rocm-openmp-extras: do not mutate llvm-amdgpu

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

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

.gitignore

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

etc/spack/defaults/concretizer.yaml

@@ -43,28 +43,6 @@ concretizer:
     # (e.g. py-setuptools, cmake etc.)
     # "full" (experimental): allows separation of the entire build-tool stack (e.g. the entire "cmake" subDAG)
     strategy: minimal
-    # Maximum number of duplicates in a DAG, when using a strategy that allows duplicates. "default" is the
-    # number used if there isn't a more specific alternative
-    max_dupes:
-      default: 1
-      # Virtuals
-      c: 2
-      cxx: 2
-      fortran: 1
-      # Regular packages
-      cmake: 2
-      gmake: 2
-      python: 2
-      python-venv: 2
-      py-cython: 2
-      py-flit-core: 2
-      py-pip: 2
-      py-setuptools: 2
-      py-wheel: 2
-      xcb-proto: 2
-      # Compilers
-      gcc: 2
-      llvm: 2
   # Option to specify compatibility between operating systems for reuse of compilers and packages
   # Specified as a key: [list] where the key is the os that is being targeted, and the list contains the OS's
   # it can reuse. Note this is a directional compatibility so mutual compatibility between two OS's

etc/spack/defaults/packages.yaml

@@ -24,14 +24,13 @@ packages:
       cxx: [gcc]
       D: [ldc]
       daal: [intel-oneapi-daal]
-      egl: [libglvnd]
       elf: [elfutils]
       fftw-api: [fftw, amdfftw]
       flame: [libflame, amdlibflame]
       fortran: [gcc]
       fortran-rt: [gcc-runtime, intel-oneapi-runtime]
       fuse: [libfuse]
-      gl: [glx, osmesa, libglvnd]
+      gl: [glx, osmesa]
       glu: [mesa-glu, openglu]
       golang: [go, gcc]
       go-or-gccgo-bootstrap: [go-bootstrap, gcc]

lib/spack/docs/basic_usage.rst

@@ -1761,24 +1761,19 @@ 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 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
+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
 using the `-a,--all` or accept specs listed on the command line to
 verify.
 
-The ``spack verify manifest`` command can also verify for individual files
-that they haven't been altered since installation time. If the given file
+The ``spack verify`` 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.
@@ -1793,22 +1788,6 @@ 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

@@ -223,10 +223,6 @@ 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

@@ -125,8 +125,6 @@ are stored in ``$spack/var/spack/cache``.  These are stored indefinitely
 by default. Can be purged with :ref:`spack clean --downloads
 <cmd-spack-clean>`.
 
-.. _Misc Cache:
-
 --------------------
 ``misc_cache``
 --------------------
@@ -336,52 +334,3 @@ 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

@@ -14,7 +14,6 @@ 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

@@ -670,45 +670,24 @@ 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:
-     - environment/relative/path/to/config.yaml
+     - relative/path/to/config.yaml
      - https://github.com/path/to/raw/config/compilers.yaml
      - /absolute/path/to/packages.yaml
-     - path: /path/to/$os/$target/environment
-       optional: true
-     - path: /path/to/os-specific/config-dir
-       when: os == "ventura"
-
-Included configuration files are required *unless* they are explicitly optional
-or the entry's condition evaluates to ``false``. Optional includes are specified
-with the ``optional`` clause and conditional with the ``when`` clause. (See
-:ref:`include-yaml` for more information on optional and conditional entries.)
-
-Files are listed using paths to individual files or directories containing them.
-Path entries may be absolute or relative to the environment or specified as 
-URLs. URLs to individual files need link to the **raw** form of the file's 
-contents (e.g., `GitHub
-<https://docs.github.com/en/repositories/working-with-files/using-files/viewing-and-understanding-files#viewing-or-copying-the-raw-file-content>`_ 
-or `GitLab
-<https://docs.gitlab.com/ee/api/repository_files.html#get-raw-file-from-repository>`_).
-Only the ``file``, ``ftp``, ``http`` and ``https`` protocols (or schemes) are
-supported. Spack-specific, environment and user path variables can be used.
-(See :ref:`config-file-variables` for more information.)
-
-.. warning::
-
-   Recursive includes are not currently processed in a breadth-first manner
-   so the value of a configuration option that is altered by multiple included
-   files may not be what you expect. This will be addressed in a future
-   update.
 
+Environments can include files or URLs. File paths can be relative or
+absolute. URLs include the path to the text for individual files or
+can be the path to a directory containing configuration files.
+Spack supports ``file``, ``http``, ``https`` and ``ftp`` protocols (or
+schemes). Spack-specific, environment and user path variables may be
+used in these paths. See :ref:`config-file-variables` for more information.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^
 Configuration precedence

lib/spack/docs/include_yaml.rst

@@ -1,51 +0,0 @@
-.. 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

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

lib/spack/docs/pipelines.rst

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

lib/spack/docs/requirements.txt

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

lib/spack/llnl/util/filesystem.py

@@ -7,7 +7,6 @@
 import fnmatch
 import glob
 import hashlib
-import io
 import itertools
 import numbers
 import os
@@ -21,7 +20,6 @@
 from contextlib import contextmanager
 from itertools import accumulate
 from typing import (
-    IO,
     Callable,
     Deque,
     Dict,
@@ -2456,69 +2454,26 @@ class WindowsSimulatedRPath:
     and vis versa.
     """
 
-    def __init__(
-        self,
-        package,
-        base_modification_prefix: Optional[Union[str, pathlib.Path]] = None,
-        link_install_prefix: bool = True,
-    ):
+    def __init__(self, package, link_install_prefix=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[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._addl_rpaths = set()
         self.link_install_prefix = link_install_prefix
-        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}")
+        self._additional_library_dependents = set()
 
     @property
     def library_dependents(self):
         """
         Set of directories where package binaries/libraries are located.
         """
-        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
+        return set([pathlib.Path(self.pkg.prefix.bin)]) | self._additional_library_dependents
 
     def add_library_dependent(self, *dest):
         """
@@ -2534,12 +2489,6 @@ 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
@@ -2628,33 +2577,6 @@ 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):
@@ -2883,20 +2805,6 @@ 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

@@ -11,11 +11,10 @@
 import re
 import sys
 import traceback
-import types
 import typing
 import warnings
 from datetime import datetime, timedelta
-from typing import Callable, Dict, Iterable, List, Mapping, Optional, Tuple, TypeVar
+from typing import Callable, Dict, Iterable, List, Tuple, TypeVar
 
 # Ignore emacs backups when listing modules
 ignore_modules = r"^\.#|~$"
@@ -708,24 +707,14 @@ def __init__(self, wrapped_object):
 
 
 class Singleton:
-    """Wrapper for lazily initialized singleton objects."""
+    """Simple wrapper for lazily initialized singleton objects."""
 
-    def __init__(self, factory: Callable[[], object]):
+    def __init__(self, factory):
         """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
@@ -733,16 +722,7 @@ def __init__(self, factory: Callable[[], object]):
     @property
     def instance(self):
         if self._instance is None:
-            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
-
+            self._instance = self.factory()
         return self._instance
 
     def __getattr__(self, name):
@@ -1100,88 +1080,3 @@ def __set__(self, instance, value):
 
     def factory(self, instance, owner):
         raise NotImplementedError("must be implemented by derived classes")
-
-
-KT = TypeVar("KT")
-VT = TypeVar("VT")
-
-
-class PriorityOrderedMapping(Mapping[KT, VT]):
-    """Mapping that iterates over key according to an integer priority. If the priority is
-    the same for two keys, insertion order is what matters.
-
-    The priority is set when the key/value pair is added. If not set, the highest current priority
-    is used.
-    """
-
-    _data: Dict[KT, VT]
-    _priorities: List[Tuple[int, KT]]
-
-    def __init__(self) -> None:
-        self._data = {}
-        # Tuple of (priority, key)
-        self._priorities = []
-
-    def __getitem__(self, key: KT) -> VT:
-        return self._data[key]
-
-    def __len__(self) -> int:
-        return len(self._data)
-
-    def __iter__(self):
-        yield from (key for _, key in self._priorities)
-
-    def __reversed__(self):
-        yield from (key for _, key in reversed(self._priorities))
-
-    def reversed_keys(self):
-        """Iterates over keys from the highest priority, to the lowest."""
-        return reversed(self)
-
-    def reversed_values(self):
-        """Iterates over values from the highest priority, to the lowest."""
-        yield from (self._data[key] for _, key in reversed(self._priorities))
-
-    def _highest_priority(self) -> int:
-        if not self._priorities:
-            return 0
-        result, _ = self._priorities[-1]
-        return result
-
-    def add(self, key: KT, *, value: VT, priority: Optional[int] = None) -> None:
-        """Adds a key/value pair to the mapping, with a specific priority.
-
-        If the priority is None, then it is assumed to be the highest priority value currently
-        in the container.
-
-        Raises:
-              ValueError: when the same priority is already in the mapping
-        """
-        if priority is None:
-            priority = self._highest_priority()
-
-        if key in self._data:
-            self.remove(key)
-
-        self._priorities.append((priority, key))
-        # We rely on sort being stable
-        self._priorities.sort(key=lambda x: x[0])
-        self._data[key] = value
-        assert len(self._data) == len(self._priorities)
-
-    def remove(self, key: KT) -> VT:
-        """Removes a key from the mapping.
-
-        Returns:
-            The value associated with the key being removed
-
-        Raises:
-            KeyError: if the key is not in the mapping
-        """
-        if key not in self._data:
-            raise KeyError(f"cannot find {key}")
-
-        popped_item = self._data.pop(key)
-        self._priorities = [(p, k) for p, k in self._priorities if k != key]
-        assert len(self._data) == len(self._priorities)
-        return popped_item

lib/spack/llnl/util/link_tree.py

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

lib/spack/llnl/util/lock.py

@@ -269,7 +269,7 @@ def __init__(
 
     @staticmethod
     def _poll_interval_generator(
-        _wait_times: Optional[Tuple[float, float, float]] = None,
+        _wait_times: Optional[Tuple[float, float, float]] = None
     ) -> Generator[float, None, None]:
         """This implements a backoff scheme for polling a contended resource
         by suggesting a succession of wait times between polls.

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

@@ -2,7 +2,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-"""Utility classes for logging the output of blocks of code."""
+"""Utility classes for logging the output of blocks of code.
+"""
 import atexit
 import ctypes
 import errno

lib/spack/spack/__init__.py

@@ -13,18 +13,6 @@
 __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:
@@ -91,6 +79,4 @@ def get_short_version() -> str:
     "get_version",
     "get_spack_commit",
     "get_short_version",
-    "package_api_version",
-    "min_package_api_version",
 ]

lib/spack/spack/audit.py

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

lib/spack/spack/binary_distribution.py

@@ -923,7 +923,7 @@ class FileTypes:
     UNKNOWN = 2
 
 
-NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7f-\x9f]")
+NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7F-\x9F]")
 
 
 def file_type(f: IO[bytes]) -> int:
@@ -2529,10 +2529,10 @@ def install_root_node(
         allow_missing: when true, allows installing a node with missing dependencies
     """
     # Early termination
-    if spec.external or not spec.concrete:
-        warnings.warn("Skipping external or abstract spec {0}".format(spec.format()))
+    if spec.external or spec.virtual:
+        warnings.warn("Skipping external or virtual package {0}".format(spec.format()))
         return
-    elif spec.installed and not force:
+    elif spec.concrete and spec.installed and not force:
         warnings.warn("Package for spec {0} already installed.".format(spec.format()))
         return
 

lib/spack/spack/bootstrap/core.py

@@ -292,12 +292,7 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
 
         # Install the spec that should make the module importable
         with spack.config.override(self.mirror_scope):
-            PackageInstaller(
-                [concrete_spec.package],
-                fail_fast=True,
-                package_use_cache=False,
-                dependencies_use_cache=False,
-            ).install()
+            PackageInstaller([concrete_spec.package], fail_fast=True).install()
 
         if _try_import_from_store(module, query_spec=concrete_spec, query_info=info):
             self.last_search = info
@@ -367,7 +362,6 @@ def ensure_module_importable_or_raise(module: str, abstract_spec: Optional[str]
     for current_config in bootstrapping_sources():
         if not source_is_enabled(current_config):
             continue
-
         with exception_handler.forward(current_config["name"], Exception):
             if create_bootstrapper(current_config).try_import(module, abstract_spec):
                 return

lib/spack/spack/build_environment.py

@@ -881,6 +881,21 @@ 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):
@@ -931,7 +946,7 @@ def setup_package(pkg, dirty, context: Context = Context.BUILD):
         for mod in pkg.compiler.modules:
             load_module(mod)
 
-    load_external_modules(setup_context)
+    load_external_modules(pkg)
 
     # Make sure nothing's strange about the Spack environment.
     validate(env_mods, tty.warn)
@@ -1220,21 +1235,6 @@ 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

@@ -12,7 +12,6 @@
 import spack.phase_callbacks
 import spack.spec
 import spack.util.prefix
-from spack.directives import depends_on
 
 from .cmake import CMakeBuilder, CMakePackage
 
@@ -372,10 +371,6 @@ class CachedCMakePackage(CMakePackage):
 
     CMakeBuilder = CachedCMakeBuilder
 
-    # These dependencies are assumed in the builder
-    depends_on("c", type="build")
-    depends_on("cxx", type="build")
-
     def flag_handler(self, name, flags):
         if name in ("cflags", "cxxflags", "cppflags", "fflags"):
             return None, None, None  # handled in the cmake cache

lib/spack/spack/build_systems/cargo.py

@@ -70,16 +70,10 @@ def build_directory(self):
         """Return the directory containing the main Cargo.toml."""
         return self.pkg.stage.source_path
 
-    @property
-    def std_build_args(self):
-        """Standard arguments for ``cargo build`` provided as a property for
-        convenience of package writers."""
-        return ["-j", str(self.pkg.module.make_jobs)]
-
     @property
     def build_args(self):
         """Arguments for ``cargo build``."""
-        return []
+        return ["-j", str(self.pkg.module.make_jobs)]
 
     @property
     def check_args(self):
@@ -94,9 +88,7 @@ def build(
     ) -> None:
         """Runs ``cargo install`` in the source directory"""
         with fs.working_dir(self.build_directory):
-            pkg.module.cargo(
-                "install", "--root", "out", "--path", ".", *self.std_build_args, *self.build_args
-            )
+            pkg.module.cargo("install", "--root", "out", "--path", ".", *self.build_args)
 
     def install(
         self, pkg: CargoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix

lib/spack/spack/build_systems/meson.py

@@ -48,9 +48,6 @@ class MesonPackage(spack.package_base.PackageBase):
         variant("strip", default=False, description="Strip targets on install")
         depends_on("meson", type="build")
         depends_on("ninja", type="build")
-        # Meson uses pkg-config for dependency detection, and this dependency is
-        # often overlooked by packages that use meson as a build system.
-        depends_on("pkgconfig", type="build")
         # Python detection in meson requires distutils to be importable, but distutils no longer
         # exists in Python 3.12. In Spack, we can't use setuptools as distutils replacement,
         # because the distutils-precedence.pth startup file that setuptools ships with is not run

lib/spack/spack/build_systems/oneapi.py

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

lib/spack/spack/ci/__init__.py

@@ -16,7 +16,6 @@
 from typing import Callable, Dict, List, Set
 from urllib.request import Request
 
-import llnl.path
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
 from llnl.util.tty.color import cescape, colorize
@@ -84,9 +83,6 @@ def get_stack_changed(env_path, rev1="HEAD^", rev2="HEAD"):
     whether or not the stack was changed.  Returns True if the environment
     manifest changed between the provided revisions (or additionally if the
     `.gitlab-ci.yml` file itself changed).  Returns False otherwise."""
-    # git returns posix paths always, normalize input to be comptaible
-    # with that
-    env_path = llnl.path.convert_to_posix_path(env_path)
     git = spack.util.git.git()
     if git:
         with fs.working_dir(spack.paths.prefix):
@@ -224,7 +220,7 @@ 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}{/hash:7}{%compiler}"
+    spec_fmt = "{name}{@version}{%compiler}{/hash:7}"
 
     if not prune:
         status = colorize("@*g{[x]}  ")
@@ -616,7 +612,7 @@ def copy_test_logs_to_artifacts(test_stage, job_test_dir):
     copy_files_to_artifacts(os.path.join(test_stage, "*", "*.txt"), job_test_dir)
 
 
-def download_and_extract_artifacts(url, work_dir) -> str:
+def download_and_extract_artifacts(url, work_dir):
     """Look for gitlab artifacts.zip at the given url, and attempt to download
         and extract the contents into the given work_dir
 
@@ -624,10 +620,6 @@ def download_and_extract_artifacts(url, work_dir) -> str:
 
         url (str): Complete url to artifacts.zip file
         work_dir (str): Path to destination where artifacts should be extracted
-
-    Output:
-
-        Artifacts root path relative to the archive root
     """
     tty.msg(f"Fetching artifacts from: {url}")
 
@@ -645,25 +637,13 @@ def download_and_extract_artifacts(url, work_dir) -> str:
         response = urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
         with open(artifacts_zip_path, "wb") as out_file:
             shutil.copyfileobj(response, out_file)
-
-        with zipfile.ZipFile(artifacts_zip_path) as zip_file:
-            zip_file.extractall(work_dir)
-            # Get the artifact root
-            artifact_root = ""
-            for f in zip_file.filelist:
-                if "spack.lock" in f.filename:
-                    artifact_root = os.path.dirname(os.path.dirname(f.filename))
-                    break
     except OSError as e:
         raise SpackError(f"Error fetching artifacts: {e}")
-    finally:
-        try:
-            os.remove(artifacts_zip_path)
-        except FileNotFoundError:
-            # If the file doesn't exist we are already raising
-            pass
 
