fix and test issue with copying by reference vs value

* [pcluster pipeline] Use local buildcache instead of upstream spack

Spack currently does not relocate compiler references from upstream spack
installations. When using a buildcache we don't need an upstream spack.

* gcc needs to be installed via postinstall to get correct deps

* quantum-espresso@gcc@12.3.0 returns ICE on neoverse_{n,v}1

* Force gitlab to pull the new container

* Revert "Force gitlab to pull the new container"

This reverts commit 3af5f4cd88.

Seems the gitlab version does not yet support "pull_policy" in .gitlab-ci.yml

* Gitlab keeps picking up wrong container. Renaming

* Update containers once more after failed build

lib/spack/spack/build_systems/r.py

@@ -7,7 +7,7 @@
 
 import llnl.util.lang as lang
 
-from spack.directives import extends, maintainers
+from spack.directives import extends
 
 from .generic import GenericBuilder, Package
 
@@ -71,8 +71,6 @@ class RPackage(Package):
 
     GenericBuilder = RBuilder
 
-    maintainers("glennpj")
-
     #: This attribute is used in UI queries that need to know the build
     #: system base class
     build_system_class = "RPackage"

lib/spack/spack/environment/environment.py

@@ -1221,28 +1221,27 @@ def remove(self, query_spec, list_name=user_speclist_name, force=False):
         old_specs = set(self.user_specs)
         new_specs = set()
         for spec in matches:
-            if spec in list_to_change:
-                try:
-                    list_to_change.remove(spec)
-                    self.update_stale_references(list_name)
-                    new_specs = set(self.user_specs)
-                except spack.spec_list.SpecListError:
-                    # define new specs list
-                    new_specs = set(self.user_specs)
-                    msg = f"Spec '{spec}' is part of a spec matrix and "
-                    msg += f"cannot be removed from list '{list_to_change}'."
-                    if force:
-                        msg += " It will be removed from the concrete specs."
-                        # Mock new specs, so we can remove this spec from concrete spec lists
-                        new_specs.remove(spec)
-                    tty.warn(msg)
+            if spec not in list_to_change:
+                continue
+            try:
+                list_to_change.remove(spec)
+                self.update_stale_references(list_name)
+                new_specs = set(self.user_specs)
+            except spack.spec_list.SpecListError:
+                # define new specs list
+                new_specs = set(self.user_specs)
+                msg = f"Spec '{spec}' is part of a spec matrix and "
+                msg += f"cannot be removed from list '{list_to_change}'."
+                if force:
+                    msg += " It will be removed from the concrete specs."
+                    # Mock new specs, so we can remove this spec from concrete spec lists
+                    new_specs.remove(spec)
+                tty.warn(msg)
+            else:
+                if list_name == user_speclist_name:
+                    self.manifest.remove_user_spec(str(spec))
                 else:
-                    if list_name == user_speclist_name:
-                        for user_spec in matches:
-                            self.manifest.remove_user_spec(str(user_spec))
-                    else:
-                        for user_spec in matches:
-                            self.manifest.remove_definition(str(user_spec), list_name=list_name)
+                    self.manifest.remove_definition(str(spec), list_name=list_name)
 
         # If force, update stale concretized specs
         for spec in old_specs - new_specs:
@@ -1346,24 +1345,48 @@ def concretize(self, force=False, tests=False):
             List of specs that have been concretized. Each entry is a tuple of
             the user spec and the corresponding concretized spec.
         """
-        if force:
-            # Clear previously concretized specs
-            self.concretized_user_specs = []
-            self.concretized_order = []
-            self.specs_by_hash = {}
+        old_concretized_user_specs = self.concretized_user_specs[:]
+        old_concretized_order = self.concretized_order[:]
+        old_specs_by_hash = self.specs_by_hash.copy()
 
-        # Pick the right concretization strategy
-        if self.unify == "when_possible":
-            return self._concretize_together_where_possible(tests=tests)
+        try:
+            if force:
+                # Clear previously concretized specs
+                self.concretized_user_specs = []
+                self.concretized_order = []
+                self.specs_by_hash = {}
 
-        if self.unify is True:
-            return self._concretize_together(tests=tests)
+            # Remove concrete specs that no longer correlate to a user spec
+            for spec in set(self.concretized_user_specs) - set(self.user_specs):
+                self.deconcretize(spec)
 
-        if self.unify is False:
-            return self._concretize_separately(tests=tests)
+            # Pick the right concretization strategy
+            if self.unify == "when_possible":
+                return self._concretize_together_where_possible(tests=tests)
 
-        msg = "concretization strategy not implemented [{0}]"
-        raise SpackEnvironmentError(msg.format(self.unify))
+            if self.unify is True:
+                return self._concretize_together(tests=tests)
+
+            if self.unify is False:
+                return self._concretize_separately(tests=tests)
+
+            msg = "concretization strategy not implemented [{0}]"
+            raise SpackEnvironmentError(msg.format(self.unify))
+        except Exception:
+            self.concretized_user_specs = old_concretized_user_specs
+            self.concretized_order = old_concretized_order
+            self.specs_by_hash = old_specs_by_hash
+            raise
+
+    def deconcretize(self, spec):
+        # spec has to be a root of the environment
+        index = self.concretized_user_specs.index(spec)
+        dag_hash = self.concretized_order.pop(index)
+        del self.concretized_user_specs[index]
+
+        # If this was the only user spec that concretized to this concrete spec, remove it
+        if dag_hash not in self.concretized_order:
+            del self.specs_by_hash[dag_hash]
 
     def _get_specs_to_concretize(
         self,

lib/spack/spack/repo.py

@@ -1239,7 +1239,7 @@ def get_pkg_class(self, pkg_name):
         try:
             module = importlib.import_module(fullname)
         except ImportError:
-            raise UnknownPackageError(pkg_name)
+            raise UnknownPackageError(fullname)
         except Exception as e:
             msg = f"cannot load package '{pkg_name}' from the '{self.namespace}' repository: {e}"
             raise RepoError(msg) from e

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

@@ -17,6 +17,7 @@
 import llnl.util.link_tree
 
 import spack.cmd.env
+import spack.concretize
 import spack.config
 import spack.environment as ev
 import spack.environment.environment
@@ -25,6 +26,7 @@
 import spack.modules
 import spack.paths
 import spack.repo
+import spack.solver.asp
 import spack.util.spack_json as sjson
 from spack.cmd.env import _env_create
 from spack.main import SpackCommand, SpackCommandError
@@ -390,6 +392,19 @@ def test_remove_after_concretize():
     assert not any(s.name == "mpileaks" for s in env_specs)
 
 
+def test_remove_before_concretize():
+    e = ev.create("test")
+    e.unify = True
+
+    e.add("mpileaks")
+    e.concretize()
+
+    e.remove("mpileaks")
+    e.concretize()
+
+    assert not list(e.concretized_specs())
+
+
 def test_remove_command():
     env("create", "test")
     assert "test" in env("list")
@@ -2746,6 +2761,51 @@ def test_virtual_spec_concretize_together(tmpdir):
     assert any(s.package.provides("mpi") for _, s in e.concretized_specs())
 
 
+@pytest.mark.parametrize(
+    "unify,method_to_fail",
+    [
+        (True, (spack.concretize, "concretize_specs_together")),
+        ("when_possible", (spack.solver.asp.Solver, "solve_in_rounds")),
+        # An earlier failure so that we test the case where the internal state
+        # has been changed, but the pointer to the internal variables has not change.
+        # This effectively tests that we are properly copying by value not by
+        # reference for the transactional concretization
+        (True, (spack.environment.Environment, "_get_specs_to_concretize")),
+    ],
+)
+def test_concretize_transactional(unify, method_to_fail, monkeypatch):
+    e = ev.create("test")
+    e.unify = unify
+
+    e.add("mpi")
+    e.add("zlib")
+    e.concretize()
+
+    # remove one spec and add another to ensure we test with changes before
+    # and after the environment is cleared during concretization
+    e.remove("zlib")
+    e.add("libelf")
+
+    def fail(*args, **kwargs):
+        raise Exception("Test failures")
+
+    location, method = method_to_fail
+    monkeypatch.setattr(location, method, fail)
+
+    first_user_specs = e.concretized_user_specs[:]
+    first_order = e.concretized_order[:]
+    first_hash_dict = e.specs_by_hash.copy()
+
+    try:
+        e.concretize()
+    except Exception:
+        pass
+
+    assert e.concretized_user_specs == first_user_specs
+    assert e.concretized_order == first_order
+    assert e.specs_by_hash == first_hash_dict
+
+
 def test_query_develop_specs():
     """Test whether a spec is develop'ed or not"""
     env("create", "test")

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

@@ -788,20 +788,17 @@ deprecated-ci-build:
 ########################################
 
 .aws-pcluster-generate-image:
-  image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
+  image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
 
 .aws-pcluster-generate:
   before_script:
-      # Setup postinstall Spack as upstream installation
+    # Use gcc from local container buildcache
     - - . "./share/spack/setup-env.sh"
       - . /etc/profile.d/modules.sh
-      - if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
-      - if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
-      - if [[ -f /bootstrap/spack/etc/spack/modules.xyaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
-      - if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
-      - if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
+      - spack mirror add local-cache /bootstrap/local-cache
+      - spack gpg trust /bootstrap/public-key
       - cd "${CI_PROJECT_DIR}" && curl -sOL https://raw.githubusercontent.com/spack/spack-configs/main/AWS/parallelcluster/postinstall.sh
-      - sed -i -e '/nohup/s/&$//' -e 's/nohup//' -e "s/spack arch -t/echo ${SPACK_TARGET_ARCH}/g" postinstall.sh
+      - sed -i -e "s/spack arch -t/echo ${SPACK_TARGET_ARCH}/g" postinstall.sh
       - /bin/bash postinstall.sh -fg
       - spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
   after_script:

share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-icelake/spack.yaml

@@ -35,18 +35,15 @@ spack:
   ci:
     pipeline-gen:
     - build-job:
-        image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
+        image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
         before_script:
         - - . "./share/spack/setup-env.sh"
           - . /etc/profile.d/modules.sh
           - spack --version
           - spack arch
-        # Setup postinstall Spack as upstream installation
-        - - if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/modules.yaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
-          - if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
+        # Use gcc from local container buildcache
+        - - spack mirror add local-cache /bootstrap/local-cache
+          - spack gpg trust /bootstrap/public-key
         - - /bin/bash "${SPACK_ARTIFACTS_ROOT}/postinstall.sh" -fg
           - spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
     - signing-job:

share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-neoverse_n1/spack.yaml

@@ -16,7 +16,7 @@ spack:
     - openfoam
     - palace
     # - py-devito
-    - quantum-espresso
+    # - quantum-espresso
     # - wrf
 
   - optimized_libs:
@@ -36,19 +36,16 @@ spack:
   ci:
     pipeline-gen:
     - build-job:
-        image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
+        image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
         tags: ["aarch64"]
         before_script:
         - - . "./share/spack/setup-env.sh"
           - . /etc/profile.d/modules.sh
           - spack --version
           - spack arch
-        # Setup postinstall Spack as upstream installation
-        - - if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/modules.yaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
-          - if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
+        # Use gcc from local container buildcache
+        - - spack mirror add local-cache /bootstrap/local-cache
+          - spack gpg trust /bootstrap/public-key
         - - /bin/bash "${SPACK_ARTIFACTS_ROOT}/postinstall.sh" -fg
           - spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
     - signing-job:

share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-neoverse_v1/spack.yaml

@@ -16,7 +16,7 @@ spack:
     - openfoam
     - palace
     # - py-devito
-    - quantum-espresso
+    # - quantum-espresso
     # - wrf
 
