rework test to parametrize by order and depth of dev spec

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

lib/spack/env/cc

@@ -241,28 +241,28 @@ case "$command" in
         mode=cpp
         debug_flags="-g"
         ;;
-    cc|c89|c99|gcc|clang|armclang|icc|icx|pgcc|nvc|xlc|xlc_r|fcc)
+    cc|c89|c99|gcc|clang|armclang|icc|icx|pgcc|nvc|xlc|xlc_r|fcc|amdclang)
         command="$SPACK_CC"
         language="C"
         comp="CC"
         lang_flags=C
         debug_flags="-g"
         ;;
-    c++|CC|g++|clang++|armclang++|icpc|icpx|dpcpp|pgc++|nvc++|xlc++|xlc++_r|FCC)
+    c++|CC|g++|clang++|armclang++|icpc|icpx|dpcpp|pgc++|nvc++|xlc++|xlc++_r|FCC|amdclang++)
         command="$SPACK_CXX"
         language="C++"
         comp="CXX"
         lang_flags=CXX
         debug_flags="-g"
         ;;
-    ftn|f90|fc|f95|gfortran|flang|armflang|ifort|ifx|pgfortran|nvfortran|xlf90|xlf90_r|nagfor|frt)
+    ftn|f90|fc|f95|gfortran|flang|armflang|ifort|ifx|pgfortran|nvfortran|xlf90|xlf90_r|nagfor|frt|amdflang)
         command="$SPACK_FC"
         language="Fortran 90"
         comp="FC"
         lang_flags=F
         debug_flags="-g"
         ;;
-    f77|xlf|xlf_r|pgf77)
+    f77|xlf|xlf_r|pgf77|amdflang)
         command="$SPACK_F77"
         language="Fortran 77"
         comp="F77"

lib/spack/env/rocmcc/amdclang

@@ -0,0 +1 @@
+../cc

lib/spack/env/rocmcc/amdclang++

@@ -0,0 +1 @@
+../cpp

lib/spack/env/rocmcc/amdflang

@@ -0,0 +1 @@
+../fc

lib/spack/spack/cmd/find.py

@@ -202,6 +202,12 @@ def display_env(env, args, decorator):
 
 
 def find(parser, args):
+    if args.bootstrap:
+        tty.warn(
+            "`spack find --bootstrap` is deprecated and will be removed in v0.19.",
+            "Use `spack --bootstrap find` instead."
+        )
+
     if args.bootstrap:
         bootstrap_store_path = spack.bootstrap.store_path()
         with spack.bootstrap.ensure_bootstrap_configuration():

lib/spack/spack/compilers/__init__.py

@@ -42,7 +42,8 @@
 
 _compiler_to_pkg = {
     'clang': 'llvm+clang',
-    'oneapi': 'intel-oneapi-compilers'
+    'oneapi': 'intel-oneapi-compilers',
+    'rocmcc': 'llvm-amdgpu'
 }
 
 

lib/spack/spack/compilers/rocmcc.py

@@ -0,0 +1,78 @@
+# Copyright 2013-2022 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)
+
+import re
+
+import llnl.util.lang
+
+import spack.compilers.clang
+
+
+class Rocmcc(spack.compilers.clang.Clang):
+    # Subclasses use possible names of C compiler
+    cc_names = ['amdclang']
+
+    # Subclasses use possible names of C++ compiler
+    cxx_names = ['amdclang++']
+
+    # Subclasses use possible names of Fortran 77 compiler
+    f77_names = ['amdflang']
+
+    # Subclasses use possible names of Fortran 90 compiler
+    fc_names = ['amdflang']
+
+    PrgEnv = 'PrgEnv-amd'
+    PrgEnv_compiler = 'amd'
+
+    @property
+    def link_paths(self):
+        link_paths = {'cc': 'rocmcc/amdclang',
+                      'cxx': 'rocmcc/amdclang++',
+                      'f77': 'rocmcc/amdflang',
+                      'fc': 'rocmcc/amdflang'}
+
+        return link_paths
+
+    @property
+    def cxx11_flag(self):
+        return "-std=c++11"
+
+    @property
+    def cxx14_flag(self):
+        return "-std=c++14"
+
+    @property
+    def cxx17_flag(self):
+        return "-std=c++17"
+
+    @property
+    def c99_flag(self):
+        return '-std=c99'
+
+    @property
+    def c11_flag(self):
+        return "-std=c11"
+
+    @classmethod
+    @llnl.util.lang.memoized
+    def extract_version_from_output(cls, output):
+        match = re.search(
+            r'llvm-project roc-(\d+)[._](\d+)[._](\d+)',
+            output
+        )
+        if match:
+            return '.'.join(match.groups())
+
+    @classmethod
+    def fc_version(cls, fortran_compiler):
+        return cls.default_version(fortran_compiler)
+
+    @classmethod
+    def f77_version(cls, f77):
+        return cls.fc_version(f77)
+
+    @property
+    def stdcxx_libs(self):
+        return ('-lstdc++', )

lib/spack/spack/dependency.py

@@ -124,7 +124,10 @@ def merge(self, other):
         # concatenate patch lists, or just copy them in
         for cond, p in other.patches.items():
             if cond in self.patches:
-                self.patches[cond].extend(other.patches[cond])
+                current_list = self.patches[cond]
+                current_list.extend(
+                    p for p in other.patches[cond] if p not in current_list
+                )
             else:
                 self.patches[cond] = other.patches[cond]
 

lib/spack/spack/fetch_strategy.py

@@ -1437,13 +1437,7 @@ def fetch(self):
         basename = os.path.basename(parsed_url.path)
 
         with working_dir(self.stage.path):
-            import spack.util.s3 as s3_util
-            s3 = s3_util.create_s3_session(self.url,
-                                           connection=s3_util.get_mirror_connection(parsed_url), url_type="fetch")  # noqa: E501
-
-            headers = s3.get_object(Bucket=parsed_url.netloc,
-                                    Key=parsed_url.path.lstrip("/"))
-            stream = headers["Body"]
+            _, headers, stream = web_util.read_from_url(self.url)
 
             with open(basename, 'wb') as f:
                 shutil.copyfileobj(stream, f)

lib/spack/spack/modules/lmod.py

@@ -188,6 +188,10 @@ def provides(self):
         if self.spec.name == 'llvm':
             provides['compiler'] = spack.spec.CompilerSpec(str(self.spec))
             provides['compiler'].name = 'clang'
+        # Special case for llvm-amdgpu
+        if self.spec.name == 'llvm-amdgpu':
+            provides['compiler'] = spack.spec.CompilerSpec(str(self.spec))
+            provides['compiler'].name = 'rocmcc'
 
         # All the other tokens in the hierarchy must be virtual dependencies
         for x in self.hierarchy_tokens:

lib/spack/spack/patch.py

@@ -97,6 +97,12 @@ def to_dict(self):
             'working_dir': self.working_dir,
         }
 
+    def __eq__(self, other):
+        return self.sha256 == other.sha256
+
+    def __hash__(self):
+        return hash(self.sha256)
+
 
 class FilePatch(Patch):
     """Describes a patch that is retrieved from a file in the repository.

lib/spack/spack/repo.py

@@ -7,6 +7,7 @@
 import contextlib
 import errno
 import functools
+import importlib
 import inspect
 import itertools
 import os
@@ -1099,7 +1100,12 @@ def get_pkg_class(self, pkg_name):
                                         % (self.namespace, namespace))
 
         class_name = nm.mod_to_class(pkg_name)
-        module = self._get_pkg_module(pkg_name)
+
+        fullname = "{0}.{1}".format(self.full_namespace, pkg_name)
+        try:
+            module = importlib.import_module(fullname)
+        except ImportError:
+            raise UnknownPackageError(pkg_name)
 
         cls = getattr(module, class_name)
         if not inspect.isclass(cls):

lib/spack/spack/solver/asp.py

@@ -1668,13 +1668,15 @@ def define_installed_packages(self, specs, possible):
         # Specs from local store
         with spack.store.db.read_transaction():
             for spec in spack.store.db.query(installed=True):
-                self._facts_from_concrete_spec(spec, possible)
+                if not spec.satisfies('dev_path=*'):
+                    self._facts_from_concrete_spec(spec, possible)
 
         # Specs from configured buildcaches
         try:
             index = spack.binary_distribution.update_cache_and_get_specs()
             for spec in index:
-                self._facts_from_concrete_spec(spec, possible)
+                if not spec.satisfies('dev_path=*'):
+                    self._facts_from_concrete_spec(spec, possible)
         except (spack.binary_distribution.FetchCacheError, IndexError):
             # this is raised when no mirrors had indices.
             # TODO: update mirror configuration so it can indicate that the source cache

lib/spack/spack/solver/concretize.lp

@@ -827,6 +827,9 @@ no_flags(Package, FlagType)
 { hash(Package, Hash) : installed_hash(Package, Hash) } 1
  :- node(Package), error("Internal error: package must resolve to at most one hash").
 
+% you can't choose an installed hash for a dev spec
+:- hash(Package, Hash), variant_set(Package, "dev_path", _).
+
 % if a hash is selected, we impose all the constraints that implies
 impose(Hash) :- hash(Package, Hash).
 

lib/spack/spack/test/cmd/find.py

@@ -333,3 +333,8 @@ def test_find_loaded(database, working_env):
     output = find('--loaded')
     expected = find()
     assert output == expected
+
+
+def test_bootstrap_deprecated():
+    output = find('--bootstrap')
+    assert "`spack find --bootstrap` is deprecated" in output

lib/spack/spack/test/concretize.py

@@ -332,7 +332,6 @@ def concretize_difficult_packages(self, a, b):
         assert s[a].version == ver(b)
 
     def test_concretize_two_virtuals(self):
-
         """Test a package with multiple virtual dependencies."""
         Spec('hypre').concretize()
 
@@ -1138,6 +1137,38 @@ def test_external_package_versions(self, spec_str, is_external, expected):
         assert s.external == is_external
         assert s.satisfies(expected)
 
+    @pytest.mark.parametrize('dev_first,spec', [
+        (True, 'dev-build-test-install'),
+        (True, 'dev-build-test-dependent'),
+        (False, 'dev-build-test-install'),
+        (False, 'dev-build-test-dependent')
+    ])
+    def test_reuse_does_not_overwrite_dev_specs(
+            self, dev_first, spec, tmpdir, mock_packages, install_mockery, mock_fetch):
+        """Test that reuse does not mix dev specs with non-dev specs.
+
+        Tests for either order (dev specs are not reused for non-dev, and
+        non-dev specs are not reused for dev specs)
+        Tests for a spec in which the root is developed and a spec in
+        which a dep is developed."""
+        # dev and non-dev specs that are otherwise identical
+        spec = Spec(spec).normalized()  # ensure dependencies present
+        dev_spec = spec.copy()
+        dev_constraint = 'dev_path=%s' % tmpdir.strpath
+        dev_spec['dev-build-test-install'].constrain(dev_constraint)
+
+        # run the test in both orders
+        first_spec = dev_spec if dev_first else spec
+        second_spec = spec if dev_first else dev_spec
+
+        # concretize and install a non-dev version
+        first_spec.concretize()
+        first_spec.package.do_install(fake=True)
+        # concretize a dev version
+        with spack.config.override("concretizer:reuse", True):
+            second_spec.concretize()
+        assert first_spec.dag_hash() != second_spec.dag_hash()
+
     @pytest.mark.regression('20292')
     @pytest.mark.parametrize('context', [
         {'add_variant': True, 'delete_variant': False},
@@ -1145,7 +1176,7 @@ def test_external_package_versions(self, spec_str, is_external, expected):
         {'add_variant': True, 'delete_variant': True}
     ])
     @pytest.mark.xfail()
-    def test_reuse_installed_packages(
+    def test_reuse_installed_packages_when_package_def_changes(
             self, context, mutable_database, repo_with_changing_recipe
     ):
         # Install a spec

lib/spack/spack/test/git_fetch.py

@@ -89,7 +89,8 @@ def test_fetch(type_of_test,
                mock_git_repository,
                config,
                mutable_mock_repo,
-               git_version):
+               git_version,
+               monkeypatch):
     """Tries to:
 
     1. Fetch the repo using a fetch strategy constructed with
@@ -107,7 +108,7 @@ def test_fetch(type_of_test,
     spec = Spec('git-test')
     spec.concretize()
     pkg = spack.repo.get(spec)
-    pkg.versions[ver('git')] = t.args
+    monkeypatch.setitem(pkg.versions, ver('git'), t.args)
 
     # Enter the stage directory and check some properties
     with pkg.stage:
@@ -137,7 +138,9 @@ def test_fetch(type_of_test,
 
 
 @pytest.mark.parametrize("type_of_test", ['branch', 'commit'])
-def test_debug_fetch(mock_packages, type_of_test, mock_git_repository, config):
+def test_debug_fetch(
+        mock_packages, type_of_test, mock_git_repository, config, monkeypatch
+):
     """Fetch the repo with debug enabled."""
     # Retrieve the right test parameters
     t = mock_git_repository.checks[type_of_test]
@@ -146,7 +149,7 @@ def test_debug_fetch(mock_packages, type_of_test, mock_git_repository, config):
     spec = Spec('git-test')
     spec.concretize()
     pkg = spack.repo.get(spec)
-    pkg.versions[ver('git')] = t.args
+    monkeypatch.setitem(pkg.versions, ver('git'), t.args)
 
     # Fetch then ensure source path exists
     with pkg.stage:
@@ -176,7 +179,7 @@ def test_needs_stage():
 
 @pytest.mark.parametrize("get_full_repo", [True, False])
 def test_get_full_repo(get_full_repo, git_version, mock_git_repository,
-                       config, mutable_mock_repo):
+                       config, mutable_mock_repo, monkeypatch):
     """Ensure that we can clone a full repository."""
 
     if git_version < ver('1.7.1'):
@@ -193,7 +196,7 @@ def test_get_full_repo(get_full_repo, git_version, mock_git_repository,
     pkg = spack.repo.get(spec)
     args = copy.copy(t.args)
     args['get_full_repo'] = get_full_repo
-    pkg.versions[ver('git')] = args
+    monkeypatch.setitem(pkg.versions, ver('git'), args)
 
     with pkg.stage:
         with spack.config.override('config:verify_ssl', secure):
@@ -222,7 +225,7 @@ def test_get_full_repo(get_full_repo, git_version, mock_git_repository,
 @pytest.mark.disable_clean_stage_check
 @pytest.mark.parametrize("submodules", [True, False])
 def test_gitsubmodule(submodules, mock_git_repository, config,
-                      mutable_mock_repo):
+                      mutable_mock_repo, monkeypatch):
     """
     Test GitFetchStrategy behavior with submodules
     """
@@ -235,7 +238,7 @@ def test_gitsubmodule(submodules, mock_git_repository, config,
     pkg = spack.repo.get(spec)
     args = copy.copy(t.args)
     args['submodules'] = submodules
-    pkg.versions[ver('git')] = args
+    monkeypatch.setitem(pkg.versions, ver('git'), args)
     pkg.do_stage()
     with working_dir(pkg.stage.source_path):
         for submodule_count in range(2):
@@ -249,7 +252,9 @@ def test_gitsubmodule(submodules, mock_git_repository, config,
 
