py-awkward: add v2.6.6 and py-awkward-cpp v35 (#46372)

* py-awkward: add v2.6.6 and py-awkward-cpp v35

* Add dependencies on python and numpy

* Add a conflict with GCC 14

* Move conflict to py-awkward-cpp

* py-awkward: 2.1.1 depends on py-awkward-cpp@12

---------

Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

.devcontainer/ubuntu20.04/devcontainer.json

@@ -1,4 +1,5 @@
 {
+  "name": "Ubuntu 20.04",
   "image": "ghcr.io/spack/ubuntu20.04-runner-amd64-gcc-11.4:2023.08.01",
   "postCreateCommand": "./.devcontainer/postCreateCommand.sh"
 }

.devcontainer/ubuntu22.04/devcontainer.json

@@ -0,0 +1,5 @@
+{
+  "name": "Ubuntu 22.04",
+  "image": "ghcr.io/spack/ubuntu-22.04:v2024-05-07",
+  "postCreateCommand": "./.devcontainer/postCreateCommand.sh"
+}

.github/workflows/audit.yaml

@@ -29,7 +29,7 @@ jobs:
         shell: ${{ matrix.system.shell }}
     steps:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: ${{inputs.python_version}}
     - name: Install Python packages

.github/workflows/bootstrap.yml

@@ -63,7 +63,7 @@ jobs:
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
         with:
           python-version: "3.12"
       - name: Bootstrap clingo
@@ -112,10 +112,10 @@ jobs:
     runs-on: ${{ matrix.runner }}
     strategy:
       matrix:
-        runner: ['macos-13', 'macos-14', "ubuntu-latest"]
+        runner: ['macos-13', 'macos-14', "ubuntu-latest", "windows-latest"]
     steps:
       - name: Setup macOS
-        if: ${{ matrix.runner != 'ubuntu-latest' }}
+        if: ${{ matrix.runner != 'ubuntu-latest' && matrix.runner != 'windows-latest'}}
         run: |
           brew install tree
           # Remove GnuPG since we want to bootstrap it
@@ -124,11 +124,16 @@ jobs:
         if: ${{ matrix.runner == 'ubuntu-latest' }}
         run: |
           sudo rm -rf $(which gpg) $(which gpg2) $(which patchelf)
+      - name: Setup Windows
+        if: ${{ matrix.runner == 'windows-latest' }}
+        run: |
+          Remove-Item -Path (Get-Command gpg).Path
+          Remove-Item -Path (Get-Command file).Path
       - name: Checkout
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
         with:
           python-version: |
             3.8
@@ -137,11 +142,20 @@ jobs:
             3.11
             3.12
       - name: Set bootstrap sources
+        env:
+          SETUP_SCRIPT_EXT: ${{ matrix.runner == 'windows-latest' && 'ps1' || 'sh' }}
+          SETUP_SCRIPT_SOURCE: ${{ matrix.runner == 'windows-latest' && './' || 'source ' }}
+        run: |
+          ${{ env.SETUP_SCRIPT_SOURCE }}share/spack/setup-env.${{ env.SETUP_SCRIPT_EXT }}
+          spack bootstrap disable github-actions-v0.4
+      - name: Disable from source bootstrap
+        if: ${{ matrix.runner != 'windows-latest' }}
         run: |
           source share/spack/setup-env.sh
-          spack bootstrap disable github-actions-v0.4
           spack bootstrap disable spack-install
       - name: Bootstrap clingo
+        # No binary clingo on Windows yet
+        if: ${{ matrix.runner != 'windows-latest' }}
         run: |
           set -e
           for ver in '3.8' '3.9' '3.10' '3.11' '3.12' ; do
@@ -164,7 +178,24 @@ jobs:
             fi
           done
       - name: Bootstrap GnuPG
+        env:
+          SETUP_SCRIPT_EXT: ${{ matrix.runner == 'windows-latest' && 'ps1' || 'sh' }}
+          SETUP_SCRIPT_SOURCE: ${{ matrix.runner == 'windows-latest' && './' || 'source ' }}
+          USER_SCOPE_PARENT_DIR: ${{ matrix.runner == 'windows-latest' && '$env:userprofile' || '$HOME' }}
+          VALIDATE_LAST_EXIT: ${{ matrix.runner == 'windows-latest' && './share/spack/qa/validate_last_exit.ps1' || '' }}
         run: |
-          source share/spack/setup-env.sh
+          ${{ env.SETUP_SCRIPT_SOURCE }}share/spack/setup-env.${{ env.SETUP_SCRIPT_EXT }}
           spack -d gpg list
-          tree ~/.spack/bootstrap/store/
+          ${{ env.VALIDATE_LAST_EXIT }}
+          tree ${{ env.USER_SCOPE_PARENT_DIR }}/.spack/bootstrap/store/
+      - name: Bootstrap File
+        env:
+          SETUP_SCRIPT_EXT: ${{ matrix.runner == 'windows-latest' && 'ps1' || 'sh' }}
+          SETUP_SCRIPT_SOURCE: ${{ matrix.runner == 'windows-latest' && './' || 'source ' }}
+          USER_SCOPE_PARENT_DIR: ${{ matrix.runner == 'windows-latest' && '$env:userprofile' || '$HOME' }}
+          VALIDATE_LAST_EXIT: ${{ matrix.runner == 'windows-latest' && './share/spack/qa/validate_last_exit.ps1' || '' }}
+        run: |
+          ${{ env.SETUP_SCRIPT_SOURCE }}share/spack/setup-env.${{ env.SETUP_SCRIPT_EXT }}
+          spack -d python share/spack/qa/bootstrap-file.py
+          ${{ env.VALIDATE_LAST_EXIT }}
+          tree ${{ env.USER_SCOPE_PARENT_DIR }}/.spack/bootstrap/store/

.github/workflows/build-containers.yml

@@ -87,7 +87,7 @@ jobs:
           fi
 
       - name: Upload Dockerfile
-        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a
+        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874
         with:
           name: dockerfiles_${{ matrix.dockerfile[0] }}
           path: dockerfiles
@@ -126,7 +126,7 @@ jobs:
     needs: deploy-images
     steps:
       - name: Merge Artifacts
-        uses: actions/upload-artifact/merge@834a144ee995460fba8ed112a2fc961b36a5ec5a
+        uses: actions/upload-artifact/merge@50769540e7f4bd5e21e526ee35c689e35e0d6874
         with:
           name: dockerfiles
           pattern: dockerfiles_*

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

@@ -17,7 +17,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: 3.9
     - name: Install Python packages

.github/workflows/unit_tests.yaml

@@ -43,7 +43,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install System packages
@@ -91,7 +91,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: '3.11'
     - name: Install System packages
@@ -151,7 +151,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: '3.11'
     - name: Install System packages
@@ -188,7 +188,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Python packages
@@ -225,7 +225,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: 3.9
     - name: Install Python packages

.github/workflows/valid-style.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: '3.11'
         cache: 'pip'
@@ -38,7 +38,7 @@ jobs:
     - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332
       with:
         fetch-depth: 0
-    - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f
+    - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3
       with:
         python-version: '3.11'
         cache: 'pip'

etc/spack/defaults/config.yaml

@@ -115,12 +115,6 @@ config:
   suppress_gpg_warnings: false
 
 
-  # If set to true, Spack will attempt to build any compiler on the spec
-  # that is not already available. If set to False, Spack will only use
-  # compilers already configured in compilers.yaml
-  install_missing_compilers: false
-
-
   # If set to true, Spack will always check checksums after downloading
   # archives. If false, Spack skips the checksum step.
   checksum: true

etc/spack/defaults/packages.yaml

@@ -72,3 +72,13 @@ packages:
     permissions:
       read: world
       write: user
+  cray-mpich:
+    buildable: false
+  cray-mvapich2:
+    buildable: false
+  fujitsu-mpi:
+    buildable: false
+  hpcx-mpi:
+    buildable: false
+  spectrum-mpi:
+    buildable: false

lib/spack/docs/conf.py

@@ -218,6 +218,7 @@ def setup(sphinx):
     ("py:class", "spack.spec.SpecfileReaderBase"),
     ("py:class", "spack.install_test.Pb"),
     ("py:class", "spack.filesystem_view.SimpleFilesystemView"),
+    ("py:class", "spack.traverse.EdgeAndDepth"),
 ]
 
 # The reST default role (used for this markup: `text`) to use for all documents.

lib/spack/docs/developer_guide.rst

@@ -181,10 +181,6 @@ Spec-related modules
 :mod:`spack.parser`
   Contains :class:`~spack.parser.SpecParser` and functions related to parsing specs.
 
-:mod:`spack.concretize`
-  Contains :class:`~spack.concretize.Concretizer` implementation,
-  which allows site administrators to change Spack's :ref:`concretization-policies`.
-
 :mod:`spack.version`
   Implements a simple :class:`~spack.version.Version` class with simple
   comparison semantics.  Also implements :class:`~spack.version.VersionRange`

lib/spack/docs/environments.rst

@@ -863,7 +863,7 @@ named list ``compilers`` is ``['%gcc', '%clang', '%intel']`` on
    spack:
      definitions:
        - compilers: ['%gcc', '%clang']
-       - when: arch.satisfies('x86_64:')
+       - when: arch.satisfies('target=x86_64:')
          compilers: ['%intel']
 
 .. note::

lib/spack/docs/pipelines.rst

@@ -663,11 +663,7 @@ build the package.
 
 When including a bootstrapping phase as in the example above, the result is that
 the bootstrapped compiler packages will be pushed to the binary mirror (and the
-local artifacts mirror) before the actual release specs are built. In this case,
-the jobs corresponding to subsequent release specs are configured to
-``install_missing_compilers``, so that if spack is asked to install a package
-with a compiler it doesn't know about, it can be quickly installed from the
-binary mirror first.
+local artifacts mirror) before the actual release specs are built.
 
 Since bootstrapping compilers is optional, those items can be left out of the
 environment/stack file, and in that case no bootstrapping will be done (only the

lib/spack/docs/requirements.txt

@@ -5,8 +5,8 @@ sphinx-rtd-theme==2.0.0
 python-levenshtein==0.25.1
 docutils==0.20.1
 pygments==2.18.0
-urllib3==2.2.2
-pytest==8.3.2
+urllib3==2.2.3
+pytest==8.3.3
 isort==5.13.2
 black==24.8.0
 flake8==7.1.1

lib/spack/llnl/util/filesystem.py

@@ -27,8 +27,6 @@
 from llnl.util.lang import dedupe, memoized
 from llnl.util.symlink import islink, readlink, resolve_link_target_relative_to_the_link, symlink
 
-from spack.util.executable import Executable, which
-
 from ..path import path_to_os_path, system_path_filter
 
 if sys.platform != "win32":
@@ -53,7 +51,6 @@
     "find_all_headers",
     "find_libraries",
     "find_system_libraries",
-    "fix_darwin_install_name",
     "force_remove",
     "force_symlink",
     "getuid",
@@ -248,42 +245,6 @@ def path_contains_subdirectory(path, root):
     return norm_path.startswith(norm_root)
 
 
-@memoized
-def file_command(*args):
-    """Creates entry point to `file` system command with provided arguments"""
-    file_cmd = which("file", required=True)
-    for arg in args:
-        file_cmd.add_default_arg(arg)
-    return file_cmd
-
-
-@memoized
-def _get_mime_type():
-    """Generate method to call `file` system command to aquire mime type
-    for a specified path
-    """
-    if sys.platform == "win32":
-        # -h option (no-dereference) does not exist in Windows
-        return file_command("-b", "--mime-type")
-    else:
-        return file_command("-b", "-h", "--mime-type")
-
-
-def mime_type(filename):
-    """Returns the mime type and subtype of a file.
-
-    Args:
-        filename: file to be analyzed
-
-    Returns:
-        Tuple containing the MIME type and subtype
-    """
-    output = _get_mime_type()(filename, output=str, error=str).strip()
-    tty.debug("==> " + output)
-    type, _, subtype = output.partition("/")
-    return type, subtype
-
-
 #: This generates the library filenames that may appear on any OS.
 library_extensions = ["a", "la", "so", "tbd", "dylib"]
 
@@ -1679,41 +1640,6 @@ def safe_remove(*files_or_dirs):
         raise
 
 
-@system_path_filter
-def fix_darwin_install_name(path):
-    """Fix install name of dynamic libraries on Darwin to have full path.
-
-    There are two parts of this task:
-
-    1. Use ``install_name('-id', ...)`` to change install name of a single lib
-    2. Use ``install_name('-change', ...)`` to change the cross linking between
-       libs. The function assumes that all libraries are in one folder and
-       currently won't follow subfolders.
-
-    Parameters:
-        path (str): directory in which .dylib files are located
-    """
-    libs = glob.glob(join_path(path, "*.dylib"))
-    for lib in libs:
-        # fix install name first:
-        install_name_tool = Executable("install_name_tool")
-        install_name_tool("-id", lib, lib)
-        otool = Executable("otool")
-        long_deps = otool("-L", lib, output=str).split("\n")
-        deps = [dep.partition(" ")[0][1::] for dep in long_deps[2:-1]]
-        # fix all dependencies:
-        for dep in deps:
-            for loc in libs:
-                # We really want to check for either
-                #     dep == os.path.basename(loc)   or
-                #     dep == join_path(builddir, os.path.basename(loc)),
-                # but we don't know builddir (nor how symbolic links look
-                # in builddir). We thus only compare the basenames.
-                if os.path.basename(dep) == os.path.basename(loc):
-                    install_name_tool("-change", dep, loc, lib)
-                    break
-
-
 def find_first(root: str, files: Union[Iterable[str], str], bfs_depth: int = 2) -> Optional[str]:
     """Find the first file matching a pattern.
 

lib/spack/spack/audit.py

@@ -46,12 +46,14 @@ def _search_duplicate_compilers(error_cls):
 import pickle
 import re
 import warnings
+from typing import Iterable, List, Set, Tuple
 from urllib.request import urlopen
 
 import llnl.util.lang
 
 import spack.config
 import spack.patch
+import spack.paths
 import spack.repo
 import spack.spec
 import spack.util.crypto
@@ -73,7 +75,9 @@ def __init__(self, summary, details):
         self.details = tuple(details)
 
     def __str__(self):
-        return self.summary + "\n" + "\n".join(["    " + detail for detail in self.details])
+        if self.details:
+            return f"{self.summary}\n" + "\n".join(f"    {detail}" for detail in self.details)
+        return self.summary
 
     def __eq__(self, other):
         if self.summary != other.summary or self.details != other.details:
@@ -257,40 +261,6 @@ def _search_duplicate_specs_in_externals(error_cls):
     return errors
 
 
-@config_packages
-def _deprecated_preferences(error_cls):
-    """Search package preferences deprecated in v0.21 (and slated for removal in v0.23)"""
-    # TODO (v0.23): remove this audit as the attributes will not be allowed in config
-    errors = []
-    packages_yaml = spack.config.CONFIG.get_config("packages")
-
-    def make_error(attribute_name, config_data, summary):
-        s = io.StringIO()
-        s.write("Occurring in the following file:\n")
-        dict_view = syaml.syaml_dict((k, v) for k, v in config_data.items() if k == attribute_name)
-        syaml.dump_config(dict_view, stream=s, blame=True)
-        return error_cls(summary=summary, details=[s.getvalue()])
-
-    if "all" in packages_yaml and "version" in packages_yaml["all"]:
-        summary = "Using the deprecated 'version' attribute under 'packages:all'"
-        errors.append(make_error("version", packages_yaml["all"], summary))
-
-    for package_name in packages_yaml:
-        if package_name == "all":
-            continue
-
-        package_conf = packages_yaml[package_name]
-        for attribute in ("compiler", "providers", "target"):
-            if attribute not in package_conf:
-                continue
-            summary = (
-                f"Using the deprecated '{attribute}' attribute " f"under 'packages:{package_name}'"
-            )
-            errors.append(make_error(attribute, package_conf, summary))
-
-    return errors
-
-
 @config_packages
 def _avoid_mismatched_variants(error_cls):
     """Warns if variant preferences have mismatched types or names."""
@@ -713,6 +683,88 @@ def _ensure_env_methods_are_ported_to_builders(pkgs, error_cls):
     return errors
 
 
+class DeprecatedMagicGlobals(ast.NodeVisitor):
+    def __init__(self, magic_globals: Iterable[str]):
+        super().__init__()
+
+        self.magic_globals: Set[str] = set(magic_globals)
+
+        # State to track whether we're in a class function
+        self.depth: int = 0
+        self.in_function: bool = False
+        self.path = (ast.Module, ast.ClassDef, ast.FunctionDef)
+
+        # Defined locals in the current function (heuristically at least)
+        self.locals: Set[str] = set()
+
+        # List of (name, lineno) tuples for references to magic globals
+        self.references_to_globals: List[Tuple[str, int]] = []
+
+    def descend_in_function_def(self, node: ast.AST) -> None:
+        if not isinstance(node, self.path[self.depth]):
+            return
+        self.depth += 1
+        if self.depth == len(self.path):
+            self.in_function = True
+        super().generic_visit(node)
+        if self.depth == len(self.path):
+            self.in_function = False
+            self.locals.clear()
+        self.depth -= 1
+
+    def generic_visit(self, node: ast.AST) -> None:
+        # Recurse into function definitions
+        if self.depth < len(self.path):
+            return self.descend_in_function_def(node)
+        elif not self.in_function:
+            return
+        elif isinstance(node, ast.Global):
+            for name in node.names:
+                if name in self.magic_globals:
+                    self.references_to_globals.append((name, node.lineno))
+        elif isinstance(node, ast.Assign):
+            # visit the rhs before lhs
+            super().visit(node.value)
+            for target in node.targets:
+                super().visit(target)
+        elif isinstance(node, ast.Name) and node.id in self.magic_globals:
+            if isinstance(node.ctx, ast.Load) and node.id not in self.locals:
+                self.references_to_globals.append((node.id, node.lineno))
+            elif isinstance(node.ctx, ast.Store):
+                self.locals.add(node.id)
+        else:
+            super().generic_visit(node)
+
+
+@package_properties
+def _uses_deprecated_globals(pkgs, error_cls):
+    """Ensure that packages do not use deprecated globals"""
+    errors = []
+
+    for pkg_name in pkgs:
+        # some packages scheduled to be removed in v0.23 are not worth fixing.
+        pkg_cls = spack.repo.PATH.get_pkg_class(pkg_name)
+        if all(v.get("deprecated", False) for v in pkg_cls.versions.values()):
+            continue
+
+        file = spack.repo.PATH.filename_for_package_name(pkg_name)
+        tree = ast.parse(open(file).read())
+        visitor = DeprecatedMagicGlobals(("std_cmake_args",))
+        visitor.visit(tree)
+        if visitor.references_to_globals:
+            errors.append(
+                error_cls(
+                    f"Package '{pkg_name}' uses deprecated globals",
+                    [
+                        f"{file}:{line} references '{name}'"
+                        for name, line in visitor.references_to_globals
+                    ],
+                )
+            )
+
+    return errors
+
+
 @package_https_directives
 def _linting_package_file(pkgs, error_cls):
     """Check for correctness of links"""

lib/spack/spack/binary_distribution.py

@@ -54,6 +54,7 @@
 import spack.util.archive
 import spack.util.crypto
 import spack.util.file_cache as file_cache
+import spack.util.filesystem as ssys
 import spack.util.gpg
 import spack.util.parallel
 import spack.util.path
@@ -105,7 +106,7 @@ class BuildCacheDatabase(spack_db.Database):
     record_fields = ("spec", "ref_count", "in_buildcache")
 
     def __init__(self, root):
-        super().__init__(root, lock_cfg=spack_db.NO_LOCK)
+        super().__init__(root, lock_cfg=spack_db.NO_LOCK, layout=None)
         self._write_transaction_impl = llnl.util.lang.nullcontext
         self._read_transaction_impl = llnl.util.lang.nullcontext
 
@@ -687,7 +688,7 @@ def get_buildfile_manifest(spec):
     # Non-symlinks.
     for rel_path in visitor.files:
         abs_path = os.path.join(root, rel_path)
-        m_type, m_subtype = fsys.mime_type(abs_path)
+        m_type, m_subtype = ssys.mime_type(abs_path)
 
         if relocate.needs_binary_relocation(m_type, m_subtype):
             # Why is this branch not part of needs_binary_relocation? :(
@@ -788,7 +789,9 @@ def sign_specfile(key: str, specfile_path: str) -> str:
     return signed_specfile_path
 
 
-def _read_specs_and_push_index(file_list, read_method, cache_prefix, db, temp_dir, concurrency):
+def _read_specs_and_push_index(
+    file_list, read_method, cache_prefix, db: BuildCacheDatabase, temp_dir, concurrency
+):
     """Read all the specs listed in the provided list, using thread given thread parallelism,
         generate the index, and push it to the mirror.
 
@@ -812,7 +815,7 @@ def _read_specs_and_push_index(file_list, read_method, cache_prefix, db, temp_di
         else:
             continue
 
-        db.add(fetched_spec, None)
+        db.add(fetched_spec)
         db.mark(fetched_spec, "in_buildcache", True)
 
     # Now generate the index, compute its hash, and push the two files to
@@ -1765,7 +1768,7 @@ def _oci_update_index(
 
     for spec_dict in spec_dicts:
         spec = Spec.from_dict(spec_dict)
-        db.add(spec, directory_layout=None)
+        db.add(spec)
         db.mark(spec, "in_buildcache", True)
 
     # Create the index.json file
@@ -2562,7 +2565,7 @@ def install_root_node(spec, unsigned=False, force=False, sha256=None):
         tty.msg('Installing "{0}" from a buildcache'.format(spec.format()))
         extract_tarball(spec, download_result, force)
         spack.hooks.post_install(spec, False)
-        spack.store.STORE.db.add(spec, spack.store.STORE.layout)
+        spack.store.STORE.db.add(spec)
 
 
 def install_single_spec(spec, unsigned=False, force=False):

lib/spack/spack/bootstrap/__init__.py

@@ -9,6 +9,7 @@
     all_core_root_specs,
     ensure_clingo_importable_or_raise,
     ensure_core_dependencies,
+    ensure_file_in_path_or_raise,
     ensure_gpg_in_path_or_raise,
     ensure_patchelf_in_path_or_raise,
 )
@@ -19,6 +20,7 @@
     "is_bootstrapping",
     "ensure_bootstrap_configuration",
     "ensure_core_dependencies",
+    "ensure_file_in_path_or_raise",
     "ensure_gpg_in_path_or_raise",
     "ensure_clingo_importable_or_raise",
     "ensure_patchelf_in_path_or_raise",

lib/spack/spack/bootstrap/core.py

@@ -472,7 +472,8 @@ def ensure_clingo_importable_or_raise() -> None:
 
 def gnupg_root_spec() -> str:
     """Return the root spec used to bootstrap GnuPG"""
-    return _root_spec("gnupg@2.3:")
+    root_spec_name = "win-gpg" if IS_WINDOWS else "gnupg"
+    return _root_spec(f"{root_spec_name}@2.3:")
 
 
 def ensure_gpg_in_path_or_raise() -> None:
@@ -482,6 +483,19 @@ def ensure_gpg_in_path_or_raise() -> None:
     )
 
 
+def file_root_spec() -> str:
+    """Return the root spec used to bootstrap file"""
+    root_spec_name = "win-file" if IS_WINDOWS else "file"
+    return _root_spec(root_spec_name)
+
+
+def ensure_file_in_path_or_raise() -> None:
+    """Ensure file is in the PATH or raise"""
+    return ensure_executables_in_path_or_raise(
+        executables=["file"], abstract_spec=file_root_spec()
+    )
+
+
 def patchelf_root_spec() -> str:
     """Return the root spec used to bootstrap patchelf"""
     # 0.13.1 is the last version not to require C++17.
@@ -565,14 +579,15 @@ def ensure_core_dependencies() -> None:
     """Ensure the presence of all the core dependencies."""
     if sys.platform.lower() == "linux":
         ensure_patchelf_in_path_or_raise()
-    if not IS_WINDOWS:
-        ensure_gpg_in_path_or_raise()
+    elif sys.platform == "win32":
+        ensure_file_in_path_or_raise()
+    ensure_gpg_in_path_or_raise()
     ensure_clingo_importable_or_raise()
 
 
 def all_core_root_specs() -> List[str]:
     """Return a list of all the core root specs that may be used to bootstrap Spack"""
-    return [clingo_root_spec(), gnupg_root_spec(), patchelf_root_spec()]
+    return [clingo_root_spec(), gnupg_root_spec(), patchelf_root_spec(), file_root_spec()]
 
 
 def bootstrapping_sources(scope: Optional[str] = None):

lib/spack/spack/bootstrap/status.py

@@ -88,7 +88,7 @@ def _core_requirements() -> List[RequiredResponseType]:
 
 def _buildcache_requirements() -> List[RequiredResponseType]:
     _buildcache_exes = {
-        "file": _missing("file", "required to analyze files for buildcaches"),
+        "file": _missing("file", "required to analyze files for buildcaches", system_only=False),
         ("gpg2", "gpg"): _missing("gpg2", "required to sign/verify buildcaches", False),
     }
     if platform.system().lower() == "darwin":

lib/spack/spack/build_environment.py

@@ -1553,21 +1553,21 @@ class ModuleChangePropagator:
 
     _PROTECTED_NAMES = ("package", "current_module", "modules_in_mro", "_set_attributes")
 
-    def __init__(self, package):
+    def __init__(self, package: spack.package_base.PackageBase) -> None:
         self._set_self_attributes("package", package)
         self._set_self_attributes("current_module", package.module)
 
         #: Modules for the classes in the MRO up to PackageBase
         modules_in_mro = []
-        for cls in type(package).__mro__:
-            module = cls.module
+        for cls in package.__class__.__mro__:
+            module = getattr(cls, "module", None)
 
-            if module == self.current_module:
-                continue
-
-            if module == spack.package_base:
+            if module is None or module is spack.package_base:
                 break
 
+            if module is self.current_module:
+                continue
+
             modules_in_mro.append(module)
         self._set_self_attributes("modules_in_mro", modules_in_mro)
         self._set_self_attributes("_set_attributes", {})

lib/spack/spack/build_systems/autotools.py

@@ -2,7 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
 import os
 import os.path
 import stat
@@ -549,13 +548,12 @@ def autoreconf(self, pkg, spec, prefix):
         tty.warn("*        a custom AUTORECONF phase in the package       *")
         tty.warn("*********************************************************")
         with fs.working_dir(self.configure_directory):
-            m = inspect.getmodule(self.pkg)
             # This line is what is needed most of the time
             # --install, --verbose, --force
             autoreconf_args = ["-ivf"]
             autoreconf_args += self.autoreconf_search_path_args
             autoreconf_args += self.autoreconf_extra_args
-            m.autoreconf(*autoreconf_args)
+            self.pkg.module.autoreconf(*autoreconf_args)
 
     @property
     def autoreconf_search_path_args(self):
@@ -579,7 +577,9 @@ def set_configure_or_die(self):
             raise RuntimeError(msg.format(self.configure_directory))
 
         # Monkey-patch the configure script in the corresponding module
-        inspect.getmodule(self.pkg).configure = Executable(self.configure_abs_path)
+        globals_for_pkg = spack.build_environment.ModuleChangePropagator(self.pkg)
+        globals_for_pkg.configure = Executable(self.configure_abs_path)
+        globals_for_pkg.propagate_changes_to_mro()
 
     def configure_args(self):
         """Return the list of all the arguments that must be passed to configure,
@@ -596,7 +596,7 @@ def configure(self, pkg, spec, prefix):
         options += self.configure_args()
 
         with fs.working_dir(self.build_directory, create=True):
-            inspect.getmodule(self.pkg).configure(*options)
+            pkg.module.configure(*options)
 
     def build(self, pkg, spec, prefix):
         """Run "make" on the build targets specified by the builder."""
@@ -604,12 +604,12 @@ def build(self, pkg, spec, prefix):
         params = ["V=1"]
         params += self.build_targets
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).make(*params)
+            pkg.module.make(*params)
 
     def install(self, pkg, spec, prefix):
         """Run "make" on the install targets specified by the builder."""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).make(*self.install_targets)
+            pkg.module.make(*self.install_targets)
 
     spack.builder.run_after("build")(execute_build_time_tests)
 

lib/spack/spack/build_systems/cargo.py

@@ -3,8 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import inspect
-
 import llnl.util.filesystem as fs
 
 import spack.builder
@@ -72,9 +70,7 @@ def check_args(self):
     def build(self, pkg, spec, prefix):
         """Runs ``cargo install`` in the source directory"""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(pkg).cargo(
-                "install", "--root", "out", "--path", ".", *self.build_args
-            )
+            pkg.module.cargo("install", "--root", "out", "--path", ".", *self.build_args)
 
     def install(self, pkg, spec, prefix):
         """Copy build files into package prefix."""
@@ -86,4 +82,4 @@ def install(self, pkg, spec, prefix):
     def check(self):
         """Run "cargo test"."""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).cargo("test", *self.check_args)
+            self.pkg.module.cargo("test", *self.check_args)

lib/spack/spack/build_systems/cmake.py

@@ -3,7 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import collections.abc
-import inspect
 import os
 import pathlib
 import platform
@@ -544,24 +543,24 @@ def cmake(self, pkg, spec, prefix):
         options += self.cmake_args()
         options.append(os.path.abspath(self.root_cmakelists_dir))
         with fs.working_dir(self.build_directory, create=True):
-            inspect.getmodule(self.pkg).cmake(*options)
+            pkg.module.cmake(*options)
 
     def build(self, pkg, spec, prefix):
         """Make the build targets"""
         with fs.working_dir(self.build_directory):
             if self.generator == "Unix Makefiles":
-                inspect.getmodule(self.pkg).make(*self.build_targets)
+                pkg.module.make(*self.build_targets)
             elif self.generator == "Ninja":
                 self.build_targets.append("-v")
-                inspect.getmodule(self.pkg).ninja(*self.build_targets)
+                pkg.module.ninja(*self.build_targets)
 
     def install(self, pkg, spec, prefix):
         """Make the install targets"""
         with fs.working_dir(self.build_directory):
             if self.generator == "Unix Makefiles":
-                inspect.getmodule(self.pkg).make(*self.install_targets)
+                pkg.module.make(*self.install_targets)
             elif self.generator == "Ninja":
-                inspect.getmodule(self.pkg).ninja(*self.install_targets)
+                pkg.module.ninja(*self.install_targets)
 
     spack.builder.run_after("build")(execute_build_time_tests)
 

lib/spack/spack/build_systems/cuda.py

@@ -3,6 +3,9 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import re
+from typing import Iterable, List
+
 import spack.variant
 from spack.directives import conflicts, depends_on, variant
 from spack.multimethod import when
@@ -44,6 +47,7 @@ class CudaPackage(PackageBase):
         "87",
         "89",
         "90",
+        "90a",
     )
 
     # FIXME: keep cuda and cuda_arch separate to make usage easier until
@@ -70,6 +74,27 @@ def cuda_flags(arch_list):
             for s in arch_list
         ]
 
+    @staticmethod
+    def compute_capabilities(arch_list: Iterable[str]) -> List[str]:
+        """Adds a decimal place to each CUDA arch.
+
+        >>> compute_capabilities(['90', '90a'])
+        ['9.0', '9.0a']
+
+        Args:
+            arch_list: A list of integer strings, optionally followed by a suffix.
+
+        Returns:
+            A list of float strings, optionally followed by a suffix
+        """
+        pattern = re.compile(r"(\d+)")
+        capabilities = []
+        for arch in arch_list:
+            _, number, letter = re.split(pattern, arch)
+            number = "{0:.1f}".format(float(number) / 10.0)
+            capabilities.append(number + letter)
+        return capabilities
+
     depends_on("cuda", when="+cuda")
 
