docs: consistently use 'managed environment' over 'named ...'

This reverts commit 3532d6ff16.

bin/spack-tmpconfig

@@ -72,6 +72,7 @@ config:
     root: $TMP_DIR/install
   misc_cache: $$user_cache_path/cache
   source_cache: $$user_cache_path/source
+  environments_root: $TMP_DIR/envs
 EOF
 cat >"$SPACK_USER_CONFIG_PATH/bootstrap.yaml" <<EOF
 bootstrap:

etc/spack/defaults/config.yaml

@@ -81,6 +81,10 @@ config:
   source_cache: $spack/var/spack/cache
 
 
+  ## Directory where spack managed environments are created and stored
+  # environments_root: $spack/var/spack/environments
+
+
   # Cache directory for miscellaneous files, like the package index.
   # This can be purged with `spack clean --misc-cache`
   misc_cache: $user_cache_path/cache

lib/spack/docs/environments.rst

@@ -58,9 +58,9 @@ Using Environments
 Here we follow a typical use case of creating, concretizing,
 installing and loading an environment.
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Creating a named Environment
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Creating a managed Environment
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 An environment is created by:
 
@@ -72,7 +72,8 @@ Spack then creates the directory ``var/spack/environments/myenv``.
 
 .. note::
 
-   All named environments are stored in the ``var/spack/environments`` folder.
+   All managed environments by default are stored in the ``var/spack/environments`` folder.
+   This location can be changed by setting the ``environments_root`` variable in ``config.yaml``.
 
 In the ``var/spack/environments/myenv`` directory, Spack creates the
 file ``spack.yaml`` and the hidden directory ``.spack-env``.
@@ -346,7 +347,7 @@ the Environment and then install the concretized specs.
    (see :ref:`build-jobs`). To speed up environment builds further, independent
    packages can be installed in parallel by launching more Spack instances. For
    example, the following will build at most four packages in parallel using
-   three background jobs:
+   three background jobs: 
 
    .. code-block:: console
 
@@ -394,7 +395,7 @@ version (and other constraints) passed as the spec argument to the
 
 For packages with ``git`` attributes, git branches, tags, and commits can
 also be used as valid concrete versions (see :ref:`version-specifier`).
-This means that for a package ``foo``, ``spack develop foo@git.main`` will clone
+This means that for a package ``foo``, ``spack develop foo@git.main`` will clone 
 the ``main`` branch of the package, and ``spack install`` will install from
 that git clone if ``foo`` is in the environment.
 Further development on ``foo`` can be tested by reinstalling the environment,
@@ -630,35 +631,6 @@ The following two Environment manifests are identical:
 Spec matrices can be used to install swaths of software across various
 toolchains.
 
-Note that ordering of matrices is important. For example, the
-following environments are identical:
-
-.. code-block:: yaml
-
-   spack:
-     specs:
-       - matrix:
-           - [hdf5@1.10.2+mpi]
-           - [^mpich, ^openmpi]
-           - ['%gcc']
-       - matrix:
-           - [hdf5@1.12.1+mpi]
-           - ['%gcc']
-           - [^mpich, ^openmpi]
-
-   spack:
-     specs:
-       - hdf5@1.10.2+mpi ^mpich%gcc
-       - hdf5@1.10.2+mpi ^openmpi%gcc
-       - hdf5@1.12.1+mpi %gcc ^mpich
-       - hdf5@1.12.1+mpi %gcc ^openmpi
-
-Notice how the first matrix applies the compiler constraints to the
-mpi dependencies, whereas the second matrix applies the compiler
-constraints directly to the root hdf5 node. This gives users the full
-breadth of expressiveness of the spec syntax through the matrix
-interface.
-
 ^^^^^^^^^^^^^^^^^^^^
 Spec List References
 ^^^^^^^^^^^^^^^^^^^^
@@ -1149,19 +1121,19 @@ index once every package is pushed. Note how this target uses the generated
 
    SPACK ?= spack
    BUILDCACHE_DIR = $(CURDIR)/tarballs
-
+   
    .PHONY: all
-
+   
    all: push
-
+   
    include env.mk
-
+   
    example/push/%: example/install/%
    	@mkdir -p $(dir $@)
    	$(info About to push $(SPEC) to a buildcache)
    	$(SPACK) -e . buildcache create --allow-root --only=package --directory $(BUILDCACHE_DIR) /$(HASH)
    	@touch $@
-
+   
    push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS))
    	$(info Updating the buildcache index)
    	$(SPACK) -e . buildcache update-index --directory $(BUILDCACHE_DIR)

lib/spack/spack/cmd/env.py

@@ -166,7 +166,7 @@ def env_activate(args):
         short_name = os.path.basename(env_path)
         ev.Environment(env).write(regenerate=False)
 
-    # Named environment
+    # Managed environment
     elif ev.exists(env_name_or_dir) and not args.dir:
         env_path = ev.root(env_name_or_dir)
         short_name = env_name_or_dir

lib/spack/spack/cmd/location.py

@@ -95,7 +95,7 @@ def location(parser, args):
             spack.cmd.require_active_env("location -e")
             path = ev.active_environment().path
         else:
-            # Get named environment path
+            # Get path of requested environment
             if not ev.exists(args.location_env):
                 tty.die("no such environment: '%s'" % args.location_env)
             path = ev.root(args.location_env)

lib/spack/spack/compilers/cce.py

@@ -89,11 +89,6 @@ def cxx14_flag(self):
             return "-std=c++14"
         return "-h std=c++14"
 
-    @property
-    def cxx17_flag(self):
-        if self.is_clang_based:
-            return "-std=c++17"
-
     @property
     def c99_flag(self):
         if self.is_clang_based:

lib/spack/spack/environment/environment.py

@@ -64,8 +64,8 @@
 _active_environment = None
 
 
-#: path where environments are stored in the spack tree
-env_path = os.path.join(spack.paths.var_path, "environments")
+#: default path where environments are stored in the spack tree
+default_env_path = os.path.join(spack.paths.var_path, "environments")
 
 
 #: Name of the input yaml file for an environment
@@ -80,6 +80,26 @@
 env_subdir_name = ".spack-env"
 
 
+def env_root_path():
+    """Override default root path if the user specified it"""
+    return spack.util.path.canonicalize_path(
+        spack.config.get("config:environments_root", default=default_env_path)
+    )
+
+
+def check_disallowed_env_config_mods(scopes):
+    for scope in scopes:
+        with spack.config.use_configuration(scope):
+            if spack.config.get("config:environments_root"):
+                raise SpackEnvironmentError(
+                    "Spack environments are prohibited from modifying 'config:environments_root' "
+                    "because it can make the definition of the environment ill-posed. Please "
+                    "remove from your environment and place it in a permanent scope such as "
+                    "defaults, system, site, etc."
+                )
+    return scopes
+
+
 def default_manifest_yaml():
     """default spack.yaml file to put in new environments"""
     return """\
@@ -216,7 +236,7 @@ def active_environment():
 
 def _root(name):
     """Non-validating version of root(), to be used internally."""
-    return os.path.join(env_path, name)
+    return os.path.join(env_root_path(), name)
 
 
 def root(name):
@@ -251,10 +271,12 @@ def read(name):
 
 
 def create(name, init_file=None, with_view=None, keep_relative=False):
-    """Create a named environment in Spack."""
+    """Create a managed environment in Spack."""
+    if not os.path.isdir(env_root_path()):
+        fs.mkdirp(env_root_path())
     validate_env_name(name)
     if exists(name):
-        raise SpackEnvironmentError("'%s': environment already exists" % name)
+        raise SpackEnvironmentError("'%s': environment already exists at %s" % (name, root(name)))
     return Environment(root(name), init_file, with_view, keep_relative)
 
 
@@ -268,10 +290,10 @@ def all_environment_names():
     """List the names of environments that currently exist."""
     # just return empty if the env path does not exist.  A read-only
     # operation like list should not try to create a directory.
-    if not os.path.exists(env_path):
+    if not os.path.exists(env_root_path()):
         return []
 
-    candidates = sorted(os.listdir(env_path))
+    candidates = sorted(os.listdir(env_root_path()))
     names = []
     for candidate in candidates:
         yaml_path = os.path.join(_root(candidate), manifest_name)
@@ -281,7 +303,7 @@ def all_environment_names():
 
 
 def all_environments():
-    """Generator for all named Environments."""
+    """Generator for all managed Environments."""
     for name in all_environment_names():
         yield read(name)
 
@@ -849,14 +871,14 @@ def clear(self, re_read=False):
     @property
     def internal(self):
         """Whether this environment is managed by Spack."""
-        return self.path.startswith(env_path)
+        return self.path.startswith(env_root_path())
 
     @property
     def name(self):
         """Human-readable representation of the environment.
 
