add regression number

Co-authored-by: jacobrking <jacobrking@users.noreply.github.com>

.github/workflows/audit.yaml

@@ -19,7 +19,7 @@ jobs:
   package-audits:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
       with:
         python-version: ${{inputs.python_version}}

.github/workflows/bootstrap.yml

@@ -24,7 +24,7 @@ jobs:
               make patch unzip which xz python3 python3-devel tree \
               cmake bison bison-devel libstdc++-static
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           fetch-depth: 0
       - name: Setup non-root user
@@ -62,7 +62,7 @@ jobs:
               make patch unzip xz-utils python3 python3-dev tree \
               cmake bison
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           fetch-depth: 0
       - name: Setup non-root user
@@ -99,7 +99,7 @@ jobs:
               bzip2 curl file g++ gcc gfortran git gnupg2 gzip \
               make patch unzip xz-utils python3 python3-dev tree
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           fetch-depth: 0
       - name: Setup non-root user
@@ -133,7 +133,7 @@ jobs:
               make patch unzip which xz python3 python3-devel tree \
               cmake bison
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           fetch-depth: 0
       - name: Setup repo
@@ -158,7 +158,7 @@ jobs:
         run: |
           brew install cmake bison@2.7 tree
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
       - name: Bootstrap clingo
         run: |
           source share/spack/setup-env.sh
@@ -179,7 +179,7 @@ jobs:
         run: |
           brew install tree
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
       - name: Bootstrap clingo
         run: |
           set -ex
@@ -204,7 +204,7 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           fetch-depth: 0
       - name: Setup repo
@@ -247,7 +247,7 @@ jobs:
               bzip2 curl file g++ gcc patchelf gfortran git gzip \
               make patch unzip xz-utils python3 python3-dev tree
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           fetch-depth: 0
       - name: Setup non-root user
@@ -283,7 +283,7 @@ jobs:
               make patch unzip xz-utils python3 python3-dev tree \
               gawk
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
         with:
           fetch-depth: 0
       - name: Setup non-root user
@@ -316,7 +316,7 @@ jobs:
           # Remove GnuPG since we want to bootstrap it
           sudo rm -rf /usr/local/bin/gpg
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
       - name: Bootstrap GnuPG
         run: |
           source share/spack/setup-env.sh
@@ -333,7 +333,7 @@ jobs:
           # Remove GnuPG since we want to bootstrap it
           sudo rm -rf /usr/local/bin/gpg
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
       - name: Bootstrap GnuPG
         run: |
           source share/spack/setup-env.sh

.github/workflows/build-containers.yml

@@ -56,7 +56,7 @@ jobs:
     if: github.repository == 'spack/spack'
     steps:
       - name: Checkout
-        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+        uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
 
       - name: Set Container Tag Normal (Nightly)
         run: |
@@ -92,13 +92,13 @@ jobs:
           path: dockerfiles
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@e81a89b1732b9c48d79cd809d8d81d79c4647a18 # @v1
+        uses: docker/setup-qemu-action@2b82ce82d56a2a04d2637cd93a637ae1b359c0a7 # @v1
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@4b4e9c3e2d4531116a6f8ba8e71fc6e2cb6e6c8c # @v1
+        uses: docker/setup-buildx-action@ecf95283f03858871ff00b787d79c419715afc34 # @v1
 
       - name: Log in to GitHub Container Registry
-        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a # @v1
+        uses: docker/login-action@465a07811f14bebb1938fbed4728c6a1ff8901fc # @v1
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
@@ -106,13 +106,13 @@ jobs:
 
       - name: Log in to DockerHub
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a # @v1
+        uses: docker/login-action@465a07811f14bebb1938fbed4728c6a1ff8901fc # @v1
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build & Deploy ${{ matrix.dockerfile[0] }}
-        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671 # @v2
+        uses: docker/build-push-action@2eb1c1961a95fc15694676618e422e8ba1d63825 # @v2
         with:
           context: dockerfiles/${{ matrix.dockerfile[0] }}
           platforms: ${{ matrix.dockerfile[1] }}

.github/workflows/ci.yaml

@@ -35,7 +35,7 @@ jobs:
       core: ${{ steps.filter.outputs.core }}
       packages: ${{ steps.filter.outputs.packages }}
     steps:
-      - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+      - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
         if: ${{ github.event_name == 'push' }}
         with:
           fetch-depth: 0

.github/workflows/nightly-win-builds.yml

@@ -14,7 +14,7 @@ jobs:
   build-paraview-deps:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
       with:
         fetch-depth: 0
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0

.github/workflows/unit_tests.yaml

@@ -47,7 +47,7 @@ jobs:
           on_develop: false
 
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
       with:
         fetch-depth: 0
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
@@ -94,7 +94,7 @@ jobs:
   shell:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
       with:
         fetch-depth: 0
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
@@ -133,7 +133,7 @@ jobs:
           dnf install -y \
               bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
               make patch tcl unzip which xz
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
     - name: Setup repo and non-root user
       run: |
           git --version
@@ -152,7 +152,7 @@ jobs:
   clingo-cffi:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
       with:
         fetch-depth: 0
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
@@ -186,7 +186,7 @@ jobs:
       matrix:
         python-version: ["3.10"]
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
       with:
         fetch-depth: 0
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2

.github/workflows/valid-style.yml

@@ -18,7 +18,7 @@ jobs:
   validate:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
       with:
         python-version: '3.11'
@@ -35,7 +35,7 @@ jobs:
   style:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
       with:
         fetch-depth: 0
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
@@ -68,7 +68,7 @@ jobs:
           dnf install -y \
               bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
               make patch tcl unzip which xz
-      - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
+      - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
       - name: Setup repo and non-root user
         run: |
           git --version
@@ -81,6 +81,7 @@ jobs:
         shell: runuser -u spack-test -- bash {0}
         run: |
           source share/spack/setup-env.sh
+          spack debug report
           spack -d bootstrap now --dev
           spack style -t black
           spack unit-test -V

.github/workflows/windows_python.yml

@@ -15,7 +15,7 @@ jobs:
   unit-tests:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
       with:
         fetch-depth: 0
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
@@ -39,7 +39,7 @@ jobs:
   unit-tests-cmd:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
       with:
         fetch-depth: 0
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
@@ -63,7 +63,7 @@ jobs:
   build-abseil:
     runs-on: windows-latest
     steps:
-    - uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
+    - uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
       with:
         fetch-depth: 0
     - uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0

lib/spack/docs/environments.rst

@@ -1132,11 +1132,11 @@ index once every package is pushed. Note how this target uses the generated
    example/push/%: example/install/%
    	@mkdir -p $(dir $@)
    	$(info About to push $(SPEC) to a buildcache)
-   	$(SPACK) -e . buildcache create --allow-root --only=package --directory $(BUILDCACHE_DIR) /$(HASH)
+   	$(SPACK) -e . buildcache push --allow-root --only=package $(BUILDCACHE_DIR) /$(HASH)
    	@touch $@
 
    push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS))
    	$(info Updating the buildcache index)
-   	$(SPACK) -e . buildcache update-index --directory $(BUILDCACHE_DIR)
+   	$(SPACK) -e . buildcache update-index $(BUILDCACHE_DIR)
    	$(info Done!)
    	@touch $@

lib/spack/docs/packaging_guide.rst

@@ -3071,7 +3071,7 @@ follows:
        # The library provided by the bar virtual package
        @property
        def bar_libs(self):
-           return find_libraries("libFooBar", root=sef.home, recursive=True)
+           return find_libraries("libFooBar", root=self.home, recursive=True)
 
        # The baz virtual package home
        @property

lib/spack/docs/requirements.txt

@@ -1,8 +1,8 @@
 sphinx==6.2.1
 sphinxcontrib-programoutput==0.17
 sphinx_design==0.4.1
-sphinx-rtd-theme==1.2.1
-python-levenshtein==0.21.0
+sphinx-rtd-theme==1.2.2
+python-levenshtein==0.21.1
 docutils==0.18.1
 pygments==2.15.1
-urllib3==2.0.2
+urllib3==2.0.3

lib/spack/spack/binary_distribution.py

@@ -760,13 +760,12 @@ def hashes_to_prefixes(spec):
     }
 
 
-def get_buildinfo_dict(spec, rel=False):
+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(),
-        "relative_rpaths": rel,
         "buildpath": spack.store.layout.root,
         "spackprefix": spack.paths.prefix,
         "relative_prefix": os.path.relpath(spec.prefix, spack.store.layout.root),
@@ -1209,9 +1208,6 @@ class PushOptions(NamedTuple):
     #: Overwrite existing tarball/metadata files in buildcache
     force: bool = False
 
-    #: Whether to use relative RPATHs
-    relative: bool = False
-
     #: Allow absolute paths to package prefixes when creating a tarball
     allow_root: bool = False
 
@@ -1281,41 +1277,17 @@ def _build_tarball_in_stage_dir(spec: Spec, out_url: str, stage_dir: str, option
         raise NoOverwriteException(url_util.format(remote_specfile_path))
 
     pkg_dir = os.path.basename(spec.prefix.rstrip(os.path.sep))
-    workdir = os.path.join(stage_dir, pkg_dir)
 
-    # TODO: We generally don't want to mutate any files, but when using relative
-    # mode, Spack unfortunately *does* mutate rpaths and links ahead of time.
-    # For now, we only make a full copy of the spec prefix when in relative mode.
-
-    if options.relative:
-        # tarfile is used because it preserves hardlink etc best.
-        binaries_dir = workdir
-        temp_tarfile_name = tarball_name(spec, ".tar")
-        temp_tarfile_path = os.path.join(tarfile_dir, temp_tarfile_name)
-        with closing(tarfile.open(temp_tarfile_path, "w")) as tar:
-            tar.add(name="%s" % spec.prefix, arcname=".")
-        with closing(tarfile.open(temp_tarfile_path, "r")) as tar:
-            tar.extractall(workdir)
-        os.remove(temp_tarfile_path)
-    else:
-        binaries_dir = spec.prefix
+    binaries_dir = spec.prefix
 
     # create info for later relocation and create tar
-    buildinfo = get_buildinfo_dict(spec, options.relative)
+    buildinfo = get_buildinfo_dict(spec)
 
-    # optionally make the paths in the binaries relative to each other
-    # in the spack install tree before creating tarball
-    if options.relative:
-        make_package_relative(workdir, spec, buildinfo, options.allow_root)
-    elif not options.allow_root:
+    if not options.allow_root:
         ensure_package_relocatable(buildinfo, binaries_dir)
 
     _do_create_tarball(tarfile_path, binaries_dir, pkg_dir, buildinfo)
 
-    # remove copy of install directory
-    if options.relative:
-        shutil.rmtree(workdir)
-
     # get the sha256 checksum of the tarball
     checksum = checksum_tarball(tarfile_path)
 
@@ -1336,7 +1308,6 @@ def _build_tarball_in_stage_dir(spec: Spec, out_url: str, stage_dir: str, option
     # This will be used to determine is the directory layout has changed.
     buildinfo = {}
     buildinfo["relative_prefix"] = os.path.relpath(spec.prefix, spack.store.layout.root)
-    buildinfo["relative_rpaths"] = options.relative
     spec_dict["buildinfo"] = buildinfo
 
     with open(specfile_path, "w") as outfile:
@@ -1596,35 +1567,6 @@ def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
     return None
 
 
-def make_package_relative(workdir, spec, buildinfo, allow_root):
-    """
-    Change paths in binaries to relative paths. Change absolute symlinks
-    to relative symlinks.
-    """
-    prefix = spec.prefix
-    old_layout_root = buildinfo["buildpath"]
-    orig_path_names = list()
-    cur_path_names = list()
-    for filename in buildinfo["relocate_binaries"]:
-        orig_path_names.append(os.path.join(prefix, filename))
-        cur_path_names.append(os.path.join(workdir, filename))
-
-    platform = spack.platforms.by_name(spec.platform)
-    if "macho" in platform.binary_formats:
-        relocate.make_macho_binaries_relative(cur_path_names, orig_path_names, old_layout_root)
-
-    if "elf" in platform.binary_formats:
-        relocate.make_elf_binaries_relative(cur_path_names, orig_path_names, old_layout_root)
-
-    allow_root or relocate.ensure_binaries_are_relocatable(cur_path_names)
-    orig_path_names = list()
-    cur_path_names = list()
-    for linkname in buildinfo.get("relocate_links", []):
-        orig_path_names.append(os.path.join(prefix, linkname))
-        cur_path_names.append(os.path.join(workdir, linkname))
-    relocate.make_link_relative(cur_path_names, orig_path_names)
-
-
 def ensure_package_relocatable(buildinfo, binaries_dir):
     """Check if package binaries are relocatable."""
     binaries = [os.path.join(binaries_dir, f) for f in buildinfo["relocate_binaries"]]

lib/spack/spack/bootstrap/environment.py

@@ -175,12 +175,12 @@ def black_root_spec() -> str:
 
 def flake8_root_spec() -> str:
     """Return the root spec used to bootstrap flake8"""
-    return _root_spec("py-flake8")
+    return _root_spec("py-flake8@3.8.2:")
 
 
 def pytest_root_spec() -> str:
     """Return the root spec used to bootstrap flake8"""
-    return _root_spec("py-pytest")
+    return _root_spec("py-pytest@6.2.4:")
 
 
 def ensure_environment_dependencies() -> None:

lib/spack/spack/build_systems/python.py

@@ -180,6 +180,51 @@ def test(self):
                 work_dir="spack-test",
             )
 
+    def update_external_dependencies(self, extendee_spec=None):
+        """
+        Ensure all external python packages have a python dependency
+
+        If another package in the DAG depends on python, we use that
+        python for the dependency of the external. If not, we assume
+        that the external PythonPackage is installed into the same
+        directory as the python it depends on.
+        """
+        # TODO: Include this in the solve, rather than instantiating post-concretization
+        if "python" not in self.spec:
+            if extendee_spec:
+                python = extendee_spec
+            elif "python" in self.spec.root:
+                python = self.spec.root["python"]
+            else:
+                python = self.get_external_python_for_prefix()
+                if not python.concrete:
+                    repo = spack.repo.path.repo_for_pkg(python)
+                    python.namespace = repo.namespace
+
+                    # Ensure architecture information is present
+                    if not python.architecture:
+                        host_platform = spack.platforms.host()
+                        host_os = host_platform.operating_system("default_os")
+                        host_target = host_platform.target("default_target")
+                        python.architecture = spack.spec.ArchSpec(
+                            (str(host_platform), str(host_os), str(host_target))
+                        )
+                    else:
+                        if not python.architecture.platform:
+                            python.architecture.platform = spack.platforms.host()
+                        if not python.architecture.os:
+                            python.architecture.os = "default_os"
+                        if not python.architecture.target:
+                            python.architecture.target = archspec.cpu.host().family.name
+
+                    # Ensure compiler information is present
+                    if not python.compiler:
+                        python.compiler = self.spec.compiler
+
+                    python.external_path = self.spec.external_path
+                    python._mark_concrete()
+            self.spec.add_dependency_edge(python, deptypes=("build", "link", "run"), virtuals=())
+
 
 class PythonPackage(PythonExtension):
     """Specialized class for packages that are built using pip."""
@@ -225,51 +270,6 @@ def list_url(cls):
             name = cls.pypi.split("/")[0]
             return "https://pypi.org/simple/" + name + "/"
 
-    def update_external_dependencies(self, extendee_spec=None):
-        """
-        Ensure all external python packages have a python dependency
-
-        If another package in the DAG depends on python, we use that
-        python for the dependency of the external. If not, we assume
-        that the external PythonPackage is installed into the same
-        directory as the python it depends on.
-        """
-        # TODO: Include this in the solve, rather than instantiating post-concretization
-        if "python" not in self.spec:
-            if extendee_spec:
-                python = extendee_spec
-            elif "python" in self.spec.root:
-                python = self.spec.root["python"]
-            else:
-                python = self.get_external_python_for_prefix()
-                if not python.concrete:
-                    repo = spack.repo.path.repo_for_pkg(python)
-                    python.namespace = repo.namespace
-
-                    # Ensure architecture information is present
-                    if not python.architecture:
-                        host_platform = spack.platforms.host()
-                        host_os = host_platform.operating_system("default_os")
-                        host_target = host_platform.target("default_target")
-                        python.architecture = spack.spec.ArchSpec(
-                            (str(host_platform), str(host_os), str(host_target))
-                        )
-                    else:
-                        if not python.architecture.platform:
-                            python.architecture.platform = spack.platforms.host()
-                        if not python.architecture.os:
-                            python.architecture.os = "default_os"
-                        if not python.architecture.target:
-                            python.architecture.target = archspec.cpu.host().family.name
-
-                    # Ensure compiler information is present
-                    if not python.compiler:
-                        python.compiler = self.spec.compiler
-
-                    python.external_path = self.spec.external_path
-                    python._mark_concrete()
-            self.spec.add_dependency_edge(python, deptypes=("build", "link", "run"))
-
     def get_external_python_for_prefix(self):
         """
         For an external package that extends python, find the most likely spec for the python

lib/spack/spack/cmd/buildcache.py

@@ -43,13 +43,6 @@ def setup_parser(subparser):
     subparsers = subparser.add_subparsers(help="buildcache sub-commands")
 
