cmake.py: include transitive run deps in CMAKE_PREFIX_PATH

- Run deps often need to be located during the build
- In cases like python-venv and python, where there's a direct build dep
  on both, but python-venv has a run dep on python, meaning we'd rather
  see python-venv in path before python topologically.

.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] }}

lib/spack/llnl/util/filesystem.py

@@ -24,6 +24,7 @@
     Callable,
     Deque,
     Dict,
+    Generator,
     Iterable,
     List,
     Match,
@@ -2838,6 +2839,25 @@ 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 llnl.util.filesystem as fs
 from llnl.util.lang import stable_partition
@@ -21,6 +21,7 @@
 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
@@ -166,15 +167,18 @@ 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 | dt.RUN, 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/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/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/traverse.py

@@ -4,7 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from collections import defaultdict
-from typing import NamedTuple, Union
+from typing import Any, Callable, List, NamedTuple, Set, Union
 
 import spack.deptypes as dt
 import spack.spec
@@ -115,6 +115,64 @@ def neighbors(self, item):
         return self.visitor.neighbors(item)
 
 
+class MixedDepthVisitor:
+    """Visits all unique edges of the sub-DAG induced by direct dependencies of type ``direct``
+    and transitive dependencies of type ``transitive``. An example use for this is traversing build
+    type dependencies non-recursively, and link dependencies recursively."""
+
+    def __init__(
+        self,
+        *,
+        direct: dt.DepFlag,
+        transitive: dt.DepFlag,
+        key: Callable[["spack.spec.Spec"], Any] = id,
+    ) -> None:
+        self.direct_type = direct
+        self.transitive_type = transitive
+        self.key = key
+        self.seen: Set[Any] = set()
+        self.seen_roots: Set[Any] = set()
+
+    def accept(self, item: EdgeAndDepth) -> bool:
+        # Do not accept duplicate root nodes. This only happens if the user starts iterating from
+        # multiple roots and lists one of the roots multiple times.
+        if item.edge.parent is None:
+            node_id = self.key(item.edge.spec)
+            if node_id in self.seen_roots:
+                return False
+            self.seen_roots.add(node_id)
+        return True
+
+    def neighbors(self, item: EdgeAndDepth) -> List[EdgeAndDepth]:
+        # If we're here through an artificial source node, it's a root, and we return all
+        # direct_type  and transitive_type edges. If we're here through a transitive_type edge, we
+        # return all transitive_type edges. To avoid returning the same edge twice:
+        # 1. If we had already encountered the current node through a transitive_type edge, we
+        #    don't need to return transitive_type edges again.
+        # 2. If we encounter the current node through a direct_type edge, and we had already seen
+        #    it through a transitive_type edge, only return the non-transitive_type, direct_type
+        #    edges.
+        node_id = self.key(item.edge.spec)
+        seen = node_id in self.seen
+        is_root = item.edge.parent is None
+        follow_transitive = is_root or bool(item.edge.depflag & self.transitive_type)
+        follow = self.direct_type if is_root else dt.NONE
+
+        if follow_transitive and not seen:
+            follow |= self.transitive_type
+            self.seen.add(node_id)
+        elif follow == dt.NONE:
+            return []
+
+        edges = item.edge.spec.edges_to_dependencies(depflag=follow)
+
+        # filter direct_type edges already followed before becuase they were also transitive_type.
+        if seen:
+            edges = [edge for edge in edges if not edge.depflag & self.transitive_type]
+
+        return sort_edges(edges)
+
+
 def get_visitor_from_args(
     cover, direction, depflag: Union[dt.DepFlag, dt.DepTypes], key=id, visited=None, visitor=None
 ):
@@ -342,9 +400,7 @@ def traverse_topo_edges_generator(edges, visitor, key=id, root=True, all_edges=F
     # maps parent identifier to a list of edges, where None is a special identifier
     # for the artificial root/source.
     node_to_edges = defaultdict(list)
-    for edge in traverse_breadth_first_edges_generator(
-        edges, CoverEdgesVisitor(visitor, key=key), root=True, depth=False
-    ):
+    for edge in traverse_breadth_first_edges_generator(edges, visitor, root=True, depth=False):
         in_edge_count[key(edge.spec)] += 1
         parent_id = key(edge.parent) if edge.parent is not None else None
         node_to_edges[parent_id].append(edge)
@@ -422,9 +478,9 @@ def traverse_edges(
     elif order not in ("post", "pre", "breadth"):
         raise ValueError(f"Unknown order {order}")
 
