scorep: ensure gcc-plugin is built, patch gcc@14 (#49257)

* scorep: ensure gcc-plugin is built, patch gcc@14
* scorep: patch only to non-deprecated versions

.github/workflows/ci.yaml

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

.github/workflows/prechecks.yml

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

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

@@ -1,7 +1,7 @@
 black==25.1.0
 clingo==5.7.1
 flake8==7.1.2
-isort==6.0.0
-mypy==1.11.2
-types-six==1.17.0.20241205
+isort==6.0.1
+mypy==1.15.0
+types-six==1.17.0.20250304
 vermin==1.6.0

.gitignore

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

etc/spack/defaults/concretizer.yaml

@@ -54,9 +54,15 @@ concretizer:
       # 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

lib/spack/docs/basic_usage.rst

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

lib/spack/docs/conf.py

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

lib/spack/docs/config_yaml.rst

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

lib/spack/docs/configuration.rst

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

lib/spack/docs/environments.rst

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

lib/spack/docs/frequently_asked_questions.rst

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

lib/spack/docs/include_yaml.rst

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

lib/spack/docs/index.rst

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

lib/spack/docs/packages_yaml.rst

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

lib/spack/docs/requirements.txt

@@ -1,13 +1,13 @@
-sphinx==8.2.0
+sphinx==8.2.3
 sphinxcontrib-programoutput==0.18
 sphinx_design==0.6.1
 sphinx-rtd-theme==3.0.2
-python-levenshtein==0.26.1
+python-levenshtein==0.27.1
 docutils==0.21.2
 pygments==2.19.1
 urllib3==2.3.0
-pytest==8.3.4
-isort==6.0.0
+pytest==8.3.5
+isort==6.0.1
 black==25.1.0
 flake8==7.1.2
 mypy==1.11.1

lib/spack/llnl/util/filesystem.py

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

lib/spack/llnl/util/lang.py

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

lib/spack/spack/__init__.py

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

lib/spack/spack/build_environment.py

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

lib/spack/spack/build_systems/cached_cmake.py

@@ -278,17 +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)

lib/spack/spack/ci/__init__.py

@@ -6,6 +6,7 @@
 import codecs
 import json
 import os
+import pathlib
 import re
 import shutil
 import stat
@@ -13,7 +14,7 @@
 import tempfile
 import zipfile
 from collections import namedtuple
-from typing import Callable, Dict, List, Set
+from typing import Callable, Dict, List, Set, Union
 from urllib.request import Request
 
 import llnl.path
@@ -23,7 +24,6 @@
 
 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
@@ -41,6 +42,7 @@
 from spack import traverse
 from spack.error import SpackError
 from spack.reporters.cdash import SPACK_CDASH_TIMEOUT
+from spack.version import GitVersion, StandardVersion
 
 from .common import (
     IS_WINDOWS,
@@ -79,6 +81,45 @@ def get_change_revisions():
     return None, None
 
 
+def get_added_versions(
+    checksums_version_dict: Dict[str, Union[StandardVersion, GitVersion]],
+    path: str,
+    from_ref: str = "HEAD~1",
+    to_ref: str = "HEAD",
+) -> List[Union[StandardVersion, GitVersion]]:
+    """Get a list of the versions added between `from_ref` and `to_ref`.
+    Args:
+       checksums_version_dict (Dict): all package versions keyed by known checksums.
+       path (str): path to the package.py
+       from_ref (str): oldest git ref, defaults to `HEAD~1`
+       to_ref (str): newer git ref, defaults to `HEAD`
+    Returns: list of versions added between refs
+    """
+    git_exe = spack.util.git.git(required=True)
+
+    # Gather git diff
+    diff_lines = git_exe("diff", from_ref, to_ref, "--", path, output=str).split("\n")
+
+    # Store added and removed versions
+    # Removed versions are tracked here to determine when versions are moved in a file
+    # and show up as both added and removed in a git diff.
+    added_checksums = set()
+    removed_checksums = set()
+
+    # Scrape diff for modified versions and prune added versions if they show up
+    # as also removed (which means they've actually just moved in the file and
+    # we shouldn't need to rechecksum them)
+    for checksum in checksums_version_dict.keys():
+        for line in diff_lines:
+            if checksum in line:
+                if line.startswith("+"):
+                    added_checksums.add(checksum)
+                if line.startswith("-"):
+                    removed_checksums.add(checksum)
+
+    return [checksums_version_dict[c] for c in added_checksums - removed_checksums]
+
+
 def get_stack_changed(env_path, rev1="HEAD^", rev2="HEAD"):
     """Given an environment manifest path and two revisions to compare, return
     whether or not the stack was changed.  Returns True if the environment
@@ -224,7 +265,7 @@ def rebuild_filter(s: spack.spec.Spec) -> RebuildDecision:
 
 def _format_pruning_message(spec: spack.spec.Spec, prune: bool, reasons: List[str]) -> str:
     reason_msg = ", ".join(reasons)
-    spec_fmt = "{name}{@version}{%compiler}{/hash:7}"
+    spec_fmt = "{name}{@version}{/hash:7}{%compiler}"
 
     if not prune:
         status = colorize("@*g{[x]}  ")
@@ -581,22 +622,25 @@ def copy_stage_logs_to_artifacts(job_spec: spack.spec.Spec, job_log_dir: str) ->
     tty.debug(f"job spec: {job_spec}")
 
     try:
-        pkg_cls = spack.repo.PATH.get_pkg_class(job_spec.name)
-        job_pkg = pkg_cls(job_spec)
-        tty.debug(f"job package: {job_pkg}")
-    except AssertionError:
-        msg = f"Cannot copy stage logs: job spec ({job_spec}) must be concrete"
-        tty.error(msg)
+        package_metadata_root = pathlib.Path(spack.store.STORE.layout.metadata_path(job_spec))
+    except spack.error.SpackError as e:
+        tty.error(f"Cannot copy logs: {str(e)}")
         return
 
-    stage_dir = job_pkg.stage.path
-    tty.debug(f"stage dir: {stage_dir}")
-    for file in [
-        job_pkg.log_path,
-        job_pkg.env_mods_path,
-        *spack.builder.create(job_pkg).archive_files,
-    ]:
-        copy_files_to_artifacts(file, job_log_dir)
+    # Get the package's archived files
+    archive_files = []
+    archive_root = package_metadata_root / "archived-files"
+    if archive_root.is_dir():
+        archive_files = [f for f in archive_root.rglob("*") if f.is_file()]
+    else:
+        msg = "Cannot copy package archived files: archived-files must be a directory"
+        tty.warn(msg)
+
+    build_log_zipped = package_metadata_root / "spack-build-out.txt.gz"
+    build_env_mods = package_metadata_root / "spack-build-env.txt"
+
+    for f in [build_log_zipped, build_env_mods, *archive_files]:
+        copy_files_to_artifacts(str(f), job_log_dir)
 
 
 def copy_test_logs_to_artifacts(test_stage, job_test_dir):

lib/spack/spack/cmd/__init__.py

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

lib/spack/spack/cmd/ci.py

@@ -4,12 +4,15 @@
 
 import json
 import os
+import re
 import shutil
+import sys
+from typing import Dict
 from urllib.parse import urlparse, urlunparse
 
 import llnl.util.filesystem as fs
-import llnl.util.tty as tty
 import llnl.util.tty.color as clr
+from llnl.util import tty
 
 import spack.binary_distribution as bindist
 import spack.ci as spack_ci
@@ -18,12 +21,22 @@
 import spack.cmd.common.arguments
 import spack.config as cfg
 import spack.environment as ev
+import spack.error
+import spack.fetch_strategy
 import spack.hash_types as ht
 import spack.mirrors.mirror
+import spack.package_base
+import spack.paths
+import spack.repo
+import spack.spec
+import spack.stage
+import spack.util.executable
+import spack.util.git
 import spack.util.gpg as gpg_util
 import spack.util.timer as timer
 import spack.util.url as url_util
 import spack.util.web as web_util
+import spack.version
 
 description = "manage continuous integration pipelines"
 section = "build"
@@ -32,6 +45,7 @@
 SPACK_COMMAND = "spack"
 INSTALL_FAIL_CODE = 1
 FAILED_CREATE_BUILDCACHE_CODE = 100
+BUILTIN = re.compile(r"var\/spack\/repos\/builtin\/packages\/([^\/]+)\/package\.py")
 
 
 def deindent(desc):
@@ -191,6 +205,16 @@ def setup_parser(subparser):
 
     reproduce.set_defaults(func=ci_reproduce)
 
+    # Verify checksums inside of ci workflows
+    verify_versions = subparsers.add_parser(
+        "verify-versions",
+        description=deindent(ci_verify_versions.__doc__),
+        help=spack.cmd.first_line(ci_verify_versions.__doc__),
+    )
+    verify_versions.add_argument("from_ref", help="git ref from which start looking at changes")
+    verify_versions.add_argument("to_ref", help="git ref to end looking at changes")
+    verify_versions.set_defaults(func=ci_verify_versions)
+
 
 def ci_generate(args):
     """generate jobs file from a CI-aware spack file
@@ -427,7 +451,7 @@ def ci_rebuild(args):
 
     # Arguments when installing the root from sources
     deps_install_args = install_args + ["--only=dependencies"]
-    root_install_args = install_args + ["--keep-stage", "--only=package"]
+    root_install_args = install_args + ["--only=package"]
 
     if cdash_handler:
         # Add additional arguments to `spack install` for CDash reporting.
@@ -464,8 +488,7 @@ def ci_rebuild(args):
                 job_spec.to_dict(hash=ht.dag_hash),
             )
 
-    # We generated the "spack install ..." command to "--keep-stage", copy
-    # any logs from the staging directory to artifacts now
+    # Copy logs and archived files from the install metadata (.spack) directory to artifacts now
     spack_ci.copy_stage_logs_to_artifacts(job_spec, job_log_dir)
 
     # If the installation succeeded and we're running stand-alone tests for
@@ -660,6 +683,159 @@ def _gitlab_artifacts_url(url: str) -> str:
     return urlunparse(parsed._replace(path="/".join(parts), fragment="", query=""))
 
 
+def validate_standard_versions(
+    pkg: spack.package_base.PackageBase, versions: spack.version.VersionList
+) -> bool:
+    """Get and test the checksum of a package version based on a tarball.
+    Args:
+      pkg spack.package_base.PackageBase: Spack package for which to validate a version checksum
+      versions spack.version.VersionList: list of package versions to validate
+    Returns: bool: result of the validation. True is valid and false is failed.
+    """
+    url_dict: Dict[spack.version.StandardVersion, str] = {}
+
+    for version in versions:
+        url = pkg.find_valid_url_for_version(version)
+        url_dict[version] = url
+
+    version_hashes = spack.stage.get_checksums_for_versions(
+        url_dict, pkg.name, fetch_options=pkg.fetch_options
+    )
+
+    valid_checksums = True
+    for version, sha in version_hashes.items():
+        if sha != pkg.versions[version]["sha256"]:
+            tty.error(
+                f"Invalid checksum found {pkg.name}@{version}\n"
+                f"    [package.py] {pkg.versions[version]['sha256']}\n"
+                f"    [Downloaded] {sha}"
+            )
+            valid_checksums = False
+            continue
+
+        tty.info(f"Validated {pkg.name}@{version} --> {sha}")
+
+    return valid_checksums
+
+
+def validate_git_versions(
+    pkg: spack.package_base.PackageBase, versions: spack.version.VersionList
+) -> bool:
+    """Get and test the commit and tag of a package version based on a git repository.
+    Args:
+      pkg spack.package_base.PackageBase: Spack package for which to validate a version
+      versions spack.version.VersionList: list of package versions to validate
+    Returns: bool: result of the validation. True is valid and false is failed.
+    """
+    valid_commit = True
+    for version in versions:
+        fetcher = spack.fetch_strategy.for_package_version(pkg, version)
+        with spack.stage.Stage(fetcher) as stage:
+            known_commit = pkg.versions[version]["commit"]
+            try:
+                stage.fetch()
+            except spack.error.FetchError:
+                tty.error(
+                    f"Invalid commit for {pkg.name}@{version}\n"
+                    f"    {known_commit} could not be checked out in the git repository."
+                )
+                valid_commit = False
+                continue
+
+            # Test if the specified tag matches the commit in the package.py
+            # We retrieve the commit associated with a tag and compare it to the
+            # commit that is located in the package.py file.
+            if "tag" in pkg.versions[version]:
+                tag = pkg.versions[version]["tag"]
+                try:
+                    with fs.working_dir(stage.source_path):
+                        found_commit = fetcher.git(
+                            "rev-list", "-n", "1", tag, output=str, error=str
+                        ).strip()
+                except spack.util.executable.ProcessError:
+                    tty.error(
+                        f"Invalid tag for {pkg.name}@{version}\n"
+                        f"    {tag} could not be found in the git repository."
+                    )
+                    valid_commit = False
+                    continue
+
+                if found_commit != known_commit:
+                    tty.error(
+                        f"Mismatched tag <-> commit found for {pkg.name}@{version}\n"
+                        f"    [package.py] {known_commit}\n"
+                        f"    [Downloaded] {found_commit}"
+                    )
+                    valid_commit = False
+                    continue
+
+            # If we have downloaded the repository, found the commit, and compared
+            # the tag (if specified) we can conclude that the version is pointing
+            # at what we would expect.
+            tty.info(f"Validated {pkg.name}@{version} --> {known_commit}")
+
+    return valid_commit
+
+
+def ci_verify_versions(args):
+    """validate version checksum & commits between git refs
+    This command takes a from_ref and to_ref arguments and
+    then parses the git diff between the two to determine which packages
+    have been modified verifies the new checksums inside of them.
+    """
+    with fs.working_dir(spack.paths.prefix):
+        # We use HEAD^1 explicitly on the merge commit created by
+        # GitHub Actions. However HEAD~1 is a safer default for the helper function.
+        files = spack.util.git.get_modified_files(from_ref=args.from_ref, to_ref=args.to_ref)
+
+    # Get a list of package names from the modified files.
+    pkgs = [(m.group(1), p) for p in files for m in [BUILTIN.search(p)] if m]
+
+    failed_version = False
+    for pkg_name, path in pkgs:
+        spec = spack.spec.Spec(pkg_name)
+        pkg = spack.repo.PATH.get_pkg_class(spec.name)(spec)
+
+        # Skip checking manual download packages and trust the maintainers
+        if pkg.manual_download:
+            tty.warn(f"Skipping manual download package: {pkg_name}")
+            continue
+
+        # Store versions checksums / commits for future loop
+        checksums_version_dict = {}
+        commits_version_dict = {}
+        for version in pkg.versions:
+            # If the package version defines a sha256 we'll use that as the high entropy
+            # string to detect which versions have been added between from_ref and to_ref
+            if "sha256" in pkg.versions[version]:
+                checksums_version_dict[pkg.versions[version]["sha256"]] = version
+
+            # If a package version instead defines a commit we'll use that as a
+            # high entropy string to detect new versions.
+            elif "commit" in pkg.versions[version]:
+                commits_version_dict[pkg.versions[version]["commit"]] = version
+
+            # TODO: enforce every version have a commit or a sha256 defined if not
+            # an infinite version (there are a lot of package's where this doesn't work yet.)
+
+        with fs.working_dir(spack.paths.prefix):
+            added_checksums = spack_ci.get_added_versions(
+                checksums_version_dict, path, from_ref=args.from_ref, to_ref=args.to_ref
+            )
+            added_commits = spack_ci.get_added_versions(
+                commits_version_dict, path, from_ref=args.from_ref, to_ref=args.to_ref
+            )
+
+        if added_checksums:
+            failed_version = not validate_standard_versions(pkg, added_checksums) or failed_version
+
+        if added_commits:
+            failed_version = not validate_git_versions(pkg, added_commits) or failed_version
+
+    if failed_version:
+        sys.exit(1)
+
+
 def ci(parser, args):
     if args.func:
         return args.func(args)

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

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

lib/spack/spack/cmd/config.py

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

lib/spack/spack/cmd/dependencies.py

@@ -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(

lib/spack/spack/cmd/dependents.py

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

lib/spack/spack/cmd/develop.py

@@ -3,11 +3,13 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
 import shutil
+from typing import Optional
 
 import llnl.util.tty as tty
 
 import spack.cmd
 import spack.config
+import spack.environment
 import spack.fetch_strategy
 import spack.repo
 import spack.spec
@@ -31,37 +33,33 @@ def setup_parser(subparser):
         "--no-clone",
         action="store_false",
         dest="clone",
-        default=None,
         help="do not clone, the package already exists at the source path",
     )
     clone_group.add_argument(
         "--clone",
         action="store_true",
         dest="clone",
-        default=None,
-        help="clone the package even if the path already exists",
+        default=True,
+        help=(
+            "(default) clone the package unless the path already exists, "
+            "use --force to overwrite"
+        ),
     )
 
     subparser.add_argument(
         "-f", "--force", help="remove any files or directories that block cloning source code"
     )
 
+    subparser.add_argument(
+        "-r",
+        "--recursive",
+        action="store_true",
+        help="traverse nodes of the graph to mark everything up to the root as a develop spec",
+    )
+
     arguments.add_common_arguments(subparser, ["spec"])
 
 
-def _update_config(spec, path):
-    find_fn = lambda section: spec.name in section
-
-    entry = {"spec": str(spec)}
-    if path != spec.name:
-        entry["path"] = path
-
-    def change_fn(section):
-        section[spec.name] = entry
-
-    spack.config.change_or_add("develop", find_fn, change_fn)
-
-
 def _retrieve_develop_source(spec: spack.spec.Spec, abspath: str) -> None:
     # "steal" the source code via staging API. We ask for a stage
     # to be created, then copy it afterwards somewhere else. It would be
@@ -83,44 +81,43 @@ def _retrieve_develop_source(spec: spack.spec.Spec, abspath: str) -> None:
     package.stage.steal_source(abspath)
 
 
-def develop(parser, args):
-    # Note: we could put develop specs in any scope, but I assume
-    # users would only ever want to do this for either (a) an active
-    # env or (b) a specified config file (e.g. that is included by
-    # an environment)
-    # TODO: when https://github.com/spack/spack/pull/35307 is merged,
-    # an active env is not required if a scope is specified
-    env = spack.cmd.require_active_env(cmd_name="develop")
-    if not args.spec:
-        if args.clone is False:
-            raise SpackError("No spec provided to spack develop command")
+def assure_concrete_spec(env: spack.environment.Environment, spec: spack.spec.Spec):
+    version = spec.versions.concrete_range_as_version
+    if not version:
+        # first check environment for a matching concrete spec
+        matching_specs = env.all_matching_specs(spec)
+        if matching_specs:
+            version = matching_specs[0].version
+            test_spec = spack.spec.Spec(f"{spec}@{version}")
+            for m_spec in matching_specs:
+                if not m_spec.satisfies(test_spec):
+                    raise SpackError(
+                        f"{spec.name}: has multiple concrete instances in the graph that can't be"
+                        " satisified by a single develop spec. To use `spack develop` ensure one"
+                        " of the following:"
+                        f"\n a) {spec.name} nodes can satisfy the same develop spec (minimally "
+                        "this means they all share the same version)"
+                        f"\n b) Provide a concrete develop spec ({spec.name}@[version]) to clearly"
+                        " indicate what should be developed"
+                    )
+        else:
+            # look up the maximum version so infintiy versions are preferred for develop
+            version = max(spec.package_class.versions.keys())
+            tty.msg(f"Defaulting to highest version: {spec.name}@{version}")
+    spec.versions = spack.version.VersionList([version])
 
-        # download all dev specs
-        for name, entry in env.dev_specs.items():
-            path = entry.get("path", name)
-            abspath = spack.util.path.canonicalize_path(path, default_wd=env.path)
 
-            if os.path.exists(abspath):
-                msg = "Skipping developer download of %s" % entry["spec"]
-                msg += " because its path already exists."
-                tty.msg(msg)
-                continue
+def setup_src_code(spec: spack.spec.Spec, src_path: str, clone: bool = True, force: bool = False):
+    """
+    Handle checking, cloning or overwriting source code
+    """
+    assert spec.versions
 
-            # Both old syntax `spack develop pkg@x` and new syntax `spack develop pkg@=x`
-            # are currently supported.
-            spec = spack.spec.parse_with_version_concrete(entry["spec"])
-            _retrieve_develop_source(spec, abspath)
+    if clone:
+        _clone(spec, src_path, force)
 
-        if not env.dev_specs:
-            tty.warn("No develop specs to download")
-
-        return
-
-    specs = spack.cmd.parse_specs(args.spec)
-    if len(specs) > 1:
-        raise SpackError("spack develop requires at most one named spec")
-
-    spec = specs[0]
+    if not clone and not os.path.exists(src_path):
+        raise SpackError(f"Provided path {src_path} does not exist")
 
     version = spec.versions.concrete_range_as_version
     if not version:
@@ -129,40 +126,114 @@ def develop(parser, args):
         tty.msg(f"Defaulting to highest version: {spec.name}@{version}")
     spec.versions = spack.version.VersionList([version])
 
-    # If user does not specify --path, we choose to create a directory in the
-    # active environment's directory, named after the spec
-    path = args.path or spec.name
-    if not os.path.isabs(path):
-        abspath = spack.util.path.canonicalize_path(path, default_wd=env.path)
-    else:
-        abspath = path
 
-    # clone default: only if the path doesn't exist
-    clone = args.clone
-    if clone is None:
-        clone = not os.path.exists(abspath)
+def _update_config(spec, path):
+    find_fn = lambda section: spec.name in section
 
-    if not clone and not os.path.exists(abspath):
-        raise SpackError("Provided path %s does not exist" % abspath)
+    entry = {"spec": str(spec)}
+    if path and path != spec.name:
+        entry["path"] = path
 
-    if clone:
-        if os.path.exists(abspath):
-            if args.force:
-                shutil.rmtree(abspath)
-            else:
-                msg = "Path %s already exists and cannot be cloned to." % abspath
-                msg += " Use `spack develop -f` to overwrite."
-                raise SpackError(msg)
+    def change_fn(section):
+        section[spec.name] = entry
 
-        _retrieve_develop_source(spec, abspath)
+    spack.config.change_or_add("develop", find_fn, change_fn)
+
+
+def update_env(
+    env: spack.environment.Environment,
+    spec: spack.spec.Spec,
+    specified_path: Optional[str] = None,
+    build_dir: Optional[str] = None,
+):
+    """
+    Update the spack.yaml file with additions or changes from a develop call
+    """
+    tty.debug(f"Updating develop config for {env.name} transactionally")
+
+    if not specified_path:
+        dev_entry = env.dev_specs.get(spec.name)
+        if dev_entry:
+            specified_path = dev_entry.get("path", None)
 
-    tty.debug("Updating develop config for {0} transactionally".format(env.name))
     with env.write_transaction():
-        if args.build_directory is not None:
+        if build_dir is not None:
             spack.config.add(
-                "packages:{}:package_attributes:build_directory:{}".format(
-                    spec.name, args.build_directory
-                ),
+                f"packages:{spec.name}:package_attributes:build_directory:{build_dir}",
                 env.scope_name,
             )
-        _update_config(spec, path)
+        # add develop spec and update path
+        _update_config(spec, specified_path)
+
+
+def _clone(spec: spack.spec.Spec, abspath: str, force: bool = False):
+    if os.path.exists(abspath):
+        if force:
+            shutil.rmtree(abspath)
+        else:
+            msg = f"Skipping developer download of {spec.name}"
+            msg += f" because its path {abspath} already exists."
+            tty.msg(msg)
+            return
+
+    # cloning can take a while and it's nice to get a message for the longer clones
+    tty.msg(f"Cloning source code for {spec}")
+    _retrieve_develop_source(spec, abspath)
+
+
+def _abs_code_path(
+    env: spack.environment.Environment, spec: spack.spec.Spec, path: Optional[str] = None
+):
+    src_path = path if path else spec.name
+    return spack.util.path.canonicalize_path(src_path, default_wd=env.path)
+
+
+def _dev_spec_generator(args, env):
+    """
+    Generator function to loop over all the develop specs based on how the command is called
+    If no specs are supplied then loop over the develop specs listed in the environment.
+    """
+    if not args.spec:
+        if args.clone is False:
+            raise SpackError("No spec provided to spack develop command")
+
+        for name, entry in env.dev_specs.items():
+            path = entry.get("path", name)
+            abspath = spack.util.path.canonicalize_path(path, default_wd=env.path)
+            # Both old syntax `spack develop pkg@x` and new syntax `spack develop pkg@=x`
+            # are currently supported.
+            spec = spack.spec.parse_with_version_concrete(entry["spec"])
+            yield spec, abspath
+    else:
+        specs = spack.cmd.parse_specs(args.spec)
+        if (args.path or args.build_directory) and len(specs) > 1:
+            raise SpackError(
+                "spack develop requires at most one named spec when using the --path or"
+                " --build-directory arguments"
+            )
+
+        for spec in specs:
+            if args.recursive:
+                concrete_specs = env.all_matching_specs(spec)
+                if not concrete_specs:
+                    tty.warn(
+                        f"{spec.name} has no matching concrete specs in the environment and "
+                        "will be skipped. `spack develop --recursive` requires a concretized"
+                        " environment"
+                    )
+                else:
+                    for s in concrete_specs:
+                        for node_spec in s.traverse(direction="parents", root=True):
+                            tty.debug(f"Recursive develop for {node_spec.name}")
+                            yield node_spec, _abs_code_path(env, node_spec, args.path)
+            else:
+                yield spec, _abs_code_path(env, spec, args.path)
+
+
+def develop(parser, args):
+    env = spack.cmd.require_active_env(cmd_name="develop")
+
+    for spec, abspath in _dev_spec_generator(args, env):
+        assure_concrete_spec(env, spec)
+        setup_src_code(spec, abspath, clone=args.clone, force=args.force)
+        update_env(env, spec, args.path, args.build_directory)

lib/spack/spack/cmd/help.py

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

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

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

lib/spack/spack/cmd/style.py

@@ -6,8 +6,9 @@
 import os
 import re
 import sys
+import warnings
 from itertools import islice, zip_longest
-from typing import Dict, List, Optional
+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")
 
@@ -507,7 +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/unit_test.py

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

lib/spack/spack/cmd/verify.py

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

lib/spack/spack/config.py

@@ -32,9 +32,10 @@
 import copy
 import functools
 import os
+import os.path
 import re
 import sys
-from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union
+from typing import Any, Callable, Dict, Generator, List, NamedTuple, Optional, Tuple, Union
 
 import jsonschema
 
@@ -42,7 +43,6 @@
 
 import spack.error
 import spack.paths
-import spack.platforms
 import spack.schema
 import spack.schema.bootstrap
 import spack.schema.cdash
@@ -54,17 +54,20 @@
 import spack.schema.develop
 import spack.schema.env
 import spack.schema.env_vars
+import spack.schema.include
+import spack.schema.merged
 import spack.schema.mirrors
 import spack.schema.modules
 import spack.schema.packages
 import spack.schema.repos
 import spack.schema.upstreams
 import spack.schema.view
-
-# Hacked yaml for configuration files preserves line numbers.
+import spack.util.remote_file_cache as rfc_util
 import spack.util.spack_yaml as syaml
-import spack.util.web as web_util
 from spack.util.cpus import cpus_available
+from spack.util.spack_yaml import get_mark_from_yaml_data
+
+from .enums import ConfigScopePriority
 
 #: Dict from section names -> schema for that section
 SECTION_SCHEMAS: Dict[str, Any] = {
@@ -72,6 +75,7 @@
     "concretizer": spack.schema.concretizer.schema,
     "definitions": spack.schema.definitions.schema,
     "env_vars": spack.schema.env_vars.schema,
+    "include": spack.schema.include.schema,
     "view": spack.schema.view.schema,
     "develop": spack.schema.develop.schema,
     "mirrors": spack.schema.mirrors.schema,
@@ -119,6 +123,17 @@
 #: Type used for raw YAML configuration
 YamlConfigDict = Dict[str, Any]
 
+#: prefix for name of included configuration scopes
+INCLUDE_SCOPE_PREFIX = "include"
+
+#: safeguard for recursive includes -- maximum include depth
+MAX_RECURSIVE_INCLUDES = 100
+
+
+def _include_cache_location():
+    """Location to cache included configuration files."""
+    return os.path.join(spack.paths.user_cache_path, "includes")
+
 
 class ConfigScope:
     def __init__(self, name: str) -> None:
@@ -126,6 +141,25 @@ def __init__(self, name: str) -> None:
         self.writable = False
         self.sections = syaml.syaml_dict()
 
+        #: names of any included scopes
+        self._included_scopes: Optional[List["ConfigScope"]] = None
+
+    @property
+    def included_scopes(self) -> List["ConfigScope"]:
+        """Memoized list of included scopes, in the order they appear in this scope."""
+        if self._included_scopes is None:
+            self._included_scopes = []
+
+            includes = self.get_section("include")
+            if includes:
+                include_paths = [included_path(data) for data in includes["include"]]
+                for path in include_paths:
+                    included_scope = include_path_scope(path)
+                    if included_scope:
+                        self._included_scopes.append(included_scope)
+
+        return self._included_scopes
+
     def get_section_filename(self, section: str) -> str:
         raise NotImplementedError
 
@@ -408,26 +442,18 @@ def _method(self, *args, **kwargs):
     return _method
 
 
-class Configuration:
-    """A full Spack configuration, from a hierarchy of config files.
+ScopeWithOptionalPriority = Union[ConfigScope, Tuple[int, ConfigScope]]
+ScopeWithPriority = Tuple[int, ConfigScope]
 
-    This class makes it easy to add a new scope on top of an existing one.
-    """
+
+class Configuration:
+    """A hierarchical configuration, merging a number of scopes at different priorities."""
 