   - optimized_libs:
@@ -36,19 +36,16 @@ spack:
   ci:
     pipeline-gen:
     - build-job:
-        image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
+        image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
         tags: ["aarch64"]
         before_script:
         - - . "./share/spack/setup-env.sh"
           - . /etc/profile.d/modules.sh
           - spack --version
           - spack arch
-        # Setup postinstall Spack as upstream installation
-        - - if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/modules.yaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
-          - if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
+        # Use gcc from local container buildcache
+        - - spack mirror add local-cache /bootstrap/local-cache
+          - spack gpg trust /bootstrap/public-key
         - - /bin/bash "${SPACK_ARTIFACTS_ROOT}/postinstall.sh" -fg
           - spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
     - signing-job:

share/spack/gitlab/cloud_pipelines/stacks/aws-pcluster-skylake/spack.yaml

@@ -35,18 +35,15 @@ spack:
   ci:
     pipeline-gen:
     - build-job:
-        image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:latest", "entrypoint": [""] }
+        image: { "name": "ghcr.io/spack/pcluster-amazonlinux-2:v2023-05-25", "entrypoint": [""] }
         before_script:
         - - . "./share/spack/setup-env.sh"
           - . /etc/profile.d/modules.sh
           - spack --version
           - spack arch
-        # Setup postinstall Spack as upstream installation
-        - - if [[ -f /bootstrap/spack/etc/spack/packages.yaml ]]; then cp /bootstrap/spack/etc/spack/packages.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/config.yaml ]]; then cp /bootstrap/spack/etc/spack/config.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/modules.yaml ]]; then cp /bootstrap/spack/etc/spack/modules.yaml ./etc/spack/; fi
-          - if [[ -f /bootstrap/spack/etc/spack/mirrors.yaml ]]; then cp /bootstrap/spack/etc/spack/mirrors.yaml ./etc/spack/; fi
-          - if [[ -d /bootstrap/spack/opt/spack ]]; then spack config add "upstreams:postinstall:install_tree:/bootstrap/spack/opt/spack"; fi
+        # Use gcc from local container buildcache
+        - - spack mirror add local-cache /bootstrap/local-cache
+          - spack gpg trust /bootstrap/public-key
         - - /bin/bash "${SPACK_ARTIFACTS_ROOT}/postinstall.sh" -fg
           - spack config --scope site add "packages:all:target:\"target=${SPACK_TARGET_ARCH}\""
     - signing-job:

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

@@ -70,6 +70,7 @@ spack:
   - charliecloud
   - conduit
   - datatransferkit
+  - dealii
   - dyninst
   - ecp-data-vis-sdk ~cuda ~rocm +adios2 +ascent +cinema +darshan +faodel +hdf5 +paraview +pnetcdf +sz +unifyfs +veloc ~visit +vtkm +zfp ^hdf5@1.14
   - exaworks

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

@@ -18,6 +18,7 @@ class Arborx(CMakePackage, CudaPackage, ROCmPackage):
     maintainers("aprokop")
 
     version("master", branch="master")
+    version("1.4", sha256="803a1018a6305cf3fea161172b3ada49537f59261279d91c2abbcce9492ee7af")
     version("1.3", sha256="3f1e17f029a460ab99f8396e2772cec908eefc4bf3868c8828907624a2d0ce5d")
     version("1.2", sha256="ed1939110b2330b7994dcbba649b100c241a2353ed2624e627a200a398096c20")
     version("1.1", sha256="2b5f2d2d5cec57c52f470c2bf4f42621b40271f870b4f80cb57e52df1acd90ce")
@@ -61,7 +62,8 @@ class Arborx(CMakePackage, CudaPackage, ROCmPackage):
     # Standalone Kokkos
     depends_on("kokkos@3.1.00:", when="~trilinos")
     depends_on("kokkos@3.4.00:", when="@1.2~trilinos")
-    depends_on("kokkos@3.6.00:", when="@1.3:~trilinos")
+    depends_on("kokkos@3.6.00:", when="@1.3~trilinos")
+    depends_on("kokkos@3.7.01:", when="@1.4:~trilinos")
     for backend in kokkos_backends:
         depends_on("kokkos+%s" % backend.lower(), when="~trilinos+%s" % backend.lower())
 
@@ -83,7 +85,8 @@ class Arborx(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("trilinos+kokkos", when="+trilinos")
     depends_on("trilinos+openmp", when="+trilinos+openmp")
     depends_on("trilinos@13.2.0:", when="@1.2+trilinos")
-    depends_on("trilinos@13.4.0:", when="@1.3:+trilinos")
+    depends_on("trilinos@13.4.0:", when="@1.3+trilinos")
+    depends_on("trilinos@14.0.0:", when="@1.4:+trilinos")
     conflicts("~serial", when="+trilinos")
     conflicts("+cuda", when="+trilinos")
 

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

@@ -0,0 +1,22 @@
+# 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 Azcopy(Package):
+    """AzCopy is a command-line utility that you can use to copy data to and from containers and
+    file shares in Azure Storage accounts.
+    """
+
+    homepage = "https://github.com/Azure/azure-storage-azcopy"
+    url = "https://github.com/Azure/azure-storage-azcopy/archive/refs/tags/v10.18.1.tar.gz"
+
+    version("10.18.1", sha256="80292625d7f1a6fc41688c5948b3a20cfdae872464d37d831e20999430819c3f")
+
+    depends_on("go", type="build")
+
+    def install(self, spec, prefix):
+        go("build", "-o", prefix.bin.azcopy)

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

@@ -12,8 +12,6 @@ class Bart(MakefilePackage, CudaPackage):
     homepage = "https://mrirecon.github.io/bart/"
     url = "https://github.com/mrirecon/bart/archive/v0.5.00.tar.gz"
 
-    maintainers("glennpj")
-
     version("0.7.00", sha256="a16afc4b632c703d95b5c34e47acd82fafc19f51f9aff442373eecfef08bfc41")
     version("0.6.00", sha256="dbbd33d1e3ed3324fe21f90a3b62cb51765fe369f21df100b46a32004928f18d")
     version("0.5.00", sha256="30eedcda0f0ef3808157542e0d67df5be49ee41e4f41487af5c850632788f643")

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

@@ -1,39 +0,0 @@
-# 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)
-
-# ----------------------------------------------------------------------------
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
-# This is a template package file for Spack.  We've put "FIXME"
-# next to all the things you'll want to change. Once you've handled
-# them, you can save this file and test your package like this:
-#
-#     spack install colima
-#
-# You can edit this file again by typing:
-#
-#     spack edit colima
-#
-# See the Spack documentation for more information on packaging.
-# ----------------------------------------------------------------------------
-
-from spack.package import *
-
-
-class Colima(MakefilePackage):
-    """FIXME: Put a proper description of your package here."""
-
-    # FIXME: Add a proper url for your package's homepage here.
-    homepage = "https://www.example.com"
-    url = "https://github.com/abiosoft/colima/archive/refs/tags/v0.5.4.tar.gz"
-
-    # FIXME: Add a list of GitHub accounts to
-    # notify when the package is updated.
-    # maintainers("github_user1", "github_user2")
-
-    version("0.5.4", sha256="9dc25fee68c02a79493d61ecf563832ce483955db102fbca64d112957ae2e6e8")
-
-    depends_on("go")

var/spack/repos/builtin/packages/daos/0001-LIBPATH-fix-for-ALT_PREFIX.2.patch

@@ -0,0 +1,42 @@
+From 08d0017f06695d4837f1c509ca39d61b32bdae2b Mon Sep 17 00:00:00 2001
+From: Sean Koyama <skoyama@anl.gov>
+Date: Mon, 6 Mar 2023 23:02:08 +0000
+Subject: [PATCH] LIBPATH fix for ALT_PREFIX
+
+---
+ site_scons/prereq_tools/base.py | 14 +++++++-------
+ 1 file changed, 7 insertions(+), 7 deletions(-)
+
+diff --git a/site_scons/prereq_tools/base.py b/site_scons/prereq_tools/base.py
+index 4df1347be..da32d3dd1 100644
+--- a/site_scons/prereq_tools/base.py
++++ b/site_scons/prereq_tools/base.py
+@@ -1247,18 +1247,18 @@ class PreReqComponent():
+             ipath = os.path.join(path, "include")
+             if not os.path.exists(ipath):
+                 ipath = None
+-            lpath = None
++            lpaths = []
+             for lib in ['lib64', 'lib']:
+-                lpath = os.path.join(path, lib)
+-                if not os.path.exists(lpath):
+-                    lpath = None
+-            if ipath is None and lpath is None:
++                lp = os.path.join(path, lib)
++                if os.path.exists(lp):
++                    lpaths.append(lp)
++            if not ipath and not lpaths:
+                 continue
+             env = self.__env.Clone()
+             if ipath:
+                 env.AppendUnique(CPPPATH=[ipath])
+-            if lpath:
+-                env.AppendUnique(LIBPATH=[lpath])
++            if lpaths:
++                env.AppendUnique(LIBPATH=lpaths)
+             if not comp.has_missing_targets(env):
+                 self.__prebuilt_path[name] = path
+                 return path
+-- 
+2.34.1
+

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

@@ -0,0 +1,70 @@
+# 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 Daos(SConsPackage):
+    """The Distributed Asynchronous Object Storage (DAOS) is an open-source
+    software-defined object store designed from the ground up for massively
+    distributed Non Volatile Memory (NVM)."""
+
+    homepage = "https://github.com/daos-stack/daos"
+    git = "https://github.com/daos-stack/daos.git"
+    maintainers("hyoklee")
+
+    version("master", branch="master", submodules=True)
+    version("2.2.0", tag="v2.2.0", submodules=True)
+    variant(
+        "debug", default=False, description="Enable debugging info and strict compile warnings"
+    )
+
+    patch("0001-LIBPATH-fix-for-ALT_PREFIX.2.patch", when="@2.2.0:")
+
+    depends_on("argobots@1.1:")
+    depends_on("boost", type="build")
+    depends_on("cmocka", type="build")
+    depends_on("go", type="build")
+    depends_on("hwloc")
+    depends_on("isa-l@2.30.0:")
+    depends_on("isa-l-crypto@2.23.0:")
+    depends_on("libfabric@1.15.1:")
+    depends_on("libfuse@3.6.1:")
+    depends_on("libuuid")
+    depends_on("libunwind")
+    depends_on("libyaml")
+    depends_on("mercury@2.2.0:+boostsys")
+    depends_on("openssl")
+    depends_on("pmdk@1.12.1:")
+    depends_on("protobuf-c@1.3.3:")
+    depends_on("py-distro")
+    depends_on("readline")
+    depends_on("scons@4.4.0:")
+    depends_on("spdk@23.01:+shared+rdma+dpdk")
+    depends_on("ucx@1.12.1:")
+
+    def build_args(self, spec, prefix):
+        args = ["PREFIX={0}".format(prefix), "USE_INSTALLED=all"]
+
+        if "+debug" in spec:
+            args.append("--debug=explain,findlibs,includes")
+
+        # Construct ALT_PREFIX and make sure that '/usr' is last.
+        alt_prefix = []
+        for node in spec.traverse():
+            alt_prefix.append(format(node.prefix))
+
+        args.extend(
+            [
+                "WARNING_LEVEL=warning",
+                "ALT_PREFIX=%s" % ":".join([str(elem) for elem in alt_prefix]),
+                "GO_BIN={0}".format(spec["go"].prefix.bin) + "/go",
+            ]
+        )
+        return args
+
+    def install_args(self, spec, prefix):
+        args = ["PREFIX={0}".format(prefix)]
+        return args

var/spack/repos/builtin/packages/dd4hep/package.py

@@ -157,6 +157,7 @@ class Dd4hep(CMakePackage):
     depends_on("lcio", when="+lcio")
     depends_on("edm4hep", when="+edm4hep")
     depends_on("podio", when="+edm4hep")
+    depends_on("podio@:0.16.03", when="@:1.23 +edm4hep")
     depends_on("podio@0.16:", when="@1.24: +edm4hep")
     depends_on("py-pytest", type=("build", "test"))
 
@@ -222,6 +223,8 @@ def setup_run_environment(self, env):
         env.set("DD4HEP", self.prefix.examples)
         env.set("DD4hep_DIR", self.prefix)
         env.set("DD4hep_ROOT", self.prefix)
+        env.set("LD_LIBRARY_PATH", self.prefix.lib)
+        env.set("LD_LIBRARY_PATH", self.prefix.lib64)
 
     def url_for_version(self, version):
         # dd4hep releases are dashes and padded with a leading zero

