sst: update core, elements, macro to 15.0.0 (#50473)

* Add tag for podio v01-03

* Update minimal root version for RNTuple support

* Make sure clang-format does not interfere with code generation

* Add edm4hep version 0.99.2 and new podio version dependency

* Keep root versions ordered for dependencies

Co-authored-by: Juan Miguel Carceller <22276694+jmcarcell@users.noreply.github.com>

---------

Co-authored-by: Juan Miguel Carceller <22276694+jmcarcell@users.noreply.github.com>

.github/workflows/import-check.yaml

@@ -6,6 +6,7 @@ on:
 jobs:
   # Check we don't make the situation with circular imports worse
   import-check:
+    continue-on-error: true
     runs-on: ubuntu-latest
     steps:
     - uses: julia-actions/setup-julia@v2

.github/workflows/sync-packages.yaml

@@ -28,7 +28,7 @@ jobs:
       run: |
         cd spack-packages
         git-filter-repo --quiet --source ../spack \
-                        --subdirectory-filter var/spack/repos \
+                        --path var/spack/repos/ --path-rename var/spack/repos/:python/ \
                         --path share/spack/gitlab/cloud_pipelines/ --path-rename share/spack/gitlab/cloud_pipelines/:.ci/gitlab/ \
                         --refs develop
     - name: Push

lib/spack/docs/basic_usage.rst

@@ -276,7 +276,7 @@ remove dependent packages *before* removing their dependencies or use the
 Garbage collection
 ^^^^^^^^^^^^^^^^^^
 
-When Spack builds software from sources, if often installs tools that are needed
+When Spack builds software from sources, it often installs tools that are needed
 just to build or test other software. These are not necessary at runtime.
 To support cases where removing these tools can be a benefit Spack provides
 the ``spack gc`` ("garbage collector") command, which will uninstall all unneeded packages:

lib/spack/docs/binary_caches.rst

@@ -89,7 +89,7 @@ You can see that the mirror is added with ``spack mirror list`` as follows:
     spack-public       https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/
 
 
-At this point, you've create a buildcache, but spack hasn't indexed it, so if
+At this point, you've created a buildcache, but Spack hasn't indexed it, so if
 you run ``spack buildcache list`` you won't see any results. You need to index
 this new build cache as follows:
 
@@ -318,7 +318,7 @@ other system dependencies. However, they are still compatible with tools like
 ``skopeo``, ``podman``, and ``docker`` for pulling and pushing.
 
 .. note::
-    The docker ``overlayfs2`` storage driver is limited to 128 layers, above which a
+    The Docker ``overlayfs2`` storage driver is limited to 128 layers, above which a
     ``max depth exceeded`` error may be produced when pulling the image. There
     are `alternative drivers <https://docs.docker.com/storage/storagedriver/>`_.
 

lib/spack/docs/bootstrapping.rst

@@ -14,7 +14,7 @@ is an entire command dedicated to the management of every aspect of bootstrappin
 
 .. command-output:: spack bootstrap --help
 
-Spack is configured to bootstrap its dependencies lazily by default; i.e. the first time they are needed and
+Spack is configured to bootstrap its dependencies lazily by default; i.e., the first time they are needed and
 can't be found. You can readily check if any prerequisite for using Spack is missing by running:
 
 .. code-block:: console
@@ -36,8 +36,8 @@ can't be found. You can readily check if any prerequisite for using Spack is mis
 
 In the case of the output shown above Spack detected that both ``clingo`` and ``gnupg``
 are missing and it's giving detailed information on why they are needed and whether
-they can be bootstrapped. The return code of this command summarizes the results, if any
-dependencies are missing the return code is ``1``, otherwise ``0``. Running a command that
+they can be bootstrapped. The return code of this command summarizes the results; if any
+dependencies are missing, the return code is ``1``, otherwise ``0``. Running a command that
 concretizes a spec, like:
 
 .. code-block:: console

lib/spack/docs/conf.py

@@ -228,7 +228,7 @@ def setup(sphinx):
     ("py:class", "spack.install_test.Pb"),
     ("py:class", "spack.filesystem_view.SimpleFilesystemView"),
     ("py:class", "spack.traverse.EdgeAndDepth"),
-    ("py:class", "archspec.cpu.microarchitecture.Microarchitecture"),
+    ("py:class", "_vendoring.archspec.cpu.microarchitecture.Microarchitecture"),
     ("py:class", "spack.compiler.CompilerCache"),
     # TypeVar that is not handled correctly
     ("py:class", "llnl.util.lang.T"),

lib/spack/docs/config_yaml.rst

@@ -148,8 +148,8 @@ this can expose you to attacks.  Use at your own risk.
 ``ssl_certs``
 --------------------
 
-Path to custom certificats for SSL verification. The value can be a
-filesytem path, or an environment variable that expands to an absolute file path.
+Path to custom certificates for SSL verification. The value can be a
+filesystem path, or an environment variable that expands to an absolute file path.
 The default value is set to the environment variable ``SSL_CERT_FILE``
 to use the same syntax used by many other applications that automatically
 detect custom certificates.

lib/spack/docs/containers.rst

@@ -11,7 +11,7 @@ Container Images
 Spack :ref:`environments` can easily be turned into container images. This page
 outlines two ways in which this can be done:
 
-1. By installing the environment on the host system, and copying the installations
+1. By installing the environment on the host system and copying the installations
    into the container image. This approach does not require any tools like Docker
    or Singularity to be installed.
 2. By generating a Docker or Singularity recipe that can be used to build the
@@ -56,8 +56,8 @@ environment roots and its runtime dependencies.
 
 .. note::
 
-  When using registries like GHCR and Docker Hub, the ``--oci-password`` flag is not
-  the password for your account, but a personal access token you need to generate separately.
+  When using registries like GHCR and Docker Hub, the ``--oci-password`` flag specifies not
+  the password for your account, but rather a personal access token you need to generate separately.
 
 The specified ``--base-image`` should have a libc that is compatible with the host system.
 For example if your host system is Ubuntu 20.04, you can use ``ubuntu:20.04``, ``ubuntu:22.04``

lib/spack/docs/getting_started.rst

@@ -20,7 +20,7 @@ be present on the machine where Spack is run:
    :header-rows: 1
 
 These requirements can be easily installed on most modern Linux systems;
-on macOS, the Command Line Tools package is required, and a full XCode suite
+on macOS, the Command Line Tools package is required, and a full Xcode suite
 may be necessary for some packages such as Qt and apple-gl. Spack is designed
 to run on HPC platforms like Cray.  Not all packages should be expected
 to work on all platforms.

lib/spack/docs/module_file_support.rst

@@ -8,7 +8,7 @@
 Modules (modules.yaml)
 ======================
 
-The use of module systems to manage user environment in a controlled way
+The use of module systems to manage user environments in a controlled way
 is a common practice at HPC centers that is sometimes embraced also by
 individual programmers on their development machines. To support this
 common practice Spack integrates with `Environment Modules
@@ -490,7 +490,7 @@ that are already in the Lmod hierarchy.
 
 
 .. note::
-   Tcl and Lua modules also allow for explicit conflicts between modulefiles.
+   Tcl and Lua modules also allow for explicit conflicts between module files.
 
    .. code-block:: yaml
 
@@ -513,7 +513,7 @@ that are already in the Lmod hierarchy.
    :meth:`~spack.spec.Spec.format` method.
 
    For Lmod and Environment Modules versions prior 4.2, it is important to
-   express the conflict on both modulefiles conflicting with each other.
+   express the conflict on both module files conflicting with each other.
 
 
 .. note::
@@ -550,7 +550,7 @@ that are already in the Lmod hierarchy.
 
 .. warning::
   Consistency of Core packages
-   The user is responsible for maintining consistency among core packages, as ``core_specs``
+   The user is responsible for maintaining consistency among core packages, as ``core_specs``
    bypasses the hierarchy that allows Lmod to safely switch between coherent software stacks.
 
 .. warning::

lib/spack/docs/packaging_guide.rst

@@ -179,7 +179,7 @@ Spack can be found at :ref:`package_class_structure`.
 
    .. code-block:: python
 
-      class Foo(CmakePackage):
+      class Foo(CMakePackage):
           def cmake_args(self):
               ...
 
@@ -1212,7 +1212,7 @@ class-level tarball URL and VCS. For example:
        version("master",  branch="master")
        version("12.12.1", md5="ecd4606fa332212433c98bf950a69cc7")
        version("12.10.1", md5="667333dbd7c0f031d47d7c5511fd0810")
-       version("12.8.1",  "9f37f683ee2b427b5540db8a20ed6b15")
+       version("12.8.1",  md5="9f37f683ee2b427b5540db8a20ed6b15")
 
 If a package contains both a ``url`` and ``git`` class-level attribute,
 Spack decides which to use based on the arguments to the ``version()``
@@ -1343,7 +1343,7 @@ Submodules
 
      version("1.0.1", tag="v1.0.1", submodules=True)
 
-  If a package has needs more fine-grained control over submodules, define
+  If a package needs more fine-grained control over submodules, define
   ``submodules`` to be a callable function that takes the package instance as
   its only argument.  The function should return a list of submodules to be fetched.
 
@@ -2308,31 +2308,19 @@ looks like this:
 
        parallel = False
 
-Similarly, you can disable parallel builds only for specific make
-commands, as ``libdwarf`` does:
+You can also disable parallel builds only for specific make
+invocation:
 
 .. code-block:: python
-   :emphasize-lines: 9, 12
+   :emphasize-lines: 5
    :linenos:
 
    class Libelf(Package):
        ...
 
        def install(self, spec, prefix):
-           configure("--prefix=" + prefix,
-                     "--enable-shared",
-                     "--disable-dependency-tracking",
-                     "--disable-debug")
-           make()
-
-           # The mkdir commands in libelf's install can fail in parallel
            make("install", parallel=False)
 
-The first make will run in parallel here, but the second will not.  If
-you set ``parallel`` to ``False`` at the package level, then each call
-to ``make()`` will be sequential by default, but packagers can call
-``make(parallel=True)`` to override it.
-
 Note that the ``--jobs`` option works out of the box for all standard
 build systems. If you are using a non-standard build system instead, you
 can use the variable ``make_jobs`` to extract the number of jobs specified
@@ -2507,7 +2495,7 @@ necessary when there are breaking changes in the dependency that the
 package cannot handle. In Spack we often add forward compatibility
 bounds only at the time a new, breaking version of a dependency is
 released. As with backward compatibility, it is typical to see a list
-of forward compatibility bounds in a package file as seperate lines:
+of forward compatibility bounds in a package file as separate lines:
 
 .. code-block:: python
 
@@ -3383,7 +3371,7 @@ the above attribute implementations:
        "/opt/spack/linux-fedora35-haswell/gcc-11.3.1/foo-1.0-ca3rczp5omy7dfzoqw4p7oc2yh3u7lt6/baz/lib/libFooBaz.so"
    ])
 
-   # baz library directories in the baz subdirectory of the foo porefix
+   # baz library directories in the baz subdirectory of the foo prefix
    >>> spec["baz"].libs.directories
    [
        "/opt/spack/linux-fedora35-haswell/gcc-11.3.1/foo-1.0-ca3rczp5omy7dfzoqw4p7oc2yh3u7lt6/baz/lib"
@@ -5740,7 +5728,7 @@ running each executable, ``foo`` and ``bar``, as independent test parts.
 .. note::
 
    The method name ``copy_test_files`` here is for illustration purposes.
-   You are free to use a name that is more suited to your package.
+   You are free to use a name that is better suited to your package.
 
    The key to copying files for stand-alone testing at build time is use
    of the ``run_after`` directive, which ensures the associated files are
@@ -7249,7 +7237,7 @@ which are not, there is the `checked_by` parameter in the license directive:
 
    license("<license>", when="<when>", checked_by="<github username>")
 
-When you have validated a github license, either when doing so explicitly or
+When you have validated a package license, either when doing so explicitly or
 as part of packaging a new package, please set the `checked_by` parameter
 to your Github username to signal that the license has been manually
 verified.

lib/spack/docs/replace_conda_homebrew.rst

@@ -214,7 +214,7 @@ package versions, simply run the following commands:
 
 Running ``spack mark -i --all`` tells Spack to mark all of the existing
 packages within an environment as "implicitly" installed. This tells
-spack's garbage collection system that these packages should be cleaned up.
+Spack's garbage collection system that these packages should be cleaned up.
 
