Merge pull request #472 from FNALssi/maintenance/merge-from-upstream-…

…2024-12-04

Merge from upstream/develop 2024-12-04

.github/workflows/build-containers.yml

@@ -120,7 +120,7 @@ jobs:
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build & Deploy ${{ matrix.dockerfile[0] }}
-        uses: docker/build-push-action@4f58ea79222b3b9dc2c8bbdd6debcef730109a75
+        uses: docker/build-push-action@48aba3b46d1b1fec4febb7c5d0c644b249a11355
         with:
           context: dockerfiles/${{ matrix.dockerfile[0] }}
           platforms: ${{ matrix.dockerfile[1] }}

.github/workflows/valid-style.yml

@@ -53,7 +53,7 @@ jobs:
         . .github/workflows/bin/setup_git.sh
     - name: Run style tests
       run: |
-          share/spack/qa/run-style-tests -s import
+          share/spack/qa/run-style-tests
   audit:
     uses: ./.github/workflows/audit.yaml
     secrets: inherit

etc/spack/defaults/packages.yaml

@@ -1271,6 +1271,8 @@ packages:
     buildable: false
   cray-mvapich2:
     buildable: false
+  egl:
+    buildable: false
   fujitsu-mpi:
     buildable: false
   hpcx-mpi:

lib/spack/docs/getting_started.rst

@@ -1326,6 +1326,7 @@ Required:
 * Microsoft Visual Studio
 * Python
 * Git
+* 7z
 
 Optional:
 * Intel Fortran (needed for some packages)
@@ -1391,6 +1392,13 @@ as the project providing Git support on Windows. This is additionally the recomm
 for installing Git on Windows, a link to which can be found above. Spack requires the
 utilities vendored by this project.
 
+"""
+7zip
+"""
+
+A tool for extracting ``.xz`` files is required for extracting source tarballs. The latest 7zip
+can be located at https://sourceforge.net/projects/sevenzip/.
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Step 2: Install and setup Spack
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

lib/spack/docs/requirements.txt

@@ -6,7 +6,7 @@ python-levenshtein==0.26.1
 docutils==0.21.2
 pygments==2.18.0
 urllib3==2.2.3
-pytest==8.3.3
+pytest==8.3.4
 isort==5.13.2
 black==24.10.0
 flake8==7.1.1

lib/spack/llnl/util/filesystem.py

@@ -24,6 +24,7 @@
     Callable,
     Deque,
     Dict,
+    Generator,
     Iterable,
     List,
     Match,
@@ -2772,22 +2773,6 @@ def prefixes(path):
     return paths
 
 
-@system_path_filter
-def md5sum(file):
-    """Compute the MD5 sum of a file.
-
-    Args:
-        file (str): file to be checksummed
-
-    Returns:
-        MD5 sum of the file's content
-    """
-    md5 = hashlib.md5()
-    with open(file, "rb") as f:
-        md5.update(f.read())
-    return md5.digest()
-
-
 @system_path_filter
 def remove_directory_contents(dir):
     """Remove all contents of a directory."""
@@ -2838,6 +2823,25 @@ def temporary_dir(
         remove_directory_contents(tmp_dir)
 
 
+@contextmanager
+def edit_in_place_through_temporary_file(file_path: str) -> Generator[str, None, None]:
+    """Context manager for modifying ``file_path`` in place, preserving its inode and hardlinks,
+    for functions or external tools that do not support in-place editing. Notice that this function
+    is unsafe in that it works with paths instead of a file descriptors, but this is by design,
+    since we assume the call site will create a new inode at the same path."""
+    tmp_fd, tmp_path = tempfile.mkstemp(
+        dir=os.path.dirname(file_path), prefix=f"{os.path.basename(file_path)}."
+    )
+    # windows cannot replace a file with open fds, so close since the call site needs to replace.
+    os.close(tmp_fd)
+    try:
+        shutil.copyfile(file_path, tmp_path, follow_symlinks=True)
+        yield tmp_path
+        shutil.copyfile(tmp_path, file_path, follow_symlinks=True)
+    finally:
+        os.unlink(tmp_path)
+
+
 def filesummary(path, print_bytes=16) -> Tuple[int, bytes]:
     """Create a small summary of the given file. Does not error
     when file does not exist.