         This is the path for directory environments, and just the name
-        for named environments.
+        for managed environments.
         """
         if self.internal:
             return os.path.basename(self.path)
@@ -1036,7 +1058,9 @@ def env_file_config_scope(self):
 
     def config_scopes(self):
         """A list of all configuration scopes for this environment."""
-        return self.included_config_scopes() + [self.env_file_config_scope()]
+        return check_disallowed_env_config_mods(
+            self.included_config_scopes() + [self.env_file_config_scope()]
+        )
 
     def destroy(self):
         """Remove this environment from Spack entirely."""
@@ -2265,12 +2289,15 @@ def _concretize_from_constraints(spec_constraints, tests=False):
         m += "concretization target. all specs must have a single name "
         m += "constraint for concretization."
         raise InvalidSpecConstraintError(m)
+    spec_constraints.remove(root_spec[0])
 
     invalid_constraints = []
     while True:
-        # Combine constraints into a single spec
-        s = Spec(" ".join([str(c) for c in spec_constraints if c not in invalid_constraints]))
-
+        # Attach all anonymous constraints to one named spec
+        s = root_spec[0].copy()
+        for c in spec_constraints:
+            if c not in invalid_constraints:
+                s.constrain(c)
         try:
             return s.concretized(tests=tests)
         except spack.spec.InvalidDependencyError as e:

lib/spack/spack/main.py

@@ -459,7 +459,7 @@ def make_argument_parser(**kwargs):
         dest="env_dir",
         metavar="DIR",
         action="store",
-        help="run with an environment directory (ignore named environments)",
+        help="run with an environment directory (ignore managed environments)",
     )
     env_group.add_argument(
         "-E",

lib/spack/spack/schema/config.py

@@ -67,6 +67,7 @@
             "license_dir": {"type": "string"},
             "source_cache": {"type": "string"},
             "misc_cache": {"type": "string"},
+            "environments_root": {"type": "string"},
             "connect_timeout": {"type": "integer", "minimum": 0},
             "verify_ssl": {"type": "boolean"},
             "suppress_gpg_warnings": {"type": "boolean"},

lib/spack/spack/spec_list.py

@@ -51,9 +51,7 @@ def specs_as_constraints(self):
             constraints = []
             for item in self.specs_as_yaml_list:
                 if isinstance(item, dict):  # matrix of specs
-                    expanded = _expand_matrix_constraints(item)
-                    for e in expanded:
-                        constraints.append([Spec(x) for x in e])
+                    constraints.extend(_expand_matrix_constraints(item))
                 else:  # individual spec
                     constraints.append([Spec(item)])
             self._constraints = constraints
@@ -64,11 +62,13 @@ def specs_as_constraints(self):
     def specs(self):
         if self._specs is None:
             specs = []
-            for item in self.specs_as_yaml_list:
-                if isinstance(item, dict):  # matrix of specs
-                    specs.extend([Spec(" ".join(x)) for x in _expand_matrix_constraints(item)])
-                else:  # individual spec
-                    specs.append(Spec(item))
+            # This could be slightly faster done directly from yaml_list,
+            # but this way is easier to maintain.
+            for constraint_list in self.specs_as_constraints:
+                spec = constraint_list[0].copy()
+                for const in constraint_list[1:]:
+                    spec.constrain(const)
+                specs.append(spec)
             self._specs = specs
 
         return self._specs
@@ -193,7 +193,11 @@ def _expand_matrix_constraints(matrix_config):
     for combo in itertools.product(*expanded_rows):
         # Construct a combined spec to test against excludes
         flat_combo = [constraint for constraint_list in combo for constraint in constraint_list]
-        test_spec = Spec(" ".join(flat_combo))
+        flat_combo = [Spec(x) for x in flat_combo]
+
+        test_spec = flat_combo[0].copy()
+        for constraint in flat_combo[1:]:
+            test_spec.constrain(constraint)
 
         # Abstract variants don't have normal satisfaction semantics
         # Convert all variants to concrete types.
@@ -209,7 +213,7 @@ def _expand_matrix_constraints(matrix_config):
             continue
 
         if sigil:
-            flat_combo[0] = sigil + flat_combo[0]
+            flat_combo[0] = Spec(sigil + str(flat_combo[0]))
 
         # Add to list of constraints
         results.append(flat_combo)

lib/spack/spack/test/cmd/concretize.py

@@ -9,8 +9,7 @@
 import spack.environment as ev
 from spack.main import SpackCommand
 
-# everything here uses the mock_env_path
-pytestmark = pytest.mark.usefixtures("mutable_mock_env_path", "config", "mutable_mock_repo")
+pytestmark = pytest.mark.usefixtures("config", "mutable_mock_repo")
 
 env = SpackCommand("env")
 add = SpackCommand("add")
@@ -21,7 +20,7 @@
 
 
 @pytest.mark.parametrize("unify", unification_strategies)
-def test_concretize_all_test_dependencies(unify):
+def test_concretize_all_test_dependencies(unify, mutable_mock_env_path):
     """Check all test dependencies are concretized."""
     env("create", "test")
 
@@ -33,7 +32,7 @@ def test_concretize_all_test_dependencies(unify):
 
 
 @pytest.mark.parametrize("unify", unification_strategies)
-def test_concretize_root_test_dependencies_not_recursive(unify):
+def test_concretize_root_test_dependencies_not_recursive(unify, mutable_mock_env_path):
     """Check that test dependencies are not concretized recursively."""
     env("create", "test")
 
@@ -45,7 +44,7 @@ def test_concretize_root_test_dependencies_not_recursive(unify):
 
 
 @pytest.mark.parametrize("unify", unification_strategies)
-def test_concretize_root_test_dependencies_are_concretized(unify):
+def test_concretize_root_test_dependencies_are_concretized(unify, mutable_mock_env_path):
     """Check that root test dependencies are concretized."""
     env("create", "test")
 

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

@@ -3236,3 +3236,20 @@ def test_relative_view_path_on_command_line_is_made_absolute(tmpdir, config):
         env("create", "--with-view", "view", "--dir", "env")
         environment = ev.Environment(os.path.join(".", "env"))
         assert os.path.samefile("view", environment.default_view.root)
+
+
+def test_environment_created_in_users_location(mutable_config, tmpdir):
+    """Test that an environment is created in a location based on the config"""
+    spack.config.set("config:environments_root", str(tmpdir.join("envs")))
+    env_dir = spack.config.get("config:environments_root")
+
+    assert tmpdir.strpath in env_dir
+    assert not os.path.isdir(env_dir)
+
+    dir_name = "user_env"
+    env("create", dir_name)
+    out = env("list")
+
+    assert dir_name in out
+    assert env_dir in ev.root(dir_name)
+    assert os.path.isdir(os.path.join(env_dir, dir_name))

lib/spack/spack/test/cmd/uninstall.py

@@ -223,7 +223,7 @@ class TestUninstallFromEnv(object):
     concretize = SpackCommand("concretize")
     find = SpackCommand("find")
 