 
 @pytest.mark.disable_clean_stage_check
-def test_gitsubmodules_delete(mock_git_repository, config, mutable_mock_repo):
+def test_gitsubmodules_delete(
+        mock_git_repository, config, mutable_mock_repo, monkeypatch
+):
     """
     Test GitFetchStrategy behavior with submodules_delete
     """
@@ -264,7 +269,7 @@ def test_gitsubmodules_delete(mock_git_repository, config, mutable_mock_repo):
     args['submodules'] = True
     args['submodules_delete'] = ['third_party/submodule0',
                                  'third_party/submodule1']
-    pkg.versions[ver('git')] = args
+    monkeypatch.setitem(pkg.versions, ver('git'), args)
     pkg.do_stage()
     with working_dir(pkg.stage.source_path):
         file_path = os.path.join(pkg.stage.source_path,

lib/spack/spack/test/hg_fetch.py

@@ -28,7 +28,8 @@ def test_fetch(
         secure,
         mock_hg_repository,
         config,
-        mutable_mock_repo
+        mutable_mock_repo,
+        monkeypatch
 ):
     """Tries to:
 
@@ -47,7 +48,7 @@ def test_fetch(
     spec = Spec('hg-test')
     spec.concretize()
     pkg = spack.repo.get(spec)
-    pkg.versions[ver('hg')] = t.args
+    monkeypatch.setitem(pkg.versions, ver('hg'), t.args)
 
     # Enter the stage directory and check some properties
     with pkg.stage:

lib/spack/spack/test/install.py

@@ -151,7 +151,9 @@ def test_failing_overwrite_install_should_keep_previous_installation(
     assert os.path.exists(spec.prefix)
 
 
-def test_dont_add_patches_to_installed_package(install_mockery, mock_fetch):
+def test_dont_add_patches_to_installed_package(
+        install_mockery, mock_fetch, monkeypatch
+):
     dependency = Spec('dependency-install')
     dependency.concretize()
     dependency.package.do_install()
@@ -160,9 +162,11 @@ def test_dont_add_patches_to_installed_package(install_mockery, mock_fetch):
     dependent = Spec('dependent-install ^/' + dependency_hash)
     dependent.concretize()
 
-    dependency.package.patches['dependency-install'] = [
+    monkeypatch.setitem(dependency.package.patches, 'dependency-install', [
         spack.patch.UrlPatch(
-            dependent.package, 'file://fake.patch', sha256='unused-hash')]
+            dependent.package, 'file://fake.patch', sha256='unused-hash'
+        )
+    ])
 
     assert dependent['dependency-install'] == dependency
 
@@ -308,52 +312,43 @@ def test_installed_upstream(install_upstream, mock_fetch):
 
 
 @pytest.mark.disable_clean_stage_check
-def test_partial_install_keep_prefix(install_mockery, mock_fetch):
+def test_partial_install_keep_prefix(install_mockery, mock_fetch, monkeypatch):
     spec = Spec('canfail').concretized()
     pkg = spack.repo.get(spec)
 
     # Normally the stage should start unset, but other tests set it
     pkg._stage = None
-    remove_prefix = spack.package.Package.remove_prefix
-    try:
-        # If remove_prefix is called at any point in this test, that is an
-        # error
-        pkg.succeed = False  # make the build fail
-        spack.package.Package.remove_prefix = mock_remove_prefix
-        with pytest.raises(spack.build_environment.ChildError):
-            pkg.do_install(keep_prefix=True)
-        assert os.path.exists(pkg.prefix)
 
-        # must clear failure markings for the package before re-installing it
-        spack.store.db.clear_failure(spec, True)
-
-        pkg.succeed = True   # make the build succeed
-        pkg.stage = MockStage(pkg.stage)
+    # If remove_prefix is called at any point in this test, that is an
+    # error
+    pkg.succeed = False  # make the build fail
+    monkeypatch.setattr(spack.package.Package, 'remove_prefix', mock_remove_prefix)
+    with pytest.raises(spack.build_environment.ChildError):
         pkg.do_install(keep_prefix=True)
-        assert pkg.installed
-        assert not pkg.stage.test_destroyed
+    assert os.path.exists(pkg.prefix)
 
-    finally:
-        spack.package.Package.remove_prefix = remove_prefix
+    # must clear failure markings for the package before re-installing it
+    spack.store.db.clear_failure(spec, True)
+
+    pkg.succeed = True   # make the build succeed
+    pkg.stage = MockStage(pkg.stage)
+    pkg.do_install(keep_prefix=True)
+    assert pkg.installed
+    assert not pkg.stage.test_destroyed
 
 
-def test_second_install_no_overwrite_first(install_mockery, mock_fetch):
+def test_second_install_no_overwrite_first(install_mockery, mock_fetch, monkeypatch):
     spec = Spec('canfail').concretized()
     pkg = spack.repo.get(spec)
-    remove_prefix = spack.package.Package.remove_prefix
-    try:
-        spack.package.Package.remove_prefix = mock_remove_prefix
+    monkeypatch.setattr(spack.package.Package, 'remove_prefix', mock_remove_prefix)
 
-        pkg.succeed = True
-        pkg.do_install()
-        assert pkg.installed
+    pkg.succeed = True
+    pkg.do_install()
+    assert pkg.installed
 
-        # If Package.install is called after this point, it will fail
-        pkg.succeed = False
-        pkg.do_install()
-
-    finally:
-        spack.package.Package.remove_prefix = remove_prefix
+    # If Package.install is called after this point, it will fail
+    pkg.succeed = False
+    pkg.do_install()
 
 
 def test_install_prefix_collision_fails(config, mock_fetch, mock_packages, tmpdir):

lib/spack/spack/test/repo.py

@@ -86,3 +86,15 @@ def test_namespace_hasattr(attr_name, exists, mutable_mock_repo):
 def test_all_package_names_is_cached_correctly():
     assert 'mpi' in spack.repo.all_package_names(include_virtuals=True)
     assert 'mpi' not in spack.repo.all_package_names(include_virtuals=False)
+
+
+@pytest.mark.regression('29203')
+def test_use_repositories_doesnt_change_class():
+    """Test that we don't create the same package module and class multiple times
+    when swapping repositories.
+    """
+    zlib_cls_outer = spack.repo.path.get_pkg_class('zlib')
+    current_paths = [r.root for r in spack.repo.path.repos]
+    with spack.repo.use_repositories(*current_paths):
+        zlib_cls_inner = spack.repo.path.get_pkg_class('zlib')
+    assert id(zlib_cls_inner) == id(zlib_cls_outer)

lib/spack/spack/test/spec_dag.py

@@ -31,7 +31,7 @@ def saved_deps():
 
 
 @pytest.fixture()
-def set_dependency(saved_deps):
+def set_dependency(saved_deps, monkeypatch):
     """Returns a function that alters the dependency information
     for a package in the ``saved_deps`` fixture.
     """
@@ -48,7 +48,7 @@ def _mock(pkg_name, spec, deptypes=all_deptypes):
 
         cond = Spec(pkg.name)
         dependency = Dependency(pkg, spec, type=deptypes)
-        pkg.dependencies[spec.name] = {cond: dependency}
+        monkeypatch.setitem(pkg.dependencies, spec.name, {cond: dependency})
     return _mock
 
 

lib/spack/spack/test/svn_fetch.py

@@ -29,7 +29,8 @@ def test_fetch(
         secure,
         mock_svn_repository,
         config,
-        mutable_mock_repo
+        mutable_mock_repo,
+        monkeypatch
 ):
     """Tries to:
 
@@ -48,7 +49,7 @@ def test_fetch(
     spec = Spec('svn-test')
     spec.concretize()
     pkg = spack.repo.get(spec)
-    pkg.versions[ver('svn')] = t.args
+    monkeypatch.setitem(pkg.versions, ver('svn'), t.args)
 
     # Enter the stage directory and check some properties
     with pkg.stage:

lib/spack/spack/test/versions.py

@@ -630,6 +630,14 @@ def test_version_wrong_idx_type():
         v['0:']
 
 
+@pytest.mark.regression('29170')
+def test_version_range_satisfies_means_nonempty_intersection():
+    x = VersionRange('3.7.0', '3')
+    y = VersionRange('3.6.0', '3.6.0')
+    assert not x.satisfies(y)
+    assert not y.satisfies(x)
+
+
 @pytest.mark.regression('26482')
 def test_version_list_with_range_included_in_concrete_version_interpreted_as_range():
     # Note: this test only tests whether we can construct a version list of a range

lib/spack/spack/version.py

@@ -167,7 +167,7 @@ def __gt__(self, other):
 
 class Version(object):
     """Class to represent versions"""
-    __slots__ = ['version', 'separators', 'string', 'commit_lookup']
+    __slots__ = ['version', 'separators', 'string', 'is_commit', 'commit_lookup']
 
     def __init__(self, string):
         if not isinstance(string, str):
@@ -189,6 +189,8 @@ def __init__(self, string):
         )
         self.separators = tuple(m[2] for m in segments)
 
+        self.is_commit = len(self.string) == 40 and COMMIT_VERSION.match(self.string)
+
     def _cmp(self, other_lookups=None):
         commit_lookup = self.commit_lookup or other_lookups
 
@@ -205,15 +207,6 @@ def _cmp(self, other_lookups=None):
 
         return self.version
 
-    @property
-    def is_commit(self):
-        """
-        Determine if the original string is referencing a commit.
-        """
-        if self.string in infinity_versions:
-            return False
-        return COMMIT_VERSION.match(self.string) is not None
-
     @property
     def dotted(self):
         """The dotted representation of the version.
@@ -586,35 +579,23 @@ def __contains__(self, other):
 
     @coerced
     def satisfies(self, other):
-        """A VersionRange satisfies another if some version in this range
-        would satisfy some version in the other range.  To do this it must
-        either:
-
-        a) Overlap with the other range
-        b) The start of this range satisfies the end of the other range.
-
-        This is essentially the same as overlaps(), but overlaps assumes
-        that its arguments are specific.  That is, 4.7 is interpreted as
-        4.7.0.0.0.0... .  This function assumes that 4.7 would be satisfied
-        by 4.7.3.5, etc.
-
-        Rationale:
-
-        If a user asks for gcc@4.5:4.7, and a package is only compatible with
-        gcc@4.7.3:4.8, then that package should be able to build under the
-        constraints.  Just using overlaps() would not work here.
-
-        Note that we don't need to check whether the end of this range
-        would satisfy the start of the other range, because overlaps()
-        already covers that case.
-
-        Note further that overlaps() is a symmetric operation, while
-        satisfies() is not.
         """
-        return (self.overlaps(other) or
-                # if either self.start or other.end are None, then this can't
-                # satisfy, or overlaps() would've taken care of it.
-                self.start and other.end and self.start.satisfies(other.end))
+        x.satisfies(y) in general means that x and y have a
+        non-zero intersection. For VersionRange this means they overlap.
+
+        `satisfies` is a commutative binary operator, meaning that
+        x.satisfies(y) if and only if y.satisfies(x).
+
+        Note: in some cases we have the keyword x.satisfies(y, strict=True)
+        to mean strict set inclusion, which is not commutative. However, this
+        lacks in VersionRange for unknown reasons.
+
+        Examples
+        - 1:3 satisfies 2:4, as their intersection is 2:3.
+        - 1:2 does not satisfy 3:4, as their intersection is empty.
+        - 4.5:4.7 satisfies 4.7.2:4.8, as their intersection is 4.7.2:4.7
+        """
+        return self.overlaps(other)
 
     @coerced
     def overlaps(self, other):

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

@@ -33,8 +33,6 @@ spack:
       variants: +bzip2 ~nls +xz
     hdf5:
       variants: +fortran +hl +shared
-      version:
-        - 1.10.7
     libfabric:
       variants: fabrics=sockets,tcp,udp,rxm
     libunwind:

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

@@ -12,7 +12,7 @@ class Amrex(CMakePackage, CudaPackage, ROCmPackage):
     mesh refinement (AMR) applications."""
 
     homepage = "https://amrex-codes.github.io/amrex/"
-    url      = "https://github.com/AMReX-Codes/amrex/releases/download/22.02/amrex-22.02.tar.gz"
+    url      = "https://github.com/AMReX-Codes/amrex/releases/download/22.03/amrex-22.03.tar.gz"
     git      = "https://github.com/AMReX-Codes/amrex.git"
 
     test_requires_compiler = True
@@ -22,6 +22,7 @@ class Amrex(CMakePackage, CudaPackage, ROCmPackage):
     maintainers = ['WeiqunZhang', 'asalmgren', 'etpalmer63']
 
     version('develop', branch='development')
+    version('22.03', sha256='2a67233e55f20b937e2da97f1ed3ab0666e12ef283b4d14c9456ebf21f36b77c')
     version('22.02', sha256='5d8dd3fa3c416b04e70188e06b7e8fc2838d78b43a2cf33a285184c77f0c1e1e')
     version('22.01', sha256='857df5b2fa8e3010b8856b81879a5be32ba7cc2e575474256eae7ef815b8354d')
     version('21.12', sha256='439f9ebf2b440fc739a7976f3ade188ec3e1de5f51a0b151e6b8dda36fa67278')

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

@@ -20,7 +20,7 @@ class Apfel(AutotoolsPackage):
     version('3.0.4', sha256='c7bfae7fe2dc0185981850f2fe6ae4842749339d064c25bf525b4ef412bbb224')
 
     depends_on('swig', when='+python')
-    depends_on('python', when='+python', type=('build', 'run'))
+    depends_on('python', type=('build', 'run'))
     depends_on('lhapdf', when='+lhapdf', type=('build', 'run'))
 
     variant('python', description='Build python wrapper', default=False)

var/spack/repos/builtin/packages/aws-parallelcluster/package.py

@@ -13,12 +13,13 @@ class AwsParallelcluster(PythonPackage):
     tool to deploy and manage HPC clusters in the AWS cloud."""
 