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

@@ -0,0 +1,94 @@
+# 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 Fds(MakefilePackage):
+    """
+    Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows,
+    with an emphasis on smoke and heat transport from fires.
+    FDS and Smokeview are free and open-source software tools provided by the National Institute
+    of Standards and Technology (NIST) of the United States Department of Commerce. Pursuant
+    to Title 17, Section 105 of the United States Code, this software is not subject to copyright
+    protection and is in the public domain. View the full disclaimer for NIST-developed software.
+    """
+
+    maintainers("kjrstory")
+    homepage = "https://pages.nist.gov/fds-smv"
+    url = "https://github.com/firemodels/fds/archive/refs/tags/FDS-6.8.0.tar.gz"
+    git = "https://github.com/firemodels/fds.git"
+
+    version("6.8.0", commit="886e0096535519b7358a3c4393c91da3caee5072")
+
+    depends_on("mpi")
+    depends_on("mkl")
+
+    build_directory = "Build"
+
+    requires(
+        "%gcc",
+        "%intel",
+        "%oneapi",
+        policy="one_of",
+        msg="FDS builds only with GNU Fortran or Intel Fortran",
+    )
+
+    requires(
+        "^intel-mkl",
+        "^intel-oneapi-mkl",
+        policy="one_of",
+        msg="FDS builds require either Intel MKL or Intel oneAPI MKL library",
+    )
+
+    requires(
+        "^openmpi",
+        when="%gcc platform=linux",
+        msg="OpenMPI can only be used with GNU Fortran on Linux platform",
+    )
+
+    requires(
+        "^intel-mpi^intel-mkl",
+        when="%intel platform=linux",
+        msg="Intel MPI and Intel MKL can only be used with Intel Fortran on Linux platform",
+    )
+
+    requires(
+        "^intel-oneapi-mpi^intel-oneapi-mkl",
+        when="%oneapi platform=linux",
+        msg="Intel oneAPI MPI and MKL can only be used with oneAPI Fortran on Linux platform",
+    )
+
+    requires(
+        "^openmpi%intel",
+        when="platform=darwin",
+        msg="OpenMPI can only be used with Intel Fortran on macOS",
+    )
+
+    def edit(self, spec, prefix):
+        env["MKL_ROOT"] = self.spec["mkl"].prefix
+        if spec.compiler.name == "oneapi":
+            env["INTEL_IFORT"] = "ifx"
+        makefile = FileFilter("Build/makefile")
+        makefile.filter(r"\.\./Scripts", "./Scripts")
+        makefile.filter(r"\.\.\\Scripts", ".\\Scripts")
+
+    @property
+    def build_targets(self):
+        spec = self.spec
+        mpi_mapping = {"openmpi": "ompi", "intel-oneapi-mpi": "impi", "intel-mpi": "impi"}
+        compiler_mapping = {"gcc": "gnu", "oneapi": "intel", "intel": "intel"}
+        platform_mapping = {"linux": "linux", "darwin": "osx"}
+        mpi_prefix = mpi_mapping[spec["mpi"].name]
+        compiler_prefix = compiler_mapping[spec.compiler.name]
+        platform_prefix = platform_mapping[spec.architecture.platform]
+        return ["{}_{}_{}".format(mpi_prefix, compiler_prefix, platform_prefix)]
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        with working_dir(self.build_directory):
+            install("*.mod", prefix.bin)
+            install("*.o", prefix.bin)
+            install("fds_" + self.build_targets[0], prefix.bin + "/fds")

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

@@ -22,8 +22,6 @@ class Fplo(MakefilePackage):
     url = "file://{0}/FPLO22.00-62.tar.gz".format(os.getcwd())
     manual_download = True
 
-    maintainers("glennpj")
-
     version("22.00-62", sha256="0d1d4e9c1e8e41900901e26c3cd08ee39dcfdeb3f2c4c8862055eaf704b6d69e")
 
     # TODO: Try to get LAPACK to work with something other than MKL. The build

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

@@ -26,8 +26,6 @@ class Gate(CMakePackage):
     homepage = "http://opengatecollaboration.org/"
     url = "https://github.com/OpenGATE/Gate/archive/v9.0.tar.gz"
 
-    maintainers("glennpj")
-
     version("9.1", sha256="aaab874198500b81d45b27cc6d6a51e72cca9519910b893a5c85c8e6d3ffa4fc")
     version("9.0", sha256="8354f392facc0b7ae2ddf0eed61cc43136195b198ba399df25e874886b8b69cb")
 

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

@@ -12,8 +12,6 @@ class Gatetools(PythonPackage):
     homepage = "https://github.com/OpenGATE/GateTools"
     pypi = "gatetools/gatetools-0.9.14.tar.gz"
 
-    maintainers("glennpj")
-
     version("0.11.2", sha256="6eef8a779278b862823ae79d6aab210db4f7889c9127b2c2e4c3a4195f9a9928")
     version("0.9.14", sha256="78fe864bb52fd4c6aeeee90d8f6c1bc5406ce02ac6f48712379efac606b5c006")
 

var/spack/repos/builtin/packages/gaudi/fmt_fix.patch

@@ -0,0 +1,22 @@
+diff --git a/GaudiHive/src/FetchLeavesFromFile.cpp b/GaudiHive/src/FetchLeavesFromFile.cpp
+index 55c60e6a1..5ed8efa91 100644
+--- a/GaudiHive/src/FetchLeavesFromFile.cpp
++++ b/GaudiHive/src/FetchLeavesFromFile.cpp
+@@ -67,7 +67,7 @@ namespace Gaudi {
+         DataObject* obj = nullptr;
+         evtSvc()
+             ->retrieveObject( m_rootNode, obj )
+-            .orThrow( fmt::format( "failed to retrieve {} from {}", m_rootNode.value(), m_dataSvcName ), name() );
++            .orThrow( fmt::format( "failed to retrieve {} from {}", m_rootNode.value(), m_dataSvcName.value() ), name() );
+       }
+       // result
+       IDataStoreLeaves::LeavesList all_leaves;
+@@ -93,7 +93,7 @@ namespace Gaudi {
+                           ->retrieveObject( reg->identifier(), obj )
+                           .orElse( [&]() {
+                             failure_msg =
+-                                fmt::format( "failed to retrieve {} from {}", reg->identifier(), m_dataSvcName );
++                                fmt::format( "failed to retrieve {} from {}", reg->identifier(), m_dataSvcName.value() );
+                             // we do not really care about the exception we throw because traverseSubTree will just use
+                             // it to abort the traversal
+                             throw GaudiException( failure_msg, name(), StatusCode::FAILURE );

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

@@ -53,6 +53,7 @@ class Gaudi(CMakePackage):
     # fixes for the cmake config which could not find newer boost versions
     patch("link_target_fixes.patch", when="@33.0:34")
     patch("link_target_fixes32.patch", when="@:32.2")
+    patch("fmt_fix.patch", when="@36.6:36.12 ^fmt@10:")
 
     # These dependencies are needed for a minimal Gaudi build
     depends_on("aida")
@@ -137,6 +138,8 @@ def setup_run_environment(self, env):
         # environment as in Gaudi.xenv
         env.prepend_path("PATH", self.prefix.scripts)
         env.prepend_path("PYTHONPATH", self.prefix.python)
+        env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib)
+        env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib64)
 
     def url_for_version(self, version):
         major = str(version[0])

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

@@ -23,8 +23,6 @@ class Gurobi(Package):
     homepage = "https://www.gurobi.com"
     manual_download = True
 
-    maintainers("glennpj")
-
     version("10.0.0", sha256="91a9ce1464f5f948809fcdfbdeb55f77698ed8a6d6cfa6985295424b6ece2bd4")
     version("9.5.2", sha256="95d8ca18b7f86116ba834a27fd6228c5b1708ae67927e7ea0e954c09374a2d0f")
     version("9.5.1", sha256="fa82859d33f08fb8aeb9da66b0fbd91718ed573c534f571aa52372c9deb891da")

var/spack/repos/builtin/packages/hdf5-vol-async/package.py

@@ -24,6 +24,7 @@ class Hdf5VolAsync(CMakePackage):
     tags = ["e4s"]
 
     version("develop", branch="develop")
+    version("1.6", tag="v1.6")
     version("1.5", tag="v1.5")
     version("1.4", tag="v1.4")
     version("1.3", tag="v1.3")

var/spack/repos/builtin/packages/hdf5-vol-daos/package.py

@@ -0,0 +1,47 @@
+# 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 Hdf5VolDaos(CMakePackage):
+    """The HDF5 DAOS VOL connector is an external VOL connector
+    that interfaces with the DAOS API"""
+
+    homepage = "https://github.com/HDFGroup/vol-daos"
+    url = (
+        "https://github.com/HDFGroup/vol-daos/releases/download/v1.2.0/hdf5_vol_daos-1.2.0.tar.bz2"
+    )
+    git = "https://github.com/HDFGroup/vol-daos.git"
+
+    maintainers("hyoklee", "soumagne")
+
+    version("master", branch="master", submodules=True)
+    version("1.2.0", sha256="669c1443605068f24c033783ef72619afcec4844902b3e0bffa19ddeea39779f")
+
+    depends_on("cmake@2.8.12.2:", type="build")
+    depends_on("daos@2.2.0:")
+    depends_on("hdf5@1.14.0:+hl+mpi+map")
+
+    def cmake_args(self):
+        """Populate cmake arguments for HDF5 DAOS."""
+        define = self.define
+
+        cmake_args = [
+            define("BUILD_SHARED_LIBS", True),
+            define("BUILD_TESTING", self.run_tests),
+            define("PC_DAOS_INCLUDEDIR", self.spec["daos"].prefix + "/include"),
+            define("PC_DAOS_LIBDIR", self.spec["daos"].prefix + "/lib64"),
+        ]
+
+        return cmake_args
+
+    def setup_run_environment(self, env):
+        env.prepend_path("HDF5_PLUGIN_PATH", self.prefix.lib)
+
+    def check(self):
+        """Unit tests fail when run in parallel."""
+
+        with working_dir(self.build_directory):
+            make("test", parallel=False)

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

@@ -24,8 +24,6 @@ class Heasoft(AutotoolsPackage):
     homepage = "https://heasarc.gsfc.nasa.gov/docs/software/lheasoft/"
     url = "https://heasarc.gsfc.nasa.gov/FTP/software/lheasoft/lheasoft6.29/heasoft-6.29src.tar.gz"
 
-    maintainers("glennpj")
-
     version("6.30", sha256="7f828f6050809653319f94d715c1b6815fbc09adfdcb61f2f0f1d7a6af10684a")
     version("6.29", sha256="534fec04baa2586326fd7240805f2606620f3b7d7078a80fdd95c9c1177c9e68")
 

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

@@ -38,6 +38,16 @@ class Hpcg(AutotoolsPackage):
         sha256="722c13837b287e979442f8372274aa5910a290aa39f1ed1ff646116be08dcae9",
         when="%arm",
     )
+    patch(
+        "https://github.com/hpcg-benchmark/hpcg/commit/e9e0b7e6cae23e1f30dd983c2ce2d3bd34d56f75.patch?full_index=1",
+        sha256="722c13837b287e979442f8372274aa5910a290aa39f1ed1ff646116be08dcae9",
+        when="%oneapi",
+    )
+    patch(
+        "https://github.com/hpcg-benchmark/hpcg/commit/e9e0b7e6cae23e1f30dd983c2ce2d3bd34d56f75.patch?full_index=1",
+        sha256="722c13837b287e979442f8372274aa5910a290aa39f1ed1ff646116be08dcae9",
+        when="%intel",
+    )
 
     depends_on("mpi@1.1:")
 
@@ -50,6 +60,8 @@ def configure(self, spec, prefix):
             not spec.satisfies("%aocc")
             and not spec.satisfies("%cce")
             and not spec.satisfies("%arm")
+            and not spec.satisfies("%intel")
+            and not spec.satisfies("%oneapi")
         ):
             CXXFLAGS += " -ftree-vectorizer-verbose=0 "
         if spec.satisfies("%cce"):

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

@@ -22,8 +22,6 @@ class Itk(CMakePackage):
     homepage = "https://itk.org/"
     url = "https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.1.1/InsightToolkit-5.1.1.tar.gz"
 
-    maintainers("glennpj")
-
     version("5.3.0", sha256="57a4471133dc8f76bde3d6eb45285c440bd40d113428884a1487472b7b71e383")
     version("5.3rc02", sha256="163aaf4a6cecd5b70ff718c1a986c746581797212fd1b629fa81f12ae4756d14")
     version(

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

@@ -23,7 +23,7 @@ class Julia(MakefilePackage):
     url = "https://github.com/JuliaLang/julia/releases/download/v1.7.0/julia-1.7.0.tar.gz"
     git = "https://github.com/JuliaLang/julia.git"
 
-    maintainers("glennpj", "vchuravy", "haampie", "giordano")
+    maintainers("vchuravy", "haampie", "giordano")
 
     version("master", branch="master")
     version("1.9.0", sha256="48f4c8a7d5f33d0bc6ce24226df20ab49e385c2d0c3767ec8dfdb449602095b2")

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

@@ -38,6 +38,10 @@ def flag_handler(self, name, flags):
         # flags, and the build system ensures that
         return (None, flags, None)
 