     # convert to typing.OrderedDict when we drop 3.6, or OrderedDict when we reach 3.9
-    scopes: Dict[str, ConfigScope]
+    scopes: lang.PriorityOrderedMapping[str, ConfigScope]
 
-    def __init__(self, *scopes: ConfigScope) -> None:
-        """Initialize a configuration with an initial list of scopes.
-
-        Args:
-            scopes: list of scopes to add to this
-                Configuration, ordered from lowest to highest precedence
-
-        """
-        self.scopes = collections.OrderedDict()
-        for scope in scopes:
-            self.push_scope(scope)
+    def __init__(self) -> None:
+        self.scopes = lang.PriorityOrderedMapping()
         self.format_updates: Dict[str, List[ConfigScope]] = collections.defaultdict(list)
 
     def ensure_unwrapped(self) -> "Configuration":
@@ -435,36 +461,59 @@ def ensure_unwrapped(self) -> "Configuration":
         return self
 
     def highest(self) -> ConfigScope:
-        """Scope with highest precedence"""
-        return next(reversed(self.scopes.values()))  # type: ignore
+        """Scope with the highest precedence"""
+        return next(self.scopes.reversed_values())  # type: ignore
 
     @_config_mutator
-    def ensure_scope_ordering(self):
-        """Ensure that scope order matches documented precedent"""
-        # FIXME: We also need to consider that custom configurations and other orderings
-        # may not be preserved correctly
-        if "command_line" in self.scopes:
-            # TODO (when dropping python 3.6): self.scopes.move_to_end
-            self.scopes["command_line"] = self.remove_scope("command_line")
+    def push_scope(
+        self, scope: ConfigScope, priority: Optional[int] = None, _depth: int = 0
+    ) -> None:
+        """Adds a scope to the Configuration, at a given priority.
 
-    @_config_mutator
-    def push_scope(self, scope: ConfigScope) -> None:
-        """Add a higher precedence scope to the Configuration."""
-        tty.debug(f"[CONFIGURATION: PUSH SCOPE]: {str(scope)}", level=2)
-        self.scopes[scope.name] = scope
+        If a priority is not given, it is assumed to be the current highest priority.
 
-    @_config_mutator
-    def pop_scope(self) -> ConfigScope:
-        """Remove the highest precedence scope and return it."""
-        name, scope = self.scopes.popitem(last=True)  # type: ignore[call-arg]
-        tty.debug(f"[CONFIGURATION: POP SCOPE]: {str(scope)}", level=2)
-        return scope
+        Args:
+            scope: scope to be added
+            priority: priority of the scope
+        """
+        # TODO: As a follow on to #48784, change this to create a graph of the
+        # TODO: includes AND ensure properly sorted such that the order included
+        # TODO: at the highest level is reflected in the value of an option that
+        # TODO: is set in multiple included files.
+        # before pushing the scope itself, push any included scopes recursively, at same priority
+        for included_scope in reversed(scope.included_scopes):
+            if _depth + 1 > MAX_RECURSIVE_INCLUDES:  # make sure we're not recursing endlessly
+                mark = ""
+                if hasattr(included_scope, "path") and syaml.marked(included_scope.path):
+                    mark = included_scope.path._start_mark  # type: ignore
+                raise RecursiveIncludeError(
+                    f"Maximum include recursion exceeded in {included_scope.name}", str(mark)
+                )
+
+            # record this inclusion so that remove_scope() can use it
+            self.push_scope(included_scope, priority=priority, _depth=_depth + 1)
+
+        tty.debug(f"[CONFIGURATION: PUSH SCOPE]: {str(scope)}, priority={priority}", level=2)
+        self.scopes.add(scope.name, value=scope, priority=priority)
 
     @_config_mutator
     def remove_scope(self, scope_name: str) -> Optional[ConfigScope]:
-        """Remove scope by name; has no effect when ``scope_name`` does not exist"""
-        scope = self.scopes.pop(scope_name, None)
-        tty.debug(f"[CONFIGURATION: POP SCOPE]: {str(scope)}", level=2)
+        """Removes a scope by name, and returns it. If the scope does not exist, returns None."""
+
+        try:
+            scope = self.scopes.remove(scope_name)
+            tty.debug(f"[CONFIGURATION: REMOVE SCOPE]: {str(scope)}", level=2)
+        except KeyError as e:
+            tty.debug(f"[CONFIGURATION: REMOVE SCOPE]: {e}", level=2)
+            return None
+
+        # transitively remove included scopes
+        for included_scope in scope.included_scopes:
+            assert (
+                included_scope.name in self.scopes
+            ), f"Included scope '{included_scope.name}' was never added to configuration!"
+            self.remove_scope(included_scope.name)
+
         return scope
 
     @property
@@ -473,15 +522,13 @@ def writable_scopes(self) -> Generator[ConfigScope, None, None]:
         return (s for s in self.scopes.values() if s.writable)
 
     def highest_precedence_scope(self) -> ConfigScope:
-        """Writable scope with highest precedence."""
-        return next(s for s in reversed(self.scopes.values()) if s.writable)  # type: ignore
+        """Writable scope with the highest precedence."""
+        return next(s for s in self.scopes.reversed_values() if s.writable)
 
     def highest_precedence_non_platform_scope(self) -> ConfigScope:
-        """Writable non-platform scope with highest precedence"""
+        """Writable non-platform scope with the highest precedence"""
         return next(
-            s
-            for s in reversed(self.scopes.values())  # type: ignore
-            if s.writable and not s.is_platform_dependent
+            s for s in self.scopes.reversed_values() if s.writable and not s.is_platform_dependent
         )
 
     def matching_scopes(self, reg_expr) -> List[ConfigScope]:
@@ -748,7 +795,7 @@ def override(
     """
     if isinstance(path_or_scope, ConfigScope):
         overrides = path_or_scope
-        CONFIG.push_scope(path_or_scope)
+        CONFIG.push_scope(path_or_scope, priority=None)
     else:
         base_name = _OVERRIDES_BASE_NAME
         # Ensure the new override gets a unique scope name
@@ -762,7 +809,7 @@ def override(
                 break
 
         overrides = InternalConfigScope(scope_name)
-        CONFIG.push_scope(overrides)
+        CONFIG.push_scope(overrides, priority=None)
         CONFIG.set(path_or_scope, value, scope=scope_name)
 
     try:
@@ -772,13 +819,86 @@ def override(
         assert scope is overrides
 
 
-def _add_platform_scope(cfg: Configuration, name: str, path: str, writable: bool = True) -> None:
+def _add_platform_scope(
+    cfg: Configuration, name: str, path: str, priority: ConfigScopePriority, writable: bool = True
+) -> None:
     """Add a platform-specific subdirectory for the current platform."""
+    import spack.platforms  # circular dependency
+
     platform = spack.platforms.host().name
     scope = DirectoryConfigScope(
         f"{name}/{platform}", os.path.join(path, platform), writable=writable
     )
-    cfg.push_scope(scope)
+    cfg.push_scope(scope, priority=priority)
+
+
+#: Class for the relevance of an optional path conditioned on a limited
+#: python code that evaluates to a boolean and or explicit specification
+#: as optional.
+class IncludePath(NamedTuple):
+    path: str
+    when: str
+    sha256: str
+    optional: bool
+
+
+def included_path(entry: Union[str, dict]) -> IncludePath:
+    """Convert the included path entry into an IncludePath.
+
+    Args:
+        entry: include configuration entry
+
+    Returns: converted entry, where an empty ``when`` means the path is
+        not conditionally included
+    """
+    if isinstance(entry, str):
+        return IncludePath(path=entry, sha256="", when="", optional=False)
+
+    path = entry["path"]
+    sha256 = entry.get("sha256", "")
+    when = entry.get("when", "")
+    optional = entry.get("optional", False)
+    return IncludePath(path=path, sha256=sha256, when=when, optional=optional)
+
+
+def include_path_scope(include: IncludePath) -> Optional[ConfigScope]:
+    """Instantiate an appropriate configuration scope for the given path.
+
+    Args:
+        include: optional include path
+
+    Returns: configuration scope
+
+    Raises:
+        ValueError: included path has an unsupported URL scheme, is required
+            but does not exist; configuration stage directory argument is missing
+        ConfigFileError: unable to access remote configuration file(s)
+    """
+    # circular dependencies
+    import spack.spec
+
+    if (not include.when) or spack.spec.eval_conditional(include.when):
+        config_path = rfc_util.local_path(include.path, include.sha256, _include_cache_location)
+        if not config_path:
+            raise ConfigFileError(f"Unable to fetch remote configuration from {include.path}")
+
+        if os.path.isdir(config_path):
+            # directories are treated as regular ConfigScopes
+            config_name = f"{INCLUDE_SCOPE_PREFIX}:{os.path.basename(config_path)}"
+            tty.debug(f"Creating DirectoryConfigScope {config_name} for '{config_path}'")
+            return DirectoryConfigScope(config_name, config_path)
+
+        if os.path.exists(config_path):
+            # files are assumed to be SingleFileScopes
+            config_name = f"{INCLUDE_SCOPE_PREFIX}:{config_path}"
+            tty.debug(f"Creating SingleFileScope {config_name} for '{config_path}'")
+            return SingleFileScope(config_name, config_path, spack.schema.merged.schema)
+
+        if not include.optional:
+            path = f" at ({config_path})" if config_path != include.path else ""
+            raise ValueError(f"Required path ({include.path}) does not exist{path}")
+
+    return None
 
 
 def config_paths_from_entry_points() -> List[Tuple[str, str]]:
@@ -806,18 +926,17 @@ def config_paths_from_entry_points() -> List[Tuple[str, str]]:
     return config_paths
 
 
-def create() -> Configuration:
+def create_incremental() -> Generator[Configuration, None, None]:
     """Singleton Configuration instance.
 
     This constructs one instance associated with this module and returns
     it. It is bundled inside a function so that configuration can be
     initialized lazily.
     """
-    cfg = Configuration()
-
     # first do the builtin, hardcoded defaults
-    builtin = InternalConfigScope("_builtin", CONFIG_DEFAULTS)
-    cfg.push_scope(builtin)
+    cfg = create_from(
+        (ConfigScopePriority.BUILTIN, InternalConfigScope("_builtin", CONFIG_DEFAULTS))
+    )
 
     # Builtin paths to configuration files in Spack
     configuration_paths = [
@@ -847,16 +966,29 @@ def create() -> Configuration:
 
     # add each scope and its platform-specific directory
     for name, path in configuration_paths:
-        cfg.push_scope(DirectoryConfigScope(name, path))
+        cfg.push_scope(DirectoryConfigScope(name, path), priority=ConfigScopePriority.CONFIG_FILES)
+        # Each scope can have per-platform overrides in subdirectories
+        _add_platform_scope(cfg, name, path, priority=ConfigScopePriority.CONFIG_FILES)
 
-        # Each scope can have per-platfom overrides in subdirectories
-        _add_platform_scope(cfg, name, path)
+        # yield the config incrementally so that each config level's init code can get
+        # data from the one below. This can be tricky, but it enables us to have a
+        # single unified config system.
+        #
+        # TODO: think about whether we want to restrict what types of config can be used
+        #     at each level. e.g., we may want to just more forcibly disallow remote
+        #     config (which uses ssl and other config options) for some of the scopes,
+        #     to make the bootstrap issues more explicit, even if allowing config scope
+        #     init to reference lower scopes is more flexible.
+        yield cfg
 
-    return cfg
+
+def create() -> Configuration:
+    """Create a configuration using create_incremental(), return the last yielded result."""
+    return list(create_incremental())[-1]
 
 
 #: This is the singleton configuration instance for Spack.
-CONFIG: Configuration = lang.Singleton(create)  # type: ignore
+CONFIG: Configuration = lang.Singleton(create_incremental)  # type: ignore
 
 
 def add_from_file(filename: str, scope: Optional[str] = None) -> None:
@@ -952,10 +1084,11 @@ def set(path: str, value: Any, scope: Optional[str] = None) -> None:
 
     Accepts the path syntax described in ``get()``.
     """
-    return CONFIG.set(path, value, scope)
+    result = CONFIG.set(path, value, scope)
+    return result
 
 
-def scopes() -> Dict[str, ConfigScope]:
+def scopes() -> lang.PriorityOrderedMapping[str, ConfigScope]:
     """Convenience function to get list of configuration scopes."""
     return CONFIG.scopes
 
@@ -1409,7 +1542,7 @@ def ensure_latest_format_fn(section: str) -> Callable[[YamlConfigDict], bool]:
 
 @contextlib.contextmanager
 def use_configuration(
-    *scopes_or_paths: Union[ConfigScope, str]
+    *scopes_or_paths: Union[ScopeWithOptionalPriority, str]
 ) -> Generator[Configuration, None, None]:
     """Use the configuration scopes passed as arguments within the context manager.
 
@@ -1424,7 +1557,7 @@ def use_configuration(
     global CONFIG
 
     # Normalize input and construct a Configuration object
-    configuration = _config_from(scopes_or_paths)
+    configuration = create_from(*scopes_or_paths)
     CONFIG.clear_caches(), configuration.clear_caches()
 
     saved_config, CONFIG = CONFIG, configuration
@@ -1435,137 +1568,44 @@ def use_configuration(
         CONFIG = saved_config
 
 
+def _normalize_input(entry: Union[ScopeWithOptionalPriority, str]) -> ScopeWithPriority:
+    if isinstance(entry, tuple):
+        return entry
+
+    default_priority = ConfigScopePriority.CONFIG_FILES
+    if isinstance(entry, ConfigScope):
+        return default_priority, entry
+
+    # Otherwise we need to construct it
+    path = os.path.normpath(entry)
+    assert os.path.isdir(path), f'"{path}" must be a directory'
+    name = os.path.basename(path)
+    return default_priority, DirectoryConfigScope(name, path)
+
+
 @lang.memoized
-def _config_from(scopes_or_paths: List[Union[ConfigScope, str]]) -> Configuration:
-    scopes = []
-    for scope_or_path in scopes_or_paths:
-        # If we have a config scope we are already done
-        if isinstance(scope_or_path, ConfigScope):
-            scopes.append(scope_or_path)
-            continue
-
-        # Otherwise we need to construct it
-        path = os.path.normpath(scope_or_path)
-        assert os.path.isdir(path), f'"{path}" must be a directory'
-        name = os.path.basename(path)
-        scopes.append(DirectoryConfigScope(name, path))
-
-    configuration = Configuration(*scopes)
-    return configuration
-
-
-def raw_github_gitlab_url(url: str) -> str:
-    """Transform a github URL to the raw form to avoid undesirable html.
+def create_from(*scopes_or_paths: Union[ScopeWithOptionalPriority, str]) -> Configuration:
+    """Creates a configuration object from the scopes passed in input.
 
     Args:
-        url: url to be converted to raw form
+        *scopes_or_paths: either a tuple of (priority, ConfigScope), or a ConfigScope, or a string
+            If priority is not given, it is assumed to be ConfigScopePriority.CONFIG_FILES. If a
+            string is given, a DirectoryConfigScope is created from it.
 
-    Returns:
-        Raw github/gitlab url or the original url
+    Examples:
+
+        >>> builtin_scope = InternalConfigScope("_builtin", {"config": {"build_jobs": 1}})
+        >>> cl_scope = InternalConfigScope("command_line", {"config": {"build_jobs": 10}})
+        >>> cfg = create_from(
+        ...     (ConfigScopePriority.COMMAND_LINE, cl_scope),
+        ...     (ConfigScopePriority.BUILTIN, builtin_scope)
+        ... )
     """
-    # Note we rely on GitHub to redirect the 'raw' URL returned here to the
-    # actual URL under https://raw.githubusercontent.com/ with '/blob'
-    # removed and or, '/blame' if needed.
-    if "github" in url or "gitlab" in url:
-        return url.replace("/blob/", "/raw/")
-
-    return url
-
-
-def collect_urls(base_url: str) -> list:
-    """Return a list of configuration URLs.
-
-    Arguments:
-        base_url: URL for a configuration (yaml) file or a directory
-            containing yaml file(s)
-
-    Returns:
-        List of configuration file(s) or empty list if none
-    """
-    if not base_url:
-        return []
-
-    extension = ".yaml"
-
-    if base_url.endswith(extension):
-        return [base_url]
-
-    # Collect configuration URLs if the base_url is a "directory".
-    _, links = web_util.spider(base_url, 0)
-    return [link for link in links if link.endswith(extension)]
-
-
-def fetch_remote_configs(url: str, dest_dir: str, skip_existing: bool = True) -> str:
-    """Retrieve configuration file(s) at the specified URL.
-
-    Arguments:
-        url: URL for a configuration (yaml) file or a directory containing
-            yaml file(s)
-        dest_dir: destination directory
-        skip_existing: Skip files that already exist in dest_dir if
-            ``True``; otherwise, replace those files
-
-    Returns:
-        Path to the corresponding file if URL is or contains a
-        single file and it is the only file in the destination directory or
-        the root (dest_dir) directory if multiple configuration files exist
-        or are retrieved.
-    """
-
-    def _fetch_file(url):
-        raw = raw_github_gitlab_url(url)
-        tty.debug(f"Reading config from url {raw}")
-        return web_util.fetch_url_text(raw, dest_dir=dest_dir)
-
-    if not url:
-        raise ConfigFileError("Cannot retrieve configuration without a URL")
-
-    # Return the local path to the cached configuration file OR to the
-    # directory containing the cached configuration files.
-    config_links = collect_urls(url)
-    existing_files = os.listdir(dest_dir) if os.path.isdir(dest_dir) else []
-
-    paths = []
-    for config_url in config_links:
-        basename = os.path.basename(config_url)
-        if skip_existing and basename in existing_files:
-            tty.warn(
-                f"Will not fetch configuration from {config_url} since a "
-                f"version already exists in {dest_dir}"
-            )
-            path = os.path.join(dest_dir, basename)
-        else:
-            path = _fetch_file(config_url)
-
-        if path:
-            paths.append(path)
-
-    if paths:
-        return dest_dir if len(paths) > 1 else paths[0]
-
-    raise ConfigFileError(f"Cannot retrieve configuration (yaml) from {url}")
-
-
-def get_mark_from_yaml_data(obj):
-    """Try to get ``spack.util.spack_yaml`` mark from YAML data.
-
-    We try the object, and if that fails we try its first member (if it's a container).
-
-    Returns:
-        mark if one is found, otherwise None.
-    """
-    # mark of object itelf
-    mark = getattr(obj, "_start_mark", None)
-    if mark:
-        return mark
-
-    # mark of first member if it is a container
-    if isinstance(obj, (list, dict)):
-        first_member = next(iter(obj), None)
-        if first_member:
-            mark = getattr(first_member, "_start_mark", None)
-
-    return mark
+    scopes_with_priority = [_normalize_input(x) for x in scopes_or_paths]
+    result = Configuration()
+    for priority, scope in scopes_with_priority:
+        result.push_scope(scope, priority=priority)
+    return result
 
 
 def determine_number_of_jobs(
@@ -1672,3 +1712,7 @@ def get_path(path, data):
 
         # give up and return None if nothing worked
         return None
+
+
+class RecursiveIncludeError(spack.error.SpackError):
+    """Too many levels of recursive includes."""

lib/spack/spack/database.py

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

lib/spack/spack/detection/path.py

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

lib/spack/spack/directives.py

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

lib/spack/spack/directory_layout.py

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

lib/spack/spack/enums.py

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

lib/spack/spack/environment/depfile.py

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

lib/spack/spack/environment/environment.py

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

lib/spack/spack/environment/shell.py

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

lib/spack/spack/filesystem_view.py

@@ -10,7 +10,7 @@
 import stat
 import sys
 import tempfile
-from typing import Callable, Dict, Optional
+from typing import Callable, Dict, List, Optional
 
 from typing_extensions import Literal
 
@@ -78,7 +78,7 @@ def view_copy(
 
     # Order of this dict is somewhat irrelevant
     prefix_to_projection = {
-        s.prefix: view.get_projection_for_spec(s)
+        str(s.prefix): view.get_projection_for_spec(s)
         for s in spec.traverse(root=True, order="breadth")
         if not s.external
     }
@@ -185,7 +185,7 @@ def __init__(
     def link(self, src: str, dst: str, spec: Optional[spack.spec.Spec] = None) -> None:
         self._link(src, dst, self, spec)
 
-    def add_specs(self, *specs, **kwargs):
+    def add_specs(self, *specs: spack.spec.Spec, **kwargs) -> None:
         """
         Add given specs to view.
 
@@ -200,19 +200,19 @@ def add_specs(self, *specs, **kwargs):
         """
         raise NotImplementedError
 
-    def add_standalone(self, spec):
+    def add_standalone(self, spec: spack.spec.Spec) -> bool:
         """
         Add (link) a standalone package into this view.
         """
         raise NotImplementedError
 
-    def check_added(self, spec):
+    def check_added(self, spec: spack.spec.Spec) -> bool:
         """
         Check if the given concrete spec is active in this view.
         """
         raise NotImplementedError
 
-    def remove_specs(self, *specs, **kwargs):
+    def remove_specs(self, *specs: spack.spec.Spec, **kwargs) -> None:
         """
         Removes given specs from view.
 
@@ -231,25 +231,25 @@ def remove_specs(self, *specs, **kwargs):
         """
         raise NotImplementedError
 
-    def remove_standalone(self, spec):
+    def remove_standalone(self, spec: spack.spec.Spec) -> None:
         """
         Remove (unlink) a standalone package from this view.
         """
         raise NotImplementedError
 
-    def get_projection_for_spec(self, spec):
+    def get_projection_for_spec(self, spec: spack.spec.Spec) -> str:
         """
         Get the projection in this view for a spec.
         """
         raise NotImplementedError
 
-    def get_all_specs(self):
+    def get_all_specs(self) -> List[spack.spec.Spec]:
         """
         Get all specs currently active in this view.
         """
         raise NotImplementedError
 
-    def get_spec(self, spec):
+    def get_spec(self, spec: spack.spec.Spec) -> Optional[spack.spec.Spec]:
         """
         Return the actual spec linked in this view (i.e. do not look it up
         in the database by name).
@@ -263,7 +263,7 @@ def get_spec(self, spec):
         """
         raise NotImplementedError
 
-    def print_status(self, *specs, **kwargs):
+    def print_status(self, *specs: spack.spec.Spec, **kwargs) -> None:
         """
         Print a short summary about the given specs, detailing whether..
             * ..they are active in the view.
@@ -643,7 +643,7 @@ def print_status(self, *specs, **kwargs):
                 specs.sort()
 
                 abbreviated = [
-                    s.cformat("{name}{@version}{%compiler}{compiler_flags}{variants}")
+                    s.cformat("{name}{@version}{compiler_flags}{variants}{%compiler}")
                     for s in specs
                 ]
 
@@ -694,7 +694,7 @@ def _sanity_check_view_projection(self, specs):
                 raise ConflictingSpecsError(current_spec, conflicting_spec)
             seen[metadata_dir] = current_spec
 
-    def add_specs(self, *specs: spack.spec.Spec) -> None:
+    def add_specs(self, *specs, **kwargs) -> None:
         """Link a root-to-leaf topologically ordered list of specs into the view."""
         assert all((s.concrete for s in specs))
         if len(specs) == 0:
@@ -831,7 +831,7 @@ def get_projection_for_spec(self, spec):
 #####################
 # utility functions #
 #####################
-def get_spec_from_file(filename):
+def get_spec_from_file(filename) -> Optional[spack.spec.Spec]:
     try:
         with open(filename, "r", encoding="utf-8") as f:
             return spack.spec.Spec.from_yaml(f)

lib/spack/spack/graph.py

@@ -482,7 +482,7 @@ class SimpleDAG(DotGraphBuilder):
     """Simple DOT graph, with nodes colored uniformly and edges without properties"""
 
     def node_entry(self, node):
-        format_option = "{name}{@version}{%compiler}{/hash:7}"
+        format_option = "{name}{@version}{/hash:7}{%compiler}"
         return node.dag_hash(), f'[label="{node.format(format_option)}"]'
 
     def edge_entry(self, edge):
@@ -515,7 +515,7 @@ def visit(self, edge):
         super().visit(edge)
 
     def node_entry(self, node):
-        node_str = node.format("{name}{@version}{%compiler}{/hash:7}")
+        node_str = node.format("{name}{@version}{/hash:7}{%compiler}")
         options = f'[label="{node_str}", group="build_dependencies", fillcolor="coral"]'
         if node.dag_hash() in self.main_unified_space:
             options = f'[label="{node_str}", group="main_psid"]'

lib/spack/spack/hash_types.py

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

lib/spack/spack/hooks/resolve_shared_libraries.py

@@ -2,200 +2,14 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import fnmatch
 import io
-import os
-import re
-from typing import Dict, List, Union
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import BaseDirectoryVisitor, visit_directory_tree
-from llnl.util.lang import stable_partition
+from llnl.util.filesystem import visit_directory_tree
 
 import spack.config
 import spack.error
-import spack.util.elf as elf
-
-#: Patterns for names of libraries that are allowed to be unresolved when *just* looking at RPATHs
-#: added by Spack. These are libraries outside of Spack's control, and assumed to be located in
-#: default search paths of the dynamic linker.
-ALLOW_UNRESOLVED = [
-    # kernel
-    "linux-vdso.so.*",
-    "libselinux.so.*",
-    # musl libc
-    "ld-musl-*.so.*",
-    # glibc
-    "ld-linux*.so.*",
-    "ld64.so.*",
-    "libanl.so.*",
-    "libc.so.*",
-    "libdl.so.*",
-    "libm.so.*",
-    "libmemusage.so.*",
-    "libmvec.so.*",
-    "libnsl.so.*",
-    "libnss_compat.so.*",
-    "libnss_db.so.*",
-    "libnss_dns.so.*",
-    "libnss_files.so.*",
-    "libnss_hesiod.so.*",
-    "libpcprofile.so.*",
-    "libpthread.so.*",
-    "libresolv.so.*",
-    "librt.so.*",
-    "libSegFault.so.*",
-    "libthread_db.so.*",
-    "libutil.so.*",
-    # gcc -- this is required even with gcc-runtime, because e.g. libstdc++ depends on libgcc_s,
-    # but the binaries we copy from the compiler don't have an $ORIGIN rpath.
-    "libasan.so.*",
-    "libatomic.so.*",
-    "libcc1.so.*",
-    "libgcc_s.so.*",
-    "libgfortran.so.*",
-    "libgomp.so.*",
-    "libitm.so.*",
-    "liblsan.so.*",
-    "libquadmath.so.*",
-    "libssp.so.*",
-    "libstdc++.so.*",
-    "libtsan.so.*",
-    "libubsan.so.*",
-    # systemd
-    "libudev.so.*",
-    # cuda driver
-    "libcuda.so.*",
-    # intel-oneapi-runtime
-    "libur_loader.so.*",
-]
-
-
-def is_compatible(parent: elf.ElfFile, child: elf.ElfFile) -> bool:
-    return (
-        child.elf_hdr.e_type == elf.ELF_CONSTANTS.ET_DYN
-        and parent.is_little_endian == child.is_little_endian
-        and parent.is_64_bit == child.is_64_bit
-        and parent.elf_hdr.e_machine == child.elf_hdr.e_machine
-    )
-
-
-def candidate_matches(current_elf: elf.ElfFile, candidate_path: bytes) -> bool:
-    try:
-        with open(candidate_path, "rb") as g:
-            return is_compatible(current_elf, elf.parse_elf(g))
-    except (OSError, elf.ElfParsingError):
-        return False
-
-
-class Problem:
-    def __init__(
-        self, resolved: Dict[bytes, bytes], unresolved: List[bytes], relative_rpaths: List[bytes]
-    ) -> None:
-        self.resolved = resolved
-        self.unresolved = unresolved
-        self.relative_rpaths = relative_rpaths
-
-
-class ResolveSharedElfLibDepsVisitor(BaseDirectoryVisitor):
-    def __init__(self, allow_unresolved_patterns: List[str]) -> None:
-        self.problems: Dict[str, Problem] = {}
-        self._allow_unresolved_regex = re.compile(
-            "|".join(fnmatch.translate(x) for x in allow_unresolved_patterns)
-        )
-
-    def allow_unresolved(self, needed: bytes) -> bool:
-        try:
-            name = needed.decode("utf-8")
-        except UnicodeDecodeError:
-            return False
-        return bool(self._allow_unresolved_regex.match(name))
-
-    def visit_file(self, root: str, rel_path: str, depth: int) -> None:
-        # We work with byte strings for paths.
-        path = os.path.join(root, rel_path).encode("utf-8")
-
-        # For $ORIGIN interpolation: should not have trailing dir seperator.
-        origin = os.path.dirname(path)
-
-        # Retrieve the needed libs + rpaths.
-        try:
-            with open(path, "rb") as f:
-                parsed_elf = elf.parse_elf(f, interpreter=False, dynamic_section=True)
-        except (OSError, elf.ElfParsingError):
-            # Not dealing with an invalid ELF file.
-            return
-
-        # If there's no needed libs all is good
-        if not parsed_elf.has_needed:
-            return
-
-        # Get the needed libs and rpaths (notice: byte strings)
-        # Don't force an encoding cause paths are just a bag of bytes.
-        needed_libs = parsed_elf.dt_needed_strs
-
-        rpaths = parsed_elf.dt_rpath_str.split(b":") if parsed_elf.has_rpath else []
-
-        # We only interpolate $ORIGIN, not $LIB and $PLATFORM, they're not really
-        # supported in general. Also remove empty paths.
-        rpaths = [x.replace(b"$ORIGIN", origin) for x in rpaths if x]
-
-        # Do not allow relative rpaths (they are relative to the current working directory)
-        rpaths, relative_rpaths = stable_partition(rpaths, os.path.isabs)
-
-        # If there's a / in the needed lib, it's opened directly, otherwise it needs
-        # a search.
-        direct_libs, search_libs = stable_partition(needed_libs, lambda x: b"/" in x)
-
-        # Do not allow relative paths in direct libs (they are relative to the current working
-        # directory)
-        direct_libs, unresolved = stable_partition(direct_libs, os.path.isabs)
-
-        resolved: Dict[bytes, bytes] = {}
-
-        for lib in search_libs:
-            if self.allow_unresolved(lib):
-                continue
-            for rpath in rpaths:
-                candidate = os.path.join(rpath, lib)
-                if candidate_matches(parsed_elf, candidate):
-                    resolved[lib] = candidate
-                    break
-            else:
-                unresolved.append(lib)
-
-        # Check if directly opened libs are compatible
-        for lib in direct_libs:
-            if candidate_matches(parsed_elf, lib):
-                resolved[lib] = lib
-            else:
-                unresolved.append(lib)
-
-        if unresolved or relative_rpaths:
-            self.problems[rel_path] = Problem(resolved, unresolved, relative_rpaths)
-
-    def visit_symlinked_file(self, root: str, rel_path: str, depth: int) -> None:
-        pass
-
-    def before_visit_dir(self, root: str, rel_path: str, depth: int) -> bool:
-        # There can be binaries in .spack/test which shouldn't be checked.
-        if rel_path == ".spack":
-            return False
-        return True
-
-    def before_visit_symlinked_dir(self, root: str, rel_path: str, depth: int) -> bool:
-        return False
-
-
-class CannotLocateSharedLibraries(spack.error.SpackError):
-    pass
-
-
-def maybe_decode(byte_str: bytes) -> Union[str, bytes]:
-    try:
-        return byte_str.decode("utf-8")
-    except UnicodeDecodeError:
-        return byte_str
+import spack.verify_libraries
 
 
 def post_install(spec, explicit):
@@ -206,36 +20,23 @@ def post_install(spec, explicit):
     if policy == "ignore" or spec.external or spec.platform not in ("linux", "freebsd"):
         return
 
