petsc: fix compilers listed in pkgconfig/petsc.pc (#48201)

* petsc: fix compilers listed in pkgconfig/petsc.pc

* Also fix reconfigure*.py

.github/workflows/bootstrap.yml

@@ -161,11 +161,7 @@ jobs:
           source share/spack/setup-env.sh
           spack -d gpg list
           tree $HOME/.spack/bootstrap/store/
-      - name: Bootstrap File
-        run: |
-          source share/spack/setup-env.sh
-          spack -d python share/spack/qa/bootstrap-file.py
-          tree $HOME/.spack/bootstrap/store/
+
 
   windows:
     runs-on: "windows-latest"
@@ -196,9 +192,3 @@ jobs:
           spack -d gpg list
           ./share/spack/qa/validate_last_exit.ps1
           tree $env:userprofile/.spack/bootstrap/store/
-      - name: Bootstrap File
-        run: |
-          ./share/spack/setup-env.ps1
-          spack -d python share/spack/qa/bootstrap-file.py
-          ./share/spack/qa/validate_last_exit.ps1
-          tree $env:userprofile/.spack/bootstrap/store/

.github/workflows/unit_tests.yaml

@@ -140,7 +140,7 @@ jobs:
     - name: Install dependencies
       run: |
           dnf install -y \
-              bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
+              bzip2 curl gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
               make patch tcl unzip which xz
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
     - name: Setup repo and non-root user

lib/spack/docs/getting_started.rst

@@ -35,7 +35,7 @@ A build matrix showing which packages are working on which systems is shown belo
       .. code-block:: console
 
          apt update
-         apt install bzip2 ca-certificates file g++ gcc gfortran git gzip lsb-release patch python3 tar unzip xz-utils zstd
+         apt install bzip2 ca-certificates g++ gcc gfortran git gzip lsb-release patch python3 tar unzip xz-utils zstd
 
    .. tab-item:: RHEL
 
@@ -148,20 +148,22 @@ The first time you concretize a spec, Spack will bootstrap automatically:
    --------------------------------
    zlib@1.2.13%gcc@9.4.0+optimize+pic+shared build_system=makefile arch=linux-ubuntu20.04-icelake
 
+The default bootstrap behavior is to use pre-built binaries. You can verify the
+active bootstrap repositories with:
+
+.. command-output:: spack bootstrap list
+
 If for security concerns you cannot bootstrap ``clingo`` from pre-built
 binaries, you have to disable fetching the binaries we generated with Github Actions.
 
 .. code-block:: console
 
-   $ spack bootstrap disable github-actions-v0.4
-   ==> "github-actions-v0.4" is now disabled and will not be used for bootstrapping
-   $ spack bootstrap disable github-actions-v0.3
-   ==> "github-actions-v0.3" is now disabled and will not be used for bootstrapping
-
-You can verify that the new settings are effective with:
-
-.. command-output:: spack bootstrap list
+   $ spack bootstrap disable github-actions-v0.6
+   ==> "github-actions-v0.6" is now disabled and will not be used for bootstrapping
+   $ spack bootstrap disable github-actions-v0.5
+   ==> "github-actions-v0.5" is now disabled and will not be used for bootstrapping
 
+You can verify that the new settings are effective with ``spack bootstrap list``.
 
 .. note::
 

lib/spack/docs/requirements.txt

@@ -5,7 +5,7 @@ sphinx-rtd-theme==3.0.2
 python-levenshtein==0.26.1
 docutils==0.21.2
 pygments==2.18.0
-urllib3==2.2.3
+urllib3==2.3.0
 pytest==8.3.4
 isort==5.13.2
 black==24.10.0

lib/spack/docs/tables/system_prerequisites.csv

@@ -8,7 +8,6 @@ unzip, , , Compress/Decompress archives
 bzip2, , , Compress/Decompress archives
 xz, , , Compress/Decompress archives
 zstd, , Optional, Compress/Decompress archives
-file, , , Create/Use Buildcaches
 lsb-release, , , Linux: identify operating system version
 gnupg2, , , Sign/Verify Buildcaches
 git, , , Manage Software Repositories

lib/spack/llnl/util/lang.py

@@ -863,8 +863,10 @@ def elide_list(line_list: List[str], max_num: int = 10) -> List[str]:
 
 if sys.version_info >= (3, 9):
     PatternStr = re.Pattern[str]
+    PatternBytes = re.Pattern[bytes]
 else:
     PatternStr = typing.Pattern[str]
+    PatternBytes = typing.Pattern[bytes]
 
 
 def fnmatch_translate_multiple(named_patterns: Dict[str, str]) -> str:

lib/spack/spack/binary_distribution.py

@@ -24,13 +24,12 @@
 import urllib.request
 import warnings
 from contextlib import closing
-from typing import Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
+from typing import IO, Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
 
 import llnl.util.filesystem as fsys
 import llnl.util.lang
 import llnl.util.tty as tty
-from llnl.util.filesystem import BaseDirectoryVisitor, mkdirp, visit_directory_tree
-from llnl.util.symlink import readlink
+from llnl.util.filesystem import mkdirp
 
 import spack.caches
 import spack.config as config
@@ -54,7 +53,6 @@
 import spack.util.archive
 import spack.util.crypto
 import spack.util.file_cache as file_cache
-import spack.util.filesystem as ssys
 import spack.util.gpg
 import spack.util.parallel
 import spack.util.path
@@ -587,129 +585,11 @@ def read_buildinfo_file(prefix):
         return syaml.load(f)
 
 
-class BuildManifestVisitor(BaseDirectoryVisitor):
-    """Visitor that collects a list of files and symlinks
-    that can be checked for need of relocation. It knows how
-    to dedupe hardlinks and deal with symlinks to files and
-    directories."""
-
-    def __init__(self):
-        # Save unique identifiers of hardlinks to avoid relocating them multiple times
-        self.visited = set()
-
-        # Lists of files we will check
-        self.files = []
-        self.symlinks = []
-
-    def seen_before(self, root, rel_path):
-        stat_result = os.lstat(os.path.join(root, rel_path))
-        if stat_result.st_nlink == 1:
-            return False
-        identifier = (stat_result.st_dev, stat_result.st_ino)
-        if identifier in self.visited:
-            return True
-        else:
-            self.visited.add(identifier)
-            return False
-
-    def visit_file(self, root, rel_path, depth):
-        if self.seen_before(root, rel_path):
-            return
-        self.files.append(rel_path)
-
-    def visit_symlinked_file(self, root, rel_path, depth):
-        # Note: symlinks *can* be hardlinked, but it is unclear if
-        # symlinks can be relinked in-place (preserving inode).
-        # Therefore, we do *not* de-dupe hardlinked symlinks.
-        self.symlinks.append(rel_path)
-
-    def before_visit_dir(self, root, rel_path, depth):
-        return os.path.basename(rel_path) not in (".spack", "man")
-
-    def before_visit_symlinked_dir(self, root, rel_path, depth):
-        # Treat symlinked directories simply as symlinks.
-        self.visit_symlinked_file(root, rel_path, depth)
-        # Never recurse into symlinked directories.
-        return False
-
-
-def file_matches(path, regex):
-    with open(path, "rb") as f:
-        contents = f.read()
-    return bool(regex.search(contents))
-
-
-def get_buildfile_manifest(spec):
-    """
-    Return a data structure with information about a build, including
-    text_to_relocate, binary_to_relocate, binary_to_relocate_fullpath
-    link_to_relocate, and other, which means it doesn't fit any of previous
-    checks (and should not be relocated). We exclude docs (man) and
-    metadata (.spack). This can be used to find a particular kind of file
-    in spack, or to generate the build metadata.
-    """
-    data = {
-        "text_to_relocate": [],
-        "binary_to_relocate": [],
-        "link_to_relocate": [],
-        "other": [],
-        "binary_to_relocate_fullpath": [],
-        "hardlinks_deduped": True,
-    }
-
-    # Guard against filesystem footguns of hardlinks and symlinks by using
-    # a visitor to retrieve a list of files and symlinks, so we don't have
-    # to worry about hardlinks of symlinked dirs and what not.
-    visitor = BuildManifestVisitor()
-    root = spec.prefix
-    visit_directory_tree(root, visitor)
-
-    # Collect a list of prefixes for this package and it's dependencies, Spack will
-    # look for them to decide if text file needs to be relocated or not
-    prefixes = [d.prefix for d in spec.traverse(root=True, deptype="all") if not d.external]
-    prefixes.append(spack.hooks.sbang.sbang_install_path())
-    prefixes.append(str(spack.store.STORE.layout.root))
-
-    # Create a giant regex that matches all prefixes
-    regex = utf8_paths_to_single_binary_regex(prefixes)
-
-    # Symlinks.
-
-    # Obvious bugs:
-    #   1. relative links are not relocated.
-    #   2. paths are used as strings.
-    for rel_path in visitor.symlinks:
-        abs_path = os.path.join(root, rel_path)
-        link = readlink(abs_path)
-        if os.path.isabs(link) and link.startswith(spack.store.STORE.layout.root):
-            data["link_to_relocate"].append(rel_path)
-
-    # Non-symlinks.
-    for rel_path in visitor.files:
-        abs_path = os.path.join(root, rel_path)
-        m_type, m_subtype = ssys.mime_type(abs_path)
-
-        if relocate.needs_binary_relocation(m_type, m_subtype):
-            # Why is this branch not part of needs_binary_relocation? :(
-            if (
-                (
-                    m_subtype in ("x-executable", "x-sharedlib", "x-pie-executable")
-                    and sys.platform != "darwin"
-                )
-                or (m_subtype in ("x-mach-binary") and sys.platform == "darwin")
-                or (not rel_path.endswith(".o"))
-            ):
-                data["binary_to_relocate"].append(rel_path)
-                data["binary_to_relocate_fullpath"].append(abs_path)
-                continue
-
-        elif relocate.needs_text_relocation(m_type, m_subtype) and file_matches(abs_path, regex):
-            data["text_to_relocate"].append(rel_path)
-            continue
-
-        data["other"].append(abs_path)
-
-    return data
+def file_matches(f: IO[bytes], regex: llnl.util.lang.PatternBytes) -> bool:
+    try:
+        return bool(regex.search(f.read()))
+    finally:
+        f.seek(0)
 
 
 def deps_to_relocate(spec):
@@ -742,17 +622,15 @@ def deps_to_relocate(spec):
 
 def get_buildinfo_dict(spec):
     """Create metadata for a tarball"""
-    manifest = get_buildfile_manifest(spec)
-
     return {
         "sbang_install_path": spack.hooks.sbang.sbang_install_path(),
         "buildpath": spack.store.STORE.layout.root,
         "spackprefix": spack.paths.prefix,
         "relative_prefix": os.path.relpath(spec.prefix, spack.store.STORE.layout.root),
-        "relocate_textfiles": manifest["text_to_relocate"],
-        "relocate_binaries": manifest["binary_to_relocate"],
-        "relocate_links": manifest["link_to_relocate"],
-        "hardlinks_deduped": manifest["hardlinks_deduped"],
+        # "relocate_textfiles": [],
+        # "relocate_binaries": [],
+        # "relocate_links": [],
+        "hardlinks_deduped": True,
         "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in deps_to_relocate(spec)},
     }
 