+    # 1.10.2 fails on macOS when trying to use the Linux getrandom() call
+    # https://dev.gnupg.org/T6442
+    patch("rndgetentropy_no_getrandom.patch", when="@=1.10.2 platform=darwin")
+
     def check(self):
         # Without this hack, `make check` fails on macOS when SIP is enabled
         # https://bugs.gnupg.org/gnupg/issue2056

var/spack/repos/builtin/packages/libgcrypt/rndgetentropy_no_getrandom.patch

@@ -0,0 +1,34 @@
+diff --git a/random/rndgetentropy.c b/random/rndgetentropy.c
+index 513da0b..d8eedce 100644
+--- a/random/rndgetentropy.c
++++ b/random/rndgetentropy.c
+@@ -81,27 +81,8 @@ _gcry_rndgetentropy_gather_random (void (*add)(const void*, size_t,
+       do
+         {
+           _gcry_pre_syscall ();
+-          if (fips_mode ())
+-            {
+-              /* DRBG chaining defined in SP 800-90A (rev 1) specify
+-               * the upstream (kernel) DRBG needs to be reseeded for
+-               * initialization of downstream (libgcrypt) DRBG. For this
+-               * in RHEL, we repurposed the GRND_RANDOM flag of getrandom API.
+-               * The libgcrypt DRBG is initialized with 48B of entropy, but
+-               * the kernel can provide only 32B at a time after reseeding
+-               * so we need to limit our requests to 32B here.
+-               * This is clarified in IG 7.19 / IG D.K. for FIPS 140-2 / 3
+-               * and might not be applicable on other FIPS modules not running
+-               * RHEL kernel.
+-               */
+-              nbytes = length < 32 ? length : 32;
+-              ret = getrandom (buffer, nbytes, GRND_RANDOM);
+-            }
+-          else
+-            {
+-              nbytes = length < sizeof (buffer) ? length : sizeof (buffer);
+-              ret = getentropy (buffer, nbytes);
+-            }
++          nbytes = length < sizeof (buffer) ? length : sizeof (buffer);
++          ret = getentropy (buffer, nbytes);
+           _gcry_post_syscall ();
+         }
+       while (ret == -1 && errno == EINTR);

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

@@ -236,7 +236,7 @@ class Llvm(CMakePackage, CudaPackage):
     # openmp dependencies
     depends_on("perl-data-dumper", type=("build"))
     depends_on("hwloc")
-    depends_on("hwloc@2.0.1:", when="@9:")
+    depends_on("hwloc@2.0.1:", when="@13")
     depends_on("elf", when="+cuda")  # libomptarget
     depends_on("libffi", when="+libomptarget")  # libomptarget
 
@@ -375,6 +375,13 @@ class Llvm(CMakePackage, CudaPackage):
     #  when/if the bugfix is merged
     patch("D133513.diff", level=0, when="@14:15+lldb+python")
 
+    # Fix hwloc@:2.3 (Conditionally disable hwloc@2.0 and hwloc@2.4 code)
+    patch(
+        "https://github.com/llvm/llvm-project/commit/3a362a9f38b95978160377ee408dbc7d14af9aad.patch?full_index=1",
+        sha256="25bc503f7855229620e56e76161cf4654945aef0be493a2d8d9e94a088157b7c",
+        when="@14:15",
+    )
+
     # The functions and attributes below implement external package
     # detection for LLVM. See:
     #

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

@@ -15,8 +15,6 @@ class Mumax(MakefilePackage, CudaPackage):
     homepage = "https://mumax.github.io"
     url = "https://github.com/mumax/3/archive/v3.10.tar.gz"
 
-    maintainers("glennpj")
-
     version(
         "3.10",
         sha256="42c858661cec3896685ff4babea11e711f71fd6ea37d20c2bed7e4a918702caa",

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

@@ -6,22 +6,23 @@
 from spack.package import *
 
 
-class Nlcglib(CMakePackage, CudaPackage):
+class Nlcglib(CMakePackage, CudaPackage, ROCmPackage):
     """Nonlinear CG methods for wave-function optimization in DFT."""
 
     homepage = "https://github.com/simonpintarelli/nlcglib"
     git = "https://github.com/simonpintarelli/nlcglib.git"
     url = "https://github.com/simonpintarelli/nlcglib/archive/v0.9.tar.gz"
 
-    maintainers("simonpintarelli")
+    maintainers = ["simonpintarelli"]
 
-    version("master", branch="master")
     version("develop", branch="develop")
+    version("master", branch="master")
 
+    version("1.0b", sha256="086c46f06a117f267cbdf1df4ad42a8512689a9610885763f463469fb15e82dc")
     version("0.9", sha256="8d5bc6b85ee714fb3d6480f767e7f43e5e7d569116cf60e48f533a7f50a37a08")
 
-    variant("wrapper", default=False, description="Use nvcc-wrapper for CUDA build")
-    variant("openmp", default=False)
+    variant("openmp", default=True)
+    variant("tests", default=False)
     variant(
         "build_type",
         default="Release",
@@ -29,38 +30,73 @@ class Nlcglib(CMakePackage, CudaPackage):
         values=("Debug", "Release", "RelWithDebInfo"),
     )
 
+    depends_on("cmake@3.21:", type="build")
+    depends_on("mpi")
     depends_on("lapack")
-    depends_on("kokkos +cuda~cuda_relocatable_device_code+cuda_lambda")
-    depends_on("kokkos-nvcc-wrapper", when="+wrapper")
-    depends_on("kokkos +cuda~cuda_relocatable_device_code+cuda_lambda+wrapper", when="+wrapper")
-    depends_on("cmake@3.15:", type="build")
-    depends_on(
-        "kokkos+cuda~cuda_relocatable_device_code+cuda_lambda+openmp+wrapper",
-        when="+openmp+wrapper",
-    )
+    depends_on("kokkos~cuda~rocm", when="~cuda~rocm")
+    depends_on("kokkos+openmp", when="+openmp")
+    depends_on("googletest", type="build", when="+tests")
+    depends_on("nlohmann-json")
+
+    with when("@:0.9"):
+        conflicts("+rocm")
+        conflicts("^kokkos@4:")
+
+    with when("+rocm"):
+        variant("magma", default=True, description="Use magma eigenvalue solver (AMDGPU)")
+        depends_on("magma+rocm", when="+magma")
+        depends_on("kokkos+rocm")
+        depends_on("rocblas")
+        depends_on("rocsolver")
+
+    with when("+cuda"):
+        depends_on("kokkos+cuda+cuda_lambda+wrapper", when="%gcc")
+        depends_on("kokkos+cuda")
 
     def cmake_args(self):
-        options = []
+        options = [
+            self.define_from_variant("USE_OPENMP", "openmp"),
+            self.define_from_variant("BUILD_TESTS", "tests"),
+            self.define_from_variant("USE_ROCM", "rocm"),
+            self.define_from_variant("USE_MAGMA", "magma"),
+            self.define_from_variant("USE_CUDA", "cuda"),
+        ]
 
-        if "+openmp" in self.spec:
-            options.append("-DUSE_OPENMP=On")
-        else:
-            options.append("-DUSE_OPENMP=Off")
         if self.spec["blas"].name in ["intel-mkl", "intel-parallel-studio"]:
-            options.append("-DLAPACK_VENDOR=MKL")
+            options += [self.define("LAPACK_VENDOR", "MKL")]
+        elif self.spec["blas"].name in ["intel-oneapi-mkl"]:
+            options += [self.define("LAPACK_VENDOR", "MKLONEAPI")]
         elif self.spec["blas"].name in ["openblas"]:
-            options.append("-DLAPACK_VENDOR=OpenBLAS")
+            options += [self.define("LAPACK_VENDOR", "OpenBLAS")]
         else:
             raise Exception("blas/lapack must be either openblas or mkl.")
 
-        options.append("-DBUILD_TESTS=OFF")
-
-        if "+wrapper" in self.spec:
-            options.append("-DCMAKE_CXX_COMPILER=%s" % self.spec["kokkos-nvcc-wrapper"].kokkos_cxx)
+        if "+cuda%gcc" in self.spec:
+            options += [
+                self.define(
+                    "CMAKE_CXX_COMPILER", "{0}".format(self.spec["kokkos-nvcc-wrapper"].kokkos_cxx)
+                )
+            ]
 
         if "+cuda" in self.spec:
-            cuda_arch = self.spec.variants["cuda_arch"].value
-            if cuda_arch[0] != "none":
-                options += ["-DCMAKE_CUDA_FLAGS=-arch=sm_{0}".format(cuda_arch[0])]
+            cuda_archs = self.spec.variants["cuda_arch"].value
+            if "@:0.9" in self.spec:
+                cuda_flags = " ".join(
+                    ["-gencode arch=compute_{0},code=sm_{0}".format(x) for x in cuda_archs]
+                )
+                options += [self.define("CMAKE_CUDA_FLAGS", cuda_flags)]
+            else:
+                options += [self.define("CMAKE_CUDA_ARCHITECTURES", cuda_archs)]
+
+        if "^cuda+allow-unsupported-compilers" in self.spec:
+            options += [self.define("CMAKE_CUDA_FLAGS", "--allow-unsupported-compiler")]
+
+        if "+rocm" in self.spec:
+            options.append(self.define("CMAKE_CXX_COMPILER", self.spec["hip"].hipcc))
+            archs = ",".join(self.spec.variants["amdgpu_target"].value)
+            options.append("-DHIP_HCC_FLAGS=--amdgpu-target={0}".format(archs))
+            options.append(
+                "-DCMAKE_CXX_FLAGS=--amdgpu-target={0} --offload-arch={0}".format(archs)
+            )
 
         return options

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

@@ -16,7 +16,7 @@ class Opencv(CMakePackage, CudaPackage):
     url = "https://github.com/opencv/opencv/archive/4.5.0.tar.gz"
     git = "https://github.com/opencv/opencv.git"
 
-    maintainers("bvanessen", "adamjstewart", "glennpj")
+    maintainers("bvanessen", "adamjstewart")
 
     version("master", branch="master")
     version("4.6.0", sha256="1ec1cba65f9f20fe5a41fda1586e01c70ea0c9a6d7b67c9e13edf0cfe2239277")

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

@@ -12,6 +12,7 @@ class PyAsttokens(PythonPackage):
     homepage = "https://github.com/gristlabs/asttokens"
     pypi = "asttokens/asttokens-2.0.5.tar.gz"
 
+    version("2.2.1", sha256="4622110b2a6f30b77e1473affaa97e711bc2f07d3f10848420ff1898edbe94f3")
     version("2.0.8", sha256="c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b")
     version("2.0.5", sha256="9a54c114f02c7a9480d56550932546a3f1fe71d8a02f1bc7ccd0ee3ee35cf4d5")
 

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

@@ -12,6 +12,7 @@ class PyBleach(PythonPackage):
     homepage = "https://github.com/mozilla/bleach"
     pypi = "bleach/bleach-3.1.0.tar.gz"
 
+    version("6.0.0", sha256="1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414")
     version("5.0.1", sha256="0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c")
     version("4.1.0", sha256="0900d8b37eba61a802ee40ac0061f8c2b5dee29c1927dd1d233e075ebf5a71da")
     version("4.0.0", sha256="ffa9221c6ac29399cc50fcc33473366edd0cf8d5e2cbbbb63296dc327fb67cc8")
@@ -19,10 +20,6 @@ class PyBleach(PythonPackage):
     version("3.1.0", sha256="3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa")
     version("1.5.0", sha256="978e758599b54cd3caa2e160d74102879b230ea8dc93871d0783721eef58bc65")
 
-    depends_on("python@3.7:", when="@5:", type=("build", "run"))
-    depends_on("python@3.6:", when="@4:", type=("build", "run"))
-    depends_on("python@2.7:2,3.5:", when="@3.1.3:", type=("build", "run"))
-    depends_on("python@2.7:2,3.4:", type=("build", "run"))
     depends_on("py-setuptools", type=("build", "run"))
     depends_on("py-six@1.9.0:", type=("build", "run"))
     depends_on("py-webencodings", type=("build", "run"))

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

@@ -14,6 +14,7 @@ class PyDask(PythonPackage):
 
     maintainers("skosukhin")
 
+    version("2023.4.1", sha256="9dc72ebb509f58f3fe518c12dd5a488c67123fdd66ccb0b968b34fd11e512153")
     version("2022.10.2", sha256="42cb43f601709575fa46ce09e74bea83fdd464187024f56954e09d9b428ceaab")
     version("2021.6.2", sha256="8588fcd1a42224b7cfcd2ebc8ad616734abb6b1a4517efd52d89c7dd66eb91f8")
     version("2021.4.1", sha256="195e4eeb154222ea7a1c368119b5f321ee4ec9d78531471fe0145a527f744aa8")
@@ -75,16 +76,24 @@ class PyDask(PythonPackage):
     depends_on("python@3.8:", type=("build", "run"), when="@2022.10.2:")
 
     depends_on("py-setuptools", type="build")
+    depends_on("py-setuptools@62.6:", type="build", when="@2023.4.1:")
+    depends_on("py-versioneer@0.28+toml", type="build", when="@2023.4.1:")
 