     # CUDA version vs Architecture
@@ -145,7 +170,8 @@ def cuda_flags(arch_list):
         conflicts("%clang@15:", when="+cuda ^cuda@:12.0")
         conflicts("%clang@16:", when="+cuda ^cuda@:12.1")
         conflicts("%clang@17:", when="+cuda ^cuda@:12.3")
-        conflicts("%clang@18:", when="+cuda ^cuda@:12.6")
+        conflicts("%clang@18:", when="+cuda ^cuda@:12.5")
+        conflicts("%clang@19:", when="+cuda ^cuda@:12.6")
 
         # https://gist.github.com/ax3l/9489132#gistcomment-3860114
         conflicts("%gcc@10", when="+cuda ^cuda@:11.4.0")

lib/spack/spack/build_systems/go.py

@@ -3,8 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import inspect
-
 import llnl.util.filesystem as fs
 
 import spack.builder
@@ -82,7 +80,7 @@ def check_args(self):
     def build(self, pkg, spec, prefix):
         """Runs ``go build`` in the source directory"""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(pkg).go("build", *self.build_args)
+            pkg.module.go("build", *self.build_args)
 
     def install(self, pkg, spec, prefix):
         """Install built binaries into prefix bin."""
@@ -95,4 +93,4 @@ def install(self, pkg, spec, prefix):
     def check(self):
         """Run ``go test .`` in the source directory"""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).go("test", *self.check_args)
+            self.pkg.module.go("test", *self.check_args)

lib/spack/spack/build_systems/makefile.py

@@ -2,7 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
 from typing import List
 
 import llnl.util.filesystem as fs
@@ -103,12 +102,12 @@ def edit(self, pkg, spec, prefix):
     def build(self, pkg, spec, prefix):
         """Run "make" on the build targets specified by the builder."""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).make(*self.build_targets)
+            pkg.module.make(*self.build_targets)
 
     def install(self, pkg, spec, prefix):
         """Run "make" on the install targets specified by the builder."""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).make(*self.install_targets)
+            pkg.module.make(*self.install_targets)
 
     spack.builder.run_after("build")(execute_build_time_tests)
 

lib/spack/spack/build_systems/meson.py

@@ -2,7 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
 import os
 from typing import List
 
@@ -195,19 +194,19 @@ def meson(self, pkg, spec, prefix):
         options += self.std_meson_args
         options += self.meson_args()
         with fs.working_dir(self.build_directory, create=True):
-            inspect.getmodule(self.pkg).meson(*options)
+            pkg.module.meson(*options)
 
     def build(self, pkg, spec, prefix):
         """Make the build targets"""
         options = ["-v"]
         options += self.build_targets
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).ninja(*options)
+            pkg.module.ninja(*options)
 
     def install(self, pkg, spec, prefix):
         """Make the install targets"""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).ninja(*self.install_targets)
+            pkg.module.ninja(*self.install_targets)
 
     spack.builder.run_after("build")(execute_build_time_tests)
 

lib/spack/spack/build_systems/msbuild.py

@@ -2,7 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
 from typing import List  # novm
 
 import llnl.util.filesystem as fs
@@ -104,7 +103,7 @@ def msbuild_install_args(self):
     def build(self, pkg, spec, prefix):
         """Run "msbuild" on the build targets specified by the builder."""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).msbuild(
+            pkg.module.msbuild(
                 *self.std_msbuild_args,
                 *self.msbuild_args(),
                 self.define_targets(*self.build_targets),
@@ -114,6 +113,6 @@ def install(self, pkg, spec, prefix):
         """Run "msbuild" on the install targets specified by the builder.
         This is INSTALL by default"""
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).msbuild(
+            pkg.module.msbuild(
                 *self.msbuild_install_args(), self.define_targets(*self.install_targets)
             )

lib/spack/spack/build_systems/nmake.py

@@ -2,7 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
 from typing import List  # novm
 
 import llnl.util.filesystem as fs
@@ -132,9 +131,7 @@ def build(self, pkg, spec, prefix):
         if self.makefile_name:
             opts.append("/F{}".format(self.makefile_name))
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).nmake(
-                *opts, *self.build_targets, ignore_quotes=self.ignore_quotes
-            )
+            pkg.module.nmake(*opts, *self.build_targets, ignore_quotes=self.ignore_quotes)
 
     def install(self, pkg, spec, prefix):
         """Run "nmake" on the install targets specified by the builder.
@@ -146,6 +143,4 @@ def install(self, pkg, spec, prefix):
             opts.append("/F{}".format(self.makefile_name))
         opts.append(self.define("PREFIX", fs.windows_sfn(prefix)))
         with fs.working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).nmake(
-                *opts, *self.install_targets, ignore_quotes=self.ignore_quotes
-            )
+            pkg.module.nmake(*opts, *self.install_targets, ignore_quotes=self.ignore_quotes)

lib/spack/spack/build_systems/octave.py

@@ -2,8 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
-
 import spack.builder
 import spack.package_base
 from spack.directives import build_system, extends
@@ -47,7 +45,7 @@ class OctaveBuilder(BaseBuilder):
 
     def install(self, pkg, spec, prefix):
         """Install the package from the archive file"""
-        inspect.getmodule(self.pkg).octave(
+        pkg.module.octave(
             "--quiet",
             "--norc",
             "--built-in-docstrings-file=/dev/null",

lib/spack/spack/build_systems/perl.py

@@ -2,7 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
 import os
 from typing import Iterable
 
@@ -134,7 +133,7 @@ def build_method(self):
     def build_executable(self):
         """Returns the executable method to build the perl package"""
         if self.build_method == "Makefile.PL":
-            build_executable = inspect.getmodule(self.pkg).make
+            build_executable = self.pkg.module.make
         elif self.build_method == "Build.PL":
             build_executable = Executable(os.path.join(self.pkg.stage.source_path, "Build"))
         return build_executable
@@ -158,7 +157,7 @@ def configure(self, pkg, spec, prefix):
             options = ["Build.PL", "--install_base", prefix]
         options += self.configure_args()
 
-        inspect.getmodule(self.pkg).perl(*options)
+        pkg.module.perl(*options)
 
     # It is possible that the shebang in the Build script that is created from
     # Build.PL may be too long causing the build to fail. Patching the shebang

lib/spack/spack/build_systems/python.py

@@ -4,7 +4,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import functools
-import inspect
 import operator
 import os
 import re
@@ -228,7 +227,7 @@ def test_imports(self) -> None:
 
         # Make sure we are importing the installed modules,
         # not the ones in the source directory
-        python = inspect.getmodule(self).python  # type: ignore[union-attr]
+        python = self.module.python
         for module in self.import_modules:
             with test_part(
                 self,
@@ -315,9 +314,9 @@ def get_external_python_for_prefix(self):
         )
 
         python_externals_detected = [
-            d.spec
-            for d in python_externals_detection.get("python", [])
-            if d.prefix == self.spec.external_path
+            spec
+            for spec in python_externals_detection.get("python", [])
+            if spec.external_path == self.spec.external_path
         ]
         if python_externals_detected:
             return python_externals_detected[0]

lib/spack/spack/build_systems/qmake.py

@@ -2,8 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
-
 from llnl.util.filesystem import working_dir
 
 import spack.builder
@@ -66,17 +64,17 @@ def qmake_args(self):
     def qmake(self, pkg, spec, prefix):
         """Run ``qmake`` to configure the project and generate a Makefile."""
         with working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).qmake(*self.qmake_args())
+            pkg.module.qmake(*self.qmake_args())
 
     def build(self, pkg, spec, prefix):
         """Make the build targets"""
         with working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).make()
+            pkg.module.make()
 
     def install(self, pkg, spec, prefix):
         """Make the install targets"""
         with working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).make("install")
+            pkg.module.make("install")
 
     def check(self):
         """Search the Makefile for a ``check:`` target and runs it if found."""

lib/spack/spack/build_systems/r.py

@@ -2,10 +2,10 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
 from typing import Optional, Tuple
 
 import llnl.util.lang as lang
+from llnl.util.filesystem import mkdirp
 
 from spack.directives import extends
 
@@ -37,6 +37,7 @@ def configure_vars(self):
 
     def install(self, pkg, spec, prefix):
         """Installs an R package."""
+        mkdirp(pkg.module.r_lib_dir)
 
         config_args = self.configure_args()
         config_vars = self.configure_vars()
@@ -44,14 +45,14 @@ def install(self, pkg, spec, prefix):
         args = ["--vanilla", "CMD", "INSTALL"]
 
         if config_args:
-            args.append("--configure-args={0}".format(" ".join(config_args)))
+            args.append(f"--configure-args={' '.join(config_args)}")
 
         if config_vars:
-            args.append("--configure-vars={0}".format(" ".join(config_vars)))
+            args.append(f"--configure-vars={' '.join(config_vars)}")
 
-        args.extend(["--library={0}".format(self.pkg.module.r_lib_dir), self.stage.source_path])
+        args.extend([f"--library={pkg.module.r_lib_dir}", self.stage.source_path])
 
-        inspect.getmodule(self.pkg).R(*args)
+        pkg.module.R(*args)
 
 
 class RPackage(Package):
@@ -80,27 +81,21 @@ class RPackage(Package):
     @lang.classproperty
     def homepage(cls):
         if cls.cran:
-            return "https://cloud.r-project.org/package=" + cls.cran
+            return f"https://cloud.r-project.org/package={cls.cran}"
         elif cls.bioc:
-            return "https://bioconductor.org/packages/" + cls.bioc
+            return f"https://bioconductor.org/packages/{cls.bioc}"
 
     @lang.classproperty
     def url(cls):
         if cls.cran:
-            return (
-                "https://cloud.r-project.org/src/contrib/"
-                + cls.cran
-                + "_"
-                + str(list(cls.versions)[0])
-                + ".tar.gz"
-            )
+            return f"https://cloud.r-project.org/src/contrib/{cls.cran}_{str(list(cls.versions)[0])}.tar.gz"
 
     @lang.classproperty
     def list_url(cls):
         if cls.cran:
-            return "https://cloud.r-project.org/src/contrib/Archive/" + cls.cran + "/"
+            return f"https://cloud.r-project.org/src/contrib/Archive/{cls.cran}/"
 
     @property
     def git(self):
         if self.bioc:
-            return "https://git.bioconductor.org/packages/" + self.bioc
+            return f"https://git.bioconductor.org/packages/{self.bioc}"

lib/spack/spack/build_systems/ruby.py

@@ -3,7 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import glob
-import inspect
 
 import spack.builder
 import spack.package_base
@@ -52,10 +51,10 @@ def build(self, pkg, spec, prefix):
         gemspecs = glob.glob("*.gemspec")
         rakefiles = glob.glob("Rakefile")
         if gemspecs:
-            inspect.getmodule(self.pkg).gem("build", "--norc", gemspecs[0])
+            pkg.module.gem("build", "--norc", gemspecs[0])
         elif rakefiles:
-            jobs = inspect.getmodule(self.pkg).make_jobs
-            inspect.getmodule(self.pkg).rake("package", "-j{0}".format(jobs))
+            jobs = pkg.module.make_jobs
+            pkg.module.rake("package", "-j{0}".format(jobs))
         else:
             # Some Ruby packages only ship `*.gem` files, so nothing to build
             pass
@@ -70,6 +69,6 @@ def install(self, pkg, spec, prefix):
             # if --install-dir is not used, GEM_PATH is deleted from the
             # environement, and Gems required to build native extensions will
             # not be found. Those extensions are built during `gem install`.
-            inspect.getmodule(self.pkg).gem(
+            pkg.module.gem(
                 "install", "--norc", "--ignore-dependencies", "--install-dir", prefix, gems[0]
             )

lib/spack/spack/build_systems/scons.py

@@ -2,8 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
-
 import spack.builder
 import spack.package_base
 from spack.directives import build_system, depends_on
@@ -63,8 +61,7 @@ def build_args(self, spec, prefix):
 
     def build(self, pkg, spec, prefix):
         """Build the package."""
-        args = self.build_args(spec, prefix)
-        inspect.getmodule(self.pkg).scons(*args)
+        pkg.module.scons(*self.build_args(spec, prefix))
 
     def install_args(self, spec, prefix):
         """Arguments to pass to install."""
@@ -72,9 +69,7 @@ def install_args(self, spec, prefix):
 
     def install(self, pkg, spec, prefix):
         """Install the package."""
-        args = self.install_args(spec, prefix)
-
-        inspect.getmodule(self.pkg).scons("install", *args)
+        pkg.module.scons("install", *self.install_args(spec, prefix))
 
     def build_test(self):
         """Run unit tests after build.

lib/spack/spack/build_systems/sip.py

@@ -2,7 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
 import os
 import re
 
@@ -86,14 +85,13 @@ def import_modules(self):
 
     def python(self, *args, **kwargs):
         """The python ``Executable``."""
-        inspect.getmodule(self).python(*args, **kwargs)
+        self.pkg.module.python(*args, **kwargs)
 
     def test_imports(self):
         """Attempts to import modules of the installed package."""
 
         # Make sure we are importing the installed modules,
         # not the ones in the source directory
-        python = inspect.getmodule(self).python
         for module in self.import_modules:
             with spack.install_test.test_part(
                 self,
@@ -101,7 +99,7 @@ def test_imports(self):
                 purpose="checking import of {0}".format(module),
                 work_dir="spack-test",
             ):
-                python("-c", "import {0}".format(module))
+                self.python("-c", "import {0}".format(module))
 
 
 @spack.builder.builder("sip")
@@ -136,7 +134,7 @@ def configure(self, pkg, spec, prefix):
         """Configure the package."""
 
         # https://www.riverbankcomputing.com/static/Docs/sip/command_line_tools.html
-        args = ["--verbose", "--target-dir", inspect.getmodule(self.pkg).python_platlib]
+        args = ["--verbose", "--target-dir", pkg.module.python_platlib]
         args.extend(self.configure_args())
 
         # https://github.com/Python-SIP/sip/commit/cb0be6cb6e9b756b8b0db3136efb014f6fb9b766
@@ -155,7 +153,7 @@ def build(self, pkg, spec, prefix):
         args = self.build_args()
 
         with working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).make(*args)
+            pkg.module.make(*args)
 
     def build_args(self):
         """Arguments to pass to build."""
@@ -166,7 +164,7 @@ def install(self, pkg, spec, prefix):
         args = self.install_args()
 
         with working_dir(self.build_directory):
-            inspect.getmodule(self.pkg).make("install", *args)
+            pkg.module.make("install", *args)
 
     def install_args(self):
         """Arguments to pass to install."""

lib/spack/spack/build_systems/waf.py

@@ -2,8 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import inspect
-
 from llnl.util.filesystem import working_dir
 
 import spack.builder
@@ -90,11 +88,11 @@ def build_directory(self):
 
     def python(self, *args, **kwargs):
         """The python ``Executable``."""
-        inspect.getmodule(self.pkg).python(*args, **kwargs)
+        self.pkg.module.python(*args, **kwargs)
 
     def waf(self, *args, **kwargs):
         """Runs the waf ``Executable``."""
-        jobs = inspect.getmodule(self.pkg).make_jobs
+        jobs = self.pkg.module.make_jobs
 
         with working_dir(self.build_directory):
             self.python("waf", "-j{0}".format(jobs), *args, **kwargs)

lib/spack/spack/builder.py

@@ -6,7 +6,6 @@
 import collections.abc
 import copy
 import functools
-import inspect
 from typing import List, Optional, Tuple
 
 from llnl.util import lang
@@ -97,11 +96,10 @@ class hierarchy (look at AspellDictPackage for an example of that)
     Args:
         pkg (spack.package_base.PackageBase): package object for which we need a builder
     """
-    package_module = inspect.getmodule(pkg)
     package_buildsystem = buildsystem_name(pkg)
     default_builder_cls = BUILDER_CLS[package_buildsystem]
     builder_cls_name = default_builder_cls.__name__
-    builder_cls = getattr(package_module, builder_cls_name, None)
+    builder_cls = getattr(pkg.module, builder_cls_name, None)
     if builder_cls:
         return builder_cls(pkg)
 

lib/spack/spack/cmd/audit.py

@@ -115,15 +115,11 @@ def audit(parser, args):
 def _process_reports(reports):
     for check, errors in reports:
         if errors:
-            msg = "{0}: {1} issue{2} found".format(
-                check, len(errors), "" if len(errors) == 1 else "s"
-            )
-            header = "@*b{" + msg + "}"
-            print(cl.colorize(header))
+            status = f"{len(errors)} issue{'' if len(errors) == 1 else 's'} found"
+            print(cl.colorize(f"{check}: @*r{{{status}}}"))
+            numdigits = len(str(len(errors)))
             for idx, error in enumerate(errors):
-                print(str(idx + 1) + ". " + str(error))
+                print(f"{idx + 1:>{numdigits}}. {error}")
             raise SystemExit(1)
         else:
-            msg = "{0}: 0 issues found.".format(check)
-            header = "@*b{" + msg + "}"
-            print(cl.colorize(header))
+            print(cl.colorize(f"{check}: @*g{{passed}}"))

lib/spack/spack/cmd/commands.py

@@ -7,6 +7,7 @@
 import copy
 import os
 import re
+import shlex
 import sys
 from argparse import ArgumentParser, Namespace
 from typing import IO, Any, Callable, Dict, Iterable, List, Optional, Sequence, Set, Tuple, Union
@@ -18,6 +19,7 @@
 import spack.cmd
 import spack.main
 import spack.paths
+import spack.platforms
 from spack.main import section_descriptions
 
 description = "list available spack commands"
@@ -139,7 +141,7 @@ def usage(self, usage: str) -> str:
 
         cmd = self.parser.prog.replace(" ", "-")
         if cmd in self.documented:
-            string += "\n:ref:`More documentation <cmd-{0}>`\n".format(cmd)
+            string = f"{string}\n:ref:`More documentation <cmd-{cmd}>`\n"
 
         return string
 
@@ -249,33 +251,27 @@ def body(
             Function body.
         """
         if positionals:
-            return """
+            return f"""
     if $list_options
     then
-        {0}
+        {self.optionals(optionals)}
     else
-        {1}
+        {self.positionals(positionals)}
     fi
-""".format(
-                self.optionals(optionals), self.positionals(positionals)
-            )
+"""
         elif subcommands:
-            return """
+            return f"""
     if $list_options
     then
-        {0}
+        {self.optionals(optionals)}
     else
-        {1}
+        {self.subcommands(subcommands)}
     fi
-""".format(
-                self.optionals(optionals), self.subcommands(subcommands)
-            )
+"""
         else:
-            return """
-    {0}
-""".format(
-                self.optionals(optionals)
-            )
+            return f"""
+    {self.optionals(optionals)}
+"""
 
     def positionals(self, positionals: Sequence[str]) -> str:
         """Return the syntax for reporting positional arguments.
@@ -304,7 +300,7 @@ def optionals(self, optionals: Sequence[str]) -> str:
         Returns:
             Syntax for optional flags.
         """
-        return 'SPACK_COMPREPLY="{0}"'.format(" ".join(optionals))
+        return f'SPACK_COMPREPLY="{" ".join(optionals)}"'
 
     def subcommands(self, subcommands: Sequence[str]) -> str:
         """Return the syntax for reporting subcommands.
@@ -315,7 +311,7 @@ def subcommands(self, subcommands: Sequence[str]) -> str:
         Returns:
             Syntax for subcommand parsers
         """
-        return 'SPACK_COMPREPLY="{0}"'.format(" ".join(subcommands))
+        return f'SPACK_COMPREPLY="{" ".join(subcommands)}"'
 
 
 # Map argument destination names to their complete commands
@@ -395,7 +391,7 @@ def _fish_dest_get_complete(prog: str, dest: str) -> Optional[str]:
     subcmd = s[1] if len(s) == 2 else ""
 
     for (prog_key, pos_key), value in _dest_to_fish_complete.items():
-        if subcmd.startswith(prog_key) and re.match("^" + pos_key + "$", dest):
+        if subcmd.startswith(prog_key) and re.match(f"^{pos_key}$", dest):
             return value
     return None
 
@@ -427,24 +423,6 @@ def format(self, cmd: Command) -> str:
             + self.complete(cmd.prog, positionals, optionals, subcommands)
         )
 
-    def _quote(self, string: str) -> str:
-        """Quote string and escape special characters if necessary.
-
-        Args:
-            string: Input string.
-
-        Returns:
-            Quoted string.
-        """
-        # Goal here is to match fish_indent behavior
-
-        # Strings without spaces (or other special characters) do not need to be escaped
-        if not any([sub in string for sub in [" ", "'", '"']]):
-            return string
-
-        string = string.replace("'", r"\'")
-        return f"'{string}'"
-
     def optspecs(
         self,
         prog: str,
@@ -463,7 +441,7 @@ def optspecs(
         optspec_var = "__fish_spack_optspecs_" + prog.replace(" ", "_").replace("-", "_")
 
         if optionals is None:
-            return "set -g %s\n" % optspec_var
+            return f"set -g {optspec_var}\n"
 
         # Build optspec by iterating over options
         args = []
@@ -490,11 +468,11 @@ def optspecs(
             long = [f[2:] for f in flags if f.startswith("--")]
 
             while len(short) > 0 and len(long) > 0:
-                arg = "%s/%s%s" % (short.pop(), long.pop(), required)
+                arg = f"{short.pop()}/{long.pop()}{required}"
             while len(short) > 0:
-                arg = "%s/%s" % (short.pop(), required)
+                arg = f"{short.pop()}/{required}"
             while len(long) > 0:
-                arg = "%s%s" % (long.pop(), required)
+                arg = f"{long.pop()}{required}"
 
             args.append(arg)
 
@@ -503,7 +481,7 @@ def optspecs(
         # indicate that such subcommand exists.
         args = " ".join(args)
 
-        return "set -g %s %s\n" % (optspec_var, args)
+        return f"set -g {optspec_var} {args}\n"
 
     @staticmethod
     def complete_head(
@@ -524,12 +502,14 @@ def complete_head(
         subcmd = s[1] if len(s) == 2 else ""
 
         if index is None:
-            return "complete -c %s -n '__fish_spack_using_command %s'" % (s[0], subcmd)
+            return f"complete -c {s[0]} -n '__fish_spack_using_command {subcmd}'"
         elif nargs in [argparse.ZERO_OR_MORE, argparse.ONE_OR_MORE, argparse.REMAINDER]:
-            head = "complete -c %s -n '__fish_spack_using_command_pos_remainder %d %s'"
+            return (
+                f"complete -c {s[0]} -n '__fish_spack_using_command_pos_remainder "
+                f"{index} {subcmd}'"
+            )
         else:
-            head = "complete -c %s -n '__fish_spack_using_command_pos %d %s'"
-        return head % (s[0], index, subcmd)
+            return f"complete -c {s[0]} -n '__fish_spack_using_command_pos {index} {subcmd}'"
 
     def complete(
         self,
@@ -597,25 +577,18 @@ def positionals(
 
             if choices is not None:
                 # If there are choices, we provide a completion for all possible values.
-                commands.append(head + " -f -a %s" % self._quote(" ".join(choices)))
+                commands.append(f"{head} -f -a {shlex.quote(' '.join(choices))}")
             else:
                 # Otherwise, we try to find a predefined completion for it
                 value = _fish_dest_get_complete(prog, args)
                 if value is not None:
-                    commands.append(head + " " + value)
+                    commands.append(f"{head} {value}")
 
         return "\n".join(commands) + "\n"
 
     def prog_comment(self, prog: str) -> str:
-        """Return a comment line for the command.
-
-        Args:
-            prog: Program name.
-
-        Returns:
-            Comment line.
-        """
-        return "\n# %s\n" % prog
+        """Return a comment line for the command."""
+        return f"\n# {prog}\n"
 
     def optionals(
         self,
@@ -658,28 +631,28 @@ def optionals(
             for f in flags:
                 if f.startswith("--"):
                     long = f[2:]
-                    prefix += " -l %s" % long
+                    prefix = f"{prefix} -l {long}"
                 elif f.startswith("-"):
                     short = f[1:]
                     assert len(short) == 1
-                    prefix += " -s %s" % short
+                    prefix = f"{prefix} -s {short}"
 
             # Check if option require argument.
             # Currently multi-argument options are not supported, so we treat it like one argument.
             if nargs != 0:
-                prefix += " -r"
+                prefix = f"{prefix} -r"
 
             if dest is not None:
                 # If there are choices, we provide a completion for all possible values.
-                commands.append(prefix + " -f -a %s" % self._quote(" ".join(dest)))
+                commands.append(f"{prefix} -f -a {shlex.quote(' '.join(dest))}")
             else:
                 # Otherwise, we try to find a predefined completion for it
                 value = _fish_dest_get_complete(prog, dest)
                 if value is not None:
-                    commands.append(prefix + " " + value)
+                    commands.append(f"{prefix} {value}")
 
             if help:
-                commands.append(prefix + " -d %s" % self._quote(help))
+                commands.append(f"{prefix} -d {shlex.quote(help)}")
 
         return "\n".join(commands) + "\n"
 
@@ -697,11 +670,11 @@ def subcommands(self, prog: str, subcommands: List[Tuple[ArgumentParser, str, st
         head = self.complete_head(prog, 0)
 
         for _, subcommand, help in subcommands:
-            command = head + " -f -a %s" % self._quote(subcommand)
+            command = f"{head} -f -a {shlex.quote(subcommand)}"
 
             if help is not None and len(help) > 0:
                 help = help.split("\n")[0]
-                command += " -d %s" % self._quote(help)
+                command = f"{command} -d {shlex.quote(help)}"
 
             commands.append(command)
 
@@ -747,7 +720,7 @@ def rst_index(out: IO) -> None:
 
         for i, cmd in enumerate(sorted(commands)):
             description = description.capitalize() if i == 0 else ""
-            ref = ":ref:`%s <spack-%s>`" % (cmd, cmd)
+            ref = f":ref:`{cmd} <spack-{cmd}>`"
             comma = "," if i != len(commands) - 1 else ""
             bar = "| " if i % 8 == 0 else "  "
             out.write(line % (description, bar + ref + comma))
@@ -858,10 +831,10 @@ def _commands(parser: ArgumentParser, args: Namespace) -> None:
 
     # check header first so we don't open out files unnecessarily
     if args.header and not os.path.exists(args.header):
-        tty.die("No such file: '%s'" % args.header)
+        tty.die(f"No such file: '{args.header}'")
 
     if args.update:
-        tty.msg("Updating file: %s" % args.update)
+        tty.msg(f"Updating file: {args.update}")
         with open(args.update, "w") as f:
             prepend_header(args, f)
             formatter(args, f)

lib/spack/spack/cmd/deprecate.py

@@ -14,7 +14,6 @@
 installation and its deprecator.
 """
 import argparse
-import os
 
 import llnl.util.tty as tty
 from llnl.util.symlink import symlink
@@ -76,12 +75,7 @@ def setup_parser(sp):
     )
 
     sp.add_argument(
-        "-l",
-        "--link-type",
-        type=str,
-        default="soft",
-        choices=["soft", "hard"],
-        help="type of filesystem link to use for deprecation (default soft)",
+        "-l", "--link-type", type=str, default=None, choices=["soft", "hard"], help="(deprecated)"
     )
 
     sp.add_argument(
@@ -91,6 +85,9 @@ def setup_parser(sp):
 
 def deprecate(parser, args):
     """Deprecate one spec in favor of another"""
+    if args.link_type is not None:
+        tty.warn("The --link-type option is deprecated and will be removed in a future release.")
+
     env = ev.active_environment()
     specs = spack.cmd.parse_specs(args.specs)
 
@@ -144,7 +141,5 @@ def deprecate(parser, args):
         if not answer:
             tty.die("Will not deprecate any packages.")
 