-    visitor = ResolveSharedElfLibDepsVisitor(
-        [*ALLOW_UNRESOLVED, *spec.package.unresolved_libraries]
+    visitor = spack.verify_libraries.ResolveSharedElfLibDepsVisitor(
+        [*spack.verify_libraries.ALLOW_UNRESOLVED, *spec.package.unresolved_libraries]
     )
     visit_directory_tree(spec.prefix, visitor)
 
-    # All good?
     if not visitor.problems:
         return
 
-    # For now just list the issues (print it in ldd style, except we don't recurse)
-    output = io.StringIO()
-    output.write("not all executables and libraries can resolve their dependencies:\n")
-    for path, problem in visitor.problems.items():
-        output.write(path)
-        output.write("\n")
-        for needed, full_path in problem.resolved.items():
-            output.write("        ")
-            if needed == full_path:
-                output.write(maybe_decode(needed))
-            else:
-                output.write(f"{maybe_decode(needed)} => {maybe_decode(full_path)}")
-            output.write("\n")
-        for not_found in problem.unresolved:
-            output.write(f"        {maybe_decode(not_found)} => not found\n")
-        for relative_rpath in problem.relative_rpaths:
-            output.write(f"        {maybe_decode(relative_rpath)} => relative rpath\n")
-
+    output = io.StringIO("not all executables and libraries can resolve their dependencies:\n")
+    visitor.write(output)
     message = output.getvalue().strip()
 
     if policy == "error":
         raise CannotLocateSharedLibraries(message)
 
     tty.warn(message)
+
+
+class CannotLocateSharedLibraries(spack.error.SpackError):
+    pass

lib/spack/spack/install_test.py

@@ -21,7 +21,6 @@
 from llnl.util.lang import nullcontext
 from llnl.util.tty.color import colorize
 
-import spack.build_environment
 import spack.config
 import spack.error
 import spack.package_base
@@ -398,7 +397,7 @@ def stand_alone_tests(self, kwargs):
         Args:
             kwargs (dict): arguments to be used by the test process
         """
-        import spack.build_environment
+        import spack.build_environment  # avoid circular dependency
 
         spack.build_environment.start_build_process(self.pkg, test_process, kwargs)
 
@@ -463,6 +462,8 @@ def write_tested_status(self):
 
 @contextlib.contextmanager
 def test_part(pkg: Pb, test_name: str, purpose: str, work_dir: str = ".", verbose: bool = False):
+    import spack.build_environment  # avoid circular dependency
+
     wdir = "." if work_dir is None else work_dir
     tester = pkg.tester
     assert test_name and test_name.startswith(

lib/spack/spack/main.py

@@ -47,6 +47,8 @@
 import spack.util.environment
 import spack.util.lock
 
+from .enums import ConfigScopePriority
+
 #: names of profile statistics
 stat_names = pstats.Stats.sort_arg_dict_default
 
@@ -872,14 +874,19 @@ def add_command_line_scopes(
         scopes = ev.environment_path_scopes(name, path)
         if scopes is None:
             if os.path.isdir(path):  # directory with config files
-                cfg.push_scope(spack.config.DirectoryConfigScope(name, path, writable=False))
-                spack.config._add_platform_scope(cfg, name, path, writable=False)
+                cfg.push_scope(
+                    spack.config.DirectoryConfigScope(name, path, writable=False),
+                    priority=ConfigScopePriority.CUSTOM,
+                )
+                spack.config._add_platform_scope(
+                    cfg, name, path, priority=ConfigScopePriority.CUSTOM, writable=False
+                )
                 continue
             else:
                 raise spack.error.ConfigError(f"Invalid configuration scope: {path}")
 
         for scope in scopes:
-            cfg.push_scope(scope)
+            cfg.push_scope(scope, priority=ConfigScopePriority.CUSTOM)
 
 
 def _main(argv=None):
@@ -952,7 +959,9 @@ def _main(argv=None):
     # Push scopes from the command line last
     if args.config_scopes:
         add_command_line_scopes(spack.config.CONFIG, args.config_scopes)
-    spack.config.CONFIG.push_scope(spack.config.InternalConfigScope("command_line"))
+    spack.config.CONFIG.push_scope(
+        spack.config.InternalConfigScope("command_line"), priority=ConfigScopePriority.COMMAND_LINE
+    )
     setup_main_options(args)
 
     # ------------------------------------------------------------------------
@@ -998,6 +1007,7 @@ def finish_parse_and_run(parser, cmd_name, main_args, env_format_error):
     args, unknown = parser.parse_known_args(main_args.command)
     # we need to inherit verbose since the install command checks for it
     args.verbose = main_args.verbose
+    args.lines = main_args.lines
 
     # Now that we know what command this is and what its args are, determine
     # whether we can continue with a bad environment and raise if not.

lib/spack/spack/modules/common.py

@@ -564,6 +564,12 @@ def __init__(self, configuration):
     def spec(self):
         return self.conf.spec
 
+    @tengine.context_property
+    def tags(self):
+        if not hasattr(self.spec.package, "tags"):
+            return []
+        return self.spec.package.tags
+
     @tengine.context_property
     def timestamp(self):
         return datetime.datetime.now()

lib/spack/spack/package_base.py

@@ -48,6 +48,7 @@
 import spack.store
 import spack.url
 import spack.util.environment
+import spack.util.executable
 import spack.util.path
 import spack.util.web
 import spack.variant
@@ -125,9 +126,10 @@ def windows_establish_runtime_linkage(self):
         # Spack should in general not modify things it has not installed
         # we can reasonably expect externals to have their link interface properly established
         if sys.platform == "win32" and not self.spec.external:
-            self.win_rpath.add_library_dependent(*self.win_add_library_dependent())
-            self.win_rpath.add_rpath(*self.win_add_rpath())
-            self.win_rpath.establish_link()
+            win_rpath = fsys.WindowsSimulatedRPath(self)
+            win_rpath.add_library_dependent(*self.win_add_library_dependent())
+            win_rpath.add_rpath(*self.win_add_rpath())
+            win_rpath.establish_link()
 
 
 #: Registers which are the detectable packages, by repo and package name
@@ -742,7 +744,6 @@ def __init__(self, spec):
         # Set up timing variables
         self._fetch_time = 0.0
 
-        self.win_rpath = fsys.WindowsSimulatedRPath(self)
         super().__init__()
 
     def __getitem__(self, key: str) -> "PackageBase":
@@ -1287,12 +1288,13 @@ def extendee_spec(self):
         if not self.extendees:
             return None
 
-        deps = []
-
         # If the extendee is in the spec's deps already, return that.
-        for dep in self.spec.traverse(deptype=("link", "run")):
-            if dep.name in self.extendees:
-                deps.append(dep)
+        deps = [
+            dep
+            for dep in self.spec.dependencies(deptype=("link", "run"))
+            for d, when in self.extendees.values()
+            if dep.satisfies(d) and self.spec.satisfies(when)
+        ]
 
         if deps:
             assert len(deps) == 1
@@ -1369,6 +1371,14 @@ def prefix(self):
     def home(self):
         return self.prefix
 
+    @property
+    def command(self) -> spack.util.executable.Executable:
+        """Returns the main executable for this package."""
+        path = os.path.join(self.home.bin, self.spec.name)
+        if fsys.is_exe(path):
+            return spack.util.executable.Executable(path)
+        raise RuntimeError(f"Unable to locate {self.spec.name} command in {self.home.bin}")
+
     @property  # type: ignore[misc]
     @memoized
     def compiler(self):

lib/spack/spack/patch.py

@@ -83,6 +83,7 @@ def __init__(
         level: int,
         working_dir: str,
         reverse: bool = False,
+        ordering_key: Optional[Tuple[str, int]] = None,
     ) -> None:
         """Initialize a new Patch instance.
 
@@ -92,6 +93,7 @@ def __init__(
             level: patch level
             working_dir: relative path *within* the stage to change to
             reverse: reverse the patch
+            ordering_key: key used to ensure patches are applied in a consistent order
         """
         # validate level (must be an integer >= 0)
         if not isinstance(level, int) or not level >= 0:
@@ -105,6 +107,13 @@ def __init__(
         self.working_dir = working_dir
         self.reverse = reverse
 
+        # The ordering key is passed when executing package.py directives, and is only relevant
+        # after a solve to build concrete specs with consistently ordered patches. For concrete
+        # specs read from a file, we add patches in the order of its patches variants and the
+        # ordering_key is irrelevant. In that case, use a default value so we don't need to branch
+        # on whether ordering_key is None where it's used, just to make static analysis happy.
+        self.ordering_key: Tuple[str, int] = ordering_key or ("", 0)
+
     def apply(self, stage: "spack.stage.Stage") -> None:
         """Apply a patch to source in a stage.
 
@@ -202,9 +211,8 @@ def __init__(
             msg += "package %s.%s does not exist." % (pkg.namespace, pkg.name)
             raise ValueError(msg)
 
-        super().__init__(pkg, abs_path, level, working_dir, reverse)
+        super().__init__(pkg, abs_path, level, working_dir, reverse, ordering_key)
         self.path = abs_path
-        self.ordering_key = ordering_key
 
     @property
     def sha256(self) -> str:
@@ -266,13 +274,11 @@ def __init__(
             archive_sha256: sha256 sum of the *archive*, if the patch is compressed
                 (only required for compressed URL patches)
         """
-        super().__init__(pkg, url, level, working_dir, reverse)
+        super().__init__(pkg, url, level, working_dir, reverse, ordering_key)
 
         self.url = url
         self._stage: Optional["spack.stage.Stage"] = None
 
-        self.ordering_key = ordering_key
-
         if allowed_archive(self.url) and not archive_sha256:
             raise spack.error.PatchDirectiveError(
                 "Compressed patches require 'archive_sha256' "

lib/spack/spack/paths.py

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

lib/spack/spack/repo.py

@@ -32,6 +32,7 @@
 import llnl.util.tty as tty
 from llnl.util.filesystem import working_dir
 
+import spack
 import spack.caches
 import spack.config
 import spack.error
@@ -49,6 +50,8 @@
 #: Package modules are imported as spack.pkg.<repo-namespace>.<pkg-name>
 ROOT_PYTHON_NAMESPACE = "spack.pkg"
 
+_API_REGEX = re.compile(r"^v(\d+)\.(\d+)$")
+
 
 def python_package_for_repo(namespace):
     """Returns the full namespace of a repository, given its relative one
@@ -909,19 +912,52 @@ def __reduce__(self):
         return RepoPath.unmarshal, self.marshal()
 
 
+def _parse_package_api_version(
+    config: Dict[str, Any],
+    min_api: Tuple[int, int] = spack.min_package_api_version,
+    max_api: Tuple[int, int] = spack.package_api_version,
+) -> Tuple[int, int]:
+    api = config.get("api")
+    if api is None:
+        package_api = (1, 0)
+    else:
+        if not isinstance(api, str):
+            raise BadRepoError(f"Invalid Package API version '{api}'. Must be of the form vX.Y")
+        api_match = _API_REGEX.match(api)
+        if api_match is None:
+            raise BadRepoError(f"Invalid Package API version '{api}'. Must be of the form vX.Y")
+        package_api = (int(api_match.group(1)), int(api_match.group(2)))
+
+    if min_api <= package_api <= max_api:
+        return package_api
+
+    min_str = ".".join(str(i) for i in min_api)
+    max_str = ".".join(str(i) for i in max_api)
+    curr_str = ".".join(str(i) for i in package_api)
+    raise BadRepoError(
+        f"Package API v{curr_str} is not supported by this version of Spack ("
+        f"must be between v{min_str} and v{max_str})"
+    )
+
+
 class Repo:
     """Class representing a package repository in the filesystem.
 
-    Each package repository must have a top-level configuration file
-    called `repo.yaml`.
+    Each package repository must have a top-level configuration file called `repo.yaml`.
 
-    Currently, `repo.yaml` must define:
+    It contains the following keys:
 
     `namespace`:
         A Python namespace where the repository's packages should live.
 
     `subdirectory`:
         An optional subdirectory name where packages are placed
+
+    `api`:
+        A string of the form vX.Y that indicates the Package API version. The default is "v1.0".
+        For the repo to be compatible with the current version of Spack, the version must be
+        greater than or equal to :py:data:`spack.min_package_api_version` and less than or equal to
+        :py:data:`spack.package_api_version`.
     """
 
     def __init__(
@@ -958,7 +994,7 @@ def check(condition, msg):
             f"{os.path.join(root, repo_config_name)} must define a namespace.",
         )
 
-        self.namespace = config["namespace"]
+        self.namespace: str = config["namespace"]
         check(
             re.match(r"[a-zA-Z][a-zA-Z0-9_.]+", self.namespace),
             f"Invalid namespace '{self.namespace}' in repo '{self.root}'. "
@@ -971,12 +1007,14 @@ def check(condition, msg):
         # Keep name components around for checking prefixes.
         self._names = self.full_namespace.split(".")
 
-        packages_dir = config.get("subdirectory", packages_dir_name)
+        packages_dir: str = config.get("subdirectory", packages_dir_name)
         self.packages_path = os.path.join(self.root, packages_dir)
         check(
             os.path.isdir(self.packages_path), f"No directory '{packages_dir}' found in '{root}'"
         )
 
+        self.package_api = _parse_package_api_version(config)
+
         # Class attribute overrides by package name
         self.overrides = overrides or {}
 
@@ -1026,7 +1064,7 @@ def is_prefix(self, fullname: str) -> bool:
         parts = fullname.split(".")
         return self._names[: len(parts)] == parts
 
-    def _read_config(self) -> Dict[str, str]:
+    def _read_config(self) -> Dict[str, Any]:
         """Check for a YAML config file in this db's root directory."""
         try:
             with open(self.config_file, encoding="utf-8") as reponame_file:
@@ -1179,9 +1217,8 @@ def all_package_paths(self) -> Generator[str, None, None]:
             yield self.package_path(name)
 
     def packages_with_tags(self, *tags: str) -> Set[str]:
-        v = set(self.tag_index[tags[0].lower()])
-        for tag in tags[1:]:
-            v.intersection_update(self.tag_index[tag.lower()])
+        v = set(self.all_package_names())
+        v.intersection_update(*(self.tag_index[tag.lower()] for tag in tags))
         return v
 
     def all_package_classes(self) -> Generator[Type["spack.package_base.PackageBase"], None, None]:
@@ -1369,6 +1406,8 @@ def create_repo(root, namespace=None, subdir=packages_dir_name):
             config.write(f"  namespace: '{namespace}'\n")
             if subdir != packages_dir_name:
                 config.write(f"  subdirectory: '{subdir}'\n")
+            x, y = spack.package_api_version
+            config.write(f"  api: v{x}.{y}\n")
 
     except OSError as e:
         # try to clean up.

lib/spack/spack/schema/__init__.py

@@ -7,8 +7,7 @@
 import warnings
 
 import jsonschema
-
-import llnl.util.lang
+import jsonschema.validators
 
 from spack.error import SpecSyntaxError
 
@@ -18,59 +17,59 @@ class DeprecationMessage(typing.NamedTuple):
     error: bool
 
 
-# jsonschema is imported lazily as it is heavy to import
-# and increases the start-up time
-def _make_validator():
-    def _validate_spec(validator, is_spec, instance, schema):
-        """Check if the attributes on instance are valid specs."""
-        import spack.spec_parser
+def _validate_spec(validator, is_spec, instance, schema):
+    """Check if all additional keys are valid specs."""
+    import spack.spec_parser
 
-        if not validator.is_type(instance, "object"):
-            return
+    if not validator.is_type(instance, "object"):
+        return
 
-        for spec_str in instance:
-            try:
-                spack.spec_parser.parse(spec_str)
-            except SpecSyntaxError:
-                yield jsonschema.ValidationError(f"the key '{spec_str}' is not a valid spec")
+    properties = schema.get("properties") or {}
 
-    def _deprecated_properties(validator, deprecated, instance, schema):
-        if not (validator.is_type(instance, "object") or validator.is_type(instance, "array")):
-            return
-
-        if not deprecated:
-            return
-
-        deprecations = {
-            name: DeprecationMessage(message=x["message"], error=x["error"])
-            for x in deprecated
-            for name in x["names"]
-        }
-
-        # Get a list of the deprecated properties, return if there is none
-        issues = [entry for entry in instance if entry in deprecations]
-        if not issues:
-            return
-
-        # Process issues
-        errors = []
-        for name in issues:
-            msg = deprecations[name].message.format(name=name)
-            if deprecations[name].error:
-                errors.append(msg)
-            else:
-                warnings.warn(msg)
-
-        if errors:
-            yield jsonschema.ValidationError("\n".join(errors))
-
-    return jsonschema.validators.extend(
-        jsonschema.Draft7Validator,
-        {"validate_spec": _validate_spec, "deprecatedProperties": _deprecated_properties},
-    )
+    for spec_str in instance:
+        if spec_str in properties:
+            continue
+        try:
+            spack.spec_parser.parse(spec_str)
+        except SpecSyntaxError:
+            yield jsonschema.ValidationError(f"the key '{spec_str}' is not a valid spec")
 
 
-Validator = llnl.util.lang.Singleton(_make_validator)
+def _deprecated_properties(validator, deprecated, instance, schema):
+    if not (validator.is_type(instance, "object") or validator.is_type(instance, "array")):
+        return
+
+    if not deprecated:
+        return
+
+    deprecations = {
+        name: DeprecationMessage(message=x["message"], error=x["error"])
+        for x in deprecated
+        for name in x["names"]
+    }
+
+    # Get a list of the deprecated properties, return if there is none
+    issues = [entry for entry in instance if entry in deprecations]
+    if not issues:
+        return
+
+    # Process issues
+    errors = []
+    for name in issues:
+        msg = deprecations[name].message.format(name=name)
+        if deprecations[name].error:
+            errors.append(msg)
+        else:
+            warnings.warn(msg)
+
+    if errors:
+        yield jsonschema.ValidationError("\n".join(errors))
+
+
+Validator = jsonschema.validators.extend(
+    jsonschema.Draft7Validator,
+    {"additionalKeysAreSpecs": _validate_spec, "deprecatedProperties": _deprecated_properties},
+)
 
 
 def _append(string: str) -> bool:

lib/spack/spack/schema/config.py

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

lib/spack/spack/schema/env.py

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

lib/spack/spack/schema/include.py

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

lib/spack/spack/schema/merged.py

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

lib/spack/spack/schema/modules.py

@@ -39,7 +39,7 @@
         "load": array_of_strings,
         "suffixes": {
             "type": "object",
-            "validate_spec": True,
+            "additionalKeysAreSpecs": True,
             "additionalProperties": {"type": "string"},  # key
         },
         "environment": spack.schema.environment.definition,
@@ -48,40 +48,44 @@
 
 projections_scheme = spack.schema.projections.properties["projections"]
 
-module_type_configuration: Dict = {
+common_props = {
+    "verbose": {"type": "boolean", "default": False},
+    "hash_length": {"type": "integer", "minimum": 0, "default": 7},
+    "include": array_of_strings,
+    "exclude": array_of_strings,
+    "exclude_implicits": {"type": "boolean", "default": False},
+    "defaults": array_of_strings,
+    "hide_implicits": {"type": "boolean", "default": False},
+    "naming_scheme": {"type": "string"},
+    "projections": projections_scheme,
+    "all": module_file_configuration,
+}
+
+tcl_configuration = {
     "type": "object",
     "default": {},
-    "validate_spec": True,
-    "properties": {
-        "verbose": {"type": "boolean", "default": False},
-        "hash_length": {"type": "integer", "minimum": 0, "default": 7},
-        "include": array_of_strings,
-        "exclude": array_of_strings,
-        "exclude_implicits": {"type": "boolean", "default": False},
-        "defaults": array_of_strings,
-        "hide_implicits": {"type": "boolean", "default": False},
-        "naming_scheme": {"type": "string"},
-        "projections": projections_scheme,
-        "all": module_file_configuration,
-    },
+    "additionalKeysAreSpecs": True,
+    "properties": {**common_props},
     "additionalProperties": module_file_configuration,
 }
 
-tcl_configuration = module_type_configuration.copy()
-
-lmod_configuration = module_type_configuration.copy()
-lmod_configuration["properties"].update(
-    {
+lmod_configuration = {
+    "type": "object",
+    "default": {},
+    "additionalKeysAreSpecs": True,
+    "properties": {
+        **common_props,
         "core_compilers": array_of_strings,
         "hierarchy": array_of_strings,
         "core_specs": array_of_strings,
         "filter_hierarchy_specs": {
             "type": "object",
-            "validate_spec": True,
+            "additionalKeysAreSpecs": True,
             "additionalProperties": array_of_strings,
         },
-    }
-)
+    },
+    "additionalProperties": module_file_configuration,
+}
 
 module_config_properties = {
     "use_view": {"anyOf": [{"type": "string"}, {"type": "boolean"}]},

lib/spack/spack/solver/asp.py

@@ -5,9 +5,12 @@
 import collections.abc
 import copy
 import enum
+import errno
 import functools
+import hashlib
 import io
 import itertools
+import json
 import os
 import pathlib
 import pprint
@@ -17,12 +20,25 @@
 import typing
 import warnings
 from contextlib import contextmanager
-from typing import Callable, Dict, Iterator, List, NamedTuple, Optional, Set, Tuple, Type, Union
+from typing import (
+    IO,
+    Callable,
+    Dict,
+    Iterator,
+    List,
+    NamedTuple,
+    Optional,
+    Set,
+    Tuple,
+    Type,
+    Union,
+)
 
 import archspec.cpu
 
 import llnl.util.lang
 import llnl.util.tty as tty
+from llnl.util.filesystem import current_file_position
 from llnl.util.lang import elide_list
 
 import spack
@@ -36,19 +52,24 @@
 import spack.error
 import spack.package_base
 import spack.package_prefs
+import spack.patch
+import spack.paths
 import spack.platforms
 import spack.repo
 import spack.solver.splicing
 import spack.spec
 import spack.store
 import spack.util.crypto
+import spack.util.hash
 import spack.util.libc
+import spack.util.module_cmd as md
 import spack.util.path
 import spack.util.timer
 import spack.variant as vt
 import spack.version as vn
 import spack.version.git_ref_lookup
 from spack import traverse
+from spack.util.file_cache import FileCache
 
 from .core import (
     AspFunction,
@@ -536,6 +557,363 @@ def format_unsolved(unsolved_specs):
                 msg += "\n\t(No candidate specs from solver)"
         return msg
 
