paraview: fix typo

This reverts commit 8f3b90619dc2bb5900ee2526927ac6d1c0ff7738.

.github/workflows/build-containers.yml

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

.github/workflows/ci.yaml

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

.github/workflows/coverage.yml

@@ -29,7 +29,8 @@ jobs:
     - run: coverage xml
 
     - name: "Upload coverage report to CodeCov"
-      uses: codecov/codecov-action@05f5a9cfad807516dbbef9929c4a42df3eb78766
+      uses: codecov/codecov-action@1e68e06f1dbfde0e4cefc87efeba9e4643565303
       with:
         verbose: true
         fail_ci_if_error: false
+        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/import-check.yaml

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

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

@@ -1,7 +1,7 @@
-black==24.10.0
+black==25.1.0
 clingo==5.7.1
-flake8==7.1.1
-isort==5.13.2
-mypy==1.8.0
-types-six==1.17.0.20241205
+flake8==7.1.2
+isort==6.0.1
+mypy==1.15.0
+types-six==1.17.0.20250304
 vermin==1.6.0

.github/workflows/valid-style.yml

@@ -20,7 +20,7 @@ jobs:
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
     - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
       with:
-        python-version: '3.11'
+        python-version: '3.13'
         cache: 'pip'
     - name: Install Python Packages
       run: |
@@ -39,7 +39,7 @@ jobs:
         fetch-depth: 0
     - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
       with:
-        python-version: '3.11'
+        python-version: '3.13'
         cache: 'pip'
     - name: Install Python packages
       run: |
@@ -58,7 +58,7 @@ jobs:
     secrets: inherit
     with:
       with_coverage: ${{ inputs.with_coverage }}
-      python_version: '3.11'
+      python_version: '3.13'
   # Check that spack can bootstrap the development environment on Python 3.6 - RHEL8
   bootstrap-dev-rhel8:
     runs-on: ubuntu-latest
@@ -86,66 +86,6 @@ jobs:
           spack -d bootstrap now --dev
           spack -d style -t black
           spack unit-test -V
-  # Check we don't make the situation with circular imports worse
-  import-check:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: julia-actions/setup-julia@v2
-      with:
-        version: '1.10'
-    - uses: julia-actions/cache@v2
-
-    # PR: use the base of the PR as the old commit
-    - name: Checkout PR base commit
-      if: github.event_name == 'pull_request'
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        ref: ${{ github.event.pull_request.base.sha }}
-        path: old
-    # not a PR: use the previous commit as the old commit
-    - name: Checkout previous commit
-      if: github.event_name != 'pull_request'
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        fetch-depth: 2
-        path: old
-    - name: Checkout previous commit
-      if: github.event_name != 'pull_request'
-      run: git -C old reset --hard HEAD^
-
-    - name: Checkout new commit
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        path: new
-    - name: Install circular import checker
-      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
-      with:
-        repository: haampie/circular-import-fighter
-        ref: b5d6ce9be35f602cca7d5a6aa0259fca10639cca
-        path: circular-import-fighter
-    - name: Install dependencies
-      working-directory: circular-import-fighter
-      run: make -j dependencies
-    - name: Problematic imports before
-      working-directory: circular-import-fighter
-      run: make SPACK_ROOT=../old SUFFIX=.old
-    - name: Problematic imports after
-      working-directory: circular-import-fighter
-      run: make SPACK_ROOT=../new SUFFIX=.new
-    - name: Compare import cycles
-      working-directory: circular-import-fighter
-      run: |
-        edges_before="$(head -n1 solution.old)"
-        edges_after="$(head -n1 solution.new)"
-        if [ "$edges_after" -gt "$edges_before" ]; then
-          printf '\033[1;31mImport check failed: %s imports need to be deleted, ' "$edges_after"
-          printf 'previously this was %s\033[0m\n'  "$edges_before"
-          printf 'Compare \033[1;97m"Problematic imports before"\033[0m and '
-          printf '\033[1;97m"Problematic imports after"\033[0m.\n'
-          exit 1
-        else
-          printf '\033[1;32mImport check passed: %s <= %s\033[0m\n' "$edges_after" "$edges_before"
-        fi
 
   # Further style checks from pylint
   pylint:

.gitignore

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

bin/spack

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

etc/spack/defaults/concretizer.yaml

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

etc/spack/defaults/packages.yaml

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

etc/spack/defaults/windows/config.yaml

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

lib/spack/docs/basic_usage.rst

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

lib/spack/docs/bootstrapping.rst

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

lib/spack/docs/build_systems/autotoolspackage.rst

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

lib/spack/docs/build_systems/custompackage.rst

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

lib/spack/docs/conf.py

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

lib/spack/docs/config_yaml.rst

@@ -25,14 +25,23 @@ These settings can be overridden in ``etc/spack/config.yaml`` or
 The location where Spack will install packages and their dependencies.
 Default is ``$spack/opt/spack``.
 
----------------------------------------------------
-``install_hash_length`` and ``install_path_scheme``
----------------------------------------------------
+---------------
+``projections``
+---------------
 
-The default Spack installation path can be very long and can create problems
-for scripts with hardcoded shebangs. Additionally, when using the Intel
-compiler, and if there is also a long list of dependencies, the compiler may
-segfault. If you see the following:
+.. warning::
+
+   Modifying projections of the install tree is strongly discouraged.
+
+By default Spack installs all packages into a unique directory relative to the install
+tree root with the following layout:
+
+.. code-block::
+
+   {architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}
+
+In very rare cases, it may be necessary to reduce the length of this path. For example,
+very old versions of the Intel compiler are known to segfault when input paths are too long:
 
      .. code-block:: console
 
@@ -40,36 +49,25 @@ segfault. If you see the following:
        ** Segmentation violation signal raised. **
        Access violation or stack overflow. Please contact Intel Support for assistance.
 
-it may be because variables containing dependency specs may be too long. There
-are two parameters to help with long path names. Firstly, the
-``install_hash_length`` parameter can set the length of the hash in the
-installation path from 1 to 32. The default path uses the full 32 characters.
+Another case is Python and R packages with many runtime dependencies, which can result
+in very large ``PYTHONPATH`` and ``R_LIBS`` environment variables. This can cause the
+``execve`` system call to fail with ``E2BIG``, preventing processes from starting.
 
-Secondly, it is also possible to modify the entire installation
-scheme. By default Spack uses
-``{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}``
-where the tokens that are available for use in this directive are the
-same as those understood by the :meth:`~spack.spec.Spec.format`
-method. Using this parameter it is possible to use a different package
-layout or reduce the depth of the installation paths. For example
+For this reason, Spack allows users to modify the installation layout through custom
+projections. For example
 
      .. code-block:: yaml
 
        config:
-         install_path_scheme: '{name}/{version}/{hash:7}'
+         install_tree:
+           root: $spack/opt/spack
+           projections:
+             all: "{name}/{version}/{hash:16}"
 
-would install packages into sub-directories using only the package
-name, version and a hash length of 7 characters.
+would install packages into sub-directories using only the package name, version and a
+hash length of 16 characters.
 
-When using either parameter to set the hash length it only affects the
-representation of the hash in the installation directory. You
-should be aware that the smaller the hash length the more likely
-naming conflicts will occur. These parameters are independent of those
-used to configure module names.
-
-.. warning:: Modifying the installation hash length or path scheme after
-   packages have been installed will prevent Spack from being
-   able to find the old installation directories.
+Notice that reducing the hash length increases the likelihood of hash collisions.
 
 --------------------
 ``build_stage``
@@ -127,6 +125,8 @@ are stored in ``$spack/var/spack/cache``.  These are stored indefinitely
 by default. Can be purged with :ref:`spack clean --downloads
 <cmd-spack-clean>`.
 
+.. _Misc Cache:
+
 --------------------
 ``misc_cache``
 --------------------
@@ -336,3 +336,52 @@ create a new alias called ``inst`` that will always call ``install -v``:
 
    aliases:
      inst: install -v
+
+-------------------------------
+``concretization_cache:enable``
+-------------------------------
+
+When set to ``true``, Spack will utilize a cache of solver outputs from
+successful concretization runs. When enabled, Spack will check the concretization
+cache prior to running the solver. If a previous request to solve a given
+problem is present in the cache, Spack will load the concrete specs and other
+solver data from the cache rather than running the solver. Specs not previously
+concretized will be added to the cache on a successful solve. The cache additionally
+holds solver statistics, so commands like ``spack solve`` will still return information
+about the run that produced a given solver result.
+
+This cache is a subcache of the :ref:`Misc Cache` and as such will be cleaned when the Misc
+Cache is cleaned.
+
+When ``false`` or ommitted, all concretization requests will be performed from scatch
+
+----------------------------
+``concretization_cache:url``
+----------------------------
+
+Path to the location where Spack will root the concretization cache. Currently this only supports
+paths on the local filesystem.
+
+Default location is under the :ref:`Misc Cache` at: ``$misc_cache/concretization``
+
+------------------------------------
+``concretization_cache:entry_limit``
+------------------------------------
+
+Sets a limit on the number of concretization results that Spack will cache. The limit is evaluated
+after each concretization run; if Spack has stored more results than the limit allows, the
+oldest concretization results are pruned until 10% of the limit has been removed.
+
+Setting this value to 0 disables the automatic pruning. It is expected users will be
+responsible for maintaining this cache.
+
+-----------------------------------
+``concretization_cache:size_limit``
+-----------------------------------
+
+Sets a limit on the size of the concretization cache in bytes. The limit is evaluated
+after each concretization run; if Spack has stored more results than the limit allows, the
+oldest concretization results are pruned until 10% of the limit has been removed.
+
+Setting this value to 0 disables the automatic pruning. It is expected users will be
+responsible for maintaining this cache.

lib/spack/docs/configuration.rst

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

lib/spack/docs/contribution_guide.rst

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

lib/spack/docs/developer_guide.rst

@@ -543,10 +543,10 @@ With either interpreter you can run a single command:
 
 .. code-block:: console
 
-   $ spack python -c 'from spack.spec import Spec; Spec("python").concretized()'
+   $ spack python -c 'from spack.concretize import concretize_one; concretize_one("python")'
    ...
 
-   $ spack python -i ipython -c 'from spack.spec import Spec; Spec("python").concretized()'
+   $ spack python -i ipython -c 'from spack.concretize import concretize_one; concretize_one("python")'
    Out[1]: ...
 
 or a file:

lib/spack/docs/environments.rst

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

lib/spack/docs/frequently_asked_questions.rst

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

lib/spack/docs/include_yaml.rst

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

lib/spack/docs/index.rst

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

lib/spack/docs/module_file_support.rst

@@ -456,14 +456,13 @@ For instance, the following config options,
        tcl:
          all:
            suffixes:
-             ^python@3: 'python{^python.version}'
+             ^python@3: 'python{^python.version.up_to_2}'
              ^openblas: 'openblas'
 
-will add a ``python-3.12.1`` version string to any packages compiled with
-Python matching the spec, ``python@3``. This is useful to know which
-version of Python a set of Python extensions is associated with. Likewise, the
-``openblas`` string is attached to any program that has openblas in the spec,
-most likely via the ``+blas`` variant specification.
+will add a ``python3.12`` to module names of packages compiled with Python 3.12, and similarly for
+all specs depending on ``python@3``. This is useful to know which version of Python a set of Python
+extensions is associated with. Likewise, the ``openblas`` string is attached to any program that
+has openblas in the spec, most likely via the ``+blas`` variant specification.
 
 The most heavyweight solution to module naming is to change the entire
 naming convention for module files. This uses the projections format

lib/spack/docs/packages_yaml.rst

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

lib/spack/docs/pipelines.rst

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

lib/spack/docs/requirements.txt

@@ -1,13 +1,13 @@
-sphinx==8.1.3
+sphinx==8.2.3
 sphinxcontrib-programoutput==0.18
 sphinx_design==0.6.1
 sphinx-rtd-theme==3.0.2
-python-levenshtein==0.26.1
+python-levenshtein==0.27.1
 docutils==0.21.2
-pygments==2.18.0
+pygments==2.19.1
 urllib3==2.3.0
-pytest==8.3.4
-isort==5.13.2
-black==24.10.0
-flake8==7.1.1
+pytest==8.3.5
+isort==6.0.1
+black==25.1.0
+flake8==7.1.2
 mypy==1.11.1

lib/spack/llnl/url.py

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

lib/spack/llnl/util/filesystem.py

@@ -7,6 +7,7 @@
 import fnmatch
 import glob
 import hashlib
+import io
 import itertools
 import numbers
 import os
@@ -20,6 +21,7 @@
 from contextlib import contextmanager
 from itertools import accumulate
 from typing import (
+    IO,
     Callable,
     Deque,
     Dict,
@@ -75,7 +77,6 @@
     "install_tree",
     "is_exe",
     "join_path",
-    "last_modification_time_recursive",
     "library_extensions",
     "mkdirp",
     "partition_path",
@@ -669,7 +670,7 @@ def copy(src, dest, _permissions=False):
         _permissions (bool): for internal use only
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* matches multiple files but *dest* is
             not a directory
     """
@@ -680,7 +681,7 @@ def copy(src, dest, _permissions=False):
 
     files = glob.glob(src)
     if not files:
-        raise IOError("No such file or directory: '{0}'".format(src))
+        raise OSError("No such file or directory: '{0}'".format(src))
     if len(files) > 1 and not os.path.isdir(dest):
         raise ValueError(
             "'{0}' matches multiple files but '{1}' is not a directory".format(src, dest)
@@ -711,7 +712,7 @@ def install(src, dest):
         dest (str): the destination file or directory
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* matches multiple files but *dest* is
             not a directory
     """
@@ -749,7 +750,7 @@ def copy_tree(
         _permissions (bool): for internal use only
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* is a parent directory of *dest*
     """
     if _permissions:
@@ -763,7 +764,7 @@ def copy_tree(
 
     files = glob.glob(src)
     if not files:
-        raise IOError("No such file or directory: '{0}'".format(src))
+        raise OSError("No such file or directory: '{0}'".format(src))
 
     # For Windows hard-links and junctions, the source path must exist to make a symlink. Add
     # all symlinks to this list while traversing the tree, then when finished, make all
@@ -844,7 +845,7 @@ def install_tree(src, dest, symlinks=True, ignore=None):
         ignore (typing.Callable): function indicating which files to ignore
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* is a parent directory of *dest*
     """
     copy_tree(src, dest, symlinks=symlinks, ignore=ignore, _permissions=True)
@@ -1470,15 +1471,36 @@ def set_executable(path):
 
 
 @system_path_filter
-def last_modification_time_recursive(path):
-    path = os.path.abspath(path)
-    times = [os.stat(path).st_mtime]
-    times.extend(
-        os.lstat(os.path.join(root, name)).st_mtime
-        for root, dirs, files in os.walk(path)
-        for name in dirs + files
-    )
-    return max(times)
+def recursive_mtime_greater_than(path: str, time: float) -> bool:
+    """Returns true if any file or dir recursively under `path` has mtime greater than `time`."""
+    # use bfs order to increase likelihood of early return
+    queue: Deque[str] = collections.deque([path])
+
+    if os.stat(path).st_mtime > time:
+        return True
+
+    while queue:
+        current = queue.popleft()
+
+        try:
+            entries = os.scandir(current)
+        except OSError:
+            continue
+
+        with entries:
+            for entry in entries:
+                try:
+                    st = entry.stat(follow_symlinks=False)
+                except OSError:
+                    continue
+
+                if st.st_mtime > time:
+                    return True
+
+                if entry.is_dir(follow_symlinks=False):
+                    queue.append(entry.path)
+
+    return False
 
 
 @system_path_filter
@@ -1740,8 +1762,7 @@ def find(
 
 
 def _log_file_access_issue(e: OSError, path: str) -> None:
-    errno_name = errno.errorcode.get(e.errno, "UNKNOWN")
-    tty.debug(f"find must skip {path}: {errno_name} {e}")
+    tty.debug(f"find must skip {path}: {e}")
 
 
 def _file_id(s: os.stat_result) -> Tuple[int, int]:
@@ -2435,26 +2456,69 @@ class WindowsSimulatedRPath:
     and vis versa.
     """
 