@@ -1042,7 +920,55 @@ def generate_key_index(key_prefix: str, tmpdir: str) -> None:
         ) from e
 
 
-def tarfile_of_spec_prefix(tar: tarfile.TarFile, prefix: str) -> None:
+class FileTypes:
+    BINARY = 0
+    TEXT = 1
+    UNKNOWN = 2
+
+
+NOT_ISO8859_1_TEXT = re.compile(b"[\x00\x7F-\x9F]")
+
+
+def file_type(f: IO[bytes]) -> int:
+    try:
+        # first check if this is an ELF or mach-o binary.
+        magic = f.read(8)
+        if len(magic) < 8:
+            return FileTypes.UNKNOWN
+        elif relocate.is_elf_magic(magic) or relocate.is_macho_magic(magic):
+            return FileTypes.BINARY
+
+        f.seek(0)
+
+        # Then try utf-8, which has a fast exponential decay in false positive rate with file size.
+        # Use chunked reads for fast early exit.
+        f_txt = io.TextIOWrapper(f, encoding="utf-8", errors="strict")
+        try:
+            while f_txt.read(1024):
+                pass
+            return FileTypes.TEXT
+        except UnicodeError:
+            f_txt.seek(0)
+            pass
+        finally:
+            f_txt.detach()
+        # Finally try iso-8859-1 heuristically. In Python, all possible 256 byte values are valid.
+        # We classify it as text if it does not contain any control characters / null bytes.
+        data = f.read(1024)
+        while data:
+            if NOT_ISO8859_1_TEXT.search(data):
+                break
+            data = f.read(1024)
+        else:
+            return FileTypes.TEXT
+        return FileTypes.UNKNOWN
+    finally:
+        f.seek(0)
+
+
+def tarfile_of_spec_prefix(
+    tar: tarfile.TarFile, prefix: str, prefixes_to_relocate: List[str]
+) -> dict:
     """Create a tarfile of an install prefix of a spec. Skips existing buildinfo file.
 
     Args:
@@ -1058,6 +984,33 @@ def tarfile_of_spec_prefix(tar: tarfile.TarFile, prefix: str) -> None:
     except OSError:
         skip = lambda entry: False
 
+    binary_regex = utf8_paths_to_single_binary_regex(prefixes_to_relocate)
+
+    relocate_binaries = []
+    relocate_links = []
+    relocate_textfiles = []
+
+    # use callbacks to add files and symlinks, so we can register which files need relocation upon
+    # extraction.
+    def add_file(tar: tarfile.TarFile, info: tarfile.TarInfo, path: str):
+        with open(path, "rb") as f:
+            relpath = os.path.relpath(path, prefix)
+            # no need to relocate anything in the .spack directory
+            if relpath.split(os.sep, 1)[0] == ".spack":
+                tar.addfile(info, f)
+                return
+            f_type = file_type(f)
+            if f_type == FileTypes.BINARY:
+                relocate_binaries.append(os.path.relpath(path, prefix))
+            elif f_type == FileTypes.TEXT and file_matches(f, binary_regex):
+                relocate_textfiles.append(os.path.relpath(path, prefix))
+            tar.addfile(info, f)
+
+    def add_symlink(tar: tarfile.TarFile, info: tarfile.TarInfo, path: str):
+        if os.path.isabs(info.linkname) and binary_regex.match(info.linkname.encode("utf-8")):
+            relocate_links.append(os.path.relpath(path, prefix))
+        tar.addfile(info)
+
     spack.util.archive.reproducible_tarfile_from_prefix(
         tar,
         prefix,
@@ -1065,29 +1018,51 @@ def tarfile_of_spec_prefix(tar: tarfile.TarFile, prefix: str) -> None:
         # used in runtimes like AWS lambda.
         include_parent_directories=True,
         skip=skip,
+        add_file=add_file,
+        add_symlink=add_symlink,
+    )
+
+    return {
+        "relocate_binaries": relocate_binaries,
+        "relocate_links": relocate_links,
+        "relocate_textfiles": relocate_textfiles,
+    }
+
+
+def create_tarball(spec: spack.spec.Spec, tarfile_path: str) -> Tuple[str, str]:
+    """Create a tarball of a spec and return the checksums of the compressed tarfile and the
+    uncompressed tarfile."""
+    return _do_create_tarball(
+        tarfile_path,
+        spec.prefix,
+        buildinfo=get_buildinfo_dict(spec),
+        prefixes_to_relocate=prefixes_to_relocate(spec),
     )
 
 
-def _do_create_tarball(tarfile_path: str, binaries_dir: str, buildinfo: dict):
+def _do_create_tarball(
+    tarfile_path: str, prefix: str, buildinfo: dict, prefixes_to_relocate: List[str]
+) -> Tuple[str, str]:
     with spack.util.archive.gzip_compressed_tarfile(tarfile_path) as (
         tar,
-        inner_checksum,
-        outer_checksum,
+        tar_gz_checksum,
+        tar_checksum,
     ):
         # Tarball the install prefix
-        tarfile_of_spec_prefix(tar, binaries_dir)
+        files_to_relocate = tarfile_of_spec_prefix(tar, prefix, prefixes_to_relocate)
+        buildinfo.update(files_to_relocate)
 
         # Serialize buildinfo for the tarball
         bstring = syaml.dump(buildinfo, default_flow_style=True).encode("utf-8")
         tarinfo = tarfile.TarInfo(
-            name=spack.util.archive.default_path_to_name(buildinfo_file_name(binaries_dir))
+            name=spack.util.archive.default_path_to_name(buildinfo_file_name(prefix))
         )
         tarinfo.type = tarfile.REGTYPE
         tarinfo.size = len(bstring)
         tarinfo.mode = 0o644
         tar.addfile(tarinfo, io.BytesIO(bstring))
 
-    return inner_checksum.hexdigest(), outer_checksum.hexdigest()
+    return tar_gz_checksum.hexdigest(), tar_checksum.hexdigest()
 
 
 class ExistsInBuildcache(NamedTuple):
@@ -1137,6 +1112,13 @@ def _exists_in_buildcache(spec: spack.spec.Spec, tmpdir: str, out_url: str) -> E
     return ExistsInBuildcache(signed, unsigned, tarball)
 
 
+def prefixes_to_relocate(spec):
+    prefixes = [s.prefix for s in deps_to_relocate(spec)]
+    prefixes.append(spack.hooks.sbang.sbang_install_path())
+    prefixes.append(str(spack.store.STORE.layout.root))
+    return prefixes
+
+
 def _url_upload_tarball_and_specfile(
     spec: spack.spec.Spec,
     tmpdir: str,
@@ -1146,7 +1128,7 @@ def _url_upload_tarball_and_specfile(
 ):
     files = BuildcacheFiles(spec, tmpdir, out_url)
     tarball = files.local_tarball()
-    checksum, _ = _do_create_tarball(tarball, spec.prefix, get_buildinfo_dict(spec))
+    checksum, _ = create_tarball(spec, tarball)
     spec_dict = spec.to_dict(hash=ht.dag_hash)
     spec_dict["buildcache_layout_version"] = CURRENT_BUILD_CACHE_LAYOUT_VERSION
     spec_dict["binary_cache_checksum"] = {"hash_algorithm": "sha256", "hash": checksum}
@@ -1470,13 +1452,11 @@ def _oci_push_pkg_blob(
     filename = os.path.join(tmpdir, f"{spec.dag_hash()}.tar.gz")
 
     # Create an oci.image.layer aka tarball of the package
-    compressed_tarfile_checksum, tarfile_checksum = _do_create_tarball(
-        filename, spec.prefix, get_buildinfo_dict(spec)
-    )
+    tar_gz_checksum, tar_checksum = create_tarball(spec, filename)
 
     blob = spack.oci.oci.Blob(
-        Digest.from_sha256(compressed_tarfile_checksum),
-        Digest.from_sha256(tarfile_checksum),
+        Digest.from_sha256(tar_gz_checksum),
+        Digest.from_sha256(tar_checksum),
         os.path.getsize(filename),
     )
 
@@ -2435,6 +2415,14 @@ def _tar_strip_component(tar: tarfile.TarFile, prefix: str):
         yield m
 
 
+def extract_buildcache_tarball(tarfile_path: str, destination: str) -> None:
+    with closing(tarfile.open(tarfile_path, "r")) as tar:
+        # Remove common prefix from tarball entries and directly extract them to the install dir.
+        tar.extractall(
+            path=destination, members=_tar_strip_component(tar, prefix=_ensure_common_prefix(tar))
+        )
+
+
 def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
     """
     extract binary tarball for given package into install area
@@ -2504,12 +2492,7 @@ def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
                 tarfile_path, size, contents, "sha256", expected, local_checksum
             )
     try:
-        with closing(tarfile.open(tarfile_path, "r")) as tar:
-            # Remove install prefix from tarfil to extract directly into spec.prefix
-            tar.extractall(
-                path=spec.prefix,
-                members=_tar_strip_component(tar, prefix=_ensure_common_prefix(tar)),
-            )
+        extract_buildcache_tarball(tarfile_path, destination=spec.prefix)
     except Exception:
         shutil.rmtree(spec.prefix, ignore_errors=True)
         _delete_staged_downloads(download_result)

lib/spack/spack/bootstrap/__init__.py

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

lib/spack/spack/bootstrap/core.py

@@ -481,19 +481,6 @@ def ensure_gpg_in_path_or_raise() -> None:
     )
 
 
-def file_root_spec() -> str:
-    """Return the root spec used to bootstrap file"""
-    root_spec_name = "win-file" if IS_WINDOWS else "file"
-    return _root_spec(root_spec_name)
-
-
-def ensure_file_in_path_or_raise() -> None:
-    """Ensure file is in the PATH or raise"""
-    return ensure_executables_in_path_or_raise(
-        executables=["file"], abstract_spec=file_root_spec()
-    )
-
-
 def patchelf_root_spec() -> str:
     """Return the root spec used to bootstrap patchelf"""
     # 0.13.1 is the last version not to require C++17.
@@ -577,15 +564,13 @@ def ensure_core_dependencies() -> None:
     """Ensure the presence of all the core dependencies."""
     if sys.platform.lower() == "linux":
         ensure_patchelf_in_path_or_raise()
-    elif sys.platform == "win32":
-        ensure_file_in_path_or_raise()
     ensure_gpg_in_path_or_raise()
     ensure_clingo_importable_or_raise()
 
 
 def all_core_root_specs() -> List[str]:
     """Return a list of all the core root specs that may be used to bootstrap Spack"""
-    return [clingo_root_spec(), gnupg_root_spec(), patchelf_root_spec(), file_root_spec()]
+    return [clingo_root_spec(), gnupg_root_spec(), patchelf_root_spec()]
 
 
 def bootstrapping_sources(scope: Optional[str] = None):

lib/spack/spack/bootstrap/status.py

@@ -3,8 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Query the status of bootstrapping on this machine"""
-import platform
-from typing import List, Optional, Sequence, Tuple, Union
+import sys
+from typing import Dict, List, Optional, Sequence, Tuple, Union
 
 import spack.util.executable
 
@@ -72,7 +72,7 @@ def _core_requirements() -> List[RequiredResponseType]:
         "bzip2": _missing("bzip2", "required to compress/decompress code archives"),
         "git": _missing("git", "required to fetch/manage git repositories"),
     }
-    if platform.system().lower() == "linux":
+    if sys.platform == "linux":
         _core_system_exes["xz"] = _missing("xz", "required to compress/decompress code archives")
 
