gcc: remove --with-ld=ld-classic (#48826)

* cp2k: add dftd4 variant

* better conflict and make support

* typo

* Update var/spack/repos/builtin/packages/cp2k/package.py

* Update var/spack/repos/builtin/packages/cp2k/package.py

.github/workflows/build-containers.yml

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

lib/spack/docs/build_systems/autotoolspackage.rst

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

lib/spack/docs/contribution_guide.rst

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

lib/spack/docs/environments.rst

@@ -112,6 +112,19 @@ the original but may concretize differently in the presence of different
 explicit or default configuration settings (e.g., a different version of
 Spack or for a different user account).
 
+Environments created from a manifest will copy any included configs
+from relative paths inside the environment. Relative paths from
+outside the environment will cause errors, and absolute paths will be
+kept absolute. For example, if ``spack.yaml`` includes:
+
+.. code-block:: yaml
+
+   spack:
+     include: [./config.yaml]
+
+then the created environment will have its own copy of the file
+``config.yaml`` copied from the location in the original environment.
+
 Create an environment from a ``spack.lock`` file using:
 
 .. code-block:: console
@@ -160,7 +173,7 @@ accepts.  If an environment already exists then spack will simply activate it
 and ignore the create-specific flags.
 
 .. code-block:: console
-   
+
    $ spack env activate --create -p myenv
    # ...
    # [creates if myenv does not exist yet]
@@ -424,8 +437,8 @@ Developing Packages in a Spack Environment
 
 The ``spack develop`` command allows one to develop Spack packages in
 an environment. It requires a spec containing a concrete version, and
-will configure Spack to install the package from local source. 
-If a version is not provided from the command line interface then spack 
+will configure Spack to install the package from local source.
+If a version is not provided from the command line interface then spack
 will automatically pick the highest version the package has defined.
 This means any infinity versions (``develop``, ``main``, ``stable``) will be
 preferred in this selection process.
@@ -435,9 +448,9 @@ set, and Spack will ensure the package and its dependents are rebuilt
 any time the environment is installed if the package's local source
 code has been modified. Spack's native implementation to check for modifications
 is to check if ``mtime`` is newer than the installation.
-A custom check can be created by overriding the ``detect_dev_src_change`` method 
-in your package class. This is particularly useful for projects using custom spack repo's 
-to drive development and want to optimize performance. 
+A custom check can be created by overriding the ``detect_dev_src_change`` method
+in your package class. This is particularly useful for projects using custom spack repo's
+to drive development and want to optimize performance.
 
 Spack ensures that all instances of a
 developed package in the environment are concretized to match the
@@ -453,7 +466,7 @@ Further development on ``foo`` can be tested by re-installing the environment,
 and eventually committed and pushed to the upstream git repo.
 
 If the package being developed supports out-of-source builds then users can use the
-``--build_directory`` flag to control the location and name of the build directory. 
+``--build_directory`` flag to control the location and name of the build directory.
 This is a shortcut to set the ``package_attributes:build_directory`` in the
 ``packages`` configuration (see :ref:`assigning-package-attributes`).
 The supplied location will become the build-directory for that package in all future builds.

lib/spack/llnl/util/filesystem.py

@@ -668,7 +668,7 @@ def copy(src, dest, _permissions=False):
         _permissions (bool): for internal use only
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* matches multiple files but *dest* is
             not a directory
     """
@@ -679,7 +679,7 @@ def copy(src, dest, _permissions=False):
 
     files = glob.glob(src)
     if not files:
-        raise IOError("No such file or directory: '{0}'".format(src))
+        raise OSError("No such file or directory: '{0}'".format(src))
     if len(files) > 1 and not os.path.isdir(dest):
         raise ValueError(
             "'{0}' matches multiple files but '{1}' is not a directory".format(src, dest)
@@ -710,7 +710,7 @@ def install(src, dest):
         dest (str): the destination file or directory
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* matches multiple files but *dest* is
             not a directory
     """
@@ -748,7 +748,7 @@ def copy_tree(
         _permissions (bool): for internal use only
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* is a parent directory of *dest*
     """
     if _permissions:
@@ -762,7 +762,7 @@ def copy_tree(
 
     files = glob.glob(src)
     if not files:
-        raise IOError("No such file or directory: '{0}'".format(src))
+        raise OSError("No such file or directory: '{0}'".format(src))
 
     # For Windows hard-links and junctions, the source path must exist to make a symlink. Add
     # all symlinks to this list while traversing the tree, then when finished, make all
@@ -843,7 +843,7 @@ def install_tree(src, dest, symlinks=True, ignore=None):
         ignore (typing.Callable): function indicating which files to ignore
 
     Raises:
-        IOError: if *src* does not match any files or directories
+        OSError: if *src* does not match any files or directories
         ValueError: if *src* is a parent directory of *dest*
     """
     copy_tree(src, dest, symlinks=symlinks, ignore=ignore, _permissions=True)

lib/spack/llnl/util/link_tree.py

@@ -308,7 +308,7 @@ class LinkTree:
 
     def __init__(self, source_root):
         if not os.path.exists(source_root):
-            raise IOError("No such file or directory: '%s'", source_root)
+            raise OSError("No such file or directory: '%s'", source_root)
 
         self._root = source_root
 

lib/spack/llnl/util/lock.py

@@ -391,7 +391,7 @@ def _poll_lock(self, op: int) -> bool:
 
             return True
 
-        except IOError as e:
+        except OSError as e:
             # EAGAIN and EACCES == locked by another process (so try again)
             if e.errno not in (errno.EAGAIN, errno.EACCES):
                 raise

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

@@ -918,7 +918,7 @@ def _writer_daemon(
                         try:
                             if stdin_file.read(1) == "v":
                                 echo = not echo
-                        except IOError as e:
+                        except OSError as e:
                             # If SIGTTIN is ignored, the system gives EIO
                             # to let the caller know the read failed b/c it
                             # was in the bg. Ignore that too.
@@ -1013,7 +1013,7 @@ def wrapped(*args, **kwargs):
         while True:
             try:
                 return function(*args, **kwargs)
-            except IOError as e:
+            except OSError as e:
                 if e.errno == errno.EINTR:
                     continue
                 raise

lib/spack/spack/build_systems/cmake.py

@@ -459,8 +459,16 @@ def cmake(
         """Runs ``cmake`` in the build directory"""
 
         # skip cmake phase if it is an incremental develop build
+        # These are the files that will re-run CMake that are generated from a successful
+        # configure step
+        primary_generator = _extract_primary_generator(self.generator)
+        if primary_generator == "Unix Makefiles":
+            configure_artifact = "Makefile"
+        elif primary_generator == "Ninja":
+            configure_artifact = "ninja.build"
+
         if spec.is_develop and os.path.isfile(
-            os.path.join(self.build_directory, "CMakeCache.txt")
+            os.path.join(self.build_directory, configure_artifact)
         ):
             return
 

lib/spack/spack/cmd/external.py

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

lib/spack/spack/cmd/test.py

@@ -177,16 +177,15 @@ def test_run(args):
         matching = spack.store.STORE.db.query_local(spec, hashes=hashes, explicit=explicit)
         if spec and not matching:
             tty.warn("No {0}installed packages match spec {1}".format(explicit_str, spec))
-            """
-            TODO: Need to write out a log message and/or CDASH Testing
-              output that package not installed IF continue to process
-              these issues here.
 
-            if args.log_format:
-                # Proceed with the spec assuming the test process
-                # to ensure report package as skipped (e.g., for CI)
-                specs_to_test.append(spec)
-            """
+            # TODO: Need to write out a log message and/or CDASH Testing
+            #   output that package not installed IF continue to process
+            #   these issues here.
+
+            # if args.log_format:
+            #     # Proceed with the spec assuming the test process
+            #     # to ensure report package as skipped (e.g., for CI)
+            #     specs_to_test.append(spec)
 
         specs_to_test.extend(matching)
 

lib/spack/spack/environment/environment.py

@@ -581,7 +581,7 @@ def _error_on_nonempty_view_dir(new_root):
     # Check if the target path lexists
     try:
         st = os.lstat(new_root)
-    except (IOError, OSError):
+    except OSError:
         return
 
     # Empty directories are fine
@@ -861,7 +861,7 @@ def regenerate(self, concrete_roots: List[Spec]) -> None:
         ):
             try:
                 shutil.rmtree(old_root)
-            except (IOError, OSError) as e:
+            except OSError as e:
                 msg = "Failed to remove old view at %s\n" % old_root
                 msg += str(e)
                 tty.warn(msg)
@@ -2554,7 +2554,7 @@ def is_latest_format(manifest):
     try:
         with open(manifest, encoding="utf-8") as f:
             data = syaml.load(f)
-    except (OSError, IOError):
+    except OSError:
         return True
     top_level_key = _top_level_key(data)
     changed = spack.schema.env.update(data[top_level_key])
@@ -2634,6 +2634,32 @@ def _ensure_env_dir():
 
     shutil.copy(envfile, target_manifest)
 
+    # Copy relative path includes that live inside the environment dir
+    try:
+        manifest = EnvironmentManifestFile(environment_dir)
+    except Exception:
+        # error handling for bad manifests is handled on other code paths
+        return
+
+    includes = manifest[TOP_LEVEL_KEY].get("include", [])
+    for include in includes:
+        if os.path.isabs(include):
+            continue
+
+        abspath = pathlib.Path(os.path.normpath(environment_dir / include))
+        common_path = pathlib.Path(os.path.commonpath([environment_dir, abspath]))
+        if common_path != environment_dir:
+            tty.debug(f"Will not copy relative include from outside environment: {include}")
+            continue
+
+        orig_abspath = os.path.normpath(envfile.parent / include)
+        if not os.path.exists(orig_abspath):
+            tty.warn(f"Included file does not exist; will not copy: '{include}'")
+            continue
+
+        fs.touchp(abspath)
+        shutil.copy(orig_abspath, abspath)
+
 
 class EnvironmentManifestFile(collections.abc.Mapping):
     """Manages the in-memory representation of a manifest file, and its synchronization

lib/spack/spack/extensions.py

@@ -187,7 +187,7 @@ def path_for_extension(target_name: str, *, paths: List[str]) -> str:
         if name == target_name:
             return path
     else:
-        raise IOError('extension "{0}" not found'.format(target_name))
+        raise OSError('extension "{0}" not found'.format(target_name))
 
 
 def get_module(cmd_name):

lib/spack/spack/filesystem_view.py

@@ -427,7 +427,7 @@ def needs_file(spec, file):
             try:
                 with open(manifest_file, "r", encoding="utf-8") as f:
                     manifest = s_json.load(f)
-            except (OSError, IOError):
+            except OSError:
                 # if we can't load it, assume it doesn't know about the file.
                 manifest = {}
             return test_path in manifest
@@ -831,7 +831,7 @@ def get_spec_from_file(filename):
     try:
         with open(filename, "r", encoding="utf-8") as f:
             return spack.spec.Spec.from_yaml(f)
-    except IOError:
+    except OSError:
         return None
 