-    def __init__(self, package, link_install_prefix=True):
+    def __init__(
+        self,
+        package,
+        base_modification_prefix: Optional[Union[str, pathlib.Path]] = None,
+        link_install_prefix: bool = True,
+    ):
         """
         Args:
             package (spack.package_base.PackageBase): Package requiring links
+            base_modification_prefix (str|pathlib.Path): Path representation indicating
+                the root directory in which to establish the simulated rpath, ie where the
+                symlinks that comprise the "rpath" behavior will be installed.
+
+                Note: This is a mutually exclusive option with `link_install_prefix` using
+                both is an error.
+
+                Default: None
             link_install_prefix (bool): Link against package's own install or stage root.
                 Packages that run their own executables during build and require rpaths to
-                the build directory during build time require this option. Default: install
+                the build directory during build time require this option.
+
+                Default: install
                 root
+
+                Note: This is a mutually exclusive option with `base_modification_prefix`, using
+                both is an error.
         """
         self.pkg = package
-        self._addl_rpaths = set()
+        self._addl_rpaths: set[str] = set()
+        if link_install_prefix and base_modification_prefix:
+            raise RuntimeError(
+                "Invalid combination of arguments given to WindowsSimulated RPath.\n"
+                "Select either `link_install_prefix` to create an install prefix rpath"
+                " or specify a `base_modification_prefix` for any other link type. "
+                "Specifying both arguments is invalid."
+            )
+        if not (link_install_prefix or base_modification_prefix):
+            raise RuntimeError(
+                "Insufficient arguments given to WindowsSimulatedRpath.\n"
+                "WindowsSimulatedRPath requires one of link_install_prefix"
+                " or base_modification_prefix to be specified."
+                " Neither was provided."
+            )
+
         self.link_install_prefix = link_install_prefix
-        self._additional_library_dependents = set()
+        if base_modification_prefix:
+            self.base_modification_prefix = pathlib.Path(base_modification_prefix)
+        else:
+            self.base_modification_prefix = pathlib.Path(self.pkg.prefix)
+        self._additional_library_dependents: set[pathlib.Path] = set()
+        if not self.link_install_prefix:
+            tty.debug(f"Generating rpath for non install context: {base_modification_prefix}")
 
     @property
     def library_dependents(self):
         """
         Set of directories where package binaries/libraries are located.
         """
-        return set([pathlib.Path(self.pkg.prefix.bin)]) | self._additional_library_dependents
+        base_pths = set()
+        if self.link_install_prefix:
+            base_pths.add(pathlib.Path(self.pkg.prefix.bin))
+        base_pths |= self._additional_library_dependents
+        return base_pths
 
     def add_library_dependent(self, *dest):
         """
@@ -2470,6 +2534,12 @@ def add_library_dependent(self, *dest):
                 new_pth = pathlib.Path(pth).parent
             else:
                 new_pth = pathlib.Path(pth)
+            path_is_in_prefix = new_pth.is_relative_to(self.base_modification_prefix)
+            if not path_is_in_prefix:
+                raise RuntimeError(
+                    f"Attempting to generate rpath symlink out of rpath context:\
+{str(self.base_modification_prefix)}"
+                )
             self._additional_library_dependents.add(new_pth)
 
     @property
@@ -2558,6 +2628,33 @@ def establish_link(self):
                 self._link(library, lib_dir)
 
 
+def make_package_test_rpath(pkg, test_dir: Union[str, pathlib.Path]):
+    """Establishes a temp Windows simulated rpath for the pkg in the testing directory
+    so an executable can test the libraries/executables with proper access
+    to dependent dlls
+
+    Note: this is a no-op on all other platforms besides Windows
+
+    Args:
+        pkg (spack.package_base.PackageBase): the package for which the rpath should be computed
+        test_dir: the testing directory in which we should construct an rpath
+    """
+    # link_install_prefix as false ensures we're not linking into the install prefix
+    mini_rpath = WindowsSimulatedRPath(pkg, link_install_prefix=False)
+    # add the testing directory as a location to install rpath symlinks
+    mini_rpath.add_library_dependent(test_dir)
+
+    # check for whether build_directory is available, if not
+    # assume the stage root is the build dir
+    build_dir_attr = getattr(pkg, "build_directory", None)
+    build_directory = build_dir_attr if build_dir_attr else pkg.stage.path
+    # add the build dir & build dir bin
+    mini_rpath.add_rpath(os.path.join(build_directory, "bin"))
+    mini_rpath.add_rpath(os.path.join(build_directory))
+    # construct rpath
+    mini_rpath.establish_link()
+
+
 @system_path_filter
 @memoized
 def can_access_dir(path):
@@ -2786,6 +2883,20 @@ def keep_modification_time(*filenames):
             os.utime(f, (os.path.getatime(f), mtime))
 
 
+@contextmanager
+def temporary_file_position(stream):
+    orig_pos = stream.tell()
+    yield
+    stream.seek(orig_pos)
+
+
+@contextmanager
+def current_file_position(stream: IO[str], loc: int, relative_to=io.SEEK_CUR):
+    with temporary_file_position(stream):
+        stream.seek(loc, relative_to)
+        yield
+
+
 @contextmanager
 def temporary_dir(
     suffix: Optional[str] = None, prefix: Optional[str] = None, dir: Optional[str] = None

lib/spack/llnl/util/lang.py

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

lib/spack/llnl/util/link_tree.py

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

lib/spack/llnl/util/lock.py

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

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

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

lib/spack/spack/__init__.py

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

lib/spack/spack/audit.py

@@ -1010,7 +1010,7 @@ def _issues_in_depends_on_directive(pkgs, error_cls):
             for dep_name, dep in deps_by_name.items():
 
                 def check_virtual_with_variants(spec, msg):
-                    if not spec.virtual or not spec.variants:
+                    if not spack.repo.PATH.is_virtual(spec.name) or not spec.variants:
                         return
                     error = error_cls(
                         f"{pkg_name}: {msg}",
@@ -1356,14 +1356,8 @@ def _test_detection_by_executable(pkgs, debug_log, error_cls):
 
             def _compare_extra_attribute(_expected, _detected, *, _spec):
                 result = []
-                # Check items are of the same type
-                if not isinstance(_detected, type(_expected)):
-                    _summary = f'{pkg_name}: error when trying to detect "{_expected}"'
-                    _details = [f"{_detected} was detected instead"]
-                    return [error_cls(summary=_summary, details=_details)]
-
                 # If they are string expected is a regex
-                if isinstance(_expected, str):
+                if isinstance(_expected, str) and isinstance(_detected, str):
                     try:
                         _regex = re.compile(_expected)
                     except re.error:
@@ -1379,7 +1373,7 @@ def _compare_extra_attribute(_expected, _detected, *, _spec):
                         _details = [f"{_detected} does not match the regex"]
                         return [error_cls(summary=_summary, details=_details)]
 
-                if isinstance(_expected, dict):
+                elif isinstance(_expected, dict) and isinstance(_detected, dict):
                     _not_detected = set(_expected.keys()) - set(_detected.keys())
                     if _not_detected:
                         _summary = f"{pkg_name}: cannot detect some attributes for spec {_spec}"
@@ -1394,6 +1388,10 @@ def _compare_extra_attribute(_expected, _detected, *, _spec):
                         result.extend(
                             _compare_extra_attribute(_expected[_key], _detected[_key], _spec=_spec)
                         )
+                else:
+                    _summary = f'{pkg_name}: error when trying to detect "{_expected}"'
+                    _details = [f"{_detected} was detected instead"]
+                    return [error_cls(summary=_summary, details=_details)]
 
                 return result
 

lib/spack/spack/binary_distribution.py

@@ -5,6 +5,7 @@
 import codecs
 import collections
 import concurrent.futures
+import contextlib
 import copy
 import hashlib
 import io
@@ -23,7 +24,7 @@
 import urllib.request
 import warnings
 from contextlib import closing
-from typing import IO, Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
+from typing import IO, Callable, Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
 
 import llnl.util.filesystem as fsys
 import llnl.util.lang
@@ -91,6 +92,9 @@
 CURRENT_BUILD_CACHE_LAYOUT_VERSION = 2
 
 
+INDEX_HASH_FILE = "index.json.hash"
+
+
 class BuildCacheDatabase(spack_db.Database):
     """A database for binary buildcaches.
 
@@ -502,7 +506,7 @@ def _fetch_and_cache_index(self, mirror_url, cache_entry={}):
         scheme = urllib.parse.urlparse(mirror_url).scheme
 
         if scheme != "oci" and not web_util.url_exists(
-            url_util.join(mirror_url, BUILD_CACHE_RELATIVE_PATH, "index.json")
+            url_util.join(mirror_url, BUILD_CACHE_RELATIVE_PATH, spack_db.INDEX_JSON_FILE)
         ):
             return False
 
@@ -591,32 +595,18 @@ def file_matches(f: IO[bytes], regex: llnl.util.lang.PatternBytes) -> bool:
         f.seek(0)
 
 
-def deps_to_relocate(spec):
-    """Return the transitive link and direct run dependencies of the spec.
-
-    This is a special traversal for dependencies we need to consider when relocating a package.
-
-    Package binaries, scripts, and other files may refer to the prefixes of  dependencies, so
-    we need to rewrite those locations when dependencies are in a different place at install time
-    than they were at build time.
-
-    This traversal covers transitive link dependencies and direct run dependencies because:
-
-    1. Spack adds RPATHs for transitive link dependencies so that packages can find needed
-       dependency libraries.
-    2. Packages may call any of their *direct* run dependencies (and may bake their paths into
-       binaries or scripts), so we also need to search for run dependency prefixes when relocating.
-
-    This returns a deduplicated list of transitive link dependencies and direct run dependencies.
-    """
-    deps = [
+def specs_to_relocate(spec: spack.spec.Spec) -> List[spack.spec.Spec]:
+    """Return the set of specs that may be referenced in the install prefix of the provided spec.
+    We currently include non-external transitive link and direct run dependencies."""
+    specs = [
         s
         for s in itertools.chain(
-            spec.traverse(root=True, deptype="link"), spec.dependencies(deptype="run")
+            spec.traverse(root=True, deptype="link", order="breadth", key=traverse.by_dag_hash),
+            spec.dependencies(deptype="run"),
         )
         if not s.external
     ]
-    return llnl.util.lang.dedupe(deps, key=lambda s: s.dag_hash())
+    return list(llnl.util.lang.dedupe(specs, key=lambda s: s.dag_hash()))
 
 
 def get_buildinfo_dict(spec):
@@ -630,7 +620,7 @@ def get_buildinfo_dict(spec):
         # "relocate_binaries": [],
         # "relocate_links": [],
         "hardlinks_deduped": True,
-        "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in deps_to_relocate(spec)},
+        "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in specs_to_relocate(spec)},
     }
 
 
@@ -683,19 +673,24 @@ def sign_specfile(key: str, specfile_path: str) -> str:
 
 
 def _read_specs_and_push_index(
-    file_list, read_method, cache_prefix, db: BuildCacheDatabase, temp_dir, concurrency
+    file_list: List[str],
+    read_method: Callable,
+    cache_prefix: str,
+    db: BuildCacheDatabase,
+    temp_dir: str,
+    concurrency: int,
 ):
     """Read all the specs listed in the provided list, using thread given thread parallelism,
         generate the index, and push it to the mirror.
 
     Args:
-        file_list (list(str)): List of urls or file paths pointing at spec files to read
+        file_list: List of urls or file paths pointing at spec files to read
         read_method: A function taking a single argument, either a url or a file path,
             and which reads the spec file at that location, and returns the spec.
-        cache_prefix (str): prefix of the build cache on s3 where index should be pushed.
+        cache_prefix: prefix of the build cache on s3 where index should be pushed.
         db: A spack database used for adding specs and then writing the index.
-        temp_dir (str): Location to write index.json and hash for pushing
-        concurrency (int): Number of parallel processes to use when fetching
+        temp_dir: Location to write index.json and hash for pushing
+        concurrency: Number of parallel processes to use when fetching
     """
     for file in file_list:
         contents = read_method(file)
@@ -713,7 +708,7 @@ def _read_specs_and_push_index(
 
     # Now generate the index, compute its hash, and push the two files to
     # the mirror.
-    index_json_path = os.path.join(temp_dir, "index.json")
+    index_json_path = os.path.join(temp_dir, spack_db.INDEX_JSON_FILE)
     with open(index_json_path, "w", encoding="utf-8") as f:
         db._write_to_file(f)
 
@@ -723,14 +718,14 @@ def _read_specs_and_push_index(
         index_hash = compute_hash(index_string)
 
     # Write the hash out to a local file
-    index_hash_path = os.path.join(temp_dir, "index.json.hash")
+    index_hash_path = os.path.join(temp_dir, INDEX_HASH_FILE)
     with open(index_hash_path, "w", encoding="utf-8") as f:
         f.write(index_hash)
 
     # Push the index itself
     web_util.push_to_url(
         index_json_path,
-        url_util.join(cache_prefix, "index.json"),
+        url_util.join(cache_prefix, spack_db.INDEX_JSON_FILE),
         keep_original=False,
         extra_args={"ContentType": "application/json", "CacheControl": "no-cache"},
     )
@@ -738,7 +733,7 @@ def _read_specs_and_push_index(
     # Push the hash
     web_util.push_to_url(
         index_hash_path,
-        url_util.join(cache_prefix, "index.json.hash"),
+        url_util.join(cache_prefix, INDEX_HASH_FILE),
         keep_original=False,
         extra_args={"ContentType": "text/plain", "CacheControl": "no-cache"},
     )
@@ -807,7 +802,7 @@ def url_read_method(url):
         try:
             _, _, spec_file = web_util.read_from_url(url)
             contents = codecs.getreader("utf-8")(spec_file).read()
-        except web_util.SpackWebError as e:
+        except (web_util.SpackWebError, OSError) as e:
             tty.error(f"Error reading specfile: {url}: {e}")
         return contents
 
@@ -875,9 +870,12 @@ def _url_generate_package_index(url: str, tmpdir: str, concurrency: int = 32):
     tty.debug(f"Retrieving spec descriptor files from {url} to build index")
 
     db = BuildCacheDatabase(tmpdir)
+    db._write()
 
     try:
-        _read_specs_and_push_index(file_list, read_fn, url, db, db.database_directory, concurrency)
+        _read_specs_and_push_index(
+            file_list, read_fn, url, db, str(db.database_directory), concurrency
+        )
     except Exception as e:
         raise GenerateIndexError(f"Encountered problem pushing package index to {url}: {e}") from e
 
@@ -925,7 +923,7 @@ class FileTypes:
     UNKNOWN = 2
 
 
-NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7F-\x9F]")
+NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7f-\x9f]")
 
 
 def file_type(f: IO[bytes]) -> int:
@@ -1112,7 +1110,7 @@ def _exists_in_buildcache(spec: spack.spec.Spec, tmpdir: str, out_url: str) -> E
 
 
 def prefixes_to_relocate(spec):
-    prefixes = [s.prefix for s in deps_to_relocate(spec)]
+    prefixes = [s.prefix for s in specs_to_relocate(spec)]
     prefixes.append(spack.hooks.sbang.sbang_install_path())
     prefixes.append(str(spack.store.STORE.layout.root))
     return prefixes
@@ -1791,7 +1789,7 @@ def _oci_update_index(
         db.mark(spec, "in_buildcache", True)
 
     # Create the index.json file
-    index_json_path = os.path.join(tmpdir, "index.json")
+    index_json_path = os.path.join(tmpdir, spack_db.INDEX_JSON_FILE)
     with open(index_json_path, "w", encoding="utf-8") as f:
         db._write_to_file(f)
 
@@ -2012,7 +2010,7 @@ def fetch_url_to_mirror(url):
 
                 # Download the config = spec.json and the relevant tarball
                 try:
-                    manifest = json.loads(response.read())
+                    manifest = json.load(response)
                     spec_digest = spack.oci.image.Digest.from_string(manifest["config"]["digest"])
                     tarball_digest = spack.oci.image.Digest.from_string(
                         manifest["layers"][-1]["digest"]
@@ -2139,10 +2137,9 @@ def fetch_url_to_mirror(url):
 
 
 def dedupe_hardlinks_if_necessary(root, buildinfo):
-    """Updates a buildinfo dict for old archives that did
-    not dedupe hardlinks. De-duping hardlinks is necessary
-    when relocating files in parallel and in-place. This
-    means we must preserve inodes when relocating."""
+    """Updates a buildinfo dict for old archives that did not dedupe hardlinks. De-duping hardlinks
+    is necessary when relocating files in parallel and in-place. This means we must preserve inodes
+    when relocating."""
 