-    link_fn = os.link if args.link_type == "hard" else symlink
-
     for dcate, dcator in zip(all_deprecate, all_deprecators):
-        dcate.package.do_deprecate(dcator, link_fn)
+        dcate.package.do_deprecate(dcator, symlink)

lib/spack/spack/cmd/info.py

@@ -48,6 +48,7 @@ def setup_parser(subparser):
     options = [
         ("--detectable", print_detectable.__doc__),
         ("--maintainers", print_maintainers.__doc__),
+        ("--namespace", print_namespace.__doc__),
         ("--no-dependencies", "do not " + print_dependencies.__doc__),
         ("--no-variants", "do not " + print_variants.__doc__),
         ("--no-versions", "do not " + print_versions.__doc__),
@@ -189,6 +190,15 @@ def print_maintainers(pkg, args):
         color.cprint(section_title("Maintainers: ") + mnt)
 
 
+def print_namespace(pkg, args):
+    """output package namespace"""
+
+    repo = spack.repo.PATH.get_repo(pkg.namespace)
+    color.cprint("")
+    color.cprint(section_title("Namespace:"))
+    color.cprint(f"    @c{{{repo.namespace}}} at {repo.root}")
+
+
 def print_phases(pkg, args):
     """output installation phases"""
 
@@ -522,6 +532,7 @@ def info(parser, args):
     # Now output optional information in expected order
     sections = [
         (args.all or args.maintainers, print_maintainers),
+        (args.all or args.namespace, print_namespace),
         (args.all or args.detectable, print_detectable),
         (args.all or args.tags, print_tags),
         (args.all or not args.no_versions, print_versions),

lib/spack/spack/compilers/__init__.py

@@ -273,24 +273,24 @@ def find_compilers(
 
     valid_compilers = {}
     for name, detected in detected_packages.items():
-        compilers = [x for x in detected if CompilerConfigFactory.from_external_spec(x.spec)]
+        compilers = [x for x in detected if CompilerConfigFactory.from_external_spec(x)]
         if not compilers:
             continue
         valid_compilers[name] = compilers
 
     def _has_fortran_compilers(x):
-        if "compilers" not in x.spec.extra_attributes:
+        if "compilers" not in x.extra_attributes:
             return False
 
-        return "fortran" in x.spec.extra_attributes["compilers"]
+        return "fortran" in x.extra_attributes["compilers"]
 
     if mixed_toolchain:
         gccs = [x for x in valid_compilers.get("gcc", []) if _has_fortran_compilers(x)]
         if gccs:
             best_gcc = sorted(
-                gccs, key=lambda x: spack.spec.parse_with_version_concrete(x.spec).version
+                gccs, key=lambda x: spack.spec.parse_with_version_concrete(x).version
             )[-1]
-            gfortran = best_gcc.spec.extra_attributes["compilers"]["fortran"]
+            gfortran = best_gcc.extra_attributes["compilers"]["fortran"]
             for name in ("llvm", "apple-clang"):
                 if name not in valid_compilers:
                     continue
@@ -298,11 +298,11 @@ def _has_fortran_compilers(x):
                 for candidate in candidates:
                     if _has_fortran_compilers(candidate):
                         continue
-                    candidate.spec.extra_attributes["compilers"]["fortran"] = gfortran
+                    candidate.extra_attributes["compilers"]["fortran"] = gfortran
 
     new_compilers = []
     for name, detected in valid_compilers.items():
-        for config in CompilerConfigFactory.from_specs([x.spec for x in detected]):
+        for config in CompilerConfigFactory.from_specs(detected):
             c = _compiler_from_config_entry(config["compiler"])
             if c in known_compilers:
                 continue

lib/spack/spack/concretize.py

@@ -19,35 +19,23 @@
 import spack.tengine
 import spack.util.path
 
-
-class Concretizer:
-    """(DEPRECATED) Only contains logic to enable/disable compiler existence checks."""
-
-    #: Controls whether we check that compiler versions actually exist
-    #: during concretization. Used for testing and for mirror creation
-    check_for_compiler_existence = None
-
-    def __init__(self):
-        if Concretizer.check_for_compiler_existence is None:
-            Concretizer.check_for_compiler_existence = not spack.config.get(
-                "config:install_missing_compilers", False
-            )
+CHECK_COMPILER_EXISTENCE = True
 
 
 @contextmanager
 def disable_compiler_existence_check():
-    saved = Concretizer.check_for_compiler_existence
-    Concretizer.check_for_compiler_existence = False
+    global CHECK_COMPILER_EXISTENCE
+    CHECK_COMPILER_EXISTENCE, saved = False, CHECK_COMPILER_EXISTENCE
     yield
-    Concretizer.check_for_compiler_existence = saved
+    CHECK_COMPILER_EXISTENCE = saved
 
 
 @contextmanager
 def enable_compiler_existence_check():
-    saved = Concretizer.check_for_compiler_existence
-    Concretizer.check_for_compiler_existence = True
+    global CHECK_COMPILER_EXISTENCE
+    CHECK_COMPILER_EXISTENCE, saved = True, CHECK_COMPILER_EXISTENCE
     yield
-    Concretizer.check_for_compiler_existence = saved
+    CHECK_COMPILER_EXISTENCE = saved
 
 
 def find_spec(spec, condition, default=None):

lib/spack/spack/container/writers/__init__.py

@@ -308,8 +308,7 @@ def __call__(self):
         return t.render(**self.to_dict())
 
 
-import spack.container.writers.docker  # noqa: E402
-
 # Import after function definition all the modules in this package,
 # so that registration of writers will happen automatically
-import spack.container.writers.singularity  # noqa: E402
+from . import docker  # noqa: F401 E402
+from . import singularity  # noqa: F401 E402

lib/spack/spack/cray_manifest.py

@@ -14,12 +14,14 @@
 import llnl.util.tty as tty
 
 import spack.cmd
+import spack.compilers
 import spack.deptypes as dt
 import spack.error
 import spack.hash_types as hash_types
 import spack.platforms
 import spack.repo
 import spack.spec
+import spack.store
 from spack.schema.cray_manifest import schema as manifest_schema
 
 #: Cray systems can store a Spack-compatible description of system
@@ -237,7 +239,7 @@ def read(path, apply_updates):
                 tty.debug(f"Include this\n{traceback.format_exc()}")
     if apply_updates:
         for spec in specs.values():
-            spack.store.STORE.db.add(spec, directory_layout=None)
+            spack.store.STORE.db.add(spec)
 
 
 class ManifestValidationError(spack.error.SpackError):

lib/spack/spack/database.py

@@ -59,7 +59,11 @@
 import spack.util.lock as lk
 import spack.util.spack_json as sjson
 import spack.version as vn
-from spack.directory_layout import DirectoryLayoutError, InconsistentInstallDirectoryError
+from spack.directory_layout import (
+    DirectoryLayout,
+    DirectoryLayoutError,
+    InconsistentInstallDirectoryError,
+)
 from spack.error import SpackError
 from spack.util.crypto import bit_length
 
@@ -203,12 +207,12 @@ class InstallRecord:
     def __init__(
         self,
         spec: "spack.spec.Spec",
-        path: str,
+        path: Optional[str],
         installed: bool,
         ref_count: int = 0,
         explicit: bool = False,
         installation_time: Optional[float] = None,
-        deprecated_for: Optional["spack.spec.Spec"] = None,
+        deprecated_for: Optional[str] = None,
         in_buildcache: bool = False,
         origin=None,
     ):
@@ -595,9 +599,11 @@ class Database:
     def __init__(
         self,
         root: str,
+        *,
         upstream_dbs: Optional[List["Database"]] = None,
         is_upstream: bool = False,
         lock_cfg: LockConfiguration = DEFAULT_LOCK_CFG,
+        layout: Optional[DirectoryLayout] = None,
     ) -> None:
         """Database for Spack installations.
 
@@ -620,6 +626,7 @@ def __init__(
         """
         self.root = root
         self.database_directory = os.path.join(self.root, _DB_DIRNAME)
+        self.layout = layout
 
         # Set up layout of database files within the db dir
         self._index_path = os.path.join(self.database_directory, "index.json")
@@ -664,14 +671,6 @@ def __init__(
 
         self.upstream_dbs = list(upstream_dbs) if upstream_dbs else []
 
-        # whether there was an error at the start of a read transaction
-        self._error = None
-
-        # For testing: if this is true, an exception is thrown when missing
-        # dependencies are detected (rather than just printing a warning
-        # message)
-        self._fail_when_missing_deps = False
-
         self._write_transaction_impl = lk.WriteTransaction
         self._read_transaction_impl = lk.ReadTransaction
 
@@ -774,7 +773,13 @@ def query_local_by_spec_hash(self, hash_key):
         with self.read_transaction():
             return self._data.get(hash_key, None)
 
-    def _assign_dependencies(self, spec_reader, hash_key, installs, data):
+    def _assign_dependencies(
+        self,
+        spec_reader: Type["spack.spec.SpecfileReaderBase"],
+        hash_key: str,
+        installs: dict,
+        data: Dict[str, InstallRecord],
+    ):
         # Add dependencies from other records in the install DB to
         # form a full spec.
         spec = data[hash_key].spec
@@ -787,26 +792,20 @@ def _assign_dependencies(self, spec_reader, hash_key, installs, data):
             for dname, dhash, dtypes, _, virtuals in spec_reader.read_specfile_dep_specs(
                 yaml_deps
             ):
-                # It is important that we always check upstream installations
-                # in the same order, and that we always check the local
-                # installation first: if a downstream Spack installs a package
-                # then dependents in that installation could be using it.
-                # If a hash is installed locally and upstream, there isn't
-                # enough information to determine which one a local package
-                # depends on, so the convention ensures that this isn't an
-                # issue.
-                upstream, record = self.query_by_spec_hash(dhash, data=data)
+                # It is important that we always check upstream installations in the same order,
+                # and that we always check the local installation first: if a downstream Spack
+                # installs a package then dependents in that installation could be using it. If a
+                # hash is installed locally and upstream, there isn't enough information to
+                # determine which one a local package depends on, so the convention ensures that
+                # this isn't an issue.
+                _, record = self.query_by_spec_hash(dhash, data=data)
                 child = record.spec if record else None
 
                 if not child:
-                    msg = "Missing dependency not in database: " "%s needs %s-%s" % (
-                        spec.cformat("{name}{/hash:7}"),
-                        dname,
-                        dhash[:7],
+                    tty.warn(
+                        f"Missing dependency not in database: "
+                        f"{spec.cformat('{name}{/hash:7}')} needs {dname}-{dhash[:7]}"
                     )
-                    if self._fail_when_missing_deps:
-                        raise MissingDependenciesError(msg)
-                    tty.warn(msg)
                     continue
 
                 spec._add_dependency(child, depflag=dt.canonicalize(dtypes), virtuals=virtuals)
@@ -846,7 +845,7 @@ def check(cond, msg):
         ):
             tty.warn(f"Spack database version changed from {version} to {_DB_VERSION}. Upgrading.")
 
-            self.reindex(spack.store.STORE.layout)
+            self.reindex()
             installs = dict(
                 (k, v.to_dict(include_fields=self._record_fields)) for k, v in self._data.items()
             )
@@ -873,8 +872,8 @@ def invalid_record(hash_key, error):
         # (i.e., its specs are a true Merkle DAG, unlike most specs.)
 
         # Pass 1: Iterate through database and build specs w/o dependencies
-        data = {}
-        installed_prefixes = set()
+        data: Dict[str, InstallRecord] = {}
+        installed_prefixes: Set[str] = set()
         for hash_key, rec in installs.items():
             try:
                 # This constructs a spec DAG from the list of all installs
@@ -911,7 +910,7 @@ def invalid_record(hash_key, error):
         self._data = data
         self._installed_prefixes = installed_prefixes
 
-    def reindex(self, directory_layout):
+    def reindex(self):
         """Build database index from scratch based on a directory layout.
 
         Locks the DB if it isn't locked already.
@@ -926,105 +925,116 @@ def _read_suppress_error():
                 if os.path.isfile(self._index_path):
                     self._read_from_file(self._index_path)
             except CorruptDatabaseError as e:
-                self._error = e
+                tty.warn(f"Reindexing corrupt database, error was: {e}")
                 self._data = {}
                 self._installed_prefixes = set()
 
-        transaction = lk.WriteTransaction(
-            self.lock, acquire=_read_suppress_error, release=self._write
-        )
-
-        with transaction:
-            if self._error:
-                tty.warn("Spack database was corrupt. Will rebuild. Error was:", str(self._error))
-                self._error = None
-
-            old_data = self._data
-            old_installed_prefixes = self._installed_prefixes
+        with lk.WriteTransaction(self.lock, acquire=_read_suppress_error, release=self._write):
+            old_installed_prefixes, self._installed_prefixes = self._installed_prefixes, set()
+            old_data, self._data = self._data, {}
             try:
-                self._construct_from_directory_layout(directory_layout, old_data)
+                self._reindex(old_data)
             except BaseException:
                 # If anything explodes, restore old data, skip write.
                 self._data = old_data
                 self._installed_prefixes = old_installed_prefixes
                 raise
 
-    def _construct_entry_from_directory_layout(
-        self, directory_layout, old_data, spec, deprecator=None
-    ):
-        # Try to recover explicit value from old DB, but
-        # default it to True if DB was corrupt. This is
-        # just to be conservative in case a command like
-        # "autoremove" is run by the user after a reindex.
-        tty.debug("RECONSTRUCTING FROM SPEC.YAML: {0}".format(spec))
-        explicit = True
-        inst_time = os.stat(spec.prefix).st_ctime
-        if old_data is not None:
-            old_info = old_data.get(spec.dag_hash())
-            if old_info is not None:
-                explicit = old_info.explicit
-                inst_time = old_info.installation_time
+    def _reindex(self, old_data: Dict[str, InstallRecord]):
+        # Specs on the file system are the source of truth for record.spec. The old database values
+        # if available are the source of truth for the rest of the record.
+        assert self.layout, "Database layout must be set to reindex"
 
-        extra_args = {"explicit": explicit, "installation_time": inst_time}
-        self._add(spec, directory_layout, **extra_args)
-        if deprecator:
-            self._deprecate(spec, deprecator)
+        specs_from_fs = self.layout.all_specs()
+        deprecated_for = self.layout.deprecated_for(specs_from_fs)
 
-    def _construct_from_directory_layout(self, directory_layout, old_data):
-        # Read first the `spec.yaml` files in the prefixes. They should be
-        # considered authoritative with respect to DB reindexing, as
-        # entries in the DB may be corrupted in a way that still makes
-        # them readable. If we considered DB entries authoritative
-        # instead, we would perpetuate errors over a reindex.
-        with directory_layout.disable_upstream_check():
-            # Initialize data in the reconstructed DB
-            self._data = {}
-            self._installed_prefixes = set()
+        known_specs: List[spack.spec.Spec] = [
+            *specs_from_fs,
+            *(deprecated for _, deprecated in deprecated_for),
+            *(rec.spec for rec in old_data.values()),
+        ]
 
-            # Start inspecting the installed prefixes
-            processed_specs = set()
+        upstream_hashes = {
+            dag_hash for upstream in self.upstream_dbs for dag_hash in upstream._data
+        }
+        upstream_hashes.difference_update(spec.dag_hash() for spec in known_specs)
 
-            for spec in directory_layout.all_specs():
-                self._construct_entry_from_directory_layout(directory_layout, old_data, spec)
-                processed_specs.add(spec)
+        def create_node(edge: spack.spec.DependencySpec, is_upstream: bool):
+            if is_upstream:
+                return
 
-            for spec, deprecator in directory_layout.all_deprecated_specs():
-                self._construct_entry_from_directory_layout(
-                    directory_layout, old_data, spec, deprecator
+            self._data[edge.spec.dag_hash()] = InstallRecord(
+                spec=edge.spec.copy(deps=False),
+                path=edge.spec.external_path if edge.spec.external else None,
+                installed=edge.spec.external,
+            )
+
+        # Store all nodes of known specs, excluding ones found in upstreams
+        tr.traverse_breadth_first_with_visitor(
+            known_specs,
+            tr.CoverNodesVisitor(
+                NoUpstreamVisitor(upstream_hashes, create_node), key=tr.by_dag_hash
+            ),
+        )
+
+        # Store the prefix and other information for specs were found on the file system
+        for s in specs_from_fs:
+            record = self._data[s.dag_hash()]
+            record.path = s.prefix
+            record.installed = True
+            record.explicit = True  # conservative assumption
+            record.installation_time = os.stat(s.prefix).st_ctime
+
+        # Deprecate specs
+        for new, old in deprecated_for:
+            self._data[old.dag_hash()].deprecated_for = new.dag_hash()
+
+        # Copy data we have from the old database
+        for old_record in old_data.values():
+            record = self._data[old_record.spec.dag_hash()]
+            record.explicit = old_record.explicit
+            record.installation_time = old_record.installation_time
+            record.origin = old_record.origin
+            record.deprecated_for = old_record.deprecated_for
+
+            # Warn when the spec has been removed from the file system (i.e. it was not detected)
+            if not record.installed and old_record.installed:
+                tty.warn(
+                    f"Spec {old_record.spec.short_spec} was marked installed in the database "
+                    "but was not found on the file system. It is now marked as missing."
                 )
-                processed_specs.add(spec)
 
-            for key, entry in old_data.items():
-                # We already took care of this spec using
-                # `spec.yaml` from its prefix.
-                if entry.spec in processed_specs:
-                    msg = "SKIPPING RECONSTRUCTION FROM OLD DB: {0}"
-                    msg += " [already reconstructed from spec.yaml]"
-                    tty.debug(msg.format(entry.spec))
-                    continue
+        def create_edge(edge: spack.spec.DependencySpec, is_upstream: bool):
+            if not edge.parent:
+                return
+            parent_record = self._data[edge.parent.dag_hash()]
+            if is_upstream:
+                upstream, child_record = self.query_by_spec_hash(edge.spec.dag_hash())
+                assert upstream and child_record, "Internal error: upstream spec not found"
+            else:
+                child_record = self._data[edge.spec.dag_hash()]
+            parent_record.spec._add_dependency(
+                child_record.spec, depflag=edge.depflag, virtuals=edge.virtuals
+            )
 
-                # If we arrived here it very likely means that
-                # we have external specs that are not dependencies
-                # of other specs. This may be the case for externally
-                # installed compilers or externally installed
-                # applications.
-                tty.debug("RECONSTRUCTING FROM OLD DB: {0}".format(entry.spec))
-                try:
-                    layout = None if entry.spec.external else directory_layout
-                    kwargs = {
-                        "spec": entry.spec,
-                        "directory_layout": layout,
-                        "explicit": entry.explicit,
-                        "installation_time": entry.installation_time,
-                    }
-                    self._add(**kwargs)
-                    processed_specs.add(entry.spec)
-                except Exception as e:
-                    # Something went wrong, so the spec was not restored
-                    # from old data
-                    tty.debug(e)
+        # Then store edges
+        tr.traverse_breadth_first_with_visitor(
+            known_specs,
+            tr.CoverEdgesVisitor(
+                NoUpstreamVisitor(upstream_hashes, create_edge), key=tr.by_dag_hash
+            ),
+        )
 
-            self._check_ref_counts()
+        # Finally update the ref counts
+        for record in self._data.values():
+            for dep in record.spec.dependencies(deptype=_TRACKED_DEPENDENCIES):
+                dep_record = self._data.get(dep.dag_hash())
+                if dep_record:  # dep might be upstream
+                    dep_record.ref_count += 1
+            if record.deprecated_for:
+                self._data[record.deprecated_for].ref_count += 1
+
+        self._check_ref_counts()
 
     def _check_ref_counts(self):
         """Ensure consistency of reference counts in the DB.
@@ -1033,7 +1043,7 @@ def _check_ref_counts(self):
 
         Does no locking.
         """
-        counts = {}
+        counts: Dict[str, int] = {}
         for key, rec in self._data.items():
             counts.setdefault(key, 0)
             for dep in rec.spec.dependencies(deptype=_TRACKED_DEPENDENCIES):
@@ -1117,29 +1127,23 @@ def _read(self):
 
     def _add(
         self,
-        spec,
-        directory_layout=None,
-        explicit=False,
-        installation_time=None,
-        allow_missing=False,
+        spec: "spack.spec.Spec",
+        explicit: bool = False,
+        installation_time: Optional[float] = None,
+        allow_missing: bool = False,
     ):
         """Add an install record for this spec to the database.
 
-        Assumes spec is installed in ``directory_layout.path_for_spec(spec)``.
-
-        Also ensures dependencies are present and updated in the DB as
-        either installed or missing.
+        Also ensures dependencies are present and updated in the DB as either installed or missing.
 
         Args:
-            spec (spack.spec.Spec): spec to be added
-            directory_layout: layout of the spec installation
+            spec: spec to be added
             explicit:
                 Possible values: True, False, any
 
-                A spec that was installed following a specific user
-                request is marked as explicit. If instead it was
-                pulled-in as a dependency of a user requested spec
-                it's considered implicit.
+                A spec that was installed following a specific user request is marked as explicit.
+                If instead it was pulled-in as a dependency of a user requested spec it's
+                considered implicit.
 
             installation_time:
                 Date and time of installation
@@ -1150,48 +1154,42 @@ def _add(
             raise NonConcreteSpecAddError("Specs added to DB must be concrete.")
 
         key = spec.dag_hash()
-        spec_pkg_hash = spec._package_hash
+        spec_pkg_hash = spec._package_hash  # type: ignore[attr-defined]
         upstream, record = self.query_by_spec_hash(key)
         if upstream:
             return
 
-        # Retrieve optional arguments
         installation_time = installation_time or _now()
 
         for edge in spec.edges_to_dependencies(depflag=_TRACKED_DEPENDENCIES):
             if edge.spec.dag_hash() in self._data:
                 continue
-            # allow missing build-only deps. This prevents excessive
-            # warnings when a spec is installed, and its build dep
-            # is missing a build dep; there's no need to install the
-            # build dep's build dep first, and there's no need to warn
-            # about it missing.
-            dep_allow_missing = allow_missing or edge.depflag == dt.BUILD
             self._add(
                 edge.spec,
-                directory_layout,
                 explicit=False,
                 installation_time=installation_time,
-                allow_missing=dep_allow_missing,
+                # allow missing build-only deps. This prevents excessive warnings when a spec is
+                # installed, and its build dep is missing a build dep; there's no need to install
+                # the build dep's build dep first, and there's no need to warn about it missing.
+                allow_missing=allow_missing or edge.depflag == dt.BUILD,
             )
 
         # Make sure the directory layout agrees whether the spec is installed
-        if not spec.external and directory_layout:
-            path = directory_layout.path_for_spec(spec)
+        if not spec.external and self.layout:
+            path = self.layout.path_for_spec(spec)
             installed = False
             try:
-                directory_layout.ensure_installed(spec)
+                self.layout.ensure_installed(spec)
                 installed = True
                 self._installed_prefixes.add(path)
             except DirectoryLayoutError as e:
                 if not (allow_missing and isinstance(e, InconsistentInstallDirectoryError)):
-                    msg = (
-                        "{0} is being {1} in the database with prefix {2}, "
-                        "but this directory does not contain an installation of "
-                        "the spec, due to: {3}"
-                    )
                     action = "updated" if key in self._data else "registered"
-                    tty.warn(msg.format(spec.short_spec, action, path, str(e)))
+                    tty.warn(
+                        f"{spec.short_spec} is being {action} in the database with prefix {path}, "
+                        "but this directory does not contain an installation of "
+                        f"the spec, due to: {e}"
+                    )
         elif spec.external_path:
             path = spec.external_path
             installed = True
@@ -1202,23 +1200,27 @@ def _add(
         if key not in self._data:
             # Create a new install record with no deps initially.
             new_spec = spec.copy(deps=False)
-            extra_args = {"explicit": explicit, "installation_time": installation_time}
-            # Commands other than 'spack install' may add specs to the DB,
-            # we can record the source of an installed Spec with 'origin'
-            if hasattr(spec, "origin"):
-                extra_args["origin"] = spec.origin
-            self._data[key] = InstallRecord(new_spec, path, installed, ref_count=0, **extra_args)
+            self._data[key] = InstallRecord(
+                new_spec,
+                path=path,
+                installed=installed,
+                ref_count=0,
+                explicit=explicit,
+                installation_time=installation_time,
+                origin=None if not hasattr(spec, "origin") else spec.origin,
+            )
 
             # Connect dependencies from the DB to the new copy.
             for dep in spec.edges_to_dependencies(depflag=_TRACKED_DEPENDENCIES):
                 dkey = dep.spec.dag_hash()
                 upstream, record = self.query_by_spec_hash(dkey)
+                assert record, f"Missing dependency {dep.spec.short_spec} in DB"
                 new_spec._add_dependency(record.spec, depflag=dep.depflag, virtuals=dep.virtuals)
                 if not upstream:
                     record.ref_count += 1
 
-            # Mark concrete once everything is built, and preserve
-            # the original hashes of concrete specs.
+            # Mark concrete once everything is built, and preserve the original hashes of concrete
+            # specs.
             new_spec._mark_concrete()
             new_spec._hash = key
             new_spec._package_hash = spec_pkg_hash
@@ -1231,7 +1233,7 @@ def _add(
         self._data[key].explicit = explicit
 
     @_autospec
-    def add(self, spec, directory_layout, explicit=False):
+    def add(self, spec: "spack.spec.Spec", *, explicit: bool = False) -> None:
         """Add spec at path to database, locking and reading DB to sync.
 
         ``add()`` will lock and read from the DB on disk.
@@ -1240,9 +1242,9 @@ def add(self, spec, directory_layout, explicit=False):
         # TODO: ensure that spec is concrete?
         # Entire add is transactional.
         with self.write_transaction():
-            self._add(spec, directory_layout, explicit=explicit)
+            self._add(spec, explicit=explicit)
 
-    def _get_matching_spec_key(self, spec, **kwargs):
+    def _get_matching_spec_key(self, spec: "spack.spec.Spec", **kwargs) -> str:
         """Get the exact spec OR get a single spec that matches."""
         key = spec.dag_hash()
         upstream, record = self.query_by_spec_hash(key)
@@ -1254,12 +1256,12 @@ def _get_matching_spec_key(self, spec, **kwargs):
         return key
 
     @_autospec
-    def get_record(self, spec, **kwargs):
+    def get_record(self, spec: "spack.spec.Spec", **kwargs) -> Optional[InstallRecord]:
         key = self._get_matching_spec_key(spec, **kwargs)
         upstream, record = self.query_by_spec_hash(key)
         return record
 
-    def _decrement_ref_count(self, spec):
+    def _decrement_ref_count(self, spec: "spack.spec.Spec") -> None:
         key = spec.dag_hash()
 
         if key not in self._data:
@@ -1276,7 +1278,7 @@ def _decrement_ref_count(self, spec):
             for dep in spec.dependencies(deptype=_TRACKED_DEPENDENCIES):
                 self._decrement_ref_count(dep)
 
-    def _increment_ref_count(self, spec):
+    def _increment_ref_count(self, spec: "spack.spec.Spec") -> None:
         key = spec.dag_hash()
 
         if key not in self._data:
@@ -1285,14 +1287,14 @@ def _increment_ref_count(self, spec):
         rec = self._data[key]
         rec.ref_count += 1
 
-    def _remove(self, spec):
+    def _remove(self, spec: "spack.spec.Spec") -> "spack.spec.Spec":
         """Non-locking version of remove(); does real work."""
         key = self._get_matching_spec_key(spec)
         rec = self._data[key]
 
         # This install prefix is now free for other specs to use, even if the
         # spec is only marked uninstalled.
-        if not rec.spec.external and rec.installed:
+        if not rec.spec.external and rec.installed and rec.path:
             self._installed_prefixes.remove(rec.path)
 
         if rec.ref_count > 0:
@@ -1316,7 +1318,7 @@ def _remove(self, spec):
         return rec.spec
 
     @_autospec
-    def remove(self, spec):
+    def remove(self, spec: "spack.spec.Spec") -> "spack.spec.Spec":
         """Removes a spec from the database.  To be called on uninstall.
 
         Reads the database, then:
@@ -1331,7 +1333,7 @@ def remove(self, spec):
         with self.write_transaction():
             return self._remove(spec)
 
-    def deprecator(self, spec):
+    def deprecator(self, spec: "spack.spec.Spec") -> Optional["spack.spec.Spec"]:
         """Return the spec that the given spec is deprecated for, or None"""
         with self.read_transaction():
             spec_key = self._get_matching_spec_key(spec)
@@ -1342,14 +1344,14 @@ def deprecator(self, spec):
             else:
                 return None
 
-    def specs_deprecated_by(self, spec):
+    def specs_deprecated_by(self, spec: "spack.spec.Spec") -> List["spack.spec.Spec"]:
         """Return all specs deprecated in favor of the given spec"""
         with self.read_transaction():
             return [
                 rec.spec for rec in self._data.values() if rec.deprecated_for == spec.dag_hash()
             ]
 
-    def _deprecate(self, spec, deprecator):
+    def _deprecate(self, spec: "spack.spec.Spec", deprecator: "spack.spec.Spec") -> None:
         spec_key = self._get_matching_spec_key(spec)
         spec_rec = self._data[spec_key]
 
@@ -1367,17 +1369,17 @@ def _deprecate(self, spec, deprecator):
         self._data[spec_key] = spec_rec
 
     @_autospec
-    def mark(self, spec, key, value):
+    def mark(self, spec: "spack.spec.Spec", key, value) -> None:
         """Mark an arbitrary record on a spec."""
         with self.write_transaction():
             return self._mark(spec, key, value)
 
-    def _mark(self, spec, key, value):
+    def _mark(self, spec: "spack.spec.Spec", key, value) -> None:
         record = self._data[self._get_matching_spec_key(spec)]
         setattr(record, key, value)
 
     @_autospec
-    def deprecate(self, spec, deprecator):
+    def deprecate(self, spec: "spack.spec.Spec", deprecator: "spack.spec.Spec") -> None:
         """Marks a spec as deprecated in favor of its deprecator"""
         with self.write_transaction():
             return self._deprecate(spec, deprecator)
@@ -1385,16 +1387,16 @@ def deprecate(self, spec, deprecator):
     @_autospec
     def installed_relatives(
         self,
-        spec,
-        direction="children",
-        transitive=True,
+        spec: "spack.spec.Spec",
+        direction: str = "children",
+        transitive: bool = True,
         deptype: Union[dt.DepFlag, dt.DepTypes] = dt.ALL,
-    ):
+    ) -> Set["spack.spec.Spec"]:
         """Return installed specs related to this one."""
         if direction not in ("parents", "children"):
             raise ValueError("Invalid direction: %s" % direction)
 
-        relatives = set()
+        relatives: Set[spack.spec.Spec] = set()
         for spec in self.query(spec):
             if transitive:
                 to_add = spec.traverse(direction=direction, root=False, deptype=deptype)
@@ -1405,17 +1407,13 @@ def installed_relatives(
 
             for relative in to_add:
                 hash_key = relative.dag_hash()
-                upstream, record = self.query_by_spec_hash(hash_key)
+                _, record = self.query_by_spec_hash(hash_key)
                 if not record:
-                    reltype = "Dependent" if direction == "parents" else "Dependency"
-                    msg = "Inconsistent state! %s %s of %s not in DB" % (
-                        reltype,
-                        hash_key,
-                        spec.dag_hash(),
+                    tty.warn(
+                        f"Inconsistent state: "
+                        f"{'dependent' if direction == 'parents' else 'dependency'} {hash_key} of "
+                        f"{spec.dag_hash()} not in DB"
                     )
-                    if self._fail_when_missing_deps:
-                        raise MissingDependenciesError(msg)
-                    tty.warn(msg)
                     continue
 
                 if not record.installed:
@@ -1425,7 +1423,7 @@ def installed_relatives(
         return relatives
 
     @_autospec
-    def installed_extensions_for(self, extendee_spec):
+    def installed_extensions_for(self, extendee_spec: "spack.spec.Spec"):
         """Returns the specs of all packages that extend the given spec"""
         for spec in self.query():
             if spec.package.extends(extendee_spec):
@@ -1684,7 +1682,7 @@ def unused_specs(
         self,
         root_hashes: Optional[Container[str]] = None,
         deptype: Union[dt.DepFlag, dt.DepTypes] = dt.LINK | dt.RUN,
-    ) -> "List[spack.spec.Spec]":
+    ) -> List["spack.spec.Spec"]:
         """Return all specs that are currently installed but not needed by root specs.
 
         By default, roots are all explicit specs in the database. If a set of root
@@ -1728,6 +1726,33 @@ def update_explicit(self, spec, explicit):
                 rec.explicit = explicit
 
 
+class NoUpstreamVisitor:
+    """Gives edges to upstream specs, but does follow edges from upstream specs."""
+
+    def __init__(
+        self,
+        upstream_hashes: Set[str],
+        on_visit: Callable[["spack.spec.DependencySpec", bool], None],
+    ):
+        self.upstream_hashes = upstream_hashes
+        self.on_visit = on_visit
+
+    def accept(self, item: tr.EdgeAndDepth) -> bool:
+        self.on_visit(item.edge, self.is_upstream(item))
+        return True
+
+    def is_upstream(self, item: tr.EdgeAndDepth) -> bool:
+        return item.edge.spec.dag_hash() in self.upstream_hashes
+
+    def neighbors(self, item: tr.EdgeAndDepth):
+        # Prune edges from upstream nodes, only follow database tracked dependencies
+        return (
+            []
+            if self.is_upstream(item)
+            else item.edge.spec.edges_to_dependencies(depflag=_TRACKED_DEPENDENCIES)
+        )
+
+
 class UpstreamDatabaseLockingError(SpackError):
     """Raised when an operation would need to lock an upstream database"""
 

lib/spack/spack/detection/__init__.py

@@ -2,17 +2,11 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-from .common import (
-    DetectedPackage,
-    executable_prefix,
-    set_virtuals_nonbuildable,
-    update_configuration,
-)
+from .common import executable_prefix, set_virtuals_nonbuildable, update_configuration
 from .path import by_path, executables_in_path
 from .test import detection_tests
 
 __all__ = [
-    "DetectedPackage",
     "by_path",
     "executables_in_path",
     "executable_prefix",

lib/spack/spack/detection/common.py

@@ -6,9 +6,9 @@
 function to update packages.yaml given a list of detected packages.
 
 Ideally, each detection method should be placed in a specific subpackage
-and implement at least a function that returns a list of DetectedPackage
-objects. The update in packages.yaml can then be done using the function
-provided here.
+and implement at least a function that returns a list of specs.
+
+The update in packages.yaml can then be done using the function provided here.
 