 Don't worry however, this will not remove your entire environment.
 Running ``spack install`` will reexamine your spack environment after

lib/spack/external/_vendoring/_pyrsistent_version.pyi

@@ -1 +0,0 @@
-from _pyrsistent_version import *

lib/spack/external/_vendoring/altgraph.pyi

@@ -1 +0,0 @@
-from altgraph import *

lib/spack/external/_vendoring/archspec/__init__.py

@@ -1,3 +1,3 @@
 """Init file to avoid namespace packages"""
 
-__version__ = "0.2.4"
+__version__ = "0.2.5"

lib/spack/external/_vendoring/archspec/cli.py

@@ -9,8 +9,8 @@
 import argparse
 import typing
 
-import archspec
-import archspec.cpu
+import _vendoring.archspec
+import _vendoring.archspec.cpu
 
 
 def _make_parser() -> argparse.ArgumentParser:
@@ -24,7 +24,7 @@ def _make_parser() -> argparse.ArgumentParser:
         "-V",
         help="Show the version and exit.",
         action="version",
-        version=f"archspec, version {archspec.__version__}",
+        version=f"archspec, version {_vendoring.archspec.__version__}",
     )
     parser.add_argument("--help", "-h", help="Show the help and exit.", action="help")
 
@@ -45,9 +45,9 @@ def _make_parser() -> argparse.ArgumentParser:
 
 
 def cpu() -> int:
-    """Run the `archspec cpu` subcommand."""
+    """Run the `_vendoring.archspec.cpu` subcommand."""
     try:
-        print(archspec.cpu.host())
+        print(_vendoring.archspec.cpu.host())
     except FileNotFoundError as exc:
         print(exc)
         return 1

lib/spack/external/_vendoring/archspec/cpu/microarchitecture.py

@@ -8,9 +8,9 @@
 import re
 import warnings
 
-import archspec
-import archspec.cpu.alias
-import archspec.cpu.schema
+import _vendoring.archspec
+import _vendoring.archspec.cpu.alias
+import _vendoring.archspec.cpu.schema
 
 from .alias import FEATURE_ALIASES
 from .schema import LazyDictionary
@@ -384,7 +384,7 @@ def fill_target_from_dict(name, data, targets):
         )
 
     known_targets = {}
-    data = archspec.cpu.schema.TARGETS_JSON["microarchitectures"]
+    data = _vendoring.archspec.cpu.schema.TARGETS_JSON["microarchitectures"]
     for name in data:
         if name in known_targets:
             # name was already brought in as ancestor to a target

lib/spack/external/_vendoring/archspec/vendor/cpuid/LICENSE

@@ -0,0 +1,20 @@
+The MIT License (MIT)
+
+Copyright (c) 2014 Anders Høst
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

lib/spack/external/_vendoring/jsonschema.pyi

@@ -1 +0,0 @@
-from jsonschema import *

lib/spack/external/_vendoring/macholib.pyi

@@ -1 +0,0 @@
-from macholib import *

lib/spack/external/_vendoring/pyrsistent/__init__.pyi

@@ -1,213 +0,0 @@
-# flake8: noqa: E704
-# from https://gist.github.com/WuTheFWasThat/091a17d4b5cab597dfd5d4c2d96faf09
-# Stubs for pyrsistent (Python 3.6)
-
-from typing import Any
-from typing import AnyStr
-from typing import Callable
-from typing import Iterable
-from typing import Iterator
-from typing import List
-from typing import Optional
-from typing import Mapping
-from typing import MutableMapping
-from typing import Sequence
-from typing import Set
-from typing import Union
-from typing import Tuple
-from typing import Type
-from typing import TypeVar
-from typing import overload
-
-# see commit 08519aa for explanation of the re-export
-from pyrsistent.typing import CheckedKeyTypeError as CheckedKeyTypeError
-from pyrsistent.typing import CheckedPMap as CheckedPMap
-from pyrsistent.typing import CheckedPSet as CheckedPSet
-from pyrsistent.typing import CheckedPVector as CheckedPVector
-from pyrsistent.typing import CheckedType as CheckedType
-from pyrsistent.typing import CheckedValueTypeError as CheckedValueTypeError
-from pyrsistent.typing import InvariantException as InvariantException
-from pyrsistent.typing import PClass as PClass
-from pyrsistent.typing import PBag as PBag
-from pyrsistent.typing import PDeque as PDeque
-from pyrsistent.typing import PList as PList
-from pyrsistent.typing import PMap as PMap
-from pyrsistent.typing import PMapEvolver as PMapEvolver
-from pyrsistent.typing import PSet as PSet
-from pyrsistent.typing import PSetEvolver as PSetEvolver
-from pyrsistent.typing import PTypeError as PTypeError
-from pyrsistent.typing import PVector as PVector
-from pyrsistent.typing import PVectorEvolver as PVectorEvolver
-
-T = TypeVar('T')
-KT = TypeVar('KT')
-VT = TypeVar('VT')
-
-def pmap(initial: Union[Mapping[KT, VT], Iterable[Tuple[KT, VT]]] = {}, pre_size: int = 0) -> PMap[KT, VT]: ...
-def m(**kwargs: VT) -> PMap[str, VT]: ...
-
-def pvector(iterable: Iterable[T] = ...) -> PVector[T]: ...
-def v(*iterable: T) -> PVector[T]: ...
-
-def pset(iterable: Iterable[T] = (), pre_size: int = 8) -> PSet[T]: ...
-def s(*iterable: T) -> PSet[T]: ...
-
-# see class_test.py for use cases
-Invariant = Tuple[bool, Optional[Union[str, Callable[[], str]]]]
-
-@overload
-def field(
-    type: Union[Type[T], Sequence[Type[T]]] = ...,
-    invariant: Callable[[Any], Union[Invariant, Iterable[Invariant]]] = lambda _: (True, None),
-    initial: Any = object(),
-    mandatory: bool = False,
-    factory: Callable[[Any], T] = lambda x: x,
-    serializer: Callable[[Any, T], Any] = lambda _, value: value,
-) -> T: ...
-# The actual return value (_PField) is irrelevant after a PRecord has been instantiated,
-# see https://github.com/tobgu/pyrsistent/blob/master/pyrsistent/_precord.py#L10
-@overload
-def field(
-    type: Any = ...,
-    invariant: Callable[[Any], Union[Invariant, Iterable[Invariant]]] = lambda _: (True, None),
-    initial: Any = object(),
-    mandatory: bool = False,
-    factory: Callable[[Any], Any] = lambda x: x,
-    serializer: Callable[[Any, Any], Any] = lambda _, value: value,
-) -> Any: ...
-
-# Use precise types for the simplest use cases, but fall back to Any for
-# everything else. See record_test.py for the wide range of possible types for
-# item_type
-@overload
-def pset_field(
-    item_type: Type[T],
-    optional: bool = False,
-    initial: Iterable[T] = ...,
-) -> PSet[T]: ...
-@overload
-def pset_field(
-    item_type: Any,
-    optional: bool = False,
-    initial: Any = (),
-) -> PSet[Any]: ...
-
-@overload
-def pmap_field(
-    key_type: Type[KT],
-    value_type: Type[VT],
-    optional: bool = False,
-    invariant: Callable[[Any], Tuple[bool, Optional[str]]] = lambda _: (True, None),
-) -> PMap[KT, VT]: ...
-@overload
-def pmap_field(
-    key_type: Any,
-    value_type: Any,
-    optional: bool = False,
-    invariant: Callable[[Any], Tuple[bool, Optional[str]]] = lambda _: (True, None),
-) -> PMap[Any, Any]: ...
-
-@overload
-def pvector_field(
-    item_type: Type[T],
-    optional: bool = False,
-    initial: Iterable[T] = ...,
-) -> PVector[T]: ...
-@overload
-def pvector_field(
-    item_type: Any,
-    optional: bool = False,
-    initial: Any = (),
-) -> PVector[Any]: ...
-
-def pbag(elements: Iterable[T]) -> PBag[T]: ...
-def b(*elements: T) -> PBag[T]: ...
-
-def plist(iterable: Iterable[T] = (), reverse: bool = False) -> PList[T]: ...
-def l(*elements: T) -> PList[T]: ...
-
-def pdeque(iterable: Optional[Iterable[T]] = None, maxlen: Optional[int] = None) -> PDeque[T]: ...
-def dq(*iterable: T) -> PDeque[T]: ...
-
-@overload
-def optional(type: T) -> Tuple[T, Type[None]]: ...
-@overload
-def optional(*typs: Any) -> Tuple[Any, ...]: ...
-
-T_PRecord = TypeVar('T_PRecord', bound='PRecord')
-class PRecord(PMap[AnyStr, Any]):
-    _precord_fields: Mapping
-    _precord_initial_values: Mapping
-
-    def __hash__(self) -> int: ...
-    def __init__(self, **kwargs: Any) -> None: ...
-    def __iter__(self) -> Iterator[Any]: ...
-    def __len__(self) -> int: ...
-    @classmethod
-    def create(
-        cls: Type[T_PRecord],
-        kwargs: Mapping,
-        _factory_fields: Optional[Iterable] = None,
-        ignore_extra: bool = False,
-    ) -> T_PRecord: ...
-    # This is OK because T_PRecord is a concrete type
-    def discard(self: T_PRecord, key: KT) -> T_PRecord: ...
-    def remove(self: T_PRecord, key: KT) -> T_PRecord: ...
-
-    def serialize(self, format: Optional[Any] = ...) -> MutableMapping: ...
-
-    # From pyrsistent documentation:
-    #   This set function differs slightly from that in the PMap
-    #   class. First of all it accepts key-value pairs. Second it accepts multiple key-value
-    #   pairs to perform one, atomic, update of multiple fields.
-    @overload
-    def set(self, key: KT, val: VT) -> Any: ...
-    @overload
-    def set(self, **kwargs: VT) -> Any: ...
-
-def immutable(
-    members: Union[str, Iterable[str]] = '',
-    name: str = 'Immutable',
-    verbose: bool = False,
-) -> Tuple: ...  # actually a namedtuple
-
-# ignore mypy warning "Overloaded function signatures 1 and 5 overlap with
-# incompatible return types"
-@overload
-def freeze(o: Mapping[KT, VT]) -> PMap[KT, VT]: ... # type: ignore
-@overload
-def freeze(o: List[T]) -> PVector[T]: ... # type: ignore
-@overload
-def freeze(o: Tuple[T, ...]) -> Tuple[T, ...]: ...
-@overload
-def freeze(o: Set[T]) -> PSet[T]: ... # type: ignore
-@overload
-def freeze(o: T) -> T: ...
-
-
-@overload
-def thaw(o: PMap[KT, VT]) -> MutableMapping[KT, VT]: ... # type: ignore
-@overload
-def thaw(o: PVector[T]) -> List[T]: ... # type: ignore
-@overload
-def thaw(o: Tuple[T, ...]) -> Tuple[T, ...]: ...
-# collections.abc.MutableSet is kind of garbage:
-# https://stackoverflow.com/questions/24977898/why-does-collections-mutableset-not-bestow-an-update-method
-@overload
-def thaw(o: PSet[T]) -> Set[T]: ... # type: ignore
-@overload
-def thaw(o: T) -> T: ...
-
-def mutant(fn: Callable) -> Callable: ...
-
-def inc(x: int) -> int: ...
-@overload
-def discard(evolver: PMapEvolver[KT, VT], key: KT) -> None: ...
-@overload
-def discard(evolver: PVectorEvolver[T], key: int) -> None: ...
-@overload
-def discard(evolver: PSetEvolver[T], key: T) -> None: ...
-def rex(expr: str) -> Callable[[Any], bool]: ...
-def ny(_: Any) -> bool: ...
-
-def get_in(keys: Iterable, coll: Mapping, default: Optional[Any] = None, no_default: bool = False) -> Any: ...

lib/spack/external/_vendoring/ruamel.pyi

@@ -1 +0,0 @@
-from ruamel import *

lib/spack/external/_vendoring/six/__init__.pyi

@@ -1 +0,0 @@
-from six import *

lib/spack/external/_vendoring/six/moves/__init__.pyi

@@ -1 +0,0 @@
-from six.moves import *

lib/spack/external/_vendoring/six/moves/configparser.pyi

@@ -1 +0,0 @@
-from six.moves.configparser import *

lib/spack/external/archspec/README.md

@@ -1,81 +0,0 @@
-[![](https://github.com/archspec/archspec/workflows/Unit%20tests/badge.svg)](https://github.com/archspec/archspec/actions)
-[![codecov](https://codecov.io/gh/archspec/archspec/branch/master/graph/badge.svg)](https://codecov.io/gh/archspec/archspec)
-[![Documentation Status](https://readthedocs.org/projects/archspec/badge/?version=latest)](https://archspec.readthedocs.io/en/latest/?badge=latest)
-
-
-# Archspec (Python bindings)
-
-Archspec aims at providing a standard set of human-understandable labels for
-various aspects of a system architecture  like CPU, network fabrics, etc. and
-APIs to detect, query and compare them.
-
-This project grew out of [Spack](https://spack.io/) and is currently under
-active development. At present it supports APIs to detect and model
-compatibility relationships among different CPU microarchitectures.
-
-## Getting started with development
-
-The `archspec` Python package needs [poetry](https://python-poetry.org/) to
-be installed from VCS sources. The preferred method to install it is via
-its custom installer outside of any virtual environment:
-```console
-$ curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
-```
-You can refer to [Poetry's documentation](https://python-poetry.org/docs/#installation)
-for further details or for other methods to install this tool. You'll also need `tox`
-to run unit test:
-```console
-$ pip install --user tox
-```
-Finally you'll need to clone the repository:
-```console
-$ git clone --recursive https://github.com/archspec/archspec.git
-```
-
-### Running unit tests
-Once you have your environment ready you can run `archspec` unit tests
-using ``tox`` from the root of the repository:
-```console
-$ tox
-  [ ... ]
-  py27: commands succeeded
-  py35: commands succeeded
-  py36: commands succeeded
-  py37: commands succeeded
-  py38: commands succeeded
-  pylint: commands succeeded
-  flake8: commands succeeded
-  black: commands succeeded
-  congratulations :)
-```
-
-## Citing Archspec
-
-If you are referencing `archspec` in a publication, please cite the following
-paper:
-
- * Massimiliano Culpo, Gregory Becker, Carlos Eduardo Arango Gutierrez, Kenneth
-   Hoste, and Todd Gamblin.
-   [**`archspec`: A library for detecting, labeling, and reasoning about
-   microarchitectures**](https://tgamblin.github.io/pubs/archspec-canopie-hpc-2020.pdf).
-   In *2nd International Workshop on Containers and New Orchestration Paradigms
-   for Isolated Environments in HPC (CANOPIE-HPC'20)*, Online Event, November
-   12, 2020.
-
-## License
-
-Archspec is distributed under the terms of both the MIT license and the
-Apache License (Version 2.0). Users may choose either license, at their
-option.
-
-All new contributions must be made under both the MIT and Apache-2.0
-licenses.
-
-See [LICENSE-MIT](https://github.com/archspec/archspec/blob/master/LICENSE-MIT),
-[LICENSE-APACHE](https://github.com/archspec/archspec/blob/master/LICENSE-APACHE),
-[COPYRIGHT](https://github.com/archspec/archspec/blob/master/COPYRIGHT), and
-[NOTICE](https://github.com/archspec/archspec/blob/master/NOTICE) for details.
-
-SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-LLNL-CODE-811653

lib/spack/external/archspec/json/COPYRIGHT

@@ -1,22 +0,0 @@
-Intellectual Property Notice
-------------------------------
-
-Archspec is licensed under the Apache License, Version 2.0 (LICENSE-APACHE
-or http://www.apache.org/licenses/LICENSE-2.0) or the MIT license,
-(LICENSE-MIT or http://opensource.org/licenses/MIT), at your option.
-
-Copyrights and patents in the Archspec project are retained by contributors.
-No copyright assignment is required to contribute to Archspec.
-
-
-SPDX usage
-------------
-
-Individual files contain SPDX tags instead of the full license text.
-This enables machine processing of license information based on the SPDX
-License Identifiers that are available here: https://spdx.org/licenses/
-
-Files that are dual-licensed as Apache-2.0 OR MIT contain the following
-text in the license header:
-
-    SPDX-License-Identifier: (Apache-2.0 OR MIT)

lib/spack/external/vendor.txt

@@ -9,3 +9,4 @@ macholib==1.16.2
   altgraph==0.17.3
 ruamel.yaml==0.17.21
 typing_extensions==4.1.1
+archspec @ git+https://github.com/archspec/archspec.git@38ce485258ffc4fc6dd6688f8dc90cb269478c47

lib/spack/spack/bootstrap/_common.py

@@ -12,10 +12,9 @@
 import warnings
 from typing import Optional, Sequence, Union
 