     push = subparsers.add_parser("push", aliases=["create"], help=push_fn.__doc__)
-    # TODO: remove from Spack 0.21
-    push.add_argument(
-        "-r",
-        "--rel",
-        action="store_true",
-        help="make all rpaths relative before creating tarballs. (deprecated)",
-    )
     push.add_argument("-f", "--force", action="store_true", help="overwrite tarball if it exists.")
     push.add_argument(
         "-u", "--unsigned", action="store_true", help="push unsigned buildcache tarballs"
@@ -63,37 +56,7 @@ def setup_parser(subparser):
     push.add_argument(
         "-k", "--key", metavar="key", type=str, default=None, help="Key for signing."
     )
-    output = push.add_mutually_exclusive_group(required=False)
-    # TODO: remove from Spack 0.21
-    output.add_argument(
-        "-d",
-        "--directory",
-        metavar="directory",
-        dest="mirror_flag",
-        type=arguments.mirror_directory,
-        help="local directory where buildcaches will be written. (deprecated)",
-    )
-    # TODO: remove from Spack 0.21
-    output.add_argument(
-        "-m",
-        "--mirror-name",
-        metavar="mirror-name",
-        dest="mirror_flag",
-        type=arguments.mirror_name,
-        help="name of the mirror where buildcaches will be written. (deprecated)",
-    )
-    # TODO: remove from Spack 0.21
-    output.add_argument(
-        "--mirror-url",
-        metavar="mirror-url",
-        dest="mirror_flag",
-        type=arguments.mirror_url,
-        help="URL of the mirror where buildcaches will be written. (deprecated)",
-    )
-    # Unfortunately we cannot add this to the mutually exclusive group above,
-    # because we have further positional arguments.
-    # TODO: require from Spack 0.21
-    push.add_argument("mirror", type=str, help="Mirror name, path, or URL.", nargs="?")
+    push.add_argument("mirror", type=str, help="Mirror name, path, or URL.")
     push.add_argument(
         "--update-index",
         "--rebuild-index",
@@ -127,13 +90,6 @@ def setup_parser(subparser):
     install.add_argument(
         "-m", "--multiple", action="store_true", help="allow all matching packages "
     )
-    # TODO: remove from Spack 0.21
-    install.add_argument(
-        "-a",
-        "--allow-root",
-        action="store_true",
-        help="allow install root string in binary files after RPATH substitution. (deprecated)",
-    )
     install.add_argument(
         "-u",
         "--unsigned",
@@ -272,71 +228,17 @@ def setup_parser(subparser):
         default=None,
         help="A quoted glob pattern identifying copy manifest files",
     )
-    source = sync.add_mutually_exclusive_group(required=False)
-    # TODO: remove in Spack 0.21
-    source.add_argument(
-        "--src-directory",
-        metavar="DIRECTORY",
-        dest="src_mirror_flag",
-        type=arguments.mirror_directory,
-        help="Source mirror as a local file path (deprecated)",
-    )
-    # TODO: remove in Spack 0.21
-    source.add_argument(
-        "--src-mirror-name",
-        metavar="MIRROR_NAME",
-        dest="src_mirror_flag",
-        type=arguments.mirror_name,
-        help="Name of the source mirror (deprecated)",
-    )
-    # TODO: remove in Spack 0.21
-    source.add_argument(
-        "--src-mirror-url",
-        metavar="MIRROR_URL",
-        dest="src_mirror_flag",
-        type=arguments.mirror_url,
-        help="URL of the source mirror (deprecated)",
-    )
-    # TODO: only support this in 0.21
-    source.add_argument(
+    sync.add_argument(
         "src_mirror",
         metavar="source mirror",
         type=arguments.mirror_name_or_url,
         help="Source mirror name, path, or URL",
-        nargs="?",
     )
-    dest = sync.add_mutually_exclusive_group(required=False)
-    # TODO: remove in Spack 0.21
-    dest.add_argument(
-        "--dest-directory",
-        metavar="DIRECTORY",
-        dest="dest_mirror_flag",
-        type=arguments.mirror_directory,
-        help="Destination mirror as a local file path (deprecated)",
-    )
-    # TODO: remove in Spack 0.21
-    dest.add_argument(
-        "--dest-mirror-name",
-        metavar="MIRROR_NAME",
-        type=arguments.mirror_name,
-        dest="dest_mirror_flag",
-        help="Name of the destination mirror (deprecated)",
-    )
-    # TODO: remove in Spack 0.21
-    dest.add_argument(
-        "--dest-mirror-url",
-        metavar="MIRROR_URL",
-        dest="dest_mirror_flag",
-        type=arguments.mirror_url,
-        help="URL of the destination mirror (deprecated)",
-    )
-    # TODO: only support this in 0.21
-    dest.add_argument(
+    sync.add_argument(
         "dest_mirror",
         metavar="destination mirror",
         type=arguments.mirror_name_or_url,
         help="Destination mirror name, path, or URL",
-        nargs="?",
     )
     sync.set_defaults(func=sync_fn)
 
@@ -344,39 +246,8 @@ def setup_parser(subparser):
     update_index = subparsers.add_parser(
         "update-index", aliases=["rebuild-index"], help=update_index_fn.__doc__
     )
-    update_index_out = update_index.add_mutually_exclusive_group(required=True)
-    # TODO: remove in Spack 0.21
-    update_index_out.add_argument(
-        "-d",
-        "--directory",
-        metavar="directory",
-        dest="mirror_flag",
-        type=arguments.mirror_directory,
-        help="local directory where buildcaches will be written (deprecated)",
-    )
-    # TODO: remove in Spack 0.21
-    update_index_out.add_argument(
-        "-m",
-        "--mirror-name",
-        metavar="mirror-name",
-        dest="mirror_flag",
-        type=arguments.mirror_name,
-        help="name of the mirror where buildcaches will be written (deprecated)",
-    )
-    # TODO: remove in Spack 0.21
-    update_index_out.add_argument(
-        "--mirror-url",
-        metavar="mirror-url",
-        dest="mirror_flag",
-        type=arguments.mirror_url,
-        help="URL of the mirror where buildcaches will be written (deprecated)",
-    )
-    # TODO: require from Spack 0.21
-    update_index_out.add_argument(
-        "mirror",
-        type=arguments.mirror_name_or_url,
-        help="Destination mirror name, path, or URL",
-        nargs="?",
+    update_index.add_argument(
+        "mirror", type=arguments.mirror_name_or_url, help="Destination mirror name, path, or URL"
     )
     update_index.add_argument(
         "-k",
@@ -436,32 +307,12 @@ def _concrete_spec_from_args(args):
 
 def push_fn(args):
     """create a binary package and push it to a mirror"""
-    if args.mirror_flag:
-        mirror = args.mirror_flag
-    elif not args.mirror:
-        raise ValueError("No mirror provided")
-    else:
-        mirror = arguments.mirror_name_or_url(args.mirror)
-
-    if args.mirror_flag:
-        tty.warn(
-            "Using flags to specify mirrors is deprecated and will be removed in "
-            "Spack 0.21, use positional arguments instead."
-        )
-
-    if args.rel:
-        tty.warn("The --rel flag is deprecated and will be removed in Spack 0.21")
-
-    # TODO: remove this in 0.21. If we have mirror_flag, the first
-    # spec is in the positional mirror arg due to argparse limitations.
-    input_specs = args.specs
-    if args.mirror_flag and args.mirror:
-        input_specs.insert(0, args.mirror)
+    mirror = arguments.mirror_name_or_url(args.mirror)
 
     url = mirror.push_url
 
     specs = bindist.specs_to_be_packaged(
-        _matching_specs(input_specs, args.spec_file),
+        _matching_specs(args.specs, args.spec_file),
         root="package" in args.things_to_install,
         dependencies="dependencies" in args.things_to_install,
     )
@@ -486,7 +337,6 @@ def push_fn(args):
                 url,
                 bindist.PushOptions(
                     force=args.force,
-                    relative=args.rel,
                     unsigned=args.unsigned,
                     allow_root=args.allow_root,
                     key=args.key,
@@ -524,9 +374,6 @@ def install_fn(args):
     if not args.specs:
         tty.die("a spec argument is required to install from a buildcache")
 
-    if args.allow_root:
-        tty.warn("The --allow-root flag is deprecated and will be removed in Spack 0.21")
-
     query = bindist.BinaryCacheQuery(all_architectures=args.otherarch)
     matches = spack.store.find(args.specs, multiple=args.multiple, query_fn=query)
     for match in matches:
@@ -710,21 +557,8 @@ def sync_fn(args):
         manifest_copy(glob.glob(args.manifest_glob))
         return 0
 
-    # If no manifest_glob, require a source and dest mirror.
-    # TODO: Simplify in Spack 0.21
-    if not (args.src_mirror_flag or args.src_mirror) or not (
-        args.dest_mirror_flag or args.dest_mirror
-    ):
-        raise ValueError("Source and destination mirror are required.")
-
-    if args.src_mirror_flag or args.dest_mirror_flag:
-        tty.warn(
-            "Using flags to specify mirrors is deprecated and will be removed in "
-            "Spack 0.21, use positional arguments instead."
-        )
-
-    src_mirror = args.src_mirror_flag if args.src_mirror_flag else args.src_mirror
-    dest_mirror = args.dest_mirror_flag if args.dest_mirror_flag else args.dest_mirror
+    src_mirror = args.src_mirror
+    dest_mirror = args.dest_mirror
 
     src_mirror_url = src_mirror.fetch_url
     dest_mirror_url = dest_mirror.push_url
@@ -803,13 +637,7 @@ def update_index(mirror: spack.mirror.Mirror, update_keys=False):
 
 def update_index_fn(args):
     """Update a buildcache index."""
-    if args.mirror_flag:
-        tty.warn(
-            "Using flags to specify mirrors is deprecated and will be removed in "
-            "Spack 0.21, use positional arguments instead."
-        )
-    mirror = args.mirror_flag if args.mirror_flag else args.mirror
-    update_index(mirror, update_keys=args.keys)
+    update_index(args.mirror, update_keys=args.keys)
 
 
 def buildcache(parser, args):

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

@@ -349,7 +349,7 @@ def install_status():
         "-I",
         "--install-status",
         action="store_true",
-        default=False,
+        default=True,
         help="show install status of packages. packages can be: "
         "installed [+], missing and needed by an installed package [-], "
         "installed in and upstream instance [^], "
@@ -357,6 +357,17 @@ def install_status():
     )
 
 
+@arg
+def no_install_status():
+    return Args(
+        "--no-install-status",
+        dest="install_status",
+        action="store_false",
+        default=True,
+        help="do not show install status annotations",
+    )
+
+
 @arg
 def no_checksum():
     return Args(

lib/spack/spack/cmd/create.py

@@ -715,7 +715,7 @@ def __call__(self, stage, url):
                 output = tar("--exclude=*/*/*", "-tf", stage.archive_file, output=str)
             except ProcessError:
                 output = ""
-        lines = output.split("\n")
+        lines = output.splitlines()
 
         # Determine the build system based on the files contained
         # in the archive.

lib/spack/spack/cmd/solve.py

@@ -44,7 +44,11 @@ def setup_parser(subparser):
     )
 
     # Below are arguments w.r.t. spec display (like spack spec)
-    arguments.add_common_arguments(subparser, ["long", "very_long", "install_status"])
+    arguments.add_common_arguments(subparser, ["long", "very_long"])
+
+    install_status_group = subparser.add_mutually_exclusive_group()
+    arguments.add_common_arguments(install_status_group, ["install_status", "no_install_status"])
+
     subparser.add_argument(
         "-y",
         "--yaml",

lib/spack/spack/cmd/spec.py

@@ -31,7 +31,11 @@ def setup_parser(subparser):
 for further documentation regarding the spec syntax, see:
     spack help --spec
 """
-    arguments.add_common_arguments(subparser, ["long", "very_long", "install_status"])
+    arguments.add_common_arguments(subparser, ["long", "very_long"])
+
+    install_status_group = subparser.add_mutually_exclusive_group()
+    arguments.add_common_arguments(install_status_group, ["install_status", "no_install_status"])
+
     format_group = subparser.add_mutually_exclusive_group()
     format_group.add_argument(
         "-y",

lib/spack/spack/cray_manifest.py

@@ -164,7 +164,10 @@ def entries_to_specs(entries):
                     continue
                 parent_spec = spec_dict[entry["hash"]]
                 dep_spec = spec_dict[dep_hash]
-                parent_spec._add_dependency(dep_spec, deptypes=deptypes)
+                parent_spec._add_dependency(dep_spec, deptypes=deptypes, virtuals=())
+
+    for spec in spec_dict.values():
+        spack.spec.reconstruct_virtuals_on_edges(spec)
 
     return spec_dict
 

lib/spack/spack/database.py

@@ -60,7 +60,7 @@
 # DB version.  This is stuck in the DB file to track changes in format.
 # Increment by one when the database format changes.
 # Versions before 5 were not integers.
-_db_version = vn.Version("6")
+_db_version = vn.Version("7")
 
 # For any version combinations here, skip reindex when upgrading.
 # Reindexing can take considerable time and is not always necessary.
@@ -72,6 +72,7 @@
     # version is saved to disk the first time the DB is written.
     (vn.Version("0.9.3"), vn.Version("5")),
     (vn.Version("5"), vn.Version("6")),
+    (vn.Version("6"), vn.Version("7")),
 ]
 
 # Default timeout for spack database locks in seconds or None (no timeout).
@@ -105,7 +106,11 @@
 
 
 def reader(version):
-    reader_cls = {vn.Version("5"): spack.spec.SpecfileV1, vn.Version("6"): spack.spec.SpecfileV3}
+    reader_cls = {
+        vn.Version("5"): spack.spec.SpecfileV1,
+        vn.Version("6"): spack.spec.SpecfileV3,
+        vn.Version("7"): spack.spec.SpecfileV4,
+    }
     return reader_cls[version]
 
 
@@ -743,7 +748,9 @@ def _assign_dependencies(self, spec_reader, hash_key, installs, data):
             spec_node_dict = spec_node_dict[spec.name]
         if "dependencies" in spec_node_dict:
             yaml_deps = spec_node_dict["dependencies"]
-            for dname, dhash, dtypes, _ in spec_reader.read_specfile_dep_specs(yaml_deps):
+            for dname, dhash, dtypes, _, virtuals in spec_reader.read_specfile_dep_specs(
+                yaml_deps
+            ):
                 # It is important that we always check upstream installations
                 # in the same order, and that we always check the local
                 # installation first: if a downstream Spack installs a package
@@ -766,7 +773,7 @@ def _assign_dependencies(self, spec_reader, hash_key, installs, data):
                     tty.warn(msg)
                     continue
 
-                spec._add_dependency(child, deptypes=dtypes)
+                spec._add_dependency(child, deptypes=dtypes, virtuals=virtuals)
 
     def _read_from_file(self, filename):
         """Fill database from file, do not maintain old data.
@@ -1172,7 +1179,7 @@ def _add(
             for dep in spec.edges_to_dependencies(deptype=_tracked_deps):
                 dkey = dep.spec.dag_hash()
                 upstream, record = self.query_by_spec_hash(dkey)
-                new_spec._add_dependency(record.spec, deptypes=dep.deptypes)
+                new_spec._add_dependency(record.spec, deptypes=dep.deptypes, virtuals=dep.virtuals)
                 if not upstream:
                     record.ref_count += 1
 

lib/spack/spack/environment/environment.py

@@ -125,7 +125,7 @@ def default_manifest_yaml():
 valid_environment_name_re = r"^\w[\w-]*$"
 
 #: version of the lockfile format. Must increase monotonically.
-lockfile_format_version = 4
+lockfile_format_version = 5
 
 
 READER_CLS = {
@@ -133,6 +133,7 @@ def default_manifest_yaml():
     2: spack.spec.SpecfileV1,
     3: spack.spec.SpecfileV2,
     4: spack.spec.SpecfileV3,
+    5: spack.spec.SpecfileV4,
 }
 
 
@@ -1548,12 +1549,13 @@ def _concretize_separately(self, tests=False):
             for h in self.specs_by_hash:
                 current_spec, computed_spec = self.specs_by_hash[h], by_hash[h]
                 for node in computed_spec.traverse():
-                    test_deps = node.dependencies(deptype="test")
-                    for test_dependency in test_deps:
+                    test_edges = node.edges_to_dependencies(deptype="test")
+                    for current_edge in test_edges:
+                        test_dependency = current_edge.spec
                         if test_dependency in current_spec[node.name]:
                             continue
                         current_spec[node.name].add_dependency_edge(
-                            test_dependency.copy(), deptypes="test"
+                            test_dependency.copy(), deptypes="test", virtuals=current_edge.virtuals
                         )
 
         results = [
@@ -2184,9 +2186,9 @@ def _read_lockfile_dict(self, d):
         # and add them to the spec
         for lockfile_key, node_dict in json_specs_by_hash.items():
             name, data = reader.name_and_data(node_dict)
-            for _, dep_hash, deptypes, _ in reader.dependencies_from_node_dict(data):
+            for _, dep_hash, deptypes, _, virtuals in reader.dependencies_from_node_dict(data):
                 specs_by_hash[lockfile_key]._add_dependency(
-                    specs_by_hash[dep_hash], deptypes=deptypes
+                    specs_by_hash[dep_hash], deptypes=deptypes, virtuals=virtuals
                 )
 
         # Traverse the root specs one at a time in the order they appear.
@@ -2378,17 +2380,28 @@ def _concretize_from_constraints(spec_constraints, tests=False):
     # Accept only valid constraints from list and concretize spec
     # Get the named spec even if out of order
     root_spec = [s for s in spec_constraints if s.name]
-    if len(root_spec) != 1:
-        m = "The constraints %s are not a valid spec " % spec_constraints
-        m += "concretization target. all specs must have a single name "
-        m += "constraint for concretization."
-        raise InvalidSpecConstraintError(m)
-    spec_constraints.remove(root_spec[0])
+    hash_spec = [s for s in spec_constraints if s.abstract_hash]
+
+    error_message = "The constraints %s are not a valid spec " % spec_constraints
+    error_message += "concretization target. all specs must have a single name "
+    error_message += "constraint for concretization."
+
+    if len(root_spec) > 1:
+        raise InvalidSpecConstraintError(error_message)
+
+    if len(root_spec) < 1:
+        if len(hash_spec) < 1:
+            raise InvalidSpecConstraintError(error_message)
+
+    if root_spec:
+        spec_constraints.remove(root_spec[0])
+
+    root_spec = root_spec[0] if root_spec else Spec()
 
     invalid_constraints = []
     while True:
         # Attach all anonymous constraints to one named spec
-        s = root_spec[0].copy()
+        s = root_spec.copy()
         for c in spec_constraints:
             if c not in invalid_constraints:
                 s.constrain(c)

lib/spack/spack/graph.py

@@ -544,6 +544,7 @@ def _static_edges(specs, deptype):
                     spack.spec.Spec(parent_name),
                     spack.spec.Spec(dependency_name),
                     deptypes=deptype,
+                    virtuals=(),
                 )
 
 

lib/spack/spack/installer.py

@@ -231,7 +231,9 @@ def _packages_needed_to_bootstrap_compiler(compiler, architecture, pkgs):
     dep.concretize()
     # mark compiler as depended-on by the packages that use it
     for pkg in pkgs:
-        dep._dependents.add(spack.spec.DependencySpec(pkg.spec, dep, deptypes=("build",)))
+        dep._dependents.add(
+            spack.spec.DependencySpec(pkg.spec, dep, deptypes=("build",), virtuals=())
+        )
     packages = [(s.package, False) for s in dep.traverse(order="post", root=False)]
 
     packages.append((dep.package, True))

lib/spack/spack/modules/common.py

@@ -40,7 +40,7 @@
 
 import llnl.util.filesystem
 import llnl.util.tty as tty
-from llnl.util.lang import dedupe
+from llnl.util.lang import dedupe, memoized
 
 import spack.build_environment
 import spack.config
@@ -672,6 +672,7 @@ def configure_options(self):
         return None
 
     @tengine.context_property
+    @memoized
     def environment_modifications(self):
         """List of environment modifications to be processed."""
         # Modifications guessed by inspecting the spec prefix
@@ -742,6 +743,19 @@ def environment_modifications(self):
 
         return [(type(x).__name__, x) for x in env if x.name not in exclude]
 
+    @tengine.context_property
+    def has_manpath_modifications(self):
+        """True if MANPATH environment variable is modified."""
+        for modification_type, cmd in self.environment_modifications:
+            if not isinstance(
+                cmd, (spack.util.environment.PrependPath, spack.util.environment.AppendPath)
+            ):
+                continue
+            if cmd.name == "MANPATH":
+                return True
+        else:
+            return False
+
     @tengine.context_property
     def autoload(self):
         """List of modules that needs to be loaded automatically."""