 The module also contains other functions that might be useful across different
 detection mechanisms.
@@ -17,9 +17,10 @@
 import itertools
 import os
 import os.path
+import pathlib
 import re
 import sys
-from typing import Dict, List, NamedTuple, Optional, Set, Tuple, Union
+from typing import Dict, List, Optional, Set, Tuple, Union
 
 import llnl.util.tty
 
@@ -30,27 +31,6 @@
 import spack.util.windows_registry
 
 
-class DetectedPackage(NamedTuple):
-    """Information on a package that has been detected."""
-
-    #: Spec that was detected
-    spec: spack.spec.Spec
-    #: Prefix of the spec
-    prefix: str
-
-    def __reduce__(self):
-        return DetectedPackage.restore, (str(self.spec), self.prefix, self.spec.extra_attributes)
-
-    @staticmethod
-    def restore(
-        spec_str: str, prefix: str, extra_attributes: Optional[Dict[str, str]]
-    ) -> "DetectedPackage":
-        spec = spack.spec.Spec.from_detection(
-            spec_str=spec_str, external_path=prefix, extra_attributes=extra_attributes
-        )
-        return DetectedPackage(spec=spec, prefix=prefix)
-
-
 def _externals_in_packages_yaml() -> Set[spack.spec.Spec]:
     """Returns all the specs mentioned as externals in packages.yaml"""
     packages_yaml = spack.config.get("packages")
@@ -65,7 +45,7 @@ def _externals_in_packages_yaml() -> Set[spack.spec.Spec]:
 
 
 def _pkg_config_dict(
-    external_pkg_entries: List[DetectedPackage],
+    external_pkg_entries: List["spack.spec.Spec"],
 ) -> Dict[str, Union[bool, List[Dict[str, ExternalEntryType]]]]:
     """Generate a package specific config dict according to the packages.yaml schema.
 
@@ -85,22 +65,19 @@ def _pkg_config_dict(
     pkg_dict = spack.util.spack_yaml.syaml_dict()
     pkg_dict["externals"] = []
     for e in external_pkg_entries:
-        if not _spec_is_valid(e.spec):
+        if not _spec_is_valid(e):
             continue
 
         external_items: List[Tuple[str, ExternalEntryType]] = [
-            ("spec", str(e.spec)),
-            ("prefix", e.prefix),
+            ("spec", str(e)),
+            ("prefix", pathlib.Path(e.external_path).as_posix()),
         ]
-        if e.spec.external_modules:
-            external_items.append(("modules", e.spec.external_modules))
+        if e.external_modules:
+            external_items.append(("modules", e.external_modules))
 
-        if e.spec.extra_attributes:
+        if e.extra_attributes:
             external_items.append(
-                (
-                    "extra_attributes",
-                    spack.util.spack_yaml.syaml_dict(e.spec.extra_attributes.items()),
-                )
+                ("extra_attributes", spack.util.spack_yaml.syaml_dict(e.extra_attributes.items()))
             )
 
         # external_items.extend(e.spec.extra_attributes.items())
@@ -221,33 +198,32 @@ def library_prefix(library_dir: str) -> str:
 
 
 def update_configuration(
-    detected_packages: Dict[str, List[DetectedPackage]],
+    detected_packages: Dict[str, List["spack.spec.Spec"]],
     scope: Optional[str] = None,
     buildable: bool = True,
 ) -> List[spack.spec.Spec]:
     """Add the packages passed as arguments to packages.yaml
 
     Args:
-        detected_packages: list of DetectedPackage objects to be added
+        detected_packages: list of specs to be added
         scope: configuration scope where to add the detected packages
         buildable: whether the detected packages are buildable or not
     """
     predefined_external_specs = _externals_in_packages_yaml()
     pkg_to_cfg, all_new_specs = {}, []
     for package_name, entries in detected_packages.items():
-        new_entries = [e for e in entries if (e.spec not in predefined_external_specs)]
+        new_entries = [s for s in entries if s not in predefined_external_specs]
 
         pkg_config = _pkg_config_dict(new_entries)
         external_entries = pkg_config.get("externals", [])
         assert not isinstance(external_entries, bool), "unexpected value for external entry"
 
-        all_new_specs.extend([x.spec for x in new_entries])
+        all_new_specs.extend(new_entries)
         if buildable is False:
             pkg_config["buildable"] = False
         pkg_to_cfg[package_name] = pkg_config
 
     pkgs_cfg = spack.config.get("packages", scope=scope)
-
     pkgs_cfg = spack.config.merge_yaml(pkgs_cfg, pkg_to_cfg)
     spack.config.set("packages", pkgs_cfg, scope=scope)
 

lib/spack/spack/detection/path.py

@@ -24,7 +24,6 @@
 import spack.util.ld_so_conf
 
 from .common import (
-    DetectedPackage,
     WindowsCompilerExternalPaths,
     WindowsKitExternalPaths,
     _convert_to_iterable,
@@ -229,7 +228,7 @@ def prefix_from_path(self, *, path: str) -> str:
 
     def detect_specs(
         self, *, pkg: Type["spack.package_base.PackageBase"], paths: List[str]
-    ) -> List[DetectedPackage]:
+    ) -> List["spack.spec.Spec"]:
         """Given a list of files matching the search patterns, returns a list of detected specs.
 
         Args:
@@ -295,16 +294,16 @@ def detect_specs(
                     warnings.warn(msg)
                     continue
 
-                if spec.external_path:
-                    prefix = spec.external_path
+                if not spec.external_path:
+                    spec.external_path = prefix
 
-                result.append(DetectedPackage(spec=spec, prefix=prefix))
+                result.append(spec)
 
         return result
 
     def find(
         self, *, pkg_name: str, repository, initial_guess: Optional[List[str]] = None
-    ) -> List[DetectedPackage]:
+    ) -> List["spack.spec.Spec"]:
         """For a given package, returns a list of detected specs.
 
         Args:
@@ -388,7 +387,7 @@ def by_path(
     *,
     path_hints: Optional[List[str]] = None,
     max_workers: Optional[int] = None,
-) -> Dict[str, List[DetectedPackage]]:
+) -> Dict[str, List["spack.spec.Spec"]]:
     """Return the list of packages that have been detected on the system, keyed by
     unqualified package name.
 

lib/spack/spack/detection/test.py

@@ -68,7 +68,7 @@ def execute(self) -> List[spack.spec.Spec]:
         with self._mock_layout() as path_hints:
             entries = by_path([self.test.pkg_name], path_hints=path_hints)
             _, unqualified_name = spack.repo.partition_package_name(self.test.pkg_name)
-            specs = set(x.spec for x in entries[unqualified_name])
+            specs = set(entries[unqualified_name])
         return list(specs)
 
     @contextlib.contextmanager

lib/spack/spack/directory_layout.py

@@ -4,17 +4,14 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import errno
-import glob
 import os
-import posixpath
 import re
 import shutil
 import sys
-from contextlib import contextmanager
 from pathlib import Path
+from typing import List, Optional, Tuple
 
 import llnl.util.filesystem as fs
-import llnl.util.tty as tty
 from llnl.util.symlink import readlink
 
 import spack.config
@@ -23,13 +20,8 @@
 import spack.util.spack_json as sjson
 from spack.error import SpackError
 
-# Note: Posixpath is used here as opposed to
-# os.path.join due to spack.spec.Spec.format
-# requiring forward slash path seperators at this stage
 default_projections = {
-    "all": posixpath.join(
-        "{architecture}", "{compiler.name}-{compiler.version}", "{name}-{version}-{hash}"
-    )
+    "all": "{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}"
 }
 
 
@@ -39,6 +31,42 @@ def _check_concrete(spec):
         raise ValueError("Specs passed to a DirectoryLayout must be concrete!")
 
 
+def _get_spec(prefix: str) -> Optional["spack.spec.Spec"]:
+    """Returns a spec if the prefix contains a spec file in the .spack subdir"""
+    for f in ("spec.json", "spec.yaml"):
+        try:
+            return spack.spec.Spec.from_specfile(os.path.join(prefix, ".spack", f))
+        except Exception:
+            continue
+    return None
+
+
+def specs_from_metadata_dirs(root: str) -> List["spack.spec.Spec"]:
+    stack = [root]
+    specs = []
+
+    while stack:
+        prefix = stack.pop()
+
+        spec = _get_spec(prefix)
+
+        if spec:
+            spec.prefix = prefix
+            specs.append(spec)
+            continue
+
+        try:
+            scandir = os.scandir(prefix)
+        except OSError:
+            continue
+
+        with scandir as entries:
+            for entry in entries:
+                if entry.is_dir(follow_symlinks=False):
+                    stack.append(entry.path)
+    return specs
+
+
 class DirectoryLayout:
     """A directory layout is used to associate unique paths with specs.
     Different installations are going to want different layouts for their
@@ -152,20 +180,9 @@ def read_spec(self, path):
     def spec_file_path(self, spec):
         """Gets full path to spec file"""
         _check_concrete(spec)
-        # Attempts to convert to JSON if possible.
-        # Otherwise just returns the YAML.
         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)
-        if os.path.exists(yaml_path) and fs.can_write_to_dir(yaml_path):
-            self.write_spec(spec, json_path)
-            try:
-                os.remove(yaml_path)
-            except OSError as err:
-                tty.debug("Could not remove deprecated {0}".format(yaml_path))
-                tty.debug(err)
-        elif os.path.exists(yaml_path):
-            return yaml_path
-        return json_path
+        return yaml_path if os.path.exists(yaml_path) else json_path
 
     def deprecated_file_path(self, deprecated_spec, deprecator_spec=None):
         """Gets full path to spec file for deprecated spec
@@ -199,23 +216,7 @@ def deprecated_file_path(self, deprecated_spec, deprecator_spec=None):
             deprecated_spec.dag_hash() + "_" + self.spec_file_name,
         )
 
-        if os.path.exists(yaml_path) and fs.can_write_to_dir(yaml_path):
-            self.write_spec(deprecated_spec, json_path)
-            try:
-                os.remove(yaml_path)
-            except (IOError, OSError) as err:
-                tty.debug("Could not remove deprecated {0}".format(yaml_path))
-                tty.debug(err)
-        elif os.path.exists(yaml_path):
-            return yaml_path
-
-        return json_path
-
-    @contextmanager
-    def disable_upstream_check(self):
-        self.check_upstream = False
-        yield
-        self.check_upstream = True
+        return yaml_path if os.path.exists(yaml_path) else json_path
 
     def metadata_path(self, spec):
         return os.path.join(spec.prefix, self.metadata_dir)
@@ -271,53 +272,6 @@ def ensure_installed(self, spec):
                 "Spec file in %s does not match hash!" % spec_file_path
             )
 
-    def all_specs(self):
-        if not os.path.isdir(self.root):
-            return []
-
-        specs = []
-        for _, path_scheme in self.projections.items():
-            path_elems = ["*"] * len(path_scheme.split(posixpath.sep))
-            # NOTE: Does not validate filename extension; should happen later
-            path_elems += [self.metadata_dir, "spec.json"]
-            pattern = os.path.join(self.root, *path_elems)
-            spec_files = glob.glob(pattern)
-            if not spec_files:  # we're probably looking at legacy yaml...
-                path_elems += [self.metadata_dir, "spec.yaml"]
-                pattern = os.path.join(self.root, *path_elems)
-                spec_files = glob.glob(pattern)
-            specs.extend([self.read_spec(s) for s in spec_files])
-        return specs
-
-    def all_deprecated_specs(self):
-        if not os.path.isdir(self.root):
-            return []
-
-        deprecated_specs = set()
-        for _, path_scheme in self.projections.items():
-            path_elems = ["*"] * len(path_scheme.split(posixpath.sep))
-            # NOTE: Does not validate filename extension; should happen later
-            path_elems += [
-                self.metadata_dir,
-                self.deprecated_dir,
-                "*_spec.*",
-            ]  # + self.spec_file_name]
-            pattern = os.path.join(self.root, *path_elems)
-            spec_files = glob.glob(pattern)
-            get_depr_spec_file = lambda x: os.path.join(
-                os.path.dirname(os.path.dirname(x)), self.spec_file_name
-            )
-            deprecated_specs |= set(
-                (self.read_spec(s), self.read_spec(get_depr_spec_file(s))) for s in spec_files
-            )
-        return deprecated_specs
-
-    def specs_by_hash(self):
-        by_hash = {}
-        for spec in self.all_specs():
-            by_hash[spec.dag_hash()] = spec
-        return by_hash
-
     def path_for_spec(self, spec):
         """Return absolute path from the root to a directory for the spec."""
         _check_concrete(spec)
@@ -383,6 +337,35 @@ def remove_install_directory(self, spec, deprecated=False):
                         raise e
             path = os.path.dirname(path)
 
+    def all_specs(self) -> List["spack.spec.Spec"]:
+        """Returns a list of all specs detected in self.root, detected by `.spack` directories.
+        Their prefix is set to the directory containing the `.spack` directory. Note that these
+        specs may follow a different layout than the current layout if it was changed after
+        installation."""
+        return specs_from_metadata_dirs(self.root)
+
+    def deprecated_for(
+        self, specs: List["spack.spec.Spec"]
+    ) -> List[Tuple["spack.spec.Spec", "spack.spec.Spec"]]:
+        """Returns a list of tuples of specs (new, old) where new is deprecated for old"""
+        spec_with_deprecated = []
+        for spec in specs:
+            try:
+                deprecated = os.scandir(
+                    os.path.join(str(spec.prefix), self.metadata_dir, self.deprecated_dir)
+                )
+            except OSError:
+                continue
+
+            with deprecated as entries:
+                for entry in entries:
+                    try:
+                        deprecated_spec = spack.spec.Spec.from_specfile(entry.path)
+                        spec_with_deprecated.append((spec, deprecated_spec))
+                    except Exception:
+                        continue
+        return spec_with_deprecated
+
 
 class DirectoryLayoutError(SpackError):
     """Superclass for directory layout errors."""

lib/spack/spack/environment/environment.py

@@ -58,9 +58,8 @@
 from spack.installer import PackageInstaller
 from spack.schema.env import TOP_LEVEL_KEY
 from spack.spec import Spec
-from spack.spec_list import InvalidSpecConstraintError, SpecList
+from spack.spec_list import SpecList
 from spack.util.path import substitute_path_variables
-from spack.variant import UnknownVariantError
 
 #: environment variable used to indicate the active environment
 spack_env_var = "SPACK_ENV"
@@ -1625,10 +1624,10 @@ def _concretize_separately(self, tests=False):
 
         # Concretize any new user specs that we haven't concretized yet
         args, root_specs, i = [], [], 0
-        for uspec, uspec_constraints in zip(self.user_specs, self.user_specs.specs_as_constraints):
+        for uspec in self.user_specs:
             if uspec not in old_concretized_user_specs:
                 root_specs.append(uspec)
-                args.append((i, [str(x) for x in uspec_constraints], tests))
+                args.append((i, str(uspec), tests))
                 i += 1
 
         # Ensure we don't try to bootstrap clingo in parallel
@@ -2508,52 +2507,11 @@ def display_specs(specs):
     print(tree_string)
 
 
-def _concretize_from_constraints(spec_constraints, tests=False):
-    # Accept only valid constraints from list and concretize spec
-    # Get the named spec even if out of order
-    root_spec = [s for s in spec_constraints if s.name]
-    if len(root_spec) != 1:
-        m = "The constraints %s are not a valid spec " % spec_constraints
-        m += "concretization target. all specs must have a single name "
-        m += "constraint for concretization."
-        raise InvalidSpecConstraintError(m)
-    spec_constraints.remove(root_spec[0])
-
-    invalid_constraints = []
-    while True:
-        # Attach all anonymous constraints to one named spec
-        s = root_spec[0].copy()
-        for c in spec_constraints:
-            if c not in invalid_constraints:
-                s.constrain(c)
-        try:
-            return s.concretized(tests=tests)
-        except spack.spec.InvalidDependencyError as e:
-            invalid_deps_string = ["^" + d for d in e.invalid_deps]
-            invalid_deps = [
-                c
-                for c in spec_constraints
-                if any(c.satisfies(invd) for invd in invalid_deps_string)
-            ]
-            if len(invalid_deps) != len(invalid_deps_string):
-                raise e
-            invalid_constraints.extend(invalid_deps)
-        except UnknownVariantError as e:
-            invalid_variants = e.unknown_variants
-            inv_variant_constraints = [
-                c for c in spec_constraints if any(name in c.variants for name in invalid_variants)
-            ]
-            if len(inv_variant_constraints) != len(invalid_variants):
-                raise e
-            invalid_constraints.extend(inv_variant_constraints)
-
-
 def _concretize_task(packed_arguments) -> Tuple[int, Spec, float]:
-    index, spec_constraints, tests = packed_arguments
-    spec_constraints = [Spec(x) for x in spec_constraints]
+    index, spec_str, tests = packed_arguments
     with tty.SuppressOutput(msg_enabled=False):
         start = time.time()
-        spec = _concretize_from_constraints(spec_constraints, tests)
+        spec = Spec(spec_str).concretized(tests=tests)
         return index, spec, time.time() - start
 
 

lib/spack/spack/installer.py

@@ -276,52 +276,6 @@ def _do_fake_install(pkg: "spack.package_base.PackageBase") -> None:
     dump_packages(pkg.spec, packages_dir)
 
 
-def _packages_needed_to_bootstrap_compiler(
-    compiler: "spack.spec.CompilerSpec", architecture: "spack.spec.ArchSpec", pkgs: list
-) -> List[Tuple["spack.package_base.PackageBase", bool]]:
-    """
-    Return a list of packages required to bootstrap `pkg`s compiler
-
-    Checks Spack's compiler configuration for a compiler that
-    matches the package spec.
-
-    Args:
-        compiler: the compiler to bootstrap
-        architecture: the architecture for which to boostrap the compiler
-        pkgs: the packages that may need their compiler installed
-
-    Return:
-        list of tuples of packages and a boolean, for concretized compiler-related
-            packages that need to be installed and bool values specify whether the
-            package is the bootstrap compiler (``True``) or one of its dependencies
-            (``False``).  The list will be empty if there are no compilers.
-    """
-    tty.debug(f"Bootstrapping {compiler} compiler")
-    compilers = spack.compilers.compilers_for_spec(compiler, arch_spec=architecture)
-    if compilers:
-        return []
-
-    dep = spack.compilers.pkg_spec_for_compiler(compiler)
-
-    # Set the architecture for the compiler package in a way that allows the
-    # concretizer to back off if needed for the older bootstrapping compiler
-    dep.constrain(f"platform={str(architecture.platform)}")
-    dep.constrain(f"os={str(architecture.os)}")
-    dep.constrain(f"target={architecture.target.microarchitecture.family.name}:")
-    # concrete CompilerSpec has less info than concrete Spec
-    # concretize as Spec to add that information
-    dep.concretize()
-    # mark compiler as depended-on by the packages that use it
-    for pkg in pkgs:
-        dep._dependents.add(
-            spack.spec.DependencySpec(pkg.spec, dep, depflag=dt.BUILD, virtuals=())
-        )
-    packages = [(s.package, False) for s in dep.traverse(order="post", root=False)]
-
-    packages.append((dep.package, True))
-    return packages
-
-
 def _hms(seconds: int) -> str:
     """
     Convert seconds to hours, minutes, seconds
@@ -451,7 +405,7 @@ def _process_external_package(pkg: "spack.package_base.PackageBase", explicit: b
 
         # Add to the DB
         tty.debug(f"{pre} registering into DB")
-        spack.store.STORE.db.add(spec, None, explicit=explicit)
+        spack.store.STORE.db.add(spec, explicit=explicit)
 
 
 def _process_binary_cache_tarball(
@@ -493,7 +447,7 @@ def _process_binary_cache_tarball(
             pkg._post_buildcache_install_hook()
 
         pkg.installed_from_binary_cache = True
-        spack.store.STORE.db.add(pkg.spec, spack.store.STORE.layout, explicit=explicit)
+        spack.store.STORE.db.add(pkg.spec, explicit=explicit)
         return True
 
 
@@ -967,26 +921,6 @@ def __init__(
             if package_id(d) != self.pkg_id
         )
 
-        # Handle bootstrapped compiler
-        #
-        # The bootstrapped compiler is not a dependency in the spec, but it is
-        # a dependency of the build task. Here we add it to self.dependencies
-        compiler_spec = self.pkg.spec.compiler
-        arch_spec = self.pkg.spec.architecture
-        strict = spack.concretize.Concretizer().check_for_compiler_existence
-        if (
-            not spack.compilers.compilers_for_spec(compiler_spec, arch_spec=arch_spec)
-            and not strict
-        ):
-            # The compiler is in the queue, identify it as dependency
-            dep = spack.compilers.pkg_spec_for_compiler(compiler_spec)
-            dep.constrain(f"platform={str(arch_spec.platform)}")
-            dep.constrain(f"os={str(arch_spec.os)}")
-            dep.constrain(f"target={arch_spec.target.microarchitecture.family.name}:")
-            dep.concretize()
-            dep_id = package_id(dep)
-            self.dependencies.add(dep_id)
-
         # List of uninstalled dependencies, which is used to establish
         # the priority of the build task.
         #
@@ -1165,53 +1099,6 @@ def __str__(self) -> str:
         installed = f"installed ({len(self.installed)}) = {self.installed}"
         return f"{self.pid}: {requests}; {tasks}; {installed}; {failed}"
 
-    def _add_bootstrap_compilers(
-        self,
-        compiler: "spack.spec.CompilerSpec",
-        architecture: "spack.spec.ArchSpec",
-        pkgs: List["spack.package_base.PackageBase"],
-        request: BuildRequest,
-        all_deps,
-    ) -> None:
-        """
-        Add bootstrap compilers and dependencies to the build queue.
-
-        Args:
-            compiler: the compiler to boostrap
-            architecture: the architecture for which to bootstrap the compiler
-            pkgs: the package list with possible compiler dependencies
-            request: the associated install request
-            all_deps (defaultdict(set)): dictionary of all dependencies and
-                associated dependents
-        """
-        packages = _packages_needed_to_bootstrap_compiler(compiler, architecture, pkgs)
-        for comp_pkg, is_compiler in packages:
-            pkgid = package_id(comp_pkg.spec)
-            if pkgid not in self.build_tasks:
-                self._add_init_task(comp_pkg, request, is_compiler, all_deps)
-            elif is_compiler:
-                # ensure it's queued as a compiler
-                self._modify_existing_task(pkgid, "compiler", True)
-
-    def _modify_existing_task(self, pkgid: str, attr, value) -> None:
-        """
-        Update a task in-place to modify its behavior.
-
-        Currently used to update the ``compiler`` field on tasks
-        that were originally created as a dependency of a compiler,
-        but are compilers in their own right.
-
-        For example, ``intel-oneapi-compilers-classic`` depends on
-        ``intel-oneapi-compilers``, which can cause the latter to be
-        queued first as a non-compiler, and only later as a compiler.
-        """
-        for i, tup in enumerate(self.build_pq):
-            key, task = tup
-            if task.pkg_id == pkgid:
-                tty.debug(f"Modifying task for {pkgid} to treat it as a compiler", level=2)
-                setattr(task, attr, value)
-                self.build_pq[i] = (key, task)
-
     def _add_init_task(
         self,
         pkg: "spack.package_base.PackageBase",
@@ -1541,42 +1428,7 @@ def _add_tasks(self, request: BuildRequest, all_deps):
             tty.warn(f"Installation request refused: {str(err)}")
             return
 
-        install_compilers = spack.config.get("config:install_missing_compilers", False)
-
         install_deps = request.install_args.get("install_deps")
-        # Bootstrap compilers first
-        if install_deps and install_compilers:
-            packages_per_compiler: Dict[
-                "spack.spec.CompilerSpec",
-                Dict["spack.spec.ArchSpec", List["spack.package_base.PackageBase"]],
-            ] = {}
-
-            for dep in request.traverse_dependencies():
-                dep_pkg = dep.package
-                compiler = dep_pkg.spec.compiler
-                arch = dep_pkg.spec.architecture
-                if compiler not in packages_per_compiler:
-                    packages_per_compiler[compiler] = {}
-
-                if arch not in packages_per_compiler[compiler]:
-                    packages_per_compiler[compiler][arch] = []
-
-                packages_per_compiler[compiler][arch].append(dep_pkg)
-
-            compiler = request.pkg.spec.compiler
-            arch = request.pkg.spec.architecture
-
-            if compiler not in packages_per_compiler:
-                packages_per_compiler[compiler] = {}
-
-            if arch not in packages_per_compiler[compiler]:
-                packages_per_compiler[compiler][arch] = []
-
-            packages_per_compiler[compiler][arch].append(request.pkg)
-
-            for compiler, archs in packages_per_compiler.items():
-                for arch, packages in archs.items():
-                    self._add_bootstrap_compilers(compiler, arch, packages, request, all_deps)
 
         if install_deps:
             for dep in request.traverse_dependencies():
@@ -1608,10 +1460,6 @@ def _add_tasks(self, request: BuildRequest, all_deps):
         fail_fast = bool(request.install_args.get("fail_fast"))
         self.fail_fast = self.fail_fast or fail_fast
 
-    def _add_compiler_package_to_config(self, pkg: "spack.package_base.PackageBase") -> None:
-        compiler_search_prefix = getattr(pkg, "compiler_search_prefix", pkg.spec.prefix)
-        spack.compilers.find_compilers([compiler_search_prefix])
-
     def _install_task(self, task: BuildTask, install_status: InstallStatus) -> None:
         """
         Perform the installation of the requested spec and/or dependency
@@ -1639,8 +1487,6 @@ def _install_task(self, task: BuildTask, install_status: InstallStatus) -> None:
         if use_cache:
             if _install_from_cache(pkg, explicit, unsigned):
                 self._update_installed(task)
-                if task.compiler:
-                    self._add_compiler_package_to_config(pkg)
                 return
             elif cache_only:
                 raise InstallError("No binary found when cache-only was specified", pkg=pkg)
@@ -1668,11 +1514,8 @@ def _install_task(self, task: BuildTask, install_status: InstallStatus) -> None:
             )
             # Note: PARENT of the build process adds the new package to
             # the database, so that we don't need to re-read from file.
-            spack.store.STORE.db.add(pkg.spec, spack.store.STORE.layout, explicit=explicit)
+            spack.store.STORE.db.add(pkg.spec, explicit=explicit)
 
-            # If a compiler, ensure it is added to the configuration
-            if task.compiler:
-                self._add_compiler_package_to_config(pkg)
         except spack.build_environment.StopPhase as e:
             # A StopPhase exception means that do_install was asked to
             # stop early from clients, and is not an error at this point
@@ -2073,10 +1916,6 @@ def install(self) -> None:
                     path = spack.util.path.debug_padded_filter(pkg.prefix)
                     _print_installed_pkg(path)
 
-                    # It's an already installed compiler, add it to the config
-                    if task.compiler:
-                        self._add_compiler_package_to_config(pkg)
-
                 else:
                     # At this point we've failed to get a write or a read
                     # lock, which means another process has taken a write

lib/spack/spack/mirror.py

@@ -29,7 +29,6 @@
 import spack.config
 import spack.error
 import spack.fetch_strategy
-import spack.mirror
 import spack.oci.image
 import spack.repo
 import spack.spec

lib/spack/spack/modules/common.py

@@ -46,7 +46,6 @@
 import spack.deptypes as dt
 import spack.environment
 import spack.error
-import spack.modules.common
 import spack.paths
 import spack.projections as proj
 import spack.repo
@@ -352,7 +351,7 @@ def get_module(module_type, spec, get_full_path, module_set_name="default", requ
     except spack.repo.UnknownPackageError:
         upstream, record = spack.store.STORE.db.query_by_spec_hash(spec.dag_hash())
     if upstream:
-        module = spack.modules.common.upstream_module_index.upstream_module(spec, module_type)
+        module = upstream_module_index.upstream_module(spec, module_type)
         if not module:
             return None
 

lib/spack/spack/package.py

@@ -104,6 +104,7 @@
 from spack.spec import InvalidSpecDetected, Spec
 from spack.util.cpus import determine_number_of_jobs
 from spack.util.executable import *
+from spack.util.filesystem import file_command, fix_darwin_install_name, mime_type
 from spack.variant import (
     any_combination_of,
     auto_or_any_combination_of,

lib/spack/spack/package_base.py

@@ -16,7 +16,6 @@
 import glob
 import hashlib
 import importlib
-import inspect
 import io
 import os
 import re
@@ -117,11 +116,10 @@ def preferred_version(pkg: "PackageBase"):
     Arguments:
         pkg: The package whose versions are to be assessed.
     """
-    # Here we sort first on the fact that a version is marked
-    # as preferred in the package, then on the fact that the
-    # version is not develop, then lexicographically
-    key_fn = lambda v: (pkg.versions[v].get("preferred", False), not v.isdevelop(), v)
-    return max(pkg.versions, key=key_fn)
+    from spack.solver.asp import concretization_version_order
+
+    version, _ = max(pkg.versions.items(), key=concretization_version_order)
+    return version
 
 
 class WindowsRPath:
@@ -1744,7 +1742,7 @@ def _has_make_target(self, target):
             bool: True if 'target' is found, else False
         """
         # Prevent altering LC_ALL for 'make' outside this function
-        make = copy.deepcopy(inspect.getmodule(self).make)
+        make = copy.deepcopy(self.module.make)
 
         # Use English locale for missing target message comparison
         make.add_default_env("LC_ALL", "C")
@@ -1794,7 +1792,7 @@ def _if_make_target_execute(self, target, *args, **kwargs):
         """
         if self._has_make_target(target):
             # Execute target
-            inspect.getmodule(self).make(target, *args, **kwargs)
+            self.module.make(target, *args, **kwargs)
 
     def _has_ninja_target(self, target):
         """Checks to see if 'target' is a valid target in a Ninja build script.
@@ -1805,7 +1803,7 @@ def _has_ninja_target(self, target):
         Returns:
             bool: True if 'target' is found, else False
         """
-        ninja = inspect.getmodule(self).ninja
+        ninja = self.module.ninja
 
         # Check if we have a Ninja build script
         if not os.path.exists("build.ninja"):
@@ -1834,7 +1832,7 @@ def _if_ninja_target_execute(self, target, *args, **kwargs):
         """
         if self._has_ninja_target(target):
             # Execute target
-            inspect.getmodule(self).ninja(target, *args, **kwargs)
+            self.module.ninja(target, *args, **kwargs)
 
     def _get_needed_resources(self):
         # We use intersects here cause it would also work if self.spec is abstract

lib/spack/spack/relocate.py

@@ -12,7 +12,6 @@
 import macholib.mach_o
 import macholib.MachO
 
-import llnl.util.filesystem as fs
 import llnl.util.lang
 import llnl.util.tty as tty
 from llnl.util.lang import memoized
@@ -25,6 +24,7 @@
 import spack.store
 import spack.util.elf as elf
 import spack.util.executable as executable
+import spack.util.filesystem as ssys
 import spack.util.path
 
 from .relocate_text import BinaryFilePrefixReplacer, TextFilePrefixReplacer
@@ -664,7 +664,7 @@ def is_binary(filename):
     Returns:
         True or False
     """
-    m_type, _ = fs.mime_type(filename)
+    m_type, _ = ssys.mime_type(filename)
 
     msg = "[{0}] -> ".format(filename)
     if m_type == "application":
@@ -692,7 +692,7 @@ def fixup_macos_rpath(root, filename):
         True if fixups were applied, else False
     """
     abspath = os.path.join(root, filename)
-    if fs.mime_type(abspath) != ("application", "x-mach-binary"):
+    if ssys.mime_type(abspath) != ("application", "x-mach-binary"):
         return False
 