-    # In topo traversal we need to construct a sub-DAG including all edges even if we are yielding
-    # a subset of them, hence "paths".
-    _cover = "paths" if order == "topo" else cover
+    # In topo traversal we need to construct a sub-DAG including all unique edges even if we are
+    # yielding a subset of them, hence "edges".
+    _cover = "edges" if order == "topo" else cover
     visitor = get_visitor_from_args(_cover, direction, deptype, key, visited)
     root_edges = with_artificial_edges(specs)
 

lib/spack/spack/util/filesystem.py

@@ -13,7 +13,7 @@
 import sys
 
 from llnl.util import tty
-from llnl.util.filesystem import join_path
+from llnl.util.filesystem import edit_in_place_through_temporary_file
 from llnl.util.lang import memoized
 
 from spack.util.executable import Executable, which
@@ -81,12 +81,11 @@ def fix_darwin_install_name(path):
     Parameters:
         path (str): directory in which .dylib files are located
     """
-    libs = glob.glob(join_path(path, "*.dylib"))
+    libs = glob.glob(os.path.join(path, "*.dylib"))
+    install_name_tool = Executable("install_name_tool")
+    otool = Executable("otool")
     for lib in libs:
-        # fix install name first:
-        install_name_tool = Executable("install_name_tool")
-        install_name_tool("-id", lib, lib)
-        otool = Executable("otool")
+        args = ["-id", lib]
         long_deps = otool("-L", lib, output=str).split("\n")
         deps = [dep.partition(" ")[0][1::] for dep in long_deps[2:-1]]
         # fix all dependencies:
@@ -98,5 +97,8 @@ def fix_darwin_install_name(path):
                 # but we don't know builddir (nor how symbolic links look
                 # in builddir). We thus only compare the basenames.
                 if os.path.basename(dep) == os.path.basename(loc):
-                    install_name_tool("-change", dep, loc, lib)
+                    args.extend(("-change", dep, loc))
                     break
+
+        with edit_in_place_through_temporary_file(lib) as tmp:
+            install_name_tool(*args, tmp)

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

@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
+
 from spack.package import *
 
 
@@ -126,6 +128,18 @@ class Dbcsr(CMakePackage, CudaPackage, ROCmPackage):
     generator("ninja")
     depends_on("ninja@1.10:", type="build")
 
+    @when("+rocm")
+    def patch(self):
+        for directory, subdirectory, files in os.walk(os.getcwd()):
+            for i in files:
+                file_path = os.path.join(directory, i)
+                filter_file("USE ISO_C_BINDING", "USE,INTRINSIC :: ISO_C_BINDING", file_path)
+                filter_file("USE ISO_FORTRAN_ENV", "USE,INTRINSIC :: ISO_FORTRAN_ENV", file_path)
+                filter_file("USE omp_lib", "USE,INTRINSIC :: omp_lib", file_path)
+                filter_file("USE OMP_LIB", "USE,INTRINSIC :: OMP_LIB", file_path)
+                filter_file("USE iso_c_binding", "USE,INTRINSIC :: iso_c_binding", file_path)
+                filter_file("USE iso_fortran_env", "USE,INTRINSIC :: iso_fortran_env", file_path)
+
     def cmake_args(self):
         spec = self.spec
 

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

@@ -22,6 +22,11 @@ class Eospac(Package):
     #   previous stable release will appear first as a new beta.
     # - alpha and beta versions are marked with 'deprecated=True' to help
     #   spack's version comparison.
+    version(
+        "6.5.12",
+        sha256="62d5f4a6a30c9acb426bd6bd972edc7fad392e5b941f950126ed0d3be5fd5162",
+        url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.5.12_39364aabc75c3312022b12e6d16d6a31f1f8945f.tgz",
+    )
     version(
         "6.5.11",
         sha256="ed821b5a1bf45df1443d5f72d86190317ed9f5bad6a7c73e23bb4365bd76e24c",