+import _vendoring.archspec.cpu
 from _vendoring.typing_extensions import TypedDict
 
-import archspec.cpu
-
 import llnl.util.filesystem as fs
 from llnl.util import tty
 
@@ -138,7 +137,7 @@ def _fix_ext_suffix(candidate_spec: "spack.spec.Spec"):
     }
 
     # If the current architecture is not problematic return
-    generic_target = archspec.cpu.host().family
+    generic_target = _vendoring.archspec.cpu.host().family
     if str(generic_target) not in _suffix_to_be_checked:
         return
 
@@ -235,7 +234,7 @@ def _root_spec(spec_str: str) -> str:
     platform = str(spack.platforms.host())
 
     spec_str += f" platform={platform}"
-    target = archspec.cpu.host().family
+    target = _vendoring.archspec.cpu.host().family
     spec_str += f" target={target}"
 
     tty.debug(f"[BOOTSTRAP ROOT SPEC] {spec_str}")

lib/spack/spack/bootstrap/clingo.py

@@ -13,7 +13,7 @@
 import sys
 from typing import Dict, Optional, Tuple
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 import spack.compilers.config
 import spack.compilers.libraries
@@ -30,7 +30,7 @@ class ClingoBootstrapConcretizer:
     def __init__(self, configuration):
         self.host_platform = spack.platforms.host()
         self.host_os = self.host_platform.default_operating_system()
-        self.host_target = archspec.cpu.host().family
+        self.host_target = _vendoring.archspec.cpu.host().family
         self.host_architecture = spack.spec.ArchSpec.default_arch()
         self.host_architecture.target = str(self.host_target)
         self.host_compiler = self._valid_compiler_or_raise()

lib/spack/spack/bootstrap/environment.py

@@ -8,7 +8,7 @@
 import sys
 from typing import Iterable, List
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 from llnl.util import tty
 
@@ -51,7 +51,7 @@ def environment_root(cls) -> pathlib.Path:
         """Environment root directory"""
         bootstrap_root_path = root_path()
         python_part = spec_for_current_python().replace("@", "")
-        arch_part = archspec.cpu.host().family
+        arch_part = _vendoring.archspec.cpu.host().family
         interpreter_part = hashlib.md5(sys.exec_prefix.encode()).hexdigest()[:5]
         environment_dir = f"{python_part}-{arch_part}-{interpreter_part}"
         return pathlib.Path(
@@ -112,7 +112,7 @@ def _write_spack_yaml_file(self) -> None:
         context = {
             "python_spec": spec_for_current_python(),
             "python_prefix": sys.exec_prefix,
-            "architecture": archspec.cpu.host().family,
+            "architecture": _vendoring.archspec.cpu.host().family,
             "environment_path": self.environment_root(),
             "environment_specs": self.spack_dev_requirements(),
             "store_path": store_path(),

lib/spack/spack/build_environment.py

@@ -59,7 +59,7 @@
     overload,
 )
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 import llnl.util.tty as tty
 from llnl.string import plural
@@ -440,10 +440,12 @@ def optimization_flags(compiler, target):
     # Try to check if the current compiler comes with a version number or
     # has an unexpected suffix. If so, treat it as a compiler with a
     # custom spec.
-    version_number, _ = archspec.cpu.version_components(compiler.version.dotted_numeric_string)
+    version_number, _ = _vendoring.archspec.cpu.version_components(
+        compiler.version.dotted_numeric_string
+    )
     try:
         result = target.optimization_flags(compiler.name, version_number)
-    except (ValueError, archspec.cpu.UnsupportedMicroarchitecture):
+    except (ValueError, _vendoring.archspec.cpu.UnsupportedMicroarchitecture):
         result = ""
 
     return result

lib/spack/spack/cmd/arch.py

@@ -5,7 +5,7 @@
 import collections
 import warnings
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 import llnl.util.tty.colify as colify
 import llnl.util.tty.color as color
@@ -92,11 +92,11 @@ def display_target_group(header, target_group):
 def arch(parser, args):
     if args.generic_target:
         # TODO: add deprecation warning in 0.24
-        print(archspec.cpu.host().generic)
+        print(_vendoring.archspec.cpu.host().generic)
         return
 
     if args.known_targets:
-        display_targets(archspec.cpu.TARGETS)
+        display_targets(_vendoring.archspec.cpu.TARGETS)
         return
 
     if args.frontend:

lib/spack/spack/cmd/mirror.py

@@ -514,17 +514,18 @@ def extend_with_dependencies(specs):
 
 
 def concrete_specs_from_cli_or_file(args):
-    tty.msg("Concretizing input specs")
     if args.specs:
-        specs = spack.cmd.parse_specs(args.specs, concretize=True)
+        specs = spack.cmd.parse_specs(args.specs, concretize=False)
         if not specs:
             raise SpackError("unable to parse specs from command line")
 
     if args.file:
-        specs = specs_from_text_file(args.file, concretize=True)
+        specs = specs_from_text_file(args.file, concretize=False)
         if not specs:
             raise SpackError("unable to parse specs from file '{}'".format(args.file))
-    return specs
+
+    concrete_specs = spack.cmd.matching_specs_from_env(specs)
+    return concrete_specs
 
 
 class IncludeFilter:
@@ -607,11 +608,6 @@ def process_mirror_stats(present, mirrored, error):
 
 def mirror_create(args):
     """create a directory to be used as a spack mirror, and fill it with package archives"""
-    if args.specs and args.all:
-        raise SpackError(
-            "cannot specify specs on command line if you chose to mirror all specs with '--all'"
-        )
-
     if args.file and args.all:
         raise SpackError(
             "cannot specify specs with a file if you chose to mirror all specs with '--all'"

lib/spack/spack/cmd/repo.py

@@ -201,7 +201,19 @@ def repo_migrate(args: Any) -> int:
         repo_v2 = None
         exit_code = 0
 
-    if exit_code == 0 and isinstance(repo_v2, spack.repo.Repo):
+    if not args.fix:
+        tty.error(
+            f"No changes were made to the repository {repo.root} with namespace "
+            f"'{repo.namespace}'. Run with --fix to apply the above changes."
+        )
+
+    elif exit_code == 1:
+        tty.error(
+            f"Repository '{repo.namespace}' could not be migrated to the latest Package API. "
+            "Please check the error messages above."
+        )
+
+    elif isinstance(repo_v2, spack.repo.Repo):
         tty.info(
             f"Repository '{repo_v2.namespace}' was successfully migrated from "
             f"package API {repo.package_api_str} to {repo_v2.package_api_str}."
@@ -212,15 +224,9 @@ def repo_migrate(args: Any) -> int:
             f"    spack repo add {shlex.quote(repo_v2.root)}"
         )
 
-    elif exit_code == 0:
+    else:
         tty.info(f"Repository '{repo.namespace}' was successfully migrated")
 
-    elif not args.fix and exit_code == 1:
-        tty.error(
-            f"No changes were made to the repository {repo.root} with namespace "
-            f"'{repo.namespace}'. Run with --fix to apply the above changes."
-        )
-
     return exit_code
 
 

lib/spack/spack/compilers/config.py

@@ -10,7 +10,7 @@
 import warnings
 from typing import Any, Dict, List, Optional, Tuple
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 import llnl.util.filesystem as fs
 import llnl.util.lang
@@ -316,7 +316,7 @@ def from_external_yaml(config: Dict[str, Any]) -> Optional[spack.spec.Spec]:
     @staticmethod
     def _finalize_external_concretization(abstract_spec):
         if CompilerFactory._GENERIC_TARGET is None:
-            CompilerFactory._GENERIC_TARGET = archspec.cpu.host().family
+            CompilerFactory._GENERIC_TARGET = _vendoring.archspec.cpu.host().family
 
         if abstract_spec.architecture:
             abstract_spec.architecture.complete_with_defaults()

lib/spack/spack/main.py

@@ -25,7 +25,7 @@
 import warnings
 from typing import List, Tuple
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 import llnl.util.lang
 import llnl.util.tty as tty
@@ -734,7 +734,7 @@ def _compatible_sys_types():
     """
     host_platform = spack.platforms.host()
     host_os = str(host_platform.default_operating_system())
-    host_target = archspec.cpu.host()
+    host_target = _vendoring.archspec.cpu.host()
     compatible_targets = [host_target] + host_target.ancestors
 
     compatible_archs = [
@@ -794,7 +794,7 @@ def shell_set(var, value):
     # print environment module system if available. This can be expensive
     # on clusters, so skip it if not needed.
     if "modules" in info:
-        generic_arch = archspec.cpu.host().family
+        generic_arch = _vendoring.archspec.cpu.host().family
         module_spec = "environment-modules target={0}".format(generic_arch)
         specs = spack.store.STORE.db.query(module_spec)
         if specs:

lib/spack/spack/package_base.py

@@ -986,7 +986,9 @@ def url_for_version(self, version):
         """
         return self._implement_all_urls_for_version(version)[0]
 
-    def update_external_dependencies(self, extendee_spec=None):
+    def _update_external_dependencies(
+        self, extendee_spec: Optional[spack.spec.Spec] = None
+    ) -> None:
         """
         Method to override in package classes to handle external dependencies
         """

lib/spack/spack/platforms/_platform.py

@@ -4,7 +4,7 @@
 import warnings
 from typing import Optional
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 import llnl.util.lang
 
@@ -38,15 +38,15 @@ def __init__(self, name):
         self.name = name
         self._init_targets()
 
-    def add_target(self, name: str, target: archspec.cpu.Microarchitecture) -> None:
+    def add_target(self, name: str, target: _vendoring.archspec.cpu.Microarchitecture) -> None:
         if name in Platform.reserved_targets:
             msg = f"{name} is a spack reserved alias and cannot be the name of a target"
             raise ValueError(msg)
         self.targets[name] = target
 
     def _init_targets(self):
-        self.default = archspec.cpu.host().name
-        for name, microarchitecture in archspec.cpu.TARGETS.items():
+        self.default = _vendoring.archspec.cpu.host().name
+        for name, microarchitecture in _vendoring.archspec.cpu.TARGETS.items():
             self.add_target(name, microarchitecture)
 
     def target(self, name):

lib/spack/spack/platforms/test.py

@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import platform
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 import spack.operating_systems
 
@@ -28,7 +28,7 @@ def __init__(self, name=None):
     def _init_targets(self):
         targets = ("aarch64", "m1") if platform.machine() == "arm64" else ("x86_64", "core2")
         for t in targets:
-            self.add_target(t, archspec.cpu.TARGETS[t])
+            self.add_target(t, _vendoring.archspec.cpu.TARGETS[t])
 
     @classmethod
     def detect(cls):

lib/spack/spack/repo_migrate.py

@@ -3,7 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import ast
-import difflib
 import os
 import re
 import shutil
@@ -83,8 +82,7 @@ def migrate_v1_to_v2(
 
     errors = False
 
-    stack: List[Tuple[str, int]] = [(repo.packages_path, 0)]
-
+    stack: List[Tuple[str, int]] = [(repo.root, 0)]
     while stack:
         path, depth = stack.pop()
 
@@ -114,7 +112,11 @@ def migrate_v1_to_v2(
                     continue
 
                 # check if this is a package
-                if depth == 0 and os.path.exists(os.path.join(entry.path, "package.py")):
+                if (
+                    depth == 1
+                    and rel_path.startswith(f"{subdirectory}{os.sep}")
+                    and os.path.exists(os.path.join(entry.path, "package.py"))
+                ):
                     if "_" in entry.name:
                         print(
                             f"Invalid package name '{entry.name}': underscores are not allowed in "
@@ -142,7 +144,7 @@ def migrate_v1_to_v2(
     rename_regex = re.compile("^(" + "|".join(re.escape(k) for k in rename.keys()) + ")")
 
     if fix:
-        os.makedirs(os.path.join(new_root, repo.subdirectory), exist_ok=True)
+        os.makedirs(new_root, exist_ok=True)
 
     def _relocate(rel_path: str) -> Tuple[str, str]:
         old = os.path.join(repo.root, rel_path)
@@ -221,16 +223,6 @@ def _relocate(rel_path: str) -> Tuple[str, str]:
     return result, (updated_repo if fix else None)
 
 
-def _spack_pkg_to_spack_repo(modulename: str) -> str:
-    # rewrite spack.pkg.builtin.foo -> spack_repo.builtin.packages.foo.package
-    parts = modulename.split(".")
-    assert parts[:2] == ["spack", "pkg"]
-    parts[0:2] = ["spack_repo"]
-    parts.insert(2, "packages")
-    parts.append("package")
-    return ".".join(parts)
-
-
 def migrate_v2_imports(
     packages_dir: str, root: str, fix: bool, out: IO[str] = sys.stdout, err: IO[str] = sys.stderr
 ) -> bool:
@@ -307,41 +299,12 @@ def migrate_v2_imports(
         #: Set of symbols of interest that are already defined through imports, assignments, or
         #: function definitions.
         defined_symbols: Set[str] = set()
+
         best_line: Optional[int] = None
+
         seen_import = False
-        module_replacements: Dict[str, str] = {}
-        parent: Dict[int, ast.AST] = {}
-
-        #: List of (line, col start, old, new) tuples of strings to be replaced inline.
-        inline_updates: List[Tuple[int, int, str, str]] = []
-
-        #: List of (line from, line to, new lines) tuples of line replacements
-        multiline_updates: List[Tuple[int, int, List[str]]] = []
-
-        with open(pkg_path, "r", encoding="utf-8", newline="") as file:
-            original_lines = file.readlines()
-
-        if len(original_lines) < 2:  # assume packagepy files have at least 2 lines...
-            continue
-
-        if original_lines[0].endswith("\r\n"):
-            newline = "\r\n"
-        elif original_lines[0].endswith("\n"):
-            newline = "\n"
-        elif original_lines[0].endswith("\r"):
-            newline = "\r"
-        else:
-            success = False
-            print(f"{pkg_path}: unknown line ending, cannot fix", file=err)
-            continue
-
-        updated_lines = original_lines.copy()
 
         for node in ast.walk(tree):
-            for child in ast.iter_child_nodes(node):
-                if isinstance(child, ast.Attribute):
-                    parent[id(child)] = node
-
             # Get the last import statement from the first block of top-level imports
             if isinstance(node, ast.Module):
                 for child in ast.iter_child_nodes(node):
@@ -361,7 +324,7 @@ def migrate_v2_imports(
 
                     if is_import:
                         if isinstance(child, (ast.stmt, ast.expr)):
-                            best_line = (getattr(child, "end_lineno", None) or child.lineno) + 1
+                            best_line = (child.end_lineno or child.lineno) + 1
 
                     if not seen_import and is_import:
                         seen_import = True
@@ -390,89 +353,12 @@ def migrate_v2_imports(
             elif isinstance(node, ast.Name) and node.id in symbol_to_module:
                 referenced_symbols.add(node.id)
 