lib/spack/spack/package_base.py

@@ -1231,6 +1231,7 @@ def dependencies_of_type(cls, *deptypes):
             if any(dt in cls.dependencies[name][cond].type for cond in conds for dt in deptypes)
         )
 
+    # TODO: allow more than one active extendee.
     @property
     def extendee_spec(self):
         """
@@ -1246,7 +1247,6 @@ def extendee_spec(self):
             if dep.name in self.extendees:
                 deps.append(dep)
 
-        # TODO: allow more than one active extendee.
         if deps:
             assert len(deps) == 1
             return deps[0]
@@ -1256,7 +1256,6 @@ def extendee_spec(self):
         if self.spec._concrete:
             return None
         else:
-            # TODO: do something sane here with more than one extendee
             # If it's not concrete, then return the spec from the
             # extends() directive since that is all we know so far.
             spec_str, kwargs = next(iter(self.extendees.items()))

lib/spack/spack/parser.py

@@ -291,7 +291,7 @@ def next_spec(
                 if root_spec.concrete:
                     raise spack.spec.RedundantSpecError(root_spec, "^" + str(dependency))
 
-                root_spec._add_dependency(dependency, deptypes=())
+                root_spec._add_dependency(dependency, deptypes=(), virtuals=())
 
             else:
                 break

lib/spack/spack/provider_index.py

@@ -292,8 +292,8 @@ def from_json(stream, repository):
         index.providers = _transform(
             providers,
             lambda vpkg, plist: (
-                spack.spec.SpecfileV3.from_node_dict(vpkg),
-                set(spack.spec.SpecfileV3.from_node_dict(p) for p in plist),
+                spack.spec.SpecfileV4.from_node_dict(vpkg),
+                set(spack.spec.SpecfileV4.from_node_dict(p) for p in plist),
             ),
         )
         return index

lib/spack/spack/solver/asp.py

@@ -2500,10 +2500,15 @@ def depends_on(self, pkg, dep, type):
         assert len(dependencies) < 2, msg
 
         if not dependencies:
-            self._specs[pkg].add_dependency_edge(self._specs[dep], deptypes=(type,))
+            self._specs[pkg].add_dependency_edge(self._specs[dep], deptypes=(type,), virtuals=())
         else:
             # TODO: This assumes that each solve unifies dependencies
-            dependencies[0].add_type(type)
+            dependencies[0].update_deptypes(deptypes=(type,))
+
+    def virtual_on_edge(self, pkg, provider, virtual):
+        dependencies = self._specs[pkg].edges_to_dependencies(name=provider)
+        assert len(dependencies) == 1
+        dependencies[0].update_virtuals((virtual,))
 
     def reorder_flags(self):
         """Order compiler flags on specs in predefined order.
@@ -2581,6 +2586,8 @@ def sort_fn(function_tuple):
             return (-2, 0)
         elif name == "external_spec_selected":
             return (0, 0)  # note out of order so this goes last
+        elif name == "virtual_on_edge":
+            return (1, 0)
         else:
             return (-1, 0)
 

lib/spack/spack/solver/concretize.lp

@@ -300,6 +300,11 @@ attr("depends_on", Package, Provider, Type)
      provider(Provider, Virtual),
      not external(Package).
 
+attr("virtual_on_edge", Package, Provider, Virtual)
+  :- dependency_holds(Package, Virtual, Type),
+     provider(Provider, Virtual),
+     not external(Package).
+
 % dependencies on virtuals also imply that the virtual is a virtual node
 attr("virtual_node", Virtual)
   :- dependency_holds(Package, Virtual, Type),

lib/spack/spack/spec.py

@@ -170,7 +170,7 @@
 )
 
 #: specfile format version. Must increase monotonically
-SPECFILE_FORMAT_VERSION = 3
+SPECFILE_FORMAT_VERSION = 4
 
 
 def colorize_spec(spec):
@@ -714,47 +714,81 @@ class DependencySpec:
         parent: starting node of the edge
         spec: ending node of the edge.
         deptypes: list of strings, representing dependency relationships.
+        virtuals: virtual packages provided from child to parent node.
     """
 
-    __slots__ = "parent", "spec", "deptypes"
+    __slots__ = "parent", "spec", "parameters"
 
-    def __init__(self, parent: "Spec", spec: "Spec", *, deptypes: dp.DependencyArgument):
+    def __init__(
+        self,
+        parent: "Spec",
+        spec: "Spec",
+        *,
+        deptypes: dp.DependencyArgument,
+        virtuals: Tuple[str, ...],
+    ):
         self.parent = parent
         self.spec = spec
-        self.deptypes = dp.canonical_deptype(deptypes)
+        self.parameters = {
+            "deptypes": dp.canonical_deptype(deptypes),
+            "virtuals": tuple(sorted(set(virtuals))),
+        }
 
-    def update_deptypes(self, deptypes: dp.DependencyArgument) -> bool:
-        deptypes = set(deptypes)
-        deptypes.update(self.deptypes)
-        deptypes = tuple(sorted(deptypes))
-        changed = self.deptypes != deptypes
+    @property
+    def deptypes(self) -> Tuple[str, ...]:
+        return self.parameters["deptypes"]
 
-        self.deptypes = deptypes
-        return changed
+    @property
+    def virtuals(self) -> Tuple[str, ...]:
+        return self.parameters["virtuals"]
+
+    def _update_edge_multivalued_property(
+        self, property_name: str, value: Tuple[str, ...]
+    ) -> bool:
+        current = self.parameters[property_name]
+        update = set(current) | set(value)
+        update = tuple(sorted(update))
+        changed = current != update
+
+        if not changed:
+            return False
+
+        self.parameters[property_name] = update
+        return True
+
+    def update_deptypes(self, deptypes: Tuple[str, ...]) -> bool:
+        """Update the current dependency types"""
+        return self._update_edge_multivalued_property("deptypes", deptypes)
+
+    def update_virtuals(self, virtuals: Tuple[str, ...]) -> bool:
+        """Update the list of provided virtuals"""
+        return self._update_edge_multivalued_property("virtuals", virtuals)
 
     def copy(self) -> "DependencySpec":
-        return DependencySpec(self.parent, self.spec, deptypes=self.deptypes)
-
-    def add_type(self, type: dp.DependencyArgument):
-        self.deptypes = dp.canonical_deptype(self.deptypes + dp.canonical_deptype(type))
+        """Return a copy of this edge"""
+        return DependencySpec(
+            self.parent, self.spec, deptypes=self.deptypes, virtuals=self.virtuals
+        )
 
     def _cmp_iter(self):
         yield self.parent.name if self.parent else None
         yield self.spec.name if self.spec else None
         yield self.deptypes
+        yield self.virtuals
 
     def __str__(self) -> str:
-        return "%s %s--> %s" % (
-            self.parent.name if self.parent else None,
-            self.deptypes,
-            self.spec.name if self.spec else None,
-        )
+        parent = self.parent.name if self.parent else None
+        child = self.spec.name if self.spec else None
+        return f"{parent} {self.deptypes}[virtuals={','.join(self.virtuals)}] --> {child}"
 
-    def canonical(self) -> Tuple[str, str, Tuple[str, ...]]:
-        return self.parent.dag_hash(), self.spec.dag_hash(), self.deptypes
+    def canonical(self) -> Tuple[str, str, Tuple[str, ...], Tuple[str, ...]]:
+        return self.parent.dag_hash(), self.spec.dag_hash(), self.deptypes, self.virtuals
 
     def flip(self) -> "DependencySpec":
-        return DependencySpec(parent=self.spec, spec=self.parent, deptypes=self.deptypes)
+        """Flip the dependency, and drop virtual information"""
+        return DependencySpec(
+            parent=self.spec, spec=self.parent, deptypes=self.deptypes, virtuals=()
+        )
 
 
 class CompilerFlag(str):
@@ -1575,10 +1609,12 @@ def _set_compiler(self, compiler):
             )
         self.compiler = compiler
 
-    def _add_dependency(self, spec: "Spec", *, deptypes: dp.DependencyArgument):
+    def _add_dependency(
+        self, spec: "Spec", *, deptypes: dp.DependencyArgument, virtuals: Tuple[str, ...]
+    ):
         """Called by the parser to add another spec as a dependency."""
         if spec.name not in self._dependencies or not spec.name:
-            self.add_dependency_edge(spec, deptypes=deptypes)
+            self.add_dependency_edge(spec, deptypes=deptypes, virtuals=virtuals)
             return
 
         # Keep the intersection of constraints when a dependency is added
@@ -1596,34 +1632,58 @@ def _add_dependency(self, spec: "Spec", *, deptypes: dp.DependencyArgument):
                 "Cannot depend on incompatible specs '%s' and '%s'" % (dspec.spec, spec)
             )
 
-    def add_dependency_edge(self, dependency_spec: "Spec", *, deptypes: dp.DependencyArgument):
+    def add_dependency_edge(
+        self,
+        dependency_spec: "Spec",
+        *,
+        deptypes: dp.DependencyArgument,
+        virtuals: Tuple[str, ...],
+    ):
         """Add a dependency edge to this spec.
 
         Args:
             dependency_spec: spec of the dependency
             deptypes: dependency types for this edge
+            virtuals: virtuals provided by this edge
         """
         deptypes = dp.canonical_deptype(deptypes)
 
         # Check if we need to update edges that are already present
         selected = self._dependencies.select(child=dependency_spec.name)
         for edge in selected:
+            has_errors, details = False, []
+            msg = f"cannot update the edge from {edge.parent.name} to {edge.spec.name}"
             if any(d in edge.deptypes for d in deptypes):
-                msg = (
-                    'cannot add a dependency on "{0.spec}" of {1} type '
-                    'when the "{0.parent}" has the edge {0!s} already'
+                has_errors = True
+                details.append(
+                    (
+                        f"{edge.parent.name} has already an edge matching any"
+                        f" of these types {str(deptypes)}"
+                    )
                 )
-                raise spack.error.SpecError(msg.format(edge, deptypes))
+
+            if any(v in edge.virtuals for v in virtuals):
+                has_errors = True
+                details.append(
+                    (
+                        f"{edge.parent.name} has already an edge matching any"
+                        f" of these virtuals {str(virtuals)}"
+                    )
+                )
+
+            if has_errors:
+                raise spack.error.SpecError(msg, "\n".join(details))
 
         for edge in selected:
             if id(dependency_spec) == id(edge.spec):
                 # If we are here, it means the edge object was previously added to
                 # both the parent and the child. When we update this object they'll
                 # both see the deptype modification.
-                edge.add_type(deptypes)
+                edge.update_deptypes(deptypes=deptypes)
+                edge.update_virtuals(virtuals=virtuals)
                 return
 
-        edge = DependencySpec(self, dependency_spec, deptypes=deptypes)
+        edge = DependencySpec(self, dependency_spec, deptypes=deptypes, virtuals=virtuals)
         self._dependencies.add(edge)
         dependency_spec._dependents.add(edge)
 
@@ -1896,12 +1956,12 @@ def lookup_hash(self):
         for node in self.traverse(root=False):
             if node.abstract_hash:
                 new = node._lookup_hash()
-                spec._add_dependency(new, deptypes=())
+                spec._add_dependency(new, deptypes=(), virtuals=())
 
         # reattach nodes that were not otherwise satisfied by new dependencies
         for node in self.traverse(root=False):
             if not any(n._satisfies(node) for n in spec.traverse()):
-                spec._add_dependency(node.copy(), deptypes=())
+                spec._add_dependency(node.copy(), deptypes=(), virtuals=())
 
         return spec
 
@@ -2036,8 +2096,14 @@ def to_node_dict(self, hash=ht.dag_hash):
                 name_tuple = ("name", name)
                 for dspec in edges_for_name:
                     hash_tuple = (hash.name, dspec.spec._cached_hash(hash))
-                    type_tuple = ("type", sorted(str(s) for s in dspec.deptypes))
-                    deps_list.append(syaml.syaml_dict([name_tuple, hash_tuple, type_tuple]))
+                    parameters_tuple = (
+                        "parameters",
+                        syaml.syaml_dict(
+                            (key, dspec.parameters[key]) for key in sorted(dspec.parameters)
+                        ),
+                    )
+                    ordered_entries = [name_tuple, hash_tuple, parameters_tuple]
+                    deps_list.append(syaml.syaml_dict(ordered_entries))
             d["dependencies"] = deps_list
 
         # Name is included in case this is replacing a virtual.
@@ -2361,7 +2427,7 @@ def spec_and_dependency_types(s):
                     dag_node, dependency_types = spec_and_dependency_types(s)
 
                 dependency_spec = spec_builder({dag_node: s_dependencies})
-                spec._add_dependency(dependency_spec, deptypes=dependency_types)
+                spec._add_dependency(dependency_spec, deptypes=dependency_types, virtuals=())
 
             return spec
 
@@ -2379,8 +2445,10 @@ def from_dict(data):
             spec = SpecfileV1.load(data)
         elif int(data["spec"]["_meta"]["version"]) == 2:
             spec = SpecfileV2.load(data)
-        else:
+        elif int(data["spec"]["_meta"]["version"]) == 3:
             spec = SpecfileV3.load(data)
+        else:
+            spec = SpecfileV4.load(data)
 
         # Any git version should
         for s in spec.traverse():
@@ -2529,6 +2597,7 @@ def _concretize_helper(self, concretizer, presets=None, visited=None):
     def _replace_with(self, concrete):
         """Replace this virtual spec with a concrete spec."""
         assert self.virtual
+        virtuals = (self.name,)
         for dep_spec in itertools.chain.from_iterable(self._dependents.values()):
             dependent = dep_spec.parent
             deptypes = dep_spec.deptypes
@@ -2539,7 +2608,11 @@ def _replace_with(self, concrete):
 
             # add the replacement, unless it is already a dep of dependent.
             if concrete.name not in dependent._dependencies:
-                dependent._add_dependency(concrete, deptypes=deptypes)
+                dependent._add_dependency(concrete, deptypes=deptypes, virtuals=virtuals)
+            else:
+                dependent.edges_to_dependencies(name=concrete.name)[0].update_virtuals(
+                    virtuals=virtuals
+                )
 
     def _expand_virtual_packages(self, concretizer):
         """Find virtual packages in this spec, replace them with providers,
@@ -3180,7 +3253,9 @@ def _merge_dependency(self, dependency, visited, spec_deps, provider_index, test
 
         # If it's a virtual dependency, try to find an existing
         # provider in the spec, and merge that.
+        virtuals = ()
         if spack.repo.path.is_virtual_safe(dep.name):
+            virtuals = (dep.name,)
             visited.add(dep.name)
             provider = self._find_provider(dep, provider_index)
             if provider:
@@ -3236,7 +3311,7 @@ def _merge_dependency(self, dependency, visited, spec_deps, provider_index, test
         # Add merged spec to my deps and recurse
         spec_dependency = spec_deps[dep.name]
         if dep.name not in self._dependencies:
-            self._add_dependency(spec_dependency, deptypes=dependency.type)
+            self._add_dependency(spec_dependency, deptypes=dependency.type, virtuals=virtuals)
 
         changed |= spec_dependency._normalize_helper(visited, spec_deps, provider_index, tests)
         return changed
@@ -3573,15 +3648,20 @@ def _constrain_dependencies(self, other):
                 changed |= edges_from_name[0].update_deptypes(
                     other._dependencies[name][0].deptypes
                 )
+                changed |= edges_from_name[0].update_virtuals(
+                    other._dependencies[name][0].virtuals
+                )
 
         # Update with additional constraints from other spec
         # operate on direct dependencies only, because a concrete dep
         # represented by hash may have structure that needs to be preserved
         for name in other.direct_dep_difference(self):
             dep_spec_copy = other._get_dependency(name)
-            dep_copy = dep_spec_copy.spec
-            deptypes = dep_spec_copy.deptypes
-            self._add_dependency(dep_copy.copy(), deptypes=deptypes)
+            self._add_dependency(
+                dep_spec_copy.spec.copy(),
+                deptypes=dep_spec_copy.deptypes,
+                virtuals=dep_spec_copy.virtuals,
+            )
             changed = True
 
         return changed
@@ -3965,7 +4045,7 @@ def spid(spec):
                 new_specs[spid(edge.spec)] = edge.spec.copy(deps=False)
 
             new_specs[spid(edge.parent)].add_dependency_edge(
-                new_specs[spid(edge.spec)], deptypes=edge.deptypes
+                new_specs[spid(edge.spec)], deptypes=edge.deptypes, virtuals=edge.virtuals
             )
 
     def copy(self, deps=True, **kwargs):
@@ -4635,12 +4715,16 @@ def from_self(name, transitive):
             if name in self_nodes:
                 for edge in self[name].edges_to_dependencies():
                     dep_name = deps_to_replace.get(edge.spec, edge.spec).name
-                    nodes[name].add_dependency_edge(nodes[dep_name], deptypes=edge.deptypes)
+                    nodes[name].add_dependency_edge(
+                        nodes[dep_name], deptypes=edge.deptypes, virtuals=edge.virtuals
+                    )
                 if any(dep not in self_nodes for dep in self[name]._dependencies):
                     nodes[name].build_spec = self[name].build_spec
             else:
                 for edge in other[name].edges_to_dependencies():
-                    nodes[name].add_dependency_edge(nodes[edge.spec.name], deptypes=edge.deptypes)
+                    nodes[name].add_dependency_edge(
+                        nodes[edge.spec.name], deptypes=edge.deptypes, virtuals=edge.virtuals
+                    )
                 if any(dep not in other_nodes for dep in other[name]._dependencies):
                     nodes[name].build_spec = other[name].build_spec
 
@@ -4730,11 +4814,40 @@ def merge_abstract_anonymous_specs(*abstract_specs: Spec):
         # Update with additional constraints from other spec
         for name in current_spec_constraint.direct_dep_difference(merged_spec):
             edge = next(iter(current_spec_constraint.edges_to_dependencies(name)))
-            merged_spec._add_dependency(edge.spec.copy(), deptypes=edge.deptypes)
+            merged_spec._add_dependency(
+                edge.spec.copy(), deptypes=edge.deptypes, virtuals=edge.virtuals
+            )
 
     return merged_spec
 
 
+def reconstruct_virtuals_on_edges(spec):
+    """Reconstruct virtuals on edges. Used to read from old DB and reindex.
+
+    Args:
+        spec: spec on which we want to reconstruct virtuals
+    """
+    # Collect all possible virtuals
+    possible_virtuals = set()
+    for node in spec.traverse():
+        try:
+            possible_virtuals.update({x for x in node.package.dependencies if Spec(x).virtual})
+        except Exception as e:
+            warnings.warn(f"cannot reconstruct virtual dependencies on package {node.name}: {e}")
+            continue
+
+    # Assume all incoming edges to provider are marked with virtuals=
+    for vspec in possible_virtuals:
+        try:
+            provider = spec[vspec]
+        except KeyError:
+            # Virtual not in the DAG
+            continue
+
+        for edge in provider.edges_from_dependents():
+            edge.update_virtuals([vspec])
+
+
 class SpecfileReaderBase:
     @classmethod
     def from_node_dict(cls, node):
@@ -4818,7 +4931,7 @@ def _load(cls, data):
 