 

lib/spack/spack/hooks/absolutify_elf_sonames.py

@@ -26,7 +26,7 @@ def is_shared_library_elf(filepath):
         with open(filepath, "rb") as f:
             elf = parse_elf(f, interpreter=True, dynamic_section=True)
             return elf.has_pt_dynamic and (elf.has_soname or not elf.has_pt_interp)
-    except (IOError, OSError, ElfParsingError):
+    except (OSError, ElfParsingError):
         return False
 
 

lib/spack/spack/hooks/sbang.py

@@ -166,7 +166,7 @@ def filter_shebangs_in_directory(directory, filenames=None):
         # Only look at executable, non-symlink files.
         try:
             st = os.lstat(path)
-        except (IOError, OSError):
+        except OSError:
             continue
 
         if stat.S_ISLNK(st.st_mode) or stat.S_ISDIR(st.st_mode) or not st.st_mode & is_exe:

lib/spack/spack/main.py

@@ -163,7 +163,7 @@ def format_help_sections(self, level):
         # lazily add all commands to the parser when needed.
         add_all_commands(self)
 
-        """Print help on subcommands in neatly formatted sections."""
+        # Print help on subcommands in neatly formatted sections.
         formatter = self._get_formatter()
 
         # Create a list of subcommand actions. Argparse internals are nasty!

lib/spack/spack/oci/opener.py

@@ -383,6 +383,7 @@ def create_opener():
     """Create an opener that can handle OCI authentication."""
     opener = urllib.request.OpenerDirector()
     for handler in [
+        urllib.request.ProxyHandler(),
         urllib.request.UnknownHandler(),
         urllib.request.HTTPSHandler(context=spack.util.web.ssl_create_default_context()),
         spack.util.web.SpackHTTPDefaultErrorHandler(),

lib/spack/spack/package.py

@@ -13,6 +13,17 @@
 # import most common types used in packages
 from typing import Dict, List, Optional
 
+
+class tty:
+    import llnl.util.tty as _tty
+
+    debug = _tty.debug
+    error = _tty.error
+    info = _tty.info
+    msg = _tty.msg
+    warn = _tty.warn
+
+
 from llnl.util.filesystem import (
     FileFilter,
     FileList,
@@ -49,7 +60,6 @@
 )
 from llnl.util.symlink import symlink
 
-# These props will be overridden when the build env is set up.
 from spack.build_environment import MakeExecutable
 from spack.build_systems.aspell_dict import AspellDictPackage
 from spack.build_systems.autotools import AutotoolsPackage
@@ -136,8 +146,10 @@
 )
 from spack.phase_callbacks import run_after, run_before
 from spack.spec import Spec
+from spack.util.environment import EnvironmentModifications
 from spack.util.executable import Executable, ProcessError, which, which_string
 from spack.util.filesystem import fix_darwin_install_name
+from spack.util.prefix import Prefix
 from spack.variant import any_combination_of, auto_or_any_combination_of, disjoint_sets
 from spack.version import Version, ver
 

lib/spack/spack/package_base.py

@@ -66,10 +66,6 @@
 ]
 FLAG_HANDLER_TYPE = Callable[[str, Iterable[str]], FLAG_HANDLER_RETURN_TYPE]
 
-"""Allowed URL schemes for spack packages."""
-_ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
-
-
 #: Filename for the Spack build/install log.
 _spack_build_logfile = "spack-build-out.txt"
 

lib/spack/spack/patch.py

@@ -6,7 +6,7 @@
 import os
 import pathlib
 import sys
-from typing import Any, Dict, Optional, Set, Tuple, Type, Union
+from typing import Any, Dict, Optional, Tuple, Type, Union
 
 import llnl.util.filesystem
 from llnl.url import allowed_archive
@@ -503,38 +503,36 @@ def patch_for_package(self, sha256: str, pkg: "spack.package_base.PackageBase")
         patch_dict["sha256"] = sha256
         return from_dict(patch_dict, repository=self.repository)
 
-    def update_packages(self, pkgs_fullname: Set[str]) -> None:
+    def update_package(self, pkg_fullname: str) -> None:
         """Update the patch cache.
 
         Args:
             pkg_fullname: package to update.
         """
         # remove this package from any patch entries that reference it.
-        if self.index:
-            empty = []
-            for sha256, package_to_patch in self.index.items():
-                remove = []
-                for fullname, patch_dict in package_to_patch.items():
-                    if patch_dict["owner"] in pkgs_fullname:
-                        remove.append(fullname)
+        empty = []
+        for sha256, package_to_patch in self.index.items():
+            remove = []
+            for fullname, patch_dict in package_to_patch.items():
+                if patch_dict["owner"] == pkg_fullname:
+                    remove.append(fullname)
 
-                for fullname in remove:
-                    package_to_patch.pop(fullname)
+            for fullname in remove:
+                package_to_patch.pop(fullname)
 
-                if not package_to_patch:
-                    empty.append(sha256)
+            if not package_to_patch:
+                empty.append(sha256)
 
-            # remove any entries that are now empty
-            for sha256 in empty:
-                del self.index[sha256]
+        # remove any entries that are now empty
+        for sha256 in empty:
+            del self.index[sha256]
 
         # update the index with per-package patch indexes
-        for pkg_fullname in pkgs_fullname:
-            pkg_cls = self.repository.get_pkg_class(pkg_fullname)
-            partial_index = self._index_patches(pkg_cls, self.repository)
-            for sha256, package_to_patch in partial_index.items():
-                p2p = self.index.setdefault(sha256, {})
-                p2p.update(package_to_patch)
+        pkg_cls = self.repository.get_pkg_class(pkg_fullname)
+        partial_index = self._index_patches(pkg_cls, self.repository)
+        for sha256, package_to_patch in partial_index.items():
+            p2p = self.index.setdefault(sha256, {})
+            p2p.update(package_to_patch)
 
     def update(self, other: "PatchCache") -> None:
         """Update this cache with the contents of another.

lib/spack/spack/provider_index.py

@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Classes and functions to manage providers of virtual dependencies"""
-from typing import Dict, Iterable, List, Optional, Set, Union
+from typing import Dict, List, Optional, Set
 
 import spack.error
 import spack.spec
@@ -26,7 +26,7 @@ class _IndexBase:
     #: Calling providers_for(spec) will find specs that provide a
     #: matching implementation of MPI. Derived class need to construct
     #: this attribute according to the semantics above.
-    providers: Dict[str, Dict["spack.spec.Spec", Set["spack.spec.Spec"]]]
+    providers: Dict[str, Dict[str, Set[str]]]
 
     def providers_for(self, virtual_spec):
         """Return a list of specs of all packages that provide virtual
@@ -99,56 +99,66 @@ def __init__(
         self.repository = repository
         self.restrict = restrict
         self.providers = {}
-        if specs:
-            self.update_packages(specs)
 
-    def update_packages(self, specs: Iterable[Union[str, "spack.spec.Spec"]]):
+        specs = specs or []
+        for spec in specs:
+            if not isinstance(spec, spack.spec.Spec):
+                spec = spack.spec.Spec(spec)
+
+            if self.repository.is_virtual_safe(spec.name):
+                continue
+
+            self.update(spec)
+
+    def update(self, spec):
         """Update the provider index with additional virtual specs.
 
         Args:
             spec: spec potentially providing additional virtual specs
         """
-        for spec in specs:
-            if not isinstance(spec, spack.spec.Spec):
-                spec = spack.spec.Spec(spec)
+        if not isinstance(spec, spack.spec.Spec):
+            spec = spack.spec.Spec(spec)
 
-            if not spec.name or self.repository.is_virtual_safe(spec.name):
-                # Only non-virtual packages with name can provide virtual specs.
-                continue
+        if not spec.name:
+            # Empty specs do not have a package
+            return
 
-            pkg_provided = self.repository.get_pkg_class(spec.name).provided
-            for provider_spec_readonly, provided_specs in pkg_provided.items():
-                for provided_spec in provided_specs:
-                    # TODO: fix this comment.
-                    # We want satisfaction other than flags
-                    provider_spec = provider_spec_readonly.copy()
-                    provider_spec.compiler_flags = spec.compiler_flags.copy()
+        msg = "cannot update an index passing the virtual spec '{}'".format(spec.name)
+        assert not self.repository.is_virtual_safe(spec.name), msg
 
-                    if spec.intersects(provider_spec, deps=False):
-                        provided_name = provided_spec.name
+        pkg_provided = self.repository.get_pkg_class(spec.name).provided
+        for provider_spec_readonly, provided_specs in pkg_provided.items():
+            for provided_spec in provided_specs:
+                # TODO: fix this comment.
+                # We want satisfaction other than flags
+                provider_spec = provider_spec_readonly.copy()
+                provider_spec.compiler_flags = spec.compiler_flags.copy()
 
-                        provider_map = self.providers.setdefault(provided_name, {})
-                        if provided_spec not in provider_map:
-                            provider_map[provided_spec] = set()
+                if spec.intersects(provider_spec, deps=False):
+                    provided_name = provided_spec.name
 
-                        if self.restrict:
-                            provider_set = provider_map[provided_spec]
+                    provider_map = self.providers.setdefault(provided_name, {})
+                    if provided_spec not in provider_map:
+                        provider_map[provided_spec] = set()
 
-                            # If this package existed in the index before,
-                            # need to take the old versions out, as they're
-                            # now more constrained.
-                            old = {s for s in provider_set if s.name == spec.name}
-                            provider_set.difference_update(old)
+                    if self.restrict:
+                        provider_set = provider_map[provided_spec]
 
-                            # Now add the new version.
-                            provider_set.add(spec)
+                        # If this package existed in the index before,
+                        # need to take the old versions out, as they're
+                        # now more constrained.
+                        old = set([s for s in provider_set if s.name == spec.name])
+                        provider_set.difference_update(old)
 
-                        else:
-                            # Before putting the spec in the map, constrain
-                            # it so that it provides what was asked for.
-                            constrained = spec.copy()
-                            constrained.constrain(provider_spec)
-                            provider_map[provided_spec].add(constrained)
+                        # Now add the new version.
+                        provider_set.add(spec)
+
+                    else:
+                        # Before putting the spec in the map, constrain
+                        # it so that it provides what was asked for.
+                        constrained = spec.copy()
+                        constrained.constrain(provider_spec)
+                        provider_map[provided_spec].add(constrained)
 
     def to_json(self, stream=None):
         """Dump a JSON representation of this object.
@@ -183,13 +193,14 @@ def merge(self, other):
 
                 spdict[provided_spec] = spdict[provided_spec].union(opdict[provided_spec])
 
-    def remove_providers(self, pkgs_fullname: Set[str]):
+    def remove_provider(self, pkg_name):
         """Remove a provider from the ProviderIndex."""
         empty_pkg_dict = []
         for pkg, pkg_dict in self.providers.items():
             empty_pset = []
             for provided, pset in pkg_dict.items():
-                pset.difference_update(pkgs_fullname)
+                same_name = set(p for p in pset if p.fullname == pkg_name)
+                pset.difference_update(same_name)
 
                 if not pset:
                     empty_pset.append(provided)

lib/spack/spack/repo.py

@@ -465,7 +465,7 @@ def read(self, stream):
         """Read this index from a provided file object."""
 