-    @pytest.fixture
+    @pytest.fixture(scope="function")
     def environment_setup(
         self, mutable_mock_env_path, config, mock_packages, mutable_database, install_mockery
     ):
@@ -242,6 +242,9 @@ def environment_setup(
             TestUninstallFromEnv.add("dt-diamond-bottom")
             TestUninstallFromEnv.concretize()
             install("--fake")
+        yield "environment_setup"
+        TestUninstallFromEnv.env("rm", "e1", "-y")
+        TestUninstallFromEnv.env("rm", "e2", "-y")
 
     def test_basic_env_sanity(self, environment_setup):
         for env_name in ["e1", "e2"]:

lib/spack/spack/test/conftest.py

@@ -1551,14 +1551,14 @@ def get_rev():
     yield t
 
 
-@pytest.fixture()
-def mutable_mock_env_path(tmpdir_factory):
+@pytest.fixture(scope="function")
+def mutable_mock_env_path(tmpdir_factory, mutable_config):
     """Fixture for mocking the internal spack environments directory."""
-    saved_path = ev.environment.env_path
+    saved_path = ev.environment.default_env_path
     mock_path = tmpdir_factory.mktemp("mock-env-path")
-    ev.environment.env_path = str(mock_path)
+    ev.environment.default_env_path = str(mock_path)
     yield mock_path
-    ev.environment.env_path = saved_path
+    ev.environment.default_env_path = saved_path
 
 
 @pytest.fixture()

lib/spack/spack/test/env.py

@@ -75,8 +75,8 @@ def test_env_change_spec(tmpdir, mock_packages, config):
   - desired_specs: ["mpileaks@2.1"]
   specs:
   - matrix:
-    - [$desired_specs]
     - [$compilers]
+    - [$desired_specs]
 """
 
 
@@ -143,3 +143,21 @@ def test_user_view_path_is_not_canonicalized_in_yaml(tmpdir, config):
         snd = ev.Environment(env_path)
         assert snd.yaml["spack"]["view"] == view
         assert os.path.samefile(snd.default_view.root, absolute_view)
+
+
+def test_environment_cant_modify_environments_root(tmpdir):
+    filename = str(tmpdir.join("spack.yaml"))
+    with open(filename, "w") as f:
+        f.write(
+            """\
+ spack:
+   config:
+     environments_root: /a/black/hole
+   view: false
+   specs: []
+ """
+        )
+    with tmpdir.as_cwd():
+        with pytest.raises(ev.SpackEnvironmentError):
+            e = ev.Environment(tmpdir.strpath)
+            ev.activate(e)

lib/spack/spack/test/spec_list.py

@@ -61,25 +61,25 @@ def test_spec_list_expansions(self):
     @pytest.mark.parametrize(
         "specs,expected",
         [
-            # Constraints are ordered carefully to apply to appropriate node
+            # Constraints are ordered randomly
             (
                 [
                     {
                         "matrix": [
-                            ["hypre", "libelf"],
-                            ["~shared"],
-                            ["^foo"],
                             ["^zmpi"],
                             ["%gcc@4.5.0"],
+                            ["hypre", "libelf"],
+                            ["~shared"],
                             ["cflags=-O3", 'cflags="-g -O0"'],
+                            ["^foo"],
                         ]
                     }
                 ],
                 [
-                    "hypre ~shared ^foo ^zmpi cflags=-O3 %gcc@4.5.0",
-                    'hypre ~shared ^foo ^zmpi cflags="-g -O0" %gcc@4.5.0',
-                    "libelf ~shared ^foo ^zmpi cflags=-O3 %gcc@4.5.0",
-                    'libelf ~shared ^foo ^zmpi cflags="-g -O0" %gcc@4.5.0',
+                    "hypre cflags=-O3 ~shared %gcc@4.5.0 ^foo ^zmpi",
+                    'hypre cflags="-g -O0" ~shared %gcc@4.5.0 ^foo ^zmpi',
+                    "libelf cflags=-O3 ~shared %gcc@4.5.0 ^foo ^zmpi",
+                    'libelf cflags="-g -O0" ~shared %gcc@4.5.0 ^foo ^zmpi',
                 ],
             ),
             # A constraint affects both the root and a dependency

share/spack/gitlab/cloud_pipelines/stacks/gpu-tests/spack.yaml

@@ -59,6 +59,8 @@ spack:
 
   specs:
   - kokkos +rocm amdgpu_target=gfx90a
+  - kokkos +wrapper +cuda cuda_arch=80 ^cuda@11.7.1
+  - raja +cuda cuda_arch=80 ^cuda@11.7.1
   - raja +cuda cuda_arch=80 ^cuda@12.0.0
 
   # FAILURES
@@ -107,6 +109,14 @@ spack:
           variables:
             CI_JOB_SIZE: large
 
+      - match:
+        - kokkos +cuda cuda_arch=80 ^cuda@11.7.1
+        - raja +cuda cuda_arch=80 ^cuda@11.7.1
+        runner-attributes:
+          tags: [ "nvidia-515.65.01", "cuda-11.7", "a100" ]
+          variables:
+            CI_JOB_SIZE: large
+
       - match:
         - kokkos +cuda cuda_arch=80 ^cuda@12.0.0
         - raja +cuda cuda_arch=80 ^cuda@12.0.0

var/spack/repos/builtin/packages/gsl-lite/package.py

@@ -1,50 +0,0 @@
-# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-
-from spack.package import *
-
-
-class GslLite(CMakePackage):
-    """A single-file header-only version of ISO C++ Guidelines Support Library
-    (GSL) for C++98, C++11, and later"""
-
-    homepage = "https://github.com/gsl-lite/gsl-lite"
-    git = "https://github.com/gsl-lite/gsl-lite.git"
-    url = "https://github.com/gsl-lite/gsl-lite/archive/refs/tags/v0.38.1.tar.gz"
-
-    maintainers("AlexanderRichert-NOAA", "climbfuji", "edwardhartnett", "Hang-Lei-NOAA")
-
-    version("0.40.0", commit="d6c8af99a1d95b3db36f26b4f22dc3bad89952de")
-    version("0.39.0", commit="d0903fa87ff579c30f608bc363582e6563570342")
-    version("0.38.1", sha256="c2fa2315fff312f3897958903ed4d4e027f73fa44235459ecb467ad7b7d62b18")
-    version("0.38.0", sha256="5d25fcd31ea66dac9e14da1cad501d95450ccfcb2768fffcd1a4170258fcbc81")
-    version("0.37.0", sha256="a31d51b73742bb234acab8d2411223cf299e760ed713f0840ffed0dabe57ca38")
-    version("0.36.0", sha256="c052cc4547b33cedee6f000393a7005915c45c6c06b35518d203db117f75c71c")
-    version("0.34.0", sha256="a7d5b2672b78704ca03df9ef65bc274d8f8cacad3ca950365eef9e25b50324c5")
-
-    variant("tests", default=False)
-    variant("cuda_tests", default=False)
-    variant("examples", default=False)
-    variant("static_analysis_demos", default=False)
-    variant("cmake_export_package_registry", default=False)
-    variant("compat_header", default=False)
-    variant("legacy_headers", default=False)
-
-    def cmake_args(self):
-        args = [
-            self.define_from_variant("GSL_LITE_OPT_BUILD_TESTS", "tests"),
-            self.define_from_variant("GSL_LITE_OPT_BUILD_CUDA_TESTS", "cuda_tests"),
-            self.define_from_variant("GSL_LITE_OPT_BUILD_EXAMPLES", "examples"),
-            self.define_from_variant(
-                "GSL_LITE_LOPT_BUILD_STATIC_ANALYSIS_DEMOS", "static_analysis_demos"
-            ),
-            self.define_from_variant(
-                "CMAKE_EXPORT_PACKAGE_REGISTRY", "cmake_export_package_registry"
-            ),
-            self.define_from_variant("GSL_LITE_OPT_INSTALL_COMPAT_HEADER", "compat_header"),
-            self.define_from_variant("GSL_LITE_OPT_INSTALL_LEGACY_HEADERS", "legacy_headers"),
-        ]
-        return args

var/spack/repos/builtin/packages/intel-tbb/package.py

@@ -255,7 +255,7 @@ def build(self, pkg, spec, prefix):
         #
         self.coerce_to_spack("build")
 