     homepage = "https://github.com/aws/aws-parallelcluster"
-    pypi = "aws-parallelcluster/aws-parallelcluster-2.11.4.tar.gz"
+    pypi = "aws-parallelcluster/aws-parallelcluster-2.11.5.tar.gz"
 
     maintainers = [
         'demartinofra', 'enrico-usai', 'lukeseawalker',
     ]
 
+    version('2.11.5', sha256='7499f88387cbe2cb73f9fddeee3363117f7ef1524d6a73e77bb07900040baebb')
     version('2.11.4', sha256='449537ccda57f91f4ec6ae0c94a8e2b1a789f08f80245fadb28f44a4351d5da4')
     version('2.11.3', sha256='7c1d74123f2f670846aed8fe1fcca5908bb46ec014e2dfc7d3ec8994447a37a0')
     version('2.11.2', sha256='60d96a5ea4dca4816ceffc4546549743abd1f6207c62f016c9c348adc64b2ec0')

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

@@ -98,9 +98,6 @@ class Axom(CachedCMakePackage, CudaPackage):
     depends_on("conduit+hdf5", when="+hdf5")
     depends_on("conduit~hdf5", when="~hdf5")
 
-    # HDF5 needs to be the same as Conduit's
-    depends_on("hdf5@1.8.19:1.8~cxx~fortran", when="+hdf5")
-
     depends_on("lua", when="+lua")
 
     depends_on("scr", when="+scr")

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

@@ -23,6 +23,7 @@ class Blt(Package):
     #  if you export targets this could cause problems in downstream
     #  projects if not handled properly. More info here:
     #  https://llnl-blt.readthedocs.io/en/develop/tutorial/exporting_targets.html
+    version('0.5.0', sha256='5f680ef922d0e0a7ff1b1a5fc8aa107cd4f543ad888cbc9b12639bea72a6ab1f')
     version('0.4.1', sha256='16cc3e067ddcf48b99358107e5035a17549f52dcc701a35cd18a9d9f536826c1')
     version('0.4.0', sha256='f3bc45d28b9b2eb6df43b75d4f6f89a1557d73d012da7b75bac1be0574767193')
     version('0.3.6', sha256='6276317c29e7ff8524fbea47d9288ddb40ac06e9f9da5e878bf9011e2c99bf71')

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

@@ -5,6 +5,8 @@
 
 import os
 
+from llnl.util import tty
+
 from spack import *
 
 
@@ -57,19 +59,19 @@ def run_sample_nested_example(self):
         """Run stand alone test: sample_nested"""
 
         test_dir = join_path(self.test_suite.current_test_cache_dir, 'examples')
+        exe = 'sample_nested'
+        source_file = 'sample_nested.c'
 
-        if not os.path.exists(test_dir):
-            print('Skipping bolt test')
+        if not os.path.isfile(join_path(test_dir, source_file)):
+            tty.warn('Skipping bolt test:'
+                     '{0} does not exist'.format(source_file))
             return
 
-        exe = 'sample_nested'
-
-        # TODO: Either change to use self.compiler.cc (so using the build-time compiler)
-        #  or add test parts that compile with the different supported compilers.
-        self.run_test('gcc',
-                      options=['-lomp', '-o', exe,
-                               '-L{0}'.format(join_path(self.prefix, 'lib')),
-                               '{0}'.format(join_path(test_dir, 'sample_nested.c'))],
+        self.run_test(exe=os.environ['CXX'],
+                      options=['-L{0}'.format(self.prefix.lib),
+                               '-I{0}'.format(self.prefix.include),
+                               '{0}'.format(join_path(test_dir, source_file)),
+                               '-o', exe, '-lomp', '-lbolt'],
                       purpose='test: compile {0} example'.format(exe),
                       work_dir=test_dir)
 
@@ -78,5 +80,4 @@ def run_sample_nested_example(self):
                       work_dir=test_dir)
 
     def test(self):
-        print("Running bolt test")
         self.run_sample_nested_example()

var/spack/repos/builtin/packages/boost/fujitsu_version_analysis-1.77.patch

@@ -0,0 +1,11 @@
+--- spack-src/tools/build/src/tools/clang-linux.jam.orig	2022-02-22 09:51:17.000000000 +0900
++++ spack-src/tools/build/src/tools/clang-linux.jam	2022-02-22 11:22:58.000000000 +0900
+@@ -97,7 +97,7 @@
+ 
+ rule get-full-version ( command-string )
+ {
+-    return [ common.match-command-output version : "version ([0-9.]+)"
++    return [ common.match-command-output version : "LLVM ([0-9.]+)"
+            : "$(command-string) --version" ] ;
+ }
+ 

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

@@ -261,7 +261,8 @@ def libs(self):
           working_dir='libs/system', level=1)
 
     # Change the method for version analysis when using Fujitsu compiler.
-    patch('fujitsu_version_analysis.patch', when='@1.67.0:%fj')
+    patch('fujitsu_version_analysis.patch', when='@1.67.0:1.76.0%fj')
+    patch('fujitsu_version_analysis-1.77.patch', when='@1.77.0:%fj')
 
     # Add option to C/C++ compile commands in clang-linux.jam
     patch('clang-linux_add_option.patch', when='@1.56.0:1.63.0')

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

@@ -22,10 +22,11 @@ class Butterflypack(CMakePackage):
 
     homepage = "https://github.com/liuyangzhuan/ButterflyPACK"
     git      = "https://github.com/liuyangzhuan/ButterflyPACK.git"
-    url      = "https://github.com/liuyangzhuan/ButterflyPACK/archive/v2.1.0.tar.gz"
+    url      = "https://github.com/liuyangzhuan/ButterflyPACK/archive/v2.1.1.tar.gz"
     maintainers = ['liuyangzhuan']
 
     version('master', branch='master')
+    version('2.1.1', sha256='0d4a1ce540c84de37e4398f72ecf685ea0c4eabceba13015add5b445a4ca3a15')
     version('2.1.0', sha256='ac76cc8d431797c1a3641b23124e3de5eb8c3a3afb71c336e7ba69c6cdf150ef')
     version('2.0.0', sha256='84f0e5ac40997409f3c80324238a07f9c700a1263b84140ed97275d67b577b80')
     version('1.2.1', sha256='cd61b0e033f55a932f13d9902e28a7abbf029c279cec9ab1b2a063525d036fa2')

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

@@ -94,9 +94,7 @@ class Charmpp(Package):
     # Other options
     variant("papi", default=False, description="Enable PAPI integration")
     variant("syncft", default=False, description="Compile with Charm++ fault tolerance support")
-    variant("smp", default=True,
-            description=(
-                "Enable SMP parallelism (does not work with +multicore)"))
+    variant("smp", default=True, description="Enable SMP parallelism")
     variant("tcp", default=False,
             description="Use TCP as transport mechanism (requires +net)")
     variant("omp", default=False, description="Support for the integrated LLVM OpenMP runtime")
@@ -134,7 +132,8 @@ class Charmpp(Package):
 
     conflicts("~tracing", "+papi")
 
-    conflicts("backend=multicore", "+smp")
+    conflicts("backend=multicore", when="~smp",
+              msg="The 'multicore' backend always uses SMP")
     conflicts("backend=ucx", when="@:6.9")
 
     # Shared-lib builds with GCC are broken on macOS:
@@ -299,7 +298,11 @@ def install(self, spec, prefix):
             options.extend(["--basedir=%s" % spec["ucx"].prefix])
         if "+papi" in spec:
             options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
-        if "+smp" in spec:
+        if "+smp" in spec and 'backend=multicore' not in spec:
+            # The 'multicore' backend always uses SMP, so we don't have to
+            # append the 'smp' option when the 'multicore' backend is active. As
+            # of Charm++ v7.0.0 it is actually a build error to append 'smp'
+            # with the 'multicore' backend.
             options.append("smp")
         if "+tcp" in spec:
             if 'backend=netlrts' not in spec:

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

@@ -77,6 +77,8 @@ class Conduit(CMakePackage):
     # set to false for systems that implicitly link mpi
     variant('blt_find_mpi', default=True, description='Use BLT CMake Find MPI logic')
     variant("hdf5", default=True, description="Build Conduit HDF5 support")
+    # TODO: remove 'compat' variant when VisIt starts distributing HDF5
+    # binaries
     variant("hdf5_compat", default=True, when='+hdf5',
             description="Build Conduit with HDF5 1.8.x (compatibility mode)")
     variant("silo", default=False, description="Build Conduit Silo support")
@@ -117,26 +119,18 @@ class Conduit(CMakePackage):
     ###############
     # HDF5
     ###############
-    # Note: cxx variant is disabled due to build issue Cyrus
-    # experienced on BGQ. When on, the static build tries
-    # to link against shared libs.
-    #
-    # Use HDF5 1.8, for wider output compatibly
-    # variants reflect we are not using hdf5's mpi or fortran features.
-    depends_on("hdf5~cxx", when="+hdf5")
-    depends_on("hdf5~shared", when="+hdf5~shared")
-    depends_on("hdf5@1.8.19:1.8", when="+hdf5+hdf5_compat")
 
-    # we need to hand this to conduit so it can properly
-    # handle downstream linking of zlib reqed by hdf5
-    depends_on("zlib", when="+hdf5")
+    depends_on("hdf5", when="+hdf5")
+    depends_on("hdf5~shared", when="+hdf5~shared")
+    # Require older HDF5 to ensure compatibility with VisIt: see #29132
+    depends_on("hdf5@1.8.0:1.8", when="+hdf5+hdf5_compat")
 
     ###############
     # Silo
     ###############
     # we are not using silo's fortran features
-    depends_on("silo~fortran", when="+silo+shared")
-    depends_on("silo~shared~fortran", when="+silo~shared")
+    depends_on("silo+shared", when="+silo+shared")
+    depends_on("silo~shared", when="+silo~shared")
 
     ###############
     # ADIOS
@@ -528,7 +522,9 @@ def hostconfig(self, spec, prefix):
 
         if "+hdf5" in spec:
             cfg.write(cmake_cache_entry("HDF5_DIR", spec['hdf5'].prefix))
-            cfg.write(cmake_cache_entry("ZLIB_DIR", spec['zlib'].prefix))
+            if 'zlib' in spec:
+                # HDF5 depends on zlib
+                cfg.write(cmake_cache_entry("ZLIB_DIR", spec['zlib'].prefix))
         else:
             cfg.write("# hdf5 not built by spack \n")
 

var/spack/repos/builtin/packages/cp2k/package.py

@@ -83,7 +83,12 @@ class Cp2k(MakefilePackage, CudaPackage):
     with when('+openmp'):
         depends_on('fftw+openmp', when='^fftw')
         depends_on('amdfftw+openmp', when='^amdfftw')
+        depends_on('cray-fftw+openmp', when='^cray-fftw')
         depends_on('openblas threads=openmp', when='^openblas')
+        # The Cray compiler wrappers will automatically add libsci_mp with
+        # -fopenmp. Since CP2K unconditionally links blas/lapack/scalapack
+        # we have to be consistent.
+        depends_on('cray-libsci+openmp', when='^cray-libsci')
 
     with when('smm=libxsmm'):
         depends_on('libxsmm@1.17:~header-only', when='@9.1:')

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

@@ -30,7 +30,7 @@ class CrayLibsci(Package):
 
     provides("blas")
     provides("lapack")
-    provides("scalapack")
+    provides("scalapack", when="+mpi")
 
     canonical_names = {
         'gcc': 'GNU',

var/spack/repos/builtin/packages/dos2unix/package.py

@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import re
+
 from spack import *
 
 
@@ -19,6 +21,8 @@ class Dos2unix(MakefilePackage):
 
     depends_on('gettext')
 
+    executables = [r'^dos2unix$']
+
     @property
     def build_targets(self):
         targets = [
@@ -29,3 +33,9 @@ def build_targets(self):
 
     def install(self, spec, prefix):
         make('prefix={0}'.format(prefix), 'install')
+
+    @classmethod
+    def determine_version(cls, exe):
+        output = Executable(exe)('--version', output=str, error=str)
+        match = re.search(r'^dos2unix\s+([\d\.]+)', output)
+        return match.group(1) if match else None

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

@@ -35,6 +35,8 @@ class Edm4hep(CMakePackage):
     depends_on('root@6.08:')
     depends_on('podio@0.14:', when='@0.4:')
     depends_on('podio@0.13.0:0.13', when='@:0.3')
+    depends_on('py-jinja2', type='build')
+    depends_on('py-pyyaml', type='build')
 
     depends_on('hepmc@:2', type='test', when='@:0.4.0')
     depends_on('hepmc3', type='test', when='@0.4.1:')

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

@@ -39,6 +39,10 @@ class Eigen(CMakePackage):
     patch('https://gitlab.com/libeigen/eigen/-/commit/6d822a1052fc665f06dc51b4729f6a38e0da0546.diff', when='@3.3.8',
           sha256='62590e9b33a8f72b608a72b87147a306e7cb20766ea53c6b8e0a183fa6cb7635')
 
+    # there is a bug in 3.3.4 that provokes a compile error with the xl compiler
+    # See https://gitlab.com/libeigen/eigen/-/issues/1555
+    patch('xlc-compilation-3.3.4.patch', when='@3.3.4%xl_r')
+
     # From http://eigen.tuxfamily.org/index.php?title=Main_Page#Requirements
     # "Eigen doesn't have any dependencies other than the C++ standard
     # library."

var/spack/repos/builtin/packages/eigen/xlc-compilation-3.3.4.patch

@@ -0,0 +1,12 @@
+diff -up /Eigen/src/Core/arch/AltiVec/PacketMath.h /Eigen/src/Core/arch/AltiVec/PacketMath.h
+--- /Eigen/src/Core/arch/AltiVec/PacketMath.h
++++ /Eigen/src/Core/arch/AltiVec/PacketMath.h
+@@ -1022,7 +1022,7 @@ ptranspose(PacketBlock<Packet2d,2>& kern
+ 
+ template<> EIGEN_STRONG_INLINE Packet2d pblend(const Selector<2>& ifPacket, const Packet2d& thenPacket, const Packet2d& elsePacket) {
+   Packet2l select = { ifPacket.select[0], ifPacket.select[1] };
+-  Packet2bl mask = vec_cmpeq(reinterpret_cast<Packet2d>(select), reinterpret_cast<Packet2d>(p2l_ONE));
++  Packet2bl mask = reinterpret_cast<Packet2bl>( vec_cmpeq(reinterpret_cast<Packet2d>(select), reinterpret_cast<Packet2d>(p2l_ONE)) );
+   return vec_sel(elsePacket, thenPacket, mask);
+ }
+ #endif // __VSX__

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

@@ -18,6 +18,8 @@ class Esmf(MakefilePackage):
     homepage = "https://www.earthsystemcog.org/projects/esmf/"
     url = 'https://github.com/esmf-org/esmf/archive/ESMF_8_0_1.tar.gz'
 