     @abc.abstractmethod
-    def update(self, pkgs_fullname: Set[str]):
+    def update(self, pkg_fullname):
         """Update the index in memory with information about a package."""
 
     @abc.abstractmethod
@@ -482,8 +482,8 @@ def _create(self):
     def read(self, stream):
         self.index = spack.tag.TagIndex.from_json(stream, self.repository)
 
-    def update(self, pkgs_fullname: Set[str]):
-        self.index.update_packages({p.split(".")[-1] for p in pkgs_fullname})
+    def update(self, pkg_fullname):
+        self.index.update_package(pkg_fullname.split(".")[-1])
 
     def write(self, stream):
         self.index.to_json(stream)
@@ -498,14 +498,15 @@ def _create(self):
     def read(self, stream):
         self.index = spack.provider_index.ProviderIndex.from_json(stream, self.repository)
 
-    def update(self, pkgs_fullname: Set[str]):
+    def update(self, pkg_fullname):
+        name = pkg_fullname.split(".")[-1]
         is_virtual = (
-            lambda name: not self.repository.exists(name)
-            or self.repository.get_pkg_class(name).virtual
+            not self.repository.exists(name) or self.repository.get_pkg_class(name).virtual
         )
-        non_virtual_pkgs_fullname = {p for p in pkgs_fullname if not is_virtual(p.split(".")[-1])}
-        self.index.remove_providers(non_virtual_pkgs_fullname)
-        self.index.update_packages(non_virtual_pkgs_fullname)
+        if is_virtual:
+            return
+        self.index.remove_provider(pkg_fullname)
+        self.index.update(pkg_fullname)
 
     def write(self, stream):
         self.index.to_json(stream)
@@ -530,8 +531,8 @@ def read(self, stream):
     def write(self, stream):
         self.index.to_json(stream)
 
-    def update(self, pkgs_fullname: Set[str]):
-        self.index.update_packages(pkgs_fullname)
+    def update(self, pkg_fullname):
+        self.index.update_package(pkg_fullname)
 
 
 class RepoIndex:
@@ -621,7 +622,9 @@ def _build_index(self, name: str, indexer: Indexer):
                 if new_index_mtime != index_mtime:
                     needs_update = self.checker.modified_since(new_index_mtime)
 
-                indexer.update({f"{self.namespace}.{pkg_name}" for pkg_name in needs_update})
+                for pkg_name in needs_update:
+                    indexer.update(f"{self.namespace}.{pkg_name}")
+
                 indexer.write(new)
 
         return indexer.index
@@ -1038,7 +1041,7 @@ def _read_config(self) -> Dict[str, str]:
 
                 return yaml_data["repo"]
 
-        except IOError:
+        except OSError:
             tty.die(f"Error reading {self.config_file} when opening {self.root}")
 
     def get(self, spec: "spack.spec.Spec") -> "spack.package_base.PackageBase":
@@ -1366,7 +1369,7 @@ def create_repo(root, namespace=None, subdir=packages_dir_name):
             if subdir != packages_dir_name:
                 config.write(f"  subdirectory: '{subdir}'\n")
 
-    except (IOError, OSError) as e:
+    except OSError as e:
         # try to clean up.
         if existed:
             shutil.rmtree(config_path, ignore_errors=True)

lib/spack/spack/spec.py

@@ -4726,7 +4726,10 @@ def __str__(self):
         bool_keys = []
         kv_keys = []
         for key in sorted_keys:
-            bool_keys.append(key) if isinstance(self[key].value, bool) else kv_keys.append(key)
+            if isinstance(self[key].value, bool):
+                bool_keys.append(key)
+            else:
+                kv_keys.append(key)
 
         # add spaces before and after key/value variants.
         string = io.StringIO()

lib/spack/spack/tag.py

@@ -5,7 +5,6 @@
 import collections
 import copy
 from collections.abc import Mapping
-from typing import Set
 
 import spack.error
 import spack.repo
@@ -111,20 +110,23 @@ def merge(self, other):
             spkgs, opkgs = self.tags[tag], other.tags[tag]
             self.tags[tag] = sorted(list(set(spkgs + opkgs)))
 
-    def update_packages(self, pkg_names: Set[str]):
-        """Updates a package in the tag index."""
+    def update_package(self, pkg_name):
+        """Updates a package in the tag index.
+
+        Args:
+            pkg_name (str): name of the package to be removed from the index
+        """
+        pkg_cls = self.repository.get_pkg_class(pkg_name)
+
         # Remove the package from the list of packages, if present
         for pkg_list in self._tag_dict.values():
-            if pkg_names.isdisjoint(pkg_list):
-                continue
-            pkg_list[:] = [pkg for pkg in pkg_list if pkg not in pkg_names]
+            if pkg_name in pkg_list:
+                pkg_list.remove(pkg_name)
 
         # Add it again under the appropriate tags
-        for pkg_name in pkg_names:
-            pkg_cls = self.repository.get_pkg_class(pkg_name)
-            for tag in getattr(pkg_cls, "tags", []):
-                tag = tag.lower()
-                self._tag_dict[tag].append(pkg_cls.name)
+        for tag in getattr(pkg_cls, "tags", []):
+            tag = tag.lower()
+            self._tag_dict[tag].append(pkg_cls.name)
 
 
 class TagIndexError(spack.error.SpackError):

lib/spack/spack/test/ci.py

@@ -328,16 +328,14 @@ def test_get_spec_filter_list(mutable_mock_env_path, mutable_mock_repo):
     e1.add("hypre")
     e1.concretize()
 
-    """
-    Concretizing the above environment results in the following graphs:
+    # Concretizing the above environment results in the following graphs:
 
-    mpileaks -> mpich (provides mpi virtual dep of mpileaks)
-             -> callpath -> dyninst -> libelf
-                                    -> libdwarf -> libelf
-                         -> mpich (provides mpi dep of callpath)
+    # mpileaks -> mpich (provides mpi virtual dep of mpileaks)
+    #          -> callpath -> dyninst -> libelf
+    #                                 -> libdwarf -> libelf
+    #                      -> mpich (provides mpi dep of callpath)
 
-    hypre -> openblas-with-lapack (provides lapack and blas virtual deps of hypre)
-    """
+    # hypre -> openblas-with-lapack (provides lapack and blas virtual deps of hypre)
 
     touched = ["libdwarf"]
 

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

@@ -1038,6 +1038,58 @@ def test_init_from_yaml(environment_from_manifest):
     assert not e2.specs_by_hash
 
 
+def test_init_from_yaml_relative_includes(tmp_path):
+    files = [
+        "relative_copied/packages.yaml",
+        "./relative_copied/compilers.yaml",
+        "repos.yaml",
+        "./config.yaml",
+    ]
+
+    manifest = f"""
+spack:
+  specs: []
+  include: {files}
+"""
+
+    e1_path = tmp_path / "e1"
+    e1_manifest = e1_path / "spack.yaml"
+    fs.mkdirp(e1_path)
+    with open(e1_manifest, "w", encoding="utf-8") as f:
+        f.write(manifest)
+
+    for f in files:
+        fs.touchp(e1_path / f)
+
+    e2 = _env_create("test2", init_file=e1_manifest)
+
+    for f in files:
+        assert os.path.exists(os.path.join(e2.path, f))
+
+
+def test_init_from_yaml_relative_includes_outside_env(tmp_path):
+    files = ["../outside_env_not_copied/repos.yaml"]
+
+    manifest = f"""
+spack:
+  specs: []
+  include: {files}
+"""
+
+    # subdir to ensure parent of environment dir is not shared
+    e1_path = tmp_path / "e1_subdir" / "e1"
+    e1_manifest = e1_path / "spack.yaml"
+    fs.mkdirp(e1_path)
+    with open(e1_manifest, "w", encoding="utf-8") as f:
+        f.write(manifest)
+
+    for f in files:
+        fs.touchp(e1_path / f)
+
+    with pytest.raises(spack.config.ConfigFileError, match="Detected 1 missing include"):
+        _ = _env_create("test2", init_file=e1_manifest)
+
+
 def test_env_view_external_prefix(tmp_path, mutable_database, mock_packages):
     fake_prefix = tmp_path / "a-prefix"
     fake_bin = fake_prefix / "bin"

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

@@ -139,7 +139,7 @@ def test_gc_except_specific_environments(mutable_database, mutable_mock_env_path
 def test_gc_except_nonexisting_dir_env(mutable_database, mutable_mock_env_path, tmpdir):
     output = gc("-ye", tmpdir.strpath, fail_on_error=False)
     assert "No such environment" in output
-    gc.returncode == 1
+    assert gc.returncode == 1
 
 
 @pytest.mark.db

lib/spack/spack/test/cmd/load.py

@@ -26,9 +26,9 @@ def test_manpath_trailing_colon(
         else ("--sh", "export %s=%s", ";")
     )
 
-    """Test that the commands generated by load add the MANPATH prefix
-    inspections. Also test that Spack correctly preserves the default/existing
-    manpath search path via a trailing colon"""
+    # Test that the commands generated by load add the MANPATH prefix
+    # inspections. Also test that Spack correctly preserves the default/existing
+    # manpath search path via a trailing colon
     install("mpileaks")
 
     sh_out = load(shell, "mpileaks")
@@ -81,7 +81,9 @@ def extract_value(output, variable):
 
         # Finally, do we list them in topo order?
         for i, pkg in enumerate(pkgs):
-            set(s.name for s in mpileaks_spec[pkg].traverse(direction="parents")) in set(pkgs[:i])
+            assert {s.name for s in mpileaks_spec[pkg].traverse(direction="parents")}.issubset(
+                pkgs[: i + 1]
+            )
 
         # Lastly, do we keep track that mpileaks was loaded?
         assert (

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

@@ -1,17 +1,6 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import pathlib
-
-import pytest
-
-import spack.concretize
-import spack.config
-import spack.environment as ev
-import spack.paths
-import spack.repo
-import spack.spec
-import spack.util.spack_yaml as syaml
 
 """
 These tests include the following package DAGs:
@@ -42,6 +31,18 @@
 y
 """
 
+import pathlib
+
+import pytest
+
+import spack.concretize
+import spack.config
+import spack.environment as ev
+import spack.paths
+import spack.repo
+import spack.spec
+import spack.util.spack_yaml as syaml
+
 