-        if spec.satisfies("%clang") or spec.satisfies("%apple-clang") or spec.satisfies("%rocmcc"):
+        if spec.satisfies("%clang") or spec.satisfies("%apple-clang"):
             tbb_compiler = "clang"
         elif spec.satisfies("%intel"):
             tbb_compiler = "icc"

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

@@ -16,7 +16,6 @@ class Libmonitor(AutotoolsPackage):
     maintainers("mwkrentel")
 
     version("master", branch="master")
-    version("2023.02.13", commit="6db182b25202552f75a087116ab57193652d150f")
     version("2022.09.02", commit="4ae16dab0ba5fbda0ffe28df523613ea22cb85ae")
     version("2021.11.08", commit="22aa52c621534f12d401fa37f6963bfca7441e20")
     version("2021.04.27", commit="a2d1b6be23410ef1ad2c9d0006672453803243c2")

var/spack/repos/builtin/packages/netcdf-fortran/nag_libtool_2.4.2.patch

@@ -0,0 +1,124 @@
+--- a/configure
++++ b/configure
+@@ -9584,6 +9584,10 @@ for cc_temp in $compiler""; do
+   esac
+ done
+ cc_basename=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
++case $cc_basename in
++  nagfor*) ;;
++  *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && cc_basename='nagfor-wrapper' ;;
++esac
+ 
+ 
+ # Only perform the check for file, if the check method requires it
+@@ -10657,6 +10661,10 @@ _LT_EOF
+ 	lf95*)				# Lahey Fortran 8.1
+ 	  whole_archive_flag_spec=
+ 	  tmp_sharedflag='--shared' ;;
++	nagfor*)
++	  whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive'
++	  compiler_needs_object=yes
++	  tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+ 	  tmp_addflag= ;;
+@@ -13415,6 +13423,10 @@ $RM -r conftest*
+   esac
+ done
+ cc_basename=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
++case $cc_basename in
++  nagfor*) ;;
++  *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && cc_basename='nagfor-wrapper' ;;
++esac
+ 
+   GCC=$G77
+   if test -n "$compiler"; then
+@@ -14252,6 +14264,10 @@ _LT_EOF
+ 	lf95*)				# Lahey Fortran 8.1
+ 	  whole_archive_flag_spec_F77=
+ 	  tmp_sharedflag='--shared' ;;
++	nagfor*)
++	  whole_archive_flag_spec_F77='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive'
++	  compiler_needs_object_F77=yes
++	  tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+ 	  tmp_addflag= ;;
+@@ -16142,6 +16158,10 @@ $RM -r conftest*
+   esac
+ done
+ cc_basename=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
++case $cc_basename in
++  nagfor*) ;;
++  *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && cc_basename='nagfor-wrapper' ;;
++esac
+ 
+ 
+   if test -n "$compiler"; then
+@@ -17142,6 +17162,10 @@ _LT_EOF
+ 	lf95*)				# Lahey Fortran 8.1
+ 	  whole_archive_flag_spec_FC=
+ 	  tmp_sharedflag='--shared' ;;
++	nagfor*)
++	  whole_archive_flag_spec_FC='${wl}--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive'
++	  compiler_needs_object_FC=yes
++	  tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+ 	  tmp_addflag= ;;
+--- a/ltmain.sh
++++ b/ltmain.sh
+@@ -180,6 +180,24 @@ func_basename ()
+     func_basename_result=`$ECHO "${1}" | $SED "$basename"`
+ } # func_basename may be replaced by extended shell implementation
+ 
++# Calculate cc_basename.  Skip known compiler wrappers and cross-prefix.
++func_cc_basename ()
++{
++    for cc_temp in $*""; do
++      case $cc_temp in
++        compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
++        distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
++        \-*) ;;
++        *) break;;
++      esac
++    done
++    func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
++    case $func_cc_basename_result in
++      nagfor*) ;;
++      *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && func_cc_basename_result='nagfor-wrapper' ;;
++    esac
++}
++
+ 
+ # func_dirname_and_basename file append nondir_replacement
+ # perform func_basename and func_dirname in a single function
+@@ -6422,6 +6440,13 @@ func_mode_link ()
+ 	# Convert "-framework foo" to "foo.ltframework"
+ 	if test -n "$inherited_linker_flags"; then
+ 	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
++
++	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
++	  func_cc_basename $CC
++	  case $func_cc_basename_result in
++	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
++	  esac
++
+ 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ 	    case " $new_inherited_linker_flags " in
+ 	      *" $tmp_inherited_linker_flag "*) ;;
+@@ -8007,6 +8032,14 @@ EOF
+ 	  ;;
+       esac
+ 
++      # Time to revert the changes made for nagfor.
++
++      func_cc_basename $CC
++      case $func_cc_basename_result in
++        nagfor*)
++          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
++      esac
++
+       # move library search paths that coincide with paths to not yet
+       # installed libraries to the beginning of the library search list
+       new_libs=

var/spack/repos/builtin/packages/netcdf-fortran/nag_libtool_2.4.6.patch

@@ -0,0 +1,96 @@
+--- a/configure
++++ b/configure
+@@ -9034,6 +9034,12 @@ func_cc_basename ()
+       esac
+     done
+     func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
++
++    # Set result to 'nagfor-wrapper' when NAG compiler is called via a wrapper (e.g. mpif90).
++    case $func_cc_basename_result in
++      nagfor*) ;;
++      *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && func_cc_basename_result='nagfor-wrapper' ;;
++    esac
+ }
+ 
+ # Check whether --enable-libtool-lock was given.
+@@ -11811,6 +11817,8 @@ _LT_EOF
+ 	  whole_archive_flag_spec=
+ 	  tmp_sharedflag='--shared' ;;
+         nagfor*)                        # NAGFOR 5.3
++          whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
++          compiler_needs_object=yes
+           tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+@@ -15663,6 +15671,8 @@ _LT_EOF
+ 	  whole_archive_flag_spec_F77=
+ 	  tmp_sharedflag='--shared' ;;
+         nagfor*)                        # NAGFOR 5.3
++          whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
++          compiler_needs_object_F77=yes
+           tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+@@ -18788,6 +18798,8 @@ _LT_EOF
+ 	  whole_archive_flag_spec_FC=
+ 	  tmp_sharedflag='--shared' ;;
+         nagfor*)                        # NAGFOR 5.3
++          whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
++          compiler_needs_object_FC=yes
+           tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+@@ -26086,6 +26098,12 @@ func_cc_basename ()
+       esac
+     done
+     func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"`
++
++    # Set result to 'nagfor-wrapper' when NAG compiler is called via a wrapper (e.g. mpif90).
++    case $func_cc_basename_result in
++      nagfor*) ;;
++      *) $cc_temp -V 2>&1 | $GREP '^NAG Fortran Compiler Release' >/dev/null 2>&1 && func_cc_basename_result='nagfor-wrapper' ;;
++    esac
+ }
+ 
+ 
+--- a/ltmain.sh
++++ b/ltmain.sh
+@@ -7868,6 +7868,13 @@ func_mode_link ()
+ 	# Convert "-framework foo" to "foo.ltframework"
+ 	if test -n "$inherited_linker_flags"; then
+ 	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
++
++	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
++	  func_cc_basename $CC
++	  case $func_cc_basename_result in
++	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
++	  esac
++
+ 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ 	    case " $new_inherited_linker_flags " in
+ 	      *" $tmp_inherited_linker_flag "*) ;;
+@@ -8890,7 +8897,8 @@ func_mode_link ()
+ 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+ 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+           # On Darwin other compilers
+-          case $CC in
++          func_cc_basename $CC
++          case $func_cc_basename_result in
+               nagfor*)
+                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+                   ;;
+@@ -9502,6 +9510,14 @@ EOF
+ 	  ;;
+       esac
+ 
++      # Time to revert the changes made for nagfor.
++
++      func_cc_basename $CC
++      case $func_cc_basename_result in
++        nagfor*)
++          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
++      esac
++
+       # move library search paths that coincide with paths to not yet
+       # installed libraries to the beginning of the library search list
+       new_libs=

var/spack/repos/builtin/packages/netcdf-fortran/package.py

@@ -37,6 +37,14 @@ class NetcdfFortran(AutotoolsPackage):
     depends_on("netcdf-c@4.7.4:", when="@4.5.3:")  # nc_def_var_szip required
     depends_on("doxygen", when="+doc", type="build")
 