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

@@ -439,6 +439,11 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage, CompilerPackage):
             sha256="1529cff128792fe197ede301a81b02036c8168cb0338df21e4bc7aafe755305a",
             when="@14.1.0 target=aarch64:",
         )
+        patch(
+            "https://raw.githubusercontent.com/Homebrew/formula-patches/f30c309442a60cfb926e780eae5d70571f8ab2cb/gcc/gcc-14.2.0-r2.diff",
+            sha256="6c0a4708f35ccf2275e6401197a491e3ad77f9f0f9ef5761860768fa6da14d3d",
+            when="@14.2.0 target=aarch64:",
+        )
         conflicts("+bootstrap", when="@11.3.0,13.1: target=aarch64:")
 
         # Use -headerpad_max_install_names in the build,

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

@@ -58,6 +58,9 @@ class Hip(CMakePackage):
     conflicts("+asan", when="os=centos7")
     conflicts("+asan", when="os=centos8")
 
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
+
     depends_on("cuda", when="+cuda")
 
     depends_on("cmake@3.16.8:", type="build")
@@ -531,12 +534,6 @@ def patch(self):
                 "clr/hipamd/hip-config-amd.cmake",
                 string=True,
             )
-            filter_file(
-                '"${ROCM_PATH}/llvm"',
-                self.spec["llvm-amdgpu"].prefix,
-                "clr/hipamd/src/hiprtc/CMakeLists.txt",
-                string=True,
-            )
         perl = self.spec["perl"].command
 
         if self.spec.satisfies("@:5.5"):
@@ -561,7 +558,12 @@ def patch(self):
                     filter_file(" -lnuma", f" -L{numactl} -lnuma", "hipBin_amd.h")
 
     def cmake_args(self):
-        args = []
+        args = [
+            # find_package(Clang) and find_package(LLVM) in clr/hipamd/src/hiprtc/CMakeLists.txt
+            # should find llvm-amdgpu
+            self.define("LLVM_ROOT", self.spec["llvm-amdgpu"].prefix),
+            self.define("Clang_ROOT", self.spec["llvm-amdgpu"].prefix),
+        ]
         if self.spec.satisfies("+rocm"):
             args.append(self.define("HSA_PATH", self.spec["hsa-rocr-dev"].prefix))
             args.append(self.define("HIP_COMPILER", "clang"))

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

@@ -19,7 +19,7 @@ class Hypre(AutotoolsPackage, CudaPackage, ROCmPackage):
     git = "https://github.com/hypre-space/hypre.git"
     tags = ["e4s", "radiuss"]
 
-    maintainers("ulrikeyang", "osborn9", "balay")
+    maintainers("ulrikeyang", "osborn9", "victorapm", "balay")
 
     test_requires_compiler = True
 
@@ -74,6 +74,7 @@ class Hypre(AutotoolsPackage, CudaPackage, ROCmPackage):
     variant(
         "superlu-dist", default=False, description="Activates support for SuperLU_Dist library"
     )
+    variant("lapack", default=True, description="Use external blas/lapack")
     variant("int64", default=False, description="Use 64bit integers")
     variant("mixedint", default=False, description="Use 64bit integers while reducing memory use")
     variant("complex", default=False, description="Use complex values")
@@ -123,8 +124,8 @@ def patch(self):  # fix sequential compilation in 'src/seq_mv'
         filter_file("\tmake", "\t$(MAKE)", "src/seq_mv/Makefile")
 
     depends_on("mpi", when="+mpi")
-    depends_on("blas")
-    depends_on("lapack")
+    depends_on("blas", when="+lapack")
+    depends_on("lapack", when="+lapack")
     depends_on("magma", when="+magma")
     depends_on("superlu-dist", when="+superlu-dist+mpi")
     depends_on("rocsparse", when="+rocm")
@@ -198,17 +199,20 @@ def url_for_version(self, version):
 
     def configure_args(self):
         spec = self.spec
-        # Note: --with-(lapack|blas)_libs= needs space separated list of names
-        lapack = spec["lapack"].libs
-        blas = spec["blas"].libs
+        configure_args = [f"--prefix={prefix}"]
 
