================================== slowest 20 test durations ============================================================
-   3.74s setup    tests/test_filter.py::test_filtering_specs[flags0-specs0-expected0]
-   0.17s call     tests/test_filter.py::test_filtering_specs[flags3-specs3-expected3]
-   0.16s call     tests/test_filter.py::test_filtering_specs[flags2-specs2-expected2]
-   0.15s call     tests/test_filter.py::test_filtering_specs[flags1-specs1-expected1]
-   0.13s call     tests/test_filter.py::test_filtering_specs[flags4-specs4-expected4]
-   0.08s call     tests/test_filter.py::test_filtering_specs[flags0-specs0-expected0]
-   0.04s teardown tests/test_filter.py::test_filtering_specs[flags4-specs4-expected4]
-   0.00s setup    tests/test_filter.py::test_filtering_specs[flags4-specs4-expected4]
-   0.00s setup    tests/test_filter.py::test_filtering_specs[flags3-specs3-expected3]
-   0.00s setup    tests/test_filter.py::test_filtering_specs[flags1-specs1-expected1]
-   0.00s setup    tests/test_filter.py::test_filtering_specs[flags2-specs2-expected2]
-   0.00s teardown tests/test_filter.py::test_filtering_specs[flags2-specs2-expected2]
-   0.00s teardown tests/test_filter.py::test_filtering_specs[flags1-specs1-expected1]
-   0.00s teardown tests/test_filter.py::test_filtering_specs[flags0-specs0-expected0]
-   0.00s teardown tests/test_filter.py::test_filtering_specs[flags3-specs3-expected3]
-   ====================================================== 3 passed, 2 xpassed in 4.51 seconds =======================================================
+   ========================================== slowest 30 durations ==========================================
+   2.31s setup    tests/test_filter.py::test_filtering_specs[kwargs0-specs0-expected0]
+   0.57s call     tests/test_filter.py::test_filtering_specs[kwargs2-specs2-expected2]
+   0.56s call     tests/test_filter.py::test_filtering_specs[kwargs4-specs4-expected4]
+   0.54s call     tests/test_filter.py::test_filtering_specs[kwargs3-specs3-expected3]
+   0.54s call     tests/test_filter.py::test_filtering_specs[kwargs1-specs1-expected1]
+   0.48s call     tests/test_filter.py::test_filtering_specs[kwargs0-specs0-expected0]
+   0.01s setup    tests/test_filter.py::test_filtering_specs[kwargs4-specs4-expected4]
+   0.01s setup    tests/test_filter.py::test_filtering_specs[kwargs2-specs2-expected2]
+   0.01s setup    tests/test_filter.py::test_filtering_specs[kwargs1-specs1-expected1]
+   0.01s setup    tests/test_filter.py::test_filtering_specs[kwargs3-specs3-expected3]
+
+   (5 durations < 0.005s hidden.  Use -vv to show these durations.)
+   =========================================== 5 passed in 5.06s ============================================

lib/spack/docs/getting_started.rst

@@ -250,10 +250,9 @@ Compiler configuration
 
 Spack has the ability to build packages with multiple compilers and
 compiler versions. Compilers can be made available to Spack by
-specifying them manually in ``compilers.yaml`` or ``packages.yaml``,
-or automatically by running ``spack compiler find``, but for
-convenience Spack will automatically detect compilers the first time
-it needs them.
+specifying them manually in ``compilers.yaml``, or automatically by
+running ``spack compiler find``, but for convenience Spack will
+automatically detect compilers the first time it needs them.
 
 .. _cmd-spack-compilers:
 
@@ -458,52 +457,6 @@ specification. The operations available to modify the environment are ``set``, `
          prepend_path: # Similar for append|remove_path
            LD_LIBRARY_PATH: /ld/paths/added/by/setvars/sh
 
-.. note::
-
-   Spack is in the process of moving compilers from a separate
-   attribute to be handled like all other packages. As part of this
-   process, the ``compilers.yaml`` section will eventually be replaced
-   by configuration in the ``packages.yaml`` section. This new
-   configuration is now available, although it is not yet the default
-   behavior.
-
-Compilers can also be configured as external packages in the
-``packages.yaml`` config file. Any external package for a compiler
-(e.g. ``gcc`` or ``llvm``) will be treated as a configured compiler
-assuming the paths to the compiler executables are determinable from
-the prefix.
-
-If the paths to the compiler executable are not determinable from the
-prefix, you can add them to the ``extra_attributes`` field using the
-``compilers`` key. The ``compilers`` key accepts compilers for ``c``,
-``cxx``, ``fortran``, and ``f77``.
-
-For all other fields from the ``compilers`` config, they can be added
-to the ``extra_attributes`` field for an external representing a
-compiler. These fields are used as-is in the internal representation
-of the compiler config.
-
-.. code-block:: yaml
-
-   packages:
-     gcc:
-       external:
-       - spec: gcc@12.2.0 arch=linux-rhel8-skylake
-         prefix: /usr
-         extra_attributes:
-           environment:
-             set:
-               GCC_ROOT: /usr
-       external:
-       - spec: llvm+clang@15.0.0 arch=linux-rhel8-skylake
-         prefix: /usr
-         extra_attributes:
-           compilers:
-             c: /usr/bin/clang-with-suffix
-             cxx: /usr/bin/clang++-with-extra-info
-             fortran: /usr/bin/gfortran
-           extra_rpaths:
-           - /usr/lib/llvm/
 
 ^^^^^^^^^^^^^^^^^^^^^^^
 Build Your Own Compiler

lib/spack/docs/gpu_configuration.rst

@@ -111,3 +111,28 @@ CUDA is split into fewer components and is simpler to specify:
          prefix: /opt/cuda/cuda-11.0.2/
 
 where ``/opt/cuda/cuda-11.0.2/lib/`` contains ``libcudart.so``.
+
+
+
+-----------------------------------
+Using an External OpenGL API
+-----------------------------------
+Depending on whether we have a graphics card or not, we may choose to use OSMesa or GLX to implement the OpenGL API.
+
+If a graphics card is unavailable, OSMesa is recommended and can typically be built with Spack.
+However, if we prefer to utilize the system GLX tailored to our graphics card, we need to declare it as an external. Here's how to do it:
+
+
+.. code-block:: yaml
+
+  packages:
+    libglx:
+      require: [opengl]
+    opengl:
+      buildable: false
+      externals:
+      - prefix: /usr/
+        spec: opengl@4.6
+
+Note that prefix has to be the root of both the libraries and the headers, using is /usr not the path the the lib.
+To know which spec for opengl is available use ``cd /usr/include/GL && grep -Ri gl_version``.

lib/spack/docs/packages_yaml.rst

@@ -97,6 +97,35 @@ Each package version and compiler listed in an external should
 have entries in Spack's packages and compiler configuration, even
 though the package and compiler may not ever be built.
 
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Extra attributes for external packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Sometimes external packages require additional attributes to be used
+effectively. This information can be defined on a per-package basis
+and stored in the ``extra_attributes`` section of the external package
+configuration. In addition to per-package information, this section
+can be used to define environment modifications to be performed
+whenever the package is used. For example, if an external package is
+built without ``rpath`` support, it may require ``LD_LIBRARY_PATH``
+settings to find its dependencies. This could be configured as
+follows:
+
+.. code-block:: yaml
+
+   packages:
+     mpich:
+       externals:
+       - spec: mpich@3.3 %clang@12.0.0 +hwloc
+         prefix: /path/to/mpich
+         extra_attributes:
+           environment:
+             prepend_path:
+               LD_LIBRARY_PATH: /path/to/hwloc/lib64
+
+See :ref:`configuration_environment_variables` for more information on
+how to configure environment modifications in Spack config files.
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Prevent packages from being built from sources
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

lib/spack/docs/packaging_guide.rst

@@ -5284,7 +5284,7 @@ installed example.
            example = which(self.prefix.bin.example)
            example()
 
-Output showing the identification of each test part after runnig the tests
+Output showing the identification of each test part after running the tests
 is illustrated below.
 
 .. code-block:: console
@@ -5781,7 +5781,7 @@ with those implemented in the package itself.
    * - `Cxx
        <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cxx>`_
      - Compiles and runs several ``hello`` programs
-   * - `Fortan
+   * - `Fortran
        <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/fortran>`_
      - Compiles and runs ``hello`` programs (``F`` and ``f90``)
    * - `Mpi

lib/spack/docs/requirements.txt

@@ -1,13 +1,13 @@
 sphinx==7.2.6
 sphinxcontrib-programoutput==0.17
 sphinx_design==0.5.0
-sphinx-rtd-theme==1.3.0
+sphinx-rtd-theme==2.0.0
 python-levenshtein==0.23.0
-docutils==0.18.1
-pygments==2.17.1
+docutils==0.20.1
+pygments==2.17.2
 urllib3==2.1.0
 pytest==7.4.3
-isort==5.12.0
-black==23.11.0
+isort==5.13.2
+black==23.12.1
 flake8==6.1.0
-mypy==1.7.0
+mypy==1.8.0

lib/spack/docs/signing.rst

@@ -142,7 +142,7 @@ Reputational Key
 ----------------
 
 The Reputational Key is the public facing key used to sign complete groups of
-development and release packages. Only one key pair exsits in this class of
+development and release packages. Only one key pair exists in this class of
 keys. In contrast to the Intermediate CI Key the Reputational Key *should* be
 used to verify package integrity. At the end of develop and release pipeline a
 final pipeline job pulls down all signed package metadata built by the pipeline,
@@ -272,7 +272,7 @@ Internal Implementation
 
 The technical implementation of the pipeline signing process includes components
 defined in Amazon Web Services, the Kubernetes cluster, at affilicated
-institutions, and the GitLab/GitLab Runner deployment. We present the techincal
+institutions, and the GitLab/GitLab Runner deployment. We present the technical
 implementation in two interdependent sections. The first addresses how secrets
 are managed through the lifecycle of a develop or release pipeline. The second
 section describes how Gitlab Runner and pipelines are configured and managed to
@@ -295,7 +295,7 @@ infrastructure.
 -----------------------
 
 Multiple intermediate CI signing keys exist, one Intermediate CI Key for jobs
-run in AWS, and one key for each affiliated institution (e.g. Univerity of
+run in AWS, and one key for each affiliated institution (e.g. University of
 Oregon). Here we describe how the Intermediate CI Key is managed in AWS:
 
 The Intermediate CI Key (including the Signing Intermediate CI Private Key is
@@ -305,7 +305,7 @@ contains an ASCII-armored export of just the *public* components of the
 Reputational Key. This secret also contains the *public* components of each of
 the affiliated institutions' Intermediate CI Key. These are potentially needed
 to verify dependent packages which may have been found in the public mirror or
-built by a protected job running on an affiliated institution's infrastrcuture
+built by a protected job running on an affiliated institution's infrastructure
 in an earlier stage of the pipeline.
 
 Procedurally the ``spack-intermediate-ci-signing-key`` secret is used in

lib/spack/llnl/util/lang.py

@@ -1047,9 +1047,9 @@ def __bool__(self):
         """Whether any exceptions were handled."""
         return bool(self.exceptions)
 
-    def forward(self, context: str) -> "GroupedExceptionForwarder":
+    def forward(self, context: str, base: type = BaseException) -> "GroupedExceptionForwarder":
         """Return a contextmanager which extracts tracebacks and prefixes a message."""
-        return GroupedExceptionForwarder(context, self)
+        return GroupedExceptionForwarder(context, self, base)
 
     def _receive_forwarded(self, context: str, exc: Exception, tb: List[str]):
         self.exceptions.append((context, exc, tb))
@@ -1072,15 +1072,18 @@ class GroupedExceptionForwarder:
     """A contextmanager to capture exceptions and forward them to a
     GroupedExceptionHandler."""
 
-    def __init__(self, context: str, handler: GroupedExceptionHandler):
+    def __init__(self, context: str, handler: GroupedExceptionHandler, base: type):
         self._context = context
         self._handler = handler
+        self._base = base
 
     def __enter__(self):
         return None
 
     def __exit__(self, exc_type, exc_value, tb):
         if exc_value is not None:
+            if not issubclass(exc_type, self._base):
+                return False
             self._handler._receive_forwarded(self._context, exc_value, traceback.format_tb(tb))
 
         # Suppress any exception from being re-raised:

lib/spack/spack/audit.py

@@ -726,13 +726,46 @@ def _unknown_variants_in_directives(pkgs, error_cls):
 
 
 @package_directives
-def _unknown_variants_in_dependencies(pkgs, error_cls):
-    """Report unknown dependencies and wrong variants for dependencies"""
+def _issues_in_depends_on_directive(pkgs, error_cls):
+    """Reports issues with 'depends_on' directives.
+
+    Issues might be unknown dependencies, unknown variants or variant values, or declaration
+    of nested dependencies.
+    """
     errors = []
     for pkg_name in pkgs:
         pkg_cls = spack.repo.PATH.get_pkg_class(pkg_name)
         filename = spack.repo.PATH.filename_for_package_name(pkg_name)
         for dependency_name, dependency_data in pkg_cls.dependencies.items():
+            # Check if there are nested dependencies declared. We don't want directives like:
+            #
+            #     depends_on('foo+bar ^fee+baz')
+            #
+            # but we'd like to have two dependencies listed instead.
+            for when, dependency_edge in dependency_data.items():
+                dependency_spec = dependency_edge.spec
+                nested_dependencies = dependency_spec.dependencies()
+                if nested_dependencies:
+                    summary = (
+                        f"{pkg_name}: invalid nested dependency "
+                        f"declaration '{str(dependency_spec)}'"
+                    )
+                    details = [
+                        f"split depends_on('{str(dependency_spec)}', when='{str(when)}') "
+                        f"into {len(nested_dependencies) + 1} directives",
+                        f"in {filename}",
+                    ]
+                    errors.append(error_cls(summary=summary, details=details))
+
+                for s in (dependency_spec, when):
+                    if s.virtual and s.variants:
+                        summary = f"{pkg_name}: virtual dependency cannot have variants"
+                        details = [
+                            f"remove variants from '{str(s)}' in depends_on directive",
+                            f"in {filename}",
+                        ]
+                        errors.append(error_cls(summary=summary, details=details))
+
             # No need to analyze virtual packages
             if spack.repo.PATH.is_virtual(dependency_name):
                 continue

lib/spack/spack/binary_distribution.py

@@ -25,7 +25,7 @@
 import warnings
 from contextlib import closing, contextmanager
 from gzip import GzipFile
-from typing import Dict, List, NamedTuple, Optional, Set, Tuple
+from typing import Dict, Iterable, List, NamedTuple, Optional, Set, Tuple
 from urllib.error import HTTPError, URLError
 
 import llnl.util.filesystem as fsys
@@ -230,7 +230,11 @@ def _associate_built_specs_with_mirror(self, cache_key, mirror_url):
                 )
                 return
 
-            spec_list = db.query_local(installed=False, in_buildcache=True)
+            spec_list = [
+                s
+                for s in db.query_local(installed=any, in_buildcache=any)
+                if s.external or db.query_local_by_spec_hash(s.dag_hash()).in_buildcache
+            ]
 
             for indexed_spec in spec_list:
                 dag_hash = indexed_spec.dag_hash()
@@ -1601,14 +1605,14 @@ def _get_valid_spec_file(path: str, max_supported_layout: int) -> Tuple[Dict, in
     return spec_dict, layout_version
 
 
-def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
+def download_tarball(spec, unsigned: Optional[bool] = False, mirrors_for_spec=None):
     """
     Download binary tarball for given package into stage area, returning
     path to downloaded tarball if successful, None otherwise.
 
     Args:
         spec (spack.spec.Spec): Concrete spec
-        unsigned (bool): Whether or not to require signed binaries
+        unsigned: if ``True`` or ``False`` override the mirror signature verification defaults
         mirrors_for_spec (list): Optional list of concrete specs and mirrors
             obtained by calling binary_distribution.get_mirrors_for_spec().
             These will be checked in order first before looking in other
@@ -1629,7 +1633,9 @@ def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
            "signature_verified": "true-if-binary-pkg-was-already-verified"
        }
     """
-    configured_mirrors = spack.mirror.MirrorCollection(binary=True).values()
+    configured_mirrors: Iterable[spack.mirror.Mirror] = spack.mirror.MirrorCollection(
+        binary=True
+    ).values()
     if not configured_mirrors:
         tty.die("Please add a spack mirror to allow download of pre-compiled packages.")
 
@@ -1647,8 +1653,16 @@ def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
     # mirror for the spec twice though.
     try_first = [i["mirror_url"] for i in mirrors_for_spec] if mirrors_for_spec else []
     try_next = [i.fetch_url for i in configured_mirrors if i.fetch_url not in try_first]
+    mirror_urls = try_first + try_next
 
-    mirrors = try_first + try_next
+    # TODO: turn `mirrors_for_spec` into a list of Mirror instances, instead of doing that here.
+    def fetch_url_to_mirror(url):
+        for mirror in configured_mirrors:
+            if mirror.fetch_url == url:
+                return mirror
+        return spack.mirror.Mirror(url)
+
+    mirrors = [fetch_url_to_mirror(url) for url in mirror_urls]
 
     tried_to_verify_sigs = []
 
@@ -1657,14 +1671,17 @@ def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
     # we remove support for deprecated spec formats and buildcache layouts.
     for try_signed in (True, False):
         for mirror in mirrors:
+            # Override mirror's default if
+            currently_unsigned = unsigned if unsigned is not None else not mirror.signed
+
             # If it's an OCI index, do things differently, since we cannot compose URLs.
-            parsed = urllib.parse.urlparse(mirror)
+            fetch_url = mirror.fetch_url
 
             # TODO: refactor this to some "nice" place.
-            if parsed.scheme == "oci":
-                ref = spack.oci.image.ImageReference.from_string(mirror[len("oci://") :]).with_tag(
-                    spack.oci.image.default_tag(spec)
-                )
+            if fetch_url.startswith("oci://"):
+                ref = spack.oci.image.ImageReference.from_string(
+                    fetch_url[len("oci://") :]
+                ).with_tag(spack.oci.image.default_tag(spec))
 
                 # Fetch the manifest
                 try:
@@ -1701,7 +1718,7 @@ def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
                         except InvalidMetadataFile as e:
                             tty.warn(
                                 f"Ignoring binary package for {spec.name}/{spec.dag_hash()[:7]} "
-                                f"from {mirror} due to invalid metadata file: {e}"
+                                f"from {fetch_url} due to invalid metadata file: {e}"
                             )
                             local_specfile_stage.destroy()
                             continue
@@ -1723,13 +1740,16 @@ def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
                     "tarball_stage": tarball_stage,
                     "specfile_stage": local_specfile_stage,
                     "signature_verified": False,
+                    "signature_required": not currently_unsigned,
                 }
 
             else:
                 ext = "json.sig" if try_signed else "json"
-                specfile_path = url_util.join(mirror, BUILD_CACHE_RELATIVE_PATH, specfile_prefix)
+                specfile_path = url_util.join(
+                    fetch_url, BUILD_CACHE_RELATIVE_PATH, specfile_prefix
+                )
                 specfile_url = f"{specfile_path}.{ext}"
-                spackfile_url = url_util.join(mirror, BUILD_CACHE_RELATIVE_PATH, tarball)
+                spackfile_url = url_util.join(fetch_url, BUILD_CACHE_RELATIVE_PATH, tarball)
                 local_specfile_stage = try_fetch(specfile_url)
                 if local_specfile_stage:
                     local_specfile_path = local_specfile_stage.save_filename
@@ -1742,21 +1762,21 @@ def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
                     except InvalidMetadataFile as e:
                         tty.warn(
                             f"Ignoring binary package for {spec.name}/{spec.dag_hash()[:7]} "
-                            f"from {mirror} due to invalid metadata file: {e}"
+                            f"from {fetch_url} due to invalid metadata file: {e}"
                         )
                         local_specfile_stage.destroy()
                         continue
 