     # Get Mach-O header commands

lib/spack/spack/rewiring.py

@@ -116,7 +116,7 @@ def rewire_node(spec, explicit):
     # spec being added to look for mismatches)
     spack.store.STORE.layout.write_spec(spec, spack.store.STORE.layout.spec_file_path(spec))
     # add to database, not sure about explicit
-    spack.store.STORE.db.add(spec, spack.store.STORE.layout, explicit=explicit)
+    spack.store.STORE.db.add(spec, explicit=explicit)
 
     # run post install hooks
     spack.hooks.post_install(spec, explicit)

lib/spack/spack/schema/__init__.py

@@ -3,22 +3,28 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """This module contains jsonschema files for all of Spack's YAML formats."""
+import typing
 import warnings
 
 import llnl.util.lang
 
 
+class DeprecationMessage(typing.NamedTuple):
+    message: str
+    error: bool
+
+
 # jsonschema is imported lazily as it is heavy to import
 # and increases the start-up time
 def _make_validator():
     import jsonschema
 
-    import spack.parser
-
     def _validate_spec(validator, is_spec, instance, schema):
         """Check if the attributes on instance are valid specs."""
         import jsonschema
 
+        import spack.parser
+
         if not validator.is_type(instance, "object"):
             return
 
@@ -32,27 +38,31 @@ def _deprecated_properties(validator, deprecated, instance, schema):
         if not (validator.is_type(instance, "object") or validator.is_type(instance, "array")):
             return
 
-        # Get a list of the deprecated properties, return if there is none
-        deprecated_properties = [x for x in instance if x in deprecated["properties"]]
-        if not deprecated_properties:
+        if not deprecated:
             return
 
-        # Retrieve the template message
-        msg_str_or_func = deprecated["message"]
-        if isinstance(msg_str_or_func, str):
-            msg = msg_str_or_func.format(properties=deprecated_properties)
-        else:
-            msg = msg_str_or_func(instance, deprecated_properties)
-            if msg is None:
-                return
+        deprecations = {
+            name: DeprecationMessage(message=x["message"], error=x["error"])
+            for x in deprecated
+            for name in x["names"]
+        }
 
-        is_error = deprecated["error"]
-        if not is_error:
-            warnings.warn(msg)
-        else:
-            import jsonschema
+        # 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
 
-            yield jsonschema.ValidationError(msg)
+        # 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.Draft4Validator,

lib/spack/spack/schema/config.py

@@ -75,7 +75,6 @@
             "verify_ssl": {"type": "boolean"},
             "ssl_certs": {"type": "string"},
             "suppress_gpg_warnings": {"type": "boolean"},
-            "install_missing_compilers": {"type": "boolean"},
             "debug": {"type": "boolean"},
             "checksum": {"type": "boolean"},
             "deprecated": {"type": "boolean"},
@@ -96,12 +95,21 @@
             "binary_index_ttl": {"type": "integer", "minimum": 0},
             "aliases": {"type": "object", "patternProperties": {r"\w[\w-]*": {"type": "string"}}},
         },
-        "deprecatedProperties": {
-            "properties": ["concretizer"],
-            "message": "Spack supports only clingo as a concretizer from v0.23. "
-            "The config:concretizer config option is ignored.",
-            "error": False,
-        },
+        "deprecatedProperties": [
+            {
+                "names": ["concretizer"],
+                "message": "Spack supports only clingo as a concretizer from v0.23. "
+                "The config:concretizer config option is ignored.",
+                "error": False,
+            },
+            {
+                "names": ["install_missing_compilers"],
+                "message": "The config:install_missing_compilers option has been deprecated in "
+                "Spack v0.23, and is currently ignored. It will be removed from config in "
+                "Spack v0.25.",
+                "error": False,
+            },
+        ],
     }
 }
 

lib/spack/spack/schema/packages.py

@@ -109,7 +109,6 @@
                     "require": requirements,
                     "prefer": prefer_and_conflict,
                     "conflict": prefer_and_conflict,
-                    "version": {},  # Here only to warn users on ignored properties
                     "target": {
                         "type": "array",
                         "default": [],
@@ -140,14 +139,6 @@
                     },
                     "variants": variants,
                 },
-                "deprecatedProperties": {
-                    "properties": ["version"],
-                    "message": "setting version preferences in the 'all' section of packages.yaml "
-                    "is deprecated and will be removed in v0.23\n\n\tThese preferences "
-                    "will be ignored by Spack. You can set them only in package-specific sections "
-                    "of the same file.\n",
-                    "error": False,
-                },
             }
         },
         "patternProperties": {
@@ -165,14 +156,11 @@
                         # version strings
                         "items": {"anyOf": [{"type": "string"}, {"type": "number"}]},
                     },
-                    "target": {},  # Here only to warn users on ignored properties
-                    "compiler": {},  # Here only to warn users on ignored properties
                     "buildable": {"type": "boolean", "default": True},
                     "permissions": permissions,
                     # If 'get_full_repo' is promoted to a Package-level
                     # attribute, it could be useful to set it here
                     "package_attributes": package_attributes,
-                    "providers": {},  # Here only to warn users on ignored properties
                     "variants": variants,
                     "externals": {
                         "type": "array",
@@ -204,18 +192,6 @@
                         },
                     },
                 },
-                "deprecatedProperties": {
-                    "properties": ["target", "compiler", "providers"],
-                    "message": "setting 'compiler:', 'target:' or 'provider:' preferences in "
-                    "a package-specific section of packages.yaml is deprecated, and will be "
-                    "removed in v0.23.\n\n\tThese preferences will be ignored by Spack, and "
-                    "can be set only in the 'all' section of the same file. "
-                    "You can run:\n\n\t\t$ spack audit configs\n\n\tto get better diagnostics, "
-                    "including files:lines where the deprecated attributes are used.\n\n"
-                    "\tUse requirements to enforce conditions on specific packages: "
-                    f"{REQUIREMENT_URL}\n",
-                    "error": False,
-                },
             }
         },
     }

lib/spack/spack/solver/asp.py

@@ -579,7 +579,7 @@ def _is_checksummed_version(version_info: Tuple[GitOrStandardVersion, dict]):
     return _is_checksummed_git_version(version)
 
 
-def _concretization_version_order(version_info: Tuple[GitOrStandardVersion, dict]):
+def concretization_version_order(version_info: Tuple[GitOrStandardVersion, dict]):
     """Version order key for concretization, where preferred > not preferred,
     not deprecated > deprecated, finite > any infinite component; only if all are
     the same, do we use default version ordering."""
@@ -1022,6 +1022,102 @@ def __iter__(self):
 ConditionSpecCache = Dict[str, Dict[ConditionSpecKey, ConditionIdFunctionPair]]
 
 
+class ConstraintOrigin(enum.Enum):
+    """Generates identifiers that can be pased into the solver attached
+    to constraints, and then later retrieved to determine the origin of
+    those constraints when ``SpecBuilder`` creates Specs from the solve
+    result.
+    """
+
+    DEPENDS_ON = 1
+    REQUIRE = 2
+
+    @staticmethod
+    def _SUFFIXES() -> Dict["ConstraintOrigin", str]:
+        return {ConstraintOrigin.DEPENDS_ON: "_dep", ConstraintOrigin.REQUIRE: "_req"}
+
+    @staticmethod
+    def append_type_suffix(pkg_id: str, kind: "ConstraintOrigin") -> str:
+        """Given a package identifier and a constraint kind, generate a string ID."""
+        suffix = ConstraintOrigin._SUFFIXES()[kind]
+        return f"{pkg_id}{suffix}"
+
+    @staticmethod
+    def strip_type_suffix(source: str) -> Tuple[int, Optional[str]]:
+        """Take a combined package/type ID generated by
+        ``append_type_suffix``, and extract the package ID and
+        an associated weight.
+        """
+        if not source:
+            return -1, None
+        for kind, suffix in ConstraintOrigin._SUFFIXES().items():
+            if source.endswith(suffix):
+                return kind.value, source[: -len(suffix)]
+        return -1, source
+
+
+class SourceContext:
+    """Tracks context in which a Spec's clause-set is generated (i.e.
+    with ``SpackSolverSetup.spec_clauses``).
+
+    Facts generated for the spec may include this context.
+    """
+
+    def __init__(self):
+        # This can be "literal" for constraints that come from a user
+        # spec (e.g. from the command line); it can be the output of
+        # `ConstraintOrigin.append_type_suffix`; the default is "none"
+        # (which means it isn't important to keep track of the source
+        # in that case).
+        self.source = "none"
+
+
+class ConditionIdContext(SourceContext):
+    """Derived from a ``ConditionContext``: for clause-sets generated by
+    imposed/required specs, stores an associated transform.
+
+    This is primarily used for tracking whether we are generating clauses
+    in the context of a required spec, or for an imposed spec.
+
+    Is not a subclass of ``ConditionContext`` because it exists in a
+    lower-level context with less information.
+    """
+
+    def __init__(self):
+        super().__init__()
+        self.transform = None
+
+
+class ConditionContext(SourceContext):
+    """Tracks context in which a condition (i.e. ``SpackSolverSetup.condition``)
+    is generated (e.g. for a `depends_on`).
+
+    This may modify the required/imposed specs generated as relevant
+    for the context.
+    """
+
+    def __init__(self):
+        super().__init__()
+        # transformation applied to facts from the required spec. Defaults
+        # to leave facts as they are.
+        self.transform_required = None
+        # transformation applied to facts from the imposed spec. Defaults
+        # to removing "node" and "virtual_node" facts.
+        self.transform_imposed = None
+
+    def requirement_context(self) -> ConditionIdContext:
+        ctxt = ConditionIdContext()
+        ctxt.source = self.source
+        ctxt.transform = self.transform_required
+        return ctxt
+
+    def impose_context(self) -> ConditionIdContext:
+        ctxt = ConditionIdContext()
+        ctxt.source = self.source
+        ctxt.transform = self.transform_imposed
+        return ctxt
+
+
 class SpackSolverSetup:
     """Class to set up and run a Spack concretization solve."""
 
@@ -1197,8 +1293,9 @@ def compiler_facts(self):
             if compiler.compiler_obj is not None:
                 c = compiler.compiler_obj
                 for flag_type, flags in c.flags.items():
+                    flag_group = " ".join(flags)
                     for flag in flags:
-                        self.gen.fact(fn.compiler_flag(compiler_id, flag_type, flag))
+                        self.gen.fact(fn.compiler_flag(compiler_id, flag_type, flag, flag_group))
 
             if compiler.available:
                 self.gen.fact(fn.compiler_available(compiler_id))
@@ -1375,7 +1472,7 @@ def _get_condition_id(
         named_cond: spack.spec.Spec,
         cache: ConditionSpecCache,
         body: bool,
-        transform: Optional[TransformFunction] = None,
+        context: ConditionIdContext,
     ) -> int:
         """Get the id for one half of a condition (either a trigger or an imposed constraint).
 
@@ -1389,15 +1486,15 @@ def _get_condition_id(
         """
         pkg_cache = cache[named_cond.name]
 
-        named_cond_key = (str(named_cond), transform)
+        named_cond_key = (str(named_cond), context.transform)
         result = pkg_cache.get(named_cond_key)
         if result:
             return result[0]
 
         cond_id = next(self._id_counter)
-        requirements = self.spec_clauses(named_cond, body=body)
-        if transform:
-            requirements = transform(named_cond, requirements)
+        requirements = self.spec_clauses(named_cond, body=body, context=context)
+        if context.transform:
+            requirements = context.transform(named_cond, requirements)
         pkg_cache[named_cond_key] = (cond_id, requirements)
 
         return cond_id
@@ -1408,8 +1505,7 @@ def condition(
         imposed_spec: Optional[spack.spec.Spec] = None,
         name: Optional[str] = None,
         msg: Optional[str] = None,
-        transform_required: Optional[TransformFunction] = None,
-        transform_imposed: Optional[TransformFunction] = remove_node,
+        context: Optional[ConditionContext] = None,
     ):
         """Generate facts for a dependency or virtual provider condition.
 
@@ -1418,10 +1514,8 @@ def condition(
             imposed_spec: the constraints that are imposed when this condition is triggered
             name: name for `required_spec` (required if required_spec is anonymous, ignored if not)
             msg: description of the condition
-            transform_required: transformation applied to facts from the required spec. Defaults
-                to leave facts as they are.
-            transform_imposed: transformation applied to facts from the imposed spec. Defaults
-                to removing "node" and "virtual_node" facts.
+            context: if provided, indicates how to modify the clause-sets for the required/imposed
+                specs based on the type of constraint they are generated for (e.g. `depends_on`)
         Returns:
             int: id of the condition created by this function
         """
@@ -1429,14 +1523,19 @@ def condition(
         if not name:
             raise ValueError(f"Must provide a name for anonymous condition: '{required_spec}'")
 
+        if not context:
+            context = ConditionContext()
+            context.transform_imposed = remove_node
+
         with spec_with_name(required_spec, name):
             # Check if we can emit the requirements before updating the condition ID counter.
             # In this way, if a condition can't be emitted but the exception is handled in the
             # caller, we won't emit partial facts.
 
             condition_id = next(self._id_counter)
+            requirement_context = context.requirement_context()
             trigger_id = self._get_condition_id(
-                required_spec, cache=self._trigger_cache, body=True, transform=transform_required
+                required_spec, cache=self._trigger_cache, body=True, context=requirement_context
             )
             self.gen.fact(fn.pkg_fact(required_spec.name, fn.condition(condition_id)))
             self.gen.fact(fn.condition_reason(condition_id, msg))
@@ -1446,8 +1545,9 @@ def condition(
             if not imposed_spec:
                 return condition_id
 
+            impose_context = context.impose_context()
             effect_id = self._get_condition_id(
-                imposed_spec, cache=self._effect_cache, body=False, transform=transform_imposed
+                imposed_spec, cache=self._effect_cache, body=False, context=impose_context
             )
             self.gen.fact(
                 fn.pkg_fact(required_spec.name, fn.condition_effect(condition_id, effect_id))
@@ -1455,8 +1555,8 @@ def condition(
 
             return condition_id
 
-    def impose(self, condition_id, imposed_spec, node=True, name=None, body=False):
-        imposed_constraints = self.spec_clauses(imposed_spec, body=body, required_from=name)
+    def impose(self, condition_id, imposed_spec, node=True, body=False):
+        imposed_constraints = self.spec_clauses(imposed_spec, body=body)
         for pred in imposed_constraints:
             # imposed "node"-like conditions are no-ops
             if not node and pred.args[0] in ("node", "virtual_node"):
@@ -1528,14 +1628,14 @@ def dependency_holds(input_spec, requirements):
                         if t & depflag
                     ]
 
-                self.condition(
-                    cond,
-                    dep.spec,
-                    name=pkg.name,
-                    msg=msg,
-                    transform_required=track_dependencies,
-                    transform_imposed=dependency_holds,
+                context = ConditionContext()
+                context.source = ConstraintOrigin.append_type_suffix(
+                    pkg.name, ConstraintOrigin.DEPENDS_ON
                 )
+                context.transform_required = track_dependencies
+                context.transform_imposed = dependency_holds
+
+                self.condition(cond, dep.spec, name=pkg.name, msg=msg, context=context)
 
                 self.gen.newline()
 
@@ -1613,17 +1713,21 @@ def emit_facts_from_requirement_rules(self, rules: List[RequirementRule]):
                     when_spec = spack.spec.Spec(pkg_name)
 
                 try:
-                    # With virtual we want to emit "node" and "virtual_node" in imposed specs
-                    transform: Optional[TransformFunction] = remove_node
-                    if virtual:
-                        transform = None
+                    context = ConditionContext()
+                    context.source = ConstraintOrigin.append_type_suffix(
+                        pkg_name, ConstraintOrigin.REQUIRE
+                    )
+                    if not virtual:
+                        context.transform_imposed = remove_node
+                    # else: for virtuals we want to emit "node" and
+                    # "virtual_node" in imposed specs
 
                     member_id = self.condition(
                         required_spec=when_spec,
                         imposed_spec=spec,
                         name=pkg_name,
-                        transform_imposed=transform,
                         msg=f"{input_spec} is a requirement for package {pkg_name}",
+                        context=context,
                     )
                 except Exception as e:
                     # Do not raise if the rule comes from the 'all' subsection, since usability
@@ -1678,6 +1782,10 @@ def external_packages(self):
             if pkg_name not in spack.repo.PATH:
                 continue
 
+            # This package is not among possible dependencies
+            if pkg_name not in self.pkgs:
+                continue
+
             # Check if the external package is buildable. If it is
             # not then "external(<pkg>)" is a fact, unless we can
             # reuse an already installed spec.
@@ -1718,7 +1826,9 @@ def external_imposition(input_spec, requirements):
                     ]
 
                 try:
-                    self.condition(spec, spec, msg=msg, transform_imposed=external_imposition)
+                    context = ConditionContext()
+                    context.transform_imposed = external_imposition
+                    self.condition(spec, spec, msg=msg, context=context)
                 except (spack.error.SpecError, RuntimeError) as e:
                     warnings.warn(f"while setting up external spec {spec}: {e}")
                     continue
@@ -1793,6 +1903,7 @@ def spec_clauses(
         expand_hashes: bool = False,
         concrete_build_deps=False,
         required_from: Optional[str] = None,
+        context: Optional[SourceContext] = None,
     ) -> List[AspFunction]:
         """Wrap a call to `_spec_clauses()` into a try/except block with better error handling.
 
@@ -1808,6 +1919,7 @@ def spec_clauses(
                 transitive=transitive,
                 expand_hashes=expand_hashes,
                 concrete_build_deps=concrete_build_deps,
+                context=context,
             )
         except RuntimeError as exc:
             msg = str(exc)
@@ -1824,6 +1936,7 @@ def _spec_clauses(
         transitive: bool = True,
         expand_hashes: bool = False,
         concrete_build_deps: bool = False,
+        context: Optional[SourceContext] = None,
     ) -> List[AspFunction]:
         """Return a list of clauses for a spec mandates are true.
 
@@ -1835,6 +1948,8 @@ def _spec_clauses(
             expand_hashes: if True, descend into hashes of concrete specs (default False)
             concrete_build_deps: if False, do not include pure build deps of concrete specs
                 (as they have no effect on runtime constraints)
+            context: tracks what constraint this clause set is generated for (e.g. a
+                `depends_on` constraint in a package.py file)
 
         Normally, if called with ``transitive=True``, ``spec_clauses()`` just generates
         hashes for the dependency requirements of concrete specs. If ``expand_hashes``
@@ -1921,13 +2036,19 @@ def _spec_clauses(
                 self.compiler_version_constraints.add(spec.compiler)
 
         # compiler flags
+        source = context.source if context else "none"
         for flag_type, flags in spec.compiler_flags.items():
+            flag_group = " ".join(flags)
             for flag in flags:
-                clauses.append(f.node_flag(spec.name, flag_type, flag))
+                clauses.append(
+                    f.node_flag(spec.name, fn.node_flag(flag_type, flag, flag_group, source))
+                )
                 if not spec.concrete and flag.propagate is True:
                     clauses.append(
                         f.propagate(
-                            spec.name, fn.node_flag(flag_type, flag), fn.edge_types("link", "run")
+                            spec.name,
+                            fn.node_flag(flag_type, flag, flag_group, source),
+                            fn.edge_types("link", "run"),
                         )
                     )
 
@@ -2009,6 +2130,7 @@ def _spec_clauses(
                             body=body,
                             expand_hashes=expand_hashes,
                             concrete_build_deps=concrete_build_deps,
+                            context=context,
                         )
                     )
 
@@ -2026,7 +2148,7 @@ def define_package_versions_and_validate_preferences(
             # like being a "develop" version or being preferred exist only at a
             # package.py level, sort them in this partial list here
             package_py_versions = sorted(
-                pkg_cls.versions.items(), key=_concretization_version_order, reverse=True
+                pkg_cls.versions.items(), key=concretization_version_order, reverse=True
             )
 
             if require_checksum and pkg_cls.has_code:
@@ -2609,10 +2731,6 @@ def define_runtime_constraints(self):
                 continue
 
             current_libc = compiler.compiler_obj.default_libc
-            # If this is a compiler yet to be built (config:install_missing_compilers:true)
-            # infer libc from the Python process
-            if not current_libc and compiler.compiler_obj.cc is None:
-                current_libc = spack.util.libc.libc_from_current_python_process()
 
             if using_libc_compatibility() and current_libc:
                 recorder("*").depends_on(
@@ -2644,7 +2762,9 @@ def literal_specs(self, specs):
                 effect_id, requirements = cache[imposed_spec_key]
             else:
                 effect_id = next(self._id_counter)
-                requirements = self.spec_clauses(spec)
+                context = SourceContext()
+                context.source = "literal"
+                requirements = self.spec_clauses(spec, context=context)
             root_name = spec.name
             for clause in requirements:
                 clause_name = clause.args[0]
@@ -3032,7 +3152,7 @@ def with_input_specs(self, input_specs: List["spack.spec.Spec"]) -> "CompilerPar
         Args:
             input_specs: specs to be concretized
         """
-        strict = spack.concretize.Concretizer().check_for_compiler_existence
+        strict = spack.concretize.CHECK_COMPILER_EXISTENCE
         default_os = str(spack.platforms.host().default_os)
         default_target = str(archspec.cpu.host().family)
         for s in traverse.traverse_nodes(input_specs):
@@ -3344,7 +3464,6 @@ def __init__(self, specs, hash_lookup=None):
         self._result = None
         self._command_line_specs = specs
         self._flag_sources = collections.defaultdict(lambda: set())
-        self._flag_compiler_defaults = set()
 
         # Pass in as arguments reusable specs and plug them in
         # from this dictionary during reconstruction
@@ -3402,14 +3521,10 @@ def node_compiler_version(self, node, compiler, version):
         self._specs[node].compiler = spack.spec.CompilerSpec(compiler)
         self._specs[node].compiler.versions = vn.VersionList([vn.Version(version)])
 
-    def node_flag_compiler_default(self, node):
-        self._flag_compiler_defaults.add(node)
-
-    def node_flag(self, node, flag_type, flag):
-        self._specs[node].compiler_flags.add_flag(flag_type, flag, False)
-
-    def node_flag_source(self, node, flag_type, source):
-        self._flag_sources[(node, flag_type)].add(source)
+    def node_flag(self, node, node_flag):
+        self._specs[node].compiler_flags.add_flag(
+            node_flag.flag_type, node_flag.flag, False, node_flag.flag_group, node_flag.source
+        )
 
     def external_spec_selected(self, node, idx):
         """This means that the external spec and index idx has been selected for this package."""
@@ -3450,15 +3565,23 @@ def virtual_on_edge(self, parent_node, provider_node, virtual):
         dependencies[0].update_virtuals((virtual,))
 
     def reorder_flags(self):
-        """Order compiler flags on specs in predefined order.
-
-        We order flags so that any node's flags will take priority over
-        those of its dependents.  That is, the deepest node in the DAG's
-        flags will appear last on the compile line, in the order they
-        were specified.
+        """For each spec, determine the order of compiler flags applied to it.
 
         The solver determines which flags are on nodes; this routine
-        imposes order afterwards.
+        imposes order afterwards. The order is:
+
+        1. Flags applied in compiler definitions should come first
+        2. Flags applied by dependents are ordered topologically (with a
+           dependency on `traverse` to resolve the partial order into a
+           stable total order)
+        3. Flags from requirements are then applied (requirements always
+           come from the package and never a parent)
+        4. Command-line flags should come last
+
+        Additionally, for each source (requirements, compiler, command line, and
+        dependents), flags from that source should retain their order and grouping:
+        e.g. for `y cflags="-z -a"` "-z" and "-a" should never have any intervening
+        flags inserted, and should always appear in that order.
         """
         # reverse compilers so we get highest priority compilers that share a spec
         compilers = dict(
@@ -3473,40 +3596,78 @@ def reorder_flags(self):
                 flagmap_from_compiler = compilers[spec.compiler].flags
 
             for flag_type in spec.compiler_flags.valid_compiler_flags():
-                from_compiler = flagmap_from_compiler.get(flag_type, [])
-                from_sources = []
-
-                # order is determined by the  DAG. A spec's flags come after any of its ancestors
-                # on the compile line
                 node = SpecBuilder.make_node(pkg=spec.name)
-                source_key = (node, flag_type)
-                if source_key in self._flag_sources:
-                    order = [
-                        SpecBuilder.make_node(pkg=s.name)
-                        for s in spec.traverse(order="post", direction="parents")
-                    ]
-                    sorted_sources = sorted(
-                        self._flag_sources[source_key], key=lambda s: order.index(s)
+
+                ordered_flags = []
+
+                # 1. Put compiler flags first
+                from_compiler = tuple(flagmap_from_compiler.get(flag_type, []))
+                extend_flag_list(ordered_flags, from_compiler)
+
+                # 2. Add all sources (the compiler is one of them, so skip any
+                # flag group that matches it exactly)
+                flag_groups = set()
+                for flag in self._specs[node].compiler_flags.get(flag_type, []):
+                    flag_groups.add(
+                        spack.spec.CompilerFlag(
+                            flag.flag_group,
+                            propagate=flag.propagate,
+                            flag_group=flag.flag_group,
+                            source=flag.source,
+                        )
                     )
 
-                    # add flags from each source, lowest to highest precedence
-                    for node in sorted_sources:
-                        all_src_flags = list()
-                        per_pkg_sources = [self._specs[node]]
-                        if node.pkg in cmd_specs:
-                            per_pkg_sources.append(cmd_specs[node.pkg])
-                        for source in per_pkg_sources:
-                            all_src_flags.extend(source.compiler_flags.get(flag_type, []))
-                        extend_flag_list(from_sources, all_src_flags)
+                # For flags that are applied by dependents, put flags from parents
+                # before children; we depend on the stability of traverse() to
+                # achieve a stable flag order for flags introduced in this manner.
+                topo_order = list(s.name for s in spec.traverse(order="post", direction="parents"))
+                lex_order = list(sorted(flag_groups))
+
+                def _order_index(flag_group):
+                    source = flag_group.source
+                    # Note: if 'require: ^dependency cflags=...' is ever possible,
+                    # this will topologically sort for require as well
+                    type_index, pkg_source = ConstraintOrigin.strip_type_suffix(source)
+                    if pkg_source in topo_order:
+                        major_index = topo_order.index(pkg_source)
+                        # If for x->y, x has multiple depends_on declarations that
+                        # are activated, and each adds cflags to y, we fall back on
+                        # alphabetical ordering to maintain a total order
+                        minor_index = lex_order.index(flag_group)
+                    else:
+                        major_index = len(topo_order) + lex_order.index(flag_group)
+                        minor_index = 0
+                    return (type_index, major_index, minor_index)
+
+                prioritized_groups = sorted(flag_groups, key=lambda x: _order_index(x))
+
+                for grp in prioritized_groups:
+                    grp_flags = tuple(
+                        x for (x, y) in spack.compiler.tokenize_flags(grp.flag_group)
+                    )
+                    if grp_flags == from_compiler:
+                        continue
+                    as_compiler_flags = list(
+                        spack.spec.CompilerFlag(
+                            x,
+                            propagate=grp.propagate,
+                            flag_group=grp.flag_group,
+                            source=grp.source,
+                        )
+                        for x in grp_flags
+                    )
+                    extend_flag_list(ordered_flags, as_compiler_flags)
+
+                # 3. Now put cmd-line flags last
+                if node.pkg in cmd_specs:
+                    cmd_flags = cmd_specs[node.pkg].compiler_flags.get(flag_type, [])
+                    extend_flag_list(ordered_flags, cmd_flags)
 
-                # compiler flags from compilers config are lowest precedence
-                ordered_compiler_flags = list(llnl.util.lang.dedupe(from_compiler + from_sources))
                 compiler_flags = spec.compiler_flags.get(flag_type, [])
+                msg = "%s does not equal %s" % (set(compiler_flags), set(ordered_flags))
+                assert set(compiler_flags) == set(ordered_flags), msg
 
-                msg = f"{set(compiler_flags)} does not equal {set(ordered_compiler_flags)}"
-                assert set(compiler_flags) == set(ordered_compiler_flags), msg
-
-                spec.compiler_flags.update({flag_type: ordered_compiler_flags})
+                spec.compiler_flags.update({flag_type: ordered_flags})
 
     def deprecated(self, node: NodeArgument, version: str) -> None:
         tty.warn(f'using "{node.pkg}@{version}" which is a deprecated version')
@@ -3570,10 +3731,9 @@ def build_specs(self, function_tuples):
                     continue
 
                 # if we've already gotten a concrete spec for this pkg,
-                # do not bother calling actions on it except for node_flag_source,
-                # since node_flag_source is tracking information not in the spec itself
+                # do not bother calling actions on it
                 spec = self._specs.get(args[0])
-                if spec and spec.concrete and name != "node_flag_source":
+                if spec and spec.concrete:
                     continue
 
             action(*args)
@@ -3633,7 +3793,8 @@ def _develop_specs_from_env(spec, env):
         assert spec.variants["dev_path"].value == path, error_msg
     else:
         spec.variants.setdefault("dev_path", spack.variant.SingleValuedVariant("dev_path", path))
-    spec.constrain(dev_info["spec"])
+
+    assert spec.satisfies(dev_info["spec"])
 
 
 def _is_reusable(spec: spack.spec.Spec, packages, local: bool) -> bool:

lib/spack/spack/solver/concretize.lp

@@ -43,9 +43,7 @@
    internal_error("Only nodes can have node_compiler_version").
 :- attr("variant_value", PackageNode, _, _), not attr("node", PackageNode),
    internal_error("variant_value true for a non-node").
-:- attr("node_flag_compiler_default", PackageNode), not attr("node", PackageNode),
-   internal_error("node_flag_compiler_default true for non-node").
-:- attr("node_flag", PackageNode, _, _), not attr("node", PackageNode),
+:- attr("node_flag", PackageNode, _), not attr("node", PackageNode),
    internal_error("node_flag assigned for non-node").
 :- attr("external_spec_selected", PackageNode, _), not attr("node", PackageNode),
    internal_error("external_spec_selected for non-node").
@@ -53,10 +51,6 @@
    internal_error("non-node depends on something").
 :- attr("depends_on", _, ChildNode, _), not attr("node", ChildNode),
    internal_error("something depends_on a non-node").
-:- attr("node_flag_source", Node, _, _), not attr("node", Node),
-   internal_error("node_flag_source assigned for a non-node").
-:- attr("node_flag_source", _, _, SourceNode), not attr("node", SourceNode),
-   internal_error("node_flag_source assigned with a non-node source").
 :- attr("virtual_node", VirtualNode), not provider(_, VirtualNode),
    internal_error("virtual node with no provider").
 :- provider(_, VirtualNode), not attr("virtual_node", VirtualNode),
@@ -154,7 +148,6 @@ unification_set(SetID, VirtualNode)
 % TODO: literals, at the moment, can only influence the "root" unification set. This needs to be extended later.
 