     # Common requirements
     depends_on("py-packaging@20:", type="build", when="@2022.10.2:")
     depends_on("py-pyyaml", type=("build", "run"), when="@2.17.1:")
     depends_on("py-pyyaml@5.3.1:", type=("build", "run"), when="@2022.10.2:")
     depends_on("py-cloudpickle@1.1.1:", type=("build", "run"), when="@2021.3.1:")
+    depends_on("py-cloudpickle@1.5.0:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-fsspec@0.6.0:", type=("build", "run"), when="@2021.3.1:")
+    depends_on("py-fsspec@2021.09.0:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-toolz@0.8.2:", type=("build", "run"), when="@2021.3.1:")
+    depends_on("py-toolz@0.10.0:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-partd@0.3.10:", type=("build", "run"), when="@2021.3.1:")
+    depends_on("py-partd@1.2.0:", type=("build", "run"), when="@2023.4.0:")
     depends_on("py-click@7.0:", type=("build", "run"), when="@2022.10.2:")
+    depends_on("py-click@8.0:", type=("build", "run"), when="@2023.4.1:")
+    depends_on("py-importlib-metadata@4.13.0:", type=("build", "run"), when="@2023.4.0:")
 
     # Requirements for dask.array
     depends_on("py-numpy", type=("build", "run"), when="@:0.17.1 +array")
@@ -94,6 +103,7 @@ class PyDask(PythonPackage):
     depends_on("py-numpy@1.15.1:", type=("build", "run"), when="@2020.12.0: +array")
     depends_on("py-numpy@1.16.0:", type=("build", "run"), when="@2021.3.1: +array")
     depends_on("py-numpy@1.18.0:", type=("build", "run"), when="@2022.10.2: +array")
+    depends_on("py-numpy@1.21.0:", type=("build", "run"), when="@2023.4.0: +array")
 
     depends_on("py-toolz", type=("build", "run"), when="@:0.6.1 +array")
     depends_on("py-toolz@0.7.2:", type=("build", "run"), when="@0.7.0: +array")
@@ -136,6 +146,7 @@ class PyDask(PythonPackage):
     depends_on("py-numpy@1.15.1:", type=("build", "run"), when="@2020.12.0: +dataframe")
     depends_on("py-numpy@1.16.0:", type=("build", "run"), when="@2021.3.1: +dataframe")
     depends_on("py-numpy@1.18.0:", type=("build", "run"), when="@2022.10.2: +dataframe")
+    depends_on("py-numpy@1.21.0:", type=("build", "run"), when="@2023.4.0: +dataframe")
 
     depends_on("py-pandas@0.16.0:", type=("build", "run"), when="+dataframe")
     depends_on("py-pandas@0.18.0:", type=("build", "run"), when="@0.9.0: +dataframe")
@@ -144,6 +155,7 @@ class PyDask(PythonPackage):
     depends_on("py-pandas@0.23.0:", type=("build", "run"), when="@2.11.0: +dataframe")
     depends_on("py-pandas@0.25.0:", type=("build", "run"), when="@2020.12.0: +dataframe")
     depends_on("py-pandas@1.0:", type=("build", "run"), when="@2022.10.2: +dataframe")
+    depends_on("py-pandas@1.3:", type=("build", "run"), when="@2023.4.0: +dataframe")
 
     depends_on("py-toolz", type=("build", "run"), when="@:0.6.1 +dataframe")
     depends_on("py-toolz@0.7.2:", type=("build", "run"), when="@0.7.0: +dataframe")
@@ -193,12 +205,15 @@ class PyDask(PythonPackage):
     )
     depends_on("py-distributed@2021.6.2", type=("build", "run"), when="@2021.6.2 +distributed")
     depends_on("py-distributed@2022.10.2", type=("build", "run"), when="@2022.10.2 +distributed")
+    depends_on("py-distributed@2023.4.1", type=("build", "run"), when="@2023.4.1 +distributed")
 
     # Requirements for dask.diagnostics
     depends_on("py-bokeh@1.0.0:", type=("build", "run"), when="@2.0.0: +diagnostics")
     depends_on("py-bokeh@1.0.0:1,2.0.1:", type=("build", "run"), when="@2.26.0: +diagnostics")
-    depends_on("py-bokeh@2.4.2:2", type=("build", "run"), when="@2022.10.2: +diagnostics")
+    depends_on("py-bokeh@2.4.2:2", type=("build", "run"), when="@2022.10.2:2023.3 +diagnostics")
+    depends_on("py-bokeh@2.4.2:", type=("build", "run"), when="@2023.4.0: +diagnostics")
     depends_on("py-jinja2", type=("build", "run"), when="@2022.10.2: +diagnostics")
+    depends_on("py-jinja2@2.10.3", type=("build", "run"), when="@2023.4.0: +diagnostics")
 
     # Requirements for dask.delayed
     depends_on("py-cloudpickle@0.2.1:", type=("build", "run"), when="@2.7.0: +delayed")

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

@@ -30,6 +30,7 @@ class PyDistributed(PythonPackage):
         "distributed.diagnostics",
     ]
 
+    version("2023.4.1", sha256="0140376338efdcf8db1d03f7c1fdbb5eab2a337b03e955d927c116824ee94ac5")
     version("2022.10.2", sha256="53f0a5bf6efab9a5ab3345cd913f6d3f3d4ea444ee2edbea331c7fef96fd67d0")
     version("2022.2.1", sha256="fb62a75af8ef33bbe1aa80a68c01a33a93c1cd5a332dd017ab44955bf7ecf65b")
     version("2021.6.2", sha256="d7d112a86ab049dcefa3b21fd1baea4212a2c03d22c24bd55ad38d21a7f5d148")
@@ -50,22 +51,29 @@ class PyDistributed(PythonPackage):
     depends_on("python@3.6:", when="@2:", type=("build", "run"))
     depends_on("python@3.7:", when="@2021.4.1:", type=("build", "run"))
     depends_on("python@3.8:", when="@2022.2.1:", type=("build", "run"))
-    depends_on("py-setuptools", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-setuptools@62.6:", type="build", when="@2023.4.1:")
+    depends_on("py-versioneer@0.28+toml", type="build", when="@2023.4.1:")
 
     # In Spack py-dask+distributed depends on py-distributed, not the other way around.
     # Hence, no need for depends_on("py-dask", ...)
     depends_on("py-click@6.6:", type=("build", "run"))
+    depends_on("py-click@8.0:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-cloudpickle@0.2.2:", type=("build", "run"), when="@:2.16.0")
     depends_on("py-cloudpickle@1.3.0:", type=("build", "run"), when="@2.17.0:2.20.0")
     depends_on("py-cloudpickle@1.5.0:", type=("build", "run"), when="@2.21.0:")
     depends_on("py-jinja2", type=("build", "run"), when="@2022.2.1:")
+    depends_on("py-jinja2@2.10.3", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-locket@1:", type=("build", "run"), when="@2022.2.1:")
     depends_on("py-msgpack", type=("build", "run"), when="@:2.10.0")
     depends_on("py-msgpack@0.6.0:", type=("build", "run"), when="@2.11.0:")
+    depends_on("py-msgpack@1.0.0:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-packaging@20.0:", type=("build", "run"), when="@2022.2.1:")
     depends_on("py-psutil@5.0:", type=("build", "run"))
+    depends_on("py-psutil@5.7.0:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-six", type=("build", "run"), when="@:1")
     depends_on("py-sortedcontainers@:1,2.0.2:", type=("build", "run"))
+    depends_on("py-sortedcontainers@2.0.5:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-tblib", type=("build", "run"), when="@:2.10.0")
     depends_on("py-tblib@1.6.0:", type=("build", "run"), when="@2.11.0:")
     depends_on("py-toolz@0.7.4:", type=("build", "run"), when="@:2.12.0")
@@ -77,8 +85,12 @@ class PyDistributed(PythonPackage):
     depends_on("py-tornado@6.0.3:", type=("build", "run"), when="^python@3.8:")
     depends_on("py-tornado@6.0.3:6.1", type=("build", "run"), when="@2022.10.2:")
     depends_on("py-zict@0.1.3:", type=("build", "run"))
+    depends_on("py-zict@2.2.0:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-pyyaml@5.3.1:", type=("build", "run"), when="@2023.4.1:")
     depends_on("py-urllib3", type=("build", "run"), when="@2022.10.2:")
+    depends_on("py-urllib3@1.24.3:", type=("build", "run"), when="@2023.4.1:")
 
     def patch(self):
-        filter_file("^dask .*", "", "requirements.txt")
+        if self.spec.satisfies("@:2023.3"):
+            filter_file("^dask .*", "", "requirements.txt")

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

@@ -16,6 +16,7 @@ class PyFiona(PythonPackage):
     maintainers("adamjstewart")
 
     version("master", branch="master")
+    version("1.9.4", sha256="49f18cbcd3b1f97128c1bb038c3451b2e1be25baa52f02ce906c25cf75af95b6")
     version("1.9.3", sha256="60f3789ad9633c3a26acf7cbe39e82e3c7a12562c59af1d599fc3e4e8f7f8f25")
     version("1.9.2", sha256="f9263c5f97206bf2eb2c010d52e8ffc54e96886b0e698badde25ff109b32952a")
     version("1.9.1", sha256="3a3725e94840a387fef48726d60db6a6791563f366939d22378a4661f8941be7")
@@ -51,8 +52,8 @@ class PyFiona(PythonPackage):
     depends_on("py-click-plugins@1:", type=("build", "run"))
     depends_on("py-cligj@0.5:", type=("build", "run"))
     depends_on("py-importlib-metadata", when="@1.9.2: ^python@:3.9", type=("build", "run"))
-    depends_on("py-munch@2.3.2:", when="@1.9:", type=("build", "run"))
-    depends_on("py-munch", type=("build", "run"))
+    depends_on("py-six", when="@1.9.4:", type=("build", "run"))
+    depends_on("py-six@1.7:", when="@:1.8", type=("build", "run"))
 
     # setup.py or release notes
     depends_on("gdal@3.1:", when="@1.9:", type=("build", "link", "run"))
@@ -60,7 +61,8 @@ class PyFiona(PythonPackage):
 
     # Historical dependencies
     depends_on("py-setuptools", when="@:1.9.1", type=("build", "run"))
-    depends_on("py-six@1.7:", when="@:1.8", type=("build", "run"))
+    depends_on("py-munch@2.3.2:", when="@1.9.0:1.9.3", type=("build", "run"))
+    depends_on("py-munch", when="@:1.8", type=("build", "run"))
 
     # error: implicit declaration of function 'OSRFixup' is invalid in C99
     conflicts("%apple-clang@12:", when="@:1.8.9")

var/spack/repos/builtin/packages/py-huggingface-hub/package.py

@@ -14,18 +14,28 @@ class PyHuggingfaceHub(PythonPackage):
     homepage = "https://github.com/huggingface/huggingface_hub"
     pypi = "huggingface_hub/huggingface_hub-0.0.10.tar.gz"
 
+    version("0.14.1", sha256="9ab899af8e10922eac65e290d60ab956882ab0bf643e3d990b1394b6b47b7fbc")
     version("0.10.1", sha256="5c188d5b16bec4b78449f8681f9975ff9d321c16046cc29bcf0d7e464ff29276")
     version("0.0.10", sha256="556765e4c7edd2d2c4c733809bae1069dca20e10ff043870ec40d53e498efae2")
     version("0.0.8", sha256="be5b9a7ed36437bb10a780d500154d426798ec16803ff3406f7a61107e4ebfc2")
 
-    depends_on("python@3.7:", when="@0.10:", type=("build", "run"))
-    depends_on("python@3.6:", type=("build", "run"))
+    variant(
+        "cli",
+        default=False,
+        when="@0.10:",
+        description="Install dependencies for CLI-specific features",
+    )
+
     depends_on("py-setuptools", type="build")
     depends_on("py-filelock", type=("build", "run"))
+    depends_on("py-fsspec", when="@0.14:", type=("build", "run"))
     depends_on("py-requests", type=("build", "run"))
+    depends_on("py-tqdm@4.42.1:", type=("build", "run"))
     depends_on("py-tqdm", type=("build", "run"))
     depends_on("py-pyyaml@5.1:", when="@0.10:", type=("build", "run"))
     depends_on("py-typing-extensions@3.7.4.3:", when="@0.10:", type=("build", "run"))
     depends_on("py-typing-extensions", when="@0.0.10:", type=("build", "run"))
     depends_on("py-importlib-metadata", when="^python@:3.7", type=("build", "run"))
     depends_on("py-packaging@20.9:", when="@0.10:", type=("build", "run"))
+
+    depends_on("py-inquirerpy@0.3.4", when="@0.14:+cli", type=("build", "run"))

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

@@ -0,0 +1,22 @@
+# 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 PyInquirerpy(PythonPackage):
+    """Python port of Inquirer.js
+    (A collection of common interactive command-line user interfaces).
+    """
+
+    homepage = "https://github.com/kazhala/InquirerPy"
+    pypi = "inquirerpy/InquirerPy-0.3.4.tar.gz"
+
+    version("0.3.4", sha256="89d2ada0111f337483cb41ae31073108b2ec1e618a49d7110b0d7ade89fc197e")
+
+    depends_on("python@3.7:3", type=("build", "run"))
+    depends_on("py-poetry-core@1:", type="build")
+    depends_on("py-prompt-toolkit@3.0.1:3", type=("build", "run"))
+    depends_on("py-pfzy@0.3.1:0.3", type=("build", "run"))