+    # The default libtool.m4 is too old to handle NAG compiler properly:
+    # https://github.com/Unidata/netcdf-fortran/issues/94
+    # Moreover, Libtool can't handle '-pthread' flag coming from libcurl,
+    # doesn't inject convenience libraries into the shared ones, and is unable
+    # to detect NAG when it is called with an MPI wrapper.
+    patch("nag_libtool_2.4.2.patch", when="@:4.4.4%nag")
+    patch("nag_libtool_2.4.6.patch", when="@4.4.5:%nag")
+
     # Enable 'make check' for NAG, which is too strict.
     patch("nag_testing.patch", when="@4.4.5%nag")
 
@@ -128,6 +136,54 @@ def configure_args(self):
 
         return config_args
 
+    @run_after("configure")
+    def patch_libtool(self):
+        """AOCC support for NETCDF-F"""
+        if "%aocc" in self.spec:
+            # Libtool does not fully support the compiler toolchain, therefore
+            # we have to patch the script. The C compiler normally gets
+            # configured correctly, the variables of interest in the
+            # 'BEGIN LIBTOOL CONFIG' section are set to non-empty values and,
+            # therefore, are not affected by the replacements below. A more
+            # robust solution would be to extend the filter_file function with
+            # an additional argument start_at and perform the replacements
+            # between the '# ### BEGIN LIBTOOL TAG CONFIG: FC' and
+            # '# ### END LIBTOOL TAG CONFIG: FC' markers for the Fortran
+            # compiler, and between the '# ### BEGIN LIBTOOL TAG CONFIG: F77'
+            # and '# ### END LIBTOOL TAG CONFIG: F77' markers for the Fortran 77
+            # compiler.
+
+            # How to pass a linker flag through the compiler:
+            filter_file(r'^wl=""$', 'wl="{0}"'.format(self.compiler.linker_arg), "libtool")
+
+            # Additional compiler flags for building library objects (we need
+            # this to enable shared libraries when building with ~pic). Note
+            # that the following will set fc_pic_flag for both FC and F77, which
+            # in the case of AOCC, should not be a problem. If it is, the
+            # aforementioned modification of the filter_file function could be
+            # a solution.
+            filter_file(
+                r'^pic_flag=""$', 'pic_flag=" {0}"'.format(self.compiler.fc_pic_flag), "libtool"
+            )
+
+            # The following is supposed to tell the compiler to use the GNU
+            # linker. However, the replacement does not happen (at least for
+            # NetCDF-Fortran 4.5.3) because the replaced substring (i.e. the
+            # first argument passed to the filter_file function) is not present
+            # in the file. The flag should probably be added to 'ldflags' in the
+            # flag_handler method above (another option is to add the flag to
+            # 'ldflags' in compilers.yaml automatically as it was done for other
+            # flags in https://github.com/spack/spack/pull/22219).
+            filter_file(
+                r"\${wl}-soname \$wl\$soname",
+                r"-fuse-ld=ld -Wl,-soname,\$soname",
+                "libtool",
+                string=True,
+            )
+
+        # TODO: resolve the NAG-related issues in a similar way: remove the
+        #  respective patch files and tune the generated libtool script instead.
+
     @when("@:4.4.5")
     def check(self):
         with working_dir(self.build_directory):

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

@@ -89,7 +89,7 @@ class Octave(AutotoolsPackage, GNUMirrorPackage):
     # Optional dependencies
     depends_on("arpack-ng", when="+arpack")
     depends_on("curl", when="+curl")
-    depends_on("fftw-api@3", when="+fftw")
+    depends_on("fftw", when="+fftw")
     depends_on("fltk", when="+fltk")
     depends_on("fontconfig", when="+fontconfig")
     depends_on("freetype", when="+freetype")
@@ -222,13 +222,12 @@ def configure_args(self):
             config_args.append("--without-curl")
 
         if "+fftw" in spec:
-            fftw_string = "fftw-api"
             config_args.extend(
                 [
-                    "--with-fftw3-includedir=%s" % spec[fftw_string].prefix.include,
-                    "--with-fftw3-libdir=%s" % spec[fftw_string].prefix.lib,
-                    "--with-fftw3f-includedir=%s" % spec[fftw_string].prefix.include,
-                    "--with-fftw3f-libdir=%s" % spec[fftw_string].prefix.lib,
+                    "--with-fftw3-includedir=%s" % spec["fftw"].prefix.include,
+                    "--with-fftw3-libdir=%s" % spec["fftw"].prefix.lib,
+                    "--with-fftw3f-includedir=%s" % spec["fftw"].prefix.include,
+                    "--with-fftw3f-libdir=%s" % spec["fftw"].prefix.lib,
                 ]
             )
         else:

var/spack/repos/builtin/packages/openmpi/nag_pthread/1.10.4_1.10.999.patch

@@ -0,0 +1,49 @@
+--- a/config/ltmain.sh
++++ b/config/ltmain.sh
+@@ -7860,14 +7860,15 @@ func_mode_link ()
+ 	func_source "$lib"
+ 
+ 	# Convert "-framework foo" to "foo.ltframework"
+-        # and "-pthread" to "-Wl,-pthread" if NAG compiler
+ 	if test -n "$inherited_linker_flags"; then
+-          case "$CC" in
+-            nagfor*)
+-	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread/-Wl,-pthread'`;;
+-            *)
+-	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`;;
+-          esac
++	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
++
++	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
++	  func_cc_basename $CC
++	  case $func_cc_basename_result in
++	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
++	  esac
++
+ 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ 	    case " $new_inherited_linker_flags " in
+ 	      *" $tmp_inherited_linker_flag "*) ;;
+@@ -8887,7 +8888,8 @@ func_mode_link ()
+ 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+ 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+           # On Darwin other compilers
+-          case $CC in
++          func_cc_basename $CC
++          case $func_cc_basename_result in
+               nagfor*)
+                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+                   ;;
+@@ -9499,6 +9501,13 @@ EOF
+ 	  ;;
+       esac
+ 
++      # Time to revert the changes made for nagfor.
++      func_cc_basename $CC
++      case $func_cc_basename_result in
++        nagfor*)
++          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
++      esac
++
+       # move library search paths that coincide with paths to not yet
+       # installed libraries to the beginning of the library search list
+       new_libs=