 % Node attributes that have multiple node arguments (usually, only the first argument is a node)
-multiple_nodes_attribute("node_flag_source").
 multiple_nodes_attribute("depends_on").
 multiple_nodes_attribute("virtual_on_edge").
 multiple_nodes_attribute("provider_set").
@@ -392,7 +385,6 @@ trigger_condition_holds(ID, RequestorNode) :-
   attr(Name, node(X, A1), A2, A3)     : condition_requirement(ID, Name, A1, A2, A3),     condition_nodes(ID, PackageNode, node(X, A1)), not multiple_nodes_attribute(Name);
   attr(Name, node(X, A1), A2, A3, A4) : condition_requirement(ID, Name, A1, A2, A3, A4), condition_nodes(ID, PackageNode, node(X, A1));
   % Special cases
-  attr("node_flag_source", node(X, A1), A2, node(Y, A3)) : condition_requirement(ID, "node_flag_source", A1, A2, A3), condition_nodes(ID, PackageNode, node(X, A1)), condition_nodes(ID, PackageNode, node(Y, A3));
   not cannot_hold(ID, PackageNode).
 
 condition_holds(ConditionID, node(X, Package))
@@ -440,13 +432,6 @@ attr(Name, node(X, A1), A2)         :- impose(ID, PackageNode), imposed_constrai
 attr(Name, node(X, A1), A2, A3)     :- impose(ID, PackageNode), imposed_constraint(ID, Name, A1, A2, A3),     imposed_nodes(ID, PackageNode, node(X, A1)), not multiple_nodes_attribute(Name).
 attr(Name, node(X, A1), A2, A3, A4) :- impose(ID, PackageNode), imposed_constraint(ID, Name, A1, A2, A3, A4), imposed_nodes(ID, PackageNode, node(X, A1)).
 
-% For node flag sources we need to look at the condition_set of the source, since it is the dependent
-% of the package on which I want to impose the constraint
-attr("node_flag_source", node(X, A1), A2, node(Y, A3))
-  :- impose(ID, node(X, A1)),
-     imposed_constraint(ID, "node_flag_source", A1, A2, A3),
-     condition_set(node(Y, A3), node(X, A1)).
-
 % Provider set is relevant only for literals, since it's the only place where `^[virtuals=foo] bar`
 % might appear in the HEAD of a rule
 attr("provider_set", node(min_dupe_id, Provider), node(min_dupe_id, Virtual))
@@ -487,8 +472,8 @@ virtual_condition_holds(node(Y, A2), Virtual)
 % we cannot have additional flag values when we are working with concrete specs
 :- attr("node", node(ID, Package)),
    attr("hash", node(ID, Package), Hash),
-   attr("node_flag", node(ID, Package), FlagType, Flag),
-   not imposed_constraint(Hash, "node_flag", Package, FlagType, Flag),
+   attr("node_flag", node(ID, Package), node_flag(FlagType, Flag, _, _)),
+   not imposed_constraint(Hash, "node_flag", Package, node_flag(FlagType, Flag, _, _)),
    internal_error("imposed hash without imposing all flag values").
 
 #defined condition/2.
@@ -789,22 +774,15 @@ required_provider(Provider, Virtual)
 
 :- provider(node(Y, Package), node(X, Virtual)), required_provider(Provider, Virtual), Package != Provider.
 
-% TODO: the following two choice rules allow the solver to add compiler
+% TODO: the following choice rule allows the solver to add compiler
 % flags if their only source is from a requirement. This is overly-specific
 % and should use a more-generic approach like in https://github.com/spack/spack/pull/37180
 
-{ attr("node_flag", node(ID, Package), FlagType, FlagValue) } :-
+{ attr("node_flag", node(ID, Package), NodeFlag) } :-
   requirement_group_member(ConditionID, Package, RequirementID),
   activate_requirement(node(ID, Package), RequirementID),
   pkg_fact(Package, condition_effect(ConditionID, EffectID)),
-  imposed_constraint(EffectID, "node_flag_set", Package, FlagType, FlagValue).
-
-{ attr("node_flag_source", node(NodeID1, Package1), FlagType, node(NodeID2, Package2)) } :-
-  requirement_group_member(ConditionID, Package1, RequirementID),
-  activate_requirement(node(NodeID1, Package1), RequirementID),
-  pkg_fact(Package1, condition_effect(ConditionID, EffectID)),
-  imposed_constraint(EffectID, "node_flag_source", Package1, FlagType, Package2),
-  imposed_nodes(EffectID, node(NodeID2, Package2), node(NodeID1, Package1)).
+  imposed_constraint(EffectID, "node_flag_set", Package, NodeFlag).
 
 requirement_weight(node(ID, Package), Group, W) :-
   W = #min {
@@ -1050,23 +1028,22 @@ variant_is_propagated(PackageNode, Variant) :-
 % 1. The same flag type is not set on this node
 % 2. This node has the same compiler as the propagation source
 
-propagated_flag(node(PackageID, Package), node_flag(FlagType, Flag), SourceNode) :-
-  propagate(node(PackageID, Package), node_flag(FlagType, Flag), _),
-  not attr("node_flag_set", node(PackageID, Package), FlagType, _),
+propagated_flag(node(PackageID, Package), node_flag(FlagType, Flag, FlagGroup, Source), SourceNode) :-
+  propagate(node(PackageID, Package), node_flag(FlagType, Flag, FlagGroup, Source), _),
+  not attr("node_flag_set", node(PackageID, Package), node_flag(FlagType, _, _, "literal")),
   % Same compiler as propagation source
   node_compiler(node(PackageID, Package), CompilerID),
   node_compiler(SourceNode, CompilerID),
-  attr("propagate", SourceNode, node_flag(FlagType, Flag), _),
+  attr("propagate", SourceNode, node_flag(FlagType, Flag, FlagGroup, Source), _),
   node(PackageID, Package) != SourceNode,
   not runtime(Package).
 
-attr("node_flag", PackageNode, FlagType, Flag) :- propagated_flag(PackageNode, node_flag(FlagType, Flag), _).
-attr("node_flag_source", PackageNode, FlagType, SourceNode) :- propagated_flag(PackageNode, node_flag(FlagType, _), SourceNode).
+attr("node_flag", PackageNode, NodeFlag) :- propagated_flag(PackageNode, NodeFlag, _).
 
 % Cannot propagate the same flag from two distinct sources
 error(100, "{0} and {1} cannot both propagate compiler flags '{2}' to {3}", Source1, Source2, Package, FlagType) :-
-  propagated_flag(node(ID, Package), node_flag(FlagType, _), node(_, Source1)),
-  propagated_flag(node(ID, Package), node_flag(FlagType, _), node(_, Source2)),
+  propagated_flag(node(ID, Package), node_flag(FlagType, _, _, _), node(_, Source1)),
+  propagated_flag(node(ID, Package), node_flag(FlagType, _, _, _), node(_, Source2)),
   Source1 < Source2.
 
 %----
@@ -1342,7 +1319,7 @@ node_compiler_weight(node(ID, Package), 100)
     not compiler_weight(CompilerID, _).
 
 % For the time being, be strict and reuse only if the compiler match one we have on the system
-error(100, "Compiler {1}@{2} requested for {0} cannot be found. Set install_missing_compilers:true if intended.", Package, Compiler, Version)
+error(100, "Compiler {1}@{2} requested for {0} cannot be found.", Package, Compiler, Version)
  :- attr("node_compiler_version", node(ID, Package), Compiler, Version),
     not node_compiler(node(ID, Package), _).
 
@@ -1353,32 +1330,18 @@ error(100, "Compiler {1}@{2} requested for {0} cannot be found. Set install_miss
 % Compiler flags
 %-----------------------------------------------------------------------------
 
-% remember where flags came from
-attr("node_flag_source", PackageNode, FlagType, PackageNode) :- attr("node_flag_set", PackageNode, FlagType, _).
-attr("node_flag_source", PackageNode, FlagType, PackageNode) :- attr("node_flag", PackageNode, FlagType, _), attr("hash", PackageNode, _).
-
 % compiler flags from compilers.yaml are put on nodes if compiler matches
-attr("node_flag", PackageNode, FlagType, Flag)
-  :- compiler_flag(CompilerID, FlagType, Flag),
+attr("node_flag", PackageNode, node_flag(FlagType, Flag, FlagGroup, CompilerID))
+  :- compiler_flag(CompilerID, FlagType, Flag, FlagGroup),
      node_compiler(PackageNode, CompilerID),
      flag_type(FlagType),
      compiler_id(CompilerID),
      compiler_name(CompilerID, CompilerName),
      compiler_version(CompilerID, Version).
 
-attr("node_flag_compiler_default", PackageNode)
-  :- not attr("node_flag_set", PackageNode, FlagType, _),
-     compiler_flag(CompilerID, FlagType, Flag),
-     node_compiler(PackageNode, CompilerID),
-     flag_type(FlagType),
-     compiler_id(CompilerID),
-     compiler_name(CompilerID, CompilerName),
-     compiler_version(CompilerID, Version).
+attr("node_flag", PackageNode, NodeFlag) :- attr("node_flag_set", PackageNode, NodeFlag).
 
-% Flag set to something
-attr("node_flag", PackageNode, FlagType, Flag) :- attr("node_flag_set", PackageNode, FlagType, Flag).
-
-#defined compiler_flag/3.
+#defined compiler_flag/4.
 
 
 %-----------------------------------------------------------------------------

lib/spack/spack/solver/core.py

@@ -230,6 +230,13 @@ class NodeArgument(NamedTuple):
     pkg: str
 
 
+class NodeFlag(NamedTuple):
+    flag_type: str
+    flag: str
+    flag_group: str
+    source: str
+
+
 def intermediate_repr(sym):
     """Returns an intermediate representation of clingo models for Spack's spec builder.
 
@@ -248,6 +255,13 @@ def intermediate_repr(sym):
             return NodeArgument(
                 id=intermediate_repr(sym.arguments[0]), pkg=intermediate_repr(sym.arguments[1])
             )
+        elif sym.name == "node_flag":
+            return NodeFlag(
+                flag_type=intermediate_repr(sym.arguments[0]),
+                flag=intermediate_repr(sym.arguments[1]),
+                flag_group=intermediate_repr(sym.arguments[2]),
+                source=intermediate_repr(sym.arguments[3]),
+            )
     except RuntimeError:
         # This happens when using clingo w/ CFFI and trying to access ".name" for symbols
         # that are not functions

lib/spack/spack/solver/display.lp

@@ -13,6 +13,7 @@
 #show attr/2.
 #show attr/3.
 #show attr/4.
+#show attr/5.
 
 % names of optimization criteria
 #show opt_criterion/2.

lib/spack/spack/spec.py

@@ -781,17 +781,49 @@ class CompilerFlag(str):
         propagate (bool): if ``True`` the flag value will
             be passed to the package's dependencies. If
             ``False`` it will not
+        flag_group (str): if this flag was introduced along
+            with several flags via a single source, then
+            this will store all such flags
+        source (str): identifies the type of constraint that
+            introduced this flag (e.g. if a package has
+            ``depends_on(... cflags=-g)``, then the ``source``
+            for "-g" would indicate ``depends_on``.
     """
 
     def __new__(cls, value, **kwargs):
         obj = str.__new__(cls, value)
         obj.propagate = kwargs.pop("propagate", False)
+        obj.flag_group = kwargs.pop("flag_group", value)
+        obj.source = kwargs.pop("source", None)
         return obj
 
 
 _valid_compiler_flags = ["cflags", "cxxflags", "fflags", "ldflags", "ldlibs", "cppflags"]
 
 
+def _shared_subset_pair_iterate(container1, container2):
+    """
+    [0, a, c, d, f]
+    [a, d, e, f]
+
+    yields [(a, a), (d, d), (f, f)]
+
+    no repeated elements
+    """
+    a_idx, b_idx = 0, 0
+    max_a, max_b = len(container1), len(container2)
+    while a_idx < max_a and b_idx < max_b:
+        if container1[a_idx] == container2[b_idx]:
+            yield (container1[a_idx], container2[b_idx])
+            a_idx += 1
+            b_idx += 1
+        else:
+            while container1[a_idx] < container2[b_idx]:
+                a_idx += 1
+            while container1[a_idx] > container2[b_idx]:
+                b_idx += 1
+
+
 class FlagMap(lang.HashableMap):
     __slots__ = ("spec",)
 
@@ -800,23 +832,9 @@ def __init__(self, spec):
         self.spec = spec
 
     def satisfies(self, other):
-        return all(f in self and self[f] == other[f] for f in other)
+        return all(f in self and set(self[f]) >= set(other[f]) for f in other)
 
     def intersects(self, other):
-        common_types = set(self) & set(other)
-        for flag_type in common_types:
-            if not self[flag_type] or not other[flag_type]:
-                # At least one of the two is empty
-                continue
-
-            if self[flag_type] != other[flag_type]:
-                return False
-
-            if not all(
-                f1.propagate == f2.propagate for f1, f2 in zip(self[flag_type], other[flag_type])
-            ):
-                # At least one propagation flag didn't match
-                return False
         return True
 
     def constrain(self, other):
@@ -824,28 +842,28 @@ def constrain(self, other):
 
         Return whether the spec changed.
         """
-        if other.spec and other.spec._concrete:
-            for k in self:
-                if k not in other:
-                    raise UnsatisfiableCompilerFlagSpecError(self[k], "<absent>")
-
         changed = False
-        for k in other:
-            if k in self and not set(self[k]) <= set(other[k]):
-                raise UnsatisfiableCompilerFlagSpecError(
-                    " ".join(f for f in self[k]), " ".join(f for f in other[k])
-                )
-            elif k not in self:
-                self[k] = other[k]
+        for flag_type in other:
+            if flag_type not in self:
+                self[flag_type] = other[flag_type]
                 changed = True
+            else:
+                extra_other = set(other[flag_type]) - set(self[flag_type])
+                if extra_other:
+                    self[flag_type] = list(self[flag_type]) + list(
+                        x for x in other[flag_type] if x in extra_other
+                    )
+                    changed = True
+
+                # Next, if any flags in other propagate, we force them to propagate in our case
+                shared = list(sorted(set(other[flag_type]) - extra_other))
+                for x, y in _shared_subset_pair_iterate(shared, sorted(self[flag_type])):
+                    if x.propagate:
+                        y.propagate = True
+
+        # TODO: what happens if flag groups with a partial (but not complete)
+        # intersection specify different behaviors for flag propagation?
 
-            # Check that the propagation values match
-            if self[k] == other[k]:
-                for i in range(len(other[k])):
-                    if self[k][i].propagate != other[k][i].propagate:
-                        raise UnsatisfiableCompilerFlagSpecError(
-                            self[k][i].propagate, other[k][i].propagate
-                        )
         return changed
 
     @staticmethod
@@ -858,7 +876,7 @@ def copy(self):
             clone[name] = compiler_flag
         return clone
 
-    def add_flag(self, flag_type, value, propagation):
+    def add_flag(self, flag_type, value, propagation, flag_group=None, source=None):
         """Stores the flag's value in CompilerFlag and adds it
         to the FlagMap
 
@@ -869,7 +887,8 @@ def add_flag(self, flag_type, value, propagation):
             propagation (bool): if ``True`` the flag value will be passed to
                 the packages' dependencies. If``False`` it will not be passed
         """
-        flag = CompilerFlag(value, propagate=propagation)
+        flag_group = flag_group or value
+        flag = CompilerFlag(value, propagate=propagation, flag_group=flag_group, source=source)
 
         if flag_type not in self:
             self[flag_type] = [flag]
@@ -1552,7 +1571,9 @@ def _get_dependency(self, name):
             raise spack.error.SpecError(err_msg.format(name, len(deps)))
         return deps[0]
 
-    def edges_from_dependents(self, name=None, depflag: dt.DepFlag = dt.ALL):
+    def edges_from_dependents(
+        self, name=None, depflag: dt.DepFlag = dt.ALL
+    ) -> List[DependencySpec]:
         """Return a list of edges connecting this node in the DAG
         to parents.
 
@@ -1562,7 +1583,9 @@ def edges_from_dependents(self, name=None, depflag: dt.DepFlag = dt.ALL):
         """
         return [d for d in self._dependents.select(parent=name, depflag=depflag)]
 
-    def edges_to_dependencies(self, name=None, depflag: dt.DepFlag = dt.ALL):
+    def edges_to_dependencies(
+        self, name=None, depflag: dt.DepFlag = dt.ALL
+    ) -> List[DependencySpec]:
         """Return a list of edges connecting this node in the DAG
         to children.
 
@@ -1661,8 +1684,9 @@ def _add_flag(self, name, value, propagate):
         elif name in valid_flags:
             assert self.compiler_flags is not None
             flags_and_propagation = spack.compiler.tokenize_flags(value, propagate)
+            flag_group = " ".join(x for (x, y) in flags_and_propagation)
             for flag, propagation in flags_and_propagation:
-                self.compiler_flags.add_flag(name, flag, propagation)
+                self.compiler_flags.add_flag(name, flag, propagation, flag_group)
         else:
             # FIXME:
             # All other flags represent variants. 'foo=true' and 'foo=false'
@@ -3887,43 +3911,43 @@ def format_attribute(match_object: Match) -> str:
             for idx, part in enumerate(parts):
                 if not part:
                     raise SpecFormatStringError("Format string attributes must be non-empty")
-                if part.startswith("_"):
+                elif part.startswith("_"):
                     raise SpecFormatStringError("Attempted to format private attribute")
-                else:
-                    if part == "variants" and isinstance(current, VariantMap):
-                        # subscript instead of getattr for variant names
+                elif isinstance(current, VariantMap):
+                    # subscript instead of getattr for variant names
+                    try:
                         current = current[part]
-                    else:
-                        # aliases
-                        if part == "arch":
-                            part = "architecture"
-                        elif part == "version":
-                            # version (singular) requires a concrete versions list. Avoid
-                            # pedantic errors by using versions (plural) when not concrete.
-                            # These two are not entirely equivalent for pkg@=1.2.3:
-                            # - version prints '1.2.3'
-                            # - versions prints '=1.2.3'
-                            if not current.versions.concrete:
-                                part = "versions"
-                        try:
-                            current = getattr(current, part)
-                        except AttributeError:
-                            parent = ".".join(parts[:idx])
-                            m = "Attempted to format attribute %s." % attribute
-                            m += "Spec %s has no attribute %s" % (parent, part)
-                            raise SpecFormatStringError(m)
-                        if isinstance(current, vn.VersionList):
-                            if current == vn.any_version:
-                                # don't print empty version lists
-                                return ""
-
-                    if callable(current):
-                        raise SpecFormatStringError("Attempted to format callable object")
-
-                    if current is None:
-                        # not printing anything
+                    except KeyError:
+                        raise SpecFormatStringError(f"Variant '{part}' does not exist")
+                else:
+                    # aliases
+                    if part == "arch":
+                        part = "architecture"
+                    elif part == "version" and not current.versions.concrete:
+                        # version (singular) requires a concrete versions list. Avoid
+                        # pedantic errors by using versions (plural) when not concrete.
+                        # These two are not entirely equivalent for pkg@=1.2.3:
+                        # - version prints '1.2.3'
+                        # - versions prints '=1.2.3'
+                        part = "versions"
+                    try:
+                        current = getattr(current, part)
+                    except AttributeError:
+                        raise SpecFormatStringError(
+                            f"Attempted to format attribute {attribute}. "
+                            f"Spec {'.'.join(parts[:idx])} has no attribute {part}"
+                        )
+                    if isinstance(current, vn.VersionList) and current == vn.any_version:
+                        # don't print empty version lists
                         return ""
 
+                if callable(current):
+                    raise SpecFormatStringError("Attempted to format callable object")
+
+                if current is None:
+                    # not printing anything
+                    return ""
+
             # Set color codes for various attributes
             color = None
             if "architecture" in parts:
@@ -4682,6 +4706,10 @@ def _load(cls, data):
 
         return hash_dict[root_spec_hash]["node_spec"]
 
+    @classmethod
+    def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
+        raise NotImplementedError("Subclasses must implement this method.")
+
 
 class SpecfileV1(SpecfileReaderBase):
     @classmethod

lib/spack/spack/stage.py

@@ -39,7 +39,6 @@
 import spack.paths
 import spack.resource
 import spack.spec
-import spack.stage
 import spack.util.crypto
 import spack.util.lock
 import spack.util.path as sup
@@ -981,8 +980,8 @@ def interactive_version_filter(
             data = buffer.getvalue().encode("utf-8")
 
             short_hash = hashlib.sha1(data).hexdigest()[:7]
-            filename = f"{spack.stage.stage_prefix}versions-{short_hash}.txt"
-            filepath = os.path.join(spack.stage.get_stage_root(), filename)
+            filename = f"{stage_prefix}versions-{short_hash}.txt"
+            filepath = os.path.join(get_stage_root(), filename)
 
             # Write contents
             with open(filepath, "wb") as f:

lib/spack/spack/store.py

@@ -173,7 +173,12 @@ def __init__(
         self.hash_length = hash_length
         self.upstreams = upstreams
         self.lock_cfg = lock_cfg
-        self.db = spack.database.Database(root, upstream_dbs=upstreams, lock_cfg=lock_cfg)
+        self.layout = spack.directory_layout.DirectoryLayout(
+            root, projections=projections, hash_length=hash_length
+        )
+        self.db = spack.database.Database(
+            root, upstream_dbs=upstreams, lock_cfg=lock_cfg, layout=self.layout
+        )
 
         timeout_format_str = (
             f"{str(lock_cfg.package_timeout)}s" if lock_cfg.package_timeout else "No timeout"
@@ -187,13 +192,9 @@ def __init__(
             self.root, default_timeout=lock_cfg.package_timeout
         )
 
-        self.layout = spack.directory_layout.DirectoryLayout(
-            root, projections=projections, hash_length=hash_length
-        )
-
     def reindex(self) -> None:
         """Convenience function to reindex the store DB with its own layout."""
-        return self.db.reindex(self.layout)
+        return self.db.reindex()
 
     def __reduce__(self):
         return Store, (
@@ -261,7 +262,7 @@ def restore(token):
 
 
 def _construct_upstream_dbs_from_install_roots(
-    install_roots: List[str], _test: bool = False
+    install_roots: List[str],
 ) -> List[spack.database.Database]:
     accumulated_upstream_dbs: List[spack.database.Database] = []
     for install_root in reversed(install_roots):
@@ -271,7 +272,6 @@ def _construct_upstream_dbs_from_install_roots(
             is_upstream=True,
             upstream_dbs=upstream_dbs,
         )
-        next_db._fail_when_missing_deps = _test
         next_db._read()
         accumulated_upstream_dbs.insert(0, next_db)
 

lib/spack/spack/test/build_environment.py

@@ -592,7 +592,7 @@ def test_setting_attributes(self, default_mock_concretization):
 
         # We can also propagate the settings to classes in the MRO
         module_wrapper.propagate_changes_to_mro()
-        for cls in type(s.package).__mro__:
+        for cls in s.package.__class__.__mro__:
             current_module = cls.module
             if current_module == spack.package_base:
                 break

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

@@ -379,9 +379,8 @@ def test_buildcache_create_install(
 def test_correct_specs_are_pushed(
     things_to_install, expected, tmpdir, monkeypatch, default_mock_concretization, temporary_store
 ):
-    # Concretize dttop and add it to the temporary database (without prefixes)
     spec = default_mock_concretization("dttop")
-    temporary_store.db.add(spec, directory_layout=None)
+    spec.package.do_install(fake=True)
     slash_hash = f"/{spec.dag_hash()}"
 
     class DontUpload(spack.binary_distribution.Uploader):

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

@@ -591,14 +591,12 @@ def test_config_prefer_upstream(
     """
 
     mock_db_root = str(tmpdir_factory.mktemp("mock_db_root"))
-    prepared_db = spack.database.Database(mock_db_root)
-
-    upstream_layout = gen_mock_layout("/a/")
+    prepared_db = spack.database.Database(mock_db_root, layout=gen_mock_layout("/a/"))
 
     for spec in ["hdf5 +mpi", "hdf5 ~mpi", "boost+debug~icu+graph", "dependency-install", "patch"]:
         dep = spack.spec.Spec(spec)
         dep.concretize()
-        prepared_db.add(dep, upstream_layout)
+        prepared_db.add(dep)
 
     downstream_db_root = str(tmpdir_factory.mktemp("mock_downstream_db_root"))
     db_for_test = spack.database.Database(downstream_db_root, upstream_dbs=[prepared_db])

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

@@ -18,8 +18,6 @@
 develop = SpackCommand("develop")
 env = SpackCommand("env")
 
-pytestmark = pytest.mark.not_on_windows("does not run on windows")
-
 
 @pytest.mark.usefixtures("mutable_mock_env_path", "mock_packages", "mock_fetch", "mutable_config")
 class TestDevelop:

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

@@ -2336,103 +2336,6 @@ def test_stack_yaml_force_remove_from_matrix(tmpdir):
             assert mpileaks_spec not in after_conc
 
 
-def test_stack_concretize_extraneous_deps(tmpdir, mock_packages):
-    # FIXME: The new concretizer doesn't handle yet soft
-    # FIXME: constraints for stacks
-    # FIXME: This now works for statically-determinable invalid deps
-    # FIXME: But it still does not work for dynamically determined invalid deps
-
-    filename = str(tmpdir.join("spack.yaml"))
-    with open(filename, "w") as f:
-        f.write(
-            """\
-spack:
-  definitions:
-    - packages: [libelf, mpileaks]
-    - install:
-        - matrix:
-            - [$packages]
-            - ['^zmpi', '^mpich']
-  specs:
-    - $install
-"""
-        )
-    with tmpdir.as_cwd():
-        env("create", "test", "./spack.yaml")
-        with ev.read("test"):
-            concretize()
-
-        test = ev.read("test")
-
-        for user, concrete in test.concretized_specs():
-            assert concrete.concrete
-            assert not user.concrete
-            if user.name == "libelf":
-                assert not concrete.satisfies("^mpi")
-            elif user.name == "mpileaks":
-                assert concrete.satisfies("^mpi")
-
-
-def test_stack_concretize_extraneous_variants(tmpdir, mock_packages):
-    filename = str(tmpdir.join("spack.yaml"))
-    with open(filename, "w") as f:
-        f.write(
-            """\
-spack:
-  definitions:
-    - packages: [libelf, mpileaks]
-    - install:
-        - matrix:
-            - [$packages]
-            - ['~shared', '+shared']
-  specs:
-    - $install
-"""
-        )
-    with tmpdir.as_cwd():
-        env("create", "test", "./spack.yaml")
-        with ev.read("test"):
-            concretize()
-
-        test = ev.read("test")
-
-        for user, concrete in test.concretized_specs():
-            assert concrete.concrete
-            assert not user.concrete
-            if user.name == "libelf":
-                assert "shared" not in concrete.variants
-            if user.name == "mpileaks":
-                assert concrete.variants["shared"].value == user.variants["shared"].value
-
-
-def test_stack_concretize_extraneous_variants_with_dash(tmpdir, mock_packages):
-    filename = str(tmpdir.join("spack.yaml"))
-    with open(filename, "w") as f:
-        f.write(
-            """\
-spack:
-  definitions:
-    - packages: [libelf, mpileaks]
-    - install:
-        - matrix:
-            - [$packages]
-            - ['shared=False', '+shared-libs']
-  specs:
-    - $install
-"""
-        )
-    with tmpdir.as_cwd():
-        env("create", "test", "./spack.yaml")
-        with ev.read("test"):
-            concretize()
-
-        ev.read("test")
-
-        # Regression test for handling of variants with dashes in them
-        # will fail before this point if code regresses
-        assert True
-
-
 def test_stack_definition_extension(tmpdir):
     filename = str(tmpdir.join("spack.yaml"))
     with open(filename, "w") as f:
@@ -4301,9 +4204,6 @@ def test_env_include_mixed_views(tmp_path, mutable_mock_env_path, mutable_config
 {''.join(includes)}
   specs:
   - mpileaks
-  packages:
-    mpileaks:
-      compiler: [gcc]
 """
     )
 

lib/spack/spack/test/cmd/external.py

@@ -44,7 +44,7 @@ def test_find_external_single_package(mock_executable):
 
     assert len(specs_by_package) == 1 and "cmake" in specs_by_package
     detected_spec = specs_by_package["cmake"]
-    assert len(detected_spec) == 1 and detected_spec[0].spec == Spec("cmake@1.foo")
+    assert len(detected_spec) == 1 and detected_spec[0] == Spec("cmake@1.foo")
 
 
 def test_find_external_two_instances_same_package(mock_executable):
@@ -61,10 +61,10 @@ def test_find_external_two_instances_same_package(mock_executable):
     )
 
     assert len(detected_specs) == 2
-    spec_to_path = {e.spec: e.prefix for e in detected_specs}
+    spec_to_path = {s: s.external_path for s in detected_specs}
     assert spec_to_path[Spec("cmake@1.foo")] == (
         spack.detection.executable_prefix(str(cmake1.parent))
-    )
+    ), spec_to_path
     assert spec_to_path[Spec("cmake@3.17.2")] == (
         spack.detection.executable_prefix(str(cmake2.parent))
     )
@@ -72,12 +72,8 @@ def test_find_external_two_instances_same_package(mock_executable):
 
 def test_find_external_update_config(mutable_config):
     entries = [
-        spack.detection.DetectedPackage(
-            Spec.from_detection("cmake@1.foo", external_path="/x/y1/"), "/x/y1/"
-        ),
-        spack.detection.DetectedPackage(
-            Spec.from_detection("cmake@3.17.2", external_path="/x/y2/"), "/x/y2/"
-        ),
+        Spec.from_detection("cmake@1.foo", external_path="/x/y1"),
+        Spec.from_detection("cmake@3.17.2", external_path="/x/y2"),
     ]
     pkg_to_entries = {"cmake": entries}
 
@@ -88,8 +84,8 @@ def test_find_external_update_config(mutable_config):
     cmake_cfg = pkgs_cfg["cmake"]
     cmake_externals = cmake_cfg["externals"]
 
-    assert {"spec": "cmake@1.foo", "prefix": "/x/y1/"} in cmake_externals
-    assert {"spec": "cmake@3.17.2", "prefix": "/x/y2/"} in cmake_externals
+    assert {"spec": "cmake@1.foo", "prefix": "/x/y1"} in cmake_externals
+    assert {"spec": "cmake@3.17.2", "prefix": "/x/y2"} in cmake_externals
 
 
 def test_get_executables(working_env, mock_executable):
@@ -229,19 +225,15 @@ def test_find_external_merge(mutable_config, mutable_mock_repo, tmp_path):
     """Checks that 'spack find external' doesn't overwrite an existing spec in packages.yaml."""
     pkgs_cfg_init = {
         "find-externals1": {
-            "externals": [{"spec": "find-externals1@1.1", "prefix": "/preexisting-prefix/"}],
+            "externals": [{"spec": "find-externals1@1.1", "prefix": "/preexisting-prefix"}],
             "buildable": False,
         }
     }
 
     mutable_config.update_config("packages", pkgs_cfg_init)
     entries = [
-        spack.detection.DetectedPackage(
-            Spec.from_detection("find-externals1@1.1", external_path="/x/y1/"), "/x/y1/"
-        ),
-        spack.detection.DetectedPackage(
-            Spec.from_detection("find-externals1@1.2", external_path="/x/y2/"), "/x/y2/"
-        ),
+        Spec.from_detection("find-externals1@1.1", external_path="/x/y1"),
+        Spec.from_detection("find-externals1@1.2", external_path="/x/y2"),
     ]
     pkg_to_entries = {"find-externals1": entries}
     scope = spack.config.default_modify_scope("packages")
@@ -251,8 +243,8 @@ def test_find_external_merge(mutable_config, mutable_mock_repo, tmp_path):
     pkg_cfg = pkgs_cfg["find-externals1"]
     pkg_externals = pkg_cfg["externals"]
 