-                    if try_signed and not unsigned:
+                    if try_signed and not currently_unsigned:
                         # If we found a signed specfile at the root, try to verify
                         # the signature immediately.  We will not download the
                         # tarball if we could not verify the signature.
                         tried_to_verify_sigs.append(specfile_url)
                         signature_verified = try_verify(local_specfile_path)
                         if not signature_verified:
-                            tty.warn("Failed to verify: {0}".format(specfile_url))
+                            tty.warn(f"Failed to verify: {specfile_url}")
 
-                    if unsigned or signature_verified or not try_signed:
+                    if currently_unsigned or signature_verified or not try_signed:
                         # We will download the tarball in one of three cases:
                         #     1. user asked for --no-check-signature
                         #     2. user didn't ask for --no-check-signature, but we
@@ -1779,6 +1799,7 @@ def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
                                 "tarball_stage": tarball_stage,
                                 "specfile_stage": local_specfile_stage,
                                 "signature_verified": signature_verified,
+                                "signature_required": not currently_unsigned,
                             }
 
                     local_specfile_stage.destroy()
@@ -1977,7 +1998,7 @@ def is_backup_file(file):
             relocate.relocate_text(text_names, prefix_to_prefix_text)
 
 
-def _extract_inner_tarball(spec, filename, extract_to, unsigned, remote_checksum):
+def _extract_inner_tarball(spec, filename, extract_to, signature_required: bool, remote_checksum):
     stagepath = os.path.dirname(filename)
     spackfile_name = tarball_name(spec, ".spack")
     spackfile_path = os.path.join(stagepath, spackfile_name)
@@ -1997,7 +2018,7 @@ def _extract_inner_tarball(spec, filename, extract_to, unsigned, remote_checksum
     else:
         raise ValueError("Cannot find spec file for {0}.".format(extract_to))
 
-    if not unsigned:
+    if signature_required:
         if os.path.exists("%s.asc" % specfile_path):
             suppress = config.get("config:suppress_gpg_warnings", False)
             try:
@@ -2046,7 +2067,7 @@ def _tar_strip_component(tar: tarfile.TarFile, prefix: str):
                 m.linkname = m.linkname[result.end() :]
 
 
-def extract_tarball(spec, download_result, unsigned=False, force=False, timer=timer.NULL_TIMER):
+def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
     """
     extract binary tarball for given package into install area
     """
@@ -2072,7 +2093,8 @@ def extract_tarball(spec, download_result, unsigned=False, force=False, timer=ti
     bchecksum = spec_dict["binary_cache_checksum"]
 
     filename = download_result["tarball_stage"].save_filename
-    signature_verified = download_result["signature_verified"]
+    signature_verified: bool = download_result["signature_verified"]
+    signature_required: bool = download_result["signature_required"]
     tmpdir = None
 
     if layout_version == 0:
@@ -2081,7 +2103,9 @@ def extract_tarball(spec, download_result, unsigned=False, force=False, timer=ti
         # and another tarball containing the actual install tree.
         tmpdir = tempfile.mkdtemp()
         try:
-            tarfile_path = _extract_inner_tarball(spec, filename, tmpdir, unsigned, bchecksum)
+            tarfile_path = _extract_inner_tarball(
+                spec, filename, tmpdir, signature_required, bchecksum
+            )
         except Exception as e:
             _delete_staged_downloads(download_result)
             shutil.rmtree(tmpdir)
@@ -2094,9 +2118,10 @@ def extract_tarball(spec, download_result, unsigned=False, force=False, timer=ti
         # the tarball.
         tarfile_path = filename
 
-        if not unsigned and not signature_verified:
+        if signature_required and not signature_verified:
             raise UnsignedPackageException(
-                "To install unsigned packages, use the --no-check-signature option."
+                "To install unsigned packages, use the --no-check-signature option, "
+                "or configure the mirror with signed: false."
             )
 
         # compute the sha256 checksum of the tarball
@@ -2209,7 +2234,7 @@ def install_root_node(spec, unsigned=False, force=False, sha256=None):
     # don't print long padded paths while extracting/relocating binaries
     with spack.util.path.filter_padding():
         tty.msg('Installing "{0}" from a buildcache'.format(spec.format()))
-        extract_tarball(spec, download_result, unsigned, force)
+        extract_tarball(spec, download_result, force)
         spack.hooks.post_install(spec, False)
         spack.store.STORE.db.add(spec, spack.store.STORE.layout)
 

lib/spack/spack/bootstrap/_common.py

@@ -16,6 +16,7 @@
 import llnl.util.filesystem as fs
 from llnl.util import tty
 
+import spack.platforms
 import spack.store
 import spack.util.environment
 import spack.util.executable
@@ -206,17 +207,19 @@ def _root_spec(spec_str: str) -> str:
     """Add a proper compiler and target to a spec used during bootstrapping.
 
     Args:
-        spec_str (str): spec to be bootstrapped. Must be without compiler and target.
+        spec_str: spec to be bootstrapped. Must be without compiler and target.
     """
-    # Add a proper compiler hint to the root spec. We use GCC for
-    # everything but MacOS and Windows.
-    if str(spack.platforms.host()) == "darwin":
+    # Add a compiler requirement to the root spec.
+    platform = str(spack.platforms.host())
+    if platform == "darwin":
         spec_str += " %apple-clang"
-    elif str(spack.platforms.host()) == "windows":
+    elif platform == "windows":
         # TODO (johnwparent): Remove version constraint when clingo patch is up
         spec_str += " %msvc@:19.37"
-    else:
+    elif platform == "linux":
         spec_str += " %gcc"
+    elif platform == "freebsd":
+        spec_str += " %clang"
 
     target = archspec.cpu.host().family
     spec_str += f" target={target}"

lib/spack/spack/bootstrap/config.py

@@ -147,7 +147,7 @@ def _add_compilers_if_missing() -> None:
             mixed_toolchain=sys.platform == "darwin"
         )
         if new_compilers:
-            spack.compilers.add_compilers_to_config(new_compilers)
+            spack.compilers.add_compilers_to_config(new_compilers, init_config=False)
 
 
 @contextlib.contextmanager

lib/spack/spack/bootstrap/core.py

@@ -386,7 +386,7 @@ def ensure_module_importable_or_raise(module: str, abstract_spec: Optional[str]
     exception_handler = GroupedExceptionHandler()
 
     for current_config in bootstrapping_sources():
-        with exception_handler.forward(current_config["name"]):
+        with exception_handler.forward(current_config["name"], Exception):
             source_is_enabled_or_raise(current_config)
             current_bootstrapper = create_bootstrapper(current_config)
             if current_bootstrapper.try_import(module, abstract_spec):
@@ -441,7 +441,7 @@ def ensure_executables_in_path_or_raise(
     exception_handler = GroupedExceptionHandler()
 
     for current_config in bootstrapping_sources():
-        with exception_handler.forward(current_config["name"]):
+        with exception_handler.forward(current_config["name"], Exception):
             source_is_enabled_or_raise(current_config)
             current_bootstrapper = create_bootstrapper(current_config)
             if current_bootstrapper.try_search_path(executables, abstract_spec):

lib/spack/spack/bootstrap/environment.py

@@ -19,7 +19,6 @@
 import spack.tengine
 import spack.util.cpus
 import spack.util.executable
-from spack.environment import depfile
 
 from ._common import _root_spec
 from .config import root_path, spec_for_current_python, store_path
@@ -86,12 +85,9 @@ def __init__(self) -> None:
         super().__init__(self.environment_root())
 
     def update_installations(self) -> None:
-        """Update the installations of this environment.
-
-        The update is done using a depfile on Linux and macOS, and using the ``install_all``
-        method of environments on Windows.
-        """
-        with tty.SuppressOutput(msg_enabled=False, warn_enabled=False):
+        """Update the installations of this environment."""
+        log_enabled = tty.is_debug() or tty.is_verbose()
+        with tty.SuppressOutput(msg_enabled=log_enabled, warn_enabled=log_enabled):
             specs = self.concretize()
         if specs:
             colorized_specs = [
@@ -100,11 +96,9 @@ def update_installations(self) -> None:
             ]
             tty.msg(f"[BOOTSTRAPPING] Installing dependencies ({', '.join(colorized_specs)})")
             self.write(regenerate=False)
-            if sys.platform == "win32":
+            with tty.SuppressOutput(msg_enabled=log_enabled, warn_enabled=log_enabled):
                 self.install_all()
-            else:
-                self._install_with_depfile()
-            self.write(regenerate=True)
+                self.write(regenerate=True)
 
     def update_syspath_and_environ(self) -> None:
         """Update ``sys.path`` and the PATH, PYTHONPATH environment variables to point to
@@ -122,25 +116,6 @@ def update_syspath_and_environ(self) -> None:
             + [str(x) for x in self.pythonpaths()]
         )
 
-    def _install_with_depfile(self) -> None:
-        model = depfile.MakefileModel.from_env(self)
-        template = spack.tengine.make_environment().get_template(
-            os.path.join("depfile", "Makefile")
-        )
-        makefile = self.environment_root() / "Makefile"
-        makefile.write_text(template.render(model.to_dict()))
-        make = spack.util.executable.which("make")
-        kwargs = {}
-        if not tty.is_debug():
-            kwargs = {"output": os.devnull, "error": os.devnull}
-        make(
-            "-C",
-            str(self.environment_root()),
-            "-j",
-            str(spack.util.cpus.determine_number_of_jobs(parallel=True)),
-            **kwargs,
-        )
-
     def _write_spack_yaml_file(self) -> None:
         tty.msg(
             "[BOOTSTRAPPING] Spack has missing dependencies, creating a bootstrapping environment"

lib/spack/spack/bootstrap/status.py

@@ -66,7 +66,6 @@ def _core_requirements() -> List[RequiredResponseType]:
     _core_system_exes = {
         "make": _missing("make", "required to build software from sources"),
         "patch": _missing("patch", "required to patch source code before building"),
-        "bash": _missing("bash", "required for Spack compiler wrapper"),
         "tar": _missing("tar", "required to manage code archives"),
         "gzip": _missing("gzip", "required to compress/decompress code archives"),
         "unzip": _missing("unzip", "required to compress/decompress code archives"),

lib/spack/spack/build_environment.py

@@ -1032,6 +1032,11 @@ def get_env_modifications(self) -> EnvironmentModifications:
                     if id(spec) in self.nodes_in_subdag:
                         pkg.setup_dependent_run_environment(run_env_mods, spec)
                 pkg.setup_run_environment(run_env_mods)
+
+                external_env = (dspec.extra_attributes or {}).get("environment", {})
+                if external_env:
+                    run_env_mods.extend(spack.schema.environment.parse(external_env))
+
                 if self.context == Context.BUILD:
                     # Don't let the runtime environment of comiler like dependencies leak into the
                     # build env

lib/spack/spack/build_systems/cached_cmake.py

@@ -9,6 +9,7 @@
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 
+import spack.build_environment
 import spack.builder
 
 from .cmake import CMakeBuilder, CMakePackage
@@ -285,6 +286,19 @@ def initconfig_hardware_entries(self):
     def std_initconfig_entries(self):
         cmake_prefix_path_env = os.environ["CMAKE_PREFIX_PATH"]
         cmake_prefix_path = cmake_prefix_path_env.replace(os.pathsep, ";")
+        cmake_rpaths_env = spack.build_environment.get_rpaths(self.pkg)
+        cmake_rpaths_path = ";".join(cmake_rpaths_env)
+        complete_rpath_list = cmake_rpaths_path
+        if "SPACK_COMPILER_EXTRA_RPATHS" in os.environ:
+            spack_extra_rpaths_env = os.environ["SPACK_COMPILER_EXTRA_RPATHS"]
+            spack_extra_rpaths_path = spack_extra_rpaths_env.replace(os.pathsep, ";")
+            complete_rpath_list = "{0};{1}".format(complete_rpath_list, spack_extra_rpaths_path)
+
+        if "SPACK_COMPILER_IMPLICIT_RPATHS" in os.environ:
+            spack_implicit_rpaths_env = os.environ["SPACK_COMPILER_IMPLICIT_RPATHS"]
+            spack_implicit_rpaths_path = spack_implicit_rpaths_env.replace(os.pathsep, ";")
+            complete_rpath_list = "{0};{1}".format(complete_rpath_list, spack_implicit_rpaths_path)
+
         return [
             "#------------------{0}".format("-" * 60),
             "# !!!! This is a generated file, edit at own risk !!!!",
@@ -292,6 +306,9 @@ def std_initconfig_entries(self):
             "# CMake executable path: {0}".format(self.pkg.spec["cmake"].command.path),
             "#------------------{0}\n".format("-" * 60),
             cmake_cache_string("CMAKE_PREFIX_PATH", cmake_prefix_path),
+            cmake_cache_string("CMAKE_INSTALL_RPATH_USE_LINK_PATH", "ON"),
+            cmake_cache_string("CMAKE_BUILD_RPATH", complete_rpath_list),
+            cmake_cache_string("CMAKE_INSTALL_RPATH", complete_rpath_list),
             self.define_cmake_cache_from_variant("CMAKE_BUILD_TYPE", "build_type"),
         ]
 

lib/spack/spack/build_systems/perl.py

@@ -10,13 +10,12 @@
 import spack.builder
 import spack.package_base
 from spack.directives import build_system, extends
-from spack.package_base import PackageBase
 from spack.util.executable import Executable
 
 from ._checks import BaseBuilder, execute_build_time_tests
 
 
-class PerlPackage(PackageBase):
+class PerlPackage(spack.package_base.PackageBase):
     """Specialized class for packages that are built using Perl."""
 
     #: This attribute is used in UI queries that need to know the build
@@ -61,6 +60,30 @@ class PerlBuilder(BaseBuilder):
     #: Callback names for build-time test
     build_time_test_callbacks = ["check"]
 
+    @property
+    def build_method(self):
+        """Searches the package for either a Makefile.PL or Build.PL.
+
+        Raises:
+            RuntimeError: if neither Makefile.PL nor Build.PL exist
+        """
+        if os.path.isfile("Makefile.PL"):
+            build_method = "Makefile.PL"
+        elif os.path.isfile("Build.PL"):
+            build_method = "Build.PL"
+        else:
+            raise RuntimeError("Unknown build_method for perl package")
+        return build_method
+
+    @property
+    def build_executable(self):
+        """Returns the executable method to build the perl package"""
+        if self.build_method == "Makefile.PL":
+            build_executable = inspect.getmodule(self.pkg).make
+        elif self.build_method == "Build.PL":
+            build_executable = Executable(os.path.join(self.pkg.stage.source_path, "Build"))
+        return build_executable
+
     def configure_args(self):
         """List of arguments passed to :py:meth:`~.PerlBuilder.configure`.
 
@@ -73,19 +96,7 @@ def configure(self, pkg, spec, prefix):
         """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`.
-
-        Raises:
-            RuntimeError: if neither Makefile.PL nor Build.PL exist
         """
-        if os.path.isfile("Makefile.PL"):
-            self.build_method = "Makefile.PL"
-            self.build_executable = inspect.getmodule(self.pkg).make
-        elif os.path.isfile("Build.PL"):
-            self.build_method = "Build.PL"
-            self.build_executable = Executable(os.path.join(self.pkg.stage.source_path, "Build"))
-        else:
-            raise RuntimeError("Unknown build_method for perl package")
-
         if self.build_method == "Makefile.PL":
             options = ["Makefile.PL", "INSTALL_BASE={0}".format(prefix)]
         elif self.build_method == "Build.PL":

lib/spack/spack/build_systems/python.py

@@ -6,13 +6,14 @@
 import os
 import re
 import shutil
-from typing import Optional
+from typing import Iterable, List, Mapping, Optional
 
 import archspec
 
 import llnl.util.filesystem as fs
 import llnl.util.lang as lang
 import llnl.util.tty as tty
+from llnl.util.filesystem import HeaderList, LibraryList
 
 import spack.builder
 import spack.config
@@ -25,14 +26,18 @@
 from spack.directives import build_system, depends_on, extends, maintainers
 from spack.error import NoHeadersError, NoLibrariesError
 from spack.install_test import test_part
+from spack.spec import Spec
+from spack.util.prefix import Prefix
 
 from ._checks import BaseBuilder, execute_install_time_tests
 
 
-def _flatten_dict(dictionary):
+def _flatten_dict(dictionary: Mapping[str, object]) -> Iterable[str]:
     """Iterable that yields KEY=VALUE paths through a dictionary.
+
     Args:
         dictionary: Possibly nested dictionary of arbitrary keys and values.
+
     Yields:
         A single path through the dictionary.
     """
@@ -50,7 +55,7 @@ class PythonExtension(spack.package_base.PackageBase):
     maintainers("adamjstewart")
 
     @property
-    def import_modules(self):
+    def import_modules(self) -> Iterable[str]:
         """Names of modules that the Python package provides.
 
         These are used to test whether or not the installation succeeded.
@@ -65,7 +70,7 @@ def import_modules(self):
         detected, this property can be overridden by the package.
 
         Returns:
-            list: list of strings of module names
+            List of strings of module names.
         """
         modules = []
         pkg = self.spec["python"].package
@@ -102,14 +107,14 @@ def import_modules(self):
         return modules
 
     @property
-    def skip_modules(self):
+    def skip_modules(self) -> Iterable[str]:
         """Names of modules that should be skipped when running tests.
 
         These are a subset of import_modules. If a module has submodules,
         they are skipped as well (meaning a.b is skipped if a is contained).
 
         Returns:
-            list: list of strings of module names
+            List of strings of module names.
         """
         return []
 
@@ -185,12 +190,12 @@ def remove_files_from_view(self, view, merge_map):
 
         view.remove_files(to_remove)
 
-    def test_imports(self):
+    def test_imports(self) -> None:
         """Attempts to import modules of the installed package."""
 
         # Make sure we are importing the installed modules,
         # not the ones in the source directory
-        python = inspect.getmodule(self).python
+        python = inspect.getmodule(self).python  # type: ignore[union-attr]
         for module in self.import_modules:
             with test_part(
                 self,
@@ -315,24 +320,27 @@ class PythonPackage(PythonExtension):
     py_namespace: Optional[str] = None
 
     @lang.classproperty
-    def homepage(cls):
+    def homepage(cls) -> Optional[str]:  # type: ignore[override]
         if cls.pypi:
             name = cls.pypi.split("/")[0]
-            return "https://pypi.org/project/" + name + "/"
+            return f"https://pypi.org/project/{name}/"
+        return None
 
     @lang.classproperty
-    def url(cls):
+    def url(cls) -> Optional[str]:
         if cls.pypi:
-            return "https://files.pythonhosted.org/packages/source/" + cls.pypi[0] + "/" + cls.pypi
+            return f"https://files.pythonhosted.org/packages/source/{cls.pypi[0]}/{cls.pypi}"
+        return None
 
     @lang.classproperty
-    def list_url(cls):
+    def list_url(cls) -> Optional[str]:  # type: ignore[override]
         if cls.pypi:
             name = cls.pypi.split("/")[0]
-            return "https://pypi.org/simple/" + name + "/"
+            return f"https://pypi.org/simple/{name}/"
+        return None
 
     @property
-    def headers(self):
+    def headers(self) -> HeaderList:
         """Discover header files in platlib."""
 
         # Remove py- prefix in package name
@@ -350,7 +358,7 @@ def headers(self):
         raise NoHeadersError(msg.format(self.spec.name, include, platlib))
 
     @property
-    def libs(self):
+    def libs(self) -> LibraryList:
         """Discover libraries in platlib."""
 
         # Remove py- prefix in package name
@@ -384,7 +392,7 @@ class PythonPipBuilder(BaseBuilder):
     install_time_test_callbacks = ["test"]
 
     @staticmethod
-    def std_args(cls):
+    def std_args(cls) -> List[str]:
         return [
             # Verbose
             "-vvv",
@@ -409,7 +417,7 @@ def std_args(cls):
         ]
 
     @property
-    def build_directory(self):
+    def build_directory(self) -> str:
         """The root directory of the Python package.
 