+    def to_dict(self, test: bool = False) -> dict:
+        """Produces dict representation of Result object
+
+        Does not include anything related to unsatisfiability as we
+        are only interested in storing satisfiable results
+        """
+        serial_node_arg = (
+            lambda node_dict: f"""{{"id": "{node_dict.id}", "pkg": "{node_dict.pkg}"}}"""
+        )
+        ret = dict()
+        ret["asp"] = self.asp
+        ret["criteria"] = self.criteria
+        ret["optimal"] = self.optimal
+        ret["warnings"] = self.warnings
+        ret["nmodels"] = self.nmodels
+        ret["abstract_specs"] = [str(x) for x in self.abstract_specs]
+        ret["satisfiable"] = self.satisfiable
+        serial_answers = []
+        for answer in self.answers:
+            serial_answer = answer[:2]
+            serial_answer_dict = {}
+            for node, spec in answer[2].items():
+                serial_answer_dict[serial_node_arg(node)] = spec.to_dict()
+            serial_answer = serial_answer + (serial_answer_dict,)
+            serial_answers.append(serial_answer)
+        ret["answers"] = serial_answers
+        ret["specs_by_input"] = {}
+        input_specs = {} if not self.specs_by_input else self.specs_by_input
+        for input, spec in input_specs.items():
+            ret["specs_by_input"][str(input)] = spec.to_dict()
+        return ret
+
+    @staticmethod
+    def from_dict(obj: dict):
+        """Returns Result object from compatible dictionary"""
+
+        def _dict_to_node_argument(dict):
+            id = dict["id"]
+            pkg = dict["pkg"]
+            return NodeArgument(id=id, pkg=pkg)
+
+        def _str_to_spec(spec_str):
+            return spack.spec.Spec(spec_str)
+
+        def _dict_to_spec(spec_dict):
+            loaded_spec = spack.spec.Spec.from_dict(spec_dict)
+            _ensure_external_path_if_external(loaded_spec)
+            spack.spec.Spec.ensure_no_deprecated(loaded_spec)
+            return loaded_spec
+
+        asp = obj.get("asp")
+        spec_list = obj.get("abstract_specs")
+        if not spec_list:
+            raise RuntimeError("Invalid json for concretization Result object")
+        if spec_list:
+            spec_list = [_str_to_spec(x) for x in spec_list]
+        result = Result(spec_list, asp)
+        result.criteria = obj.get("criteria")
+        result.optimal = obj.get("optimal")
+        result.warnings = obj.get("warnings")
+        result.nmodels = obj.get("nmodels")
+        result.satisfiable = obj.get("satisfiable")
+        result._unsolved_specs = []
+        answers = []
+        for answer in obj.get("answers", []):
+            loaded_answer = answer[:2]
+            answer_node_dict = {}
+            for node, spec in answer[2].items():
+                answer_node_dict[_dict_to_node_argument(json.loads(node))] = _dict_to_spec(spec)
+            loaded_answer.append(answer_node_dict)
+            answers.append(tuple(loaded_answer))
+        result.answers = answers
+        result._concrete_specs_by_input = {}
+        result._concrete_specs = []
+        for input, spec in obj.get("specs_by_input", {}).items():
+            result._concrete_specs_by_input[_str_to_spec(input)] = _dict_to_spec(spec)
+            result._concrete_specs.append(_dict_to_spec(spec))
+        return result
+
+
+class ConcretizationCache:
+    """Store for Spack concretization results and statistics
+
+    Serializes solver result objects and statistics to json and stores
+    at a given endpoint in a cache associated by the sha256 of the
+    asp problem and the involved control files.
+    """
+
+    def __init__(self, root: Union[str, None] = None):
+        root = root or spack.config.get(
+            "config:concretization_cache:url", spack.paths.default_conc_cache_path
+        )
+        self.root = pathlib.Path(spack.util.path.canonicalize_path(root))
+        self._fc = FileCache(self.root)
+        self._cache_manifest = ".cache_manifest"
+        self._manifest_queue: List[Tuple[pathlib.Path, int]] = []
+
+    def cleanup(self):
+        """Prunes the concretization cache according to configured size and entry
+        count limits. Cleanup is done in FIFO ordering."""
+        # TODO: determine a better default
+        entry_limit = spack.config.get("config:concretization_cache:entry_limit", 1000)
+        bytes_limit = spack.config.get("config:concretization_cache:size_limit", 3e8)
+        # lock the entire buildcache as we're removing a lot of data from the
+        # manifest and cache itself
+        with self._fc.read_transaction(self._cache_manifest) as f:
+            count, cache_bytes = self._extract_cache_metadata(f)
+            if not count or not cache_bytes:
+                return
+            entry_count = int(count)
+            manifest_bytes = int(cache_bytes)
+            # move beyond the metadata entry
+            f.readline()
+            if entry_count > entry_limit and entry_limit > 0:
+                with self._fc.write_transaction(self._cache_manifest) as (old, new):
+                    # prune the oldest 10% or until we have removed 10% of
+                    # total bytes starting from oldest entry
+                    # TODO: make this configurable?
+                    prune_count = entry_limit // 10
+                    lines_to_prune = f.readlines(prune_count)
+                    for i, line in enumerate(lines_to_prune):
+                        sha, cache_entry_bytes = self._parse_manifest_entry(line)
+                        if sha and cache_entry_bytes:
+                            cache_path = self._cache_path_from_hash(sha)
+                            if self._fc.remove(cache_path):
+                                entry_count -= 1
+                                manifest_bytes -= int(cache_entry_bytes)
+                        else:
+                            tty.warn(
+                                f"Invalid concretization cache entry: '{line}' on line: {i+1}"
+                            )
+                    self._write_manifest(f, entry_count, manifest_bytes)
+
+            elif manifest_bytes > bytes_limit and bytes_limit > 0:
+                with self._fc.write_transaction(self._cache_manifest) as (old, new):
+                    # take 10% of current size off
+                    prune_amount = bytes_limit // 10
+                    total_pruned = 0
+                    i = 0
+                    while total_pruned < prune_amount:
+                        sha, manifest_cache_bytes = self._parse_manifest_entry(f.readline())
+                        if sha and manifest_cache_bytes:
+                            entry_bytes = int(manifest_cache_bytes)
+                            cache_path = self.root / sha[:2] / sha
+                            if self._safe_remove(cache_path):
+                                entry_count -= 1
+                                entry_bytes -= entry_bytes
+                                total_pruned += entry_bytes
+                        else:
+                            tty.warn(
+                                "Invalid concretization cache entry "
+                                f"'{sha} {manifest_cache_bytes}' on line: {i}"
+                            )
+                        i += 1
+                    self._write_manifest(f, entry_count, manifest_bytes)
+            for cache_dir in self.root.iterdir():
+                if cache_dir.is_dir() and not any(cache_dir.iterdir()):
+                    self._safe_remove(cache_dir)
+
+    def cache_entries(self):
+        """Generator producing cache entries"""
+        for cache_dir in self.root.iterdir():
+            # ensure component is cache entry directory
+            # not metadata file
+            if cache_dir.is_dir():
+                for cache_entry in cache_dir.iterdir():
+                    if not cache_entry.is_dir():
+                        yield cache_entry
+                    else:
+                        raise RuntimeError(
+                            "Improperly formed concretization cache. "
+                            f"Directory {cache_entry.name} is improperly located "
+                            "within the concretization cache."
+                        )
+
+    def _parse_manifest_entry(self, line):
+        """Returns parsed manifest entry lines
+        with handling for invalid reads."""
+        if line:
+            cache_values = line.strip("\n").split(" ")
+            if len(cache_values) < 2:
+                tty.warn(f"Invalid cache entry at {line}")
+                return None, None
+        return None, None
+
+    def _write_manifest(self, manifest_file, entry_count, entry_bytes):
+        """Writes new concretization cache manifest file.
+
+        Arguments:
+            manifest_file: IO stream opened for readin
+                            and writing wrapping the manifest file
+                            with cursor at calltime set to location
+                            where manifest should be truncated
+            entry_count: new total entry count
+            entry_bytes: new total entry bytes count
+
+        """
+        persisted_entries = manifest_file.readlines()
+        manifest_file.truncate(0)
+        manifest_file.write(f"{entry_count} {entry_bytes}\n")
+        manifest_file.writelines(persisted_entries)
+
+    def _results_from_cache(self, cache_entry_buffer: IO[str]) -> Union[Result, None]:
+        """Returns a Results object from the concretizer cache
+
+        Reads the cache hit and uses `Result`'s own deserializer
+        to produce a new Result object
+        """
+
+        with current_file_position(cache_entry_buffer, 0):
+            cache_str = cache_entry_buffer.read()
+            # TODO: Should this be an error if None?
+            # Same for _stats_from_cache
+            if cache_str:
+                cache_entry = json.loads(cache_str)
+                result_json = cache_entry["results"]
+                return Result.from_dict(result_json)
+        return None
+
+    def _stats_from_cache(self, cache_entry_buffer: IO[str]) -> Union[List, None]:
+        """Returns concretization statistic from the
+        concretization associated with the cache.
+
+        Deserialzes the the json representation of the
+        statistics covering the cached concretization run
+        and returns the Python data structures
+        """
+        with current_file_position(cache_entry_buffer, 0):
+            cache_str = cache_entry_buffer.read()
+            if cache_str:
+                return json.loads(cache_str)["statistics"]
+        return None
+
+    def _extract_cache_metadata(self, cache_stream: IO[str]):
+        """Extracts and returns cache entry count and bytes count from head of manifest
+        file"""
+        # make sure we're always reading from the beginning of the stream
+        # concretization cache manifest data lives at the top of the file
+        with current_file_position(cache_stream, 0):
+            return self._parse_manifest_entry(cache_stream.readline())
+
+    def _prefix_digest(self, problem: str) -> Tuple[str, str]:
+        """Return the first two characters of, and the full, sha256 of the given asp problem"""
+        prob_digest = hashlib.sha256(problem.encode()).hexdigest()
+        prefix = prob_digest[:2]
+        return prefix, prob_digest
+
+    def _cache_path_from_problem(self, problem: str) -> pathlib.Path:
+        """Returns a Path object representing the path to the cache
+        entry for the given problem"""
+        prefix, digest = self._prefix_digest(problem)
+        return pathlib.Path(prefix) / digest
+
+    def _cache_path_from_hash(self, hash: str) -> pathlib.Path:
+        """Returns a Path object representing the cache entry
+        corresponding to the given sha256 hash"""
+        return pathlib.Path(hash[:2]) / hash
+
+    def _lock_prefix_from_cache_path(self, cache_path: str):
+        """Returns the bit location corresponding to a given cache entry path
+        for file locking"""
+        return spack.util.hash.base32_prefix_bits(
+            spack.util.hash.b32_hash(cache_path), spack.util.crypto.bit_length(sys.maxsize)
+        )
+
+    def flush_manifest(self):
+        """Updates the concretization cache manifest file after a cache write operation
+        Updates the current byte count and entry counts and writes to the head of the
+        manifest file"""
+        manifest_file = self.root / self._cache_manifest
+        manifest_file.touch(exist_ok=True)
+        with open(manifest_file, "r+", encoding="utf-8") as f:
+            # check if manifest is empty
+            count, cache_bytes = self._extract_cache_metadata(f)
+            if not count or not cache_bytes:
+                # cache is unintialized
+                count = 0
+                cache_bytes = 0
+            f.seek(0, io.SEEK_END)
+            for manifest_update in self._manifest_queue:
+                entry_path, entry_bytes = manifest_update
+                count += 1
+                cache_bytes += entry_bytes
+                f.write(f"{entry_path.name} {entry_bytes}")
+            f.seek(0, io.SEEK_SET)
+            new_stats = f"{int(count)+1} {int(cache_bytes)}\n"
+            f.write(new_stats)
+
+    def _register_cache_update(self, cache_path: pathlib.Path, bytes_written: int):
+        """Adds manifest entry to update queue for later updates to the manifest"""
+        self._manifest_queue.append((cache_path, bytes_written))
+
+    def _safe_remove(self, cache_dir: pathlib.Path):
+        """Removes cache entries with handling for the case where the entry has been
+        removed already or there are multiple cache entries in a directory"""
+        try:
+            if cache_dir.is_dir():
+                cache_dir.rmdir()
+            else:
+                cache_dir.unlink()
+            return True
+        except FileNotFoundError:
+            # This is acceptable, removal is idempotent
+            pass
+        except OSError as e:
+            if e.errno == errno.ENOTEMPTY:
+                # there exists another cache entry in this directory, don't clean yet
+                pass
+        return False
+
+    def store(self, problem: str, result: Result, statistics: List, test: bool = False):
+        """Creates entry in concretization cache for problem if none exists,
+        storing the concretization Result object and statistics in the cache
+        as serialized json joined as a single file.
+
+        Hash membership is computed based on the sha256 of the provided asp
+        problem.
+        """
+        cache_path = self._cache_path_from_problem(problem)
+        if self._fc.init_entry(cache_path):
+            # if an entry for this conc hash exists already, we're don't want
+            # to overwrite, just exit
+            tty.debug(f"Cache entry {cache_path} exists, will not be overwritten")
+            return
+        with self._fc.write_transaction(cache_path) as (old, new):
+            if old:
+                # Entry for this conc hash exists already, do not overwrite
+                tty.debug(f"Cache entry {cache_path} exists, will not be overwritten")
+                return
+            cache_dict = {"results": result.to_dict(test=test), "statistics": statistics}
+            bytes_written = new.write(json.dumps(cache_dict))
+            self._register_cache_update(cache_path, bytes_written)
+
+    def fetch(self, problem: str) -> Union[Tuple[Result, List], Tuple[None, None]]:
+        """Returns the concretization cache result for a lookup based on the given problem.
+
+        Checks the concretization cache for the given problem, and either returns the
+        Python objects cached on disk representing the concretization results and statistics
+        or returns none if no cache entry was found.
+        """
+        cache_path = self._cache_path_from_problem(problem)
+        result, statistics = None, None
+        with self._fc.read_transaction(cache_path) as f:
+            if f:
+                result = self._results_from_cache(f)
+                statistics = self._stats_from_cache(f)
+        if result and statistics:
+            tty.debug(f"Concretization cache hit at {str(cache_path)}")
+            return result, statistics
+        tty.debug(f"Concretization cache miss at {str(cache_path)}")
+        return None, None
+
+
+CONC_CACHE: ConcretizationCache = llnl.util.lang.Singleton(
+    lambda: ConcretizationCache()
+)  # type: ignore
+
 
 def _normalize_packages_yaml(packages_yaml):
     normalized_yaml = copy.copy(packages_yaml)
@@ -804,6 +1182,15 @@ def solve(self, setup, specs, reuse=None, output=None, control=None, allow_depre
         if sys.platform == "win32":
             tty.debug("Ensuring basic dependencies {win-sdk, wgl} available")
             spack.bootstrap.core.ensure_winsdk_external_or_raise()
+        control_files = ["concretize.lp", "heuristic.lp", "display.lp"]
+        if not setup.concretize_everything:
+            control_files.append("when_possible.lp")
+        if using_libc_compatibility():
+            control_files.append("libc_compatibility.lp")
+        else:
+            control_files.append("os_compatibility.lp")
+        if setup.enable_splicing:
+            control_files.append("splices.lp")
 
         timer.start("setup")
         asp_problem = setup.setup(specs, reuse=reuse, allow_deprecated=allow_deprecated)
@@ -813,123 +1200,133 @@ def solve(self, setup, specs, reuse=None, output=None, control=None, allow_depre
             return Result(specs), None, None
         timer.stop("setup")
 
-        timer.start("load")
-        # Add the problem instance
-        self.control.add("base", [], asp_problem)
-        # Load the file itself
+        timer.start("cache-check")
+        timer.start("ordering")
+        # ensure deterministic output
+        problem_repr = "\n".join(sorted(asp_problem.split("\n")))
+        timer.stop("ordering")
         parent_dir = os.path.dirname(__file__)
-        self.control.load(os.path.join(parent_dir, "concretize.lp"))
-        self.control.load(os.path.join(parent_dir, "heuristic.lp"))
-        self.control.load(os.path.join(parent_dir, "display.lp"))
-        if not setup.concretize_everything:
-            self.control.load(os.path.join(parent_dir, "when_possible.lp"))
+        full_path = lambda x: os.path.join(parent_dir, x)
+        abs_control_files = [full_path(x) for x in control_files]
+        for ctrl_file in abs_control_files:
+            with open(ctrl_file, "r", encoding="utf-8") as f:
+                problem_repr += "\n" + f.read()
 
-        # Binary compatibility is based on libc on Linux, and on the os tag elsewhere
-        if using_libc_compatibility():
-            self.control.load(os.path.join(parent_dir, "libc_compatibility.lp"))
-        else:
-            self.control.load(os.path.join(parent_dir, "os_compatibility.lp"))
-        if setup.enable_splicing:
-            self.control.load(os.path.join(parent_dir, "splices.lp"))
+        result = None
+        conc_cache_enabled = spack.config.get("config:concretization_cache:enable", True)
+        if conc_cache_enabled:
+            result, concretization_stats = CONC_CACHE.fetch(problem_repr)
 
-        timer.stop("load")
+        timer.stop("cache-check")
+        if not result:
+            timer.start("load")
+            # Add the problem instance
+            self.control.add("base", [], asp_problem)
+            # Load the files
+            [self.control.load(lp) for lp in abs_control_files]
+            timer.stop("load")
 
-        # Grounding is the first step in the solve -- it turns our facts
-        # and first-order logic rules into propositional logic.
-        timer.start("ground")
-        self.control.ground([("base", [])])
-        timer.stop("ground")
+            # Grounding is the first step in the solve -- it turns our facts
+            # and first-order logic rules into propositional logic.
+            timer.start("ground")
+            self.control.ground([("base", [])])
+            timer.stop("ground")
 
-        # With a grounded program, we can run the solve.
-        models = []  # stable models if things go well
-        cores = []  # unsatisfiable cores if they do not
+            # With a grounded program, we can run the solve.
+            models = []  # stable models if things go well
+            cores = []  # unsatisfiable cores if they do not
 
-        def on_model(model):
-            models.append((model.cost, model.symbols(shown=True, terms=True)))
+            def on_model(model):
+                models.append((model.cost, model.symbols(shown=True, terms=True)))
 
-        solve_kwargs = {
-            "assumptions": setup.assumptions,
-            "on_model": on_model,
-            "on_core": cores.append,
-        }
+            solve_kwargs = {
+                "assumptions": setup.assumptions,
+                "on_model": on_model,
+                "on_core": cores.append,
+            }
 
-        if clingo_cffi():
-            solve_kwargs["on_unsat"] = cores.append
+            if clingo_cffi():
+                solve_kwargs["on_unsat"] = cores.append
 
-        timer.start("solve")
-        time_limit = spack.config.CONFIG.get("concretizer:timeout", -1)
-        error_on_timeout = spack.config.CONFIG.get("concretizer:error_on_timeout", True)
-        # Spack uses 0 to set no time limit, clingo API uses -1
-        if time_limit == 0:
-            time_limit = -1
-        with self.control.solve(**solve_kwargs, async_=True) as handle:
-            finished = handle.wait(time_limit)
-            if not finished:
-                specs_str = ", ".join(llnl.util.lang.elide_list([str(s) for s in specs], 4))
-                header = f"Spack is taking more than {time_limit} seconds to solve for {specs_str}"
-                if error_on_timeout:
-                    raise UnsatisfiableSpecError(f"{header}, stopping concretization")
-                warnings.warn(f"{header}, using the best configuration found so far")
-                handle.cancel()
+            timer.start("solve")
+            time_limit = spack.config.CONFIG.get("concretizer:timeout", -1)
+            error_on_timeout = spack.config.CONFIG.get("concretizer:error_on_timeout", True)
+            # Spack uses 0 to set no time limit, clingo API uses -1
+            if time_limit == 0:
+                time_limit = -1
+            with self.control.solve(**solve_kwargs, async_=True) as handle:
+                finished = handle.wait(time_limit)
+                if not finished:
+                    specs_str = ", ".join(llnl.util.lang.elide_list([str(s) for s in specs], 4))
+                    header = (
+                        f"Spack is taking more than {time_limit} seconds to solve for {specs_str}"
+                    )
+                    if error_on_timeout:
+                        raise UnsatisfiableSpecError(f"{header}, stopping concretization")
+                    warnings.warn(f"{header}, using the best configuration found so far")
+                    handle.cancel()
 
-            solve_result = handle.get()
-        timer.stop("solve")
+                solve_result = handle.get()
+            timer.stop("solve")
 
-        # once done, construct the solve result
-        result = Result(specs)
-        result.satisfiable = solve_result.satisfiable
+            # once done, construct the solve result
+            result = Result(specs)
+            result.satisfiable = solve_result.satisfiable
 
-        if result.satisfiable:
-            timer.start("construct_specs")
-            # get the best model
-            builder = SpecBuilder(specs, hash_lookup=setup.reusable_and_possible)
-            min_cost, best_model = min(models)
+            if result.satisfiable:
+                timer.start("construct_specs")
+                # get the best model
+                builder = SpecBuilder(specs, hash_lookup=setup.reusable_and_possible)
+                min_cost, best_model = min(models)
 
-            # first check for errors
-            error_handler = ErrorHandler(best_model, specs)
-            error_handler.raise_if_errors()
+                # first check for errors
+                error_handler = ErrorHandler(best_model, specs)
+                error_handler.raise_if_errors()
 
-            # build specs from spec attributes in the model
-            spec_attrs = [(name, tuple(rest)) for name, *rest in extract_args(best_model, "attr")]
-            answers = builder.build_specs(spec_attrs)
+                # build specs from spec attributes in the model
+                spec_attrs = [
+                    (name, tuple(rest)) for name, *rest in extract_args(best_model, "attr")
+                ]
+                answers = builder.build_specs(spec_attrs)
 
-            # add best spec to the results
-            result.answers.append((list(min_cost), 0, answers))
+                # add best spec to the results
+                result.answers.append((list(min_cost), 0, answers))
 
-            # get optimization criteria
-            criteria_args = extract_args(best_model, "opt_criterion")
-            result.criteria = build_criteria_names(min_cost, criteria_args)
+                # get optimization criteria
+                criteria_args = extract_args(best_model, "opt_criterion")
+                result.criteria = build_criteria_names(min_cost, criteria_args)
 
-            # record the number of models the solver considered
-            result.nmodels = len(models)
+                # record the number of models the solver considered
+                result.nmodels = len(models)
 
-            # record the possible dependencies in the solve
-            result.possible_dependencies = setup.pkgs
-            timer.stop("construct_specs")
-            timer.stop()
-        elif cores:
-            result.control = self.control
-            result.cores.extend(cores)
+                # record the possible dependencies in the solve
+                result.possible_dependencies = setup.pkgs
+                timer.stop("construct_specs")
+                timer.stop()
+            elif cores:
+                result.control = self.control
+                result.cores.extend(cores)
 
+            result.raise_if_unsat()
+
+            if result.satisfiable and result.unsolved_specs and setup.concretize_everything:
+                unsolved_str = Result.format_unsolved(result.unsolved_specs)
+                raise InternalConcretizerError(
+                    "Internal Spack error: the solver completed but produced specs"
+                    " that do not satisfy the request. Please report a bug at "
+                    f"https://github.com/spack/spack/issues\n\t{unsolved_str}"
+                )
+            if conc_cache_enabled:
+                CONC_CACHE.store(problem_repr, result, self.control.statistics, test=setup.tests)
+            concretization_stats = self.control.statistics
         if output.timers:
             timer.write_tty()
             print()
 
         if output.stats:
             print("Statistics:")
-            pprint.pprint(self.control.statistics)
-
-        result.raise_if_unsat()
-
-        if result.satisfiable and result.unsolved_specs and setup.concretize_everything:
-            unsolved_str = Result.format_unsolved(result.unsolved_specs)
-            raise InternalConcretizerError(
-                "Internal Spack error: the solver completed but produced specs"
-                " that do not satisfy the request. Please report a bug at "
-                f"https://github.com/spack/spack/issues\n\t{unsolved_str}"
-            )
-
-        return result, timer, self.control.statistics
+            pprint.pprint(concretization_stats)
+        return result, timer, concretization_stats
 
 
 class ConcreteSpecsByHash(collections.abc.Mapping):
@@ -1371,7 +1768,7 @@ def effect_rules(self):
             return
 
         self.gen.h2("Imposed requirements")
-        for name in self._effect_cache:
+        for name in sorted(self._effect_cache):
             cache = self._effect_cache[name]
             for (spec_str, _), (effect_id, requirements) in cache.items():
                 self.gen.fact(fn.pkg_fact(name, fn.effect_id(effect_id)))
@@ -1424,8 +1821,8 @@ def define_variant(
 
         elif isinstance(values, vt.DisjointSetsOfValues):
             union = set()
-            for sid, s in enumerate(values.sets):
-                for value in s:
+            for sid, s in enumerate(sorted(values.sets)):
+                for value in sorted(s):
                     pkg_fact(fn.variant_value_from_disjoint_sets(vid, value, sid))
                 union.update(s)
             values = union
@@ -1606,7 +2003,7 @@ def package_provider_rules(self, pkg):
             self.gen.fact(fn.pkg_fact(pkg.name, fn.possible_provider(vpkg_name)))
 
         for when, provided in pkg.provided.items():
-            for vpkg in provided:
+            for vpkg in sorted(provided):
                 if vpkg.name not in self.possible_virtuals:
                     continue
 
@@ -1621,8 +2018,8 @@ def package_provider_rules(self, pkg):
             condition_id = self.condition(
                 when, required_name=pkg.name, msg="Virtuals are provided together"
             )
-            for set_id, virtuals_together in enumerate(sets_of_virtuals):
-                for name in virtuals_together:
+            for set_id, virtuals_together in enumerate(sorted(sets_of_virtuals)):
+                for name in sorted(virtuals_together):
                     self.gen.fact(
                         fn.pkg_fact(pkg.name, fn.provided_together(condition_id, set_id, name))
                     )
@@ -1656,13 +2053,16 @@ def track_dependencies(input_spec, requirements):
                     return requirements + [fn.attr("track_dependencies", input_spec.name)]
 
                 def dependency_holds(input_spec, requirements):
-                    return remove_node(input_spec, requirements) + [
+                    result = remove_node(input_spec, requirements) + [
                         fn.attr(
                             "dependency_holds", pkg.name, input_spec.name, dt.flag_to_string(t)
                         )
                         for t in dt.ALL_FLAGS
                         if t & depflag
                     ]
+                    if input_spec.name not in pkg.extendees:
+                        return result
+                    return result + [fn.attr("extends", pkg.name, input_spec.name)]
 
                 context = ConditionContext()
                 context.source = ConstraintOrigin.append_type_suffix(
@@ -1729,7 +2129,7 @@ def package_splice_rules(self, pkg):
                     for map in pkg.variants.values():
                         for k in map:
                             filt_match_variants.add(k)
-                    filt_match_variants = list(filt_match_variants)
+                    filt_match_variants = sorted(filt_match_variants)
                     variant_constraints = self._gen_match_variant_splice_constraints(
                         pkg, cond, spec_to_splice, hash_var, splice_node, filt_match_variants
                     )
@@ -1834,8 +2234,8 @@ def emit_facts_from_requirement_rules(self, rules: List[RequirementRule]):
                 spec.attach_git_version_lookup()
 
                 when_spec = spec
-                if virtual:
-                    when_spec = spack.spec.Spec(pkg_name)
+                if virtual and spec.name != pkg_name:
+                    when_spec = spack.spec.Spec(f"^[virtuals={pkg_name}] {spec.name}")
 
                 try:
                     context = ConditionContext()
@@ -2259,7 +2659,7 @@ def define_package_versions_and_validate_preferences(
     ):
         """Declare any versions in specs not declared in packages."""
         packages_yaml = spack.config.get("packages")
-        for pkg_name in possible_pkgs:
+        for pkg_name in sorted(possible_pkgs):
             pkg_cls = self.pkg_class(pkg_name)
 
             # All the versions from the corresponding package.py file. Since concepts
@@ -2587,7 +2987,7 @@ def define_variant_values(self):
         """
         # Tell the concretizer about possible values from specs seen in spec_clauses().
         # We might want to order these facts by pkg and name if we are debugging.
-        for pkg_name, variant_def_id, value in self.variant_values_from_specs:
+        for pkg_name, variant_def_id, value in sorted(self.variant_values_from_specs):
             try:
                 vid = self.variant_ids_by_def_id[variant_def_id]
             except KeyError:
@@ -2625,6 +3025,8 @@ def concrete_specs(self):
             # Declare as possible parts of specs that are not in package.py
             # - Add versions to possible versions
             # - Add OS to possible OS's
+
+            # is traverse deterministic?
             for dep in spec.traverse():
                 self.possible_versions[dep.name].add(dep.version)
                 if isinstance(dep.version, vn.GitVersion):
@@ -2862,7 +3264,7 @@ def define_runtime_constraints(self):
         recorder.consume_facts()
 
     def literal_specs(self, specs):
-        for spec in specs:
+        for spec in sorted(specs):
             self.gen.h2("Spec: %s" % str(spec))
             condition_id = next(self._id_counter)
             trigger_id = next(self._id_counter)
@@ -3363,7 +3765,7 @@ def consume_facts(self):
             # on the available compilers)
             self._setup.pkg_version_rules(runtime_pkg)
 
-        for imposed_spec, when_spec in self.runtime_conditions:
+        for imposed_spec, when_spec in sorted(self.runtime_conditions):
             msg = f"{when_spec} requires {imposed_spec} at runtime"
             _ = self._setup.condition(when_spec, imposed_spec=imposed_spec, msg=msg)
 
@@ -3702,11 +4104,11 @@ def build_specs(self, function_tuples):
         roots = [spec.root for spec in self._specs.values()]
         roots = dict((id(r), r) for r in roots)
         for root in roots.values():
-            spack.spec.Spec.inject_patches_variant(root)
+            _inject_patches_variant(root)
 
         # Add external paths to specs with just external modules
         for s in self._specs.values():
-            spack.spec.Spec.ensure_external_path_if_external(s)
+            _ensure_external_path_if_external(s)
 
         for s in self._specs.values():
             _develop_specs_from_env(s, ev.active_environment())
@@ -3778,6 +4180,92 @@ def execute_explicit_splices(self):
         return specs
 
 
+def _inject_patches_variant(root: spack.spec.Spec) -> None:
+    # This dictionary will store object IDs rather than Specs as keys
+    # since the Spec __hash__ will change as patches are added to them
+    spec_to_patches: Dict[int, Set[spack.patch.Patch]] = {}
+    for s in root.traverse():
+        # After concretizing, assign namespaces to anything left.
+        # Note that this doesn't count as a "change".  The repository
+        # configuration is constant throughout a spack run, and
+        # normalize and concretize evaluate Packages using Repo.get(),
+        # which respects precedence.  So, a namespace assignment isn't
+        # changing how a package name would have been interpreted and
+        # we can do it as late as possible to allow as much
+        # compatibility across repositories as possible.
+        if s.namespace is None:
+            s.namespace = spack.repo.PATH.repo_for_pkg(s.name).namespace
+
+        if s.concrete:
+            continue
+
+        # Add any patches from the package to the spec.
+        node_patches = {
+            patch
+            for cond, patch_list in spack.repo.PATH.get_pkg_class(s.fullname).patches.items()
+            if s.satisfies(cond)
+            for patch in patch_list
+        }
+        if node_patches:
+            spec_to_patches[id(s)] = node_patches
+
+    # Also record all patches required on dependencies by depends_on(..., patch=...)
+    for dspec in root.traverse_edges(deptype=dt.ALL, cover="edges", root=False):
+        if dspec.spec.concrete:
+            continue
+
+        pkg_deps = spack.repo.PATH.get_pkg_class(dspec.parent.fullname).dependencies
+
+        edge_patches: List[spack.patch.Patch] = []
+        for cond, deps_by_name in pkg_deps.items():
+            if not dspec.parent.satisfies(cond):
+                continue
+
+            dependency = deps_by_name.get(dspec.spec.name)
+            if not dependency:
+                continue
+
+            for pcond, patch_list in dependency.patches.items():
+                if dspec.spec.satisfies(pcond):
+                    edge_patches.extend(patch_list)
+
+        if edge_patches:
+            spec_to_patches.setdefault(id(dspec.spec), set()).update(edge_patches)
+
+    for spec in root.traverse():
+        if id(spec) not in spec_to_patches:
+            continue
+
+        patches = list(spec_to_patches[id(spec)])
+        variant: vt.MultiValuedVariant = spec.variants.setdefault(
+            "patches", vt.MultiValuedVariant("patches", ())
+        )
+        variant.value = tuple(p.sha256 for p in patches)
+        # FIXME: Monkey patches variant to store patches order
+        ordered_hashes = [(*p.ordering_key, p.sha256) for p in patches if p.ordering_key]
+        ordered_hashes.sort()
+        tty.debug(
+            f"Ordered hashes [{spec.name}]: "
+            + ", ".join("/".join(str(e) for e in t) for t in ordered_hashes)
+        )
+        setattr(
+            variant, "_patches_in_order_of_appearance", [sha256 for _, _, sha256 in ordered_hashes]
+        )
+
+
+def _ensure_external_path_if_external(spec: spack.spec.Spec) -> None:
+    if not spec.external_modules or spec.external_path:
+        return
+
+    # Get the path from the module the package can override the default
+    # (this is mostly needed for Cray)
+    pkg_cls = spack.repo.PATH.get_pkg_class(spec.name)
+    package = pkg_cls(spec)
+    spec.external_path = getattr(package, "external_prefix", None) or md.path_from_modules(
+        spec.external_modules
+    )
+
+
 def _develop_specs_from_env(spec, env):
     dev_info = env.dev_specs.get(spec.name, {}) if env else {}
     if not dev_info:
@@ -4134,6 +4622,9 @@ def solve_with_stats(
         reusable_specs.extend(self.selector.reusable_specs(specs))
         setup = SpackSolverSetup(tests=tests)
         output = OutputConfiguration(timers=timers, stats=stats, out=out, setup_only=setup_only)
+
+        CONC_CACHE.flush_manifest()
+        CONC_CACHE.cleanup()
         return self.driver.solve(
             setup, specs, reuse=reusable_specs, output=output, allow_deprecated=allow_deprecated
         )
@@ -4203,6 +4694,9 @@ def solve_in_rounds(
             for spec in result.specs:
                 reusable_specs.extend(spec.traverse())
 
+        CONC_CACHE.flush_manifest()
+        CONC_CACHE.cleanup()
+
 
 class UnsatisfiableSpecError(spack.error.UnsatisfiableSpecError):
     """There was an issue with the spec that was requested (i.e. a user error)."""

lib/spack/spack/solver/concretize.lp

@@ -524,6 +524,16 @@ error(10, "'{0}' is not a valid dependency for any package in the DAG", Package)
   :- attr("node", node(ID, Package)),
      not needed(node(ID, Package)).
 
+
+% Extensions depending on each other must all extend the same node (e.g. all Python packages
+% depending on each other must depend on the same Python interpreter)
+error(100, "{0} and {1} must depend on the same {2}", ExtensionParent, ExtensionChild, ExtendeePackage)
+  :- depends_on(ExtensionParent, ExtensionChild),
+     attr("extends", ExtensionParent, ExtendeePackage),
+     depends_on(ExtensionParent, node(X, ExtendeePackage)),
+     depends_on(ExtensionChild,  node(Y, ExtendeePackage)),
+     X != Y.
+
 #defined dependency_type/2.
 
 %-----------------------------------------------------------------------------
@@ -587,6 +597,13 @@ attr("virtual_on_edge", PackageNode, ProviderNode, Virtual)
 attr("virtual_on_incoming_edges", ProviderNode, Virtual)
   :- attr("virtual_on_edge", _, ProviderNode, Virtual).
 