-        configure_args = [
-            "--prefix=%s" % prefix,
-            "--with-lapack-libs=%s" % " ".join(lapack.names),
-            "--with-lapack-lib-dirs=%s" % " ".join(lapack.directories),
-            "--with-blas-libs=%s" % " ".join(blas.names),
-            "--with-blas-lib-dirs=%s" % " ".join(blas.directories),
-        ]
+        # Note: --with-(lapack|blas)_libs= needs space separated list of names
+        if spec.satisfies("+lapack"):
+            configure_args.append("--with-lapack")
+            configure_args.append("--with-blas")
+            configure_args.append("--with-lapack-libs=%s" % " ".join(spec["lapack"].libs.names))
+            configure_args.append("--with-blas-libs=%s" % " ".join(spec["blas"].libs.names))
+            configure_args.append(
+                "--with-lapack-lib-dirs=%s" % " ".join(spec["lapack"].libs.directories)
+            )
+            configure_args.append(
+                "--with-blas-lib-dirs=%s" % " ".join(spec["blas"].libs.directories)
+            )
 
         if spec.satisfies("+mpi"):
             os.environ["CC"] = spec["mpi"].mpicc
@@ -245,7 +249,9 @@ def configure_args(self):
             configure_args.append("--without-superlu")
             # MLI and FEI do not build without superlu on Linux
             configure_args.append("--without-mli")
-            configure_args.append("--without-fei")
+            # FEI option was removed in hypre 2.17
+            if self.version < Version("2.17.0"):
+                configure_args.append("--without-fei")
 
         if spec.satisfies("+superlu-dist"):
             configure_args.append(

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

@@ -22,6 +22,12 @@ class IntelOneapiDpl(IntelOneApiLibraryPackage):
 
     homepage = "https://github.com/oneapi-src/oneDPL"
 
+    version(
+        "2022.7.1",
+        url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/de3c613f-829c-4bdc-aa2b-6129eece3bd9/intel-onedpl-2022.7.1.15_offline.sh",
+        sha256="737f8d29f50fcb26abf7a39373305c177d8b91a70dbc5fed9d41aabfcc8bad5a",
+        expand=False,
+    )
     version(
         "2022.7.0",
         url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/85ad74ff-f4fa-45e2-b50d-67d637d42baa/intel-onedpl-2022.7.0.647_offline.sh",

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

@@ -21,6 +21,12 @@ class IntelOneapiMpi(IntelOneApiLibraryPackage):
 
     homepage = "https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/mpi-library.html"
 
+    version(
+        "2021.14.1",
+        url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/1acd5e79-796c-401a-ab31-a3dc7b20c6a2/intel-mpi-2021.14.1.7_offline.sh",
+        sha256="6459b9fc81fad9b9955de7fd9904e67fcf2ada3564ce0a74b9c14ea8fb533ddf",
+        expand=False,
+    )
     version(
         "2021.14.0",
         url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/4b14b28c-2ca6-4559-a0ca-8a157627e0c8/intel-mpi-2021.14.0.791_offline.sh",

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

@@ -383,6 +383,7 @@ def cmake_args(self):
         # - MVAPICH --> mvapich
         # - HPE MPT --> mpt
         # - Cray MPICH --> mpich
+        # - HPC-X --> openmpi
 
         if self.spec.satisfies("^mpich"):
             args.append(self.define("MPI_STACK", "mpich"))
@@ -398,6 +399,8 @@ def cmake_args(self):
             args.append(self.define("MPI_STACK", "mpt"))
         elif self.spec.satisfies("^cray-mpich"):
             args.append(self.define("MPI_STACK", "mpich"))
+        elif self.spec.satisfies("^hpcx-mpi"):
+            args.append(self.define("MPI_STACK", "openmpi"))
         else:
             raise InstallError("Unsupported MPI stack")
 