         This is usually the directory containing one of the following files:
@@ -420,51 +428,51 @@ def build_directory(self):
         """
         return self.pkg.stage.source_path
 
-    def config_settings(self, spec, prefix):
+    def config_settings(self, spec: Spec, prefix: Prefix) -> Mapping[str, object]:
         """Configuration settings to be passed to the PEP 517 build backend.
 
         Requires pip 22.1 or newer for keys that appear only a single time,
         or pip 23.1 or newer if the same key appears multiple times.
 
         Args:
-            spec (spack.spec.Spec): build spec
-            prefix (spack.util.prefix.Prefix): installation prefix
+            spec: Build spec.
+            prefix: Installation prefix.
 
         Returns:
-            dict: Possibly nested dictionary of KEY, VALUE settings
+            Possibly nested dictionary of KEY, VALUE settings.
         """
         return {}
 
-    def install_options(self, spec, prefix):
+    def install_options(self, spec: Spec, prefix: Prefix) -> Iterable[str]:
         """Extra arguments to be supplied to the setup.py install command.
 
         Requires pip 23.0 or older.
 
         Args:
-            spec (spack.spec.Spec): build spec
-            prefix (spack.util.prefix.Prefix): installation prefix
+            spec: Build spec.
+            prefix: Installation prefix.
 
         Returns:
-            list: list of options
+            List of options.
         """
         return []
 
-    def global_options(self, spec, prefix):
+    def global_options(self, spec: Spec, prefix: Prefix) -> Iterable[str]:
         """Extra global options to be supplied to the setup.py call before the install
         or bdist_wheel command.
 
         Deprecated in pip 23.1.
 
         Args:
-            spec (spack.spec.Spec): build spec
-            prefix (spack.util.prefix.Prefix): installation prefix
+            spec: Build spec.
+            prefix: Installation prefix.
 
         Returns:
-            list: list of options
+            List of options.
         """
         return []
 
-    def install(self, pkg, spec, prefix):
+    def install(self, pkg: PythonPackage, spec: Spec, prefix: Prefix) -> None:
         """Install everything from build directory."""
 
         args = PythonPipBuilder.std_args(pkg) + [f"--prefix={prefix}"]

lib/spack/spack/build_systems/rocm.py

@@ -108,6 +108,8 @@ class ROCmPackage(PackageBase):
         "gfx90a:xnack+",
         "gfx90c",
         "gfx940",
+        "gfx941",
+        "gfx942",
         "gfx1010",
         "gfx1011",
         "gfx1012",
@@ -168,6 +170,8 @@ def hip_flags(amdgpu_target):
     depends_on("llvm-amdgpu@4.3.0:", when="amdgpu_target=gfx90a:xnack-")
     depends_on("llvm-amdgpu@4.3.0:", when="amdgpu_target=gfx90a:xnack+")
     depends_on("llvm-amdgpu@5.2.0:", when="amdgpu_target=gfx940")
+    depends_on("llvm-amdgpu@5.7.0:", when="amdgpu_target=gfx941")
+    depends_on("llvm-amdgpu@5.7.0:", when="amdgpu_target=gfx942")
     depends_on("llvm-amdgpu@4.5.0:", when="amdgpu_target=gfx1013")
     depends_on("llvm-amdgpu@3.8.0:", when="amdgpu_target=gfx1030")
     depends_on("llvm-amdgpu@3.9.0:", when="amdgpu_target=gfx1031")

lib/spack/spack/ci.py

@@ -1253,6 +1253,7 @@ def main_script_replacements(cmd):
                 op=lambda cmd: cmd.replace("mirror_prefix", temp_storage_url_prefix),
             )
 
+            cleanup_job["dependencies"] = []
             output_object["cleanup"] = cleanup_job
 
         if (
@@ -1276,6 +1277,7 @@ def main_script_replacements(cmd):
                 if buildcache_destination
                 else remote_mirror_override or remote_mirror_url
             )
+            signing_job["dependencies"] = []
 
             output_object["sign-pkgs"] = signing_job
 
@@ -1296,6 +1298,7 @@ def main_script_replacements(cmd):
             final_job["when"] = "always"
             final_job["retry"] = service_job_retries
             final_job["interruptible"] = True
+            final_job["dependencies"] = []
 
             output_object["rebuild-index"] = final_job
 

lib/spack/spack/cmd/__init__.py

@@ -6,10 +6,8 @@
 import argparse
 import os
 import re
-import shlex
 import sys
-from textwrap import dedent
-from typing import List, Match, Tuple
+from typing import List, Union
 
 import llnl.string
 import llnl.util.tty as tty
@@ -147,89 +145,37 @@ def get_command(cmd_name):
     return getattr(get_module(cmd_name), pname)
 
 
-class _UnquotedFlags:
-    """Use a heuristic in `.extract()` to detect whether the user is trying to set
-    multiple flags like the docker ENV attribute allows (e.g. 'cflags=-Os -pipe').
+def quote_kvp(string: str) -> str:
+    """For strings like ``name=value`` or ``name==value``, quote and escape the value if needed.
 
-    If the heuristic finds a match (which can be checked with `__bool__()`), a warning
-    message explaining how to quote multiple flags correctly can be generated with
-    `.report()`.
+    This is a compromise to respect quoting of key-value pairs on the CLI. The shell
+    strips quotes from quoted arguments, so we cannot know *exactly* how CLI arguments
+    were quoted. To compensate, we re-add quotes around anything staritng with ``name=``
+    or ``name==``, and we assume the rest of the argument is the value. This covers the
+    common cases of passign flags, e.g., ``cflags="-O2 -g"`` on the command line.
     """
+    match = spack.parser.SPLIT_KVP.match(string)
+    if not match:
+        return string
 
-    flags_arg_pattern = re.compile(
-        r'^({0})=([^\'"].*)$'.format("|".join(spack.spec.FlagMap.valid_compiler_flags()))
-    )
-
-    def __init__(self, all_unquoted_flag_pairs: List[Tuple[Match[str], str]]):
-        self._flag_pairs = all_unquoted_flag_pairs
-
-    def __bool__(self) -> bool:
-        return bool(self._flag_pairs)
-
-    @classmethod
-    def extract(cls, sargs: str) -> "_UnquotedFlags":
-        all_unquoted_flag_pairs: List[Tuple[Match[str], str]] = []
-        prev_flags_arg = None
-        for arg in shlex.split(sargs):
-            if prev_flags_arg is not None:
-                all_unquoted_flag_pairs.append((prev_flags_arg, arg))
-            prev_flags_arg = cls.flags_arg_pattern.match(arg)
-        return cls(all_unquoted_flag_pairs)
-
-    def report(self) -> str:
-        single_errors = [
-            "({0}) {1} {2} => {3}".format(
-                i + 1,
-                match.group(0),
-                next_arg,
-                '{0}="{1} {2}"'.format(match.group(1), match.group(2), next_arg),
-            )
-            for i, (match, next_arg) in enumerate(self._flag_pairs)
-        ]
-        return dedent(
-            """\
-        Some compiler or linker flags were provided without quoting their arguments,
-        which now causes spack to try to parse the *next* argument as a spec component
-        such as a variant instead of an additional compiler or linker flag. If the
-        intent was to set multiple flags, try quoting them together as described below.
-
-        Possible flag quotation errors (with the correctly-quoted version after the =>):
-        {0}"""
-        ).format("\n".join(single_errors))
+    key, delim, value = match.groups()
+    return f"{key}{delim}{spack.parser.quote_if_needed(value)}"
 
 
-def parse_specs(args, **kwargs):
+def parse_specs(
+    args: Union[str, List[str]], concretize: bool = False, tests: bool = False
+) -> List[spack.spec.Spec]:
     """Convenience function for parsing arguments from specs.  Handles common
     exceptions and dies if there are errors.
     """
-    concretize = kwargs.get("concretize", False)
-    normalize = kwargs.get("normalize", False)
-    tests = kwargs.get("tests", False)
+    args = [args] if isinstance(args, str) else args
+    arg_string = " ".join([quote_kvp(arg) for arg in args])
 
-    sargs = args
-    if not isinstance(args, str):
-        sargs = " ".join(args)
-    unquoted_flags = _UnquotedFlags.extract(sargs)
-
-    try:
-        specs = spack.parser.parse(sargs)
-        for spec in specs:
-            if concretize:
-                spec.concretize(tests=tests)  # implies normalize
-            elif normalize:
-                spec.normalize(tests=tests)
-        return specs
-
-    except spack.error.SpecError as e:
-        msg = e.message
-        if e.long_message:
-            msg += e.long_message
-        # Unquoted flags will be read as a variant or hash
-        if unquoted_flags and ("variant" in msg or "hash" in msg):
-            msg += "\n\n"
-            msg += unquoted_flags.report()
-
-        raise spack.error.SpackError(msg) from e
+    specs = spack.parser.parse(arg_string)
+    for spec in specs:
+        if concretize:
+            spec.concretize(tests=tests)
+    return specs
 
 
 def matching_spec_from_env(spec):

lib/spack/spack/cmd/add.py

@@ -6,7 +6,7 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
+from spack.cmd.common import arguments
 
 description = "add a spec to an environment"
 section = "environments"

lib/spack/spack/cmd/bootstrap.py

@@ -15,13 +15,13 @@
 import spack.bootstrap
 import spack.bootstrap.config
 import spack.bootstrap.core
-import spack.cmd.common.arguments
 import spack.config
 import spack.main
 import spack.mirror
 import spack.spec
 import spack.stage
 import spack.util.path
+from spack.cmd.common import arguments
 
 description = "manage bootstrap configuration"
 section = "system"
@@ -68,12 +68,8 @@
 
 
 def _add_scope_option(parser):
-    scopes = spack.config.scopes()
     parser.add_argument(
-        "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        help="configuration scope to read/modify",
+        "--scope", action=arguments.ConfigScope, help="configuration scope to read/modify"
     )
 
 
@@ -106,7 +102,7 @@ def setup_parser(subparser):
     disable.add_argument("name", help="name of the source to be disabled", nargs="?", default=None)
 
     reset = sp.add_parser("reset", help="reset bootstrapping configuration to Spack defaults")
-    spack.cmd.common.arguments.add_common_arguments(reset, ["yes_to_all"])
+    arguments.add_common_arguments(reset, ["yes_to_all"])
 
     root = sp.add_parser("root", help="get/set the root bootstrap directory")
     _add_scope_option(root)

lib/spack/spack/cmd/buildcache.py

@@ -21,7 +21,6 @@
 
 import spack.binary_distribution as bindist
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.environment as ev
 import spack.error
@@ -38,8 +37,10 @@
 import spack.util.crypto
 import spack.util.url as url_util
 import spack.util.web as web_util
+from spack import traverse
 from spack.build_environment import determine_number_of_jobs
 from spack.cmd import display_specs
+from spack.cmd.common import arguments
 from spack.oci.image import (
     Digest,
     ImageReference,
@@ -76,7 +77,19 @@ def setup_parser(subparser: argparse.ArgumentParser):
     )
     push_sign = push.add_mutually_exclusive_group(required=False)
     push_sign.add_argument(
-        "--unsigned", "-u", action="store_true", help="push unsigned buildcache tarballs"
+        "--unsigned",
+        "-u",
+        action="store_false",
+        dest="signed",
+        default=None,
+        help="push unsigned buildcache tarballs",
+    )
+    push_sign.add_argument(
+        "--signed",
+        action="store_true",
+        dest="signed",
+        default=None,
+        help="push signed buildcache tarballs",
     )
     push_sign.add_argument(
         "--key", "-k", metavar="key", type=str, default=None, help="key for signing"
@@ -110,7 +123,14 @@ def setup_parser(subparser: argparse.ArgumentParser):
         help="stop pushing on first failure (default is best effort)",
     )
     push.add_argument(
-        "--base-image", default=None, help="specify the base image for the buildcache. "
+        "--base-image", default=None, help="specify the base image for the buildcache"
+    )
+    push.add_argument(
+        "--tag",
+        "-t",
+        default=None,
+        help="when pushing to an OCI registry, tag an image containing all root specs and their "
+        "runtime dependencies",
     )
     arguments.add_common_arguments(push, ["specs", "jobs"])
     push.set_defaults(func=push_fn)
@@ -182,23 +202,22 @@ def setup_parser(subparser: argparse.ArgumentParser):
     )
 
     # used to construct scope arguments below
-    scopes = spack.config.scopes()
-
     check.add_argument(
         "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_modify_scope(),
+        action=arguments.ConfigScope,
+        default=lambda: spack.config.default_modify_scope(),
         help="configuration scope containing mirrors to check",
     )
-    check_spec_or_specfile = check.add_mutually_exclusive_group(required=True)
-    check_spec_or_specfile.add_argument(
+    # Unfortunately there are 3 ways to do the same thing here:
+    check_specs = check.add_mutually_exclusive_group()
+    check_specs.add_argument(
         "-s", "--spec", help="check single spec instead of release specs file"
     )
-    check_spec_or_specfile.add_argument(
+    check_specs.add_argument(
         "--spec-file",
         help="check single spec from json or yaml file instead of release specs file",
     )
+    arguments.add_common_arguments(check, ["specs"])
 
     check.set_defaults(func=check_fn)
 
@@ -320,26 +339,36 @@ def push_fn(args):
         )
 
     if args.specs or args.spec_file:
-        specs = _matching_specs(spack.cmd.parse_specs(args.specs or args.spec_file))
+        roots = _matching_specs(spack.cmd.parse_specs(args.specs or args.spec_file))
     else:
-        specs = spack.cmd.require_active_env("buildcache push").all_specs()
+        roots = spack.cmd.require_active_env(cmd_name="buildcache push").concrete_roots()
 
     if args.allow_root:
         tty.warn(
             "The flag `--allow-root` is the default in Spack 0.21, will be removed in Spack 0.22"
         )
 
+    mirror: spack.mirror.Mirror = args.mirror
+
     # Check if this is an OCI image.
     try:
-        image_ref = spack.oci.oci.image_from_mirror(args.mirror)
+        target_image = spack.oci.oci.image_from_mirror(mirror)
     except ValueError:
-        image_ref = None
+        target_image = None
+
+    push_url = mirror.push_url
+
+    # When neither --signed, --unsigned nor --key are specified, use the mirror's default.
+    if args.signed is None and not args.key:
+        unsigned = not mirror.signed
+    else:
+        unsigned = not (args.key or args.signed)
 
     # For OCI images, we require dependencies to be pushed for now.
-    if image_ref:
+    if target_image:
         if "dependencies" not in args.things_to_install:
             tty.die("Dependencies must be pushed for OCI images.")
-        if not args.unsigned:
+        if not unsigned:
             tty.warn(
                 "Code signing is currently not supported for OCI images. "
                 "Use --unsigned to silence this warning."
@@ -347,26 +376,48 @@ def push_fn(args):
 
     # This is a list of installed, non-external specs.
     specs = bindist.specs_to_be_packaged(
-        specs,
+        roots,
         root="package" in args.things_to_install,
         dependencies="dependencies" in args.things_to_install,
     )
 
-    url = args.mirror.push_url
-
     # When pushing multiple specs, print the url once ahead of time, as well as how
     # many specs are being pushed.
     if len(specs) > 1:
-        tty.info(f"Selected {len(specs)} specs to push to {url}")
+        tty.info(f"Selected {len(specs)} specs to push to {push_url}")
 
     failed = []
 
     # TODO: unify this logic in the future.
-    if image_ref:
+    if target_image:
+        base_image = ImageReference.from_string(args.base_image) if args.base_image else None
         with tempfile.TemporaryDirectory(
             dir=spack.stage.get_stage_root()
         ) as tmpdir, _make_pool() as pool:
-            skipped = _push_oci(args, image_ref, specs, tmpdir, pool)
+            skipped, base_images, checksums = _push_oci(
+                target_image=target_image,
+                base_image=base_image,
+                installed_specs_with_deps=specs,
+                force=args.force,
+                tmpdir=tmpdir,
+                pool=pool,
+            )
+
+            # Apart from creating manifests for each individual spec, we allow users to create a
+            # separate image tag for all root specs and their runtime dependencies.
+            if args.tag:
+                tagged_image = target_image.with_tag(args.tag)
+                # _push_oci may not populate base_images if binaries were already in the registry
+                for spec in roots:
+                    _update_base_images(
+                        base_image=base_image,
+                        target_image=target_image,
+                        spec=spec,
+                        base_image_cache=base_images,
+                    )
+                _put_manifest(base_images, checksums, tagged_image, tmpdir, None, None, *roots)
+                tty.info(f"Tagged {tagged_image}")
+
     else:
         skipped = []
 
@@ -374,10 +425,10 @@ def push_fn(args):
             try:
                 bindist.push_or_raise(
                     spec,
-                    url,
+                    push_url,
                     bindist.PushOptions(
                         force=args.force,
-                        unsigned=args.unsigned,
+                        unsigned=unsigned,
                         key=args.key,
                         regenerate_index=args.update_index,
                     ),
@@ -385,7 +436,7 @@ def push_fn(args):
 
                 msg = f"{_progress(i, len(specs))}Pushed {_format_spec(spec)}"
                 if len(specs) == 1:
-                    msg += f" to {url}"
+                    msg += f" to {push_url}"
                 tty.info(msg)
 
             except bindist.NoOverwriteException:
@@ -427,11 +478,11 @@ def push_fn(args):
     # Update the index if requested
     # TODO: remove update index logic out of bindist; should be once after all specs are pushed
     # not once per spec.
-    if image_ref and len(skipped) < len(specs) and args.update_index:
+    if target_image and len(skipped) < len(specs) and args.update_index:
         with tempfile.TemporaryDirectory(
             dir=spack.stage.get_stage_root()
         ) as tmpdir, _make_pool() as pool:
-            _update_index_oci(image_ref, tmpdir, pool)
+            _update_index_oci(target_image, tmpdir, pool)
 
 
 def _get_spack_binary_blob(image_ref: ImageReference) -> Optional[spack.oci.oci.Blob]:
@@ -497,17 +548,21 @@ def _archspec_to_gooarch(spec: spack.spec.Spec) -> str:
 def _put_manifest(
     base_images: Dict[str, Tuple[dict, dict]],
     checksums: Dict[str, spack.oci.oci.Blob],
-    spec: spack.spec.Spec,
     image_ref: ImageReference,
     tmpdir: str,
+    extra_config: Optional[dict],
+    annotations: Optional[dict],
+    *specs: spack.spec.Spec,
 ):
-    architecture = _archspec_to_gooarch(spec)
+    architecture = _archspec_to_gooarch(specs[0])
 
     dependencies = list(
         reversed(
             list(
                 s
-                for s in spec.traverse(order="topo", deptype=("link", "run"), root=True)
+                for s in traverse.traverse_nodes(
+                    specs, order="topo", deptype=("link", "run"), root=True
+                )
                 if not s.external
             )
         )
@@ -516,7 +571,7 @@ def _put_manifest(
     base_manifest, base_config = base_images[architecture]
     env = _retrieve_env_dict_from_config(base_config)
 
-    spack.user_environment.environment_modifications_for_specs(spec).apply_modifications(env)
+    spack.user_environment.environment_modifications_for_specs(*specs).apply_modifications(env)
 
     # Create an oci.image.config file
     config = copy.deepcopy(base_config)
@@ -528,20 +583,14 @@ def _put_manifest(
     # Set the environment variables
     config["config"]["Env"] = [f"{k}={v}" for k, v in env.items()]
 