+% This is needed to allow requirement on virtuals,
+% when a virtual root is requested
+attr("virtual_on_incoming_edges", ProviderNode, Virtual)
+  :- attr("virtual_root", node(min_dupe_id, Virtual)),
+     attr("root", ProviderNode),
+     provider(ProviderNode, node(min_dupe_id, Virtual)).
+
 % dependencies on virtuals also imply that the virtual is a virtual node
 1 { attr("virtual_node", node(0..X-1, Virtual)) : max_dupes(Virtual, X) }
   :- node_depends_on_virtual(PackageNode, Virtual).
@@ -943,12 +960,14 @@ error(100, "Cannot set variant '{0}' for package '{1}' because the variant condi
      build(node(ID, Package)).
 
 % at most one variant value for single-valued variants.
-error(100, "'{0}' required multiple values for single-valued variant '{1}'", Package, Variant)
+error(100, "'{0}' requires conflicting variant values 'Spec({1}={2})' and 'Spec({1}={3})'", Package, Variant, Value1, Value2)
   :- attr("node", node(ID, Package)),
      node_has_variant(node(ID, Package), Variant, _),
      variant_single_value(node(ID, Package), Variant),
-     build(node(ID, Package)),
-     2 { attr("variant_value", node(ID, Package), Variant, Value) }.
+     attr("variant_value", node(ID, Package), Variant, Value1),
+     attr("variant_value", node(ID, Package), Variant, Value2),
+     Value1 < Value2,
+     build(node(ID, Package)).
 
 error(100, "No valid value for variant '{1}' of package '{0}'", Package, Variant)
   :- attr("node", node(ID, Package)),

lib/spack/spack/solver/error_messages.lp

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

lib/spack/spack/solver/requirements.py

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

lib/spack/spack/spec.py

@@ -97,9 +97,7 @@
 import spack.spec_parser
 import spack.store
 import spack.traverse
-import spack.util.executable
 import spack.util.hash
-import spack.util.module_cmd as md
 import spack.util.prefix
 import spack.util.spack_json as sjson
 import spack.util.spack_yaml as syaml
@@ -176,15 +174,17 @@
 #:     Spec(Spec("string").format()) == Spec("string)"
 DEFAULT_FORMAT = (
     "{name}{@versions}"
-    "{%compiler.name}{@compiler.versions}{compiler_flags}"
+    "{compiler_flags}"
     "{variants}{ namespace=namespace_if_anonymous}{ arch=architecture}{/abstract_hash}"
+    " {%compiler.name}{@compiler.versions}"
 )
 
 #: Display format, which eliminates extra `@=` in the output, for readability.
 DISPLAY_FORMAT = (
     "{name}{@version}"
-    "{%compiler.name}{@compiler.version}{compiler_flags}"
+    "{compiler_flags}"
     "{variants}{ namespace=namespace_if_anonymous}{ arch=architecture}{/abstract_hash}"
+    " {%compiler.name}{@compiler.version}"
 )
 
 #: Regular expression to pull spec contents out of clearsigned signature
@@ -799,7 +799,7 @@ def update_deptypes(self, depflag: dt.DepFlag) -> bool:
         self.depflag = new
         return True
 
-    def update_virtuals(self, virtuals: Tuple[str, ...]) -> bool:
+    def update_virtuals(self, virtuals: Iterable[str]) -> bool:
         """Update the list of provided virtuals"""
         old = self.virtuals
         self.virtuals = tuple(sorted(set(virtuals).union(self.virtuals)))
@@ -1109,28 +1109,6 @@ def clear(self):
         self.edges.clear()
 
 
-def _command_default_handler(spec: "Spec"):
-    """Default handler when looking for the 'command' attribute.
-
-    Tries to search for ``spec.name`` in the ``spec.home.bin`` directory.
-
-    Parameters:
-        spec: spec that is being queried
-
-    Returns:
-        Executable: An executable of the command
-
-    Raises:
-        RuntimeError: If the command is not found
-    """
-    home = getattr(spec.package, "home")
-    path = os.path.join(home.bin, spec.name)
-
-    if fs.is_exe(path):
-        return spack.util.executable.Executable(path)
-    raise RuntimeError(f"Unable to locate {spec.name} command in {home.bin}")
-
-
 def _headers_default_handler(spec: "Spec"):
     """Default handler when looking for the 'headers' attribute.
 
@@ -1334,9 +1312,7 @@ class SpecBuildInterface(lang.ObjectWrapper):
     home = ForwardQueryToPackage("home", default_handler=None)
     headers = ForwardQueryToPackage("headers", default_handler=_headers_default_handler)
     libs = ForwardQueryToPackage("libs", default_handler=_libs_default_handler)
-    command = ForwardQueryToPackage(
-        "command", default_handler=_command_default_handler, _indirect=True
-    )
+    command = ForwardQueryToPackage("command", default_handler=None, _indirect=True)
 
     def __init__(
         self,
@@ -1514,7 +1490,7 @@ def __init__(self, spec_like=None, *, external_path=None, external_modules=None)
         self.abstract_hash = None
 
         # initial values for all spec hash types
-        for h in ht.hashes:
+        for h in ht.HASHES:
             setattr(self, h.attr, None)
 
         # cache for spec's prefix, computed lazily by prefix property
@@ -2107,32 +2083,34 @@ def long_spec(self):
     def short_spec(self):
         """Returns a version of the spec with the dependencies hashed
         instead of completely enumerated."""
-        spec_format = "{name}{@version}{%compiler.name}{@compiler.version}"
-        spec_format += "{variants}{ arch=architecture}{/hash:7}"
-        return self.format(spec_format)
+        return self.format(
+            "{name}{@version}{variants}{ arch=architecture}"
+            "{/hash:7}{%compiler.name}{@compiler.version}"
+        )
 
     @property
     def cshort_spec(self):
         """Returns an auto-colorized version of ``self.short_spec``."""
-        spec_format = "{name}{@version}{%compiler.name}{@compiler.version}"
-        spec_format += "{variants}{ arch=architecture}{/hash:7}"
-        return self.cformat(spec_format)
+        return self.cformat(
+            "{name}{@version}{variants}{ arch=architecture}"
+            "{/hash:7}{%compiler.name}{@compiler.version}"
+        )
 
     @property
-    def prefix(self):
+    def prefix(self) -> spack.util.prefix.Prefix:
         if not self._concrete:
-            raise spack.error.SpecError("Spec is not concrete: " + str(self))
+            raise spack.error.SpecError(f"Spec is not concrete: {self}")
 
         if self._prefix is None:
-            upstream, record = spack.store.STORE.db.query_by_spec_hash(self.dag_hash())
+            _, record = spack.store.STORE.db.query_by_spec_hash(self.dag_hash())
             if record and record.path:
-                self.prefix = record.path
+                self.set_prefix(record.path)
             else:
-                self.prefix = spack.store.STORE.layout.path_for_spec(self)
+                self.set_prefix(spack.store.STORE.layout.path_for_spec(self))
+        assert self._prefix is not None
         return self._prefix
 
-    @prefix.setter
-    def prefix(self, value):
+    def set_prefix(self, value: str) -> None:
         self._prefix = spack.util.prefix.Prefix(llnl.path.convert_to_platform_path(value))
 
     def spec_hash(self, hash):
@@ -2195,30 +2173,16 @@ def package_hash(self):
     def dag_hash(self, length=None):
         """This is Spack's default hash, used to identify installations.
 
-        Same as the full hash (includes package hash and build/link/run deps).
-        Tells us when package files and any dependencies have changes.
-
         NOTE: Versions of Spack prior to 0.18 only included link and run deps.
+        NOTE: Versions of Spack prior to 1.0 only did not include test deps.
 
         """
         return self._cached_hash(ht.dag_hash, length)
 
-    def process_hash(self, length=None):
-        """Hash used to transfer specs among processes.
-
-        This hash includes build and test dependencies and is only used to
-        serialize a spec and pass it around among processes.
-        """
-        return self._cached_hash(ht.process_hash, length)
-
     def dag_hash_bit_prefix(self, bits):
         """Get the first <bits> bits of the DAG hash as an integer type."""
         return spack.util.hash.base32_prefix_bits(self.dag_hash(), bits)
 
-    def process_hash_bit_prefix(self, bits):
-        """Get the first <bits> bits of the DAG hash as an integer type."""
-        return spack.util.hash.base32_prefix_bits(self.process_hash(), bits)
-
     def _lookup_hash(self):
         """Lookup just one spec with an abstract hash, returning a spec from the the environment,
         store, or finally, binary caches."""
@@ -2738,7 +2702,7 @@ def spec_and_dependency_types(
         return spec_builder(spec_dict)
 
     @staticmethod
-    def from_dict(data):
+    def from_dict(data) -> "Spec":
         """Construct a spec from JSON/YAML.
 
         Args:
@@ -2761,7 +2725,7 @@ def from_dict(data):
         return spec
 
     @staticmethod
-    def from_yaml(stream):
+    def from_yaml(stream) -> "Spec":
         """Construct a spec from YAML.
 
         Args:
@@ -2771,7 +2735,7 @@ def from_yaml(stream):
         return Spec.from_dict(data)
 
     @staticmethod
-    def from_json(stream):
+    def from_json(stream) -> "Spec":
         """Construct a spec from JSON.
 
         Args:
@@ -2781,7 +2745,7 @@ def from_json(stream):
             data = sjson.load(stream)
             return Spec.from_dict(data)
         except Exception as e:
-            raise sjson.SpackJSONError("error parsing JSON spec:", str(e)) from e
+            raise sjson.SpackJSONError("error parsing JSON spec:", e) from e
 
     @staticmethod
     def extract_json_from_clearsig(data):
@@ -2845,94 +2809,6 @@ def _patches_assigned(self):
 
         return True
 
-    @staticmethod
-    def inject_patches_variant(root):
-        # This dictionary will store object IDs rather than Specs as keys
-        # since the Spec __hash__ will change as patches are added to them
-        spec_to_patches = {}
-        for s in root.traverse():
-            # After concretizing, assign namespaces to anything left.
-            # Note that this doesn't count as a "change".  The repository
-            # configuration is constant throughout a spack run, and
-            # normalize and concretize evaluate Packages using Repo.get(),
-            # which respects precedence.  So, a namespace assignment isn't
-            # changing how a package name would have been interpreted and
-            # we can do it as late as possible to allow as much
-            # compatibility across repositories as possible.
-            if s.namespace is None:
-                s.namespace = spack.repo.PATH.repo_for_pkg(s.name).namespace
-
-            if s.concrete:
-                continue
-
-            # Add any patches from the package to the spec.
-            patches = set()
-            for cond, patch_list in spack.repo.PATH.get_pkg_class(s.fullname).patches.items():
-                if s.satisfies(cond):
-                    for patch in patch_list:
-                        patches.add(patch)
-            if patches:
-                spec_to_patches[id(s)] = patches
-
-        # Also record all patches required on dependencies by
-        # depends_on(..., patch=...)
-        for dspec in root.traverse_edges(deptype=all, cover="edges", root=False):
-            if dspec.spec.concrete:
-                continue
-
-            pkg_deps = spack.repo.PATH.get_pkg_class(dspec.parent.fullname).dependencies
-
-            patches = []
-            for cond, deps_by_name in pkg_deps.items():
-                if not dspec.parent.satisfies(cond):
-                    continue
-
-                dependency = deps_by_name.get(dspec.spec.name)
-                if not dependency:
-                    continue
-
-                for pcond, patch_list in dependency.patches.items():
-                    if dspec.spec.satisfies(pcond):
-                        patches.extend(patch_list)
-
-            if patches:
-                all_patches = spec_to_patches.setdefault(id(dspec.spec), set())
-                for patch in patches:
-                    all_patches.add(patch)
-
-        for spec in root.traverse():
-            if id(spec) not in spec_to_patches:
-                continue
-
-            patches = list(lang.dedupe(spec_to_patches[id(spec)]))
-            mvar = spec.variants.setdefault("patches", vt.MultiValuedVariant("patches", ()))
-            mvar.value = tuple(p.sha256 for p in patches)
-            # FIXME: Monkey patches mvar to store patches order
-            full_order_keys = list(tuple(p.ordering_key) + (p.sha256,) for p in patches)
-            ordered_hashes = sorted(full_order_keys)
-            tty.debug(
-                "Ordered hashes [{0}]: ".format(spec.name)
-                + ", ".join("/".join(str(e) for e in t) for t in ordered_hashes)
-            )
-            mvar._patches_in_order_of_appearance = list(t[-1] for t in ordered_hashes)
-
-    @staticmethod
-    def ensure_external_path_if_external(external_spec):
-        if external_spec.external_modules and not external_spec.external_path:
-            compiler = spack.compilers.compiler_for_spec(
-                external_spec.compiler, external_spec.architecture
-            )
-            for mod in compiler.modules:
-                md.load_module(mod)
-
-            # Get the path from the module the package can override the default
-            # (this is mostly needed for Cray)
-            pkg_cls = spack.repo.PATH.get_pkg_class(external_spec.name)
-            package = pkg_cls(external_spec)
-            external_spec.external_path = getattr(
-                package, "external_prefix", md.path_from_modules(external_spec.external_modules)
-            )
-
     @staticmethod
     def ensure_no_deprecated(root):
         """Raise if a deprecated spec is in the dag.
@@ -3673,11 +3549,11 @@ def _dup(self, other: "Spec", deps: Union[bool, dt.DepTypes, dt.DepFlag] = True)
 
         if self._concrete:
             self._dunder_hash = other._dunder_hash
-            for h in ht.hashes:
+            for h in ht.HASHES:
                 setattr(self, h.attr, getattr(other, h.attr, None))
         else:
             self._dunder_hash = None
-            for h in ht.hashes:
+            for h in ht.HASHES:
                 setattr(self, h.attr, None)
 
         return changed
@@ -3869,16 +3745,6 @@ def _cmp_iter(self):
         # serialized before the hash change and one after, are considered different.
         yield self.dag_hash() if self.concrete else None
 
-        # This needs to be in _cmp_iter so that no specs with different process hashes
-        # are considered the same by `__hash__` or `__eq__`.
-        #
-        # TODO: We should eventually unify the `_cmp_*` methods with `to_node_dict` so
-        # TODO: there aren't two sources of truth, but this needs some thought, since
-        # TODO: they exist for speed.  We should benchmark whether it's really worth
-        # TODO: having two types of hashing now that we use `json` instead of `yaml` for
-        # TODO: spec hashing.
-        yield self.process_hash() if self.concrete else None
-
         def deps():
             for dep in sorted(itertools.chain.from_iterable(self._dependencies.values())):
                 yield dep.spec.name
@@ -4532,7 +4398,7 @@ def clear_caches(self, ignore: Tuple[str, ...] = ()) -> None:
         """
         Clears all cached hashes in a Spec, while preserving other properties.
         """
-        for h in ht.hashes:
+        for h in ht.HASHES:
             if h.attr not in ignore:
                 if hasattr(self, h.attr):
                     setattr(self, h.attr, None)
@@ -4541,18 +4407,12 @@ def clear_caches(self, ignore: Tuple[str, ...] = ()) -> None:
                 setattr(self, attr, None)
 
     def __hash__(self):
-        # If the spec is concrete, we leverage the process hash and just use
-        # a 64-bit prefix of it. The process hash has the advantage that it's
-        # computed once per concrete spec, and it's saved -- so if we read
-        # concrete specs we don't need to recompute the whole hash. This is
-        # good for large, unchanging specs.
-        #
-        # We use the process hash instead of the DAG hash here because the DAG
-        # hash includes the package hash, which can cause infinite recursion,
-        # and which isn't defined unless the spec has a known package.
+        # If the spec is concrete, we leverage the dag hash and just use a 64-bit prefix of it.
+        # The dag hash has the advantage that it's computed once per concrete spec, and it's saved
+        # -- so if we read concrete specs we don't need to recompute the whole hash.
         if self.concrete:
             if not self._dunder_hash:
-                self._dunder_hash = self.process_hash_bit_prefix(64)
+                self._dunder_hash = self.dag_hash_bit_prefix(64)
             return self._dunder_hash
 
         # This is the normal hash for lazy_lexicographic_ordering. It's
@@ -4561,7 +4421,7 @@ def __hash__(self):
         return hash(lang.tuplify(self._cmp_iter))
 
     def __reduce__(self):
-        return Spec.from_dict, (self.to_dict(hash=ht.process_hash),)
+        return Spec.from_dict, (self.to_dict(hash=ht.dag_hash),)
 
     def attach_git_version_lookup(self):
         # Add a git lookup method for GitVersions
@@ -4704,17 +4564,6 @@ def constrain(self, other: "VariantMap") -> bool:
 
         return changed
 
-    @property
-    def concrete(self):
-        """Returns True if the spec is concrete in terms of variants.
-
-        Returns:
-            bool: True or False
-        """
-        return self.spec._concrete or all(
-            v in self for v in spack.repo.PATH.get_pkg_class(self.spec.fullname).variant_names()
-        )
-
     def copy(self) -> "VariantMap":
         clone = VariantMap(self.spec)
         for name, variant in self.items():
@@ -4841,33 +4690,51 @@ def merge_abstract_anonymous_specs(*abstract_specs: Spec):
     return merged_spec
 
 
-def reconstruct_virtuals_on_edges(spec):
-    """Reconstruct virtuals on edges. Used to read from old DB and reindex.
+def reconstruct_virtuals_on_edges(spec: Spec) -> None:
+    """Reconstruct virtuals on edges. Used to read from old DB and reindex."""
+    virtuals_needed: Dict[str, Set[str]] = {}
+    virtuals_provided: Dict[str, Set[str]] = {}
+    for edge in spec.traverse_edges(cover="edges", root=False):
+        parent_key = edge.parent.dag_hash()
+        if parent_key not in virtuals_needed:
+            # Construct which virtuals are needed by parent
+            virtuals_needed[parent_key] = set()
+            try:
+                parent_pkg = edge.parent.package
+            except Exception as e:
+                warnings.warn(
+                    f"cannot reconstruct virtual dependencies on {edge.parent.name}: {e}"
+                )
+                continue
 
-    Args:
-        spec: spec on which we want to reconstruct virtuals
-    """
-    # Collect all possible virtuals
-    possible_virtuals = set()
-    for node in spec.traverse():
-        try:
-            possible_virtuals.update(
-                {x for x in node.package.dependencies if spack.repo.PATH.is_virtual(x)}
+            virtuals_needed[parent_key].update(
+                name
+                for name, when_deps in parent_pkg.dependencies_by_name(when=True).items()
+                if spack.repo.PATH.is_virtual(name)
+                and any(edge.parent.satisfies(x) for x in when_deps)
             )
-        except Exception as e:
-            warnings.warn(f"cannot reconstruct virtual dependencies on package {node.name}: {e}")
+
+        if not virtuals_needed[parent_key]:
             continue
 
-    # Assume all incoming edges to provider are marked with virtuals=
-    for vspec in possible_virtuals:
-        try:
-            provider = spec[vspec]
-        except KeyError:
-            # Virtual not in the DAG
+        child_key = edge.spec.dag_hash()
+        if child_key not in virtuals_provided:
+            virtuals_provided[child_key] = set()
+            try:
+                child_pkg = edge.spec.package
+            except Exception as e:
+                warnings.warn(
+                    f"cannot reconstruct virtual dependencies on {edge.parent.name}: {e}"
+                )
+                continue
+            virtuals_provided[child_key].update(x.name for x in child_pkg.virtuals_provided)
+
+        if not virtuals_provided[child_key]:
             continue
 
-        for edge in provider.edges_from_dependents():
-            edge.update_virtuals([vspec])
+        virtuals_to_add = virtuals_needed[parent_key] & virtuals_provided[child_key]
+        if virtuals_to_add:
+            edge.update_virtuals(virtuals_to_add)
 
 
 class SpecfileReaderBase:
@@ -4876,7 +4743,7 @@ def from_node_dict(cls, node):
         spec = Spec()
 
         name, node = cls.name_and_data(node)
-        for h in ht.hashes:
+        for h in ht.HASHES:
             setattr(spec, h.attr, node.get(h.name, None))
 
         spec.name = name
@@ -5059,7 +4926,7 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
         """
         for dep_name, elt in deps.items():
             if isinstance(elt, dict):
-                for h in ht.hashes:
+                for h in ht.HASHES:
                     if h.name in elt:
                         dep_hash, deptypes = elt[h.name], elt["type"]
                         hash_type = h.name
@@ -5102,7 +4969,7 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
             dep_name = dep["name"]
             if isinstance(elt, dict):
                 # new format: elements of dependency spec are keyed.
-                for h in ht.hashes:
+                for h in ht.HASHES:
                     if h.name in elt:
                         dep_hash, deptypes, hash_type, virtuals = cls.extract_info_from_dep(elt, h)
                         break
@@ -5212,6 +5079,13 @@ def get_host_environment() -> Dict[str, Any]:
     }
 
 
+def eval_conditional(string):
+    """Evaluate conditional definitions using restricted variable scope."""
+    valid_variables = get_host_environment()
+    valid_variables.update({"re": re, "env": os.environ})
+    return eval(string, valid_variables)
+
+
 class SpecParseError(spack.error.SpecError):
     """Wrapper for ParseError for when we're parsing specs."""
 
@@ -5370,8 +5244,10 @@ def __init__(self, spec):
 
 class AmbiguousHashError(spack.error.SpecError):
     def __init__(self, msg, *specs):
-        spec_fmt = "{namespace}.{name}{@version}{%compiler}{compiler_flags}"
-        spec_fmt += "{variants}{ arch=architecture}{/hash:7}"
+        spec_fmt = (
+            "{namespace}.{name}{@version}{compiler_flags}{variants}"
+            "{ arch=architecture}{/hash:7}{%compiler}"
+        )
         specs_str = "\n  " + "\n  ".join(spec.format(spec_fmt) for spec in specs)
         super().__init__(msg + specs_str)
 

lib/spack/spack/spec_parser.py

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

lib/spack/spack/test/architecture.py

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

lib/spack/spack/test/bindist.py

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

lib/spack/spack/test/build_environment.py

@@ -388,7 +388,7 @@ def test_wrapper_variables(
     root = spack.concretize.concretize_one("dt-diamond")
 
     for s in root.traverse():
-        s.prefix = "/{0}-prefix/".format(s.name)
+        s.set_prefix(f"/{s.name}-prefix/")
 
     dep_pkg = root["dt-diamond-left"].package
     dep_lib_paths = ["/test/path/to/ex1.so", "/test/path/to/subdir/ex2.so"]
@@ -396,7 +396,7 @@ def test_wrapper_variables(
     dep_libs = LibraryList(dep_lib_paths)
 
     dep2_pkg = root["dt-diamond-right"].package
-    dep2_pkg.spec.prefix = str(installation_dir_with_headers)
+    dep2_pkg.spec.set_prefix(str(installation_dir_with_headers))
 
     setattr(dep_pkg, "libs", dep_libs)
     try:
@@ -542,7 +542,7 @@ def test_build_jobs_sequential_is_sequential():
         spack.config.determine_number_of_jobs(
             parallel=False,
             max_cpus=8,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("command_line", {"config": {"build_jobs": 8}}),
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 8}}),
             ),
@@ -556,7 +556,7 @@ def test_build_jobs_command_line_overrides():
         spack.config.determine_number_of_jobs(
             parallel=True,
             max_cpus=1,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("command_line", {"config": {"build_jobs": 10}}),
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 1}}),
             ),
@@ -567,7 +567,7 @@ def test_build_jobs_command_line_overrides():
         spack.config.determine_number_of_jobs(
             parallel=True,
             max_cpus=100,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("command_line", {"config": {"build_jobs": 10}}),
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 100}}),
             ),
@@ -581,7 +581,7 @@ def test_build_jobs_defaults():
         spack.config.determine_number_of_jobs(
             parallel=True,
             max_cpus=10,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 1}})
             ),
         )
@@ -591,7 +591,7 @@ def test_build_jobs_defaults():
         spack.config.determine_number_of_jobs(
             parallel=True,
             max_cpus=10,
-            config=spack.config.Configuration(
+            config=spack.config.create_from(
                 spack.config.InternalConfigScope("defaults", {"config": {"build_jobs": 100}})
             ),
         )

lib/spack/spack/test/build_systems.py

@@ -403,8 +403,8 @@ def test_autoreconf_search_path_args_multiple(default_mock_concretization, tmpdi
     aclocal_fst = str(tmpdir.mkdir("fst").mkdir("share").mkdir("aclocal"))
     aclocal_snd = str(tmpdir.mkdir("snd").mkdir("share").mkdir("aclocal"))
     build_dep_one, build_dep_two = spec.dependencies(deptype="build")
-    build_dep_one.prefix = str(tmpdir.join("fst"))
-    build_dep_two.prefix = str(tmpdir.join("snd"))
+    build_dep_one.set_prefix(str(tmpdir.join("fst")))
+    build_dep_two.set_prefix(str(tmpdir.join("snd")))
     assert spack.build_systems.autotools._autoreconf_search_path_args(spec) == [
         "-I",
         aclocal_fst,
@@ -422,8 +422,8 @@ def test_autoreconf_search_path_args_skip_automake(default_mock_concretization,
     aclocal_snd = str(tmpdir.mkdir("snd").mkdir("share").mkdir("aclocal"))
     build_dep_one, build_dep_two = spec.dependencies(deptype="build")
     build_dep_one.name = "automake"
-    build_dep_one.prefix = str(tmpdir.join("fst"))
-    build_dep_two.prefix = str(tmpdir.join("snd"))
+    build_dep_one.set_prefix(str(tmpdir.join("fst")))
+    build_dep_two.set_prefix(str(tmpdir.join("snd")))
     assert spack.build_systems.autotools._autoreconf_search_path_args(spec) == ["-I", aclocal_snd]
 
 
@@ -434,7 +434,7 @@ def test_autoreconf_search_path_args_external_order(default_mock_concretization,
     aclocal_snd = str(tmpdir.mkdir("snd").mkdir("share").mkdir("aclocal"))
     build_dep_one, build_dep_two = spec.dependencies(deptype="build")
     build_dep_one.external_path = str(tmpdir.join("fst"))
-    build_dep_two.prefix = str(tmpdir.join("snd"))
+    build_dep_two.set_prefix(str(tmpdir.join("snd")))
     assert spack.build_systems.autotools._autoreconf_search_path_args(spec) == [
         "-I",
         aclocal_snd,
@@ -447,8 +447,8 @@ def test_autoreconf_search_path_skip_nonexisting(default_mock_concretization, tm
     """Skip -I flags for non-existing directories"""
     spec = default_mock_concretization("dttop")
     build_dep_one, build_dep_two = spec.dependencies(deptype="build")
-    build_dep_one.prefix = str(tmpdir.join("fst"))
-    build_dep_two.prefix = str(tmpdir.join("snd"))
+    build_dep_one.set_prefix(str(tmpdir.join("fst")))
+    build_dep_two.set_prefix(str(tmpdir.join("snd")))
     assert spack.build_systems.autotools._autoreconf_search_path_args(spec) == []
 
 

lib/spack/spack/test/cc.py

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

lib/spack/spack/test/ci.py

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

lib/spack/spack/test/cmd/buildcache.py

@@ -214,9 +214,7 @@ def verify_mirror_contents():
             if in_env_pkg in p:
                 found_pkg = True
 
-        if not found_pkg:
-            print("Expected to find {0} in {1}".format(in_env_pkg, dest_mirror_dir))
-            assert False
+        assert found_pkg, f"Expected to find {in_env_pkg} in {dest_mirror_dir}"
 