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

@@ -12,11 +12,13 @@ class PyPartd(PythonPackage):
     homepage = "https://github.com/dask/partd/"
     pypi = "partd/partd-0.3.8.tar.gz"
 
+    version("1.4.0", sha256="aa0ff35dbbcc807ae374db56332f4c1b39b46f67bf2975f5151e0b4186aed0d5")
     version("1.1.0", sha256="6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0")
     version("0.3.10", sha256="33722a228ebcd1fa6f44b1631bdd4cff056376f89eb826d7d880b35b637bcfba")
     version("0.3.8", sha256="67291f1c4827cde3e0148b3be5d69af64b6d6169feb9ba88f0a6cfe77089400f")
 
     depends_on("python@3.5:", type=("build", "run"), when="@1.1.0:")
+    depends_on("python@3.7:", type=("build", "run"), when="@1.4.0:")
     depends_on("py-setuptools", type="build")
     depends_on("py-locket", type=("build", "run"))
     depends_on("py-toolz", type=("build", "run"))

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

@@ -17,13 +17,15 @@ class PyPastml(PythonPackage):
     maintainers("snehring")
 
     version("1.9.40", sha256="5334bc8de70a968117240b90d90878ac935be18de6e6e485fb1a8f90cd539fea")
+    version("1.9.38", sha256="43bf7d2a3a9b9b67da7c5881ecdeb2ee9cccd1585b8f65700e53761609945cc6")
 
     depends_on("python@3.8:", type=("build", "run"))
     depends_on("py-setuptools", type="build")
 
     depends_on("py-ete3@3.1.1:", type=("build", "run"))
     depends_on("py-pandas@1.0.0:", type=("build", "run"))
-    depends_on("py-numpy@1.22:", type=("build", "run"))
+    depends_on("py-numpy@1.19.0:", type=("build", "run"), when="@1.9.38")
+    depends_on("py-numpy@1.22:", type=("build", "run"), when="@1.9.40")
     depends_on("py-jinja2@2.11.0:", type=("build", "run"))
     depends_on("py-scipy@1.5.0:", type=("build", "run"))
     depends_on("py-itolapi@4.0.0:", type=("build", "run"))

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

@@ -0,0 +1,18 @@
+# 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 PyPfzy(PythonPackage):
+    """Python port of the fzy fuzzy string matching algorithm."""
+
+    homepage = "https://github.com/kazhala/pfzy"
+    pypi = "pfzy/pfzy-0.3.4.tar.gz"
+
+    version("0.3.4", sha256="717ea765dd10b63618e7298b2d98efd819e0b30cd5905c9707223dceeb94b3f1")
+
+    depends_on("python@3.7:3", type=("build", "run"))
+    depends_on("py-poetry-core@1:", type="build")

var/spack/repos/builtin/packages/py-topiary-asr/package.py

@@ -23,7 +23,8 @@ class PyTopiaryAsr(PythonPackage):
     depends_on("py-setuptools", type="build")
 
     depends_on("py-biopython", type=("build", "run"))
-    depends_on("py-numpy@:1.21", type=("build", "run"))
+    depends_on("py-numpy@:1.21", type=("build", "run"), when="@0.9.9")
+    depends_on("py-numpy", type=("build", "run"), when="@main")
     depends_on("py-pandas", type=("build", "run"))
     depends_on("py-matplotlib", type=("build", "run"))
     depends_on("py-ete3", type=("build", "run"))

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

@@ -12,7 +12,10 @@ class PyZict(PythonPackage):
     homepage = "https://zict.readthedocs.io/en/latest/"
     pypi = "zict/zict-1.0.0.tar.gz"
 
+    version("3.0.0", sha256="e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5")
     version("1.0.0", sha256="e34dd25ea97def518fb4c77f2c27078f3a7d6c965b0a3ac8fe5bdb0a8011a310")
 
+    depends_on("python@3.8:", when="@3.0.0:", type=("build", "run"))
+
     depends_on("py-setuptools", type="build")
-    depends_on("py-heapdict", type=("build", "run"))
+    depends_on("py-heapdict", type=("build", "run"), when="@:2.2.0")

var/spack/repos/builtin/packages/r-a4/package.py

@@ -14,6 +14,7 @@ class RA4(RPackage):
 
     bioc = "a4"
 
+    version("1.48.0", commit="89ef9f4afdde5270acecc7c65be3752b71237eba")
     version("1.46.0", commit="1b8f1300025fb0940e7f24cff7ffec9fca02d0e4")
     version("1.44.0", commit="5b0fc5a9971d8f3688ad1f88a4f5ee1498e91633")
     version("1.42.0", commit="fc26809e2bce7cd50d99d6f6dd5f85c38342fdea")

var/spack/repos/builtin/packages/r-a4base/package.py

@@ -14,6 +14,7 @@ class RA4base(RPackage):
 
     bioc = "a4Base"
 
+    version("1.48.0", commit="26d5793de3163091125feeed1de82e5406777b60")
     version("1.46.0", commit="be70ae723bb6031cdf9540d62dc6113761074e88")
     version("1.44.0", commit="9ae69e03118c7b14df0e6c9e3b25362b09f25bbe")
     version("1.42.0", commit="d7296e2792020e9c5b1c19101104326ee8bebfe6")

var/spack/repos/builtin/packages/r-a4classif/package.py

@@ -15,6 +15,7 @@ class RA4classif(RPackage):
 
     bioc = "a4Classif"
 
+    version("1.48.0", commit="1e2ff90d5af6332beac630395a7494c8fd30aff4")
     version("1.46.0", commit="96794183a76ab7da7a1863ccd421640254447af5")
     version("1.44.0", commit="df0fce781f9bc480a1159d958c9a63c314a9ed01")
     version("1.42.0", commit="820854a7ca9ed0c295479a25b7e3375c6d01d0b5")

var/spack/repos/builtin/packages/r-a4core/package.py

@@ -14,6 +14,7 @@ class RA4core(RPackage):
 
     bioc = "a4Core"
 
+    version("1.48.0", commit="3dd09f0a662745fcfd3fee7048301f3524e8ac5c")
     version("1.46.0", commit="8999fe146be6d04ae36c725d2b6324a6ce8ceb83")
     version("1.44.0", commit="61a7f3a51a41af615bfd4c22984e4c4a82874e8c")
     version("1.42.0", commit="6985950b72c2a0f20ec44fe2067d8864e004bfaa")

var/spack/repos/builtin/packages/r-a4preproc/package.py

@@ -14,6 +14,7 @@ class RA4preproc(RPackage):
 
     bioc = "a4Preproc"
 
+    version("1.48.0", commit="d3bf8b82d7cabd2ef77253bb9a741dcde3ca3a41")
     version("1.46.0", commit="8463958692c73fd655a6dfec39ea99c915513719")
     version("1.44.0", commit="252381265b96b83803a93e0c2014dd6b0574e57f")
     version("1.42.0", commit="773a91e884d2ada16fe9cf57d5ed53c0155e3fa2")

var/spack/repos/builtin/packages/r-a4reporting/package.py

@@ -14,6 +14,7 @@ class RA4reporting(RPackage):
 
     bioc = "a4Reporting"
 
+    version("1.48.0", commit="de8c4b76f6b7ef502d77d55289df0d64fe70447c")
     version("1.46.0", commit="00b82d25bef4d518ae92f615d3a6f7931c0618dc")
     version("1.44.0", commit="bfe83507daf53e2e327474ea3012f0dc920efac1")
     version("1.42.0", commit="b0d715b9cdac80bc412f0a9a6b33941c4a7582bb")

var/spack/repos/builtin/packages/r-absseq/package.py

@@ -17,6 +17,7 @@ class RAbsseq(RPackage):
 
     bioc = "ABSSeq"
 
+    version("1.54.0", commit="5e7de8c2a6532073012660f22243c9f7a5568ef6")
     version("1.52.0", commit="07038c047775e17d5d29909927d2143efb63e9cb")
     version("1.50.0", commit="4f384d04ebaae6ea0b56e5cff9a9dcdcb6c8afb0")
     version("1.48.0", commit="b237c967d44d075ca306c35e92df8b66a60ce72d")

var/spack/repos/builtin/packages/r-acde/package.py

@@ -22,6 +22,7 @@ class RAcde(RPackage):
 
     bioc = "acde"
 
+    version("1.30.0", commit="4c16b9fd6c91a433bf1345252e022571c4983cb5")
     version("1.28.0", commit="0edccca7be2475fa2ae3b3c36d0d64924c37b3c0")
     version("1.26.0", commit="dfef9a435062e948efd5eda22942a0d500baa992")
     version("1.24.0", commit="0c3c4d47af7eaff37420032ea5245743a65124cf")

var/spack/repos/builtin/packages/r-acgh/package.py

@@ -16,6 +16,7 @@ class RAcgh(RPackage):
 
     bioc = "aCGH"
 
+    version("1.78.0", commit="75df3a4839af66ce177d1bbc3cec4ac03c21dc8e")
     version("1.76.0", commit="c6068522854ed0b1c3feb006619ef25590f70ad6")
     version("1.74.0", commit="e7ba380af0da138788eb6c86f5dbe453269c0810")
     version("1.72.0", commit="b5d4022ac487125194d3913f1b8c2948db6e2792")

var/spack/repos/builtin/packages/r-acme/package.py

@@ -21,6 +21,7 @@ class RAcme(RPackage):
 
     bioc = "ACME"
 
+    version("2.56.0", commit="083af1249e67db11fd471babe67b146eb9c1700c")
     version("2.54.0", commit="8d39d9d6623adf427f5eba308790e1de01213870")
     version("2.52.0", commit="14a97c722d0201654af9e583e7e462b458c28a77")
     version("2.50.0", commit="d55a19a8c091e8ea5fd35041520107a7f7603e14")

var/spack/repos/builtin/packages/r-adsplit/package.py

@@ -16,6 +16,7 @@ class RAdsplit(RPackage):
 
     bioc = "adSplit"
 
+    version("1.70.0", commit="a08a994215a459b856eae051c778e2b9144f52d9")
     version("1.68.0", commit="705977b5e1cb7dd69793cc673fa215baaba42af5")
     version("1.66.0", commit="64580a6f7a9bc6b16334267c90df48fbb839cc16")
     version("1.64.0", commit="32f150eb51c66b867301dceeb527de5b97f9f490")

var/spack/repos/builtin/packages/r-affxparser/package.py

@@ -20,6 +20,7 @@ class RAffxparser(RPackage):
 
     bioc = "affxparser"
 
+    version("1.72.0", commit="6e976af32f77835143f6b4e0c01c6016dc1b331c")
     version("1.70.0", commit="28f94cd3477e9500942be89cbcb5cad1bbb369fe")
     version("1.68.1", commit="821a01a2df18115a3b7864b3f45418255b7123eb")
     version("1.66.0", commit="2ea72d4c924ac14bdd807b23563c8501c226ce3a")

var/spack/repos/builtin/packages/r-affy/package.py

@@ -15,6 +15,7 @@ class RAffy(RPackage):
 
     bioc = "affy"
 
+    version("1.78.0", commit="cc7eac358b6e10ee86a7a93d2e436758f6fbd9b5")
     version("1.76.0", commit="3bb309388d5d6402c356d4a5270ee83c5b88942f")
     version("1.74.0", commit="2266c4a46eda7e5b64f7f3e17e8b61e7b85579ff")
     version("1.72.0", commit="3750b4eb8e5224b19100f6c881b67e568d8968a2")

var/spack/repos/builtin/packages/r-affycomp/package.py

@@ -14,6 +14,7 @@ class RAffycomp(RPackage):
 
     bioc = "affycomp"
 
+    version("1.76.0", commit="8bfc628de26a739c5e0cb47aa22bfda7c8d0a922")
     version("1.74.0", commit="1160d6395f23085456938ba2bd38fb45597fc92f")
     version("1.72.0", commit="c52baea98b80abd4a99380ac9d4b68ef91869d40")
     version("1.70.0", commit="487f6775975092475581a6c02ddb27590559cf07")

var/spack/repos/builtin/packages/r-affycontam/package.py

@@ -14,6 +14,7 @@ class RAffycontam(RPackage):
 
     bioc = "affyContam"
 
+    version("1.58.0", commit="5e91d79d7653a4f484b62eae7fd7e908de8cb9b6")
     version("1.56.0", commit="e2b8a4fba1648255eadce954a848f2dd8e22bcb3")
     version("1.54.0", commit="c5208b48b8881983ff53a4713244327e8ad13b78")
     version("1.52.0", commit="47c1d86da330f157d3ece0e26b0657d66a5ca0c9")

var/spack/repos/builtin/packages/r-affycoretools/package.py

@@ -15,6 +15,7 @@ class RAffycoretools(RPackage):
 
     bioc = "affycoretools"
 