-            # Find lines where spack.pkg is used.
-            elif (
-                isinstance(node, ast.Attribute)
-                and isinstance(node.value, ast.Name)
-                and node.value.id == "spack"
-                and node.attr == "pkg"
-            ):
-                # go as many attrs up until we reach a known module name to be replaced
-                known_module = "spack.pkg"
-                ancestor = node
-                while True:
-                    next_parent = parent.get(id(ancestor))
-                    if next_parent is None or not isinstance(next_parent, ast.Attribute):
-                        break
-                    ancestor = next_parent
-                    known_module = f"{known_module}.{ancestor.attr}"
-                    if known_module in module_replacements:
-                        break
-
-                inline_updates.append(
-                    (
-                        ancestor.lineno,
-                        ancestor.col_offset,
-                        known_module,
-                        module_replacements[known_module],
-                    )
-                )
-
+            # Register imported symbols to make this operation idempotent
             elif isinstance(node, ast.ImportFrom):
-                # Keep track of old style spack.pkg imports, to be replaced.
-                if node.module and node.module.startswith("spack.pkg.") and node.level == 0:
-
-                    depth = node.module.count(".")
-
-                    # simple case of find and replace
-                    # from spack.pkg.builtin.my_pkg import MyPkg
-                    # -> from spack_repo.builtin.packages.my_pkg.package import MyPkg
-                    if depth == 3:
-                        module_replacements[node.module] = _spack_pkg_to_spack_repo(node.module)
-                        inline_updates.append(
-                            (
-                                node.lineno,
-                                node.col_offset,
-                                node.module,
-                                module_replacements[node.module],
-                            )
-                        )
-
-                    # non-trivial possible multiline case
-                    # from spack.pkg.builtin import (boost, cmake as foo)
-                    # -> import spack_repo.builtin.packages.boost.package as boost
-                    # -> import spack_repo.builtin.packages.cmake.package as foo
-                    elif depth == 2 and node.end_lineno is not None:
-                        _, _, namespace = node.module.rpartition(".")
-                        indent = original_lines[node.lineno - 1][: node.col_offset]
-                        multiline_updates.append(
-                            (
-                                node.lineno,
-                                node.end_lineno + 1,
-                                [
-                                    f"{indent}import spack_repo.{namespace}.packages."
-                                    f"{alias.name}.package as {alias.asname or alias.name}"
-                                    f"{newline}"
-                                    for alias in node.names
-                                ],
-                            )
-                        )
-
-                    else:
-                        success = False
-                        print(
-                            f"{pkg_path}:{node.lineno}: don't know how to rewrite `{node.module}`",
-                            file=err,
-                        )
-
-                # Subtract the symbols that are imported so we don't repeatedly add imports.
                 for alias in node.names:
                     if alias.name in symbol_to_module:
-                        if alias.asname is None:
-                            defined_symbols.add(alias.name)
-
-                        # error when symbols are explicitly imported that are no longer available
-                        if node.module == "spack.package" and node.level == 0:
+                        defined_symbols.add(alias.name)
+                        if node.module == "spack.package":
                             success = False
                             print(
                                 f"{pkg_path}:{node.lineno}: `{alias.name}` is imported from "
@@ -483,84 +369,59 @@ def migrate_v2_imports(
                     if alias.asname and alias.asname in symbol_to_module:
                         defined_symbols.add(alias.asname)
 
-            elif isinstance(node, ast.Import):
-                # normal imports are easy find and replace since they are single lines.
-                for alias in node.names:
-                    if alias.asname and alias.asname in symbol_to_module:
-                        defined_symbols.add(alias.name)
-                    elif alias.asname is None and alias.name.startswith("spack.pkg."):
-                        module_replacements[alias.name] = _spack_pkg_to_spack_repo(alias.name)
-                        inline_updates.append(
-                            (
-                                alias.lineno,
-                                alias.col_offset,
-                                alias.name,
-                                module_replacements[alias.name],
-                            )
-                        )
-
         # Remove imported symbols from the referenced symbols
         referenced_symbols.difference_update(defined_symbols)
 
-        # Sort from last to first so we can modify without messing up the line / col offsets
-        inline_updates.sort(reverse=True)
-
-        # Nothing to change here.
-        if not inline_updates and not referenced_symbols:
+        if not referenced_symbols:
             continue
 
-        # First do module replacements of spack.pkg imports
-        for line, col, old, new in inline_updates:
-            updated_lines[line - 1] = updated_lines[line - 1][:col] + updated_lines[line - 1][
-                col:
-            ].replace(old, new, 1)
+        if best_line is None:
+            print(f"{pkg_path}: failed to update imports", file=err)
+            success = False
+            continue
 
-        # Then insert new imports for symbols referenced in the package
-        if referenced_symbols:
-            if best_line is None:
-                print(f"{pkg_path}: failed to update imports", file=err)
-                success = False
-                continue
+        # Add the missing imports right after the last import statement
+        with open(pkg_path, "r", encoding="utf-8", newline="") as file:
+            lines = file.readlines()
 
-            # Group missing symbols by their module
-            missing_imports_by_module: Dict[str, list] = {}
-            for symbol in referenced_symbols:
-                module = symbol_to_module[symbol]
-                if module not in missing_imports_by_module:
-                    missing_imports_by_module[module] = []
-                missing_imports_by_module[module].append(symbol)
+        # Group missing symbols by their module
+        missing_imports_by_module: Dict[str, list] = {}
+        for symbol in referenced_symbols:
+            module = symbol_to_module[symbol]
+            if module not in missing_imports_by_module:
+                missing_imports_by_module[module] = []
+            missing_imports_by_module[module].append(symbol)
 
-            new_lines = [
-                f"from {module} import {', '.join(sorted(symbols))}{newline}"
-                for module, symbols in sorted(missing_imports_by_module.items())
-            ]
+        new_lines = [
+            f"from {module} import {', '.join(sorted(symbols))}\n"
+            for module, symbols in sorted(missing_imports_by_module.items())
+        ]
 
-            if not seen_import:
-                new_lines.extend((newline, newline))
+        if not seen_import:
+            new_lines.extend(("\n", "\n"))
 
-            multiline_updates.append((best_line, best_line, new_lines))
-
-        multiline_updates.sort(reverse=True)
-        for start, end, new_lines in multiline_updates:
-            updated_lines[start - 1 : end - 1] = new_lines
-
-        if not fix:
+        if not fix:  # only print the diff
+            success = False  # packages need to be fixed, but we didn't do it
+            diff_start, diff_end = max(1, best_line - 3), min(best_line + 2, len(lines))
+            num_changed = diff_end - diff_start + 1
+            num_added = num_changed + len(new_lines)
             rel_pkg_path = os.path.relpath(pkg_path, start=root)
-            diff = difflib.unified_diff(
-                original_lines,
-                updated_lines,
-                n=3,
-                fromfile=f"a/{rel_pkg_path}",
-                tofile=f"b/{rel_pkg_path}",
-            )
-            out.write("".join(diff))
+            out.write(f"--- a/{rel_pkg_path}\n+++ b/{rel_pkg_path}\n")
+            out.write(f"@@ -{diff_start},{num_changed} +{diff_start},{num_added} @@\n")
+            for line in lines[diff_start - 1 : best_line - 1]:
+                out.write(f" {line}")
+            for line in new_lines:
+                out.write(f"+{line}")
+            for line in lines[best_line - 1 : diff_end]:
+                out.write(f" {line}")
             continue
 
+        lines[best_line - 1 : best_line - 1] = new_lines
+
         tmp_file = pkg_path + ".tmp"
 
-        # binary mode to avoid newline conversion issues; utf-8 was already required upon read.
-        with open(tmp_file, "wb") as file:
-            file.write("".join(updated_lines).encode("utf-8"))
+        with open(tmp_file, "w", encoding="utf-8", newline="") as file:
+            file.writelines(lines)
 
         os.replace(tmp_file, pkg_path)
 

lib/spack/spack/solver/asp.py

@@ -34,7 +34,7 @@
     Union,
 )
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 import llnl.util.lang
 import llnl.util.tty as tty
@@ -1617,7 +1617,7 @@ def target_ranges(self, spec, single_target_fn):
         target = spec.architecture.target
 
         # Check if the target is a concrete target
-        if str(target) in archspec.cpu.TARGETS:
+        if str(target) in _vendoring.archspec.cpu.TARGETS:
             return [single_target_fn(spec.name, target)]
 
         self.target_constraints.add(target)
@@ -2753,7 +2753,7 @@ def _supported_targets(self, compiler_name, compiler_version, targets):
                         compiler_name, compiler_version.dotted_numeric_string
                     )
                 supported.append(target)
-            except archspec.cpu.UnsupportedMicroarchitecture:
+            except _vendoring.archspec.cpu.UnsupportedMicroarchitecture:
                 continue
             except ValueError:
                 continue
@@ -2818,7 +2818,7 @@ def target_defaults(self, specs):
             if not spec.architecture or not spec.architecture.target:
                 continue
 
-            target = archspec.cpu.TARGETS.get(spec.target.name)
+            target = _vendoring.archspec.cpu.TARGETS.get(spec.target.name)
             if not target:
                 self.target_ranges(spec, None)
                 continue
@@ -2830,7 +2830,7 @@ def target_defaults(self, specs):
                         candidate_targets.append(ancestor)
 
         platform = spack.platforms.host()
-        uarch = archspec.cpu.TARGETS.get(platform.default)
+        uarch = _vendoring.archspec.cpu.TARGETS.get(platform.default)
         best_targets = {uarch.family.name}
         for compiler in self.possible_compilers:
             supported = self._supported_targets(compiler.name, compiler.version, candidate_targets)
@@ -2938,7 +2938,7 @@ def _all_targets_satisfiying(single_constraint):
                 return [single_constraint]
 
             t_min, _, t_max = single_constraint.partition(":")
-            for test_target in archspec.cpu.TARGETS.values():
+            for test_target in _vendoring.archspec.cpu.TARGETS.values():
                 # Check lower bound
                 if t_min and not t_min <= test_target:
                     continue
@@ -3894,7 +3894,7 @@ def external_spec_selected(self, node, idx):
 
         if extendee_spec:
             extendee_node = SpecBuilder.make_node(pkg=extendee_spec.name)
-            package.update_external_dependencies(self._specs.get(extendee_node, None))
+            package._update_external_dependencies(self._specs.get(extendee_node))
 
     def depends_on(self, parent_node, dependency_node, type):
         dependency_spec = self._specs[dependency_node]

lib/spack/spack/solver/input_analysis.py

@@ -5,7 +5,7 @@
 import collections
 from typing import Dict, List, NamedTuple, Set, Tuple, Union
 
-import archspec.cpu
+import _vendoring.archspec.cpu
 
 from llnl.util import lang, tty
 
@@ -34,7 +34,7 @@ def unreachable(self, *, pkg_name: str, when_spec: spack.spec.Spec) -> bool:
         """
         raise NotImplementedError
 
-    def candidate_targets(self) -> List[archspec.cpu.Microarchitecture]:
+    def candidate_targets(self) -> List[_vendoring.archspec.cpu.Microarchitecture]:
         """Returns a list of targets that are candidate for concretization"""
         raise NotImplementedError
 
@@ -70,7 +70,7 @@ def __init__(self, *, configuration: spack.config.Configuration, repo: spack.rep
         self.configuration = configuration
         self.repo = repo
         self._platform_condition = spack.spec.Spec(
-            f"platform={spack.platforms.host()} target={archspec.cpu.host().family}:"
+            f"platform={spack.platforms.host()} target={_vendoring.archspec.cpu.host().family}:"
         )
 
         try:
@@ -110,10 +110,10 @@ def unreachable(self, *, pkg_name: str, when_spec: spack.spec.Spec) -> bool:
         """
         return False
 
-    def candidate_targets(self) -> List[archspec.cpu.Microarchitecture]:
+    def candidate_targets(self) -> List[_vendoring.archspec.cpu.Microarchitecture]:
         """Returns a list of targets that are candidate for concretization"""
         platform = spack.platforms.host()
-        default_target = archspec.cpu.TARGETS[platform.default]
+        default_target = _vendoring.archspec.cpu.TARGETS[platform.default]
 
         # Construct the list of targets which are compatible with the host
         candidate_targets = [default_target] + default_target.ancestors
@@ -125,7 +125,7 @@ def candidate_targets(self) -> List[archspec.cpu.Microarchitecture]:
             additional_targets_in_family = sorted(
                 [
                     t
-                    for t in archspec.cpu.TARGETS.values()
+                    for t in _vendoring.archspec.cpu.TARGETS.values()
                     if (t.family.name == default_target.family.name and t not in candidate_targets)
                 ],
                 key=lambda x: len(x.ancestors),

lib/spack/spack/spec.py

@@ -74,10 +74,9 @@
     overload,
 )
 
+import _vendoring.archspec.cpu
 from _vendoring.typing_extensions import Literal
 