-    # From the OCI v1.0 spec:
-    # > Any extra fields in the Image JSON struct are considered implementation
-    # > specific and MUST be ignored by any implementations which are unable to
-    # > interpret them.
-    # We use this to store the Spack spec, so we can use it to create an index.
-    spec_dict = spec.to_dict(hash=ht.dag_hash)
-    spec_dict["buildcache_layout_version"] = 1
-    spec_dict["binary_cache_checksum"] = {
-        "hash_algorithm": "sha256",
-        "hash": checksums[spec.dag_hash()].compressed_digest.digest,
-    }
-    config.update(spec_dict)
+    if extra_config:
+        # From the OCI v1.0 spec:
+        # > Any extra fields in the Image JSON struct are considered implementation
+        # > specific and MUST be ignored by any implementations which are unable to
+        # > interpret them.
+        config.update(extra_config)
 
-    config_file = os.path.join(tmpdir, f"{spec.dag_hash()}.config.json")
+    config_file = os.path.join(tmpdir, f"{specs[0].dag_hash()}.config.json")
 
     with open(config_file, "w") as f:
         json.dump(config, f, separators=(",", ":"))
@@ -572,48 +621,69 @@ def _put_manifest(
                 for s in dependencies
             ),
         ],
-        "annotations": {"org.opencontainers.image.description": spec.format()},
     }
 
-    image_ref_for_spec = image_ref.with_tag(default_tag(spec))
+    if annotations:
+        oci_manifest["annotations"] = annotations
 
     # Finally upload the manifest
-    upload_manifest_with_retry(image_ref_for_spec, oci_manifest=oci_manifest)
+    upload_manifest_with_retry(image_ref, oci_manifest=oci_manifest)
 
     # delete the config file
     os.unlink(config_file)
 
-    return image_ref_for_spec
+
+def _update_base_images(
+    *,
+    base_image: Optional[ImageReference],
+    target_image: ImageReference,
+    spec: spack.spec.Spec,
+    base_image_cache: Dict[str, Tuple[dict, dict]],
+):
+    """For a given spec and base image, copy the missing layers of the base image with matching
+    arch to the registry of the target image. If no base image is specified, create a dummy
+    manifest and config file."""
+    architecture = _archspec_to_gooarch(spec)
+    if architecture in base_image_cache:
+        return
+    if base_image is None:
+        base_image_cache[architecture] = (
+            default_manifest(),
+            default_config(architecture, "linux"),
+        )
+    else:
+        base_image_cache[architecture] = copy_missing_layers_with_retry(
+            base_image, target_image, architecture
+        )
 
 
 def _push_oci(
-    args,
-    image_ref: ImageReference,
+    *,
+    target_image: ImageReference,
+    base_image: Optional[ImageReference],
     installed_specs_with_deps: List[Spec],
     tmpdir: str,
     pool: multiprocessing.pool.Pool,
-) -> List[str]:
+    force: bool = False,
+) -> Tuple[List[str], Dict[str, Tuple[dict, dict]], Dict[str, spack.oci.oci.Blob]]:
     """Push specs to an OCI registry
 
     Args:
-        args: The command line arguments.
-        image_ref: The image reference.
+        image_ref: The target OCI image
+        base_image: Optional base image, which will be copied to the target registry.
         installed_specs_with_deps: The installed specs to push, excluding externals,
             including deps, ordered from roots to leaves.
+        force: Whether to overwrite existing layers and manifests in the buildcache.
 
     Returns:
-        List[str]: The list of skipped specs (already in the buildcache).
+        A tuple consisting of the list of skipped specs already in the build cache,
+        a dictionary mapping architectures to base image manifests and configs,
+        and a dictionary mapping each spec's dag hash to a blob.
     """
 
     # Reverse the order
     installed_specs_with_deps = list(reversed(installed_specs_with_deps))
 
-    # The base image to use for the package. When not set, we use
-    # the OCI registry only for storage, and do not use any base image.
-    base_image_ref: Optional[ImageReference] = (
-        ImageReference.from_string(args.base_image) if args.base_image else None
-    )
-
     # Spec dag hash -> blob
     checksums: Dict[str, spack.oci.oci.Blob] = {}
 
@@ -623,11 +693,11 @@ def _push_oci(
     # Specs not uploaded because they already exist
     skipped = []
 
-    if not args.force:
+    if not force:
         tty.info("Checking for existing specs in the buildcache")
         to_be_uploaded = []
 
-        tags_to_check = (image_ref.with_tag(default_tag(s)) for s in installed_specs_with_deps)
+        tags_to_check = (target_image.with_tag(default_tag(s)) for s in installed_specs_with_deps)
         available_blobs = pool.map(_get_spack_binary_blob, tags_to_check)
 
         for spec, maybe_blob in zip(installed_specs_with_deps, available_blobs):
@@ -640,46 +710,63 @@ def _push_oci(
         to_be_uploaded = installed_specs_with_deps
 
     if not to_be_uploaded:
-        return skipped
+        return skipped, base_images, checksums
 
     tty.info(
-        f"{len(to_be_uploaded)} specs need to be pushed to {image_ref.domain}/{image_ref.name}"
+        f"{len(to_be_uploaded)} specs need to be pushed to "
+        f"{target_image.domain}/{target_image.name}"
     )
 
     # Upload blobs
     new_blobs = pool.starmap(
-        _push_single_spack_binary_blob, ((image_ref, spec, tmpdir) for spec in to_be_uploaded)
+        _push_single_spack_binary_blob, ((target_image, spec, tmpdir) for spec in to_be_uploaded)
     )
 
     # And update the spec to blob mapping
     for spec, blob in zip(to_be_uploaded, new_blobs):
         checksums[spec.dag_hash()] = blob
 
-    # Copy base image layers, probably fine to do sequentially.
+    # Copy base images if necessary
     for spec in to_be_uploaded:
-        architecture = _archspec_to_gooarch(spec)
-        # Get base image details, if we don't have them yet
-        if architecture in base_images:
-            continue
-        if base_image_ref is None:
-            base_images[architecture] = (default_manifest(), default_config(architecture, "linux"))
-        else:
-            base_images[architecture] = copy_missing_layers_with_retry(
-                base_image_ref, image_ref, architecture
-            )
+        _update_base_images(
+            base_image=base_image,
+            target_image=target_image,
+            spec=spec,
+            base_image_cache=base_images,
+        )
+
+    def extra_config(spec: Spec):
+        spec_dict = spec.to_dict(hash=ht.dag_hash)
+        spec_dict["buildcache_layout_version"] = 1
+        spec_dict["binary_cache_checksum"] = {
+            "hash_algorithm": "sha256",
+            "hash": checksums[spec.dag_hash()].compressed_digest.digest,
+        }
+        return spec_dict
 
     # Upload manifests
     tty.info("Uploading manifests")
-    pushed_image_ref = pool.starmap(
+    pool.starmap(
         _put_manifest,
-        ((base_images, checksums, spec, image_ref, tmpdir) for spec in to_be_uploaded),
+        (
+            (
+                base_images,
+                checksums,
+                target_image.with_tag(default_tag(spec)),
+                tmpdir,
+                extra_config(spec),
+                {"org.opencontainers.image.description": spec.format()},
+                spec,
+            )
+            for spec in to_be_uploaded
+        ),
     )
 
     # Print the image names of the top-level specs
-    for spec, ref in zip(to_be_uploaded, pushed_image_ref):
-        tty.info(f"Pushed {_format_spec(spec)} to {ref}")
+    for spec in to_be_uploaded:
+        tty.info(f"Pushed {_format_spec(spec)} to {target_image.with_tag(default_tag(spec))}")
 
-    return skipped
+    return skipped, base_images, checksums
 
 
 def _config_from_tag(image_ref: ImageReference, tag: str) -> Optional[dict]:
@@ -816,15 +903,24 @@ def check_fn(args: argparse.Namespace):
     exit code is non-zero, then at least one of the indicated specs needs to be rebuilt
     """
     if args.spec_file:
+        specs_arg = (
+            args.spec_file if os.path.sep in args.spec_file else os.path.join(".", args.spec_file)
+        )
         tty.warn(
             "The flag `--spec-file` is deprecated and will be removed in Spack 0.22. "
-            "Use --spec instead."
+            f"Use `spack buildcache check {specs_arg}` instead."
         )
+    elif args.spec:
+        specs_arg = args.spec
+        tty.warn(
+            "The flag `--spec` is deprecated and will be removed in Spack 0.23. "
+            f"Use `spack buildcache check {specs_arg}` instead."
+        )
+    else:
+        specs_arg = args.specs
 
-    specs = spack.cmd.parse_specs(args.spec or args.spec_file)
-
-    if specs:
-        specs = _matching_specs(specs)
+    if specs_arg:
+        specs = _matching_specs(spack.cmd.parse_specs(specs_arg))
     else:
         specs = spack.cmd.require_active_env("buildcache check").all_specs()
 

lib/spack/spack/cmd/change.py

@@ -4,7 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
+from spack.cmd.common import arguments
 
 description = "change an existing spec in an environment"
 section = "environments"

lib/spack/spack/cmd/ci.py

@@ -16,6 +16,7 @@
 import spack.cmd.buildcache as buildcache
 import spack.config as cfg
 import spack.environment as ev
+import spack.environment.depfile
 import spack.hash_types as ht
 import spack.mirror
 import spack.util.gpg as gpg_util
@@ -606,7 +607,9 @@ def ci_rebuild(args):
             "SPACK_INSTALL_FLAGS={}".format(args_to_string(deps_install_args)),
             "-j$(nproc)",
             "install-deps/{}".format(
-                ev.depfile.MakefileSpec(job_spec).safe_format("{name}-{version}-{hash}")
+                spack.environment.depfile.MakefileSpec(job_spec).safe_format(
+                    "{name}-{version}-{hash}"
+                )
             ),
         ],
         spack_cmd + ["install"] + root_install_args,

lib/spack/spack/cmd/clean.py

@@ -12,13 +12,13 @@
 
 import spack.bootstrap
 import spack.caches
-import spack.cmd.common.arguments as arguments
 import spack.cmd.test
 import spack.config
 import spack.repo
 import spack.stage
 import spack.store
 import spack.util.path
+from spack.cmd.common import arguments
 from spack.paths import lib_path, var_path
 
 description = "remove temporary build files and/or downloaded archives"

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

@@ -67,12 +67,13 @@ class ConstraintAction(argparse.Action):
 
     def __call__(self, parser, namespace, values, option_string=None):
         # Query specs from command line
-        self.values = values
-        namespace.constraint = values
+        self.constraint = namespace.constraint = values
+        self.constraint_specs = namespace.constraint_specs = []
         namespace.specs = self._specs
 
     def _specs(self, **kwargs):
-        qspecs = spack.cmd.parse_specs(self.values)
+        # store parsed specs in spec.constraint after a call to specs()
+        self.constraint_specs[:] = spack.cmd.parse_specs(self.constraint)
 
         # If an environment is provided, we'll restrict the search to
         # only its installed packages.
@@ -81,12 +82,12 @@ def _specs(self, **kwargs):
             kwargs["hashes"] = set(env.all_hashes())
 
         # return everything for an empty query.
-        if not qspecs:
+        if not self.constraint_specs:
             return spack.store.STORE.db.query(**kwargs)
 
         # Return only matching stuff otherwise.
         specs = {}
-        for spec in qspecs:
+        for spec in self.constraint_specs:
             for s in spack.store.STORE.db.query(spec, **kwargs):
                 # This is fast for already-concrete specs
                 specs[s.dag_hash()] = s
@@ -124,6 +125,33 @@ def __call__(self, parser, namespace, values, option_string=None):
         setattr(namespace, self.dest, deptype)
 
 
+class ConfigScope(argparse.Action):
+    """Pick the currently configured config scopes."""
+
+    def __init__(self, *args, **kwargs) -> None:
+        kwargs.setdefault("metavar", spack.config.SCOPES_METAVAR)
+        super().__init__(*args, **kwargs)
+
+    @property
+    def default(self):
+        return self._default() if callable(self._default) else self._default
+
+    @default.setter
+    def default(self, value):
+        self._default = value
+
+    @property
+    def choices(self):
+        return spack.config.scopes().keys()
+
+    @choices.setter
+    def choices(self, value):
+        pass
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, values)
+
+
 def _cdash_reporter(namespace):
     """Helper function to create a CDash reporter. This function gets an early reference to the
     argparse namespace under construction, so it can later use it to create the object.
@@ -357,10 +385,11 @@ def install_status():
         "--install-status",
         action="store_true",
         default=True,
-        help="show install status of packages\n\npackages can be: "
-        "installed [+], missing and needed by an installed package [-], "
-        "installed in an upstream instance [^], "
-        "or not installed (no annotation)",
+        help=(
+            "show install status of packages\n"
+            "[+] installed       [^] installed in an upstream\n"
+            " -  not installed   [-] missing dep of installed package\n"
+        ),
     )
 
 

lib/spack/spack/cmd/common/confirmation.py

@@ -21,10 +21,11 @@ def confirm_action(specs: List[spack.spec.Spec], participle: str, noun: str):
         participle: action expressed as a participle, e.g. "uninstalled"
         noun: action expressed as a noun, e.g. "uninstallation"
     """
-    tty.msg(f"The following {len(specs)} packages will be {participle}:\n")
     spack.cmd.display_specs(specs, **display_args)
-    print("")
-    answer = tty.get_yes_or_no("Do you want to proceed?", default=False)
+    print()
+    answer = tty.get_yes_or_no(
+        f"{len(specs)} packages will be {participle}. Do you want to proceed?", default=False
+    )
     if not answer:
         tty.msg(f"Aborting {noun}")
         sys.exit(0)

lib/spack/spack/cmd/common/env_utility.py

@@ -8,13 +8,13 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.deptypes as dt
 import spack.error
 import spack.paths
 import spack.spec
 import spack.store
 from spack import build_environment, traverse
+from spack.cmd.common import arguments
 from spack.context import Context
 from spack.util.environment import dump_environment, pickle_environment
 

lib/spack/spack/cmd/compiler.py

@@ -14,6 +14,7 @@
 import spack.compilers
 import spack.config
 import spack.spec
+from spack.cmd.common import arguments
 
 description = "manage compilers"
 section = "system"
@@ -23,8 +24,6 @@
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar="SUBCOMMAND", dest="compiler_command")
 
-    scopes = spack.config.scopes()
-
     # Find
     find_parser = sp.add_parser(
         "find",
@@ -47,9 +46,8 @@ def setup_parser(subparser):
     find_parser.add_argument("add_paths", nargs=argparse.REMAINDER)
     find_parser.add_argument(
         "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_modify_scope("compilers"),
+        action=arguments.ConfigScope,
+        default=lambda: spack.config.default_modify_scope("compilers"),
         help="configuration scope to modify",
     )
 
@@ -60,32 +58,20 @@ def setup_parser(subparser):
     )
     remove_parser.add_argument("compiler_spec")
     remove_parser.add_argument(
-        "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=None,
-        help="configuration scope to modify",
+        "--scope", action=arguments.ConfigScope, default=None, help="configuration scope to modify"
     )
 
     # List
     list_parser = sp.add_parser("list", help="list available compilers")
     list_parser.add_argument(
-        "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_list_scope(),
-        help="configuration scope to read from",
+        "--scope", action=arguments.ConfigScope, help="configuration scope to read from"
     )
 
     # Info
     info_parser = sp.add_parser("info", help="show compiler paths")
     info_parser.add_argument("compiler_spec")
     info_parser.add_argument(
-        "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_list_scope(),
-        help="configuration scope to read from",
+        "--scope", action=arguments.ConfigScope, help="configuration scope to read from"
     )
 
 
@@ -103,7 +89,7 @@ def compiler_find(args):
         paths, scope=None, mixed_toolchain=args.mixed_toolchain
     )
     if new_compilers:
-        spack.compilers.add_compilers_to_config(new_compilers, scope=args.scope)
+        spack.compilers.add_compilers_to_config(new_compilers, scope=args.scope, init_config=False)
         n = len(new_compilers)
         s = "s" if n > 1 else ""
 

lib/spack/spack/cmd/compilers.py

@@ -3,7 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import spack.config
+from spack.cmd.common import arguments
 from spack.cmd.compiler import compiler_list
 
 description = "list available compilers"
@@ -12,13 +12,8 @@
 
 
 def setup_parser(subparser):
-    scopes = spack.config.scopes()
-
     subparser.add_argument(
-        "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        help="configuration scope to read/modify",
+        "--scope", action=arguments.ConfigScope, help="configuration scope to read/modify"
     )
 
 

lib/spack/spack/cmd/config.py

@@ -5,12 +5,12 @@
 import collections
 import os
 import shutil
+import sys
 from typing import List
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 
-import spack.cmd.common.arguments
 import spack.config
 import spack.environment as ev
 import spack.repo
@@ -18,6 +18,7 @@
 import spack.schema.packages
 import spack.store
 import spack.util.spack_yaml as syaml
+from spack.cmd.common import arguments
 from spack.util.editor import editor
 
 description = "get and set configuration options"
@@ -26,14 +27,9 @@
 
 
 def setup_parser(subparser):
-    scopes = spack.config.scopes()
-
     # User can only choose one
     subparser.add_argument(
-        "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        help="configuration scope to read/modify",
+        "--scope", action=arguments.ConfigScope, help="configuration scope to read/modify"
     )
 
     sp = subparser.add_subparsers(metavar="SUBCOMMAND", dest="config_command")
@@ -53,6 +49,7 @@ def setup_parser(subparser):
     blame_parser.add_argument(
         "section",
         help="configuration section to print\n\noptions: %(choices)s",
+        nargs="?",
         metavar="section",
         choices=spack.config.SECTION_SCHEMAS,
     )
@@ -101,13 +98,13 @@ def setup_parser(subparser):
     setup_parser.add_parser = add_parser
 
     update = sp.add_parser("update", help="update configuration files to the latest format")
-    spack.cmd.common.arguments.add_common_arguments(update, ["yes_to_all"])
+    arguments.add_common_arguments(update, ["yes_to_all"])
     update.add_argument("section", help="section to update")
 
     revert = sp.add_parser(
         "revert", help="revert configuration files to their state before update"
     )
-    spack.cmd.common.arguments.add_common_arguments(revert, ["yes_to_all"])
+    arguments.add_common_arguments(revert, ["yes_to_all"])
     revert.add_argument("section", help="section to update")
 
 
@@ -136,32 +133,50 @@ def _get_scope_and_section(args):
     return scope, section
 
 
+def print_configuration(args, *, blame: bool) -> None:
+    if args.scope and args.section is None:
+        tty.die(f"the argument --scope={args.scope} requires specifying a section.")
+
+    if args.section is not None:
+        spack.config.CONFIG.print_section(args.section, blame=blame, scope=args.scope)
+        return
+
+    print_flattened_configuration(blame=blame)
+
+
+def print_flattened_configuration(*, blame: bool) -> None:
+    """Prints to stdout a flattened version of the configuration.
+
+    Args:
+        blame: if True, shows file provenance for each entry in the configuration.
+    """
+    env = ev.active_environment()
+    if env is not None:
+        pristine = env.manifest.pristine_yaml_content
+        flattened = pristine.copy()
+        flattened[spack.schema.env.TOP_LEVEL_KEY] = pristine[spack.schema.env.TOP_LEVEL_KEY].copy()
+    else:
+        flattened = syaml.syaml_dict()
+        flattened[spack.schema.env.TOP_LEVEL_KEY] = syaml.syaml_dict()
+
+    for config_section in spack.config.SECTION_SCHEMAS:
+        current = spack.config.get(config_section)
+        flattened[spack.schema.env.TOP_LEVEL_KEY][config_section] = current
+    syaml.dump_config(flattened, stream=sys.stdout, default_flow_style=False, blame=blame)
+
+
 def config_get(args):
     """Dump merged YAML configuration for a specific section.
 