     # Executables that are not bootstrapped yet
@@ -87,17 +87,16 @@ def _core_requirements() -> List[RequiredResponseType]:
 
 
 def _buildcache_requirements() -> List[RequiredResponseType]:
-    _buildcache_exes = {
-        "file": _missing("file", "required to analyze files for buildcaches", system_only=False),
-        ("gpg2", "gpg"): _missing("gpg2", "required to sign/verify buildcaches", False),
+    _buildcache_exes: Dict[ExecutablesType, str] = {
+        ("gpg2", "gpg"): _missing("gpg2", "required to sign/verify buildcaches", False)
     }
-    if platform.system().lower() == "darwin":
+    if sys.platform == "darwin":
         _buildcache_exes["otool"] = _missing("otool", "required to relocate binaries")
 
     # Executables that are not bootstrapped yet
     result = [_required_system_executable(exe, msg) for exe, msg in _buildcache_exes.items()]
 
-    if platform.system().lower() == "linux":
+    if sys.platform == "linux":
         result.append(
             _required_executable(
                 "patchelf",

lib/spack/spack/cmd/bootstrap.py

@@ -29,7 +29,7 @@
 
 
 # Tarball to be downloaded if binary packages are requested in a local mirror
-BINARY_TARBALL = "https://github.com/spack/spack-bootstrap-mirrors/releases/download/v0.4/bootstrap-buildcache.tar.gz"
+BINARY_TARBALL = "https://github.com/spack/spack-bootstrap-mirrors/releases/download/v0.6/bootstrap-buildcache.tar.gz"
 
 #: Subdirectory where to create the mirror
 LOCAL_MIRROR_DIR = "bootstrap_cache"
@@ -51,9 +51,9 @@
     },
 }
 
-CLINGO_JSON = "$spack/share/spack/bootstrap/github-actions-v0.4/clingo.json"
-GNUPG_JSON = "$spack/share/spack/bootstrap/github-actions-v0.4/gnupg.json"
-PATCHELF_JSON = "$spack/share/spack/bootstrap/github-actions-v0.4/patchelf.json"
+CLINGO_JSON = "$spack/share/spack/bootstrap/github-actions-v0.6/clingo.json"
+GNUPG_JSON = "$spack/share/spack/bootstrap/github-actions-v0.6/gnupg.json"
+PATCHELF_JSON = "$spack/share/spack/bootstrap/github-actions-v0.6/patchelf.json"
 
 # Metadata for a generated source mirror
 SOURCE_METADATA = {

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

@@ -529,6 +529,7 @@ def __call__(self, parser, namespace, values, option_string):
         # the const from the constructor or a value from the CLI.
         # Note that this is only called if the argument is actually
         # specified on the command line.
+        spack.config.CONFIG.ensure_scope_ordering()
         spack.config.set(self.config_path, self.const, scope="command_line")
 
 

lib/spack/spack/config.py

@@ -431,6 +431,19 @@ def ensure_unwrapped(self) -> "Configuration":
         """Ensure we unwrap this object from any dynamic wrapper (like Singleton)"""
         return self
 
+    def highest(self) -> ConfigScope:
+        """Scope with highest precedence"""
+        return next(reversed(self.scopes.values()))  # type: ignore
+
+    @_config_mutator
+    def ensure_scope_ordering(self):
+        """Ensure that scope order matches documented precedent"""
+        # FIXME: We also need to consider that custom configurations and other orderings
+        # may not be preserved correctly
+        if "command_line" in self.scopes:
+            # TODO (when dropping python 3.6): self.scopes.move_to_end
+            self.scopes["command_line"] = self.remove_scope("command_line")
+
     @_config_mutator
     def push_scope(self, scope: ConfigScope) -> None:
         """Add a higher precedence scope to the Configuration."""

lib/spack/spack/environment/environment.py

@@ -3043,11 +3043,13 @@ def prepare_config_scope(self) -> None:
         """Add the manifest's scopes to the global configuration search path."""
         for scope in self.env_config_scopes:
             spack.config.CONFIG.push_scope(scope)
+        spack.config.CONFIG.ensure_scope_ordering()
 
     def deactivate_config_scope(self) -> None:
         """Remove any of the manifest's scopes from the global config path."""
         for scope in self.env_config_scopes:
             spack.config.CONFIG.remove_scope(scope.name)
+        spack.config.CONFIG.ensure_scope_ordering()
 
     @contextlib.contextmanager
     def use_config(self):

lib/spack/spack/package.py

@@ -103,7 +103,7 @@
 from spack.phase_callbacks import run_after, run_before
 from spack.spec import InvalidSpecDetected, Spec
 from spack.util.executable import *
-from spack.util.filesystem import file_command, fix_darwin_install_name, mime_type
+from spack.util.filesystem import fix_darwin_install_name
 from spack.variant import any_combination_of, auto_or_any_combination_of, disjoint_sets
 from spack.version import Version, ver
 

lib/spack/spack/relocate.py

@@ -23,7 +23,6 @@
 import spack.store
 import spack.util.elf as elf
 import spack.util.executable as executable
-import spack.util.filesystem as ssys
 
 from .relocate_text import BinaryFilePrefixReplacer, TextFilePrefixReplacer
 
@@ -350,32 +349,6 @@ def _set_elf_rpaths_and_interpreter(
         return None
 
 
-def needs_binary_relocation(m_type, m_subtype):
-    """Returns True if the file with MIME type/subtype passed as arguments
-    needs binary relocation, False otherwise.
-
-    Args:
-        m_type (str): MIME type of the file
-        m_subtype (str): MIME subtype of the file
-    """
-    subtypes = ("x-executable", "x-sharedlib", "x-mach-binary", "x-pie-executable")
-    if m_type == "application":
-        if m_subtype in subtypes:
-            return True
-    return False
-
-
-def needs_text_relocation(m_type, m_subtype):
-    """Returns True if the file with MIME type/subtype passed as arguments
-    needs text relocation, False otherwise.
-
-    Args:
-        m_type (str): MIME type of the file
-        m_subtype (str): MIME subtype of the file
-    """
-    return m_type == "text"
-
-
 def relocate_macho_binaries(
     path_names, old_layout_root, new_layout_root, prefix_to_prefix, rel, old_prefix, new_prefix
 ):
@@ -623,24 +596,32 @@ def relocate_text_bin(binaries, prefixes):
     return BinaryFilePrefixReplacer.from_strings_or_bytes(prefixes).apply(binaries)
 
 
-def is_binary(filename):
-    """Returns true if a file is binary, False otherwise
+def is_macho_magic(magic: bytes) -> bool:
+    return (
+        # In order of popularity: 64-bit mach-o le/be, 32-bit mach-o le/be.
+        magic.startswith(b"\xCF\xFA\xED\xFE")
+        or magic.startswith(b"\xFE\xED\xFA\xCF")
+        or magic.startswith(b"\xCE\xFA\xED\xFE")
+        or magic.startswith(b"\xFE\xED\xFA\xCE")
+        # universal binaries: 0xcafebabe be (most common?) or 0xbebafeca le (not sure if exists).
+        # Here we need to disambiguate mach-o and JVM class files. In mach-o the next 4 bytes are
+        # the number of binaries; in JVM class files it's the java version number. We assume there
+        # are less than 10 binaries in a universal binary.
+        or (magic.startswith(b"\xCA\xFE\xBA\xBE") and int.from_bytes(magic[4:8], "big") < 10)
+        or (magic.startswith(b"\xBE\xBA\xFE\xCA") and int.from_bytes(magic[4:8], "little") < 10)
+    )
 
-    Args:
-        filename: file to be tested
 
-    Returns:
-        True or False
-    """
-    m_type, _ = ssys.mime_type(filename)
+def is_elf_magic(magic: bytes) -> bool:
+    return magic.startswith(b"\x7FELF")
 
-    msg = "[{0}] -> ".format(filename)
-    if m_type == "application":
-        tty.debug(msg + "BINARY FILE")
-        return True
 
-    tty.debug(msg + "TEXT FILE")
-    return False
+def is_binary(filename: str) -> bool:
+    """Returns true iff a file is likely binary"""
+    with open(filename, "rb") as f:
+        magic = f.read(8)
+
+    return is_macho_magic(magic) or is_elf_magic(magic)
 
 
 # Memoize this due to repeated calls to libraries in the same directory.
@@ -649,6 +630,14 @@ def _exists_dir(dirname):
     return os.path.isdir(dirname)
 
 
+def is_macho_binary(path):
+    try:
+        with open(path, "rb") as f:
+            return is_macho_magic(f.read(4))
+    except OSError:
+        return False
+
+
 def fixup_macos_rpath(root, filename):
     """Apply rpath fixups to the given file.
 
@@ -660,7 +649,8 @@ def fixup_macos_rpath(root, filename):
         True if fixups were applied, else False
     """
     abspath = os.path.join(root, filename)
-    if ssys.mime_type(abspath) != ("application", "x-mach-binary"):
+
+    if not is_macho_binary(abspath):
         return False
 
     # Get Mach-O header commands

lib/spack/spack/rewiring.py

@@ -4,12 +4,8 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
-import re
 import shutil
 import tempfile
-from collections import OrderedDict
-
-from llnl.util.symlink import readlink, symlink
 
 import spack.binary_distribution as bindist
 import spack.deptypes as dt
@@ -20,19 +16,6 @@
 import spack.store
 
 
-def _relocate_spliced_links(links, orig_prefix, new_prefix):
-    """Re-linking function which differs from `relocate.relocate_links` by
-    reading the old link rather than the new link, since the latter wasn't moved
-    in our case. This still needs to be called after the copy to destination
-    because it expects the new directory structure to be in place."""
-    for link in links:
-        link_target = readlink(os.path.join(orig_prefix, link))
-        link_target = re.sub("^" + orig_prefix, new_prefix, link_target)
-        new_link_path = os.path.join(new_prefix, link)
-        os.unlink(new_link_path)
-        symlink(link_target, new_link_path)
-
-
 def rewire(spliced_spec):
     """Given a spliced spec, this function conducts all the rewiring on all
     nodes in the DAG of that spec."""
@@ -54,13 +37,17 @@ def rewire_node(spec, explicit):
     the splice. The resulting package is then 'installed.'"""
     tempdir = tempfile.mkdtemp()
 