     # New archives don't need this.
     if buildinfo.get("hardlinks_deduped", False):
@@ -2171,65 +2168,48 @@ def dedupe_hardlinks_if_necessary(root, buildinfo):
         buildinfo[key] = new_list
 
 
-def relocate_package(spec):
-    """
-    Relocate the given package
-    """
-    workdir = str(spec.prefix)
-    buildinfo = read_buildinfo_file(workdir)
-    new_layout_root = str(spack.store.STORE.layout.root)
-    new_prefix = str(spec.prefix)
-    new_rel_prefix = str(os.path.relpath(new_prefix, new_layout_root))
-    new_spack_prefix = str(spack.paths.prefix)
-
-    old_sbang_install_path = None
-    if "sbang_install_path" in buildinfo:
-        old_sbang_install_path = str(buildinfo["sbang_install_path"])
+def relocate_package(spec: spack.spec.Spec) -> None:
+    """Relocate binaries and text files in the given spec prefix, based on its buildinfo file."""
+    spec_prefix = str(spec.prefix)
+    buildinfo = read_buildinfo_file(spec_prefix)
     old_layout_root = str(buildinfo["buildpath"])
-    old_spack_prefix = str(buildinfo.get("spackprefix"))
-    old_rel_prefix = buildinfo.get("relative_prefix")
-    old_prefix = os.path.join(old_layout_root, old_rel_prefix)
-    rel = buildinfo.get("relative_rpaths", False)
 
-    # In the past prefix_to_hash was the default and externals were not dropped, so prefixes
-    # were not unique.
+    # Warn about old style tarballs created with the --rel flag (removed in Spack v0.20)
+    if buildinfo.get("relative_rpaths", False):
+        tty.warn(
+            f"Tarball for {spec} uses relative rpaths, which can cause library loading issues."
+        )
+
+    # In Spack 0.19 and older prefix_to_hash was the default and externals were not dropped, so
+    # prefixes were not unique.
     if "hash_to_prefix" in buildinfo:
         hash_to_old_prefix = buildinfo["hash_to_prefix"]
     elif "prefix_to_hash" in buildinfo:
-        hash_to_old_prefix = dict((v, k) for (k, v) in buildinfo["prefix_to_hash"].items())
+        hash_to_old_prefix = {v: k for (k, v) in buildinfo["prefix_to_hash"].items()}
     else:
-        hash_to_old_prefix = dict()
+        raise NewLayoutException(
+            "Package tarball was created from an install prefix with a different directory layout "
+            "and an older buildcache create implementation. It cannot be relocated."
+        )
 
-    if old_rel_prefix != new_rel_prefix and not hash_to_old_prefix:
-        msg = "Package tarball was created from an install "
-        msg += "prefix with a different directory layout and an older "
-        msg += "buildcache create implementation. It cannot be relocated."
-        raise NewLayoutException(msg)
+    prefix_to_prefix: Dict[str, str] = {}
 
-    # Spurious replacements (e.g. sbang) will cause issues with binaries
-    # For example, the new sbang can be longer than the old one.
-    # Hence 2 dictionaries are maintained here.
-    prefix_to_prefix_text = collections.OrderedDict()
-    prefix_to_prefix_bin = collections.OrderedDict()
+    if "sbang_install_path" in buildinfo:
+        old_sbang_install_path = str(buildinfo["sbang_install_path"])
+        prefix_to_prefix[old_sbang_install_path] = spack.hooks.sbang.sbang_install_path()
 
-    if old_sbang_install_path:
-        install_path = spack.hooks.sbang.sbang_install_path()
-        prefix_to_prefix_text[old_sbang_install_path] = install_path
+    # First match specific prefix paths. Possibly the *local* install prefix of some dependency is
+    # in an upstream, so we cannot assume the original spack store root can be mapped uniformly to
+    # the new spack store root.
 
-    # First match specific prefix paths. Possibly the *local* install prefix
-    # of some dependency is in an upstream, so we cannot assume the original
-    # spack store root can be mapped uniformly to the new spack store root.
-    #
-    # If the spec is spliced, we need to handle the simultaneous mapping
-    # from the old install_tree to the new install_tree and from the build_spec
-    # to the spliced spec.
-    # Because foo.build_spec is foo for any non-spliced spec, we can simplify
-    # by checking for spliced-in nodes by checking for nodes not in the build_spec
-    # without any explicit check for whether the spec is spliced.
-    # An analog in this algorithm is any spec that shares a name or provides the same virtuals
-    # in the context of the relevant root spec. This ensures that the analog for a spec s
-    # is the spec that s replaced when we spliced.
-    relocation_specs = deps_to_relocate(spec)
+    # If the spec is spliced, we need to handle the simultaneous mapping from the old install_tree
+    # to the new install_tree and from the build_spec to the spliced spec. Because foo.build_spec
+    # is foo for any non-spliced spec, we can simplify by checking for spliced-in nodes by checking
+    # for nodes not in the build_spec without any explicit check for whether the spec is spliced.
+    # An analog in this algorithm is any spec that shares a name or provides the same virtuals in
+    # the context of the relevant root spec. This ensures that the analog for a spec s is the spec
+    # that s replaced when we spliced.
+    relocation_specs = specs_to_relocate(spec)
     build_spec_ids = set(id(s) for s in spec.build_spec.traverse(deptype=dt.ALL & ~dt.BUILD))
     for s in relocation_specs:
         analog = s
@@ -2248,98 +2228,66 @@ def relocate_package(spec):
         lookup_dag_hash = analog.dag_hash()
         if lookup_dag_hash in hash_to_old_prefix:
             old_dep_prefix = hash_to_old_prefix[lookup_dag_hash]
-            prefix_to_prefix_bin[old_dep_prefix] = str(s.prefix)
-            prefix_to_prefix_text[old_dep_prefix] = str(s.prefix)
+            prefix_to_prefix[old_dep_prefix] = str(s.prefix)
 
     # Only then add the generic fallback of install prefix -> install prefix.
-    prefix_to_prefix_text[old_prefix] = new_prefix
-    prefix_to_prefix_bin[old_prefix] = new_prefix
-    prefix_to_prefix_text[old_layout_root] = new_layout_root
-    prefix_to_prefix_bin[old_layout_root] = new_layout_root
+    prefix_to_prefix[old_layout_root] = str(spack.store.STORE.layout.root)
 
-    # This is vestigial code for the *old* location of sbang. Previously,
-    # sbang was a bash script, and it lived in the spack prefix. It is
-    # now a POSIX script that lives in the install prefix. Old packages
-    # will have the old sbang location in their shebangs.
-    orig_sbang = "#!/bin/bash {0}/bin/sbang".format(old_spack_prefix)
-    new_sbang = spack.hooks.sbang.sbang_shebang_line()
-    prefix_to_prefix_text[orig_sbang] = new_sbang
+    # Delete identity mappings from prefix_to_prefix
+    prefix_to_prefix = {k: v for k, v in prefix_to_prefix.items() if k != v}
 
-    tty.debug("Relocating package from", "%s to %s." % (old_layout_root, new_layout_root))
+    # If there's nothing to relocate, we're done.
+    if not prefix_to_prefix:
+        return
 
-    # Old archives maybe have hardlinks repeated.
-    dedupe_hardlinks_if_necessary(workdir, buildinfo)
+    for old, new in prefix_to_prefix.items():
+        tty.debug(f"Relocating: {old} => {new}.")
 
-    def is_backup_file(file):
-        return file.endswith("~")
+    # Old archives may have hardlinks repeated.
+    dedupe_hardlinks_if_necessary(spec_prefix, buildinfo)
 
     # Text files containing the prefix text
-    text_names = list()
-    for filename in buildinfo["relocate_textfiles"]:
-        text_name = os.path.join(workdir, filename)
-        # Don't add backup files generated by filter_file during install step.
-        if not is_backup_file(text_name):
-            text_names.append(text_name)
+    textfiles = [os.path.join(spec_prefix, f) for f in buildinfo["relocate_textfiles"]]
+    binaries = [os.path.join(spec_prefix, f) for f in buildinfo.get("relocate_binaries")]
+    links = [os.path.join(spec_prefix, f) for f in buildinfo.get("relocate_links", [])]
 
-    # If we are not installing back to the same install tree do the relocation
-    if old_prefix != new_prefix:
-        files_to_relocate = [
-            os.path.join(workdir, filename) for filename in buildinfo.get("relocate_binaries")
-        ]
-        # If the buildcache was not created with relativized rpaths
-        # do the relocation of path in binaries
-        platform = spack.platforms.by_name(spec.platform)
-        if "macho" in platform.binary_formats:
-            relocate.relocate_macho_binaries(
-                files_to_relocate,
-                old_layout_root,
-                new_layout_root,
-                prefix_to_prefix_bin,
-                rel,
-                old_prefix,
-                new_prefix,
-            )
-        elif "elf" in platform.binary_formats and not rel:
-            # The new ELF dynamic section relocation logic only handles absolute to
-            # absolute relocation.
-            relocate.new_relocate_elf_binaries(files_to_relocate, prefix_to_prefix_bin)
-        elif "elf" in platform.binary_formats and rel:
-            relocate.relocate_elf_binaries(
-                files_to_relocate,
-                old_layout_root,
-                new_layout_root,
-                prefix_to_prefix_bin,
-                rel,
-                old_prefix,
-                new_prefix,
-            )
+    platform = spack.platforms.by_name(spec.platform)
+    if "macho" in platform.binary_formats:
+        relocate.relocate_macho_binaries(binaries, prefix_to_prefix)
+    elif "elf" in platform.binary_formats:
+        relocate.relocate_elf_binaries(binaries, prefix_to_prefix)
 
-        # Relocate links to the new install prefix
-        links = [os.path.join(workdir, f) for f in buildinfo.get("relocate_links", [])]
-        relocate.relocate_links(links, prefix_to_prefix_bin)
+    relocate.relocate_links(links, prefix_to_prefix)
+    relocate.relocate_text(textfiles, prefix_to_prefix)
+    changed_files = relocate.relocate_text_bin(binaries, prefix_to_prefix)
 
-        # For all buildcaches
-        # relocate the install prefixes in text files including dependencies
-        relocate.relocate_text(text_names, prefix_to_prefix_text)
+    # Add ad-hoc signatures to patched macho files when on macOS.
+    if "macho" in platform.binary_formats and sys.platform == "darwin":
+        codesign = which("codesign")
+        if not codesign:
+            return
+        for binary in changed_files:
+            # preserve the original inode by running codesign on a copy
+            with fsys.edit_in_place_through_temporary_file(binary) as tmp_binary:
+                codesign("-fs-", tmp_binary)
 
-        # relocate the install prefixes in binary files including dependencies
-        changed_files = relocate.relocate_text_bin(files_to_relocate, prefix_to_prefix_bin)
+    install_manifest = os.path.join(
+        spec.prefix,
+        spack.store.STORE.layout.metadata_dir,
+        spack.store.STORE.layout.manifest_file_name,
+    )
+    if not os.path.exists(install_manifest):
+        spec_id = spec.format("{name}/{hash:7}")
+        tty.warn("No manifest file in tarball for spec %s" % spec_id)
 
-        # Add ad-hoc signatures to patched macho files when on macOS.
-        if "macho" in platform.binary_formats and sys.platform == "darwin":
-            codesign = which("codesign")
-            if not codesign:
-                return
-            for binary in changed_files:
-                # preserve the original inode by running codesign on a copy
-                with fsys.edit_in_place_through_temporary_file(binary) as tmp_binary:
-                    codesign("-fs-", tmp_binary)
+    # overwrite old metadata with new
+    if spec.spliced:
+        # rewrite spec on disk
+        spack.store.STORE.layout.write_spec(spec, spack.store.STORE.layout.spec_file_path(spec))
 
-    # If we are installing back to the same location
-    # relocate the sbang location if the spack directory changed
-    else:
-        if old_spack_prefix != new_spack_prefix:
-            relocate.relocate_text(text_names, prefix_to_prefix_text)
+        # de-cache the install manifest
+        with contextlib.suppress(FileNotFoundError):
+            os.unlink(install_manifest)
 
 
 def _extract_inner_tarball(spec, filename, extract_to, signature_required: bool, remote_checksum):
@@ -2507,15 +2455,6 @@ def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
     except Exception as e:
         shutil.rmtree(spec.prefix, ignore_errors=True)
         raise e
-    else:
-        manifest_file = os.path.join(
-            spec.prefix,
-            spack.store.STORE.layout.metadata_dir,
-            spack.store.STORE.layout.manifest_file_name,
-        )
-        if not os.path.exists(manifest_file):
-            spec_id = spec.format("{name}/{hash:7}")
-            tty.warn("No manifest file in tarball for spec %s" % spec_id)
     finally:
         if tmpdir:
             shutil.rmtree(tmpdir, ignore_errors=True)
@@ -2590,10 +2529,10 @@ def install_root_node(
         allow_missing: when true, allows installing a node with missing dependencies
     """
     # Early termination
-    if spec.external or spec.virtual:
-        warnings.warn("Skipping external or virtual package {0}".format(spec.format()))
+    if spec.external or not spec.concrete:
+        warnings.warn("Skipping external or abstract spec {0}".format(spec.format()))
         return
-    elif spec.concrete and spec.installed and not force:
+    elif spec.installed and not force:
         warnings.warn("Package for spec {0} already installed.".format(spec.format()))
         return
 
@@ -2620,10 +2559,6 @@ def install_root_node(
         tty.msg('Installing "{0}" from a buildcache'.format(spec.format()))
         extract_tarball(spec, download_result, force)
         spec.package.windows_establish_runtime_linkage()
-        if spec.spliced:  # overwrite old metadata with new
-            spack.store.STORE.layout.write_spec(
-                spec, spack.store.STORE.layout.spec_file_path(spec)
-            )
         spack.hooks.post_install(spec, False)
         spack.store.STORE.db.add(spec, allow_missing=allow_missing)
 
@@ -2661,11 +2596,14 @@ def try_direct_fetch(spec, mirrors=None):
         )
         try:
             _, _, fs = web_util.read_from_url(buildcache_fetch_url_signed_json)
+            specfile_contents = codecs.getreader("utf-8")(fs).read()
             specfile_is_signed = True
-        except web_util.SpackWebError as e1:
+        except (web_util.SpackWebError, OSError) as e1:
             try:
                 _, _, fs = web_util.read_from_url(buildcache_fetch_url_json)
-            except web_util.SpackWebError as e2:
+                specfile_contents = codecs.getreader("utf-8")(fs).read()
+                specfile_is_signed = False
+            except (web_util.SpackWebError, OSError) as e2:
                 tty.debug(
                     f"Did not find {specfile_name} on {buildcache_fetch_url_signed_json}",
                     e1,
@@ -2675,7 +2613,6 @@ def try_direct_fetch(spec, mirrors=None):
                     f"Did not find {specfile_name} on {buildcache_fetch_url_json}", e2, level=2
                 )
                 continue
-        specfile_contents = codecs.getreader("utf-8")(fs).read()
 
         # read the spec from the build cache file. All specs in build caches
         # are concrete (as they are built) so we need to mark this spec
@@ -2769,8 +2706,9 @@ def get_keys(install=False, trust=False, force=False, mirrors=None):
 
         try:
             _, _, json_file = web_util.read_from_url(keys_index)
-            json_index = sjson.load(codecs.getreader("utf-8")(json_file))
-        except web_util.SpackWebError as url_err:
+            json_index = sjson.load(json_file)
+        except (web_util.SpackWebError, OSError, ValueError) as url_err:
+            # TODO: avoid repeated request
             if web_util.url_exists(keys_index):
                 tty.error(
                     f"Unable to find public keys in {url_util.format(fetch_url)},"
@@ -3017,14 +2955,14 @@ def __init__(self, url, local_hash, urlopen=web_util.urlopen):
 
     def get_remote_hash(self):
         # Failure to fetch index.json.hash is not fatal
-        url_index_hash = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, "index.json.hash")
+        url_index_hash = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, INDEX_HASH_FILE)
         try:
             response = self.urlopen(urllib.request.Request(url_index_hash, headers=self.headers))
-        except (TimeoutError, urllib.error.URLError):
+            remote_hash = response.read(64)
+        except OSError:
             return None
 
         # Validate the hash
-        remote_hash = response.read(64)
         if not re.match(rb"[a-f\d]{64}$", remote_hash):
             return None
         return remote_hash.decode("utf-8")
@@ -3038,17 +2976,17 @@ def conditional_fetch(self) -> FetchIndexResult:
             return FetchIndexResult(etag=None, hash=None, data=None, fresh=True)
 
         # Otherwise, download index.json
-        url_index = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, "index.json")
+        url_index = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, spack_db.INDEX_JSON_FILE)
 
         try:
             response = self.urlopen(urllib.request.Request(url_index, headers=self.headers))
-        except (TimeoutError, urllib.error.URLError) as e:
-            raise FetchIndexError("Could not fetch index from {}".format(url_index), e) from e
+        except OSError as e:
+            raise FetchIndexError(f"Could not fetch index from {url_index}", e) from e
 
         try:
             result = codecs.getreader("utf-8")(response).read()
-        except ValueError as e:
-            raise FetchIndexError("Remote index {} is invalid".format(url_index), e) from e
+        except (ValueError, OSError) as e:
+            raise FetchIndexError(f"Remote index {url_index} is invalid") from e
 
         computed_hash = compute_hash(result)
 