     With no arguments and an active environment, print the contents of
     the environment's manifest file (spack.yaml).
     """
-    scope, section = _get_scope_and_section(args)
-
-    if section is not None:
-        spack.config.CONFIG.print_section(section)
-
-    elif scope and scope.startswith("env:"):
-        config_file = spack.config.CONFIG.get_config_filename(scope, section)
-        if os.path.exists(config_file):
-            with open(config_file) as f:
-                print(f.read())
-        else:
-            tty.die("environment has no %s file" % ev.manifest_name)
-
-    else:
-        tty.die("`spack config get` requires a section argument or an active environment.")
+    print_configuration(args, blame=False)
 
 
 def config_blame(args):
     """Print out line-by-line blame of merged YAML."""
-    spack.config.CONFIG.print_section(args.section, blame=True)
+    print_configuration(args, blame=True)
 
 
 def config_edit(args):

lib/spack/spack/cmd/deconcretize.py

@@ -10,10 +10,10 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.cmd.common.confirmation as confirmation
 import spack.environment as ev
 import spack.spec
+from spack.cmd.common import arguments
 
 description = "remove specs from the concretized lockfile of an environment"
 section = "environments"

lib/spack/spack/cmd/dependencies.py

@@ -9,11 +9,11 @@
 from llnl.util.tty.colify import colify
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 import spack.package_base
 import spack.repo
 import spack.store
+from spack.cmd.common import arguments
 
 description = "show dependencies of a package"
 section = "basic"

lib/spack/spack/cmd/dependents.py

@@ -9,10 +9,10 @@
 from llnl.util.tty.colify import colify
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 import spack.repo
 import spack.store
+from spack.cmd.common import arguments
 
 description = "show packages that depend on another"
 section = "basic"

lib/spack/spack/cmd/deprecate.py

@@ -20,9 +20,9 @@
 from llnl.util.symlink import symlink
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 import spack.store
+from spack.cmd.common import arguments
 from spack.database import InstallStatuses
 from spack.error import SpackError
 

lib/spack/spack/cmd/dev_build.py

@@ -9,9 +9,9 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.repo
+from spack.cmd.common import arguments
 
 description = "developer build: build from code in current working directory"
 section = "build"

lib/spack/spack/cmd/develop.py

@@ -8,10 +8,10 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.spec
 import spack.util.path
 import spack.version
+from spack.cmd.common import arguments
 from spack.error import SpackError
 
 description = "add a spec to an environment's dev-build information"
@@ -45,10 +45,41 @@ def setup_parser(subparser):
     arguments.add_common_arguments(subparser, ["spec"])
 
 
-def develop(parser, args):
-    env = spack.cmd.require_active_env(cmd_name="develop")
+def _update_config(spec, path):
+    find_fn = lambda section: spec.name in section
 
+    entry = {"spec": str(spec)}
+    if path != spec.name:
+        entry["path"] = path
+
+    def change_fn(section):
+        section[spec.name] = entry
+
+    spack.config.change_or_add("develop", find_fn, change_fn)
+
+
+def _retrieve_develop_source(spec, abspath):
+    # "steal" the source code via staging API. We ask for a stage
+    # to be created, then copy it afterwards somewhere else. It would be
+    # better if we can create the `source_path` directly into its final
+    # destination.
+    pkg_cls = spack.repo.PATH.get_pkg_class(spec.name)
+    # We construct a package class ourselves, rather than asking for
+    # Spec.package, since Spec only allows this when it is concrete
+    package = pkg_cls(spec)
+    if isinstance(package.stage[0].fetcher, spack.fetch_strategy.GitFetchStrategy):
+        package.stage[0].fetcher.get_full_repo = True
+        # If we retrieved this version before and cached it, we may have
+        # done so without cloning the full git repo; likewise, any
+        # mirror might store an instance with truncated history.
+        package.stage[0].disable_mirrors()
+
+    package.stage.steal_source(abspath)
+
+
+def develop(parser, args):
     if not args.spec:
+        env = spack.cmd.require_active_env(cmd_name="develop")
         if args.clone is False:
             raise SpackError("No spec provided to spack develop command")
 
@@ -66,7 +97,7 @@ def develop(parser, args):
             # Both old syntax `spack develop pkg@x` and new syntax `spack develop pkg@=x`
             # are currently supported.
             spec = spack.spec.parse_with_version_concrete(entry["spec"])
-            env.develop(spec=spec, path=path, clone=True)
+            _retrieve_develop_source(spec, abspath)
 
         if not env.dev_specs:
             tty.warn("No develop specs to download")
@@ -81,12 +112,16 @@ def develop(parser, args):
     version = spec.versions.concrete_range_as_version
     if not version:
         raise SpackError("Packages to develop must have a concrete version")
-
     spec.versions = spack.version.VersionList([version])
 
-    # default path is relative path to spec.name
+    # If user does not specify --path, we choose to create a directory in the
+    # active environment's directory, named after the spec
     path = args.path or spec.name
-    abspath = spack.util.path.canonicalize_path(path, default_wd=env.path)
+    if not os.path.isabs(path):
+        env = spack.cmd.require_active_env(cmd_name="develop")
+        abspath = spack.util.path.canonicalize_path(path, default_wd=env.path)
+    else:
+        abspath = path
 
     # clone default: only if the path doesn't exist
     clone = args.clone
@@ -96,15 +131,24 @@ def develop(parser, args):
     if not clone and not os.path.exists(abspath):
         raise SpackError("Provided path %s does not exist" % abspath)
 
-    if clone and os.path.exists(abspath):
-        if args.force:
-            shutil.rmtree(abspath)
-        else:
-            msg = "Path %s already exists and cannot be cloned to." % abspath
-            msg += " Use `spack develop -f` to overwrite."
-            raise SpackError(msg)
+    if clone:
+        if os.path.exists(abspath):
+            if args.force:
+                shutil.rmtree(abspath)
+            else:
+                msg = "Path %s already exists and cannot be cloned to." % abspath
+                msg += " Use `spack develop -f` to overwrite."
+                raise SpackError(msg)
 
+        _retrieve_develop_source(spec, abspath)
+
+    # Note: we could put develop specs in any scope, but I assume
+    # users would only ever want to do this for either (a) an active
+    # env or (b) a specified config file (e.g. that is included by
+    # an environment)
+    # TODO: when https://github.com/spack/spack/pull/35307 is merged,
+    # an active env is not required if a scope is specified
+    env = spack.cmd.require_active_env(cmd_name="develop")
+    tty.debug("Updating develop config for {0} transactionally".format(env.name))
     with env.write_transaction():
-        changed = env.develop(spec, path, clone)
-        if changed:
-            env.write()
+        _update_config(spec, path)

lib/spack/spack/cmd/diff.py

@@ -10,11 +10,11 @@
 from llnl.util.tty.color import cprint, get_color_when
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 import spack.solver.asp as asp
 import spack.util.environment
 import spack.util.spack_json as sjson
+from spack.cmd.common import arguments
 
 description = "compare two specs"
 section = "basic"
@@ -44,6 +44,9 @@ def setup_parser(subparser):
         action="append",
         help="select the attributes to show (defaults to all)",
     )
+    subparser.add_argument(
+        "--ignore", action="append", help="omit diffs related to these dependencies"
+    )
 
 
 def shift(asp_function):
@@ -54,7 +57,7 @@ def shift(asp_function):
     return asp.AspFunction(first, rest)
 
 
-def compare_specs(a, b, to_string=False, color=None):
+def compare_specs(a, b, to_string=False, color=None, ignore_packages=None):
     """
     Generate a comparison, including diffs (for each side) and an intersection.
 
@@ -73,6 +76,14 @@ def compare_specs(a, b, to_string=False, color=None):
     if color is None:
         color = get_color_when()
 
+    a = a.copy()
+    b = b.copy()
+
+    if ignore_packages:
+        for pkg_name in ignore_packages:
+            a.trim(pkg_name)
+            b.trim(pkg_name)
+
     # Prepare a solver setup to parse differences
     setup = asp.SpackSolverSetup()
 
@@ -209,7 +220,7 @@ def diff(parser, args):
 
     # Calculate the comparison (c)
     color = False if args.dump_json else get_color_when()
-    c = compare_specs(specs[0], specs[1], to_string=True, color=color)
+    c = compare_specs(specs[0], specs[1], to_string=True, color=color, ignore_packages=args.ignore)
 
     # Default to all attributes
     attributes = args.attribute or ["all"]

lib/spack/spack/cmd/env.py

@@ -20,7 +20,6 @@
 import spack.cmd
 import spack.cmd.common
 import spack.cmd.common.arguments
-import spack.cmd.common.arguments as arguments
 import spack.cmd.install
 import spack.cmd.modules
 import spack.cmd.uninstall
@@ -31,6 +30,7 @@
 import spack.schema.env
 import spack.spec
 import spack.tengine
+from spack.cmd.common import arguments
 from spack.util.environment import EnvironmentModifications
 
 description = "manage virtual environments"

lib/spack/spack/cmd/extensions.py

@@ -10,10 +10,10 @@
 from llnl.util.tty.colify import colify
 
 import spack.cmd as cmd
-import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 import spack.repo
 import spack.store
+from spack.cmd.common import arguments
 
 description = "list extensions for package"
 section = "extensions"

lib/spack/spack/cmd/external.py

@@ -14,12 +14,12 @@
 
 import spack
 import spack.cmd
-import spack.cmd.common.arguments
 import spack.config
 import spack.cray_manifest as cray_manifest
 import spack.detection
 import spack.error
 import spack.util.environment
+from spack.cmd.common import arguments
 
 description = "manage external packages in Spack configuration"
 section = "config"
@@ -29,8 +29,6 @@
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar="SUBCOMMAND", dest="external_command")
 
-    scopes = spack.config.scopes()
-
     find_parser = sp.add_parser("find", help="add external packages to packages.yaml")
     find_parser.add_argument(
         "--not-buildable",
@@ -48,15 +46,14 @@ def setup_parser(subparser):
     )
     find_parser.add_argument(
         "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_modify_scope("packages"),
+        action=arguments.ConfigScope,
+        default=lambda: spack.config.default_modify_scope("packages"),
         help="configuration scope to modify",
     )
     find_parser.add_argument(
         "--all", action="store_true", help="search for all packages that Spack knows about"
     )
-    spack.cmd.common.arguments.add_common_arguments(find_parser, ["tags", "jobs"])
+    arguments.add_common_arguments(find_parser, ["tags", "jobs"])
     find_parser.add_argument("packages", nargs=argparse.REMAINDER)
     find_parser.epilog = (
         'The search is by default on packages tagged with the "build-tools" or '

lib/spack/spack/cmd/fetch.py

@@ -6,11 +6,11 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.environment as ev
 import spack.repo
 import spack.traverse
+from spack.cmd.common import arguments
 
 description = "fetch archives for packages"
 section = "build"

lib/spack/spack/cmd/find.py

@@ -12,9 +12,9 @@
 
 import spack.bootstrap
 import spack.cmd as cmd
-import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 import spack.repo
+from spack.cmd.common import arguments
 from spack.database import InstallStatuses
 
 description = "list and search installed packages"
@@ -261,10 +261,8 @@ def find(parser, args):
 
     # Exit early with an error code if no package matches the constraint
     if not results and args.constraint:
-        msg = "No package matches the query: {0}"
-        msg = msg.format(" ".join(args.constraint))
-        tty.msg(msg)
-        raise SystemExit(1)
+        constraint_str = " ".join(str(s) for s in args.constraint_specs)
+        tty.die(f"No package matches the query: {constraint_str}")
 
     # If tags have been specified on the command line, filter by tags
     if args.tags:

lib/spack/spack/cmd/gc.py

@@ -8,6 +8,7 @@
 import spack.cmd.common.arguments
 import spack.cmd.common.confirmation
 import spack.cmd.uninstall
+import spack.deptypes as dt
 import spack.environment as ev
 import spack.store
 
@@ -17,31 +18,91 @@
 
 
 def setup_parser(subparser):
+    subparser.add_argument(
+        "-E",
+        "--except-any-environment",
+        action="store_true",
+        help="remove everything unless needed by an environment",
+    )
+    subparser.add_argument(
+        "-e",
+        "--except-environment",
+        metavar="ENV",
+        action="append",
+        default=[],
+        help="remove everything unless needed by specified environment\n"
+        "you can list multiple environments, or specify directory\n"
+        "environments by path.",
+    )
+    subparser.add_argument(
+        "-b",
+        "--keep-build-dependencies",
+        action="store_true",
+        help="do not remove installed build-only dependencies of roots\n"
+        "(default is to keep only link & run dependencies)",
+    )
     spack.cmd.common.arguments.add_common_arguments(subparser, ["yes_to_all"])
 
 
+def roots_from_environments(args, active_env):
+    # if we're using -E or -e, make a list of environments whose roots we should consider.
+    all_environments = []
+
+    # -E will garbage collect anything not needed by any env, including the current one
+    if args.except_any_environment:
+        all_environments += list(ev.all_environments())
+        if active_env:
+            all_environments.append(active_env)
+
+    # -e says "also preserve things needed by this particular env"
+    for env_name_or_dir in args.except_environment:
+        print("HMM", env_name_or_dir)
+        if ev.exists(env_name_or_dir):
+            env = ev.read(env_name_or_dir)
+        elif ev.is_env_dir(env_name_or_dir):
+            env = ev.Environment(env_name_or_dir)
+        else:
+            tty.die(f"No such environment: '{env_name_or_dir}'")
+        all_environments.append(env)
+
+    # add root hashes from all considered environments to list of roots
+    root_hashes = set()
+    for env in all_environments:
+        root_hashes |= set(env.concretized_order)
+
+    return root_hashes
+
+
 def gc(parser, args):
-    specs = spack.store.STORE.db.unused_specs
+    deptype = dt.LINK | dt.RUN
+    if args.keep_build_dependencies:
+        deptype |= dt.BUILD
 
-    # Restrict garbage collection to the active environment
-    # speculating over roots that are yet to be installed
-    env = ev.active_environment()
-    if env:
-        msg = 'Restricting the garbage collection to the "{0}" environment'
-        tty.msg(msg.format(env.name))
-        env.concretize()
-        roots = [s for s in env.roots()]
-        all_hashes = set([s.dag_hash() for r in roots for s in r.traverse()])
-        lr_hashes = set([s.dag_hash() for r in roots for s in r.traverse(deptype=("link", "run"))])
-        maybe_to_be_removed = all_hashes - lr_hashes
-        specs = [s for s in specs if s.dag_hash() in maybe_to_be_removed]
+    active_env = ev.active_environment()
 
-    if not specs:
-        msg = "There are no unused specs. Spack's store is clean."
-        tty.msg(msg)
-        return
+    # wrap the whole command with a read transaction to avoid multiple
+    with spack.store.STORE.db.read_transaction():
+        if args.except_environment or args.except_any_environment:
+            # if either of these is specified, we ignore the active environment and garbage
+            # collect anything NOT in specified environments.
+            root_hashes = roots_from_environments(args, active_env)
 
-    if not args.yes_to_all:
-        spack.cmd.common.confirmation.confirm_action(specs, "uninstalled", "uninstallation")
+        elif active_env:
+            # only gc what's in current environment
+            tty.msg(f"Restricting garbage collection to environment '{active_env.name}'")
+            root_hashes = set(spack.store.STORE.db.all_hashes())  # keep everything
+            root_hashes -= set(active_env.all_hashes())  # except this env
+            root_hashes |= set(active_env.concretized_order)  # but keep its roots
+        else:
+            # consider all explicit specs roots (the default for db.unused_specs())
+            root_hashes = None
 
-    spack.cmd.uninstall.do_uninstall(specs, force=False)
+        specs = spack.store.STORE.db.unused_specs(root_hashes=root_hashes, deptype=deptype)
+        if not specs:
+            tty.msg("There are no unused specs. Spack's store is clean.")
+            return
+
+        if not args.yes_to_all:
+            spack.cmd.common.confirmation.confirm_action(specs, "uninstalled", "uninstall")
+
+        spack.cmd.uninstall.do_uninstall(specs, force=False)

lib/spack/spack/cmd/gpg.py

@@ -7,11 +7,11 @@
 import os
 
 import spack.binary_distribution
-import spack.cmd.common.arguments as arguments
 import spack.mirror
 import spack.paths
 import spack.util.gpg
 import spack.util.url
+from spack.cmd.common import arguments
 
 description = "handle GPG actions for spack"
 section = "packaging"

lib/spack/spack/cmd/graph.py

@@ -5,10 +5,10 @@
 from llnl.util import tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.environment as ev
 import spack.store
+from spack.cmd.common import arguments
 from spack.graph import DAGWithDependencyTypes, SimpleDAG, graph_ascii, graph_dot, static_graph_dot
 
 description = "generate graphs of package dependency relationships"

lib/spack/spack/cmd/info.py

@@ -11,13 +11,13 @@
 import llnl.util.tty.color as color
 from llnl.util.tty.colify import colify
 
-import spack.cmd.common.arguments as arguments
 import spack.deptypes as dt
 import spack.fetch_strategy as fs
 import spack.install_test
 import spack.repo
 import spack.spec
 import spack.version
+from spack.cmd.common import arguments
 from spack.package_base import preferred_version
 
 description = "get detailed information on a particular package"
@@ -327,7 +327,7 @@ def _variants_by_name_when(pkg):
     """Adaptor to get variants keyed by { name: { when: { [Variant...] } }."""
     # TODO: replace with pkg.variants_by_name(when=True) when unified directive dicts are merged.
     variants = {}
-    for name, (variant, whens) in pkg.variants.items():
+    for name, (variant, whens) in sorted(pkg.variants.items()):
         for when in whens:
             variants.setdefault(name, {}).setdefault(when, []).append(variant)
     return variants

lib/spack/spack/cmd/install.py

@@ -14,7 +14,6 @@
 
 import spack.build_environment
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.environment as ev
 import spack.fetch_strategy
@@ -23,6 +22,7 @@
 import spack.report
 import spack.spec
 import spack.store
+from spack.cmd.common import arguments
 from spack.error import SpackError
 from spack.installer import PackageInstaller
 
@@ -162,8 +162,8 @@ def setup_parser(subparser):
         "--no-check-signature",
         action="store_true",
         dest="unsigned",
-        default=False,
-        help="do not check signatures of binary packages",
+        default=None,
+        help="do not check signatures of binary packages (override mirror config)",
     )
     subparser.add_argument(
         "--show-log-on-error",

lib/spack/spack/cmd/list.py

@@ -15,9 +15,9 @@
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 
-import spack.cmd.common.arguments as arguments
 import spack.deptypes as dt
 import spack.repo
+from spack.cmd.common import arguments
 from spack.version import VersionList
 
 description = "list and search available packages"

lib/spack/spack/cmd/load.py

@@ -8,12 +8,12 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.cmd.find
 import spack.environment as ev
 import spack.store
 import spack.user_environment as uenv
 import spack.util.environment
+from spack.cmd.common import arguments
 
 description = "add package to the user environment"
 section = "user environment"
@@ -98,15 +98,15 @@ def load(parser, args):
         spack.cmd.display_specs(results)
         return
 