 @pytest.fixture
 def test_repo(mutable_config, monkeypatch, mock_stage):

lib/spack/spack/test/install.py

@@ -458,7 +458,7 @@ def test_log_install_without_build_files(install_mockery):
     spec = spack.concretize.concretize_one("trivial-install-test-package")
 
     # Attempt installing log without the build log file
-    with pytest.raises(IOError, match="No such file or directory"):
+    with pytest.raises(OSError, match="No such file or directory"):
         spack.installer.log(spec.package)
 
 

lib/spack/spack/test/installer.py

@@ -470,7 +470,7 @@ def _repoerr(repo, name):
 
     # The call to install_tree will raise the exception since not mocking
     # creation of dependency package files within *install* directories.
-    with pytest.raises(IOError, match=path if sys.platform != "win32" else ""):
+    with pytest.raises(OSError, match=path if sys.platform != "win32" else ""):
         inst.dump_packages(spec, path)
 
     # Now try the error path, which requires the mock directory structure

lib/spack/spack/test/llnl/util/filesystem.py

@@ -82,7 +82,7 @@ def test_non_existing_src(self, stage):
         """Test using a non-existing source."""
 
         with fs.working_dir(str(stage)):
-            with pytest.raises(IOError, match="No such file or directory"):
+            with pytest.raises(OSError, match="No such file or directory"):
                 fs.copy("source/none", "dest")
 
     def test_multiple_src_file_dest(self, stage):
@@ -139,7 +139,7 @@ def test_non_existing_src(self, stage):
         """Test using a non-existing source."""
 
         with fs.working_dir(str(stage)):
-            with pytest.raises(IOError, match="No such file or directory"):
+            with pytest.raises(OSError, match="No such file or directory"):
                 fs.install("source/none", "dest")
 
     def test_multiple_src_file_dest(self, stage):
@@ -220,7 +220,7 @@ def test_non_existing_src(self, stage):
         """Test using a non-existing source."""
 
         with fs.working_dir(str(stage)):
-            with pytest.raises(IOError, match="No such file or directory"):
+            with pytest.raises(OSError, match="No such file or directory"):
                 fs.copy_tree("source/none", "dest")
 
     def test_parent_dir(self, stage):
@@ -301,7 +301,7 @@ def test_non_existing_src(self, stage):
         """Test using a non-existing source."""
 
         with fs.working_dir(str(stage)):
-            with pytest.raises(IOError, match="No such file or directory"):
+            with pytest.raises(OSError, match="No such file or directory"):
                 fs.install_tree("source/none", "dest")
 
     def test_parent_dir(self, stage):

lib/spack/spack/test/llnl/util/lock.py

@@ -93,28 +93,26 @@
     pass
 
 
-"""This is a list of filesystem locations to test locks in.  Paths are
-expanded so that %u is replaced with the current username. '~' is also
-legal and will be expanded to the user's home directory.
-
-Tests are skipped for directories that don't exist, so you'll need to
-update this with the locations of NFS, Lustre, and other mounts on your
-system.
-"""
+#: This is a list of filesystem locations to test locks in.  Paths are
+#: expanded so that %u is replaced with the current username. '~' is also
+#: legal and will be expanded to the user's home directory.
+#:
+#: Tests are skipped for directories that don't exist, so you'll need to
+#: update this with the locations of NFS, Lustre, and other mounts on your
+#: system.
 locations = [
     tempfile.gettempdir(),
     os.path.join("/nfs/tmp2/", getpass.getuser()),
     os.path.join("/p/lscratch*/", getpass.getuser()),
 ]
 
-"""This is the longest a failed multiproc test will take.
-Barriers will time out and raise an exception after this interval.
-In MPI mode, barriers don't time out (they hang).  See mpi_multiproc_test.
-"""
+#: This is the longest a failed multiproc test will take.
+#: Barriers will time out and raise an exception after this interval.
+#: In MPI mode, barriers don't time out (they hang).  See mpi_multiproc_test.
 barrier_timeout = 5
 
-"""This is the lock timeout for expected failures.
-This may need to be higher for some filesystems."""
+#: This is the lock timeout for expected failures.
+#: This may need to be higher for some filesystems.
 lock_fail_timeout = 0.1
 
 
@@ -286,9 +284,8 @@ def wait(self):
     comm.Barrier()  # barrier after each MPI test.
 
 
-"""``multiproc_test()`` should be called by tests below.
-``multiproc_test()`` will work for either MPI runs or for local runs.
-"""
+#: ``multiproc_test()`` should be called by tests below.
+#: ``multiproc_test()`` will work for either MPI runs or for local runs.
 multiproc_test = mpi_multiproc_test if mpi else local_multiproc_test
 
 
@@ -1339,7 +1336,7 @@ def test_poll_lock_exception(tmpdir, monkeypatch, err_num, err_msg):
     """Test poll lock exception handling."""
 
     def _lockf(fd, cmd, len, start, whence):
-        raise IOError(err_num, err_msg)
+        raise OSError(err_num, err_msg)
 
     with tmpdir.as_cwd():
         lockfile = "lockfile"
@@ -1351,7 +1348,7 @@ def _lockf(fd, cmd, len, start, whence):
         if err_num in [errno.EAGAIN, errno.EACCES]:
             assert not lock._poll_lock(fcntl.LOCK_EX)
         else:
-            with pytest.raises(IOError, match=err_msg):
+            with pytest.raises(OSError, match=err_msg):
                 lock._poll_lock(fcntl.LOCK_EX)
 
         monkeypatch.undo()

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

@@ -238,10 +238,7 @@ def test_exclude(self, modulefile_content, module_configuration, host_architectu
 
         assert len([x for x in content if "module load " in x]) == 1
 
-        # Catch "Exception" to avoid using FileNotFoundError on Python 3
-        # and IOError on Python 2 or common bases like EnvironmentError
-        # which are not officially documented
-        with pytest.raises(Exception):
+        with pytest.raises(FileNotFoundError):
             modulefile_content(f"callpath target={host_architecture_str}")
 
         content = modulefile_content(f"zmpi target={host_architecture_str}")

lib/spack/spack/test/reporters.py

@@ -132,7 +132,8 @@ def test_reporters_extract_skipped(state):
     parts = spack.reporters.extract.extract_test_parts("fake", outputs)
 
     assert len(parts) == 1
-    parts[0]["completed"] == expected
+
+    assert parts[0]["completed"] == spack.reporters.extract.completed["skipped"]
 
 
 def test_reporters_skip_new():

lib/spack/spack/test/sbang.py

@@ -198,7 +198,7 @@ def script_dir(sbang_line):
     ],
 )
 def test_shebang_interpreter_regex(shebang, interpreter):
-    sbang.get_interpreter(shebang) == interpreter
+    assert sbang.get_interpreter(shebang) == interpreter
 
 
 def test_shebang_handling(script_dir, sbang_line):

lib/spack/spack/test/spec_dag.py

@@ -428,31 +428,29 @@ def test_copy_through_spec_build_interface(self):
         c2 = s["mpileaks"]["mpileaks"].copy()
         assert c0 == c1 == c2 == s
 
-    """
-    Here is the graph with deptypes labeled (assume all packages have a 'dt'
-    prefix). Arrows are marked with the deptypes ('b' for 'build', 'l' for
-    'link', 'r' for 'run').
+    # Here is the graph with deptypes labeled (assume all packages have a 'dt'
+    # prefix). Arrows are marked with the deptypes ('b' for 'build', 'l' for
+    # 'link', 'r' for 'run').
 
-        use -bl-> top
+    #     use -bl-> top
 
-        top -b->  build1
-        top -bl-> link1
-        top -r->  run1
+    #     top -b->  build1
+    #     top -bl-> link1
+    #     top -r->  run1
 
-        build1 -b->  build2
-        build1 -bl-> link2
-        build1 -r->  run2
+    #     build1 -b->  build2
+    #     build1 -bl-> link2
+    #     build1 -r->  run2
 
-        link1 -bl-> link3
+    #     link1 -bl-> link3
 
-        run1 -bl-> link5
-        run1 -r->  run3
+    #     run1 -bl-> link5
+    #     run1 -r->  run3
 
-        link3 -b->  build2
-        link3 -bl-> link4
+    #     link3 -b->  build2
+    #     link3 -bl-> link4
 
-        run3 -b-> build3
-    """
+    #     run3 -b-> build3
 
     @pytest.mark.parametrize(
         "spec_str,deptypes,expected",

lib/spack/spack/test/stage.py

@@ -125,7 +125,7 @@ def check_expand_archive(stage, stage_name, expected_file_list):
 
         assert os.path.isfile(fn)
         with open(fn, encoding="utf-8") as _file:
-            _file.read() == contents
+            assert _file.read() == contents
 
 
 def check_fetch(stage, stage_name):

lib/spack/spack/test/tag.py

@@ -154,6 +154,7 @@ def test_tag_no_tags(mock_packages):
 def test_tag_update_package(mock_packages):
     mock_index = mock_packages.tag_index
     index = spack.tag.TagIndex(repository=mock_packages)
-    index.update_packages(set(spack.repo.all_package_names()))
+    for name in spack.repo.all_package_names():
+        index.update_package(name)
 
     ensure_tags_results_equal(mock_index.tags, index.tags)

lib/spack/spack/test/util/compression.py

@@ -20,12 +20,7 @@
 
 datadir = os.path.join(spack_root, "lib", "spack", "spack", "test", "data", "compression")
 
-ext_archive = {}
-[
-    ext_archive.update({ext: ".".join(["Foo", ext])})
-    for ext in llnl.url.ALLOWED_ARCHIVE_TYPES
-    if "TAR" not in ext
-]
+ext_archive = {ext: f"Foo.{ext}" for ext in llnl.url.ALLOWED_ARCHIVE_TYPES if "TAR" not in ext}
 # Spack does not use Python native handling for tarballs or zip
 # Don't test tarballs or zip in native test
 native_archive_list = [

lib/spack/spack/test/util/editor.py

@@ -204,13 +204,13 @@ def test_no_editor():
     def assert_exec(exe, args):
         assert False
 
-    with pytest.raises(EnvironmentError, match=r"No text editor found.*"):
+    with pytest.raises(OSError, match=r"No text editor found.*"):
         ed.editor("/path/to/file", exec_fn=assert_exec)
 
     def assert_exec(exe, args):
         return False
 
-    with pytest.raises(EnvironmentError, match=r"No text editor found.*"):
+    with pytest.raises(OSError, match=r"No text editor found.*"):
         ed.editor("/path/to/file", exec_fn=assert_exec)
 