-    return artifact_root
+    with zipfile.ZipFile(artifacts_zip_path) as zip_file:
+        zip_file.extractall(work_dir)
+
+    os.remove(artifacts_zip_path)
 
 
 def get_spack_info():
@@ -777,7 +757,7 @@ def setup_spack_repro_version(repro_dir, checkout_commit, merge_commit=None):
     return True
 
 
-def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime, use_local_head):
+def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime):
     """Given a url to gitlab artifacts.zip from a failed 'spack ci rebuild' job,
     attempt to setup an environment in which the failure can be reproduced
     locally.  This entails the following:
@@ -791,11 +771,8 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime, use_local_head)
     commands to run to reproduce the build once inside the container.
     """
     work_dir = os.path.realpath(work_dir)
-    if os.path.exists(work_dir) and os.listdir(work_dir):
-        raise SpackError(f"Cannot run reproducer in non-emptry working dir:\n  {work_dir}")
-
     platform_script_ext = "ps1" if IS_WINDOWS else "sh"
-    artifact_root = download_and_extract_artifacts(url, work_dir)
+    download_and_extract_artifacts(url, work_dir)
 
     gpg_path = None
     if gpg_url:
@@ -857,9 +834,6 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime, use_local_head)
     with open(repro_file, encoding="utf-8") as fd:
         repro_details = json.load(fd)
 
-    spec_file = fs.find(work_dir, repro_details["job_spec_json"])[0]
-    reproducer_spec = spack.spec.Spec.from_specfile(spec_file)
-
     repro_dir = os.path.dirname(repro_file)
     rel_repro_dir = repro_dir.replace(work_dir, "").lstrip(os.path.sep)
 
@@ -920,20 +894,17 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime, use_local_head)
     commit_regex = re.compile(r"commit\s+([^\s]+)")
     merge_commit_regex = re.compile(r"Merge\s+([^\s]+)\s+into\s+([^\s]+)")
 
-    if use_local_head:
-        commit_1 = "HEAD"
+    # Try the more specific merge commit regex first
+    m = merge_commit_regex.search(spack_info)
+    if m:
+        # This was a merge commit and we captured the parents
+        commit_1 = m.group(1)
+        commit_2 = m.group(2)
     else:
-        # Try the more specific merge commit regex first
-        m = merge_commit_regex.search(spack_info)
+        # Not a merge commit, just get the commit sha
+        m = commit_regex.search(spack_info)
         if m:
-            # This was a merge commit and we captured the parents
             commit_1 = m.group(1)
-            commit_2 = m.group(2)
-        else:
-            # Not a merge commit, just get the commit sha
-            m = commit_regex.search(spack_info)
-            if m:
-                commit_1 = m.group(1)
 
     setup_result = False
     if commit_1:
@@ -1008,8 +979,6 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime, use_local_head)
             "entrypoint", entrypoint_script, work_dir, run=False, exit_on_failure=False
         )
 
-        # Attempt to create a unique name for the reproducer container
-        container_suffix = "_" + reproducer_spec.dag_hash() if reproducer_spec else ""
         docker_command = [
             runtime,
             "run",
@@ -1017,14 +986,14 @@ def reproduce_ci_job(url, work_dir, autostart, gpg_url, runtime, use_local_head)
             "-t",
             "--rm",
             "--name",
-            f"spack_reproducer{container_suffix}",
+            "spack_reproducer",
             "-v",
             ":".join([work_dir, mounted_workdir, "Z"]),
             "-v",
             ":".join(
                 [
-                    os.path.join(work_dir, artifact_root),
-                    os.path.join(mount_as_dir, artifact_root),
+                    os.path.join(work_dir, "jobs_scratch_dir"),
+                    os.path.join(mount_as_dir, "jobs_scratch_dir"),
                     "Z",
                 ]
             ),

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}{ arch=architecture} {%compiler.name}{@compiler.version}"
+    format_string = "{name}{@version}{%compiler.name}{@compiler.version}{ arch=architecture}"
     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
@@ -471,11 +471,12 @@ def get_arg(name, default=None):
         nfmt = "{fullname}" if namespaces else "{name}"
         ffmt = ""
         if full_compiler or flags:
-            ffmt += "{compiler_flags} {%compiler.name}"
+            ffmt += "{%compiler.name}"
             if full_compiler:
                 ffmt += "{@compiler.version}"
+            ffmt += " {compiler_flags}"
         vfmt = "{variants}" if variants else ""
-        format_string = nfmt + "{@version}" + vfmt + ffmt
+        format_string = nfmt + "{@version}" + ffmt + vfmt
 
     def fmt(s, depth=0):
         """Formatter function for all output specs"""

lib/spack/spack/cmd/checksum.py

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

lib/spack/spack/cmd/ci.py

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

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

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

lib/spack/spack/cmd/config.py

@@ -350,12 +350,9 @@ 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=write_scope)
+            spack.config.add(update_path, scope=ideal_scope_to_modify)
     else:
         raise ValueError("'config change' can currently only change 'require' sections")
 

lib/spack/spack/cmd/debug.py

@@ -2,11 +2,23 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
 import platform
+import re
+import sys
+from datetime import datetime
+from glob import glob
+
+import llnl.util.tty as tty
+from llnl.util.filesystem import working_dir
 
 import spack
+import spack.paths
 import spack.platforms
 import spack.spec
+import spack.store
+import spack.util.git
+from spack.util.executable import which
 
 description = "debugging commands for troubleshooting Spack"
 section = "developer"
@@ -15,9 +27,63 @@
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar="SUBCOMMAND", dest="debug_command")
+    sp.add_parser("create-db-tarball", help="create a tarball of Spack's installation metadata")
     sp.add_parser("report", help="print information useful for bug reports")
 
 
+def _debug_tarball_suffix():
+    now = datetime.now()
+    suffix = now.strftime("%Y-%m-%d-%H%M%S")
+
+    git = spack.util.git.git()
+    if not git:
+        return "nobranch-nogit-%s" % suffix
+
+    with working_dir(spack.paths.prefix):
+        if not os.path.isdir(".git"):
+            return "nobranch.nogit.%s" % suffix
+
+        # Get symbolic branch name and strip any special chars (mainly '/')
+        symbolic = git("rev-parse", "--abbrev-ref", "--short", "HEAD", output=str).strip()
+        symbolic = re.sub(r"[^\w.-]", "-", symbolic)
+
+        # Get the commit hash too.
+        commit = git("rev-parse", "--short", "HEAD", output=str).strip()
+
+        if symbolic == commit:
+            return "nobranch.%s.%s" % (commit, suffix)
+        else:
+            return "%s.%s.%s" % (symbolic, commit, suffix)
+
+
+def create_db_tarball(args):
+    tar = which("tar")
+    tarball_name = "spack-db.%s.tar.gz" % _debug_tarball_suffix()
+    tarball_path = os.path.abspath(tarball_name)
+
+    base = os.path.basename(str(spack.store.STORE.root))
+    transform_args = []
+    # Currently --transform and -s are not supported by Windows native tar
+    if "GNU" in tar("--version", output=str):
+        transform_args = ["--transform", "s/^%s/%s/" % (base, tarball_name)]
+    elif sys.platform != "win32":
+        transform_args = ["-s", "/^%s/%s/" % (base, tarball_name)]
+
+    wd = os.path.dirname(str(spack.store.STORE.root))
+    with working_dir(wd):
+        files = [spack.store.STORE.db._index_path]
+        files += glob("%s/*/*/*/.spack/spec.json" % base)
+        files += glob("%s/*/*/*/.spack/spec.yaml" % base)
+        files = [os.path.relpath(f) for f in files]
+
+        args = ["-czf", tarball_path]
+        args += transform_args
+        args += files
+        tar(*args)
+
+    tty.msg("Created %s" % tarball_name)
+
+
 def report(args):
     host_platform = spack.platforms.host()
     host_os = host_platform.default_operating_system()
@@ -29,5 +95,5 @@ def report(args):
 
 
 def debug(parser, args):
-    if args.debug_command == "report":
-        report(args)
+    action = {"create-db-tarball": create_db_tarball, "report": report}
+    action[args.debug_command](args)

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}{/hash:7}{%compiler}"
+        format_string = "{name}{@version}{%compiler}{/hash:7}"
         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}{/hash:7}{%compiler}"
+        format_string = "{name}{@version}{%compiler}{/hash:7}"
         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/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 @B{fabrics=psm,mrail,sock} @g{%gcc}
+      mvapich2 @g{%gcc} @B{fabrics=psm,mrail,sock}
           mvapich2, built with gcc compiler, with support for multiple fabrics
 """
 

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

@@ -383,10 +383,8 @@ 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_flags}{variants}"
-                "{arch=architecture} {%compiler}"
-            )
+            spec_fmt = "{hash:7} {name}{@version}{%compiler}"
+            spec_fmt += "{compiler_flags}{variants}{arch=architecture}"
             msg += "\t" + s.cformat(spec_fmt) + "\n"
         tty.die(msg, "In this context exactly *one* match is needed.")
 

lib/spack/spack/cmd/providers.py

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

lib/spack/spack/cmd/unit_test.py

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

lib/spack/spack/cmd/verify.py

@@ -2,48 +2,35 @@
 #
 # 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 = "verify spack installations on disk"
+description = "check that all spack packages are on disk as installed"
 section = "admin"
 level = "long"
 
-MANIFEST_SUBPARSER: Optional[argparse.ArgumentParser] = None
 
+def setup_parser(subparser):
+    setup_parser.parser = subparser
 
-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(
+    subparser.add_argument(
         "-l", "--local", action="store_true", help="verify only locally installed packages"
     )
-    MANIFEST_SUBPARSER.add_argument(
+    subparser.add_argument(
         "-j", "--json", action="store_true", help="ouptut json-formatted errors"
     )
-    MANIFEST_SUBPARSER.add_argument("-a", "--all", action="store_true", help="verify all packages")
-    MANIFEST_SUBPARSER.add_argument(
+    subparser.add_argument("-a", "--all", action="store_true", help="verify all packages")
+    subparser.add_argument(
         "specs_or_files", nargs=argparse.REMAINDER, help="specs or files to verify"
     )
 
-    manifest_sp_type = MANIFEST_SUBPARSER.add_mutually_exclusive_group()
-    manifest_sp_type.add_argument(
+    type = subparser.add_mutually_exclusive_group()
+    type.add_argument(
         "-s",
         "--specs",
         action="store_const",
@@ -52,7 +39,7 @@ def setup_parser(subparser: argparse.ArgumentParser):
         default="specs",
         help="treat entries as specs (default)",
     )
-    manifest_sp_type.add_argument(
+    type.add_argument(
         "-f",
         "--files",
         action="store_const",
@@ -62,67 +49,14 @@ def setup_parser(subparser: argparse.ArgumentParser):
         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:
-            MANIFEST_SUBPARSER.error("cannot use --all with --files")
+            setup_parser.parser.print_help()
+            return 1
 
         for file in args.specs_or_files:
             results = spack.verify.check_file_manifest(file)
@@ -153,7 +87,8 @@ def verify_manifest(args):
         env = ev.active_environment()
         specs = list(map(lambda x: spack.cmd.disambiguate_spec(x, env, local=local), spec_args))
     else:
-        MANIFEST_SUBPARSER.error("use --all or specify specs to verify")
+        setup_parser.parser.print_help()
+        return 1
 
     for spec in specs:
         tty.debug("Verifying package %s")

lib/spack/spack/concretize.py

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

lib/spack/spack/config.py

@@ -32,10 +32,9 @@
 import copy
 import functools
 import os
-import os.path
 import re
 import sys
-from typing import Any, Callable, Dict, Generator, List, NamedTuple, Optional, Tuple, Union
+from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union
 
 import jsonschema
 
@@ -43,6 +42,7 @@
 
 import spack.error
 import spack.paths
+import spack.platforms
 import spack.schema
 import spack.schema.bootstrap
 import spack.schema.cdash
@@ -54,20 +54,17 @@
 import spack.schema.develop
 import spack.schema.env
 import spack.schema.env_vars
-import spack.schema.include
-import spack.schema.merged
 import spack.schema.mirrors
 import spack.schema.modules
 import spack.schema.packages
 import spack.schema.repos
 import spack.schema.upstreams
 import spack.schema.view
-import spack.util.remote_file_cache as rfc_util
-import spack.util.spack_yaml as syaml
-from spack.util.cpus import cpus_available
-from spack.util.spack_yaml import get_mark_from_yaml_data
 
-from .enums import ConfigScopePriority
+# Hacked yaml for configuration files preserves line numbers.
+import spack.util.spack_yaml as syaml
+import spack.util.web as web_util
+from spack.util.cpus import cpus_available
 
 #: Dict from section names -> schema for that section
 SECTION_SCHEMAS: Dict[str, Any] = {
@@ -75,7 +72,6 @@
     "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,
@@ -123,17 +119,6 @@
 #: 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:
@@ -141,9 +126,6 @@ def __init__(self, name: str) -> None:
         self.writable = False
         self.sections = syaml.syaml_dict()
 
-        #: names of any included scopes
-        self.included_scopes: List[str] = []
-
     def get_section_filename(self, section: str) -> str:
         raise NotImplementedError
 
@@ -426,18 +408,26 @@ def _method(self, *args, **kwargs):
     return _method
 
 
-ScopeWithOptionalPriority = Union[ConfigScope, Tuple[int, ConfigScope]]
-ScopeWithPriority = Tuple[int, ConfigScope]
-
-
 class Configuration:
-    """A hierarchical configuration, merging a number of scopes at different priorities."""
+    """A full Spack configuration, from a hierarchy of config files.
+
+    This class makes it easy to add a new scope on top of an existing one.
+    """
 
     # convert to typing.OrderedDict when we drop 3.6, or OrderedDict when we reach 3.9
-    scopes: lang.PriorityOrderedMapping[str, ConfigScope]
+    scopes: Dict[str, ConfigScope]
 
-    def __init__(self) -> None:
-        self.scopes = lang.PriorityOrderedMapping()
+    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)
         self.format_updates: Dict[str, List[ConfigScope]] = collections.defaultdict(list)
 
     def ensure_unwrapped(self) -> "Configuration":
@@ -445,64 +435,36 @@ def ensure_unwrapped(self) -> "Configuration":
         return self
 
     def highest(self) -> ConfigScope:
-        """Scope with the highest precedence"""
-        return next(self.scopes.reversed_values())  # type: ignore
+        """Scope with highest precedence"""
+        return next(reversed(self.scopes.values()))  # type: ignore
 
     @_config_mutator
-    def push_scope(
-        self, scope: ConfigScope, priority: Optional[int] = None, _depth: int = 0
-    ) -> None:
-        """Adds a scope to the Configuration, at a given priority.
+    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")
 
-        If a priority is not given, it is assumed to be the current highest 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
 
-        Args:
-            scope: scope to be added
-            priority: priority of the scope
-        """
-        tty.debug(f"[CONFIGURATION: PUSH SCOPE]: {str(scope)}, priority={priority}", level=2)
-
-        # TODO: As a follow on to #48784, change this to create a graph of the
-        # TODO: includes AND ensure properly sorted such that the order included
-        # TODO: at the highest level is reflected in the value of an option that
-        # TODO: is set in multiple included files.
-        # before pushing the scope itself, push any included scopes recursively, at same priority
-        includes = scope.get_section("include")
-        if includes:
-            include_paths = [included_path(data) for data in includes["include"]]
-            for path in reversed(include_paths):
-                included_scope = include_path_scope(path)
-                if not included_scope:
-                    continue
-
-                if _depth + 1 > MAX_RECURSIVE_INCLUDES:  # make sure we're not recursing endlessly
-                    mark = path.path._start_mark if syaml.marked(path.path) else ""  # type: ignore
-                    raise RecursiveIncludeError(
-                        f"Maximum include recursion exceeded in {path.path}", str(mark)
-                    )
-
-                # record this inclusion so that remove_scope() can use it
-                scope.included_scopes.append(included_scope.name)
-                self.push_scope(included_scope, priority=priority, _depth=_depth + 1)
-
-        self.scopes.add(scope.name, value=scope, priority=priority)
+    @_config_mutator
+    def 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
 
     @_config_mutator
     def remove_scope(self, scope_name: str) -> Optional[ConfigScope]:
-        """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 inc in scope.included_scopes:
-            assert inc in self.scopes, f"Included scope '{inc}' was never added to configuration!"
-            self.remove_scope(inc)
-        scope.included_scopes.clear()  # clean up includes for bookkeeping
-
+        """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)
         return scope
 
     @property
@@ -511,13 +473,15 @@ 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 the highest precedence."""
-        return next(s for s in self.scopes.reversed_values() if s.writable)
+        """Writable scope with highest precedence."""
+        return next(s for s in reversed(self.scopes.values()) if s.writable)  # type: ignore
 
     def highest_precedence_non_platform_scope(self) -> ConfigScope:
-        """Writable non-platform scope with the highest precedence"""
+        """Writable non-platform scope with highest precedence"""
         return next(
-            s for s in self.scopes.reversed_values() if s.writable and not s.is_platform_dependent
+            s
+            for s in reversed(self.scopes.values())  # type: ignore
+            if s.writable and not s.is_platform_dependent
         )
 
     def matching_scopes(self, reg_expr) -> List[ConfigScope]:
@@ -784,7 +748,7 @@ def override(
     """
     if isinstance(path_or_scope, ConfigScope):
         overrides = path_or_scope
-        CONFIG.push_scope(path_or_scope, priority=None)
+        CONFIG.push_scope(path_or_scope)
     else:
         base_name = _OVERRIDES_BASE_NAME
         # Ensure the new override gets a unique scope name
@@ -798,7 +762,7 @@ def override(
                 break
 
         overrides = InternalConfigScope(scope_name)
-        CONFIG.push_scope(overrides, priority=None)
+        CONFIG.push_scope(overrides)
         CONFIG.set(path_or_scope, value, scope=scope_name)
 
     try:
@@ -808,86 +772,13 @@ def override(
         assert scope is overrides
 
 
-def _add_platform_scope(
-    cfg: Configuration, name: str, path: str, priority: ConfigScopePriority, writable: bool = True
-) -> None:
+def _add_platform_scope(cfg: Configuration, name: str, path: str, 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, 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
+    cfg.push_scope(scope)
 
 
 def config_paths_from_entry_points() -> List[Tuple[str, str]]:
@@ -915,17 +806,18 @@ def config_paths_from_entry_points() -> List[Tuple[str, str]]:
     return config_paths
 
 
-def create_incremental() -> Generator[Configuration, None, None]:
+def create() -> Configuration:
     """Singleton Configuration instance.
 