+    maintainers = ['climbfuji']
+
     version('8.2.0',  sha256='3693987aba2c8ae8af67a0e222bea4099a48afe09b8d3d334106f9d7fc311485')
     version('8.1.1',  sha256='58c2e739356f21a1b32673aa17a713d3c4af9d45d572f4ba9168c357d586dc75')
     version('8.0.1',  sha256='9172fb73f3fe95c8188d889ee72fdadb4f978b1d969e1d8e401e8d106def1d84')
@@ -126,10 +128,14 @@ def edit(self, spec, prefix):
         # C++ compilers are being used to build the ESMF library.
         if self.compiler.name == 'gcc':
             os.environ['ESMF_COMPILER'] = 'gfortran'
+            gfortran_major_version = int(spack.compiler.get_compiler_version_output(
+                self.compiler.fc, '-dumpversion').split('.')[0])
         elif self.compiler.name == 'intel':
             os.environ['ESMF_COMPILER'] = 'intel'
-        elif self.compiler.name == 'clang':
+        elif self.compiler.name in ['clang', 'apple-clang']:
             os.environ['ESMF_COMPILER'] = 'gfortranclang'
+            gfortran_major_version = int(spack.compiler.get_compiler_version_output(
+                self.compiler.fc, '-dumpversion').split('.')[0])
         elif self.compiler.name == 'nag':
             os.environ['ESMF_COMPILER'] = 'nag'
         elif self.compiler.name == 'pgi':
@@ -154,9 +160,18 @@ def edit(self, spec, prefix):
             # Build an optimized version of the library.
             os.environ['ESMF_BOPT'] = 'O'
 
-        if self.spec.satisfies('%gcc@10:'):
+        if self.compiler.name in ['gcc', 'clang', 'apple-clang'] and \
+                gfortran_major_version >= 10:
             os.environ['ESMF_F90COMPILEOPTS'] = '-fallow-argument-mismatch'
 
+        #######
+        # OS  #
+        #######
+
+        # ESMF_OS must be set for Cray systems
+        if 'platform=cray' in self.spec:
+            os.environ['ESMF_OS'] = 'Unicos'
+
         #######
         # MPI #
         #######
@@ -276,3 +291,9 @@ def edit(self, spec, prefix):
 
     def check(self):
         make('check', parallel=False)
+
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        env.set('ESMFMKFILE', os.path.join(self.prefix.lib, 'esmf.mk'))
+
+    def setup_run_environment(self, env):
+        env.set('ESMFMKFILE', os.path.join(self.prefix.lib, 'esmf.mk'))

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

@@ -37,7 +37,7 @@ def patch(self):
     def configure_args(self):
         args = ['--with-boost={0}'.format(self.spec['boost'].prefix)]
 
-        if self.spec.satisfies('polatform=darwin'):
+        if self.spec.satisfies('platform=darwin'):
             args += ['--with-darwinports', '--with-fink']
 
         return args

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

@@ -14,6 +14,8 @@ class Fmt(CMakePackage):
     homepage = "https://fmt.dev/"
     url      = "https://github.com/fmtlib/fmt/releases/download/7.1.3/fmt-7.1.3.zip"
 
+    version('8.1.1', sha256='23778bad8edba12d76e4075da06db591f3b0e3c6c04928ced4a7282ca3400e5d')
+    version('8.1.0', sha256='d8e9f093b2241c3a9fc3895e23231ef9de00c762cfa0a9c65e4748755bc352ae')
     version('8.0.1', sha256='a627a56eab9554fc1e5dd9a623d0768583b3a383ff70a4312ba68f94c9d415bf')
     version('7.1.3', sha256='5d98c504d0205f912e22449ecdea776b78ce0bb096927334f80781e720084c9f')
     version('7.1.2', sha256='4d6968ab7c01e95cc76df136755703defb985105a117b83057e4fd5d53680ea7')

var/spack/repos/builtin/packages/git-lfs/package.py

@@ -20,6 +20,11 @@ class GitLfs(MakefilePackage):
 
     executables = ['^git-lfs$']
 
+    maintainers = ['sethrj']
+
+    version('3.1.2', sha256='5c9bc449068d0104ea124c25f596af16da85e7b5bf256bc544d8ce5f4fe231f2')
+    version('2.13.3', sha256='f8bd7a06e61e47417eb54c3a0db809ea864a9322629b5544b78661edab17b950')
+    version('2.12.1', sha256='2b2e70f1233f7efe9a010771510391a07527ec7c0af721ecf8edabac5d60f62b')
     version('2.11.0', sha256='8183c4cbef8cf9c2e86b0c0a9822451e2df272f89ceb357c498bfdf0ff1b36c7')
     version('2.10.0', sha256='07fd5c57a1039d5717dc192affbe3268ec2fd03accdca462cb504c0b4194cd23')
     version('2.9.0', sha256='f1963ad88747577ffeeb854649aeacaa741c59be74683da4d46b129a72d111b7')
@@ -29,11 +34,16 @@ class GitLfs(MakefilePackage):
     version('2.7.0', sha256='1c829ddd163be2206a44edb366bd7f6d84c5afae3496687405ca9d2a5f3af07b')
     version('2.6.1', sha256='e17cd9d4e66d1116be32f7ddc7e660c7f8fabbf510bc01b01ec15a22dd934ead')
 
-    depends_on('go@1.5:', type='build')
+    depends_on('go@1.17:', type='build', when='@2.13:')
+    depends_on('go@1.5:', type='build', when='@:2.12')
     depends_on('git@1.8.2:', type='run')
 
     patch('patches/issue-10702.patch', when='@2.7.0:2.7.1')
 
+    # Mysterious syscall failures of old versions on new systems
+    conflicts('os=bigsur', when='@:2.11')
+    conflicts('os=monterey', when='@:2.11')
+
     parallel = False
 
     @classmethod

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

@@ -14,6 +14,7 @@ class Gmp(AutotoolsPackage, GNUMirrorPackage):
     gnu_mirror_path = "gmp/gmp-6.1.2.tar.bz2"
 
     version('6.2.1', sha256='eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c')
+    version('6.2.0', sha256='f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea')
     version('6.1.2',  sha256='5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2')
     version('6.1.1',  sha256='a8109865f2893f1373b0a8ed5ff7429de8db696fc451b1036bd7bdf95bbeffd6')
     version('6.1.0',  sha256='498449a994efeba527885c10405993427995d3f86b8768d8cdf8d9dd7c6b73e8')

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

@@ -42,10 +42,11 @@ class Go(Package):
 
     maintainers = ['alecbcs']
 
-    version('1.17.3',  sha256='705c64251e5b25d5d55ede1039c6aa22bea40a7a931d14c370339853643c3df0')
-    version('1.17.2',  sha256='2255eb3e4e824dd7d5fcdc2e7f84534371c186312e546fb1086a34c17752f431')
-    version('1.17.1',  sha256='49dc08339770acd5613312db8c141eaf61779995577b89d93b541ef83067e5b1')
-    version('1.17',    sha256='3a70e5055509f347c0fb831ca07a2bf3b531068f349b14a3c652e9b5b67beb5d')
+    version('1.17.7', sha256='c108cd33b73b1911a02b697741df3dea43e01a5c4e08e409e8b3a0e3745d2b4d')
+    version('1.17.3', sha256='705c64251e5b25d5d55ede1039c6aa22bea40a7a931d14c370339853643c3df0', deprecated=True)
+    version('1.17.2',  sha256='2255eb3e4e824dd7d5fcdc2e7f84534371c186312e546fb1086a34c17752f431', deprecated=True)
+    version('1.17.1',  sha256='49dc08339770acd5613312db8c141eaf61779995577b89d93b541ef83067e5b1', deprecated=True)
+    version('1.17',    sha256='3a70e5055509f347c0fb831ca07a2bf3b531068f349b14a3c652e9b5b67beb5d', deprecated=True)
     version('1.16.10', sha256='a905472011585e403d00d2a41de7ced29b8884309d73482a307f689fd0f320b5')
     version('1.16.9',  sha256='0a1cc7fd7bd20448f71ebed64d846138850d5099b18cf5cc10a4fc45160d8c3d')
     version('1.16.6',  sha256='a3a5d4bc401b51db065e4f93b523347a4d343ae0c0b08a65c3423b05a138037d')

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

@@ -27,7 +27,7 @@ class Groff(AutotoolsPackage, GNUMirrorPackage):
     # See brew scripts for groff for guidance:
     # https://github.com/Homebrew/homebrew-core/blob/master/Formula/groff.rb
     # Seems troublesome...netpbm requires groff?
-    variant('pdf', default=True, description='Build the `gropdf` executable.')
+    variant('pdf', default=False, description='Build the `gropdf` executable.')
     variant('x', default=False, description='Enable set of graphical options')
     variant('uchardet', default=True,
             description='Builds preconv with uchardet library for '

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

@@ -20,11 +20,12 @@ class Gurobi(Package):
     # to set up a mirror, see
     # https://spack.readthedocs.io/en/latest/mirrors.html
 
-    homepage = "https://www.gurobi.com/index"
+    homepage = "https://www.gurobi.com"
     manual_download = True
 
     maintainers = ['glennpj']
 
+    version('9.5.1', sha256='fa82859d33f08fb8aeb9da66b0fbd91718ed573c534f571aa52372c9deb891da')
     version('9.1.2', sha256='7f60bd675f79476bb2b32cd632aa1d470f8246f2b033b7652d8de86f6e7e429b')
     version('7.5.2', '01f6dbb8d165838cca1664a1a14e4a85')
 
@@ -35,9 +36,7 @@ class Gurobi(Package):
     license_url      = 'http://www.gurobi.com/downloads/download-center'
 
     extends('python')
-    depends_on('python@2.7,3.6:', type=('build', 'run'))
-    depends_on('py-pip', type='build')
-    depends_on('py-wheel', type='build')
+    depends_on('python@2.7,3.6:')
 
     def url_for_version(self, version):
         return "file://{0}/gurobi{1}_linux64.tar.gz".format(os.getcwd(), version)
@@ -58,5 +57,5 @@ def install(self, spec, prefix):
     @run_after('install')
     def gurobipy(self):
         with working_dir('linux64'):
-            args = std_pip_args + ['--prefix=' + self.prefix, '.']
-            pip(*args)
+            python = which('python')
+            python('setup.py', 'install', '--prefix={0}'.format(self.prefix))

var/spack/repos/builtin/packages/hdf5/package.py

@@ -108,6 +108,8 @@ class Hdf5(CMakePackage):
     conflicts('+java', when='@:1.9')
     # The Java wrappers cannot be built without shared libs.
     conflicts('+java', when='~shared')
+    # Fortran cannot be built with shared
+    conflicts('+fortran', when='+shared@:1.8')
 
     # There are several officially unsupported combinations of the features:
     # 1. Thread safety is not guaranteed via high-level C-API but in some cases

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

@@ -18,6 +18,7 @@ class Hiop(CMakePackage, CudaPackage, ROCmPackage):
     maintainers = ['ashermancinelli', 'CameronRutherford']
 
     # Most recent tagged snapshot is the preferred version when profiling.
+    version('0.5.4', commit='a37a7a677884e95d1c0ad37936aef3778fc91c3e')
     version('0.5.3', commit='698e8d0fdc0ff9975d8714339ff8c782b70d85f9')
     version('0.5.2', commit='662ad76dee1f501f648a8bec9a490cb5881789e9')
     version('0.5.1', commit='6789bbb55824e68e428c2df1009d647af81f9cf1')
@@ -64,10 +65,16 @@ class Hiop(CMakePackage, CudaPackage, ROCmPackage):
 
     depends_on('magma+cuda', when='+cuda')
     depends_on('magma+rocm', when='+rocm')
-    depends_on('magma@2.5.4:', when='@0.4:+cuda')
-    depends_on('magma@2.6.1:', when='@0.4.6:+cuda')
-    depends_on('magma@2.5.4:', when='@0.4:+rocm')
-    depends_on('magma@2.6.1:', when='@0.4.6:+rocm')
+
+    # Depends on Magma when +rocm or +cuda
+    magma_ver_constraints = (
+        ('2.5.4', '0.4'),
+        ('2.6.1', '0.4.6'),
+        ('2.6.2', '0.5.4'),
+    )
+    for (magma_v, hiop_v) in magma_ver_constraints:
+        depends_on('magma@{0}:'.format(magma_v), when='@{0}:+cuda'.format(hiop_v))
+        depends_on('magma@{0}:'.format(magma_v), when='@{0}:+rocm'.format(hiop_v))
 
     depends_on('raja+openmp', when='+raja')
     depends_on('raja@0.14.0:', when='@0.5.0:+raja')

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

@@ -0,0 +1,36 @@
+# Copyright 2013-2022 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 import *
+
+
+class Hztool(AutotoolsPackage):
+    """HZTool is a library of routines which will allow you to reproduce an
+    experimental result using the four-vector final state from Monte Carlo
+    generators."""
+
+    homepage = "https://hztool.hepforge.org"
+    url      = "https://hztool.hepforge.org/downloads/?f=hztool-4.3.2.tar.gz"
+    list_url = "https://hztool.hepforge.org/downloads/"
+
+    maintainers = ['wdconinc']
+
+    tags = ['hep']
+
+    version('4.3.2', sha256='2a8d334abd96a7a9f70d53cfbb46f35902ccd1108861333a87542f8357152fd4')
+    version('4.3',   sha256='af1a302c16e9f0bfbfdd77a486a5f47553d81d1d049bc83cc72321ba285af264')
+    version('4.2',   sha256='87b74b2e424a1e6bd990cc12a0bfcba15854a6451ffa20aff8dc4bdfed559160')
+    version('4.1',   sha256='a24b5d483d1dacaa991958956e838601a426133c74885b3aa2fc27c98b42d22a')
+    version('4.0',   sha256='e6f6955159da46156bf9182f61754a59dd14e407d40c2448e3f821d55bf963a0')
+
+    def patch(self):
+        filter_file('-fno-automatic',
+                    '-fno-automatic -fallow-argument-mismatch',
+                    'configure.ac')
+
+    def configure_args(self):
+        args = []
+        args.append('--disable-docs')
+        return args