         # Pass 0: Determine hash type
         for node in nodes:
-            for _, _, _, dhash_type in cls.dependencies_from_node_dict(node):
+            for _, _, _, dhash_type, _ in cls.dependencies_from_node_dict(node):
                 any_deps = True
                 if dhash_type:
                     hash_type = dhash_type
@@ -4849,8 +4962,10 @@ def _load(cls, data):
         # Pass 2: Finish construction of all DAG edges (including build specs)
         for node_hash, node in hash_dict.items():
             node_spec = node["node_spec"]
-            for _, dhash, dtypes, _ in cls.dependencies_from_node_dict(node):
-                node_spec._add_dependency(hash_dict[dhash]["node_spec"], deptypes=dtypes)
+            for _, dhash, dtypes, _, virtuals in cls.dependencies_from_node_dict(node):
+                node_spec._add_dependency(
+                    hash_dict[dhash]["node_spec"], deptypes=dtypes, virtuals=virtuals
+                )
             if "build_spec" in node.keys():
                 _, bhash, _ = cls.build_spec_from_node_dict(node, hash_type=hash_type)
                 node_spec._build_spec = hash_dict[bhash]["node_spec"]
@@ -4884,9 +4999,10 @@ def load(cls, data):
         for node in nodes:
             # get dependency dict from the node.
             name, data = cls.name_and_data(node)
-            for dname, _, dtypes, _ in cls.dependencies_from_node_dict(data):
-                deps[name]._add_dependency(deps[dname], deptypes=dtypes)
+            for dname, _, dtypes, _, virtuals in cls.dependencies_from_node_dict(data):
+                deps[name]._add_dependency(deps[dname], deptypes=dtypes, virtuals=virtuals)
 
+        reconstruct_virtuals_on_edges(result)
         return result
 
     @classmethod
@@ -4915,18 +5031,20 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
                     if h.name in elt:
                         dep_hash, deptypes = elt[h.name], elt["type"]
                         hash_type = h.name
+                        virtuals = []
                         break
                 else:  # We never determined a hash type...
                     raise spack.error.SpecError("Couldn't parse dependency spec.")
             else:
                 raise spack.error.SpecError("Couldn't parse dependency types in spec.")
-            yield dep_name, dep_hash, list(deptypes), hash_type
+            yield dep_name, dep_hash, list(deptypes), hash_type, list(virtuals)
 
 
 class SpecfileV2(SpecfileReaderBase):
     @classmethod
     def load(cls, data):
         result = cls._load(data)
+        reconstruct_virtuals_on_edges(result)
         return result
 
     @classmethod
@@ -4960,7 +5078,7 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
                     raise spack.error.SpecError("Couldn't parse dependency spec.")
             else:
                 raise spack.error.SpecError("Couldn't parse dependency types in spec.")
-            result.append((dep_name, dep_hash, list(deptypes), hash_type))
+            result.append((dep_name, dep_hash, list(deptypes), hash_type, list(virtuals)))
         return result
 
     @classmethod
@@ -4980,6 +5098,20 @@ class SpecfileV3(SpecfileV2):
     pass
 
 
+class SpecfileV4(SpecfileV2):
+    @classmethod
+    def extract_info_from_dep(cls, elt, hash):
+        dep_hash = elt[hash.name]
+        deptypes = elt["parameters"]["deptypes"]
+        hash_type = hash.name
+        virtuals = elt["parameters"]["virtuals"]
+        return dep_hash, deptypes, hash_type, virtuals
+
+    @classmethod
+    def load(cls, data):
+        return cls._load(data)
+
+
 class LazySpecCache(collections.defaultdict):
     """Cache for Specs that uses a spec_like as key, and computes lazily
     the corresponding value ``Spec(spec_like``.

lib/spack/spack/test/bindist.py

@@ -201,12 +201,12 @@ def test_default_rpaths_create_install_default_layout(mirror_dir):
     install_cmd("--no-cache", sy_spec.name)
 
     # Create a buildache
-    buildcache_cmd("push", "-au", "-d", mirror_dir, cspec.name, sy_spec.name)
+    buildcache_cmd("push", "-au", mirror_dir, cspec.name, sy_spec.name)
     # Test force overwrite create buildcache (-f option)
-    buildcache_cmd("push", "-auf", "-d", mirror_dir, cspec.name)
+    buildcache_cmd("push", "-auf", mirror_dir, cspec.name)
 
     # Create mirror index
-    buildcache_cmd("update-index", "-d", mirror_dir)
+    buildcache_cmd("update-index", mirror_dir)
     # List the buildcaches in the mirror
     buildcache_cmd("list", "-alv")
 
@@ -214,13 +214,13 @@ def test_default_rpaths_create_install_default_layout(mirror_dir):
     uninstall_cmd("-y", "--dependents", gspec.name)
 
     # Test installing from build caches
-    buildcache_cmd("install", "-au", cspec.name, sy_spec.name)
+    buildcache_cmd("install", "-u", cspec.name, sy_spec.name)
 
     # This gives warning that spec is already installed
-    buildcache_cmd("install", "-au", cspec.name)
+    buildcache_cmd("install", "-u", cspec.name)
 
     # Test overwrite install
-    buildcache_cmd("install", "-afu", cspec.name)
+    buildcache_cmd("install", "-fu", cspec.name)
 
     buildcache_cmd("keys", "-f")
     buildcache_cmd("list")
@@ -246,35 +246,10 @@ def test_default_rpaths_install_nondefault_layout(mirror_dir):
 
     # Install some packages with dependent packages
     # test install in non-default install path scheme
-    buildcache_cmd("install", "-au", cspec.name, sy_spec.name)
+    buildcache_cmd("install", "-u", cspec.name, sy_spec.name)
 
     # Test force install in non-default install path scheme
-    buildcache_cmd("install", "-auf", cspec.name)
-
-
-@pytest.mark.requires_executables(*args)
-@pytest.mark.maybeslow
-@pytest.mark.nomockstage
-@pytest.mark.usefixtures("default_config", "cache_directory", "install_dir_default_layout")
-def test_relative_rpaths_create_default_layout(mirror_dir):
-    """
-    Test the creation and installation of buildcaches with relative
-    rpaths into the default directory layout scheme.
-    """
-
-    gspec, cspec = Spec("garply").concretized(), Spec("corge").concretized()
-
-    # Install 'corge' without using a cache
-    install_cmd("--no-cache", cspec.name)
-
-    # Create build cache with relative rpaths
-    buildcache_cmd("push", "-aur", "-d", mirror_dir, cspec.name)
-
-    # Create mirror index
-    buildcache_cmd("update-index", "-d", mirror_dir)
-
-    # Uninstall the package and deps
-    uninstall_cmd("-y", "--dependents", gspec.name)
+    buildcache_cmd("install", "-uf", cspec.name)
 
 
 @pytest.mark.requires_executables(*args)
@@ -291,19 +266,19 @@ def test_relative_rpaths_install_default_layout(mirror_dir):
     gspec, cspec = Spec("garply").concretized(), Spec("corge").concretized()
 
     # Install buildcache created with relativized rpaths
-    buildcache_cmd("install", "-auf", cspec.name)
+    buildcache_cmd("install", "-uf", cspec.name)
 
     # This gives warning that spec is already installed
-    buildcache_cmd("install", "-auf", cspec.name)
+    buildcache_cmd("install", "-uf", cspec.name)
 
     # Uninstall the package and deps
     uninstall_cmd("-y", "--dependents", gspec.name)
 
     # Install build cache
-    buildcache_cmd("install", "-auf", cspec.name)
+    buildcache_cmd("install", "-uf", cspec.name)
 
     # Test overwrite install
-    buildcache_cmd("install", "-auf", cspec.name)
+    buildcache_cmd("install", "-uf", cspec.name)
 
 
 @pytest.mark.requires_executables(*args)
@@ -320,7 +295,7 @@ def test_relative_rpaths_install_nondefault(mirror_dir):
     cspec = Spec("corge").concretized()
 
     # Test install in non-default install path scheme and relative path
-    buildcache_cmd("install", "-auf", cspec.name)
+    buildcache_cmd("install", "-uf", cspec.name)
 
 
 def test_push_and_fetch_keys(mock_gnupghome):
@@ -401,7 +376,7 @@ def test_spec_needs_rebuild(monkeypatch, tmpdir):
     install_cmd(s.name)
 
     # Put installed package in the buildcache
-    buildcache_cmd("push", "-u", "-a", "-d", mirror_dir.strpath, s.name)
+    buildcache_cmd("push", "-u", "-a", mirror_dir.strpath, s.name)
 
     rebuild = bindist.needs_rebuild(s, mirror_url)
 
@@ -430,8 +405,8 @@ def test_generate_index_missing(monkeypatch, tmpdir, mutable_config):
     install_cmd("--no-cache", s.name)
 
     # Create a buildcache and update index
-    buildcache_cmd("push", "-uad", mirror_dir.strpath, s.name)
-    buildcache_cmd("update-index", "-d", mirror_dir.strpath)
+    buildcache_cmd("push", "-ua", mirror_dir.strpath, s.name)
+    buildcache_cmd("update-index", mirror_dir.strpath)
 
     # Check package and dependency in buildcache
     cache_list = buildcache_cmd("list", "--allarch")
@@ -443,7 +418,7 @@ def test_generate_index_missing(monkeypatch, tmpdir, mutable_config):
     os.remove(*libelf_files)
 
     # Update index
-    buildcache_cmd("update-index", "-d", mirror_dir.strpath)
+    buildcache_cmd("update-index", mirror_dir.strpath)
 
     with spack.config.override("config:binary_index_ttl", 0):
         # Check dependency not in buildcache
@@ -519,10 +494,10 @@ def test_update_sbang(tmpdir, test_mirror):
     install_cmd("--no-cache", old_spec.name)
 
     # Create a buildcache with the installed spec.
-    buildcache_cmd("push", "-u", "-a", "-d", mirror_dir, old_spec_hash_str)
+    buildcache_cmd("push", "-u", "-a", mirror_dir, old_spec_hash_str)
 
     # Need to force an update of the buildcache index
-    buildcache_cmd("update-index", "-d", mirror_dir)
+    buildcache_cmd("update-index", mirror_dir)
 
     # Uninstall the original package.
     uninstall_cmd("-y", old_spec_hash_str)
@@ -538,7 +513,7 @@ def test_update_sbang(tmpdir, test_mirror):
         assert new_spec.dag_hash() == old_spec.dag_hash()
 
         # Install package from buildcache
-        buildcache_cmd("install", "-a", "-u", "-f", new_spec.name)
+        buildcache_cmd("install", "-u", "-f", new_spec.name)
 
         # Continue blowing away caches
         bindist.clear_spec_cache()

lib/spack/spack/test/build_system_guess.py

@@ -3,8 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import sys
-
 import pytest
 
 import spack.cmd.create
@@ -12,8 +10,6 @@
 import spack.util.executable
 import spack.util.url as url_util
 
-pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
-
 
 @pytest.fixture(
     scope="function",

lib/spack/spack/test/ci.py

@@ -291,7 +291,7 @@ def make_build_job(name, deps, stage, use_artifact_buildcache, optimize, use_dep
     def make_rebuild_index_job(use_artifact_buildcache, optimize, use_dependencies):
         result = {
             "stage": "stage-rebuild-index",
-            "script": "spack buildcache update-index --mirror-url s3://mirror",
+            "script": "spack buildcache update-index s3://mirror",
             "tags": ["tag-0", "tag-1"],
             "image": {"name": "spack/centos7", "entrypoint": [""]},
             "after_script": ['rm -rf "./spack"'],

lib/spack/spack/test/cmd/buildcache.py

@@ -85,7 +85,7 @@ def tests_buildcache_create(install_mockery, mock_fetch, monkeypatch, tmpdir):
     pkg = "trivial-install-test-package"
     install(pkg)
 
-    buildcache("push", "-d", str(tmpdir), "--unsigned", pkg)
+    buildcache("push", "--unsigned", str(tmpdir), pkg)
 
     spec = Spec(pkg).concretized()
     tarball_path = spack.binary_distribution.tarball_path_name(spec, ".spack")
@@ -105,7 +105,7 @@ def tests_buildcache_create_env(
         add(pkg)
         install()
 
-        buildcache("push", "-d", str(tmpdir), "--unsigned")
+        buildcache("push", "--unsigned", str(tmpdir))
 
     spec = Spec(pkg).concretized()
     tarball_path = spack.binary_distribution.tarball_path_name(spec, ".spack")
@@ -118,7 +118,7 @@ def test_buildcache_create_fails_on_noargs(tmpdir):
     """Ensure that buildcache create fails when given no args or
     environment."""
     with pytest.raises(spack.main.SpackCommandError):
-        buildcache("push", "-d", str(tmpdir), "--unsigned")
+        buildcache("push", "--unsigned", str(tmpdir))
 
 
 def test_buildcache_create_fail_on_perm_denied(install_mockery, mock_fetch, monkeypatch, tmpdir):
@@ -127,7 +127,7 @@ def test_buildcache_create_fail_on_perm_denied(install_mockery, mock_fetch, monk
 
     tmpdir.chmod(0)
     with pytest.raises(OSError) as error:
-        buildcache("push", "-d", str(tmpdir), "--unsigned", "trivial-install-test-package")
+        buildcache("push", "--unsigned", str(tmpdir), "trivial-install-test-package")
     assert error.value.errno == errno.EACCES
     tmpdir.chmod(0o700)
 
@@ -159,11 +159,11 @@ def test_update_key_index(
     # Put installed package in the buildcache, which, because we're signing
     # it, should result in the public key getting pushed to the buildcache
     # as well.
-    buildcache("push", "-a", "-d", mirror_dir.strpath, s.name)
+    buildcache("push", "-a", mirror_dir.strpath, s.name)
 
     # Now make sure that when we pass the "--keys" argument to update-index
     # it causes the index to get update.
-    buildcache("update-index", "--keys", "-d", mirror_dir.strpath)
+    buildcache("update-index", "--keys", mirror_dir.strpath)
 
     key_dir_list = os.listdir(os.path.join(mirror_dir.strpath, "build_cache", "_pgp"))
 
@@ -213,27 +213,25 @@ def verify_mirror_contents():
     # Install a package and put it in the buildcache
     s = Spec(out_env_pkg).concretized()
     install(s.name)
-    buildcache("push", "-u", "-f", "-a", "--mirror-url", src_mirror_url, s.name)
+    buildcache("push", "-u", "-f", "-a", src_mirror_url, s.name)
 
     env("create", "test")
     with ev.read("test"):
         add(in_env_pkg)
         install()
-        buildcache("push", "-u", "-f", "-a", "--mirror-url", src_mirror_url, in_env_pkg)
+        buildcache("push", "-u", "-f", "-a", src_mirror_url, in_env_pkg)
 
         # Now run the spack buildcache sync command with all the various options
         # for specifying mirrors
 
         # Use urls to specify mirrors
-        buildcache(
-            "sync", "--src-mirror-url", src_mirror_url, "--dest-mirror-url", dest_mirror_url
-        )
+        buildcache("sync", src_mirror_url, dest_mirror_url)
 
         verify_mirror_contents()
         shutil.rmtree(dest_mirror_dir)
 
         # Use local directory paths to specify fs locations
-        buildcache("sync", "--src-directory", src_mirror_dir, "--dest-directory", dest_mirror_dir)
+        buildcache("sync", src_mirror_dir, dest_mirror_dir)
 
         verify_mirror_contents()
         shutil.rmtree(dest_mirror_dir)
@@ -242,7 +240,7 @@ def verify_mirror_contents():
         mirror("add", "src", src_mirror_url)
         mirror("add", "dest", dest_mirror_url)
 
-        buildcache("sync", "--src-mirror-name", "src", "--dest-mirror-name", "dest")
+        buildcache("sync", "src", "dest")
 
         verify_mirror_contents()
 
@@ -260,7 +258,7 @@ def test_buildcache_create_install(
     pkg = "trivial-install-test-package"
     install(pkg)
 
-    buildcache("push", "-d", str(tmpdir), "--unsigned", pkg)
+    buildcache("push", "--unsigned", str(tmpdir), pkg)
 
     spec = Spec(pkg).concretized()
     tarball_path = spack.binary_distribution.tarball_path_name(spec, ".spack")
@@ -324,12 +322,12 @@ def fake_push(node, push_url, options):
 
     monkeypatch.setattr(spack.binary_distribution, "push_or_raise", fake_push)
 
-    buildcache_create_args = ["create", "-d", str(tmpdir), "--unsigned"]
+    buildcache_create_args = ["create", "--unsigned"]
 
     if things_to_install != "":
         buildcache_create_args.extend(["--only", things_to_install])
 
-    buildcache_create_args.extend([slash_hash])
+    buildcache_create_args.extend([str(tmpdir), slash_hash])
 
     buildcache(*buildcache_create_args)
 

lib/spack/spack/test/cmd/ci.py

@@ -1055,7 +1055,7 @@ def test_ci_nothing_to_rebuild(
     )
 
     install_cmd("archive-files")
-    buildcache_cmd("push", "-a", "-f", "-u", "--mirror-url", mirror_url, "archive-files")
+    buildcache_cmd("push", "-a", "-f", "-u", mirror_url, "archive-files")
 
     filename = str(tmpdir.join("spack.yaml"))
     with open(filename, "w") as f:
@@ -1155,8 +1155,8 @@ def test_ci_generate_mirror_override(
         second_ci_yaml = str(tmpdir.join(".gitlab-ci-2.yml"))
         with ev.read("test"):
             install_cmd()
-            buildcache_cmd("push", "-u", "--mirror-url", mirror_url, "patchelf")
-            buildcache_cmd("update-index", "--mirror-url", mirror_url, output=str)
+            buildcache_cmd("push", "-u", mirror_url, "patchelf")
+            buildcache_cmd("update-index", mirror_url, output=str)
 
             # This generate should not trigger a rebuild of patchelf, since it's in
             # the main mirror referenced in the environment.
@@ -1297,7 +1297,7 @@ def test_push_mirror_contents(
             mirror_cmd("rm", "test-ci")
 
             # Test generating buildcache index while we have bin mirror
-            buildcache_cmd("update-index", "--mirror-url", mirror_url)
+            buildcache_cmd("update-index", mirror_url)
             index_path = os.path.join(buildcache_path, "index.json")
             with open(index_path) as idx_fd:
                 index_object = json.load(idx_fd)
@@ -1613,7 +1613,7 @@ def test_ci_rebuild_index(
                 ypfd.write(spec_json)
 
             install_cmd("--add", "--keep-stage", "-f", json_path)
-            buildcache_cmd("push", "-u", "-a", "-f", "--mirror-url", mirror_url, "callpath")
+            buildcache_cmd("push", "-u", "-a", "-f", mirror_url, "callpath")
             ci_cmd("rebuild-index")
 
             buildcache_path = os.path.join(mirror_dir.strpath, "build_cache")
@@ -1647,7 +1647,7 @@ def test_ci_generate_bootstrap_prune_dag(
     install_cmd("gcc@=12.2.0%gcc@10.2.1")
 