     This constructs one instance associated with this module and returns
     it. It is bundled inside a function so that configuration can be
     initialized lazily.
     """
+    cfg = Configuration()
+
     # first do the builtin, hardcoded defaults
-    cfg = create_from(
-        (ConfigScopePriority.BUILTIN, InternalConfigScope("_builtin", CONFIG_DEFAULTS))
-    )
+    builtin = InternalConfigScope("_builtin", CONFIG_DEFAULTS)
+    cfg.push_scope(builtin)
 
     # Builtin paths to configuration files in Spack
     configuration_paths = [
@@ -955,29 +847,16 @@ def create_incremental() -> Generator[Configuration, None, None]:
 
     # add each scope and its platform-specific directory
     for name, path in configuration_paths:
-        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)
+        cfg.push_scope(DirectoryConfigScope(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
+        # Each scope can have per-platfom overrides in subdirectories
+        _add_platform_scope(cfg, name, path)
 
-
-def create() -> Configuration:
-    """Create a configuration using create_incremental(), return the last yielded result."""
-    return list(create_incremental())[-1]
+    return cfg
 
 
 #: This is the singleton configuration instance for Spack.
-CONFIG: Configuration = lang.Singleton(create_incremental)  # type: ignore
+CONFIG: Configuration = lang.Singleton(create)  # type: ignore
 
 
 def add_from_file(filename: str, scope: Optional[str] = None) -> None:
@@ -1073,11 +952,10 @@ def set(path: str, value: Any, scope: Optional[str] = None) -> None:
 
     Accepts the path syntax described in ``get()``.
     """
-    result = CONFIG.set(path, value, scope)
-    return result
+    return CONFIG.set(path, value, scope)
 
 
-def scopes() -> lang.PriorityOrderedMapping[str, ConfigScope]:
+def scopes() -> Dict[str, ConfigScope]:
     """Convenience function to get list of configuration scopes."""
     return CONFIG.scopes
 
@@ -1531,7 +1409,7 @@ def ensure_latest_format_fn(section: str) -> Callable[[YamlConfigDict], bool]:
 
 @contextlib.contextmanager
 def use_configuration(
-    *scopes_or_paths: Union[ScopeWithOptionalPriority, str]
+    *scopes_or_paths: Union[ConfigScope, str]
 ) -> Generator[Configuration, None, None]:
     """Use the configuration scopes passed as arguments within the context manager.
 
@@ -1546,7 +1424,7 @@ def use_configuration(
     global CONFIG
 
     # Normalize input and construct a Configuration object
-    configuration = create_from(*scopes_or_paths)
+    configuration = _config_from(scopes_or_paths)
     CONFIG.clear_caches(), configuration.clear_caches()
 
     saved_config, CONFIG = CONFIG, configuration
@@ -1557,44 +1435,137 @@ 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 create_from(*scopes_or_paths: Union[ScopeWithOptionalPriority, str]) -> Configuration:
-    """Creates a configuration object from the scopes passed in input.
+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.
 
     Args:
-        *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.
+        url: url to be converted to raw form
 
-    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)
-        ... )
+    Returns:
+        Raw github/gitlab url or the original url
     """
-    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
+    # 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
 
 
 def determine_number_of_jobs(
@@ -1701,7 +1672,3 @@ 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

@@ -41,8 +41,6 @@
     Union,
 )
 
-import spack.repo
-
 try:
     import uuid
 
@@ -1558,12 +1556,7 @@ def _query(
         # If we did fine something, the query spec can't be virtual b/c we matched an actual
         # package installation, so skip the virtual check entirely. If we *didn't* find anything,
         # check all the deferred specs *if* the query is virtual.
-        if (
-            not results
-            and query_spec is not None
-            and deferred
-            and spack.repo.PATH.is_virtual(query_spec.name)
-        ):
+        if not results and query_spec is not None and deferred and query_spec.virtual:
             results = [spec for spec in deferred if spec.satisfies(query_spec)]
 
         return results

lib/spack/spack/detection/common.py

@@ -310,7 +310,7 @@ def find_windows_kit_roots() -> List[str]:
 
     @staticmethod
     def find_windows_kit_bin_paths(
-        kit_base: Union[Optional[str], Optional[list]] = None,
+        kit_base: Union[Optional[str], Optional[list]] = None
     ) -> List[str]:
         """Returns Windows kit bin directory per version"""
         kit_base = WindowsKitExternalPaths.find_windows_kit_roots() if not kit_base else kit_base
@@ -325,7 +325,7 @@ def find_windows_kit_bin_paths(
 
     @staticmethod
     def find_windows_kit_lib_paths(
-        kit_base: Union[Optional[str], Optional[list]] = None,
+        kit_base: Union[Optional[str], Optional[list]] = None
     ) -> List[str]:
         """Returns Windows kit lib directory per version"""
         kit_base = WindowsKitExternalPaths.find_windows_kit_roots() if not kit_base else kit_base

lib/spack/spack/detection/path.py

@@ -243,7 +243,7 @@ def prefix_from_path(self, *, path: str) -> str:
         raise NotImplementedError("must be implemented by derived classes")
 
     def detect_specs(
-        self, *, pkg: Type["spack.package_base.PackageBase"], paths: Iterable[str]
+        self, *, pkg: Type["spack.package_base.PackageBase"], paths: List[str]
     ) -> List["spack.spec.Spec"]:
         """Given a list of files matching the search patterns, returns a list of detected specs.
 
@@ -259,8 +259,6 @@ def detect_specs(
             )
             return []
 
-        from spack.repo import PATH as repo_path
-
         result = []
         for candidate_path, items_in_prefix in _group_by_prefix(
             llnl.util.lang.dedupe(paths)
@@ -307,10 +305,7 @@ def detect_specs(
 
                 resolved_specs[spec] = candidate_path
                 try:
-                    # Validate the spec calling a package specific method
-                    pkg_cls = repo_path.get_pkg_class(spec.name)
-                    validate_fn = getattr(pkg_cls, "validate_detected_spec", lambda x, y: None)
-                    validate_fn(spec, spec.extra_attributes)
+                    spec.validate_detection()
                 except Exception as e:
                     msg = (
                         f'"{spec}" has been detected on the system but will '

lib/spack/spack/directives.py

@@ -568,7 +568,7 @@ def patch(
     """
 
     def _execute_patch(
-        pkg_or_dep: Union[Type[spack.package_base.PackageBase], Dependency],
+        pkg_or_dep: Union[Type[spack.package_base.PackageBase], Dependency]
     ) -> None:
         pkg = pkg_or_dep.pkg if isinstance(pkg_or_dep, Dependency) else pkg_or_dep
 

lib/spack/spack/directory_layout.py

@@ -25,7 +25,7 @@
 }
 
 
-def _check_concrete(spec: "spack.spec.Spec") -> None:
+def _check_concrete(spec):
     """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.set_prefix(prefix)
+            spec.prefix = prefix
             specs.append(spec)
             continue
 
@@ -84,7 +84,7 @@ class DirectoryLayout:
 
     def __init__(
         self,
-        root: str,
+        root,
         *,
         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) -> Tuple[str]:
+    def hidden_file_regexes(self):
         return ("^{0}$".format(re.escape(self.metadata_dir)),)
 
-    def relative_path_for_spec(self, spec: "spack.spec.Spec") -> str:
+    def relative_path_for_spec(self, spec):
         _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: "spack.spec.Spec", path: str) -> None:
+    def write_spec(self, spec, path):
         """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: "spack.spec.Spec", path: str) -> None:
             # 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: "spack.spec.Spec") -> None:
+    def write_host_environment(self, spec):
         """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: "spack.spec.Spec") -> None:
         with open(env_file, "w", encoding="utf-8") as fd:
             sjson.dump(environ, fd)
 
-    def read_spec(self, path: str) -> "spack.spec.Spec":
+    def read_spec(self, path):
         """Read the contents of a file and parse them as a spec"""
         try:
             with open(path, encoding="utf-8") as f:
@@ -159,28 +159,26 @@ def read_spec(self, path: str) -> "spack.spec.Spec":
                     # Too late for conversion; spec_file_path() already called.
                     spec = spack.spec.Spec.from_yaml(f)
                 else:
-                    raise SpecReadError(f"Did not recognize spec file extension: {extension}")
+                    raise SpecReadError(
+                        "Did not recognize spec file extension:" " {0}".format(extension)
+                    )
         except Exception as e:
             if spack.config.get("config:debug"):
                 raise
-            raise SpecReadError(f"Unable to read file: {path}", f"Cause: {e}")
+            raise SpecReadError("Unable to read file: %s" % path, "Cause: " + str(e))
 
         # Specs read from actual installations are always concrete
         spec._mark_concrete()
         return spec
 
-    def spec_file_path(self, spec: "spack.spec.Spec") -> str:
+    def spec_file_path(self, spec):
         """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: "spack.spec.Spec",
-        deprecator_spec: Optional["spack.spec.Spec"] = None,
-    ) -> str:
+    def deprecated_file_path(self, deprecated_spec, deprecator_spec=None):
         """Gets full path to spec file for deprecated spec
 
         If the deprecator_spec is provided, use that. Otherwise, assume
@@ -214,16 +212,16 @@ def deprecated_file_path(
 
         return yaml_path if os.path.exists(yaml_path) else json_path
 
-    def metadata_path(self, spec: "spack.spec.Spec") -> str:
+    def metadata_path(self, spec):
         return os.path.join(spec.prefix, self.metadata_dir)
 
-    def env_metadata_path(self, spec: "spack.spec.Spec") -> str:
+    def env_metadata_path(self, spec):
         return os.path.join(self.metadata_path(spec), "install_environment.json")
 
-    def build_packages_path(self, spec: "spack.spec.Spec") -> str:
+    def build_packages_path(self, spec):
         return os.path.join(self.metadata_path(spec), self.packages_dir)
 
-    def create_install_directory(self, spec: "spack.spec.Spec") -> None:
+    def create_install_directory(self, spec):
         _check_concrete(spec)
 
         # Create install directory with properly configured permissions
@@ -241,7 +239,7 @@ def create_install_directory(self, spec: "spack.spec.Spec") -> None:
 
         self.write_spec(spec, self.spec_file_path(spec))
 
-    def ensure_installed(self, spec: "spack.spec.Spec") -> None:
+    def ensure_installed(self, spec):
         """
         Throws InconsistentInstallDirectoryError if:
         1. spec prefix does not exist
@@ -268,7 +266,7 @@ def ensure_installed(self, spec: "spack.spec.Spec") -> None:
                 "Spec file in %s does not match hash!" % spec_file_path
             )
 
-    def path_for_spec(self, spec: "spack.spec.Spec") -> str:
+    def path_for_spec(self, spec):
         """Return absolute path from the root to a directory for the spec."""
         _check_concrete(spec)
 
@@ -279,13 +277,23 @@ def path_for_spec(self, spec: "spack.spec.Spec") -> str:
         assert not path.startswith(self.root)
         return os.path.join(self.root, path)
 
-    def remove_install_directory(self, spec: "spack.spec.Spec", deprecated: bool = False) -> None:
+    def remove_install_directory(self, spec, deprecated=False):
         """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:
@@ -296,16 +304,7 @@ def remove_install_directory(self, spec: "spack.spec.Spec", deprecated: bool = F
                     raise RemoveFailedError(spec, path, e) from e
         elif os.path.exists(path):
             try:
-                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)
+                shutil.rmtree(path, **kwargs)
             except OSError as e:
                 raise RemoveFailedError(spec, path, e) from e
 

lib/spack/spack/enums.py

@@ -12,13 +12,3 @@ 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}{variants}{ arch=architecture} {%compiler}"
+                    "{name}{@version}{%compiler}{variants}{arch=architecture}"
                 ),
                 item.buildcache_flag,
             )

lib/spack/spack/environment/environment.py

@@ -10,6 +10,8 @@
 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
 
@@ -30,6 +32,7 @@
 import spack.paths
 import spack.repo
 import spack.schema.env
+import spack.schema.merged
 import spack.spec
 import spack.spec_list
 import spack.store
@@ -40,6 +43,7 @@
 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
@@ -47,8 +51,6 @@
 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
@@ -385,7 +387,6 @@ 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
 
@@ -402,8 +403,8 @@ 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 substituted and expanded path is the same (e.g. when absolute)
-            if entry["path"] == expanded_path:
+            # Skip if the expanded path is the same (e.g. when absolute)
+            if dev_path == expanded_path:
                 continue
 
             tty.debug("Expanding develop path for {0} to {1}".format(name, expanded_path))
@@ -418,34 +419,6 @@ 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.
 
@@ -573,6 +546,13 @@ 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"""
@@ -1005,7 +985,7 @@ def _process_definition(self, entry):
         """Process a single spec definition item."""
         when_string = entry.get("when")
         if when_string is not None:
-            when = spack.spec.eval_conditional(when_string)
+            when = _eval_conditional(when_string)
             assert len([x for x in entry if x != "when"]) == 1
         else:
             when = True
@@ -1550,6 +1530,9 @@ 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:
@@ -2409,8 +2392,6 @@ def invalidate_repository_cache(self):
 
     def __enter__(self):
         self._previous_active = _active_environment
-        if self._previous_active:
-            deactivate()
         activate(self)
         return self
 
@@ -2660,23 +2641,20 @@ 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:
-        included_path = spack.config.included_path(include)
-        path = included_path.path
-        if os.path.isabs(path):
+        if os.path.isabs(include):
             continue
 
-        abspath = pathlib.Path(os.path.normpath(environment_dir / path))
+        abspath = pathlib.Path(os.path.normpath(environment_dir / include))
         common_path = pathlib.Path(os.path.commonpath([environment_dir, abspath]))
         if common_path != environment_dir:
-            tty.debug(f"Will not copy relative include file from outside environment: {path}")
+            tty.debug(f"Will not copy relative include from outside environment: {include}")
             continue
 
-        orig_abspath = os.path.normpath(envfile.parent / path)
+        orig_abspath = os.path.normpath(envfile.parent / include)
         if not os.path.exists(orig_abspath):
-            tty.warn(f"Included file does not exist; will not copy: '{path}'")
+            tty.warn(f"Included file does not exist; will not copy: '{include}'")
             continue
 
         fs.touchp(abspath)
@@ -2899,7 +2877,7 @@ def extract_name(_item):
                 continue
 
             condition_str = item.get("when", "True")
-            if not spack.spec.eval_conditional(condition_str):
+            if not _eval_conditional(condition_str):
                 continue
 
             yield idx, item
@@ -2960,20 +2938,127 @@ 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
@@ -2982,12 +3067,14 @@ 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, priority=ConfigScopePriority.ENVIRONMENT)
+            spack.config.CONFIG.push_scope(scope)
+        spack.config.CONFIG.ensure_scope_ordering()
 
     def deactivate_config_scope(self) -> None:
         """Remove any of the manifest's scopes from the global config path."""
         for scope in self.env_config_scopes:
             spack.config.CONFIG.remove_scope(scope.name)
+        spack.config.CONFIG.ensure_scope_ordering()
 
     @contextlib.contextmanager
     def use_config(self):

lib/spack/spack/filesystem_view.py

@@ -9,8 +9,7 @@
 import shutil
 import stat
 import sys
-import tempfile
-from typing import Callable, Dict, List, Optional
+from typing import Callable, Dict, Optional
 
 from typing_extensions import Literal
 
@@ -78,7 +77,7 @@ def view_copy(
 
     # Order of this dict is somewhat irrelevant
     prefix_to_projection = {
-        str(s.prefix): view.get_projection_for_spec(s)
+        s.prefix: view.get_projection_for_spec(s)
         for s in spec.traverse(root=True, order="breadth")
         if not s.external
     }
@@ -185,7 +184,7 @@ 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: spack.spec.Spec, **kwargs) -> None:
+    def add_specs(self, *specs, **kwargs):
         """
         Add given specs to view.
 
@@ -200,19 +199,19 @@ def add_specs(self, *specs: spack.spec.Spec, **kwargs) -> None:
         """
         raise NotImplementedError
 
-    def add_standalone(self, spec: spack.spec.Spec) -> bool:
+    def add_standalone(self, spec):
         """
         Add (link) a standalone package into this view.
         """
         raise NotImplementedError
 
-    def check_added(self, spec: spack.spec.Spec) -> bool:
+    def check_added(self, spec):
         """
         Check if the given concrete spec is active in this view.
         """
         raise NotImplementedError
 
-    def remove_specs(self, *specs: spack.spec.Spec, **kwargs) -> None:
+    def remove_specs(self, *specs, **kwargs):
         """
         Removes given specs from view.
 