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

@@ -0,0 +1,26 @@
+# Copyright 2013-2021 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 import *
+
+
+class Kakoune(MakefilePackage):
+    """mawww's experiment for a better code editor."""
+
+    homepage = "https://www.kakoune.org"
+    url      = "https://github.com/mawww/kakoune/releases/download/v2021.11.08/kakoune-2021.11.08.tar.bz2"
+
+    maintainers = ['Bambi']
+
+    version('2021.11.08', sha256='aa30889d9da11331a243a8f40fe4f6a8619321b19217debac8f565e06eddb5f4')
+
+    depends_on('ncurses')
+
+    conflicts('%gcc@:8', when='@2021.11.08', msg='GCC version must be at least 9.0!')
+
+    build_targets = ['all', 'man']
+
+    def edit(self, spec, prefix):
+        env['PREFIX'] = prefix

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

@@ -136,6 +136,7 @@ class Kokkos(CMakePackage, CudaPackage, ROCmPackage):
         "72": 'volta72',
         "75": 'turing75',
         "80": 'ampere80',
+        "86": 'ampere86',
     }
     cuda_arches = spack_cuda_arch_map.values()
     conflicts("+cuda", when="cuda_arch=none")

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

@@ -27,3 +27,9 @@ def setup_run_environment(self, env):
             env.set('LANDSFCUTIL_LIB' + suffix, lib[0])
             env.set('LANDSFCUTIL_INC' + suffix,
                     join_path(self.prefix, 'include_' + suffix))
+
+    def flag_handler(self, name, flags):
+        if self.spec.satisfies('%fj'):
+            if name == 'fflags':
+                flags.append('-Free')
+        return (None, None, flags)

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

@@ -197,9 +197,12 @@ class Lbann(CMakePackage, CudaPackage, ROCmPackage):
     depends_on('cnpy', when='+numpy')
     depends_on('nccl', when='@0.94:0.98.2 +cuda')
 
-    depends_on('conduit@0.4.0: +hdf5~hdf5_compat ~python', when='@0.94:0 +conduit')
-    depends_on('conduit@0.5.0:0.6 +hdf5~hdf5_compat ~python', when='@0.100:0.101 +conduit')
-    depends_on('conduit@0.6.0: +hdf5~hdf5_compat~fortran~parmetis ~python', when='@:0.90,0.99:')
+    # Note that conduit defaults to +fortran +parmetis +python, none of which are
+    # necessary by LBANN: you may want to disable those options in your
+    # packages.yaml
+    depends_on('conduit@0.4.0: +hdf5', when='@0.94:0 +conduit')
+    depends_on('conduit@0.5.0:0.6 +hdf5', when='@0.100:0.101 +conduit')
+    depends_on('conduit@0.6.0: +hdf5', when='@:0.90,0.99:')
 
     # LBANN can use Python in two modes 1) as part of an extensible framework
     # and 2) to drive the front end model creation and launch

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

@@ -11,24 +11,30 @@ class Lhapdf(AutotoolsPackage):
        used for evaluating PDFs from discretised data files. """
 
     homepage = "https://lhapdf.hepforge.org/"
-    url      = "https://lhapdf.hepforge.org/downloads/?f=LHAPDF-6.2.3.tar.gz"
+    git      = "https://gitlab.com/hepcedar/lhapdf"
+    # the tarballs from hepforge include bundled cython sources
+    # that may break the build when using incompatible python versions
+    # thus use the release tarball from gitlab that does not include lhapdf.cxx
+    url      = "https://gitlab.com/hepcedar/lhapdf/-/archive/lhapdf-6.4.0/lhapdf-lhapdf-6.4.0.tar.gz"
 
     tags = ['hep']
 
-    version('6.3.0', sha256='ed4d8772b7e6be26d1a7682a13c87338d67821847aa1640d78d67d2cef8b9b5d')
-    version('6.2.3', sha256='d6e63addc56c57b6286dc43ffc56d901516f4779a93a0f1547e14b32cfd82dd1')
+    version('6.4.0', sha256='155702c36df46de30c5f7fa249193a9a0eea614191de1606301e06cd8062fc29')
+    version('6.3.0', sha256='864468439c7662bbceed6c61c7132682ec83381a23c9c9920502fdd7329dd816')
+    version('6.2.3', sha256='37200a1ab70247250a141dfed7419d178f9a83bd23a4f8a38e203d4e27b41308')
+
+    variant('python', default=True, description="Build python bindings")
 
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
     depends_on('libtool',  type='build')
     depends_on('m4',       type='build')
 
-    depends_on('python',        type=('build', 'run'))
-    depends_on('py-cython',     type='build')
-    depends_on('py-setuptools', type='build')
-
-    extends('python')
+    extends('python', when='+python')
+    depends_on('py-cython',     type='build', when='+python')
+    depends_on('py-setuptools', type='build', when='+python')
 
     def configure_args(self):
         args = ['FCFLAGS=-O3', 'CFLAGS=-O3', 'CXXFLAGS=-O3']
+        args.extend(self.enable_or_disable('python'))
         return args

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

@@ -32,6 +32,7 @@ class Libdrm(Package):
     depends_on('docbook-xsl', type='build')
     depends_on('libpciaccess@0.10:')
     depends_on('libpthread-stubs')
+    depends_on('meson', type='build', when='@2.4.101:')
 
     def url_for_version(self, version):
         if version <= Version('2.4.100'):

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

@@ -11,9 +11,11 @@ class Libpipeline(AutotoolsPackage):
     in a flexible and convenient way."""
 
     homepage = "http://libpipeline.nongnu.org/"
-    url      = "https://git.savannah.nongnu.org/cgit/libpipeline.git/snapshot/libpipeline-1.4.2.tar.gz"
+    git = "https://gitlab.com/cjwatson/libpipeline"
+    url = "https://download.savannah.nongnu.org/releases/libpipeline/libpipeline-1.5.5.tar.gz"
 
-    version('1.4.2', sha256='ac8b103b281ff63129c4fa6a8cc40bb5863e3a4266343d6e3bb5788de1ede488')
+    version('1.5.5', sha256='0c8367f8b82bb721b50647a647115b6e62a37e3b2e954a9685e4d933f30c00cc')
+    version('1.4.2', sha256='fef1fc9aa40ce8796f18cd1aecd888a9484a9556c8b0f8d07c863578277679be')
 
     depends_on('pkgconfig', type='build')
     depends_on('check', type='test')

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

@@ -15,6 +15,7 @@ class Libtree(MakefilePackage):
     maintainers = ['haampie']
 
     version('master', branch='master')
+    version('3.1.0', sha256='8057edb2dd77b0acf6ceab6868741993979dccd41fc41a58bde743f11666d781')
     version('3.0.3', sha256='7e4589b617775cb3a2b4b8fe03f80b81e43ef16046d680f1517ce52d7be9893f')
     version('3.0.2', sha256='f07c9cf3394cacd1eab15d42b97b9b6787d8bd3b7f6746fe0f39e7d951eebaac')
     version('3.0.1', sha256='20d3cd66f5c74058de9dd594af8ffd639c795d27ab435c588a3cd43911c1604f')

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

@@ -34,7 +34,7 @@ class Libzmq(AutotoolsPackage):
     variant("drafts", default=False,
             description="Build and install draft classes and methods")
 
-    variant("docs", default=True,
+    variant("docs", default=False,
             description="Build documentation")
 
     variant("libbsd", when='@4.3.3:', default=(sys.platform != 'darwin'),

var/spack/repos/builtin/packages/llvm/llvm12-thread.patch

@@ -0,0 +1,31 @@
+diff --git a/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake b/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake
+index e3c2a580396e..5f76992d193e 100644
+--- a/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake
++++ b/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake
+@@ -249,3 +249,6 @@ if (NOT LIBOMPTARGET_CUDA_TOOLKIT_ROOT_DIR_PRESET AND
+     endif()
+   endif()
+ endif()
++
++find_package(Threads REQUIRED)
++set(OPENMP_PTHREAD_LIB ${CMAKE_THREAD_LIBS_INIT})
+diff --git a/openmp/libomptarget/src/CMakeLists.txt b/openmp/libomptarget/src/CMakeLists.txt
+index 15e6c3bbaf1f..3e5a73504a08 100644
+--- a/openmp/libomptarget/src/CMakeLists.txt
++++ b/openmp/libomptarget/src/CMakeLists.txt
+@@ -30,6 +30,7 @@ if(OPENMP_STANDALONE_BUILD OR (NOT OPENMP_ENABLE_LIBOMPTARGET_PROFILING))
+   add_library(omptarget SHARED ${LIBOMPTARGET_SRC_FILES})
+   target_link_libraries(omptarget
+     ${CMAKE_DL_LIBS}
++    ${OPENMP_PTHREAD_LIB}
+     "-Wl,--version-script=${CMAKE_CURRENT_SOURCE_DIR}/exports")
+ else()
+   set(LLVM_LINK_COMPONENTS
+@@ -37,6 +38,7 @@ else()
+     )
+   add_llvm_library(omptarget SHARED ${LIBOMPTARGET_SRC_FILES}
+       LINK_LIBS ${CMAKE_DL_LIBS}
++      ${OPENMP_PTHREAD_LIB}
+       "-Wl,--version-script=${CMAKE_CURRENT_SOURCE_DIR}/exports"
+       )
+   target_compile_definitions(omptarget PUBLIC OMPTARGET_PROFILE_ENABLED)

var/spack/repos/builtin/packages/llvm/llvm13-fujitsu.patch

@@ -0,0 +1,15 @@
+--- spack-src/libcxx/include/__config.org	2022-02-03 14:36:11.000000000 +0900
++++ spack-src/libcxx/include/__config	2022-02-04 08:39:59.000000000 +0900
+@@ -52,7 +52,11 @@
+ #  elif __cplusplus <= 201703L
+ #    define _LIBCPP_STD_VER 17
+ #  elif __cplusplus <= 202002L
+-#    define _LIBCPP_STD_VER 20
++#    if defined(__FUJITSU) || defined(__CLANG_FUJITSU)
++#      define _LIBCPP_STD_VER 17
++#    else
++#      define _LIBCPP_STD_VER 20
++#    endif
+ #  else
+ #    define _LIBCPP_STD_VER 21  // current year, or date of c++2b ratification
+ #  endif

var/spack/repos/builtin/packages/llvm/llvm13-thread.patch

@@ -0,0 +1,19 @@
+--- spack-src/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake.org	2022-02-08 14:58:13.000000000 +0900
++++ spack-src/openmp/libomptarget/cmake/Modules/LibomptargetGetDependencies.cmake	2022-02-08 13:58:53.000000000 +0900
+@@ -276,4 +276,5 @@
+   endif()
+ endif()
+
+-set(OPENMP_PTHREAD_LIB ${LLVM_PTHREAD_LIB})
++find_package(Threads REQUIRED)
++set(OPENMP_PTHREAD_LIB ${CMAKE_THREAD_LIBS_INIT})
+--- spack-src/openmp/libomptarget/src/CMakeLists.txt.org	2022-02-09 08:49:35.000000000 +0900
++++ spack-src/openmp/libomptarget/src/CMakeLists.txt	2022-02-09 08:50:18.000000000 +0900
+@@ -36,6 +36,7 @@
+ endif()
+ target_link_libraries(omptarget PRIVATE
+   ${CMAKE_DL_LIBS}
++  ${OPENMP_PTHREAD_LIB}
+   "-Wl,--version-script=${CMAKE_CURRENT_SOURCE_DIR}/exports")
+ 
+ # Install libomptarget under the lib destination folder.

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

@@ -238,6 +238,8 @@ class Llvm(CMakePackage, CudaPackage):
     conflicts("%gcc@:5.0", when="@8:")
     # clang/lib: a lambda parameter cannot shadow an explicitly captured entity
     conflicts("%clang@8:", when="@:4")
+    # Internal compiler error on gcc 8.4 on aarch64 https://bugzilla.redhat.com/show_bug.cgi?id=1958295
+    conflicts('%gcc@8.4:8.4.9', when='@12: target=aarch64:')
 
     # When these versions are concretized, but not explicitly with +libcxx, these
     # conflicts will enable clingo to set ~libcxx, making the build successful:
@@ -347,6 +349,13 @@ class Llvm(CMakePackage, CudaPackage):
 
     patch('llvm-gcc11.patch', when='@9:11%gcc@11:')
 
+    # add -lpthread to build OpenMP libraries with Fujitsu compiler
+    patch('llvm12-thread.patch', when='@12 %fj')
+    patch('llvm13-thread.patch', when='@13 %fj')
+
+    # avoid build failed with Fujitsu compiler
+    patch('llvm13-fujitsu.patch', when='@13 %fj')
+
     # The functions and attributes below implement external package
     # detection for LLVM. See:
     #

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

@@ -0,0 +1,44 @@
+# Copyright 2013-2021 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 import *
+
+
+class Madx(CMakePackage):
+    """MAD-X (Methodical Accelerator Design) is an application
+    for designing particle accelerators."""
+
+    homepage = "https://github.com/MethodicalAcceleratorDesign/MAD-X"
+    url      = "https://github.com/MethodicalAcceleratorDesign/MAD-X/archive/refs/tags/5.07.00.tar.gz"
+    git      = "https://github.com/MethodicalAcceleratorDesign/MAD-X.git"
+
+    maintainers = ['wdconinc']
+
+    # Supported MAD-X versions
+    version('5.08.01', sha256='89c943fcb474344a4f7d28de98e8eae0aec40f779bf908daff79043bf3520555')
+    version('5.08.00', sha256='0b3fe2aca8899289ef7bfb98d745f13b8c4082e239f54f2662c9cad8d1e63a53')
+    version('5.07.00', sha256='77c0ec591dc3ea76cf57c60a5d7c73b6c0d66cca1fa7c4eb25a9071e8fc67e60')
+
+    variant('x11', default=True, description='Turn on plotting using X11')
+
+    # patch for gcc-11 to avoid error due to variable shadowing
+    patch('https://github.com/MethodicalAcceleratorDesign/MAD-X/commit/e7a434290df675b894f70026ce0c7c217330cce5.patch',
+          sha256='ba9d00692250ab1eeeb7235a4ba7d899ecbbb4588f3ec08afc22d228dc1ea437',
+          when='@:5.07.00')
+
+    depends_on('cmake@2.8:', type='build')
+
+    depends_on("libx11")
+    depends_on("zlib")
+
+    def cmake_args(self):
+        args = [
+            self.define('MADX_STATIC', False),  # Turn on for static linking
+            self.define('MADX_LAPACK', True),  # Use system blas/lapack installation
+            self.define('MADX_NTPSA', True),  # Build with NTPSA
+            self.define('MADX_ONLINE', False),  # Build with Online model
+            self.define_from_variant('MADX_X11', 'x11'),  # Turn on plotting using X11
+        ]
+        return args