-import archspec.cpu
-
 import llnl.path
 import llnl.string
 import llnl.util.filesystem as fs
@@ -217,10 +216,12 @@ def ensure_modern_format_string(fmt: str) -> None:
         )
 
 
-def _make_microarchitecture(name: str) -> archspec.cpu.Microarchitecture:
-    if isinstance(name, archspec.cpu.Microarchitecture):
+def _make_microarchitecture(name: str) -> _vendoring.archspec.cpu.Microarchitecture:
+    if isinstance(name, _vendoring.archspec.cpu.Microarchitecture):
         return name
-    return archspec.cpu.TARGETS.get(name, archspec.cpu.generic_microarchitecture(name))
+    return _vendoring.archspec.cpu.TARGETS.get(
+        name, _vendoring.archspec.cpu.generic_microarchitecture(name)
+    )
 
 
 @lang.lazy_lexicographic_ordering
@@ -364,7 +365,7 @@ def target(self, value):
         # will assumed to be the host machine's platform.
 
         def target_or_none(t):
-            if isinstance(t, archspec.cpu.Microarchitecture):
+            if isinstance(t, _vendoring.archspec.cpu.Microarchitecture):
                 return t
             if t and t != "None":
                 return _make_microarchitecture(t)

lib/spack/spack/test/architecture.py

@@ -3,10 +3,9 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import platform
 
+import _vendoring.archspec.cpu
 import pytest
 
-import archspec.cpu
-
 import spack.concretize
 import spack.operating_systems
 import spack.platforms
@@ -125,7 +124,8 @@ def test_satisfy_strict_constraint_when_not_concrete(architecture_tuple, constra
 )
 @pytest.mark.usefixtures("mock_packages", "config")
 @pytest.mark.skipif(
-    str(archspec.cpu.host().family) != "x86_64", reason="tests are for x86_64 uarch ranges"
+    str(_vendoring.archspec.cpu.host().family) != "x86_64",
+    reason="tests are for x86_64 uarch ranges",
 )
 def test_concretize_target_ranges(root_target_range, dep_target_range, result, monkeypatch):
     spec = spack.concretize.concretize_one(

lib/spack/spack/test/build_environment.py

@@ -8,10 +8,9 @@
 import sys
 from typing import Dict, Optional, Tuple
 
+import _vendoring.archspec.cpu
 import pytest
 
-import archspec.cpu
-
 from llnl.path import Path, convert_to_platform_path
 from llnl.util.filesystem import HeaderList, LibraryList
 
@@ -727,14 +726,15 @@ def test_rpath_with_duplicate_link_deps():
 @pytest.mark.filterwarnings("ignore:microarchitecture specific")
 @pytest.mark.not_on_windows("Windows doesn't support the compiler wrapper")
 def test_optimization_flags(compiler_spec, target_name, expected_flags, compiler_factory):
-    target = archspec.cpu.TARGETS[target_name]
+    target = _vendoring.archspec.cpu.TARGETS[target_name]
     compiler = spack.spec.parse_with_version_concrete(compiler_spec)
     opt_flags = spack.build_environment.optimization_flags(compiler, target)
     assert opt_flags == expected_flags
 
 
 @pytest.mark.skipif(
-    str(archspec.cpu.host().family) != "x86_64", reason="tests check specific x86_64 uarch flags"
+    str(_vendoring.archspec.cpu.host().family) != "x86_64",
+    reason="tests check specific x86_64 uarch flags",
 )
 @pytest.mark.not_on_windows("Windows doesn't support the compiler wrapper")
 def test_optimization_flags_are_using_node_target(default_mock_concretization, monkeypatch):

lib/spack/spack/test/build_systems.py

@@ -5,11 +5,10 @@
 import glob
 import os
 
+import _vendoring.archspec.cpu
 import py.path
 import pytest
 
-import archspec.cpu
-
 import llnl.util.filesystem as fs
 
 import spack
@@ -217,7 +216,8 @@ def test_autotools_gnuconfig_replacement_disabled(self, mutable_database):
 
     @pytest.mark.disable_clean_stage_check
     @pytest.mark.skipif(
-        str(archspec.cpu.host().family) != "x86_64", reason="test data is specific for x86_64"
+        str(_vendoring.archspec.cpu.host().family) != "x86_64",
+        reason="test data is specific for x86_64",
     )
     def test_autotools_gnuconfig_replacement_no_gnuconfig(self, mutable_database, monkeypatch):
         """

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

@@ -61,6 +61,26 @@ def test_mirror_from_env(mutable_mock_env_path, tmp_path, mock_packages, mock_fe
         assert mirror_res == expected
 
 
+# Test for command line-specified spec in concretized environment
+def test_mirror_spec_from_env(mutable_mock_env_path, tmp_path, mock_packages, mock_fetch):
+    mirror_dir = str(tmp_path / "mirror-B")
+    env_name = "test"
+
+    env("create", env_name)
+    with ev.read(env_name):
+        add("simple-standalone-test@0.9")
+        concretize()
+        with spack.config.override("config:checksum", False):
+            mirror("create", "-d", mirror_dir, "simple-standalone-test")
+
+    e = ev.read(env_name)
+    assert set(os.listdir(mirror_dir)) == set([s.name for s in e.user_specs])
+    spec = e.concrete_roots()[0]
+    mirror_res = os.listdir(os.path.join(mirror_dir, spec.name))
+    expected = ["%s.tar.gz" % spec.format("{name}-{version}")]
+    assert mirror_res == expected
+
+
 @pytest.fixture
 def source_for_pkg_with_hash(mock_packages, tmpdir):
     s = spack.concretize.concretize_one("trivial-pkg-with-valid-hash")
@@ -401,8 +421,7 @@ def test_all_specs_with_all_versions_dont_concretize(self):
     @pytest.mark.parametrize(
         "cli_args,error_str",
         [
-            # Passed more than one among -f --all and specs
-            ({"specs": "hdf5", "file": None, "all": True}, "cannot specify specs on command line"),
+            # Passed more than one among -f --all
             (
                 {"specs": None, "file": "input.txt", "all": True},
                 "cannot specify specs with a file if",

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

@@ -95,47 +95,24 @@ class _7zip(Package):
     pass
 """
 
-# this is written like this to be explicit about line endings and indentation
-OLD_NUMPY = (
-    b"# some comment\r\n"
-    b"\r\n"
-    b"import spack.pkg.builtin.foo, spack.pkg.builtin.bar\r\n"
-    b"from spack.package import *\r\n"
-    b"from something.unrelated import AutotoolsPackage\r\n"
-    b"\r\n"
-    b"if True:\r\n"
-    b"\tfrom spack.pkg.builtin import (\r\n"
-    b"\t\tfoo,\r\n"
-    b"\t\tbar as baz,\r\n"
-    b"\t)\r\n"
-    b"\r\n"
-    b"class PyNumpy(CMakePackage, AutotoolsPackage):\r\n"
-    b"\tgenerator('ninja')\r\n"
-    b"\r\n"
-    b"\tdef example(self):\r\n"
-    b"\t\t# unchanged comment: spack.pkg.builtin.foo.something\r\n"
-    b"\t\treturn spack.pkg.builtin.foo.example(), foo, baz\r\n"
-)
+OLD_NUMPY = b"""\
+# some comment
 
-NEW_NUMPY = (
-    b"# some comment\r\n"
-    b"\r\n"
-    b"import spack_repo.builtin.packages.foo.package, spack_repo.builtin.packages.bar.package\r\n"
-    b"from spack_repo.builtin.build_systems.cmake import CMakePackage, generator\r\n"
-    b"from spack.package import *\r\n"
-    b"from something.unrelated import AutotoolsPackage\r\n"
-    b"\r\n"
-    b"if True:\r\n"
-    b"\timport spack_repo.builtin.packages.foo.package as foo\r\n"
-    b"\timport spack_repo.builtin.packages.bar.package as baz\r\n"
-    b"\r\n"
-    b"class PyNumpy(CMakePackage, AutotoolsPackage):\r\n"
-    b"\tgenerator('ninja')\r\n"
-    b"\r\n"
-    b"\tdef example(self):\r\n"
-    b"\t\t# unchanged comment: spack.pkg.builtin.foo.something\r\n"
-    b"\t\treturn spack_repo.builtin.packages.foo.package.example(), foo, baz\r\n"
-)
+from spack.package import *
+
+class PyNumpy(CMakePackage):
+    generator("ninja")
+"""
+
+NEW_NUMPY = b"""\
+# some comment
+
+from spack_repo.builtin.build_systems.cmake import CMakePackage, generator
+from spack.package import *
+
+class PyNumpy(CMakePackage):
+    generator("ninja")
+"""
 
 
 def test_repo_migrate(tmp_path: pathlib.Path, config):
@@ -165,6 +142,7 @@ def test_repo_migrate(tmp_path: pathlib.Path, config):
     assert pkg_py_numpy_new.read_bytes() == NEW_NUMPY
 
 
+@pytest.mark.not_on_windows("Known failure on windows")
 def test_migrate_diff(git: Executable, tmp_path: pathlib.Path):
     root, _ = spack.repo.create_repo(str(tmp_path), "foo", package_api=(2, 0))
     r = pathlib.Path(root)

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

@@ -4,10 +4,9 @@
 
 import os
 
+import _vendoring.archspec.cpu
 import pytest
 
-import archspec.cpu
-
 import spack.concretize
 import spack.config
 import spack.paths
@@ -86,7 +85,8 @@ def test_external_nodes_do_not_have_runtimes(runtime_repo, mutable_config, tmp_p
             {"pkg-a": "gcc-runtime@9.4.0", "pkg-b": "gcc-runtime@9.4.0"},
             1,
             marks=pytest.mark.skipif(
-                str(archspec.cpu.host().family) != "x86_64", reason="test data is x86_64 specific"
+                str(_vendoring.archspec.cpu.host().family) != "x86_64",
+                reason="test data is x86_64 specific",
             ),
         ),
         pytest.param(
@@ -98,7 +98,8 @@ def test_external_nodes_do_not_have_runtimes(runtime_repo, mutable_config, tmp_p
             },
             2,
             marks=pytest.mark.skipif(
-                str(archspec.cpu.host().family) != "x86_64", reason="test data is x86_64 specific"
+                str(_vendoring.archspec.cpu.host().family) != "x86_64",
+                reason="test data is x86_64 specific",
             ),
         ),
     ],

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

@@ -6,11 +6,10 @@
 import platform
 import sys
 
+import _vendoring.archspec.cpu
 import _vendoring.jinja2
 import pytest
 
-import archspec.cpu
-
 import llnl.util.lang
 
 import spack.binary_distribution
@@ -146,12 +145,12 @@ def current_host(request, monkeypatch):
 
     monkeypatch.setattr(spack.platforms.Test, "default", cpu)
     if not is_preference:
-        target = archspec.cpu.TARGETS[cpu]
-        monkeypatch.setattr(archspec.cpu, "host", lambda: target)
+        target = _vendoring.archspec.cpu.TARGETS[cpu]
+        monkeypatch.setattr(_vendoring.archspec.cpu, "host", lambda: target)
         yield target
     else:
-        target = archspec.cpu.TARGETS["sapphirerapids"]
-        monkeypatch.setattr(archspec.cpu, "host", lambda: target)
+        target = _vendoring.archspec.cpu.TARGETS["sapphirerapids"]
+        monkeypatch.setattr(_vendoring.archspec.cpu, "host", lambda: target)
         with spack.config.override("packages:all", {"target": [cpu]}):
             yield target
 
@@ -383,7 +382,7 @@ def test_different_compilers_get_different_flags(
                 "gcc": {"externals": [gcc11_with_flags]},
             },
         )
-        t = archspec.cpu.host().family
+        t = _vendoring.archspec.cpu.host().family
         client = spack.concretize.concretize_one(
             Spec(
                 f"cmake-client platform=test os=redhat6 target={t} %gcc@11.1.0"
@@ -976,7 +975,7 @@ def test_noversion_pkg(self, spec):
     def test_adjusting_default_target_based_on_compiler(
         self, spec, compiler_spec, best_achievable, current_host, compiler_factory, mutable_config
     ):
-        best_achievable = archspec.cpu.TARGETS[best_achievable]
+        best_achievable = _vendoring.archspec.cpu.TARGETS[best_achievable]
         expected = best_achievable if best_achievable < current_host else current_host
         mutable_config.set(
             "packages", {"gcc": {"externals": [compiler_factory(spec=f"{compiler_spec}")]}}
@@ -1645,7 +1644,7 @@ def test_target_granularity(self):
         # The test architecture uses core2 as the default target. Check that when
         # we configure Spack for "generic" granularity we concretize for x86_64
         default_target = spack.platforms.test.Test.default
-        generic_target = archspec.cpu.TARGETS[default_target].generic.name
+        generic_target = _vendoring.archspec.cpu.TARGETS[default_target].generic.name
         s = Spec("python")
         assert spack.concretize.concretize_one(s).satisfies("target=%s" % default_target)
         with spack.config.override("concretizer:targets", {"granularity": "generic"}):
@@ -2011,7 +2010,7 @@ def test_installed_specs_disregard_conflicts(self, mutable_database, monkeypatch
     def test_require_targets_are_allowed(self, mutable_config, mutable_database):
         """Test that users can set target constraints under the require attribute."""
         # Configuration to be added to packages.yaml
-        required_target = archspec.cpu.TARGETS[spack.platforms.test.Test.default].family
+        required_target = _vendoring.archspec.cpu.TARGETS[spack.platforms.test.Test.default].family
         external_conf = {"all": {"require": f"target={required_target}"}}
         mutable_config.set("packages", external_conf)
 

lib/spack/spack/test/conftest.py

@@ -20,13 +20,12 @@
 import tempfile
 import xml.etree.ElementTree
 
+import _vendoring.archspec.cpu
+import _vendoring.archspec.cpu.microarchitecture
+import _vendoring.archspec.cpu.schema
 import py
 import pytest
 
-import archspec.cpu
-import archspec.cpu.microarchitecture
-import archspec.cpu.schema
-
 import llnl.util.lang
 import llnl.util.lock
 import llnl.util.tty as tty
@@ -372,12 +371,12 @@ def clean_test_environment():
 def _host():
     """Mock archspec host so there is no inconsistency on the Windows platform
     This function cannot be local as it needs to be pickleable"""
-    return archspec.cpu.Microarchitecture("x86_64", [], "generic", [], {}, 0)
+    return _vendoring.archspec.cpu.Microarchitecture("x86_64", [], "generic", [], {}, 0)
 