-    # copy anything installed to a temporary directory
-    shutil.copytree(spec.build_spec.prefix, os.path.join(tempdir, spec.dag_hash()))
+    # Copy spec.build_spec.prefix to spec.prefix through a temporary tarball
+    tarball = os.path.join(tempdir, f"{spec.dag_hash()}.tar.gz")
+    bindist.create_tarball(spec.build_spec, tarball)
 
     spack.hooks.pre_install(spec)
+    bindist.extract_buildcache_tarball(tarball, destination=spec.prefix)
+    buildinfo = bindist.read_buildinfo_file(spec.prefix)
+
     # compute prefix-to-prefix for every node from the build spec to the spliced
     # spec
-    prefix_to_prefix = OrderedDict({spec.build_spec.prefix: spec.prefix})
+    prefix_to_prefix = {spec.build_spec.prefix: spec.prefix}
     build_spec_ids = set(id(s) for s in spec.build_spec.traverse(deptype=dt.ALL & ~dt.BUILD))
     for s in bindist.deps_to_relocate(spec):
         analog = s
@@ -77,19 +64,17 @@ def rewire_node(spec, explicit):
 
         prefix_to_prefix[analog.prefix] = s.prefix
 
-    manifest = bindist.get_buildfile_manifest(spec.build_spec)
     platform = spack.platforms.by_name(spec.platform)
 
     text_to_relocate = [
-        os.path.join(tempdir, spec.dag_hash(), rel_path)
-        for rel_path in manifest.get("text_to_relocate", [])
+        os.path.join(spec.prefix, rel_path) for rel_path in buildinfo["relocate_textfiles"]
     ]
     if text_to_relocate:
         relocate.relocate_text(files=text_to_relocate, prefixes=prefix_to_prefix)
-
+    links = [os.path.join(spec.prefix, f) for f in buildinfo["relocate_links"]]
+    relocate.relocate_links(links, prefix_to_prefix)
     bins_to_relocate = [
-        os.path.join(tempdir, spec.dag_hash(), rel_path)
-        for rel_path in manifest.get("binary_to_relocate", [])
+        os.path.join(spec.prefix, rel_path) for rel_path in buildinfo["relocate_binaries"]
     ]
     if bins_to_relocate:
         if "macho" in platform.binary_formats:
@@ -113,22 +98,18 @@ def rewire_node(spec, explicit):
                 spec.prefix,
             )
         relocate.relocate_text_bin(binaries=bins_to_relocate, prefixes=prefix_to_prefix)
-    # Copy package into place, except for spec.json (because spec.json
-    # describes the old spec and not the new spliced spec).
-    shutil.copytree(
-        os.path.join(tempdir, spec.dag_hash()),
-        spec.prefix,
-        ignore=shutil.ignore_patterns("spec.json", "install_manifest.json"),
-    )
-    if manifest.get("link_to_relocate"):
-        _relocate_spliced_links(
-            manifest.get("link_to_relocate"), spec.build_spec.prefix, spec.prefix
-        )
     shutil.rmtree(tempdir)
-    # Above, we did not copy spec.json: instead, here we write the new
-    # (spliced) spec into spec.json, without this, Database.add would fail on
-    # the next line (because it checks the spec.json in the prefix against the
-    # spec being added to look for mismatches)
+    install_manifest = os.path.join(
+        spec.prefix,
+        spack.store.STORE.layout.metadata_dir,
+        spack.store.STORE.layout.manifest_file_name,
+    )
+    try:
+        os.unlink(install_manifest)
+    except FileNotFoundError:
+        pass
+    # Write the spliced spec into spec.json. Without this, Database.add would fail because it
+    # checks the spec.json in the prefix against the spec being added to look for mismatches
     spack.store.STORE.layout.write_spec(spec, spack.store.STORE.layout.spec_file_path(spec))
     # add to database, not sure about explicit
     spack.store.STORE.db.add(spec, explicit=explicit)

lib/spack/spack/test/bindist.py

@@ -23,7 +23,7 @@
 
 import archspec.cpu
 
-from llnl.util.filesystem import copy_tree, join_path, visit_directory_tree
+from llnl.util.filesystem import copy_tree, join_path
 from llnl.util.symlink import readlink
 
 import spack.binary_distribution as bindist
@@ -43,7 +43,7 @@
 import spack.util.spack_yaml as syaml
 import spack.util.url as url_util
 import spack.util.web as web_util
-from spack.binary_distribution import CannotListKeys, GenerateIndexError, get_buildfile_manifest
+from spack.binary_distribution import CannotListKeys, GenerateIndexError
 from spack.directory_layout import DirectoryLayout
 from spack.paths import test_path
 from spack.spec import Spec
@@ -623,60 +623,21 @@ def test_FetchCacheError_pretty_printing_single():
     assert str_e.rstrip() == str_e
 
 
-def test_build_manifest_visitor(tmpdir):
-    dir = "directory"
-    file = os.path.join("directory", "file")
-
-    with tmpdir.as_cwd():
-        # Create a file inside a directory
-        os.mkdir(dir)
-        with open(file, "wb") as f:
-            f.write(b"example file")
-
-        # Symlink the dir
-        os.symlink(dir, "symlink_to_directory")
-
-        # Symlink the file
-        os.symlink(file, "symlink_to_file")
-
-        # Hardlink the file
-        os.link(file, "hardlink_of_file")
-
-        # Hardlinked symlinks: seems like this is only a thing on Linux,
-        # on Darwin the symlink *target* is hardlinked, on Linux the
-        # symlink *itself* is hardlinked.
-        if sys.platform.startswith("linux"):
-            os.link("symlink_to_file", "hardlink_of_symlink_to_file")
-            os.link("symlink_to_directory", "hardlink_of_symlink_to_directory")
-
-    visitor = bindist.BuildManifestVisitor()
-    visit_directory_tree(str(tmpdir), visitor)
-
-    # We de-dupe hardlinks of files, so there should really be just one file
-    assert len(visitor.files) == 1
-
-    # We do not de-dupe symlinks, cause it's unclear how to update symlinks
-    # in-place, preserving inodes.
-    if sys.platform.startswith("linux"):
-        assert len(visitor.symlinks) == 4  # includes hardlinks of symlinks.
-    else:
-        assert len(visitor.symlinks) == 2
-
-    with tmpdir.as_cwd():
-        assert not any(os.path.islink(f) or os.path.isdir(f) for f in visitor.files)
-        assert all(os.path.islink(f) for f in visitor.symlinks)
-
-
-def test_text_relocate_if_needed(install_mockery, temporary_store, mock_fetch, monkeypatch, capfd):
+def test_text_relocate_if_needed(install_mockery, temporary_store, mock_fetch, tmp_path):
     install_cmd("needs-text-relocation")
+    spec = temporary_store.db.query_one("needs-text-relocation")
+    tgz_path = tmp_path / "relocatable.tar.gz"
+    bindist.create_tarball(spec, str(tgz_path))
 
-    specs = temporary_store.db.query("needs-text-relocation")
-    assert len(specs) == 1
-    manifest = get_buildfile_manifest(specs[0])
+    # extract the .spack/binary_distribution file
+    with tarfile.open(tgz_path) as tar:
+        entry_name = next(x for x in tar.getnames() if x.endswith(".spack/binary_distribution"))
+        bd_file = tar.extractfile(entry_name)
+        manifest = syaml.load(bd_file)
 
-    assert join_path("bin", "exe") in manifest["text_to_relocate"]
-    assert join_path("bin", "otherexe") not in manifest["text_to_relocate"]
-    assert join_path("bin", "secretexe") not in manifest["text_to_relocate"]
+    assert join_path("bin", "exe") in manifest["relocate_textfiles"]
+    assert join_path("bin", "otherexe") not in manifest["relocate_textfiles"]
+    assert join_path("bin", "secretexe") not in manifest["relocate_textfiles"]
 
 
 def test_etag_fetching_304():
@@ -917,7 +878,7 @@ def test_tarball_doesnt_include_buildinfo_twice(tmp_path: Path):
     tarball = str(tmp_path / "prefix.tar.gz")
 
     bindist._do_create_tarball(
-        tarfile_path=tarball, binaries_dir=str(p), buildinfo={"metadata": "new"}
+        tarfile_path=tarball, prefix=str(p), buildinfo={"metadata": "new"}, prefixes_to_relocate=[]
     )
 
     expected_prefix = str(p).lstrip("/")
@@ -926,7 +887,10 @@ def test_tarball_doesnt_include_buildinfo_twice(tmp_path: Path):
     # and that the tarball contains the new one, not the old one.
     with tarfile.open(tarball) as tar:
         assert syaml.load(tar.extractfile(f"{expected_prefix}/.spack/binary_distribution")) == {
-            "metadata": "new"
+            "metadata": "new",
+            "relocate_binaries": [],
+            "relocate_textfiles": [],
+            "relocate_links": [],
         }
         assert tar.getnames() == [
             *_all_parents(expected_prefix),
@@ -951,11 +915,15 @@ def test_reproducible_tarball_is_reproducible(tmp_path: Path):
 
     # Create a tarball with a certain mtime of bin/app
     os.utime(app, times=(0, 0))
-    bindist._do_create_tarball(tarball_1, binaries_dir=str(p), buildinfo=buildinfo)
+    bindist._do_create_tarball(
+        tarball_1, prefix=str(p), buildinfo=buildinfo, prefixes_to_relocate=[]
+    )
 
     # Do it another time with different mtime of bin/app
     os.utime(app, times=(10, 10))
-    bindist._do_create_tarball(tarball_2, binaries_dir=str(p), buildinfo=buildinfo)
+    bindist._do_create_tarball(
+        tarball_2, prefix=str(p), buildinfo=buildinfo, prefixes_to_relocate=[]
+    )
 
     # They should be bitwise identical:
     assert filecmp.cmp(tarball_1, tarball_2, shallow=False)
@@ -1001,7 +969,7 @@ def test_tarball_normalized_permissions(tmpdir):
     ) as f:
         f.write("hello world")
 
-    bindist._do_create_tarball(tarball, binaries_dir=p.strpath, buildinfo={})
+    bindist._do_create_tarball(tarball, prefix=p.strpath, buildinfo={}, prefixes_to_relocate=[])
 
     expected_prefix = p.strpath.lstrip("/")
 
@@ -1120,7 +1088,7 @@ def test_tarfile_of_spec_prefix(tmpdir):
     file = tmpdir.join("example.tar")
 
     with tarfile.open(file, mode="w") as tar:
-        bindist.tarfile_of_spec_prefix(tar, prefix.strpath)
+        bindist.tarfile_of_spec_prefix(tar, prefix.strpath, prefixes_to_relocate=[])
 
     expected_prefix = prefix.strpath.lstrip("/")
 

lib/spack/spack/test/config.py

@@ -1441,3 +1441,30 @@ def test_config_path_dsl(path, it_should_work, expected_parsed):
     else:
         with pytest.raises(ValueError):
             spack.config.ConfigPath._validate(path)
+
+
+@pytest.mark.regression("48254")
+def test_env_activation_preserves_config_scopes(mutable_mock_env_path):
+    """Check that the "command_line" scope remains the highest priority scope, when we activate,
+    or deactivate, environments.
+    """
+    expected_cl_scope = spack.config.CONFIG.highest()
+    assert expected_cl_scope.name == "command_line"
+
+    # Creating an environment pushes a new scope
+    ev.create("test")
+    with ev.read("test"):
+        assert spack.config.CONFIG.highest() == expected_cl_scope
+
+        # No active environment pops the scope
+        with ev.no_active_environment():
+            assert spack.config.CONFIG.highest() == expected_cl_scope
+        assert spack.config.CONFIG.highest() == expected_cl_scope
+
+        # Switch the environment to another one
+        ev.create("test-2")
+        with ev.read("test-2"):
+            assert spack.config.CONFIG.highest() == expected_cl_scope
+        assert spack.config.CONFIG.highest() == expected_cl_scope
+
+    assert spack.config.CONFIG.highest() == expected_cl_scope

lib/spack/spack/test/packaging.py

@@ -36,8 +36,6 @@
     macho_find_paths,
     macho_make_paths_normal,
     macho_make_paths_relative,
-    needs_binary_relocation,
-    needs_text_relocation,
     relocate_links,
     relocate_text,
 )
@@ -193,16 +191,6 @@ def test_relocate_links(tmpdir):
         assert readlink("to_self_but_relative") == "relative"
 