var/spack/repos/builtin/packages/openmpi/nag_pthread/2.0.0_2.1.1.patch

@@ -0,0 +1,40 @@
+--- a/config/ltmain.sh
++++ b/config/ltmain.sh
+@@ -7862,6 +7862,13 @@ func_mode_link ()
+ 	# Convert "-framework foo" to "foo.ltframework"
+ 	if test -n "$inherited_linker_flags"; then
+ 	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
++
++	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
++	  func_cc_basename $CC
++	  case $func_cc_basename_result in
++	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
++	  esac
++
+ 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ 	    case " $new_inherited_linker_flags " in
+ 	      *" $tmp_inherited_linker_flag "*) ;;
+@@ -8881,7 +8888,8 @@ func_mode_link ()
+ 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+ 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+           # On Darwin other compilers
+-          case $CC in
++          func_cc_basename $CC
++          case $func_cc_basename_result in
+               nagfor*)
+                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+                   ;;
+@@ -9493,6 +9501,13 @@ EOF
+ 	  ;;
+       esac
+ 
++      # Time to revert the changes made for nagfor.
++      func_cc_basename $CC
++      case $func_cc_basename_result in
++        nagfor*)
++          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
++      esac
++
+       # move library search paths that coincide with paths to not yet
+       # installed libraries to the beginning of the library search list
+       new_libs=

var/spack/repos/builtin/packages/openmpi/nag_pthread/2.1.2_2.1.3_3.0.0.patch

@@ -0,0 +1,49 @@
+--- a/config/ltmain.sh
++++ b/config/ltmain.sh
+@@ -7860,14 +7860,15 @@ func_mode_link ()
+ 	func_source "$lib"
+ 
+ 	# Convert "-framework foo" to "foo.ltframework"
+-        # and "-pthread" to "-Wl,-pthread" if NAG compiler
+ 	if test -n "$inherited_linker_flags"; then
+-          case "$CC" in
+-            nagfor*)
+-	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread/-Wl,-pthread/g'`;;
+-            *)
+-	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`;;
+-          esac
++	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
++
++	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
++	  func_cc_basename $CC
++	  case $func_cc_basename_result in
++	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
++	  esac
++
+ 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ 	    case " $new_inherited_linker_flags " in
+ 	      *" $tmp_inherited_linker_flag "*) ;;
+@@ -8887,7 +8888,8 @@ func_mode_link ()
+ 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+ 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+           # On Darwin other compilers
+-          case $CC in
++          func_cc_basename $CC
++          case $func_cc_basename_result in
+               nagfor*)
+                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+                   ;;
+@@ -9499,6 +9501,13 @@ EOF
+ 	  ;;
+       esac
+ 
++      # Time to revert the changes made for nagfor.
++      func_cc_basename $CC
++      case $func_cc_basename_result in
++        nagfor*)
++          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
++      esac
++
+       # move library search paths that coincide with paths to not yet
+       # installed libraries to the beginning of the library search list
+       new_libs=

var/spack/repos/builtin/packages/openmpi/nag_pthread/2.1.4_2.1.999_3.0.1_4.patch

@@ -0,0 +1,49 @@
+--- a/config/ltmain.sh
++++ b/config/ltmain.sh
+@@ -7860,14 +7860,15 @@ func_mode_link ()
+ 	func_source "$lib"
+ 
+ 	# Convert "-framework foo" to "foo.ltframework"
+-        # and "-pthread" to "-Wl,-pthread" if NAG compiler
+ 	if test -n "$inherited_linker_flags"; then
+-          case "$CC" in
+-            *nagfor*)
+-	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g' | $SED 's/-pthread/-Wl,-pthread/g'`;;
+-            *)
+-	      tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`;;
+-          esac
++	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
++
++	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
++	  func_cc_basename $CC
++	  case $func_cc_basename_result in
++	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
++	  esac
++
+ 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ 	    case " $new_inherited_linker_flags " in
+ 	      *" $tmp_inherited_linker_flag "*) ;;
+@@ -8887,7 +8888,8 @@ func_mode_link ()
+ 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+ 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+           # On Darwin other compilers
+-          case $CC in
++          func_cc_basename $CC
++          case $func_cc_basename_result in
+               nagfor*)
+                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+                   ;;
+@@ -9499,6 +9501,13 @@ EOF
+ 	  ;;
+       esac
+ 
++      # Time to revert the changes made for nagfor.
++      func_cc_basename $CC
++      case $func_cc_basename_result in
++        nagfor*)
++          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
++      esac
++
+       # move library search paths that coincide with paths to not yet
+       # installed libraries to the beginning of the library search list
+       new_libs=

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

@@ -382,6 +382,14 @@ class Openmpi(AutotoolsPackage, CudaPackage):
     patch("btl_vader.patch", when="@3.0.1:3.0.2")
     patch("btl_vader.patch", when="@3.1.0:3.1.2")
 
+    # Make NAG compiler pass the -pthread option to the linker:
+    # https://github.com/open-mpi/ompi/pull/6378
+    # We support only versions based on Libtool 2.4.6.
+    patch("nag_pthread/2.1.4_2.1.999_3.0.1_4.patch", when="@2.1.4:2.1,3.0.1:4%nag")
+    patch("nag_pthread/2.1.2_2.1.3_3.0.0.patch", when="@2.1.2:2.1.3,3.0.0%nag")
+    patch("nag_pthread/2.0.0_2.1.1.patch", when="@2.0.0:2.1.1%nag")
+    patch("nag_pthread/1.10.4_1.10.999.patch", when="@1.10.4:1.10%nag")
+
     # Fix MPI_Sizeof() in the "mpi" Fortran module for compilers that do not
     # support "IGNORE TKR" functionality (e.g. NAG).
     # The issue has been resolved upstream in two steps:

var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_master.patch

@@ -0,0 +1,10 @@
+--- a/m4/libtool.m4
++++ b/m4/libtool.m4
+@@ -5282,7 +5282,6 @@ _LT_EOF
+ 	tmp_sharedflag='-shared'
+ 	case $cc_basename,$host_cpu in
+         pgcc*)				# Portland Group C compiler
+-	  _LT_TAGVAR(whole_archive_flag_spec, $1)='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
+ 	  tmp_addflag=' $pic_flag'
+ 	  ;;
+ 	pgf77* | pgf90* | pgf95* | pgfortran*)

var/spack/repos/builtin/packages/parallel-netcdf/cray_pgi_libtool_release.patch

@@ -0,0 +1,26 @@
+--- a/configure
++++ b/configure
+@@ -11858,7 +11858,6 @@ _LT_EOF
+ 	tmp_sharedflag='-shared'
+ 	case $cc_basename,$host_cpu in
+         pgcc*)				# Portland Group C compiler
+-	  whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
+ 	  tmp_addflag=' $pic_flag'
+ 	  ;;
+ 	pgf77* | pgf90* | pgf95* | pgfortran*)
+@@ -21326,7 +21325,6 @@ _LT_EOF
+ 	tmp_sharedflag='-shared'
+ 	case $cc_basename,$host_cpu in
+         pgcc*)				# Portland Group C compiler
+-	  whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
+ 	  tmp_addflag=' $pic_flag'
+ 	  ;;
+ 	pgf77* | pgf90* | pgf95* | pgfortran*)
+@@ -25066,7 +25064,6 @@ _LT_EOF
+ 	tmp_sharedflag='-shared'
+ 	case $cc_basename,$host_cpu in
+         pgcc*)				# Portland Group C compiler
+-	  whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
+ 	  tmp_addflag=' $pic_flag'
+ 	  ;;
+ 	pgf77* | pgf90* | pgf95* | pgfortran*)