-    assert {"spec": "find-externals1@1.1", "prefix": "/preexisting-prefix/"} in pkg_externals
-    assert {"spec": "find-externals1@1.2", "prefix": "/x/y2/"} in pkg_externals
+    assert {"spec": "find-externals1@1.1", "prefix": "/preexisting-prefix"} in pkg_externals
+    assert {"spec": "find-externals1@1.2", "prefix": "/x/y2"} in pkg_externals
 
 
 def test_list_detectable_packages(mutable_config, mutable_mock_repo):
@@ -278,7 +270,7 @@ def _determine_variants(cls, exes, version_str):
 
     assert len(detected_specs) == 1
 
-    gcc = detected_specs[0].spec
+    gcc = detected_specs[0]
     assert gcc.name == "gcc"
     assert gcc.external_path == os.path.sep + os.path.join("opt", "gcc", "bin")
 

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

@@ -334,7 +334,6 @@ def test_find_command_basic_usage(database):
     assert "mpileaks" in output
 
 
-@pytest.mark.not_on_windows("envirnment is not yet supported on windows")
 @pytest.mark.regression("9875")
 def test_find_prefix_in_env(
     mutable_mock_env_path, install_mockery, mock_fetch, mock_packages, mock_archive

lib/spack/spack/test/cmd/gc.py

@@ -16,8 +16,6 @@
 add = spack.main.SpackCommand("add")
 install = spack.main.SpackCommand("install")
 
-pytestmark = pytest.mark.not_on_windows("does not run on windows")
-
 
 @pytest.mark.db
 def test_gc_without_build_dependency(mutable_database):

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

@@ -19,7 +19,6 @@
 
 import spack.cmd.common.arguments
 import spack.cmd.install
-import spack.compilers as compilers
 import spack.config
 import spack.environment as ev
 import spack.hash_types as ht
@@ -29,7 +28,7 @@
 from spack.error import SpackError
 from spack.main import SpackCommand
 from spack.parser import SpecSyntaxError
-from spack.spec import CompilerSpec, Spec
+from spack.spec import Spec
 
 install = SpackCommand("install")
 env = SpackCommand("env")
@@ -916,68 +915,6 @@ def test_cdash_configure_warning(tmpdir, mock_fetch, install_mockery, capfd):
         assert "foo: No such file or directory" in content
 
 
-@pytest.mark.not_on_windows("ArchSpec gives test platform debian rather than windows")
-def test_compiler_bootstrap(
-    install_mockery, mock_packages, mock_fetch, mock_archive, mutable_config, monkeypatch
-):
-    monkeypatch.setattr(spack.concretize.Concretizer, "check_for_compiler_existence", False)
-    spack.config.set("config:install_missing_compilers", True)
-    assert CompilerSpec("gcc@=12.0") not in compilers.all_compiler_specs()
-
-    # Test succeeds if it does not raise an error
-    install("pkg-a%gcc@=12.0")
-
-
-@pytest.mark.not_on_windows("Binary mirrors not supported on windows")
-def test_compiler_bootstrap_from_binary_mirror(
-    install_mockery, mock_packages, mock_fetch, mock_archive, mutable_config, monkeypatch, tmpdir
-):
-    """
-    Make sure installing compiler from buildcache registers compiler
-    """
-
-    # Create a temp mirror directory for buildcache usage
-    mirror_dir = tmpdir.join("mirror_dir")
-    mirror_url = "file://{0}".format(mirror_dir.strpath)
-
-    # Install a compiler, because we want to put it in a buildcache
-    install("gcc@=10.2.0")
-
-    # Put installed compiler in the buildcache
-    buildcache("push", "-u", "-f", mirror_dir.strpath, "gcc@10.2.0")
-
-    # Now uninstall the compiler
-    uninstall("-y", "gcc@10.2.0")
-
-    monkeypatch.setattr(spack.concretize.Concretizer, "check_for_compiler_existence", False)
-    spack.config.set("config:install_missing_compilers", True)
-    assert CompilerSpec("gcc@=10.2.0") not in compilers.all_compiler_specs()
-
-    # Configure the mirror where we put that buildcache w/ the compiler
-    mirror("add", "test-mirror", mirror_url)
-
-    # Now make sure that when the compiler is installed from binary mirror,
-    # it also gets configured as a compiler.  Test succeeds if it does not
-    # raise an error
-    install("--no-check-signature", "--cache-only", "--only", "dependencies", "pkg-b%gcc@=10.2.0")
-    install("--no-cache", "--only", "package", "pkg-b%gcc@10.2.0")
-
-
-@pytest.mark.not_on_windows("ArchSpec gives test platform debian rather than windows")
-@pytest.mark.regression("16221")
-def test_compiler_bootstrap_already_installed(
-    install_mockery, mock_packages, mock_fetch, mock_archive, mutable_config, monkeypatch
-):
-    monkeypatch.setattr(spack.concretize.Concretizer, "check_for_compiler_existence", False)
-    spack.config.set("config:install_missing_compilers", True)
-
-    assert CompilerSpec("gcc@=12.0") not in compilers.all_compiler_specs()
-
-    # Test succeeds if it does not raise an error
-    install("gcc@=12.0")
-    install("pkg-a%gcc@=12.0")
-
-
 def test_install_fails_no_args(tmpdir):
     # ensure no spack.yaml in directory
     with tmpdir.as_cwd():

lib/spack/spack/test/cmd/providers.py

@@ -31,7 +31,6 @@ def test_it_just_runs(pkg):
                 "mpilander",
                 "mvapich2",
                 "openmpi",
-                "openmpi@1.6.5",
                 "openmpi@1.7.5:",
                 "openmpi@2.0.0:",
                 "spectrum-mpi",

lib/spack/spack/test/cmd/reindex.py

@@ -2,9 +2,10 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import os
+import shutil
 
 import spack.store
+from spack.database import Database
 from spack.main import SpackCommand
 
 install = SpackCommand("install")
@@ -23,31 +24,55 @@ def test_reindex_basic(mock_packages, mock_archive, mock_fetch, install_mockery)
     assert spack.store.STORE.db.query() == all_installed
 
 
-def test_reindex_db_deleted(mock_packages, mock_archive, mock_fetch, install_mockery):
+def _clear_db(tmp_path):
+    empty_db = Database(str(tmp_path))
+    with empty_db.write_transaction():
+        pass
+    shutil.rmtree(spack.store.STORE.db.database_directory)
+    shutil.copytree(empty_db.database_directory, spack.store.STORE.db.database_directory)
+    # force a re-read of the database
+    assert len(spack.store.STORE.db.query()) == 0
+
+
+def test_reindex_db_deleted(mock_packages, mock_archive, mock_fetch, install_mockery, tmp_path):
     install("libelf@0.8.13")
     install("libelf@0.8.12")
 
     all_installed = spack.store.STORE.db.query()
 
-    os.remove(spack.store.STORE.db._index_path)
+    _clear_db(tmp_path)
+
     reindex()
 
     assert spack.store.STORE.db.query() == all_installed
 
 
 def test_reindex_with_deprecated_packages(
-    mock_packages, mock_archive, mock_fetch, install_mockery
+    mock_packages, mock_archive, mock_fetch, install_mockery, tmp_path
 ):
     install("libelf@0.8.13")
     install("libelf@0.8.12")
 
     deprecate("-y", "libelf@0.8.12", "libelf@0.8.13")
 
-    all_installed = spack.store.STORE.db.query(installed=any)
-    non_deprecated = spack.store.STORE.db.query(installed=True)
+    db = spack.store.STORE.db
+
+    all_installed = db.query(installed=any)
+    non_deprecated = db.query(installed=True)
+
+    _clear_db(tmp_path)
 
-    os.remove(spack.store.STORE.db._index_path)
     reindex()
 
-    assert spack.store.STORE.db.query(installed=any) == all_installed
-    assert spack.store.STORE.db.query(installed=True) == non_deprecated
+    assert db.query(installed=any) == all_installed
+    assert db.query(installed=True) == non_deprecated
+
+    old_libelf = db.query_local_by_spec_hash(
+        db.query_local("libelf@0.8.12", installed=any)[0].dag_hash()
+    )
+    new_libelf = db.query_local_by_spec_hash(
+        db.query_local("libelf@0.8.13", installed=True)[0].dag_hash()
+    )
+    assert old_libelf.deprecated_for == new_libelf.spec.dag_hash()
+    assert new_libelf.deprecated_for is None
+    assert new_libelf.ref_count == 1

lib/spack/spack/test/cmd/stage.py

@@ -50,7 +50,6 @@ def fake_stage(pkg, mirror_only=False):
     return expected_path
 
 
-@pytest.mark.not_on_windows("PermissionError")
 def test_stage_path(check_stage_path):
     """Verify that --path only works with single specs."""
     stage("--path={0}".format(check_stage_path), "trivial-install-test-package")

lib/spack/spack/test/cmd/undevelop.py

@@ -2,10 +2,6 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-
-import pytest
-
 import spack.environment as ev
 import spack.spec
 from spack.main import SpackCommand
@@ -14,8 +10,6 @@
 env = SpackCommand("env")
 concretize = SpackCommand("concretize")
 
-pytestmark = pytest.mark.not_on_windows("does not run on windows")
-
 
 def test_undevelop(tmpdir, mutable_config, mock_packages, mutable_mock_env_path):
     # setup environment

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

@@ -205,7 +205,6 @@ def _warn(*args, **kwargs):
 
 # Note: I want to use https://docs.pytest.org/en/7.1.x/how-to/skipping.html#skip-all-test-functions-of-a-class-or-module
 # the style formatter insists on separating these two lines.
-@pytest.mark.not_on_windows("Envs unsupported on Windows")
 class TestUninstallFromEnv:
     """Tests an installation with two environments e1 and e2, which each have
     shared package installations:

lib/spack/spack/test/concretize.py

@@ -13,6 +13,7 @@
 
 import llnl.util.lang
 
+import spack.binary_distribution
 import spack.compiler
 import spack.compilers
 import spack.concretize
@@ -400,14 +401,6 @@ def test_spec_flags_maintain_order(self, mutable_config, gcc11_with_flags):
                 s.compiler_flags[x] == ["-O0", "-g"] for x in ("cflags", "cxxflags", "fflags")
             )
 
-    @pytest.mark.xfail(reason="Broken, needs to be fixed")
-    def test_compiler_flags_from_compiler_and_dependent(self):
-        client = Spec("cmake-client %clang@12.2.0 platform=test os=fe target=fe cflags==-g")
-        client.concretize()
-        cmake = client["cmake"]
-        for spec in [client, cmake]:
-            assert spec.compiler_flags["cflags"] == ["-O3", "-g"]
-
     def test_compiler_flags_differ_identical_compilers(self, mutable_config, clang12_with_flags):
         mutable_config.set("compilers", [clang12_with_flags])
         # Correct arch to use test compiler that has flags
@@ -441,6 +434,13 @@ def test_compiler_flags_differ_identical_compilers(self, mutable_config, clang12
                 ["hypre cflags='-g'", "^openblas cflags='-O3'"],
                 ["^openblas cflags='-g'"],
             ),
+            # Setting propagation on parent and dependency -> the
+            # dependency propagation flags override
+            (
+                "hypre cflags=='-g' ^openblas cflags=='-O3'",
+                ["hypre cflags='-g'", "^openblas cflags='-O3'"],
+                ["^openblas cflags='-g'"],
+            ),
             # Propagation doesn't go across build dependencies
             (
                 "cmake-client cflags=='-O2 -g'",
@@ -648,20 +648,6 @@ def test_external_package(self):
         assert "externalprereq" not in spec
         assert spec["externaltool"].compiler.satisfies("gcc")
 
-    def test_external_package_module(self):
-        # No tcl modules on darwin/linux machines
-        # and Windows does not (currently) allow for bash calls
-        # TODO: improved way to check for this.
-        platform = spack.platforms.real_host().name
-        if platform == "darwin" or platform == "linux" or platform == "windows":
-            return
-
-        spec = Spec("externalmodule")
-        spec.concretize()
-        assert spec["externalmodule"].external_modules == ["external-module"]
-        assert "externalprereq" not in spec
-        assert spec["externalmodule"].compiler.satisfies("gcc")
-
     def test_nobuild_package(self):
         """Test that a non-buildable package raise an error if no specs
         in packages.yaml are compatible with the request.
@@ -775,15 +761,15 @@ def test_regression_issue_7239(self):
         s = Spec("mpileaks")
         s.concretize()
 
-        assert llnl.util.lang.ObjectWrapper not in type(s).__mro__
+        assert llnl.util.lang.ObjectWrapper not in s.__class__.__mro__
 
         # Spec wrapped in a build interface
         build_interface = s["mpileaks"]
-        assert llnl.util.lang.ObjectWrapper in type(build_interface).__mro__
+        assert llnl.util.lang.ObjectWrapper in build_interface.__class__.__mro__
 
         # Mimics asking the build interface from a build interface
         build_interface = s["mpileaks"]["mpileaks"]
-        assert llnl.util.lang.ObjectWrapper in type(build_interface).__mro__
+        assert llnl.util.lang.ObjectWrapper in build_interface.__class__.__mro__
 
     @pytest.mark.regression("7705")
     def test_regression_issue_7705(self):
@@ -1301,7 +1287,7 @@ def mock_fn(*args, **kwargs):
             return [first_spec]
 
         if mock_db:
-            temporary_store.db.add(first_spec, None)
+            temporary_store.db.add(first_spec)
         else:
             monkeypatch.setattr(spack.binary_distribution, "update_cache_and_get_specs", mock_fn)
 
@@ -1366,7 +1352,7 @@ def test_no_reuse_when_variant_condition_does_not_hold(self, mutable_database, m
     def test_reuse_with_flags(self, mutable_database, mutable_config):
         spack.config.set("concretizer:reuse", True)
         spec = Spec("pkg-a cflags=-g cxxflags=-g").concretized()
-        spack.store.STORE.db.add(spec, None)
+        spec.package.do_install(fake=True)
 
         testspec = Spec("pkg-a cflags=-g")
         testspec.concretize()
@@ -2109,11 +2095,13 @@ def test_external_python_extension_find_dependency_from_detection(self, monkeypa
         """Test that python extensions have access to a python dependency
 
         when python isn't otherwise in the DAG"""
-        python_spec = Spec("python@=detected")
         prefix = os.path.sep + "fake"
+        python_spec = Spec.from_detection("python@=detected", external_path=prefix)
 
         def find_fake_python(classes, path_hints):
-            return {"python": [spack.detection.DetectedPackage(python_spec, prefix=path_hints[0])]}
+            return {
+                "python": [Spec.from_detection("python@=detected", external_path=path_hints[0])]
+            }
 
         monkeypatch.setattr(spack.detection, "by_path", find_fake_python)
         external_conf = {
@@ -2128,7 +2116,8 @@ def find_fake_python(classes, path_hints):
 
         assert "python" in spec["py-extension1"]
         assert spec["python"].prefix == prefix
-        assert spec["python"] == python_spec
+        assert spec["python"].external
+        assert spec["python"].satisfies(python_spec)
 
     def test_external_python_extension_find_unified_python(self):
         """Test that python extensions use the same python as other specs in unified env"""
@@ -2386,26 +2375,6 @@ def test_externals_with_platform_explicitly_set(self, tmp_path):
         s = Spec("mpich").concretized()
         assert s.external
 
-    @pytest.mark.regression("43875")
-    def test_concretize_missing_compiler(self, mutable_config, monkeypatch):
-        """Tests that Spack can concretize a spec with a missing compiler when the
-        option is active.
-        """
-
-        def _default_libc(self):
-            if self.cc is None:
-                return None
-            return Spec("glibc@=2.28")
-
-        monkeypatch.setattr(spack.concretize.Concretizer, "check_for_compiler_existence", False)
-        monkeypatch.setattr(spack.compiler.Compiler, "default_libc", property(_default_libc))
-        monkeypatch.setattr(
-            spack.util.libc, "libc_from_current_python_process", lambda: Spec("glibc@=2.28")
-        )
-        mutable_config.set("config:install_missing_compilers", True)
-        s = Spec("pkg-a %gcc@=13.2.0").concretized()
-        assert s.satisfies("%gcc@13.2.0")
-
     @pytest.mark.regression("43267")
     def test_spec_with_build_dep_from_json(self, tmp_path):
         """Tests that we can correctly concretize a spec, when we express its dependency as a
@@ -2959,7 +2928,7 @@ def test_concretization_version_order():
     result = [
         v
         for v, _ in sorted(
-            versions, key=spack.solver.asp._concretization_version_order, reverse=True
+            versions, key=spack.solver.asp.concretization_version_order, reverse=True
         )
     ]
     assert result == [

lib/spack/spack/test/concretize_errors.py

@@ -8,8 +8,6 @@
 import spack.solver.asp
 import spack.spec
 
-pytestmark = [pytest.mark.not_on_windows("Windows uses old concretizer")]
-
 version_error_messages = [
     "Cannot satisfy 'fftw@:1.0' and 'fftw@1.1:",
     "        required because quantum-espresso depends on fftw@:1.0",

lib/spack/spack/test/concretize_requirements.py

@@ -19,8 +19,6 @@
 from spack.test.conftest import create_test_repo
 from spack.util.url import path_to_file_url
 
-pytestmark = [pytest.mark.not_on_windows("Windows uses old concretizer")]
-
 
 def update_packages_config(conf_str):
     conf = syaml.load_config(conf_str)

lib/spack/spack/test/container/cli.py

@@ -27,7 +27,6 @@ def test_listing_possible_os():
         assert expected_os in output
 
 
-@pytest.mark.not_on_windows("test unsupported on Windows")
 @pytest.mark.maybeslow
 @pytest.mark.requires_executables("git")
 def test_bootstrap_phase(minimal_configuration, config_dumper, capsys):

lib/spack/spack/test/database.py

@@ -7,6 +7,7 @@
 import functools
 import json
 import os
+import re
 import shutil
 import sys
 
@@ -40,20 +41,21 @@
 @pytest.fixture()
 def upstream_and_downstream_db(tmpdir, gen_mock_layout):
     mock_db_root = str(tmpdir.mkdir("mock_db_root"))
-    upstream_write_db = spack.database.Database(mock_db_root)
-    upstream_db = spack.database.Database(mock_db_root, is_upstream=True)
+    upstream_layout = gen_mock_layout("/a/")
+    upstream_write_db = spack.database.Database(mock_db_root, layout=upstream_layout)
+    upstream_db = spack.database.Database(mock_db_root, is_upstream=True, layout=upstream_layout)
     # Generate initial DB file to avoid reindex
     with open(upstream_write_db._index_path, "w") as db_file:
         upstream_write_db._write_to_file(db_file)
-    upstream_layout = gen_mock_layout("/a/")
 
     downstream_db_root = str(tmpdir.mkdir("mock_downstream_db_root"))
-    downstream_db = spack.database.Database(downstream_db_root, upstream_dbs=[upstream_db])
+    downstream_db = spack.database.Database(
+        downstream_db_root, upstream_dbs=[upstream_db], layout=gen_mock_layout("/b/")
+    )
     with open(downstream_db._index_path, "w") as db_file:
         downstream_db._write_to_file(db_file)
-    downstream_layout = gen_mock_layout("/b/")
 
-    yield upstream_write_db, upstream_db, upstream_layout, downstream_db, downstream_layout
+    yield upstream_write_db, upstream_db, downstream_db
 
 
 @pytest.mark.parametrize(
@@ -69,14 +71,14 @@ def upstream_and_downstream_db(tmpdir, gen_mock_layout):
 def test_query_by_install_tree(
     install_tree, result, upstream_and_downstream_db, mock_packages, monkeypatch, config
 ):
-    up_write_db, up_db, up_layout, down_db, down_layout = upstream_and_downstream_db
+    up_write_db, up_db, down_db = upstream_and_downstream_db
 
     # Set the upstream DB to contain "pkg-c" and downstream to contain "pkg-b")
     b = spack.spec.Spec("pkg-b").concretized()
     c = spack.spec.Spec("pkg-c").concretized()
-    up_write_db.add(c, up_layout)
+    up_write_db.add(c)
     up_db._read()
-    down_db.add(b, down_layout)
+    down_db.add(b)
 
     specs = down_db.query(install_tree=install_tree.format(u=up_db.root, d=down_db.root))
     assert [s.name for s in specs] == result
@@ -86,9 +88,7 @@ def test_spec_installed_upstream(
     upstream_and_downstream_db, mock_custom_repository, config, monkeypatch
 ):
     """Test whether Spec.installed_upstream() works."""
-    upstream_write_db, upstream_db, upstream_layout, downstream_db, downstream_layout = (
-        upstream_and_downstream_db
-    )
+    upstream_write_db, upstream_db, downstream_db = upstream_and_downstream_db
 
     # a known installed spec should say that it's installed
     with spack.repo.use_repositories(mock_custom_repository):
@@ -96,7 +96,7 @@ def test_spec_installed_upstream(
         assert not spec.installed
         assert not spec.installed_upstream
 
-        upstream_write_db.add(spec, upstream_layout)
+        upstream_write_db.add(spec)
         upstream_db._read()
 
         monkeypatch.setattr(spack.store.STORE, "db", downstream_db)
@@ -112,9 +112,7 @@ def test_spec_installed_upstream(
 
 @pytest.mark.usefixtures("config")
 def test_installed_upstream(upstream_and_downstream_db, tmpdir):
-    upstream_write_db, upstream_db, upstream_layout, downstream_db, downstream_layout = (
-        upstream_and_downstream_db
-    )
+    upstream_write_db, upstream_db, downstream_db = upstream_and_downstream_db
 
     builder = spack.repo.MockRepositoryBuilder(tmpdir.mkdir("mock.repo"))
     builder.add_package("x")
@@ -125,7 +123,7 @@ def test_installed_upstream(upstream_and_downstream_db, tmpdir):
     with spack.repo.use_repositories(builder.root):
         spec = spack.spec.Spec("w").concretized()
         for dep in spec.traverse(root=False):
-            upstream_write_db.add(dep, upstream_layout)
+            upstream_write_db.add(dep)
         upstream_db._read()
 
         for dep in spec.traverse(root=False):
@@ -135,11 +133,11 @@ def test_installed_upstream(upstream_and_downstream_db, tmpdir):
                 upstream_db.get_by_hash(dep.dag_hash())
 
         new_spec = spack.spec.Spec("w").concretized()
-        downstream_db.add(new_spec, downstream_layout)
+        downstream_db.add(new_spec)
         for dep in new_spec.traverse(root=False):
             upstream, record = downstream_db.query_by_spec_hash(dep.dag_hash())
             assert upstream
-            assert record.path == upstream_layout.path_for_spec(dep)
+            assert record.path == upstream_db.layout.path_for_spec(dep)
         upstream, record = downstream_db.query_by_spec_hash(new_spec.dag_hash())
         assert not upstream
         assert record.installed
@@ -148,32 +146,32 @@ def test_installed_upstream(upstream_and_downstream_db, tmpdir):
         downstream_db._check_ref_counts()
 
 
-@pytest.mark.usefixtures("config")
-def test_removed_upstream_dep(upstream_and_downstream_db, tmpdir):
-    upstream_write_db, upstream_db, upstream_layout, downstream_db, downstream_layout = (
-        upstream_and_downstream_db
-    )
+def test_removed_upstream_dep(upstream_and_downstream_db, tmpdir, capsys, config):
+    upstream_write_db, upstream_db, downstream_db = upstream_and_downstream_db
 
     builder = spack.repo.MockRepositoryBuilder(tmpdir.mkdir("mock.repo"))
     builder.add_package("z")
     builder.add_package("y", dependencies=[("z", None, None)])
 
     with spack.repo.use_repositories(builder):
-        spec = spack.spec.Spec("y").concretized()
+        y = spack.spec.Spec("y").concretized()
+        z = y["z"]
 
-        upstream_write_db.add(spec["z"], upstream_layout)
+        # add dependency to upstream, dependents to downstream
+        upstream_write_db.add(z)
+        upstream_db._read()
+        downstream_db.add(y)
+
+        # remove the dependency from the upstream DB
+        upstream_write_db.remove(z)
         upstream_db._read()
 
-        new_spec = spack.spec.Spec("y").concretized()
-        downstream_db.add(new_spec, downstream_layout)
-
-        upstream_write_db.remove(new_spec["z"])
-        upstream_db._read()
-
-        new_downstream = spack.database.Database(downstream_db.root, upstream_dbs=[upstream_db])
-        new_downstream._fail_when_missing_deps = True
-        with pytest.raises(spack.database.MissingDependenciesError):
-            new_downstream._read()
+        # then rereading the downstream DB should warn about the missing dep
+        downstream_db._read_from_file(downstream_db._index_path)
+        assert (
+            f"Missing dependency not in database: y/{y.dag_hash(7)} needs z"
+            in capsys.readouterr().err
+        )
 
 
 @pytest.mark.usefixtures("config")
@@ -182,9 +180,7 @@ def test_add_to_upstream_after_downstream(upstream_and_downstream_db, tmpdir):
     DB. When a package is recorded as installed in both, the results should
     refer to the downstream DB.
     """
-    upstream_write_db, upstream_db, upstream_layout, downstream_db, downstream_layout = (
-        upstream_and_downstream_db
-    )
+    upstream_write_db, upstream_db, downstream_db = upstream_and_downstream_db
 
     builder = spack.repo.MockRepositoryBuilder(tmpdir.mkdir("mock.repo"))
     builder.add_package("x")
@@ -192,8 +188,8 @@ def test_add_to_upstream_after_downstream(upstream_and_downstream_db, tmpdir):
     with spack.repo.use_repositories(builder.root):
         spec = spack.spec.Spec("x").concretized()
 
-        downstream_db.add(spec, downstream_layout)
-        upstream_write_db.add(spec, upstream_layout)
+        downstream_db.add(spec)
+        upstream_write_db.add(spec)
         upstream_db._read()
 
         upstream, record = downstream_db.query_by_spec_hash(spec.dag_hash())
@@ -207,33 +203,22 @@ def test_add_to_upstream_after_downstream(upstream_and_downstream_db, tmpdir):
         try:
             orig_db = spack.store.STORE.db
             spack.store.STORE.db = downstream_db
-            assert queried_spec.prefix == downstream_layout.path_for_spec(spec)
+            assert queried_spec.prefix == downstream_db.layout.path_for_spec(spec)
         finally:
             spack.store.STORE.db = orig_db
 
 
-@pytest.mark.usefixtures("config", "temporary_store")
-def test_cannot_write_upstream(tmpdir, gen_mock_layout):
-    roots = [str(tmpdir.mkdir(x)) for x in ["a", "b"]]
-    layouts = [gen_mock_layout(x) for x in ["/ra/", "/rb/"]]
-
-    builder = spack.repo.MockRepositoryBuilder(tmpdir.mkdir("mock.repo"))
-    builder.add_package("x")
-
+def test_cannot_write_upstream(tmp_path, mock_packages, config):
     # Instantiate the database that will be used as the upstream DB and make
     # sure it has an index file
-    upstream_db_independent = spack.database.Database(roots[1])
-    with upstream_db_independent.write_transaction():
+    with spack.database.Database(str(tmp_path)).write_transaction():
         pass
 
-    upstream_dbs = spack.store._construct_upstream_dbs_from_install_roots([roots[1]], _test=True)
+    # Create it as an upstream
+    db = spack.database.Database(str(tmp_path), is_upstream=True)
 
-    with spack.repo.use_repositories(builder.root):
-        spec = spack.spec.Spec("x")
-        spec.concretize()
-
-        with pytest.raises(spack.database.ForbiddenLockError):
-            upstream_dbs[0].add(spec, layouts[1])
+    with pytest.raises(spack.database.ForbiddenLockError):
+        db.add(spack.spec.Spec("pkg-a").concretized())
 
 
 @pytest.mark.usefixtures("config", "temporary_store")
@@ -248,17 +233,17 @@ def test_recursive_upstream_dbs(tmpdir, gen_mock_layout):
 
     with spack.repo.use_repositories(builder.root):
         spec = spack.spec.Spec("x").concretized()
-        db_c = spack.database.Database(roots[2])
-        db_c.add(spec["z"], layouts[2])
+        db_c = spack.database.Database(roots[2], layout=layouts[2])
+        db_c.add(spec["z"])
 
-        db_b = spack.database.Database(roots[1], upstream_dbs=[db_c])
-        db_b.add(spec["y"], layouts[1])
+        db_b = spack.database.Database(roots[1], upstream_dbs=[db_c], layout=layouts[1])
+        db_b.add(spec["y"])
 
-        db_a = spack.database.Database(roots[0], upstream_dbs=[db_b, db_c])
-        db_a.add(spec["x"], layouts[0])
+        db_a = spack.database.Database(roots[0], upstream_dbs=[db_b, db_c], layout=layouts[0])
+        db_a.add(spec["x"])
 
         upstream_dbs_from_scratch = spack.store._construct_upstream_dbs_from_install_roots(
-            [roots[1], roots[2]], _test=True
+            [roots[1], roots[2]]
         )
         db_a_from_scratch = spack.database.Database(
             roots[0], upstream_dbs=upstream_dbs_from_scratch
@@ -366,7 +351,7 @@ def _check_db_sanity(database):
     _check_merkleiness()
 
 
-def _check_remove_and_add_package(database, spec):
+def _check_remove_and_add_package(database: spack.database.Database, spec):
     """Remove a spec from the DB, then add it and make sure everything's
     still ok once it is added.  This checks that it was
     removed, that it's back when added again, and that ref
@@ -386,7 +371,7 @@ def _check_remove_and_add_package(database, spec):
     assert concrete_spec not in remaining
 
     # add it back and make sure everything is ok.
-    database.add(concrete_spec, spack.store.STORE.layout)
+    database.add(concrete_spec)
     installed = database.query()
     assert concrete_spec in installed
     assert installed == original
@@ -396,7 +381,7 @@ def _check_remove_and_add_package(database, spec):
     database._check_ref_counts()
 
 
-def _mock_install(spec):
+def _mock_install(spec: str):
     s = spack.spec.Spec(spec).concretized()
     s.package.do_install(fake=True)
 
@@ -636,7 +621,7 @@ def test_080_root_ref_counts(mutable_database):
     assert mutable_database.get_record("mpich").ref_count == 1
 
     # Put the spec back
-    mutable_database.add(rec.spec, spack.store.STORE.layout)
+    mutable_database.add(rec.spec)
 
     # record is present again
     assert len(mutable_database.query("mpileaks ^mpich", installed=any)) == 1
@@ -998,9 +983,12 @@ def test_reindex_removed_prefix_is_not_installed(mutable_database, mock_store, c
     # Reindex should pick up libelf as a dependency of libdwarf
     spack.store.STORE.reindex()
 
-    # Reindexing should warn about libelf not being found on the filesystem
-    err = capfd.readouterr()[1]
-    assert "this directory does not contain an installation of the spec" in err
+    # Reindexing should warn about libelf not found on the filesystem
+    assert re.search(
+        "libelf@0.8.13.+ was marked installed in the database "
+        "but was not found on the file system",
+        capfd.readouterr().err,
+    )
 
     # And we should still have libelf in the database, but not installed.
     assert not mutable_database.query_one("libelf", installed=True)
@@ -1117,9 +1105,9 @@ def test_database_construction_doesnt_use_globals(tmpdir, config, nullify_global
 def test_database_read_works_with_trailing_data(tmp_path, default_mock_concretization):
     # Populate a database
     root = str(tmp_path)
-    db = spack.database.Database(root)
+    db = spack.database.Database(root, layout=None)
     spec = default_mock_concretization("pkg-a")
-    db.add(spec, directory_layout=None)
+    db.add(spec)
     specs_in_db = db.query_local()
     assert spec in specs_in_db
 