+    constraint_specs = spack.cmd.parse_specs(args.constraint)
     specs = [
-        spack.cmd.disambiguate_spec(spec, env, first=args.load_first)
-        for spec in spack.cmd.parse_specs(args.constraint)
+        spack.cmd.disambiguate_spec(spec, env, first=args.load_first) for spec in constraint_specs
     ]
 
     if not args.shell:
-        specs_str = " ".join(args.constraint) or "SPECS"
+        specs_str = " ".join(str(s) for s in constraint_specs) or "SPECS"
         spack.cmd.common.shell_init_instructions(
-            "spack load", "    eval `spack load {sh_arg} %s`" % specs_str
+            "spack load", f"    eval `spack load {{sh_arg}} {specs_str}`"
         )
         return 1
 

lib/spack/spack/cmd/location.py

@@ -9,11 +9,11 @@
 
 import spack.builder
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 import spack.paths
 import spack.repo
 import spack.stage
+from spack.cmd.common import arguments
 
 description = "print out locations of packages and spack directories"
 section = "basic"

lib/spack/spack/cmd/mark.py

@@ -8,11 +8,11 @@
 from llnl.util import tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.error
 import spack.package_base
 import spack.repo
 import spack.store
+from spack.cmd.common import arguments
 from spack.database import InstallStatuses
 
 description = "mark packages as explicitly or implicitly installed"

lib/spack/spack/cmd/mirror.py

@@ -11,7 +11,6 @@
 
 import spack.caches
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.concretize
 import spack.config
 import spack.environment as ev
@@ -20,6 +19,7 @@
 import spack.spec
 import spack.util.path
 import spack.util.web as web_util
+from spack.cmd.common import arguments
 from spack.error import SpackError
 
 description = "manage mirrors (source and binary)"
@@ -88,18 +88,14 @@ def setup_parser(subparser):
         "--mirror-url", metavar="mirror_url", type=str, help="find mirror to destroy by url"
     )
 
-    # used to construct scope arguments below
-    scopes = spack.config.scopes()
-
     # Add
     add_parser = sp.add_parser("add", help=mirror_add.__doc__)
     add_parser.add_argument("name", help="mnemonic name for mirror", metavar="mirror")
     add_parser.add_argument("url", help="url of mirror directory from 'spack mirror create'")
     add_parser.add_argument(
         "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_modify_scope(),
+        action=arguments.ConfigScope,
+        default=lambda: spack.config.default_modify_scope(),
         help="configuration scope to modify",
     )
     add_parser.add_argument(
@@ -111,15 +107,31 @@ def setup_parser(subparser):
             "and source use `--type binary --type source` (default)"
         ),
     )
+    add_parser_signed = add_parser.add_mutually_exclusive_group(required=False)
+    add_parser_signed.add_argument(
+        "--unsigned",
+        help="do not require signing and signature verification when pushing and installing from "
+        "this build cache",
+        action="store_false",
+        default=None,
+        dest="signed",
+    )
+    add_parser_signed.add_argument(
+        "--signed",
+        help="require signing and signature verification when pushing and installing from this "
+        "build cache",
+        action="store_true",
+        default=None,
+        dest="signed",
+    )
     arguments.add_connection_args(add_parser, False)
     # Remove
     remove_parser = sp.add_parser("remove", aliases=["rm"], help=mirror_remove.__doc__)
     remove_parser.add_argument("name", help="mnemonic name for mirror", metavar="mirror")
     remove_parser.add_argument(
         "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_modify_scope(),
+        action=arguments.ConfigScope,
+        default=lambda: spack.config.default_modify_scope(),
         help="configuration scope to modify",
     )
 
@@ -136,9 +148,8 @@ def setup_parser(subparser):
     )
     set_url_parser.add_argument(
         "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_modify_scope(),
+        action=arguments.ConfigScope,
+        default=lambda: spack.config.default_modify_scope(),
         help="configuration scope to modify",
     )
     arguments.add_connection_args(set_url_parser, False)
@@ -163,11 +174,27 @@ def setup_parser(subparser):
         ),
     )
     set_parser.add_argument("--url", help="url of mirror directory from 'spack mirror create'")
+    set_parser_unsigned = set_parser.add_mutually_exclusive_group(required=False)
+    set_parser_unsigned.add_argument(
+        "--unsigned",
+        help="do not require signing and signature verification when pushing and installing from "
+        "this build cache",
+        action="store_false",
+        default=None,
+        dest="signed",
+    )
+    set_parser_unsigned.add_argument(
+        "--signed",
+        help="require signing and signature verification when pushing and installing from this "
+        "build cache",
+        action="store_true",
+        default=None,
+        dest="signed",
+    )
     set_parser.add_argument(
         "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_modify_scope(),
+        action=arguments.ConfigScope,
+        default=lambda: spack.config.default_modify_scope(),
         help="configuration scope to modify",
     )
     arguments.add_connection_args(set_parser, False)
@@ -175,11 +202,7 @@ def setup_parser(subparser):
     # List
     list_parser = sp.add_parser("list", help=mirror_list.__doc__)
     list_parser.add_argument(
-        "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_list_scope(),
-        help="configuration scope to read from",
+        "--scope", action=arguments.ConfigScope, help="configuration scope to read from"
     )
 
 
@@ -194,6 +217,7 @@ def mirror_add(args):
         or args.type
         or args.oci_username
         or args.oci_password
+        or args.signed is not None
     ):
         connection = {"url": args.url}
         if args.s3_access_key_id and args.s3_access_key_secret:
@@ -209,6 +233,8 @@ def mirror_add(args):
         if args.type:
             connection["binary"] = "binary" in args.type
             connection["source"] = "source" in args.type
+        if args.signed is not None:
+            connection["signed"] = args.signed
         mirror = spack.mirror.Mirror(connection, name=args.name)
     else:
         mirror = spack.mirror.Mirror(args.url, name=args.name)
@@ -241,6 +267,8 @@ def _configure_mirror(args):
         changes["endpoint_url"] = args.s3_endpoint_url
     if args.oci_username and args.oci_password:
         changes["access_pair"] = [args.oci_username, args.oci_password]
+    if getattr(args, "signed", None) is not None:
+        changes["signed"] = args.signed
 
     # argparse cannot distinguish between --binary and --no-binary when same dest :(
     # notice that set-url does not have these args, so getattr

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

@@ -14,11 +14,11 @@
 from llnl.util.tty import color
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.modules
 import spack.modules.common
 import spack.repo
+from spack.cmd.common import arguments
 
 description = "manipulate module files"
 section = "environment"
@@ -388,21 +388,15 @@ def modules_cmd(parser, args, module_type, callbacks=callbacks):
         callbacks[args.subparser_name](module_type, specs, args)
 
     except MultipleSpecsMatch:
-        msg = "the constraint '{query}' matches multiple packages:\n"
+        query = " ".join(str(s) for s in args.constraint_specs)
+        msg = f"the constraint '{query}' matches multiple packages:\n"
         for s in specs:
             spec_fmt = "{hash:7} {name}{@version}{%compiler}"
             spec_fmt += "{compiler_flags}{variants}{arch=architecture}"
             msg += "\t" + s.cformat(spec_fmt) + "\n"
-        tty.error(msg.format(query=args.constraint))
-        tty.die(
-            "In this context exactly **one** match is needed: "
-            "please specify your constraints better."
-        )
+        tty.die(msg, "In this context exactly *one* match is needed.")
 
     except NoSpecMatches:
-        msg = "the constraint '{query}' matches no package."
-        tty.error(msg.format(query=args.constraint))
-        tty.die(
-            "In this context exactly **one** match is needed: "
-            "please specify your constraints better."
-        )
+        query = " ".join(str(s) for s in args.constraint_specs)
+        msg = f"the constraint '{query}' matches no package."
+        tty.die(msg, "In this context exactly *one* match is needed.")

lib/spack/spack/cmd/patch.py

@@ -6,12 +6,12 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.environment as ev
 import spack.package_base
 import spack.repo
 import spack.traverse
+from spack.cmd.common import arguments
 
 description = "patch expanded archive sources in preparation for install"
 section = "build"

lib/spack/spack/cmd/pkg.py

@@ -12,11 +12,11 @@
 from llnl.util.tty.colify import colify
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.paths
 import spack.repo
 import spack.util.executable as exe
 import spack.util.package_hash as ph
+from spack.cmd.common import arguments
 
 description = "query packages associated with particular git revisions"
 section = "developer"

lib/spack/spack/cmd/remove.py

@@ -6,7 +6,7 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
+from spack.cmd.common import arguments
 
 description = "remove specs from an environment"
 section = "environments"

lib/spack/spack/cmd/repo.py

@@ -11,6 +11,7 @@
 import spack.config
 import spack.repo
 import spack.util.path
+from spack.cmd.common import arguments
 
 description = "manage package source repositories"
 section = "config"
@@ -19,7 +20,6 @@
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar="SUBCOMMAND", dest="repo_command")
-    scopes = spack.config.scopes()
 
     # Create
     create_parser = sp.add_parser("create", help=repo_create.__doc__)
@@ -42,11 +42,7 @@ def setup_parser(subparser):
     # List
     list_parser = sp.add_parser("list", help=repo_list.__doc__)
     list_parser.add_argument(
-        "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_list_scope(),
-        help="configuration scope to read from",
+        "--scope", action=arguments.ConfigScope, help="configuration scope to read from"
     )
 
     # Add
@@ -54,9 +50,8 @@ def setup_parser(subparser):
     add_parser.add_argument("path", help="path to a Spack package repository directory")
     add_parser.add_argument(
         "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_modify_scope(),
+        action=arguments.ConfigScope,
+        default=lambda: spack.config.default_modify_scope(),
         help="configuration scope to modify",
     )
 
@@ -67,9 +62,8 @@ def setup_parser(subparser):
     )
     remove_parser.add_argument(
         "--scope",
-        choices=scopes,
-        metavar=spack.config.SCOPES_METAVAR,
-        default=spack.config.default_modify_scope(),
+        action=arguments.ConfigScope,
+        default=lambda: spack.config.default_modify_scope(),
         help="configuration scope to modify",
     )
 

lib/spack/spack/cmd/restage.py

@@ -6,8 +6,8 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.repo
+from spack.cmd.common import arguments
 
 description = "revert checked out package source code"
 section = "build"

lib/spack/spack/cmd/solve.py

@@ -12,12 +12,12 @@
 
 import spack
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.environment
 import spack.hash_types as ht
 import spack.package_base
 import spack.solver.asp as asp
+from spack.cmd.common import arguments
 
 description = "concretize a specs using an ASP solver"
 section = "developer"

lib/spack/spack/cmd/spec.py

@@ -10,11 +10,11 @@
 
 import spack
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 import spack.hash_types as ht
 import spack.spec
 import spack.store
+from spack.cmd.common import arguments
 
 description = "show what would be installed, given a spec"
 section = "build"

lib/spack/spack/cmd/stage.py

@@ -8,13 +8,13 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.environment as ev
 import spack.package_base
 import spack.repo
 import spack.stage
 import spack.traverse
+from spack.cmd.common import arguments
 
 description = "expand downloaded archive in preparation for install"
 section = "build"

lib/spack/spack/cmd/test.py

@@ -15,12 +15,12 @@
 from llnl.util.tty import colify
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.environment as ev
 import spack.install_test
 import spack.package_base
 import spack.repo
 import spack.report
+from spack.cmd.common import arguments
 
 description = "run spack's tests for an install"
 section = "admin"

lib/spack/spack/cmd/tutorial.py

@@ -10,11 +10,11 @@
 from llnl.util.filesystem import working_dir
 
 import spack
-import spack.cmd.common.arguments as arguments
 import spack.config
 import spack.paths
 import spack.util.git
 import spack.util.gpg
+from spack.cmd.common import arguments
 from spack.util.spack_yaml import syaml_dict
 
 description = "set up spack for our tutorial (WARNING: modifies config!)"

lib/spack/spack/cmd/undevelop.py

@@ -6,7 +6,7 @@
 import llnl.util.tty as tty
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
+from spack.cmd.common import arguments
 
 description = "remove specs from an environment"
 section = "environments"
@@ -17,21 +17,51 @@ def setup_parser(subparser):
     subparser.add_argument(
         "-a", "--all", action="store_true", help="remove all specs from (clear) the environment"
     )
+
     arguments.add_common_arguments(subparser, ["specs"])
 
 
+def _update_config(specs_to_remove, remove_all=False):
+    def change_fn(dev_config):
+        modified = False
+        for spec in specs_to_remove:
+            if spec.name in dev_config:
+                tty.msg("Undevelop: removing {0}".format(spec.name))
+                del dev_config[spec.name]
+                modified = True
+        if remove_all and dev_config:
+            dev_config.clear()
+            modified = True
+        return modified
+
+    spack.config.update_all("develop", change_fn)
+
+
 def undevelop(parser, args):
-    env = spack.cmd.require_active_env(cmd_name="undevelop")
-
+    remove_specs = None
+    remove_all = False
     if args.all:
-        specs = env.dev_specs.keys()
+        remove_all = True
     else:
-        specs = spack.cmd.parse_specs(args.specs)
+        remove_specs = spack.cmd.parse_specs(args.specs)
 
+    # TODO: when https://github.com/spack/spack/pull/35307 is merged,
+    # an active env is not required if a scope is specified
+    env = spack.cmd.require_active_env(cmd_name="undevelop")
     with env.write_transaction():
-        changed = False
-        for spec in specs:
-            tty.msg("Removing %s from environment %s development specs" % (spec, env.name))
-            changed |= env.undevelop(spec)
-        if changed:
-            env.write()
+        _update_config(remove_specs, remove_all)
+
+    updated_all_dev_specs = set(spack.config.get("develop"))
+    remove_spec_names = set(x.name for x in remove_specs)
+
+    if remove_all:
+        not_fully_removed = updated_all_dev_specs
+    else:
+        not_fully_removed = updated_all_dev_specs & remove_spec_names
+
+    if not_fully_removed:
+        tty.msg(
+            "The following specs could not be removed as develop specs"
+            " - see `spack config blame develop` to locate files requiring"
+            f" manual edits: {', '.join(not_fully_removed)}"
+        )

lib/spack/spack/cmd/uninstall.py

@@ -10,13 +10,13 @@
 from llnl.util.tty.colify import colify
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.cmd.common.confirmation as confirmation
 import spack.environment as ev
 import spack.package_base
 import spack.spec
 import spack.store
 import spack.traverse as traverse
+from spack.cmd.common import arguments
 from spack.database import InstallStatuses
 
 description = "remove installed packages"
@@ -277,7 +277,7 @@ def uninstall_specs(args, specs):
         return
 
     if not args.yes_to_all:
-        confirmation.confirm_action(uninstall_list, "uninstalled", "uninstallation")
+        confirmation.confirm_action(uninstall_list, "uninstalled", "uninstall")
 
     # Uninstall everything on the list
     do_uninstall(uninstall_list, args.force)

lib/spack/spack/cmd/unit_test.py

@@ -227,9 +227,7 @@ def unit_test(parser, args, unknown_args):
     # has been used, then test that extension.
     pytest_root = spack.paths.spack_root
     if args.extension:
-        target = args.extension
-        extensions = spack.extensions.get_extension_paths()
-        pytest_root = spack.extensions.path_for_extension(target, *extensions)
+        pytest_root = spack.extensions.load_extension(args.extension)
 
     # pytest.ini lives in the root of the spack repository.
     with llnl.util.filesystem.working_dir(pytest_root):

lib/spack/spack/cmd/unload.py

@@ -7,10 +7,10 @@
 import sys
 
 import spack.cmd
-import spack.cmd.common.arguments as arguments
 import spack.error
 import spack.user_environment as uenv
 import spack.util.environment
+from spack.cmd.common import arguments
 
 description = "remove package from the user environment"
 section = "user environment"

lib/spack/spack/cmd/versions.py

@@ -8,9 +8,9 @@
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 
-import spack.cmd.common.arguments as arguments
 import spack.repo
 import spack.spec
+from spack.cmd.common import arguments
 from spack.version import infinity_versions, ver
 
 description = "list available versions of a package"

lib/spack/spack/compiler.py

@@ -334,40 +334,6 @@ def __init__(
         # used for version checks for API, e.g. C++11 flag
         self._real_version = None
 
-    def __eq__(self, other):
-        return (
-            self.cc == other.cc
-            and self.cxx == other.cxx
-            and self.fc == other.fc
-            and self.f77 == other.f77
-            and self.spec == other.spec
-            and self.operating_system == other.operating_system
-            and self.target == other.target
-            and self.flags == other.flags
-            and self.modules == other.modules
-            and self.environment == other.environment
-            and self.extra_rpaths == other.extra_rpaths
-            and self.enable_implicit_rpaths == other.enable_implicit_rpaths
-        )
-
-    def __hash__(self):
-        return hash(
-            (
-                self.cc,
-                self.cxx,
-                self.fc,
-                self.f77,
-                self.spec,
-                self.operating_system,
-                self.target,
-                str(self.flags),
-                str(self.modules),
-                str(self.environment),
-                str(self.extra_rpaths),
-                self.enable_implicit_rpaths,
-            )
-        )
-
     def verify_executables(self):
         """Raise an error if any of the compiler executables is not valid.
 

lib/spack/spack/compilers/__init__.py

@@ -109,7 +109,7 @@ def _to_dict(compiler):
     return {"compiler": d}
 
 
-def get_compiler_config(scope=None, init_config=False):
+def get_compiler_config(scope=None, init_config=True):
     """Return the compiler configuration for the specified architecture."""
 
     config = spack.config.get("compilers", scope=scope) or []
@@ -118,8 +118,6 @@ def get_compiler_config(scope=None, init_config=False):
 
     merged_config = spack.config.get("compilers")
     if merged_config:
-        # Config is empty for this scope
-        # Do not init config because there is a non-empty scope
         return config
 
     _init_compiler_config(scope=scope)
@@ -127,105 +125,6 @@ def get_compiler_config(scope=None, init_config=False):
     return config
 
 
-def get_compiler_config_from_packages(scope=None):
-    """Return the compiler configuration from packages.yaml"""
-    config = spack.config.get("packages", scope=scope)
-    if not config:
-        return []
-
-    packages = []
-    compiler_package_names = supported_compilers() + list(package_name_to_compiler_name.keys())
-    for name, entry in config.items():
-        if name not in compiler_package_names:
-            continue
-        externals_config = entry.get("externals", None)
-        if not externals_config:
-            continue
-        packages.extend(_compiler_config_from_package_config(externals_config))
-
-    return packages
-
-
-def _compiler_config_from_package_config(config):
-    compilers = []
-    for entry in config:
-        compiler = _compiler_config_from_external(entry)
-        if compiler:
-            compilers.append(compiler)
-
-    return compilers
-
-
-def _compiler_config_from_external(config):
-    spec = spack.spec.parse_with_version_concrete(config["spec"])
-    # use str(spec.versions) to allow `@x.y.z` instead of `@=x.y.z`
-    compiler_spec = spack.spec.CompilerSpec(
-        package_name_to_compiler_name.get(spec.name, spec.name), spec.version
-    )
-
-    extra_attributes = config.get("extra_attributes", {})
-    prefix = config.get("prefix", None)
-
-    compiler_class = class_for_compiler_name(compiler_spec.name)
-    paths = extra_attributes.get("compilers", {})
-
-    # compilers format has cc/fc/f77, externals format has "c/fortran"
-    if "c" in paths:
-        paths["cc"] = paths.pop("c")
-    if "fortran" in paths:
-        fc = paths.pop("fortran")
-        paths["fc"] = fc
-        if "f77" not in paths:
-            paths["f77"] = fc
-
-    compiler_langs = ["cc", "cxx", "fc", "f77"]
-    for lang in compiler_langs:
-        if paths.setdefault(lang, None):
-            continue
-
-        if not prefix:
-            continue
-
-        # Check for files that satisfy the naming scheme for this compiler
-        bindir = os.path.join(prefix, "bin")
-        for f, regex in itertools.product(os.listdir(bindir), compiler_class.search_regexps(lang)):
-            if regex.match(f):
-                paths[lang] = os.path.join(bindir, f)
-
-    if all(v is None for v in paths.values()):
-        return None
-
-    if not spec.architecture:
-        host_platform = spack.platforms.host()
-        operating_system = host_platform.operating_system("default_os")
-        target = host_platform.target("default_target").microarchitecture
-    else:
-        target = spec.target
-        if not target:
-            host_platform = spack.platforms.host()
-            target = host_platform.target("default_target").microarchitecture
-
-        operating_system = spec.os
-        if not operating_system:
-            host_platform = spack.platforms.host()
-            operating_system = host_platform.operating_system("default_os")
-
-    compiler_entry = {
-        "compiler": {
-            "spec": str(compiler_spec),
-            "paths": paths,
-            "flags": extra_attributes.get("flags", {}),
-            "operating_system": str(operating_system),
-            "target": str(target.family),
-            "modules": config.get("modules", []),
-            "environment": extra_attributes.get("environment", {}),
-            "extra_rpaths": extra_attributes.get("extra_rpaths", []),
-            "implicit_rpaths": extra_attributes.get("implicit_rpaths", None),
-        }
-    }
-    return compiler_entry
-
-
 def _init_compiler_config(*, scope):
     """Compiler search used when Spack has no compilers."""
     compilers = find_compilers()
@@ -243,20 +142,17 @@ def compiler_config_files():
         compiler_config = config.get("compilers", scope=name)
         if compiler_config:
             config_files.append(config.get_config_filename(name, "compilers"))
-        compiler_config_from_packages = get_compiler_config_from_packages(scope=name)
-        if compiler_config_from_packages:
-            config_files.append(config.get_config_filename(name, "packages"))
     return config_files
 
 
-def add_compilers_to_config(compilers, scope=None):
+def add_compilers_to_config(compilers, scope=None, init_config=True):
     """Add compilers to the config for the specified architecture.
 