 
@@ -220,5 +220,5 @@ def test_exec_fn_executable(editor_var, good_exe, bad_exe):
     assert ed.editor(exec_fn=ed.executable)
 
     os.environ[editor_var] = bad_exe
-    with pytest.raises(EnvironmentError, match=r"No text editor found.*"):
+    with pytest.raises(OSError, match=r"No text editor found.*"):
         ed.editor(exec_fn=ed.executable)

lib/spack/spack/util/editor.py

@@ -9,7 +9,7 @@
 defined by the EDITOR environment variable if VISUAL is not set or the
 specified editor fails (e.g. no DISPLAY for a graphical editor). If
 neither variable is set, we fall back to one of several common editors,
-raising an EnvironmentError if we are unable to find one.
+raising an OSError if we are unable to find one.
 """
 import os
 import shlex
@@ -141,7 +141,7 @@ def try_env_var(var):
         return True
 
     # Fail if nothing could be found
-    raise EnvironmentError(
+    raise OSError(
         "No text editor found! Please set the VISUAL and/or EDITOR "
         "environment variable(s) to your preferred text editor."
     )

lib/spack/spack/util/ld_so_conf.py

@@ -46,7 +46,7 @@ def _process_ld_so_conf_queue(queue):
         try:
             with open(p, "rb") as f:
                 lines = f.readlines()
-        except (IOError, OSError):
+        except OSError:
             continue
 
         for line in lines:
@@ -132,7 +132,7 @@ def host_dynamic_linker_search_paths():
 
             if os.path.exists(possible_conf):
                 conf_file = possible_conf
-    except (IOError, OSError, elf_utils.ElfParsingError):
+    except (OSError, elf_utils.ElfParsingError):
         pass
 
     # Note: ld_so_conf doesn't error if the file does not exist.

share/spack/gitlab/cloud_pipelines/.gitlab-ci.yml

@@ -59,11 +59,6 @@ default:
     SPACK_TARGET_PLATFORM: "linux"
     SPACK_TARGET_ARCH: "aarch64"
 
-.linux_power:
-  variables:
-    SPACK_TARGET_PLATFORM: "linux"
-    SPACK_TARGET_ARCH: "ppc64le"
-
 .win64-msvc2019:
   variables:
     SPACK_TARGET_PLATFORM: "win64"
@@ -352,35 +347,6 @@ e4s-oneapi-build:
     - artifacts: True
       job: e4s-oneapi-generate
 
-########################################
-# E4S on Power
-########################################
-.e4s-power-generate-tags-and-image:
-  image: { "name": "ghcr.io/spack/ubuntu20.04-runner-ppc64-gcc-11.4:2023.08.01", "entrypoint": [""] }
-  tags: ["spack", "public", "large", "ppc64le"]
-
-.e4s-power:
-  extends: [".linux_power"]
-  variables:
-    SPACK_CI_STACK_NAME: e4s-power
-
-e4s-power-generate:
-  extends: [ ".e4s-power", ".generate-x86_64", ".e4s-power-generate-tags-and-image"]
-  variables:
-    # Override concretization pool for metal runners
-    SPACK_CONCRETIZE_JOBS: 16
-
-e4s-power-build:
-  extends: [ ".e4s-power", ".build" ]
-  trigger:
-    include:
-      - artifact: jobs_scratch_dir/cloud-ci-pipeline.yml
-        job: e4s-power-generate
-    strategy: depend
-  needs:
-    - artifacts: True
-      job: e4s-power-generate
-
 #########################################
 # Build tests for different build-systems
 #########################################

share/spack/gitlab/cloud_pipelines/configs/linux/ppc64le/ci.yaml

@@ -1,22 +0,0 @@
-ci:
-  pipeline-gen:
-  - build-job:
-      tags: ["ppc64le"]
-      # Power runners overrides the default script
-      # - don't download make
-      # - no intermediate keys
-      script::
-      - uname -a || true
-      - grep -E 'vendor|model name' /proc/cpuinfo 2>/dev/null | sort -u || head -n10 /proc/cpuinfo 2>/dev/null || true
-      - nproc
-      - . "./share/spack/setup-env.sh"
-      - spack --version
-      - spack arch
-      - cd ${SPACK_CONCRETE_ENV_DIR}
-      - spack env activate --without-view .
-      - if [ -n "$SPACK_BUILD_JOBS" ]; then spack config add "config:build_jobs:$SPACK_BUILD_JOBS"; fi
-      - spack config add "config:install_tree:projections:${SPACK_JOB_SPEC_PKG_NAME}:'morepadding/{architecture}/{compiler.name}-{compiler.version}/{name}-{version}-{hash}'"
-      - mkdir -p ${SPACK_ARTIFACTS_ROOT}/user_data
-      - if [[ -r /mnt/key/e4s.gpg ]]; then spack gpg trust /mnt/key/e4s.gpg; fi
-      - if [[ -r /mnt/key/spack_public_key.gpg ]]; then spack gpg trust /mnt/key/spack_public_key.gpg; fi
-      - spack --color=always --backtrace ci rebuild > >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_out.txt) 2> >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_err.txt >&2)

share/spack/gitlab/cloud_pipelines/configs/linux/ppc64le/concretizer.yaml

@@ -1,3 +0,0 @@
-concretizer:
-  targets:
-    granularity: generic

share/spack/gitlab/cloud_pipelines/stacks/e4s-power/spack.yaml

@@ -1,271 +0,0 @@
-spack:
-  view: false
-
-  concretizer:
-    reuse: false
-    unify: false
-
-  packages:
-    all:
-      require: "%gcc@9.4.0 target=ppc64le"
-      compiler: [gcc@9.4.0]
-      providers:
-        blas: [openblas]
-        mpi: [mpich]
-      variants: +mpi cuda_arch=70
-    binutils:
-      variants: +ld +gold +headers +libiberty ~nls
-    hdf5:
-      variants: +fortran +hl +shared
-    libfabric:
-      variants: fabrics=sockets,tcp,udp,rxm
-    openblas:
-      variants: threads=openmp
-    trilinos:
-      variants: +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext
-        +ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu
-        +nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos
-        +teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
-    xz:
-      variants: +pic
-    mpi:
-      require: mpich
-    mpich:
-      require: '~wrapperrpath ~hwloc %gcc@9.4.0 target=ppc64le'
-    ncurses:
-      require: '@6.3 +termlib %gcc@9.4.0 target=ppc64le'
-    faodel:
-      require: "~tcmalloc %gcc@9.4.0 target=ppc64le"
-    tbb:
-      require: intel-tbb
-    vtk-m:
-      require: "+examples %gcc@9.4.0 target=ppc64le"
-    cuda:
-      require: "@11.4.4 %gcc@9.4.0 target=ppc64le"
-    paraview:
-      require: "+examples %gcc@9.4.0 target=ppc64le"
-
-
-  specs:
-  # CPU
-  - adios
-  - alquimia
-  - aml
-  - amrex
-  - arborx
-  - argobots
-  - axom
-  - bolt
-  - boost
-  - bricks
-  - butterflypack
-  - cabana
-  - caliper
-  - chai
-  - chapel ~rocm ~cuda
-  - charliecloud
-  - conduit
-  - cp2k +mpi
-  - datatransferkit
-  - drishti
-  - dxt-explorer
-  - dyninst
-  - exaworks
-  - fftx
-  - flecsi
-  - flit
-  - flux-core
-  - fortrilinos
-  - gasnet
-  - ginkgo
-  - globalarrays
-  - gmp
-  - gotcha
-  - gptune
-  - gromacs +cp2k ^cp2k +mpi build_system=cmake
-  - h5bench
-  - hdf5-vol-async
-  - hdf5-vol-cache
-  - hdf5-vol-log
-  - heffte +fftw
-  - hpctoolkit
-  - hpx networking=mpi
-  - hypre
-  - kokkos +openmp
-  - kokkos-kernels +openmp
-  - laghos
-  - lammps
-  - lbann
-  - legion
-  - libnrm
-  - libquo
-  - libunwind
-  - loki
-  - mercury
-  - metall
-  - mfem
-  - mgard +serial +openmp +timing +unstructured ~cuda
-  - mpark-variant
-  - mpifileutils ~xattr
-  - nccmp
-  - nco
-  - netlib-scalapack
-  - nrm
-  - nvhpc
-  - nwchem
-  - omega-h
-  - openfoam
-  - openmpi
-  - openpmd-api
-  - papi
-  - papyrus
-  - paraview ~cuda ~rocm
-  - parsec ~cuda
-  - pdt
-  - petsc
-  - plasma
-  - plumed
-  - precice
-  - pruners-ninja
-  - pumi
-  - py-amrex
-  - py-h5py
-  - py-jupyterhub
-  - py-libensemble
-  - py-petsc4py
-  - qthreads scheduler=distrib
-  - quantum-espresso
-  - raja
-  - rempi
-  - scr
-  - slate ~cuda
-  - slepc
-  - stc
-  - strumpack ~slate
-  - sundials
-  - superlu
-  - superlu-dist
-  - swig@4.0.2-fortran
-  - sz3
-  - tasmanian
-  - tau +mpi +python                       # +syscall fails: https://github.com/spack/spack/pull/40830#issuecomment-1790799772; tau: has issue with `spack env depfile` build
-  - trilinos +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext +ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu +nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos +teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
-  - turbine
-  - umap
-  - umpire
-  - upcxx
-  - wannier90
-  - warpx +python
-  - wps
-  - wrf
-  - xyce +mpi +shared +pymi +pymi_static_tpls
-  # INCLUDED IN ECP DAV CPU
-  - adios2
-  - ascent
-  - darshan-runtime
-  - darshan-util
-  - faodel
-  - hdf5
-  - libcatalyst
-  - parallel-netcdf
-  - py-cinemasci
-  - sz
-  - unifyfs
-  - veloc
-  # - visit                                 # libext, libxkbfile, libxrender, libxt, silo (https://github.com/spack/spack/issues/39538), cairo
-  - vtk-m
-  - zfp
-  # - ecp-data-vis-sdk ~cuda ~rocm +adios2 +ascent +cinema +darshan +faodel +hdf5 ~paraview +pnetcdf +sz +unifyfs +veloc ~visit +vtkm +zfp # +visit: libext, libxkbfile, libxrender, libxt, silo (https://github.com/spack/spack/issues/39538), cairo
-  # --
-  # - dealii                                # fltk: https://github.com/spack/spack/issues/38791
-  # - geopm-runtime                         # cairo: *** No autoreconf found, please install it ***
-  # - glvis                                 # glvis: https://github.com/spack/spack/issues/42839
-  # - libpressio +bitgrooming +bzip2 ~cuda ~cusz +fpzip +hdf5 +libdistributed +lua +openmp +python +sz +sz3 +unix +zfp # py-numcodecs: gcc: error: unrecognized command line option '-mno-sse2'; did you mean '-mno-isel'? gcc: error: unrecognized command line option '-mno-avx2'
-  # - phist +mpi                            # ghost@develop: gcc-9: error: unrecognized command line option '-march=native'; did you mean '-mcpu=native'?
-  # - variorum                              # variorum: https://github.com/spack/spack/issues/38786
-
-  # PYTHON PACKAGES
-  - opencv +python3
-  - py-jax
-  - py-jupyterlab
-  - py-matplotlib
-  - py-mpi4py
-  - py-notebook
-  - py-numba
-  - py-numpy
-  - py-openai
-  - py-pandas
-  - py-plotly
-  - py-pooch
-  - py-pytest
-  - py-scikit-learn
-  - py-scipy
-  - py-seaborn
-  # - py-horovod        # py-torch, py-tensorflow
-  # - py-tensorflow     # error
-  # - py-torch          # error
-
-  # CUDA NOARCH
-  - bricks +cuda
-  - cabana +cuda ^kokkos +wrapper +cuda_lambda +cuda cuda_arch=70
-  - flux-core +cuda
-  - hpctoolkit +cuda
-  - papi +cuda
-  - tau +mpi +cuda
-  # --
-  # - legion +cuda                          # legion: needs NVIDIA driver
-
-  # CUDA 70
-  - amrex +cuda cuda_arch=70
-  - arborx +cuda cuda_arch=70 ^kokkos +wrapper
-  - caliper +cuda cuda_arch=70
-  - chai +cuda cuda_arch=70 ^umpire ~shared
-  - ecp-data-vis-sdk ~rocm +adios2 ~ascent +hdf5 +vtkm +zfp ~paraview +cuda cuda_arch=70
-  - exago +mpi +python +raja +hiop ~rocm +cuda cuda_arch=70 ~ipopt ^hiop@1.0.0 ~sparse +mpi +raja ~rocm +cuda cuda_arch=70 #^raja@0.14.0
-  - flecsi +cuda cuda_arch=70
-  - ginkgo +cuda cuda_arch=70
-  - gromacs +cuda cuda_arch=70
-  - heffte +cuda cuda_arch=70
-  - hpx +cuda cuda_arch=70
-  - hypre +cuda cuda_arch=70
-  - kokkos +wrapper +cuda cuda_arch=70
-  - kokkos-kernels +cuda cuda_arch=70 ^kokkos +wrapper +cuda cuda_arch=70
-  - magma +cuda cuda_arch=70
-  - mfem +cuda cuda_arch=70
-  - mgard +serial +openmp +timing +unstructured +cuda cuda_arch=70
-  - omega-h +cuda cuda_arch=70
-  - parsec +cuda cuda_arch=70
-  - petsc +cuda cuda_arch=70
-  - raja +cuda cuda_arch=70
-  - slate +cuda cuda_arch=70
-  - slepc +cuda cuda_arch=70
-  - strumpack ~slate +cuda cuda_arch=70
-  - sundials +cuda cuda_arch=70
-  - superlu-dist +cuda cuda_arch=70
-  - tasmanian +cuda cuda_arch=70
-  - umpire ~shared +cuda cuda_arch=70
-  # INCLUDED IN ECP DAV CUDA
-  - adios2 +cuda cuda_arch=70
-  # - ascent +cuda cuda_arch=70             # ascent: https://github.com/spack/spack/issues/38045
-  - paraview +cuda cuda_arch=70
-  - vtk-m +cuda cuda_arch=70
-  - zfp +cuda cuda_arch=70
-  # --
-  # - axom +cuda cuda_arch=70               # axom: https://github.com/spack/spack/issues/29520
-  # - cp2k +mpi +cuda cuda_arch=70          # dbcsr
-  # - cusz +cuda cuda_arch=70               # cusz: https://github.com/spack/spack/issues/38787
-  # - dealii +cuda cuda_arch=70             # fltk: https://github.com/spack/spack/issues/38791
-  # - lammps +cuda cuda_arch=70             # lammps: needs NVIDIA driver
-  # - lbann +cuda cuda_arch=70              # lbann: https://github.com/spack/spack/issues/38788
-  # - libpressio +bitgrooming +bzip2 +fpzip +hdf5 +libdistributed +lua +openmp +python +sz +sz3 +unix +zfp +json +remote +netcdf +cusz +mgard +cuda cuda_arch=70 ^cusz +cuda cuda_arch=70 # depends_on("cuda@11.7.1:", when="+cuda")
-  # - py-torch +cuda cuda_arch=70           # skipped
-  # - trilinos +cuda cuda_arch=70           # trilinos: https://github.com/trilinos/Trilinos/issues/11630
-  # - upcxx +cuda cuda_arch=70              # upcxx: needs NVIDIA driver
-
-  ci:
-    pipeline-gen:
-    - build-job:
-        image: ghcr.io/spack/ubuntu20.04-runner-ppc64-gcc-11.4:2023.08.01
-
-  cdash:
-    build-group: E4S Power