     # Put installed compiler in the buildcache
-    buildcache_cmd("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, "gcc@12.2.0%gcc@10.2.1")
+    buildcache_cmd("push", "-u", "-a", "-f", mirror_dir.strpath, "gcc@12.2.0%gcc@10.2.1")
 
     # Now uninstall the compiler
     uninstall_cmd("-y", "gcc@12.2.0%gcc@10.2.1")
@@ -1662,7 +1662,7 @@ def test_ci_generate_bootstrap_prune_dag(
     install_cmd("--no-check-signature", "b%gcc@=12.2.0")
 
     # Put spec built with installed compiler in the buildcache
-    buildcache_cmd("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, "b%gcc@12.2.0")
+    buildcache_cmd("push", "-u", "-a", "-f", mirror_dir.strpath, "b%gcc@12.2.0")
 
     # Now uninstall the spec
     uninstall_cmd("-y", "b%gcc@12.2.0")

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

@@ -2402,6 +2402,21 @@ def test_env_activate_default_view_root_unconditional(mutable_mock_env_path):
     )
 
 
+@pytest.mark.regression("38510")
+def test_concretize_separately_abstract_hash(install_mockery, mock_fetch):
+    """Check that a root can have no name if it has a hash."""
+    s = Spec("trivial-install-test-package").concretized()
+    install(str(s))
+
+    e = ev.create("test")
+    e.unify = False
+
+    e.add(f"/{s.dag_hash()}")
+    e.concretize()
+
+    assert list(e.concretized_specs()) == [(Spec(f"/{s.dag_hash()}"), s)]
+
+
 def test_concretize_user_specs_together():
     e = ev.create("coconcretization")
     e.unify = True

lib/spack/spack/test/cmd/graph.py

@@ -3,16 +3,12 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import sys
-
 import pytest
 
 from spack.main import SpackCommand, SpackCommandError
 
 graph = SpackCommand("graph")
 
-pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
-
 
 @pytest.mark.db
 @pytest.mark.usefixtures("mock_packages", "database")

lib/spack/spack/test/cmd/info.py

@@ -4,7 +4,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import argparse
-import sys
 
 import pytest
 
@@ -13,8 +12,6 @@
 
 info = SpackCommand("info")
 
-pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="Not yet implemented on Windows")
-
 
 @pytest.fixture(scope="module")
 def parser():

lib/spack/spack/test/cmd/install.py

@@ -966,7 +966,7 @@ def test_compiler_bootstrap_from_binary_mirror(
     install("gcc@=10.2.0")
 
     # Put installed compiler in the buildcache
-    buildcache("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, "gcc@10.2.0")
+    buildcache("push", "-u", "-a", "-f", mirror_dir.strpath, "gcc@10.2.0")
 
     # Now uninstall the compiler
     uninstall("-y", "gcc@10.2.0")
@@ -1138,7 +1138,7 @@ def install_use_buildcache(opt):
 
     # Populate the buildcache
     install(package_name)
-    buildcache("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, package_name, dependency_name)
+    buildcache("push", "-u", "-a", "-f", mirror_dir.strpath, package_name, dependency_name)
 
     # Uninstall the all of the packages for clean slate
     uninstall("-y", "-a")

lib/spack/spack/test/cmd/mark.py

@@ -3,8 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import sys
-
 import pytest
 
 import spack.store
@@ -15,8 +13,6 @@
 install = SpackCommand("install")
 uninstall = SpackCommand("uninstall")
 
-pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
-
 
 @pytest.mark.db
 def test_mark_mode_required(mutable_database):

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

@@ -235,7 +235,7 @@ def test_mirror_destroy(
 
     # Put a binary package in a buildcache
     install("--no-cache", spec_name)
-    buildcache("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, spec_name)
+    buildcache("push", "-u", "-a", "-f", mirror_dir.strpath, spec_name)
 
     contents = os.listdir(mirror_dir.strpath)
     assert "build_cache" in contents
@@ -245,7 +245,7 @@ def test_mirror_destroy(
 
     assert not os.path.exists(mirror_dir.strpath)
 
-    buildcache("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, spec_name)
+    buildcache("push", "-u", "-a", "-f", mirror_dir.strpath, spec_name)
 
     contents = os.listdir(mirror_dir.strpath)
     assert "build_cache" in contents

lib/spack/spack/test/cmd/spec.py

@@ -157,7 +157,7 @@ def _parse_types(string):
 
 
 def test_spec_deptypes_nodes():
-    output = spec("--types", "--cover", "nodes", "dt-diamond")
+    output = spec("--types", "--cover", "nodes", "--no-install-status", "dt-diamond")
     types = _parse_types(output)
 
     assert types["dt-diamond"] == ["    "]
@@ -167,7 +167,7 @@ def test_spec_deptypes_nodes():
 
 
 def test_spec_deptypes_edges():
-    output = spec("--types", "--cover", "edges", "dt-diamond")
+    output = spec("--types", "--cover", "edges", "--no-install-status", "dt-diamond")
     types = _parse_types(output)
 
     assert types["dt-diamond"] == ["    "]

lib/spack/spack/test/concretize.py

@@ -2170,3 +2170,14 @@ def test_concretization_with_compilers_supporting_target_any(self):
         with spack.config.override("compilers", compiler_configuration):
             s = spack.spec.Spec("a").concretized()
         assert s.satisfies("%gcc@12.1.0")
+
+    @pytest.mark.parametrize("spec_str", ["mpileaks", "mpileaks ^mpich"])
+    def test_virtuals_are_annotated_on_edges(self, spec_str, default_mock_concretization):
+        """Tests that information on virtuals is annotated on DAG edges"""
+        spec = default_mock_concretization(spec_str)
+        mpi_provider = spec["mpi"].name
+
+        edges = spec.edges_to_dependencies(name=mpi_provider)
+        assert len(edges) == 1 and edges[0].virtuals == ("mpi",)
+        edges = spec.edges_to_dependencies(name="callpath")
+        assert len(edges) == 1 and edges[0].virtuals == ()

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

@@ -167,6 +167,37 @@ def test_prepend_path_separator(self, modulefile_content, module_configuration):
         assert len([x for x in content if 'append_path("SPACE", "qux", " ")' in x]) == 1
         assert len([x for x in content if 'remove_path("SPACE", "qux", " ")' in x]) == 1
 
+    @pytest.mark.regression("11355")
+    def test_manpath_setup(self, modulefile_content, module_configuration):
+        """Tests specific setup of MANPATH environment variable."""
+
+        module_configuration("autoload_direct")
+
+        # no manpath set by module
+        content = modulefile_content("mpileaks")
+        assert len([x for x in content if 'append_path("MANPATH", "", ":")' in x]) == 0
+
+        # manpath set by module with prepend_path
+        content = modulefile_content("module-manpath-prepend")
+        assert (
+            len([x for x in content if 'prepend_path("MANPATH", "/path/to/man", ":")' in x]) == 1
+        )
+        assert (
+            len([x for x in content if 'prepend_path("MANPATH", "/path/to/share/man", ":")' in x])
+            == 1
+        )
+        assert len([x for x in content if 'append_path("MANPATH", "", ":")' in x]) == 1
+
+        # manpath set by module with append_path
+        content = modulefile_content("module-manpath-append")
+        assert len([x for x in content if 'append_path("MANPATH", "/path/to/man", ":")' in x]) == 1
+        assert len([x for x in content if 'append_path("MANPATH", "", ":")' in x]) == 1
+
+        # manpath set by module with setenv
+        content = modulefile_content("module-manpath-setenv")
+        assert len([x for x in content if 'setenv("MANPATH", "/path/to/man")' in x]) == 1
+        assert len([x for x in content if 'append_path("MANPATH", "", ":")' in x]) == 0
+
     def test_help_message(self, modulefile_content, module_configuration):
         """Tests the generation of module help message."""
 

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

@@ -37,6 +37,11 @@ def test_autoload_direct(self, modulefile_content, module_configuration):
         module_configuration("autoload_direct")
         content = modulefile_content(mpileaks_spec_string)
 
+        assert (
+            len([x for x in content if "if {![info exists ::env(LMOD_VERSION_MAJOR)]} {" in x])
+            == 1
+        )
+        assert len([x for x in content if "depends-on " in x]) == 2
         assert len([x for x in content if "module load " in x]) == 2
 
         # dtbuild1 has
@@ -46,6 +51,11 @@ def test_autoload_direct(self, modulefile_content, module_configuration):
         # Just make sure the 'build' dependency is not there
         content = modulefile_content("dtbuild1")
 
+        assert (
+            len([x for x in content if "if {![info exists ::env(LMOD_VERSION_MAJOR)]} {" in x])
+            == 1
+        )
+        assert len([x for x in content if "depends-on " in x]) == 2
         assert len([x for x in content if "module load " in x]) == 2
 
         # The configuration file sets the verbose keyword to False
@@ -58,6 +68,11 @@ def test_autoload_all(self, modulefile_content, module_configuration):
         module_configuration("autoload_all")
         content = modulefile_content(mpileaks_spec_string)
 
+        assert (
+            len([x for x in content if "if {![info exists ::env(LMOD_VERSION_MAJOR)]} {" in x])
+            == 1
+        )
+        assert len([x for x in content if "depends-on " in x]) == 5
         assert len([x for x in content if "module load " in x]) == 5
 
         # dtbuild1 has
@@ -67,6 +82,11 @@ def test_autoload_all(self, modulefile_content, module_configuration):
         # Just make sure the 'build' dependency is not there
         content = modulefile_content("dtbuild1")
 
+        assert (
+            len([x for x in content if "if {![info exists ::env(LMOD_VERSION_MAJOR)]} {" in x])
+            == 1
+        )
+        assert len([x for x in content if "depends-on " in x]) == 2
         assert len([x for x in content if "module load " in x]) == 2
 
     def test_prerequisites_direct(self, modulefile_content, module_configuration):
@@ -103,6 +123,7 @@ def test_alter_environment(self, modulefile_content, module_configuration):
         assert len([x for x in content if x.startswith("prepend-path CMAKE_PREFIX_PATH")]) == 0
         assert len([x for x in content if 'setenv FOO "foo"' in x]) == 0
         assert len([x for x in content if "unsetenv BAR" in x]) == 0
+        assert len([x for x in content if "depends-on foo/bar" in x]) == 1
         assert len([x for x in content if "module load foo/bar" in x]) == 1
         assert len([x for x in content if "setenv LIBDWARF_ROOT" in x]) == 1
 
@@ -121,6 +142,46 @@ def test_prepend_path_separator(self, modulefile_content, module_configuration):
         assert len([x for x in content if 'append-path --delim " " SPACE "qux"' in x]) == 1
         assert len([x for x in content if 'remove-path --delim " " SPACE "qux"' in x]) == 1
 
+    @pytest.mark.regression("11355")
+    def test_manpath_setup(self, modulefile_content, module_configuration):
+        """Tests specific setup of MANPATH environment variable."""
+
+        module_configuration("autoload_direct")
+
+        # no manpath set by module
+        content = modulefile_content("mpileaks")
+        assert len([x for x in content if 'append-path --delim ":" MANPATH ""' in x]) == 0
+
+        # manpath set by module with prepend-path
+        content = modulefile_content("module-manpath-prepend")
+        assert (
+            len([x for x in content if 'prepend-path --delim ":" MANPATH "/path/to/man"' in x])
+            == 1
+        )
+        assert (
+            len(
+                [
+                    x
+                    for x in content
+                    if 'prepend-path --delim ":" MANPATH "/path/to/share/man"' in x
+                ]
+            )
+            == 1
+        )
+        assert len([x for x in content if 'append-path --delim ":" MANPATH ""' in x]) == 1
+
+        # manpath set by module with append-path
+        content = modulefile_content("module-manpath-append")
+        assert (
+            len([x for x in content if 'append-path --delim ":" MANPATH "/path/to/man"' in x]) == 1
+        )
+        assert len([x for x in content if 'append-path --delim ":" MANPATH ""' in x]) == 1
+
+        # manpath set by module with setenv
+        content = modulefile_content("module-manpath-setenv")
+        assert len([x for x in content if 'setenv MANPATH "/path/to/man"' in x]) == 1
+        assert len([x for x in content if 'append-path --delim ":" MANPATH ""' in x]) == 0
+
     def test_help_message(self, modulefile_content, module_configuration):
         """Tests the generation of module help message."""
 
@@ -394,10 +455,16 @@ def test_autoload_with_constraints(self, modulefile_content, module_configuratio
 
         # Test the mpileaks that should have the autoloaded dependencies
         content = modulefile_content("mpileaks ^mpich2")
+        assert len([x for x in content if "depends-on " in x]) == 2
         assert len([x for x in content if "module load " in x]) == 2
 
         # Test the mpileaks that should NOT have the autoloaded dependencies
         content = modulefile_content("mpileaks ^mpich")
+        assert (
+            len([x for x in content if "if {![info exists ::env(LMOD_VERSION_MAJOR)]} {" in x])
+            == 0
+        )
+        assert len([x for x in content if "depends-on " in x]) == 0
         assert len([x for x in content if "module load " in x]) == 0
 
     def test_modules_no_arch(self, factory, module_configuration):

lib/spack/spack/test/packaging.py

@@ -100,7 +100,7 @@ def test_buildcache(mock_archive, tmpdir):
     parser = argparse.ArgumentParser()
     buildcache.setup_parser(parser)
 
-    create_args = ["create", "-a", "-f", "-d", mirror_path, pkghash]
+    create_args = ["create", "-a", "-f", mirror_path, pkghash]
     # Create a private key to sign package with if gpg2 available
     spack.util.gpg.create(
         name="test key 1", expires="0", email="spack@googlegroups.com", comment="Spack test key"
@@ -116,7 +116,7 @@ def test_buildcache(mock_archive, tmpdir):
     # Uninstall the package
     pkg.do_uninstall(force=True)
 
-    install_args = ["install", "-a", "-f", pkghash]
+    install_args = ["install", "-f", pkghash]
     args = parser.parse_args(install_args)
     # Test install
     buildcache.buildcache(parser, args)
@@ -131,30 +131,6 @@ def test_buildcache(mock_archive, tmpdir):
     assert buildinfo["relocate_textfiles"] == ["dummy.txt"]
     assert buildinfo["relocate_links"] == ["link_to_dummy.txt"]
 
-    # create build cache with relative path
-    create_args.insert(create_args.index("-a"), "-f")
-    create_args.insert(create_args.index("-a"), "-r")
-    args = parser.parse_args(create_args)
-    buildcache.buildcache(parser, args)
-
-    # Uninstall the package
-    pkg.do_uninstall(force=True)
-
-    args = parser.parse_args(install_args)
-    buildcache.buildcache(parser, args)
-
-    # test overwrite install
-    install_args.insert(install_args.index("-a"), "-f")
-    args = parser.parse_args(install_args)
-    buildcache.buildcache(parser, args)
-
-    files = os.listdir(spec.prefix)
-    assert "link_to_dummy.txt" in files
-    assert "dummy.txt" in files
-    #    assert os.path.realpath(
-    #        os.path.join(spec.prefix, 'link_to_dummy.txt')
-    #    ) == os.path.realpath(os.path.join(spec.prefix, 'dummy.txt'))
-
     args = parser.parse_args(["keys"])
     buildcache.buildcache(parser, args)
 

lib/spack/spack/test/spec_dag.py

@@ -125,7 +125,7 @@ def _mock_installed(self):
     # use the installed C.  It should *not* force A to use the installed D
     # *if* we're doing a fresh installation.
     a_spec = Spec(a)
-    a_spec._add_dependency(c_spec, deptypes=("build", "link"))
+    a_spec._add_dependency(c_spec, deptypes=("build", "link"), virtuals=())
     a_spec.concretize()
     assert spack.version.Version("2") == a_spec[c][d].version
     assert spack.version.Version("2") == a_spec[e].version
@@ -148,7 +148,7 @@ def test_specify_preinstalled_dep(tmpdir, monkeypatch):
         monkeypatch.setattr(Spec, "installed", property(lambda x: x.name != "a"))
 
         a_spec = Spec("a")
-        a_spec._add_dependency(b_spec, deptypes=("build", "link"))
+        a_spec._add_dependency(b_spec, deptypes=("build", "link"), virtuals=())
         a_spec.concretize()
 
         assert set(x.name for x in a_spec.traverse()) == set(["a", "b", "c"])
@@ -989,9 +989,9 @@ def test_synthetic_construction_of_split_dependencies_from_same_package(mock_pac
     link_run_spec = Spec("c@=1.0").concretized()
     build_spec = Spec("c@=2.0").concretized()
 
-    root.add_dependency_edge(link_run_spec, deptypes="link")
-    root.add_dependency_edge(link_run_spec, deptypes="run")
-    root.add_dependency_edge(build_spec, deptypes="build")
+    root.add_dependency_edge(link_run_spec, deptypes="link", virtuals=())
+    root.add_dependency_edge(link_run_spec, deptypes="run", virtuals=())
+    root.add_dependency_edge(build_spec, deptypes="build", virtuals=())
 
     # Check dependencies from the perspective of root
     assert len(root.dependencies()) == 2
@@ -1017,7 +1017,7 @@ def test_synthetic_construction_bootstrapping(mock_packages, config):
     root = Spec("b@=2.0").concretized()
     bootstrap = Spec("b@=1.0").concretized()
 
-    root.add_dependency_edge(bootstrap, deptypes="build")
+    root.add_dependency_edge(bootstrap, deptypes="build", virtuals=())
 
     assert len(root.dependencies()) == 1
     assert root.dependencies()[0].name == "b"
@@ -1036,7 +1036,7 @@ def test_addition_of_different_deptypes_in_multiple_calls(mock_packages, config)
     bootstrap = Spec("b@=1.0").concretized()
 
     for current_deptype in ("build", "link", "run"):
-        root.add_dependency_edge(bootstrap, deptypes=current_deptype)
+        root.add_dependency_edge(bootstrap, deptypes=current_deptype, virtuals=())
 
         # Check edges in dependencies
         assert len(root.edges_to_dependencies()) == 1
@@ -1063,9 +1063,9 @@ def test_adding_same_deptype_with_the_same_name_raises(
     c1 = Spec("b@=1.0").concretized()
     c2 = Spec("b@=2.0").concretized()
 
-    p.add_dependency_edge(c1, deptypes=c1_deptypes)
+    p.add_dependency_edge(c1, deptypes=c1_deptypes, virtuals=())
     with pytest.raises(spack.error.SpackError):
-        p.add_dependency_edge(c2, deptypes=c2_deptypes)
+        p.add_dependency_edge(c2, deptypes=c2_deptypes, virtuals=())
 
 
 @pytest.mark.regression("33499")
@@ -1084,16 +1084,16 @@ def test_indexing_prefers_direct_or_transitive_link_deps():
     z3_flavor_1 = Spec("z3 +through_a1")
     z3_flavor_2 = Spec("z3 +through_z1")
 