 
 @pytest.fixture(scope="function")
 def archspec_host_is_spack_test_host(monkeypatch):
-    monkeypatch.setattr(archspec.cpu, "host", _host)
+    monkeypatch.setattr(_vendoring.archspec.cpu, "host", _host)
 
 
 # Hooks to add command line options or set other custom behaviors.
@@ -728,14 +727,14 @@ def mock_uarch_json(tmpdir_factory):
 
 @pytest.fixture(scope="session")
 def mock_uarch_configuration(mock_uarch_json):
-    """Create mock dictionaries for the archspec.cpu."""
+    """Create mock dictionaries for the _vendoring.archspec.cpu."""
 
     def load_json():
         with open(mock_uarch_json, encoding="utf-8") as f:
             return json.load(f)
 
     targets_json = load_json()
-    targets = archspec.cpu.microarchitecture._known_microarchitectures()
+    targets = _vendoring.archspec.cpu.microarchitecture._known_microarchitectures()
 
     yield targets_json, targets
 
@@ -744,8 +743,8 @@ def load_json():
 def mock_targets(mock_uarch_configuration, monkeypatch):
     """Use this fixture to enable mock uarch targets for testing."""
     targets_json, targets = mock_uarch_configuration
-    monkeypatch.setattr(archspec.cpu.schema, "TARGETS_JSON", targets_json)
-    monkeypatch.setattr(archspec.cpu.microarchitecture, "TARGETS", targets)
+    monkeypatch.setattr(_vendoring.archspec.cpu.schema, "TARGETS_JSON", targets_json)
+    monkeypatch.setattr(_vendoring.archspec.cpu.microarchitecture, "TARGETS", targets)
 
 
 @pytest.fixture(scope="session")
@@ -773,7 +772,7 @@ def configuration_dir(tmpdir_factory, linux_os):
     config_template = test_config / "config.yaml"
     config.write(config_template.read_text().format(install_tree_root, locks))
 
-    target = str(archspec.cpu.host().family)
+    target = str(_vendoring.archspec.cpu.host().family)
     compilers = tmpdir.join("site", "packages.yaml")
     compilers_template = test_config / "packages.yaml"
     compilers.write(compilers_template.read_text().format(linux_os=linux_os, target=target))
@@ -2117,7 +2116,7 @@ def _factory(*, spec):
 @pytest.fixture()
 def host_architecture_str():
     """Returns the broad architecture family (x86_64, aarch64, etc.)"""
-    return str(archspec.cpu.host().family)
+    return str(_vendoring.archspec.cpu.host().family)
 
 
 def _true(x):

lib/spack/spack/test/cray_manifest.py

@@ -11,10 +11,9 @@
 import json
 import os
 
+import _vendoring.archspec.cpu
 import pytest
 
-import archspec.cpu
-
 import spack
 import spack.cmd
 import spack.cmd.external
@@ -104,7 +103,7 @@ def spec_json(self):
 
 @pytest.fixture
 def _common_arch(test_platform):
-    generic = archspec.cpu.TARGETS[test_platform.default].family
+    generic = _vendoring.archspec.cpu.TARGETS[test_platform.default].family
     return JsonArchEntry(platform=test_platform.name, os="redhat6", target=generic.name)
 
 

lib/spack/spack/test/modules/lmod.py

@@ -4,10 +4,9 @@
 
 import os
 
+import _vendoring.archspec.cpu
 import pytest
 
-import archspec.cpu
-
 import spack.concretize
 import spack.config
 import spack.environment as ev
@@ -221,7 +220,8 @@ def test_setenv_raw_value(self, modulefile_content, module_configuration):
         assert len([x for x in content if 'setenv("FOO", "{{name}}, {name}, {{}}, {}")' in x]) == 1
 
     @pytest.mark.skipif(
-        str(archspec.cpu.host().family) != "x86_64", reason="test data is specific for x86_64"
+        str(_vendoring.archspec.cpu.host().family) != "x86_64",
+        reason="test data is specific for x86_64",
     )
     def test_help_message(self, modulefile_content, module_configuration):
         """Tests the generation of module help message."""

lib/spack/spack/test/modules/tcl.py

@@ -4,10 +4,9 @@
 
 import os
 
+import _vendoring.archspec.cpu
 import pytest
 
-import archspec.cpu
-
 import spack.concretize
 import spack.modules.common
 import spack.modules.tcl
@@ -186,7 +185,8 @@ def test_setenv_raw_value(self, modulefile_content, module_configuration):
         assert len([x for x in content if "setenv FOO {{{name}}, {name}, {{}}, {}}" in x]) == 1
 
     @pytest.mark.skipif(
-        str(archspec.cpu.host().family) != "x86_64", reason="test data is specific for x86_64"
+        str(_vendoring.archspec.cpu.host().family) != "x86_64",
+        reason="test data is specific for x86_64",
     )
     def test_help_message(self, modulefile_content, module_configuration):
         """Tests the generation of module help message."""

lib/spack/spack/variant.py

@@ -208,7 +208,7 @@ def variant_type(self) -> VariantType:
         else:
             return VariantType.SINGLE
 
-    def __str__(self):
+    def __str__(self) -> str:
         return (
             f"Variant('{self.name}', "
             f"default='{self.default}', "
@@ -491,14 +491,14 @@ class DisjointSetsOfValues(collections.abc.Sequence):
         *sets (list): mutually exclusive sets of values
     """
 
-    _empty_set = set(("none",))
+    _empty_set = {"none"}
 
-    def __init__(self, *sets):
+    def __init__(self, *sets: Tuple[str, ...]) -> None:
         self.sets = [set(_flatten(x)) for x in sets]
 
         # 'none' is a special value and can appear only in a set of
         # a single element
-        if any("none" in s and s != set(("none",)) for s in self.sets):
+        if any("none" in s and s != {"none"} for s in self.sets):
             raise spack.error.SpecError(
                 "The value 'none' represents the empty set,"
                 " and must appear alone in a set. Use the "

pyproject.toml

@@ -75,7 +75,6 @@ section-order = [
   "future",
   "standard-library",
   "third-party",
-  "archspec",
   "llnl",
   "spack",
   "first-party",
@@ -84,7 +83,6 @@ section-order = [
 
 [tool.ruff.lint.isort.sections]
 spack = ["spack"]
-archspec = ["archspec"]
 llnl = ["llnl"]
 
 [tool.ruff.lint.per-file-ignores]
@@ -104,13 +102,11 @@ sections = [
   "FUTURE",
   "STDLIB",
   "THIRDPARTY",
-  "ARCHSPEC",
   "LLNL",
   "FIRSTPARTY",
   "LOCALFOLDER",
 ]
 known_first_party = "spack"
-known_archspec = "archspec"
 known_llnl = "llnl"
 known_third_party = ["ruamel", "six"]
 src_paths = "lib"
@@ -264,6 +260,9 @@ substitute = [
   { match = "from attr", replace = "from _vendoring.attr" },
   { match = "import jsonschema", replace = "import _vendoring.jsonschema" },
   { match = "from jsonschema", replace = "from _vendoring.jsonschema" },
+  { match = "archspec.cpu", replace = "_vendoring.archspec.cpu" },
+  { match = "archspec.__version__", replace = "_vendoring.archspec.__version__" },
+  { match = "import archspec", replace = "import _vendoring.archspec" },
 ]
 drop = [
   # contains unnecessary scripts
@@ -285,11 +284,21 @@ drop = [
   "pvectorc.*.so",
   # Trim jsonschema tests
   "jsonschema/tests",
+  "archspec/json/tests",
+  "archspec/vendor/cpuid/.gitignore",
+  "pyrsistent/__init__.pyi",
 ]
 
 [tool.vendoring.typing-stubs]
-six = ["six.__init__", "six.moves.__init__", "six.moves.configparser"]
+_pyrsistent_version = []
+altgraph = []
+archspec = []
 distro = []
+jsonschema = []
+macholib = []
+pyrsistent = []
+ruamel = []
+six = []
 
 [tool.vendoring.license.directories]
 setuptools = "pkg_resources"

share/spack/gitlab/cloud_pipelines/stacks/hep/spack.yaml

@@ -69,7 +69,7 @@ spack:
   - alpgen
   - ampt
   - apfel +lhapdf +python
-  - celeritas ~cuda +openmp ~rocm +vecgeom
+  - celeritas ~cuda +openmp ~rocm +vecgeom +covfie
   - cepgen
   - cernlib +shared
   - collier
@@ -130,12 +130,12 @@ spack:
 
   # CUDA
   #- acts +cuda +traccc cuda_arch=80
-  #- celeritas +cuda ~openmp +vecgeom cuda_arch=80
+  #- celeritas +cuda ~openmp +vecgeom cuda_arch=80 +covfie
   - root +cuda +cudnn +tmva-gpu
   - vecgeom +cuda cuda_arch=80
 
   # ROCm
-  - celeritas +rocm amdgpu_target=gfx90a ~openmp ~vecgeom  # only available with ORANGE
+  - celeritas +rocm amdgpu_target=gfx90a ~openmp ~vecgeom # only available with ORANGE
 
   ci:
     pipeline-gen:

var/spack/repos/spack_repo/builtin/build_systems/python.py

@@ -10,7 +10,7 @@
 import stat
 from typing import Dict, Iterable, List, Mapping, Optional, Tuple
 
-import archspec
+import _vendoring.archspec.cpu
 
 import llnl.util.filesystem as fs
 from llnl.util.lang import ClassProperty, classproperty, match_predicate
@@ -250,7 +250,7 @@ def test_imports(self) -> None:
             ):
                 python("-c", f"import {module}")
 
-    def update_external_dependencies(self, extendee_spec=None):
+    def _update_external_dependencies(self, extendee_spec: Optional[Spec] = None) -> None:
         """
         Ensure all external python packages have a python dependency
 
@@ -286,7 +286,7 @@ def update_external_dependencies(self, extendee_spec=None):
                         if not python.architecture.os:
                             python.architecture.os = platform.default_operating_system()
                         if not python.architecture.target:
-                            python.architecture.target = archspec.cpu.host().family.name
+                            python.architecture.target = _vendoring.archspec.cpu.host().family.name
 
                     python.external_path = self.spec.external_path
                     python._mark_concrete()

var/spack/repos/spack_repo/builtin/packages/additivefoam/assets/assets_1.0.0/Allwmake

@@ -1,4 +1,5 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
 
-applications/Allwmake $targetType $*
+wmake $targetType applications/solvers/additiveFoam/movingHeatSource
+wmake $targetType applications/solvers/additiveFoam

var/spack/repos/spack_repo/builtin/packages/additivefoam/assets/assets_1.0.0/applications/Allwmake

@@ -1,5 +0,0 @@
-#!/bin/sh
-cd ${0%/*} || exit 1    # Run from this directory
-
-wmake libso solvers/additiveFoam/movingHeatSource
-wmake solvers/additiveFoam

var/spack/repos/spack_repo/builtin/packages/additivefoam/assets/assets_main/Allwmake

@@ -1,4 +1,4 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # Run from this directory
 
-applications/Allwmake $targetType $*
+./applications/solvers/additiveFoam/Allwmake $targetType $*

var/spack/repos/spack_repo/builtin/packages/additivefoam/assets/assets_main/applications/Allwmake

@@ -1,9 +0,0 @@
-#!/bin/sh
-cd ${0%/*} || exit 1    # Run from this directory
-
-# Parse arguments for library compilation
-. $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
-
-wmake $targetType solvers/additiveFoam/functionObjects/ExaCA
-wmake $targetType solvers/additiveFoam/movingHeatSource
-wmake $targetType solvers/additiveFoam

var/spack/repos/spack_repo/builtin/packages/additivefoam/package.py

@@ -15,9 +15,9 @@
 class Additivefoam(Package):
     """AdditiveFOAM is a heat and mass transfer software for Additive Manufacturing (AM)"""
 
-    homepage = "https://github.com/ORNL/AdditiveFOAM"
+    homepage = "https://ornl.github.io/AdditiveFOAM/"
     git = "https://github.com/ORNL/AdditiveFOAM.git"
-    url = "https://github.com/ORNL/AdditiveFOAM/archive/1.0.0.tar.gz"
+    url = "https://github.com/ORNL/AdditiveFOAM/archive/1.1.0.tar.gz"
 
     maintainers("streeve", "colemanjs", "gknapp1")
 
@@ -26,16 +26,17 @@ class Additivefoam(Package):
     license("GPL-3.0-only")
 
     version("main", branch="main")
+    version("1.1.0", sha256="a13770bd66fe10224705fb3a2bfb557e63e0aea98c917b0084cf8b91eaa53ee2")
     version("1.0.0", sha256="abbdf1b0230cd2f26f526be76e973f508978611f404fe8ec4ecdd7d5df88724c")
 
     depends_on("cxx", type="build")  # generated
 
     depends_on("openfoam-org@10")
 
-    common = ["spack-derived-Allwmake"]
-    assets = [join_path("applications", "Allwmake"), "Allwmake"]
+    common = []
+    assets = ["Allwmake"]
 
-    build_script = "./spack-derived-Allwmake"
+    build_script = "./Allwmake"
 
     phases = ["configure", "build", "install"]
 
@@ -56,15 +57,49 @@ def add_extra_files(self, common, local_prefix, local):
             openfoam.install(join_path(indir, f), join_path(outdir, f))
 
     def patch(self):
+        """Patches build by adding Allwmake from the asset directory based on
+        the spec version.
+
+        For all versions after 1.0.0 there is an Allwmake script in
+        the AdditiveFOAM repository that can be called by the spack assets_main/Allwmake
+        script, whereas the assets_1.0.0/Allwmake script contains the
+        build instructions."""
         spec = self.spec
-        asset_dir = ""
-        if Version("main") in spec.versions:
-            asset_dir = "assets_main"
-        elif Version("1.0.0") in spec.versions:
+        asset_dir = "assets_main"
+        if Version("1.0.0") in spec.versions:
             asset_dir = "assets_1.0.0"
         self.add_extra_files(self.common, asset_dir, self.assets)
 