var/spack/repos/builtin/packages/7zip/package.py

@@ -100,10 +100,8 @@ def install(self, spec, prefix):
                 for ext in exts:
                     glob_str = os.path.join(pth, ext)
                     files = glob.glob(glob_str)
-                    [
+                    for x in files:
                         shutil.copy(
                             os.path.join(self._7z_src_dir, x),
                             os.path.join(prefix, os.path.basename(x)),
                         )
-                        for x in files
-                    ]

var/spack/repos/builtin/packages/abinit/package.py

@@ -179,7 +179,7 @@ def configure_args(self):
             if spec.satisfies("@:8"):
                 oapp("--with-dft-flavor=atompaw+libxc")
             else:
-                "--without-wannier90",
+                oapp("--without-wannier90")
 
         if spec.satisfies("+mpi"):
             oapp(f"CC={spec['mpi'].mpicc}")

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

@@ -5,11 +5,8 @@
 import inspect
 import os
 
-import llnl.util.tty as tty
-
 import spack.pkg.builtin.openfoam as openfoam
 from spack.package import *
-from spack.version import Version
 
 
 class Additivefoam(Package):

var/spack/repos/builtin/packages/amdlibflame/package.py

@@ -202,8 +202,8 @@ def configure_args(self):
             args.append("--enable-void-return-complex")
 
         if spec.satisfies("@3.0:3.1 %aocc"):
-            """To enabled Fortran to C calling convention for
-            complex types when compiling with aocc flang"""
+            # To enable Fortran to C calling convention for complex types when compiling with
+            # aocc flang
             args.append("--enable-f2c-dotc")
 
         if spec.satisfies("@3.0.1: +ilp64"):

var/spack/repos/builtin/packages/anaconda3/package.py

@@ -6,7 +6,6 @@
 from os.path import split
 
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 
 class Anaconda3(Package):

var/spack/repos/builtin/packages/aocc/package.py

@@ -2,7 +2,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from llnl.util import tty
 
 from spack.package import *
 from spack.pkg.builtin.llvm import LlvmDetection

var/spack/repos/builtin/packages/aocl-da/package.py

@@ -5,7 +5,6 @@
 import os
 
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 
 class AoclDa(CMakePackage):

var/spack/repos/builtin/packages/apcomp/package.py

@@ -6,8 +6,6 @@
 import os
 import socket
 
-import llnl.util.tty as tty
-
 from spack.build_systems.cmake import CMakeBuilder
 from spack.package import *
 

var/spack/repos/builtin/packages/arkouda/package.py

@@ -3,8 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
-import llnl.util.tty as tty
-
 from spack.package import *
 from spack.util.environment import set_env
 

var/spack/repos/builtin/packages/ascent/package.py

@@ -9,8 +9,6 @@
 import sys
 from os import environ as env
 
-import llnl.util.tty as tty
-
 from spack.package import *
 
 

var/spack/repos/builtin/packages/bcl2fastq2/package.py

@@ -5,8 +5,6 @@
 import glob
 import os
 
-import llnl.util.tty as tty
-
 from spack.package import *
 from spack.pkg.builtin.boost import Boost
 

var/spack/repos/builtin/packages/binutils/package.py

@@ -160,8 +160,11 @@ class Binutils(AutotoolsPackage, GNUMirrorPackage):
 
     with when("platform=darwin"):
         conflicts("+gold", msg="Binutils cannot build linkers on macOS")
+        # 2.41 doesn't seem to have any problems.
         conflicts(
-            "libs=shared", when="@2.37:2.40", msg="https://github.com/spack/spack/issues/35817"
+            "libs=shared",
+            when="@2.37:2.40,2.42:",
+            msg="https://github.com/spack/spack/issues/35817",
         )
 
     conflicts(

var/spack/repos/builtin/packages/bohrium/package.py

@@ -4,8 +4,6 @@
 
 import os
 
-import llnl.util.tty as tty
-
 from spack.package import *
 from spack.package_test import compare_output
 from spack.pkg.builtin.boost import Boost

var/spack/repos/builtin/packages/cdo/package.py

@@ -19,6 +19,11 @@ class Cdo(AutotoolsPackage):
 
     maintainers("skosukhin", "Try2Code")
 
+    version(
+        "2.5.0",
+        sha256="e865c05c1b52fd76b80e33421554db81b38b75210820bdc40e8690f4552f68e2",
+        url="https://code.mpimet.mpg.de/attachments/download/29786/cdo-2.5.0.tar.gz",
+    )
     version(
         "2.4.4",
         sha256="49f50bd18dacd585e9518cfd4f55548f692426edfb3b27ddcd1c653eab53d063",

var/spack/repos/builtin/packages/charmpp/package.py

@@ -396,7 +396,7 @@ def install(self, spec, prefix):
                         copy(filepath, tmppath)
                         os.remove(filepath)
                         os.rename(tmppath, filepath)
-                    except (IOError, OSError):
+                    except OSError:
                         pass
 
         tmp_path = join_path(builddir, "tmp")

var/spack/repos/builtin/packages/clingo-bootstrap/package.py

@@ -8,7 +8,6 @@
 import spack.user_environment
 from spack.package import *
 from spack.pkg.builtin.clingo import Clingo
-from spack.util.environment import EnvironmentModifications
 
 
 class ClingoBootstrap(Clingo):

var/spack/repos/builtin/packages/cmake/package.py

@@ -30,11 +30,13 @@ class Cmake(Package):
     license("BSD-3-Clause")
 
     version("master", branch="master")
+    version("3.31.5", sha256="66fb53a145648be56b46fa9e8ccade3a4d0dfc92e401e52ce76bdad1fea43d27")
     version("3.31.4", sha256="a6130bfe75f5ba5c73e672e34359f7c0a1931521957e8393a5c2922c8b0f7f25")
     version("3.31.3", sha256="fac45bc6d410b49b3113ab866074888d6c9e9dc81a141874446eb239ac38cb87")
     version("3.31.2", sha256="42abb3f48f37dbd739cdfeb19d3712db0c5935ed5c2aef6c340f9ae9114238a2")
     version("3.31.1", sha256="c4fc2a9bd0cd5f899ccb2fb81ec422e175090bc0de5d90e906dd453b53065719")
     version("3.31.0", sha256="300b71db6d69dcc1ab7c5aae61cbc1aa2778a3e00cbd918bc720203e311468c3")
+    version("3.30.7", sha256="470e44d9c7caa3bd869ef953071b84f565b5d378d0a9eccbbbcd72031f21b9de")
     version("3.30.6", sha256="a7aa25cdd8545156fe0fec95ebbd53cb2b5173a8717e227f6e8a755185c168cf")
     version("3.30.5", sha256="9f55e1a40508f2f29b7e065fa08c29f82c402fa0402da839fffe64a25755a86d")
     version("3.30.4", sha256="c759c97274f1e7aaaafcb1f0d261f9de9bf3a5d6ecb7e2df616324a46fe704b2")

var/spack/repos/builtin/packages/conda4aarch64/package.py

@@ -3,7 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 
 class Conda4aarch64(Package):

var/spack/repos/builtin/packages/conduit/package.py

@@ -8,8 +8,6 @@
 import socket
 from os import environ as env
 
-import llnl.util.tty as tty
-
 from spack.package import *
 
 

var/spack/repos/builtin/packages/cp2k/package.py

@@ -38,10 +38,11 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
     git = "https://github.com/cp2k/cp2k.git"
     list_url = "https://github.com/cp2k/cp2k/releases"
 