     Arguments:
         compilers: a list of Compiler objects.
         scope: configuration scope to modify.
     """
-    compiler_config = get_compiler_config(scope, init_config=False)
+    compiler_config = get_compiler_config(scope, init_config)
     for compiler in compilers:
         if not compiler.cc:
             tty.debug(f"{compiler.spec} does not have a C compiler")
@@ -288,9 +184,6 @@ def remove_compiler_from_config(compiler_spec, scope=None):
     for current_scope in candidate_scopes:
         removal_happened |= _remove_compiler_from_scope(compiler_spec, scope=current_scope)
 
-    msg = "`spack compiler remove` will not remove compilers defined in packages.yaml"
-    msg += "\nTo remove these compilers, either edit the config or use `spack external remove`"
-    tty.debug(msg)
     return removal_happened
 
 
@@ -305,7 +198,7 @@ def _remove_compiler_from_scope(compiler_spec, scope):
          True if one or more compiler entries were actually removed, False otherwise
     """
     assert scope is not None, "a specific scope is needed when calling this function"
-    compiler_config = get_compiler_config(scope, init_config=False)
+    compiler_config = get_compiler_config(scope)
     filtered_compiler_config = [
         compiler_entry
         for compiler_entry in compiler_config
@@ -328,14 +221,7 @@ def all_compilers_config(scope=None, init_config=True):
     """Return a set of specs for all the compiler versions currently
     available to build with.  These are instances of CompilerSpec.
     """
-    from_packages_yaml = get_compiler_config_from_packages(scope)
-    if from_packages_yaml:
-        init_config = False
-    from_compilers_yaml = get_compiler_config(scope, init_config)
-
-    result = from_compilers_yaml + from_packages_yaml
-    key = lambda c: _compiler_from_config_entry(c["compiler"])
-    return list(llnl.util.lang.dedupe(result, key=key))
+    return get_compiler_config(scope, init_config)
 
 
 def all_compiler_specs(scope=None, init_config=True):
@@ -502,7 +388,7 @@ def find_specs_by_arch(compiler_spec, arch_spec, scope=None, init_config=True):
 
 
 def all_compilers(scope=None, init_config=True):
-    config = all_compilers_config(scope, init_config=init_config)
+    config = get_compiler_config(scope, init_config=init_config)
     compilers = list()
     for items in config:
         items = items["compiler"]
@@ -517,7 +403,10 @@ def compilers_for_spec(
     """This gets all compilers that satisfy the supplied CompilerSpec.
     Returns an empty list if none are found.
     """
-    config = all_compilers_config(scope, init_config)
+    if use_cache:
+        config = all_compilers_config(scope, init_config)
+    else:
+        config = get_compiler_config(scope, init_config)
 
     matches = set(find(compiler_spec, scope, init_config))
     compilers = []
@@ -693,7 +582,9 @@ def get_compiler_duplicates(compiler_spec, arch_spec):
 
     scope_to_compilers = {}
     for scope in config.scopes:
-        compilers = compilers_for_spec(compiler_spec, arch_spec=arch_spec, scope=scope)
+        compilers = compilers_for_spec(
+            compiler_spec, arch_spec=arch_spec, scope=scope, use_cache=False
+        )
         if compilers:
             scope_to_compilers[scope] = compilers
 

lib/spack/spack/compilers/cce.py

@@ -20,16 +20,16 @@ def __init__(self, *args, **kwargs):
             self.version_argument = "-V"
 
     # Subclasses use possible names of C compiler
-    cc_names = ["craycc", "cc"]
+    cc_names = ["craycc"]
 
     # Subclasses use possible names of C++ compiler
-    cxx_names = ["crayCC", "CC"]
+    cxx_names = ["crayCC"]
 
     # Subclasses use possible names of Fortran 77 compiler
-    f77_names = ["crayftn", "ftn"]
+    f77_names = ["crayftn"]
 
     # Subclasses use possible names of Fortran 90 compiler
-    fc_names = ["crayftn", "ftn"]
+    fc_names = ["crayftn"]
 
     # MacPorts builds gcc versions with prefixes and -mp-X.Y suffixes.
     suffixes = [r"-mp-\d\.\d"]

lib/spack/spack/config.py

@@ -35,12 +35,9 @@
 import os
 import re
 import sys
-from contextlib import contextmanager
-from typing import Dict, List, Optional, Union
+from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Type, Union
 
-import llnl.util.lang
-import llnl.util.tty as tty
-from llnl.util.filesystem import mkdirp, rename
+from llnl.util import filesystem, lang, tty
 
 import spack.compilers
 import spack.paths
@@ -70,6 +67,7 @@
     "compilers": spack.schema.compilers.schema,
     "concretizer": spack.schema.concretizer.schema,
     "definitions": spack.schema.definitions.schema,
+    "develop": spack.schema.develop.schema,
     "mirrors": spack.schema.mirrors.schema,
     "repos": spack.schema.repos.schema,
     "packages": spack.schema.packages.schema,
@@ -113,28 +111,34 @@
 #: Base name for the (internal) overrides scope.
 _OVERRIDES_BASE_NAME = "overrides-"
 
+#: Type used for raw YAML configuration
+YamlConfigDict = Dict[str, Any]
+
 
 class ConfigScope:
     """This class represents a configuration scope.
 
     A scope is one directory containing named configuration files.
-    Each file is a config "section" (e.g., mirrors, compilers, etc).
+    Each file is a config "section" (e.g., mirrors, compilers, etc.).
     """
 
-    def __init__(self, name, path):
+    def __init__(self, name, path) -> None:
         self.name = name  # scope name.
         self.path = path  # path to directory containing configs.
         self.sections = syaml.syaml_dict()  # sections read from config files.
 
     @property
-    def is_platform_dependent(self):
+    def is_platform_dependent(self) -> bool:
+        """Returns true if the scope name is platform specific"""
         return os.sep in self.name
 
-    def get_section_filename(self, section):
+    def get_section_filename(self, section: str) -> str:
+        """Returns the filename associated with a given section"""
         _validate_section_name(section)
-        return os.path.join(self.path, "%s.yaml" % section)
+        return os.path.join(self.path, f"{section}.yaml")
 
-    def get_section(self, section):
+    def get_section(self, section: str) -> Optional[YamlConfigDict]:
+        """Returns the data associated with a given section"""
         if section not in self.sections:
             path = self.get_section_filename(section)
             schema = SECTION_SCHEMAS[section]
@@ -142,39 +146,44 @@ def get_section(self, section):
             self.sections[section] = data
         return self.sections[section]
 
-    def _write_section(self, section):
+    def _write_section(self, section: str) -> None:
         filename = self.get_section_filename(section)
         data = self.get_section(section)
+        if data is None:
+            return
 
         # We copy data here to avoid adding defaults at write time
         validate_data = copy.deepcopy(data)
         validate(validate_data, SECTION_SCHEMAS[section])
 
         try:
-            mkdirp(self.path)
+            filesystem.mkdirp(self.path)
             with open(filename, "w") as f:
                 syaml.dump_config(data, stream=f, default_flow_style=False)
-        except (syaml.SpackYAMLError, IOError) as e:
+        except (syaml.SpackYAMLError, OSError) as e:
             raise ConfigFileError(f"cannot write to '{filename}'") from e
 
-    def clear(self):
+    def clear(self) -> None:
         """Empty cached config information."""
         self.sections = syaml.syaml_dict()
 
-    def __repr__(self):
-        return "<ConfigScope: %s: %s>" % (self.name, self.path)
+    def __repr__(self) -> str:
+        return f"<ConfigScope: {self.name}: {self.path}>"
 
 
 class SingleFileScope(ConfigScope):
     """This class represents a configuration scope in a single YAML file."""
 
-    def __init__(self, name, path, schema, yaml_path=None):
+    def __init__(
+        self, name: str, path: str, schema: YamlConfigDict, yaml_path: Optional[List[str]] = None
+    ) -> None:
         """Similar to ``ConfigScope`` but can be embedded in another schema.
 
         Arguments:
             schema (dict): jsonschema for the file to read
             yaml_path (list): path in the schema where config data can be
                 found.
+
                 If the schema accepts the following yaml data, the yaml_path
                 would be ['outer', 'inner']
 
@@ -186,18 +195,18 @@ def __init__(self, name, path, schema, yaml_path=None):
                          install_tree: $spack/opt/spack
         """
         super().__init__(name, path)
-        self._raw_data = None
+        self._raw_data: Optional[YamlConfigDict] = None
         self.schema = schema
         self.yaml_path = yaml_path or []
 
     @property
-    def is_platform_dependent(self):
+    def is_platform_dependent(self) -> bool:
         return False
 
-    def get_section_filename(self, section):
+    def get_section_filename(self, section) -> str:
         return self.path
 
-    def get_section(self, section):
+    def get_section(self, section: str) -> Optional[YamlConfigDict]:
         # read raw data from the file, which looks like:
         # {
         #   'config': {
@@ -246,8 +255,8 @@ def get_section(self, section):
 
         return self.sections.get(section, None)
 
-    def _write_section(self, section):
-        data_to_write = self._raw_data
+    def _write_section(self, section: str) -> None:
+        data_to_write: Optional[YamlConfigDict] = self._raw_data
 
         # If there is no existing data, this section SingleFileScope has never
         # been written to disk. We need to construct the portion of the data
@@ -277,18 +286,18 @@ def _write_section(self, section):
         validate(data_to_write, self.schema)
         try:
             parent = os.path.dirname(self.path)
-            mkdirp(parent)
+            filesystem.mkdirp(parent)
 
-            tmp = os.path.join(parent, ".%s.tmp" % os.path.basename(self.path))
+            tmp = os.path.join(parent, f".{os.path.basename(self.path)}.tmp")
             with open(tmp, "w") as f:
                 syaml.dump_config(data_to_write, stream=f, default_flow_style=False)
-            rename(tmp, self.path)
+            filesystem.rename(tmp, self.path)
 
-        except (syaml.SpackYAMLError, IOError) as e:
+        except (syaml.SpackYAMLError, OSError) as e:
             raise ConfigFileError(f"cannot write to config file {str(e)}") from e
 
-    def __repr__(self):
-        return "<SingleFileScope: %s: %s>" % (self.name, self.path)
+    def __repr__(self) -> str:
+        return f"<SingleFileScope: {self.name}: {self.path}>"
 
 
 class ImmutableConfigScope(ConfigScope):
@@ -297,11 +306,11 @@ class ImmutableConfigScope(ConfigScope):
     This is used for ConfigScopes passed on the command line.
     """
 
-    def _write_section(self, section):
-        raise ConfigError("Cannot write to immutable scope %s" % self)
+    def _write_section(self, section) -> None:
+        raise ConfigError(f"Cannot write to immutable scope {self}")
 
-    def __repr__(self):
-        return "<ImmutableConfigScope: %s: %s>" % (self.name, self.path)
+    def __repr__(self) -> str:
+        return f"<ImmutableConfigScope: {self.name}: {self.path}>"
 
 
 class InternalConfigScope(ConfigScope):
@@ -312,56 +321,58 @@ class InternalConfigScope(ConfigScope):
     override settings from files.
     """
 
-    def __init__(self, name, data=None):
+    def __init__(self, name: str, data: Optional[YamlConfigDict] = None) -> None:
         super().__init__(name, None)
         self.sections = syaml.syaml_dict()
 
-        if data:
+        if data is not None:
             data = InternalConfigScope._process_dict_keyname_overrides(data)
             for section in data:
                 dsec = data[section]
                 validate({section: dsec}, SECTION_SCHEMAS[section])
                 self.sections[section] = _mark_internal(syaml.syaml_dict({section: dsec}), name)
 
-    def get_section_filename(self, section):
+    def get_section_filename(self, section: str) -> str:
         raise NotImplementedError("Cannot get filename for InternalConfigScope.")
 
-    def get_section(self, section):
+    def get_section(self, section: str) -> Optional[YamlConfigDict]:
         """Just reads from an internal dictionary."""
         if section not in self.sections:
             self.sections[section] = None
         return self.sections[section]
 
-    def _write_section(self, section):
+    def _write_section(self, section: str) -> None:
         """This only validates, as the data is already in memory."""
         data = self.get_section(section)
         if data is not None:
             validate(data, SECTION_SCHEMAS[section])
         self.sections[section] = _mark_internal(data, self.name)
 
-    def __repr__(self):
-        return "<InternalConfigScope: %s>" % self.name
+    def __repr__(self) -> str:
+        return f"<InternalConfigScope: {self.name}>"
 
-    def clear(self):
+    def clear(self) -> None:
         # no cache to clear here.
         pass
 
     @staticmethod
-    def _process_dict_keyname_overrides(data):
+    def _process_dict_keyname_overrides(data: YamlConfigDict) -> YamlConfigDict:
         """Turn a trailing `:' in a key name into an override attribute."""
-        result = {}
+        # Below we have a lot of type directives, since we hack on types and monkey-patch them
+        # by adding attributes that otherwise they won't have.
+        result: YamlConfigDict = {}
         for sk, sv in data.items():
             if sk.endswith(":"):
                 key = syaml.syaml_str(sk[:-1])
-                key.override = True
+                key.override = True  # type: ignore[attr-defined]
             elif sk.endswith("+"):
                 key = syaml.syaml_str(sk[:-1])
-                key.prepend = True
+                key.prepend = True  # type: ignore[attr-defined]
             elif sk.endswith("-"):
                 key = syaml.syaml_str(sk[:-1])
-                key.append = True
+                key.append = True  # type: ignore[attr-defined]
             else:
-                key = sk
+                key = sk  # type: ignore[assignment]
 
             if isinstance(sv, dict):
                 result[key] = InternalConfigScope._process_dict_keyname_overrides(sv)
@@ -394,7 +405,7 @@ class Configuration:
     # convert to typing.OrderedDict when we drop 3.6, or OrderedDict when we reach 3.9
     scopes: Dict[str, ConfigScope]
 
-    def __init__(self, *scopes: ConfigScope):
+    def __init__(self, *scopes: ConfigScope) -> None:
         """Initialize a configuration with an initial list of scopes.
 
         Args:
@@ -405,26 +416,26 @@ def __init__(self, *scopes: ConfigScope):
         self.scopes = collections.OrderedDict()
         for scope in scopes:
             self.push_scope(scope)
-        self.format_updates: Dict[str, List[str]] = collections.defaultdict(list)
+        self.format_updates: Dict[str, List[ConfigScope]] = collections.defaultdict(list)
 
     @_config_mutator
-    def push_scope(self, scope: ConfigScope):
+    def push_scope(self, scope: ConfigScope) -> None:
         """Add a higher precedence scope to the Configuration."""
-        tty.debug("[CONFIGURATION: PUSH SCOPE]: {}".format(str(scope)), level=2)
+        tty.debug(f"[CONFIGURATION: PUSH SCOPE]: {str(scope)}", level=2)
         self.scopes[scope.name] = scope
 
     @_config_mutator
     def pop_scope(self) -> ConfigScope:
         """Remove the highest precedence scope and return it."""
         name, scope = self.scopes.popitem(last=True)  # type: ignore[call-arg]
-        tty.debug("[CONFIGURATION: POP SCOPE]: {}".format(str(scope)), level=2)
+        tty.debug(f"[CONFIGURATION: POP SCOPE]: {str(scope)}", level=2)
         return scope
 
     @_config_mutator
     def remove_scope(self, scope_name: str) -> Optional[ConfigScope]:
         """Remove scope by name; has no effect when ``scope_name`` does not exist"""
         scope = self.scopes.pop(scope_name, None)
-        tty.debug("[CONFIGURATION: POP SCOPE]: {}".format(str(scope)), level=2)
+        tty.debug(f"[CONFIGURATION: POP SCOPE]: {str(scope)}", level=2)
         return scope
 
     @property
@@ -481,16 +492,16 @@ def _validate_scope(self, scope: Optional[str]) -> ConfigScope:
 
         else:
             raise ValueError(
-                "Invalid config scope: '%s'.  Must be one of %s" % (scope, self.scopes.keys())
+                f"Invalid config scope: '{scope}'.  Must be one of {self.scopes.keys()}"
             )
 
-    def get_config_filename(self, scope, section) -> str:
+    def get_config_filename(self, scope: str, section: str) -> str:
         """For some scope and section, get the name of the configuration file."""
         scope = self._validate_scope(scope)
         return scope.get_section_filename(section)
 
     @_config_mutator
-    def clear_caches(self):
+    def clear_caches(self) -> None:
         """Clears the caches for configuration files,
 
         This will cause files to be re-read upon the next request."""
@@ -500,7 +511,7 @@ def clear_caches(self):
     @_config_mutator
     def update_config(
         self, section: str, update_data: Dict, scope: Optional[str] = None, force: bool = False
-    ):
+    ) -> None:
         """Update the configuration file for a particular scope.
 
         Overwrites contents of a section in a scope with update_data,
@@ -514,10 +525,10 @@ def update_config(
         format will fail to update unless ``force`` is True.
 
         Args:
-            section (str): section of the configuration to be updated
-            update_data (dict): data to be used for the update
-            scope (str): scope to be updated
-            force (str): force the update
+            section: section of the configuration to be updated
+            update_data: data to be used for the update
+            scope: scope to be updated
+            force: force the update
         """
         if self.format_updates.get(section) and not force:
             msg = (
@@ -546,7 +557,7 @@ def update_config(
 
         scope._write_section(section)
 
-    def get_config(self, section, scope=None):
+    def get_config(self, section: str, scope: Optional[str] = None) -> YamlConfigDict:
         """Get configuration settings for a section.
 
         If ``scope`` is ``None`` or not provided, return the merged contents
@@ -573,12 +584,12 @@ def get_config(self, section, scope=None):
         """
         return self._get_config_memoized(section, scope)
 
-    @llnl.util.lang.memoized
-    def _get_config_memoized(self, section, scope):
+    @lang.memoized
+    def _get_config_memoized(self, section: str, scope: Optional[str]) -> YamlConfigDict:
         _validate_section_name(section)
 
         if scope is None:
-            scopes = self.scopes.values()
+            scopes = list(self.scopes.values())
         else:
             scopes = [self._validate_scope(scope)]
 
@@ -613,7 +624,7 @@ def _get_config_memoized(self, section, scope):
             ret = syaml.syaml_dict(ret)
         return ret
 
-    def get(self, path, default=None, scope=None):
+    def get(self, path: str, default: Optional[Any] = None, scope: Optional[str] = None) -> Any:
         """Get a config section or a single value from one.
 
         Accepts a path syntax that allows us to grab nested config map
@@ -644,7 +655,7 @@ def get(self, path, default=None, scope=None):
         return value
 
     @_config_mutator
-    def set(self, path, value, scope=None):
+    def set(self, path: str, value: Any, scope: Optional[str] = None) -> None:
         """Convenience function for setting single values in config files.
 
         Accepts the path syntax described in ``get()``.
@@ -686,21 +697,22 @@ def set(self, path, value, scope=None):
 
     def __iter__(self):
         """Iterate over scopes in this configuration."""
-        for scope in self.scopes.values():
-            yield scope
+        yield from self.scopes.values()
 
-    def print_section(self, section, blame=False):
+    def print_section(self, section: str, blame: bool = False, *, scope=None) -> None:
         """Print a configuration to stdout."""
         try:
             data = syaml.syaml_dict()
-            data[section] = self.get_config(section)
+            data[section] = self.get_config(section, scope=scope)
             syaml.dump_config(data, stream=sys.stdout, default_flow_style=False, blame=blame)
-        except (syaml.SpackYAMLError, IOError) as e:
+        except (syaml.SpackYAMLError, OSError) as e:
             raise ConfigError(f"cannot read '{section}' configuration") from e
 
 
-@contextmanager
-def override(path_or_scope, value=None):
+@contextlib.contextmanager
+def override(
+    path_or_scope: Union[ConfigScope, str], value: Optional[Any] = None
+) -> Generator[Union[lang.Singleton, Configuration], None, None]:
     """Simple way to override config settings within a context.
 
     Arguments:
@@ -718,10 +730,10 @@ def override(path_or_scope, value=None):
     else:
         base_name = _OVERRIDES_BASE_NAME
         # Ensure the new override gets a unique scope name
-        current_overrides = [s.name for s in CONFIG.matching_scopes(r"^{0}".format(base_name))]
+        current_overrides = [s.name for s in CONFIG.matching_scopes(rf"^{base_name}")]
         num_overrides = len(current_overrides)
         while True:
-            scope_name = "{0}{1}".format(base_name, num_overrides)
+            scope_name = f"{base_name}{num_overrides}"
             if scope_name in current_overrides:
                 num_overrides += 1
             else:
@@ -738,12 +750,13 @@ def override(path_or_scope, value=None):
         assert scope is overrides
 
 
-#: configuration scopes added on the command line
-#: set by ``spack.main.main()``.
+#: configuration scopes added on the command line set by ``spack.main.main()``
 COMMAND_LINE_SCOPES: List[str] = []
 
 
-def _add_platform_scope(cfg, scope_type, name, path):
+def _add_platform_scope(
+    cfg: Union[Configuration, lang.Singleton], scope_type: Type[ConfigScope], name: str, path: str
+) -> None:
     """Add a platform-specific subdirectory for the current platform."""
     platform = spack.platforms.host().name
     plat_name = os.path.join(name, platform)
@@ -751,7 +764,9 @@ def _add_platform_scope(cfg, scope_type, name, path):
     cfg.push_scope(scope_type(plat_name, plat_path))
 
 
-def _add_command_line_scopes(cfg, command_line_scopes):
+def _add_command_line_scopes(
+    cfg: Union[Configuration, lang.Singleton], command_line_scopes: List[str]
+) -> None:
     """Add additional scopes from the --config-scope argument.
 
     Command line scopes are named after their position in the arg list.
@@ -760,26 +775,22 @@ def _add_command_line_scopes(cfg, command_line_scopes):
         # We ensure that these scopes exist and are readable, as they are
         # provided on the command line by the user.
         if not os.path.isdir(path):
-            raise ConfigError("config scope is not a directory: '%s'" % path)
+            raise ConfigError(f"config scope is not a directory: '{path}'")
         elif not os.access(path, os.R_OK):
-            raise ConfigError("config scope is not readable: '%s'" % path)
+            raise ConfigError(f"config scope is not readable: '{path}'")
 
         # name based on order on the command line
-        name = "cmd_scope_%d" % i
+        name = f"cmd_scope_{i:d}"
         cfg.push_scope(ImmutableConfigScope(name, path))
         _add_platform_scope(cfg, ImmutableConfigScope, name, path)
 
 
-def create():
+def create() -> Configuration:
     """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.
-
-    Return:
-        (Configuration): object for accessing spack configuration
-
     """
     cfg = Configuration()
 
@@ -828,16 +839,25 @@ def create():
 
 
 #: This is the singleton configuration instance for Spack.
-CONFIG: Union[Configuration, llnl.util.lang.Singleton] = llnl.util.lang.Singleton(create)
+CONFIG: Union[Configuration, lang.Singleton] = lang.Singleton(create)
 
 
-def add_from_file(filename, scope=None):
+def add_from_file(filename: str, scope: Optional[str] = None) -> None:
     """Add updates to a config from a filename"""
     # Extract internal attributes, if we are dealing with an environment
     data = read_config_file(filename)
+    if data is None:
+        return
+
     if spack.schema.env.TOP_LEVEL_KEY in data:
         data = data[spack.schema.env.TOP_LEVEL_KEY]
 
+    msg = (
+        "unexpected 'None' value when retrieving configuration. "
+        "Please submit a bug-report at https://github.com/spack/spack/issues"
+    )
+    assert data is not None, msg
+
     # update all sections from config dict
     # We have to iterate on keys to keep overrides from the file
     for section in data.keys():
@@ -855,7 +875,7 @@ def add_from_file(filename, scope=None):
             CONFIG.set(section, new, scope)
 
 
-def add(fullpath, scope=None):
+def add(fullpath: str, scope: Optional[str] = None) -> None:
     """Add the given configuration to the specified config scope.
     Add accepts a path. If you want to add from a filename, use add_from_file"""
     components = process_config_path(fullpath)
@@ -903,12 +923,12 @@ def add(fullpath, scope=None):
     CONFIG.set(path, new, scope)
 
 
-def get(path, default=None, scope=None):
+def get(path: str, default: Optional[Any] = None, scope: Optional[str] = None) -> Any:
     """Module-level wrapper for ``Configuration.get()``."""
     return CONFIG.get(path, default, scope)
 
 
-def set(path, value, scope=None):
+def set(path: str, value: Any, scope: Optional[str] = None) -> None:
     """Convenience function for setting single values in config files.
 
     Accepts the path syntax described in ``get()``.
@@ -916,32 +936,113 @@ def set(path, value, scope=None):
     return CONFIG.set(path, value, scope)
 
 
-def add_default_platform_scope(platform):
+def add_default_platform_scope(platform: str) -> None:
     plat_name = os.path.join("defaults", platform)
     plat_path = os.path.join(CONFIGURATION_DEFAULTS_PATH[1], platform)
     CONFIG.push_scope(ConfigScope(plat_name, plat_path))
 
 
-def scopes():
+def scopes() -> Dict[str, ConfigScope]:
     """Convenience function to get list of configuration scopes."""
     return CONFIG.scopes
 
 
-def _validate_section_name(section):
+def writable_scopes() -> List[ConfigScope]:
+    """
+    Return list of writable scopes
+    """
+    return list(
+        reversed(
+            list(
+                x
+                for x in CONFIG.scopes.values()
+                if not isinstance(x, (InternalConfigScope, ImmutableConfigScope))
+            )
+        )
+    )
+
+
+def writable_scope_names() -> List[str]:
+    return list(x.name for x in writable_scopes())
+
+
+def matched_config(cfg_path: str) -> List[Tuple[str, Any]]:
+    return [(scope, get(cfg_path, scope=scope)) for scope in writable_scope_names()]
+
+
+def change_or_add(
+    section_name: str, find_fn: Callable[[str], bool], update_fn: Callable[[str], None]
+) -> None:
+    """Change or add a subsection of config, with additional logic to
+    select a reasonable scope where the change is applied.
+
+    Search through config scopes starting with the highest priority:
+    the first matching a criteria (determined by ``find_fn``) is updated;
+    if no such config exists, find the first config scope that defines
+    any config for the named section; if no scopes define any related
+    config, then update the highest-priority config scope.
+    """
+    configs_by_section = matched_config(section_name)
+
+    found = False
+    for scope, section in configs_by_section:
+        found = find_fn(section)
+        if found:
+            break
+
+    if found:
+        update_fn(section)
+        spack.config.set(section_name, section, scope=scope)
+        return
+
+    # If no scope meets the criteria specified by ``find_fn``,
+    # then look for a scope that has any content (for the specified
+    # section name)
+    for scope, section in configs_by_section:
+        if section:
+            update_fn(section)
+            found = True
+            break
+
+    if found:
+        spack.config.set(section_name, section, scope=scope)
+        return
+
+    # If no scopes define any config for the named section, then
+    # modify the highest-priority scope.
+    scope, section = configs_by_section[0]
+    update_fn(section)
+    spack.config.set(section_name, section, scope=scope)
+
+
+def update_all(section_name: str, change_fn: Callable[[str], bool]) -> None:
+    """Change a config section, which may have details duplicated
+    across multiple scopes.
+    """
+    configs_by_section = matched_config("develop")
+
+    for scope, section in configs_by_section:
+        modified = change_fn(section)
+        if modified:
+            spack.config.set(section_name, section, scope=scope)
+
+
+def _validate_section_name(section: str) -> None:
     """Exit if the section is not a valid section."""
     if section not in SECTION_SCHEMAS:
         raise ConfigSectionError(
-            "Invalid config section: '%s'. Options are: %s"
-            % (section, " ".join(SECTION_SCHEMAS.keys()))
+            f"Invalid config section: '{section}'. Options are: {' '.join(SECTION_SCHEMAS.keys())}"
         )
 
 
-def validate(data, schema, filename=None):
+def validate(
+    data: YamlConfigDict, schema: YamlConfigDict, filename: Optional[str] = None
+) -> YamlConfigDict:
     """Validate data read in from a Spack YAML file.
 
     Arguments:
-        data (dict or list): data read from a Spack YAML file
-        schema (dict or list): jsonschema to validate data
+        data: data read from a Spack YAML file
+        schema: jsonschema to validate data
 
     This leverages the line information (start_mark, end_mark) stored
     on Spack YAML structures.
@@ -964,7 +1065,9 @@ def validate(data, schema, filename=None):
     return test_data
 
 
-def read_config_file(filename, schema=None):
+def read_config_file(
+    filename: str, schema: Optional[YamlConfigDict] = None
+) -> Optional[YamlConfigDict]:
     """Read a YAML configuration file.
 
     User can provide a schema for validation. If no schema is provided,
@@ -976,17 +1079,17 @@ def read_config_file(filename, schema=None):
 
     if not os.path.exists(filename):
         # Ignore nonexistent files.
-        tty.debug("Skipping nonexistent config path {0}".format(filename), level=3)
+        tty.debug(f"Skipping nonexistent config path {filename}", level=3)
         return None
 
     elif not os.path.isfile(filename):
-        raise ConfigFileError("Invalid configuration. %s exists but is not a file." % filename)
+        raise ConfigFileError(f"Invalid configuration. {filename} exists but is not a file.")
 
     elif not os.access(filename, os.R_OK):
-        raise ConfigFileError("Config file is not readable: {0}".format(filename))
+        raise ConfigFileError(f"Config file is not readable: {filename}")
 
     try:
-        tty.debug("Reading config from file {0}".format(filename))
+        tty.debug(f"Reading config from file {filename}")
         with open(filename) as f:
             data = syaml.load_config(f)
 
@@ -1004,11 +1107,11 @@ def read_config_file(filename, schema=None):
     except syaml.SpackYAMLError as e:
         raise ConfigFileError(str(e)) from e
 
-    except IOError as e:
+    except OSError as e:
         raise ConfigFileError(f"Error reading configuration file {filename}: {str(e)}") from e
 
 
-def _override(string):
+def _override(string: str) -> bool:
     """Test if a spack YAML string is an override.
 
     See ``spack_yaml`` for details.  Keys in Spack YAML can end in `::`,
@@ -1019,7 +1122,7 @@ def _override(string):
     return hasattr(string, "override") and string.override
 
 
-def _append(string):
+def _append(string: str) -> bool:
     """Test if a spack YAML string is an override.
 
     See ``spack_yaml`` for details.  Keys in Spack YAML can end in `+:`,
@@ -1033,7 +1136,7 @@ def _append(string):
     return getattr(string, "append", False)
 
 
-def _prepend(string):
+def _prepend(string: str) -> bool:
     """Test if a spack YAML string is an override.
 
     See ``spack_yaml`` for details.  Keys in Spack YAML can end in `+:`,
@@ -1105,7 +1208,7 @@ def get_valid_type(path):
                     return types[schema_type]()
     else:
         return type(None)
-    raise ConfigError("Cannot determine valid type for path '%s'." % path)
+    raise ConfigError(f"Cannot determine valid type for path '{path}'.")
 
 
 def remove_yaml(dest, source):
@@ -1233,7 +1336,7 @@ def they_are(t):
     return copy.copy(source)
 
 
-def process_config_path(path):
+def process_config_path(path: str) -> List[str]:
     """Process a path argument to config.set() that may contain overrides ('::' or
     trailing ':')
 
@@ -1246,29 +1349,29 @@ def process_config_path(path):
     """
     result = []
     if path.startswith(":"):
-        raise syaml.SpackYAMLError("Illegal leading `:' in path `{0}'".format(path), "")
+        raise syaml.SpackYAMLError(f"Illegal leading `:' in path `{path}'", "")
     seen_override_in_path = False
     while path:
         front, sep, path = path.partition(":")
         if (sep and not path) or path.startswith(":"):
             if seen_override_in_path:
                 raise syaml.SpackYAMLError(
-                    "Meaningless second override" " indicator `::' in path `{0}'".format(path), ""
+                    f"Meaningless second override indicator `::' in path `{path}'", ""
                 )
             path = path.lstrip(":")
             front = syaml.syaml_str(front)
-            front.override = True
+            front.override = True  # type: ignore[attr-defined]
             seen_override_in_path = True
 
         elif front.endswith("+"):
             front = front.rstrip("+")
             front = syaml.syaml_str(front)
-            front.prepend = True
+            front.prepend = True  # type: ignore[attr-defined]
 
         elif front.endswith("-"):
             front = front.rstrip("-")
             front = syaml.syaml_str(front)
-            front.append = True
+            front.append = True  # type: ignore[attr-defined]
 
         result.append(front)
 
@@ -1288,7 +1391,7 @@ def process_config_path(path):
 #
 # Settings for commands that modify configuration
 #
-def default_modify_scope(section="config"):
+def default_modify_scope(section: str = "config") -> str:
     """Return the config scope that commands should modify by default.
 
     Commands that modify configuration by default modify the *highest*
@@ -1304,23 +1407,15 @@ def default_modify_scope(section="config"):
         return CONFIG.highest_precedence_non_platform_scope().name
 
 
-def default_list_scope():
-    """Return the config scope that is listed by default.
-
-    Commands that list configuration list *all* scopes (merged) by default.
-    """
-    return None
-
-
-def _update_in_memory(data, section):
+def _update_in_memory(data: YamlConfigDict, section: str) -> bool:
     """Update the format of the configuration data in memory.
 
     This function assumes the section is valid (i.e. validation
     is responsibility of the caller)
 
     Args:
-        data (dict): configuration data
-        section (str): section of the configuration to update
+        data: configuration data
+        section: section of the configuration to update
 
     Returns:
         True if the data was changed, False otherwise
@@ -1330,14 +1425,14 @@ def _update_in_memory(data, section):
     return changed
 
 
-def ensure_latest_format_fn(section):
+def ensure_latest_format_fn(section: str) -> Callable[[YamlConfigDict], bool]:
     """Return a function that takes as input a dictionary read from
     a configuration file and update it to the latest format.
 
     The function returns True if there was any update, False otherwise.
 
     Args:
-        section (str): section of the configuration e.g. "packages",
+        section: section of the configuration e.g. "packages",
             "config", etc.
     """
     # The line below is based on the fact that every module we need
@@ -1348,7 +1443,9 @@ def ensure_latest_format_fn(section):
 
 
 @contextlib.contextmanager
-def use_configuration(*scopes_or_paths):
+def use_configuration(
+    *scopes_or_paths: Union[ConfigScope, str]
+) -> Generator[Configuration, None, None]:
     """Use the configuration scopes passed as arguments within the
     context manager.
 
@@ -1372,8 +1469,8 @@ def use_configuration(*scopes_or_paths):
         CONFIG = saved_config
 
 
-@llnl.util.lang.memoized
-def _config_from(scopes_or_paths):
+@lang.memoized
+def _config_from(scopes_or_paths: List[Union[ConfigScope, str]]) -> Configuration:
     scopes = []
     for scope_or_path in scopes_or_paths:
         # If we have a config scope we are already done
@@ -1383,7 +1480,7 @@ def _config_from(scopes_or_paths):
 
         # Otherwise we need to construct it
         path = os.path.normpath(scope_or_path)
-        assert os.path.isdir(path), '"{0}" must be a directory'.format(path)
+        assert os.path.isdir(path), f'"{path}" must be a directory'
         name = os.path.basename(path)
         scopes.append(ConfigScope(name, path))
 
@@ -1391,13 +1488,14 @@ def _config_from(scopes_or_paths):
     return configuration
 
 
-def raw_github_gitlab_url(url):
+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
 
-    Returns: (str) raw github/gitlab url or the original url
+    Returns:
+        Raw github/gitlab url or the original url
     """
     # Note we rely on GitHub to redirect the 'raw' URL returned here to the
     # actual URL under https://raw.githubusercontent.com/ with '/blob'
@@ -1450,7 +1548,7 @@ def fetch_remote_configs(url: str, dest_dir: str, skip_existing: bool = True) ->
 
     def _fetch_file(url):
         raw = raw_github_gitlab_url(url)
-        tty.debug("Reading config from url {0}".format(raw))
+        tty.debug(f"Reading config from url {raw}")
         return web_util.fetch_url_text(raw, dest_dir=dest_dir)
 
     if not url:
@@ -1466,8 +1564,8 @@ def _fetch_file(url):
         basename = os.path.basename(config_url)
         if skip_existing and basename in existing_files:
             tty.warn(
-                "Will not fetch configuration from {0} since a version already"
-                "exists in {1}".format(config_url, dest_dir)
+                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:
@@ -1479,7 +1577,7 @@ def _fetch_file(url):
     if paths:
         return dest_dir if len(paths) > 1 else paths[0]
 
-    raise ConfigFileError("Cannot retrieve configuration (yaml) from {0}".format(url))
+    raise ConfigFileError(f"Cannot retrieve configuration (yaml) from {url}")
 
 
 class ConfigError(SpackError):
@@ -1497,7 +1595,13 @@ class ConfigFileError(ConfigError):
 class ConfigFormatError(ConfigError):
     """Raised when a configuration format does not match its schema."""
 
-    def __init__(self, validation_error, data, filename=None, line=None):
+    def __init__(
+        self,
+        validation_error,
+        data: YamlConfigDict,
+        filename: Optional[str] = None,
+        line: Optional[int] = None,
+    ) -> None:
         # spack yaml has its own file/line marks -- try to find them
         # we prioritize these over the inputs
         self.validation_error = validation_error
@@ -1511,11 +1615,11 @@ def __init__(self, validation_error, data, filename=None, line=None):
         # construct location
         location = "<unknown file>"
         if filename:
-            location = "%s" % filename
+            location = f"{filename}"
         if line is not None:
-            location += ":%d" % line
+            location += f":{line:d}"
 
-        message = "%s: %s" % (location, validation_error.message)
+        message = f"{location}: {validation_error.message}"
         super().__init__(message)
 
     def _get_mark(self, validation_error, data):

lib/spack/spack/cray_manifest.py

@@ -227,7 +227,7 @@ def read(path, apply_updates):
     if apply_updates and compilers:
         for compiler in compilers:
             try:
-                spack.compilers.add_compilers_to_config([compiler])
+                spack.compilers.add_compilers_to_config([compiler], init_config=False)
             except Exception:
                 warnings.warn(
                     f"Could not add compiler {str(compiler.spec)}: "