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

@@ -702,8 +702,10 @@ def find_optional_library(name, prefix):
         if "+mpi" in spec:
             options += ["MPICXX=%s" % spec["mpi"].mpicxx]
             hypre = spec["hypre"]
-            # The hypre package always links with 'blas' and 'lapack'.
-            all_hypre_libs = hypre.libs + hypre["lapack"].libs + hypre["blas"].libs
+            all_hypre_libs = hypre.libs
+            if "+lapack" in hypre:
+                all_hypre_libs += hypre["lapack"].libs + hypre["blas"].libs
+
             hypre_gpu_libs = ""
             if "+cuda" in hypre:
                 hypre_gpu_libs = " -lcusparse -lcurand -lcublas"

var/spack/repos/builtin/packages/netlib-scalapack/package.py

@@ -92,6 +92,8 @@ def cmake_args(self):
             or spec.satisfies("%apple-clang")
             or spec.satisfies("%oneapi")
             or spec.satisfies("%arm")
+            or spec.satisfies("%cce")
+            or spec.satisfies("%rocmcc")
         ):
             c_flags.append("-Wno-error=implicit-function-declaration")
 
@@ -116,6 +118,8 @@ class NetlibScalapack(ScalapackBase):
     git = "https://github.com/Reference-ScaLAPACK/scalapack"
     tags = ["e4s"]
 
+    maintainers("etiennemlb")
+
     license("BSD-3-Clause-Open-MPI")
 
     version("2.2.0", sha256="40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57")

var/spack/repos/builtin/packages/nghttp2/package.py

@@ -15,6 +15,7 @@ class Nghttp2(AutotoolsPackage):
 
     license("MIT")
 
+    version("1.64.0", sha256="20e73f3cf9db3f05988996ac8b3a99ed529f4565ca91a49eb0550498e10621e8")
     version("1.63.0", sha256="9318a2cc00238f5dd6546212109fb833f977661321a2087f03034e25444d3dbb")
     version("1.62.1", sha256="d0b0b9d00500ee4aa3bfcac00145d3b1ef372fd301c35bff96cf019c739db1b4")
     version("1.62.0", sha256="482e41a46381d10adbdfdd44c1942ed5fd1a419e0ab6f4a5ff5b61468fe6f00d")

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

@@ -19,6 +19,7 @@ class PyJoblib(PythonPackage):
 
     license("BSD-3-Clause")
 
+    version("1.4.2", sha256="2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e")
     version("1.2.0", sha256="e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018")
     version("1.1.0", sha256="4158fcecd13733f8be669be0683b96ebdbbd38d23559f54dca7205aea1bf1e35")
     version("1.0.1", sha256="9c17567692206d2f3fb9ecf5e991084254fe631665c450b443761c4186a613f7")
@@ -35,7 +36,10 @@ class PyJoblib(PythonPackage):
     version("0.10.2", sha256="3123553bdad83b143428033537c9e1939caf4a4d8813dade6a2246948c94494b")
     version("0.10.0", sha256="49b3a0ba956eaa2f077e1ebd230b3c8d7b98afc67520207ada20a4d8b8efd071")
 
-    depends_on("python@3.7:", when="@1.2:", type=("build", "run"))
-    depends_on("python@3.6:", when="@0.15:", type=("build", "run"))
-    depends_on("python@2.7:2.8,3.4:", type=("build", "run"))
-    depends_on("py-setuptools", type=("build", "run"))
+    with default_args(type=("build", "run")):
+        # https://github.com/joblib/joblib/pull/1361
+        depends_on("python@:3.11", when="@:1.2")
+
+    with default_args(type="build"):
+        depends_on("py-setuptools@61.2:", when="@1.4:")
+        depends_on("py-setuptools")

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

@@ -23,6 +23,7 @@ class PyKeras(PythonPackage):
     maintainers("adamjstewart")
     license("Apache-2.0")
 