     # Install a package and put it in the buildcache
     s = spack.concretize.concretize_one(out_env_pkg)

lib/spack/spack/test/cmd/ci.py

@@ -22,7 +22,11 @@
 import spack.hash_types as ht
 import spack.main
 import spack.paths as spack_paths
+import spack.repo
+import spack.spec
+import spack.stage
 import spack.util.spack_yaml as syaml
+import spack.version
 from spack.ci import gitlab as gitlab_generator
 from spack.ci.common import PipelineDag, PipelineOptions, SpackCIConfig
 from spack.ci.generator_registry import generator
@@ -867,7 +871,7 @@ def test_push_to_build_cache(
             logs_dir = scratch / "logs_dir"
             logs_dir.mkdir()
             ci.copy_stage_logs_to_artifacts(concrete_spec, str(logs_dir))
-            assert "spack-build-out.txt" in os.listdir(logs_dir)
+            assert "spack-build-out.txt.gz" in os.listdir(logs_dir)
 
             dl_dir = scratch / "download_dir"
             buildcache_cmd("download", "--spec-file", json_path, "--path", str(dl_dir))
@@ -1841,3 +1845,216 @@ def test_ci_generate_alternate_target(
 
     assert pipeline_doc.startswith("unittestpipeline")
     assert "externaltest" in pipeline_doc
+
+
+@pytest.fixture
+def fetch_versions_match(monkeypatch):
+    """Fake successful checksums returned from downloaded tarballs."""
+
+    def get_checksums_for_versions(url_by_version, package_name, **kwargs):
+        pkg_cls = spack.repo.PATH.get_pkg_class(package_name)
+        return {v: pkg_cls.versions[v]["sha256"] for v in url_by_version}
+
+    monkeypatch.setattr(spack.stage, "get_checksums_for_versions", get_checksums_for_versions)
+
+
+@pytest.fixture
+def fetch_versions_invalid(monkeypatch):
+    """Fake successful checksums returned from downloaded tarballs."""
+
+    def get_checksums_for_versions(url_by_version, package_name, **kwargs):
+        return {
+            v: "abcdef1234567890abcdef1234567890abcdef1234567890abcdef1234567890"
+            for v in url_by_version
+        }
+
+    monkeypatch.setattr(spack.stage, "get_checksums_for_versions", get_checksums_for_versions)
+
+
+@pytest.mark.parametrize("versions", [["2.1.4"], ["2.1.4", "2.1.5"]])
+def test_ci_validate_standard_versions_valid(capfd, mock_packages, fetch_versions_match, versions):
+    spec = spack.spec.Spec("diff-test")
+    pkg = spack.repo.PATH.get_pkg_class(spec.name)(spec)
+    version_list = [spack.version.Version(v) for v in versions]
+
+    assert spack.cmd.ci.validate_standard_versions(pkg, version_list)
+
+    out, err = capfd.readouterr()
+    for version in versions:
+        assert f"Validated diff-test@{version}" in out
+
+
+@pytest.mark.parametrize("versions", [["2.1.4"], ["2.1.4", "2.1.5"]])
+def test_ci_validate_standard_versions_invalid(
+    capfd, mock_packages, fetch_versions_invalid, versions
+):
+    spec = spack.spec.Spec("diff-test")
+    pkg = spack.repo.PATH.get_pkg_class(spec.name)(spec)
+    version_list = [spack.version.Version(v) for v in versions]
+
+    assert spack.cmd.ci.validate_standard_versions(pkg, version_list) is False
+
+    out, err = capfd.readouterr()
+    for version in versions:
+        assert f"Invalid checksum found diff-test@{version}" in err
+
+
+@pytest.mark.parametrize("versions", [[("1.0", -2)], [("1.1", -4), ("2.0", -6)]])
+def test_ci_validate_git_versions_valid(
+    capfd, monkeypatch, mock_packages, mock_git_version_info, versions
+):
+    spec = spack.spec.Spec("diff-test")
+    pkg = spack.repo.PATH.get_pkg_class(spec.name)(spec)
+    version_list = [spack.version.Version(v) for v, _ in versions]
+
+    repo_path, filename, commits = mock_git_version_info
+    version_commit_dict = {
+        spack.version.Version(v): {"tag": f"v{v}", "commit": commits[c]} for v, c in versions
+    }
+
+    pkg_class = spec.package_class
+
+    monkeypatch.setattr(pkg_class, "git", repo_path)
+    monkeypatch.setattr(pkg_class, "versions", version_commit_dict)
+
+    assert spack.cmd.ci.validate_git_versions(pkg, version_list)
+
+    out, err = capfd.readouterr()
+    for version in version_list:
+        assert f"Validated diff-test@{version}" in out
+
+
+@pytest.mark.parametrize("versions", [[("1.0", -3)], [("1.1", -5), ("2.0", -5)]])
+def test_ci_validate_git_versions_bad_tag(
+    capfd, monkeypatch, mock_packages, mock_git_version_info, versions
+):
+    spec = spack.spec.Spec("diff-test")
+    pkg = spack.repo.PATH.get_pkg_class(spec.name)(spec)
+    version_list = [spack.version.Version(v) for v, _ in versions]
+
+    repo_path, filename, commits = mock_git_version_info
+    version_commit_dict = {
+        spack.version.Version(v): {"tag": f"v{v}", "commit": commits[c]} for v, c in versions
+    }
+
+    pkg_class = spec.package_class
+
+    monkeypatch.setattr(pkg_class, "git", repo_path)
+    monkeypatch.setattr(pkg_class, "versions", version_commit_dict)
+
+    assert spack.cmd.ci.validate_git_versions(pkg, version_list) is False
+
+    out, err = capfd.readouterr()
+    for version in version_list:
+        assert f"Mismatched tag <-> commit found for diff-test@{version}" in err
+
+
+@pytest.mark.parametrize("versions", [[("1.0", -2)], [("1.1", -4), ("2.0", -6), ("3.0", -6)]])
+def test_ci_validate_git_versions_invalid(
+    capfd, monkeypatch, mock_packages, mock_git_version_info, versions
+):
+    spec = spack.spec.Spec("diff-test")
+    pkg = spack.repo.PATH.get_pkg_class(spec.name)(spec)
+    version_list = [spack.version.Version(v) for v, _ in versions]
+
+    repo_path, filename, commits = mock_git_version_info
+    version_commit_dict = {
+        spack.version.Version(v): {
+            "tag": f"v{v}",
+            "commit": "abcdefabcdefabcdefabcdefabcdefabcdefabc",
+        }
+        for v, c in versions
+    }
+
+    pkg_class = spec.package_class
+
+    monkeypatch.setattr(pkg_class, "git", repo_path)
+    monkeypatch.setattr(pkg_class, "versions", version_commit_dict)
+
+    assert spack.cmd.ci.validate_git_versions(pkg, version_list) is False
+
+    out, err = capfd.readouterr()
+    for version in version_list:
+        assert f"Invalid commit for diff-test@{version}" in err
+
+
+@pytest.fixture
+def verify_standard_versions_valid(monkeypatch):
+    def validate_standard_versions(pkg, versions):
+        for version in versions:
+            print(f"Validated {pkg.name}@{version}")
+        return True
+
+    monkeypatch.setattr(spack.cmd.ci, "validate_standard_versions", validate_standard_versions)
+
+
+@pytest.fixture
+def verify_git_versions_valid(monkeypatch):
+    def validate_git_versions(pkg, versions):
+        for version in versions:
+            print(f"Validated {pkg.name}@{version}")
+        return True
+
+    monkeypatch.setattr(spack.cmd.ci, "validate_git_versions", validate_git_versions)
+
+
+@pytest.fixture
+def verify_standard_versions_invalid(monkeypatch):
+    def validate_standard_versions(pkg, versions):
+        for version in versions:
+            print(f"Invalid checksum found {pkg.name}@{version}")
+        return False
+
+    monkeypatch.setattr(spack.cmd.ci, "validate_standard_versions", validate_standard_versions)
+
+
+@pytest.fixture
+def verify_git_versions_invalid(monkeypatch):
+    def validate_git_versions(pkg, versions):
+        for version in versions:
+            print(f"Invalid commit for {pkg.name}@{version}")
+        return False
+
+    monkeypatch.setattr(spack.cmd.ci, "validate_git_versions", validate_git_versions)
+
+
+def test_ci_verify_versions_valid(
+    monkeypatch,
+    mock_packages,
+    mock_git_package_changes,
+    verify_standard_versions_valid,
+    verify_git_versions_valid,
+):
+    repo_path, _, commits = mock_git_package_changes
+    monkeypatch.setattr(spack.paths, "prefix", repo_path)
+
+    out = ci_cmd("verify-versions", commits[-1], commits[-3])
+    assert "Validated diff-test@2.1.5" in out
+    assert "Validated diff-test@2.1.6" in out
+
+
+def test_ci_verify_versions_standard_invalid(
+    monkeypatch,
+    mock_packages,
+    mock_git_package_changes,
+    verify_standard_versions_invalid,
+    verify_git_versions_invalid,
+):
+    repo_path, _, commits = mock_git_package_changes
+
+    monkeypatch.setattr(spack.paths, "prefix", repo_path)
+
+    out = ci_cmd("verify-versions", commits[-1], commits[-3], fail_on_error=False)
+    assert "Invalid checksum found diff-test@2.1.5" in out
+    assert "Invalid commit for diff-test@2.1.6" in out
+
+
+def test_ci_verify_versions_manual_package(monkeypatch, mock_packages, mock_git_package_changes):
+    repo_path, _, commits = mock_git_package_changes
+    monkeypatch.setattr(spack.paths, "prefix", repo_path)
+
+    pkg_class = spack.spec.Spec("diff-test").package_class
+    monkeypatch.setattr(pkg_class, "manual_download", True)
+
+    out = ci_cmd("verify-versions", commits[-1], commits[-2])
+    assert "Skipping manual download package: diff-test" in out

lib/spack/spack/test/cmd/commands.py

@@ -5,6 +5,7 @@
 import filecmp
 import os
 import shutil
+import textwrap
 
 import pytest
 
@@ -259,15 +260,25 @@ def test_update_completion_arg(shell, tmpdir, monkeypatch):
 def test_updated_completion_scripts(shell, tmpdir):
     """Make sure our shell tab completion scripts remain up-to-date."""
 
-    msg = (
+    width = 72
+    lines = textwrap.wrap(
         "It looks like Spack's command-line interface has been modified. "
-        "Please update Spack's shell tab completion scripts by running:\n\n"
-        "    spack commands --update-completion\n\n"
-        "and adding the changed files to your pull request."
+        "If differences are more than your global 'include:' scopes, please "
+        "update Spack's shell tab completion scripts by running:",
+        width,
     )
+    lines.append("\n    spack commands --update-completion\n")
+    lines.extend(
+        textwrap.wrap(
+            "and adding the changed files (minus your global 'include:' scopes) "
+            "to your pull request.",
+            width,
+        )
+    )
+    msg = "\n".join(lines)
 
     header = os.path.join(spack.paths.share_path, shell, f"spack-completion.{shell}")
-    script = "spack-completion.{0}".format(shell)
+    script = f"spack-completion.{shell}"
     old_script = os.path.join(spack.paths.share_path, script)
     new_script = str(tmpdir.join(script))
 

lib/spack/spack/test/cmd/config.py

@@ -213,7 +213,7 @@ def test_config_add_update_dict(mutable_empty_config):
 
 def test_config_with_c_argument(mutable_empty_config):
     # I don't know how to add a spack argument to a Spack Command, so we test this way
-    config_file = "config:install_root:root:/path/to/config.yaml"
+    config_file = "config:install_tree:root:/path/to/config.yaml"
     parser = spack.main.make_argument_parser()
     args = parser.parse_args(["-c", config_file])
     assert config_file in args.config_vars
@@ -221,7 +221,7 @@ def test_config_with_c_argument(mutable_empty_config):
     # Add the path to the config
     config("add", args.config_vars[0], scope="command_line")
     output = config("get", "config")
-    assert "config:\n  install_root:\n    root: /path/to/config.yaml" in output
+    assert "config:\n  install_tree:\n    root: /path/to/config.yaml" in output
 
 
 def test_config_add_ordered_dict(mutable_empty_config):

lib/spack/spack/test/cmd/deprecate.py

@@ -15,6 +15,9 @@
 deprecate = SpackCommand("deprecate")
 find = SpackCommand("find")
 
+# Unit tests should not be affected by the user's managed environments
+pytestmark = pytest.mark.usefixtures("mutable_mock_env_path")
+
 
 def test_deprecate(mock_packages, mock_archive, mock_fetch, install_mockery):
     install("--fake", "libelf@0.8.13")

lib/spack/spack/test/cmd/develop.py

@@ -16,6 +16,7 @@
 import spack.stage
 import spack.util.git
 import spack.util.path
+from spack.error import SpackError
 from spack.main import SpackCommand
 
 add = SpackCommand("add")
@@ -159,6 +160,7 @@ def check_path(stage, dest):
             # Create path to allow develop to modify env
             fs.mkdirp(abspath)
             develop("--no-clone", "-p", path, "mpich@1.0")
+            self.check_develop(e, spack.spec.Spec("mpich@=1.0"), path)
 
             # Remove path to ensure develop with no args runs staging code
             os.rmdir(abspath)
@@ -218,6 +220,40 @@ def test_develop_full_git_repo(
         assert len(commits) > 1
 
 
+def test_recursive(mutable_mock_env_path, install_mockery, mock_fetch):
+    env("create", "test")
+
+    with ev.read("test") as e:
+        add("indirect-mpich@1.0")
+        e.concretize()
+        specs = e.all_specs()
+
+        assert len(specs) > 1
+        develop("--recursive", "mpich")
+
+        expected_dev_specs = ["mpich", "direct-mpich", "indirect-mpich"]
+        for spec in expected_dev_specs:
+            assert spec in e.dev_specs
+
+
+def test_develop_fails_with_multiple_concrete_versions(
+    mutable_mock_env_path, install_mockery, mock_fetch
+):
+    env("create", "test")
+
+    with ev.read("test") as e:
+        add("indirect-mpich@1.0")
+        add("indirect-mpich@0.9")
+        e.unify = False
+        e.concretize()
+
+        with pytest.raises(SpackError) as develop_error:
+            develop("indirect-mpich", fail_on_error=True)
+
+        error_str = "has multiple concrete instances in the graph"
+        assert error_str in str(develop_error.value)
+
+
 def test_concretize_dev_path_with_at_symbol_in_env(mutable_mock_env_path, tmpdir, mock_packages):
     spec_like = "develop-test@develop"
 

lib/spack/spack/test/cmd/env.py

@@ -1067,13 +1067,17 @@ def test_init_from_yaml_relative_includes(tmp_path):
         assert os.path.exists(os.path.join(e2.path, f))
 
 
+# TODO: Should we be supporting relative path rewrites when creating new env from existing?
+# TODO: If so, then this should confirm that the absolute include paths in the new env exist.
 def test_init_from_yaml_relative_includes_outside_env(tmp_path):
-    files = ["../outside_env_not_copied/repos.yaml"]
+    """Ensure relative includes to files outside the environment fail."""
+    files = ["../outside_env/repos.yaml"]
 
     manifest = f"""
 spack:
   specs: []
-  include: {files}
+  include:
+  - path: {files[0]}
 """
 
     # subdir to ensure parent of environment dir is not shared
@@ -1086,7 +1090,7 @@ def test_init_from_yaml_relative_includes_outside_env(tmp_path):
     for f in files:
         fs.touchp(e1_path / f)
 
-    with pytest.raises(spack.config.ConfigFileError, match="Detected 1 missing include"):
+    with pytest.raises(ValueError, match="does not exist"):
         _ = _env_create("test2", init_file=e1_manifest)
 
 
@@ -1186,14 +1190,14 @@ def test_env_with_config(environment_from_manifest):
 
 
 def test_with_config_bad_include_create(environment_from_manifest):
-    """Confirm missing include paths raise expected exception and error."""
-    with pytest.raises(spack.config.ConfigFileError, match="2 missing include path"):
+    """Confirm missing required include raises expected exception."""
+    err = "does not exist"
+    with pytest.raises(ValueError, match=err):
         environment_from_manifest(
             """
 spack:
   include:
   - /no/such/directory
-  - no/such/file.yaml
 """
         )
 
@@ -1203,34 +1207,25 @@ def test_with_config_bad_include_activate(environment_from_manifest, tmpdir):
     include1 = env_root / "include1.yaml"
     include1.touch()
 
-    abs_include_path = os.path.abspath(tmpdir.join("subdir").ensure("include2.yaml"))
-
     spack_yaml = env_root / ev.manifest_name
     spack_yaml.write_text(
-        f"""
+        """
 spack:
   include:
   - ./include1.yaml
-  - {abs_include_path}
 """
     )
 
     with ev.Environment(env_root) as e:
         e.concretize()
 
-    # we've created an environment with some included config files (which do
-    # in fact exist): now we remove them and check that we get a sensible
-    # error message
+    # We've created an environment with included config file (which does
+    # exist). Now we remove it and check that we get a sensible error.
 
-    os.remove(abs_include_path)
     os.remove(include1)
-    with pytest.raises(spack.config.ConfigFileError) as exc:
+    with pytest.raises(ValueError, match="does not exist"):
         ev.activate(ev.Environment(env_root))
 
-    err = exc.value.message
-    assert "missing include" in err
-    assert abs_include_path in err
-    assert "include1.yaml" in err
     assert ev.active_environment() is None
 
 
@@ -1338,8 +1333,10 @@ def test_config_change_existing(mutable_mock_env_path, tmp_path, mock_packages,
     included file scope.
     """
 
+    env_path = tmp_path / "test_config"
+    fs.mkdirp(env_path)
     included_file = "included-packages.yaml"
-    included_path = tmp_path / included_file
+    included_path = env_path / included_file
     with open(included_path, "w", encoding="utf-8") as f:
         f.write(
             """\
@@ -1355,7 +1352,7 @@ def test_config_change_existing(mutable_mock_env_path, tmp_path, mock_packages,
 """
         )
 
-    spack_yaml = tmp_path / ev.manifest_name
+    spack_yaml = env_path / ev.manifest_name
     spack_yaml.write_text(
         f"""\
 spack:
@@ -1369,7 +1366,8 @@ def test_config_change_existing(mutable_mock_env_path, tmp_path, mock_packages,
 """
     )
 
-    e = ev.Environment(tmp_path)
+    mutable_config.set("config:misc_cache", str(tmp_path / "cache"))
+    e = ev.Environment(env_path)
     with e:
         # List of requirements, flip a variant
         config("change", "packages:mpich:require:~debug")
@@ -1459,19 +1457,6 @@ def test_env_with_included_config_file_url(tmpdir, mutable_empty_config, package
     assert cfg["mpileaks"]["version"] == ["2.2"]
 
 
-def test_env_with_included_config_missing_file(tmpdir, mutable_empty_config):
-    """Test inclusion of a missing configuration file raises FetchError
-    noting missing file."""
-
-    spack_yaml = tmpdir.join("spack.yaml")
-    missing_file = tmpdir.join("packages.yaml")
-    with spack_yaml.open("w") as f:
-        f.write("spack:\n  include:\n    - {0}\n".format(missing_file.strpath))
-
-    with pytest.raises(spack.error.ConfigError, match="missing include path"):
-        ev.Environment(tmpdir.strpath)
-
-
 def test_env_with_included_config_scope(mutable_mock_env_path, packages_file):
     """Test inclusion of a package file from the environment's configuration
     stage directory. This test is intended to represent a case where a remote
@@ -1566,7 +1551,7 @@ def test_env_with_included_config_precedence(tmp_path):
 
 
 def test_env_with_included_configs_precedence(tmp_path):
-    """Test precendence of multiple included configuration files."""
+    """Test precedence of multiple included configuration files."""
     file1 = "high-config.yaml"
     file2 = "low-config.yaml"
 
@@ -1794,7 +1779,7 @@ def test_roots_display_with_variants():
     with ev.read("test"):
         out = find(output=str)
 
-    assert "boost +shared" in out
+    assert "boost+shared" in out
 
 
 def test_uninstall_keeps_in_env(mock_stage, mock_fetch, install_mockery):
@@ -3080,14 +3065,26 @@ def test_stack_view_activate_from_default(
 
 def test_envvar_set_in_activate(tmp_path, mock_packages, install_mockery):
     spack_yaml = tmp_path / "spack.yaml"
+    env_vars_yaml = tmp_path / "env_vars.yaml"
+
+    env_vars_yaml.write_text(
+        """
+env_vars:
+  set:
+    CONFIG_ENVAR_SET_IN_ENV_LOAD: "True"
+"""
+    )
+
     spack_yaml.write_text(
         """
 spack:
+  include:
+  - env_vars.yaml
   specs:
     - cmake%gcc
   env_vars:
     set:
-      ENVAR_SET_IN_ENV_LOAD: "True"
+      SPACK_ENVAR_SET_IN_ENV_LOAD: "True"
 """
     )
 
@@ -3098,12 +3095,16 @@ def test_envvar_set_in_activate(tmp_path, mock_packages, install_mockery):
     test_env = ev.read("test")
     output = env("activate", "--sh", "test")
 
-    assert "ENVAR_SET_IN_ENV_LOAD=True" in output
+    assert "SPACK_ENVAR_SET_IN_ENV_LOAD=True" in output
+    assert "CONFIG_ENVAR_SET_IN_ENV_LOAD=True" in output
 
     with test_env:
-        with spack.util.environment.set_env(ENVAR_SET_IN_ENV_LOAD="True"):
+        with spack.util.environment.set_env(
+            SPACK_ENVAR_SET_IN_ENV_LOAD="True", CONFIG_ENVAR_SET_IN_ENV_LOAD="True"
+        ):
             output = env("deactivate", "--sh")
-            assert "unset ENVAR_SET_IN_ENV_LOAD" in output
+            assert "unset SPACK_ENVAR_SET_IN_ENV_LOAD" in output
+            assert "unset CONFIG_ENVAR_SET_IN_ENV_LOAD" in output
 
 
 def test_stack_view_no_activate_without_default(
@@ -4277,21 +4278,31 @@ def test_unify_when_possible_works_around_conflicts():
     assert len([x for x in e.all_specs() if x.satisfies("mpich")]) == 1
 
 
+# Using mock_include_cache to ensure the "remote" file is cached in a temporary
+# location and not polluting the user cache.
 def test_env_include_packages_url(
-    tmpdir, mutable_empty_config, mock_spider_configs, mock_curl_configs
+    tmpdir, mutable_empty_config, mock_fetch_url_text, mock_curl_configs, mock_include_cache
 ):
     """Test inclusion of a (GitHub) URL."""
     develop_url = "https://github.com/fake/fake/blob/develop/"
     default_packages = develop_url + "etc/fake/defaults/packages.yaml"
+    sha256 = "a422e35b3a18869d0611a4137b37314131749ecdc070a7cd7183f488da81201a"
     spack_yaml = tmpdir.join("spack.yaml")
     with spack_yaml.open("w") as f:
-        f.write("spack:\n  include:\n    - {0}\n".format(default_packages))
-    assert os.path.isfile(spack_yaml.strpath)
+        f.write(
+            f"""\
+spack:
+  include:
+  - path: {default_packages}
+    sha256: {sha256}
+"""
+        )
 
     with spack.config.override("config:url_fetch_method", "curl"):
         env = ev.Environment(tmpdir.strpath)
         ev.activate(env)
 
+        # Make sure a setting from test/data/config/packages.yaml is present
         cfg = spack.config.get("packages")
         assert "mpich" in cfg["all"]["providers"]["mpi"]
 
@@ -4360,7 +4371,7 @@ def test_env_view_disabled(tmp_path, mutable_mock_env_path):
 
 
 @pytest.mark.parametrize("first", ["false", "true", "custom"])
-def test_env_include_mixed_views(tmp_path, mutable_mock_env_path, mutable_config, first):
+def test_env_include_mixed_views(tmp_path, mutable_config, mutable_mock_env_path, first):
     """Ensure including path and boolean views in different combinations result
     in the creation of only the first view if it is not disabled."""
     false_yaml = tmp_path / "false-view.yaml"

lib/spack/spack/test/cmd/find.py

@@ -320,7 +320,7 @@ def test_find_very_long(database, config):
 @pytest.mark.db
 def test_find_show_compiler(database, config):
     output = find("--no-groups", "--show-full-compiler", "mpileaks")
-    assert "mpileaks@2.3%gcc@10.2.1" in output
+    assert "mpileaks@2.3 %gcc@10.2.1" in output
 
 
 @pytest.mark.db
@@ -464,7 +464,7 @@ def test_environment_with_version_range_in_compiler_doesnt_fail(tmp_path):
 
     with test_environment:
         output = find()
-    assert "zlib%gcc@12.1.0" in output
+    assert "zlib %gcc@12.1.0" in output
 
 
 _pkga = (

lib/spack/spack/test/cmd/install.py

@@ -718,10 +718,11 @@ def test_install_deps_then_package(tmpdir, mock_fetch, install_mockery):
     assert os.path.exists(root.prefix)
 
 
+# Unit tests should not be affected by the user's managed environments
 @pytest.mark.not_on_windows("Environment views not supported on windows. Revisit after #34701")
 @pytest.mark.regression("12002")
 def test_install_only_dependencies_in_env(
-    tmpdir, mock_fetch, install_mockery, mutable_mock_env_path
+    tmpdir, mutable_mock_env_path, mock_fetch, install_mockery
 ):
     env("create", "test")
 
@@ -735,9 +736,10 @@ def test_install_only_dependencies_in_env(
         assert not os.path.exists(root.prefix)
 
 
+# Unit tests should not be affected by the user's managed environments
 @pytest.mark.regression("12002")
 def test_install_only_dependencies_of_all_in_env(
-    tmpdir, mock_fetch, install_mockery, mutable_mock_env_path
+    tmpdir, mutable_mock_env_path, mock_fetch, install_mockery
 ):
     env("create", "--without-view", "test")
 
@@ -757,7 +759,8 @@ def test_install_only_dependencies_of_all_in_env(
                 assert os.path.exists(dep.prefix)
 
 
-def test_install_no_add_in_env(tmpdir, mock_fetch, install_mockery, mutable_mock_env_path):
+# Unit tests should not be affected by the user's managed environments
+def test_install_no_add_in_env(tmpdir, mutable_mock_env_path, mock_fetch, install_mockery):
     # To test behavior of --add option, we create the following environment:
     #
     #     mpileaks
@@ -898,7 +901,6 @@ def test_cdash_configure_warning(tmpdir, mock_fetch, install_mockery, capfd):
         specfile = "./spec.json"
         with open(specfile, "w", encoding="utf-8") as f:
             f.write(spec.to_json())
-        print(spec.to_json())
         install("--log-file=cdash_reports", "--log-format=cdash", specfile)
         # Verify Configure.xml exists with expected contents.
         report_dir = tmpdir.join("cdash_reports")
@@ -933,9 +935,10 @@ def test_install_fails_no_args_suggests_env_activation(tmpdir):
     assert "using the `spack.yaml` in this directory" in output
 
 
+# Unit tests should not be affected by the user's managed environments
 @pytest.mark.not_on_windows("Environment views not supported on windows. Revisit after #34701")
 def test_install_env_with_tests_all(
-    tmpdir, mock_packages, mock_fetch, install_mockery, mutable_mock_env_path
+    tmpdir, mutable_mock_env_path, mock_packages, mock_fetch, install_mockery
 ):
     env("create", "test")
     with ev.read("test"):
@@ -945,9 +948,10 @@ def test_install_env_with_tests_all(
         assert os.path.exists(test_dep.prefix)
 
 
+# Unit tests should not be affected by the user's managed environments
 @pytest.mark.not_on_windows("Environment views not supported on windows. Revisit after #34701")
 def test_install_env_with_tests_root(
-    tmpdir, mock_packages, mock_fetch, install_mockery, mutable_mock_env_path
+    tmpdir, mutable_mock_env_path, mock_packages, mock_fetch, install_mockery
 ):
     env("create", "test")
     with ev.read("test"):
@@ -957,9 +961,10 @@ def test_install_env_with_tests_root(
         assert not os.path.exists(test_dep.prefix)
 
 
+# Unit tests should not be affected by the user's managed environments
 @pytest.mark.not_on_windows("Environment views not supported on windows. Revisit after #34701")
 def test_install_empty_env(
-    tmpdir, mock_packages, mock_fetch, install_mockery, mutable_mock_env_path
+    tmpdir, mutable_mock_env_path, mock_packages, mock_fetch, install_mockery
 ):
     env_name = "empty"
     env("create", env_name)
@@ -995,9 +1000,17 @@ def test_installation_fail_tests(install_mockery, mock_fetch, name, method):
     assert "See test log for details" in output
 
 
+# Unit tests should not be affected by the user's managed environments
 @pytest.mark.not_on_windows("Buildcache not supported on windows")
 def test_install_use_buildcache(
-    capsys, mock_packages, mock_fetch, mock_archive, mock_binary_index, tmpdir, install_mockery
+    capsys,
+    mutable_mock_env_path,
+    mock_packages,
+    mock_fetch,
+    mock_archive,
+    mock_binary_index,
+    tmpdir,
+    install_mockery,
 ):
     """
     Make sure installing with use-buildcache behaves correctly.

lib/spack/spack/test/cmd/mark.py

@@ -12,6 +12,9 @@
 install = SpackCommand("install")
 uninstall = SpackCommand("uninstall")
 
+# Unit tests should not be affected by the user's managed environments
+pytestmark = pytest.mark.usefixtures("mutable_mock_env_path")
+
 
 @pytest.mark.db
 def test_mark_mode_required(mutable_database):

lib/spack/spack/test/cmd/mirror.py

@@ -38,8 +38,9 @@ def test_regression_8083(tmpdir, capfd, mock_packages, mock_fetch, config):
     assert "as it is an external spec" in output
 
 
+# Unit tests should not be affected by the user's managed environments
 @pytest.mark.regression("12345")
-def test_mirror_from_env(tmp_path, mock_packages, mock_fetch, mutable_mock_env_path):
+def test_mirror_from_env(mutable_mock_env_path, tmp_path, mock_packages, mock_fetch):
     mirror_dir = str(tmp_path / "mirror")
     env_name = "test"
 
@@ -342,8 +343,16 @@ def test_mirror_name_collision(mutable_config):
         mirror("add", "first", "1")
 
 
+# Unit tests should not be affected by the user's managed environments
 def test_mirror_destroy(
-    install_mockery, mock_packages, mock_fetch, mock_archive, mutable_config, monkeypatch, tmpdir
+    mutable_mock_env_path,
+    install_mockery,
+    mock_packages,
+    mock_fetch,
+    mock_archive,
+    mutable_config,
+    monkeypatch,
+    tmpdir,
 ):
     # Create a temp mirror directory for buildcache usage
     mirror_dir = tmpdir.join("mirror_dir")

lib/spack/spack/test/cmd/pkg.py

@@ -42,7 +42,7 @@ def mock_pkg_git_repo(git, tmp_path_factory):
     repo_dir = root_dir / "builtin.mock"
     shutil.copytree(spack.paths.mock_packages_path, str(repo_dir))
 
-    repo_cache = spack.util.file_cache.FileCache(str(root_dir / "cache"))
+    repo_cache = spack.util.file_cache.FileCache(root_dir / "cache")
     mock_repo = spack.repo.RepoPath(str(repo_dir), cache=repo_cache)
     mock_repo_packages = mock_repo.repos[0].packages_path
 

lib/spack/spack/test/cmd/repo.py

@@ -5,9 +5,13 @@
 
 import pytest
 
+import spack.config
+import spack.environment as ev
 import spack.main
+from spack.main import SpackCommand
 
 repo = spack.main.SpackCommand("repo")
+env = SpackCommand("env")
 
 
 def test_help_option():
@@ -33,3 +37,33 @@ def test_create_add_list_remove(mutable_config, tmpdir):
     repo("remove", "--scope=site", str(tmpdir))
     output = repo("list", "--scope=site", output=str)
     assert "mockrepo" not in output
+
+
+def test_env_repo_path_vars_substitution(
+    tmpdir, install_mockery, mutable_mock_env_path, monkeypatch
+):
+    """Test Spack correctly substitues repo paths with environment variables when creating an
+    environment from a manifest file."""
+
+    monkeypatch.setenv("CUSTOM_REPO_PATH", ".")
+
+    # setup environment from spack.yaml
+    envdir = tmpdir.mkdir("env")
+    with envdir.as_cwd():
+        with open("spack.yaml", "w", encoding="utf-8") as f:
+            f.write(
+                """\
+spack:
+  specs: []
+
+  repos:
+    - $CUSTOM_REPO_PATH
+"""
+            )
+        # creating env from manifest file
+        env("create", "test", "./spack.yaml")
+        # check that repo path was correctly substituted with the environment variable
+        current_dir = os.getcwd()
+        with ev.read("test") as newenv:
+            repos_specs = spack.config.get("repos", default={}, scope=newenv.scope_name)
+            assert current_dir in repos_specs

lib/spack/spack/test/cmd/spec.py

@@ -13,7 +13,10 @@
 import spack.store
 from spack.main import SpackCommand, SpackCommandError
 