@@ -3082,7 +3020,7 @@ def __init__(self, url, etag, urlopen=web_util.urlopen):
 
     def conditional_fetch(self) -> FetchIndexResult:
         # Just do a conditional fetch immediately
-        url = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, "index.json")
+        url = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, spack_db.INDEX_JSON_FILE)
         headers = {"User-Agent": web_util.SPACK_USER_AGENT, "If-None-Match": f'"{self.etag}"'}
 
         try:
@@ -3092,12 +3030,12 @@ def conditional_fetch(self) -> FetchIndexResult:
                 # Not modified; that means fresh.
                 return FetchIndexResult(etag=None, hash=None, data=None, fresh=True)
             raise FetchIndexError(f"Could not fetch index {url}", e) from e
-        except (TimeoutError, urllib.error.URLError) as e:
+        except OSError as e:  # URLError, socket.timeout, etc.
             raise FetchIndexError(f"Could not fetch index {url}", e) from e
 
         try:
             result = codecs.getreader("utf-8")(response).read()
-        except ValueError as e:
+        except (ValueError, OSError) as e:
             raise FetchIndexError(f"Remote index {url} is invalid", e) from e
 
         headers = response.headers
@@ -3129,11 +3067,11 @@ def conditional_fetch(self) -> FetchIndexResult:
                     headers={"Accept": "application/vnd.oci.image.manifest.v1+json"},
                 )
             )
-        except (TimeoutError, urllib.error.URLError) as e:
+        except OSError as e:
             raise FetchIndexError(f"Could not fetch manifest from {url_manifest}", e) from e
 
         try:
-            manifest = json.loads(response.read())
+            manifest = json.load(response)
         except Exception as e:
             raise FetchIndexError(f"Remote index {url_manifest} is invalid", e) from e
 
@@ -3148,14 +3086,16 @@ def conditional_fetch(self) -> FetchIndexResult:
             return FetchIndexResult(etag=None, hash=None, data=None, fresh=True)
 
         # Otherwise fetch the blob / index.json
-        response = self.urlopen(
-            urllib.request.Request(
-                url=self.ref.blob_url(index_digest),
-                headers={"Accept": "application/vnd.oci.image.layer.v1.tar+gzip"},
+        try:
+            response = self.urlopen(
+                urllib.request.Request(
+                    url=self.ref.blob_url(index_digest),
+                    headers={"Accept": "application/vnd.oci.image.layer.v1.tar+gzip"},
+                )
             )
-        )
-
-        result = codecs.getreader("utf-8")(response).read()
+            result = codecs.getreader("utf-8")(response).read()
+        except (OSError, ValueError) as e:
+            raise FetchIndexError(f"Remote index {url_manifest} is invalid", e) from e
 
         # Make sure the blob we download has the advertised hash
         if compute_hash(result) != index_digest.digest:

lib/spack/spack/bootstrap/_common.py

@@ -5,12 +5,14 @@
 import fnmatch
 import glob
 import importlib
-import os.path
+import os
 import re
 import sys
 import sysconfig
 import warnings
-from typing import Dict, Optional, Sequence, Union
+from typing import Optional, Sequence, Union
+
+from typing_extensions import TypedDict
 
 import archspec.cpu
 
@@ -18,13 +20,17 @@
 from llnl.util import tty
 
 import spack.platforms
+import spack.spec
 import spack.store
 import spack.util.environment
 import spack.util.executable
 
 from .config import spec_for_current_python
 
-QueryInfo = Dict[str, "spack.spec.Spec"]
+
+class QueryInfo(TypedDict, total=False):
+    spec: spack.spec.Spec
+    command: spack.util.executable.Executable
 
 
 def _python_import(module: str) -> bool:
@@ -211,7 +217,9 @@ def _executables_in_store(
             ):
                 spack.util.environment.path_put_first("PATH", [bin_dir])
                 if query_info is not None:
-                    query_info["command"] = spack.util.executable.which(*executables, path=bin_dir)
+                    query_info["command"] = spack.util.executable.which(
+                        *executables, path=bin_dir, required=True
+                    )
                     query_info["spec"] = concrete_spec
                 return True
     return False

lib/spack/spack/bootstrap/clingo.py

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

lib/spack/spack/bootstrap/config.py

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

lib/spack/spack/bootstrap/core.py

@@ -25,7 +25,6 @@
 import functools
 import json
 import os
-import os.path
 import sys
 import uuid
 from typing import Any, Callable, Dict, List, Optional, Tuple
@@ -34,8 +33,10 @@
 from llnl.util.lang import GroupedExceptionHandler
 
 import spack.binary_distribution
+import spack.concretize
 import spack.config
 import spack.detection
+import spack.error
 import spack.mirrors.mirror
 import spack.platforms
 import spack.spec
@@ -44,10 +45,17 @@
 import spack.util.executable
 import spack.util.path
 import spack.util.spack_yaml
+import spack.util.url
 import spack.version
 from spack.installer import PackageInstaller
 
-from ._common import _executables_in_store, _python_import, _root_spec, _try_import_from_store
+from ._common import (
+    QueryInfo,
+    _executables_in_store,
+    _python_import,
+    _root_spec,
+    _try_import_from_store,
+)
 from .clingo import ClingoBootstrapConcretizer
 from .config import spack_python_interpreter, spec_for_current_python
 
@@ -89,8 +97,12 @@ def __init__(self, conf: ConfigDictionary) -> None:
         self.name = conf["name"]
         self.metadata_dir = spack.util.path.canonicalize_path(conf["metadata"])
 
-        # Promote (relative) paths to file urls
-        self.url = spack.mirrors.mirror.Mirror(conf["info"]["url"]).fetch_url
+        # Check for relative paths, and turn them into absolute paths
+        # root is the metadata_dir
+        maybe_url = conf["info"]["url"]
+        if spack.util.url.is_path_instead_of_url(maybe_url) and not os.path.isabs(maybe_url):
+            maybe_url = os.path.join(self.metadata_dir, maybe_url)
+        self.url = spack.mirrors.mirror.Mirror(maybe_url).fetch_url
 
     @property
     def mirror_scope(self) -> spack.config.InternalConfigScope:
@@ -134,7 +146,7 @@ class BuildcacheBootstrapper(Bootstrapper):
 
     def __init__(self, conf) -> None:
         super().__init__(conf)
-        self.last_search: Optional[ConfigDictionary] = None
+        self.last_search: Optional[QueryInfo] = None
         self.config_scope_name = f"bootstrap_buildcache-{uuid.uuid4()}"
 
     @staticmethod
@@ -211,14 +223,14 @@ def _install_and_test(
                 for _, pkg_hash, pkg_sha256 in item["binaries"]:
                     self._install_by_hash(pkg_hash, pkg_sha256, bincache_platform)
 
-                info: ConfigDictionary = {}
+                info: QueryInfo = {}
                 if test_fn(query_spec=abstract_spec, query_info=info):
                     self.last_search = info
                     return True
         return False
 
     def try_import(self, module: str, abstract_spec_str: str) -> bool:
-        info: ConfigDictionary
+        info: QueryInfo
         test_fn, info = functools.partial(_try_import_from_store, module), {}
         if test_fn(query_spec=abstract_spec_str, query_info=info):
             return True
@@ -231,7 +243,7 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
         return self._install_and_test(abstract_spec, bincache_platform, data, test_fn)
 
     def try_search_path(self, executables: Tuple[str], abstract_spec_str: str) -> bool:
-        info: ConfigDictionary
+        info: QueryInfo
         test_fn, info = functools.partial(_executables_in_store, executables), {}
         if test_fn(query_spec=abstract_spec_str, query_info=info):
             self.last_search = info
@@ -249,11 +261,11 @@ class SourceBootstrapper(Bootstrapper):
 
     def __init__(self, conf) -> None:
         super().__init__(conf)
-        self.last_search: Optional[ConfigDictionary] = None
+        self.last_search: Optional[QueryInfo] = None
         self.config_scope_name = f"bootstrap_source-{uuid.uuid4()}"
 
     def try_import(self, module: str, abstract_spec_str: str) -> bool:
-        info: ConfigDictionary = {}
+        info: QueryInfo = {}
         if _try_import_from_store(module, abstract_spec_str, query_info=info):
             self.last_search = info
             return True
@@ -270,17 +282,22 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
                 bootstrapper = ClingoBootstrapConcretizer(configuration=spack.config.CONFIG)
                 concrete_spec = bootstrapper.concretize()
             else:
-                concrete_spec = spack.spec.Spec(
+                abstract_spec = spack.spec.Spec(
                     abstract_spec_str + " ^" + spec_for_current_python()
                 )
-                concrete_spec.concretize()
+                concrete_spec = spack.concretize.concretize_one(abstract_spec)
 
         msg = "[BOOTSTRAP MODULE {0}] Try installing '{1}' from sources"
         tty.debug(msg.format(module, abstract_spec_str))
 
         # Install the spec that should make the module importable
         with spack.config.override(self.mirror_scope):
-            PackageInstaller([concrete_spec.package], fail_fast=True).install()
+            PackageInstaller(
+                [concrete_spec.package],
+                fail_fast=True,
+                package_use_cache=False,
+                dependencies_use_cache=False,
+            ).install()
 
         if _try_import_from_store(module, query_spec=concrete_spec, query_info=info):
             self.last_search = info
@@ -288,7 +305,7 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
         return False
 
     def try_search_path(self, executables: Tuple[str], abstract_spec_str: str) -> bool:
-        info: ConfigDictionary = {}
+        info: QueryInfo = {}
         if _executables_in_store(executables, abstract_spec_str, query_info=info):
             self.last_search = info
             return True
@@ -299,7 +316,7 @@ def try_search_path(self, executables: Tuple[str], abstract_spec_str: str) -> bo
         # might reduce compilation time by a fair amount
         _add_externals_if_missing()
 
-        concrete_spec = spack.spec.Spec(abstract_spec_str).concretized()
+        concrete_spec = spack.concretize.concretize_one(abstract_spec_str)
         msg = "[BOOTSTRAP] Try installing '{0}' from sources"
         tty.debug(msg.format(abstract_spec_str))
         with spack.config.override(self.mirror_scope):
@@ -316,11 +333,9 @@ def create_bootstrapper(conf: ConfigDictionary):
     return _bootstrap_methods[btype](conf)
 
 
-def source_is_enabled_or_raise(conf: ConfigDictionary):
-    """Raise ValueError if the source is not enabled for bootstrapping"""
-    trusted, name = spack.config.get("bootstrap:trusted"), conf["name"]
-    if not trusted.get(name, False):
-        raise ValueError("source is not trusted")
+def source_is_enabled(conf: ConfigDictionary) -> bool:
+    """Returns true if the source is not enabled for bootstrapping"""
+    return spack.config.get("bootstrap:trusted").get(conf["name"], False)
 
 
 def ensure_module_importable_or_raise(module: str, abstract_spec: Optional[str] = None):
@@ -350,24 +365,24 @@ def ensure_module_importable_or_raise(module: str, abstract_spec: Optional[str]
     exception_handler = GroupedExceptionHandler()
 
     for current_config in bootstrapping_sources():
+        if not source_is_enabled(current_config):
+            continue
+
         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):
+            if create_bootstrapper(current_config).try_import(module, abstract_spec):
                 return
 
-    assert exception_handler, (
-        f"expected at least one exception to have been raised at this point: "
-        f"while bootstrapping {module}"
-    )
     msg = f'cannot bootstrap the "{module}" Python module '
     if abstract_spec:
         msg += f'from spec "{abstract_spec}" '
-    if tty.is_debug():
+
+    if not exception_handler:
+        msg += ": no bootstrapping sources are enabled"
+    elif spack.error.debug or spack.error.SHOW_BACKTRACE:
         msg += exception_handler.grouped_message(with_tracebacks=True)
     else:
         msg += exception_handler.grouped_message(with_tracebacks=False)
-        msg += "\nRun `spack --debug ...` for more detailed errors"
+        msg += "\nRun `spack --backtrace ...` for more detailed errors"
     raise ImportError(msg)
 
 
@@ -405,8 +420,9 @@ def ensure_executables_in_path_or_raise(
     exception_handler = GroupedExceptionHandler()
 
     for current_config in bootstrapping_sources():
+        if not source_is_enabled(current_config):
+            continue
         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):
                 # Additional environment variables needed
@@ -414,6 +430,7 @@ def ensure_executables_in_path_or_raise(
                     current_bootstrapper.last_search["spec"],
                     current_bootstrapper.last_search["command"],
                 )
+                assert cmd is not None, "expected an Executable"
                 cmd.add_default_envmod(
                     spack.user_environment.environment_modifications_for_specs(
                         concrete_spec, set_package_py_globals=False
@@ -421,18 +438,17 @@ def ensure_executables_in_path_or_raise(
                 )
                 return cmd
 
-    assert exception_handler, (
-        f"expected at least one exception to have been raised at this point: "
-        f"while bootstrapping {executables_str}"
-    )
     msg = f"cannot bootstrap any of the {executables_str} executables "
     if abstract_spec:
         msg += f'from spec "{abstract_spec}" '
-    if tty.is_debug():
+
+    if not exception_handler:
+        msg += ": no bootstrapping sources are enabled"
+    elif spack.error.debug or spack.error.SHOW_BACKTRACE:
         msg += exception_handler.grouped_message(with_tracebacks=True)
     else:
         msg += exception_handler.grouped_message(with_tracebacks=False)
-        msg += "\nRun `spack --debug ...` for more detailed errors"
+        msg += "\nRun `spack --backtrace ...` for more detailed errors"
     raise RuntimeError(msg)
 
 

lib/spack/spack/bootstrap/status.py

@@ -63,7 +63,6 @@ def _missing(name: str, purpose: str, system_only: bool = True) -> str:
 
 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"),
         "tar": _missing("tar", "required to manage code archives"),
         "gzip": _missing("gzip", "required to compress/decompress code archives"),

lib/spack/spack/build_environment.py

@@ -44,7 +44,19 @@
 from enum import Flag, auto
 from itertools import chain
 from multiprocessing.connection import Connection
-from typing import Callable, Dict, List, Optional, Set, Tuple
+from typing import (
+    Callable,
+    Dict,
+    List,
+    Optional,
+    Sequence,
+    Set,
+    TextIO,
+    Tuple,
+    Type,
+    Union,
+    overload,
+)
 
 import archspec.cpu
 
@@ -146,48 +158,128 @@ def get_effective_jobs(jobs, parallel=True, supports_jobserver=False):
 
 
 class MakeExecutable(Executable):
-    """Special callable executable object for make so the user can specify
-    parallelism options on a per-invocation basis.  Specifying
-    'parallel' to the call will override whatever the package's
-    global setting is, so you can either default to true or false and
-    override particular calls. Specifying 'jobs_env' to a particular
-    call will name an environment variable which will be set to the
-    parallelism level (without affecting the normal invocation with
-    -j).
+    """Special callable executable object for make so the user can specify parallelism options
+    on a per-invocation basis.
     """
 
-    def __init__(self, name, jobs, **kwargs):
-        supports_jobserver = kwargs.pop("supports_jobserver", True)
-        super().__init__(name, **kwargs)
+    def __init__(self, name: str, *, jobs: int, supports_jobserver: bool = True) -> None:
+        super().__init__(name)
         self.supports_jobserver = supports_jobserver
         self.jobs = jobs
 
-    def __call__(self, *args, **kwargs):
-        """parallel, and jobs_env from kwargs are swallowed and used here;
-        remaining arguments are passed through to the superclass.
-        """
-        parallel = kwargs.pop("parallel", True)
-        jobs_env = kwargs.pop("jobs_env", None)
-        jobs_env_supports_jobserver = kwargs.pop("jobs_env_supports_jobserver", False)
+    @overload
+    def __call__(
+        self,
+        *args: str,
+        parallel: bool = ...,
+        jobs_env: Optional[str] = ...,
+        jobs_env_supports_jobserver: bool = ...,
+        fail_on_error: bool = ...,
+        ignore_errors: Union[int, Sequence[int]] = ...,
+        ignore_quotes: Optional[bool] = ...,
+        timeout: Optional[int] = ...,
+        env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
+        extra_env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
+        input: Optional[TextIO] = ...,
+        output: Union[Optional[TextIO], str] = ...,
+        error: Union[Optional[TextIO], str] = ...,
+        _dump_env: Optional[Dict[str, str]] = ...,
+    ) -> None: ...
 