+    version("3.7.0", sha256="a4451a5591e75dfb414d0b84a3fd2fb9c0240cc87ebe7e397f547ce10b0e67b7")
     version("3.6.0", sha256="405727525a3522ed8f9ec0b46e0667e4c65fcf714a067322c16a00d902ded41d")
     version("3.5.0", sha256="53ae4f9472ec9d9c6941c82a3fda86969724ace3b7630a94ba0a1f17ba1065c3")
     version("3.4.1", sha256="34cd9aeaa008914715149234c215657ca758e1b473bd2aab2e211ac967d1f8fe")
@@ -74,10 +75,12 @@ class PyKeras(PythonPackage):
     )
 
     with default_args(type="build"):
+        # pyproject.toml
+        depends_on("py-setuptools@61:", when="@3.7:")
         depends_on("py-setuptools")
 
     with default_args(type=("build", "run")):
-        # setup.py
+        # pyproject.toml
         depends_on("python@3.9:", when="@3:")
         depends_on("python@3.8:", when="@2.12:")
         depends_on("py-absl-py", when="@2.6:")
@@ -98,7 +101,8 @@ class PyKeras(PythonPackage):
 
         # requirements-tensorflow-cuda.txt
         with when("backend=tensorflow"):
-            depends_on("py-tensorflow@2.17", when="@3.5:")
+            depends_on("py-tensorflow@2.18", when="@3.7:")
+            depends_on("py-tensorflow@2.17", when="@3.5:3.6")
             depends_on("py-tensorflow@2.16.1:2.16", when="@3.0:3.4")
 
         # requirements-jax-cuda.txt
@@ -109,13 +113,15 @@ class PyKeras(PythonPackage):
 
         # requirements-torch-cuda.txt
         with when("backend=torch"):
-            depends_on("py-torch@2.4.1", when="@3.6:")
+            depends_on("py-torch@2.5.1", when="@3.7:")
+            depends_on("py-torch@2.4.1", when="@3.6")
             depends_on("py-torch@2.4.0", when="@3.5")
             depends_on("py-torch@2.2.1", when="@3.1:3.4")
             depends_on("py-torch@2.1.2", when="@3.0.3:3.0.5")
             depends_on("py-torch@2.1.1", when="@3.0.1:3.0.2")
             depends_on("py-torch@2.1.0", when="@3.0.0")
-            depends_on("py-torchvision@0.19.1", when="@3.6:")
+            depends_on("py-torchvision@0.20.1", when="@3.7:")
+            depends_on("py-torchvision@0.19.1", when="@3.6")
             depends_on("py-torchvision@0.19.0", when="@3.5")
             depends_on("py-torchvision@0.17.1", when="@3.1:3.4")
             depends_on("py-torchvision@0.16.2", when="@3.0.3:3.0.5")

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

@@ -73,6 +73,7 @@ class PyPandas(PythonPackage):
     variant("excel", when="@1.4:", default=False, description="Build with support for Excel")
 
     depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
     with default_args(type="build"):
         depends_on("py-meson-python@0.13.1:", when="@2.1:")

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

@@ -33,7 +33,8 @@ class PyPyvista(PythonPackage):
     depends_on("pil", type=("build", "run"))
     depends_on("py-pooch", when="@0.37:", type=("build", "run"))
     depends_on("py-scooby@0.5.1:", type=("build", "run"))
-    depends_on("vtk+python", type=("build", "run"))
+    # https://github.com/pyvista/pyvista/issues/6857
+    depends_on("vtk@:9.3+python", type=("build", "run"))
     depends_on("py-typing-extensions", when="^python@:3.7", type=("build", "run"))
 
     # Historical dependencies

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

@@ -30,3 +30,6 @@ class PyRiver(PythonPackage):
     depends_on("py-numpy@1.22:", type=("build", "run"))
     depends_on("py-scipy@1.5:", type=("build", "run"))
     depends_on("py-pandas@1.3:", type=("build", "run"))
+
+    # https://github.com/online-ml/river/pull/1632
+    depends_on("py-numpy@:1", when="@:0.21", type=("build", "run"))

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

@@ -14,6 +14,10 @@ class PyScooby(PythonPackage):
 
     license("MIT")
 