-pytestmark = pytest.mark.usefixtures("mutable_config", "mutable_mock_repo")
+# Unit tests should not be affected by the user's managed environments
+pytestmark = pytest.mark.usefixtures(
+    "mutable_mock_env_path", "mutable_config", "mutable_mock_repo"
+)
 
 spec = SpackCommand("spec")
 

lib/spack/spack/test/cmd/style.py

@@ -409,3 +409,108 @@ def test_case_sensitive_imports(tmp_path: pathlib.Path):
 def test_pkg_imports():
     assert spack.cmd.style._module_part(spack.paths.prefix, "spack.pkg.builtin.boost") is None
     assert spack.cmd.style._module_part(spack.paths.prefix, "spack.pkg") is None
+
+
+def test_spec_strings(tmp_path):
+    (tmp_path / "example.py").write_text(
+        """\
+def func(x):
+    print("dont fix %s me" % x, 3)
+    return x.satisfies("+foo %gcc +bar") and x.satisfies("%gcc +baz")
+"""
+    )
+    (tmp_path / "example.json").write_text(
+        """\
+{
+    "spec": [
+        "+foo %gcc +bar~nope   ^dep %clang +yup @3.2 target=x86_64 /abcdef ^another   %gcc   ",
+        "%gcc +baz"
+    ],
+    "%gcc x=y": 2
+}
+"""
+    )
+    (tmp_path / "example.yaml").write_text(
+        """\
+spec:
+  - "+foo   %gcc +bar"
+  - "%gcc +baz"
+  - "this is fine %clang"
+"%gcc x=y": 2
+"""
+    )
+
+    issues = set()
+
+    def collect_issues(path: str, line: int, col: int, old: str, new: str):
+        issues.add((path, line, col, old, new))
+
+    # check for issues with custom handler
+    spack.cmd.style._check_spec_strings(
+        [
+            str(tmp_path / "nonexistent.py"),
+            str(tmp_path / "example.py"),
+            str(tmp_path / "example.json"),
+            str(tmp_path / "example.yaml"),
+        ],
+        handler=collect_issues,
+    )
+
+    assert issues == {
+        (
+            str(tmp_path / "example.json"),
+            3,
+            9,
+            "+foo %gcc +bar~nope   ^dep %clang +yup @3.2 target=x86_64 /abcdef ^another   %gcc   ",
+            "+foo +bar~nope %gcc   ^dep +yup @3.2 target=x86_64 /abcdef %clang ^another   %gcc   ",
+        ),
+        (str(tmp_path / "example.json"), 4, 9, "%gcc +baz", "+baz %gcc"),
+        (str(tmp_path / "example.json"), 6, 5, "%gcc x=y", "x=y %gcc"),
+        (str(tmp_path / "example.py"), 3, 23, "+foo %gcc +bar", "+foo +bar %gcc"),
+        (str(tmp_path / "example.py"), 3, 57, "%gcc +baz", "+baz %gcc"),
+        (str(tmp_path / "example.yaml"), 2, 5, "+foo   %gcc +bar", "+foo +bar   %gcc"),
+        (str(tmp_path / "example.yaml"), 3, 5, "%gcc +baz", "+baz %gcc"),
+        (str(tmp_path / "example.yaml"), 5, 1, "%gcc x=y", "x=y %gcc"),
+    }
+
+    # fix the issues in the files
+    spack.cmd.style._check_spec_strings(
+        [
+            str(tmp_path / "nonexistent.py"),
+            str(tmp_path / "example.py"),
+            str(tmp_path / "example.json"),
+            str(tmp_path / "example.yaml"),
+        ],
+        handler=spack.cmd.style._spec_str_fix_handler,
+    )
+
+    assert (
+        (tmp_path / "example.json").read_text()
+        == """\
+{
+    "spec": [
+        "+foo +bar~nope %gcc   ^dep +yup @3.2 target=x86_64 /abcdef %clang ^another   %gcc   ",
+        "+baz %gcc"
+    ],
+    "x=y %gcc": 2
+}
+"""
+    )
+    assert (
+        (tmp_path / "example.py").read_text()
+        == """\
+def func(x):
+    print("dont fix %s me" % x, 3)
+    return x.satisfies("+foo +bar %gcc") and x.satisfies("+baz %gcc")
+"""
+    )
+    assert (
+        (tmp_path / "example.yaml").read_text()
+        == """\
+spec:
+  - "+foo +bar   %gcc"
+  - "+baz %gcc"
+  - "this is fine %clang"
+"x=y %gcc": 2
+"""
+    )

lib/spack/spack/test/cmd/uninstall.py

@@ -16,6 +16,9 @@
 uninstall = SpackCommand("uninstall")
 install = SpackCommand("install")
 
+# Unit tests should not be affected by the user's managed environments
+pytestmark = pytest.mark.usefixtures("mutable_mock_env_path")
+
 
 class MockArgs:
     def __init__(self, packages, all=False, force=False, dependents=False):
@@ -220,9 +223,7 @@ class TestUninstallFromEnv:
     find = SpackCommand("find")
 
     @pytest.fixture(scope="function")
-    def environment_setup(
-        self, mutable_mock_env_path, mock_packages, mutable_database, install_mockery
-    ):
+    def environment_setup(self, mock_packages, mutable_database, install_mockery):
         TestUninstallFromEnv.env("create", "e1")
         e1 = spack.environment.read("e1")
         with e1:

lib/spack/spack/test/cmd/unit_test.py

@@ -50,7 +50,7 @@ def test_list_long(capsys):
 def test_list_long_with_pytest_arg(capsys):
     with capsys.disabled():
         output = spack_test("--list-long", cmd_test_py)
-    print(output)
+
     assert "unit_test.py::\n" in output
     assert "test_list" in output
     assert "test_list_with_pytest_arg" in output

lib/spack/spack/test/cmd/verify.py

@@ -4,19 +4,31 @@
 
 """Tests for the `spack verify` command"""
 import os
+import platform
+
+import pytest
 
 import llnl.util.filesystem as fs
 
+import spack.cmd.verify
 import spack.concretize
+import spack.installer
 import spack.store
+import spack.util.executable
 import spack.util.spack_json as sjson
 import spack.verify
-from spack.main import SpackCommand
+from spack.main import SpackCommand, SpackCommandError
 
 verify = SpackCommand("verify")
 install = SpackCommand("install")
 
 
+def skip_unless_linux(f):
+    return pytest.mark.skipif(
+        str(platform.system()) != "Linux", reason="only tested on linux for now"
+    )(f)
+
+
 def test_single_file_verify_cmd(tmpdir):
     # Test the verify command interface to verifying a single file.
     filedir = os.path.join(str(tmpdir), "a", "b", "c", "d")
@@ -36,15 +48,14 @@ def test_single_file_verify_cmd(tmpdir):
     with open(manifest_file, "w", encoding="utf-8") as f:
         sjson.dump({filepath: data}, f)
 
-    results = verify("-f", filepath, fail_on_error=False)
-    print(results)
+    results = verify("manifest", "-f", filepath, fail_on_error=False)
     assert not results
 
     os.utime(filepath, (0, 0))
     with open(filepath, "w", encoding="utf-8") as f:
         f.write("I changed.")
 
-    results = verify("-f", filepath, fail_on_error=False)
+    results = verify("manifest", "-f", filepath, fail_on_error=False)
 
     expected = ["hash"]
     mtime = os.stat(filepath).st_mtime
@@ -55,7 +66,7 @@ def test_single_file_verify_cmd(tmpdir):
     assert filepath in results
     assert all(x in results for x in expected)
 
-    results = verify("-fj", filepath, fail_on_error=False)
+    results = verify("manifest", "-fj", filepath, fail_on_error=False)
     res = sjson.load(results)
     assert len(res) == 1
     errors = res.pop(filepath)
@@ -69,18 +80,68 @@ def test_single_spec_verify_cmd(tmpdir, mock_packages, mock_archive, mock_fetch,
     prefix = s.prefix
     hash = s.dag_hash()
 
-    results = verify("/%s" % hash, fail_on_error=False)
+    results = verify("manifest", "/%s" % hash, fail_on_error=False)
     assert not results
 
     new_file = os.path.join(prefix, "new_file_for_verify_test")
     with open(new_file, "w", encoding="utf-8") as f:
         f.write("New file")
 
-    results = verify("/%s" % hash, fail_on_error=False)
+    results = verify("manifest", "/%s" % hash, fail_on_error=False)
     assert new_file in results
     assert "added" in results
 
-    results = verify("-j", "/%s" % hash, fail_on_error=False)
+    results = verify("manifest", "-j", "/%s" % hash, fail_on_error=False)
     res = sjson.load(results)
     assert len(res) == 1
     assert res[new_file] == ["added"]
+
+
+@pytest.mark.requires_executables("gcc")
+@skip_unless_linux
+def test_libraries(tmp_path, install_mockery, mock_fetch):
+    gcc = spack.util.executable.which("gcc", required=True)
+    s = spack.concretize.concretize_one("libelf")
+    spack.installer.PackageInstaller([s.package]).install()
+    os.mkdir(s.prefix.bin)
+
+    # There are no ELF files so the verification should pass
+    verify("libraries", f"/{s.dag_hash()}")
+
+    # Now put main_with_rpath linking to libf.so inside the prefix and verify again. This should
+    # work because libf.so can be located in the rpath.
+    (tmp_path / "f.c").write_text("void f(void){return;}")
+    (tmp_path / "main.c").write_text("void f(void); int main(void){f();return 0;}")
+
+    gcc("-shared", "-fPIC", "-o", str(tmp_path / "libf.so"), str(tmp_path / "f.c"))
+    gcc(
+        "-o",
+        str(s.prefix.bin.main_with_rpath),
+        str(tmp_path / "main.c"),
+        "-L",
+        str(tmp_path),
+        f"-Wl,-rpath,{tmp_path}",
+        "-lf",
+    )
+    verify("libraries", f"/{s.dag_hash()}")
+
+    # Now put main_without_rpath linking to libf.so inside the prefix and verify again. This should
+    # fail because libf.so cannot be located in the rpath.
+    gcc(
+        "-o",
+        str(s.prefix.bin.main_without_rpath),
+        str(tmp_path / "main.c"),
+        "-L",
+        str(tmp_path),
+        "-lf",
+    )
+
+    with pytest.raises(SpackCommandError):
+        verify("libraries", f"/{s.dag_hash()}")
+
+    # Check the error message
+    msg = spack.cmd.verify._verify_libraries(s, [])
+    assert msg is not None and "libf.so => not found" in msg
+
+    # And check that we can make it pass by ignoring it.
+    assert spack.cmd.verify._verify_libraries(s, ["libf.so"]) is None

lib/spack/spack/test/cmd/versions.py

@@ -59,13 +59,6 @@ def mock_fetch_remote_versions(*args, **kwargs):
     assert v.strip(" \n\t") == "99.99.99\n  3.2.1"
 
 
-@pytest.mark.maybeslow
-def test_no_versions():
-    """Test a package for which no remote versions are available."""
-
-    versions("converge")
-
-
 @pytest.mark.maybeslow
 def test_no_unchecksummed_versions():
     """Test a package for which no unchecksummed versions are available."""

lib/spack/spack/test/concretization/compiler_runtimes.py

@@ -92,7 +92,7 @@ def test_external_nodes_do_not_have_runtimes(runtime_repo, mutable_config, tmp_p
         # Same as before, but tests that we can reuse from a more generic target
         pytest.param(
             "pkg-a%gcc@9.4.0",
-            "pkg-b%gcc@10.2.1 target=x86_64",
+            "pkg-b target=x86_64 %gcc@10.2.1",
             {"pkg-a": "gcc-runtime@9.4.0", "pkg-b": "gcc-runtime@9.4.0"},
             1,
             marks=pytest.mark.skipif(
@@ -101,7 +101,7 @@ def test_external_nodes_do_not_have_runtimes(runtime_repo, mutable_config, tmp_p
         ),
         pytest.param(
             "pkg-a%gcc@10.2.1",
-            "pkg-b%gcc@9.4.0 target=x86_64",
+            "pkg-b target=x86_64 %gcc@9.4.0",
             {
                 "pkg-a": "gcc-runtime@10.2.1 target=x86_64",
                 "pkg-b": "gcc-runtime@9.4.0 target=x86_64",

lib/spack/spack/test/concretization/core.py

@@ -121,7 +121,7 @@ def binary_compatibility(monkeypatch, request):
         "mpileaks ^mpi@1.2:2",
         # conflict not triggered
         "conflict",
-        "conflict%clang~foo",
+        "conflict~foo%clang",
         "conflict-parent%gcc",
     ]
 )
@@ -387,8 +387,8 @@ def test_different_compilers_get_different_flags(
         t = archspec.cpu.host().family
         client = spack.concretize.concretize_one(
             Spec(
-                f"cmake-client %gcc@11.1.0 platform=test os=redhat6 target={t}"
-                f" ^cmake %clang@12.2.0 platform=test os=redhat6 target={t}"
+                f"cmake-client platform=test os=redhat6 target={t} %gcc@11.1.0"
+                f" ^cmake platform=test os=redhat6 target={t} %clang@12.2.0"
             )
         )
         cmake = client["cmake"]
@@ -403,7 +403,7 @@ def test_spec_flags_maintain_order(self, mutable_config, gcc11_with_flags):
         for successive concretizations.
         """
         mutable_config.set("compilers", [gcc11_with_flags])
-        spec_str = "libelf %gcc@11.1.0 os=redhat6"
+        spec_str = "libelf os=redhat6 %gcc@11.1.0"
         for _ in range(3):
             s = spack.concretize.concretize_one(spec_str)
             assert all(
@@ -414,7 +414,7 @@ def test_compiler_flags_differ_identical_compilers(self, mutable_config, clang12
         mutable_config.set("compilers", [clang12_with_flags])
         # Correct arch to use test compiler that has flags
         t = archspec.cpu.host().family
-        spec = Spec(f"pkg-a %clang@12.2.0 platform=test os=redhat6 target={t}")
+        spec = Spec(f"pkg-a platform=test os=redhat6 target={t} %clang@12.2.0")
 
         # Get the compiler that matches the spec (
         compiler = spack.compilers.compiler_for_spec("clang@=12.2.0", spec.architecture)
@@ -488,13 +488,13 @@ def test_architecture_deep_inheritance(self, mock_targets, compiler_factory):
         # CNL compiler has no target attribute, and this is essential to make detection pass
         del cnl_compiler["compiler"]["target"]
         with spack.config.override("compilers", [cnl_compiler]):
-            spec_str = "mpileaks %gcc@4.5.0 os=CNL target=nocona ^dyninst os=CNL ^callpath os=CNL"
+            spec_str = "mpileaks os=CNL target=nocona %gcc@4.5.0 ^dyninst os=CNL ^callpath os=CNL"
             spec = spack.concretize.concretize_one(spec_str)
             for s in spec.traverse(root=False):
                 assert s.architecture.target == spec.architecture.target
 
     def test_compiler_flags_from_user_are_grouped(self):
-        spec = Spec('pkg-a%gcc cflags="-O -foo-flag foo-val" platform=test')
+        spec = Spec('pkg-a cflags="-O -foo-flag foo-val" platform=test %gcc')
         spec = spack.concretize.concretize_one(spec)
         cflags = spec.compiler_flags["cflags"]
         assert any(x == "-foo-flag foo-val" for x in cflags)
@@ -804,7 +804,7 @@ def test_external_and_virtual(self, mutable_config):
         assert spec["stuff"].compiler.satisfies("gcc")
 
     def test_compiler_child(self):
-        s = Spec("mpileaks%clang target=x86_64 ^dyninst%gcc")
+        s = Spec("mpileaks target=x86_64 %clang ^dyninst%gcc")
         s = spack.concretize.concretize_one(s)
         assert s["mpileaks"].satisfies("%clang")
         assert s["dyninst"].satisfies("%gcc")
@@ -826,7 +826,7 @@ def test_conflict_in_all_directives_true(self):
         with pytest.raises(spack.error.SpackError):
             s = spack.concretize.concretize_one(s)
 
-    @pytest.mark.parametrize("spec_str", ["conflict@10.0%clang+foo"])
+    @pytest.mark.parametrize("spec_str", ["conflict@10.0+foo%clang"])
     def test_no_conflict_in_external_specs(self, spec_str):
         # Modify the configuration to have the spec with conflict
         # registered as an external
@@ -940,9 +940,9 @@ def test_noversion_pkg(self, spec):
         "spec, best_achievable",
         [
             ("mpileaks%gcc@=4.4.7 ^dyninst@=10.2.1 target=x86_64:", "core2"),
-            ("mpileaks%gcc@=4.8 target=x86_64:", "haswell"),
-            ("mpileaks%gcc@=5.3.0 target=x86_64:", "broadwell"),
-            ("mpileaks%apple-clang@=5.1.0 target=x86_64:", "x86_64"),
+            ("mpileaks target=x86_64: %gcc@=4.8", "haswell"),
+            ("mpileaks target=x86_64: %gcc@=5.3.0", "broadwell"),
+            ("mpileaks target=x86_64: %apple-clang@=5.1.0", "x86_64"),
         ],
     )
     @pytest.mark.regression("13361", "20537")
@@ -1286,7 +1286,7 @@ def test_compiler_match_is_preferred_to_newer_version(self, compiler_factory):
         with spack.config.override(
             "compilers", [compiler_factory(spec="gcc@10.1.0", operating_system="redhat6")]
         ):
-            spec_str = "simple-inheritance+openblas %gcc@10.1.0 os=redhat6"
+            spec_str = "simple-inheritance+openblas os=redhat6 %gcc@10.1.0"
             s = spack.concretize.concretize_one(spec_str)
             assert "openblas@0.2.15" in s
             assert s["openblas"].satisfies("%gcc@10.1.0")
@@ -1319,7 +1319,7 @@ def test_custom_compiler_version(self, mutable_config, compiler_factory, monkeyp
             "compilers", [compiler_factory(spec="gcc@10foo", operating_system="redhat6")]
         )
         monkeypatch.setattr(spack.compiler.Compiler, "real_version", "10.2.1")
-        s = spack.concretize.concretize_one("pkg-a %gcc@10foo os=redhat6")
+        s = spack.concretize.concretize_one("pkg-a os=redhat6 %gcc@10foo")
         assert "%gcc@10foo" in s
 
     def test_all_patches_applied(self):
@@ -1531,8 +1531,8 @@ def test_external_with_non_default_variant_as_dependency(self):
             ("mpileaks", "os=debian6"),
             # To trigger the bug in 22871 we need to have the same compiler
             # spec available on both operating systems
-            ("mpileaks%gcc@10.2.1 platform=test os=debian6", "os=debian6"),
-            ("mpileaks%gcc@10.2.1 platform=test os=redhat6", "os=redhat6"),
+            ("mpileaks platform=test os=debian6 %gcc@10.2.1", "os=debian6"),
+            ("mpileaks platform=test os=redhat6 %gcc@10.2.1", "os=redhat6"),
         ],
     )
     def test_os_selection_when_multiple_choices_are_possible(
@@ -2018,7 +2018,6 @@ def test_git_ref_version_is_equivalent_to_specified_version(self, git_ref):
         s = Spec("develop-branch-version@git.%s=develop" % git_ref)
         c = spack.concretize.concretize_one(s)
         assert git_ref in str(c)
-        print(str(c))
         assert s.satisfies("@develop")
         assert s.satisfies("@0.1:")
 
@@ -2888,6 +2887,23 @@ def test_specifying_different_versions_build_deps(self):
         assert any(x.satisfies(hdf5_str) for x in result.specs)
         assert any(x.satisfies(pinned_str) for x in result.specs)
 
+    @pytest.mark.regression("44289")
+    def test_all_extensions_depend_on_same_extendee(self):
+        """Tests that we don't reuse dependencies that bring in a different extendee"""
+        setuptools = spack.concretize.concretize_one("py-setuptools ^python@3.10")
+
+        solver = spack.solver.asp.Solver()
+        setup = spack.solver.asp.SpackSolverSetup()
+        result, _, _ = solver.driver.solve(
+            setup, [Spec("py-floating ^python@3.11")], reuse=list(setuptools.traverse())
+        )
+        assert len(result.specs) == 1
+
+        floating = result.specs[0]
+        assert all(setuptools.dag_hash() != x.dag_hash() for x in floating.traverse())
+        pythons = [x for x in floating.traverse() if x.name == "python"]
+        assert len(pythons) == 1 and pythons[0].satisfies("@3.11")
+
 
 @pytest.mark.parametrize(
     "v_str,v_opts,checksummed",
@@ -2997,7 +3013,7 @@ def test_virtuals_provided_together_but_only_one_required_in_dag(self):
 
 
 def test_reusable_externals_match(mock_packages, tmpdir):
-    spec = Spec("mpich@4.1%gcc@13.1.0~debug build_system=generic arch=linux-ubuntu23.04-zen2")
+    spec = Spec("mpich@4.1~debug build_system=generic arch=linux-ubuntu23.04-zen2 %gcc@13.1.0")
     spec.external_path = tmpdir.strpath
     spec.external_modules = ["mpich/4.1"]
     spec._mark_concrete()
@@ -3015,7 +3031,7 @@ def test_reusable_externals_match(mock_packages, tmpdir):
 
 
 def test_reusable_externals_match_virtual(mock_packages, tmpdir):
-    spec = Spec("mpich@4.1%gcc@13.1.0~debug build_system=generic arch=linux-ubuntu23.04-zen2")
+    spec = Spec("mpich@4.1~debug build_system=generic arch=linux-ubuntu23.04-zen2 %gcc@13.1.0")
     spec.external_path = tmpdir.strpath
     spec.external_modules = ["mpich/4.1"]
     spec._mark_concrete()
@@ -3033,7 +3049,7 @@ def test_reusable_externals_match_virtual(mock_packages, tmpdir):
 
 
 def test_reusable_externals_different_prefix(mock_packages, tmpdir):
-    spec = Spec("mpich@4.1%gcc@13.1.0~debug build_system=generic arch=linux-ubuntu23.04-zen2")
+    spec = Spec("mpich@4.1~debug build_system=generic arch=linux-ubuntu23.04-zen2 %gcc@13.1.0")
     spec.external_path = "/other/path"
     spec.external_modules = ["mpich/4.1"]
     spec._mark_concrete()
@@ -3052,7 +3068,7 @@ def test_reusable_externals_different_prefix(mock_packages, tmpdir):
 
 @pytest.mark.parametrize("modules", [None, ["mpich/4.1", "libfabric/1.19"]])
 def test_reusable_externals_different_modules(mock_packages, tmpdir, modules):
-    spec = Spec("mpich@4.1%gcc@13.1.0~debug build_system=generic arch=linux-ubuntu23.04-zen2")
+    spec = Spec("mpich@4.1~debug build_system=generic arch=linux-ubuntu23.04-zen2 %gcc@13.1.0")
     spec.external_path = tmpdir.strpath
     spec.external_modules = modules
     spec._mark_concrete()
@@ -3070,7 +3086,7 @@ def test_reusable_externals_different_modules(mock_packages, tmpdir, modules):
 
 
 def test_reusable_externals_different_spec(mock_packages, tmpdir):
-    spec = Spec("mpich@4.1%gcc@13.1.0~debug build_system=generic arch=linux-ubuntu23.04-zen2")
+    spec = Spec("mpich@4.1~debug build_system=generic arch=linux-ubuntu23.04-zen2 %gcc@13.1.0")
     spec.external_path = tmpdir.strpath
     spec._mark_concrete()
     assert not spack.solver.asp._is_reusable(
@@ -3238,3 +3254,54 @@ def test_spec_unification(unify, mutable_config, mock_packages):
     maybe_fails = pytest.raises if unify is True else llnl.util.lang.nullcontext
     with maybe_fails(spack.solver.asp.UnsatisfiableSpecError):
         _ = spack.cmd.parse_specs([a_restricted, b], concretize=True)
+
+
+def test_concretization_cache_roundtrip(use_concretization_cache, monkeypatch, mutable_config):
+    """Tests whether we can write the results of a clingo solve to the cache
+    and load the same spec request from the cache to produce identical specs"""
+    # Force determinism:
+    # Solver setup is normally non-deterministic due to non-determinism in
+    # asp solver setup logic generation. The only other inputs to the cache keys are
+    # the .lp files, which are invariant over the course of this test.
+    # This method forces the same setup to be produced for the same specs
+    # which gives us a guarantee of cache hits, as it removes the only
+    # element of non deterministic solver setup for the same spec
+    # Basically just a quick and dirty memoization
+    solver_setup = spack.solver.asp.SpackSolverSetup.setup
+
+    def _setup(self, specs, *, reuse=None, allow_deprecated=False):
+        if not getattr(_setup, "cache_setup", None):
+            cache_setup = solver_setup(self, specs, reuse=reuse, allow_deprecated=allow_deprecated)
+            setattr(_setup, "cache_setup", cache_setup)
+        return getattr(_setup, "cache_setup")
+
+    # monkeypatch our forced determinism setup method into solver setup
+    monkeypatch.setattr(spack.solver.asp.SpackSolverSetup, "setup", _setup)
+
+    assert spack.config.get("config:concretization_cache:enable")
+
+    # run one standard concretization to populate the cache and the setup method
+    # memoization
+    h = spack.concretize.concretize_one("hdf5")
+
+    # due to our forced determinism above, we should not be observing
+    # cache misses, assert that we're not storing any new cache entries
+    def _ensure_no_store(self, problem: str, result, statistics, test=False):
+        # always throw, we never want to reach this code path
+        assert False, "Concretization cache hit expected"
+
+    # Assert that we're actually hitting the cache
+    cache_fetch = spack.solver.asp.ConcretizationCache.fetch
+
+    def _ensure_cache_hits(self, problem: str):
+        result, statistics = cache_fetch(self, problem)
+        assert result, "Expected successful concretization cache hit"
+        assert statistics, "Expected statistics to be non null on cache hit"
+        return result, statistics
+
+    monkeypatch.setattr(spack.solver.asp.ConcretizationCache, "store", _ensure_no_store)
+    monkeypatch.setattr(spack.solver.asp.ConcretizationCache, "fetch", _ensure_cache_hits)
+    # ensure subsequent concretizations of the same spec produce the same spec
+    # object
+    for _ in range(5):
+        assert h == spack.concretize.concretize_one("hdf5")

lib/spack/spack/test/concretization/errors.py

@@ -29,8 +29,7 @@
 ]
 
 variant_error_messages = [
-    "'fftw' required multiple values for single-valued variant 'mpi'",
-    "    Requested '~mpi' and '+mpi'",
+    "'fftw' requires conflicting variant values '~mpi' and '+mpi'",
     "        required because quantum-espresso depends on fftw+mpi when +invino",
     "          required because quantum-espresso+invino ^fftw~mpi requested explicitly",
     "        required because quantum-espresso+invino ^fftw~mpi requested explicitly",

lib/spack/spack/test/concretization/flag_mixing.py

@@ -94,7 +94,7 @@ def test_mix_spec_and_compiler_cfg(concretize_scope, test_repo):
     conf_str = _compiler_cfg_one_entry_with_cflags("-Wall")
     update_concretize_scope(conf_str, "compilers")
 
-    s1 = spack.concretize.concretize_one('y %gcc@12.100.100 cflags="-O2"')
+    s1 = spack.concretize.concretize_one('y cflags="-O2" %gcc@12.100.100')
     assert s1.satisfies('cflags="-Wall -O2"')
 
 
@@ -182,7 +182,7 @@ def test_propagate_and_compiler_cfg(concretize_scope, test_repo):
     conf_str = _compiler_cfg_one_entry_with_cflags("-f2")
     update_concretize_scope(conf_str, "compilers")
 
-    root_spec = spack.concretize.concretize_one("v %gcc@12.100.100 cflags=='-f1'")
+    root_spec = spack.concretize.concretize_one("v cflags=='-f1' %gcc@12.100.100")
     assert root_spec["y"].satisfies("cflags='-f1 -f2'")
 
 
@@ -229,7 +229,7 @@ def test_dev_mix_flags(tmp_path, concretize_scope, mutable_mock_env_path, test_r
     env_content = f"""\
 spack:
   specs:
-  - y %gcc@12.100.100 cflags=='-fsanitize=address'
+  - y cflags=='-fsanitize=address' %gcc@12.100.100
   develop:
     y:
       spec: y cflags=='-fsanitize=address'

lib/spack/spack/test/concretization/requirements.py

@@ -359,10 +359,10 @@ def test_one_package_multiple_oneof_groups(concretize_scope, test_repo):
     update_packages_config(conf_str)
 
     s1 = spack.concretize.concretize_one("y@2.5")
-    assert s1.satisfies("%clang~shared")
+    assert s1.satisfies("~shared%clang")
 
     s2 = spack.concretize.concretize_one("y@2.4")
-    assert s2.satisfies("%gcc+shared")
+    assert s2.satisfies("+shared%gcc")
 
 
 @pytest.mark.regression("34241")
@@ -377,11 +377,14 @@ def test_require_cflags(concretize_scope, mock_packages):
 """
     update_packages_config(conf_str)
 