@@ -231,25 +230,25 @@ def remove_specs(self, *specs: spack.spec.Spec, **kwargs) -> None:
         """
         raise NotImplementedError
 
-    def remove_standalone(self, spec: spack.spec.Spec) -> None:
+    def remove_standalone(self, spec):
         """
         Remove (unlink) a standalone package from this view.
         """
         raise NotImplementedError
 
-    def get_projection_for_spec(self, spec: spack.spec.Spec) -> str:
+    def get_projection_for_spec(self, spec):
         """
         Get the projection in this view for a spec.
         """
         raise NotImplementedError
 
-    def get_all_specs(self) -> List[spack.spec.Spec]:
+    def get_all_specs(self):
         """
         Get all specs currently active in this view.
         """
         raise NotImplementedError
 
-    def get_spec(self, spec: spack.spec.Spec) -> Optional[spack.spec.Spec]:
+    def get_spec(self, spec):
         """
         Return the actual spec linked in this view (i.e. do not look it up
         in the database by name).
@@ -263,7 +262,7 @@ def get_spec(self, spec: spack.spec.Spec) -> Optional[spack.spec.Spec]:
         """
         raise NotImplementedError
 
-    def print_status(self, *specs: spack.spec.Spec, **kwargs) -> None:
+    def print_status(self, *specs, **kwargs):
         """
         Print a short summary about the given specs, detailing whether..
             * ..they are active in the view.
@@ -643,7 +642,7 @@ def print_status(self, *specs, **kwargs):
                 specs.sort()
 
                 abbreviated = [
-                    s.cformat("{name}{@version}{compiler_flags}{variants}{%compiler}")
+                    s.cformat("{name}{@version}{%compiler}{compiler_flags}{variants}")
                     for s in specs
                 ]
 
@@ -694,7 +693,7 @@ def _sanity_check_view_projection(self, specs):
                 raise ConflictingSpecsError(current_spec, conflicting_spec)
             seen[metadata_dir] = current_spec
 
-    def add_specs(self, *specs, **kwargs) -> None:
+    def add_specs(self, *specs: spack.spec.Spec) -> 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:
@@ -709,10 +708,7 @@ def add_specs(self, *specs, **kwargs) -> None:
         def skip_list(file):
             return os.path.basename(file) == spack.store.STORE.layout.metadata_dir
 
-        # Determine if the root is on a case-insensitive filesystem
-        normalize_paths = is_folder_on_case_insensitive_filesystem(self._root)
-
-        visitor = SourceMergeVisitor(ignore=skip_list, normalize_paths=normalize_paths)
+        visitor = SourceMergeVisitor(ignore=skip_list)
 
         # Gather all the directories to be made and files to be linked
         for spec in specs:
@@ -831,7 +827,7 @@ def get_projection_for_spec(self, spec):
 #####################
 # utility functions #
 #####################
-def get_spec_from_file(filename) -> Optional[spack.spec.Spec]:
+def get_spec_from_file(filename):
     try:
         with open(filename, "r", encoding="utf-8") as f:
             return spack.spec.Spec.from_yaml(f)
@@ -888,8 +884,3 @@ def get_dependencies(specs):
 
 class ConflictingProjectionsError(SpackError):
     """Raised when a view has a projections file and is given one manually."""
-
-
-def is_folder_on_case_insensitive_filesystem(path: str) -> bool:
-    with tempfile.NamedTemporaryFile(dir=path, prefix=".sentinel") as sentinel:
-        return os.path.exists(os.path.join(path, os.path.basename(sentinel.name).upper()))

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}{/hash:7}{%compiler}"
+        format_option = "{name}{@version}{%compiler}{/hash:7}"
         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}{/hash:7}{%compiler}")
+        node_str = node.format("{name}{@version}{%compiler}{/hash:7}")
         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/hooks/resolve_shared_libraries.py

@@ -2,14 +2,198 @@
 #
 # 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 visit_directory_tree
+from llnl.util.filesystem import BaseDirectoryVisitor, visit_directory_tree
+from llnl.util.lang import stable_partition
 
 import spack.config
 import spack.error
-import spack.verify_libraries
+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.*",
+]
+
+
+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
 
 
 def post_install(spec, explicit):
@@ -20,23 +204,36 @@ def post_install(spec, explicit):
     if policy == "ignore" or spec.external or spec.platform not in ("linux", "freebsd"):
         return
 
-    visitor = spack.verify_libraries.ResolveSharedElfLibDepsVisitor(
-        [*spack.verify_libraries.ALLOW_UNRESOLVED, *spec.package.unresolved_libraries]
+    visitor = ResolveSharedElfLibDepsVisitor(
+        [*ALLOW_UNRESOLVED, *spec.package.unresolved_libraries]
     )
     visit_directory_tree(spec.prefix, visitor)
 
+    # All good?
     if not visitor.problems:
         return
 
-    output = io.StringIO("not all executables and libraries can resolve their dependencies:\n")
-    visitor.write(output)
+    # 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")
+
     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

@@ -21,6 +21,7 @@
 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
@@ -397,7 +398,7 @@ def stand_alone_tests(self, kwargs):
         Args:
             kwargs (dict): arguments to be used by the test process
         """
-        import spack.build_environment  # avoid circular dependency
+        import spack.build_environment
 
         spack.build_environment.start_build_process(self.pkg, test_process, kwargs)
 
@@ -462,8 +463,6 @@ 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

@@ -47,8 +47,6 @@
 import spack.util.environment
 import spack.util.lock
 
-from .enums import ConfigScopePriority
-
 #: names of profile statistics
 stat_names = pstats.Stats.sort_arg_dict_default
 
@@ -874,19 +872,14 @@ 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),
-                    priority=ConfigScopePriority.CUSTOM,
-                )
-                spack.config._add_platform_scope(
-                    cfg, name, path, priority=ConfigScopePriority.CUSTOM, writable=False
-                )
+                cfg.push_scope(spack.config.DirectoryConfigScope(name, path, writable=False))
+                spack.config._add_platform_scope(cfg, name, path, writable=False)
                 continue
             else:
                 raise spack.error.ConfigError(f"Invalid configuration scope: {path}")
 
         for scope in scopes:
-            cfg.push_scope(scope, priority=ConfigScopePriority.CUSTOM)
+            cfg.push_scope(scope)
 
 
 def _main(argv=None):
@@ -959,9 +952,7 @@ 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"), priority=ConfigScopePriority.COMMAND_LINE
-    )
+    spack.config.CONFIG.push_scope(spack.config.InternalConfigScope("command_line"))
     setup_main_options(args)
 
     # ------------------------------------------------------------------------
@@ -1007,7 +998,6 @@ 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

@@ -330,17 +330,18 @@ class BaseConfiguration:
     default_projections = {"all": "{name}/{version}-{compiler.name}-{compiler.version}"}
 
     def __init__(self, spec: spack.spec.Spec, module_set_name: str, explicit: bool) -> None:
+        # Module where type(self) is defined
+        m = inspect.getmodule(self)
+        assert m is not None  # make mypy happy
+        self.module = m
         # Spec for which we want to generate a module file
         self.spec = spec
         self.name = module_set_name
         self.explicit = explicit
-        # Dictionary of configuration options that should be applied to the spec
+        # Dictionary of configuration options that should be applied
+        # to the spec
         self.conf = merge_config_rules(self.module.configuration(self.name), self.spec)
 
-    @property
-    def module(self):
-        return inspect.getmodule(self)
-
     @property
     def projections(self):
         """Projection from specs to module names"""
@@ -774,6 +775,10 @@ def __init__(
     ) -> None:
         self.spec = spec
 
+        # This class is meant to be derived. Get the module of the
+        # actual writer.
+        self.module = inspect.getmodule(self)
+        assert self.module is not None  # make mypy happy
         m = self.module
 
         # Create the triplet of configuration/layout/context
@@ -811,10 +816,6 @@ def __init__(
             name = type(self).__name__
             raise ModulercHeaderNotDefined(msg.format(name))
 
-    @property
-    def module(self):
-        return inspect.getmodule(self)
-
     def _get_template(self):
         """Gets the template that will be rendered for this spec."""
         # Get templates and put them in the order of importance:

lib/spack/spack/modules/lmod.py

@@ -209,7 +209,7 @@ def provides(self):
         # All the other tokens in the hierarchy must be virtual dependencies
         for x in self.hierarchy_tokens:
             if self.spec.package.provides(x):
-                provides[x] = self.spec
+                provides[x] = self.spec[x]
         return provides
 
     @property

lib/spack/spack/package_base.py

@@ -125,10 +125,9 @@ 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:
-            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()
+            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()
 
 
 #: Registers which are the detectable packages, by repo and package name
@@ -743,6 +742,7 @@ 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":

lib/spack/spack/patch.py

@@ -83,7 +83,6 @@ def __init__(
         level: int,
         working_dir: str,
         reverse: bool = False,
-        ordering_key: Optional[Tuple[str, int]] = None,
     ) -> None:
         """Initialize a new Patch instance.
 
@@ -93,7 +92,6 @@ 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:
@@ -107,13 +105,6 @@ 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.
 
@@ -211,8 +202,9 @@ 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, ordering_key)
+        super().__init__(pkg, abs_path, level, working_dir, reverse)
         self.path = abs_path
+        self.ordering_key = ordering_key
 
     @property
     def sha256(self) -> str:
@@ -274,11 +266,13 @@ 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, ordering_key)
+        super().__init__(pkg, url, level, working_dir, reverse)
 
         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

@@ -108,8 +108,6 @@ 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/relocate.py

@@ -283,21 +283,21 @@ def relocate_text_bin(binaries: Iterable[str], prefix_to_prefix: PrefixToPrefix)
 def is_macho_magic(magic: bytes) -> bool:
     return (
         # In order of popularity: 64-bit mach-o le/be, 32-bit mach-o le/be.
-        magic.startswith(b"\xcf\xfa\xed\xfe")
-        or magic.startswith(b"\xfe\xed\xfa\xcf")
-        or magic.startswith(b"\xce\xfa\xed\xfe")
-        or magic.startswith(b"\xfe\xed\xfa\xce")
+        magic.startswith(b"\xCF\xFA\xED\xFE")
+        or magic.startswith(b"\xFE\xED\xFA\xCF")
+        or magic.startswith(b"\xCE\xFA\xED\xFE")
+        or magic.startswith(b"\xFE\xED\xFA\xCE")
         # universal binaries: 0xcafebabe be (most common?) or 0xbebafeca le (not sure if exists).
         # Here we need to disambiguate mach-o and JVM class files. In mach-o the next 4 bytes are
         # the number of binaries; in JVM class files it's the java version number. We assume there
         # are less than 10 binaries in a universal binary.
-        or (magic.startswith(b"\xca\xfe\xba\xbe") and int.from_bytes(magic[4:8], "big") < 10)
-        or (magic.startswith(b"\xbe\xba\xfe\xca") and int.from_bytes(magic[4:8], "little") < 10)
+        or (magic.startswith(b"\xCA\xFE\xBA\xBE") and int.from_bytes(magic[4:8], "big") < 10)
+        or (magic.startswith(b"\xBE\xBA\xFE\xCA") and int.from_bytes(magic[4:8], "little") < 10)
     )
 
 
 def is_elf_magic(magic: bytes) -> bool:
-    return magic.startswith(b"\x7fELF")
+    return magic.startswith(b"\x7FELF")
 
 
 def is_binary(filename: str) -> bool:
@@ -406,8 +406,8 @@ def fixup_macos_rpaths(spec):
     entries which makes it harder to adjust with ``install_name_tool
     -delete_rpath``.
     """
-    if spec.external or not spec.concrete:
-        tty.warn("external/abstract spec cannot be fixed up: {0!s}".format(spec))
+    if spec.external or spec.virtual:
+        tty.warn("external or virtual package cannot be fixed up: {0!s}".format(spec))
         return False
 
     if "platform=darwin" not in spec:

lib/spack/spack/repo.py

@@ -32,7 +32,6 @@
 import llnl.util.tty as tty
 from llnl.util.filesystem import working_dir
 
-import spack
 import spack.caches
 import spack.config
 import spack.error
@@ -50,8 +49,6 @@
 #: 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
@@ -912,52 +909,19 @@ 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`.
 
-    It contains the following keys:
+    Currently, `repo.yaml` must define:
 
     `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__(
@@ -994,7 +958,7 @@ def check(condition, msg):
             f"{os.path.join(root, repo_config_name)} must define a namespace.",
         )
 
-        self.namespace: str = config["namespace"]
+        self.namespace = config["namespace"]
         check(
             re.match(r"[a-zA-Z][a-zA-Z0-9_.]+", self.namespace),
             f"Invalid namespace '{self.namespace}' in repo '{self.root}'. "
@@ -1007,14 +971,12 @@ def check(condition, msg):
         # Keep name components around for checking prefixes.
         self._names = self.full_namespace.split(".")
 
-        packages_dir: str = config.get("subdirectory", packages_dir_name)
+        packages_dir = 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 {}
 
@@ -1064,7 +1026,7 @@ def is_prefix(self, fullname: str) -> bool:
         parts = fullname.split(".")
         return self._names[: len(parts)] == parts
 
-    def _read_config(self) -> Dict[str, Any]:
+    def _read_config(self) -> Dict[str, str]:
         """Check for a YAML config file in this db's root directory."""
         try:
             with open(self.config_file, encoding="utf-8") as reponame_file:
@@ -1406,8 +1368,6 @@ 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/reporters/cdash.py

@@ -177,7 +177,7 @@ def build_report_for_package(self, report_dir, package, duration):
         # something went wrong pre-cdash "configure" phase b/c we have an exception and only
         # "update" was encounterd.
         # dump the report in the configure line so teams can see what the issue is
-        if len(phases_encountered) == 1 and package.get("exception"):
+        if len(phases_encountered) == 1 and package["exception"]:
             # TODO this mapping is not ideal since these are pre-configure errors
             # we need to determine if a more appropriate cdash phase can be utilized
             # for now we will add a message to the log explaining this

lib/spack/spack/schema/__init__.py

@@ -7,7 +7,8 @@
 import warnings
 
 import jsonschema
-import jsonschema.validators
+
+import llnl.util.lang
 
 from spack.error import SpecSyntaxError
 
@@ -17,59 +18,59 @@ class DeprecationMessage(typing.NamedTuple):
     error: bool
 
 
-def _validate_spec(validator, is_spec, instance, schema):
-    """Check if all additional keys are valid specs."""
-    import spack.spec_parser
+# 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
 
-    if not validator.is_type(instance, "object"):
-        return
+        if not validator.is_type(instance, "object"):
+            return
 
-    properties = schema.get("properties") or {}
+        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")
 
-    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")
+    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},
+    )
 
 
-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},
-)
+Validator = llnl.util.lang.Singleton(_make_validator)
 
 
 def _append(string: str) -> bool:

lib/spack/spack/schema/concretizer.py

@@ -84,11 +84,7 @@
             "duplicates": {
                 "type": "object",
                 "properties": {
-                    "strategy": {"type": "string", "enum": ["none", "minimal", "full"]},
-                    "max_dupes": {
-                        "type": "object",
-                        "additional_properties": {"type": "integer", "minimum": 1},
-                    },
+                    "strategy": {"type": "string", "enum": ["none", "minimal", "full"]}
                 },
             },
             "static_analysis": {"type": "boolean"},

lib/spack/spack/schema/config.py

@@ -58,15 +58,6 @@
                     {"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/cray_manifest.py

@@ -3,12 +3,12 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 """Schema for Cray descriptive manifest: this describes a set of
-installed packages on the system and also specifies dependency
-relationships between them (so this provides more information than
-external entries in packages configuration).
+   installed packages on the system and also specifies dependency
+   relationships between them (so this provides more information than
+   external entries in packages configuration).
 