 
-def test_needs_relocation():
-    assert needs_binary_relocation("application", "x-sharedlib")
-    assert needs_binary_relocation("application", "x-executable")
-    assert not needs_binary_relocation("application", "x-octet-stream")
-    assert not needs_binary_relocation("text", "x-")
-    assert needs_text_relocation("text", "x-")
-    assert not needs_text_relocation("symbolic link to", "x-")
-    assert needs_binary_relocation("application", "x-mach-binary")
-
-
 def test_replace_paths(tmpdir):
     with tmpdir.as_cwd():
         suffix = "dylib" if platform.system().lower() == "darwin" else "so"

lib/spack/spack/util/archive.py

@@ -10,7 +10,7 @@
 import tarfile
 from contextlib import closing, contextmanager
 from gzip import GzipFile
-from typing import Callable, Dict, Tuple
+from typing import Callable, Dict, List, Tuple
 
 from llnl.util.symlink import readlink
 
@@ -130,6 +130,15 @@ def default_path_to_name(path: str) -> str:
     return pathlib.PurePath(*p.parts[1:]).as_posix() if p.is_absolute() else p.as_posix()
 
 
+def default_add_file(tar: tarfile.TarFile, file_info: tarfile.TarInfo, path: str) -> None:
+    with open(path, "rb") as f:
+        tar.addfile(file_info, f)
+
+
+def default_add_link(tar: tarfile.TarFile, file_info: tarfile.TarInfo, path: str) -> None:
+    tar.addfile(file_info)
+
+
 def reproducible_tarfile_from_prefix(
     tar: tarfile.TarFile,
     prefix: str,
@@ -137,6 +146,9 @@ def reproducible_tarfile_from_prefix(
     include_parent_directories: bool = False,
     skip: Callable[[os.DirEntry], bool] = lambda entry: False,
     path_to_name: Callable[[str], str] = default_path_to_name,
+    add_file: Callable[[tarfile.TarFile, tarfile.TarInfo, str], None] = default_add_file,
+    add_symlink: Callable[[tarfile.TarFile, tarfile.TarInfo, str], None] = default_add_link,
+    add_hardlink: Callable[[tarfile.TarFile, tarfile.TarInfo, str], None] = default_add_link,
 ) -> None:
     """Create a tarball from a given directory. Only adds regular files, symlinks and dirs.
     Skips devices, fifos. Preserves hardlinks. Normalizes permissions like git. Tar entries are
@@ -170,8 +182,10 @@ def reproducible_tarfile_from_prefix(
             tar.addfile(dir_info)
 
     dir_stack = [prefix]
+    new_dirs: List[str] = []
     while dir_stack:
         dir = dir_stack.pop()
+        new_dirs.clear()
 
         # Add the dir before its contents
         dir_info = tarfile.TarInfo(path_to_name(dir))
@@ -183,7 +197,6 @@ def reproducible_tarfile_from_prefix(
         with os.scandir(dir) as it:
             entries = sorted(it, key=lambda entry: entry.name)
 
-        new_dirs = []
         for entry in entries:
             if skip(entry):
                 continue
@@ -201,7 +214,7 @@ def reproducible_tarfile_from_prefix(
                 # st_mode field of the stat structure is unspecified." So we set it to
                 # something sensible without lstat'ing the link.
                 file_info.mode = 0o755
-                tar.addfile(file_info)
+                add_symlink(tar, file_info, entry.path)
 
             elif entry.is_file(follow_symlinks=False):
                 # entry.stat has zero (st_ino, st_dev, st_nlink) on Windows: use lstat.
@@ -216,15 +229,13 @@ def reproducible_tarfile_from_prefix(
                     if ident in hardlink_to_tarinfo_name:
                         file_info.type = tarfile.LNKTYPE
                         file_info.linkname = hardlink_to_tarinfo_name[ident]
-                        tar.addfile(file_info)
+                        add_hardlink(tar, file_info, entry.path)
                         continue
                     hardlink_to_tarinfo_name[ident] = file_info.name
 
                 # If file not yet seen, copy it
                 file_info.type = tarfile.REGTYPE
                 file_info.size = s.st_size
-
-                with open(entry.path, "rb") as f:
-                    tar.addfile(file_info, f)
+                add_file(tar, file_info, entry.path)
 
         dir_stack.extend(reversed(new_dirs))  # we pop, so reverse to stay alphabetical

lib/spack/spack/util/filesystem.py

@@ -10,62 +10,10 @@
 
 import glob
 import os
-import sys
 
-from llnl.util import tty
 from llnl.util.filesystem import edit_in_place_through_temporary_file
-from llnl.util.lang import memoized
 
-from spack.util.executable import Executable, which
-
-
-def _ensure_file_on_win():
-    """Ensures the file command is available on Windows
-    If not, it is bootstrapped.
-    No-op on all other platforms"""
-    if sys.platform != "win32":
-        return
-    import spack.bootstrap
-
-    with spack.bootstrap.ensure_bootstrap_configuration():
-        spack.bootstrap.ensure_file_in_path_or_raise()
-
-
-@memoized
-def file_command(*args):
-    """Creates entry point to `file` system command with provided arguments"""
-    _ensure_file_on_win()
-    file_cmd = which("file", required=True)
-    for arg in args:
-        file_cmd.add_default_arg(arg)
-    return file_cmd
-
-
-@memoized
-def _get_mime_type():
-    """Generate method to call `file` system command to aquire mime type
-    for a specified path
-    """
-    if sys.platform == "win32":
-        # -h option (no-dereference) does not exist in Windows
-        return file_command("-b", "--mime-type")
-    else:
-        return file_command("-b", "-h", "--mime-type")
-
-
-def mime_type(filename):
-    """Returns the mime type and subtype of a file.
-
-    Args:
-        filename: file to be analyzed
-
-    Returns:
-        Tuple containing the MIME type and subtype
-    """
-    output = _get_mime_type()(filename, output=str, error=str).strip()
-    tty.debug("==> " + output)
-    type, _, subtype = output.partition("/")
-    return type, subtype
+from spack.util.executable import Executable
 
 
 def fix_darwin_install_name(path):

share/spack/qa/bootstrap-file.py

@@ -1,4 +0,0 @@
-from spack.util.filesystem import file_command
-
-if __name__ == "__main__":
-    file_command()

var/spack/repos/builtin/packages/amr-wind/package.py

@@ -21,6 +21,11 @@ class AmrWind(CMakePackage, CudaPackage, ROCmPackage):
     license("BSD-3-Clause")
 
     version("main", branch="main", submodules=True)
+    version("3.3.1", tag="v3.3.1", submodules=True)
+    version("3.3.0", tag="v3.3.0", submodules=True)
+    version("3.2.3", tag="v3.2.3", submodules=True)
+    version("3.2.2", tag="v3.2.2", submodules=True)
+    version("3.2.1", tag="v3.2.1", submodules=True)
     version("3.2.0", tag="v3.2.0", submodules=True)
     version("3.1.7", tag="v3.1.7", submodules=True)
     version("3.1.6", tag="v3.1.6", submodules=True)
@@ -77,6 +82,7 @@ class AmrWind(CMakePackage, CudaPackage, ROCmPackage):
     variant(
         "waves2amr", default=False, description="Enable Waves2AMR support for ocean wave input"
     )
+    variant("fft", default=False, description="Enable FFT support for MAC projection")
 
     depends_on("mpi", when="+mpi")
     depends_on("hdf5~mpi", when="+hdf5~mpi")
@@ -102,6 +108,7 @@ class AmrWind(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("helics@:3.3.2", when="+helics")
     depends_on("helics@:3.3.2+mpi", when="+helics+mpi")
     depends_on("fftw", when="@2.1: +waves2amr")
+    depends_on("fftw", when="@3.3.1: +fft")
 
     for arch in CudaPackage.cuda_arch_values:
         depends_on("hypre+cuda cuda_arch=%s" % arch, when="+cuda+hypre cuda_arch=%s" % arch)
@@ -137,6 +144,10 @@ def cmake_args(self):
             "rocm",
             "tests",
             "tiny_profile",
+            "fft",
+            "helics",
+            "umpire",
+            "sycl",
         ]
         args = [self.define_from_variant("AMR_WIND_ENABLE_%s" % v.upper(), v) for v in vs]
 
@@ -161,19 +172,19 @@ def cmake_args(self):
             args.append("-DAMReX_AMD_ARCH=" + ";".join(str(x) for x in targets))
 
         if spec.satisfies("+umpire"):
-            args.append(self.define_from_variant("AMR_WIND_ENABLE_UMPIRE", "umpire"))
             args.append(define("UMPIRE_DIR", spec["umpire"].prefix))
 
         if spec.satisfies("+helics"):
-            args.append(self.define_from_variant("AMR_WIND_ENABLE_HELICS", "helics"))
             args.append(define("HELICS_DIR", spec["helics"].prefix))
 
         if spec.satisfies("+waves2amr"):
             args.append(self.define_from_variant("AMR_WIND_ENABLE_W2A", "waves2amr"))
             args.append(define("FFTW_DIR", spec["fftw"].prefix))
 
+        if spec.satisfies("+fft"):
+            args.append(define("FFTW_DIR", spec["fftw"].prefix))
+
         if spec.satisfies("+sycl"):
-            args.append(define("AMR_WIND_ENABLE_SYCL", True))
             requires(
                 "%dpcpp",
                 "%oneapi",

var/spack/repos/builtin/packages/cray-mvapich2/package.py

@@ -53,11 +53,6 @@ def setup_dependent_package(self, module, dependent_spec):
         spec.mpifc = dependent_module.spack_fc
         spec.mpif77 = dependent_module.spack_f77
 
-        spec.mpicxx_shared_libs = [
-            join_path(self.prefix.lib, "libmpicxx.{0}".format(dso_suffix)),
-            join_path(self.prefix.lib, "libmpi.{0}".format(dso_suffix)),
-        ]
-
     def install(self, spec, prefix):
         raise InstallError(
             self.spec.format(

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

@@ -15,6 +15,7 @@ class Freeglut(CMakePackage, SourceforgePackage):
 
     license("MIT")
 