+    def setup_build_environment(self, env):
+        """Set up the build environment variables."""
+
+        # Ensure that the directories exist
+        mkdirp(self.prefix.bin)
+        mkdirp(self.prefix.lib)
+
+        # Add to the environment
+        env.set("FOAM_USER_APPBIN", self.prefix.bin)
+        env.set("FOAM_USER_LIBBIN", self.prefix.lib)
+
+    def setup_run_environment(self, env):
+        """Set up the run environment variables."""
+
+        # Add to the environment
+        env.prepend_path("PATH", self.prefix.bin)
+        env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib)
+
+    def activate(self, spec, prefix):
+        """Activate the package to modify the environment."""
+        self.setup_run_environment(self.spec.environment())
+
+    def deactivate(self, spec, prefix):
+        """Deactivate the package and clean up the environment."""
+        env = self.spec.environment()
+        env.pop("FOAM_USER_APPBIN", None)
+        env.pop("FOAM_USER_LIBBIN", None)
+
     def configure(self, spec, prefix):
+        """Configure the environment for building."""
         pass
 
     def build(self, spec, prefix):

var/spack/repos/spack_repo/builtin/packages/amdsmi/package.py

@@ -21,6 +21,7 @@ class Amdsmi(CMakePackage):
     libraries = ["libamd_smi"]
 
     license("MIT")
+    version("6.4.0", sha256="6f0200ba7305171e9dadbfcd41ff00c194b98d2b88e0555c57739ef01c767233")
     version("6.3.3", sha256="e23abc65a1cd75764d7da049b91cce2a095b287279efcd4f90b4b9b63b974dd5")
     version("6.3.2", sha256="1ed452eedfe51ac6e615d7bfe0bd7a0614f21113874ae3cbea7df72343cc2d13")
     version("6.3.1", sha256="a3a5a711052e813b9be9304d5e818351d3797f668ec2a455e61253a73429c355")
@@ -38,6 +39,7 @@ class Amdsmi(CMakePackage):
     version("5.5.1", sha256="b794c7fd562fd92f2c9f2bbdc2d5dded7486101fcd4598f2e8c3484c9a939281")
     version("5.5.0", sha256="dcfbd96e93afcf86b1261464e008e9ef7e521670871a1885e6eaffc7cdc8f555")
 
+    depends_on("c", type="build")
     depends_on("cxx", type="build")  # generated
 
     depends_on("cmake@3.11:")

var/spack/repos/spack_repo/builtin/packages/aqlprofile/package.py

@@ -10,6 +10,20 @@
 from spack.package import *
 
 _versions = {
+    "6.4.0": {
+        "apt": (
+            "5ec56bc3c227ad37227072bd513c58c9501e1ceefb06692ad4812f337853dca4",
+            "https://repo.radeon.com/rocm/apt/6.4/pool/main/h/hsa-amd-aqlprofile/hsa-amd-aqlprofile_1.0.0.60400-47~22.04_amd64.deb",
+        ),
+        "yum": (
+            "22ed4c6a999ca6823e5e6bf9f4ab560cba68025f354346b1ac2ebb4757239c56",
+            "https://repo.radeon.com/rocm/rhel8/6.4/main/hsa-amd-aqlprofile-1.0.0.60400-47.el8.x86_64.rpm",
+        ),
+        "zyp": (
+            "7a4c9ca0e6ca178c65776f9b1d9d01ca7576eaa555fdcbf49a42def1ce6d6041",
+            "https://repo.radeon.com/rocm/zyp/6.4/main/hsa-amd-aqlprofile-1.0.0.60400-sles156.47.x86_64.rpm",
+        ),
+    },
     "6.3.3": {
         "apt": (
             "5fe2b18e75e8c0a66069af8446399796818f7340a9ef5f2b52adaa79ee8e2a37",
@@ -307,6 +321,7 @@ class Aqlprofile(Package):
         "6.3.1",
         "6.3.2",
         "6.3.3",
+        "6.4.0",
     ]:
         depends_on(f"hsa-rocr-dev@{ver}", when=f"@{ver}")
 

var/spack/repos/spack_repo/builtin/packages/aws_ofi_nccl/package.py

@@ -19,6 +19,7 @@ class AwsOfiNccl(AutotoolsPackage):
     maintainers("bvanessen")
 
     version("master", branch="master")
+    version("1.14.2", sha256="e523ea08ce0caeff5c949b2134b4897186d793ce908904dd9d47bb08230b9bbd")
     version("1.13.0", sha256="50dd231a0a99cec29300df46b8e828139ced15322a3c3c41b1d22dcc9a62ec02")
     version("1.12.1", sha256="821f0929c016e5448785bbc6795af5096559ecfc6c9479eb3818cafa61424576")
     version("1.12.0", sha256="93029207103b75f4dc15f023b3b8692851202b52b7e2824723dd5d328f0ea65b")
@@ -51,7 +52,7 @@ class AwsOfiNccl(AutotoolsPackage):
     depends_on("libtool", type="build")
 
     def url_for_version(self, version):
-        if version < Version("1.7.0"):
+        if version < Version("1.7.0") or version >= Version("1.14.0"):
             return super().url_for_version(version)
         url_fmt = "https://github.com/aws/aws-ofi-nccl/archive/v{0}-aws.tar.gz"
         return url_fmt.format(version)

var/spack/repos/spack_repo/builtin/packages/blast2go/package.py

@@ -4,23 +4,19 @@
 
 from spack_repo.builtin.build_systems.generic import Package
 
-import archspec
-
 from spack.package import *
 
 
 class Blast2go(Package):
     """Blast2GO is a bioinformatics platform for high-quality functional
-    annotation and analysis of genomic datasets."""
+    annotation and analysis of genomic datasets.
+    """
 
     homepage = "https://www.blast2go.com/"
 
     version("5.2.5", sha256="c37aeda25f96ac0553b52da6b5af3167d50671ddbfb3b39bcb11afe5d0643891")
 
-    for t in set(
-        [str(x.family) for x in archspec.cpu.TARGETS.values() if str(x.family) != "x86_64"]
-    ):
-        conflicts("target={0}:".format(t), msg="blast2go is available x86_64 only")
+    requires("target=x86_64:", msg="blast2go is available x86_64 only")
 
     depends_on("bash", type="build")
     depends_on("blast-plus", type="run")

var/spack/repos/spack_repo/builtin/packages/celeritas/package.py

@@ -19,12 +19,17 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     git = "https://github.com/celeritas-project/celeritas.git"
     url = "https://github.com/celeritas-project/celeritas/releases/download/v0.1.0/celeritas-0.1.0.tar.gz"
 
-    maintainers("sethrj")
+    maintainers("sethrj", "drbenmorgan")
 
     license("Apache-2.0")
 
+    sanity_check_is_file = ["bin/celer-sim"]
+
     version("develop", branch="develop", get_full_repo=True)
 
+    version("0.6.0", sha256="c776dee357ecff42f85ed02c328f24b092400af28e67af2c0e195ce8f67613b0")
+    version("0.5.3", sha256="4d1fe1f34e899c3599898fb6d44686d2582a41b0872784514aa8c562597b3ee6")
+    version("0.5.2", sha256="46311c096b271d0331b82c02485ac6bf650d5b0f7bd948fb01aef5058f8824e3")
     version("0.5.1", sha256="182d5466fbd98ba9400b343b55f6a06e03b77daed4de1dd16f632ac0a3620249")
     version("0.5.0", sha256="4a8834224d96fd01897e5872ac109f60d91ef0bd7b63fac05a73dcdb61a5530e")
     version("0.4.4", sha256="8b5ae63aa2d50c2ecf48d752424e4a33c50c07d9f0f5ca5448246de3286fd836")
@@ -59,11 +64,13 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
         multi=False,
         description="C++ standard version",
     )
+    variant("covfie", default=False, when="@0.6:", description="Enable covfie magnetic fields")
     variant("debug", default=False, description="Enable runtime debug assertions")
     variant("doc", default=False, description="Build and install documentation")
     variant("geant4", default=True, description="Enable Geant4 integration")
     variant("hepmc3", default=True, description="Use HepMC3 I/O interfaces")
     variant("openmp", default=False, description="Use OpenMP multithreading")
+    variant("perfetto", default=False, when="@0.5:", description="Use Perfetto profiling")
     variant("root", default=False, description="Use ROOT I/O")
     variant("shared", default=True, description="Build shared libraries")
     variant("swig", default=False, when="@:0.4", description="Generate SWIG Python bindings")
@@ -75,7 +82,9 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("cmake@3.18:", type="build", when="+cuda+vecgeom")
     depends_on("cmake@3.22:", type="build", when="+rocm")
 
+    depends_on("cli11", when="@0.6:")
     depends_on("nlohmann-json")
+    depends_on("covfie@0.13:", when="+covfie")
     depends_on("geant4@10.5:11.1", when="@0.3.1:0.4.1 +geant4")
     depends_on("geant4@10.5:11.2", when="@0.4.2:0.4 +geant4")
     depends_on("geant4@10.5:", when="@0.5: +geant4")
@@ -104,14 +113,20 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     for _std in _cxxstd_values:
         for _pkg in ["geant4", "root", "vecgeom"]:
             depends_on(f"{_pkg} cxxstd={_std}", when=f"+{_pkg} cxxstd={_std}")
+        # NOTE: as a private dependency, covfie cxxstd can differ from the
+        # celeritas "public" standard
 
     # Ensure consistent CUDA architectures
     depends_on("vecgeom +cuda cuda_arch=none", when="+vecgeom +cuda cuda_arch=none")
     for _arch in CudaPackage.cuda_arch_values:
-        depends_on(f"vecgeom +cuda cuda_arch={_arch}", when=f"+vecgeom +cuda cuda_arch={_arch}")
+        for _pkg in ["covfie", "vecgeom"]:
+            depends_on(f"{_pkg} +cuda cuda_arch={_arch}", when=f"+{_pkg} +cuda cuda_arch={_arch}")
 
+    conflicts("+rocm", when="+covfie", msg="HIP support is not yet available with covfie")
     conflicts("+rocm", when="+cuda", msg="AMD and NVIDIA accelerators are incompatible")
     conflicts("+rocm", when="+vecgeom", msg="HIP support is only available with ORANGE")
+    for _arch in ["cuda", "rocm"]:
+        conflicts("+perfetto", when=f"+{_arch}", msg="Perfetto is only used for CPU profiling")
 
     # geant4@11.3.0 now returns const G4Element::GetElementTable()
     patch(
@@ -134,7 +149,18 @@ def cmake_args(self):
             define("CELERITAS_USE_Python", True),
         ]
 
-        for pkg in ["CUDA", "Geant4", "HepMC3", "OpenMP", "ROOT", "SWIG", "VecGeom"]:
+        # NOTE: package names are stylized like the dependency asks: Find{pkg}.cmake
+        for pkg in [
+            "covfie",
+            "CUDA",
+            "Geant4",
+            "HepMC3",
+            "OpenMP",
+            "Perfetto",
+            "ROOT",
+            "SWIG",
+            "VecGeom",
+        ]:
             args.append(from_variant("CELERITAS_USE_" + pkg, pkg.lower()))
 
         if self.spec.satisfies("+cuda"):
@@ -162,8 +188,9 @@ def cmake_args(self):
             args.extend(
                 (
                     define(f"CELERITAS_BUILTIN_{pkg}", False)
-                    for pkg in ["GTest", "nlohmann_json", "G4VG"]
+                    for pkg in ["covfie", "CLI11", "GTest", "nlohmann_json", "G4VG"]
                 )
             )
+            # NOTE: Perfetto is always vendored!
 
         return args

var/spack/repos/spack_repo/builtin/packages/chafa/package.py

@@ -13,13 +13,15 @@ class Chafa(AutotoolsPackage):
     suitable for display in a terminal."""
 
     homepage = "https://hpjansson.org/chafa/"
-    url = "https://hpjansson.org/chafa/releases/chafa-1.14.5.tar.xz"
+    url = "https://hpjansson.org/chafa/releases/chafa-1.16.1.tar.xz"
     git = "https://github.com/hpjansson/chafa.git"
 
     license("LGPL-3.0-or-later", checked_by="Buldram")
     maintainers("Buldram")
 
     version("master", branch="master")
+    version("1.16.1", sha256="4a25debb71530baf0a748b15cfee6b8da6b513f696d9484987eaf410ecce1129")
+    version("1.16.0", sha256="bf863e57b6200b696bde1742aa95d7feb8cd23b9df1e91e91859b2b1e54fd290")
     version("1.14.5", sha256="7b5b384d5fb76a641d00af0626ed2115fb255ea371d9bef11f8500286a7b09e5")
     version("1.14.4", sha256="d0708a63f05b79269dae862a42671e38aece47fbd4fc852904bca51a65954454")
     version("1.14.3", sha256="f3d5530a96c8e55eea180448896e973093e0302f4cbde45d028179af8cfd90f3")
@@ -75,6 +77,19 @@ def configure_args(self):
             *self.with_or_without("jxl"),
         ]
 
+    @run_after("install")
+    def install_completions(self):
+        mkdirp(zsh_completion_path(self.prefix))
+        install(
+            "tools/completions/zsh-completion.zsh", zsh_completion_path(self.prefix) / "_chafa"
+        )
+        if self.spec.satisfies("@1.16.1:"):
+            mkdirp(fish_completion_path(self.prefix))
+            install(
+                "tools/completions/fish-completion.fish",
+                fish_completion_path(self.prefix) / "chafa.fish",
+            )
+
     @run_after("install", when="+man")
     def install_man(self):
         mkdirp(prefix.share.man.man1)

var/spack/repos/spack_repo/builtin/packages/comgr/package.py

@@ -31,6 +31,7 @@ def url_for_version(self, version):
     license("NCSA")
 
     version("master", branch="amd-stg-open", deprecated=True)
+    version("6.4.0", sha256="dca1c145a23f05229d5d646241f9d1d3c5dbf1d745b338ae020eabe33beb965c")
     version("6.3.3", sha256="4df9aba24e574edf23844c0d2d9dda112811db5c2b08c9428604a21b819eb23d")
     version("6.3.2", sha256="1f52e45660ea508d3fe717a9903fe27020cee96de95a3541434838e0193a4827")
     version("6.3.1", sha256="e9c2481cccacdea72c1f8d3970956c447cec47e18dfb9712cbbba76a2820552c")
@@ -94,6 +95,7 @@ def url_for_version(self, version):
         "6.3.1",
         "6.3.2",
         "6.3.3",
+        "6.4.0",
         "master",
     ]:
         # llvm libs are linked statically, so this *could* be a build dep
@@ -123,6 +125,7 @@ def url_for_version(self, version):
         "6.3.1",
         "6.3.2",
         "6.3.3",
+        "6.4.0",
     ]:
         depends_on(f"rocm-core@{ver}", when=f"@{ver}")
 

var/spack/repos/spack_repo/builtin/packages/compiler_wrapper/package.py

@@ -6,10 +6,9 @@
 import sys
 from typing import List
 
+import _vendoring.archspec.cpu
 from spack_repo.builtin.build_systems.generic import Package
 