+    version("1.72.0", commit="229ae09efc1a66e64ea395019c32d16387bf81ac")
     version("1.70.0", commit="f09a788aa83e1e052a7c5f148a451a99fe9c9c96")
     version("1.68.1", commit="69546b1fe5edd71eca130d53d33f0fb0fcf62c97")
     version("1.66.0", commit="6bf769d70e196634097f465ed2fa85cce5312a6d")

var/spack/repos/builtin/packages/r-affydata/package.py

@@ -15,6 +15,7 @@ class RAffydata(RPackage):
 
     bioc = "affydata"
 
+    version("1.48.0", commit="037b86c86c114761ff1bcca64ab4e0bcd68063d3")
     version("1.46.0", commit="870745b886df9f1fbbd6130d266c0ef96f3afa66")
     version("1.44.0", commit="f18304a356cee8cd7297bab362b13c40e50439df")
     version("1.42.0", commit="4b54c1206bedd27ff9be32affc999a279f4e96f0")

var/spack/repos/builtin/packages/r-affyilm/package.py

@@ -16,6 +16,7 @@ class RAffyilm(RPackage):
 
     bioc = "affyILM"
 
+    version("1.52.0", commit="08ed8c60921ba1b9e04fa90e156eef1a3c899d15")
     version("1.50.0", commit="185cd8e4712a3378ce7a156d4940224bbb2c4122")
     version("1.48.0", commit="4603a4c4d6c2330a8a56a7bb657dc56c51a9393a")
     version("1.46.0", commit="67ffbfa6c881ed83d15604bf4463fe5dba81036b")

var/spack/repos/builtin/packages/r-affyio/package.py

@@ -15,6 +15,7 @@ class RAffyio(RPackage):
 
     bioc = "affyio"
 
+    version("1.70.0", commit="95560567e27088863c64e868a8e5069fc725b8d7")
     version("1.68.0", commit="33080c5eeb14c0ca40f0d231706af4e0c2c1ef8b")
     version("1.66.0", commit="3a0b90704fc46cddd99a72b985a6bdb348f69b50")
     version("1.64.0", commit="aa7ce48f3f4110431f6f488d45961fde4019ffb0")

var/spack/repos/builtin/packages/r-affyplm/package.py

@@ -17,6 +17,7 @@ class RAffyplm(RPackage):
 
     bioc = "affyPLM"
 
+    version("1.76.0", commit="45557df5a32f56aa5240439737c5718738fb4c27")
     version("1.74.0", commit="5f76ef92e69deabc19c5395eaec4adb85c66b63d")
     version("1.72.0", commit="394c0a8e213f188d0b1d01e20516df8bf1bc5c09")
     version("1.70.0", commit="64abfec92b347aa340b54a8c7b2fbd524fe9c312")
@@ -34,3 +35,4 @@ class RAffyplm(RPackage):
     depends_on("r-gcrma", type=("build", "run"))
     depends_on("r-preprocesscore@1.5.1:", type=("build", "run"))
     depends_on("r-zlibbioc", type=("build", "run"))
+    depends_on("zlib")

var/spack/repos/builtin/packages/r-affyrnadegradation/package.py

@@ -18,6 +18,7 @@ class RAffyrnadegradation(RPackage):
 
     bioc = "AffyRNADegradation"
 
+    version("1.46.0", commit="431ae61c9b3809829697ef71672c57171d93311e")
     version("1.44.0", commit="63881f41fc67cc7322b189446dcffb4e1060e303")
     version("1.42.0", commit="5775f41f538b3c8ee4d07d38cec1b49c548cebe6")
     version("1.40.0", commit="8539a91ee464d692a267bb17c91dc1ef9a231f41")

var/spack/repos/builtin/packages/r-agdex/package.py

@@ -14,6 +14,7 @@ class RAgdex(RPackage):
 
     bioc = "AGDEX"
 
+    version("1.48.0", commit="917920b397493b0ea40093044ebe36fff7c389ad")
     version("1.46.0", commit="d7c38e8bdcaa7b0261117c605e7f61e2b07e8316")
     version("1.44.0", commit="9d3eb90eaf7bf093c7fa73facb3df89506a85185")
     version("1.42.0", commit="175cf1b384b0942103d841b1feb9e4f7d141ba06")

var/spack/repos/builtin/packages/r-agilp/package.py

@@ -13,6 +13,7 @@ class RAgilp(RPackage):
 
     bioc = "agilp"
 
+    version("3.32.0", commit="8291f7b7c1b6167952568f51593116afc6d0fc27")
     version("3.30.0", commit="a2c898dc901ccdda4b8582caff079ab20b1bfc28")
     version("3.28.0", commit="2c6dfccc76473b5bef13b75fa59adf46b3381f55")
     version("3.26.0", commit="3170fe2b1cc459d5e2ca7f61a127aac17cd66a96")

var/spack/repos/builtin/packages/r-agimicrorna/package.py

@@ -14,6 +14,7 @@ class RAgimicrorna(RPackage):
 
     bioc = "AgiMicroRna"
 
+    version("2.50.0", commit="a812b0f4f215b093ca685889b65de60c6701b695")
     version("2.48.0", commit="4c163b1b730150a3a60a3815bd8c08fa04d71fc1")
     version("2.46.0", commit="8c6d73e1c3f1f9cc019bdb219b19e6179bb1efe4")
     version("2.44.0", commit="8b308baa3b1b0afc0855ea263630a288689e3864")

var/spack/repos/builtin/packages/r-aims/package.py

@@ -17,6 +17,7 @@ class RAims(RPackage):
 
     bioc = "AIMS"
 
+    version("1.32.0", commit="019415a6362e805465d43c157606e1774aed9e51")
     version("1.30.0", commit="2ab61159c5aa0902cc33fc1502f7853b66912cce")
     version("1.28.0", commit="84608df638b5694c08158ed77ad2c8a64c4e594b")
     version("1.26.0", commit="5dcf60eb4cdcf563ea848482c9c488f465c27bbd")

var/spack/repos/builtin/packages/r-aldex2/package.py

@@ -23,6 +23,7 @@ class RAldex2(RPackage):
 
     bioc = "ALDEx2"
 
+    version("1.32.0", commit="ba32b9a9b6a8f42906ea094318f00116f15e42eb")
     version("1.30.0", commit="cb6670515a8722f9cfedac12a8c2747a5298ee46")
     version("1.28.1", commit="f8d8ba6d2439bff75ab80f5466c9a047c31ed0a6")
     version("1.26.0", commit="0876a2eac08d3f1c01df7414d97d391c80182ada")

var/spack/repos/builtin/packages/r-allelicimbalance/package.py

@@ -14,6 +14,7 @@ class RAllelicimbalance(RPackage):
 
     bioc = "AllelicImbalance"
 
+    version("1.38.0", commit="75a3b0fefe635a0892eae338d0fdd4a9e091f957")
     version("1.36.0", commit="cb4910c1fd58cc4272c21251a8f120990e1aa431")
     version("1.34.0", commit="290708ccc4ceae1fbb9e9257cb254916449d389b")
     version("1.32.0", commit="428ab8c96bb15fab45e4084da25f98b01b9d60b6")

var/spack/repos/builtin/packages/r-alpine/package.py

@@ -14,6 +14,7 @@ class RAlpine(RPackage):
 
     bioc = "alpine"
 
+    version("1.26.0", commit="1e317dbf2973eb4b6a3ffbf52bc0faacec76a616")
     version("1.24.0", commit="7e734d49881761cafaacea096ce757531b6bd522")
     version("1.22.0", commit="6107a82962f07e0434e93f261cd375eaaa171d91")
     version("1.20.0", commit="9348ef14128aa6be10cca1987736ddbc385df7e9")

var/spack/repos/builtin/packages/r-altcdfenvs/package.py

@@ -13,6 +13,7 @@ class RAltcdfenvs(RPackage):
 
     bioc = "altcdfenvs"
 
+    version("2.62.0", commit="aedf0e9f98639d60b327e50957e504cf24b64bbb")
     version("2.60.0", commit="0bc0b4493b8e9fe2eb47fb8e9377123ce8f472bb")
     version("2.58.0", commit="08255a777ffa1e1414d3dd3062d95bfdd3dfd47c")
     version("2.56.0", commit="941e00b97a33662a8230991e387070324b2e76bf")

var/spack/repos/builtin/packages/r-anaquin/package.py

@@ -17,6 +17,7 @@ class RAnaquin(RPackage):
 
     bioc = "Anaquin"
 
+    version("2.24.0", commit="0eefabdc4036b98505032c460d08375839b1fc3e")
     version("2.22.0", commit="d848a9bd7bf9d1d62202cc477300bf1a65b3e36c")
     version("2.20.0", commit="61598dd3430b09b57f31d7d550ea95126a2d73c8")
     version("2.18.0", commit="c8e3df3e299c32daac0dda23cea59a18673d886b")

var/spack/repos/builtin/packages/r-aneufinder/package.py

@@ -15,6 +15,7 @@ class RAneufinder(RPackage):
 
     bioc = "AneuFinder"
 
+    version("1.28.0", commit="e17d810171bdab1c6a26a3ab7b7931db4e073e7e")
     version("1.26.0", commit="7cd59a1e24c6512f2e4fcbe2c53a0d3cd2d06217")
     version("1.24.0", commit="4c6906eee514eba3e8ac159654a6953e37a99bba")
     version("1.22.0", commit="ea0beb3d827c2dd4bc56708a839a93c55304918b")
@@ -33,7 +34,7 @@ class RAneufinder(RPackage):
     depends_on("r-aneufinderdata", type=("build", "run"))
     depends_on("r-foreach", type=("build", "run"))
     depends_on("r-doparallel", type=("build", "run"))
-    depends_on("r-biocgenerics", type=("build", "run"), when="@1.4.0:1.6.0")
+    depends_on("r-biocgenerics", type=("build", "run"), when="@1.4.0:")
     depends_on("r-biocgenerics@0.31.6:", type=("build", "run"), when="@1.18.0:")
     depends_on("r-s4vectors", type=("build", "run"))
     depends_on("r-genomeinfodb", type=("build", "run"))
@@ -47,5 +48,5 @@ class RAneufinder(RPackage):
     depends_on("r-reshape2", type=("build", "run"))
     depends_on("r-ggdendro", type=("build", "run"))
     depends_on("r-ggrepel", type=("build", "run"))
-    depends_on("r-reordercluster", type=("build", "run"))
     depends_on("r-mclust", type=("build", "run"))
+    depends_on("r-reordercluster", type=("build", "run"), when="@:1.26.0")

var/spack/repos/builtin/packages/r-aneufinderdata/package.py

@@ -14,6 +14,7 @@ class RAneufinderdata(RPackage):
 
     bioc = "AneuFinderData"
 
+    version("1.28.0", commit="d04255e60173ce478d31b1e1e5c73e6ed9e3b20c")
     version("1.26.0", commit="4b810599b62a3fb39239bfd98ed960c93989e86b")
     version("1.24.0", commit="cf6f3852702aab28e3170fc56b695d00b7389666")
     version("1.22.0", commit="ae8eec3b0afdc351dc447aad2024df5b2c75e56b")

var/spack/repos/builtin/packages/r-annaffy/package.py

@@ -16,6 +16,7 @@ class RAnnaffy(RPackage):
 
     bioc = "annaffy"
 
+    version("1.72.0", commit="7cb439706a7e93fb5b44ead374010077a44ea78b")
     version("1.70.0", commit="c99e81259adb39b5d8e954fd7afe7f93675229bc")
     version("1.68.0", commit="fa930c0bbdca9828a130ab06d86c65d451380830")
     version("1.66.0", commit="aa1afa1509754128d27508228c1f39f51a8da043")

var/spack/repos/builtin/packages/r-annotate/package.py

@@ -13,6 +13,7 @@ class RAnnotate(RPackage):
 
     bioc = "annotate"
 
+    version("1.78.0", commit="ca6415a463ec682f340ba5d1dc6246a92e836143")
     version("1.76.0", commit="0181d5c41d594e36be06adb6a02302db0ad2c507")
     version("1.74.0", commit="200c71743417792880f8171d59b2ac0ddd3902a8")
     version("1.72.0", commit="67ac76a9ff6d60dc1620763d3aa98aef39443110")

var/spack/repos/builtin/packages/r-annotationdbi/package.py

@@ -14,6 +14,7 @@ class RAnnotationdbi(RPackage):
 
     bioc = "AnnotationDbi"
 