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

@@ -23,7 +23,8 @@ class Magma(CMakePackage, CudaPackage, ROCmPackage):
     test_requires_compiler = True
 
     version('master', branch='master')
-    version('2.6.1', sha256='6cd83808c6e8bc7a44028e05112b3ab4e579bcc73202ed14733f66661127e213')
+    version('2.6.2rc1', commit='5959b8783e45f1809812ed96ae762f38ee701972')
+    version('2.6.1', sha256='6cd83808c6e8bc7a44028e05112b3ab4e579bcc73202ed14733f66661127e213', preferred=True)
     version('2.6.0', sha256='50cdd384f44f06a34469e7125f8b2ffae13c1975d373c3f1510d91be2b7638ec')
     version('2.5.4', sha256='7734fb417ae0c367b418dea15096aef2e278a423e527c615aab47f0683683b67')
     version('2.5.3', sha256='c602d269a9f9a3df28f6a4f593be819abb12ed3fa413bba1ff8183de721c5ef6')
@@ -76,19 +77,31 @@ class Magma(CMakePackage, CudaPackage, ROCmPackage):
     patch('cmake-W.patch', when='@2.5.0:%nvhpc')
 
     @run_before('cmake')
-    def generate_cuda(self):
-        if '@master' in self.spec:
-            backend = 'cuda'
-            cuda_arch = self.spec.variants['cuda_arch'].value
-            gpu_target = ' '.join('sm_{0}'.format(i) for i in cuda_arch)
-            if '+rocm' in self.spec:
-                backend = 'hip'
-                gpu_target = self.spec.variants['amdgpu_target'].value
-            with open('make.inc', 'w') as inc:
-                inc.write('FORT = true\n')
-                inc.write('GPU_TARGET = %s\n' % gpu_target)
-                inc.write('BACKEND = %s\n' % backend)
-            make('generate')
+    def generate_gpu_config(self):
+        """If not an official release, a generation step is required to build"""
+        spec = self.spec
+
+        # 2.6.2rc1 is not an official release
+        should_generate = ('@master' in spec) or ('@2.6.2rc1' in spec)
+
+        if not should_generate:
+            return
+
+        backend = 'cuda' if '+cuda' in spec else 'hip'
+
+        gpu_target = ''
+        if '+cuda' in spec:
+            cuda_archs = spec.variants['cuda_arch'].value
+            gpu_target = ' '.join('sm_{0}'.format(i) for i in cuda_archs)
+        else:
+            gpu_target = spec.variants['amdgpu_target'].value
+
+        with open('make.inc', 'w') as inc:
+            inc.write('FORT = true\n')
+            inc.write('GPU_TARGET = {0}\n'.format(gpu_target))
+            inc.write('BACKEND = {0}\n'.format(backend))
+
+        make('generate')
 
     def cmake_args(self):
         spec = self.spec

var/spack/repos/builtin/packages/man-db/package.py

@@ -13,14 +13,18 @@ class ManDb(AutotoolsPackage):
     flat-text whatis databases."""
 
     homepage = "https://www.nongnu.org/man-db/"
-    url      = "https://git.savannah.nongnu.org/cgit/man-db.git/snapshot/man-db-2.7.6.1.tar.gz"
+    git      = "https://gitlab.com/cjwatson/man-db"
+    url      = "https://download.savannah.nongnu.org/releases/man-db/man-db-2.10.1.tar.xz"
 
-    version('2.7.6.1', sha256='dd913662e341fc01e6721878b6cbe1001886cc3bfa6632b095937bba3238c779')
+    version('2.10.1', sha256='2ffd8f2e80122fe72e60c740c851e6a3e15c9a7921185eb4752c1c672824bed6')
+    version('2.7.6.1', sha256='08edbc52f24aca3eebac429b5444efd48b9b90b9b84ca0ed5507e5c13ed10f3f')
 
-    depends_on('autoconf')
-    depends_on('automake')
+    depends_on('pkgconf', type='build')
     depends_on('gettext')
-    depends_on('libpipeline')
+    depends_on('libpipeline@1.5.0:', when='@2.8.0:')
+    depends_on('libpipeline@1.4.0:', when='@2.7.1:')
+    depends_on('libpipeline@1.3.0:', when='@2.6.7:')
+    depends_on('libpipeline@1.1.0:', when='@2.6.0:')
     depends_on('flex')
     depends_on('gdbm')
     depends_on('groff', type=('build', 'link', 'run'))
@@ -38,3 +42,6 @@ def configure_args(self):
             '--with-systemdtmpfilesdir={0}/tmp'.format(self.prefix)
         ]
         return args
+
+    def install(self, spec, prefix):
+        make('install', 'DESTDIR=%s' % prefix)

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

@@ -44,7 +44,7 @@ class Mesa(MesonPackage):
     depends_on('zlib@1.2.3:')
 
     # Internal options
-    variant('llvm', default=True, description="Enable LLVM.")
+    variant('llvm', default=False, description="Enable LLVM.")
     _SWR_AUTO_VALUE = 'auto'
     _SWR_ENABLED_VALUES = (_SWR_AUTO_VALUE, 'avx', 'avx2', 'knl', 'skx')
     _SWR_DISABLED_VALUES = ('none',)

var/spack/repos/builtin/packages/mesa18/package.py

@@ -41,7 +41,7 @@ class Mesa18(AutotoolsPackage):
     depends_on('ncurses+termlib')
 
     # Internal options
-    variant('llvm', default=True, description="Enable LLVM.")
+    variant('llvm', default=False, description="Enable LLVM.")
     _SWR_ENABLED_VALUES = ('avx', 'avx2', 'knl', 'skx')
     variant('swr', values=any_combination_of(*_SWR_ENABLED_VALUES),
             description="Enable the SWR driver.")

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

@@ -16,6 +16,7 @@ class Meshtool(MakefilePackage):
 
     version('master', branch='master')
     # Version to use with openCARP releases
+    version('oc9.0', commit='6c5cfbd067120901f15a04bf63beec409bda6dc9')
     version('oc8.2', commit='6c5cfbd067120901f15a04bf63beec409bda6dc9')
     version('oc8.1', commit="6c5cfbd067120901f15a04bf63beec409bda6dc9")
     version('oc7.0', commit="6c5cfbd067120901f15a04bf63beec409bda6dc9")

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

@@ -13,6 +13,7 @@ class Mumps(Package):
     homepage = "http://mumps.enseeiht.fr"
     url      = "http://mumps.enseeiht.fr/MUMPS_5.3.5.tar.gz"
 
+    version('5.4.1', sha256='93034a1a9fe0876307136dcde7e98e9086e199de76f1c47da822e7d4de987fa8')
     version('5.4.0', sha256='c613414683e462da7c152c131cebf34f937e79b30571424060dd673368bbf627')
     version('5.3.5', sha256='e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4')
     version('5.3.3', sha256='27e7749ac05006bf8e81a457c865402bb72a42bf3bc673da49de1020f0f32011')

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

@@ -14,7 +14,7 @@ class Mvapich2(AutotoolsPackage):
     platforms (x86 (Intel and AMD), ARM and OpenPOWER)"""
 
     homepage = "https://mvapich.cse.ohio-state.edu/userguide/userguide_spack/"
-    url = "https://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.6.tar.gz"
+    url = "https://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.7.tar.gz"
     list_url = "https://mvapich.cse.ohio-state.edu/downloads/"
 
     maintainers = ['natshineman', 'harisubramoni', 'ndcontini']
@@ -22,6 +22,7 @@ class Mvapich2(AutotoolsPackage):
     executables = ['^mpiname$']
 
     # Prefer the latest stable release
+    version('2.3.7', sha256='4b6ad2c8c270e1fabcd073c49edb6bf95af93780f4a487bc48404a8ca384f34e')
     version('2.3.6', sha256='b3a62f2a05407191b856485f99da05f5e769d6381cd63e2fcb83ee98fc46a249')
     version('2.3.5', sha256='f9f467fec5fc981a89a7beee0374347b10c683023c76880f92a1a0ad4b961a8c')
     version('2.3.4', sha256='7226a45c7c98333c8e5d2888119cce186199b430c13b7b1dca1769909e68ea7a')

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

@@ -16,6 +16,7 @@ class Nss(MakefilePackage):
     homepage = "https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS"
     url      = "https://ftp.mozilla.org/pub/security/nss/releases/NSS_3_67_RTM/src/nss-3.67.tar.gz"
 
+    version('3.75', sha256='fd571507827284644f4dd522a032acda2286835f6683ed22a1c2d3878cc58582')
     version('3.73', sha256='566d3a68da9b10d7da9ef84eb4fe182f8f04e20d85c55d1bf360bb2c0096d8e5')
     # Everything before 3.73 is vulnerable (CVE-2021-43527)
     version('3.67', sha256='f6549a9148cd27b394b40c77fa73111d5ea23cdb51d796665de1b7458f88ce7f', deprecated=True)

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

@@ -18,7 +18,8 @@ class Opencarp(CMakePackage):
 
     maintainers = ['MarieHouillon']
 
-    version('8.2', commit='dbfd16fd', submodules=False, no_cache=True, preferred=True)
+    version('9.0', commit='c0167599', submodules=False, no_cache=True, preferred=True)
+    version('8.2', commit='dbfd16fd', submodules=False, no_cache=True)
     version('8.1', commit='28eb2e97', submodules=False, no_cache=True)
     version('7.0', commit='78da9195', submodules=False, no_cache=True)
     version('master', branch='master', submodules=False, no_cache=True)
@@ -34,14 +35,14 @@ class Opencarp(CMakePackage):
     depends_on('binutils')
     depends_on('gengetopt')
     depends_on('pkgconfig')
-    depends_on('python@:3.8')
+    depends_on('python')
     depends_on('zlib')
     depends_on('perl')
 
     depends_on('py-carputils')
     depends_on('meshtool')
     # Use specific versions of carputils and meshtool for releases
-    for ver in ['8.2', '7.0', '8.1']:
+    for ver in ['9.0', '8.2', '7.0', '8.1']:
         depends_on('py-carputils@oc' + ver, when='@' + ver + ' +carputils')
         depends_on('meshtool@oc' + ver, when='@' + ver + ' +meshtool')
 

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

@@ -92,6 +92,9 @@ class Paraview(CMakePackage, CudaPackage):
     conflicts('build_edition=core', when='@:5.7')
     # before 5.3.0, ParaView didn't have VTK-m
     conflicts('use_vtkm=on', when='@:5.3')
+    # paraview@5.9.0 is recommended when using the xl compiler
+    # See https://gitlab.kitware.com/paraview/paraview/-/merge_requests/4433
+    conflicts('paraview@:5.8', when='%xl_r', msg='Use paraview@5.9.0 with %xl_r. Earlier versions are not able to build with xl.')
 
     # We only support one single Architecture
     for _arch, _other_arch in itertools.permutations(CudaPackage.cuda_arch_values, 2):
@@ -219,6 +222,10 @@ class Paraview(CMakePackage, CudaPackage):
     # https://gitlab.kitware.com/vtk/vtk/-/merge_requests/8653
     patch('vtk-adios2-module-no-kit.patch', when='@5.8:5.10')
 
+    # Patch for paraview 5.9.0%xl_r
+    # https://gitlab.kitware.com/vtk/vtk/-/merge_requests/7591
+    patch('xlc-compilation-pv590.patch', when='@5.9.0%xl_r')
+
     @property
     def generator(self):
         # https://gitlab.kitware.com/paraview/paraview/-/issues/21223

var/spack/repos/builtin/packages/paraview/xlc-compilation-pv590.patch

@@ -0,0 +1,39 @@
+diff --git a/VTK/Common/DataModel/vtkStaticCellLinksTemplate.txx b/VTK/Common/DataModel/vtkStaticCellLinksTemplate.txx
+index 514c0ee..66edca2 100644
+--- a/VTK/Common/DataModel/vtkStaticCellLinksTemplate.txx
++++ b/VTK/Common/DataModel/vtkStaticCellLinksTemplate.txx
+@@ -356,7 +356,7 @@ void vtkStaticCellLinksTemplate<TIds>::ThreadedBuildLinks(
+
+   // Create an array of atomics with initial count=0. This will keep
+   // track of point uses. Count them in parallel.
+-  std::atomic<TIds>* counts = new std::atomic<TIds>[numPts] {};
++  std::atomic<TIds>* counts = new std::atomic<TIds>[numPts] ();
+   CountUses<TIds> count(cellArray, counts);
+   vtkSMPTools::For(0, numCells, count);
+
+diff --git a/VTK/Filters/Core/vtkBinnedDecimation.cxx b/VTK/Filters/Core/vtkBinnedDecimation.cxx
+index 0736c56..8403908 100644
+--- a/VTK/Filters/Core/vtkBinnedDecimation.cxx
++++ b/VTK/Filters/Core/vtkBinnedDecimation.cxx
+@@ -632,7 +632,7 @@ void BinPointsDecimate(int genMode, vtkIdType numPts, PointsT* pts, vtkPointData
+   // is a problem because a ptId can == zero; as a workaround, we'll
+   // initially use negative ids, and convert to positive ids in the
+   // final composition.
+-  std::atomic<TIds>* ptMap = new std::atomic<TIds>[numBins] {};
++  std::atomic<TIds>* ptMap = new std::atomic<TIds>[numBins] ();
+
+   // Is the triangle output? And eventually the offset into the output cell array.
+   TIds* triMap = new TIds[numTris + 1];
+diff --git a/VTK/Filters/Core/vtkWindowedSincPolyDataFilter.cxx b/VTK/Filters/Core/vtkWindowedSincPolyDataFilter.cxx
+index 15e47a1..7baef33 100644
+--- a/VTK/Filters/Core/vtkWindowedSincPolyDataFilter.cxx
++++ b/VTK/Filters/Core/vtkWindowedSincPolyDataFilter.cxx
+@@ -348,7 +348,7 @@ struct PointConnectivity : PointConnectivityBase
+     // accommodate more smoothing edges (although after a certain point,
+     // additional edges make little difference, especially at the cost of
+     // memory and speed).
+-    this->Offsets = new std::atomic<TIds>[this->NumPts + 1] {}; // Initialized to zero
++    this->Offsets = new std::atomic<TIds>[this->NumPts + 1] (); // Initialized to zero
+     this->Edges = nullptr;                                      // initially until constructed
+     this->EdgeCounts = new EDGE_COUNT_TYPE[this->NumPts];       // values set later
+   }