@@ -1140,3 +1128,53 @@ def test_database_errors_with_just_a_version_key(tmp_path):
 
     with pytest.raises(spack.database.InvalidDatabaseVersionError):
         spack.database.Database(root).query_local()
+
+
+def test_reindex_with_upstreams(tmp_path, monkeypatch, mock_packages, config):
+    # Reindexing should not put install records of upstream entries into the local database. Here
+    # we install `mpileaks` locally with dependencies in the upstream. And we even install
+    # `mpileaks` with the same hash in the upstream. After reindexing, `mpileaks` should still be
+    # in the local db, and `callpath` should not.
+    mpileaks = spack.spec.Spec("mpileaks").concretized()
+    callpath = mpileaks.dependencies("callpath")[0]
+
+    upstream_store = spack.store.create(
+        {"config": {"install_tree": {"root": str(tmp_path / "upstream")}}}
+    )
+    monkeypatch.setattr(spack.store, "STORE", upstream_store)
+    callpath.package.do_install(fake=True)
+
+    local_store = spack.store.create(
+        {
+            "config": {"install_tree": {"root": str(tmp_path / "local")}},
+            "upstreams": {"my-upstream": {"install_tree": str(tmp_path / "upstream")}},
+        }
+    )
+    monkeypatch.setattr(spack.store, "STORE", local_store)
+    mpileaks.package.do_install(fake=True)
+
+    # Sanity check that callpath is from upstream.
+    assert not local_store.db.query_local("callpath")
+    assert local_store.db.query("callpath")
+
+    # Install mpileaks also upstream with the same hash to ensure that determining upstreamness
+    # checks local installs before upstream databases, even when the local database is being
+    # reindexed.
+    monkeypatch.setattr(spack.store, "STORE", upstream_store)
+    mpileaks.package.do_install(fake=True)
+
+    # Delete the local database
+    shutil.rmtree(local_store.db.database_directory)
+
+    # Create a new instance s.t. we don't have cached specs in memory
+    reindexed_local_store = spack.store.create(
+        {
+            "config": {"install_tree": {"root": str(tmp_path / "local")}},
+            "upstreams": {"my-upstream": {"install_tree": str(tmp_path / "upstream")}},
+        }
+    )
+    reindexed_local_store.db.reindex()
+
+    assert not reindexed_local_store.db.query_local("callpath")
+    assert reindexed_local_store.db.query("callpath") == [callpath]
+    assert reindexed_local_store.db.query_local("mpileaks") == [mpileaks]

lib/spack/spack/test/detection.py

@@ -11,11 +11,7 @@
 def test_detection_update_config(mutable_config):
     # mock detected package
     detected_packages = collections.defaultdict(list)
-    detected_packages["cmake"] = [
-        spack.detection.common.DetectedPackage(
-            spec=spack.spec.Spec("cmake@3.27.5"), prefix="/usr/bin"
-        )
-    ]
+    detected_packages["cmake"] = [spack.spec.Spec("cmake@3.27.5", external_path="/usr/bin")]
 
     # update config for new package
     spack.detection.common.update_configuration(detected_packages)

lib/spack/spack/test/env.py

@@ -860,3 +860,33 @@ def test_env_view_on_non_empty_dir_errors(tmp_path, config, mock_packages, tempo
     env.install_all(fake=True)
     with pytest.raises(ev.SpackEnvironmentError, match="because it is a non-empty dir"):
         env.regenerate_views()
+
+
+@pytest.mark.parametrize(
+    "matrix_line", [("^zmpi", "^mpich"), ("~shared", "+shared"), ("shared=False", "+shared-libs")]
+)
+@pytest.mark.regression("40791")
+def test_stack_enforcement_is_strict(tmp_path, matrix_line, config, mock_packages):
+    """Ensure that constraints in matrices are applied strictly after expansion, to avoid
+    inconsistencies between abstract user specs and concrete specs.
+    """
+    manifest = tmp_path / "spack.yaml"
+    manifest.write_text(
+        f"""\
+spack:
+  definitions:
+    - packages: [libelf, mpileaks]
+    - install:
+        - matrix:
+            - [$packages]
+            - [{", ".join(item for item in matrix_line)}]
+  specs:
+    - $install
+  concretizer:
+    unify: false
+"""
+    )
+    # Here we raise different exceptions depending on whether we solve serially or not
+    with pytest.raises(Exception):
+        with ev.Environment(tmp_path) as e:
+            e.concretize()

lib/spack/spack/test/flag_mixing.py

@@ -0,0 +1,333 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import pytest
+
+import spack.build_systems.generic
+import spack.config
+import spack.environment as ev
+import spack.error
+import spack.package_base
+import spack.repo
+import spack.util.spack_yaml as syaml
+import spack.version
+from spack.spec import Spec
+from spack.test.conftest import create_test_repo
+
+"""
+These tests include the following package DAGs:
+
+Firstly, w, x, y where w and x apply cflags to y.
+
+w
+|\
+x |
+|/
+y
+
+Secondly, v, y which where v does not apply cflags to y - this is for testing
+mixing with compiler flag propagation in the absence of compiler flags applied
+by dependents.
+
+v
+|
+y
+
+Finally, a diamond dag to check that the topological order is resolved into
+a total order:
+
+t
+|\
+u x
+|/
+y
+"""
+
+_pkgx = (
+    "x",
+    """\
+class X(Package):
+    version("1.1")
+    version("1.0")
+
+    variant("activatemultiflag", default=False)
+    depends_on('y cflags="-d1"', when="~activatemultiflag")
+    depends_on('y cflags="-d1 -d2"', when="+activatemultiflag")
+""",
+)
+
+
+_pkgy = (
+    "y",
+    """\
+class Y(Package):
+    version("2.1")
+    version("2.0")
+""",
+)
+
+
+_pkgw = (
+    "w",
+    """\
+class W(Package):
+    version("3.1")
+    version("3.0")
+
+    variant("moveflaglater", default=False)
+
+    depends_on('x +activatemultiflag')
+    depends_on('y cflags="-d0"', when="~moveflaglater")
+    depends_on('y cflags="-d3"', when="+moveflaglater")
+""",
+)
+
+
+_pkgv = (
+    "v",
+    """\
+class V(Package):
+    version("4.1")
+    version("4.0")
+
+    depends_on("y")
+""",
+)
+
+
+_pkgt = (
+    "t",
+    """\
+class T(Package):
+    version("5.0")
+
+    depends_on("u")
+    depends_on("x+activatemultiflag")
+    depends_on("y cflags='-c1 -c2'")
+""",
+)
+
+
+_pkgu = (
+    "u",
+    """\
+class U(Package):
+    version("6.0")
+
+    depends_on("y cflags='-e1 -e2'")
+""",
+)
+
+
+@pytest.fixture
+def _create_test_repo(tmpdir, mutable_config):
+    yield create_test_repo(tmpdir, [_pkgt, _pkgu, _pkgv, _pkgw, _pkgx, _pkgy])
+
+
+@pytest.fixture
+def test_repo(_create_test_repo, monkeypatch, mock_stage):
+    with spack.repo.use_repositories(_create_test_repo) as mock_repo_path:
+        yield mock_repo_path
+
+
+def update_concretize_scope(conf_str, section):
+    conf = syaml.load_config(conf_str)
+    spack.config.set(section, conf[section], scope="concretize")
+
+
+def test_mix_spec_and_requirements(concretize_scope, test_repo):
+    conf_str = """\
+packages:
+  y:
+    require: cflags="-c"
+"""
+    update_concretize_scope(conf_str, "packages")
+
+    s1 = Spec('y cflags="-a"').concretized()
+    assert s1.satisfies('cflags="-a -c"')
+
+
+def test_mix_spec_and_dependent(concretize_scope, test_repo):
+    s1 = Spec('x ^y cflags="-a"').concretized()
+    assert s1["y"].satisfies('cflags="-a -d1"')
+
+
+def _compiler_cfg_one_entry_with_cflags(cflags):
+    return f"""\
+compilers::
+- compiler:
+    spec: gcc@12.100.100
+    paths:
+      cc: /usr/bin/fake-gcc
+      cxx: /usr/bin/fake-g++
+      f77: null
+      fc: null
+    flags:
+      cflags: {cflags}
+    operating_system: debian6
+    modules: []
+"""
+
+
+def test_mix_spec_and_compiler_cfg(concretize_scope, test_repo):
+    conf_str = _compiler_cfg_one_entry_with_cflags("-Wall")
+    update_concretize_scope(conf_str, "compilers")
+
+    s1 = Spec('y %gcc@12.100.100 cflags="-O2"').concretized()
+    assert s1.satisfies('cflags="-Wall -O2"')
+
+
+@pytest.mark.parametrize(
+    "cmd_flags,req_flags,cmp_flags,dflags,expected_order",
+    [
+        ("-a -b", "-c", None, False, "-c -a -b"),
+        ("-x7 -x4", "-x5 -x6", None, False, "-x5 -x6 -x7 -x4"),
+        ("-x7 -x4", "-x5 -x6", "-x3 -x8", False, "-x3 -x8 -x5 -x6 -x7 -x4"),
+        ("-x7 -x4", "-x5 -x6", "-x3 -x8", True, "-x3 -x8 -d1 -d2 -x5 -x6 -x7 -x4"),
+        ("-x7 -x4", None, "-x3 -x8", False, "-x3 -x8 -x7 -x4"),
+        ("-x7 -x4", None, "-x3 -x8", True, "-x3 -x8 -d1 -d2 -x7 -x4"),
+        # The remaining test cover cases of intersection
+        ("-a -b", "-a -c", None, False, "-c -a -b"),
+        ("-a -b", None, "-a -c", False, "-c -a -b"),
+        ("-a -b", "-a -c", "-a -d", False, "-d -c -a -b"),
+        ("-a -d2 -d1", "-d2 -c", "-d1 -b", True, "-b -c -a -d2 -d1"),
+        ("-a", "-d0 -d2 -c", "-d1 -b", True, "-b -d1 -d0 -d2 -c -a"),
+    ],
+)
+def test_flag_order_and_grouping(
+    concretize_scope, test_repo, cmd_flags, req_flags, cmp_flags, dflags, expected_order
+):
+    """Check consistent flag ordering and grouping on a package "y"
+    with flags introduced from a variety of sources.
+
+    The ordering rules are explained in ``asp.SpecBuilder.reorder_flags``.
+    """
+    if req_flags:
+        conf_str = f"""\
+packages:
+  y:
+    require: cflags="{req_flags}"
+"""
+        update_concretize_scope(conf_str, "packages")
+
+    if cmp_flags:
+        conf_str = _compiler_cfg_one_entry_with_cflags(cmp_flags)
+        update_concretize_scope(conf_str, "compilers")
+
+    compiler_spec = ""
+    if cmp_flags:
+        compiler_spec = "%gcc@12.100.100"
+
+    if dflags:
+        spec_str = f"x+activatemultiflag {compiler_spec} ^y"
+        expected_dflags = "-d1 -d2"
+    else:
+        spec_str = f"y {compiler_spec}"
+        expected_dflags = None
+
+    if cmd_flags:
+        spec_str += f' cflags="{cmd_flags}"'
+
+    root_spec = Spec(spec_str).concretized()
+    spec = root_spec["y"]
+    satisfy_flags = " ".join(x for x in [cmd_flags, req_flags, cmp_flags, expected_dflags] if x)
+    assert spec.satisfies(f'cflags="{satisfy_flags}"')
+    assert spec.compiler_flags["cflags"] == expected_order.split()
+
+
+def test_two_dependents_flag_mixing(concretize_scope, test_repo):
+    root_spec1 = Spec("w~moveflaglater").concretized()
+    spec1 = root_spec1["y"]
+    assert spec1.compiler_flags["cflags"] == "-d0 -d1 -d2".split()
+
+    root_spec2 = Spec("w+moveflaglater").concretized()
+    spec2 = root_spec2["y"]
+    assert spec2.compiler_flags["cflags"] == "-d3 -d1 -d2".split()
+
+
+def test_propagate_and_compiler_cfg(concretize_scope, test_repo):
+    conf_str = _compiler_cfg_one_entry_with_cflags("-f2")
+    update_concretize_scope(conf_str, "compilers")
+
+    root_spec = Spec("v %gcc@12.100.100 cflags=='-f1'").concretized()
+    assert root_spec["y"].satisfies("cflags='-f1 -f2'")
+
+
+# Note: setting flags on a dependency overrides propagation, which
+# is tested in test/concretize.py:test_compiler_flag_propagation
+
+
+def test_propagate_and_pkg_dep(concretize_scope, test_repo):
+    root_spec1 = Spec("x ~activatemultiflag cflags=='-f1'").concretized()
+    assert root_spec1["y"].satisfies("cflags='-f1 -d1'")
+
+
+def test_propagate_and_require(concretize_scope, test_repo):
+    conf_str = """\
+packages:
+  y:
+    require: cflags="-f2"
+"""
+    update_concretize_scope(conf_str, "packages")
+
+    root_spec1 = Spec("v cflags=='-f1'").concretized()
+    assert root_spec1["y"].satisfies("cflags='-f1 -f2'")
+
+    # Next, check that a requirement does not "undo" a request for
+    # propagation from the command-line spec
+    conf_str = """\
+packages:
+  v:
+    require: cflags="-f1"
+"""
+    update_concretize_scope(conf_str, "packages")
+
+    root_spec2 = Spec("v cflags=='-f1'").concretized()
+    assert root_spec2["y"].satisfies("cflags='-f1'")
+
+    # Note: requirements cannot enforce propagation: any attempt to do
+    # so will generate a concretization error; this likely relates to
+    # the note about #37180 in concretize.lp
+
+
+def test_dev_mix_flags(tmp_path, concretize_scope, mutable_mock_env_path, test_repo):
+    src_dir = tmp_path / "x-src"
+
+    env_content = f"""\
+spack:
+  specs:
+  - y %gcc@12.100.100 cflags=='-fsanitize=address'
+  develop:
+    y:
+      spec: y cflags=='-fsanitize=address'
+      path: {src_dir}
+"""
+
+    conf_str = _compiler_cfg_one_entry_with_cflags("-f1")
+    update_concretize_scope(conf_str, "compilers")
+
+    manifest_file = tmp_path / ev.manifest_name
+    manifest_file.write_text(env_content)
+    e = ev.create("test", manifest_file)
+    with e:
+        e.concretize()
+    e.write()
+
+    (result,) = list(j for i, j in e.concretized_specs() if j.name == "y")
+
+    assert result["y"].satisfies("cflags='-fsanitize=address -f1'")
+
+
+def test_diamond_dep_flag_mixing(concretize_scope, test_repo):
+    """A diamond where each dependent applies flags to the bottom
+    dependency. The goal is to ensure that the flag ordering is
+    (a) topological and (b) repeatable for elements not subject to
+    this partial ordering (i.e. the flags for the left and right
+    nodes of the diamond always appear in the same order).
+    `Spec.traverse` is responsible for handling both of these needs.
+    """
+    root_spec1 = Spec("t").concretized()
+    spec1 = root_spec1["y"]
+    assert spec1.satisfies('cflags="-c1 -c2 -d1 -d2 -e1 -e2"')
+    assert spec1.compiler_flags["cflags"] == "-c1 -c2 -e1 -e2 -d1 -d2".split()

lib/spack/spack/test/install.py

@@ -11,6 +11,8 @@
 
 import llnl.util.filesystem as fs
 
+import spack.config
+import spack.database
 import spack.error
 import spack.mirror
 import spack.patch
@@ -255,8 +257,8 @@ def install_upstream(tmpdir_factory, gen_mock_layout, install_mockery):
     installs are using the upstream installs).
     """
     mock_db_root = str(tmpdir_factory.mktemp("mock_db_root"))
-    prepared_db = spack.database.Database(mock_db_root)
     upstream_layout = gen_mock_layout("/a/")
+    prepared_db = spack.database.Database(mock_db_root, layout=upstream_layout)
     spack.config.CONFIG.push_scope(
         spack.config.InternalConfigScope(
             name="install-upstream-fixture",
@@ -266,8 +268,7 @@ def install_upstream(tmpdir_factory, gen_mock_layout, install_mockery):
 
     def _install_upstream(*specs):
         for spec_str in specs:
-            s = spack.spec.Spec(spec_str).concretized()
-            prepared_db.add(s, upstream_layout)
+            prepared_db.add(Spec(spec_str).concretized())
         downstream_root = str(tmpdir_factory.mktemp("mock_downstream_db_root"))
         return downstream_root, upstream_layout
 
@@ -280,7 +281,7 @@ def test_installed_upstream_external(install_upstream, mock_fetch):
     """
     store_root, _ = install_upstream("externaltool")
     with spack.store.use_store(store_root):
-        dependent = spack.spec.Spec("externaltest")
+        dependent = Spec("externaltest")
         dependent.concretize()
 
         new_dependency = dependent["externaltool"]
@@ -299,8 +300,8 @@ def test_installed_upstream(install_upstream, mock_fetch):
     """
     store_root, upstream_layout = install_upstream("dependency-install")
     with spack.store.use_store(store_root):
-        dependency = spack.spec.Spec("dependency-install").concretized()
-        dependent = spack.spec.Spec("dependent-install").concretized()
+        dependency = Spec("dependency-install").concretized()
+        dependent = Spec("dependent-install").concretized()
 
         new_dependency = dependent["dependency-install"]
         assert new_dependency.installed_upstream
@@ -607,7 +608,7 @@ def test_install_from_binary_with_missing_patch_succeeds(
         s.to_json(f)
 
     # And register it in the database
-    temporary_store.db.add(s, directory_layout=temporary_store.layout, explicit=True)
+    temporary_store.db.add(s, explicit=True)
 
     # Push it to a binary cache
     mirror = spack.mirror.Mirror.from_local_path(str(tmp_path / "my_build_cache"))

lib/spack/spack/test/installer.py

@@ -12,8 +12,6 @@
 import py
 import pytest
 
-import archspec.cpu
-
 import llnl.util.filesystem as fs
 import llnl.util.lock as ulk
 import llnl.util.tty as tty
@@ -435,76 +433,6 @@ def test_fake_install(install_mockery):
     assert os.path.isdir(pkg.prefix.lib)
 
 
-def test_packages_needed_to_bootstrap_compiler_none(install_mockery):
-    spec = spack.spec.Spec("trivial-install-test-package")
-    spec.concretize()
-    assert spec.concrete
-
-    packages = inst._packages_needed_to_bootstrap_compiler(
-        spec.compiler, spec.architecture, [spec.package]
-    )
-    assert not packages
-
-
-@pytest.mark.xfail(reason="fails when assuming Spec.package can only be called on concrete specs")
-def test_packages_needed_to_bootstrap_compiler_packages(install_mockery, monkeypatch):
-    spec = spack.spec.Spec("trivial-install-test-package")
-    spec.concretize()
-
-    def _conc_spec(compiler):
-        return spack.spec.Spec("pkg-a").concretized()
-
-    # Ensure we can get past functions that are precluding obtaining
-    # packages.
-    monkeypatch.setattr(spack.compilers, "compilers_for_spec", _none)
-    monkeypatch.setattr(spack.compilers, "pkg_spec_for_compiler", _conc_spec)
-    monkeypatch.setattr(spack.spec.Spec, "concretize", _noop)
-
-    packages = inst._packages_needed_to_bootstrap_compiler(
-        spec.compiler, spec.architecture, [spec.package]
-    )
-    assert packages
-
-
-def test_update_tasks_for_compiler_packages_as_compiler(mock_packages, config, monkeypatch):
-    spec = spack.spec.Spec("trivial-install-test-package").concretized()
-    installer = inst.PackageInstaller([spec.package], {})
-
-    # Add a task to the queue
-    installer._add_init_task(spec.package, installer.build_requests[0], False, {})
-
-    # monkeypatch to make the list of compilers be what we test
-    def fake_package_list(compiler, architecture, pkgs):
-        return [(spec.package, True)]
-
-    monkeypatch.setattr(inst, "_packages_needed_to_bootstrap_compiler", fake_package_list)
-
-    installer._add_bootstrap_compilers("fake", "fake", "fake", None, {})
-
-    # Check that the only task is now a compiler task
-    assert len(installer.build_pq) == 1
-    assert installer.build_pq[0][1].compiler
-
-
-@pytest.mark.skipif(
-    str(archspec.cpu.host().family) != "x86_64",
-    reason="OneAPI compiler is not supported on other architectures",
-)
-def test_bootstrapping_compilers_with_different_names_from_spec(
-    install_mockery, mutable_config, mock_fetch, archspec_host_is_spack_test_host
-):
-    """Tests that, when we bootstrap '%oneapi' we can translate it to the
-    'intel-oneapi-compilers' package.
-    """
-    with spack.config.override("config:install_missing_compilers", True):
-        with spack.concretize.disable_compiler_existence_check():
-            spec = spack.spec.Spec("trivial-install-test-package%oneapi@=22.2.0").concretized()
-            spec.package.do_install()
-            assert (
-                spack.spec.CompilerSpec("oneapi@=22.2.0") in spack.compilers.all_compiler_specs()
-            )
-
-
 def test_dump_packages_deps_ok(install_mockery, tmpdir, mock_packages):
     """Test happy path for dump_packages with dependencies."""
 
@@ -696,26 +624,6 @@ def test_check_deps_status_upstream(install_mockery, monkeypatch):
         assert inst.package_id(dep) in installer.installed
 
 
-def test_add_bootstrap_compilers(install_mockery, monkeypatch):
-    from collections import defaultdict
-
-    def _pkgs(compiler, architecture, pkgs):
-        spec = spack.spec.Spec("mpi").concretized()
-        return [(spec.package, True)]
-
-    installer = create_installer(["trivial-install-test-package"], {})
-    request = installer.build_requests[0]
-    all_deps = defaultdict(set)
-
-    monkeypatch.setattr(inst, "_packages_needed_to_bootstrap_compiler", _pkgs)
-    installer._add_bootstrap_compilers("fake", "fake", [request.pkg], request, all_deps)
-
-    ids = list(installer.build_tasks)
-    assert len(ids) == 1
-    task = installer.build_tasks[ids[0]]
-    assert task.compiler
-
-
 def test_prepare_for_install_on_installed(install_mockery, monkeypatch):
     """Test of _prepare_for_install's early return for installed task path."""
     installer = create_installer(["dependent-install"], {})
@@ -729,18 +637,6 @@ def test_prepare_for_install_on_installed(install_mockery, monkeypatch):
     installer._prepare_for_install(task)
 
 
-def test_installer_init_requests(install_mockery):
-    """Test of installer initial requests."""
-    spec_name = "dependent-install"
-    with spack.config.override("config:install_missing_compilers", True):
-        installer = create_installer([spec_name], {})
-
-        # There is only one explicit request in this case
-        assert len(installer.build_requests) == 1
-        request = installer.build_requests[0]
-        assert request.pkg.name == spec_name
-
-
 def test_install_task_use_cache(install_mockery, monkeypatch):
     installer = create_installer(["trivial-install-test-package"], {})
     request = installer.build_requests[0]

lib/spack/spack/test/package_class.py

@@ -286,6 +286,7 @@ def compilers(compiler, arch_spec):
 
 
 # TODO (post-34236): Remove when remove deprecated run_test(), etc.
+@pytest.mark.not_on_windows("echo not available on Windows")
 @pytest.mark.parametrize(
     "msg,installed,purpose,expected",
     [

lib/spack/spack/test/schema.py

@@ -105,25 +105,21 @@ def test_schema_validation(meta_schema, config_name):
 
 def test_deprecated_properties(module_suffixes_schema):
     # Test that an error is reported when 'error: True'
-    msg_fmt = r"deprecated properties detected [properties={properties}]"
-    module_suffixes_schema["deprecatedProperties"] = {
-        "properties": ["tcl"],
-        "message": msg_fmt,
-        "error": True,
-    }
+    msg_fmt = r"{name} is deprecated"
+    module_suffixes_schema["deprecatedProperties"] = [
+        {"names": ["tcl"], "message": msg_fmt, "error": True}
+    ]
     v = spack.schema.Validator(module_suffixes_schema)
     data = {"tcl": {"all": {"suffixes": {"^python": "py"}}}}
 
-    expected_match = "deprecated properties detected"
+    expected_match = "tcl is deprecated"
     with pytest.raises(jsonschema.ValidationError, match=expected_match):
         v.validate(data)
 
     # Test that just a warning is reported when 'error: False'
-    module_suffixes_schema["deprecatedProperties"] = {
-        "properties": ["tcl"],
-        "message": msg_fmt,
-        "error": False,
-    }
+    module_suffixes_schema["deprecatedProperties"] = [
+        {"names": ["tcl"], "message": msg_fmt, "error": False}
+    ]
     v = spack.schema.Validator(module_suffixes_schema)
     data = {"tcl": {"all": {"suffixes": {"^python": "py"}}}}
     # The next validation doesn't raise anymore

lib/spack/spack/test/spec_semantics.py

@@ -245,6 +245,65 @@ def test_abstract_specs_can_constrain_each_other(self, lhs, rhs, expected):
         assert c1 == c2
         assert c1 == expected
 
+    @pytest.mark.parametrize(
+        "lhs,rhs,expected_lhs,expected_rhs,propagated_lhs,propagated_rhs",
+        [
+            (
+                'mpich cppflags="-O3"',
+                'mpich cppflags="-O2"',
+                'mpich cppflags="-O3 -O2"',
+                'mpich cppflags="-O2 -O3"',
+                [],
+                [],
+            ),
+            (
+                'mpich cflags="-O3 -g"',
+                'mpich cflags=="-O3"',
+                'mpich cflags="-O3 -g"',
+                'mpich cflags=="-O3 -g"',
+                [("cflags", "-O3")],
+                [("cflags", "-O3")],
+            ),
+        ],
+    )
+    def test_constrain_compiler_flags(
+        self, lhs, rhs, expected_lhs, expected_rhs, propagated_lhs, propagated_rhs
+    ):
+        """Constraining is asymmetric for compiler flags. Also note that
+        Spec equality does not account for flag propagation, so the checks
+        here are manual.
+        """
+        lhs, rhs, expected_lhs, expected_rhs = (
+            Spec(lhs),
+            Spec(rhs),
+            Spec(expected_lhs),
+            Spec(expected_rhs),
+        )
+
+        assert lhs.intersects(rhs)
+        assert rhs.intersects(lhs)
+
+        c1, c2 = lhs.copy(), rhs.copy()
+        c1.constrain(rhs)
+        c2.constrain(lhs)
+
+        assert c1 == expected_lhs
+        assert c2 == expected_rhs
+        for x in [c1, c2]:
+            assert x.satisfies(lhs)
+            assert x.satisfies(rhs)
+
+        def _propagated_flags(_spec):
+            result = set()
+            for flagtype in _spec.compiler_flags:
+                for flag in _spec.compiler_flags[flagtype]:
+                    if flag.propagate:
+                        result.add((flagtype, flag))
+            return result
+
+        assert set(propagated_lhs) <= _propagated_flags(c1)
+        assert set(propagated_rhs) <= _propagated_flags(c2)
+
     def test_constrain_specs_by_hash(self, default_mock_concretization, database):
         """Test that Specs specified only by their hashes can constrain eachother."""
         mpich_dag_hash = "/" + database.query_one("mpich").dag_hash()
@@ -311,14 +370,11 @@ def test_concrete_specs_which_satisfies_abstract(self, lhs, rhs, default_mock_co
             ("mpich~~foo", "mpich++foo"),
             ("mpich++foo", "mpich~~foo"),
             ("mpich foo==True", "mpich foo==False"),
-            ('mpich cppflags="-O3"', 'mpich cppflags="-O2"'),
-            ('mpich cppflags="-O3"', 'mpich cppflags=="-O3"'),
             ("libelf@0:2.0", "libelf@2.1:3"),
             ("libelf@0:2.5%gcc@4.8:4.9", "libelf@2.1:3%gcc@4.5:4.7"),
             ("libelf+debug", "libelf~debug"),
             ("libelf+debug~foo", "libelf+debug+foo"),
             ("libelf debug=True", "libelf debug=False"),
-            ('libelf cppflags="-O3"', 'libelf cppflags="-O2"'),
             ("libelf platform=test target=be os=be", "libelf target=fe os=fe"),
             ("namespace=builtin.mock", "namespace=builtin"),
         ],
@@ -347,10 +403,6 @@ def test_constraining_abstract_specs_with_empty_intersection(self, lhs, rhs):
             ("mpich", "mpich++foo"),
             ("mpich", "mpich~~foo"),
             ("mpich", "mpich foo==1"),
-            # Flags semantics is currently different from other variant
-            ("mpich", 'mpich cflags="-O3"'),
-            ("mpich cflags=-O3", 'mpich cflags="-O3 -Ofast"'),
-            ("mpich cflags=-O2", 'mpich cflags="-O3"'),
             ("multivalue-variant foo=bar", "multivalue-variant +foo"),
             ("multivalue-variant foo=bar", "multivalue-variant ~foo"),
             ("multivalue-variant fee=bar", "multivalue-variant fee=baz"),
@@ -689,6 +741,13 @@ def test_spec_formatting(self, default_mock_concretization):
             ("{/hash}", "/", lambda s: "/" + s.dag_hash()),
         ]
 
+        variants_segments = [
+            ("{variants.debug}", spec, "debug"),
+            ("{variants.foo}", spec, "foo"),
+            ("{^pkg-a.variants.bvv}", spec["pkg-a"], "bvv"),
+            ("{^pkg-a.variants.foo}", spec["pkg-a"], "foo"),
+        ]
+
         other_segments = [
             ("{spack_root}", spack.paths.spack_root),
             ("{spack_install}", spack.store.STORE.layout.root),
@@ -716,6 +775,12 @@ def check_prop(check_spec, fmt_str, prop, getter):
             callpath, fmt_str = depify("callpath", named_str, sigil)
             assert spec.format(fmt_str) == getter(callpath)
 
+        for named_str, test_spec, variant_name in variants_segments:
+            assert test_spec.format(named_str) == str(test_spec.variants[variant_name])
+            assert test_spec.format(named_str[:-1] + ".value}") == str(
+                test_spec.variants[variant_name].value
+            )
+
         for named_str, expected in other_segments:
             actual = spec.format(named_str)
             assert expected == actual
@@ -775,6 +840,7 @@ def test_spec_formatting_sigil_mismatches(self, default_mock_concretization, fmt
             r"{dag_hash}",
             r"{foo}",
             r"{+variants.debug}",
+            r"{variants.this_variant_does_not_exist}",
         ],
     )
     def test_spec_formatting_bad_formats(self, default_mock_concretization, fmt_str):
@@ -1451,8 +1517,8 @@ def test_abstract_contains_semantic(lhs, rhs, expected, mock_packages):
         (CompilerSpec, "gcc@5", "gcc@5-tag", (True, False, True)),
         # Flags (flags are a map, so for convenience we initialize a full Spec)
         # Note: the semantic is that of sv variants, not mv variants
-        (Spec, "cppflags=-foo", "cppflags=-bar", (False, False, False)),
-        (Spec, "cppflags='-bar -foo'", "cppflags=-bar", (False, False, False)),
+        (Spec, "cppflags=-foo", "cppflags=-bar", (True, False, False)),
+        (Spec, "cppflags='-bar -foo'", "cppflags=-bar", (True, True, False)),
         (Spec, "cppflags=-foo", "cppflags=-foo", (True, True, True)),
         (Spec, "cppflags=-foo", "cflags=-foo", (True, False, False)),
         # Versions