var/spack/repos/builtin/packages/parallel-netcdf/nag_libtool.patch

@@ -0,0 +1,69 @@
+--- a/configure
++++ b/configure
+@@ -11745,6 +11745,8 @@ _LT_EOF
+ 	  whole_archive_flag_spec=
+ 	  tmp_sharedflag='--shared' ;;
+         nagfor*)                        # NAGFOR 5.3
++          whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
++          compiler_needs_object=yes
+           tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+@@ -21030,6 +21032,8 @@ _LT_EOF
+ 	  whole_archive_flag_spec_F77=
+ 	  tmp_sharedflag='--shared' ;;
+         nagfor*)                        # NAGFOR 5.3
++          whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
++          compiler_needs_object_F77=yes
+           tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+@@ -24765,6 +24769,8 @@ _LT_EOF
+ 	  whole_archive_flag_spec_FC=
+ 	  tmp_sharedflag='--shared' ;;
+         nagfor*)                        # NAGFOR 5.3
++          whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test  -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive'
++          compiler_needs_object_FC=yes
+           tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+--- a/scripts/ltmain.sh
++++ b/scripts/ltmain.sh
+@@ -7862,6 +7862,13 @@ func_mode_link ()
+ 	# Convert "-framework foo" to "foo.ltframework"
+ 	if test -n "$inherited_linker_flags"; then
+ 	  tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'`
++
++	  # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor
++	  func_cc_basename $CC
++	  case $func_cc_basename_result in
++	    nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;;
++	  esac
++
+ 	  for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ 	    case " $new_inherited_linker_flags " in
+ 	      *" $tmp_inherited_linker_flag "*) ;;
+@@ -8881,7 +8888,8 @@ func_mode_link ()
+ 	  xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+ 	  verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+           # On Darwin other compilers
+-          case $CC in
++          func_cc_basename $CC
++          case $func_cc_basename_result in
+               nagfor*)
+                   verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision"
+                   ;;
+@@ -9493,6 +9501,13 @@ EOF
+ 	  ;;
+       esac
+ 
++      # Time to revert the changes made for nagfor.
++      func_cc_basename $CC
++      case $func_cc_basename_result in
++        nagfor*)
++          new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;;
++      esac
++
+       # move library search paths that coincide with paths to not yet
+       # installed libraries to the beginning of the library search list
+       new_libs=

var/spack/repos/builtin/packages/parallel-netcdf/package.py

@@ -79,6 +79,23 @@ def url_for_version(self, version):
     # (see below).
     conflicts("+shared", when="@:1.9%nag+fortran")
 
+    # https://github.com/Parallel-NetCDF/PnetCDF/pull/59
+    patch("nag_libtool.patch", when="@1.9:1.12.1%nag")
+
+    # We could apply the patch unconditionally. However, it fixes a problem
+    # that manifests itself only when we build shared libraries with Spack on
+    # a Cray system with PGI compiler. Based on the name of the $CC executable,
+    # Libtool "thinks" that it works with PGI compiler directly but on a Cray
+    # system it actually works with the Cray's wrapper. PGI compiler (at least
+    # since the version 15.7) "understands" two formats of the
+    # '--whole-archive' argument. Unluckily, Cray's wrapper "understands" only
+    # one of them but Libtool switches to another one. The following patch
+    # discards the switching.
+    patch("cray_pgi_libtool_release.patch", when="@1.8:999%pgi+shared platform=cray")
+    # Given that the bug manifests itself in rather specific conditions, it is
+    # not reported upstream.
+    patch("cray_pgi_libtool_master.patch", when="@master%pgi+shared platform=cray")
+
     @property
     def libs(self):
         libraries = ["libpnetcdf"]

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

@@ -1,26 +0,0 @@
-# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack.package import *
-
-
-class PyFortls(PythonPackage):
-    """A Language Server for Fortran providing code completion, diagnostics, hovering and more."""
-
-    homepage = "https://fortls.fortran-lang.org"
-    pypi = "fortls/fortls-2.13.0.tar.gz"
-
-    maintainers("RMeli")
-
-    version("2.13.0", sha256="23c5013e8dd8e1d65bf07be610d0827bc48aa7331a7a7ce13612d4c646d0db31")
-
-    depends_on("py-setuptools@45:", type="build")
-    depends_on("py-packaging", type=("build", "run"))
-    depends_on("py-setuptools-scm@6.2:+toml", type="build")
-    depends_on("py-setuptools-scm-git-archive", type="build")
-
-    depends_on("py-json5", type=("build", "run"))
-    depends_on("py-importlib-metadata", type=("build", "run"), when="^python@:3.7")
-    depends_on("py-typing-extensions", type=("build", "run"), when="^python@:3.7")

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

@@ -37,7 +37,6 @@ class PyMatplotlib(PythonPackage):
         "pylab",
     ]
 
-    version("3.7.0", sha256="8f6efd313430d7ef70a38a3276281cb2e8646b3a22b3b21eb227da20e15e6813")
     version("3.6.3", sha256="1f4d69707b1677560cd952544ee4962f68ff07952fb9069ff8c12b56353cb8c9")
     version("3.6.2", sha256="b03fd10a1709d0101c054883b550f7c4c5e974f751e2680318759af005964990")
     version("3.6.1", sha256="e2d1b7225666f7e1bcc94c0bc9c587a82e3e8691da4757e357e5c2515222ee37")
@@ -139,12 +138,16 @@ class PyMatplotlib(PythonPackage):
     # https://matplotlib.org/stable/devel/dependencies.html
     # Runtime dependencies
     # Mandatory dependencies
+    extends("python", ignore=r"bin/nosetests.*$|bin/pbr$")
     depends_on("python@3.8:", when="@3.6:", type=("build", "link", "run"))
+    depends_on("python@3.7:", when="@3.4:", type=("build", "link", "run"))
+    depends_on("python@3.6:", when="@3.1:", type=("build", "link", "run"))
+    depends_on("python@3.5:", when="@3:", type=("build", "link", "run"))
+    depends_on("python@2.7:2.8,3.4:", when="@:2", type=("build", "link", "run"))
     depends_on("py-contourpy@1.0.1:", when="@3.6:", type=("build", "run"))
     depends_on("py-cycler@0.10:", type=("build", "run"))
     depends_on("py-fonttools@4.22:", when="@3.5:", type=("build", "run"))
     depends_on("py-kiwisolver@1.0.1:", type=("build", "run"), when="@2.2.0:")
-    depends_on("py-numpy@1.20:", when="@3.7:", type=("build", "run"))
     depends_on("py-numpy@1.19:", when="@3.6:", type=("build", "run"))
     depends_on("py-numpy@1.17:", when="@3.5:", type=("build", "run"))
     depends_on("py-numpy@1.16:", when="@3.4:", type=("build", "run"))
@@ -153,13 +156,11 @@ class PyMatplotlib(PythonPackage):
     depends_on("py-packaging@20:", when="@3.6:", type=("build", "run"))
     depends_on("py-packaging", when="@3.5:", type=("build", "run"))
     depends_on("pil@6.2:", when="@3.3:", type=("build", "run"))
-    depends_on("py-pyparsing@2.3.1:", when="@3.7:", type=("build", "run"))
     depends_on("py-pyparsing@2.2.1:", when="@3.4:", type=("build", "run"))
     depends_on("py-pyparsing@2.0.3,2.0.5:2.1.1,2.1.3:2.1.5,2.1.7:", type=("build", "run"))
     depends_on("py-python-dateutil@2.7:", when="@3.4:", type=("build", "run"))
     depends_on("py-python-dateutil@2.1:", type=("build", "run"))
     depends_on("py-setuptools", type=("build", "run"))
-    depends_on("py-importlib-resources@3.2:", when="@3.7: ^python@:3.9", type=("build", "run"))
 
     # Historical dependencies
     depends_on("py-pytz", type=("build", "run"), when="@:2")
@@ -224,7 +225,6 @@ class PyMatplotlib(PythonPackage):
     # Dependencies for building matplotlib
     # Setup dependencies
     depends_on("py-certifi@2020.6.20:", when="@3.3.1:", type="build")
-    depends_on("py-pybind11@2.6:", when="@3.7:", type="build")
     depends_on("py-setuptools-scm@7:", when="@3.6:", type="build")
     depends_on("py-setuptools-scm@4:6", when="@3.5", type="build")
     depends_on("py-setuptools-scm-git-archive", when="@3.5", type="build")

var/spack/repos/builtin/packages/py-radiant-mlhub/package.py

@@ -14,8 +14,6 @@ class PyRadiantMlhub(PythonPackage):
 
     maintainers("adamjstewart")
 