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

@@ -16,16 +16,16 @@ class Parsec(CMakePackage, CudaPackage):
     """
 
     homepage    = "https://icl.utk.edu/dte"
-    git         = "https://bitbucket.org/icldistcomp/parsec.git"
-    url         = "https://bitbucket.org/icldistcomp/parsec/get/parsec-3.0.2012.tar.bz2"
-    list_url    = "https://bitbucket.org/icldistcomp/parsec/downloads/?tab=tags"
+    git         = "https://github.com/icldisco/parsec.git"
+    url         = "https://github.com/ICLDisco/parsec/archive/refs/tags/parsec-3.0.2012.tar.gz"
+    list_url    = "https://github.com/ICLDisco/parsec/tags"
     maintainers = ['abouteiller', 'bosilca', 'herault']
-    tags = ['e4s']
+    tags        = ['e4s']
 
     test_requires_compiler = True
 
     version('master', branch='master')
-    version('3.0.2012', sha256='f565bcfffe106be8237b6aea3e83a5770607b7236606414b6f270244fa6ec3bc')
+    version('3.0.2012', sha256='f565bcfffe106be8237b6aea3e83a5770607b7236606414b6f270244fa6ec3bc', url='https://bitbucket.org/icldistcomp/parsec/get/parsec-3.0.2012.tar.bz2')
     version('1.1.0', sha256='d2928033c121000ae0a554f1e7f757c1f22274a8b74457ecd52744ae1f70b95a', url='https://bitbucket.org/icldistcomp/parsec/get/v1.1.0.tar.bz2')
 
     variant('build_type', default='RelWithDebInfo', description='CMake build type', values=('Debug', 'Release', 'RelWithDebInfo'))
@@ -38,7 +38,7 @@ class Parsec(CMakePackage, CudaPackage):
     # TODO: Spack does not handle cross-compilation atm
     # variant('xcompile', default=False, description='Cross compile')
 
-    depends_on('cmake@3.16:', type='build')
+    depends_on('cmake@3.18:', type='build')
     depends_on('python', type='build')
     depends_on('flex', type='build')
     depends_on('bison', type='build')

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

@@ -16,6 +16,7 @@ class Pika(CMakePackage, CudaPackage, ROCmPackage):
     url = "https://github.com/pika-org/pika/archive/0.0.0.tar.gz"
     maintainers = ['msimberg', 'albestro', 'teonnik']
 
+    version('0.2.0', sha256='712bb519f22bdc9d5ee4ac374d251a54a0af4c9e4e7f62760b8ab9a177613d12')
     version('0.1.0', sha256='aa0ae2396cd264d821a73c4c7ecb118729bb3de042920c9248909d33755e7327')
     version('main', git='https://github.com/pika-org/pika.git', branch='main')
 
@@ -44,6 +45,7 @@ class Pika(CMakePackage, CudaPackage, ROCmPackage):
 
     variant('examples', default=False, description='Build and install examples')
     variant('mpi', default=False, description='Enable MPI support')
+    variant('apex', default=False, description='Enable APEX support', when='@0.2.0:')
 
     # Build dependencies
     depends_on('git', type='build')
@@ -63,6 +65,7 @@ class Pika(CMakePackage, CudaPackage, ROCmPackage):
 
     depends_on('mpi', when='+mpi')
     depends_on('cuda@11:', when='+cuda')
+    depends_on('apex', when='+apex')
 
     for cxxstd in cxxstds:
         depends_on(
@@ -89,6 +92,7 @@ def cmake_args(self):
             self.define_from_variant('PIKA_WITH_CUDA', 'cuda'),
             self.define_from_variant('PIKA_WITH_HIP', 'rocm'),
             self.define_from_variant('PIKA_WITH_MPI', 'mpi'),
+            self.define_from_variant('PIKA_WITH_APEX', 'apex'),
             self.define('PIKA_WITH_TESTS', self.run_tests),
             self.define_from_variant(
                 'PIKA_WITH_GENERIC_CONTEXT_COROUTINES', 'generic_coroutines'),

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

@@ -11,6 +11,7 @@ class PyBilliard(PythonPackage):
 
     pypi = "billiard/billiard-3.5.0.5.tar.gz"
 
+    version('3.6.4.0', sha256='299de5a8da28a783d51b197d496bef4f1595dd023a93a4f59dde1886ae905547')
     version('3.6.3.0', sha256='d91725ce6425f33a97dfa72fb6bfef0e47d4652acd98a032bd1a7fbf06d5fa6a')
     version('3.6.1.0', sha256='b8809c74f648dfe69b973c8e660bcec00603758c9db8ba89d7719f88d5f01f26')
     version('3.6.0.0', sha256='756bf323f250db8bf88462cd042c992ba60d8f5e07fc5636c24ba7d6f4261d84')

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

@@ -14,20 +14,21 @@ class PyCarputils(PythonPackage):
 
     version('master', branch='master')
     # Version to use with openCARP releases
+    version('oc9.0', commit='e79e66b25c7bfaf405fad595019594ab9aa83392')
     version('oc8.2', commit='e60f639c0f39ad71c8ae11814de1f3aa726e8352')
     version('oc8.1', commit='a4210fcb0fe17226a1744ee9629f85b629decba3')
     version('oc7.0', commit='4c04db61744f2fb7665594d7c810699c5c55c77c')
 
     depends_on('git')
 
-    depends_on('python@:3.8', type=('build', 'run'))
+    depends_on('python', type=('build', 'run'))
     depends_on('py-pip', type='build')
     depends_on('py-numpy@1.14.5:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('py-python-dateutil', type='run')
-    depends_on('py-scipy@:1.5.4', type='run')
-    depends_on('py-matplotlib@:3.3.3', type='run')
-    depends_on('py-pandas@:1.1.4', type='run')
-    depends_on('py-tables@3.6.1', type='run')
-    depends_on('py-six@:1.14.0', type='run')
+    depends_on('py-scipy@1.5.0:', type='run')
+    depends_on('py-matplotlib@3.0.0:', type='run')
+    depends_on('py-pandas', type='run')
+    depends_on('py-tables@3.6.1:', type='run')
+    depends_on('py-six@1.12.0:', type='run')
     depends_on('py-ruamel-yaml', type='run')

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

@@ -65,8 +65,8 @@ class PyCelery(PythonPackage):
     depends_on('py-click-repl@0.2.0:', when="@5.2.0:", type=('build', 'run'))
     depends_on('py-pytz@2019.3:', type=('build', 'run'))
     depends_on('py-pytz@2021.3:', type=('build', 'run'), when="@5.2.3")
-    depends_on('py-billiard@3.6.3:3', type=('build', 'run'))
-    depends_on('py-billiard@3.6.4:3', type=('build', 'run'), when="@5.2.3")
+    depends_on('py-billiard@3.6.3.0:3', type=('build', 'run'))
+    depends_on('py-billiard@3.6.4.0:3', type=('build', 'run'), when="@5.2.3")
     depends_on('py-kombu@4.6.11', when="@4.3.0:4",  type=('build', 'run'))
     depends_on('py-kombu@5.0.0:', when="@5.0.0:5.0", type=('build', 'run'))
     depends_on('py-kombu@5.2.3:5', when="@5.2.0:5.2", type=('build', 'run'))

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

@@ -0,0 +1,21 @@
+# Copyright 2013-2022 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 import *
+
+
+class PyColorio(PythonPackage):
+    """Tools for color research"""
+
+    homepage = "https://github.com/nschloe/colorio"
+    pypi     = "colorio/colorio-0.11.2.tar.gz"
+
+    version('0.11.2', sha256='aa45d8e0a2e506c4019d4fb488d34a107d7f803c8e8ff355e2e57c01f6f1cd81')
+
+    depends_on('python@3.7:', type=('build', 'run'))
+    depends_on('py-flit-core@3.2:3.6', type='build')
+    depends_on('py-numpy@1.20:', type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-npx', type=('build', 'run'))

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

@@ -0,0 +1,23 @@
+# Copyright 2013-2022 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 import *
+
+
+class PyControl(PythonPackage):
+    """The Python Control Systems Library is a Python module that implements
+    basic operations for analysis and design of feedback control systems."""
+
+    homepage = "https://python-control.org/"
+    pypi     = "control/control-0.9.1.tar.gz"
+
+    maintainers = ['haralmha']
+
+    version('0.9.1', sha256='8c9084bf386eafcf5d74008f780fae6dec68d243d18a380c866ac10a3549f8d3')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))

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

@@ -11,6 +11,7 @@ class PyFutures(PythonPackage):
 
     pypi = "futures/futures-3.0.5.tar.gz"
 
+    version('3.3.0', sha256='7e033af76a5e35f58e56da7a91e687706faf4e7bdfb2cbc3f2cca6b9bcda9794')
     version('3.2.0', sha256='9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265')
     version('3.0.5', sha256='0542525145d5afc984c88f914a0c85c77527f65946617edb5274f72406f981df')
 

var/spack/repos/builtin/packages/py-googleapis-common-protos/package.py

@@ -12,7 +12,9 @@ class PyGoogleapisCommonProtos(PythonPackage):
     homepage = "https://github.com/googleapis/googleapis"
     pypi = "googleapis-common-protos/googleapis-common-protos-1.6.0.tar.gz"
 
+    version('1.55.0', sha256='53eb313064738f45d5ac634155ae208e121c963659627b90dfcb61ef514c03e1')
     version('1.6.0', sha256='e61b8ed5e36b976b487c6e7b15f31bb10c7a0ca7bd5c0e837f4afab64b53a0c6')
 
     depends_on('py-setuptools', type='build')
-    depends_on('py-protobuf@3.6.0:', type=('build', 'run'))
+    depends_on('py-protobuf@3.6.0:3', type=('build', 'run'))
+    depends_on('py-protobuf@3.12.0:3', type=('build', 'run'), when='@1.55.0:')

var/spack/repos/builtin/packages/py-h5py/package.py

@@ -36,38 +36,39 @@ class PyH5py(PythonPackage):
     variant('mpi', default=True, description='Build with MPI support')
 
     # Python versions
-    depends_on('python@3.6:', type=('build', 'run'), when='@3.0.0:3.1')
-    depends_on('python@3.7:', type=('build', 'run'), when='@3.2.0:')
+    depends_on('python@3.6:', type=('build', 'run'), when='@3:3.1')
+    depends_on('python@3.7:', type=('build', 'run'), when='@3.2:')
 
     # Build dependencies
     depends_on('py-cython@0.23:', type='build', when='@:2')
-    depends_on('py-cython@0.29:', type=('build'), when='@3.0.0:^python@:3.7')
-    depends_on('py-cython@0.29.14:', type=('build'), when='@3.0.0:^python@3.8.0:3.8')
-    depends_on('py-cython@0.29.15:', type=('build'), when='@3.0.0:^python@3.9.0:')
+    depends_on('py-cython@0.29:', type=('build'), when='@3: ^python@:3.7')
+    depends_on('py-cython@0.29.14:', type=('build'), when='@3: ^python@3.8.0:3.8')
+    depends_on('py-cython@0.29.15:', type=('build'), when='@3: ^python@3.9.0:')
     depends_on('py-pkgconfig', type='build')
     depends_on('py-setuptools', type='build')
-    depends_on('py-wheel', type='build', when='@3.0.0:')
+    depends_on('py-wheel', type='build', when='@3:')
 
     # Build and runtime dependencies
     depends_on('py-cached-property@1.5:', type=('build', 'run'), when='^python@:3.7')
     depends_on('py-numpy@1.7:', type=('build', 'run'), when='@:2')
-    depends_on('py-numpy@1.12:', type=('build', 'run'), when='@3.0.0:^python@3.6.0:3.6')
-    depends_on('py-numpy@1.14.5:', type=('build', 'run'), when='@3.0.0:^python@3.7.0:3.7')
-    depends_on('py-numpy@1.17.5:', type=('build', 'run'), when='@3.0.0:^python@3.8.0:3.8')
-    depends_on('py-numpy@1.19.3:', type=('build', 'run'), when='@3.0.0:^python@3.9.0:')
+    depends_on('py-numpy@1.12:', type=('build', 'run'), when='@3: ^python@3.6.0:3.6')
+    depends_on('py-numpy@1.14.5:', type=('build', 'run'), when='@3: ^python@3.7.0:3.7')
+    depends_on('py-numpy@1.17.5:', type=('build', 'run'), when='@3: ^python@3.8.0:3.8')
+    depends_on('py-numpy@1.19.3:', type=('build', 'run'), when='@3: ^python@3.9.0:')
     depends_on('py-six', type=('build', 'run'), when='@:2')
 
-    # Link dependencies
-    depends_on('hdf5@1.8.4:1.11+hl', when='@:2')
-    depends_on('hdf5@1.8.4:+hl', when='@3.0.0:')
+    # Link dependencies (py-h5py v2 cannot build against HDF5 1.12 regardless
+    # of API setting)
+    depends_on('hdf5@1.8.4:1.11 +hl', when='@:2')
+    depends_on('hdf5@1.8.4: +hl', when='@3:')
 
     # MPI dependencies
     depends_on('hdf5+mpi', when='+mpi')
     depends_on('mpi', when='+mpi')
     depends_on('py-mpi4py', when='@:2 +mpi', type=('build', 'run'))
-    depends_on('py-mpi4py@3.0.0:', when='@3.0.0:3.2+mpi^python@3.0.0:3.7', type=('build', 'run'))
-    depends_on('py-mpi4py@3.0.2:', when='@3.3.0:+mpi^python@3.0.0:3.7', type=('build', 'run'))
-    depends_on('py-mpi4py@3.0.3:', when='@3.0.0:+mpi^python@3.8.0:', type=('build', 'run'))
+    depends_on('py-mpi4py@3:', when='@3:3.2+mpi^python@3:3.7', type=('build', 'run'))
+    depends_on('py-mpi4py@3.0.2:', when='@3.3.0:+mpi^python@3:3.7', type=('build', 'run'))
+    depends_on('py-mpi4py@3.0.3:', when='@3:+mpi^python@3.8.0:', type=('build', 'run'))
 
     def setup_build_environment(self, env):
         env.set('HDF5_DIR', self.spec['hdf5'].prefix)

var/spack/repos/builtin/packages/py-importlib-metadata/package.py

@@ -19,6 +19,7 @@ class PyImportlibMetadata(PythonPackage):
     version('3.10.1', sha256='c9356b657de65c53744046fa8f7358afe0714a1af7d570c00c3835c2d724a7c1')
     version('3.10.0', sha256='c9db46394197244adf2f0b08ec5bc3cf16757e9590b02af1fca085c16c0d600a')
     version('2.0.0', sha256='77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da')
+    version('1.7.0', sha256='90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83')
     version('1.2.0', sha256='41e688146d000891f32b1669e8573c57e39e5060e7f5f647aa617cd9a9568278')
     version('0.23',  sha256='aa18d7378b00b40847790e7c27e11673d7fed219354109d0e7b9e5b25dc3ad26')
     version('0.19',  sha256='23d3d873e008a513952355379d93cbcab874c58f4f034ff657c7a87422fa64e8')

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

@@ -16,11 +16,19 @@ class PyJupytext(PythonPackage):
 
     maintainers = ['vvolkl']
 
+    version('1.13.6', sha256='c6c25918ddb6403d0d8504e08d35f6efc447baf0dbeb6a28b73adf39e866a0c4')
     version('1.13.0', sha256='fb220af65d2bd32d01c779b0e935c4c2b71e3f5f2f01bf1bab10d5f23fe121d4')
 
-    depends_on('py-setuptools', type='build')
+    depends_on('python@3.6:3', type=('build', 'run'))
+    depends_on('py-setuptools@40.8.0:', type='build')
     depends_on('py-nbformat', type=('build', 'run'))
     depends_on('py-pyyaml', type=('build', 'run'))
     depends_on('py-toml', type=('build', 'run'))
     depends_on('py-mdit-py-plugins', type=('build', 'run'))
     depends_on('py-markdown-it-py@1.0:1', type=('build', 'run'))
+    # todo: in order to use jupytext as a jupyterlab extension,
+    # some additional dependencies need to be added (and checked):
+    depends_on('py-jupyterlab@3', type=('build', 'run'))
+    # TODO: replace this after concretizer learns how to concretize separate build deps
+    depends_on('py-jupyter-packaging7', type='build')
+    # depends_on('py-jupyter-packaging@0.7.9:0.7', type='build')```

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

@@ -10,13 +10,16 @@ class PyMako(PythonPackage):
     """A super-fast templating language that borrows the best
        ideas from the existing templating languages."""
 