-    maintainers("dev-zero", "mtaillefumier")
+    maintainers("dev-zero", "mtaillefumier", "RMeli", "abussy")
 
     license("GPL-2.0-or-later")
 
+    version("2025.1", sha256="65c8ad5488897b0f995919b9fa77f2aba4b61677ba1e3c19bb093d5c08a8ce1d")
     version("2024.3", sha256="a6eeee773b6b1fb417def576e4049a89a08a0ed5feffcd7f0b33c7d7b48f19ba")
     version("2024.2", sha256="cc3e56c971dee9e89b705a1103765aba57bf41ad39a11c89d3de04c8b8cdf473")
     version("2024.1", sha256="a7abf149a278dfd5283dc592a2c4ae803b37d040df25d62a5e35af5c4557668f")
@@ -115,7 +116,9 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
     )
     variant("pytorch", default=False, description="Enable libtorch support")
     variant("quip", default=False, description="Enable quip support")
+    variant("dftd4", when="@2024.2:", default=False, description="Enable DFT-D4 support")
     variant("mpi_f08", default=False, description="Use MPI F08 module")
+    variant("smeagol", default=False, description="Enable libsmeagol support", when="@2025.2:")
 
     variant(
         "enable_regtests",
@@ -260,6 +263,8 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
         depends_on("plumed+mpi", when="+mpi")
         depends_on("plumed~mpi", when="~mpi")
 
+    depends_on("libsmeagol", when="+smeagol")
+
     # while we link statically against PEXSI, its own deps may be linked in
     # dynamically, therefore can't set this as pure build-type dependency.
     depends_on("pexsi+fortran@0.10.0:", when="+pexsi")
@@ -290,6 +295,8 @@ class Cp2k(MakefilePackage, CMakePackage, CudaPackage, ROCmPackage):
 
     depends_on("spglib", when="+spglib")
 
+    depends_on("dftd4@3.6.0: build_system=cmake", when="+dftd4")
+
     with when("build_system=cmake"):
         depends_on("cmake@3.22:", type="build")
 
@@ -621,6 +628,18 @@ def edit(self, pkg, spec, prefix):
             ldflags += [spglib.search_flags]
             libs.append(spglib.ld_flags)
 
+        if spec.satisfies("+dftd4"):
+            cppflags += ["-D__DFTD4"]
+            dftd4 = spec["dftd4"].libs
+            ldflags += [dftd4.search_flags]
+            libs.append(dftd4.ld_flags)
+
+        if spec.satisfies("+smeagol"):
+            cppflags += ["-D__SMEAGOL"]
+            smeagol = spec["libsmeagol"].libs
+            ldflags += [smeagol.search_flags]
+            libs.append(smeagol.ld_flags)
+
         cc = spack_cc if "~mpi" in spec else spec["mpi"].mpicc
         cxx = spack_cxx if "~mpi" in spec else spec["mpi"].mpicxx
         fc = spack_fc if "~mpi" in spec else spec["mpi"].mpifc
@@ -763,8 +782,8 @@ def edit(self, pkg, spec, prefix):
                     "Point environment variable LIBSMM_PATH to "
                     "the absolute path of the libsmm.a file"
                 )
-            except IOError:
-                raise IOError(
+            except OSError:
+                raise OSError(
                     "The file LIBSMM_PATH pointed to does not "
                     "exist. Note that it must be absolute path."
                 )
@@ -994,7 +1013,9 @@ def cmake_args(self):
             self.define_from_variant("CP2K_USE_VORI", "libvori"),
             self.define_from_variant("CP2K_USE_SPLA", "spla"),
             self.define_from_variant("CP2K_USE_QUIP", "quip"),
+            self.define_from_variant("CP2K_USE_DFTD4", "dftd4"),
             self.define_from_variant("CP2K_USE_MPI_F08", "mpi_f08"),
+            self.define_from_variant("CP2K_USE_LIBSMEAGOL", "smeagol"),
         ]
 
         # we force the use elpa openmp threading support. might need to be revisited though

var/spack/repos/builtin/packages/cuda/package.py

@@ -7,8 +7,6 @@
 import re
 from glob import glob
 
-import llnl.util.tty as tty
-
 from spack.package import *
 
 # FIXME Remove hack for polymorphic versions
@@ -741,7 +739,7 @@ def install(self, spec, prefix):
                 os.remove("/tmp/cuda-installer.log")
             except OSError:
                 if spec.satisfies("@10.1:"):
-                    tty.die(
+                    raise InstallError(
                         "The cuda installer will segfault due to the "
                         "presence of /tmp/cuda-installer.log "
                         "please remove the file and try again "

var/spack/repos/builtin/packages/dray/package.py

@@ -5,8 +5,6 @@
 import os
 import socket
 
-import llnl.util.tty as tty
-
 from spack.build_systems.cmake import CMakeBuilder
 from spack.package import *
 

var/spack/repos/builtin/packages/dyninst/package.py

@@ -63,8 +63,9 @@ class Dyninst(CMakePackage):
 
     variant("stat_dysect", default=False, description="Patch for STAT's DySectAPI")
 
-    boost_libs = "+atomic+chrono+date_time+filesystem+system+thread+timer"
-    "+container+random+exception"
+    boost_libs = (
+        "+atomic+chrono+date_time+filesystem+system+thread+timer+container+random+exception"
+    )
 
     depends_on("boost@1.61.0:" + boost_libs, when="@10.1.0:")
     depends_on("boost@1.61.0:1.69" + boost_libs, when="@:10.0")

var/spack/repos/builtin/packages/elemental/package.py

@@ -150,7 +150,7 @@ def cmake_args(self):
                     ),
                     "-DCUSTOM_BLAS_SUFFIX:BOOL=TRUE",
                 ]
-            ),
+            )
             if spec.satisfies("+scalapack"):
                 args.extend(
                     [
@@ -159,7 +159,7 @@ def cmake_args(self):
                         ),
                         "-DCUSTOM_LAPACK_SUFFIX:BOOL=TRUE",
                     ]
-                ),
+                )
         else:
             math_libs = spec["lapack"].libs + spec["blas"].libs
 

var/spack/repos/builtin/packages/embree/package.py

@@ -80,7 +80,7 @@ def cmake_args(self):
             avx512_suffix = ""
             if spec.satisfies("@:3.12"):
                 avx512_suffix = "SKX"
-            args.append(self.define("EMBREE_ISA_AVX512" + avx512_suffix, True)),
+            args.append(self.define("EMBREE_ISA_AVX512" + avx512_suffix, True))
             if spec.satisfies("%gcc@:7"):
                 # remove unsupported -mprefer-vector-width=256, otherwise copied
                 # from common/cmake/gnu.cmake

var/spack/repos/builtin/packages/fasta/package.py

@@ -41,7 +41,7 @@ def makefile_name(self):
         elif self.spec.satisfies("platform=linux target=x86_64:"):
             name = "Makefile.linux64_sse2"
         else:
-            tty.die(
+            raise InstallError(
                 """Unsupported platform/target, must be
 Darwin (assumes 64-bit)
 Linux x86_64

var/spack/repos/builtin/packages/fmt/package.py

@@ -118,12 +118,7 @@ def cmake_args(self):
             args.append("-DBUILD_SHARED_LIBS=ON")
 
         if spec.satisfies("+pic"):
-            args.extend(
-                [
-                    "-DCMAKE_C_FLAGS={0}".format(self.compiler.cc_pic_flag),
-                    "-DCMAKE_CXX_FLAGS={0}".format(self.compiler.cxx_pic_flag),
-                ]
-            )
+            args.append(self.define("CMAKE_POSITION_INDEPENDENT_CODE", True))
 
         args.append("-DCMAKE_CXX_STANDARD={0}".format(spec.variants["cxxstd"].value))
         # Require standard at configure time to guarantee the

var/spack/repos/builtin/packages/foam-extend/package.py

@@ -32,8 +32,6 @@
 import os
 import re
 
-import llnl.util.tty as tty
-
 from spack.package import *
 from spack.pkg.builtin.openfoam import (
     OpenfoamArch,
@@ -41,7 +39,6 @@
     rewrite_environ_files,
     write_environ,
 )
-from spack.util.environment import EnvironmentModifications
 
 
 class FoamExtend(Package):
@@ -173,7 +170,7 @@ def setup_run_environment(self, env):
         if minimal:
             # pre-build or minimal environment
             tty.info("foam-extend minimal env {0}".format(self.prefix))
-            env.set("FOAM_INST_DIR", os.path.dirname(self.projectdir)),
+            env.set("FOAM_INST_DIR", os.path.dirname(self.projectdir))
             env.set("FOAM_PROJECT_DIR", self.projectdir)
             env.set("WM_PROJECT_DIR", self.projectdir)
             for d in ["wmake", self.archbin]:  # bin added automatically

var/spack/repos/builtin/packages/freeipmi/package.py

@@ -2,7 +2,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import llnl.util.tty as tty
 
 from spack.package import *
 

var/spack/repos/builtin/packages/freesurfer/package.py

@@ -6,7 +6,6 @@
 import os
 
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 
 class Freesurfer(Package):

var/spack/repos/builtin/packages/fsl/package.py

@@ -7,7 +7,6 @@
 
 import spack.util.environment
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 
 class Fsl(Package, CudaPackage):

var/spack/repos/builtin/packages/gasnet/package.py

@@ -3,8 +3,8 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
+import warnings
 