lib/spack/spack/binary_distribution.py

@@ -2334,7 +2334,9 @@ def is_backup_file(file):
             if not codesign:
                 return
             for binary in changed_files:
-                codesign("-fs-", binary)
+                # preserve the original inode by running codesign on a copy
+                with fsys.edit_in_place_through_temporary_file(binary) as tmp_binary:
+                    codesign("-fs-", tmp_binary)
 
     # If we are installing back to the same location
     # relocate the sbang location if the spack directory changed

lib/spack/spack/build_systems/cmake.py

@@ -9,7 +9,7 @@
 import re
 import sys
 from itertools import chain
-from typing import Any, List, Optional, Set, Tuple
+from typing import Any, List, Optional, Tuple
 
 import archspec.cpu
 
@@ -23,6 +23,7 @@
 import spack.phase_callbacks
 import spack.spec
 import spack.util.prefix
+from spack import traverse
 from spack.directives import build_system, conflicts, depends_on, variant
 from spack.multimethod import when
 from spack.util.environment import filter_system_paths
@@ -168,15 +169,18 @@ def _values(x):
 def get_cmake_prefix_path(pkg: spack.package_base.PackageBase) -> List[str]:
     """Obtain the CMAKE_PREFIX_PATH entries for a package, based on the cmake_prefix_path package
     attribute of direct build/test and transitive link dependencies."""
-    # Add direct build/test deps
-    selected: Set[str] = {s.dag_hash() for s in pkg.spec.dependencies(deptype=dt.BUILD | dt.TEST)}
-    # Add transitive link deps
-    selected.update(s.dag_hash() for s in pkg.spec.traverse(root=False, deptype=dt.LINK))
-    # Separate out externals so they do not shadow Spack prefixes
-    externals, spack_built = stable_partition(
-        (s for s in pkg.spec.traverse(root=False, order="topo") if s.dag_hash() in selected),
-        lambda x: x.external,
+    edges = traverse.traverse_topo_edges_generator(
+        traverse.with_artificial_edges([pkg.spec]),
+        visitor=traverse.MixedDepthVisitor(
+            direct=dt.BUILD | dt.TEST, transitive=dt.LINK, key=traverse.by_dag_hash
+        ),
+        key=traverse.by_dag_hash,
+        root=False,
+        all_edges=False,  # cover all nodes, not all edges
     )
+    ordered_specs = [edge.spec for edge in edges]
+    # Separate out externals so they do not shadow Spack prefixes
+    externals, spack_built = stable_partition((s for s in ordered_specs), lambda x: x.external)
 
     return filter_system_paths(
         path for spec in chain(spack_built, externals) for path in spec.package.cmake_prefix_paths

lib/spack/spack/cmd/style.py

@@ -323,8 +323,6 @@ def process_files(file_list, is_args):
             rewrite_and_print_output(output, args, pat, replacement)
 
     packages_isort_args = (
-        "--rm",
-        "spack",
         "--rm",
         "spack.pkgkit",
         "--rm",

lib/spack/spack/compilers/intel.py

@@ -124,8 +124,8 @@ def setup_custom_environment(self, pkg, env):
         # Edge cases for Intel's oneAPI compilers when using the legacy classic compilers:
         # Always pass flags to disable deprecation warnings, since these warnings can
         # confuse tools that parse the output of compiler commands (e.g. version checks).
-        if self.real_version >= Version("2021") and self.real_version <= Version("2023"):
+        if self.real_version >= Version("2021") and self.real_version < Version("2024"):
             env.append_flags("SPACK_ALWAYS_CFLAGS", "-diag-disable=10441")
             env.append_flags("SPACK_ALWAYS_CXXFLAGS", "-diag-disable=10441")
-        if self.real_version >= Version("2021") and self.real_version <= Version("2024"):
+        if self.real_version >= Version("2021") and self.real_version < Version("2025"):
             env.append_flags("SPACK_ALWAYS_FFLAGS", "-diag-disable=10448")