-This does not specify a configuration - it is an input format
-that is consumed and transformed into Spack DB records.
+   This does not specify a configuration - it is an input format
+   that is consumed and transformed into Spack DB records.
 """
 from typing import Any, Dict
 

lib/spack/spack/schema/env.py

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

lib/spack/spack/schema/include.py

@@ -1,41 +0,0 @@
-# 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

@@ -21,7 +21,6 @@
 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
@@ -41,7 +40,6 @@
     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,
@@ -50,6 +48,7 @@
     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",
-            "additionalKeysAreSpecs": True,
+            "validate_spec": True,
             "additionalProperties": {"type": "string"},  # key
         },
         "environment": spack.schema.environment.definition,
@@ -48,44 +48,40 @@
 
 projections_scheme = spack.schema.projections.properties["projections"]
 
-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 = {
+module_type_configuration: Dict = {
     "type": "object",
     "default": {},
-    "additionalKeysAreSpecs": True,
-    "properties": {**common_props},
+    "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,
+    },
     "additionalProperties": module_file_configuration,
 }
 
-lmod_configuration = {
-    "type": "object",
-    "default": {},
-    "additionalKeysAreSpecs": True,
-    "properties": {
-        **common_props,
+tcl_configuration = module_type_configuration.copy()
+
+lmod_configuration = module_type_configuration.copy()
+lmod_configuration["properties"].update(
+    {
         "core_compilers": array_of_strings,
         "hierarchy": array_of_strings,
         "core_specs": array_of_strings,
         "filter_hierarchy_specs": {
             "type": "object",
-            "additionalKeysAreSpecs": True,
+            "validate_spec": 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

@@ -5,12 +5,8 @@
 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
@@ -20,25 +16,12 @@
 import typing
 import warnings
 from contextlib import contextmanager
-from typing import (
-    IO,
-    Callable,
-    Dict,
-    Iterator,
-    List,
-    NamedTuple,
-    Optional,
-    Set,
-    Tuple,
-    Type,
-    Union,
-)
+from typing import 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
@@ -50,27 +33,21 @@
 import spack.deptypes as dt
 import spack.environment as ev
 import spack.error
-import spack.hash_types as ht
 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,
@@ -96,19 +73,17 @@
 #: Enable the addition of a runtime node
 WITH_RUNTIME = sys.platform != "win32"
 
-
-class OutputConfiguration(NamedTuple):
-    """Data class that contains configuration on what a clingo solve should output."""
-
-    #: Print out coarse timers for different solve phases
-    timers: bool
-    #: Whether to output Clingo's internal solver statistics
-    stats: bool
-    #: Optional output stream for the generated ASP program
-    out: Optional[io.IOBase]
-    #: If True, stop after setup and don't solve
-    setup_only: bool
-
+#: Data class that contain configuration on what a
+#: clingo solve should output.
+#:
+#: Args:
+#:     timers (bool):  Print out coarse timers for different solve phases.
+#:     stats (bool): Whether to output Clingo's internal solver statistics.
+#:     out: Optional output stream for the generated ASP program.
+#:     setup_only (bool): if True, stop after setup and don't solve (default False).
+OutputConfiguration = collections.namedtuple(
+    "OutputConfiguration", ["timers", "stats", "out", "setup_only"]
+)
 
 #: Default output configuration for a solve
 DEFAULT_OUTPUT_CONFIGURATION = OutputConfiguration(
@@ -523,7 +498,7 @@ def _compute_specs_from_answer_set(self):
             # The specs must be unified to get here, so it is safe to associate any satisfying spec
             # with the input. Multiple inputs may be matched to the same concrete spec
             node = SpecBuilder.make_node(pkg=input_spec.name)
-            if spack.repo.PATH.is_virtual(input_spec.name):
+            if input_spec.virtual:
                 providers = [
                     spec.name for spec in answer.values() if spec.package.provides(input_spec.name)
                 ]
@@ -558,364 +533,6 @@ 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}"}}"""
-        )
-        spec_hash_type = ht.process_hash if test else ht.dag_hash
-        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(hash=spec_hash_type)
-            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(hash=spec_hash_type)
-        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)
@@ -1184,15 +801,6 @@ 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)
@@ -1202,133 +810,123 @@ def solve(self, setup, specs, reuse=None, output=None, control=None, allow_depre
             return Result(specs), None, None
         timer.stop("setup")
 
-        timer.start("cache-check")
-        timer.start("ordering")
-        # ensure deterministic output
-        problem_repr = "\n".join(sorted(asp_problem.split("\n")))
-        timer.stop("ordering")
+        timer.start("load")
+        # Add the problem instance
+        self.control.add("base", [], asp_problem)
+        # Load the file itself
         parent_dir = os.path.dirname(__file__)
-        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()
+        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"))
 
-        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)
+        # 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"))
 
-        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")
+        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(concretization_stats)
-        return result, timer, concretization_stats
+            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
 
 
 class ConcreteSpecsByHash(collections.abc.Mapping):
@@ -1770,7 +1368,7 @@ def effect_rules(self):
             return
 
         self.gen.h2("Imposed requirements")
-        for name in sorted(self._effect_cache):
+        for name in 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)))
@@ -1823,8 +1421,8 @@ def define_variant(
 
         elif isinstance(values, vt.DisjointSetsOfValues):
             union = set()
-            for sid, s in enumerate(sorted(values.sets)):
-                for value in sorted(s):
+            for sid, s in enumerate(values.sets):
+                for value in s:
                     pkg_fact(fn.variant_value_from_disjoint_sets(vid, value, sid))
                 union.update(s)
             values = union
@@ -2005,7 +1603,7 @@ 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 sorted(provided):
+            for vpkg in provided:
                 if vpkg.name not in self.possible_virtuals:
                     continue
 
@@ -2020,8 +1618,8 @@ 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(sorted(sets_of_virtuals)):
-                for name in sorted(virtuals_together):
+            for set_id, virtuals_together in enumerate(sets_of_virtuals):
+                for name in virtuals_together:
                     self.gen.fact(
                         fn.pkg_fact(pkg.name, fn.provided_together(condition_id, set_id, name))
                     )
@@ -2055,16 +1653,13 @@ def track_dependencies(input_spec, requirements):
                     return requirements + [fn.attr("track_dependencies", input_spec.name)]
 
                 def dependency_holds(input_spec, requirements):
-                    result = remove_node(input_spec, requirements) + [
+                    return 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(
@@ -2131,7 +1726,7 @@ def package_splice_rules(self, pkg):
                     for map in pkg.variants.values():
                         for k in map:
                             filt_match_variants.add(k)
-                    filt_match_variants = sorted(filt_match_variants)
+                    filt_match_variants = list(filt_match_variants)
                     variant_constraints = self._gen_match_variant_splice_constraints(
                         pkg, cond, spec_to_splice, hash_var, splice_node, filt_match_variants
                     )
@@ -2485,11 +2080,7 @@ def _spec_clauses(
         f: Union[Type[_Head], Type[_Body]] = _Body if body else _Head
 
         if spec.name:
-            clauses.append(
-                f.node(spec.name)
-                if not spack.repo.PATH.is_virtual(spec.name)
-                else f.virtual_node(spec.name)
-            )
+            clauses.append(f.node(spec.name) if not spec.virtual else f.virtual_node(spec.name))
         if spec.namespace:
             clauses.append(f.namespace(spec.name, spec.namespace))
 
@@ -2516,7 +2107,7 @@ def _spec_clauses(
 
             for value in variant.value_as_tuple:
                 # ensure that the value *can* be valid for the spec
-                if spec.name and not spec.concrete and not spack.repo.PATH.is_virtual(spec.name):
+                if spec.name and not spec.concrete and not spec.virtual:
                     variant_defs = vt.prevalidate_variant_value(
                         self.pkg_class(spec.name), variant, spec
                     )
@@ -2661,7 +2252,7 @@ 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 sorted(possible_pkgs):
+        for pkg_name in possible_pkgs:
             pkg_cls = self.pkg_class(pkg_name)
 
             # All the versions from the corresponding package.py file. Since concepts
@@ -2989,7 +2580,7 @@ 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 sorted(self.variant_values_from_specs):
+        for pkg_name, variant_def_id, value in self.variant_values_from_specs:
             try:
                 vid = self.variant_ids_by_def_id[variant_def_id]
             except KeyError:
@@ -3027,8 +2618,6 @@ 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):
@@ -3078,9 +2667,7 @@ def setup(
         # Fail if we already know an unreachable node is requested
         for spec in specs:
             missing_deps = [
-                str(d)
-                for d in spec.traverse()
-                if d.name not in self.pkgs and not spack.repo.PATH.is_virtual(d.name)
+                str(d) for d in spec.traverse() if d.name not in self.pkgs and not d.virtual
             ]
             if missing_deps:
                 raise spack.spec.InvalidDependencyError(spec.name, missing_deps)
@@ -3266,7 +2853,7 @@ def define_runtime_constraints(self):
         recorder.consume_facts()
 
     def literal_specs(self, specs):
-        for spec in sorted(specs):
+        for spec in specs:
             self.gen.h2("Spec: %s" % str(spec))
             condition_id = next(self._id_counter)
             trigger_id = next(self._id_counter)
@@ -3297,11 +2884,7 @@ def literal_specs(self, specs):
                     pkg_name = clause.args[1]
                     self.gen.fact(fn.mentioned_in_literal(trigger_id, root_name, pkg_name))
 
-            requirements.append(
-                fn.attr(
-                    "virtual_root" if spack.repo.PATH.is_virtual(spec.name) else "root", spec.name
-                )
-            )
+            requirements.append(fn.attr("virtual_root" if spec.virtual else "root", spec.name))
             cache[imposed_spec_key] = (effect_id, requirements)
             self.gen.fact(fn.pkg_fact(spec.name, fn.condition_effect(condition_id, effect_id)))
 
@@ -3767,7 +3350,7 @@ def consume_facts(self):
             # on the available compilers)
             self._setup.pkg_version_rules(runtime_pkg)
 
-        for imposed_spec, when_spec in sorted(self.runtime_conditions):
+        for imposed_spec, when_spec in self.runtime_conditions:
             msg = f"{when_spec} requires {imposed_spec} at runtime"
             _ = self._setup.condition(when_spec, imposed_spec=imposed_spec, msg=msg)
 
@@ -4106,11 +3689,11 @@ 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():
-            _inject_patches_variant(root)
+            spack.spec.Spec.inject_patches_variant(root)
 
         # Add external paths to specs with just external modules
         for s in self._specs.values():
-            _ensure_external_path_if_external(s)
+            spack.spec.Spec.ensure_external_path_if_external(s)
 
         for s in self._specs.values():
             _develop_specs_from_env(s, ev.active_environment())
@@ -4182,92 +3765,6 @@ 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:
@@ -4588,10 +4085,10 @@ def _check_input_and_extract_concrete_specs(specs):
         reusable = []
         for root in specs:
             for s in root.traverse():
+                if s.virtual:
+                    continue
                 if s.concrete:
                     reusable.append(s)
-                elif spack.repo.PATH.is_virtual(s.name):
-                    continue
                 spack.spec.Spec.ensure_valid_variants(s)
         return reusable
 
@@ -4624,9 +4121,6 @@ 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
         )
@@ -4696,9 +4190,6 @@ 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

@@ -265,7 +265,6 @@ error(100, "Cannot select a single version for virtual '{0}'", Virtual)
 % If we select a deprecated version, mark the package as deprecated
 attr("deprecated", node(ID, Package), Version) :-
      attr("version", node(ID, Package), Version),
-     not external(node(ID, Package)),
      pkg_fact(Package, deprecated_version(Version)).
 
 error(100, "Package '{0}' needs the deprecated version '{1}', and this is not allowed", Package, Version)
@@ -524,16 +523,6 @@ 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.
 
 %-----------------------------------------------------------------------------

lib/spack/spack/solver/input_analysis.py

@@ -381,9 +381,7 @@ def __init__(
             self.all_types = dt.LINK | dt.RUN | dt.BUILD
 
         self._possible_dependencies: Set[str] = set()
-        self._possible_virtuals: Set[str] = {
-            x.name for x in specs if spack.repo.PATH.is_virtual(x.name)
-        }
+        self._possible_virtuals: Set[str] = set(x.name for x in specs if x.virtual)
 
     def possible_dependencies(self) -> Set[str]:
         """Returns the list of possible dependencies"""
@@ -468,29 +466,16 @@ def possible_packages_facts(self, gen, fn):
         gen.newline()
 
         gen.h2("Packages with at multiple possible nodes (build-tools)")
-        default = spack.config.CONFIG.get("concretizer:duplicates:max_dupes:default", 2)
         for package_name in sorted(self.possible_dependencies() & build_tools):
-            max_dupes = spack.config.CONFIG.get(
-                f"concretizer:duplicates:max_dupes:{package_name}", default
-            )
-            gen.fact(fn.max_dupes(package_name, max_dupes))
-            if max_dupes > 1:
-                gen.fact(fn.multiple_unification_sets(package_name))
+            gen.fact(fn.max_dupes(package_name, 2))
+            gen.fact(fn.multiple_unification_sets(package_name))
         gen.newline()
 
-        gen.h2("Maximum number of nodes (link-run virtuals)")
-        for package_name in sorted(self._link_run_virtuals):
+        gen.h2("Maximum number of nodes (virtual packages)")
+        for package_name in sorted(self.possible_virtuals()):
             gen.fact(fn.max_dupes(package_name, 1))
         gen.newline()
 
-        gen.h2("Maximum number of nodes (other virtuals)")
-        for package_name in sorted(self.possible_virtuals() - self._link_run_virtuals):
-            max_dupes = spack.config.CONFIG.get(
-                f"concretizer:duplicates:max_dupes:{package_name}", default
-            )
-            gen.fact(fn.max_dupes(package_name, max_dupes))
-        gen.newline()
-
         gen.h2("Possible package in link-run subDAG")
         for name in sorted(self._link_run):
             gen.fact(fn.possible_in_link_run(name))

lib/spack/spack/solver/requirements.py

@@ -10,7 +10,7 @@
 import spack.error
 import spack.package_base
 import spack.spec
-from spack.util.spack_yaml import get_mark_from_yaml_data
+from spack.config import get_mark_from_yaml_data
 
 
 class RequirementKind(enum.Enum):
@@ -165,8 +165,7 @@ def _rules_from_requirements(
 
                 # validate specs from YAML first, and fail with line numbers if parsing fails.
                 constraints = [
-                    parse_spec_from_yaml_string(constraint, named=kind == RequirementKind.VIRTUAL)
-                    for constraint in constraints
+                    parse_spec_from_yaml_string(constraint) for constraint in constraints
                 ]
                 when_str = requirement.get("when")
                 when = parse_spec_from_yaml_string(when_str) if when_str else spack.spec.Spec()
@@ -204,7 +203,7 @@ def reject_requirement_constraint(
                 s.validate_or_raise()
             except spack.error.SpackError as e:
                 tty.debug(
-                    f"[{__name__}] Rejecting the default '{constraint}' requirement "
+                    f"[SETUP] Rejecting the default '{constraint}' requirement "
                     f"on '{pkg_name}': {str(e)}",
                     level=2,
                 )
@@ -212,37 +211,21 @@ def reject_requirement_constraint(
         return False
 
 
-def parse_spec_from_yaml_string(string: str, *, named: bool = False) -> spack.spec.Spec:
+def parse_spec_from_yaml_string(string: str) -> 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.
 
-    Args:
+    Arguments:
         string: a string representing a ``Spec`` from config YAML.
-        named: if True, the spec must have a name
+
     """
     try:
-        result = spack.spec.Spec(string)
+        return 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

@@ -52,7 +52,6 @@
 import enum
 import io
 import itertools
-import json
 import os
 import pathlib
 import platform
@@ -99,6 +98,7 @@
 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
@@ -175,17 +175,15 @@
 #:     Spec(Spec("string").format()) == Spec("string)"
 DEFAULT_FORMAT = (
     "{name}{@versions}"
-    "{compiler_flags}"
+    "{%compiler.name}{@compiler.versions}{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_flags}"
+    "{%compiler.name}{@compiler.version}{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
@@ -800,7 +798,7 @@ def update_deptypes(self, depflag: dt.DepFlag) -> bool:
         self.depflag = new
         return True
 
-    def update_virtuals(self, virtuals: Iterable[str]) -> bool:
+    def update_virtuals(self, virtuals: Tuple[str, ...]) -> bool:
         """Update the list of provided virtuals"""
         old = self.virtuals
         self.virtuals = tuple(sorted(set(virtuals).union(self.virtuals)))
@@ -1339,20 +1337,14 @@ class SpecBuildInterface(lang.ObjectWrapper):
         "command", default_handler=_command_default_handler, _indirect=True
     )
 
-    def __init__(
-        self,
-        spec: "Spec",
-        name: str,
-        query_parameters: List[str],
-        _parent: "Spec",
-        is_virtual: bool,
-    ):
+    def __init__(self, spec: "Spec", name: str, query_parameters: List[str], _parent: "Spec"):
         super().__init__(spec)
         # Adding new attributes goes after super() call since the ObjectWrapper
         # resets __dict__ to behave like the passed object
         original_spec = getattr(spec, "wrapped_obj", spec)
         self.wrapped_obj = original_spec
-        self.token = original_spec, name, query_parameters, _parent, is_virtual
+        self.token = original_spec, name, query_parameters, _parent
+        is_virtual = spack.repo.PATH.is_virtual(name)
         self.last_query = QueryState(
             name=name, extra_parameters=query_parameters, isvirtual=is_virtual
         )
@@ -1923,12 +1915,6 @@ def package_class(self):
 
     @property
     def virtual(self):
-        warnings.warn(
-            "`Spec.virtual` is deprecated and will be removed in version 1.0.0. Use "
-            "`spack.repo.PATH.is_virtual(spec.name)` instead.",
-            category=spack.error.SpackAPIWarning,
-            stacklevel=2,
-        )
         return spack.repo.PATH.is_virtual(self.name)
 
     @property
@@ -2108,34 +2094,32 @@ def long_spec(self):
     def short_spec(self):
         """Returns a version of the spec with the dependencies hashed
         instead of completely enumerated."""
-        return self.format(
-            "{name}{@version}{variants}{ arch=architecture}"
-            "{/hash:7}{%compiler.name}{@compiler.version}"
-        )
+        spec_format = "{name}{@version}{%compiler.name}{@compiler.version}"
+        spec_format += "{variants}{ arch=architecture}{/hash:7}"
+        return self.format(spec_format)
 
     @property
     def cshort_spec(self):
         """Returns an auto-colorized version of ``self.short_spec``."""
-        return self.cformat(
-            "{name}{@version}{variants}{ arch=architecture}"
-            "{/hash:7}{%compiler.name}{@compiler.version}"
-        )
+        spec_format = "{name}{@version}{%compiler.name}{@compiler.version}"
+        spec_format += "{variants}{ arch=architecture}{/hash:7}"
+        return self.cformat(spec_format)
 
     @property
-    def prefix(self) -> spack.util.prefix.Prefix:
+    def prefix(self):
         if not self._concrete:
-            raise spack.error.SpecError(f"Spec is not concrete: {self}")
+            raise spack.error.SpecError("Spec is not concrete: " + str(self))
 
         if self._prefix is None:
-            _, record = spack.store.STORE.db.query_by_spec_hash(self.dag_hash())
+            upstream, record = spack.store.STORE.db.query_by_spec_hash(self.dag_hash())
             if record and record.path:
-                self.set_prefix(record.path)
+                self.prefix = record.path
             else:
-                self.set_prefix(spack.store.STORE.layout.path_for_spec(self))
-        assert self._prefix is not None
+                self.prefix = spack.store.STORE.layout.path_for_spec(self)
         return self._prefix
 
-    def set_prefix(self, value: str) -> None:
+    @prefix.setter
+    def prefix(self, value):
         self._prefix = spack.util.prefix.Prefix(llnl.path.convert_to_platform_path(value))
 
     def spec_hash(self, hash):
@@ -2149,9 +2133,7 @@ def spec_hash(self, hash):
         if hash.override is not None:
             return hash.override(self)
         node_dict = self.to_node_dict(hash=hash)
-        json_text = json.dumps(
-            node_dict, ensure_ascii=True, indent=None, separators=(",", ":"), sort_keys=False
-        )
+        json_text = sjson.dump(node_dict)
         # This implements "frankenhashes", preserving the last 7 characters of the
         # original hash when splicing so that we can avoid relocation issues
         out = spack.util.hash.b32_hash(json_text)
@@ -2712,7 +2694,7 @@ def name_and_dependency_types(s: str) -> Tuple[str, dt.DepFlag]:
                 return name, depflag
 
             def spec_and_dependency_types(
-                s: Union[Spec, Tuple[Spec, str]],
+                s: Union[Spec, Tuple[Spec, str]]
             ) -> Tuple[Spec, dt.DepFlag]:
                 """Given a non-string key in the literal, extracts the spec
                 and its dependency types.
@@ -2741,7 +2723,7 @@ def spec_and_dependency_types(
         return spec_builder(spec_dict)
 
     @staticmethod
-    def from_dict(data) -> "Spec":
+    def from_dict(data):
         """Construct a spec from JSON/YAML.
 