+    @overload
+    def __call__(
+        self,
+        *args: str,
+        parallel: bool = ...,
+        jobs_env: Optional[str] = ...,
+        jobs_env_supports_jobserver: bool = ...,
+        fail_on_error: bool = ...,
+        ignore_errors: Union[int, Sequence[int]] = ...,
+        ignore_quotes: Optional[bool] = ...,
+        timeout: Optional[int] = ...,
+        env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
+        extra_env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
+        input: Optional[TextIO] = ...,
+        output: Union[Type[str], Callable] = ...,
+        error: Union[Optional[TextIO], str, Type[str], Callable] = ...,
+        _dump_env: Optional[Dict[str, str]] = ...,
+    ) -> str: ...
+
+    @overload
+    def __call__(
+        self,
+        *args: str,
+        parallel: bool = ...,
+        jobs_env: Optional[str] = ...,
+        jobs_env_supports_jobserver: bool = ...,
+        fail_on_error: bool = ...,
+        ignore_errors: Union[int, Sequence[int]] = ...,
+        ignore_quotes: Optional[bool] = ...,
+        timeout: Optional[int] = ...,
+        env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
+        extra_env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
+        input: Optional[TextIO] = ...,
+        output: Union[Optional[TextIO], str, Type[str], Callable] = ...,
+        error: Union[Type[str], Callable] = ...,
+        _dump_env: Optional[Dict[str, str]] = ...,
+    ) -> str: ...
+
+    def __call__(
+        self,
+        *args: str,
+        parallel: bool = True,
+        jobs_env: Optional[str] = None,
+        jobs_env_supports_jobserver: bool = False,
+        **kwargs,
+    ) -> Optional[str]:
+        """Runs this "make" executable in a subprocess.
+
+        Args:
+            parallel: if False, parallelism is disabled
+            jobs_env: environment variable that will be set to the current level of parallelism
+            jobs_env_supports_jobserver: whether the jobs env supports a job server
+
+        For all the other **kwargs, refer to the base class.
+        """
         jobs = get_effective_jobs(
             self.jobs, parallel=parallel, supports_jobserver=self.supports_jobserver
         )
         if jobs is not None:
-            args = ("-j{0}".format(jobs),) + args
+            args = (f"-j{jobs}",) + args
 
         if jobs_env:
-            # Caller wants us to set an environment variable to
-            # control the parallelism.
+            # Caller wants us to set an environment variable to control the parallelism
             jobs_env_jobs = get_effective_jobs(
                 self.jobs, parallel=parallel, supports_jobserver=jobs_env_supports_jobserver
             )
             if jobs_env_jobs is not None:
-                kwargs["extra_env"] = {jobs_env: str(jobs_env_jobs)}
+                extra_env = kwargs.setdefault("extra_env", {})
+                extra_env.update({jobs_env: str(jobs_env_jobs)})
 
         return super().__call__(*args, **kwargs)
 
 
+class UndeclaredDependencyError(spack.error.SpackError):
+    """Raised if a dependency is invoking an executable through a module global, without
+    declaring a dependency on it.
+    """
+
+
+class DeprecatedExecutable:
+    def __init__(self, pkg: str, exe: str, exe_pkg: str) -> None:
+        self.pkg = pkg
+        self.exe = exe
+        self.exe_pkg = exe_pkg
+
+    def __call__(self, *args, **kwargs):
+        raise UndeclaredDependencyError(
+            f"{self.pkg} is using {self.exe} without declaring a dependency on {self.exe_pkg}"
+        )
+
+    def add_default_env(self, key: str, value: str):
+        self.__call__()
+
+
 def clean_environment():
     # Stuff in here sanitizes the build environment to eliminate
     # anything the user has set that may interfere. We apply it immediately
@@ -209,11 +301,13 @@ def clean_environment():
     env.unset("CPLUS_INCLUDE_PATH")
     env.unset("OBJC_INCLUDE_PATH")
 
+    # prevent configure scripts from sourcing variables from config site file (AC_SITE_LOAD).
+    env.set("CONFIG_SITE", os.devnull)
     env.unset("CMAKE_PREFIX_PATH")
+
     env.unset("PYTHONPATH")
     env.unset("R_HOME")
     env.unset("R_ENVIRON")
-
     env.unset("LUA_PATH")
     env.unset("LUA_CPATH")
 
@@ -621,10 +715,9 @@ def set_package_py_globals(pkg, context: Context = Context.BUILD):
         module.std_meson_args = spack.build_systems.meson.MesonBuilder.std_args(pkg)
         module.std_pip_args = spack.build_systems.python.PythonPipBuilder.std_args(pkg)
 
-    # TODO: make these build deps that can be installed if not found.
-    module.make = MakeExecutable("make", jobs)
-    module.gmake = MakeExecutable("gmake", jobs)
-    module.ninja = MakeExecutable("ninja", jobs, supports_jobserver=False)
+    module.make = DeprecatedExecutable(pkg.name, "make", "gmake")
+    module.gmake = DeprecatedExecutable(pkg.name, "gmake", "gmake")
+    module.ninja = DeprecatedExecutable(pkg.name, "ninja", "ninja")
     # TODO: johnwparent: add package or builder support to define these build tools
     # for now there is no entrypoint for builders to define these on their
     # own
@@ -788,21 +881,6 @@ def get_rpath_deps(pkg: spack.package_base.PackageBase) -> List[spack.spec.Spec]
     return _get_rpath_deps_from_spec(pkg.spec, pkg.transitive_rpaths)
 
 
-def load_external_modules(pkg):
-    """Traverse a package's spec DAG and load any external modules.
-
-    Traverse a package's dependencies and load any external modules
-    associated with them.
-
-    Args:
-        pkg (spack.package_base.PackageBase): package to load deps for
-    """
-    for dep in list(pkg.spec.traverse()):
-        external_modules = dep.external_modules or []
-        for external_module in external_modules:
-            load_module(external_module)
-
-
 def setup_package(pkg, dirty, context: Context = Context.BUILD):
     """Execute all environment setup routines."""
     if context not in (Context.BUILD, Context.TEST):
@@ -853,7 +931,7 @@ def setup_package(pkg, dirty, context: Context = Context.BUILD):
         for mod in pkg.compiler.modules:
             load_module(mod)
 
-    load_external_modules(pkg)
+    load_external_modules(setup_context)
 
     # Make sure nothing's strange about the Spack environment.
     validate(env_mods, tty.warn)
@@ -1142,6 +1220,21 @@ def _make_runnable(self, dep: spack.spec.Spec, env: EnvironmentModifications):
                 env.prepend_path("PATH", bin_dir)
 
 
+def load_external_modules(context: SetupContext) -> None:
+    """Traverse a package's spec DAG and load any external modules.
+
+    Traverse a package's dependencies and load any external modules
+    associated with them.
+
+    Args:
+        context: A populated SetupContext object
+    """
+    for spec, _ in context.external:
+        external_modules = spec.external_modules or []
+        for external_module in external_modules:
+            load_module(external_module)
+
+
 def _setup_pkg_and_run(
     serialized_pkg: "spack.subprocess_context.PackageInstallContext",
     function: Callable,

lib/spack/spack/build_systems/aspell_dict.py

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

lib/spack/spack/build_systems/autotools.py

@@ -2,7 +2,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
-import os.path
 import stat
 import subprocess
 from typing import Callable, List, Optional, Set, Tuple, Union
@@ -356,6 +355,13 @@ def _do_patch_libtool_configure(self) -> None:
             )
             # Support Libtool 2.4.2 and older:
             x.filter(regex=r'^(\s*test \$p = "-R")(; then\s*)$', repl=r'\1 || test x-l = x"$p"\2')
+            # Configure scripts generated with libtool < 2.5.4 have a faulty test for the
+            # -single_module linker flag. A deprecation warning makes it think the default is
+            # -multi_module, triggering it to use problematic linker flags (such as ld -r). The
+            # linker default is `-single_module` from (ancient) macOS 10.4, so override by setting
+            # `lt_cv_apple_cc_single_mod=yes`. See the fix in libtool commit
+            # 82f7f52123e4e7e50721049f7fa6f9b870e09c9d.
+            x.filter("lt_cv_apple_cc_single_mod=no", "lt_cv_apple_cc_single_mod=yes", string=True)
 
     @spack.phase_callbacks.run_after("configure")
     def _do_patch_libtool(self) -> None:
@@ -527,7 +533,7 @@ def build_directory(self) -> str:
         return build_dir
 
     @spack.phase_callbacks.run_before("autoreconf")
-    def delete_configure_to_force_update(self) -> None:
+    def _delete_configure_to_force_update(self) -> None:
         if self.force_autoreconf:
             fs.force_remove(self.configure_abs_path)
 
@@ -540,7 +546,7 @@ def autoreconf_search_path_args(self) -> List[str]:
         return _autoreconf_search_path_args(self.spec)
 
     @spack.phase_callbacks.run_after("autoreconf")
-    def set_configure_or_die(self) -> None:
+    def _set_configure_or_die(self) -> None:
         """Ensure the presence of a "configure" script, or raise. If the "configure"
         is found, a module level attribute is set.
 
@@ -564,10 +570,7 @@ def configure_args(self) -> List[str]:
         return []
 
     def autoreconf(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Not needed usually, configure should be already there"""
 
@@ -596,10 +599,7 @@ def autoreconf(
             self.pkg.module.autoreconf(*autoreconf_args)
 
     def configure(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Run "configure", with the arguments specified by the builder and an
         appropriately set prefix.
@@ -612,10 +612,7 @@ def configure(
             pkg.module.configure(*options)
 
     def build(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Run "make" on the build targets specified by the builder."""
         # See https://autotools.io/automake/silent.html
@@ -625,10 +622,7 @@ def build(
             pkg.module.make(*params)
 
     def install(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Run "make" on the install targets specified by the builder."""
         with fs.working_dir(self.build_directory):
@@ -825,7 +819,7 @@ def installcheck(self) -> None:
             self.pkg._if_make_target_execute("installcheck")
 
     @spack.phase_callbacks.run_after("install")
-    def remove_libtool_archives(self) -> None:
+    def _remove_libtool_archives(self) -> None:
         """Remove all .la files in prefix sub-folders if the package sets
         ``install_libtool_archives`` to be False.
         """

lib/spack/spack/build_systems/cached_cmake.py

@@ -10,6 +10,9 @@
 import llnl.util.tty as tty
 
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
+from spack.directives import depends_on
 
 from .cmake import CMakeBuilder, CMakePackage
 
@@ -275,17 +278,24 @@ def initconfig_hardware_entries(self):
             entries.append("# ROCm")
             entries.append("#------------------{0}\n".format("-" * 30))
 
-            # Explicitly setting HIP_ROOT_DIR may be a patch that is no longer necessary
-            entries.append(cmake_cache_path("HIP_ROOT_DIR", "{0}".format(spec["hip"].prefix)))
-            llvm_bin = spec["llvm-amdgpu"].prefix.bin
-            llvm_prefix = spec["llvm-amdgpu"].prefix
-            # Some ROCm systems seem to point to /<path>/rocm-<ver>/ and
-            # others point to /<path>/rocm-<ver>/llvm
-            if os.path.basename(os.path.normpath(llvm_prefix)) != "llvm":
-                llvm_bin = os.path.join(llvm_prefix, "llvm/bin/")
-            entries.append(
-                cmake_cache_filepath("CMAKE_HIP_COMPILER", os.path.join(llvm_bin, "clang++"))
-            )
+            if spec.satisfies("^blt@0.7:"):
+                rocm_root = os.path.dirname(spec["llvm-amdgpu"].prefix)
+                entries.append(cmake_cache_path("ROCM_PATH", rocm_root))
+            else:
+                # Explicitly setting HIP_ROOT_DIR may be a patch that is no longer necessary
+                entries.append(cmake_cache_path("HIP_ROOT_DIR", "{0}".format(spec["hip"].prefix)))
+                llvm_bin = spec["llvm-amdgpu"].prefix.bin
+                llvm_prefix = spec["llvm-amdgpu"].prefix
+                # Some ROCm systems seem to point to /<path>/rocm-<ver>/ and
+                # others point to /<path>/rocm-<ver>/llvm
+                if os.path.basename(os.path.normpath(llvm_prefix)) != "llvm":
+                    llvm_bin = os.path.join(llvm_prefix, "llvm/bin/")
+                entries.append(
+                    cmake_cache_filepath(
+                        "CMAKE_HIP_COMPILER", os.path.join(llvm_bin, "amdclang++")
+                    )
+                )
+
             archs = self.spec.variants["amdgpu_target"].value
             if archs[0] != "none":
                 arch_str = ";".join(archs)
@@ -293,12 +303,26 @@ def initconfig_hardware_entries(self):
                 entries.append(cmake_cache_string("AMDGPU_TARGETS", arch_str))
                 entries.append(cmake_cache_string("GPU_TARGETS", arch_str))
 
+            if spec.satisfies("%gcc"):
+                entries.append(
+                    cmake_cache_string(
+                        "CMAKE_HIP_FLAGS", f"--gcc-toolchain={self.pkg.compiler.prefix}"
+                    )
+                )
+
         return entries
 
     def std_initconfig_entries(self):
         cmake_prefix_path_env = os.environ["CMAKE_PREFIX_PATH"]
         cmake_prefix_path = cmake_prefix_path_env.replace(os.pathsep, ";")
-
+        complete_rpath_list = ";".join(
+            [
+                self.pkg.spec.prefix.lib,
+                self.pkg.spec.prefix.lib64,
+                *os.environ.get("SPACK_COMPILER_EXTRA_RPATHS", "").split(":"),
+                *os.environ.get("SPACK_COMPILER_IMPLICIT_RPATHS", "").split(":"),
+            ]
+        )
         return [
             "#------------------{0}".format("-" * 60),
             "# !!!! This is a generated file, edit at own risk !!!!",
@@ -307,6 +331,8 @@ def std_initconfig_entries(self):
             "#------------------{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"),
         ]
 
@@ -314,7 +340,9 @@ def initconfig_package_entries(self):
         """This method is to be overwritten by the package"""
         return []
 
-    def initconfig(self, pkg, spec, prefix):
+    def initconfig(
+        self, pkg: "CachedCMakePackage", spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         cache_entries = (
             self.std_initconfig_entries()
             + self.initconfig_compiler_entries()
@@ -351,6 +379,10 @@ class CachedCMakePackage(CMakePackage):
 
     CMakeBuilder = CachedCMakeBuilder
 
+    # These dependencies are assumed in the builder
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
+
     def flag_handler(self, name, flags):
         if name in ("cflags", "cxxflags", "cppflags", "fflags"):
             return None, None, None  # handled in the cmake cache

lib/spack/spack/build_systems/cargo.py

@@ -7,6 +7,8 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, depends_on
 from spack.multimethod import when
 
@@ -68,6 +70,12 @@ def build_directory(self):
         """Return the directory containing the main Cargo.toml."""
         return self.pkg.stage.source_path
 
+    @property
+    def std_build_args(self):
+        """Standard arguments for ``cargo build`` provided as a property for
+        convenience of package writers."""
+        return ["-j", str(self.pkg.module.make_jobs)]
+
     @property
     def build_args(self):
         """Arguments for ``cargo build``."""
@@ -78,12 +86,21 @@ def check_args(self):
         """Argument for ``cargo test`` during check phase"""
         return []
 
-    def build(self, pkg, spec, prefix):
+    def setup_build_environment(self, env):
+        env.set("CARGO_HOME", self.stage.path)
+
+    def build(
+        self, pkg: CargoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Runs ``cargo install`` in the source directory"""
         with fs.working_dir(self.build_directory):
-            pkg.module.cargo("install", "--root", "out", "--path", ".", *self.build_args)
+            pkg.module.cargo(
+                "install", "--root", "out", "--path", ".", *self.std_build_args, *self.build_args
+            )
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: CargoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Copy build files into package prefix."""
         with fs.working_dir(self.build_directory):
             fs.install_tree("out", prefix)

lib/spack/spack/build_systems/cmake.py

@@ -11,6 +11,7 @@
 from typing import Any, List, Optional, Tuple
 
 import llnl.util.filesystem as fs
+from llnl.util import tty
 from llnl.util.lang import stable_partition
 
 import spack.builder
@@ -454,18 +455,27 @@ def cmake_args(self) -> List[str]:
         return []
 
     def cmake(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: CMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Runs ``cmake`` in the build directory"""
 