-    root.add_dependency_edge(a1, deptypes=("build", "run", "test"))
+    root.add_dependency_edge(a1, deptypes=("build", "run", "test"), virtuals=())
 
     # unique package as a dep of a build/run/test type dep.
-    a1.add_dependency_edge(a2, deptypes="all")
-    a1.add_dependency_edge(z3_flavor_1, deptypes="all")
+    a1.add_dependency_edge(a2, deptypes="all", virtuals=())
+    a1.add_dependency_edge(z3_flavor_1, deptypes="all", virtuals=())
 
     # chain of link type deps root -> z1 -> z2 -> z3
-    root.add_dependency_edge(z1, deptypes="link")
-    z1.add_dependency_edge(z2, deptypes="link")
-    z2.add_dependency_edge(z3_flavor_2, deptypes="link")
+    root.add_dependency_edge(z1, deptypes="link", virtuals=())
+    z1.add_dependency_edge(z2, deptypes="link", virtuals=())
+    z2.add_dependency_edge(z3_flavor_2, deptypes="link", virtuals=())
 
     # Indexing should prefer the link-type dep.
     assert "through_z1" in root["z3"].variants

lib/spack/spack/test/spec_semantics.py

@@ -971,7 +971,7 @@ def test_error_message_unknown_variant(self):
     def test_satisfies_dependencies_ordered(self):
         d = Spec("zmpi ^fake")
         s = Spec("mpileaks")
-        s._add_dependency(d, deptypes=())
+        s._add_dependency(d, deptypes=(), virtuals=())
         assert s.satisfies("mpileaks ^zmpi ^fake")
 
     @pytest.mark.parametrize("transitive", [True, False])
@@ -1018,6 +1018,7 @@ def test_is_extension_after_round_trip_to_dict(config, mock_packages, spec_str):
 
 
 def test_malformed_spec_dict():
+    # FIXME: This test was really testing the specific implementation with an ad-hoc test
     with pytest.raises(SpecError, match="malformed"):
         Spec.from_dict(
             {"spec": {"_meta": {"version": 2}, "nodes": [{"dependencies": {"name": "foo"}}]}}
@@ -1025,6 +1026,7 @@ def test_malformed_spec_dict():
 
 
 def test_spec_dict_hashless_dep():
+    # FIXME: This test was really testing the specific implementation with an ad-hoc test
     with pytest.raises(SpecError, match="Couldn't parse"):
         Spec.from_dict(
             {
@@ -1118,7 +1120,7 @@ def test_concretize_partial_old_dag_hash_spec(mock_packages, config):
 
     # add it to an abstract spec as a dependency
     top = Spec("dt-diamond")
-    top.add_dependency_edge(bottom, deptypes=())
+    top.add_dependency_edge(bottom, deptypes=(), virtuals=())
 
     # concretize with the already-concrete dependency
     top.concretize()

lib/spack/spack/test/spec_yaml.py

@@ -43,12 +43,6 @@ def check_json_round_trip(spec):
     assert spec.eq_dag(spec_from_json)
 
 
-def test_simple_spec():
-    spec = Spec("mpileaks")
-    check_yaml_round_trip(spec)
-    check_json_round_trip(spec)
-
-
 def test_read_spec_from_signed_json():
     spec_dir = os.path.join(spack.paths.test_path, "data", "mirrors", "signed_json")
     file_name = (
@@ -70,13 +64,6 @@ def check_spec(spec_to_check):
         check_spec(s)
 
 
-def test_normal_spec(mock_packages):
-    spec = Spec("mpileaks+debug~opt")
-    spec.normalize()
-    check_yaml_round_trip(spec)
-    check_json_round_trip(spec)
-
-
 @pytest.mark.parametrize(
     "invalid_yaml", ["playing_playlist: {{ action }} playlist {{ playlist_name }}"]
 )
@@ -95,37 +82,28 @@ def test_invalid_json_spec(invalid_json, error_message):
     assert error_message in exc_msg
 
 
-def test_external_spec(config, mock_packages):
-    spec = Spec("externaltool")
-    spec.concretize()
-    check_yaml_round_trip(spec)
-    check_json_round_trip(spec)
-
-    spec = Spec("externaltest")
-    spec.concretize()
-    check_yaml_round_trip(spec)
-    check_json_round_trip(spec)
-
-
-def test_ambiguous_version_spec(mock_packages):
-    spec = Spec("mpileaks@1.0:5.0,6.1,7.3+debug~opt")
-    spec.normalize()
-    check_yaml_round_trip(spec)
-    check_json_round_trip(spec)
-
-
-def test_concrete_spec(config, mock_packages):
-    spec = Spec("mpileaks+debug~opt")
-    spec.concretize()
-    check_yaml_round_trip(spec)
-    check_json_round_trip(spec)
-
-
-def test_yaml_multivalue(config, mock_packages):
-    spec = Spec('multivalue-variant foo="bar,baz"')
-    spec.concretize()
-    check_yaml_round_trip(spec)
-    check_json_round_trip(spec)
+@pytest.mark.parametrize(
+    "abstract_spec",
+    [
+        # Externals
+        "externaltool",
+        "externaltest",
+        # Ambiguous version spec
+        "mpileaks@1.0:5.0,6.1,7.3+debug~opt",
+        # Variants
+        "mpileaks+debug~opt",
+        'multivalue-variant foo="bar,baz"',
+        # Virtuals on edges
+        "callpath",
+        "mpileaks",
+    ],
+)
+def test_roundtrip_concrete_specs(abstract_spec, default_mock_concretization):
+    check_yaml_round_trip(Spec(abstract_spec))
+    check_json_round_trip(Spec(abstract_spec))
+    concrete_spec = default_mock_concretization(abstract_spec)
+    check_yaml_round_trip(concrete_spec)
+    check_json_round_trip(concrete_spec)
 
 
 def test_yaml_subdag(config, mock_packages):
@@ -506,6 +484,8 @@ def test_legacy_yaml(tmpdir, install_mockery, mock_packages):
         ("specfiles/hdf5.v017.json.gz", "xqh5iyjjtrp2jw632cchacn3l7vqzf3m", spack.spec.SpecfileV2),
         # Use "full hash" everywhere, see https://github.com/spack/spack/pull/28504
         ("specfiles/hdf5.v019.json.gz", "iulacrbz7o5v5sbj7njbkyank3juh6d3", spack.spec.SpecfileV3),
+        # Add properties on edges, see https://github.com/spack/spack/pull/34821
+        ("specfiles/hdf5.v020.json.gz", "vlirlcgazhvsvtundz4kug75xkkqqgou", spack.spec.SpecfileV4),
     ],
 )
 def test_load_json_specfiles(specfile, expected_hash, reader_cls):

lib/spack/spack/test/traverse.py

@@ -19,7 +19,7 @@ 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], deptypes=deptypes)
+        specs[parent].add_dependency_edge(specs[child], deptypes=deptypes, virtuals=())
     return specs
 
 

lib/spack/spack/test/web.py

@@ -4,7 +4,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import collections
 import os
-import sys
 
 import pytest
 
@@ -34,7 +33,6 @@ def _create_url(relative_url):
 root_with_fragment = _create_url("index_with_fragment.html")
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
 @pytest.mark.parametrize(
     "depth,expected_found,expected_not_found,expected_text",
     [
@@ -99,20 +97,17 @@ def test_spider_no_response(monkeypatch):
     assert not pages and not links
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
 def test_find_versions_of_archive_0():
     versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=0)
     assert Version("0.0.0") in versions
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
 def test_find_versions_of_archive_1():
     versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=1)
     assert Version("0.0.0") in versions
     assert Version("1.0.0") in versions
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
 def test_find_versions_of_archive_2():
     versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=2)
     assert Version("0.0.0") in versions
@@ -120,14 +115,12 @@ def test_find_versions_of_archive_2():
     assert Version("2.0.0") in versions
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
 def test_find_exotic_versions_of_archive_2():
     versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=2)
     # up for grabs to make this better.
     assert Version("2.0.0b2") in versions
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
 def test_find_versions_of_archive_3():
     versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=3)
     assert Version("0.0.0") in versions
@@ -137,7 +130,6 @@ def test_find_versions_of_archive_3():
     assert Version("4.5") in versions
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
 def test_find_exotic_versions_of_archive_3():
     versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=3)
     assert Version("2.0.0b2") in versions
@@ -145,7 +137,6 @@ def test_find_exotic_versions_of_archive_3():
     assert Version("4.5-rc5") in versions
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
 def test_find_versions_of_archive_with_fragment():
     versions = spack.util.web.find_versions_of_archive(
         root_tarball, root_with_fragment, list_depth=0
@@ -206,7 +197,6 @@ def test_etag_parser():
     assert spack.util.web.parse_etag("abc def") is None
 
 
-@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
 def test_list_url(tmpdir):
     testpath = str(tmpdir)
     testpath_url = url_util.path_to_file_url(testpath)

lib/spack/spack/traverse.py

@@ -211,7 +211,9 @@ def get_visitor_from_args(cover, direction, deptype, key=id, visited=None, visit
 def with_artificial_edges(specs):
     """Initialize a list of edges from an imaginary root node to the root specs."""
     return [
-        EdgeAndDepth(edge=spack.spec.DependencySpec(parent=None, spec=s, deptypes=()), depth=0)
+        EdgeAndDepth(
+            edge=spack.spec.DependencySpec(parent=None, spec=s, deptypes=(), virtuals=()), depth=0
+        )
         for s in specs
     ]
 

lib/spack/spack/util/web.py

@@ -17,6 +17,7 @@
 import traceback
 import urllib.parse
 from html.parser import HTMLParser
+from pathlib import Path, PurePosixPath
 from urllib.error import URLError
 from urllib.request import HTTPSHandler, Request, build_opener
 
@@ -498,7 +499,8 @@ def list_url(url, recursive=False):
 
     if local_path:
         if recursive:
-            return list(_iter_local_prefix(local_path))
+            # convert backslash to forward slash as required for URLs
+            return [str(PurePosixPath(Path(p))) for p in list(_iter_local_prefix(local_path))]
         return [
             subpath
             for subpath in os.listdir(local_path)
@@ -738,7 +740,8 @@ def find_versions_of_archive(
 
         # We'll be a bit more liberal and just look for the archive
         # part, not the full path.
-        url_regex = os.path.basename(url_regex)
+        # this is a URL so it is a posixpath even on Windows
+        url_regex = PurePosixPath(url_regex).name
 
         # We need to add a / to the beginning of the regex to prevent
         # Spack from picking up similarly named packages like:

share/spack/spack-completion.bash

@@ -498,7 +498,7 @@ _spack_buildcache() {
 _spack_buildcache_push() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -r --rel -f --force -u --unsigned -a --allow-root -k --key -d --directory -m --mirror-name --mirror-url --update-index --rebuild-index --spec-file --only"
+        SPACK_COMPREPLY="-h --help -f --force -u --unsigned -a --allow-root -k --key --update-index --rebuild-index --spec-file --only"
     else
         _mirrors
     fi
@@ -507,7 +507,7 @@ _spack_buildcache_push() {
 _spack_buildcache_create() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -r --rel -f --force -u --unsigned -a --allow-root -k --key -d --directory -m --mirror-name --mirror-url --update-index --rebuild-index --spec-file --only"
+        SPACK_COMPREPLY="-h --help -f --force -u --unsigned -a --allow-root -k --key --update-index --rebuild-index --spec-file --only"
     else
         _mirrors
     fi
@@ -516,7 +516,7 @@ _spack_buildcache_create() {
 _spack_buildcache_install() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -f --force -m --multiple -a --allow-root -u --unsigned -o --otherarch"
+        SPACK_COMPREPLY="-h --help -f --force -m --multiple -u --unsigned -o --otherarch"
     else
         _all_packages
     fi
@@ -563,7 +563,7 @@ _spack_buildcache_save_specfile() {
 _spack_buildcache_sync() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help --manifest-glob --src-directory --src-mirror-name --src-mirror-url --dest-directory --dest-mirror-name --dest-mirror-url"
+        SPACK_COMPREPLY="-h --help --manifest-glob"
     else
         SPACK_COMPREPLY=""
     fi
@@ -572,7 +572,7 @@ _spack_buildcache_sync() {
 _spack_buildcache_update_index() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -d --directory -m --mirror-name --mirror-url -k --keys"
+        SPACK_COMPREPLY="-h --help -k --keys"
     else
         _mirrors
     fi
@@ -581,7 +581,7 @@ _spack_buildcache_update_index() {
 _spack_buildcache_rebuild_index() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -d --directory -m --mirror-name --mirror-url -k --keys"
+        SPACK_COMPREPLY="-h --help -k --keys"
     else
         _mirrors
     fi
@@ -1695,7 +1695,7 @@ _spack_restage() {
 _spack_solve() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help --show -l --long -L --very-long -I --install-status -y --yaml -j --json -c --cover -N --namespaces -t --types --timers --stats -U --fresh --reuse --reuse-deps"
+        SPACK_COMPREPLY="-h --help --show -l --long -L --very-long -I --install-status --no-install-status -y --yaml -j --json -c --cover -N --namespaces -t --types --timers --stats -U --fresh --reuse --reuse-deps"
     else
         _all_packages
     fi
@@ -1704,7 +1704,7 @@ _spack_solve() {
 _spack_spec() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -l --long -L --very-long -I --install-status -y --yaml -j --json --format -c --cover -N --namespaces -t --types -U --fresh --reuse --reuse-deps"
+        SPACK_COMPREPLY="-h --help -l --long -L --very-long -I --install-status --no-install-status -y --yaml -j --json --format -c --cover -N --namespaces -t --types -U --fresh --reuse --reuse-deps"
     else
         _all_packages
     fi

share/spack/templates/container/Dockerfile

@@ -37,7 +37,7 @@ RUN find -L {{ paths.view }}/* -type f -exec readlink -f '{}' \; | \
 
 # Modifications to the environment that are necessary to run
 RUN cd {{ paths.environment }} && \
-    spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
+    spack env activate --sh -d . > activate.sh
 
 {% if extra_instructions.build %}
 {{ extra_instructions.build }}
@@ -53,7 +53,13 @@ COPY --from=builder {{ paths.environment }} {{ paths.environment }}
 COPY --from=builder {{ paths.store }} {{ paths.store }}
 COPY --from=builder {{ paths.hidden_view }} {{ paths.hidden_view }}
 COPY --from=builder {{ paths.view }} {{ paths.view }}
-COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
+
+RUN { \
+      echo '#!/bin/sh' \
+      && echo '.' {{ paths.environment }}/activate.sh \
+      && echo 'exec "$@"'; \
+    } > /entrypoint.sh \
+&&  chmod a+x /entrypoint.sh
 
 {% block final_stage %}
 
@@ -70,6 +76,6 @@ RUN {% if os_package_update %}{{ os_packages_final.update }} \
 {% for label, value in labels.items() %}
 LABEL "{{ label }}"="{{ value }}"
 {% endfor %}
-ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l", "-c", "$*", "--" ]
+ENTRYPOINT [ "/entrypoint.sh" ]
 CMD [ "/bin/bash" ]
 {% endif %}

share/spack/templates/modules/modulefile.lua

@@ -84,6 +84,10 @@ setenv("{{ cmd.name }}", "{{ cmd.value }}")
 unsetenv("{{ cmd.name }}")
 {% endif %}
 {% endfor %}
+{# Make sure system man pages are enabled by appending trailing delimiter to MANPATH #}
+{% if has_manpath_modifications %}
+append_path("MANPATH", "", ":")
+{% endif %}
 {% endblock %}
 
 {% block footer %}

share/spack/templates/modules/modulefile.tcl

@@ -26,9 +26,17 @@ proc ModulesHelp { } {
 {% endblock %}
 
 {% block autoloads %}
+{% if autoload|length > 0 %}
+if {![info exists ::env(LMOD_VERSION_MAJOR)]} {
 {% for module in autoload %}
-module load {{ module }}
+    module load {{ module }}
 {% endfor %}
+} else {
+{% for module in autoload %}
+    depends-on {{ module }}
+{% endfor %}
+}
+{% endif %}
 {% endblock %}
 {#  #}
 {% block prerequisite %}
@@ -58,6 +66,10 @@ unsetenv {{ cmd.name }}
 {% endif %}
 {#  #}
 {% endfor %}
+{# Make sure system man pages are enabled by appending trailing delimiter to MANPATH #}
+{% if has_manpath_modifications %}
+append-path --delim ":" MANPATH ""
+{% endif %}
 {% endblock %}
 
 {% block footer %}

var/spack/repos/builtin.mock/packages/module-manpath-append/package.py

@@ -0,0 +1,16 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class ModuleManpathAppend(Package):
+    homepage = "http://www.llnl.gov"
+    url = "http://www.llnl.gov/module-manpath-append-1.0.tar.gz"
+
+    version("1.0", "0123456789abcdef0123456789abcdef")
+
+    def setup_run_environment(self, env):
+        env.append_path("MANPATH", "/path/to/man")

var/spack/repos/builtin.mock/packages/module-manpath-prepend/package.py

@@ -0,0 +1,17 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class ModuleManpathPrepend(Package):
+    homepage = "http://www.llnl.gov"
+    url = "http://www.llnl.gov/module-manpath-prepend-1.0.tar.gz"
+
+    version("1.0", "0123456789abcdef0123456789abcdef")
+
+    def setup_run_environment(self, env):
+        env.prepend_path("MANPATH", "/path/to/man")
+        env.prepend_path("MANPATH", "/path/to/share/man")

var/spack/repos/builtin.mock/packages/module-manpath-setenv/package.py

@@ -0,0 +1,16 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class ModuleManpathSetenv(Package):
+    homepage = "http://www.llnl.gov"
+    url = "http://www.llnl.gov/module-manpath-setenv-1.0.tar.gz"
+
+    version("1.0", "0123456789abcdef0123456789abcdef")
+
+    def setup_run_environment(self, env):
+        env.set("MANPATH", "/path/to/man")

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

@@ -27,7 +27,8 @@ class Abinit(AutotoolsPackage):
     homepage = "https://www.abinit.org/"
     url = "https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz"
 
-    version("9.8.3", sha256="65fb93217336a72d1554cc6991127203958cc7df59921782251a86569e33a357")
+    version("9.8.4", sha256="a086d5045f0093b432e6a044d5f71f7edf5a41a62d67b3677cb0751d330c564a")
+    version("9.8.3", sha256="de823878aea2c20098f177524fbb4b60de9b1b5971b2e835ec244dfa3724589b")
     version("9.6.1", sha256="b6a12760fd728eb4aacca431ae12150609565bedbaa89763f219fcd869f79ac6")
     version("9.4.2", sha256="d40886f5c8b138bb4aa1ca05da23388eb70a682790cfe5020ecce4db1b1a76bc")
     version("8.10.3", sha256="ed626424b4472b93256622fbb9c7645fa3ffb693d4b444b07d488771ea7eaa75")