         Args:
@@ -2764,7 +2746,7 @@ def from_dict(data) -> "Spec":
         return spec
 
     @staticmethod
-    def from_yaml(stream) -> "Spec":
+    def from_yaml(stream):
         """Construct a spec from YAML.
 
         Args:
@@ -2774,7 +2756,7 @@ def from_yaml(stream) -> "Spec":
         return Spec.from_dict(data)
 
     @staticmethod
-    def from_json(stream) -> "Spec":
+    def from_json(stream):
         """Construct a spec from JSON.
 
         Args:
@@ -2784,7 +2766,7 @@ def from_json(stream) -> "Spec":
             data = sjson.load(stream)
             return Spec.from_dict(data)
         except Exception as e:
-            raise sjson.SpackJSONError("error parsing JSON spec:", e) from e
+            raise sjson.SpackJSONError("error parsing JSON spec:", str(e)) from e
 
     @staticmethod
     def extract_json_from_clearsig(data):
@@ -2832,6 +2814,24 @@ def from_detection(
         s.extra_attributes = extra_attributes
         return s
 
+    def validate_detection(self):
+        """Validate the detection of an external spec.
+
+        This method is used as part of Spack's detection protocol, and is
+        not meant for client code use.
+        """
+        # Assert that _extra_attributes is a Mapping and not None,
+        # which likely means the spec was created with Spec.from_detection
+        msg = 'cannot validate "{0}" since it was not created ' "using Spec.from_detection".format(
+            self
+        )
+        assert isinstance(self.extra_attributes, collections.abc.Mapping), msg
+
+        # Validate the spec calling a package specific method
+        pkg_cls = spack.repo.PATH.get_pkg_class(self.name)
+        validate_fn = getattr(pkg_cls, "validate_detected_spec", lambda x, y: None)
+        validate_fn(self, self.extra_attributes)
+
     def _patches_assigned(self):
         """Whether patches have been assigned to this spec by the concretizer."""
         # FIXME: _patches_in_order_of_appearance is attached after concretization
@@ -2848,6 +2848,94 @@ 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.
@@ -3002,7 +3090,7 @@ def validate_or_raise(self):
         # FIXME: raise just the first one encountered
         for spec in self.traverse():
             # raise an UnknownPackageError if the spec's package isn't real.
-            if spec.name and not spack.repo.PATH.is_virtual(spec.name):
+            if (not spec.virtual) and spec.name:
                 spack.repo.PATH.get_pkg_class(spec.fullname)
 
             # validate compiler in addition to the package name.
@@ -3011,7 +3099,7 @@ def validate_or_raise(self):
                     raise UnsupportedCompilerError(spec.compiler.name)
 
             # Ensure correctness of variants (if the spec is not virtual)
-            if not spack.repo.PATH.is_virtual(spec.name):
+            if not spec.virtual:
                 Spec.ensure_valid_variants(spec)
                 substitute_abstract_variants(spec)
 
@@ -3246,9 +3334,7 @@ def intersects(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
 
         # If the names are different, we need to consider virtuals
         if self.name != other.name and self.name and other.name:
-            self_virtual = spack.repo.PATH.is_virtual(self.name)
-            other_virtual = spack.repo.PATH.is_virtual(other.name)
-            if self_virtual and other_virtual:
+            if self.virtual and other.virtual:
                 # Two virtual specs intersect only if there are providers for both
                 lhs = spack.repo.PATH.providers_for(str(self))
                 rhs = spack.repo.PATH.providers_for(str(other))
@@ -3256,8 +3342,8 @@ def intersects(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
                 return bool(intersection)
 
             # A provider can satisfy a virtual dependency.
-            elif self_virtual or other_virtual:
-                virtual_spec, non_virtual_spec = (self, other) if self_virtual else (other, self)
+            elif self.virtual or other.virtual:
+                virtual_spec, non_virtual_spec = (self, other) if self.virtual else (other, self)
                 try:
                     # Here we might get an abstract spec
                     pkg_cls = spack.repo.PATH.get_pkg_class(non_virtual_spec.fullname)
@@ -3327,20 +3413,12 @@ def _intersects_dependencies(self, other):
         # These two loops handle cases where there is an overly restrictive
         # vpkg in one spec for a provider in the other (e.g., mpi@3: is not
         # compatible with mpich2)
-        for spec in self.traverse():
-            if (
-                spack.repo.PATH.is_virtual(spec.name)
-                and spec.name in other_index
-                and not other_index.providers_for(spec)
-            ):
+        for spec in self.virtual_dependencies():
+            if spec.name in other_index and not other_index.providers_for(spec):
                 return False
 
-        for spec in other.traverse():
-            if (
-                spack.repo.PATH.is_virtual(spec.name)
-                and spec.name in self_index
-                and not self_index.providers_for(spec)
-            ):
+        for spec in other.virtual_dependencies():
+            if spec.name in self_index and not self_index.providers_for(spec):
                 return False
 
         return True
@@ -3370,9 +3448,7 @@ def satisfies(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
         # If the names are different, we need to consider virtuals
         if self.name != other.name and self.name and other.name:
             # A concrete provider can satisfy a virtual dependency.
-            if not spack.repo.PATH.is_virtual(self.name) and spack.repo.PATH.is_virtual(
-                other.name
-            ):
+            if not self.virtual and other.virtual:
                 try:
                     # Here we might get an abstract spec
                     pkg_cls = spack.repo.PATH.get_pkg_class(self.fullname)
@@ -3440,7 +3516,7 @@ def satisfies(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
         lhs_edges: Dict[str, Set[DependencySpec]] = collections.defaultdict(set)
         for rhs_edge in other.traverse_edges(root=False, cover="edges"):
             # If we are checking for ^mpi we need to verify if there is any edge
-            if spack.repo.PATH.is_virtual(rhs_edge.spec.name):
+            if rhs_edge.spec.virtual:
                 rhs_edge.update_virtuals(virtuals=(rhs_edge.spec.name,))
 
             if not rhs_edge.virtuals:
@@ -3484,6 +3560,10 @@ def satisfies(self, other: Union[str, "Spec"], deps: bool = True) -> bool:
             for rhs in other.traverse(root=False)
         )
 
+    def virtual_dependencies(self):
+        """Return list of any virtual deps in this spec."""
+        return [spec for spec in self.traverse() if spec.virtual]
+
     @property  # type: ignore[misc] # decorated prop not supported in mypy
     def patches(self):
         """Return patch objects for any patch sha256 sums on this Spec.
@@ -3673,23 +3753,30 @@ def __getitem__(self, name: str):
             csv = query_parameters.pop().strip()
             query_parameters = re.split(r"\s*,\s*", csv)
 
-        # Consider all direct dependencies and transitive runtime dependencies
-        order = itertools.chain(
-            self.edges_to_dependencies(depflag=dt.ALL),
-            self.traverse_edges(deptype=dt.LINK | dt.RUN, order="breadth", cover="edges"),
+        order = lambda: itertools.chain(
+            self.traverse_edges(deptype=dt.LINK, order="breadth", cover="edges"),
+            self.edges_to_dependencies(depflag=dt.BUILD | dt.RUN | dt.TEST),
+            self.traverse_edges(deptype=dt.ALL, order="breadth", cover="edges"),
         )
 
+        # Consider runtime dependencies and direct build/test deps before transitive dependencies,
+        # and prefer matches closest to the root.
         try:
-            edge = next((e for e in order if e.spec.name == name or name in e.virtuals))
-        except StopIteration as e:
-            raise KeyError(f"No spec with name {name} in {self}") from e
+            child: Spec = next(
+                e.spec
+                for e in itertools.chain(
+                    (e for e in order() if e.spec.name == name or name in e.virtuals),
+                    # for historical reasons
+                    (e for e in order() if e.spec.concrete and e.spec.package.provides(name)),
+                )
+            )
+        except StopIteration:
+            raise KeyError(f"No spec with name {name} in {self}")
 
         if self._concrete:
-            return SpecBuildInterface(
-                edge.spec, name, query_parameters, _parent=self, is_virtual=name in edge.virtuals
-            )
+            return SpecBuildInterface(child, name, query_parameters, _parent=self)
 
-        return edge.spec
+        return child
 
     def __contains__(self, spec):
         """True if this spec or some dependency satisfies the spec.
@@ -3705,11 +3792,8 @@ def __contains__(self, spec):
         # if anonymous or same name, we only have to look at the root
         if not spec.name or spec.name == self.name:
             return self.satisfies(spec)
-        try:
-            dep = self[spec.name]
-        except KeyError:
-            return False
-        return dep.satisfies(spec)
+        else:
+            return any(s.satisfies(spec) for s in self.traverse(root=False))
 
     def eq_dag(self, other, deptypes=True, vs=None, vo=None):
         """True if the full dependency DAGs of specs are equal."""
@@ -4619,6 +4703,17 @@ 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():
@@ -4745,51 +4840,31 @@ def merge_abstract_anonymous_specs(*abstract_specs: Spec):
     return merged_spec
 
 
-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
+def reconstruct_virtuals_on_edges(spec):
+    """Reconstruct virtuals on edges. Used to read from old DB and reindex.
 
-            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)
-            )
-
-        if not virtuals_needed[parent_key]:
+    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 Spec(x).virtual})
+        except Exception as e:
+            warnings.warn(f"cannot reconstruct virtual dependencies on package {node.name}: {e}")
             continue
 
-        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]:
+    # 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
             continue
 
-        virtuals_to_add = virtuals_needed[parent_key] & virtuals_provided[child_key]
-        if virtuals_to_add:
-            edge.update_virtuals(virtuals_to_add)
+        for edge in provider.edges_from_dependents():
+            edge.update_virtuals([vspec])
 
 
 class SpecfileReaderBase:
@@ -5134,13 +5209,6 @@ 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."""
 
@@ -5299,10 +5367,8 @@ def __init__(self, spec):
 
 class AmbiguousHashError(spack.error.SpecError):
     def __init__(self, msg, *specs):
-        spec_fmt = (
-            "{namespace}.{name}{@version}{compiler_flags}{variants}"
-            "{ arch=architecture}{/hash:7}{%compiler}"
-        )
+        spec_fmt = "{namespace}.{name}{@version}{%compiler}{compiler_flags}"
+        spec_fmt += "{variants}{ arch=architecture}{/hash:7}"
         specs_str = "\n  " + "\n  ".join(spec.format(spec_fmt) for spec in specs)
         super().__init__(msg + specs_str)
 

lib/spack/spack/spec_parser.py

@@ -485,18 +485,23 @@ 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.
     """
-    parser = SpecParser(text)
+    stripped_text = text.strip()
+    parser = SpecParser(stripped_text)
     result = parser.next_spec(initial_spec)
-    next_token = parser.ctx.next_token
+    last_token = parser.ctx.current_token
 
-    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}}}")
+    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}}}")
         raise ValueError(message)
 
     if result is None:
-        raise ValueError("expected a single spec, but got none")
+        message = "a single spec was requested, but none was parsed:"
+        message += f"\n{text}"
+        raise ValueError(message)
 
     return result
 

lib/spack/spack/test/abi_splicing.py

@@ -1,7 +1,7 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-"""Test ABI-based splicing of dependencies"""
+""" Test ABI-based splicing of dependencies """
 
 from typing import List
 

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 foobar=bar target={root_target_range} %gcc@10 ^pkg-b target={dep_target_range}"
+        f"pkg-a %gcc@10 foobar=bar target={root_target_range} ^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

@@ -200,11 +200,7 @@ 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",
-    "mutable_mock_env_path",
+    "default_config", "cache_directory", "install_dir_default_layout", "temporary_mirror"
 )
 def test_default_rpaths_create_install_default_layout(temporary_mirror_dir):
     """
@@ -276,11 +272,7 @@ 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",
-    "mutable_mock_env_path",
+    "default_config", "cache_directory", "install_dir_default_layout", "temporary_mirror"
 )
 def test_relative_rpaths_install_default_layout(temporary_mirror_dir):
     """
@@ -577,6 +569,7 @@ 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
@@ -1140,7 +1133,7 @@ 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 arch=linux-ubuntu23.04-zen2 %gcc@13.1.0")
+    spec = Spec("gmake@4.4.1%gcc@13.1.0 arch=linux-ubuntu23.04-zen2")
     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.set_prefix(f"/{s.name}-prefix/")
+        s.prefix = "/{0}-prefix/".format(s.name)
 
     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.set_prefix(str(installation_dir_with_headers))
+    dep2_pkg.spec.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.create_from(
+            config=spack.config.Configuration(
                 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.create_from(
+            config=spack.config.Configuration(
                 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.create_from(
+            config=spack.config.Configuration(
                 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.create_from(
+            config=spack.config.Configuration(
                 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.create_from(
+            config=spack.config.Configuration(
                 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.set_prefix(str(tmpdir.join("fst")))
-    build_dep_two.set_prefix(str(tmpdir.join("snd")))
+    build_dep_one.prefix = str(tmpdir.join("fst"))
+    build_dep_two.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.set_prefix(str(tmpdir.join("fst")))
-    build_dep_two.set_prefix(str(tmpdir.join("snd")))
+    build_dep_one.prefix = str(tmpdir.join("fst"))
+    build_dep_two.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.set_prefix(str(tmpdir.join("snd")))
+    build_dep_two.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.set_prefix(str(tmpdir.join("fst")))
-    build_dep_two.set_prefix(str(tmpdir.join("snd")))
+    build_dep_one.prefix = str(tmpdir.join("fst"))
+    build_dep_two.prefix = str(tmpdir.join("snd"))
     assert spack.build_systems.autotools._autoreconf_search_path_args(spec) == []
 
 

lib/spack/spack/test/cc.py

@@ -210,6 +210,7 @@ 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

@@ -347,6 +347,7 @@ 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/build_env.py

@@ -12,7 +12,7 @@
 build_env = SpackCommand("build-env")
 
 
-@pytest.mark.parametrize("pkg", [("pkg-c",), ("pkg-c", "--")])
+@pytest.mark.parametrize("pkg", [("zlib",), ("zlib", "--")])
 @pytest.mark.usefixtures("config", "mock_packages", "working_env")
 def test_it_just_runs(pkg):
     build_env(*pkg)
@@ -38,7 +38,7 @@ def test_build_env_requires_a_spec(args):
 @pytest.mark.usefixtures("config", "mock_packages", "working_env")
 def test_dump(shell_as, shell, tmpdir):
     with tmpdir.as_cwd():
-        build_env("--dump", _out_file, "pkg-c")
+        build_env("--dump", _out_file, "zlib")
         with open(_out_file, encoding="utf-8") as f:
             if shell == "pwsh":
                 assert any(line.startswith("$Env:PATH") for line in f.readlines())
@@ -51,7 +51,7 @@ def test_dump(shell_as, shell, tmpdir):
 @pytest.mark.usefixtures("config", "mock_packages", "working_env")
 def test_pickle(tmpdir):
     with tmpdir.as_cwd():
-        build_env("--pickle", _out_file, "pkg-c")
+        build_env("--pickle", _out_file, "zlib")
         environment = pickle.load(open(_out_file, "rb"))
         assert isinstance(environment, dict)
         assert "PATH" in environment

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

@@ -148,7 +148,7 @@ def test_update_key_index(
     s = spack.concretize.concretize_one("libdwarf")
 
     # Install a package
-    install("--fake", s.name)
+    install(s.name)
 
     # Put installed package in the buildcache, which, because we're signing
     # it, should result in the public key getting pushed to the buildcache
@@ -178,7 +178,7 @@ def test_buildcache_autopush(tmp_path, install_mockery, mock_fetch):
     s = spack.concretize.concretize_one("libdwarf")
 
     # Install and generate build cache index
-    PackageInstaller([s.package], fake=True, explicit=True).install()
+    PackageInstaller([s.package], explicit=True).install()
 
     metadata_file = spack.binary_distribution.tarball_name(s, ".spec.json")
 
@@ -214,11 +214,13 @@ def verify_mirror_contents():
             if in_env_pkg in p:
                 found_pkg = True
 
-        assert found_pkg, f"Expected to find {in_env_pkg} in {dest_mirror_dir}"
+        if not found_pkg:
+            print("Expected to find {0} in {1}".format(in_env_pkg, dest_mirror_dir))
+            assert False
 
     # Install a package and put it in the buildcache
     s = spack.concretize.concretize_one(out_env_pkg)
-    install("--fake", s.name)
+    install(s.name)
     buildcache("push", "-u", "-f", src_mirror_url, s.name)
 
     env("create", "test")

lib/spack/spack/test/cmd/checksum.py

@@ -3,7 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import argparse
-import pathlib
 
 import pytest
 
@@ -23,15 +22,7 @@
 
 
 @pytest.fixture
-def no_add(monkeypatch):
-    def add_versions_to_pkg(pkg, version_lines, open_in_editor):
-        raise AssertionError("Should not be called")
-
-    monkeypatch.setattr(spack.cmd.checksum, "add_versions_to_pkg", add_versions_to_pkg)
-
-
-@pytest.fixture
-def can_fetch_versions(monkeypatch, no_add):
+def can_fetch_versions(monkeypatch):
     """Fake successful version detection."""
 