+    version("0.10.0", sha256="7ea33c262c0cc6a33c6eeeb5648df787be4f22660e53c114e5fff1b811a8854f")
     version("0.5.7", sha256="ae2c2b6f5f5d10adf7aaab32409028f1e28d3ce833664bdd1e8c2072e8da169a")
 
+    # https://github.com/banesullivan/scooby/pull/83
+    depends_on("python@:3.11", when="@:0.5", type=("build", "run"))
     depends_on("py-setuptools", type="build")
+    depends_on("py-setuptools-scm", when="@0.10:", type="build")

var/spack/repos/builtin/packages/py-torch-cluster/package.py

@@ -18,7 +18,8 @@ class PyTorchCluster(PythonPackage):
 
     version("1.6.3", sha256="78d5a930a5bbd0d8788df8c6d66addd68d6dd292fe3edb401e3dacba26308152")
 
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
     depends_on("python", type=("build", "link", "run"))
     depends_on("py-setuptools", type="build")

var/spack/repos/builtin/packages/py-torch-scatter/package.py

@@ -18,7 +18,8 @@ class PyTorchScatter(PythonPackage):
 
     version("2.1.2", sha256="69b3aa435f2424ac6a1bfb6ff702da6eb73b33ca0db38fb26989c74159258e47")
 
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
     depends_on("python", type=("build", "link", "run"))
     depends_on("py-setuptools", type="build")

var/spack/repos/builtin/packages/py-torch-spline-conv/package.py

@@ -18,7 +18,8 @@ class PyTorchSplineConv(PythonPackage):
 
     version("1.2.2", sha256="ed45a81da29f774665dbdd4709d7e534cdf16d2e7006dbd06957f35bd09661b2")
 
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
     depends_on("python", type=("build", "link", "run"))
     depends_on("py-setuptools", type="build")

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

@@ -17,6 +17,7 @@ class Raylib(CMakePackage):
 
     license("Zlib", checked_by="georgemalerbo")
 
+    version("5.5", sha256="aea98ecf5bc5c5e0b789a76de0083a21a70457050ea4cc2aec7566935f5e258e")
     version("5.0", sha256="98f049b9ea2a9c40a14e4e543eeea1a7ec3090ebdcd329c4ca2cf98bc9793482")
 
     depends_on("c", type="build")  # generated

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

@@ -40,7 +40,8 @@ class Rocfft(CMakePackage):
         version("5.3.3", sha256="678c18710578c1fb36a0009311bb79de7607c3468f9102cfba56a866ebb7ff78")
         version("5.3.0", sha256="d655c5541c4aff4267e80e36d002fc3a55c2f84a0ae8631197c12af3bf03fa7d")
 
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
     amdgpu_targets = ROCmPackage.amdgpu_targets
 

var/spack/repos/builtin/packages/roctracer-dev/package.py

@@ -41,7 +41,8 @@ class RoctracerDev(CMakePackage, ROCmPackage):
         version("5.3.3", sha256="f2cb1e6bb69ea1a628c04f984741f781ae1d8498dc58e15795bb03015f924d13")
         version("5.3.0", sha256="36f1da60863a113bb9fe2957949c661f00a702e249bb0523cda1fb755c053808")
 
-    depends_on("cxx", type="build")  # generated
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
 
     variant("asan", default=False, description="Build with address-sanitizer enabled or disabled")
 

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

@@ -12,7 +12,7 @@ class Rsync(AutotoolsPackage):
     """An open source utility that provides fast incremental file transfer."""
 
     homepage = "https://rsync.samba.org"
-    url = "https://download.samba.org/pub/rsync/src/rsync-3.2.4.tar.gz"
+    url = "https://download.samba.org/pub/rsync/src/rsync-3.3.0.tar.gz"
 
     license("GPL-3.0-or-later")
 