-import spack.main
 from spack.package import *
 
 
@@ -147,7 +147,7 @@ def install(self, spec, prefix):
                 git = which("git")
                 git("describe", "--long", "--always", output="version.git")
             except ProcessError:
-                spack.main.send_warning_to_tty("Omitting version stamp due to git error")
+                warnings.warn("Omitting version stamp due to git error")
 
         # The GASNet-EX library has a highly multi-dimensional configure space,
         # to accomodate the varying behavioral requirements of each client runtime.

var/spack/repos/builtin/packages/gaussian-view/package.py

@@ -5,8 +5,6 @@
 
 import os
 
-import llnl.util.tty as tty
-
 import spack.tengine
 from spack.package import *
 

var/spack/repos/builtin/packages/gcc-runtime/package.py

@@ -8,8 +8,6 @@
 
 from macholib import MachO, mach_o
 
-from llnl.util import tty
-
 from spack.package import *
 from spack.util.elf import delete_needed_from_elf, parse_elf
 

var/spack/repos/builtin/packages/gcc/package.py

@@ -7,7 +7,6 @@
 
 import archspec.cpu
 
-import llnl.util.tty as tty
 from llnl.util.symlink import readlink
 
 import spack.compiler
@@ -801,11 +800,6 @@ def configure_args(self):
                     "--with-as=" + binutils.join("as"),
                 ]
             )
-        elif spec.satisfies("%apple-clang@15:"):
-            # https://github.com/iains/gcc-darwin-arm64/issues/117
-            # https://github.com/iains/gcc-12-branch/issues/22
-            # https://github.com/iains/gcc-13-branch/issues/8
-            options.append("--with-ld=/Library/Developer/CommandLineTools/usr/bin/ld-classic")
 
         # enable_bootstrap
         if spec.satisfies("+bootstrap"):

var/spack/repos/builtin/packages/gem5/package.py

@@ -3,7 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
-import spack.config
 from spack.package import *
 
 
@@ -64,7 +63,7 @@ def install(self, spec, prefix):
     def build_args(self, spec, prefix):
         args = []
         args.append("build/ALL/gem5.opt")
-        args.append(f"-j{spack.config.determine_number_of_jobs(parallel=True)}")
+        args.append(f"-j{determine_number_of_jobs(parallel=True)}")
         args.append("--ignore-style")
 
         return args

var/spack/repos/builtin/packages/genie/package.py

@@ -6,7 +6,6 @@
 import os
 
 from spack.package import *
-from spack.version import Version
 
 
 class Genie(Package):

var/spack/repos/builtin/packages/gromacs/package.py

@@ -4,8 +4,6 @@
 
 import os
 
-import llnl.util.filesystem as fs
-
 import spack.build_systems.cmake
 from spack.package import *
 
@@ -660,7 +658,7 @@ def build_test_binaries(self):
         not be intended with ``--test``.
         """
         if self.pkg.run_tests:
-            with fs.working_dir(self.build_directory):
+            with working_dir(self.build_directory):
                 make("tests")
 
     def check(self):
@@ -669,7 +667,7 @@ def check(self):
         Override the standard CMakeBuilder behavior. GROMACS has both `test`
         and `check` targets, but we are only interested in the latter.
         """
-        with fs.working_dir(self.build_directory):
+        with working_dir(self.build_directory):
             if self.generator == "Unix Makefiles":
                 make("check")
             elif self.generator == "Ninja":

var/spack/repos/builtin/packages/gurobi/package.py

@@ -53,7 +53,7 @@ def patch(self):
     def setup_run_environment(self, env):
         env.set("GUROBI_HOME", self.prefix)
         env.set("GRB_LICENSE_FILE", join_path(self.prefix, "gurobi.lic"))
-        env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib),
+        env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib)
 
     def install(self, spec, prefix):
         install_tree("linux64", prefix)

var/spack/repos/builtin/packages/h5bench/package.py

@@ -74,8 +74,8 @@ def setup_build_tests(self):
         filter_file("mpirun", f"{launcher}", filename)
         filter_file(r"-n 2", "-n 1 --timeout 240", filename)
 
-        """Copy the example source files after the package is installed to an
-        install test subdirectory for use during `spack test run`."""
+        # Copy the example source files after the package is installed to an
+        # install test subdirectory for use during `spack test run`.
         cache_extra_test_sources(self, ["tests", "samples"])
 
     def mpi_launcher(self):

var/spack/repos/builtin/packages/hdf5/package.py

@@ -8,7 +8,6 @@
 import sys
 
 import llnl.util.lang
-import llnl.util.tty as tty
 
 from spack.package import *
 

var/spack/repos/builtin/packages/heasoft/package.py

@@ -4,10 +4,7 @@
 
 import os
 
-import llnl.util.tty as tty
-
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 
 class Heasoft(AutotoolsPackage):

var/spack/repos/builtin/packages/hip/package.py

@@ -8,7 +8,6 @@
 import spack.build_environment
 from spack.hooks.sbang import filter_shebang
 from spack.package import *
-from spack.util.prefix import Prefix
 
 
 class Hip(CMakePackage):
@@ -667,12 +666,12 @@ def cmake_args(self):
         if self.spec.satisfies("@5.6.0:"):
             args.append(self.define("ROCCLR_PATH", self.stage.source_path + "/clr/rocclr"))
             args.append(self.define("AMD_OPENCL_PATH", self.stage.source_path + "/clr/opencl"))
-            args.append(self.define("CLR_BUILD_HIP", True)),
-            args.append(self.define("CLR_BUILD_OCL", False)),
+            args.append(self.define("CLR_BUILD_HIP", True))
+            args.append(self.define("CLR_BUILD_OCL", False))
         if self.spec.satisfies("@5.6:5.7"):
-            args.append(self.define("HIPCC_BIN_DIR", self.stage.source_path + "/hipcc/bin")),
+            args.append(self.define("HIPCC_BIN_DIR", self.stage.source_path + "/hipcc/bin"))
         if self.spec.satisfies("@6.0:"):
-            args.append(self.define("HIPCC_BIN_DIR", self.spec["hipcc"].prefix.bin)),
+            args.append(self.define("HIPCC_BIN_DIR", self.spec["hipcc"].prefix.bin))
         return args
 
     test_src_dir_old = "samples"

var/spack/repos/builtin/packages/hipblaslt/package.py

@@ -29,6 +29,7 @@ class Hipblaslt(CMakePackage):
 
     depends_on("c", type="build")
     depends_on("cxx", type="build")
+    depends_on("cmake@3.25.2:", type="build", when="@6.2.0:")
 
     amdgpu_targets = ROCmPackage.amdgpu_targets
 

var/spack/repos/builtin/packages/hpctoolkit/package.py

@@ -6,8 +6,6 @@
 import os
 import tempfile
 
-import llnl.util.tty as tty
-
 import spack.build_systems.autotools
 import spack.build_systems.meson
 from spack.package import *
@@ -118,6 +116,12 @@ class Hpctoolkit(AutotoolsPackage, MesonPackage):
         when="build_system=autotools",
     )
     variant("viewer", default=True, description="Include hpcviewer.")
+    variant(
+        "docs",
+        default=False,
+        description="Include extra documentation (user's manual)",
+        when="@develop",
+    )
 
     variant(
         "python", default=False, description="Support unwinding Python source.", when="@2023.03:"
@@ -185,6 +189,10 @@ class Hpctoolkit(AutotoolsPackage, MesonPackage):
     depends_on("zlib-api")
     depends_on("zlib+shared", when="^[virtuals=zlib-api] zlib")
 
+    depends_on("py-docutils", type="build", when="@develop")
+    depends_on("py-sphinx", type="build", when="+docs")
+    depends_on("py-myst-parser@0.19:", type="build", when="+docs")
+
     depends_on("cuda", when="+cuda")
     depends_on("oneapi-level-zero", when="+level_zero")
     depends_on("oneapi-igc", when="+gtpin")
@@ -402,6 +410,8 @@ def meson_args(self):
         spec = self.spec
 
         args = [
+            "-Dmanpages=enabled",
+            "-Dmanual=" + ("enabled" if spec.satisfies("+docs") else "disabled"),
             "-Dhpcprof_mpi=" + ("enabled" if spec.satisfies("+mpi") else "disabled"),
             "-Dpython=" + ("enabled" if spec.satisfies("+python") else "disabled"),
             "-Dpapi=" + ("enabled" if spec.satisfies("+papi") else "disabled"),

var/spack/repos/builtin/packages/hpx-kokkos/package.py

@@ -2,8 +2,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import llnl.util.filesystem as fs
-
 from spack.package import *
 
 
@@ -95,7 +93,7 @@ def cmake_args(self):
 
     def check(self):
         if self.run_tests:
-            with fs.working_dir(self.build_directory):
+            with working_dir(self.build_directory):
                 cmake("--build", ".", "--target", "tests")
                 cmake("--build", ".", "--target", "benchmarks")
                 ctest("--output-on-failure")

var/spack/repos/builtin/packages/intel-oneapi-compilers/package.py

@@ -7,7 +7,6 @@
 
 from spack.build_environment import dso_suffix
 from spack.package import *
-from spack.util.environment import EnvironmentModifications
 
 versions = [
     {

var/spack/repos/builtin/packages/intel-oneapi-runtime/package.py

@@ -3,8 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
 
-from llnl.util import tty
-
 from spack.package import *
 from spack.pkg.builtin.gcc_runtime import get_elf_libraries
 

var/spack/repos/builtin/packages/intel/package.py

@@ -3,8 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import re
 
-import llnl.util.tty as tty
-
 import spack.compiler
 from spack.package import *
 

var/spack/repos/builtin/packages/jdk/package.py

@@ -6,7 +6,6 @@
 import re
 
 from spack.package import *
-from spack.util.prefix import Prefix
 
 
 class Jdk(Package):

var/spack/repos/builtin/packages/julia/package.py

@@ -6,7 +6,6 @@
 import os
 
 from spack.package import *
-from spack.version import ver
 
 
 def get_best_target(microarch, compiler_name, compiler_version):

var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py

@@ -20,6 +20,8 @@ class KokkosNvccWrapper(Package):
 
     license("BSD-3-Clause")
 
+    version("4.5.01", sha256="e0008c89d7f03ebbe31eb3c89d40fe529b4e4072b40331ae6b9d6599f02dff44")
+    version("4.5.00", sha256="7f7d8db54e5d2b0d4109ac6aa05732abd25b17d004cce5e21f56005952954e68")
     version("4.4.01", sha256="3f7096d17eaaa4004c7497ac082bf1ae3ff47b5104149e54af021a89414c3682")
     version("4.4.00", sha256="c638980cb62c34969b8c85b73e68327a2cb64f763dd33e5241f5fd437170205a")
     version("4.3.01", sha256="5998b7c732664d6b5e219ccc445cd3077f0e3968b4be480c29cd194b4f45ec70")