lib/spack/spack/compilers/oneapi.py

@@ -155,10 +155,10 @@ def setup_custom_environment(self, pkg, env):
         # icx+icpx+ifx or icx+icpx+ifort. But to be on the safe side (some users may
         # want to try to swap icpx against icpc, for example), and since the Intel LLVM
         # compilers accept these diag-disable flags, we apply them for all compilers.
-        if self.real_version >= Version("2021") and self.real_version <= Version("2023"):
+        if self.real_version >= Version("2021") and self.real_version < Version("2024"):
             env.append_flags("SPACK_ALWAYS_CFLAGS", "-diag-disable=10441")
             env.append_flags("SPACK_ALWAYS_CXXFLAGS", "-diag-disable=10441")
-        if self.real_version >= Version("2021") and self.real_version <= Version("2024"):
+        if self.real_version >= Version("2021") and self.real_version < Version("2025"):
             env.append_flags("SPACK_ALWAYS_FFLAGS", "-diag-disable=10448")
 
         # 2024 release bumped the libsycl version because of an ABI

lib/spack/spack/relocate.py

@@ -13,6 +13,7 @@
 import macholib.mach_o
 import macholib.MachO
 
+import llnl.util.filesystem as fs
 import llnl.util.lang
 import llnl.util.tty as tty
 from llnl.util.lang import memoized
@@ -275,10 +276,10 @@ def modify_macho_object(cur_path, rpaths, deps, idpath, paths_to_paths):
 
     # Deduplicate and flatten
     args = list(itertools.chain.from_iterable(llnl.util.lang.dedupe(args)))
+    install_name_tool = executable.Executable("install_name_tool")
     if args:
-        args.append(str(cur_path))
-        install_name_tool = executable.Executable("install_name_tool")
-        install_name_tool(*args)
+        with fs.edit_in_place_through_temporary_file(cur_path) as temp_path:
+            install_name_tool(*args, temp_path)
 
 
 def macholib_get_paths(cur_path):
@@ -717,8 +718,8 @@ def fixup_macos_rpath(root, filename):
         # No fixes needed
         return False
 
-    args.append(abspath)
-    executable.Executable("install_name_tool")(*args)
+    with fs.edit_in_place_through_temporary_file(abspath) as temp_path:
+        executable.Executable("install_name_tool")(*args, temp_path)
     return True
 
 

lib/spack/spack/schema/config.py

@@ -106,8 +106,8 @@
             {
                 "names": ["install_missing_compilers"],
                 "message": "The config:install_missing_compilers option has been deprecated in "
-                "Spack v0.23, and is currently ignored. It will be removed from config in "
-                "Spack v0.25.",
+                "Spack v0.23, and is currently ignored. It will be removed from config after "
+                "Spack v1.0.",
                 "error": False,
             },
         ],

lib/spack/spack/stage.py

@@ -488,7 +488,7 @@ def _generate_fetchers(self, mirror_only=False) -> Generator["fs.FetchStrategy",
             # Insert fetchers in the order that the URLs are provided.
             fetchers[:0] = (
                 fs.from_url_scheme(
-                    url_util.join(mirror.fetch_url, self.mirror_layout.path),
+                    url_util.join(mirror.fetch_url, *self.mirror_layout.path.split(os.sep)),
                     checksum=digest,
                     expand=expand,
                     extension=extension,