@@ -20,16 +20,42 @@ class Rsync(AutotoolsPackage):
     version("3.2.7", sha256="4e7d9d3f6ed10878c58c5fb724a67dacf4b6aac7340b13e488fb2dc41346f2bb")
     version("3.2.6", sha256="fb3365bab27837d41feaf42e967c57bd3a47bc8f10765a3671efd6a3835454d3")
     version("3.2.5", sha256="2ac4d21635cdf791867bc377c35ca6dda7f50d919a58be45057fd51600c69aba")
-    version("3.2.4", sha256="6f761838d08052b0b6579cf7f6737d93e47f01f4da04c5d24d3447b7f2a5fad1")
-    version("3.2.3", sha256="becc3c504ceea499f4167a260040ccf4d9f2ef9499ad5683c179a697146ce50e")
-    version("3.2.2", sha256="644bd3841779507665211fd7db8359c8a10670c57e305b4aab61b4e40037afa8")
-    version("3.1.3", sha256="55cc554efec5fdaad70de921cd5a5eeb6c29a95524c715f3bbf849235b0800c0")
-    version("3.1.2", sha256="ecfa62a7fa3c4c18b9eccd8c16eaddee4bd308a76ea50b5c02a5840f09c0a1c2")
-    version("3.1.1", sha256="7de4364fcf5fe42f3bdb514417f1c40d10bbca896abe7e7f2c581c6ea08a2621")
 
-    depends_on("c", type="build")  # generated
-    depends_on("cxx", type="build")  # generated
+    # Releases before 3.2.5 are deprecated because of CVE-2022-29154
+    # https://nvd.nist.gov/vuln/detail/CVE-2022-29154
+    version(
+        "3.2.4",
+        sha256="6f761838d08052b0b6579cf7f6737d93e47f01f4da04c5d24d3447b7f2a5fad1",
+        deprecated=True,
+    )
+    version(
+        "3.2.3",
+        sha256="becc3c504ceea499f4167a260040ccf4d9f2ef9499ad5683c179a697146ce50e",
+        deprecated=True,
+    )
+    version(
+        "3.2.2",
+        sha256="644bd3841779507665211fd7db8359c8a10670c57e305b4aab61b4e40037afa8",
+        deprecated=True,
+    )
+    version(
+        "3.1.3",
+        sha256="55cc554efec5fdaad70de921cd5a5eeb6c29a95524c715f3bbf849235b0800c0",
+        deprecated=True,
+    )
+    version(
+        "3.1.2",
+        sha256="ecfa62a7fa3c4c18b9eccd8c16eaddee4bd308a76ea50b5c02a5840f09c0a1c2",
+        deprecated=True,
+    )
+    version(
+        "3.1.1",
+        sha256="7de4364fcf5fe42f3bdb514417f1c40d10bbca896abe7e7f2c581c6ea08a2621",
+        deprecated=True,
+    )
 
+    depends_on("c", type="build")
+    depends_on("cxx", type="build")
     depends_on("zlib-api")
     depends_on("popt")
     depends_on("openssl", when="@3.2:")

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

@@ -304,6 +304,9 @@ class Seacas(CMakePackage):
         when="@:2023-10-24",
     )
 
+    # Based on install-tpl.sh script, cereal seems to only be used when faodel enabled
+    depends_on("cereal", when="@2021-04-02: +faodel")
+
     def setup_run_environment(self, env):
         env.prepend_path("PYTHONPATH", self.prefix.lib)
 
@@ -486,6 +489,15 @@ def cmake_args(self):
             if pkg.lower() in spec:
                 options.append(define(pkg + "_ROOT", spec[pkg.lower()].prefix))
 
+        if "+faodel" in spec:
+            # faodel headers are under $faodel_prefix/include/faodel but seacas
+            # leaves off the faodel part
+            faodel_incdir = spec["faodel"].prefix.include
+            faodel_incdir2 = spec["faodel"].prefix.include.faodel
+            faodel_incdirs = [faodel_incdir, faodel_incdir2]
+            options.append(define("Faodel_INCLUDE_DIRS", ";".join(faodel_incdirs)))
+            options.append(define("Faodel_LIBRARY_DIRS", spec["faodel"].prefix.lib))
+
         options.append(from_variant("TPL_ENABLE_ADIOS2", "adios2"))
         if "+adios2" in spec:
             options.append(define("ADIOS2_ROOT", spec["adios2"].prefix))