+    homepage = "https://www.makotemplates.org/"
     pypi = "Mako/Mako-1.0.1.tar.gz"
+    git = "https://github.com/sqlalchemy/mako"
 
+    version('1.1.6', sha256='4e9e345a41924a954251b95b4b28e14a301145b544901332e658907a7464b6b2')
     version('1.1.5', sha256='169fa52af22a91900d852e937400e79f535496191c63712e3b9fda5a9bed6fc3')
     version('1.1.4', sha256='17831f0b7087c313c0ffae2bcbbd3c1d5ba9eeac9c38f2eb7b50e8c99fe9d5ab')
     version('1.0.4', sha256='fed99dbe4d0ddb27a33ee4910d8708aca9ef1fe854e668387a9ab9a90cbf9059')
     version('1.0.1', sha256='45f0869febea59dab7efd256fb451c377cbb7947bef386ff0bb44627c31a8d1c')
 
+    depends_on('python@2.7:2,3.4:', when='@1.1.0:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('py-markupsafe@0.9.2:', type=('build', 'run'))
-    depends_on('python@2.7:2,3.4:', when='@1.1.0:')

var/spack/repos/builtin/packages/py-matplotlib-inline/package.py

@@ -9,9 +9,10 @@
 class PyMatplotlibInline(PythonPackage):
     """Inline Matplotlib backend for Jupyter."""
 
-    homepage = "https://github.com/martinRenou/matplotlib-inline"
+    homepage = "https://github.com/ipython/matplotlib-inline"
     pypi     = "matplotlib-inline/matplotlib-inline-0.1.2.tar.gz"
 
+    version('0.1.3', sha256='a04bfba22e0d1395479f866853ec1ee28eea1485c1d69a6faf00dc3e24ff34ee')
     version('0.1.2', sha256='f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e')
 
     depends_on('python@3.5:', type=('build', 'run'))

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

@@ -7,24 +7,24 @@
 
 
 class PyMistune(PythonPackage):
-    """
-    Python markdown parser
-    """
-    homepage = "https://mistune.readthedocs.org/en/latest/"
-    url      = "https://github.com/lepture/mistune/archive/v0.7.1.tar.gz"
+    """A sane Markdown parser with useful plugins and renderers."""
 
-    version('0.8.4', sha256='a1443771ea9ed7268a0cb3cf31462604ae148938ba32070bd5c54545f8f36a5d')
-    version('0.8.3', sha256='666c93fc10cb0aa924a373898a709eba4d43f4e453264a4c7396878ec8145a4a')
-    version('0.8.2', sha256='997c6d723350093760ccd48b722344b3330a5f947dec264e129160b85037784e')
-    version('0.8.1', sha256='77ae24a5accfd62d23f945d7e6598392194f8ca6ef1bd70ddc81e151ac3eb1fe')
-    version('0.8',   sha256='f479dc2ceac7d593231e77448cb5cf7194fdbebad1d88fcdb78eacac1c042f6e')
-    version('0.7.4', sha256='5030d5e3e0ec90fbdaed0f52d3c756ffb30e4ab46c3de159c97482c09569abcb')
-    version('0.7.3', sha256='c4f391e61d3b5e8fbb112669a5c6960fb04b71b61d35f0f09a201809545b1676')
-    version('0.7.2', sha256='a3fe17dfad99bd353485879a5c05827dd2932219da8b078212a21797f6cdbf0b')
-    version('0.7.1', sha256='d6684534174caa30e0169e106a7152aee14507796a610b76be9fe9b335b18410')
-    version('0.7', sha256='9b2cac8053d21dde5f2b3edb01948dac8ee5c3a85eeeeb6913c3ddf2f773c7b6')
-    version('0.6', sha256='c2d976c06c099edb525b8ac3745f3d3b5c49af6189edb6de390ddf9c248913cf')
-    version('0.5.1', sha256='c4ecfbb99acbb034c4f4580496502bde6b33f3dfc47873c59ee7e509c05dc822')
-    version('0.5', sha256='3320b7fd80e44a1ac27658e19e67215f464c080b02c8af9fce57050d411560d2')
+    homepage = "https://github.com/lepture/mistune"
+    pypi     = "mistune/mistune-2.0.2.tar.gz"
+
+    version('2.0.2', sha256='6fc88c3cb49dba8b16687b41725e661cf85784c12e8974a29b9d336dd596c3a1')
+    version('0.8.4', sha256='59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e')
+    version('0.8.3', sha256='bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619')
+    version('0.8.2', sha256='c50f2fb3a058120c5696f08af9d57877a9c76e879f19af5835fb2c6a4e56a67b')
+    version('0.8.1', sha256='4c0f66924ce28f03b95b210ea57e57bd0b59f479edd91c2fa4fe59331eae4a82')
+    version('0.8',   sha256='dc3f43e7cf0abb95cdfecbf82d85c419108d5f13e1844b2a8a2fc0abf24c7a47')
+    version('0.7.4', sha256='8517af9f5cd1857bb83f9a23da75aa516d7538c32a2c5d5c56f3789a9e4cd22f')
+    version('0.7.3', sha256='21d0e869df3b9189f248e022f1c9763cf9069e1a2f00676f1f1852bd7f98b713')
+    version('0.7.2', sha256='626f2516adcde4af608eaf83635ff20ff7e577c1898ad4d0f0fcd8c094399840')
+    version('0.7.1', sha256='6076dedf768348927d991f4371e5a799c6a0158b16091df08ee85ee231d929a7')
+    version('0.7',   sha256='1daa2e55f5de63ecde7c446c4677c0447006752f78ad2c9c1c3c3452d395f89f')
+    version('0.6',   sha256='d54a69365d01bc97412a39c11674a8aae3f333586e91f38895cc1ad818e13dc5')
+    version('0.5.1', sha256='cc66489a28845c0e1848ae290af5b555074eb76185136ca058e8eed1faa89692')
+    version('0.5',   sha256='d53d868cfd10cf757160e88adb5760fce95f7026a243f15a02b7c604238e5869')
 
     depends_on('py-setuptools', type='build')

var/spack/repos/builtin/packages/py-ml-collections/package.py

@@ -0,0 +1,24 @@
+# Copyright 2013-2022 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 import *
+
+
+class PyMlCollections(PythonPackage):
+    """ML Collections is a library of Python collections designed for ML usecases."""
+
+    homepage = "https://https://github.com/google/ml_collections"
+    pypi     = "ml_collections/ml_collections-0.1.0.tar.gz"
+
+    version('0.1.1', sha256='3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc')
+
+    depends_on('python@2.6:', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-pyyaml', type=('build', 'run'))
+    depends_on('py-absl-py', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-contextlib2', type=('build', 'run'))
+    depends_on('py-dataclasses', type=('build', 'run'), when='python@:3.6')
+    depends_on('py-typing', type=('build', 'run'), when='python@:3.5')

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

@@ -3,19 +3,23 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from spack import *
+
 
 class PyMultidict(PythonPackage):
     """Multidict is dict-like collection of key-value pairs where key
     might be occurred more than once in the container."""
 
     homepage = "https://github.com/aio-libs/multidict"
-    url      = "https://github.com/aio-libs/multidict/archive/v4.7.6.tar.gz"
+    pypi     = "multidict/multidict-6.0.2.tar.gz"
 
-    version('5.2.0', sha256='70039c8d0f4883816de230619c9d4ee1b8527b3628a42783e8bc26de4fee1154')
-    version('5.1.0', sha256='1798708288851b808d2d03ea6046ca51bc44c228aaea12c9643a0a481ee41d8c')
-    version('4.7.6', sha256='449035f89a12f189579ff83811424c71e4a39e335bcb8045145ad084b7bde2dc')
+    version('6.0.2', sha256='5ff3bd75f38e4c43f1f470f2df7a4d430b821c4ce22be384e1459cb57d6bb013')
+    version('5.2.0', sha256='0dd1c93edb444b33ba2274b66f63def8a327d607c6c790772f448a53b6ea59ce')
+    version('5.1.0', sha256='25b4e5f22d3a37ddf3effc0710ba692cfc792c2b9edfb9c05aefe823256e84d5')
+    version('4.7.6', sha256='fbb77a75e529021e7c4a8d4e823d88ef4d23674a202be4f5addffc72cbb91430')
 
-    depends_on('py-setuptools', type='build')
-    depends_on('py-setuptools@40:', type='build', when='@5.1.0:')
+    depends_on('python@3.7:', when='@6:', type=('build', 'run'))
+    depends_on('python@3.6:', when='@5.1:', type=('build', 'run'))
     depends_on('python@3.5:', type=('build', 'run'))
-    depends_on('python@3.6:', type=('build', 'run'), when='@5.1.0:')
+    depends_on('py-pip@18:', when='@:4', type='build')
+    depends_on('py-setuptools@40:', type='build')

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

@@ -0,0 +1,19 @@
+# Copyright 2013-2022 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 import *
+
+
+class PyNpx(PythonPackage):
+    """Some useful extensions for NumPy"""
+
+    homepage = "https://github.com/nschloe/npx"
+    pypi     = "npx/npx-0.1.0.tar.gz"
+
+    version('0.1.0', sha256='3edec9508326b6724d7c176dbcba2098508788241b8a671aab583d0c72b2f05b')
+
+    depends_on('python@3.7:', type=('build', 'run'))
+    depends_on('py-flit-core@3.2:3', type='build')
+    depends_on('py-numpy@1.20.0:', type=('build', 'run'))

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

@@ -0,0 +1,23 @@
+# Copyright 2013-2022 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 import *
+
+
+class PyParam(PythonPackage):
+    """Param is a library providing Parameters: Python attributes extended to have
+    features such as type and range checking, dynamically generated values,
+    documentation strings, default values, etc., each of which is inherited from
+    parent classes if not specified in a subclass."""
+
+    homepage = "https://param.holoviz.org/"
+    pypi     = "param/param-1.12.0.tar.gz"
+
+    maintainers = ['haralmha']
+
+    version('1.12.0', sha256='35d0281c8e3beb6dd469f46ff0b917752a54bed94d1b0c567346c76d0ff59c4a')
+
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')

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

@@ -0,0 +1,23 @@
+# Copyright 2013-2022 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 import *
+
+
+class PyPriority(PythonPackage):
+    """Priority is a pure-Python implementation of the priority
+    logic for HTTP/2, set out in RFC 7540 Section 5.3 (Stream
+    Priority). This logic allows for clients to express a
+    preference for how the server allocates its (limited)
+    resources to the many outstanding HTTP requests that may be
+    running over a single HTTP/2 connection."""
+
+    homepage = "https://github.com/python-hyper/priority/"
+    pypi     = "priority/priority-2.0.0.tar.gz"
+
+    version('2.0.0', sha256='c965d54f1b8d0d0b19479db3924c7c36cf672dbf2aec92d43fbdaf4492ba18c0')
+
+    depends_on('python@3.6.1:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')

var/spack/repos/builtin/packages/py-setuptools-scm/package.py

@@ -14,6 +14,7 @@ class PySetuptoolsScm(PythonPackage):
 
     version('6.3.2',  sha256='a49aa8081eeb3514eb9728fa5040f2eaa962d6c6f4ec9c32f6c1fba88f88a0f2')
     version('6.0.1',  sha256='d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92')
+    version('5.0.2', sha256='83a0cedd3449e3946307811a4c7b9d89c4b5fd464a2fb5eeccd0a5bb158ae5c8')
     version('4.1.2',  sha256='a8994582e716ec690f33fec70cca0f85bd23ec974e3f783233e4879090a7faa8')
     version('3.5.0',  sha256='5bdf21a05792903cafe7ae0c9501182ab52497614fa6b1750d9dbae7b60c1a87')
     version('3.3.3',  sha256='bd25e1fb5e4d603dcf490f1fde40fb4c595b357795674c3e5cb7f6217ab39ea5')
@@ -27,6 +28,7 @@ class PySetuptoolsScm(PythonPackage):
     depends_on('python@3.6:', when='@6:', type=('build', 'run'))
 
     depends_on('py-setuptools@34.4:', type=('build', 'run'))
+    depends_on('py-setuptools@42:', type=('build', 'run'), when='@5:')
     depends_on('py-setuptools@45:', type=('build', 'run'), when='@6:')
 
     depends_on('py-toml', when='+toml @:6.1.0', type=('build', 'run'))

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

@@ -13,8 +13,10 @@ class PyTestpath(PythonPackage):
     homepage = "https://github.com/jupyter/testpath"
     pypi = "testpath/testpath-0.4.2.tar.gz"
 
+    version('0.6.0', sha256='2f1b97e6442c02681ebe01bd84f531028a7caea1af3825000f52345c30285e0f')
     version('0.5.0', sha256='1acf7a0bcd3004ae8357409fc33751e16d37ccc650921da1094a86581ad1e417')
     version('0.4.2', sha256='b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8')
 
     depends_on('python@3.5:', type=('build', 'run'), when='@0.5.0:')
-    depends_on('py-flit-core@3.2.0:3.2', type='build')
+    depends_on('py-flit-core@3.2.0:3.2', type='build', when='@:0.5.0')
+    depends_on('py-flit-core@3.2.0:3', type='build', when='@0.6.0:')