-    version("0.5.5", sha256="93cabc3c8e9ba343cdb3b0bfaec01bf7a36aae75704fabfe96c8bf5cab9fa899")
-    version("0.5.3", sha256="f111983910e41f2ce40bf401ccf9e33b393e52cc1989f8f8b74c6b4e2bdd0127")
     version("0.5.2", sha256="d310afce962508a44c60f5738fef164c50e78f76c3e85813653824b39a189ca3")
     version("0.5.1", sha256="b7daff4a127e96e27c64eda66e393d9727e61a87c887f86738753486cc44fa46")
     version("0.5.0", sha256="fff788aaa5f8afcb0f6eabff4147eaaf7de375f0a43ecaf2238033fc3a62e2c2")
@@ -25,9 +23,10 @@ class PyRadiantMlhub(PythonPackage):
     version("0.3.0", sha256="dd66479f12317e7bf366abe8d692841485e9497918c30ab14cd6db9e69ce3dbb")
     version("0.2.2", sha256="0d9f634b7e29c7f7294b81a10cf712ac63251949a9c5a07aa6c64c0d5b77e1ba")
     version("0.2.1", sha256="75a2f096b09a87191238fe557dc64dda8c44156351b4026c784c848c7d84b6fb")
-    version("0.2.0", sha256="4a3e4c301c5e74f282bbf77b7d65db5a1d6c2a4dc6d18637eff6e1228ca2eb9d")
 
     depends_on("python@3.8:", when="@0.5:", type=("build", "run"))
+    depends_on("python@3.7:", when="@0.3:", type=("build", "run"))
+    depends_on("python@3.6:", type=("build", "run"))
     depends_on("py-setuptools", type="build")
     depends_on("py-click@7.1.2:8", when="@0.3:", type=("build", "run"))
     depends_on("py-click@7.1.2:7.1", when="@:0.2", type=("build", "run"))
@@ -49,7 +48,4 @@ class PyRadiantMlhub(PythonPackage):
     depends_on("py-tqdm@4.64:4", when="@0.5.0:0.5.1", type=("build", "run"))
     depends_on("py-tqdm@4.56:4", when="@0.3:0.4", type=("build", "run"))
     depends_on("py-tqdm@4.56", when="@:0.2", type=("build", "run"))
-    depends_on("py-urllib3@1.26.11:1.26", when="@0.5.5:", type=("build", "run"))
-
-    # Historical dependencies
     depends_on("py-typing-extensions@3.7:", when="@0.4.1:0.4 ^python@:3.7", type=("build", "run"))

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

@@ -20,7 +20,6 @@ class PyRasterio(PythonPackage):
     maintainers("adamjstewart")
 
     version("master", branch="master")
-    version("1.3.6", sha256="c8b90eb10e16102d1ab0334a7436185f295de1c07f0d197e206d1c005fc33905")
     version("1.3.5", sha256="92358c3d4d5d6f3c7cd2812c8832d5175abce02b11bc101ac9548ff07163e8e2")
     version("1.3.4", sha256="5a8771405276ecf00b8ee927bd0a81ec21778dcfc97e4a37d0b388f10c9a41a8")
     version("1.3.3", sha256="b6fb1f12489f3a678c05ddcb78a74f0b6f63836219f51c0541e505f5e5208e7d")
@@ -34,32 +33,32 @@ class PyRasterio(PythonPackage):
     version("1.0.24", sha256="4839479621045211f66868ec49625979693450bc2e476f23e7e8ac4804eaf452")
     version("1.0a12", sha256="47d460326e04c64590ff56952271a184a6307f814efc34fb319c12e690585f3c")
 
-    # From pyproject.toml
-    depends_on("py-cython@0.29.29:", when="@1.3.3:", type="build")
-    depends_on("py-cython@0.29.24:0.29", when="@1.3.0:1.3.2", type="build")
-
-    # From setup.py
+    # From README.rst
     depends_on("python@3.8:", when="@1.3:", type=("build", "link", "run"))
     depends_on("python@3.6:3.9", when="@1.2", type=("build", "link", "run"))
     depends_on("python@2.7:2.8,3.5:3.8", when="@1.1", type=("build", "link", "run"))
     depends_on("python@2.7:2.8,3.5:3.7", when="@:1.0", type=("build", "link", "run"))
-    depends_on("py-affine", type=("build", "run"))
-    depends_on("py-attrs", type=("build", "run"))
-    depends_on("py-certifi", when="@1.2:", type=("build", "run"))
-    depends_on("py-click@4:", when="@1.2.4:", type=("build", "run"))
-    depends_on("py-click@4:7", when="@:1.2.3", type=("build", "run"))
-    depends_on("py-cligj@0.5:", type=("build", "run"))
     depends_on("py-numpy@1.18:", when="@1.3:", type=("build", "link", "run"))
     depends_on("py-numpy@1.15:", when="@1.2:", type=("build", "link", "run"))
     depends_on("py-numpy", type=("build", "link", "run"))
-    depends_on("py-snuggs@1.4.1:", type=("build", "run"))
-    depends_on("py-click-plugins", type=("build", "run"))
-    depends_on("py-setuptools", type=("build", "run"))
-
-    # From README.rst and setup.py
     depends_on("gdal@3.1:", when="@1.3:")
     depends_on("gdal@2.4:3.3", when="@1.2.7:1.2")
     depends_on("gdal@2.3:3.2", when="@1.2.0:1.2.6")
     depends_on("gdal@1.11:3.2", when="@1.1.0:1.1")
     depends_on("gdal@1.11:3.0", when="@1.0.25:1.0")
     depends_on("gdal@1.11:2", when="@:1.0.24")
+
+    # From pyproject.toml
+    depends_on("py-cython@0.29.29:", when="@1.3.3:", type="build")
+    depends_on("py-cython@0.29.24:0.29", when="@1.3.0:1.3.2", type="build")
+
+    # From setup.py
+    depends_on("py-affine", type=("build", "run"))
+    depends_on("py-attrs", type=("build", "run"))
+    depends_on("py-certifi", when="@1.2:", type=("build", "run"))
+    depends_on("py-click@4:", when="@1.2.4:", type=("build", "run"))
+    depends_on("py-click@4:7", when="@:1.2.3", type=("build", "run"))
+    depends_on("py-cligj@0.5:", type=("build", "run"))
+    depends_on("py-snuggs@1.4.1:", type=("build", "run"))
+    depends_on("py-click-plugins", type=("build", "run"))
+    depends_on("py-setuptools", type=("build", "run"))

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

@@ -14,7 +14,6 @@ class Shtools(MakefilePackage):
 
     maintainers("eschnett")
 
-    version("4.10.1", sha256="f4fb5c86841fe80136b520d2040149eafd4bc2d49da6b914d8a843b812f20b61")
     version("4.9.1", sha256="5c22064f9daf6e9aa08cace182146993aa6b25a6ea593d92572c59f4013d53c2")
     version("4.8", sha256="c36fc86810017e544abbfb12f8ddf6f101a1ac8b89856a76d7d9801ffc8dac44")
     version("4.5", sha256="1975a2a2bcef8c527d321be08c13c2bc479e0d6b81c468a3203f95df59be4f89")
@@ -25,12 +24,12 @@ class Shtools(MakefilePackage):
 
     # The Makefile expects the "other" libtool, not the GNU libtool we have in
     # Spack
-    patch("nolibtool.patch", when="@:4.9")
+    patch("nolibtool.patch")
 
     variant("openmp", default=True, description="Enable OpenMP support")
 
     depends_on("blas")
-    depends_on("fftw precision=double")
+    depends_on("fftw")
     depends_on("lapack")
     depends_on("py-flake8", type="test")