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

@@ -1249,3 +1249,14 @@ def test_find_input_types(tmp_path: pathlib.Path):
 
     with pytest.raises(TypeError):
         fs.find(1, "file.txt")  # type: ignore
+
+
+def test_edit_in_place_through_temporary_file(tmp_path):
+    (tmp_path / "example.txt").write_text("Hello")
+    current_ino = os.stat(tmp_path / "example.txt").st_ino
+    with fs.edit_in_place_through_temporary_file(tmp_path / "example.txt") as temporary:
+        os.unlink(temporary)
+        with open(temporary, "w") as f:
+            f.write("World")
+    assert (tmp_path / "example.txt").read_text() == "World"
+    assert os.stat(tmp_path / "example.txt").st_ino == current_ino

lib/spack/spack/test/traverse.py

@@ -20,9 +20,8 @@ def create_dag(nodes, edges):
     """
     specs = {name: Spec(name) for name in nodes}
     for parent, child, deptypes in edges:
-        specs[parent].add_dependency_edge(
-            specs[child], depflag=dt.canonicalize(deptypes), virtuals=()
-        )
+        depflag = deptypes if isinstance(deptypes, dt.DepFlag) else dt.canonicalize(deptypes)
+        specs[parent].add_dependency_edge(specs[child], depflag=depflag, virtuals=())
     return specs
 
 
@@ -454,3 +453,61 @@ def test_topo_is_bfs_for_trees(cover):
     assert list(traverse.traverse_nodes([binary_tree["A"]], order="topo", cover=cover)) == list(
         traverse.traverse_nodes([binary_tree["A"]], order="breadth", cover=cover)
     )
+
+
+@pytest.mark.parametrize("roots", [["A"], ["A", "B"], ["B", "A"], ["A", "B", "A"]])
+@pytest.mark.parametrize("order", ["breadth", "post", "pre"])
+@pytest.mark.parametrize("include_root", [True, False])
+def test_mixed_depth_visitor(roots, order, include_root):
+    """Test that the MixedDepthVisitor lists unique edges that are reachable either directly from
+    roots through build type edges, or transitively through link type edges. The tests ensures that
+    unique edges are listed exactly once."""
+    my_graph = create_dag(
+        nodes=["A", "B", "C", "D", "E", "F", "G", "H", "I"],
+        edges=(
+            ("A", "B", dt.LINK | dt.RUN),
+            ("A", "C", dt.BUILD),
+            ("A", "D", dt.BUILD | dt.RUN),
+            ("A", "H", dt.LINK),
+            ("A", "I", dt.RUN),
+            ("B", "D", dt.BUILD | dt.LINK),
+            ("C", "E", dt.BUILD | dt.LINK | dt.RUN),
+            ("D", "F", dt.LINK),
+            ("D", "G", dt.BUILD | dt.RUN),
+            ("H", "B", dt.LINK),
+        ),
+    )
+    starting_points = traverse.with_artificial_edges([my_graph[root] for root in roots])
+    visitor = traverse.MixedDepthVisitor(direct=dt.BUILD, transitive=dt.LINK)
+
+    if order == "pre":
+        edges = traverse.traverse_depth_first_edges_generator(
+            starting_points, visitor, post_order=False, root=include_root
+        )
+    elif order == "post":
+        edges = traverse.traverse_depth_first_edges_generator(
+            starting_points, visitor, post_order=True, root=include_root
+        )
+    elif order == "breadth":
+        edges = traverse.traverse_breadth_first_edges_generator(
+            starting_points, visitor, root=include_root
+        )
+
+    artificial_edges = [(None, root) for root in roots] if include_root else []
+    simple_edges = [
+        (None if edge.parent is None else edge.parent.name, edge.spec.name) for edge in edges
+    ]
+
+    # make sure that every edge is listed exactly once and that the right edges are listed
+    assert len(simple_edges) == len(set(simple_edges))
+    assert set(simple_edges) == {
+        # the roots
+        *artificial_edges,
+        ("A", "B"),
+        ("A", "C"),
+        ("A", "D"),
+        ("A", "H"),
+        ("B", "D"),
+        ("D", "F"),
+        ("H", "B"),
+    }

lib/spack/spack/test/versions.py

@@ -607,6 +607,9 @@ def test_stringify_version(version_str):
     v.string = None
     assert str(v) == version_str
 
+    v.string = None
+    assert v.string == version_str
+
 
 def test_len():
     a = Version("1.2.3.4")