+    version("3.6.0", sha256="9c3d4d6516fbfa0280edc93c77698fb7303e443c1aaaf37d269e3288a6c3ea52")
     version("3.2.2", sha256="c5944a082df0bba96b5756dddb1f75d0cd72ce27b5395c6c1dde85c2ff297a50")
     version("3.2.1", sha256="d4000e02102acaf259998c870e25214739d1f16f67f99cb35e4f46841399da68")
     version("3.0.0", sha256="2a43be8515b01ea82bcfa17d29ae0d40bd128342f0930cd1f375f1ff999f76a2")
@@ -42,17 +43,17 @@ class Freeglut(CMakePackage, SourceforgePackage):
     patch(
         "https://gitweb.gentoo.org/repo/gentoo.git/plain/media-libs/freeglut/files/freeglut-3.2.1-gcc10-fno-common.patch?id=f9102571b69d9fc05471a592fda252681fdfdef1",
         sha256="898e8fb314cbe728d791e9ea69829313143cda039c008f0ca06c1b5730922aa7",
-        when="@3.2.1 %gcc@10.0:",
+        when="@3:3.2.1 %gcc@10.0:",
     )
     patch(
         "https://gitweb.gentoo.org/repo/gentoo.git/plain/media-libs/freeglut/files/freeglut-3.2.1-gcc10-fno-common.patch?id=f9102571b69d9fc05471a592fda252681fdfdef1",
         sha256="898e8fb314cbe728d791e9ea69829313143cda039c008f0ca06c1b5730922aa7",
-        when="@3.2.1 %clang@11.0:",
+        when="@3:3.2.1 %clang@11.0:",
     )
     patch(
         "https://gitweb.gentoo.org/repo/gentoo.git/plain/media-libs/freeglut/files/freeglut-3.2.1-gcc10-fno-common.patch?id=f9102571b69d9fc05471a592fda252681fdfdef1",
         sha256="898e8fb314cbe728d791e9ea69829313143cda039c008f0ca06c1b5730922aa7",
-        when="@3.2.1 %aocc@2.3.0:",
+        when="@3:3.2.1 %aocc@2.3.0:",
     )
 
     def cmake_args(self):

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

@@ -169,8 +169,12 @@ def setup_run_environment(self, env):
         # environment as in Gaudi.xenv
         env.prepend_path("PATH", self.prefix.scripts)
         env.prepend_path("PYTHONPATH", self.prefix.python)
-        for d in self.libs.directories:
-            env.prepend_path("LD_LIBRARY_PATH", d)
+
+        # Note: ROOT dependency automatically sets up ROOT environment vars
+
+        # ...but Gaudi additionally requires a path variable about itself
+        for lib_path in [self.prefix.lib, self.prefix.lib64]:
+            env.prepend_path("LD_LIBRARY_PATH", lib_path)
 
     def url_for_version(self, version):
         major = str(version[0])

var/spack/repos/builtin/packages/gsl/gsl-2.8-cblas.patch

@@ -0,0 +1,323 @@
+ Makefile.am                     |   8 +-
+ ax_cblas.m4                     |  69 +++++
+ bspline/Makefile.am             |   2 +-
+ configure.ac                    |  10 +
+ eigen/Makefile.am               |   2 +-
+ gsl-config.in                   |   4 +-
+ gsl.pc.in                       |   2 +-
+ interpolation/Makefile.am       |   2 +-
+ linalg/Makefile.am              |   2 +-
+ multifit/Makefile.am            |   4 +-
+ multimin/Makefile.am            |   4 +-
+ multiroots/Makefile.am          |   2 +-
+ ode-initval/Makefile.am         |   2 +-
+ poly/Makefile.am                |   2 +-
+ specfunc/Makefile.am            |   2 +-
+ wavelet/Makefile.am             |   2 +-
+ 31 files changed, 1157 insertions(+), 19 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index c522001..4513bc8 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -19,7 +19,7 @@ EXTRA_DIST = autogen.sh gsl-config.in gsl.pc.in configure.ac THANKS BUGS gsl.spe
+ 
+ lib_LTLIBRARIES = libgsl.la
+ libgsl_la_SOURCES = version.c
+-libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS)
++libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) @CBLAS_LINK_LIBS@
+ libgsl_la_LDFLAGS = $(GSL_LDFLAGS) -version-info $(GSL_LT_VERSION)
+ noinst_HEADERS = templates_on.h templates_off.h build.h
+ 
+@@ -29,10 +29,10 @@ m4data_DATA = gsl.m4
+ bin_PROGRAMS = gsl-randist gsl-histogram
+ 
+ gsl_randist_SOURCES = gsl-randist.c
+-gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la
++gsl_randist_LDADD = libgsl.la
+ 
+ gsl_histogram_SOURCES = gsl-histogram.c
+-gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la
++gsl_histogram_LDADD = libgsl.la
+ 
+ check_SCRIPTS = test_gsl_histogram.sh pkgconfig.test
+ TESTS = test_gsl_histogram.sh pkgconfig.test
+@@ -51,6 +51,8 @@ edit = $(SED) \
+ 	-e 's|@GSL_CFLAGS[@]|$(GSL_CFLAGS)|g' \
+ 	-e 's|@GSL_LIBM[@]|$(GSL_LIBM)|g' \
+ 	-e 's|@GSL_LIBS[@]|$(GSL_LIBS)|g' \
++	-e 's|@CBLAS_CFLAGS[@]|$(CBLAS_CFLAGS)|g' \
++	-e 's|@CBLAS_LIBS[@]|$(CBLAS_LIBS)|g' \
+ 	-e 's|@LIBS[@]|$(LIBS)|g' \
+ 	-e 's|@VERSION[@]|$(VERSION)|g'
+ 
+diff --git a/ax_cblas.m4 b/ax_cblas.m4
+new file mode 100644
+index 0000000..6ef143a
+--- /dev/null
++++ b/ax_cblas.m4
+@@ -0,0 +1,69 @@
++AC_DEFUN([AX_CBLAS],[
++
++  ext_cblas=no
++  ext_cblas_libs="-lcblas"
++  ext_cblas_cflags=""
++
++  AC_ARG_WITH(cblas-external,
++	[AS_HELP_STRING([--with-cblas-external], 
++			[Use external CBLAS library (default is no)])],
++	[with_ext_cblas=$withval],
++	[with_ext_cblas=no])
++
++  case $with_ext_cblas in
++	no) ext_cblas=no ;;
++	yes) ext_cblas=yes ;;
++	-* | */* | *.a | *.so | *.so.* | *.o) 
++	   ext_cblas=yes
++	   ext_cblas_libs="$with_cblas" ;;
++	*) ext_cblas=yes
++	   ext_cblas_libs="-l$with_cblas" ;;
++  esac
++
++  AC_ARG_WITH(cblas-external-libs,
++	[AS_HELP_STRING([--with-cblas-external-libs=<libs>],
++			[External cblas libraries to link with (default is "$ext_cblas_libs")])],
++	[ext_cblas_libs=$withval],
++	[])
++
++  AC_ARG_WITH(cblas-external-cflags,
++	[AS_HELP_STRING([--with-cblas-external-cflags=<flags>],
++			[Pre-processing flags to compile with external cblas ("-I<dir>")])],
++	[ext_cblas_cflags=$withval],
++	[])
++
++  if test x$ext_cblas != xno; then
++	if test "x$CBLAS_LIBS" = x; then
++	   CBLAS_LIBS="$ext_cblas_libs"
++     	fi
++     	if test "x$CBLAS_CFLAGS" = x; then
++       	   CBLAS_CFLAGS="$ext_cblas_cflags"
++   	fi
++
++   	CFLAGS_sav="$CFLAGS"
++   	CFLAGS="$CFLAGS $CBLAS_CFLAGS"
++   	AC_CHECK_HEADER(cblas.h, ,
++		[AC_MSG_ERROR([
++	   	*** Header file cblas.h not found.
++	   	*** If you installed cblas header in a non standard place,
++	   	*** specify its install prefix using the following option
++	   	***  --with-cblas-external-cflags="-I<include_dir>"])
++	 	])
++   	CFLAGS="$CFLAGS_sav"
++
++   	LIBS_sav="$LIBS"
++   	LIBS="$LIBS $CBLAS_LIBS -lm"
++   	AC_MSG_CHECKING([for cblas_sgemm in $CBLAS_LIBS])
++   	AC_TRY_LINK_FUNC(cblas_sgemm, [ext_cblas=yes],
++    		[AC_MSG_ERROR([
++	    	*** Linking with cblas with $LIBS failed.
++       	    	*** If you installed cblas library in a non standard place,
++   	    	*** specify its install prefix using the following option
++	    	***  --with-cblas-external-libs="-L<lib_dir> -l<lib>"])
++	 	])
++   	AC_MSG_RESULT($ext_cblas)
++   	LIBS="$LIBS_sav"
++	AC_SUBST([CBLAS_CFLAGS])
++	AC_SUBST([CBLAS_LIBS])
++ fi
++])
+diff --git a/bspline/Makefile.am b/bspline/Makefile.am
+index 3f4f950..d413036 100644
+--- a/bspline/Makefile.am
++++ b/bspline/Makefile.am
+@@ -12,6 +12,6 @@ check_PROGRAMS = test
+ 
+ TESTS = $(check_PROGRAMS)
+ 
+-test_LDADD = libgslbspline.la ../multifit/libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la ../poly/libgslpoly.la ../integration/libgslintegration.la ../rng/libgslrng.la ../sort/libgslsort.la
++test_LDADD = libgslbspline.la ../multifit/libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la ../poly/libgslpoly.la ../integration/libgslintegration.la ../rng/libgslrng.la ../sort/libgslsort.la
+ 
+ test_SOURCES = test.c
+diff --git a/configure.ac b/configure.ac
+index a26fc1e..564d426 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -208,6 +208,16 @@ if test "x$LIBS" = "x" ; then
+   AC_CHECK_LIB(m, cos)
+ fi
+ 
++sinclude(ax_cblas.m4)
++AX_CBLAS
++if test "x$CBLAS_LIBS" != "x"; then
++   CBLAS_LINK_LIBS="$CBLAS_LIBS"
++else
++   CBLAS_LINK_LIBS="\$(top_builddir)/cblas/libgslcblas.la"
++   CBLAS_LIBS="-lgslcblas"
++fi
++AC_SUBST(CBLAS_LINK_LIBS)
++
+ dnl Remember to put a definition in acconfig.h for each of these
+ AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1
+ #include <fenv.h>]) 
+diff --git a/eigen/Makefile.am b/eigen/Makefile.am
+index c28bfde..14197a4 100644
+--- a/eigen/Makefile.am
++++ b/eigen/Makefile.am
+@@ -11,7 +11,7 @@ noinst_HEADERS =  qrstep.c
+ 
+ TESTS = $(check_PROGRAMS)
+ 
+-test_LDADD = libgsleigen.la  ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la
++test_LDADD = libgsleigen.la  ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la
+ 
+ test_SOURCES = test.c
+ 
+diff --git a/gsl-config.in b/gsl-config.in
+old mode 100755
+new mode 100644
+index 3f3fa61..c9c4262
+--- a/gsl-config.in
++++ b/gsl-config.in
+@@ -58,11 +58,11 @@ while test $# -gt 0; do
+ 	;;
+ 
+     --cflags)
+-       	echo @GSL_CFLAGS@ 
++       	echo @GSL_CFLAGS@ @CBLAS_CFLAGS@ 
+        	;;
+ 
+     --libs)
+-        : ${GSL_CBLAS_LIB=-lgslcblas}
++        : ${GSL_CBLAS_LIB=@CBLAS_LIBS@}
+ 	echo @GSL_LIBS@ $GSL_CBLAS_LIB @GSL_LIBM@
+        	;;
+ 
+diff --git a/gsl.pc.in b/gsl.pc.in
+index 5e9ef21..5a7a0f3 100644
+--- a/gsl.pc.in
++++ b/gsl.pc.in
+@@ -2,7 +2,7 @@ prefix=@prefix@
+ exec_prefix=@exec_prefix@
+ libdir=@libdir@
+ includedir=@includedir@
+-GSL_CBLAS_LIB=-lgslcblas
++GSL_CBLAS_LIB=@CBLAS_LIBS@
+ 
+ Name: GSL
+ Description: GNU Scientific Library
+diff --git a/interpolation/Makefile.am b/interpolation/Makefile.am
+index 1d80755..e45bd51 100644
+--- a/interpolation/Makefile.am
++++ b/interpolation/Makefile.am
+@@ -12,7 +12,7 @@ AM_CPPFLAGS = -I$(top_srcdir)
+ 
+ TESTS = $(check_PROGRAMS)
+ 
+-test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
++test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+ 
+ test_SOURCES = test.c
+ 
+diff --git a/linalg/Makefile.am b/linalg/Makefile.am
+index a6c15b0..447ebbe 100644
+--- a/linalg/Makefile.am
++++ b/linalg/Makefile.am
+@@ -13,4 +13,4 @@ TESTS = $(check_PROGRAMS)
+ check_PROGRAMS = test
+ 
+ test_SOURCES = test.c
+-test_LDADD = libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../rng/libgslrng.la
++test_LDADD = libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../rng/libgslrng.la
+diff --git a/multifit/Makefile.am b/multifit/Makefile.am
+index 988614e..793b485 100644
+--- a/multifit/Makefile.am
++++ b/multifit/Makefile.am
+@@ -67,8 +67,8 @@ check_PROGRAMS = test #demo
+ TESTS = $(check_PROGRAMS)
+ 
+ test_SOURCES = test.c
+-test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la ../min/libgslmin.la
++test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la  ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la ../min/libgslmin.la
+ 
+ #demo_SOURCES = demo.c
+-#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
++#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la
+ 
+diff --git a/multimin/Makefile.am b/multimin/Makefile.am
+index 7071359..65a488a 100644
+--- a/multimin/Makefile.am
++++ b/multimin/Makefile.am
+@@ -13,8 +13,8 @@ check_PROGRAMS = test #demo
+ TESTS = $(check_PROGRAMS) 
+ 
+ test_SOURCES = test.c test_funcs.c test_funcs.h
+-test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
++test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+ 
+ #demo_SOURCES = demo.c 
+-#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
++#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+ 
+diff --git a/multiroots/Makefile.am b/multiroots/Makefile.am
+index a351c3f..6178448 100644
+--- a/multiroots/Makefile.am
++++ b/multiroots/Makefile.am
+@@ -15,5 +15,5 @@ check_PROGRAMS = test
+ TESTS = $(check_PROGRAMS)
+ 
+ test_SOURCES = test.c test_funcs.c test_funcs.h
+-test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
++test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+ 
+diff --git a/ode-initval/Makefile.am b/ode-initval/Makefile.am
+index 9c774b5..346c381 100644
+--- a/ode-initval/Makefile.am
++++ b/ode-initval/Makefile.am
+@@ -12,7 +12,7 @@ check_PROGRAMS = test
+ 
+ TESTS = $(check_PROGRAMS)
+ 
+-test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la 
++test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la 
+ 
+ test_SOURCES = test.c
+ 
+diff --git a/poly/Makefile.am b/poly/Makefile.am
+index f1dae5d..e0f8e83 100644
+--- a/poly/Makefile.am
++++ b/poly/Makefile.am
+@@ -10,7 +10,7 @@ noinst_HEADERS = balance.c companion.c qr.c
+ 
+ TESTS = $(check_PROGRAMS)
+ 
+-check_PROGRAMS = test
++#check_PROGRAMS = test
+ 
+ test_SOURCES = test.c
+ test_LDADD = libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../sort/libgslsort.la
+diff --git a/specfunc/Makefile.am b/specfunc/Makefile.am
+index eba9ab2..772cc7e 100644
+--- a/specfunc/Makefile.am
++++ b/specfunc/Makefile.am
+@@ -12,7 +12,7 @@ TESTS = $(check_PROGRAMS)
+ 
+ check_PROGRAMS = test
+ 
+-test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la  ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../block/libgslblock.la ../complex/libgslcomplex.la ../poly/libgslpoly.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
++test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la  ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../block/libgslblock.la ../complex/libgslcomplex.la ../poly/libgslpoly.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+ 
+ test_SOURCES = test_sf.c test_sf.h test_airy.c test_bessel.c test_coulomb.c test_dilog.c test_gamma.c test_hyperg.c test_legendre.c test_mathieu.c
+   
+diff --git a/wavelet/Makefile.am b/wavelet/Makefile.am
+index 9da20d8..8cdbd77 100644
+--- a/wavelet/Makefile.am
++++ b/wavelet/Makefile.am
+@@ -10,7 +10,7 @@ check_PROGRAMS = test
+ 
+ TESTS = $(check_PROGRAMS)
+ 
+-test_LDADD = libgslwavelet.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
++test_LDADD = libgslwavelet.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la  ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la
+ 
+ test_SOURCES = test.c
+ 