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

@@ -16,6 +16,7 @@ class Alglib(MakefilePackage):
     homepage = "https://www.alglib.net/"
     url = "https://www.alglib.net/translator/re/alglib-3.11.0.cpp.gpl.tgz"
 
+    version("4.00.0", sha256="827b5f559713a3e8c7c1452ed1ffd5227adb9622d1a165ceb70c117c8ed3ccb4")
     version("3.20.0", sha256="e7357f0f894313ff1b640ec9cb5e8b63f06d2d3411c2143a374aa0e9740da8a9")
     version("3.11.0", sha256="34e391594aac89fb354bdaf58c42849489cd1199197398ba98bb69961f42bdb0")
 

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

@@ -0,0 +1,54 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Binder(CMakePackage):
+    """
+    Binder is a tool for automatic generation of Python bindings
+    for C++11 projects using Pybind11 and Clang LibTooling libraries.
+    That is, Binder, takes a C++ project and compiles it into objects
+    and functions that are all usable within Python.
+    Binder is different from prior tools in that it handles special
+    features new in C++11.
+    """
+
+    homepage = "https://github.com/RosettaCommons/binder"
+    git = "https://github.com/RosettaCommons/binder.git"
+
+    maintainers("lyskov", "kliegeois")
+
+    version("master", branch="master")
+    version("1.3.0", tag="v1.3.0")
+    version("1.2.0", tag="v1.2.0")
+    version("1.1.0", tag="v1.0.0")
+    version("1.0.0", tag="v1.0.0")
+
+    # Add dependencies
+    depends_on("llvm+clang+llvm_dylib@7.0:9")
+
+    def cmake_args(self):
+        spec = self.spec
+        llvm_dir = spec["llvm"].prefix
+        clang_dir = spec["llvm"].prefix
+        options = []
+
+        options.extend(
+            [
+                "-DLLVM_DIR:FILEPATH={0}".format(llvm_dir),
+                "-DClang_DIR:FILEPATH={0}".format(clang_dir),
+                "-DCMAKE_CXX_FLAGS=-Wl,--verbose",
+                "-DBINDER_ENABLE_TEST=OFF",
+            ]
+        )
+        return options
+
+    def setup_dependent_package(self, module, dependent_spec):
+        llvm_dir = self.spec["llvm"].prefix
+        self.spec.clang_include_dirs = llvm_dir.include
+        self.spec.LibClang_include_dir = llvm_dir.lib.clang.join(
+            format(self.spec["llvm"].version)
+        ).include

var/spack/repos/builtin/packages/bioconductor-ebseq/package.py

@@ -0,0 +1,29 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class BioconductorEbseq(RPackage):
+    """An R package for gene and isoform differential expression analysis of RNA-seq data.
+
+    R/EBSeq is an R package for identifying genes and isoforms differentially
+    expressed (DE) across two or more biological conditions in an RNA-seq
+    experiment. Details can be found in Leng et al., 2013. It provides the syntax
+    required for identifying DE genes and isoforms in a two-group RNA-seq
+    experiment as well for identifying DE genes across more than two conditions
+    (the commands for identifying DE isoforms across more than two conditions
+    are the same as those required for gene-level analysis)."""
+
+    homepage = "https://www.biostat.wisc.edu/~kendzior/EBSEQ/"
+    url = "https://bioconductor.org/packages/release/bioc/src/contrib/EBSeq_1.40.0.tar.gz"
+
+    bioc = "ebseq"
+
+    version("1.40.0", sha256="a5d3a88743d61062c6d68a426b19c53a4afd2fa216abc884d42c187780994378")
+
+    depends_on("r-blockmodeling")
+    depends_on("r-gplots")
+    depends_on("r-testthat")

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

@@ -12,5 +12,6 @@ class Blogbench(AutotoolsPackage):
     homepage = "https://openbenchmarking.org/test/pts/blogbench"
     url = "https://download.pureftpd.org/pub/blogbench/blogbench-1.1.tar.gz"
 
+    version("1.2", sha256="1eabdb1ac0ad8ff6f5b9de36b2ef9b684a35b6e40aea0424e3dd4d6cd923c1af")
     version("1.1", sha256="8cded059bfdbccb7be35bb6a2272ecfdbe3fbea43d53c92ba5572ac24f26c4df")
     version("1.0", sha256="dc29261a19064a8fb64d39b27607f19d3b33ce3795908e717404167687ef33be")

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

@@ -21,6 +21,7 @@ class Ccache(CMakePackage):
 
     executables = ["^ccache$"]
 
+    version("4.8.1", sha256="869903c1891beb8bee87f1ec94d8a0dad18c2add4072c456acbc85cdfc23ca63")
     version("4.8", sha256="ac4b01748fd59cfe07e070c34432b91bdd0fd8640e1e653a80b01d6a523186b0")
     version("4.7.4", sha256="dc283906b73bd7c461178ca472a459e9d86b5523405035921bd8204e77620264")
     version("4.7.3", sha256="577841df9e9d9659d58a2f4e0f6eaceb7e29816988ffb2b12390e17b109b4ac4")

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

@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from glob import glob
+
 from spack.package import *
 
 
@@ -16,12 +18,19 @@ class Cdhit(MakefilePackage):
     version("4.8.1", sha256="f8bc3cdd7aebb432fcd35eed0093e7a6413f1e36bbd2a837ebc06e57cdb20b70")
     version("4.6.8", sha256="37d685e4aa849314401805fe4d4db707e1d06070368475e313d6f3cb8fb65949")
 
+    maintainers("snehring")
+
     variant("openmp", default=True, description="Compile with multi-threading support")
     variant("zlib", default=True, description="Compile with zlib")
 
     depends_on("perl", type=("build", "run"))
+    depends_on("perl-text-nsp", type="run")
     depends_on("zlib", when="+zlib", type="link")
 
+    def patch(self):
+        for f in glob("*.pl"):
+            filter_file("^#!/usr/bin/perl.*$", "#!/usr/bin/env perl", f)
+
     def build(self, spec, prefix):
         mkdirp(prefix.bin)
         make_args = []

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

@@ -17,6 +17,7 @@ class Cgal(CMakePackage):
     homepage = "https://www.cgal.org/"
     url = "https://github.com/CGAL/cgal/releases/download/v5.4.1/CGAL-5.4.1.tar.xz"
 
+    version("5.5.2", sha256="b2b05d5616ecc69facdc24417cce0b04fb4321491d107db45103add520e3d8c3")
     version("5.4.1", sha256="4c3dd7ee4d36d237111a4d72b6e14170093271595d5b695148532daa95323d76")
     version("5.1.5", sha256="b1bb8a6053aa12baa5981aef20a542cd3e617a86826963fb8fb6852b1a0da97c")
     version("5.0.3", sha256="e5a3672e35e5e92e3c1b4452cd3c1d554f3177dc512bd98b29edf21866a4288c")

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

@@ -14,6 +14,7 @@ class Cloc(Package):
     homepage = "https://github.com/AlDanial/cloc/"
     url = "https://github.com/AlDanial/cloc/archive/v1.90.tar.gz"
 
+    version("1.96.1", sha256="f0551d98dcce9ca2e78b984adf8e8cc7c6002037a1155e5294338c435e4a1af1")
     version("1.90", sha256="60b429dd2aa5cd65707b359dcbcbeb710c8e4db880886528ced0962c67e52548")
     version("1.84", sha256="c3f0a6bd2319110418ccb3e55a7a1b6d0edfd7528bfd2ae5d530938abe90f254")
     version("1.80", sha256="082f53530eee3f9ee84ec449eca59a77ff114250cd7daf9519679537b5b21d67")

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

@@ -159,6 +159,10 @@ class Comgr(CMakePackage):
 
     root_cmakelists_dir = join_path("lib", "comgr")
 
+    def cmake_args(self):
+        args = [self.define("BUILD_TESTING", self.run_tests)]
+        return args
+
     @classmethod
     def determine_version(cls, lib):
         match = re.search(r"lib\S*\.so\.\d+\.\d+\.(\d)(\d\d)(\d\d)", lib)

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

@@ -14,6 +14,7 @@ class Consul(MakefilePackage):
     homepage = "https://www.consul.io"
     url = "https://github.com/hashicorp/consul/archive/v1.8.1.tar.gz"
 
+    version("1.15.3", sha256="5137e9831b4bc094c8ce5be64c661dc0d9a96ee9509d756030d60d4bcca42503")
     version("1.8.1", sha256="c173e9866e6181b3679a942233adade118976414f6ca2da8deaea0fa2bba9b06")
     version("1.8.0", sha256="a87925bde6aecddf532dfd050e907b6a0a6447cdd5dc4f49b46d97c9f73b58f9")
     version("1.7.6", sha256="893abad7563c1f085303705f72d8789b338236972123f0ab6d2be24dbb58c2ac")

var/spack/repos/builtin/packages/cpp-httplib/package.py

@@ -12,6 +12,7 @@ class CppHttplib(CMakePackage):
     homepage = "https://github.com/yhirose/cpp-httplib/"
     url = "https://github.com/yhirose/cpp-httplib/archive/v0.5.10.tar.gz"
 
+    version("0.12.5", sha256="b488f3fa9c6bf35608c3d9a5b69be52e016bbf2fbfe67e5ee684eadb2655493e")
     version("0.12.3", sha256="175ced3c9cdaf221e9edf210297568d8f7d402a41d6db01254ac9e0b25487c54")
     version("0.5.9", sha256="c9e7aef3b0d4e80ee533d10413508d8a6e09a67d0d59646c43111f3993de006e")
     version("0.5.8", sha256="184d4fe79fc836ee26aa8635b3240879af4c6f17257fc7063d0b77a0cf856dfc")

var/spack/repos/builtin/packages/ctffind/fix_return_types.patch

@@ -0,0 +1,34 @@
+--- a/src/programs/ctffind/ctffind.cpp	2023-06-02 16:47:21.975662000 +0200
++++ b/src/programs/ctffind/ctffind.cpp	2023-06-02 16:48:06.565418037 +0200
+@@ -267,11 +267,11 @@
+ float FindRotationalAlignmentBetweenTwoStacksOfImages(Image *self, Image *other_image, int number_of_images, float search_half_range, float search_step_size, float minimum_radius, float maximum_radius);
+ void ComputeImagesWithNumberOfExtremaAndCTFValues(CTF *ctf, Image *number_of_extrema, Image *ctf_values);
+ int ReturnSpectrumBinNumber(int number_of_bins, float number_of_extrema_profile[], Image *number_of_extrema, long address, Image *ctf_values, float ctf_values_profile[]);
+-bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_renormalized[], float number_of_extrema_profile[], float ctf_values_profile[]);
++void ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_renormalized[], float number_of_extrema_profile[], float ctf_values_profile[]);
+ void ComputeEquiPhaseAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Curve *epa_pre_max, Curve *epa_post_max);
+ void OverlayCTF( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins_in_1d_spectra, double spatial_frequency[], double rotational_average_astig[], float number_of_extrema_profile[], float ctf_values_profile[], Curve *equiphase_average_pre_max, Curve *equiphase_average_post_max);
+ void ComputeFRCBetween1DSpectrumAndFit( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[], double frc[], double frc_sigma[], int first_fit_bin);
+-bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit );
++void RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit );
+ void Renormalize1DSpectrumForFRC( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[]);
+ float ReturnAzimuthToUseFor1DPlots(CTF *ctf);
+ 
+@@ -2419,7 +2419,7 @@
+ 
+ // Rescale the spectrum and its 1D rotational avereage so that the peaks and troughs are at 0.0 and 1.0. The location of peaks and troughs are worked out
+ // by parsing the suppilied 1D average_fit array
+-bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit )
++void RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit )
+ {
+ 	MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated");
+ 	MyDebugAssertTrue(number_of_bins > 1,"Bad number of bins: %i\n",number_of_bins);
+@@ -2762,7 +2762,7 @@
+ }
+ 
+ //
+-bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_rank[], float number_of_extrema_profile[], float ctf_values_profile[])
++void ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_rank[], float number_of_extrema_profile[], float ctf_values_profile[])
+ {
+ 	MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated");
+ 	MyDebugAssertTrue(number_of_extrema->is_in_memory,"Number of extrema image not allocated");

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

@@ -34,6 +34,7 @@ def url_for_version(self, version):
 
     patch("configure.patch", when="@4.1.8")
     patch("power9.patch", when="@4.1.14 target=power9le")
+    patch("fix_return_types.patch", when="@4.1.13:4.1.14")
 
     def configure_args(self):
         config_args = []

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

@@ -26,6 +26,7 @@ class Curl(NMakePackage, AutotoolsPackage):
 
     maintainers("alecbcs")
 
+    version("8.1.2", sha256="b54974d32fd610acace92e3df1f643144015ac65847f0a041fdc17db6f43f243")
     version("8.0.1", sha256="9b6b1e96b748d04b968786b6bdf407aa5c75ab53a3d37c1c8c81cdb736555ccf")
     version("7.88.1", sha256="8224b45cce12abde039c12dc0711b7ea85b104b9ad534d6e4c5b4e188a61c907")
 

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

@@ -14,6 +14,7 @@ class Direnv(Package):
 
     maintainers("acastanedam", "alecbcs")
 
+    version("2.32.3", sha256="c66f6d1000f28f919c6106b5dcdd0a0e54fb553602c63c60bf59d9bbdf8bd33c")
     version("2.32.2", sha256="352b3a65e8945d13caba92e13e5666e1854d41749aca2e230938ac6c64fa8ef9")
     version("2.32.1", sha256="dc7df9a9e253e1124748aa74da94bf2b96f5a61d581c60d52d3f8e8dc86ecfde")
     version("2.31.0", sha256="f82694202f584d281a166bd5b7e877565f96a94807af96325c8f43643d76cb44")

var/spack/repos/builtin/packages/dla-future/package.py

@@ -0,0 +1,135 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class DlaFuture(CMakePackage, CudaPackage, ROCmPackage):
+    """DLA-Future library: Distributed Linear Algebra with Future"""
+
+    homepage = "https://github.com/eth-cscs/DLA-Future"
+    url = "https://github.com/eth-cscs/DLA-Future/archive/v0.0.0.tar.gz"
+    git = "https://github.com/eth-cscs/DLA-Future.git"
+    maintainers = ["rasolca", "albestro", "msimberg", "aurianer"]
+
+    version("0.1.0", sha256="f7ffcde22edabb3dc24a624e2888f98829ee526da384cd752b2b271c731ca9b1")
+    version("master", branch="master")
+
+    variant("shared", default=True, description="Build shared libraries.")
+
+    variant("doc", default=False, description="Build documentation.")
+
+    variant("miniapps", default=False, description="Build miniapps.")
+
+    depends_on("cmake@3.22:", type="build")
+    depends_on("doxygen", type="build", when="+doc")
+    depends_on("mpi")
+    depends_on("blaspp@2022.05.00:")
+    depends_on("lapackpp@2022.05.00:")
+
+    depends_on("umpire~examples")
+    depends_on("umpire+cuda~shared", when="+cuda")
+    depends_on("umpire+rocm~shared", when="+rocm")
+    depends_on("umpire@4.1.0:")
+
+    depends_on("pika@0.15.1:")
+    depends_on("pika-algorithms@0.1:")
+    depends_on("pika +mpi")
+    depends_on("pika +cuda", when="+cuda")
+    depends_on("pika +rocm", when="+rocm")
+
+    conflicts("^pika cxxstd=20", when="+cuda")
+
+    depends_on("whip +cuda", when="+cuda")
+    depends_on("whip +rocm", when="+rocm")
+
+    depends_on("rocblas", when="+rocm")
+    depends_on("rocprim", when="+rocm")
+    depends_on("rocsolver", when="+rocm")
+    depends_on("rocthrust", when="+rocm")
+
+    conflicts("+cuda", when="+rocm")
+
+    with when("+rocm"):
+        for val in ROCmPackage.amdgpu_targets:
+            depends_on("pika amdgpu_target={0}".format(val), when="amdgpu_target={0}".format(val))
+            depends_on(
+                "rocsolver amdgpu_target={0}".format(val), when="amdgpu_target={0}".format(val)
+            )
+            depends_on(
+                "rocblas amdgpu_target={0}".format(val), when="amdgpu_target={0}".format(val)
+            )
+            depends_on(
+                "rocprim amdgpu_target={0}".format(val), when="amdgpu_target={0}".format(val)
+            )
+            depends_on(
+                "rocthrust amdgpu_target={0}".format(val), when="amdgpu_target={0}".format(val)
+            )
+            depends_on("whip amdgpu_target={0}".format(val), when="amdgpu_target={0}".format(val))
+            depends_on(
+                "umpire amdgpu_target={0}".format(val), when="amdgpu_target={0}".format(val)
+            )
+
+    with when("+cuda"):
+        for val in CudaPackage.cuda_arch_values:
+            depends_on("pika cuda_arch={0}".format(val), when="cuda_arch={0}".format(val))
+            depends_on("umpire cuda_arch={0}".format(val), when="cuda_arch={0}".format(val))
+
+    def cmake_args(self):
+        spec = self.spec
+        args = []
+
+        args.append(self.define_from_variant("BUILD_SHARED_LIBS", "shared"))
+
+        # BLAS/LAPACK
+        if "^mkl" in spec:
+            vmap = {
+                "none": "seq",
+                "openmp": "omp",
+                "tbb": "tbb",
+            }  # Map MKL variants to LAPACK target name
+            # TODO: Generalise for intel-oneapi-mkl
+            args += [
+                self.define("DLAF_WITH_MKL", True),
+                self.define(
+                    "MKL_LAPACK_TARGET",
+                    "mkl::mkl_intel_32bit_{0}_dyn".format(
+                        vmap[spec["intel-mkl"].variants["threads"].value]
+                    ),
+                ),
+            ]
+        else:
+            args.append(self.define("DLAF_WITH_MKL", False))
+            args.append(
+                self.define(
+                    "LAPACK_LIBRARY",
+                    " ".join([spec[dep].libs.ld_flags for dep in ["blas", "lapack"]]),
+                )
+            )
+
+        # CUDA/HIP
+        args.append(self.define_from_variant("DLAF_WITH_CUDA", "cuda"))
+        args.append(self.define_from_variant("DLAF_WITH_HIP", "rocm"))
+        if "+rocm" in spec:
+            archs = self.spec.variants["amdgpu_target"].value
+            if "none" not in archs:
+                arch_str = ";".join(archs)
+                args.append(self.define("CMAKE_HIP_ARCHITECTURES", arch_str))
+        if "+cuda" in spec:
+            archs = self.spec.variants["cuda_arch"].value
+            if "none" not in archs:
+                arch_str = ";".join(archs)
+                args.append(self.define("CMAKE_CUDA_ARCHITECTURES", arch_str))
+
+        # DOC
+        args.append(self.define_from_variant("DLAF_BUILD_DOC", "doc"))
+
+        # TEST
+        args.append(self.define("DLAF_BUILD_TESTING", self.run_tests))
+
+        # MINIAPPS
+        args.append(self.define_from_variant("DLAF_BUILD_MINIAPPS", "miniapps"))
+
+        return args