-import archspec.cpu
-
 from llnl.util import lang
 
 import spack.compilers.libraries
@@ -183,12 +182,12 @@ def setup_dependent_build_environment(
             env.set(f"SPACK_{wrapper_var_name}_RPATH_ARG", compiler_pkg.rpath_arg)
 
             uarch = dependent_spec.architecture.target
-            version_number, _ = archspec.cpu.version_components(
+            version_number, _ = _vendoring.archspec.cpu.version_components(
                 compiler_pkg.spec.version.dotted_numeric_string
             )
             try:
                 isa_arg = uarch.optimization_flags(compiler_pkg.archspec_name(), version_number)
-            except (ValueError, archspec.cpu.UnsupportedMicroarchitecture):
+            except (ValueError, _vendoring.archspec.cpu.UnsupportedMicroarchitecture):
                 isa_arg = ""
 
             if isa_arg:

var/spack/repos/spack_repo/builtin/packages/composable_kernel/package.py

@@ -21,6 +21,7 @@ class ComposableKernel(CMakePackage):
     license("MIT")
 
     version("master", branch="develop", deprecated=True)
+    version("6.4.0", sha256="8dbfea0bdc4950ca60e8d1ea43edf1f515c4a34e47ead951415c49a0669a3baf")
     version("6.3.3", sha256="b7102efba044455416a6127af1951019fe8365a653ea7eb0b1d83bb4542c9309")
     version("6.3.2", sha256="875237fe493ff040f8f63b827cddf2ff30a8d3aa18864f87d0e35323c7d62a2d")
     version("6.3.1", sha256="3e8c8c832ca3f9ceb99ab90f654b93b7db876f08d90eda87a70bc629c854052a")
@@ -65,6 +66,7 @@ class ComposableKernel(CMakePackage):
 
     for ver in [
         "master",
+        "6.4.0",
         "6.3.3",
         "6.3.2",
         "6.3.1",

var/spack/repos/spack_repo/builtin/packages/cryoef/package.py

@@ -0,0 +1,32 @@
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack_repo.builtin.build_systems.makefile import MakefilePackage
+
+from spack.package import *
+
+
+class Cryoef(MakefilePackage):
+    """An open-source software package for robust analysis of the orientation distribution
+    of cryoelectron microscopy data."""
+
+    homepage = "https://www.mrc-lmb.cam.ac.uk/crusso/cryoEF"
+    url = "https://www.mrc-lmb.cam.ac.uk/crusso/cryoEF/cryoEF_v1.1.0.tar.gz"
+
+    version("1.1.0", sha256="655ed8543a0226754bdeb6e0dd4efc0467f15dc4c9c963c44ef7b8d3d0e41b62")
+
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
+    depends_on("fftw-api@3")
+
+    def patch(self):
+        filter_file(
+            "-lfftw3", f"-lfftw3 {self.spec['fftw-api'].libs.ld_flags} -no-pie", "Makefile"
+        )
+
+    def install(self, spec, prefix):
+        install_tree("TestData", prefix.TestData)
+        install_tree("bin", prefix.bin)
+        install_tree("lib", prefix.lib)
+        install("PlotOD.py", prefix.bin)

var/spack/repos/spack_repo/builtin/packages/cyrus_sasl/package.py

@@ -41,3 +41,4 @@ class CyrusSasl(AutotoolsPackage):
     depends_on("groff", type="build")
     depends_on("openssl", type="link")
     depends_on("libxcrypt", type="link")
+    depends_on("krb5", type="link")

var/spack/repos/spack_repo/builtin/packages/direnv/package.py

@@ -22,6 +22,7 @@ class Direnv(GoPackage):
 
     # Versions (newest to oldest)
     version("master", branch="master")
+    version("2.36.0", sha256="edb89ca67ef46a792d4e20177dae9dbd229e26dcbcfb17baa9645c1ff7cc47b0")
     version("2.35.0", sha256="a7aaec49d1b305f0745dad364af967fb3dc9bb5befc9f29d268d528b5a474e57")
     version("2.34.0", sha256="3d7067e71500e95d69eac86a271a6b6fc3f2f2817ba0e9a589524bf3e73e007c")
     version("2.33.0", sha256="8ef18051aa6bdcd6b59f04f02acdd0b78849b8ddbdbd372d4957af7889c903ea")
@@ -34,5 +35,6 @@ class Direnv(GoPackage):
     version("2.11.3", sha256="2d34103a7f9645059270763a0cfe82085f6d9fe61b2a85aca558689df0e7b006")
 
     # Build dependencies
+    depends_on("go@1.24:", type="build", when="@2.36:")
     depends_on("go@1.20:", type="build", when="@2.33:")
     depends_on("go@1.16:", type="build", when="@2.28:")

var/spack/repos/spack_repo/builtin/packages/e2fsprogs/package.py

@@ -26,6 +26,7 @@ class E2fsprogs(AutotoolsPackage):
     depends_on("c", type="build")  # generated
     depends_on("cxx", type="build")  # generated
 
+    depends_on("uuid")
     depends_on("texinfo", type="build")
     depends_on("fuse", when="+fuse2fs")
     depends_on("pkgconfig", when="+fuse2fs")

var/spack/repos/spack_repo/builtin/packages/edm4hep/package.py

@@ -22,6 +22,7 @@ class Edm4hep(CMakePackage):
     license("Apache-2.0")
 
     version("main", branch="main")
+    version("0.99.2", sha256="b3e7abb61fd969e4c9aef55dd6839a2186bf0b0d3801174fe6e0b9df8e0ebace")
     version("0.99.1", sha256="84d990f09dbd0ad2198596c0c51238a4b15391f51febfb15dd3d191dc7aae9f4")
     version("0.99", sha256="3636e8c14474237029bf1a8be11c53b57ad3ed438fd70a7e9b87c5d08f1f2ea6")
     version("0.10.5", sha256="003c8e0c8e1d1844592d43d41384f4320586fbfa51d4d728ae0870b9c4f78d81")
@@ -79,6 +80,7 @@ class Edm4hep(CMakePackage):
     depends_on("podio@1:", when="@0.99:")
     depends_on("podio@0.15:", when="@:0.10.5")
     depends_on("podio@:1.1", when="@:0.99.0")
+    depends_on("podio@1.3:", when="@0.99.2:")
     for _std in _cxxstd_values:
         for _v in _std:
             depends_on(f"podio cxxstd={_v.value}", when=f"cxxstd={_v.value}")
@@ -109,6 +111,8 @@ def cmake_args(self):
             self.define("BUILD_TESTING", self.run_tests),
             self.define_from_variant("EDM4HEP_WITH_JSON", "json"),
         ]
+        if self.spec.satisfies("@:0.99.1 ^podio@1.3:"):
+            args.append(self.define("PODIO_USE_CLANG_FORMAT", False))
         return args
 
     def setup_run_environment(self, env: EnvironmentModifications) -> None:

var/spack/repos/spack_repo/builtin/packages/fairlogger/package.py

@@ -16,67 +16,20 @@ class Fairlogger(CMakePackage):
     maintainers("dennisklein", "ChristianTackeGSI")
 
     version("develop", branch="dev", get_full_repo=True)
-    version("1.11.1", sha256="bba5814f101d705792499e43b387190d8b8c7592466171ae045d4926485f2f70")
-    version("1.10.4", sha256="2fa321893f2c8c599cca160db243299ce1e941fbfb3f935b1139caa943bc0dba")
-    version("1.9.3", sha256="0c02076ed708372d5ae7bdebcefc8e45a8cbfa480eea781308336d60a2781f3a")
+    version("2.2.0", sha256="8dfb11e3aa0a9c545f3dfb310d261956727cea558d4123fd8c9c98e135e4d02b")
     version(
-        "1.9.0",
-        sha256="13bcaa0d4129f8d4e69a0a2ece8e5b7073760082c8aa028e3fc0c11106503095",
+        "1.11.1",
+        sha256="bba5814f101d705792499e43b387190d8b8c7592466171ae045d4926485f2f70",
         deprecated=True,
     )
     version(
-        "1.8.0",
-        sha256="3f0a38dba1411b542d998e02badcc099c057b33a402954fc5c2ab74947a0c42c",
+        "1.10.4",
+        sha256="2fa321893f2c8c599cca160db243299ce1e941fbfb3f935b1139caa943bc0dba",
         deprecated=True,
     )
     version(
-        "1.7.0",
-        sha256="ef467f0a70afc0549442323d70b165fa0b0b4b4e6f17834573ca15e8e0b007e4",
-        deprecated=True,
-    )
-    version(
-        "1.6.2",
-        sha256="5c6ef0c0029eb451fee71756cb96e6c5011040a9813e8889667b6f3b6b04ed03",
-        deprecated=True,
-    )
-    version(
-        "1.6.1",
-        sha256="3894580f4c398d724ba408e410e50f70c9f452e8cfaf7c3ff8118c08df28eaa8",
-        deprecated=True,
-    )
-    version(
-        "1.6.0",
-        sha256="721e8cadfceb2f63014c2a727e098babc6deba653baab8866445a772385d0f5b",
-        deprecated=True,
-    )
-    version(
-        "1.5.0",
-        sha256="8e74e0b1e50ee86f4fca87a44c6b393740b32099ac3880046bf252c31c58dd42",
-        deprecated=True,
-    )
-    version(
-        "1.4.0",
-        sha256="75457e86984cc03ce87d6ad37adc5aab1910cabd39a9bbe5fb21ce2475a91138",
-        deprecated=True,
-    )
-    version(
-        "1.3.0",
-        sha256="5cedea2773f7091d69aae9fd8f724e6e47929ee3784acdd295945a848eb36b93",
-        deprecated=True,
-    )
-    version(
-        "1.2.0",
-        sha256="bc0e049cf84ceb308132d8679e7f22fcdca5561dda314d5233d0d5fe2b0f8c62",
-        deprecated=True,
-    )
-    version(
-        "1.1.0",
-        sha256="e185e5bd07df648224f85e765d18579fae0de54adaab9a194335e3ad6d3d29f7",
-        deprecated=True,
-    )
-    version(
-        "1.0.6",
-        sha256="2fc266a6e494adda40837be406aef8d9838f385ffd64fbfafb1164833906b4e0",
+        "1.9.3",
+        sha256="0c02076ed708372d5ae7bdebcefc8e45a8cbfa480eea781308336d60a2781f3a",
         deprecated=True,
     )
 
@@ -92,14 +45,21 @@ class Fairlogger(CMakePackage):
     variant(
         "cxxstd",
         default="default",
-        values=("default", conditional("11", when="@:1.9"), "14", "17", "20"),
+        values=(
+            "default",
+            conditional("11", when="@:1.9"),
+            conditional("14", when="@:1"),
+            "17",
+            "20",
+            "23",
+            "26",
+        ),
         multi=False,
         description="Use the specified C++ standard when building.",
     )
     variant(
         "pretty", default=False, description="Use BOOST_PRETTY_FUNCTION macro (Supported by 1.4+)."
     )
-    conflicts("+pretty", when="@:1.3")
 
     depends_on("cxx", type="build")  # generated
 
@@ -108,14 +68,15 @@ class Fairlogger(CMakePackage):
 
     depends_on("boost", when="+pretty")
     conflicts("^boost@1.70:", when="^cmake@:3.14")
+    depends_on("fmt")
     depends_on("fmt@:8", when="@:1.9")
-    depends_on("fmt@5.3.0:5", when="@1.6.0:1.6.1")
-    depends_on("fmt@5.3.0:", when="@1.6.2:")
 
     def patch(self):
         """FairLogger gets its version number from git.
-        But the tarball doesn't have that information, so
-        we patch the spack version into CMakeLists.txt"""
+
+        The tarball doesn't have that information, so we patch the spack
+        version into CMakeLists.txt.
+        """
         if not self.spec.satisfies("@develop"):
             filter_file(
                 r"(get_git_version\(.*)\)",
@@ -123,14 +84,17 @@ def patch(self):
                 "CMakeLists.txt",
             )
 
+        if self.spec.satisfies("@:1"):
+            filter_file(r"(LANGUAGES C CXX)", r"LANGUAGES CXX", "CMakeLists.txt")
+
     def cmake_args(self):
-        args = [self.define("DISABLE_COLOR", True)]
+        args = [
+            self.define("DISABLE_COLOR", True),
+            self.define_from_variant("USE_BOOST_PRETTY_FUNCTION", "pretty"),
+            self.define("USE_EXTERNAL_FMT", True),
+        ]
         if self.spec.variants["cxxstd"].value != "default":
             args.append(self.define_from_variant("CMAKE_CXX_STANDARD", "cxxstd"))
-        if self.spec.satisfies("@1.4:"):
-            args.append(self.define_from_variant("USE_BOOST_PRETTY_FUNCTION", "pretty"))
-        if self.spec.satisfies("@1.6:"):
-            args.append(self.define("USE_EXTERNAL_FMT", True))
         if self.spec.satisfies("^boost@:1.69"):
             args.append(self.define("Boost_NO_BOOST_CMAKE", True))
         return args

var/spack/repos/spack_repo/builtin/packages/fairmq/package.py

@@ -57,6 +57,7 @@ class Fairmq(CMakePackage):
         depends_on("git")
 
     depends_on("boost@1.66: +container+program_options+filesystem+date_time+regex")
+    conflicts("^boost@1.88:")
     depends_on("fairlogger@1.6: +pretty")
     depends_on("libzmq@4.1.4:")