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

@@ -39,7 +39,8 @@ class Gsl(AutotoolsPackage, GNUMirrorPackage):
 
     # from https://dev.gentoo.org/~mgorny/dist/gsl-2.3-cblas.patch.bz2
     patch("gsl-2.3-cblas.patch", when="@2.3:2.5+external-cblas")
-    patch("gsl-2.6-cblas.patch", when="@2.6: +external-cblas")
+    patch("gsl-2.6-cblas.patch", when="@2.6:2.7 +external-cblas")
+    patch("gsl-2.8-cblas.patch", when="@2.8: +external-cblas")
 
     conflicts("+external-cblas", when="@:2.2")
 

var/spack/repos/builtin/packages/herwig3/package.py

@@ -16,6 +16,7 @@ class Herwig3(AutotoolsPackage):
 
     license("GPL-3.0-only")
 
+    version("7.3.0", sha256="2624819d2dff105ba952ea1b5cf12eb6f4926d4951774a41907699e2f567686c")
     version("7.2.3", sha256="5599899379b01b09e331a2426d78d39b7f6ec126db2543e9d340aefe6aa50f84")
     version("7.2.2", sha256="53e06b386df5bc20fe268b6c8ba50f1e62b6744e577d383ec836ea3fc672c383")
     version("7.2.1", sha256="d4fff32f21c5c08a4b2e563c476b079859c2c8e3b78d853a8a60da96d5eea686")
@@ -33,6 +34,7 @@ class Herwig3(AutotoolsPackage):
     depends_on("thepeg@2.2.1", when="@7.2.1")
     depends_on("thepeg@2.2.2", when="@7.2.2")
     depends_on("thepeg@2.2.3", when="@7.2.3")
+    depends_on("thepeg@2.3.0", when="@7.3.0")
     depends_on("evtgen")
 
     depends_on("boost +math+test")

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

@@ -29,6 +29,7 @@ class Legion(CMakePackage, ROCmPackage):
 
     maintainers("pmccormick", "streichler", "elliottslaughter")
     tags = ["e4s"]
+    version("24.12.0", tag="legion-24.12.0", commit="2f087ebe433a19f9a3abd05382f951027933bad9")
     version("24.09.0", tag="legion-24.09.0", commit="4a03402467547b99530042cfe234ceec2cd31b2e")
     version("24.06.0", tag="legion-24.06.0", commit="3f27977943626ef23038ef0049b7ad1b389caad1")
     version("24.03.0", tag="legion-24.03.0", commit="c61071541218747e35767317f6f89b83f374f264")

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

@@ -6,15 +6,16 @@
 from spack.package import *
 
 
-class Libzip(CMakePackage, AutotoolsPackage):
+class Libzip(CMakePackage):
     """libzip is a C library for reading, creating,
     and modifying zip archives."""
 
     homepage = "https://libzip.org/"
-
+    maintainers("prudhomm")
     license("BSD-3-Clause")
 
     # current versions are released on GitHub
+    version("1.11.1", sha256="c0e6fa52a62ba11efd30262290dc6970947aef32e0cc294ee50e9005ceac092a")
     version("1.10.1", sha256="9669ae5dfe3ac5b3897536dc8466a874c8cf2c0e3b1fdd08d75b273884299363")
     version("1.9.2", sha256="fd6a7f745de3d69cf5603edc9cb33d2890f0198e415255d0987a0cf10d824c6f")
     version("1.8.0", sha256="30ee55868c0a698d3c600492f2bea4eb62c53849bcf696d21af5eb65f3f3839e")
@@ -24,17 +25,6 @@ class Libzip(CMakePackage, AutotoolsPackage):
         sha256="06eb8e9141fd19e2788cabaea9c9c2fd4d488d9e1484eb474bbfcac78e7b1d88",
         url="https://github.com/nih-at/libzip/releases/download/rel-1-6-1/libzip-1.6.1.tar.gz",
     )
-    # older releases are available on libzip.org
-    version(
-        "1.3.2",
-        sha256="ab4c34eb6c3a08b678cd0f2450a6c57a13e9618b1ba34ee45d00eb5327316457",
-        deprecated=True,
-    )
-    version(
-        "1.2.0",
-        sha256="6cf9840e427db96ebf3936665430bab204c9ebbd0120c326459077ed9c907d9f",
-        deprecated=True,
-    )
 
     depends_on("c", type="build")  # generated
     depends_on("cxx", type="build")  # generated
@@ -46,14 +36,25 @@ def url_for_version(self, version):
 
     depends_on("zlib-api")
 
-    # Build system
-    build_system(
-        conditional("cmake", when="@1.4:"), conditional("autotools", when="@:1.3"), default="cmake"
-    )
+    variant("gnutls", default=True, description="Enable gnutls support")
+    variant("bzip2", default=True, description="Enable bzip2 support")
+    variant("lzma", default=True, description="Enable lzma support")
+    variant("openssl", default=True, description="Enable openssl support")
+    variant("zstd", default=True, description="Enable zstd support", when="@1.8:")
+    variant("mbedtls", default=True, description="Enable mbedtls support")
+    depends_on("gnutls", when="+gnutls")
+    depends_on("bzip2", when="+bzip2")
+    depends_on("lzma", when="+lzma")
+    depends_on("openssl", when="+openssl")
+    depends_on("mbedtls", when="+mbedtls")
+    depends_on("zstd", when="+zstd")
 
-    @property
-    def headers(self):
-        # Up to version 1.3.0 zipconf.h was installed outside of self.prefix.include
-        return find_all_headers(
-            self.prefix if self.spec.satisfies("@:1.3.0") else self.prefix.include
-        )
+    def cmake_args(self):
+        return [
+            self.define_from_variant("ENABLE_GNUTLS", "gnutls"),
+            self.define_from_variant("ENABLE_MBEDTLS", "mbedtls"),
+            self.define_from_variant("ENABLE_OPENSSL", "openssl"),
+            self.define_from_variant("ENABLE_BZIP2", "bzip2"),
+            self.define_from_variant("ENABLE_LZMA", "lzma"),
+            self.define_from_variant("ENABLE_ZSTD", "zstd"),
+        ]

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

@@ -8,7 +8,6 @@
 import sys
 
 import spack.compilers
-from spack.build_environment import dso_suffix
 from spack.package import *
 
 
@@ -482,11 +481,6 @@ def setup_dependent_package(self, module, dependent_spec):
             spec.mpifc = join_path(self.prefix.bin, "mpif90")
             spec.mpif77 = join_path(self.prefix.bin, "mpif77")
 