-    spec_mpich2 = spack.concretize.concretize_one("mpich2")
-    assert spec_mpich2.satisfies("cflags=-g")
+    mpich2 = spack.concretize.concretize_one("mpich2")
+    assert mpich2.satisfies("cflags=-g")
 
-    spec_mpi = spack.concretize.concretize_one("mpi")
-    assert spec_mpi.satisfies("mpich cflags=-O1")
+    mpileaks = spack.concretize.concretize_one("mpileaks")
+    assert mpileaks["mpi"].satisfies("mpich cflags=-O1")
+
+    mpi = spack.concretize.concretize_one("mpi")
+    assert mpi.satisfies("mpich cflags=-O1")
 
 
 def test_requirements_for_package_that_is_not_needed(concretize_scope, test_repo):
@@ -499,7 +502,7 @@ def test_default_requirements_with_all(spec_str, requirement_str, concretize_sco
     "requirements,expectations",
     [
         (("%gcc", "%clang"), ("%gcc", "%clang")),
-        (("%gcc~shared", "@1.0"), ("%gcc~shared", "@1.0+shared")),
+        (("~shared%gcc", "@1.0"), ("~shared%gcc", "@1.0+shared")),
     ],
 )
 def test_default_and_package_specific_requirements(
@@ -754,7 +757,7 @@ def test_skip_requirement_when_default_requirement_condition_cannot_be_met(
     update_packages_config(packages_yaml)
     s = spack.concretize.concretize_one("mpileaks")
 
-    assert s.satisfies("%clang+shared")
+    assert s.satisfies("+shared %clang")
     # Sanity checks that 'callpath' doesn't have the shared variant, but that didn't
     # cause failures during concretization.
     assert "shared" not in s["callpath"].variants
@@ -982,6 +985,52 @@ def test_requiring_package_on_multiple_virtuals(concretize_scope, mock_packages)
             ["%clang"],
             ["%gcc"],
         ),
+        # Test using preferences on virtuals
+        (
+            """
+            packages:
+              all:
+                providers:
+                  mpi: [mpich]
+              mpi:
+                prefer:
+                - zmpi
+        """,
+            "mpileaks",
+            ["^[virtuals=mpi] zmpi"],
+            ["^[virtuals=mpi] mpich"],
+        ),
+        (
+            """
+            packages:
+              all:
+                providers:
+                  mpi: [mpich]
+              mpi:
+                prefer:
+                - zmpi
+        """,
+            "mpileaks ^[virtuals=mpi] mpich",
+            ["^[virtuals=mpi] mpich"],
+            ["^[virtuals=mpi] zmpi"],
+        ),
+        # Tests that strong preferences can be overridden by requirements
+        (
+            """
+                packages:
+                  all:
+                    providers:
+                      mpi: [zmpi]
+                  mpi:
+                    require:
+                    - mpich
+                    prefer:
+                    - zmpi
+            """,
+            "mpileaks",
+            ["^[virtuals=mpi] mpich"],
+            ["^[virtuals=mpi] zmpi"],
+        ),
     ],
 )
 def test_strong_preferences_packages_yaml(
@@ -1032,6 +1081,16 @@ def test_strong_preferences_packages_yaml(
         """,
             "multivalue-variant@=2.3 %clang",
         ),
+        # Test using conflict on virtual
+        (
+            """
+        packages:
+          mpi:
+            conflict:
+            - mpich
+    """,
+            "mpileaks ^[virtuals=mpi] mpich",
+        ),
     ],
 )
 def test_conflict_packages_yaml(packages_yaml, spec_str, concretize_scope, mock_packages):
@@ -1125,3 +1184,69 @@ def test_strong_preferences_higher_priority_than_reuse(concretize_scope, mock_pa
         )
         ascent = result.specs[0]
     assert ascent["adios2"].dag_hash() == reused_spec.dag_hash(), ascent
+
+
+@pytest.mark.parametrize(
+    "packages_yaml,err_match",
+    [
+        (
+            """
+packages:
+  mpi:
+    require:
+    - "+bzip2"
+""",
+            "expected a named spec",
+        ),
+        (
+            """
+packages:
+  mpi:
+    require:
+    - one_of: ["+bzip2", openmpi]
+""",
+            "expected a named spec",
+        ),
+        (
+            """
+packages:
+  mpi:
+    require:
+    - "^mpich"
+""",
+            "Did you mean",
+        ),
+    ],
+)
+def test_anonymous_spec_cannot_be_used_in_virtual_requirements(
+    packages_yaml, err_match, concretize_scope, mock_packages
+):
+    """Tests that using anonymous specs in requirements for virtual packages raises an
+    appropriate error message.
+    """
+    update_packages_config(packages_yaml)
+    with pytest.raises(spack.error.SpackError, match=err_match):
+        spack.concretize.concretize_one("mpileaks")
+
+
+def test_virtual_requirement_respects_any_of(concretize_scope, mock_packages):
+    """Tests that "any of" requirements can be used with virtuals"""
+    conf_str = """\
+        packages:
+          mpi:
+            require:
+            - any_of: ["mpich2", "mpich"]
+        """
+    update_packages_config(conf_str)
+
+    s = spack.concretize.concretize_one("mpileaks")
+    assert s.satisfies("^[virtuals=mpi] mpich2")
+
+    s = spack.concretize.concretize_one("mpileaks ^mpich2")
+    assert s.satisfies("^[virtuals=mpi] mpich2")
+
+    s = spack.concretize.concretize_one("mpileaks ^mpich")
+    assert s.satisfies("^[virtuals=mpi] mpich")
+
+    with pytest.raises(spack.error.SpackError):
+        spack.concretize.concretize_one("mpileaks ^[virtuals=mpi] zmpi")

lib/spack/spack/test/config.py

@@ -11,8 +11,7 @@
 
 import pytest
 
-import llnl.util.tty as tty
-from llnl.util.filesystem import join_path, touch, touchp
+from llnl.util.filesystem import join_path, touch
 
 import spack
 import spack.config
@@ -26,6 +25,7 @@
 import spack.schema.compilers
 import spack.schema.config
 import spack.schema.env
+import spack.schema.include
 import spack.schema.mirrors
 import spack.schema.repos
 import spack.spec
@@ -33,6 +33,8 @@
 import spack.util.path as spack_path
 import spack.util.spack_yaml as syaml
 
+from ..enums import ConfigScopePriority
+
 # sample config data
 config_low = {
     "config": {
@@ -49,22 +51,9 @@
 
 config_override_list = {"config": {"build_stage:": ["pathd", "pathe"]}}
 
-config_merge_dict = {"config": {"info": {"a": 3, "b": 4}}}
+config_merge_dict = {"config": {"aliases": {"ls": "find", "dev": "develop"}}}
 
-config_override_dict = {"config": {"info:": {"a": 7, "c": 9}}}
-
-
-@pytest.fixture()
-def write_config_file(tmpdir):
-    """Returns a function that writes a config file."""
-
-    def _write(config, data, scope):
-        config_yaml = tmpdir.join(scope, config + ".yaml")
-        config_yaml.ensure()
-        with config_yaml.open("w") as f:
-            syaml.dump_config(data, f)
-
-    return _write
+config_override_dict = {"config": {"aliases:": {"be": "build-env", "deps": "dependencies"}}}
 
 
 @pytest.fixture()
@@ -710,10 +699,7 @@ def assert_marked(obj):
 
 
 def test_internal_config_from_data():
-    config = spack.config.Configuration()
-
-    # add an internal config initialized from an inline dict
-    config.push_scope(
+    config = spack.config.create_from(
         spack.config.InternalConfigScope(
             "_builtin", {"config": {"verify_ssl": False, "build_jobs": 6}}
         )
@@ -1038,6 +1024,16 @@ def test_bad_config_yaml(tmpdir):
         )
 
 
+def test_bad_include_yaml(tmpdir):
+    with pytest.raises(spack.config.ConfigFormatError, match="is not of type"):
+        check_schema(
+            spack.schema.include.schema,
+            """\
+include: $HOME/include.yaml
+""",
+        )
+
+
 def test_bad_mirrors_yaml(tmpdir):
     with pytest.raises(spack.config.ConfigFormatError):
         check_schema(
@@ -1102,9 +1098,9 @@ def test_internal_config_section_override(mock_low_high_config, write_config_fil
 
 def test_internal_config_dict_override(mock_low_high_config, write_config_file):
     write_config_file("config", config_merge_dict, "low")
-    wanted_dict = config_override_dict["config"]["info:"]
+    wanted_dict = config_override_dict["config"]["aliases:"]
     mock_low_high_config.push_scope(spack.config.InternalConfigScope("high", config_override_dict))
-    assert mock_low_high_config.get("config:info") == wanted_dict
+    assert mock_low_high_config.get("config:aliases") == wanted_dict
 
 
 def test_internal_config_list_override(mock_low_high_config, write_config_file):
@@ -1136,10 +1132,10 @@ def test_set_list_override(mock_low_high_config, write_config_file):
 
 def test_set_dict_override(mock_low_high_config, write_config_file):
     write_config_file("config", config_merge_dict, "low")
-    wanted_dict = config_override_dict["config"]["info:"]
-    with spack.config.override("config:info:", wanted_dict):
-        assert wanted_dict == mock_low_high_config.get("config:info")
-    assert config_merge_dict["config"]["info"] == mock_low_high_config.get("config:info")
+    wanted_dict = config_override_dict["config"]["aliases:"]
+    with spack.config.override("config:aliases:", wanted_dict):
+        assert wanted_dict == mock_low_high_config.get("config:aliases")
+    assert config_merge_dict["config"]["aliases"] == mock_low_high_config.get("config:aliases")
 
 
 def test_set_bad_path(config):
@@ -1225,7 +1221,7 @@ def test_user_config_path_is_default_when_env_var_is_empty(working_env):
 
 
 def test_default_install_tree(monkeypatch, default_config):
-    s = spack.spec.Spec("nonexistent@x.y.z %none@a.b.c arch=foo-bar-baz")
+    s = spack.spec.Spec("nonexistent@x.y.z arch=foo-bar-baz %none@a.b.c")
     monkeypatch.setattr(s, "dag_hash", lambda length: "abc123")
     _, _, projections = spack.store.parse_install_tree(spack.config.get("config"))
     assert s.format(projections["all"]) == "foo-bar-baz/none-a.b.c/nonexistent-x.y.z-abc123"
@@ -1265,134 +1261,6 @@ def test_user_cache_path_is_default_when_env_var_is_empty(working_env):
     assert os.path.expanduser("~%s.spack" % os.sep) == spack.paths._get_user_cache_path()
 
 
-github_url = "https://github.com/fake/fake/{0}/develop"
-gitlab_url = "https://gitlab.fake.io/user/repo/-/blob/config/defaults"
-
-
-@pytest.mark.parametrize(
-    "url,isfile",
-    [
-        (github_url.format("tree"), False),
-        ("{0}/README.md".format(github_url.format("blob")), True),
-        ("{0}/etc/fake/defaults/packages.yaml".format(github_url.format("blob")), True),
-        (gitlab_url, False),
-        (None, False),
-    ],
-)
-def test_config_collect_urls(mutable_empty_config, mock_spider_configs, url, isfile):
-    with spack.config.override("config:url_fetch_method", "curl"):
-        urls = spack.config.collect_urls(url)
-        if url:
-            if isfile:
-                expected = 1 if url.endswith(".yaml") else 0
-                assert len(urls) == expected
-            else:
-                # Expect multiple configuration files for a "directory"
-                assert len(urls) > 1
-        else:
-            assert not urls
-
-
-@pytest.mark.parametrize(
-    "url,isfile,fail",
-    [
-        (github_url.format("tree"), False, False),
-        (gitlab_url, False, False),
-        ("{0}/README.md".format(github_url.format("blob")), True, True),
-        ("{0}/compilers.yaml".format(gitlab_url), True, False),
-        (None, False, True),
-    ],
-)
-def test_config_fetch_remote_configs(
-    tmpdir, mutable_empty_config, mock_collect_urls, mock_curl_configs, url, isfile, fail
-):
-    def _has_content(filename):
-        # The first element of all configuration files for this test happen to
-        # be the basename of the file so this check leverages that feature. If
-        # that changes, then this check will need to change accordingly.
-        element = "{0}:".format(os.path.splitext(os.path.basename(filename))[0])
-        with open(filename, "r", encoding="utf-8") as fd:
-            for line in fd:
-                if element in line:
-                    return True
-        tty.debug("Expected {0} in '{1}'".format(element, filename))
-        return False
-
-    dest_dir = join_path(tmpdir.strpath, "defaults")
-    if fail:
-        msg = "Cannot retrieve configuration"
-        with spack.config.override("config:url_fetch_method", "curl"):
-            with pytest.raises(spack.config.ConfigFileError, match=msg):
-                spack.config.fetch_remote_configs(url, dest_dir)
-    else:
-        with spack.config.override("config:url_fetch_method", "curl"):
-            path = spack.config.fetch_remote_configs(url, dest_dir)
-            assert os.path.exists(path)
-            if isfile:
-                # Ensure correct file is "fetched"
-                assert os.path.basename(path) == os.path.basename(url)
-                # Ensure contents of the file has expected config element
-                assert _has_content(path)
-            else:
-                for filename in os.listdir(path):
-                    assert _has_content(join_path(path, filename))
-
-
-@pytest.fixture(scope="function")
-def mock_collect_urls(mock_config_data, monkeypatch):
-    """Mock the collection of URLs to avoid mocking spider."""
-
-    _, config_files = mock_config_data
-
-    def _collect(base_url):
-        if not base_url:
-            return []
-
-        ext = os.path.splitext(base_url)[1]
-        if ext:
-            return [base_url] if ext == ".yaml" else []
-
-        return [join_path(base_url, f) for f in config_files]
-
-    monkeypatch.setattr(spack.config, "collect_urls", _collect)
-
-    yield
-
-
-@pytest.mark.parametrize(
-    "url,skip",
-    [(github_url.format("tree"), True), ("{0}/compilers.yaml".format(gitlab_url), True)],
-)
-def test_config_fetch_remote_configs_skip(
-    tmpdir, mutable_empty_config, mock_collect_urls, mock_curl_configs, url, skip
-):
-    """Ensure skip fetching remote config file if it already exists when
-    required and not skipping if replacing it."""
-
-    def check_contents(filename, expected):
-        with open(filename, "r", encoding="utf-8") as fd:
-            lines = fd.readlines()
-            if expected:
-                assert lines[0] == "compilers:"
-            else:
-                assert not lines
-
-    dest_dir = join_path(tmpdir.strpath, "defaults")
-    filename = "compilers.yaml"
-
-    # Create a stage directory with an empty configuration file
-    path = join_path(dest_dir, filename)
-    touchp(path)
-
-    # Do NOT replace the existing cached configuration file if skipping
-    expected = None if skip else "compilers:"
-
-    with spack.config.override("config:url_fetch_method", "curl"):
-        path = spack.config.fetch_remote_configs(url, dest_dir, skip)
-        result_filename = path if path.endswith(".yaml") else join_path(path, filename)
-        check_contents(result_filename, expected)
-
-
 def test_config_file_dir_failure(tmpdir, mutable_empty_config):
     with pytest.raises(spack.config.ConfigFileError, match="not a file"):
         spack.config.read_config_file(tmpdir.strpath)
@@ -1445,7 +1313,7 @@ def test_config_path_dsl(path, it_should_work, expected_parsed):
 
 
 @pytest.mark.regression("48254")
-def test_env_activation_preserves_config_scopes(mutable_mock_env_path):
+def test_env_activation_preserves_command_line_scope(mutable_mock_env_path):
     """Check that the "command_line" scope remains the highest priority scope, when we activate,
     or deactivate, environments.
     """
@@ -1469,3 +1337,51 @@ def test_env_activation_preserves_config_scopes(mutable_mock_env_path):
         assert spack.config.CONFIG.highest() == expected_cl_scope
 
     assert spack.config.CONFIG.highest() == expected_cl_scope
+
+
+@pytest.mark.regression("48414")
+@pytest.mark.regression("49188")
+def test_env_activation_preserves_config_scopes(mutable_mock_env_path):
+    """Check that the priority of scopes is respected when merging configuration files."""
+    custom_scope = spack.config.InternalConfigScope("custom_scope")
+    spack.config.CONFIG.push_scope(custom_scope, priority=ConfigScopePriority.CUSTOM)
+    expected_scopes_without_env = ["custom_scope", "command_line"]
+    expected_scopes_with_first_env = ["custom_scope", "env:test", "command_line"]
+    expected_scopes_with_second_env = ["custom_scope", "env:test-2", "command_line"]
+
+    def highest_priority_scopes(config, *, nscopes):
+        return list(config.scopes)[-nscopes:]
+
+    assert highest_priority_scopes(spack.config.CONFIG, nscopes=2) == expected_scopes_without_env
+    # Creating an environment pushes a new scope
+    ev.create("test")
+    with ev.read("test"):
+        assert (
+            highest_priority_scopes(spack.config.CONFIG, nscopes=3)
+            == expected_scopes_with_first_env
+        )
+
+        # No active environment pops the scope
+        with ev.no_active_environment():
+            assert (
+                highest_priority_scopes(spack.config.CONFIG, nscopes=2)
+                == expected_scopes_without_env
+            )
+        assert (
+            highest_priority_scopes(spack.config.CONFIG, nscopes=3)
+            == expected_scopes_with_first_env
+        )
+
+        # Switch the environment to another one
+        ev.create("test-2")
+        with ev.read("test-2"):
+            assert (
+                highest_priority_scopes(spack.config.CONFIG, nscopes=3)
+                == expected_scopes_with_second_env
+            )
+        assert (
+            highest_priority_scopes(spack.config.CONFIG, nscopes=3)
+            == expected_scopes_with_first_env
+        )
+
+    assert highest_priority_scopes(spack.config.CONFIG, nscopes=2) == expected_scopes_without_env

lib/spack/spack/test/conftest.py

@@ -30,7 +30,15 @@
 import llnl.util.lang
 import llnl.util.lock
 import llnl.util.tty as tty
-from llnl.util.filesystem import copy_tree, mkdirp, remove_linked_tree, touchp, working_dir
+from llnl.util.filesystem import (
+    copy,
+    copy_tree,
+    join_path,
+    mkdirp,
+    remove_linked_tree,
+    touchp,
+    working_dir,
+)
 
 import spack.binary_distribution
 import spack.bootstrap.core
@@ -65,6 +73,9 @@
 from spack.installer import PackageInstaller
 from spack.main import SpackCommand
 from spack.util.pattern import Bunch
+from spack.util.remote_file_cache import raw_github_gitlab_url
+
+from ..enums import ConfigScopePriority
 
 mirror_cmd = SpackCommand("mirror")
 
@@ -150,7 +161,7 @@ def mock_git_version_info(git, tmpdir, override_git_repos_cache_path):
     version tags on multiple branches, and version order is not equal to time
     order or topological order.
     """
-    repo_path = str(tmpdir.mkdir("git_repo"))
+    repo_path = str(tmpdir.mkdir("git_version_info_repo"))
     filename = "file.txt"
 
     def commit(message):
@@ -231,6 +242,84 @@ def latest_commit():
     yield repo_path, filename, commits
 
 
+@pytest.fixture
+def mock_git_package_changes(git, tmpdir, override_git_repos_cache_path):
+    """Create a mock git repo with known structure of package edits
+
+    The structure of commits in this repo is as follows::
+
+       o diff-test: modification to make manual download package
+       |
+       o diff-test: add v1.2 (from a git ref)
+       |
+       o diff-test: add v1.1 (from source tarball)
+       |
+       o diff-test: new package (testing multiple added versions)
+
+    The repo consists of a single package.py file for DiffTest.
+
+    Important attributes of the repo for test coverage are: multiple package
+    versions are added with some coming from a tarball and some from git refs.
+    """
+    repo_path = str(tmpdir.mkdir("git_package_changes_repo"))
+    filename = "var/spack/repos/builtin/packages/diff-test/package.py"
+
+    def commit(message):
+        global commit_counter
+        git(
+            "commit",
+            "--no-gpg-sign",
+            "--date",
+            "2020-01-%02d 12:0:00 +0300" % commit_counter,
+            "-am",
+            message,
+        )
+        commit_counter += 1
+
+    with working_dir(repo_path):
+        git("init")
+
+        git("config", "user.name", "Spack")
+        git("config", "user.email", "spack@spack.io")
+
+        commits = []
+
+        def latest_commit():
+            return git("rev-list", "-n1", "HEAD", output=str, error=str).strip()
+
+        os.makedirs(os.path.dirname(filename))
+
+        # add pkg-a as a new package to the repository
+        shutil.copy2(f"{spack.paths.test_path}/data/conftest/diff-test/package-0.txt", filename)
+        git("add", filename)
+        commit("diff-test: new package")
+        commits.append(latest_commit())
+
+        # add v2.1.5 to pkg-a
+        shutil.copy2(f"{spack.paths.test_path}/data/conftest/diff-test/package-1.txt", filename)
+        git("add", filename)
+        commit("diff-test: add v2.1.5")
+        commits.append(latest_commit())
+
+        # add v2.1.6 to pkg-a
+        shutil.copy2(f"{spack.paths.test_path}/data/conftest/diff-test/package-2.txt", filename)
+        git("add", filename)
+        commit("diff-test: add v2.1.6")
+        commits.append(latest_commit())
+
+        # convert pkg-a to a manual download package
+        shutil.copy2(f"{spack.paths.test_path}/data/conftest/diff-test/package-3.txt", filename)
+        git("add", filename)
+        commit("diff-test: modification to make manual download package")
+        commits.append(latest_commit())
+
+        # The commits are ordered with the last commit first in the list
+        commits = list(reversed(commits))
+
+    # Return the git directory to install, the filename used, and the commits
+    yield repo_path, filename, commits
+
+
 @pytest.fixture(autouse=True)
 def clear_recorded_monkeypatches():
     yield
@@ -339,6 +428,16 @@ def pytest_collection_modifyitems(config, items):
             item.add_marker(skip_as_slow)
 
 
+@pytest.fixture(scope="function")
+def use_concretization_cache(mutable_config, tmpdir):
+    """Enables the use of the concretization cache"""
+    spack.config.set("config:concretization_cache:enable", True)
+    # ensure we have an isolated concretization cache
+    new_conc_cache_loc = str(tmpdir.mkdir("concretization"))
+    spack.config.set("config:concretization_cache:path", new_conc_cache_loc)
+    yield
+
+
 #
 # These fixtures are applied to all tests
 #
@@ -723,11 +822,23 @@ def configuration_dir(tmpdir_factory, linux_os):
 def _create_mock_configuration_scopes(configuration_dir):
     """Create the configuration scopes used in `config` and `mutable_config`."""
     return [
-        spack.config.InternalConfigScope("_builtin", spack.config.CONFIG_DEFAULTS),
-        spack.config.DirectoryConfigScope("site", str(configuration_dir.join("site"))),
-        spack.config.DirectoryConfigScope("system", str(configuration_dir.join("system"))),
-        spack.config.DirectoryConfigScope("user", str(configuration_dir.join("user"))),
-        spack.config.InternalConfigScope("command_line"),
+        (
+            ConfigScopePriority.BUILTIN,
+            spack.config.InternalConfigScope("_builtin", spack.config.CONFIG_DEFAULTS),
+        ),
+        (
+            ConfigScopePriority.CONFIG_FILES,
+            spack.config.DirectoryConfigScope("site", str(configuration_dir.join("site"))),
+        ),
+        (
+            ConfigScopePriority.CONFIG_FILES,
+            spack.config.DirectoryConfigScope("system", str(configuration_dir.join("system"))),
+        ),
+        (
+            ConfigScopePriority.CONFIG_FILES,
+            spack.config.DirectoryConfigScope("user", str(configuration_dir.join("user"))),
+        ),
+        (ConfigScopePriority.COMMAND_LINE, spack.config.InternalConfigScope("command_line")),
     ]
 
 
@@ -794,13 +905,11 @@ def mock_wsdk_externals(monkeypatch_session):
 def concretize_scope(mutable_config, tmpdir):
     """Adds a scope for concretization preferences"""
     tmpdir.ensure_dir("concretize")
-    mutable_config.push_scope(
+    with spack.config.override(
         spack.config.DirectoryConfigScope("concretize", str(tmpdir.join("concretize")))
-    )
+    ):
+        yield str(tmpdir.join("concretize"))
 
-    yield str(tmpdir.join("concretize"))
-
-    mutable_config.pop_scope()
     spack.repo.PATH._provider_index = None
 
 
@@ -1669,7 +1778,7 @@ def installation_dir_with_headers(tmpdir_factory):
 ##########
 
 
-@pytest.fixture(params=["conflict%clang+foo", "conflict-parent@0.9^conflict~foo"])
+@pytest.fixture(params=["conflict+foo%clang", "conflict-parent@0.9^conflict~foo"])
 def conflict_spec(request):
     """Specs which violate constraints specified with the "conflicts"
     directive in the "conflict" package.
@@ -1884,35 +1993,21 @@ def __call__(self, *args, **kwargs):
 
 
 @pytest.fixture(scope="function")
-def mock_spider_configs(mock_config_data, monkeypatch):
-    """
-    Mock retrieval of configuration file URLs from the web by grabbing
-    them from the test data configuration directory.
-    """
-    config_data_dir, config_files = mock_config_data
+def mock_fetch_url_text(tmpdir, mock_config_data, monkeypatch):
+    """Mock spack.util.web.fetch_url_text."""
 
-    def _spider(*args, **kwargs):
-        root_urls = args[0]
-        if not root_urls:
-            return [], set()
+    stage_dir, config_files = mock_config_data
 
-        root_urls = [root_urls] if isinstance(root_urls, str) else root_urls
+    def _fetch_text_file(url, dest_dir):
+        raw_url = raw_github_gitlab_url(url)
+        mkdirp(dest_dir)
+        basename = os.path.basename(raw_url)
+        src = join_path(stage_dir, basename)
+        dest = join_path(dest_dir, basename)
+        copy(src, dest)
+        return dest
 
-        # Any URL with an extension will be treated like a file; otherwise,
-        # it is considered a directory/folder and we'll grab all available
-        # files.
-        urls = []
-        for url in root_urls:
-            if os.path.splitext(url)[1]:
-                urls.append(url)
-            else:
-                urls.extend([os.path.join(url, f) for f in config_files])
-
-        return [], set(urls)
-
-    monkeypatch.setattr(spack.util.web, "spider", _spider)
-
-    yield
+    monkeypatch.setattr(spack.util.web, "fetch_url_text", _fetch_text_file)
 
 
 @pytest.fixture(scope="function")
@@ -2126,8 +2221,7 @@ def _c_compiler_always_exists():
 @pytest.fixture(scope="session")
 def mock_test_cache(tmp_path_factory):
     cache_dir = tmp_path_factory.mktemp("cache")
-    print(cache_dir)
-    return spack.util.file_cache.FileCache(str(cache_dir))
+    return spack.util.file_cache.FileCache(cache_dir)
 
 
 class MockHTTPResponse(io.IOBase):
@@ -2176,3 +2270,27 @@ def info(self):
 @pytest.fixture()
 def mock_runtimes(config, mock_packages):
     return mock_packages.packages_with_tags("runtime")
+
+
+@pytest.fixture()
+def write_config_file(tmpdir):
+    """Returns a function that writes a config file."""
+
+    def _write(config, data, scope):
+        config_yaml = tmpdir.join(scope, config + ".yaml")
+        config_yaml.ensure()
+        with config_yaml.open("w") as f:
+            syaml.dump_config(data, f)
+        return config_yaml
+
+    return _write
+
+
+def _include_cache_root():
+    return join_path(str(tempfile.mkdtemp()), "user_cache", "includes")
+
+
+@pytest.fixture()
+def mock_include_cache(monkeypatch):
+    """Override the include cache directory so tests don't pollute user cache."""
+    monkeypatch.setattr(spack.config, "_include_cache_location", _include_cache_root)

lib/spack/spack/test/data/config/config.yaml

@@ -14,3 +14,5 @@ config:
   checksum: true
   dirty: false
   locks: {1}
+  concretization_cache:
+    enable: false

lib/spack/spack/test/data/conftest/diff-test/package-0.txt

@@ -0,0 +1,19 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class DiffTest(AutotoolsPackage):
+    """zlib replacement with optimizations for next generation systems."""
+
+    homepage = "https://github.com/zlib-ng/zlib-ng"
+    url = "https://github.com/zlib-ng/zlib-ng/archive/2.0.0.tar.gz"
+    git = "https://github.com/zlib-ng/zlib-ng.git"
+
+    license("Zlib")
+
+    version("2.1.4", sha256="a0293475e6a44a3f6c045229fe50f69dc0eebc62a42405a51f19d46a5541e77a")
+    version("2.0.0", sha256="86993903527d9b12fc543335c19c1d33a93797b3d4d37648b5addae83679ecd8")
+    version("2.0.7", sha256="6c0853bb27738b811f2b4d4af095323c3d5ce36ceed6b50e5f773204fb8f7200")

lib/spack/spack/test/data/conftest/diff-test/package-1.txt

@@ -0,0 +1,20 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class DiffTest(AutotoolsPackage):
+    """zlib replacement with optimizations for next generation systems."""
+
+    homepage = "https://github.com/zlib-ng/zlib-ng"
+    url = "https://github.com/zlib-ng/zlib-ng/archive/2.0.0.tar.gz"
+    git = "https://github.com/zlib-ng/zlib-ng.git"
+
+    license("Zlib")
+
+    version("2.1.5", sha256="3f6576971397b379d4205ae5451ff5a68edf6c103b2f03c4188ed7075fbb5f04")
+    version("2.1.4", sha256="a0293475e6a44a3f6c045229fe50f69dc0eebc62a42405a51f19d46a5541e77a")
+    version("2.0.7", sha256="6c0853bb27738b811f2b4d4af095323c3d5ce36ceed6b50e5f773204fb8f7200")
+    version("2.0.0", sha256="86993903527d9b12fc543335c19c1d33a93797b3d4d37648b5addae83679ecd8")