     def fetch_remote_versions(pkg, concurrency):
@@ -54,7 +45,7 @@ def url_exists(url, curl=None):
 
 
 @pytest.fixture
-def cannot_fetch_versions(monkeypatch, no_add):
+def cannot_fetch_versions(monkeypatch):
     """Fake unsuccessful version detection."""
 
     def fetch_remote_versions(pkg, concurrency):
@@ -97,6 +88,7 @@ def test_checksum_args(arguments, expected):
         (["--batch", "preferred-test"], "version of preferred-test"),
         (["--latest", "preferred-test"], "Found 1 version"),
         (["--preferred", "preferred-test"], "Found 1 version"),
+        (["--add-to-package", "preferred-test"], "Added 0 new versions to"),
         (["--verify", "preferred-test"], "Verified 1 of 1"),
         (["--verify", "zlib", "1.2.13"], "1.2.13  [-] No previous checksum"),
     ],
@@ -279,12 +271,15 @@ def test_checksum_interactive_unrecognized_command():
     assert interactive_version_filter(v.copy(), input=input) == v
 
 
-def test_checksum_versions(mock_packages, can_fetch_versions, monkeypatch):
+def test_checksum_versions(mock_packages, can_fetch_versions):
     pkg_cls = spack.repo.PATH.get_pkg_class("zlib")
     versions = [str(v) for v in pkg_cls.versions]
     output = spack_checksum("zlib", *versions)
     assert "Found 3 versions" in output
     assert "version(" in output
+    output = spack_checksum("--add-to-package", "zlib", *versions)
+    assert "Found 3 versions" in output
+    assert "Added 0 new versions to" in output
 
 
 def test_checksum_missing_version(mock_packages, cannot_fetch_versions):
@@ -292,6 +287,7 @@ def test_checksum_missing_version(mock_packages, cannot_fetch_versions):
     assert "Could not find any remote versions" in output
     output = spack_checksum("--add-to-package", "preferred-test", "99.99.99", fail_on_error=False)
     assert "Could not find any remote versions" in output
+    assert "Added 1 new versions to" not in output
 
 
 def test_checksum_deprecated_version(mock_packages, can_fetch_versions):
@@ -301,6 +297,8 @@ def test_checksum_deprecated_version(mock_packages, can_fetch_versions):
         "--add-to-package", "deprecated-versions", "1.1.0", fail_on_error=False
     )
     assert "Version 1.1.0 is deprecated" in output
+    # TODO alecbcs: broken assertion.
+    # assert "Added 0 new versions to" not in output
 
 
 def test_checksum_url(mock_packages, config):
@@ -339,52 +337,3 @@ def test_checksum_manual_download_fails(mock_packages, monkeypatch):
     monkeypatch.setattr(spack.package_base.PackageBase, "download_instr", error)
     with pytest.raises(ManualDownloadRequiredError, match=error):
         spack_checksum(name, *versions)
-
-
-def test_upate_package_contents(tmp_path: pathlib.Path):
-    """Test that the package.py file is updated with the new versions."""
-    pkg_path = tmp_path / "package.py"
-    pkg_path.write_text(
-        """\
-from spack.package import *
-
-class Zlib(Package):
-    homepage = "http://zlib.net"
-    url = "http://zlib.net/fossils/zlib-1.2.11.tar.gz"
-
-    version("1.2.11", sha256="c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1")
-    version("1.2.8", sha256="36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d")
-    version("1.2.3", sha256="1795c7d067a43174113fdf03447532f373e1c6c57c08d61d9e4e9be5e244b05e")
-    variant("pic", default=True, description="test")
-
-    def install(self, spec, prefix):
-        make("install")
-"""
-    )
-    version_lines = """\
-    version("1.2.13", sha256="abcdef1234567890abcdef1234567890abcdef1234567890abcdef1234567890")
-    version("1.2.5", sha256="abcdef1234567890abcdef1234567890abcdef1234567890abcdef1234567890")
-    version("1.2.3", sha256="1795c7d067a43174113fdf03447532f373e1c6c57c08d61d9e4e9be5e244b05e")
-"""
-    # two new versions are added
-    assert spack.cmd.checksum.add_versions_to_pkg(str(pkg_path), version_lines) == 2
-    assert (
-        pkg_path.read_text()
-        == """\
-from spack.package import *
-
-class Zlib(Package):
-    homepage = "http://zlib.net"
-    url = "http://zlib.net/fossils/zlib-1.2.11.tar.gz"
-
-    version("1.2.13", sha256="abcdef1234567890abcdef1234567890abcdef1234567890abcdef1234567890")  # FIXME
-    version("1.2.11", sha256="c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1")
-    version("1.2.8", sha256="36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d")
-    version("1.2.5", sha256="abcdef1234567890abcdef1234567890abcdef1234567890abcdef1234567890")  # FIXME
-    version("1.2.3", sha256="1795c7d067a43174113fdf03447532f373e1c6c57c08d61d9e4e9be5e244b05e")
-    variant("pic", default=True, description="test")
-
-    def install(self, spec, prefix):
-        make("install")
-"""
-    )

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

@@ -28,7 +28,6 @@
 from spack.ci.generator_registry import generator
 from spack.cmd.ci import FAILED_CREATE_BUILDCACHE_CODE
 from spack.database import INDEX_JSON_FILE
-from spack.error import SpackError
 from spack.schema.buildcache_spec import schema as specfile_schema
 from spack.schema.database_index import schema as db_idx_schema
 from spack.spec import Spec
@@ -171,9 +170,7 @@ def test_ci_generate_with_env(ci_generate_test, tmp_path, mock_binary_index):
     url: https://my.fake.cdash
     project: Not used
     site: Nothing
-""",
-        "--artifacts-root",
-        str(tmp_path / "my_artifacts_root"),
+"""
     )
     yaml_contents = syaml.load(outputfile.read_text())
 
@@ -195,7 +192,7 @@ def test_ci_generate_with_env(ci_generate_test, tmp_path, mock_binary_index):
 
     assert "variables" in yaml_contents
     assert "SPACK_ARTIFACTS_ROOT" in yaml_contents["variables"]
-    assert yaml_contents["variables"]["SPACK_ARTIFACTS_ROOT"] == "my_artifacts_root"
+    assert yaml_contents["variables"]["SPACK_ARTIFACTS_ROOT"] == "jobs_scratch_dir"
 
 
 def test_ci_generate_with_env_missing_section(ci_generate_test, tmp_path, mock_binary_index):
@@ -1065,7 +1062,7 @@ def test_ci_rebuild_index(
             with open(tmp_path / "spec.json", "w", encoding="utf-8") as f:
                 f.write(concrete_spec.to_json(hash=ht.dag_hash))
 
-            install_cmd("--fake", "--add", "-f", str(tmp_path / "spec.json"))
+            install_cmd("--add", "-f", str(tmp_path / "spec.json"))
             buildcache_cmd("push", "-u", "-f", mirror_url, "callpath")
             ci_cmd("rebuild-index")
 
@@ -1325,50 +1322,44 @@ def test_ci_reproduce(
         env.concretize()
         env.write()
 
-    def fake_download_and_extract_artifacts(url, work_dir, merge_commit_test=True):
-        with working_dir(tmp_path), ev.Environment(".") as env:
-            if not os.path.exists(repro_dir):
-                repro_dir.mkdir()
+        repro_dir.mkdir()
 
-            job_spec = env.concrete_roots()[0]
-            with open(repro_dir / "archivefiles.json", "w", encoding="utf-8") as f:
-                f.write(job_spec.to_json(hash=ht.dag_hash))
-                artifacts_root = repro_dir / "jobs_scratch_dir"
-                pipeline_path = artifacts_root / "pipeline.yml"
+        job_spec = env.concrete_roots()[0]
+        with open(repro_dir / "archivefiles.json", "w", encoding="utf-8") as f:
+            f.write(job_spec.to_json(hash=ht.dag_hash))
 
-                ci_cmd(
-                    "generate",
-                    "--output-file",
-                    str(pipeline_path),
-                    "--artifacts-root",
-                    str(artifacts_root),
+        artifacts_root = repro_dir / "scratch_dir"
+        pipeline_path = artifacts_root / "pipeline.yml"
+
+        ci_cmd(
+            "generate",
+            "--output-file",
+            str(pipeline_path),
+            "--artifacts-root",
+            str(artifacts_root),
+        )
+
+        job_name = gitlab_generator.get_job_name(job_spec)
+
+        with open(repro_dir / "repro.json", "w", encoding="utf-8") as f:
+            f.write(
+                json.dumps(
+                    {
+                        "job_name": job_name,
+                        "job_spec_json": "archivefiles.json",
+                        "ci_project_dir": str(repro_dir),
+                    }
                 )
+            )
 
-                job_name = gitlab_generator.get_job_name(job_spec)
+        with open(repro_dir / "install.sh", "w", encoding="utf-8") as f:
+            f.write("#!/bin/sh\n\n#fake install\nspack install blah\n")
 
-                with open(repro_dir / "repro.json", "w", encoding="utf-8") as f:
-                    f.write(
-                        json.dumps(
-                            {
-                                "job_name": job_name,
-                                "job_spec_json": "archivefiles.json",
-                                "ci_project_dir": str(repro_dir),
-                            }
-                        )
-                    )
+        with open(repro_dir / "spack_info.txt", "w", encoding="utf-8") as f:
+            f.write(f"\nMerge {last_two_git_commits[1]} into {last_two_git_commits[0]}\n\n")
 
-                with open(repro_dir / "install.sh", "w", encoding="utf-8") as f:
-                    f.write("#!/bin/sh\n\n#fake install\nspack install blah\n")
-
-                with open(repro_dir / "spack_info.txt", "w", encoding="utf-8") as f:
-                    if merge_commit_test:
-                        f.write(
-                            f"\nMerge {last_two_git_commits[1]} into {last_two_git_commits[0]}\n\n"
-                        )
-                    else:
-                        f.write(f"\ncommit {last_two_git_commits[1]}\n\n")
-
-            return "jobs_scratch_dir"
+    def fake_download_and_extract_artifacts(url, work_dir):
+        pass
 
     monkeypatch.setattr(ci, "download_and_extract_artifacts", fake_download_and_extract_artifacts)
     rep_out = ci_cmd(
@@ -1384,64 +1375,6 @@ def fake_download_and_extract_artifacts(url, work_dir, merge_commit_test=True):
     # Make sure we tell the user where it is when not in interactive mode
     assert f"$ {repro_dir}/start.sh" in rep_out
 
-    # Ensure the correct commits are used
-    assert f"checkout_commit: {last_two_git_commits[0]}" in rep_out
-    assert f"merge_commit: {last_two_git_commits[1]}" in rep_out
-
-    # Test re-running in dirty working dir
-    with pytest.raises(SpackError, match=f"{repro_dir}"):
-        rep_out = ci_cmd(
-            "reproduce-build",
-            "https://example.com/api/v1/projects/1/jobs/2/artifacts",
-            "--working-dir",
-            str(repro_dir),
-            output=str,
-        )
-
-    # Cleanup between  tests
-    shutil.rmtree(repro_dir)
-
-    # Test --use-local-head
-    rep_out = ci_cmd(
-        "reproduce-build",
-        "https://example.com/api/v1/projects/1/jobs/2/artifacts",
-        "--use-local-head",
-        "--working-dir",
-        str(repro_dir),
-        output=str,
-    )
-
-    # Make sure we are checkout out the HEAD commit without a merge commit
-    assert "checkout_commit: HEAD" in rep_out
-    assert "merge_commit: None" in rep_out
-
-    # Test the case where the spack_info.txt is not a merge commit
-    monkeypatch.setattr(
-        ci,
-        "download_and_extract_artifacts",
-        lambda url, wd: fake_download_and_extract_artifacts(url, wd, False),
-    )
-
-    # Cleanup between  tests
-    shutil.rmtree(repro_dir)
-
-    rep_out = ci_cmd(
-        "reproduce-build",
-        "https://example.com/api/v1/projects/1/jobs/2/artifacts",
-        "--working-dir",
-        str(repro_dir),
-        output=str,
-    )
-    # Make sure the script was generated
-    assert (repro_dir / "start.sh").exists()
-
-    # Make sure we tell the user where it is when not in interactive mode
-    assert f"$ {repro_dir}/start.sh" in rep_out
-
-    # Ensure the correct commit is used (different than HEAD)
-    assert f"checkout_commit: {last_two_git_commits[1]}" in rep_out
-    assert "merge_commit: None" in rep_out
-
 
 @pytest.mark.parametrize(
     "url_in,url_out",

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

@@ -5,7 +5,6 @@
 import filecmp
 import os
 import shutil
-import textwrap
 
 import pytest
 
@@ -260,25 +259,15 @@ 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."""
 
-    width = 72
-    lines = textwrap.wrap(
+    msg = (
         "It looks like Spack's command-line interface has been modified. "
-        "If differences are more than your global 'include:' scopes, please "
-        "update Spack's shell tab completion scripts by running:",
-        width,
+        "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."
     )
-    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 = f"spack-completion.{shell}"
+    script = "spack-completion.{0}".format(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_tree:root:/path/to/config.yaml"
+    config_file = "config:install_root: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_tree:\n    root: /path/to/config.yaml" in output
+    assert "config:\n  install_root:\n    root: /path/to/config.yaml" in output
 
 
 def test_config_add_ordered_dict(mutable_empty_config):
@@ -335,7 +335,7 @@ def test_config_add_override_leaf_from_file(mutable_empty_config, tmpdir):
 
 
 def test_config_add_update_dict_from_file(mutable_empty_config, tmpdir):
-    config("add", "packages:all:require:['%gcc']")
+    config("add", "packages:all:compiler:[gcc]")
 
     # contents to add to file
     contents = """spack:
@@ -357,7 +357,7 @@ def test_config_add_update_dict_from_file(mutable_empty_config, tmpdir):
     expected = """packages:
   all:
     target: [x86_64]
-    require: ['%gcc']
+    compiler: [gcc]
 """
 
     assert expected == output
@@ -606,6 +606,7 @@ def test_config_prefer_upstream(
     packages = syaml.load(open(cfg_file, encoding="utf-8"))["packages"]
 
     # Make sure only the non-default variants are set.
+    assert packages["all"] == {"compiler": ["gcc@=10.2.1"]}
     assert packages["boost"] == {"variants": "+debug +graph", "version": ["1.63.0"]}
     assert packages["dependency-install"] == {"version": ["2.0"]}
     # Ensure that neither variant gets listed for hdf5, since they conflict

lib/spack/spack/test/cmd/debug.py

@@ -2,16 +2,52 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
 import platform
 
+import pytest
+
 import spack
 import spack.platforms
 import spack.spec
+from spack.database import INDEX_JSON_FILE
 from spack.main import SpackCommand
+from spack.util.executable import which
 
 debug = SpackCommand("debug")
 
 
+@pytest.mark.db
+def test_create_db_tarball(tmpdir, database):
+    with tmpdir.as_cwd():
+        debug("create-db-tarball")
+
+        # get the first non-dotfile to avoid coverage files in the directory
+        files = os.listdir(os.getcwd())
+        tarball_name = next(
+            f for f in files if not f.startswith(".") and not f.startswith("tests")
+        )
+
+        # debug command made an archive
+        assert os.path.exists(tarball_name)
+
+        # print contents of archive
+        tar = which("tar")
+        contents = tar("tzf", tarball_name, output=str)
+
+        # DB file is included
+        assert INDEX_JSON_FILE in contents
+
+        # specfiles from all installs are included
+        for spec in database.query():
+            # externals won't have a specfile
+            if spec.external:
+                continue
+
+            spec_suffix = "%s/.spack/spec.json" % spec.dag_hash()
+            assert spec_suffix in contents
+
+
 def test_report():
     out = debug("report")
     host_platform = spack.platforms.host()

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

@@ -15,21 +15,18 @@
 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")
-    install("--fake", "libelf@0.8.10")
+    install("libelf@0.8.13")
+    install("libelf@0.8.10")
 
-    all_installed = spack.store.STORE.db.query("libelf")
+    all_installed = spack.store.STORE.db.query()
     assert len(all_installed) == 2
 
     deprecate("-y", "libelf@0.8.10", "libelf@0.8.13")
 
-    non_deprecated = spack.store.STORE.db.query("libelf")
-    all_available = spack.store.STORE.db.query("libelf", installed=InstallRecordStatus.ANY)
+    non_deprecated = spack.store.STORE.db.query()
+    all_available = spack.store.STORE.db.query(installed=InstallRecordStatus.ANY)
     assert all_available == all_installed
     assert non_deprecated == spack.store.STORE.db.query("libelf@0.8.13")
 
@@ -42,24 +39,24 @@ def test_deprecate_fails_no_such_package(mock_packages, mock_archive, mock_fetch
     output = deprecate("-y", "libelf@0.8.10", "libelf@0.8.13", fail_on_error=False)
     assert "Spec 'libelf@0.8.10' matches no installed packages" in output
 
-    install("--fake", "libelf@0.8.10")
+    install("libelf@0.8.10")
 
     output = deprecate("-y", "libelf@0.8.10", "libelf@0.8.13", fail_on_error=False)
     assert "Spec 'libelf@0.8.13' matches no installed packages" in output
 
 
-def test_deprecate_install(mock_packages, mock_archive, mock_fetch, install_mockery, monkeypatch):
-    """Tests that the -i option allows us to deprecate in favor of a spec
-    that is not yet installed.
-    """
-    install("--fake", "libelf@0.8.10")
-    to_deprecate = spack.store.STORE.db.query("libelf")
+def test_deprecate_install(mock_packages, mock_archive, mock_fetch, install_mockery):
+    """Tests that the ```-i`` option allows us to deprecate in favor of a spec
+    that is not yet installed."""
+    install("libelf@0.8.10")
+
+    to_deprecate = spack.store.STORE.db.query()
     assert len(to_deprecate) == 1
 
     deprecate("-y", "-i", "libelf@0.8.10", "libelf@0.8.13")
 