-        spec.mpicxx_shared_libs = [
-            join_path(self.prefix.lib, "libmpicxx.{0}".format(dso_suffix)),
-            join_path(self.prefix.lib, "libmpi.{0}".format(dso_suffix)),
-        ]
-
     def autoreconf(self, spec, prefix):
         """Not needed usually, configure should be already there"""
         # If configure exists nothing needs to be done

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

@@ -4,7 +4,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import itertools
-import os.path
 import re
 import sys
 
@@ -242,10 +241,6 @@ def setup_dependent_package(self, module, dependent_spec):
         self.spec.mpicxx = join_path(self.prefix.bin, "mpicxx")
         self.spec.mpifc = join_path(self.prefix.bin, "mpif90")
         self.spec.mpif77 = join_path(self.prefix.bin, "mpif77")
-        self.spec.mpicxx_shared_libs = [
-            os.path.join(self.prefix.lib, "libmpicxx.{0}".format(dso_suffix)),
-            os.path.join(self.prefix.lib, "libmpi.{0}".format(dso_suffix)),
-        ]
 
     @run_before("configure")
     def die_without_fortran(self):

var/spack/repos/builtin/packages/mvapich2-gdr/package.py

@@ -3,7 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os.path
 import sys
 
 from spack.package import *
@@ -184,10 +183,6 @@ def setup_dependent_package(self, module, dependent_spec):
         self.spec.mpicxx = join_path(self.prefix.bin, "mpicxx")
         self.spec.mpifc = join_path(self.prefix.bin, "mpif90")
         self.spec.mpif77 = join_path(self.prefix.bin, "mpif77")
-        self.spec.mpicxx_shared_libs = [
-            os.path.join(self.prefix.lib, "libmpicxx.{0}".format(dso_suffix)),
-            os.path.join(self.prefix.lib, "libmpi.{0}".format(dso_suffix)),
-        ]
 
     def configure_args(self):
         spec = self.spec

var/spack/repos/builtin/packages/mvapich2/package.py

@@ -399,10 +399,6 @@ def setup_dependent_package(self, module, dependent_spec):
         self.spec.mpicxx = join_path(self.prefix.bin, "mpicxx")
         self.spec.mpifc = join_path(self.prefix.bin, "mpif90")
         self.spec.mpif77 = join_path(self.prefix.bin, "mpif77")
-        self.spec.mpicxx_shared_libs = [
-            os.path.join(self.prefix.lib, "libmpicxx.{0}".format(dso_suffix)),
-            os.path.join(self.prefix.lib, "libmpi.{0}".format(dso_suffix)),
-        ]
 
     @run_before("configure")
     def die_without_fortran(self):

var/spack/repos/builtin/packages/mvapich2x/package.py

@@ -3,7 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os.path
 import sys
 
 from spack.package import *
@@ -239,10 +238,6 @@ def setup_dependent_package(self, module, dependent_spec):
         self.spec.mpicxx = join_path(self.prefix.bin, "mpicxx")
         self.spec.mpifc = join_path(self.prefix.bin, "mpif90")
         self.spec.mpif77 = join_path(self.prefix.bin, "mpif77")
-        self.spec.mpicxx_shared_libs = [
-            os.path.join(self.prefix.lib, "libmpicxx.{0}".format(dso_suffix)),
-            os.path.join(self.prefix.lib, "libmpi.{0}".format(dso_suffix)),
-        ]
 
     def configure_args(self):
         spec = self.spec

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

@@ -36,5 +36,5 @@ def cmake_args(self):
 
     def setup_run_environment(self, env):
         env.set("OPENDATADETECTOR_DATA", join_path(self.prefix.share, "OpenDataDetector"))
-        for d in self.libs.directories:
-            env.prepend_path("LD_LIBRARY_PATH", d)
+        for lib_path in [self.prefix.lib, self.prefix.lib64]:
+            env.prepend_path("LD_LIBRARY_PATH", lib_path)

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

@@ -274,12 +274,16 @@ def configure(self, spec, prefix):
             f.write("fortran_compiler = {0}\n".format(env["SPACK_FC"]))
             if self.spec.satisfies("@1.3.1") and not is_intel:
                 f.write("gfortran_f_flags = -ffree-line-length-none\n")
-            if self.spec.satisfies("@2.1.1:") and not is_intel:
+            if self.spec.satisfies("@2.1.1") and not is_intel:
                 f.write("gfortran_f_flags = -ffree-line-length-none " + "-fdollar-ok ")
                 if self.spec.target.family == "aarch64":
                     f.write("-mcmodel=small\n")
                 else:
                     f.write("-mcmodel=medium\n")
+            if self.spec.satisfies("@2.1.2:") and not is_intel:
+                f.write("gfortran_f_flags = -ffree-line-length-none " + "-fdollar-ok\n")
+                if self.spec.target.family == "aarch64":
+                    f.write("cmodel = small\n")
 
         if self.spec.satisfies("@:1 processes=lcg.coll"):
             copy(join_path(os.path.dirname(__file__), "sft1.coll"), "lcg.coll")

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

@@ -931,10 +931,6 @@ def setup_dependent_package(self, module, dependent_spec):
         self.spec.mpicxx = join_path(self.prefix.bin, "mpic++")
         self.spec.mpifc = join_path(self.prefix.bin, "mpif90")
         self.spec.mpif77 = join_path(self.prefix.bin, "mpif77")
-        self.spec.mpicxx_shared_libs = [
-            join_path(self.prefix.lib, "libmpi_cxx.{0}".format(dso_suffix)),
-            join_path(self.prefix.lib, "libmpi.{0}".format(dso_suffix)),
-        ]
 
     # Most of the following with_or_without methods might seem redundant
     # because Spack compiler wrapper adds the required -I and -L flags, which

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

@@ -302,7 +302,8 @@ class Petsc(Package, CudaPackage, ROCmPackage):
     # older versions of petsc did not support mumps when +int64
     conflicts("+mumps", when="@:3.12+int64")
 
-    filter_compiler_wrappers("petscvariables", relative_root="lib/petsc/conf")
+    filter_compiler_wrappers("petscvariables", "reconfigure*.py", relative_root="lib/petsc/conf")
+    filter_compiler_wrappers("petsc.pc", "PETSc.pc", relative_root="lib/pkgconfig")
 
     @run_before("configure")
     def check_fortran_compiler(self):

var/spack/repos/builtin/packages/py-fitter/package.py

@@ -12,20 +12,23 @@ class PyFitter(PythonPackage):
     most probable distribution and the best parameters."""
 
     homepage = "https://github.com/cokelaer/fitter"
-    pypi = "fitter/fitter-1.5.1.tar.gz"
+    pypi = "fitter/fitter-1.6.0.tar.gz"
 
     maintainers("carsonwoods")
 
     license("GPL-3.0-or-later")
 
+    version("1.6.0", sha256="908223d75b35d3846984bfb2fed1d2a926da5a30b95b704aa95b2a894227c0af")
+    version("1.5.2", sha256="afb33a8b1e24cdbc9318f55be72534e07028f25240ab76a4b081d27d1ed677d9")
     version("1.5.1", sha256="893b35ad0a84c3b96b63ec203a6a79effdba98777aed966ae61709f5e1e8cf99")
 
-    depends_on("py-setuptools", type="build")
-
-    depends_on("py-pandas", type=("build", "run"))
-    depends_on("py-numpy", type=("build", "run"))
-    depends_on("py-scipy@0.18:", type=("build", "run"))
-    depends_on("py-tqdm", type=("build", "run"))
-    depends_on("py-joblib", type=("build", "run"))
-    depends_on("py-click", type=("build", "run"))
-    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-poetry-core@1:", when="@1.6:", type="build")
+    depends_on("py-setuptools", when="@:1.6", type="build")
+    depends_on("python@3.8:3", type=("build", "run"))
+    depends_on("py-click@8.1.6:8", type=("build", "run"))
+    depends_on("py-joblib@1.3.1:1", type=("build", "run"))
+    depends_on("py-matplotlib@3.7.2:3", type=("build", "run"))
+    depends_on("py-numpy@1.20.0:1", type=("build", "run"))
+    depends_on("py-pandas@0.23.4:2", type=("build", "run"))
+    depends_on("py-scipy@0.18:1", type=("build", "run"))
+    depends_on("py-tqdm@4.65.1:4", type=("build", "run"))

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

@@ -364,7 +364,7 @@ def determine_variants(cls, exes, version_str):
                 variants += "~tix"
 
         # Some modules are platform-dependent
-        if sys.platform != "win32":
+        if sys.platform != "win32" and Version(version_str) < Version("3.13"):
             try:
                 python("-c", "import crypt", error=os.devnull)
                 variants += "+crypt"

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

@@ -869,6 +869,6 @@ def setup_dependent_run_environment(
         # automatically prepending dependent package library paths to
         # ROOT_LIBRARY_PATH (for @6.26:) or LD_LIBRARY_PATH (for older
         # versions).
-        for lib_path in (dependent_spec.prefix.lib, dependent_spec.prefix.lib64):
+        for lib_path in [dependent_spec.prefix.lib, dependent_spec.prefix.lib64]:
             if os.path.exists(lib_path):
                 env.prepend_path(self.root_library_path, lib_path)

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

@@ -65,6 +65,7 @@ class Silo(AutotoolsPackage):
     variant("hzip", default=True, description="Enable hzip support")
     variant("fpzip", default=True, description="Enable fpzip support")
 
+    depends_on("python", type=("build", "link"), when="+python")
     depends_on("perl", type="build")
     depends_on("m4", type="build", when="+shared")
     depends_on("autoconf", type="build", when="+shared")
@@ -129,6 +130,8 @@ def flag_handler(self, name, flags):
             if spec.satisfies("%oneapi"):
                 flags.append("-Wno-error=int")
                 flags.append("-Wno-error=int-conversion")
+            if spec.satisfies("+python"):
+                flags.append(f"-I {spec['python'].headers.directories[0]}")
             if "+hdf5" in spec:
                 # @:4.10 can use up to the 1.10 API
                 if "@:4.10" in spec:

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

@@ -71,7 +71,8 @@ class Thepeg(AutotoolsPackage):
     depends_on("hepmc3", when="hepmc=3")
     conflicts("hepmc=3", when="@:2.1", msg="HepMC3 support was added in 2.2.0")
     depends_on("fastjet", when="@2.0.0:")
-    depends_on("rivet", when="@2.0.3: +rivet")
+    depends_on("rivet@:3 hepmc=2", when="@2.0.3: +rivet hepmc=2")
+    depends_on("rivet@:3 hepmc=3", when="@2.0.3: +rivet hepmc=3")
     depends_on("boost +test", when="@2.1.1:")
 
     depends_on("autoconf", type="build")

var/spack/repos/tutorial/packages/mpich/package.py

@@ -93,11 +93,6 @@ def setup_dependent_package(self, module, dependent_spec):
         self.spec.mpifc = join_path(self.prefix.bin, "mpif90")
         self.spec.mpif77 = join_path(self.prefix.bin, "mpif77")
 
-        self.spec.mpicxx_shared_libs = [
-            join_path(self.prefix.lib, "libmpicxx.{0}".format(dso_suffix)),
-            join_path(self.prefix.lib, "libmpi.{0}".format(dso_suffix)),
-        ]
-
     def autoreconf(self, spec, prefix):
         """Not needed usually, configure should be already there"""
         # If configure exists nothing needs to be done