-        # skip cmake phase if it is an incremental develop build
-        if spec.is_develop and os.path.isfile(
-            os.path.join(self.build_directory, "CMakeCache.txt")
-        ):
-            return
+        if spec.is_develop:
+            # skip cmake phase if it is an incremental develop build
+
+            # Determine the files that will re-run CMake that are generated from a successful
+            # configure step based on state
+            primary_generator = _extract_primary_generator(self.generator)
+            configure_artifact = "Makefile"
+            if primary_generator == "Ninja":
+                configure_artifact = "ninja.build"
+
+            if os.path.isfile(os.path.join(self.build_directory, configure_artifact)):
+                tty.msg(
+                    "Incremental build criteria satisfied."
+                    "Skipping CMake configure step. To force configuration run"
+                    f" `spack clean {pkg.name}`"
+                )
+                return
 
         options = self.std_cmake_args
         options += self.cmake_args()
@@ -474,10 +484,7 @@ def cmake(
             pkg.module.cmake(*options)
 
     def build(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: CMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Make the build targets"""
         with fs.working_dir(self.build_directory):
@@ -488,10 +495,7 @@ def build(
                 pkg.module.ninja(*self.build_targets)
 
     def install(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: CMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Make the install targets"""
         with fs.working_dir(self.build_directory):

lib/spack/spack/build_systems/cuda.py

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

lib/spack/spack/build_systems/generic.py

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

lib/spack/spack/build_systems/go.py

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

lib/spack/spack/build_systems/lua.py

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

lib/spack/spack/build_systems/makefile.py

@@ -98,29 +98,20 @@ def build_directory(self) -> str:
         return self.pkg.stage.source_path
 
     def edit(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: MakefilePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Edit the Makefile before calling make. The default is a no-op."""
         pass
 
     def build(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: MakefilePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Run "make" on the build targets specified by the builder."""
         with fs.working_dir(self.build_directory):
             pkg.module.make(*self.build_targets)
 
     def install(
-        self,
-        pkg: spack.package_base.PackageBase,
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
+        self, pkg: MakefilePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
     ) -> None:
         """Run "make" on the install targets specified by the builder."""
         with fs.working_dir(self.build_directory):

lib/spack/spack/build_systems/maven.py

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

lib/spack/spack/build_systems/meson.py

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

lib/spack/spack/build_systems/msbuild.py

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

lib/spack/spack/build_systems/nmake.py

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

lib/spack/spack/build_systems/octave.py

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

lib/spack/spack/build_systems/oneapi.py

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

lib/spack/spack/build_systems/perl.py

@@ -10,8 +10,11 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
-from spack.directives import build_system, extends
+import spack.spec
+import spack.util.prefix
+from spack.directives import build_system, depends_on, extends
 from spack.install_test import SkipTest, test_part
+from spack.multimethod import when
 from spack.util.executable import Executable
 
 from ._checks import BuilderWithDefaults, execute_build_time_tests
@@ -28,7 +31,9 @@ class PerlPackage(spack.package_base.PackageBase):
 
     build_system("perl")
 
-    extends("perl", when="build_system=perl")
+    with when("build_system=perl"):
+        extends("perl")
+        depends_on("gmake", type="build")
 
     @property
     @memoized
@@ -146,7 +151,9 @@ def configure_args(self):
         """
         return []
 
-    def configure(self, pkg, spec, prefix):
+    def configure(
+        self, pkg: PerlPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Run Makefile.PL or Build.PL with arguments consisting of
         an appropriate installation base directory followed by the
         list returned by :py:meth:`~.PerlBuilder.configure_args`.
@@ -170,7 +177,9 @@ def fix_shebang(self):
             repl = "#!/usr/bin/env perl"
             filter_file(pattern, repl, "Build", backup=False)
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: PerlPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Builds a Perl package."""
         self.build_executable()
 
@@ -181,6 +190,8 @@ def check(self):
         """Runs built-in tests of a Perl package."""
         self.build_executable("test")
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: PerlPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Installs a Perl package."""
         self.build_executable("install")

lib/spack/spack/build_systems/python.py

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

lib/spack/spack/build_systems/qmake.py

@@ -6,6 +6,8 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
+import spack.spec
+import spack.util.prefix
 from spack.directives import build_system, depends_on
 
 from ._checks import BuilderWithDefaults, execute_build_time_tests
@@ -27,6 +29,7 @@ class QMakePackage(spack.package_base.PackageBase):
     build_system("qmake")
 
     depends_on("qmake", type="build", when="build_system=qmake")
+    depends_on("gmake", type="build")
 
 
 @spack.builder.builder("qmake")
@@ -61,17 +64,23 @@ def qmake_args(self):
         """List of arguments passed to qmake."""
         return []
 
-    def qmake(self, pkg, spec, prefix):
+    def qmake(
+        self, pkg: QMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Run ``qmake`` to configure the project and generate a Makefile."""
         with working_dir(self.build_directory):
             pkg.module.qmake(*self.qmake_args())
 
-    def build(self, pkg, spec, prefix):
+    def build(
+        self, pkg: QMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Make the build targets"""
         with working_dir(self.build_directory):
             pkg.module.make()
 
-    def install(self, pkg, spec, prefix):
+    def install(
+        self, pkg: QMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+    ) -> None:
         """Make the install targets"""
         with working_dir(self.build_directory):
             pkg.module.make("install")

lib/spack/spack/build_systems/r.py

@@ -94,7 +94,7 @@ def list_url(cls):
         if cls.cran:
             return f"https://cloud.r-project.org/src/contrib/Archive/{cls.cran}/"
 
-    @property
-    def git(self):
-        if self.bioc:
-            return f"https://git.bioconductor.org/packages/{self.bioc}"
+    @lang.classproperty
+    def git(cls):
+        if cls.bioc:
+            return f"https://git.bioconductor.org/packages/{cls.bioc}"

lib/spack/spack/build_systems/racket.py

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

lib/spack/spack/build_systems/rocm.py

@@ -140,7 +140,7 @@ class ROCmPackage(PackageBase):
         when="+rocm",
     )
 
-    depends_on("llvm-amdgpu", when="+rocm")
+    depends_on("llvm-amdgpu", type="build", when="+rocm")
     depends_on("hsa-rocr-dev", when="+rocm")
     depends_on("hip +rocm", when="+rocm")
 

lib/spack/spack/build_systems/ruby.py

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

lib/spack/spack/build_systems/scons.py

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

lib/spack/spack/build_systems/sip.py

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

lib/spack/spack/build_systems/waf.py

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

lib/spack/spack/ci/__init__.py

@@ -6,6 +6,7 @@
 import codecs
 import json
 import os
+import pathlib
 import re
 import shutil
 import stat
@@ -14,16 +15,15 @@
 import zipfile
 from collections import namedtuple
 from typing import Callable, Dict, List, Set
-from urllib.error import HTTPError, URLError
-from urllib.request import HTTPHandler, Request, build_opener
+from urllib.request import Request
 
+import llnl.path
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 from llnl.util.tty.color import cescape, colorize
 
 import spack
 import spack.binary_distribution as bindist
-import spack.builder
 import spack.concretize
 import spack.config as cfg
 import spack.environment as ev
@@ -33,6 +33,7 @@
 import spack.paths
 import spack.repo
 import spack.spec
+import spack.store
 import spack.util.git
 import spack.util.gpg as gpg_util
 import spack.util.spack_yaml as syaml
@@ -63,6 +64,8 @@
 
 PushResult = namedtuple("PushResult", "success url")
 
+urlopen = web_util.urlopen  # alias for mocking in tests
+
 
 def get_change_revisions():
     """If this is a git repo get the revisions to use when checking
@@ -82,6 +85,9 @@ def get_stack_changed(env_path, rev1="HEAD^", rev2="HEAD"):
     whether or not the stack was changed.  Returns True if the environment
     manifest changed between the provided revisions (or additionally if the
     `.gitlab-ci.yml` file itself changed).  Returns False otherwise."""
+    # git returns posix paths always, normalize input to be comptaible
+    # with that
+    env_path = llnl.path.convert_to_posix_path(env_path)
     git = spack.util.git.git()
     if git:
         with fs.working_dir(spack.paths.prefix):
@@ -219,7 +225,7 @@ def rebuild_filter(s: spack.spec.Spec) -> RebuildDecision:
 
 def _format_pruning_message(spec: spack.spec.Spec, prune: bool, reasons: List[str]) -> str:
     reason_msg = ", ".join(reasons)
-    spec_fmt = "{name}{@version}{%compiler}{/hash:7}"
+    spec_fmt = "{name}{@version}{/hash:7}{%compiler}"
 
     if not prune:
         status = colorize("@*g{[x]}  ")
@@ -472,12 +478,9 @@ def generate_pipeline(env: ev.Environment, args) -> None:
     # Use all unpruned specs to populate the build group for this set
     cdash_config = cfg.get("cdash")
     if options.cdash_handler and options.cdash_handler.auth_token:
-        try:
-            options.cdash_handler.populate_buildgroup(
-                [options.cdash_handler.build_name(s) for s in pipeline_specs]
-            )
-        except (SpackError, HTTPError, URLError, TimeoutError) as err:
-            tty.warn(f"Problem populating buildgroup: {err}")
+        options.cdash_handler.populate_buildgroup(
+            [options.cdash_handler.build_name(s) for s in pipeline_specs]
+        )
     elif cdash_config:
         # warn only if there was actually a CDash configuration.
         tty.warn("Unable to populate buildgroup without CDash credentials")
@@ -579,22 +582,25 @@ def copy_stage_logs_to_artifacts(job_spec: spack.spec.Spec, job_log_dir: str) ->
     tty.debug(f"job spec: {job_spec}")
 
     try:
-        pkg_cls = spack.repo.PATH.get_pkg_class(job_spec.name)
-        job_pkg = pkg_cls(job_spec)
-        tty.debug(f"job package: {job_pkg}")
-    except AssertionError:
-        msg = f"Cannot copy stage logs: job spec ({job_spec}) must be concrete"
-        tty.error(msg)
+        package_metadata_root = pathlib.Path(spack.store.STORE.layout.metadata_path(job_spec))
+    except spack.error.SpackError as e:
+        tty.error(f"Cannot copy logs: {str(e)}")
         return
 
-    stage_dir = job_pkg.stage.path
-    tty.debug(f"stage dir: {stage_dir}")
-    for file in [
-        job_pkg.log_path,
-        job_pkg.env_mods_path,
-        *spack.builder.create(job_pkg).archive_files,
-    ]:
-        copy_files_to_artifacts(file, job_log_dir)
+    # Get the package's archived files
+    archive_files = []
+    archive_root = package_metadata_root / "archived-files"
+    if archive_root.is_dir():
+        archive_files = [f for f in archive_root.rglob("*") if f.is_file()]
+    else:
+        msg = "Cannot copy package archived files: archived-files must be a directory"
+        tty.warn(msg)
+
+    build_log_zipped = package_metadata_root / "spack-build-out.txt.gz"
+    build_env_mods = package_metadata_root / "spack-build-env.txt"
+
+    for f in [build_log_zipped, build_env_mods, *archive_files]:
+        copy_files_to_artifacts(str(f), job_log_dir)
 
 
 def copy_test_logs_to_artifacts(test_stage, job_test_dir):
@@ -614,7 +620,7 @@ def copy_test_logs_to_artifacts(test_stage, job_test_dir):
     copy_files_to_artifacts(os.path.join(test_stage, "*", "*.txt"), job_test_dir)
 
 
-def download_and_extract_artifacts(url, work_dir):
+def download_and_extract_artifacts(url, work_dir) -> str:
     """Look for gitlab artifacts.zip at the given url, and attempt to download
         and extract the contents into the given work_dir
 
@@ -622,6 +628,10 @@ def download_and_extract_artifacts(url, work_dir):
 
         url (str): Complete url to artifacts.zip file
         work_dir (str): Path to destination where artifacts should be extracted
+
+    Output:
+
+        Artifacts root path relative to the archive root
     """
     tty.msg(f"Fetching artifacts from: {url}")
 
@@ -631,31 +641,33 @@ def download_and_extract_artifacts(url, work_dir):
     if token:
         headers["PRIVATE-TOKEN"] = token
 
-    opener = build_opener(HTTPHandler)
-
-    request = Request(url, headers=headers)
-    request.get_method = lambda: "GET"
-
-    response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
-    response_code = response.getcode()
-
-    if response_code != 200:
-        msg = f"Error response code ({response_code}) in reproduce_ci_job"
-        raise SpackError(msg)
-
+    request = Request(url, headers=headers, method="GET")
     artifacts_zip_path = os.path.join(work_dir, "artifacts.zip")
+    os.makedirs(work_dir, exist_ok=True)
 
-    if not os.path.exists(work_dir):
-        os.makedirs(work_dir)
+    try:
+        response = urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
+        with open(artifacts_zip_path, "wb") as out_file:
+            shutil.copyfileobj(response, out_file)
 
-    with open(artifacts_zip_path, "wb") as out_file:
-        shutil.copyfileobj(response, out_file)
+        with zipfile.ZipFile(artifacts_zip_path) as zip_file:
+            zip_file.extractall(work_dir)
+            # Get the artifact root
+            artifact_root = ""
+            for f in zip_file.filelist:
+                if "spack.lock" in f.filename:
+                    artifact_root = os.path.dirname(os.path.dirname(f.filename))
+                    break
+    except OSError as e:
+        raise SpackError(f"Error fetching artifacts: {e}")
+    finally:
+        try:
+            os.remove(artifacts_zip_path)
+        except FileNotFoundError:
+            # If the file doesn't exist we are already raising
+            pass
 
-    zip_file = zipfile.ZipFile(artifacts_zip_path)
-    zip_file.extractall(work_dir)
-    zip_file.close()
-
-    os.remove(artifacts_zip_path)
+    return artifact_root
 
 
 def get_spack_info():
@@ -769,7 +781,7 @@ def setup_spack_repro_version(repro_dir, checkout_commit, merge_commit=None):
     return True
 
 
-def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
+def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime, use_local_head):
     """Given a url to gitlab artifacts.zip from a failed 'spack ci rebuild' job,
     attempt to setup an environment in which the failure can be reproduced
     locally.  This entails the following:
@@ -783,8 +795,11 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     commands to run to reproduce the build once inside the container.
     """
     work_dir = os.path.realpath(work_dir)
+    if os.path.exists(work_dir) and os.listdir(work_dir):
+        raise SpackError(f"Cannot run reproducer in non-emptry working dir:\n  {work_dir}")
+
     platform_script_ext = "ps1" if IS_WINDOWS else "sh"
-    download_and_extract_artifacts(url, work_dir)
+    artifact_root = download_and_extract_artifacts(url, work_dir)
 
     gpg_path = None
     if gpg_url:
@@ -846,6 +861,9 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     with open(repro_file, encoding="utf-8") as fd:
         repro_details = json.load(fd)
 
+    spec_file = fs.find(work_dir, repro_details["job_spec_json"])[0]
+    reproducer_spec = spack.spec.Spec.from_specfile(spec_file)
+
     repro_dir = os.path.dirname(repro_file)
     rel_repro_dir = repro_dir.replace(work_dir, "").lstrip(os.path.sep)
 
@@ -906,17 +924,20 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     commit_regex = re.compile(r"commit\s+([^\s]+)")
     merge_commit_regex = re.compile(r"Merge\s+([^\s]+)\s+into\s+([^\s]+)")
 
-    # Try the more specific merge commit regex first
-    m = merge_commit_regex.search(spack_info)
-    if m:
-        # This was a merge commit and we captured the parents
-        commit_1 = m.group(1)
-        commit_2 = m.group(2)
+    if use_local_head:
+        commit_1 = "HEAD"
     else:
-        # Not a merge commit, just get the commit sha
-        m = commit_regex.search(spack_info)
+        # Try the more specific merge commit regex first
+        m = merge_commit_regex.search(spack_info)
         if m:
+            # This was a merge commit and we captured the parents
             commit_1 = m.group(1)
+            commit_2 = m.group(2)
+        else:
+            # Not a merge commit, just get the commit sha
+            m = commit_regex.search(spack_info)
+            if m:
+                commit_1 = m.group(1)
 
     setup_result = False
     if commit_1:
@@ -991,6 +1012,8 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
             "entrypoint", entrypoint_script, work_dir, run=False, exit_on_failure=False
         )
 
+        # Attempt to create a unique name for the reproducer container
+        container_suffix = "_" + reproducer_spec.dag_hash() if reproducer_spec else ""
         docker_command = [
             runtime,
             "run",
@@ -998,14 +1021,14 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
             "-t",
             "--rm",
             "--name",
-            "spack_reproducer",
+            f"spack_reproducer{container_suffix}",
             "-v",
             ":".join([work_dir, mounted_workdir, "Z"]),
             "-v",
             ":".join(
                 [
-                    os.path.join(work_dir, "jobs_scratch_dir"),
-                    os.path.join(mount_as_dir, "jobs_scratch_dir"),
+                    os.path.join(work_dir, artifact_root),
+                    os.path.join(mount_as_dir, artifact_root),
                     "Z",
                 ]
             ),

lib/spack/spack/ci/common.py

@@ -1,23 +1,21 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import codecs
 import copy
 import json
 import os
 import re
-import ssl
 import sys
 import time
 from collections import deque
 from enum import Enum
 from typing import Dict, Generator, List, Optional, Set, Tuple
 from urllib.parse import quote, urlencode, urlparse
-from urllib.request import HTTPHandler, HTTPSHandler, Request, build_opener
+from urllib.request import Request
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
-from llnl.util.lang import Singleton, memoized
+from llnl.util.lang import memoized
 
 import spack.binary_distribution as bindist
 import spack.config as cfg
@@ -35,32 +33,11 @@
 from spack.reporters.cdash import SPACK_CDASH_TIMEOUT
 from spack.reporters.cdash import build_stamp as cdash_build_stamp
 