-    non_deprecated = spack.store.STORE.db.query("libelf")
-    deprecated = spack.store.STORE.db.query("libelf", installed=InstallRecordStatus.DEPRECATED)
+    non_deprecated = spack.store.STORE.db.query()
+    deprecated = spack.store.STORE.db.query(installed=InstallRecordStatus.DEPRECATED)
     assert deprecated == to_deprecate
     assert len(non_deprecated) == 1
     assert non_deprecated[0].satisfies("libelf@0.8.13")
@@ -67,8 +64,8 @@ def test_deprecate_install(mock_packages, mock_archive, mock_fetch, install_mock
 
 def test_deprecate_deps(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Test that the deprecate command deprecates all dependencies properly."""
-    install("--fake", "libdwarf@20130729 ^libelf@0.8.13")
-    install("--fake", "libdwarf@20130207 ^libelf@0.8.10")
+    install("libdwarf@20130729 ^libelf@0.8.13")
+    install("libdwarf@20130207 ^libelf@0.8.10")
 
     new_spec = spack.concretize.concretize_one("libdwarf@20130729^libelf@0.8.13")
     old_spec = spack.concretize.concretize_one("libdwarf@20130207^libelf@0.8.10")
@@ -84,14 +81,14 @@ def test_deprecate_deps(mock_packages, mock_archive, mock_fetch, install_mockery
     assert all_available == all_installed
     assert sorted(all_available) == sorted(deprecated + non_deprecated)
 
-    assert sorted(non_deprecated) == sorted(new_spec.traverse())
-    assert sorted(deprecated) == sorted([old_spec, old_spec["libelf"]])
+    assert sorted(non_deprecated) == sorted(list(new_spec.traverse()))
+    assert sorted(deprecated) == sorted(list(old_spec.traverse()))
 
 
 def test_uninstall_deprecated(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Tests that we can still uninstall deprecated packages."""
-    install("--fake", "libelf@0.8.13")
-    install("--fake", "libelf@0.8.10")
+    install("libelf@0.8.13")
+    install("libelf@0.8.10")
 
     deprecate("-y", "libelf@0.8.10", "libelf@0.8.13")
 
@@ -107,9 +104,9 @@ def test_uninstall_deprecated(mock_packages, mock_archive, mock_fetch, install_m
 
 def test_deprecate_already_deprecated(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Tests that we can re-deprecate a spec to change its deprecator."""
-    install("--fake", "libelf@0.8.13")
-    install("--fake", "libelf@0.8.12")
-    install("--fake", "libelf@0.8.10")
+    install("libelf@0.8.13")
+    install("libelf@0.8.12")
+    install("libelf@0.8.10")
 
     deprecated_spec = spack.concretize.concretize_one("libelf@0.8.10")
 
@@ -120,8 +117,8 @@ def test_deprecate_already_deprecated(mock_packages, mock_archive, mock_fetch, i
 
     deprecate("-y", "libelf@0.8.10", "libelf@0.8.13")
 
-    non_deprecated = spack.store.STORE.db.query("libelf")
-    all_available = spack.store.STORE.db.query("libelf", installed=InstallRecordStatus.ANY)
+    non_deprecated = spack.store.STORE.db.query()
+    all_available = spack.store.STORE.db.query(installed=InstallRecordStatus.ANY)
     assert len(non_deprecated) == 2
     assert len(all_available) == 3
 
@@ -132,9 +129,9 @@ def test_deprecate_already_deprecated(mock_packages, mock_archive, mock_fetch, i
 def test_deprecate_deprecator(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Tests that when a deprecator spec is deprecated, its deprecatee specs
     are updated to point to the new deprecator."""
-    install("--fake", "libelf@0.8.13")
-    install("--fake", "libelf@0.8.12")
-    install("--fake", "libelf@0.8.10")
+    install("libelf@0.8.13")
+    install("libelf@0.8.12")
+    install("libelf@0.8.10")
 
     first_deprecated_spec = spack.concretize.concretize_one("libelf@0.8.10")
     second_deprecated_spec = spack.concretize.concretize_one("libelf@0.8.12")
@@ -147,8 +144,8 @@ def test_deprecate_deprecator(mock_packages, mock_archive, mock_fetch, install_m
 
     deprecate("-y", "libelf@0.8.12", "libelf@0.8.13")
 
-    non_deprecated = spack.store.STORE.db.query("libelf")
-    all_available = spack.store.STORE.db.query("libelf", installed=InstallRecordStatus.ANY)
+    non_deprecated = spack.store.STORE.db.query()
+    all_available = spack.store.STORE.db.query(installed=InstallRecordStatus.ANY)
     assert len(non_deprecated) == 1
     assert len(all_available) == 3
 
@@ -161,8 +158,8 @@ def test_deprecate_deprecator(mock_packages, mock_archive, mock_fetch, install_m
 def test_concretize_deprecated(mock_packages, mock_archive, mock_fetch, install_mockery):
     """Tests that the concretizer throws an error if we concretize to a
     deprecated spec"""
-    install("--fake", "libelf@0.8.13")
-    install("--fake", "libelf@0.8.10")
+    install("libelf@0.8.13")
+    install("libelf@0.8.10")
 
     deprecate("-y", "libelf@0.8.10", "libelf@0.8.13")
 

lib/spack/spack/test/cmd/dev_build.py

@@ -127,15 +127,16 @@ def test_dev_build_before_until(tmpdir, install_mockery):
         assert not_installed in out
 
 
-def _print_spack_short_spec(*args):
-    print(f"SPACK_SHORT_SPEC={os.environ['SPACK_SHORT_SPEC']}")
+def print_spack_cc(*args):
+    # Eat arguments and print environment variable to test
+    print(os.environ.get("CC", ""))
 
 
 def test_dev_build_drop_in(tmpdir, mock_packages, monkeypatch, install_mockery, working_env):
-    monkeypatch.setattr(os, "execvp", _print_spack_short_spec)
+    monkeypatch.setattr(os, "execvp", print_spack_cc)
     with tmpdir.as_cwd():
         output = dev_build("-b", "edit", "--drop-in", "sh", "dev-build-test-install@0.0.0")
-        assert "SPACK_SHORT_SPEC=dev-build-test-install@0.0.0" in output
+        assert os.path.join("lib", "spack", "env") in output
 
 
 def test_dev_build_fails_already_installed(tmpdir, install_mockery):

lib/spack/spack/test/cmd/diff.py

@@ -194,7 +194,7 @@ def test_diff_cmd(install_mockery, mock_fetch, mock_archive, mock_packages):
 
 def test_load_first(install_mockery, mock_fetch, mock_archive, mock_packages):
     """Test with and without the --first option"""
-    install_cmd("--fake", "mpileaks")
+    install_cmd("mpileaks")
 
     # Only one version of mpileaks will work
     diff_cmd("mpileaks", "mpileaks")

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

@@ -1067,17 +1067,13 @@ 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):
-    """Ensure relative includes to files outside the environment fail."""
-    files = ["../outside_env/repos.yaml"]
+    files = ["../outside_env_not_copied/repos.yaml"]
 
     manifest = f"""
 spack:
   specs: []
-  include:
-  - path: {files[0]}
+  include: {files}
 """
 
     # subdir to ensure parent of environment dir is not shared
@@ -1090,7 +1086,7 @@ def test_init_from_yaml_relative_includes_outside_env(tmp_path):
     for f in files:
         fs.touchp(e1_path / f)
 
-    with pytest.raises(ValueError, match="does not exist"):
+    with pytest.raises(spack.config.ConfigFileError, match="Detected 1 missing include"):
         _ = _env_create("test2", init_file=e1_manifest)
 
 
@@ -1190,14 +1186,14 @@ def test_env_with_config(environment_from_manifest):
 
 
 def test_with_config_bad_include_create(environment_from_manifest):
-    """Confirm missing required include raises expected exception."""
-    err = "does not exist"
-    with pytest.raises(ValueError, match=err):
+    """Confirm missing include paths raise expected exception and error."""
+    with pytest.raises(spack.config.ConfigFileError, match="2 missing include path"):
         environment_from_manifest(
             """
 spack:
   include:
   - /no/such/directory
+  - no/such/file.yaml
 """
         )
 
@@ -1207,25 +1203,34 @@ 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 included config file (which does
-    # exist). Now we remove it and check that we get a sensible error.
+    # 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
 
+    os.remove(abs_include_path)
     os.remove(include1)
-    with pytest.raises(ValueError, match="does not exist"):
+    with pytest.raises(spack.config.ConfigFileError) as exc:
         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
 
 
@@ -1333,10 +1338,8 @@ 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 = env_path / included_file
+    included_path = tmp_path / included_file
     with open(included_path, "w", encoding="utf-8") as f:
         f.write(
             """\
@@ -1352,7 +1355,7 @@ def test_config_change_existing(mutable_mock_env_path, tmp_path, mock_packages,
 """
         )
 
-    spack_yaml = env_path / ev.manifest_name
+    spack_yaml = tmp_path / ev.manifest_name
     spack_yaml.write_text(
         f"""\
 spack:
@@ -1366,8 +1369,7 @@ def test_config_change_existing(mutable_mock_env_path, tmp_path, mock_packages,
 """
     )
 
-    mutable_config.set("config:misc_cache", str(tmp_path / "cache"))
-    e = ev.Environment(env_path)
+    e = ev.Environment(tmp_path)
     with e:
         # List of requirements, flip a variant
         config("change", "packages:mpich:require:~debug")
@@ -1457,6 +1459,19 @@ 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
@@ -1551,7 +1566,7 @@ def test_env_with_included_config_precedence(tmp_path):
 
 
 def test_env_with_included_configs_precedence(tmp_path):
-    """Test precedence of multiple included configuration files."""
+    """Test precendence of multiple included configuration files."""
     file1 = "high-config.yaml"
     file2 = "low-config.yaml"
 
@@ -1735,10 +1750,7 @@ def check_stage(spec):
         spec = spack.concretize.concretize_one(spec)
         for dep in spec.traverse():
             stage_name = f"{stage_prefix}{dep.name}-{dep.version}-{dep.dag_hash()}"
-            if dep.external:
-                assert not os.path.exists(os.path.join(root, stage_name))
-            else:
-                assert os.path.isdir(os.path.join(root, stage_name))
+            assert os.path.isdir(os.path.join(root, stage_name))
 
     check_stage("mpileaks")
     check_stage("zmpi")
@@ -1779,7 +1791,7 @@ 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):
@@ -3063,10 +3075,11 @@ def test_stack_view_activate_from_default(
         assert "FOOBAR=mpileaks" in shell
 
 
-def test_envvar_set_in_activate(tmp_path, mock_packages, install_mockery):
-    spack_yaml = tmp_path / "spack.yaml"
-    spack_yaml.write_text(
-        """
+def test_envvar_set_in_activate(tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery):
+    filename = str(tmpdir.join("spack.yaml"))
+    with open(filename, "w", encoding="utf-8") as f:
+        f.write(
+            """\
 spack:
   specs:
     - cmake%gcc
@@ -3074,21 +3087,21 @@ def test_envvar_set_in_activate(tmp_path, mock_packages, install_mockery):
     set:
       ENVAR_SET_IN_ENV_LOAD: "True"
 """
-    )
+        )
+    with tmpdir.as_cwd():
+        env("create", "test", "./spack.yaml")
+        with ev.read("test"):
+            install()
 
-    env("create", "test", str(spack_yaml))
-    with ev.read("test"):
-        install("--fake")
+        test_env = ev.read("test")
+        output = env("activate", "--sh", "test")
 
-    test_env = ev.read("test")
-    output = env("activate", "--sh", "test")
+        assert "ENVAR_SET_IN_ENV_LOAD=True" in output
 
-    assert "ENVAR_SET_IN_ENV_LOAD=True" in output
-
-    with test_env:
-        with spack.util.environment.set_env(ENVAR_SET_IN_ENV_LOAD="True"):
-            output = env("deactivate", "--sh")
-            assert "unset ENVAR_SET_IN_ENV_LOAD" in output
+        with test_env:
+            with spack.util.environment.set_env(ENVAR_SET_IN_ENV_LOAD="True"):
+                output = env("deactivate", "--sh")
+                assert "unset ENVAR_SET_IN_ENV_LOAD" in output
 
 
 def test_stack_view_no_activate_without_default(
@@ -4262,31 +4275,21 @@ 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_fetch_url_text, mock_curl_configs, mock_include_cache
+    tmpdir, mutable_empty_config, mock_spider_configs, mock_curl_configs
 ):
     """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(
-            f"""\
-spack:
-  include:
-  - path: {default_packages}
-    sha256: {sha256}
-"""
-        )
+        f.write("spack:\n  include:\n    - {0}\n".format(default_packages))
+    assert os.path.isfile(spack_yaml.strpath)
 
     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"]
 
@@ -4355,7 +4358,7 @@ 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_config, mutable_mock_env_path, first):
+def test_env_include_mixed_views(tmp_path, mutable_mock_env_path, mutable_config, 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

@@ -233,27 +233,21 @@ def test_display_json_deps(database, capsys):
 @pytest.mark.db
 def test_find_format(database, config):
     output = find("--format", "{name}-{^mpi.name}", "mpileaks")
-    assert set(output.strip().split("\n")) == {
-        "mpileaks-zmpi",
-        "mpileaks-mpich",
-        "mpileaks-mpich2",
-    }
+    assert set(output.strip().split("\n")) == set(
+        ["mpileaks-zmpi", "mpileaks-mpich", "mpileaks-mpich2"]
+    )
 
     output = find("--format", "{name}-{version}-{compiler.name}-{^mpi.name}", "mpileaks")
     assert "installed package" not in output
-    assert set(output.strip().split("\n")) == {
-        "mpileaks-2.3-gcc-zmpi",
-        "mpileaks-2.3-gcc-mpich",
-        "mpileaks-2.3-gcc-mpich2",
-    }
+    assert set(output.strip().split("\n")) == set(
+        ["mpileaks-2.3-gcc-zmpi", "mpileaks-2.3-gcc-mpich", "mpileaks-2.3-gcc-mpich2"]
+    )
 
     output = find("--format", "{name}-{^mpi.name}-{hash:7}", "mpileaks")
     elements = output.strip().split("\n")
-    assert set(e[:-7] for e in elements) == {
-        "mpileaks-zmpi-",
-        "mpileaks-mpich-",
-        "mpileaks-mpich2-",
-    }
+    assert set(e[:-7] for e in elements) == set(
+        ["mpileaks-zmpi-", "mpileaks-mpich-", "mpileaks-mpich2-"]
+    )
 
     # hashes are in base32
     for e in elements:
@@ -320,7 +314,7 @@ 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
@@ -354,7 +348,7 @@ def test_find_prefix_in_env(
     """Test `find` formats requiring concrete specs work in environments."""
     env("create", "test")
     with ev.read("test"):
-        install("--fake", "--add", "mpileaks")
+        install("--add", "mpileaks")
         find("-p")
         find("-l")
         find("-L")
@@ -464,7 +458,7 @@ 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

@@ -718,11 +718,10 @@ 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, mutable_mock_env_path, mock_fetch, install_mockery
+    tmpdir, mock_fetch, install_mockery, mutable_mock_env_path
 ):
     env("create", "test")
 
@@ -736,10 +735,9 @@ 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, mutable_mock_env_path, mock_fetch, install_mockery
+    tmpdir, mock_fetch, install_mockery, mutable_mock_env_path
 ):
     env("create", "--without-view", "test")
 
@@ -759,8 +757,7 @@ def test_install_only_dependencies_of_all_in_env(
                 assert os.path.exists(dep.prefix)
 
 
-# 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):
+def test_install_no_add_in_env(tmpdir, mock_fetch, install_mockery, mutable_mock_env_path):
     # To test behavior of --add option, we create the following environment:
     #
     #     mpileaks
@@ -901,6 +898,7 @@ 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")
@@ -935,10 +933,9 @@ 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, mutable_mock_env_path, mock_packages, mock_fetch, install_mockery
+    tmpdir, mock_packages, mock_fetch, install_mockery, mutable_mock_env_path
 ):
     env("create", "test")
     with ev.read("test"):
@@ -948,10 +945,9 @@ 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, mutable_mock_env_path, mock_packages, mock_fetch, install_mockery
+    tmpdir, mock_packages, mock_fetch, install_mockery, mutable_mock_env_path
 ):
     env("create", "test")
     with ev.read("test"):
@@ -961,10 +957,9 @@ 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, mutable_mock_env_path, mock_packages, mock_fetch, install_mockery
+    tmpdir, mock_packages, mock_fetch, install_mockery, mutable_mock_env_path
 ):
     env_name = "empty"
     env("create", env_name)
@@ -1000,17 +995,9 @@ 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,
-    mutable_mock_env_path,
-    mock_packages,
-    mock_fetch,
-    mock_archive,
-    mock_binary_index,
-    tmpdir,
-    install_mockery,
+    capsys, 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

@@ -12,9 +12,6 @@
 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

@@ -38,9 +38,8 @@ 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(mutable_mock_env_path, tmp_path, mock_packages, mock_fetch):
+def test_mirror_from_env(tmp_path, mock_packages, mock_fetch, mutable_mock_env_path):
     mirror_dir = str(tmp_path / "mirror")
     env_name = "test"
 
@@ -343,16 +342,8 @@ 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(
-    mutable_mock_env_path,
-    install_mockery,
-    mock_packages,
-    mock_fetch,
-    mock_archive,
-    mutable_config,
-    monkeypatch,
-    tmpdir,
+    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")