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

@@ -50,13 +50,17 @@ def cmake_args(self):
 
         return args
 
-    def test(self):
+    def test_dla(self):
+        """prepare, run, and confirm dla results"""
         test01 = find(self.prefix.share, "01_spindimer")[0]
         copy(join_path(test01, "std.toml"), ".")
+
         # prepare
-        pythonexe = self.spec["python"].command.path
+        python = self.spec["python"].command
         opts = [self.spec.prefix.bin.dla_pre, "std.toml"]
-        self.run_test(pythonexe, options=opts)
+        with test_part(self, "test_dla_pre", purpose="prepare dla"):
+            python(*opts)
+
         # (mpi) run
         opts = []
         if self.spec.satisfies("+mpi"):
@@ -66,6 +70,11 @@ def test(self):
         else:
             exe_name = "dla"
         opts.append("param.in")
-        expected = ["R ene = -3.74300000e-01 2.96344394e-03"]
-        self.run_test(exe_name, options=opts)
-        self.run_test("cat", options=["sample.log"], expected=expected)
+        with test_part(self, "test_dla_run", purpose="run dla"):
+            exe = which(exe_name)
+            exe(*opts)
+
+        with test_part(self, "test_dla_results", purpose="confirming dla results"):
+            cat = which("cat")
+            out = cat("sample.log", output=str.split, error=str.split)
+            assert "R ene = -3.74300000e-01 2.96344394e-03" in out

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

@@ -51,13 +51,9 @@ def cache_test_sources(self):
         """Save off the pdb sources for stand-alone testing."""
         self.cache_extra_test_sources("pdb")
 
-    def test(self):
-        """Perform stand-alone/smoke test on installed package."""
-        pdb_path = join_path(self.test_suite.current_test_cache_dir, "pdb")
-        self.run_test(
-            "mkdssp",
-            options=["1ALK.pdb", "1alk.dssp"],
-            purpose="test: calculating structure for example",
-            installed=True,
-            work_dir=pdb_path,
-        )
+    def test_mkdssp(self):
+        """calculate structure for example"""
+        pdb_path = self.test_suite.current_test_cache_dir.pdb
+        mkdssp = which(self.prefix.bin.mkdssp)
+        with working_dir(pdb_path):
+            mkdssp("1ALK.pdb", "1alk.dssp")

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

@@ -33,12 +33,8 @@ def check_install(self):
         print("stdout received fromm dust is '{}".format(output))
         assert "Dust " in output
 
-    def test(self):
-        """Run this smoke test when requested explicitly"""
-
-        dustpath = join_path(self.spec["dust"].prefix.bin, "dust")
-        options = ["--version"]
-        purpose = "Check dust can execute (with option '--version')"
-        expected = ["Dust "]
-
-        self.run_test(dustpath, options=options, expected=expected, status=[0], purpose=purpose)
+    def test_run(self):
+        """check dust can execute (with option '--version')"""
+        dust = which(self.prefix.bin.dust)
+        out = dust("--version", output=str.split, error=str.split)
+        assert "Dust " in out

var/spack/repos/builtin/packages/ecp-data-vis-sdk/package.py

@@ -107,7 +107,7 @@ class EcpDataVisSdk(BundlePackage, CudaPackage, ROCmPackage):
         propagate=["cuda", "hdf5", "sz", "zfp", "fortran"] + cuda_arch_variants,
     )
 
-    dav_sdk_depends_on("darshan-runtime+mpi", when="+darshan", propagate=["hdf5"])
+    dav_sdk_depends_on("darshan-runtime+mpi", when="+darshan")
     dav_sdk_depends_on("darshan-util", when="+darshan")
 
     dav_sdk_depends_on("faodel+shared+mpi network=libfabric", when="+faodel", propagate=["hdf5"])
@@ -171,7 +171,8 @@ class EcpDataVisSdk(BundlePackage, CudaPackage, ROCmPackage):
     # ParaView needs @5.11: in order to use CUDA/ROCM, therefore it is the minimum
     # required version since GPU capability is desired for ECP
     dav_sdk_depends_on(
-        "paraview@5.11:+mpi+openpmd+python+kits+shared+catalyst+libcatalyst+raytracing",
+        "paraview@5.11:+mpi+openpmd+python+kits+shared+catalyst+libcatalyst+raytracing"
+        " use_vtkm=on",
         when="+paraview",
         propagate=["adios2", "cuda", "hdf5", "rocm"] + amdgpu_target_variants + cuda_arch_variants,
     )

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

@@ -19,6 +19,7 @@ class Edm4hep(CMakePackage):
     tags = ["hep", "key4hep"]
 
     version("master", branch="master")
+    version("0.9", sha256="170ef84822761c4b02da9047f2b4d0dd0f48ed1c027b10171d4207b1542fbd5c")
     version("0.8", sha256="102d57167885eba3bea79f6b6647e5303ad8732c5784590abdcdd816b2411c79")
     version("0.7.2", sha256="e289280d5de2c0a3b542bf9dfe04b9f6471b0a0fcf33f5c8101ea7252e2a7643")
     version("0.7.1", sha256="82e215a532f548a73a6f6094eaa8b436c553994e135f6d63a674543dc89a9f1b")

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

@@ -15,6 +15,7 @@ class Etcd(Package):
 
     maintainers("alecbcs")
 
+    version("3.5.9", sha256="ab24d74b66ba1ed7d2bc391839d961e7215f0f3d674c3a9592dad6dc67a7b223")
     version("3.4.23", sha256="055c608c4898d25f23aefbc845ff074bf5e8a07e61ed41dbd5cc4d4f59c93093")
 
     depends_on("go@1.19:")

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

@@ -14,6 +14,13 @@ class Fairmq(CMakePackage):
     maintainers("dennisklein", "ChristianTackeGSI")
 
     version("dev", branch="dev", submodules=True, get_full_repo=True)
+    version(
+        "1.6.0",
+        tag="v1.6.0",
+        commit="42d27af20fb5cbbbc0b0fdfef1c981d51a8baf87",
+        submodules=True,
+        no_cache=True,
+    )
     version(
         "1.5.0",
         tag="v1.5.0",

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

@@ -13,6 +13,7 @@ class Fastp(MakefilePackage):
     homepage = "https://github.com/OpenGene/fastp"
     url = "https://github.com/OpenGene/fastp/archive/v0.20.0.tar.gz"
 
+    version("0.23.4", sha256="4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5")
     version("0.23.3", sha256="a37ee4b5dcf836a5a19baec645657b71d9dcd69ee843998f41f921e9b67350e3")
     version("0.20.0", sha256="8d751d2746db11ff233032fc49e3bcc8b53758dd4596fdcf4b4099a4d702ac22")
 

var/spack/repos/builtin/packages/fastq-screen/package.py

@@ -12,16 +12,31 @@ class FastqScreen(Package):
     the library matches with what you expect."""
 
     homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
-    url = "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.11.2.tar.gz"
+    url = "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.tar.gz"
 
-    version("0.11.2", sha256="a179df1f5803b42bbbb2b50af05ea18ae6fefcbf7020ca2feeb0d3c598a65207")
+    version("0.15.3", sha256="002750d78ca50fe0f789e24445e10988e16244f81b4f0189bf2fc4ee8b680be5")
+    version(
+        "0.11.2",
+        sha256="a179df1f5803b42bbbb2b50af05ea18ae6fefcbf7020ca2feeb0d3c598a65207",
+        url="https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.11.2.tar.gz",
+    )
 
+    variant("bismark", default=False, description="Enable bisulfite mapping with bismark")
+    variant("bowtie", default=False, description="Enable mapping with bowtie")
+    variant("bwa", default=False, description="Enable mapping with bwa")
+
+    # general dependencies
     depends_on("perl", type="run")
     depends_on("perl-gdgraph", type="run")
-    depends_on("bowtie")
-    depends_on("bowtie2")
-    depends_on("bwa")
-    depends_on("samtools")
+    depends_on("bowtie2", type="run")
+    depends_on("samtools", type="run")
+    # variant dependencies
+    depends_on("bismark", type="run", when="+bismark")
+    depends_on("bowtie", type="run", when="+bowtie")
+    depends_on("bwa", type="run", when="+bwa")
+
+    def patch(self):
+        filter_file("/usr/bin/perl", self.spec["perl"].command.path, "fastq_screen", backup=False)
 
     def install(self, spec, prefix):
         install_tree(".", prefix.bin)

var/spack/repos/builtin/packages/flux-core/package.py

@@ -20,6 +20,7 @@ class FluxCore(AutotoolsPackage):
     maintainers("grondo")
 
     version("master", branch="master")
+    version("0.51.0", sha256="e57b71b708482f20d2a2195a000c0c3b9176faa6aaadfad4d2117f8671ca67ce")
     version("0.50.0", sha256="77414299a7ca081199aa0f57bcaea3e05860e2095df73c0f6b7672b88fadf683")
     version("0.49.0", sha256="9b8d7af1d8aaa7ee110bcb9815b6b8647af686de949097c9bb2a0269d5551051")
     version("0.48.0", sha256="32c1bfdde44123e90606422807d381406874bb6dbec170ddb493f905208cc275")

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

@@ -23,6 +23,7 @@ class Freeipmi(AutotoolsPackage):
     homepage = "https://www.gnu.org/software/freeipmi/"
     url = "https://ftp.gnu.org/gnu/freeipmi/freeipmi-1.6.4.tar.gz"
 
+    version("1.6.9", sha256="f25e1c35f3d0f1b5a99cc31ecc2353ca83ed46a15163842fba870127dc9c8206")
     version("1.6.4", sha256="65dfbb95a30438ba247f01a58498862a37d2e71c8c950bcfcee459d079241a3c")
 
     depends_on("libgcrypt")

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

@@ -26,7 +26,7 @@ class FrontistrBase(CMakePackage):
     # depends_on('revocap-coupler')
     depends_on("metis")
     depends_on("mumps")
-    depends_on("trilinos@:12.18.1")
+    depends_on("trilinos@:13.0.1")
 
     def cmake_args(self):
         define = self.define

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

@@ -13,5 +13,6 @@ class Ftxui(CMakePackage):
     homepage = "https://arthursonzogni.github.io"
     url = "https://github.com/ArthurSonzogni/FTXUI/archive/refs/tags/v2.0.0.tar.gz"
 
+    version("4.1.1", sha256="9009d093e48b3189487d67fc3e375a57c7b354c0e43fc554ad31bec74a4bc2dd")
     version("4.0.0", sha256="7276e4117429ebf8e34ea371c3ea4e66eb99e0f234cb4c5c85fca17174a53dfa")
     version("2.0.0", sha256="d891695ef22176f0c09f8261a37af9ad5b262dd670a81e6b83661a23abc2c54f")

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

@@ -17,6 +17,7 @@ class Fzf(MakefilePackage):
 
     executables = ["^fzf$"]
 
+    version("0.41.1", sha256="982682eaac377c8a55ae8d7491fcd0e888d6c13915d01da9ebb6b7c434d7f4b5")
     version("0.40.0", sha256="9597f297a6811d300f619fff5aadab8003adbcc1566199a43886d2ea09109a65")
 
     depends_on("go@1.17:", type="build")

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

@@ -82,12 +82,7 @@ class Gaudi(CMakePackage):
 
     # Testing dependencies
     # Note: gaudi only builds examples when testing enabled
-    for pv in (
-        ["catch2", "@36.8:"],
-        ["py-nose", "@35:"],
-        ["py-pytest", "@36.2:"],
-        ["py-qmtest", "@35:"],
-    ):
+    for pv in (["catch2", "@36.8:"], ["py-nose", "@35:"], ["py-pytest", "@36.2:"]):
         depends_on(pv[0], when=pv[1], type="test")
         depends_on(pv[0], when=pv[1] + " +examples")
 

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

@@ -84,7 +84,7 @@ class Gdb(AutotoolsPackage, GNUMirrorPackage):
     depends_on("source-highlight", when="+source-highlight")
     depends_on("ncurses", when="+tui")
     depends_on("gmp", when="@11.1:")
-    depends_on("elfutils@0.178:+debuginfod", when="@11.1:+debuginfod")
+    depends_on("elfutils@0.179:+debuginfod", when="@10.1:+debuginfod")
 
     build_directory = "spack-build"
 

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

@@ -232,6 +232,13 @@ class Gromacs(CMakePackage, CudaPackage):
         for gmx_ver, plumed_vers in plumed_patches.items():
             depends_on("plumed@{0}".format(plumed_vers), when="@{0}+plumed".format(gmx_ver))
 
+    variant(
+        "intel_provided_gcc",
+        default=False,
+        description="Use this if Intel compiler is installed through spack."
+        + "The g++ location is written to icp{c,x}.cfg",
+    )
+
     depends_on("fftw-api@3")
     depends_on("cmake@2.8.8:3", type="build")
     depends_on("cmake@3.4.3:3", type="build", when="@2018:")
@@ -244,7 +251,8 @@ class Gromacs(CMakePackage, CudaPackage):
     depends_on("sycl", when="+sycl")
     depends_on("lapack", when="+lapack")
     depends_on("blas", when="+blas")
-    depends_on("gcc", when="%oneapi")
+    depends_on("gcc", when="%oneapi ~intel_provided_gcc")
+    depends_on("gcc", when="%intel ~intel_provided_gcc")
 
     depends_on("hwloc@1.0:1", when="+hwloc@2016:2018")
     depends_on("hwloc", when="+hwloc@2019:")
@@ -254,6 +262,14 @@ class Gromacs(CMakePackage, CudaPackage):
 
     depends_on("nvhpc", when="+cufftmp")
 
+    requires(
+        "%intel",
+        "%oneapi",
+        policy="one_of",
+        when="+intel_provided_gcc",
+        msg="Only attempt to find gcc libs for Intel compiler if Intel compiler is used.",
+    )
+
     patch("gmxDetectCpu-cmake-3.14.patch", when="@2018:2019.3^cmake@3.14.0:")
     patch("gmxDetectSimd-cmake-3.14.patch", when="@5.0:2017^cmake@3.14.0:")
 
@@ -431,8 +447,16 @@ def cmake_args(self):
         if self.spec.satisfies("@2020:"):
             options.append("-DGMX_INSTALL_LEGACY_API=ON")
 
-        if self.spec.satisfies("%oneapi"):
-            options.append("-DGMX_GPLUSPLUS_PATH=%s/g++" % self.spec["gcc"].prefix.bin)
+        if self.spec.satisfies("%oneapi") or self.spec.satisfies("%intel"):
+            # If intel-oneapi-compilers was installed through spack the gcc is added to the
+            # configuration file.
+            if self.spec.satisfies("+intel_provided_gcc") and os.path.exists(
+                ".".join([os.environ["SPACK_CXX"], "cfg"])
+            ):
+                with open(".".join([os.environ["SPACK_CXX"], "cfg"]), "r") as f:
+                    options.append("-DCMAKE_CXX_FLAGS={}".format(f.read()))
+            else:
+                options.append("-DGMX_GPLUSPLUS_PATH=%s/g++" % self.spec["gcc"].prefix.bin)
 
         if "+double" in self.spec:
             options.append("-DGMX_DOUBLE:BOOL=ON")

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

@@ -20,6 +20,9 @@ class Gxsview(QMakePackage):
     # Support email for questions ohnishi@m.mpat.go.jp
     maintainers("cessenat")
 
+    version(
+        "2023.05.29", sha256="1e768fd7afd22198b7f73adeb42f4ccf7e0ff68996a3843b1ea138225c4c1da3"
+    )
     version(
         "2022.11.04", sha256="28c299e4f87836b93e4a42934777364a166e35d305050ee5623a1b7cbc0ab561"
     )

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

@@ -16,6 +16,7 @@ class Hashcat(MakefilePackage):
     homepage = "https://hashcat.net/hashcat/"
     url = "https://github.com/hashcat/hashcat/archive/v6.1.1.tar.gz"
 
+    version("6.2.6", sha256="b25e1077bcf34908cc8f18c1a69a2ec98b047b2cbcf0f51144dcf3ba1e0b7b2a")
     version("6.1.1", sha256="39c140bbb3c0bdb1564bfa9b9a1cff49115a42f4c9c19e9b066b617aea309f80")
     version("6.1.0", sha256="916f92434e3b36a126be1d1247a95cd3b32b4d814604960a2ca325d4cc0542d1")
     version("6.0.0", sha256="e8e70f2a5a608a4e224ccf847ad2b8e4d68286900296afe00eb514d8c9ec1285")

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

@@ -18,6 +18,7 @@ class Hbase(Package):
     list_url = "https://archive.apache.org/dist/hbase"
     list_depth = 1
 
+    version("2.5.4", sha256="ffb929d1ffcaf0309e1617833f3b36645a9c9d9c10b47d6baccc7e50c6d0ed33")
     version("2.5.3", sha256="874f239c341a6a4a646051c79fda9e838242481b70463bf8daa28ba7239576c2")
     version("2.4.9", sha256="ed282a165fe0910b27d143f3ea21d552110bc155fd5456250a05dc51b0f0b6bd")
     version("2.2.5", sha256="25d08f8f038d9de5beb43dfb0392e8a8b34eae7e0f2670d6c2c172abc3855194")

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

@@ -47,6 +47,8 @@ class Hpcviewer(Package):
     maintainers("mwkrentel")
 
     darwin_sha = {
+        ("2023.05", "aarch64"): "b34e1ebc021e91c7260cc91a888e966a81913691de04c5e972da613d0dc34294",
+        ("2023.05", "x86_64"): "689c2c18f70d53a8e1f27527f65d30c61b6f70db98f63378a97f236926ef1ac5",
         ("2023.04", "aarch64"): "85fc1c8823e2ef442666d60e98674a55315771e57205a0d2cef739d39fea699f",
         ("2023.04", "x86_64"): "6a2497d52414ca131089a4819006e5bfe1d4b35e28bf66874105bfe051d658d4",
         ("2023.02", "aarch64"): "05356fcd0a84f70b07f556b55a02954aae05419d9fa12f0f64f8e2399566e622",
@@ -65,6 +67,9 @@ class Hpcviewer(Package):
     }
 
     viewer_sha = {
+        ("2023.05", "aarch64"): "901b58b73890180b1cb7572d91c1b6cc205a5d3d50927c50d05d2b05554918c6",
+        ("2023.05", "ppc64le"): "d948e4777aea3a0c06300aedd4ce04e28f97b3ac306f78d672a5f692152bbdef",
+        ("2023.05", "x86_64"): "8c51df8b958ec600c9b7547461d7e9abb0e07a048d4031f58efd47df7ec79091",
         ("2023.04", "aarch64"): "826c6a83c88eda980f9106843863853804a74f117ef53bfdd0973429c121949a",
         ("2023.04", "ppc64le"): "4804ea59101d0301e9a2284b77757919ffc114330becc071bb69d3fc5f5df261",
         ("2023.04", "x86_64"): "24aad913a156996cd372439a4b2ae8a6d90aab0e2f5281f1fa81b5be9c9b9278",