-
-def _urlopen():
-    error_handler = web_util.SpackHTTPDefaultErrorHandler()
-
-    # One opener with HTTPS ssl enabled
-    with_ssl = build_opener(
-        HTTPHandler(), HTTPSHandler(context=web_util.ssl_create_default_context()), error_handler
-    )
-
-    # One opener with HTTPS ssl disabled
-    without_ssl = build_opener(
-        HTTPHandler(), HTTPSHandler(context=ssl._create_unverified_context()), error_handler
-    )
-
-    # And dynamically dispatch based on the config:verify_ssl.
-    def dispatch_open(fullurl, data=None, timeout=None, verify_ssl=True):
-        opener = with_ssl if verify_ssl else without_ssl
-        timeout = timeout or cfg.get("config:connect_timeout", 1)
-        return opener.open(fullurl, data, timeout)
-
-    return dispatch_open
-
-
 IS_WINDOWS = sys.platform == "win32"
 SPACK_RESERVED_TAGS = ["public", "protected", "notary"]
-_dyn_mapping_urlopener = Singleton(_urlopen)
+
+# this exists purely for testing purposes
+_urlopen = web_util.urlopen
 
 
 def copy_files_to_artifacts(src, artifacts_dir):
@@ -279,26 +256,25 @@ def copy_test_results(self, source, dest):
         reports = fs.join_path(source, "*_Test*.xml")
         copy_files_to_artifacts(reports, dest)
 
-    def create_buildgroup(self, opener, headers, url, group_name, group_type):
+    def create_buildgroup(self, headers, url, group_name, group_type):
         data = {"newbuildgroup": group_name, "project": self.project, "type": group_type}
 
         enc_data = json.dumps(data).encode("utf-8")
 
         request = Request(url, data=enc_data, headers=headers)
 
-        response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
-        response_code = response.getcode()
-
-        if response_code not in [200, 201]:
-            msg = f"Creating buildgroup failed (response code = {response_code})"
-            tty.warn(msg)
+        try:
+            response_text = _urlopen(request, timeout=SPACK_CDASH_TIMEOUT).read()
+        except OSError as e:
+            tty.warn(f"Failed to create CDash buildgroup: {e}")
             return None
 
-        response_text = response.read()
-        response_json = json.loads(response_text)
-        build_group_id = response_json["id"]
-
-        return build_group_id
+        try:
+            response_json = json.loads(response_text)
+            return response_json["id"]
+        except (json.JSONDecodeError, KeyError) as e:
+            tty.warn(f"Failed to parse CDash response: {e}")
+            return None
 
     def populate_buildgroup(self, job_names):
         url = f"{self.url}/api/v1/buildgroup.php"
@@ -308,16 +284,11 @@ def populate_buildgroup(self, job_names):
             "Content-Type": "application/json",
         }
 
-        opener = build_opener(HTTPHandler)
-
-        parent_group_id = self.create_buildgroup(opener, headers, url, self.build_group, "Daily")
-        group_id = self.create_buildgroup(
-            opener, headers, url, f"Latest {self.build_group}", "Latest"
-        )
+        parent_group_id = self.create_buildgroup(headers, url, self.build_group, "Daily")
+        group_id = self.create_buildgroup(headers, url, f"Latest {self.build_group}", "Latest")
 
         if not parent_group_id or not group_id:
-            msg = f"Failed to create or retrieve buildgroups for {self.build_group}"
-            tty.warn(msg)
+            tty.warn(f"Failed to create or retrieve buildgroups for {self.build_group}")
             return
 
         data = {
@@ -329,15 +300,12 @@ def populate_buildgroup(self, job_names):
 
         enc_data = json.dumps(data).encode("utf-8")
 
-        request = Request(url, data=enc_data, headers=headers)
-        request.get_method = lambda: "PUT"
+        request = Request(url, data=enc_data, headers=headers, method="PUT")
 
-        response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
-        response_code = response.getcode()
-
-        if response_code != 200:
-            msg = f"Error response code ({response_code}) in populate_buildgroup"
-            tty.warn(msg)
+        try:
+            _urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
+        except OSError as e:
+            tty.warn(f"Failed to populate CDash buildgroup: {e}")
 
     def report_skipped(self, spec: spack.spec.Spec, report_dir: str, reason: Optional[str]):
         """Explicitly report skipping testing of a spec (e.g., it's CI
@@ -735,9 +703,6 @@ def _apply_section(dest, src):
                 for value in header.values():
                     value = os.path.expandvars(value)
 
-                verify_ssl = mapping.get("verify_ssl", spack.config.get("config:verify_ssl", True))
-                timeout = mapping.get("timeout", spack.config.get("config:connect_timeout", 1))
-
                 required = mapping.get("require", [])
                 allowed = mapping.get("allow", [])
                 ignored = mapping.get("ignore", [])
@@ -771,19 +736,15 @@ def job_query(job):
                         endpoint_url._replace(query=query).geturl(), headers=header, method="GET"
                     )
                     try:
-                        response = _dyn_mapping_urlopener(
-                            request, verify_ssl=verify_ssl, timeout=timeout
-                        )
+                        response = _urlopen(request)
+                        config = json.load(response)
                     except Exception as e:
                         # For now just ignore any errors from dynamic mapping and continue
                         # This is still experimental, and failures should not stop CI
                         # from running normally
-                        tty.warn(f"Failed to fetch dynamic mapping for query:\n\t{query}")
-                        tty.warn(f"{e}")
+                        tty.warn(f"Failed to fetch dynamic mapping for query:\n\t{query}: {e}")
                         continue
 
-                    config = json.load(codecs.getreader("utf-8")(response))
-
                     # Strip ignore keys
                     if ignored:
                         for key in ignored:

lib/spack/spack/cmd/__init__.py

@@ -171,7 +171,9 @@ def quote_kvp(string: str) -> str:
 
 
 def parse_specs(
-    args: Union[str, List[str]], concretize: bool = False, tests: bool = False
+    args: Union[str, List[str]],
+    concretize: bool = False,
+    tests: spack.concretize.TestsType = False,
 ) -> List[spack.spec.Spec]:
     """Convenience function for parsing arguments from specs.  Handles common
     exceptions and dies if there are errors.
@@ -183,11 +185,13 @@ def parse_specs(
     if not concretize:
         return specs
 
-    to_concretize = [(s, None) for s in specs]
+    to_concretize: List[spack.concretize.SpecPairInput] = [(s, None) for s in specs]
     return _concretize_spec_pairs(to_concretize, tests=tests)
 
 
-def _concretize_spec_pairs(to_concretize, tests=False):
+def _concretize_spec_pairs(
+    to_concretize: List[spack.concretize.SpecPairInput], tests: spack.concretize.TestsType = False
+) -> List[spack.spec.Spec]:
     """Helper method that concretizes abstract specs from a list of abstract,concrete pairs.
 
     Any spec with a concrete spec associated with it will concretize to that spec. Any spec
@@ -198,7 +202,7 @@ def _concretize_spec_pairs(to_concretize, tests=False):
     # Special case for concretizing a single spec
     if len(to_concretize) == 1:
         abstract, concrete = to_concretize[0]
-        return [concrete or abstract.concretized()]
+        return [concrete or spack.concretize.concretize_one(abstract, tests=tests)]
 
     # Special case if every spec is either concrete or has an abstract hash
     if all(
@@ -250,9 +254,9 @@ def matching_spec_from_env(spec):
     """
     env = ev.active_environment()
     if env:
-        return env.matching_spec(spec) or spec.concretized()
+        return env.matching_spec(spec) or spack.concretize.concretize_one(spec)
     else:
-        return spec.concretized()
+        return spack.concretize.concretize_one(spec)
 
 
 def matching_specs_from_env(specs):
@@ -293,7 +297,7 @@ def disambiguate_spec(
 
 def disambiguate_spec_from_hashes(
     spec: spack.spec.Spec,
-    hashes: List[str],
+    hashes: Optional[List[str]],
     local: bool = False,
     installed: Union[bool, InstallRecordStatus] = True,
     first: bool = False,
@@ -326,7 +330,7 @@ def ensure_single_spec_or_die(spec, matching_specs):
     if len(matching_specs) <= 1:
         return
 
-    format_string = "{name}{@version}{%compiler.name}{@compiler.version}{ arch=architecture}"
+    format_string = "{name}{@version}{ arch=architecture} {%compiler.name}{@compiler.version}"
     args = ["%s matches multiple packages." % spec, "Matching packages:"]
     args += [
         colorize("  @K{%s} " % s.dag_hash(7)) + s.cformat(format_string) for s in matching_specs
@@ -467,12 +471,11 @@ def get_arg(name, default=None):
         nfmt = "{fullname}" if namespaces else "{name}"
         ffmt = ""
         if full_compiler or flags:
-            ffmt += "{%compiler.name}"
+            ffmt += "{compiler_flags} {%compiler.name}"
             if full_compiler:
                 ffmt += "{@compiler.version}"
-            ffmt += " {compiler_flags}"
         vfmt = "{variants}" if variants else ""
-        format_string = nfmt + "{@version}" + ffmt + vfmt
+        format_string = nfmt + "{@version}" + vfmt + ffmt
 
     def fmt(s, depth=0):
         """Formatter function for all output specs"""

lib/spack/spack/cmd/arch.py

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

lib/spack/spack/cmd/bootstrap.py

@@ -1,7 +1,7 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import os.path
+import os
 import shutil
 import sys
 import tempfile
@@ -14,9 +14,9 @@
 import spack.bootstrap
 import spack.bootstrap.config
 import spack.bootstrap.core
+import spack.concretize
 import spack.config
 import spack.mirrors.utils
-import spack.spec
 import spack.stage
 import spack.util.path
 import spack.util.spack_yaml
@@ -397,7 +397,7 @@ def _mirror(args):
         llnl.util.tty.msg(msg.format(spec_str, mirror_dir))
         # Suppress tty from the call below for terser messages
         llnl.util.tty.set_msg_enabled(False)
-        spec = spack.spec.Spec(spec_str).concretized()
+        spec = spack.concretize.concretize_one(spec_str)
         for node in spec.traverse():
             spack.mirrors.utils.create(mirror_dir, [node])
         llnl.util.tty.set_msg_enabled(True)
@@ -436,6 +436,7 @@ def write_metadata(subdir, metadata):
         shutil.copy(spack.util.path.canonicalize_path(GNUPG_JSON), abs_directory)
         shutil.copy(spack.util.path.canonicalize_path(PATCHELF_JSON), abs_directory)
         instructions += cmd.format("local-binaries", rel_directory)
+        instructions += "  % spack buildcache update-index <final-path>/bootstrap_cache\n"
     print(instructions)
 
 

lib/spack/spack/cmd/buildcache.py

@@ -16,6 +16,7 @@
 
 import spack.binary_distribution as bindist
 import spack.cmd
+import spack.concretize
 import spack.config
 import spack.deptypes as dt
 import spack.environment as ev
@@ -554,8 +555,7 @@ def check_fn(args: argparse.Namespace):
         tty.msg("No specs provided, exiting.")
         return
 
-    for spec in specs:
-        spec.concretize()
+    specs = [spack.concretize.concretize_one(s) for s in specs]
 
     # Next see if there are any configured binary mirrors
     configured_mirrors = spack.config.get("mirrors", scope=args.scope)
@@ -623,7 +623,7 @@ def save_specfile_fn(args):
     root = specs[0]
 
     if not root.concrete:
-        root.concretize()
+        root = spack.concretize.concretize_one(root)
 
     save_dependency_specfiles(
         root, args.specfile_dir, dependencies=spack.cmd.parse_specs(args.specs)

lib/spack/spack/cmd/checksum.py

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

lib/spack/spack/cmd/ci.py

@@ -176,6 +176,11 @@ def setup_parser(subparser):
     reproduce.add_argument(
         "-s", "--autostart", help="Run docker reproducer automatically", action="store_true"
     )
+    reproduce.add_argument(
+        "--use-local-head",
+        help="Use the HEAD of the local Spack instead of reproducing a commit",
+        action="store_true",
+    )
     gpg_group = reproduce.add_mutually_exclusive_group(required=False)
     gpg_group.add_argument(
         "--gpg-file", help="Path to public GPG key for validating binary cache installs"
@@ -422,7 +427,7 @@ def ci_rebuild(args):
 
     # Arguments when installing the root from sources
     deps_install_args = install_args + ["--only=dependencies"]
-    root_install_args = install_args + ["--keep-stage", "--only=package"]
+    root_install_args = install_args + ["--only=package"]
 
     if cdash_handler:
         # Add additional arguments to `spack install` for CDash reporting.
@@ -459,8 +464,7 @@ def ci_rebuild(args):
                 job_spec.to_dict(hash=ht.dag_hash),
             )
 
-    # We generated the "spack install ..." command to "--keep-stage", copy
-    # any logs from the staging directory to artifacts now
+    # Copy logs and archived files from the install metadata (.spack) directory to artifacts now
     spack_ci.copy_stage_logs_to_artifacts(job_spec, job_log_dir)
 
     # If the installation succeeded and we're running stand-alone tests for
@@ -608,7 +612,12 @@ def ci_reproduce(args):
         gpg_key_url = None
 
     return spack_ci.reproduce_ci_job(
-        args.job_url, args.working_dir, args.autostart, gpg_key_url, args.runtime
+        args.job_url,
+        args.working_dir,
+        args.autostart,
+        gpg_key_url,
+        args.runtime,
+        args.use_local_head,
     )
 
 

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

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

lib/spack/spack/cmd/config.py

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

lib/spack/spack/cmd/containerize.py

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

lib/spack/spack/cmd/debug.py

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

lib/spack/spack/cmd/dependencies.py

@@ -9,9 +9,9 @@
 
 import spack.cmd
 import spack.environment as ev
-import spack.package_base
 import spack.store
 from spack.cmd.common import arguments
+from spack.solver.input_analysis import create_graph_analyzer
 
 description = "show dependencies of a package"
 section = "basic"
@@ -55,7 +55,7 @@ def dependencies(parser, args):
         env = ev.active_environment()
         spec = spack.cmd.disambiguate_spec(specs[0], env)
 
-        format_string = "{name}{@version}{%compiler}{/hash:7}"
+        format_string = "{name}{@version}{/hash:7}{%compiler}"
         if sys.stdout.isatty():
             tty.msg("Dependencies of %s" % spec.format(format_string, color=True))
         deps = spack.store.STORE.db.installed_relatives(
@@ -68,15 +68,17 @@ def dependencies(parser, args):
 
     else:
         spec = specs[0]
-        dependencies = spack.package_base.possible_dependencies(
+        dependencies, virtuals, _ = create_graph_analyzer().possible_dependencies(
             spec,
             transitive=args.transitive,
             expand_virtuals=args.expand_virtuals,
-            depflag=args.deptype,
+            allowed_deps=args.deptype,
         )
+        if not args.expand_virtuals:
+            dependencies.update(virtuals)
 
         if spec.name in dependencies:
-            del dependencies[spec.name]
+            dependencies.remove(spec.name)
 
         if dependencies:
             colify(sorted(dependencies))

lib/spack/spack/cmd/dependents.py

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

lib/spack/spack/cmd/deprecate.py

@@ -18,6 +18,7 @@
 from llnl.util.symlink import symlink
 
 import spack.cmd
+import spack.concretize
 import spack.environment as ev
 import spack.installer
 import spack.store
@@ -103,7 +104,7 @@ def deprecate(parser, args):
     )
 
     if args.install:
-        deprecator = specs[1].concretized()
+        deprecator = spack.concretize.concretize_one(specs[1])
     else:
         deprecator = spack.cmd.disambiguate_spec(specs[1], env, local=True)
 

lib/spack/spack/cmd/dev_build.py

@@ -10,6 +10,7 @@
 import spack.build_environment
 import spack.cmd
 import spack.cmd.common.arguments
+import spack.concretize
 import spack.config
 import spack.repo
 from spack.cmd.common import arguments
@@ -113,8 +114,8 @@ def dev_build(self, args):
     source_path = os.path.abspath(source_path)
 
     # Forces the build to run out of the source directory.
-    spec.constrain("dev_path=%s" % source_path)
-    spec.concretize()
+    spec.constrain(f'dev_path="{source_path}"')
+    spec = spack.concretize.concretize_one(spec)
 
     if spec.installed:
         tty.error("Already installed in %s" % spec.prefix)

lib/spack/spack/cmd/develop.py

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

lib/spack/spack/cmd/external.py

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

lib/spack/spack/cmd/help.py

@@ -54,10 +54,6 @@
       @m{target=target}                 specific <target> processor
       @m{arch=platform-os-target}       shortcut for all three above
 