+    version("1.62.0", commit="7ca03a0332d0a284ea27d16edb7b386c86cf99ea")
     version("1.60.0", commit="cd61bd1b1538e2f1f411fd7087820749ecf39da8")
     version("1.58.0", commit="05fcf7a28a6b15b195da23474d7ba89bd0cfd891")
     version("1.56.2", commit="13fdc4a93852199ca6ec120a2fe1078f9f445f67")

var/spack/repos/builtin/packages/r-annotationfilter/package.py

@@ -15,6 +15,7 @@ class RAnnotationfilter(RPackage):
 
     bioc = "AnnotationFilter"
 
+    version("1.24.0", commit="172d9c149d9025154f7b26982d07f571499b03e8")
     version("1.22.0", commit="c9fea4a829ce9419b6e0af987915b2d469358597")
     version("1.20.0", commit="2818aff6502fd6fe819521cd8d97695ef6f9198e")
     version("1.18.0", commit="60a9b666d7362d7ed5c357fd4a5d2744d8598c20")

var/spack/repos/builtin/packages/r-annotationforge/package.py

@@ -14,6 +14,7 @@ class RAnnotationforge(RPackage):
 
     bioc = "AnnotationForge"
 
+    version("1.42.0", commit="2eac005012b11317c33c8b0062b968b2ac378308")
     version("1.40.0", commit="f77d3a942eb6b18c18888b7af3f0e652596cf19f")
     version("1.38.1", commit="2dcedf353bc57bf80818e6adb1f7129c21886f6b")
     version("1.38.0", commit="1f77750562ea3a01f0f1a46c299184fc31196ffd")

var/spack/repos/builtin/packages/r-annotationhub/package.py

@@ -20,6 +20,7 @@ class RAnnotationhub(RPackage):
 
     bioc = "AnnotationHub"
 
+    version("3.8.0", commit="975022dd33706824bd02f67cc9c3a42f3567f4a5")
     version("3.6.0", commit="3315a73b7803a92412ed18209dd37b378195b86f")
     version("3.4.0", commit="e74e54ca44f50c2c15c60f8620e3d1721f8f5b6d")
     version("3.2.1", commit="ad1dfe86f0b0ea4711cc9cdb89e073e8794ec9aa")

var/spack/repos/builtin/packages/r-aroma-light/package.py

@@ -16,6 +16,7 @@ class RAromaLight(RPackage):
 
     bioc = "aroma.light"
 
+    version("3.30.0", commit="a1882c2126622cb389a7ef1ef5b5c565e603a282")
     version("3.28.0", commit="7749dd7033e9885ec2546a5cac0562bac2fea04d")
     version("3.26.0", commit="7ead7517a77bc8b4b4b42aace69957a17e8fe016")
     version("3.24.0", commit="3ff48b8f546acc9803b3c652363cac78d3b81ae5")

var/spack/repos/builtin/packages/r-bamsignals/package.py

@@ -16,6 +16,7 @@ class RBamsignals(RPackage):
 
     bioc = "bamsignals"
 
+    version("1.32.0", commit="34bfc4e8b58e47c3b94347fd2976aeae07fc28c2")
     version("1.30.0", commit="aac37dffd6f6876b4626866e3d40bb7af75620fe")
     version("1.28.0", commit="27b70be6f73747d9d32054da043f4a37ea55b917")
     version("1.26.0", commit="d57643441d04f77db0907637dc9e7cd5bed5842f")

var/spack/repos/builtin/packages/r-basilisk-utils/package.py

@@ -0,0 +1,24 @@
+# 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 RBasiliskUtils(RPackage):
+    """Basilisk Installation Utilities.
+
+    Implements utilities for installation of the basilisk package, primarily
+    for creation of the underlying Conda instance. This allows us to avoid
+    re-writing the same R code in both the configure script (for centrally
+    administered R installations) and in the lazy installation mechanism (for
+    distributed package binaries). It is highly unlikely that developers - or,
+    heaven forbid, end-users! - will need to interact with this package
+    directly; they should be using the basilisk package instead."""
+
+    bioc = "basilisk.utils"
+
+    version("1.12.0", commit="8314f9a72ecc0f20b180431aec93647320de8c2c")
+
+    depends_on("r-dir-expiry", type=("build", "run"))

var/spack/repos/builtin/packages/r-basilisk/package.py

@@ -0,0 +1,24 @@
+# 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 RBasilisk(RPackage):
+    """Freezing Python Dependencies Inside Bioconductor Packages.
+
+    Installs a self-contained conda instance that is managed by the
+    R/Bioconductor installation machinery. This aims to provide a consistent
+    Python environment that can be used reliably by Bioconductor packages.
+    Functions are also provided to enable smooth interoperability of multiple
+    Python environments in a single R session."""
+
+    bioc = "basilisk"
+
+    version("1.12.0", commit="26c1c354526eb8d806268427a7c40b31bb89f489")
+
+    depends_on("r-reticulate", type=("build", "run"))
+    depends_on("r-dir-expiry", type=("build", "run"))
+    depends_on("r-basilisk-utils", type=("build", "run"))

var/spack/repos/builtin/packages/r-beachmat/package.py

@@ -17,6 +17,7 @@ class RBeachmat(RPackage):
 
     bioc = "beachmat"
 
+    version("2.16.0", commit="4cc8e50dcae767a2ef84ffc7a581ea182f05f300")
     version("2.14.0", commit="5a4b85f4a22f3447f12d03157ab95de73f6137c6")
     version("2.12.0", commit="3e6af145bdcdf0a0b722d8256ba1a38b8a36b2f5")
     version("2.10.0", commit="b7cc532d4a5b26d9073135cc9945258ea08e5079")
@@ -34,7 +35,7 @@ class RBeachmat(RPackage):
     depends_on("r-delayedarray@0.15.14:", type=("build", "run"), when="@2.6.4")
     depends_on("r-biocgenerics", type=("build", "run"), when="@1.4.0:")
     depends_on("r-matrix", type=("build", "run"), when="@2.6.4:")
-    depends_on("r-rcpp@0.12.14:", type=("build", "run"), when="@1.0.2:1.4.0")
+    depends_on("r-rcpp@0.12.14:", type=("build", "run"), when="@1.0.2:")
     depends_on("r-rcpp", type=("build", "run"), when="@2.10.0:")
 
     depends_on("r-rhdf5lib", type=("build", "run"), when="@1.0.2:1.4.0")

var/spack/repos/builtin/packages/r-biobase/package.py

@@ -14,6 +14,7 @@ class RBiobase(RPackage):
 
     bioc = "Biobase"
 
+    version("2.60.0", commit="8dc10d2d26dc0847740ff2b4f16cc1ae2e936464")
     version("2.58.0", commit="767f2f33f158f233616178e12ce08cdb03d2a5a2")
     version("2.56.0", commit="3b2dd91b333677c2f27257c7624014a55e73c52b")
     version("2.54.0", commit="8215d76ce44899e6d10fe8a2f503821a94ef6b40")

var/spack/repos/builtin/packages/r-biocfilecache/package.py

@@ -16,6 +16,7 @@ class RBiocfilecache(RPackage):
 
     bioc = "BiocFileCache"
 
+    version("2.8.0", commit="d088b3224bcee4661d954c77fe38ba8c45ecc51a")
     version("2.6.0", commit="f5b8368c1402b15e8db8eab59217f1176e902e6f")
     version("2.4.0", commit="2c00eee40d95fddad223f115f959b09e1a14f75d")
     version("2.2.1", commit="cc912123408803193bf37395f4d18baa8dcd6f47")
@@ -31,7 +32,7 @@ class RBiocfilecache(RPackage):
     depends_on("r-dbplyr@1.0.0:", type=("build", "run"), when="@1.2.3:")
     depends_on("r-rsqlite", type=("build", "run"))
     depends_on("r-dbi", type=("build", "run"))
-    depends_on("r-rappdirs", type=("build", "run"))
     depends_on("r-filelock", type=("build", "run"), when="@2.2.1:")
     depends_on("r-curl", type=("build", "run"), when="@1.6.0:")
     depends_on("r-httr", type=("build", "run"))
+    depends_on("r-rappdirs", type=("build", "run"), when="@:2.6.0")

var/spack/repos/builtin/packages/r-biocgenerics/package.py

@@ -13,6 +13,7 @@ class RBiocgenerics(RPackage):
 
     bioc = "BiocGenerics"
 
+    version("0.46.0", commit="a90f0c5976a24417e47e009ba602fc98515ac9ab")
     version("0.44.0", commit="d7cd9c19958bd8d4573d980494188fa15ab16e45")
     version("0.42.0", commit="3582d47b836387afc08157f3d6a5013fd64334ed")
     version("0.40.0", commit="0bc1e0ed4d20c7101cd782a14f6373e27478acfc")

var/spack/repos/builtin/packages/r-biocio/package.py

@@ -22,11 +22,13 @@ class RBiocio(RPackage):
 
     bioc = "BiocIO"
 
+    version("1.10.0", commit="1368ff1a7ddbb62515a87a88d7ec39981de557d5")
     version("1.8.0", commit="4a719fa41e014b7b948f7b245e581ede6a04eda1")
     version("1.6.0", commit="60c8aa1a961e43bf0ee5d563a6d9fcec84f7f8f8")
     version("1.4.0", commit="c335932526a38c75dbfa4970c1d90b8a21466d37")
 
     depends_on("r@4.0.0:", type=("build", "run"))
     depends_on("r@4.0:", type=("build", "run"), when="@1.8.0:")
+    depends_on("r@4.3.0:", type=("build", "run"), when="@1.10.0:")
     depends_on("r-biocgenerics", type=("build", "run"))
     depends_on("r-s4vectors", type=("build", "run"))

var/spack/repos/builtin/packages/r-biocneighbors/package.py

@@ -21,6 +21,7 @@ class RBiocneighbors(RPackage):
 
     bioc = "BiocNeighbors"
 
+    version("1.18.0", commit="4b19ef2a76baa0b001c426bad540ab9295bec78e")
     version("1.16.0", commit="3b227beead424314aab5ef847222f8f4243c684f")
     version("1.14.0", commit="670a1bd4d82636d28fbff50cea2157e16bb1a858")
     version("1.12.0", commit="3c8a290f75adc944b408e6e77a36f3a0c1509c4c")

var/spack/repos/builtin/packages/r-biocparallel/package.py

@@ -15,6 +15,7 @@ class RBiocparallel(RPackage):
 
     bioc = "BiocParallel"
 
+    version("1.34.0", commit="f3bbc0a2d38da034c50ca1e4704fc4ee99a2dc9e")
     version("1.32.1", commit="6c85dbad596a74a6d3022173a4a11c6b81a4a2c2")
     version("1.30.4", commit="1229ebe9f6d8305f9f61e562464f83f9ba86e699")
     version("1.30.2", commit="e7e109f7a94dbfbc50f926be030c7ad8c1a053db")

var/spack/repos/builtin/packages/r-biocsingular/package.py

@@ -17,6 +17,7 @@ class RBiocsingular(RPackage):
 
     bioc = "BiocSingular"
 
+    version("1.16.0", commit="0db9a691d4eb21551c532d8bde8f64dcc19b6c66")
     version("1.14.0", commit="6dc42b30110e498f6694f18037f991c1006c71b7")
     version("1.12.0", commit="7d1b8f4954e9e6f2c30a5111cdab9aabc8bcc3a6")
     version("1.10.0", commit="6615ae8cb124aba6507447c1081bd2eba655e57d")

var/spack/repos/builtin/packages/r-biocstyle/package.py

@@ -14,6 +14,7 @@ class RBiocstyle(RPackage):
 
     bioc = "BiocStyle"
 
+    version("2.28.0", commit="b358aa5d3f9c68629e9abf50ffceccbf77226ea8")
     version("2.26.0", commit="add035498bdce76d71a0afa22a063c2d8e5588bc")
     version("2.24.0", commit="53095b534b7e6c80a33a67b5f2db0db8f00db902")
     version("2.22.0", commit="86250b637afa3a3463fac939b99c0402b47876ea")

var/spack/repos/builtin/packages/r-biocversion/package.py

@@ -14,6 +14,7 @@ class RBiocversion(RPackage):
 
     bioc = "BiocVersion"
 
+    version("3.17.1", commit="a2d0c4c489be1cafdb51bf8d205161429b09ac7f")
     version("3.16.0", commit="c681e06fe30ea6815f958c1a3c74c090863680ba")
     version("3.15.2", commit="818ab03b6a3551993b712e3702126040f9fb7600")
     version("3.14.0", commit="aa56d93d0ea5dcdbf301f120502981740fd91e1e")
@@ -22,3 +23,4 @@ class RBiocversion(RPackage):
     depends_on("r@4.0.0:", type=("build", "run"))
     depends_on("r@4.1.0:", type=("build", "run"), when="@3.14.0:")
     depends_on("r@4.2.0:", type=("build", "run"), when="@3.15.2:")
+    depends_on("r@4.3.0:", type=("build", "run"), when="@3.17.1:")