-    cross-compiling:
-      @m{os=backend} or @m{os=be}           build for compute node (backend)
-      @m{os=frontend} or @m{os=fe}          build for login node (frontend)
-
     dependencies:
       ^dependency [constraints]     specify constraints on dependencies
       ^@K{/hash}                        build with a specific installed
@@ -77,7 +73,7 @@
       boxlib @B{dim=2}                  boxlib built for 2 dimensions
       libdwarf @g{%intel} ^libelf@g{%gcc}
           libdwarf, built with intel compiler, linked to libelf built with gcc
-      mvapich2 @g{%gcc} @B{fabrics=psm,mrail,sock}
+      mvapich2 @B{fabrics=psm,mrail,sock} @g{%gcc}
           mvapich2, built with gcc compiler, with support for multiple fabrics
 """
 

lib/spack/spack/cmd/install.py

@@ -13,6 +13,7 @@
 from llnl.util import lang, tty
 
 import spack.cmd
+import spack.concretize
 import spack.config
 import spack.environment as ev
 import spack.paths
@@ -450,7 +451,7 @@ def concrete_specs_from_file(args):
             else:
                 s = spack.spec.Spec.from_json(f)
 
-        concretized = s.concretized()
+        concretized = spack.concretize.concretize_one(s)
         if concretized.dag_hash() != s.dag_hash():
             msg = 'skipped invalid file "{0}". '
             msg += "The file does not contain a concrete spec."

lib/spack/spack/cmd/make_installer.py

@@ -7,9 +7,9 @@
 
 from llnl.path import convert_to_posix_path
 
+import spack.concretize
 import spack.paths
 import spack.util.executable
-from spack.spec import Spec
 
 description = "generate Windows installer"
 section = "admin"
@@ -65,8 +65,7 @@ def make_installer(parser, args):
     """
     if sys.platform == "win32":
         output_dir = args.output_dir
-        cmake_spec = Spec("cmake")
-        cmake_spec.concretize()
+        cmake_spec = spack.concretize.concretize_one("cmake")
         cmake_path = os.path.join(cmake_spec.prefix, "bin", "cmake.exe")
         cpack_path = os.path.join(cmake_spec.prefix, "bin", "cpack.exe")
         spack_source = args.spack_source

lib/spack/spack/cmd/mirror.py

@@ -492,7 +492,7 @@ def extend_with_additional_versions(specs, num_versions):
         mirror_specs = spack.mirrors.utils.get_all_versions(specs)
     else:
         mirror_specs = spack.mirrors.utils.get_matching_versions(specs, num_versions=num_versions)
-    mirror_specs = [x.concretized() for x in mirror_specs]
+    mirror_specs = [spack.concretize.concretize_one(x) for x in mirror_specs]
     return mirror_specs
 
 
@@ -545,7 +545,7 @@ def _not_license_excluded(self, x):
         package does not explicitly forbid redistributing source."""
         if self.private:
             return True
-        elif x.package_class.redistribute_source(x):
+        elif spack.repo.PATH.get_pkg_class(x.fullname).redistribute_source(x):
             return True
         else:
             tty.debug(

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

@@ -5,7 +5,7 @@
 """Implementation details of the ``spack module`` command."""
 
 import collections
-import os.path
+import os
 import shutil
 import sys
 
@@ -383,8 +383,10 @@ def modules_cmd(parser, args, module_type, callbacks=callbacks):
         query = " ".join(str(s) for s in args.constraint_specs)
         msg = f"the constraint '{query}' matches multiple packages:\n"
         for s in specs:
-            spec_fmt = "{hash:7} {name}{@version}{%compiler}"
-            spec_fmt += "{compiler_flags}{variants}{arch=architecture}"
+            spec_fmt = (
+                "{hash:7} {name}{@version}{compiler_flags}{variants}"
+                "{arch=architecture} {%compiler}"
+            )
             msg += "\t" + s.cformat(spec_fmt) + "\n"
         tty.die(msg, "In this context exactly *one* match is needed.")
 

lib/spack/spack/cmd/providers.py

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

lib/spack/spack/cmd/style.py

@@ -6,8 +6,9 @@
 import os
 import re
 import sys
-from itertools import zip_longest
-from typing import Dict, List, Optional
+import warnings
+from itertools import islice, zip_longest
+from typing import Callable, Dict, List, Optional
 
 import llnl.util.tty as tty
 import llnl.util.tty.color as color
@@ -16,6 +17,9 @@
 import spack.paths
 import spack.repo
 import spack.util.git
+import spack.util.spack_yaml
+from spack.spec_parser import SPEC_TOKENIZER, SpecTokens
+from spack.tokenize import Token
 from spack.util.executable import Executable, which
 
 description = "runs source code style checks on spack"
@@ -198,6 +202,13 @@ def setup_parser(subparser):
         action="append",
         help="specify tools to skip (choose from %s)" % ", ".join(tool_names),
     )
+    subparser.add_argument(
+        "--spec-strings",
+        action="store_true",
+        help="upgrade spec strings in Python, JSON and YAML files for compatibility with Spack "
+        "v1.0 and v0.x. Example: spack style --spec-strings $(git ls-files). Note: this flag "
+        "will be removed in Spack v1.0.",
+    )
 
     subparser.add_argument("files", nargs=argparse.REMAINDER, help="specific files to check")
 
@@ -423,7 +434,8 @@ def _run_import_check(
             continue
 
         for m in is_abs_import.finditer(contents):
-            if contents.count(m.group(1)) == 1:
+            # Find at most two occurences: the first is the import itself, the second is its usage.
+            if len(list(islice(re.finditer(rf"{re.escape(m.group(1))}(?!\w)", contents), 2))) == 1:
                 to_remove.append(m.group(0))
                 exit_code = 1
                 print(f"{pretty_path}: redundant import: {m.group(1)}", file=out)
@@ -438,7 +450,7 @@ def _run_import_check(
             module = _module_part(root, m.group(0))
             if not module or module in to_add:
                 continue
-            if re.search(rf"import {re.escape(module)}\b(?!\.)", contents):
+            if re.search(rf"import {re.escape(module)}(?!\w|\.)", contents):
                 continue
             to_add.add(module)
             exit_code = 1
@@ -506,7 +518,196 @@ def _bootstrap_dev_dependencies():
         spack.bootstrap.ensure_environment_dependencies()
 
 
+IS_PROBABLY_COMPILER = re.compile(r"%[a-zA-Z_][a-zA-Z0-9\-]")
+
+
+def _spec_str_reorder_compiler(idx: int, blocks: List[List[Token]]) -> None:
+    # only move the compiler to the back if it exists and is not already at the end
+    if not 0 <= idx < len(blocks) - 1:
+        return
+    # if there's only whitespace after the compiler, don't move it
+    if all(token.kind == SpecTokens.WS for block in blocks[idx + 1 :] for token in block):
+        return
+    # rotate left and always add at least one WS token between compiler and previous token
+    compiler_block = blocks.pop(idx)
+    if compiler_block[0].kind != SpecTokens.WS:
+        compiler_block.insert(0, Token(SpecTokens.WS, " "))
+    # delete the WS tokens from the new first block if it was at the very start, to prevent leading
+    # WS tokens.
+    while idx == 0 and blocks[0][0].kind == SpecTokens.WS:
+        blocks[0].pop(0)
+    blocks.append(compiler_block)
+
+
+def _spec_str_format(spec_str: str) -> Optional[str]:
+    """Given any string, try to parse as spec string, and rotate the compiler token to the end
+    of each spec instance. Returns the formatted string if it was changed, otherwise None."""
+    # We parse blocks of tokens that include leading whitespace, and move the compiler block to
+    # the end when we hit a dependency ^... or the end of a string.
+    # [@3.1][ +foo][ +bar][ %gcc@3.1][ +baz]
+    # [@3.1][ +foo][ +bar][ +baz][ %gcc@3.1]
+
+    current_block: List[Token] = []
+    blocks: List[List[Token]] = []
+    compiler_block_idx = -1
+    in_edge_attr = False
+
+    for token in SPEC_TOKENIZER.tokenize(spec_str):
+        if token.kind == SpecTokens.UNEXPECTED:
+            # parsing error, we cannot fix this string.
+            return None
+        elif token.kind in (SpecTokens.COMPILER, SpecTokens.COMPILER_AND_VERSION):
+            # multiple compilers are not supported in Spack v0.x, so early return
+            if compiler_block_idx != -1:
+                return None
+            current_block.append(token)
+            blocks.append(current_block)
+            current_block = []
+            compiler_block_idx = len(blocks) - 1
+        elif token.kind in (
+            SpecTokens.START_EDGE_PROPERTIES,
+            SpecTokens.DEPENDENCY,
+            SpecTokens.UNQUALIFIED_PACKAGE_NAME,
+            SpecTokens.FULLY_QUALIFIED_PACKAGE_NAME,
+        ):
+            _spec_str_reorder_compiler(compiler_block_idx, blocks)
+            compiler_block_idx = -1
+            if token.kind == SpecTokens.START_EDGE_PROPERTIES:
+                in_edge_attr = True
+            current_block.append(token)
+            blocks.append(current_block)
+            current_block = []
+        elif token.kind == SpecTokens.END_EDGE_PROPERTIES:
+            in_edge_attr = False
+            current_block.append(token)
+            blocks.append(current_block)
+            current_block = []
+        elif in_edge_attr:
+            current_block.append(token)
+        elif token.kind in (
+            SpecTokens.VERSION_HASH_PAIR,
+            SpecTokens.GIT_VERSION,
+            SpecTokens.VERSION,
+            SpecTokens.PROPAGATED_BOOL_VARIANT,
+            SpecTokens.BOOL_VARIANT,
+            SpecTokens.PROPAGATED_KEY_VALUE_PAIR,
+            SpecTokens.KEY_VALUE_PAIR,
+            SpecTokens.DAG_HASH,
+        ):
+            current_block.append(token)
+            blocks.append(current_block)
+            current_block = []
+        elif token.kind == SpecTokens.WS:
+            current_block.append(token)
+        else:
+            raise ValueError(f"unexpected token {token}")
+
+    if current_block:
+        blocks.append(current_block)
+    _spec_str_reorder_compiler(compiler_block_idx, blocks)
+
+    new_spec_str = "".join(token.value for block in blocks for token in block)
+    return new_spec_str if spec_str != new_spec_str else None
+
+
+SpecStrHandler = Callable[[str, int, int, str, str], None]
+
+
+def _spec_str_default_handler(path: str, line: int, col: int, old: str, new: str):
+    """A SpecStrHandler that prints formatted spec strings and their locations."""
+    print(f"{path}:{line}:{col}: `{old}` -> `{new}`")
+
+
+def _spec_str_fix_handler(path: str, line: int, col: int, old: str, new: str):
+    """A SpecStrHandler that updates formatted spec strings in files."""
+    with open(path, "r", encoding="utf-8") as f:
+        lines = f.readlines()
+    new_line = lines[line - 1].replace(old, new)
+    if new_line == lines[line - 1]:
+        tty.warn(f"{path}:{line}:{col}: could not apply fix: `{old}` -> `{new}`")
+        return
+    lines[line - 1] = new_line
+    print(f"{path}:{line}:{col}: fixed `{old}` -> `{new}`")
+    with open(path, "w", encoding="utf-8") as f:
+        f.writelines(lines)
+
+
+def _spec_str_ast(path: str, tree: ast.AST, handler: SpecStrHandler) -> None:
+    """Walk the AST of a Python file and apply handler to formatted spec strings."""
+    has_constant = sys.version_info >= (3, 8)
+    for node in ast.walk(tree):
+        if has_constant and isinstance(node, ast.Constant) and isinstance(node.value, str):
+            current_str = node.value
+        elif not has_constant and isinstance(node, ast.Str):
+            current_str = node.s
+        else:
+            continue
+        if not IS_PROBABLY_COMPILER.search(current_str):
+            continue
+        new = _spec_str_format(current_str)
+        if new is not None:
+            handler(path, node.lineno, node.col_offset, current_str, new)
+
+
+def _spec_str_json_and_yaml(path: str, data: dict, handler: SpecStrHandler) -> None:
+    """Walk a YAML or JSON data structure and apply handler to formatted spec strings."""
+    queue = [data]
+    seen = set()
+
+    while queue:
+        current = queue.pop(0)
+        if id(current) in seen:
+            continue
+        seen.add(id(current))
+        if isinstance(current, dict):
+            queue.extend(current.values())
+            queue.extend(current.keys())
+        elif isinstance(current, list):
+            queue.extend(current)
+        elif isinstance(current, str) and IS_PROBABLY_COMPILER.search(current):
+            new = _spec_str_format(current)
+            if new is not None:
+                mark = getattr(current, "_start_mark", None)
+                if mark:
+                    line, col = mark.line + 1, mark.column + 1
+                else:
+                    line, col = 0, 0
+                handler(path, line, col, current, new)
+
+
+def _check_spec_strings(
+    paths: List[str], handler: SpecStrHandler = _spec_str_default_handler
+) -> None:
+    """Open Python, JSON and YAML files, and format their string literals that look like spec
+    strings. A handler is called for each formatting, which can be used to print or apply fixes."""
+    for path in paths:
+        is_json_or_yaml = path.endswith(".json") or path.endswith(".yaml") or path.endswith(".yml")
+        is_python = path.endswith(".py")
+        if not is_json_or_yaml and not is_python:
+            continue
+
+        try:
+            with open(path, "r", encoding="utf-8") as f:
+                # skip files that are likely too large to be user code or config
+                if os.fstat(f.fileno()).st_size > 1024 * 1024:
+                    warnings.warn(f"skipping {path}: too large.")
+                    continue
+                if is_json_or_yaml:
+                    _spec_str_json_and_yaml(path, spack.util.spack_yaml.load_config(f), handler)
+                elif is_python:
+                    _spec_str_ast(path, ast.parse(f.read()), handler)
+        except (OSError, spack.util.spack_yaml.SpackYAMLError, SyntaxError, ValueError):
+            warnings.warn(f"skipping {path}")
+            continue
+
+
 def style(parser, args):
+    if args.spec_strings:
+        if not args.files:
+            tty.die("No files provided to check spec strings.")
+        handler = _spec_str_fix_handler if args.fix else _spec_str_default_handler
+        return _check_spec_strings(args.files, handler)
+
     # save initial working directory for relativizing paths later
     args.initial_working_dir = os.getcwd()
 

lib/spack/spack/cmd/test.py

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

lib/spack/spack/cmd/tutorial.py

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

lib/spack/spack/cmd/uninstall.py

@@ -144,7 +144,7 @@ def is_installed(spec):
         record = spack.store.STORE.db.query_local_by_spec_hash(spec.dag_hash())
         return record and record.installed
 
-    specs = traverse.traverse_nodes(
+    all_specs = traverse.traverse_nodes(
         specs,
         root=False,
         order="breadth",
@@ -155,7 +155,7 @@ def is_installed(spec):
     )
 
     with spack.store.STORE.db.read_transaction():
-        return [spec for spec in specs if is_installed(spec)]
+        return [spec for spec in all_specs if is_installed(spec)]
 
 
 def dependent_environments(

lib/spack/spack/cmd/unit_test.py

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

lib/spack/spack/cmd/verify.py

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

lib/spack/spack/compiler.py

@@ -749,12 +749,18 @@ def __init__(self, compiler, feature, flag_name, ver_string=None):
 class CompilerCacheEntry:
     """Deserialized cache entry for a compiler"""
 
-    __slots__ = ["c_compiler_output", "real_version"]
+    __slots__ = ("c_compiler_output", "real_version")
 
     def __init__(self, c_compiler_output: Optional[str], real_version: str):
         self.c_compiler_output = c_compiler_output
         self.real_version = real_version
 
+    @property
+    def empty(self) -> bool:
+        """Sometimes the compiler is temporarily broken, preventing us from getting output. The
+        call site determines if that is a problem."""
+        return self.c_compiler_output is None
+
     @classmethod
     def from_dict(cls, data: Dict[str, Optional[str]]):
         if not isinstance(data, dict):
@@ -792,9 +798,10 @@ def __init__(self, cache: "FileCache") -> None:
         self.cache.init_entry(self.name)
         self._data: Dict[str, Dict[str, Optional[str]]] = {}
 
-    def _get_entry(self, key: str) -> Optional[CompilerCacheEntry]:
+    def _get_entry(self, key: str, *, allow_empty: bool) -> Optional[CompilerCacheEntry]:
         try:
-            return CompilerCacheEntry.from_dict(self._data[key])
+            entry = CompilerCacheEntry.from_dict(self._data[key])
+            return entry if allow_empty or not entry.empty else None
         except ValueError:
             del self._data[key]
         except KeyError:
@@ -812,7 +819,7 @@ def get(self, compiler: Compiler) -> CompilerCacheEntry:
             self._data = {}
 
         key = self._key(compiler)
-        value = self._get_entry(key)
+        value = self._get_entry(key, allow_empty=False)
         if value is not None:
             return value
 
@@ -826,7 +833,7 @@ def get(self, compiler: Compiler) -> CompilerCacheEntry:
                 self._data = {}
 
             # Use cache entry that may have been created by another process in the meantime.
-            entry = self._get_entry(key)
+            entry = self._get_entry(key, allow_empty=True)
 
             # Finally compute the cache entry
             if entry is None: