simmodsuite: depends on rpc

Sun RPC support was optional starting with glibc version 2.26 and was removed in version 2.32. On newer operating systems (e.g., RHEL8) libtirpc is required to satisfy the xdr symbols.

lib/spack/docs/module_file_support.rst

@@ -308,7 +308,7 @@ the variable ``FOOBAR`` will be unset.
      spec constraints are instead evaluated top to bottom.
 
 """"""""""""""""""""""""""""""""""""""""""""
-Blacklist or whitelist specific module files
+Exclude or include specific module files
 """"""""""""""""""""""""""""""""""""""""""""
 
 You can use anonymous specs also to prevent module files from being written or
@@ -322,8 +322,8 @@ your system. If you write a configuration file like:
    modules:
      default:
        tcl:
-         whitelist: ['gcc', 'llvm']  # Whitelist will have precedence over blacklist
-         blacklist: ['%gcc@4.4.7']   # Assuming gcc@4.4.7 is the system compiler
+         include: ['gcc', 'llvm']  # include will have precedence over exclude
+         exclude: ['%gcc@4.4.7']   # Assuming gcc@4.4.7 is the system compiler
 
 you will prevent the generation of module files for any package that
 is compiled with ``gcc@4.4.7``, with the only exception of any ``gcc``
@@ -490,7 +490,7 @@ satisfies a default, Spack will generate the module file in the
 appropriate path, and will generate a default symlink to the module
 file as well.
 
-.. warning:: 
+.. warning::
   If Spack is configured to generate multiple default packages in the
   same directory, the last modulefile to be generated will be the
   default module.
@@ -589,7 +589,7 @@ Filter out environment modifications
 Modifications to certain environment variables in module files are there by
 default, for instance because they are generated by prefix inspections.
 If you want to prevent modifications to some environment variables, you can
-do so by using the environment blacklist:
+do so by using the ``exclude_env_vars``:
 
 .. code-block:: yaml
 
@@ -599,7 +599,7 @@ do so by using the environment blacklist:
          all:
            filter:
              # Exclude changes to any of these variables
-             environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+             exclude_env_vars: ['CPATH', 'LIBRARY_PATH']
 
 The configuration above will generate module files that will not contain
 modifications to either ``CPATH`` or ``LIBRARY_PATH``.

lib/spack/spack/binary_distribution.py

@@ -618,7 +618,7 @@ def get_buildfile_manifest(spec):
     Return a data structure with information about a build, including
     text_to_relocate, binary_to_relocate, binary_to_relocate_fullpath
     link_to_relocate, and other, which means it doesn't fit any of previous
-    checks (and should not be relocated). We blacklist docs (man) and
+    checks (and should not be relocated). We exclude docs (man) and
     metadata (.spack). This can be used to find a particular kind of file
     in spack, or to generate the build metadata.
     """
@@ -626,12 +626,12 @@ def get_buildfile_manifest(spec):
             "link_to_relocate": [], "other": [],
             "binary_to_relocate_fullpath": []}
 
-    blacklist = (".spack", "man")
+    exclude_list = (".spack", "man")
 
     # Do this at during tarball creation to save time when tarball unpacked.
     # Used by make_package_relative to determine binaries to change.
     for root, dirs, files in os.walk(spec.prefix, topdown=True):
-        dirs[:] = [d for d in dirs if d not in blacklist]
+        dirs[:] = [d for d in dirs if d not in exclude_list]
 
         # Directories may need to be relocated too.
         for directory in dirs:

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

@@ -403,4 +403,4 @@ def add_s3_connection_args(subparser, add_help):
         default=None)
     subparser.add_argument(
         '--s3-endpoint-url',
-        help="Access Token to use to connect to this S3 mirror")
+        help="Endpoint URL to use to connect to this S3 mirror")

lib/spack/spack/cmd/edit.py

@@ -104,9 +104,9 @@ def edit(parser, args):
             path = os.path.join(path, name)
             if not os.path.exists(path):
                 files = glob.glob(path + '*')
-                blacklist = ['.pyc', '~']  # blacklist binaries and backups
+                exclude_list = ['.pyc', '~']  # exclude binaries and backups
                 files = list(filter(
-                    lambda x: all(s not in x for s in blacklist), files))
+                    lambda x: all(s not in x for s in exclude_list), files))
                 if len(files) > 1:
                     m = 'Multiple files exist with the name {0}.'.format(name)
                     m += ' Please specify a suffix. Files are:\n\n'

lib/spack/spack/cmd/modules/__init__.py

@@ -131,7 +131,7 @@ def check_module_set_name(name):
 
 _missing_modules_warning = (
     "Modules have been omitted for one or more specs, either"
-    " because they were blacklisted or because the spec is"
+    " because they were excluded or because the spec is"
     " associated with a package that is installed upstream and"
     " that installation has not generated a module file. Rerun"
     " this command with debug output enabled for more details.")
@@ -180,7 +180,7 @@ def loads(module_type, specs, args, out=None):
     for spec, mod in modules:
         if not mod:
             module_output_for_spec = (
-                '## blacklisted or missing from upstream: {0}'.format(
+                '## excluded or missing from upstream: {0}'.format(
                     spec.format()))
         else:
             d['exclude'] = '## ' if spec.name in exclude_set else ''
@@ -293,8 +293,8 @@ def refresh(module_type, specs, args):
         cls(spec, args.module_set_name) for spec in specs
         if spack.repo.path.exists(spec.name)]
 
-    # Filter blacklisted packages early
-    writers = [x for x in writers if not x.conf.blacklisted]
+    # Filter excluded packages early
+    writers = [x for x in writers if not x.conf.excluded]
 
     # Detect name clashes in module files
     file2writer = collections.defaultdict(list)

lib/spack/spack/cmd/stage.py

@@ -24,6 +24,7 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-p', '--path', dest='path',
         help="path to stage package, does not add to spack tree")
+    arguments.add_concretizer_args(subparser)
 
 
 def stage(parser, args):

lib/spack/spack/fetch_strategy.py

@@ -337,9 +337,7 @@ def fetch(self):
                 continue
 
             try:
-                partial_file, save_file = self._fetch_from_url(url)
-                if save_file and (partial_file is not None):
-                    llnl.util.filesystem.rename(partial_file, save_file)
+                self._fetch_from_url(url)
                 break
             except FailedDownloadError as e:
                 errors.append(str(e))
@@ -389,9 +387,7 @@ def _check_headers(self, headers):
 
     @_needs_stage
     def _fetch_urllib(self, url):
-        save_file = None
-        if self.stage.save_filename:
-            save_file = self.stage.save_filename
+        save_file = self.stage.save_filename
         tty.msg('Fetching {0}'.format(url))
 
         # Run urllib but grab the mime type from the http headers
@@ -401,16 +397,18 @@ def _fetch_urllib(self, url):
             # clean up archive on failure.
             if self.archive_file:
                 os.remove(self.archive_file)
-            if save_file and os.path.exists(save_file):
+            if os.path.lexists(save_file):
                 os.remove(save_file)
             msg = 'urllib failed to fetch with error {0}'.format(e)
             raise FailedDownloadError(url, msg)
 
+        if os.path.lexists(save_file):
+            os.remove(save_file)
+
         with open(save_file, 'wb') as _open_file:
             shutil.copyfileobj(response, _open_file)
 
         self._check_headers(str(headers))
-        return None, save_file
 
     @_needs_stage
     def _fetch_curl(self, url):
@@ -471,7 +469,7 @@ def _fetch_curl(self, url):
             if self.archive_file:
                 os.remove(self.archive_file)
 
-            if partial_file and os.path.exists(partial_file):
+            if partial_file and os.path.lexists(partial_file):
                 os.remove(partial_file)
 
             if curl.returncode == 22:
@@ -498,7 +496,9 @@ def _fetch_curl(self, url):
                     "Curl failed with error %d" % curl.returncode)
 
         self._check_headers(headers)
-        return partial_file, save_file
+
+        if save_file and (partial_file is not None):
+            fs.rename(partial_file, save_file)
 
     @property  # type: ignore # decorated properties unsupported in mypy
     @_needs_stage
@@ -613,7 +613,7 @@ def fetch(self):
 
         # remove old symlink if one is there.
         filename = self.stage.save_filename
-        if os.path.exists(filename):
+        if os.path.lexists(filename):
             os.remove(filename)
 
         # Symlink to local cached archive.

lib/spack/spack/installer.py

@@ -2212,7 +2212,8 @@ def flag_installed(self, installed):
     @property
     def explicit(self):
         """The package was explicitly requested by the user."""
-        return self.pkg == self.request.pkg
+        return self.pkg == self.request.pkg and \
+            self.request.install_args.get('explicit', True)
 
     @property
     def key(self):

lib/spack/spack/modules/common.py

@@ -54,6 +54,34 @@
 import spack.util.spack_yaml as syaml
 
 
+def get_deprecated(dictionary, name, old_name, default):
+    """Get a deprecated property from a ``dict``.
+
+    Arguments:
+        dictionary (dict): dictionary to get a value from.
+        name (str): New name for the property. If present, supersedes ``old_name``.
+        old_name (str): Deprecated name for the property. If present, a warning
+            is printed.
+        default (object): value to return if neither name is found.
+    """
+    value = default
+
+    # always warn if old name is present
+    if old_name in dictionary:
+        value = dictionary.get(old_name, value)
+        main_msg = "`{}:` is deprecated in module config and will be removed in v0.20."
+        details = (
+            "Use `{}:` instead. You can run `spack config update` to translate your "
+            "configuration files automatically."
+        )
+        tty.warn(main_msg.format(old_name), details.format(name))
+
+    # name overrides old name if present
+    value = dictionary.get(name, value)
+
+    return value
+
+
 #: config section for this file
 def configuration(module_set_name):
     config_path = 'modules:%s' % module_set_name
@@ -351,14 +379,14 @@ def get_module(
 
     Retrieve the module file for the given spec if it is available. If the
     module is not available, this will raise an exception unless the module
-    is blacklisted or if the spec is installed upstream.
+    is excluded or if the spec is installed upstream.
 
     Args:
         module_type: the type of module we want to retrieve (e.g. lmod)
         spec: refers to the installed package that we want to retrieve a module
             for
-        required: if the module is required but blacklisted, this function will
-            print a debug message. If a module is missing but not blacklisted,
+        required: if the module is required but excluded, this function will
+            print a debug message. If a module is missing but not excluded,
             then an exception is raised (regardless of whether it is required)
         get_full_path: if ``True``, this returns the full path to the module.
             Otherwise, this returns the module name.
@@ -386,13 +414,13 @@ def get_module(
     else:
         writer = spack.modules.module_types[module_type](spec, module_set_name)
         if not os.path.isfile(writer.layout.filename):
-            if not writer.conf.blacklisted:
+            if not writer.conf.excluded:
                 err_msg = "No module available for package {0} at {1}".format(
                     spec, writer.layout.filename
                 )
                 raise ModuleNotFoundError(err_msg)
             elif required:
-                tty.debug("The module configuration has blacklisted {0}: "
+                tty.debug("The module configuration has excluded {0}: "
                           "omitting it".format(spec))
             else:
                 return None
@@ -483,26 +511,30 @@ def hash(self):
         return None
 
     @property
-    def blacklisted(self):
-        """Returns True if the module has been blacklisted,
-        False otherwise.
-        """
+    def excluded(self):
+        """Returns True if the module has been excluded, False otherwise."""
+
         # A few variables for convenience of writing the method
         spec = self.spec
         conf = self.module.configuration(self.name)
 
-        # Compute the list of whitelist rules that match
-        wlrules = conf.get('whitelist', [])
-        whitelist_matches = [x for x in wlrules if spec.satisfies(x)]
+        # Compute the list of include rules that match
+        # DEPRECATED: remove 'whitelist' in v0.20
+        include_rules = get_deprecated(conf, "include", "whitelist", [])
+        include_matches = [x for x in include_rules if spec.satisfies(x)]
 
-        # Compute the list of blacklist rules that match
-        blrules = conf.get('blacklist', [])
-        blacklist_matches = [x for x in blrules if spec.satisfies(x)]
+        # Compute the list of exclude rules that match
+        # DEPRECATED: remove 'blacklist' in v0.20
+        exclude_rules = get_deprecated(conf, "exclude", "blacklist", [])
+        exclude_matches = [x for x in exclude_rules if spec.satisfies(x)]
 
-        # Should I blacklist the module because it's implicit?
-        blacklist_implicits = conf.get('blacklist_implicits')
+        # Should I exclude the module because it's implicit?
+        # DEPRECATED: remove 'blacklist_implicits' in v0.20
+        exclude_implicits = get_deprecated(
+            conf, "exclude_implicits", "blacklist_implicits", None
+        )
         installed_implicitly = not spec._installed_explicitly()
-        blacklisted_as_implicit = blacklist_implicits and installed_implicitly
+        excluded_as_implicit = exclude_implicits and installed_implicitly
 
         def debug_info(line_header, match_list):
             if match_list:
@@ -511,15 +543,15 @@ def debug_info(line_header, match_list):
                 for rule in match_list:
                     tty.debug('\t\tmatches rule: {0}'.format(rule))
 
-        debug_info('WHITELIST', whitelist_matches)
-        debug_info('BLACKLIST', blacklist_matches)
+        debug_info('INCLUDE', include_matches)
+        debug_info('EXCLUDE', exclude_matches)
 
-        if blacklisted_as_implicit:
-            msg = '\tBLACKLISTED_AS_IMPLICIT : {0}'.format(spec.cshort_spec)
+        if excluded_as_implicit:
+            msg = '\tEXCLUDED_AS_IMPLICIT : {0}'.format(spec.cshort_spec)
             tty.debug(msg)
 
-        is_blacklisted = blacklist_matches or blacklisted_as_implicit
-        if not whitelist_matches and is_blacklisted:
+        is_excluded = exclude_matches or excluded_as_implicit
+        if not include_matches and is_excluded:
             return True
 
         return False
@@ -544,17 +576,22 @@ def specs_to_prereq(self):
         return self._create_list_for('prerequisites')
 
     @property
-    def environment_blacklist(self):
+    def exclude_env_vars(self):
         """List of variables that should be left unmodified."""
-        return self.conf.get('filter', {}).get('environment_blacklist', {})
+        filter = self.conf.get('filter', {})
+
+        # DEPRECATED: remove in v0.20
+        return get_deprecated(
+            filter, "exclude_env_vars", "environment_blacklist", {}
+        )
 
     def _create_list_for(self, what):
-        whitelist = []
+        include = []
         for item in self.conf[what]:
             conf = type(self)(item, self.name)
-            if not conf.blacklisted:
-                whitelist.append(item)
-        return whitelist
+            if not conf.excluded:
+                include.append(item)
+        return include
 
     @property
     def verbose(self):
@@ -733,8 +770,8 @@ def environment_modifications(self):
         # Modifications required from modules.yaml
         env.extend(self.conf.env)
 
-        # List of variables that are blacklisted in modules.yaml
-        blacklist = self.conf.environment_blacklist
+        # List of variables that are excluded in modules.yaml
+        exclude = self.conf.exclude_env_vars
 
         # We may have tokens to substitute in environment commands
 
@@ -758,7 +795,7 @@ def environment_modifications(self):
                 pass
             x.name = str(x.name).replace('-', '_')
 
-        return [(type(x).__name__, x) for x in env if x.name not in blacklist]
+        return [(type(x).__name__, x) for x in env if x.name not in exclude]
 
     @tengine.context_property
     def autoload(self):
@@ -831,9 +868,9 @@ def write(self, overwrite=False):
                 existing file. If False the operation is skipped an we print
                 a warning to the user.
         """
-        # Return immediately if the module is blacklisted
-        if self.conf.blacklisted:
-            msg = '\tNOT WRITING: {0} [BLACKLISTED]'
+        # Return immediately if the module is excluded
+        if self.conf.excluded:
+            msg = '\tNOT WRITING: {0} [EXCLUDED]'
             tty.debug(msg.format(self.spec.cshort_spec))
             return
 

lib/spack/spack/s3_handler.py

@@ -3,7 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from io import BufferedReader
+from io import BufferedReader, IOBase
 
 import six
 import six.moves.urllib.error as urllib_error
@@ -23,11 +23,15 @@
 # https://github.com/python/cpython/pull/3249
 class WrapStream(BufferedReader):
     def __init__(self, raw):
-        raw.readable = lambda: True
-        raw.writable = lambda: False
-        raw.seekable = lambda: False
-        raw.closed = False
-        raw.flush = lambda: None
+        # In botocore >=1.23.47, StreamingBody inherits from IOBase, so we
+        # only add missing attributes in older versions.
+        # https://github.com/boto/botocore/commit/a624815eabac50442ed7404f3c4f2664cd0aa784
+        if not isinstance(raw, IOBase):
+            raw.readable = lambda: True
+            raw.writable = lambda: False
+            raw.seekable = lambda: False
+            raw.closed = False
+            raw.flush = lambda: None
         super(WrapStream, self).__init__(raw)
 
     def detach(self):

lib/spack/spack/schema/modules.py

@@ -18,9 +18,13 @@
 #:
 #: THIS NEEDS TO BE UPDATED FOR EVERY NEW KEYWORD THAT
 #: IS ADDED IMMEDIATELY BELOW THE MODULE TYPE ATTRIBUTE
-spec_regex = r'(?!hierarchy|core_specs|verbose|hash_length|whitelist|' \
-             r'blacklist|projections|naming_scheme|core_compilers|all|' \
-             r'defaults)(^\w[\w-]*)'
+spec_regex = (
+    r'(?!hierarchy|core_specs|verbose|hash_length|defaults|'
+    r'whitelist|blacklist|'  # DEPRECATED: remove in 0.20.
+    r'include|exclude|'      # use these more inclusive/consistent options
+    r'projections|naming_scheme|core_compilers|all)(^\w[\w-]*)'
+
+)
 
 #: Matches a valid name for a module set
 valid_module_set_name = r'^(?!arch_folder$|lmod$|roots$|enable$|prefix_inspections$|'\
@@ -50,12 +54,21 @@
             'default': {},
             'additionalProperties': False,
             'properties': {
+                # DEPRECATED: remove in 0.20.
                 'environment_blacklist': {
                     'type': 'array',
                     'default': [],
                     'items': {
                         'type': 'string'
                     }
+                },
+                # use exclude_env_vars instead
+                'exclude_env_vars': {
+                    'type': 'array',
+                    'default': [],
+                    'items': {
+                        'type': 'string'
+                    }
                 }
             }
         },
@@ -95,12 +108,20 @@
                 'minimum': 0,
                 'default': 7
             },
+            # DEPRECATED: remove in 0.20.
             'whitelist': array_of_strings,
             'blacklist': array_of_strings,
             'blacklist_implicits': {
                 'type': 'boolean',
                 'default': False
             },
+            # whitelist/blacklist have been replaced with include/exclude
+            'include': array_of_strings,
+            'exclude': array_of_strings,
+            'exclude_implicits': {
+                'type': 'boolean',
+                'default': False
+            },
             'defaults': array_of_strings,
             'naming_scheme': {
                 'type': 'string'  # Can we be more specific here?
@@ -224,14 +245,51 @@ def deprecation_msg_default_module_set(instance, props):
 }
 
 
-def update(data):
-    """Update the data in place to remove deprecated properties.
+# deprecated keys and their replacements
+exclude_include_translations = {
+    "whitelist": "include",
+    "blacklist": "exclude",
+    "blacklist_implicits": "exclude_implicits",
+    "environment_blacklist": "exclude_env_vars",
+}
 
-    Args:
-        data (dict): dictionary to be updated
 
-    Returns:
-        True if data was changed, False otherwise
+def update_keys(data, key_translations):
+    """Change blacklist/whitelist to exclude/include.
+
+    Arguments:
+        data (dict): data from a valid modules configuration.
+        key_translations (dict): A dictionary of keys to translate to
+            their respective values.
+
+    Return:
+        (bool) whether anything was changed in data
+    """
+    changed = False
+
+    if isinstance(data, dict):
+        keys = list(data.keys())
+        for key in keys:
+            value = data[key]
+
+            translation = key_translations.get(key)
+            if translation:
+                data[translation] = data.pop(key)
+                changed = True
+
+            changed |= update_keys(value, key_translations)
+
+    elif isinstance(data, list):
+        for elt in data:
+            changed |= update_keys(elt, key_translations)
+
+    return changed
+
+
+def update_default_module_set(data):
+    """Update module configuration to move top-level keys inside default module set.
+
+    This change was introduced in v0.18 (see 99083f1706 or #28659).
     """
     changed = False
 
@@ -258,3 +316,21 @@ def update(data):
         data['default'] = default
 
     return changed
+
+
+def update(data):
+    """Update the data in place to remove deprecated properties.
+
+    Args:
+        data (dict): dictionary to be updated
+
+    Returns:
+        True if data was changed, False otherwise
+    """
+    # deprecated top-level module config (everything in default module set)
+    changed = update_default_module_set(data)
+
+    # translate blacklist/whitelist to exclude/include
+    changed |= update_keys(data, exclude_include_translations)
+
+    return changed

lib/spack/spack/test/cmd/module.py

@@ -149,16 +149,20 @@ def test_find_recursive():
 
 
 @pytest.mark.db
-def test_find_recursive_blacklisted(database, module_configuration):
-    module_configuration('blacklist')
+# DEPRECATED: remove blacklist in v0.20
+@pytest.mark.parametrize("config_name", ["exclude", "blacklist"])
+def test_find_recursive_excluded(database, module_configuration, config_name):
+    module_configuration(config_name)
 
     module('lmod', 'refresh', '-y', '--delete-tree')
     module('lmod', 'find', '-r', 'mpileaks ^mpich')
 
 
 @pytest.mark.db
-def test_loads_recursive_blacklisted(database, module_configuration):
-    module_configuration('blacklist')
+# DEPRECATED: remove blacklist in v0.20
+@pytest.mark.parametrize("config_name", ["exclude", "blacklist"])
+def test_loads_recursive_excluded(database, module_configuration, config_name):
+    module_configuration(config_name)
 
     module('lmod', 'refresh', '-y', '--delete-tree')
     output = module('lmod', 'loads', '-r', 'mpileaks ^mpich')
@@ -166,7 +170,7 @@ def test_loads_recursive_blacklisted(database, module_configuration):
 
     assert any(re.match(r'[^#]*module load.*mpileaks', ln) for ln in lines)
     assert not any(re.match(r'[^#]module load.*callpath', ln) for ln in lines)
-    assert any(re.match(r'## blacklisted or missing.*callpath', ln)
+    assert any(re.match(r'## excluded or missing.*callpath', ln)
                for ln in lines)
 
     # TODO: currently there is no way to separate stdout and stderr when

lib/spack/spack/test/cmd/stage.py

@@ -8,6 +8,7 @@
 
 import pytest
 
+import spack.config
 import spack.environment as ev
 import spack.repo
 from spack.main import SpackCommand
@@ -122,3 +123,13 @@ def fake_stage(pkg, mirror_only=False):
 
     # assert that all were staged
     assert len(expected) == 0
+
+
+@pytest.mark.disable_clean_stage_check
+def test_concretizer_arguments(mock_packages, mock_fetch):
+    """Make sure stage also has --reuse and --fresh flags."""
+    stage("--reuse", "trivial-install-test-package")
+    assert spack.config.get("concretizer:reuse", None) is True
+
+    stage("--fresh", "trivial-install-test-package")
+    assert spack.config.get("concretizer:reuse", None) is False

lib/spack/spack/test/conftest.py

@@ -1003,7 +1003,7 @@ def __call__(self, filename):
 
 
 @pytest.fixture()
-def module_configuration(monkeypatch, request):
+def module_configuration(monkeypatch, request, mutable_config):
     """Reads the module configuration file from the mock ones prepared
     for tests and monkeypatches the right classes to hook it in.
     """
@@ -1018,6 +1018,8 @@ def module_configuration(monkeypatch, request):
         spack.paths.test_path, 'data', 'modules', writer_key
     )
 
+    # ConfigUpdate, when called, will modify configuration, so we need to use
+    # the mutable_config fixture
     return ConfigUpdate(root_for_conf, writer_mod, writer_key, monkeypatch)
 
 

lib/spack/spack/test/data/modules/lmod/alter_environment.yaml

@@ -10,7 +10,7 @@ lmod:
   all:
     autoload: none
     filter:
-      environment_blacklist:
+      exclude_env_vars:
         - CMAKE_PREFIX_PATH
     environment:
       set:

lib/spack/spack/test/data/modules/lmod/blacklist.yaml

@@ -1,3 +1,5 @@
+# DEPRECATED: remove this in v0.20
+# See `exclude.yaml` for the new syntax
 enable:
   - lmod
 lmod:

lib/spack/spack/test/data/modules/lmod/blacklist_environment.yaml

@@ -0,0 +1,30 @@
+# DEPRECATED: remove this in v0.20
+# See `alter_environment.yaml` for the new syntax
+enable:
+  - lmod
+lmod:
+  core_compilers:
+    - 'clang@3.3'
+
+  hierarchy:
+    - mpi
+
+  all:
+    autoload: none
+    filter:
+      environment_blacklist:
+        - CMAKE_PREFIX_PATH
+    environment:
+      set:
+        '{name}_ROOT': '{prefix}'
+
+  'platform=test target=x86_64':
+    environment:
+      set:
+        FOO: 'foo'
+      unset:
+        - BAR
+
+  'platform=test target=core2':
+    load:
+      - 'foo/bar'

lib/spack/spack/test/data/modules/lmod/exclude.yaml

@@ -0,0 +1,12 @@
+enable:
+  - lmod
+lmod:
+  core_compilers:
+    - 'clang@3.3'
+  hierarchy:
+    - mpi
+  exclude:
+    - callpath
+
+  all:
+    autoload: direct

lib/spack/spack/test/data/modules/tcl/alter_environment.yaml

@@ -4,7 +4,7 @@ tcl:
   all:
     autoload: none
     filter:
-      environment_blacklist:
+      exclude_env_vars:
         - CMAKE_PREFIX_PATH
     environment:
       set:

lib/spack/spack/test/data/modules/tcl/blacklist.yaml

@@ -1,3 +1,5 @@
+# DEPRECATED: remove this in v0.20
+# See `exclude.yaml` for the new syntax
 enable:
   - tcl
 tcl:

lib/spack/spack/test/data/modules/tcl/blacklist_environment.yaml

@@ -0,0 +1,25 @@
+# DEPRECATED: remove this in v0.20
+# See `alter_environment.yaml` for the new syntax
+enable:
+  - tcl
+tcl:
+  all:
+    autoload: none
+    filter:
+      environment_blacklist:
+        - CMAKE_PREFIX_PATH
+    environment:
+      set:
+        '{name}_ROOT': '{prefix}'
+
+  'platform=test target=x86_64':
+    environment:
+      set:
+        FOO: 'foo'
+        OMPI_MCA_mpi_leave_pinned: '1'
+      unset:
+        - BAR
+
+  'platform=test target=core2':
+    load:
+      - 'foo/bar'

lib/spack/spack/test/data/modules/tcl/blacklist_implicits.yaml

@@ -1,3 +1,5 @@
+# DEPRECATED: remove this in v0.20
+# See `exclude_implicits.yaml` for the new syntax
 enable:
   - tcl
 tcl:

lib/spack/spack/test/data/modules/tcl/exclude.yaml

@@ -0,0 +1,10 @@
+enable:
+  - tcl
+tcl:
+  include:
+    - zmpi
+  exclude:
+    - callpath
+    - mpi
+  all:
+    autoload: direct

lib/spack/spack/test/data/modules/tcl/exclude_implicits.yaml

@@ -0,0 +1,6 @@
+enable:
+  - tcl
+tcl:
+  exclude_implicits: true
+  all:
+    autoload: direct

lib/spack/spack/test/environment_modifications.py

@@ -379,40 +379,40 @@ def test_clear(env):
     assert len(env) == 0
 
 
-@pytest.mark.parametrize('env,blacklist,whitelist', [
-    # Check we can blacklist a literal
+@pytest.mark.parametrize('env,exclude,include', [
+    # Check we can exclude a literal
     ({'SHLVL': '1'}, ['SHLVL'], []),
-    # Check whitelist takes precedence
+    # Check include takes precedence
     ({'SHLVL': '1'}, ['SHLVL'], ['SHLVL']),
 ])
-def test_sanitize_literals(env, blacklist, whitelist):
+def test_sanitize_literals(env, exclude, include):
 
-    after = environment.sanitize(env, blacklist, whitelist)
+    after = environment.sanitize(env, exclude, include)
 
-    # Check that all the whitelisted variables are there
-    assert all(x in after for x in whitelist)
+    # Check that all the included variables are there
+    assert all(x in after for x in include)
 
-    # Check that the blacklisted variables that are not
-    # whitelisted are there
-    blacklist = list(set(blacklist) - set(whitelist))
-    assert all(x not in after for x in blacklist)
+    # Check that the excluded variables that are not
+    # included are there
+    exclude = list(set(exclude) - set(include))
+    assert all(x not in after for x in exclude)
 
 
-@pytest.mark.parametrize('env,blacklist,whitelist,expected,deleted', [
-    # Check we can blacklist using a regex
+@pytest.mark.parametrize('env,exclude,include,expected,deleted', [
+    # Check we can exclude using a regex
     ({'SHLVL': '1'}, ['SH.*'], [], [], ['SHLVL']),
-    # Check we can whitelist using a regex
+    # Check we can include using a regex
     ({'SHLVL': '1'}, ['SH.*'], ['SH.*'], ['SHLVL'], []),
-    # Check regex to blacklist Modules v4 related vars
+    # Check regex to exclude Modules v4 related vars
     ({'MODULES_LMALTNAME': '1', 'MODULES_LMCONFLICT': '2'},
      ['MODULES_(.*)'], [], [], ['MODULES_LMALTNAME', 'MODULES_LMCONFLICT']),
     ({'A_modquar': '1', 'b_modquar': '2', 'C_modshare': '3'},
      [r'(\w*)_mod(quar|share)'], [], [],
      ['A_modquar', 'b_modquar', 'C_modshare']),
 ])
-def test_sanitize_regex(env, blacklist, whitelist, expected, deleted):
+def test_sanitize_regex(env, exclude, include, expected, deleted):
 
-    after = environment.sanitize(env, blacklist, whitelist)
+    after = environment.sanitize(env, exclude, include)
 
     assert all(x in after for x in expected)
     assert all(x not in after for x in deleted)
@@ -460,7 +460,7 @@ def test_from_environment_diff(before, after, search_list):
 @pytest.mark.skipif(sys.platform == 'win32',
                     reason="LMod not supported on Windows")
 @pytest.mark.regression('15775')
-def test_blacklist_lmod_variables():
+def test_exclude_lmod_variables():
     # Construct the list of environment modifications
     file = os.path.join(datadir, 'sourceme_lmod.sh')
     env = EnvironmentModifications.from_sourcing_file(file)

lib/spack/spack/test/installer.py

@@ -1176,6 +1176,18 @@ def test_install_skip_patch(install_mockery, mock_fetch):
     assert inst.package_id(spec.package) in installer.installed
 
 
+def test_install_implicit(install_mockery, mock_fetch):
+    """Test the path skip_patch install path."""
+    spec_name = 'trivial-install-test-package'
+    const_arg = installer_args([spec_name],
+                               {'fake': False})
+    installer = create_installer(const_arg)
+    pkg = installer.build_requests[0].pkg
+    assert not create_build_task(pkg, {'explicit': False}).explicit
+    assert create_build_task(pkg, {'explicit': True}).explicit
+    assert create_build_task(pkg).explicit
+
+
 def test_overwrite_install_backup_success(temporary_store, config, mock_packages,
                                           tmpdir):
     """

lib/spack/spack/test/modules/common.py

@@ -11,7 +11,9 @@
 import spack.error
 import spack.modules.tcl
 import spack.package_base
+import spack.schema.modules
 import spack.spec
+import spack.util.spack_yaml as syaml
 from spack.modules.common import UpstreamModuleIndex
 from spack.spec import Spec
 
@@ -226,3 +228,34 @@ def find_nothing(*args):
     assert module_path
 
     spack.package_base.PackageBase.uninstall_by_spec(spec)
+
+
+# DEPRECATED: remove blacklist in v0.20
+@pytest.mark.parametrize("module_type, old_config,new_config", [
+    ("tcl",  "blacklist.yaml",             "exclude.yaml"),
+    ("tcl",  "blacklist_implicits.yaml",   "exclude_implicits.yaml"),
+    ("tcl",  "blacklist_environment.yaml", "alter_environment.yaml"),
+    ("lmod", "blacklist.yaml",             "exclude.yaml"),
+    ("lmod", "blacklist_environment.yaml", "alter_environment.yaml"),
+])
+def test_exclude_include_update(module_type, old_config, new_config):
+    module_test_data_root = os.path.join(
+        spack.paths.test_path, 'data', 'modules', module_type
+    )
+    with open(os.path.join(module_test_data_root, old_config)) as f:
+        old_yaml = syaml.load(f)
+    with open(os.path.join(module_test_data_root, new_config)) as f:
+        new_yaml = syaml.load(f)
+
+    # ensure file that needs updating is translated to the right thing.
+    assert spack.schema.modules.update_keys(
+        old_yaml, spack.schema.modules.exclude_include_translations
+    )
+    assert new_yaml == old_yaml
+
+    # ensure a file that doesn't need updates doesn't get updated
+    original_new_yaml = new_yaml.copy()
+    assert not spack.schema.modules.update_keys(
+        new_yaml, spack.schema.modules.exclude_include_translations
+    )
+    original_new_yaml == new_yaml

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

@@ -110,10 +110,16 @@ def test_autoload_all(self, modulefile_content, module_configuration):
 
         assert len([x for x in content if 'depends_on(' in x]) == 5
 
-    def test_alter_environment(self, modulefile_content, module_configuration):
+    # DEPRECATED: remove blacklist in v0.20
+    @pytest.mark.parametrize(
+        "config_name", ["alter_environment", "blacklist_environment"]
+    )
+    def test_alter_environment(
+            self, modulefile_content, module_configuration, config_name
+    ):
         """Tests modifications to run-time environment."""
 
-        module_configuration('alter_environment')
+        module_configuration(config_name)
         content = modulefile_content('mpileaks platform=test target=x86_64')
 
         assert len(
@@ -145,10 +151,11 @@ def test_prepend_path_separator(self, modulefile_content,
             elif re.match(r'[a-z]+_path\("SEMICOLON"', line):
                 assert line.endswith('"bar", ";")')
 
-    def test_blacklist(self, modulefile_content, module_configuration):
-        """Tests blacklisting the generation of selected modules."""
+    @pytest.mark.parametrize("config_name", ["exclude", "blacklist"])
+    def test_exclude(self, modulefile_content, module_configuration, config_name):
+        """Tests excluding the generation of selected modules."""
 
-        module_configuration('blacklist')
+        module_configuration(config_name)
         content = modulefile_content(mpileaks_spec_string)
 
         assert len([x for x in content if 'depends_on(' in x]) == 1

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

@@ -97,10 +97,16 @@ def test_prerequisites_all(self, modulefile_content, module_configuration):
 
         assert len([x for x in content if 'prereq' in x]) == 5
 
-    def test_alter_environment(self, modulefile_content, module_configuration):
+    # DEPRECATED: remove blacklist in v0.20
+    @pytest.mark.parametrize(
+        "config_name", ["alter_environment", "blacklist_environment"]
+    )
+    def test_alter_environment(
+            self, modulefile_content, module_configuration, config_name
+    ):
         """Tests modifications to run-time environment."""
 
-        module_configuration('alter_environment')
+        module_configuration(config_name)
         content = modulefile_content('mpileaks platform=test target=x86_64')
 
         assert len([x for x in content
@@ -129,10 +135,11 @@ def test_alter_environment(self, modulefile_content, module_configuration):
         assert len([x for x in content if 'module load foo/bar' in x]) == 1
         assert len([x for x in content if 'setenv LIBDWARF_ROOT' in x]) == 1
 
-    def test_blacklist(self, modulefile_content, module_configuration):
-        """Tests blacklisting the generation of selected modules."""
+    @pytest.mark.parametrize("config_name", ["exclude", "blacklist"])
+    def test_exclude(self, modulefile_content, module_configuration, config_name):
+        """Tests excluding the generation of selected modules."""
 
-        module_configuration('blacklist')
+        module_configuration(config_name)
         content = modulefile_content('mpileaks ^zmpi')
 
         assert len([x for x in content if 'is-loaded' in x]) == 1
@@ -359,24 +366,27 @@ def test_extend_context(
 
     @pytest.mark.regression('4400')
     @pytest.mark.db
-    def test_blacklist_implicits(
-            self, modulefile_content, module_configuration, database
+    @pytest.mark.parametrize(
+        "config_name", ["exclude_implicits", "blacklist_implicits"]
+    )
+    def test_exclude_implicits(
+            self, modulefile_content, module_configuration, database, config_name
     ):
-        module_configuration('blacklist_implicits')
+        module_configuration(config_name)
 
         # mpileaks has been installed explicitly when setting up
         # the tests database
         mpileaks_specs = database.query('mpileaks')
         for item in mpileaks_specs:
             writer = writer_cls(item, 'default')
-            assert not writer.conf.blacklisted
+            assert not writer.conf.excluded
 
         # callpath is a dependency of mpileaks, and has been pulled
         # in implicitly
         callpath_specs = database.query('callpath')
         for item in callpath_specs:
             writer = writer_cls(item, 'default')
-            assert writer.conf.blacklisted
+            assert writer.conf.excluded
 
     @pytest.mark.regression('9624')
     @pytest.mark.db

lib/spack/spack/util/environment.py

@@ -673,10 +673,10 @@ def from_sourcing_file(filename, *arguments, **kwargs):
                 (default: ``&> /dev/null``)
             concatenate_on_success (str): operator used to execute a command
                 only when the previous command succeeds (default: ``&&``)
-            blacklist ([str or re]): ignore any modifications of these
+            exclude ([str or re]): ignore any modifications of these
                 variables (default: [])
-            whitelist ([str or re]): always respect modifications of these
-                variables (default: []). has precedence over blacklist.
+            include ([str or re]): always respect modifications of these
+                variables (default: []). Supersedes any excluded variables.
             clean (bool): in addition to removing empty entries,
                 also remove duplicate entries (default: False).
         """
@@ -687,13 +687,13 @@ def from_sourcing_file(filename, *arguments, **kwargs):
             msg = 'Trying to source non-existing file: {0}'.format(filename)
             raise RuntimeError(msg)
 
-        # Prepare a whitelist and a blacklist of environment variable names
-        blacklist = kwargs.get('blacklist', [])
-        whitelist = kwargs.get('whitelist', [])
+        # Prepare include and exclude lists of environment variable names
+        exclude = kwargs.get('exclude', [])
+        include = kwargs.get('include', [])
         clean = kwargs.get('clean', False)
 
         # Other variables unrelated to sourcing a file
-        blacklist.extend([
+        exclude.extend([
             # Bash internals
             'SHLVL', '_', 'PWD', 'OLDPWD', 'PS1', 'PS2', 'ENV',
             # Environment modules v4
@@ -706,12 +706,12 @@ def from_sourcing_file(filename, *arguments, **kwargs):
         # Compute the environments before and after sourcing
         before = sanitize(
             environment_after_sourcing_files(os.devnull, **kwargs),
-            blacklist=blacklist, whitelist=whitelist
+            exclude=exclude, include=include
         )
         file_and_args = (filename,) + arguments
         after = sanitize(
             environment_after_sourcing_files(file_and_args, **kwargs),
-            blacklist=blacklist, whitelist=whitelist
+            exclude=exclude, include=include
         )
 
         # Delegate to the other factory
@@ -881,22 +881,6 @@ def validate(env, errstream):
         set_or_unset_not_first(variable, list_of_changes, errstream)
 
 
-def filter_environment_blacklist(env, variables):
-    """Generator that filters out any change to environment variables present in
-    the input list.
-
-    Args:
-        env: list of environment modifications
-        variables: list of variable names to be filtered
-
-    Returns:
-        items in env if they are not in variables
-    """
-    for item in env:
-        if item.name not in variables:
-            yield item
-
-
 def inspect_path(root, inspections, exclude=None):
     """Inspects ``root`` to search for the subdirectories in ``inspections``.
     Adds every path found to a list of prepend-path commands and returns it.
@@ -1060,17 +1044,15 @@ def _source_single_file(file_and_args, environment):
     return current_environment
 
 
-def sanitize(environment, blacklist, whitelist):
+def sanitize(environment, exclude, include):
     """Returns a copy of the input dictionary where all the keys that
-    match a blacklist pattern and don't match a whitelist pattern are
+    match an excluded pattern and don't match an included pattern are
     removed.
 
     Args:
         environment (dict): input dictionary
-        blacklist (list): literals or regex patterns to be
-            blacklisted
-        whitelist (list): literals or regex patterns to be
-            whitelisted
+        exclude (list): literals or regex patterns to be excluded
+        include (list): literals or regex patterns to be included
     """
 
     def set_intersection(fullset, *args):
@@ -1088,9 +1070,9 @@ def set_intersection(fullset, *args):
     # Don't modify input, make a copy instead
     environment = sjson.decode_json_dict(dict(environment))
 
-    # Retain (whitelist) has priority over prune (blacklist)
-    prune = set_intersection(set(environment), *blacklist)
-    prune -= set_intersection(prune, *whitelist)
+    # include supersedes any excluded items
+    prune = set_intersection(set(environment), *exclude)
+    prune -= set_intersection(prune, *include)
     for k in prune:
         environment.pop(k, None)
 

lib/spack/spack/util/s3.py

@@ -14,9 +14,18 @@
 def get_mirror_connection(url, url_type="push"):
     connection = {}
     # Try to find a mirror for potential connection information
-    for mirror in spack.mirror.MirrorCollection().values():
-        if "%s://%s" % (url.scheme, url.netloc) == mirror.push_url:
-            connection = mirror.to_dict()[url_type]
+    # Check to see if desired file starts with any of the mirror URLs
+    rebuilt_path = url_util.format(url)
+    # Gather dict of push URLS point to the value of the whole mirror
+    mirror_dict = {x.push_url: x for x in spack.mirror.MirrorCollection().values()}  # noqa: E501
+    # Ensure most specific URLs (longest) are presented first
+    mirror_url_keys = mirror_dict.keys()
+    mirror_url_keys = sorted(mirror_url_keys, key=len, reverse=True)
+    for mURL in mirror_url_keys:
+        # See if desired URL starts with the mirror's push URL
+        if rebuilt_path.startswith(mURL):
+            connection = mirror_dict[mURL].to_dict()[url_type]
+            break
     return connection
 
 

lib/spack/spack/util/web.py

@@ -391,7 +391,7 @@ def list_url(url, recursive=False):
                 if os.path.isfile(os.path.join(local_path, subpath))]
 
     if url.scheme == 's3':
-        s3 = s3_util.create_s3_session(url)
+        s3 = s3_util.create_s3_session(url, connection=s3_util.get_mirror_connection(url))  # noqa: E501
         if recursive:
             return list(_iter_s3_prefix(s3, url))
 

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

@@ -264,9 +264,11 @@ e4s-mac-protected-build:
 
 e4s-pr-generate:
   extends: [ ".e4s", ".pr-generate"]
+  image: ecpe4s/ubuntu22.04-runner-x86_64:2022-07-01
 
 e4s-protected-generate:
   extends: [ ".e4s", ".protected-generate"]
+  image: ecpe4s/ubuntu22.04-runner-x86_64:2022-07-01
 
 e4s-pr-build:
   extends: [ ".e4s", ".pr-build" ]

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

@@ -15,23 +15,16 @@ spack:
 
   packages:
     all:
-      compiler:
-        - gcc@7.5.0
+      compiler: [gcc@11.2.0]
       providers:
-        blas:
-          - openblas
-        mpi:
-          - mpich
-      target:
-        - x86_64
+        blas: [openblas]
+        mpi: [mpich]
+      target: [x86_64]
       variants: +mpi
     binutils:
       variants: +ld +gold +headers +libiberty ~nls
-      version:
-        - 2.36.1
-    doxygen:
-      version:
-        - 1.8.20
+    cuda:
+      version: [11.7.0]
     elfutils:
       variants: +bzip2 ~nls +xz
     hdf5:
@@ -40,187 +33,197 @@ spack:
       variants: fabrics=sockets,tcp,udp,rxm
     libunwind:
       variants: +pic +xz
-    mesa:
-      variants: ~llvm
-    mesa18:
-      variants: ~llvm
     mpich:
       variants: ~wrapperrpath
     ncurses:
       variants: +termlib
     openblas:
       variants: threads=openmp
-    openturns:
-      version: [1.18]
+    python:
+      version: [3.8.13]
     trilinos:
-      variants: +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext +ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu +nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos +teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
+      variants: +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext
+        +ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu
+        +nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos
+        +teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
     xz:
       variants: +pic
-
-  definitions:
-
-  - cuda_specs:
-    - amrex +cuda cuda_arch=70
-    - caliper +cuda cuda_arch=70
-    - chai ~benchmarks ~tests +cuda cuda_arch=70 ^umpire ~shared
-    - ginkgo +cuda cuda_arch=70
-    - heffte +cuda cuda_arch=70
-    - hpx +cuda cuda_arch=70
-    - hypre +cuda cuda_arch=70
-    - kokkos +wrapper +cuda cuda_arch=70
-    - kokkos-kernels +cuda cuda_arch=70 ^kokkos +wrapper +cuda cuda_arch=70
-    - magma +cuda cuda_arch=70
-    - mfem +cuda cuda_arch=70
-    - parsec +cuda cuda_arch=70
-    - petsc +cuda cuda_arch=70
-    - raja +cuda cuda_arch=70
-    - slate +cuda cuda_arch=70
-    - slepc +cuda cuda_arch=70
-    - strumpack ~slate +cuda cuda_arch=70
-    - sundials +cuda cuda_arch=70
-    - superlu-dist +cuda cuda_arch=70
-    - tasmanian +cuda cuda_arch=70
-    # Trilinos: enable CUDA, Kokkos, and important Tpetra-era solver packages;
-    # disable Epetra; disable ETI to speed up CI; disable all other TPLs
-    - trilinos@13.2.0 +cuda cuda_arch=70 +wrapper    +amesos2 +belos +ifpack2 +kokkos +muelu +nox +stratimikos +tpetra    ~amesos ~anasazi ~aztec ~epetraext ~ifpack ~isorropia ~ml ~teko ~tempus ~zoltan ~zoltan2     ~explicit_template_instantiation ~adios2~basker~boost~chaco~complex~debug~dtk~epetraextbtf~epetraextexperimental~epetraextgraphreorderings~exodus~float~fortran~gtest~hypre~intrepid~intrepid2~ipo~mesquite~minitensor~mumps~openmp~phalanx~piro~rocm~rol~rythmos~sacado~scorec~shards~shared~shylu~stk~stokhos~strumpack~suite-sparse~superlu~superlu-dist~trilinoscouplings~x11
-    - umpire ~shared +cuda cuda_arch=70
-    - vtk-m +cuda cuda_arch=70
-    - zfp +cuda cuda_arch=70
-   #- ascent ~shared +cuda cuda_arch=70
-   #- axom +cuda cuda_arch=70 ^umpire ~shared
-   #- dealii +cuda cuda_arch=70 # gmsh
-   #- flecsi +cuda cuda_arch=70
-   #- paraview +cuda cuda_arch=70
-
-  - rocm_specs:
-    - kokkos +rocm amdgpu_target=gfx906
-    #- amrex +rocm amdgpu_target=gfx906
-    #- chai +rocm ~benchmarks amdgpu_target=gfx906
-    #- ginkgo +rocm amdgpu_target=gfx906 # needs hip<4.1
-    #- raja +rocm ~openmp amdgpu_target=gfx906 # blt 0.3.6 issue with rocm
-    #- slate +rocm amdgpu_target=gfx906
-    #- strumpack +rocm ~slate amdgpu_target=gfx906
-    #- sundials +rocm amdgpu_target=gfx906
-    #- tasmanian +rocm amdgpu_target=gfx906
-    #- umpire+rocm amdgpu_target=gfx906 # blt 0.3.6 issue with rocm
-
-  - default_specs:
-    - adios
-    - adios2
-    - aml
-    - amrex
-    - arborx
-    - archer
-    - argobots
-    - ascent
-    - axom
-    - bolt
-    - cabana
-    - caliper
-    - chai ~benchmarks ~tests
-    - conduit
-    - darshan-runtime
-    - darshan-util
-    - datatransferkit
-    - dyninst
-    - faodel
-    - flecsi@1.4.2 +external_cinch
-    - flit
-    - flux-core
-    - fortrilinos
-    - gasnet
-    - ginkgo
-    - globalarrays
-    - gmp
-    - gotcha
-    - gptune
-    - h5bench
-    - hdf5
-    - heffte +fftw
-    - hpctoolkit
-    - hpx
-    - hypre
-    - kokkos +openmp
-    - kokkos-kernels +openmp
-    - lammps
-    - legion
-    - libnrm
-    - libquo
-    - libunwind
-    - llvm targets=amdgpu,nvptx +clang +compiler-rt +libcxx +lld +lldb +llvm_dylib +flang ~cuda
-    - loki
-    - mercury
-    - metall
-    - mfem
-    - mpark-variant
-    - mpifileutils ~xattr
-    - nccmp
-    - nco
-    - ninja
-    - nrm
-    - omega-h
-    - openmpi
-    - openpmd-api
-    - papi
-    - papyrus@1.0.1
-    - parallel-netcdf
-    - parsec ~cuda
-    - pdt
-    - petsc
-    - phist
-    - plasma
-    - precice
-    - pumi
-    - py-jupyterhub
-    - py-libensemble
-    - py-petsc4py
-    - py-warpx ^warpx dims=2
-    - py-warpx ^warpx dims=3
-    - py-warpx ^warpx dims=rz
-    - qthreads scheduler=distrib
-    - raja
-    - rempi
-    - scr
-    - slate ~cuda
-    - slepc
-    - stc
-    - strumpack ~slate
-    - sundials
-    - superlu
-    - superlu-dist
-    - swig
-    - swig@4.0.2-fortran
-    - sz
-    - tasmanian
-    - tau +mpi +python
-    - trilinos +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext +ifpack +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu +nox +piro +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos +teko +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
-    - turbine
-    - umap
-    - umpire
-    - unifyfs@0.9.1
-    - upcxx
-    - variorum
-    - veloc
-    - wannier90
-    - zfp
-    #- dealii
-    #- geopm
-    #- qt
-    #- qwt
-
-  - arch:
-    - '%gcc target=x86_64'
-
+    mesa:
+      version: [21.3.8]
 
   specs:
+  # CPU
+  - adios
+  - adios2
+  - alquimia
+  - aml
+  - amrex
+  - arborx
+  - archer
+  - argobots
+  - ascent
+  - axom
+  - bolt
+  - bricks
+  - butterflypack
+  - cabana
+  - chai ~benchmarks ~tests
+  - conduit
+  - darshan-runtime
+  - darshan-util
+  - datatransferkit
+  - dyninst
+  - exaworks
+  - faodel
+  - flecsi
+  - flit
+  - flux-core
+  - fortrilinos
+  - gasnet
+  - ginkgo
+  - globalarrays
+  - gmp
+  - gptune
+  - hdf5 +fortran +hl +shared
+  - heffte +fftw
+  - hpctoolkit
+  - hpx networking=mpi
+  - hypre
+  - kokkos +openmp
+  - kokkos-kernels +openmp
+  - lammps
+  - legion
+  - libnrm
+  - libquo
+  - libunwind
+  - mercury
+  - metall
+  - mfem
+  - mpark-variant
+  - mpifileutils ~xattr
+  - nccmp
+  - nco
+  - netlib-scalapack
+  - nrm
+  - nvhpc
+  - omega-h
+  - openmpi
+  - openpmd-api
+  - papi
+  - papyrus
+  - parallel-netcdf
+  - parsec ~cuda
+  - pdt
+  - petsc
+  - phist
+  - plasma
+  - plumed
+  - precice
+  - pumi
+  - py-cinemasci
+  - py-jupyterhub
+  - py-libensemble
+  - py-petsc4py
+  - py-warpx ^warpx dims=2
+  - py-warpx ^warpx dims=3
+  - py-warpx ^warpx dims=rz
+  - qthreads scheduler=distrib
+  - raja
+  - scr
+  - slate ~cuda
+  - slepc
+  - stc
+  - strumpack ~slate
+  - sundials
+  - superlu
+  - superlu-dist
+  - swig
+  - swig@4.0.2-fortran
+  - sz
+  - tasmanian
+  - tau +mpi +python
+  - trilinos@13.0.1 +amesos +amesos2 +anasazi +aztec +belos +boost +epetra +epetraext +ifpack
+    +ifpack2 +intrepid +intrepid2 +isorropia +kokkos +ml +minitensor +muelu +nox +piro
+    +phalanx +rol +rythmos +sacado +stk +shards +shylu +stokhos +stratimikos +teko
+    +tempus +tpetra +trilinoscouplings +zoltan +zoltan2 +superlu-dist gotype=long_long
+  - turbine
+  - umap
+  - umpire
+  - upcxx
+  - veloc
+  - vtk-m
+  - wannier90
+  - zfp
 
-  - matrix:
-    - - $default_specs
-    - - $arch
+  # CUDA
+  - adios2 +cuda cuda_arch=80
+  - arborx +cuda cuda_arch=80 ^kokkos@3.6.00 +wrapper
+  - bricks +cuda
+  - cabana +cuda ^kokkos@3.6.00 +wrapper +cuda_lambda +cuda cuda_arch=80
+  - chai ~benchmarks ~tests +cuda cuda_arch=80 ^umpire@6.0.0 ~shared
+  - flux-core +cuda
+  - ginkgo +cuda cuda_arch=80
+  - heffte +cuda cuda_arch=80
+  - hpctoolkit +cuda
+  - hpx +cuda cuda_arch=80
+  - hypre +cuda cuda_arch=80
+  - kokkos-kernels +cuda cuda_arch=80 ^kokkos +wrapper +cuda cuda_arch=80
+  - kokkos +wrapper +cuda cuda_arch=80
+  - magma +cuda cuda_arch=80
+  - mfem +cuda cuda_arch=80
+  - papi +cuda
+  - petsc +cuda cuda_arch=80
+  - raja +cuda cuda_arch=80
+  - slate +cuda cuda_arch=80
+  - slepc +cuda cuda_arch=80
+  - strumpack ~slate +cuda cuda_arch=80
+  - sundials +cuda cuda_arch=80
+  - superlu-dist +cuda cuda_arch=80
+  - tasmanian +cuda cuda_arch=80
+  - tau +mpi +cuda
+  - umpire ~shared +cuda cuda_arch=80
+  - vtk-m +cuda cuda_arch=80
+  - zfp +cuda cuda_arch=80
 
-  - matrix:
-    - - $cuda_specs
-    - - $arch
+  # ROCm
+  - amrex +rocm amdgpu_target=gfx90a
+  - arborx +rocm amdgpu_target=gfx90a
+  - gasnet +rocm amdgpu_target=gfx90a
+  - ginkgo +rocm amdgpu_target=gfx90a
+  - heffte +rocm amdgpu_target=gfx90a
+  - hpx +rocm amdgpu_target=gfx90a
+  - kokkos +rocm amdgpu_target=gfx90a
+  - magma ~cuda +rocm amdgpu_target=gfx90a
+  - petsc +rocm amdgpu_target=gfx90a
+  - slepc +rocm amdgpu_target=gfx90a ^petsc +rocm amdgpu_target=gfx90a
+  - strumpack ~slate +rocm amdgpu_target=gfx90a
+  - superlu-dist +rocm amdgpu_target=gfx90a
+  - tau +mpi +rocm
+  - upcxx +rocm amdgpu_target=gfx90a
+
+  # CPU failures
+  #- caliper        # /usr/bin/ld: ../../libcaliper.so.2.7.0: undefined reference to `_dl_sym'
+  #- charliecloud   # autogen.sh: 6: [[: not found
+  #- geopm          # /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: error:'__builtin_strncpy' specified bound 512 equals destination size [-Werror=stringop-truncation]
+  #- gotcha         # /usr/bin/ld: ../../libgotcha.so.2.0.2: undefined reference to `_dl_sym' 
+  #- h5bench        # commons/h5bench_util.h:196: multiple definition of `has_vol_async';
+  #- loki           # ../include/loki/Singleton.h:158:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  #- paraview +qt   # llvm@14
+  #- pruners-ninja  # test/ninja_test_util.c:34: multiple definition of `a';
+  #- rempi          # rempi_message_manager.h:53:3: error: 'string' does not name a type
+  #- unifyfs        # gotcha: /usr/bin/ld: ../../libgotcha.so.2.0.2: undefined reference to `_dl_sym' 
+  #- variorum       # /usr/bin/ld: Intel/CMakeFiles/variorum_intel.dir/Broadwell_4F.c.o:(.bss+0x0): multiple definition of `g_platform';
+
+  # CUDA failures
+  #- caliper +cuda cuda_arch=80               # /usr/bin/ld: ../../libcaliper.so.2.7.0: undefined reference to `_dl_sym'
+  #- parsec +cuda cuda_arch=80                # parsec/mca/device/cuda/transfer.c:168: multiple definition of `parsec_CUDA_d2h_max_flows';
+  #- trilinos@13.2.0 +cuda cuda_arch=80       # /usr/include/c++/11/bits/std_function.h:435:145: error: parameter packs not expanded with '...':
+
+  # ROCm failures
+  #- chai ~benchmarks +rocm amdgpu_target=gfx90a  # umpire: Target "blt_hip" INTERFACE_INCLUDE_DIRECTORIES property contains path: "/tmp/root/spack-stage/spack-stage-umpire-2022.03.1-by6rldnpdowaaoqgxkeqejwyx5uxo2sv/spack-src/HIP_CLANG_INCLUDE_PATH-NOTFOUND/.." which is prefixed in the source directory.
+  #- hpctoolkit +rocm                             # roctracer-dev: core/memory_pool.h:155:64: error: 'int pthread_yield()' is deprecated: pthread_yield is deprecated, use sched_yield instead [-Werror=deprecated-declarations]
+  #- raja ~openmp +rocm amdgpu_target=gfx90a      # cmake: Could NOT find ROCPRIM (missing: ROCPRIM_INCLUDE_DIRS)
+  #- umpire +rocm amdgpu_target=gfx90a            # Target "blt_hip" INTERFACE_INCLUDE_DIRECTORIES property contains path: "/tmp/root/spack-stage/spack-stage-umpire-2022.03.1-by6rldnpdowaaoqgxkeqejwyx5uxo2sv/spack-src/HIP_CLANG_INCLUDE_PATH-NOTFOUND/.." which is prefixed in the source directory.
 
   mirrors: { "mirror": "s3://spack-binaries/develop/e4s" }
 
@@ -237,10 +240,14 @@ spack:
       - if [[ -r /mnt/key/spack_public_key.gpg ]]; then spack gpg trust /mnt/key/spack_public_key.gpg; fi
       - spack -d ci rebuild > >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_out.txt) 2> >(tee ${SPACK_ARTIFACTS_ROOT}/user_data/pipeline_err.txt >&2)
 
-    image: { "name": "ghcr.io/spack/e4s-ubuntu-18.04:v2021-10-18", "entrypoint": [""] }
+    image: ecpe4s/ubuntu22.04-runner-x86_64:2022-07-01
+    
     mappings:
       - match:
+          - hipblas
           - llvm
+          - llvm-amdgpu
+          - rocblas
         runner-attributes:
           tags: [ "spack", "huge", "x86_64" ]
           variables:
@@ -402,7 +409,7 @@ spack:
             KUBERNETES_CPU_REQUEST: "500m"
             KUBERNETES_MEMORY_REQUEST: "500M"
 
-      - match: ['os=ubuntu18.04']
+      - match: ['os=ubuntu22.04']
         runner-attributes:
           tags: ["spack", "x86_64"]
           variables:
@@ -414,7 +421,7 @@ spack:
       before_script:
         - . "./share/spack/setup-env.sh"
         - spack --version
-      image: { "name": "ghcr.io/spack/e4s-ubuntu-18.04:v2021-10-18", "entrypoint": [""] }
+      image: ecpe4s/ubuntu22.04-runner-x86_64:2022-07-01
       tags: ["spack", "public", "x86_64"]
 
     signing-job-attributes:

share/spack/spack-completion.bash

@@ -1688,7 +1688,7 @@ _spack_spec() {
 _spack_stage() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -n --no-checksum --deprecated -p --path"
+        SPACK_COMPREPLY="-h --help -n --no-checksum --deprecated -p --path -U --fresh --reuse"
     else
         _all_packages
     fi

share/spack/templates/container/Dockerfile

@@ -19,8 +19,7 @@ RUN mkdir {{ paths.environment }} \
 {{ manifest }} > {{ paths.environment }}/spack.yaml
 
 # Install the software, remove unnecessary deps
-RUN spack install --fail-fast && \
-    spack gc -y
+RUN cd {{ paths.environment }} && spack env activate . && spack install --fail-fast && spack gc -y
 {% if strip %}
 
 # Strip all the binaries

var/spack/repos/builtin/packages/adios2/package.py

@@ -21,6 +21,7 @@ class Adios2(CMakePackage, CudaPackage):
     tags = ['e4s']
 
     version('master', branch='master')
+    version('2.8.2', sha256='9909f6409dc44b2c28c1fda0042dab4b711f25ec3277ef0cb6ffc40f5483910d')
     version('2.8.1', sha256='3f515b442bbd52e3189866b121613fe3b59edb8845692ea86fad83d1eba35d93')
     version('2.8.0', sha256='5af3d950e616989133955c2430bd09bcf6bad3a04cf62317b401eaf6e7c2d479')
     version('2.7.1', sha256='c8e237fd51f49d8a62a0660db12b72ea5067512aa7970f3fcf80b70e3f87ca3e')

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

@@ -16,6 +16,7 @@ class Gperftools(AutotoolsPackage):
     url      = "https://github.com/gperftools/gperftools/releases/download/gperftools-2.7/gperftools-2.7.tar.gz"
     maintainers = ['albestro', 'eschnett', 'msimberg', 'teonnik']
 
+    version('2.10', sha256='83e3bfdd28b8bcf53222c3798d4d395d52dadbbae59e8730c4a6d31a9c3732d8')
     version('2.9.1', sha256='ea566e528605befb830671e359118c2da718f721c27225cbbc93858c7520fee3')
     version('2.8.1', sha256='12f07a8ba447f12a3ae15e6e3a6ad74de35163b787c0c7b76288d7395f2f74e0')
     version('2.7', sha256='1ee8c8699a0eff6b6a203e59b43330536b22bbcbe6448f54c7091e5efb0763c9')
@@ -36,5 +37,9 @@ def configure_args(self):
                                        variant='dynamic_sized_delete_support')
         args += self.enable_or_disable("debugalloc")
         args += self.enable_or_disable("libunwind")
+        if self.spec.satisfies('+libunwind'):
+            args += [
+                "LDFLAGS=-lunwind"
+            ]
 
         return args

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

@@ -14,7 +14,9 @@ class Interproscan(Package):
 
     homepage = "https://www.ebi.ac.uk/interpro/interproscan.html"
     url      = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz"
+    maintainers = ['snehring']
 
+    version('5.56-89.0', sha256='75e6a8f86ca17356a2f77f75b07d6d8fb7b397c9575f6e9716b64983e490b230')
     version('5.38-76.0', sha256='cb191ff8eee275689b789167a57b368ea5c06bbcd36b4de23e8bbbbdc0fc7434')
     version('5.36-75.0', sha256='383d7431e47c985056c856ceb6d4dcf7ed2559a4a3d5c210c01ce3975875addb')
     version('4.8',

var/spack/repos/builtin/packages/kallisto/htslib_configure.patch

@@ -0,0 +1,12 @@
+--- a/ext/htslib/configure.ac	2022-01-16 23:02:18.000000000 -0600
++++ b/ext/htslib/configure.ac	2022-07-16 18:45:33.283586367 -0500
+@@ -46,7 +46,9 @@
+    the PACKAGE_* defines are unused and are overridden by the more
+    accurate PACKAGE_VERSION as computed by the Makefile.  */])
+ 
++AC_CANONICAL_HOST
+ AC_PROG_CC
++AC_PROG_INSTALL
+ AC_PROG_RANLIB
+ 
+ dnl Avoid chicken-and-egg problem where pkg-config supplies the

var/spack/repos/builtin/packages/kallisto/limits.patch

@@ -0,0 +1,9 @@
+--- a/src/MinCollector.cpp	2020-02-16 16:27:33.000000000 -0600
++++ b/src/MinCollector.cpp	2022-07-17 13:09:47.698229720 -0500
+@@ -1,5 +1,6 @@
+ #include "MinCollector.h"
+ #include <algorithm>
++#include <limits>
+ 
+ // utility functions
+ 

var/spack/repos/builtin/packages/kallisto/link_zlib.patch

@@ -0,0 +1,10 @@
+--- a/src/CMakeLists.txt	2017-03-20 05:38:35.000000000 -0500
++++ b/src/CMakeLists.txt	2022-07-17 12:56:04.456804708 -0500
+@@ -32,6 +32,7 @@
+ 
+ if ( ZLIB_FOUND )
+     include_directories( ${ZLIB_INCLUDE_DIRS} )
++    target_link_libraries(kallisto kallisto_core ${ZLIB_LIBRARIES})
+ else()
+     message(FATAL_ERROR "zlib not found. Required for to output files" )
+ endif( ZLIB_FOUND )

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

@@ -17,8 +17,15 @@ class Kallisto(CMakePackage):
     version('0.46.2', sha256='c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2')
     version('0.43.1', sha256='7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400')
 
+    # HDF5 support is optional beginning with version 0.46.2.
+    variant('hdf5',
+            when='@0.46.2:',
+            default=False,
+            description='Build with HDF5 support')
+
     depends_on('zlib')
-    depends_on('hdf5')
+    depends_on('hdf5', when='@:0.43')
+    depends_on('hdf5', when='+hdf5')
 
     # htslib isn't built in time to be used....
     parallel = False
@@ -30,6 +37,19 @@ class Kallisto(CMakePackage):
     depends_on('libtool',  type='build', when='@0.44.0:')
     depends_on('m4',       type='build', when='@0.44.0:')
 
+    patch('link_zlib.patch', when='@:0.43')
+    patch('limits.patch', when='@:0.46')
+    patch('htslib_configure.patch', when='@0.44.0:^autoconf@2.70:')
+
+    @run_before('cmake')
+    def autoreconf(self):
+        # Versions of autoconf greater than 2.69 need config.guess and
+        # config.sub in the tree.
+        if self.spec.satisfies('@0.44.0:^autoconf@2.70:'):
+            with working_dir(join_path(self.stage.source_path, 'ext', 'htslib')):
+                autoreconf = which('autoreconf')
+                autoreconf('--install')
+
     # Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args
     # causes bits of cmake's output to end up in the autoconf-generated
     # configure script.
@@ -41,8 +61,10 @@ def std_cmake_args(self):
         setting.
         """
         a = super(Kallisto, self).std_cmake_args
-        if (self.spec.version >= Version('0.44.0')):
+        if self.spec.satisfies('@0.44.0:'):
             args = [i for i in a if i != '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON']
+            if self.spec.satisfies('@0.46.2:'):
+                args.append(self.define_from_variant('USE_HDF5', 'hdf5'))
         else:
             args = a
 

var/spack/repos/builtin/packages/kraken2/package.py

@@ -18,6 +18,7 @@ class Kraken2(Package):
 
     maintainers = ['rberg2']
 
+    version('2.1.2', sha256='e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3')
     version('2.1.1', sha256='8f3e928cdb32b9e8e6f55b44703d1557b2a5fc3f30f63e8d16e465e19a81dee4')
     version('2.0.8-beta', sha256='f2a91fc57a40b3e87df8ac2ea7c0ff1060cc9295c95de417ee53249ee3f7ad8e')
     version('2.0.7-beta', sha256='baa160f5aef73327e1a79e6d1c54b64b2fcdaee0be31b456f7bc411d1897a744')

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

@@ -34,9 +34,11 @@ class Lhapdf(AutotoolsPackage):
     extends('python', when='+python')
     depends_on('py-cython',     type='build', when='+python')
     depends_on('py-setuptools', type='build', when='+python')
+    depends_on('gettext',       type='build', when='+python')
 
     def configure_args(self):
         args = ['FCFLAGS=-O3', 'CFLAGS=-O3', 'CXXFLAGS=-O3',
-                'LIBS=-L' + self.spec['python'].prefix.lib]
+                'LIBS=-L' + self.spec['python'].prefix.lib +
+                ' -L' + self.spec['gettext'].prefix.lib]
         args.extend(self.enable_or_disable('python'))
         return args

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

@@ -110,6 +110,10 @@ class Openssl(Package):   # Uses Fake Autotools, should subclass Package
     depends_on('ca-certificates-mozilla', type=('build', 'run'), when='certs=mozilla')
     depends_on('nasm', when='platform=windows')
 
+    patch('https://github.com/openssl/openssl/commit/f9e578e720bb35228948564192adbe3bc503d5fb.patch?full_index=1',
+          sha256='3fdcf2d1e47c34f3a012f23306322c5a35cad55b180c9b6fb34537b55884645c',
+          when='@1.1.1q')
+
     @classmethod
     def determine_version(cls, exe):
         output = Executable(exe)('version', output=str, error=str)

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

@@ -0,0 +1,40 @@
+# 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.package import *
+
+
+class PyBlight(PythonPackage):
+    """A catch-all compile-tool wrapper."""
+
+    homepage = "https://github.com/trailofbits/blight"
+    pypi     = "blight/blight-0.0.47.tar.gz"
+
+    maintainers = ['woodruffw']
+
+    version('0.0.47', sha256='eb4a881adb98e03a0a855b95bfcddb0f4b3ca568b00cb45b571f047ae75c5667')
+
+    variant('dev', default=False, description='Install dependencies to help with development')
+
+    depends_on('python@3.7:', type=('build', 'run'))
+
+    # In process of changing build backend after 0.0.47 release.
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-click@7.1:8', type=('build', 'run'))
+    depends_on('py-typing-extensions', type=('build', 'run'))
+    depends_on('py-pydantic@1.7:1', type=('build', 'run'))
+
+    depends_on('py-flake8', type=('build', 'run'), when='+dev')
+    depends_on('py-black', type=('build', 'run'), when='+dev')
+    # blight uses pyproject.toml to configure isort. isort added
+    # support in 5.0.0
+    depends_on('py-isort@5.0.0:', type=('build', 'run'), when='+dev')
+    depends_on('py-pytest', type=('build', 'run'), when='+dev')
+    depends_on('py-pytest-cov', type=('build', 'run'), when='+dev')
+    depends_on('py-coverage+toml', type=('build', 'run'), when='+dev')
+    depends_on('py-twine', type=('build', 'run'), when='+dev')
+    depends_on('py-pdoc3', type=('build', 'run'), when='+dev')
+    depends_on('py-mypy', type=('build', 'run'), when='@0.0.5:+dev')

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

@@ -10,18 +10,20 @@ class PyFparser(PythonPackage):
     """Parser for Fortran 77..2003 code."""
 
     homepage = "https://github.com/stfc/fparser"
-    url      = "https://github.com/stfc/fparser/archive/0.0.5.tar.gz"
     git      = "https://github.com/stfc/fparser.git"
+    pypi     = "fparser/fparser-0.0.16.tar.gz"
 
     version('develop', branch='master')
-    version('0.0.6', sha256='6ced61573257d11037d25c02d5f0ea92ca9bf1783018bf5f0de30d245ae631ac')
-    version('0.0.5', sha256='7668b331b9423d15353d502ab26d1d561acd5247882dab672f1e45565dabaf08')
+    version('0.0.16', sha256='a06389b95a1b9ed12f8141b69c67343da5ba0a29277b2997b02573a93af14e13')
+    version('0.0.6', sha256='bf8a419cb528df1bfc24ddd26d63f2ebea6f1e103f1a259d8d3a6c9b1cd53012')
+    version('0.0.5', sha256='f3b5b0ac56fd22abed558c0fb0ba4f28edb8de7ef24cfda8ca8996562215822f')
 
     depends_on('py-setuptools', type='build')
 
     depends_on('py-numpy', type=('build', 'run'), when='@:0.0.5')
-    depends_on('py-nose', type='build')
-    depends_on('py-six', type='build', when='@0.0.6:')
+    depends_on('py-nose', type=('build', 'run'), when='@:0.0.7')
+    # six is unused as of 0.0.15, but still listed in setup.py
+    depends_on('py-six', type=('build', 'run'), when='@0.0.6:')
 
     depends_on('py-pytest', type='test')
 

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

@@ -14,6 +14,7 @@ class PyGeocube(PythonPackage):
 
     maintainers = ['adamjstewart']
 
+    version('0.3.2', sha256='71ff0228f1ef44e3a649d29a045ff7e2a2094a5cfca30fadab8f88f4ec23a41d')
     version('0.3.1', sha256='5c97131010cd8d556a5fad2a3824452120640ac33a6a45b6ca9ee3c28f2e266f')
     version('0.0.17', sha256='bf8da0fa96d772ebaea0b98bafa0ba5b8639669d5feb07465d4255af177bddc0')
 

var/spack/repos/builtin/packages/py-horovod/eigen.patch

@@ -0,0 +1,711 @@
+--- spack-src/third_party/eigen/Eigen/src/Core/arch/NEON/PacketMath.h.orig	2022-03-02 16:22:53.000000000 +0900
++++ spack-src/third_party/eigen/Eigen/src/Core/arch/NEON/PacketMath.h	2022-03-03 14:11:43.000000000 +0900
+@@ -1922,13 +1922,13 @@
+ template<> EIGEN_STRONG_INLINE void pstoreu<uint64_t>(uint64_t* to, const Packet2ul& from)
+ { EIGEN_DEBUG_UNALIGNED_STORE vst1q_u64(to,from); }
+ 
+-template<> EIGEN_DEVICE_FUNC inline Packet2f pgather<float, Packet2f>(const float* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2f pgather<float, Packet2f>(const float* from, Index stride)
+ {
+   Packet2f res = vld1_dup_f32(from);
+   res = vld1_lane_f32(from + 1*stride, res, 1);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet4f pgather<float, Packet4f>(const float* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4f pgather<float, Packet4f>(const float* from, Index stride)
+ {
+   Packet4f res = vld1q_dup_f32(from);
+   res = vld1q_lane_f32(from + 1*stride, res, 1);
+@@ -1936,14 +1936,14 @@
+   res = vld1q_lane_f32(from + 3*stride, res, 3);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet4c pgather<int8_t, Packet4c>(const int8_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4c pgather<int8_t, Packet4c>(const int8_t* from, Index stride)
+ {
+   Packet4c res;
+   for (int i = 0; i != 4; i++)
+     reinterpret_cast<int8_t*>(&res)[i] = *(from + i * stride);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet8c pgather<int8_t, Packet8c>(const int8_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8c pgather<int8_t, Packet8c>(const int8_t* from, Index stride)
+ {
+   Packet8c res = vld1_dup_s8(from);
+   res = vld1_lane_s8(from + 1*stride, res, 1);
+@@ -1955,7 +1955,7 @@
+   res = vld1_lane_s8(from + 7*stride, res, 7);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet16c pgather<int8_t, Packet16c>(const int8_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet16c pgather<int8_t, Packet16c>(const int8_t* from, Index stride)
+ {
+   Packet16c res = vld1q_dup_s8(from);
+   res = vld1q_lane_s8(from + 1*stride, res, 1);
+@@ -1975,14 +1975,14 @@
+   res = vld1q_lane_s8(from + 15*stride, res, 15);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet4uc pgather<uint8_t, Packet4uc>(const uint8_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4uc pgather<uint8_t, Packet4uc>(const uint8_t* from, Index stride)
+ {
+   Packet4uc res;
+   for (int i = 0; i != 4; i++)
+     reinterpret_cast<uint8_t*>(&res)[i] = *(from + i * stride);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet8uc pgather<uint8_t, Packet8uc>(const uint8_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8uc pgather<uint8_t, Packet8uc>(const uint8_t* from, Index stride)
+ {
+   Packet8uc res = vld1_dup_u8(from);
+   res = vld1_lane_u8(from + 1*stride, res, 1);
+@@ -1994,7 +1994,7 @@
+   res = vld1_lane_u8(from + 7*stride, res, 7);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet16uc pgather<uint8_t, Packet16uc>(const uint8_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet16uc pgather<uint8_t, Packet16uc>(const uint8_t* from, Index stride)
+ {
+   Packet16uc res = vld1q_dup_u8(from);
+   res = vld1q_lane_u8(from + 1*stride, res, 1);
+@@ -2014,7 +2014,7 @@
+   res = vld1q_lane_u8(from + 15*stride, res, 15);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet4s pgather<int16_t, Packet4s>(const int16_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4s pgather<int16_t, Packet4s>(const int16_t* from, Index stride)
+ {
+   Packet4s res = vld1_dup_s16(from);
+   res = vld1_lane_s16(from + 1*stride, res, 1);
+@@ -2022,7 +2022,7 @@
+   res = vld1_lane_s16(from + 3*stride, res, 3);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet8s pgather<int16_t, Packet8s>(const int16_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8s pgather<int16_t, Packet8s>(const int16_t* from, Index stride)
+ {
+   Packet8s res = vld1q_dup_s16(from);
+   res = vld1q_lane_s16(from + 1*stride, res, 1);
+@@ -2034,7 +2034,7 @@
+   res = vld1q_lane_s16(from + 7*stride, res, 7);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet4us pgather<uint16_t, Packet4us>(const uint16_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4us pgather<uint16_t, Packet4us>(const uint16_t* from, Index stride)
+ {
+   Packet4us res = vld1_dup_u16(from);
+   res = vld1_lane_u16(from + 1*stride, res, 1);
+@@ -2042,7 +2042,7 @@
+   res = vld1_lane_u16(from + 3*stride, res, 3);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet8us pgather<uint16_t, Packet8us>(const uint16_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8us pgather<uint16_t, Packet8us>(const uint16_t* from, Index stride)
+ {
+   Packet8us res = vld1q_dup_u16(from);
+   res = vld1q_lane_u16(from + 1*stride, res, 1);
+@@ -2054,13 +2054,13 @@
+   res = vld1q_lane_u16(from + 7*stride, res, 7);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet2i pgather<int32_t, Packet2i>(const int32_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2i pgather<int32_t, Packet2i>(const int32_t* from, Index stride)
+ {
+   Packet2i res = vld1_dup_s32(from);
+   res = vld1_lane_s32(from + 1*stride, res, 1);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet4i pgather<int32_t, Packet4i>(const int32_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4i pgather<int32_t, Packet4i>(const int32_t* from, Index stride)
+ {
+   Packet4i res = vld1q_dup_s32(from);
+   res = vld1q_lane_s32(from + 1*stride, res, 1);
+@@ -2068,13 +2068,13 @@
+   res = vld1q_lane_s32(from + 3*stride, res, 3);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet2ui pgather<uint32_t, Packet2ui>(const uint32_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2ui pgather<uint32_t, Packet2ui>(const uint32_t* from, Index stride)
+ {
+   Packet2ui res = vld1_dup_u32(from);
+   res = vld1_lane_u32(from + 1*stride, res, 1);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet4ui pgather<uint32_t, Packet4ui>(const uint32_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4ui pgather<uint32_t, Packet4ui>(const uint32_t* from, Index stride)
+ {
+   Packet4ui res = vld1q_dup_u32(from);
+   res = vld1q_lane_u32(from + 1*stride, res, 1);
+@@ -2082,37 +2082,37 @@
+   res = vld1q_lane_u32(from + 3*stride, res, 3);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet2l pgather<int64_t, Packet2l>(const int64_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2l pgather<int64_t, Packet2l>(const int64_t* from, Index stride)
+ {
+   Packet2l res = vld1q_dup_s64(from);
+   res = vld1q_lane_s64(from + 1*stride, res, 1);
+   return res;
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet2ul pgather<uint64_t, Packet2ul>(const uint64_t* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2ul pgather<uint64_t, Packet2ul>(const uint64_t* from, Index stride)
+ {
+   Packet2ul res = vld1q_dup_u64(from);
+   res = vld1q_lane_u64(from + 1*stride, res, 1);
+   return res;
+ }
+ 
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<float, Packet2f>(float* to, const Packet2f& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<float, Packet2f>(float* to, const Packet2f& from, Index stride)
+ {
+   vst1_lane_f32(to + stride*0, from, 0);
+   vst1_lane_f32(to + stride*1, from, 1);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<float, Packet4f>(float* to, const Packet4f& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<float, Packet4f>(float* to, const Packet4f& from, Index stride)
+ {
+   vst1q_lane_f32(to + stride*0, from, 0);
+   vst1q_lane_f32(to + stride*1, from, 1);
+   vst1q_lane_f32(to + stride*2, from, 2);
+   vst1q_lane_f32(to + stride*3, from, 3);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<int8_t, Packet4c>(int8_t* to, const Packet4c& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<int8_t, Packet4c>(int8_t* to, const Packet4c& from, Index stride)
+ {
+   for (int i = 0; i != 4; i++)
+     *(to + i * stride) = reinterpret_cast<const int8_t*>(&from)[i];
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<int8_t, Packet8c>(int8_t* to, const Packet8c& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<int8_t, Packet8c>(int8_t* to, const Packet8c& from, Index stride)
+ {
+   vst1_lane_s8(to + stride*0, from, 0);
+   vst1_lane_s8(to + stride*1, from, 1);
+@@ -2123,7 +2123,7 @@
+   vst1_lane_s8(to + stride*6, from, 6);
+   vst1_lane_s8(to + stride*7, from, 7);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<int8_t, Packet16c>(int8_t* to, const Packet16c& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<int8_t, Packet16c>(int8_t* to, const Packet16c& from, Index stride)
+ {
+   vst1q_lane_s8(to + stride*0, from, 0);
+   vst1q_lane_s8(to + stride*1, from, 1);
+@@ -2142,12 +2142,12 @@
+   vst1q_lane_s8(to + stride*14, from, 14);
+   vst1q_lane_s8(to + stride*15, from, 15);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<uint8_t, Packet4uc>(uint8_t* to, const Packet4uc& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<uint8_t, Packet4uc>(uint8_t* to, const Packet4uc& from, Index stride)
+ {
+   for (int i = 0; i != 4; i++)
+     *(to + i * stride) = reinterpret_cast<const uint8_t*>(&from)[i];
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<uint8_t, Packet8uc>(uint8_t* to, const Packet8uc& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<uint8_t, Packet8uc>(uint8_t* to, const Packet8uc& from, Index stride)
+ {
+   vst1_lane_u8(to + stride*0, from, 0);
+   vst1_lane_u8(to + stride*1, from, 1);
+@@ -2158,7 +2158,7 @@
+   vst1_lane_u8(to + stride*6, from, 6);
+   vst1_lane_u8(to + stride*7, from, 7);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<uint8_t, Packet16uc>(uint8_t* to, const Packet16uc& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<uint8_t, Packet16uc>(uint8_t* to, const Packet16uc& from, Index stride)
+ {
+   vst1q_lane_u8(to + stride*0, from, 0);
+   vst1q_lane_u8(to + stride*1, from, 1);
+@@ -2177,14 +2177,14 @@
+   vst1q_lane_u8(to + stride*14, from, 14);
+   vst1q_lane_u8(to + stride*15, from, 15);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<int16_t, Packet4s>(int16_t* to, const Packet4s& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<int16_t, Packet4s>(int16_t* to, const Packet4s& from, Index stride)
+ {
+   vst1_lane_s16(to + stride*0, from, 0);
+   vst1_lane_s16(to + stride*1, from, 1);
+   vst1_lane_s16(to + stride*2, from, 2);
+   vst1_lane_s16(to + stride*3, from, 3);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<int16_t, Packet8s>(int16_t* to, const Packet8s& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<int16_t, Packet8s>(int16_t* to, const Packet8s& from, Index stride)
+ {
+   vst1q_lane_s16(to + stride*0, from, 0);
+   vst1q_lane_s16(to + stride*1, from, 1);
+@@ -2195,14 +2195,14 @@
+   vst1q_lane_s16(to + stride*6, from, 6);
+   vst1q_lane_s16(to + stride*7, from, 7);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<uint16_t, Packet4us>(uint16_t* to, const Packet4us& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<uint16_t, Packet4us>(uint16_t* to, const Packet4us& from, Index stride)
+ {
+   vst1_lane_u16(to + stride*0, from, 0);
+   vst1_lane_u16(to + stride*1, from, 1);
+   vst1_lane_u16(to + stride*2, from, 2);
+   vst1_lane_u16(to + stride*3, from, 3);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<uint16_t, Packet8us>(uint16_t* to, const Packet8us& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<uint16_t, Packet8us>(uint16_t* to, const Packet8us& from, Index stride)
+ {
+   vst1q_lane_u16(to + stride*0, from, 0);
+   vst1q_lane_u16(to + stride*1, from, 1);
+@@ -2213,36 +2213,36 @@
+   vst1q_lane_u16(to + stride*6, from, 6);
+   vst1q_lane_u16(to + stride*7, from, 7);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<int32_t, Packet2i>(int32_t* to, const Packet2i& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<int32_t, Packet2i>(int32_t* to, const Packet2i& from, Index stride)
+ {
+   vst1_lane_s32(to + stride*0, from, 0);
+   vst1_lane_s32(to + stride*1, from, 1);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<int32_t, Packet4i>(int32_t* to, const Packet4i& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<int32_t, Packet4i>(int32_t* to, const Packet4i& from, Index stride)
+ {
+   vst1q_lane_s32(to + stride*0, from, 0);
+   vst1q_lane_s32(to + stride*1, from, 1);
+   vst1q_lane_s32(to + stride*2, from, 2);
+   vst1q_lane_s32(to + stride*3, from, 3);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<uint32_t, Packet2ui>(uint32_t* to, const Packet2ui& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<uint32_t, Packet2ui>(uint32_t* to, const Packet2ui& from, Index stride)
+ {
+   vst1_lane_u32(to + stride*0, from, 0);
+   vst1_lane_u32(to + stride*1, from, 1);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<uint32_t, Packet4ui>(uint32_t* to, const Packet4ui& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<uint32_t, Packet4ui>(uint32_t* to, const Packet4ui& from, Index stride)
+ {
+   vst1q_lane_u32(to + stride*0, from, 0);
+   vst1q_lane_u32(to + stride*1, from, 1);
+   vst1q_lane_u32(to + stride*2, from, 2);
+   vst1q_lane_u32(to + stride*3, from, 3);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<int64_t, Packet2l>(int64_t* to, const Packet2l& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<int64_t, Packet2l>(int64_t* to, const Packet2l& from, Index stride)
+ {
+   vst1q_lane_s64(to + stride*0, from, 0);
+   vst1q_lane_s64(to + stride*1, from, 1);
+ }
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<uint64_t, Packet2ul>(uint64_t* to, const Packet2ul& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<uint64_t, Packet2ul>(uint64_t* to, const Packet2ul& from, Index stride)
+ {
+   vst1q_lane_u64(to + stride*0, from, 0);
+   vst1q_lane_u64(to + stride*1, from, 1);
+@@ -2457,23 +2457,23 @@
+ template<> EIGEN_STRONG_INLINE uint64_t predux<Packet2ul>(const Packet2ul& a)
+ { return vgetq_lane_u64(a, 0) + vgetq_lane_u64(a, 1); }
+ 
+-template<> EIGEN_DEVICE_FUNC inline Packet4c predux_half_dowto4(const Packet8c& a)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4c predux_half_dowto4(const Packet8c& a)
+ {
+   return vget_lane_s32(vreinterpret_s32_s8(vadd_s8(a,
+       vreinterpret_s8_s32(vrev64_s32(vreinterpret_s32_s8(a))))), 0);
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet8c predux_half_dowto4(const Packet16c& a)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8c predux_half_dowto4(const Packet16c& a)
+ { return vadd_s8(vget_high_s8(a), vget_low_s8(a)); }
+-template<> EIGEN_DEVICE_FUNC inline Packet4uc predux_half_dowto4(const Packet8uc& a)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4uc predux_half_dowto4(const Packet8uc& a)
+ {
+   return vget_lane_u32(vreinterpret_u32_u8(vadd_u8(a,
+       vreinterpret_u8_u32(vrev64_u32(vreinterpret_u32_u8(a))))), 0);
+ }
+-template<> EIGEN_DEVICE_FUNC inline Packet8uc predux_half_dowto4(const Packet16uc& a)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8uc predux_half_dowto4(const Packet16uc& a)
+ { return vadd_u8(vget_high_u8(a), vget_low_u8(a)); }
+-template<> EIGEN_DEVICE_FUNC inline Packet4s predux_half_dowto4(const Packet8s& a)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4s predux_half_dowto4(const Packet8s& a)
+ { return vadd_s16(vget_high_s16(a), vget_low_s16(a)); }
+-template<> EIGEN_DEVICE_FUNC inline Packet4us predux_half_dowto4(const Packet8us& a)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4us predux_half_dowto4(const Packet8us& a)
+ { return vadd_u16(vget_high_u16(a), vget_low_u16(a)); }
+ 
+ // Other reduction functions:
+@@ -2752,13 +2752,13 @@
+   return vget_lane_u32(vpmax_u32(tmp, tmp), 0);
+ }
+ 
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet2f, 2>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet2f, 2>& kernel)
+ {
+   const float32x2x2_t z = vzip_f32(kernel.packet[0], kernel.packet[1]);
+   kernel.packet[0] = z.val[0];
+   kernel.packet[1] = z.val[1];
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet4f, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet4f, 4>& kernel)
+ {
+   const float32x4x2_t tmp1 = vzipq_f32(kernel.packet[0], kernel.packet[1]);
+   const float32x4x2_t tmp2 = vzipq_f32(kernel.packet[2], kernel.packet[3]);
+@@ -2768,7 +2768,7 @@
+   kernel.packet[2] = vcombine_f32(vget_low_f32(tmp1.val[1]), vget_low_f32(tmp2.val[1]));
+   kernel.packet[3] = vcombine_f32(vget_high_f32(tmp1.val[1]), vget_high_f32(tmp2.val[1]));
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet4c, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet4c, 4>& kernel)
+ {
+   const int8x8_t a = vreinterpret_s8_s32(vset_lane_s32(kernel.packet[2], vdup_n_s32(kernel.packet[0]), 1));
+   const int8x8_t b = vreinterpret_s8_s32(vset_lane_s32(kernel.packet[3], vdup_n_s32(kernel.packet[1]), 1));
+@@ -2781,7 +2781,7 @@
+   kernel.packet[2] = vget_lane_s32(vreinterpret_s32_s16(zip16.val[1]), 0);
+   kernel.packet[3] = vget_lane_s32(vreinterpret_s32_s16(zip16.val[1]), 1);
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet8c, 8>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet8c, 8>& kernel)
+ {
+   int8x8x2_t zip8[4];
+   uint16x4x2_t zip16[4];
+@@ -2811,7 +2811,7 @@
+     }
+   }
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet16c, 16>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet16c, 16>& kernel)
+ {
+   int8x16x2_t zip8[8];
+   uint16x8x2_t zip16[8];
+@@ -2858,7 +2858,7 @@
+     }
+   }
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet4uc, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet4uc, 4>& kernel)
+ {
+   const uint8x8_t a = vreinterpret_u8_u32(vset_lane_u32(kernel.packet[2], vdup_n_u32(kernel.packet[0]), 1));
+   const uint8x8_t b = vreinterpret_u8_u32(vset_lane_u32(kernel.packet[3], vdup_n_u32(kernel.packet[1]), 1));
+@@ -2871,7 +2871,7 @@
+   kernel.packet[2] = vget_lane_u32(vreinterpret_u32_u16(zip16.val[1]), 0);
+   kernel.packet[3] = vget_lane_u32(vreinterpret_u32_u16(zip16.val[1]), 1);
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet8uc, 8>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet8uc, 8>& kernel)
+ {
+   uint8x8x2_t zip8[4];
+   uint16x4x2_t zip16[4];
+@@ -2901,7 +2901,7 @@
+     }
+   }
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet16uc, 16>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet16uc, 16>& kernel)
+ {
+   uint8x16x2_t zip8[8];
+   uint16x8x2_t zip16[8];
+@@ -2946,7 +2946,7 @@
+     }
+   }
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet4s, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet4s, 4>& kernel)
+ {
+   const int16x4x2_t zip16_1 = vzip_s16(kernel.packet[0], kernel.packet[1]);
+   const int16x4x2_t zip16_2 = vzip_s16(kernel.packet[2], kernel.packet[3]);
+@@ -2960,7 +2960,7 @@
+   kernel.packet[3] = vreinterpret_s16_u32(zip32_2.val[1]);
+ }
+ 
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet8s, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet8s, 4>& kernel)
+ {
+   const int16x8x2_t zip16_1 = vzipq_s16(kernel.packet[0], kernel.packet[1]);
+   const int16x8x2_t zip16_2 = vzipq_s16(kernel.packet[2], kernel.packet[3]);
+@@ -2974,7 +2974,7 @@
+   kernel.packet[3] = vreinterpretq_s16_u32(zip32_2.val[1]);
+ }
+ 
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet16uc, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet16uc, 4>& kernel)
+ {
+   const uint8x16x2_t zip8_1 = vzipq_u8(kernel.packet[0], kernel.packet[1]);
+   const uint8x16x2_t zip8_2 = vzipq_u8(kernel.packet[2], kernel.packet[3]);
+@@ -2988,7 +2988,7 @@
+   kernel.packet[3] = vreinterpretq_u8_u16(zip16_2.val[1]);
+ }
+ 
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet8s, 8>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet8s, 8>& kernel)
+ {
+   const int16x8x2_t zip16_1 = vzipq_s16(kernel.packet[0], kernel.packet[1]);
+   const int16x8x2_t zip16_2 = vzipq_s16(kernel.packet[2], kernel.packet[3]);
+@@ -3009,7 +3009,7 @@
+   kernel.packet[6] = vreinterpretq_s16_u32(vcombine_u32(vget_low_u32(zip32_2.val[1]), vget_low_u32(zip32_4.val[1])));
+   kernel.packet[7] = vreinterpretq_s16_u32(vcombine_u32(vget_high_u32(zip32_2.val[1]), vget_high_u32(zip32_4.val[1])));
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet4us, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet4us, 4>& kernel)
+ {
+   const uint16x4x2_t zip16_1 = vzip_u16(kernel.packet[0], kernel.packet[1]);
+   const uint16x4x2_t zip16_2 = vzip_u16(kernel.packet[2], kernel.packet[3]);
+@@ -3022,7 +3022,7 @@
+   kernel.packet[2] = vreinterpret_u16_u32(zip32_2.val[0]);
+   kernel.packet[3] = vreinterpret_u16_u32(zip32_2.val[1]);
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet8us, 8>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet8us, 8>& kernel)
+ {
+   const uint16x8x2_t zip16_1 = vzipq_u16(kernel.packet[0], kernel.packet[1]);
+   const uint16x8x2_t zip16_2 = vzipq_u16(kernel.packet[2], kernel.packet[3]);
+@@ -3043,13 +3043,13 @@
+   kernel.packet[6] = vreinterpretq_u16_u32(vcombine_u32(vget_low_u32(zip32_2.val[1]), vget_low_u32(zip32_4.val[1])));
+   kernel.packet[7] = vreinterpretq_u16_u32(vcombine_u32(vget_high_u32(zip32_2.val[1]), vget_high_u32(zip32_4.val[1])));
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet2i, 2>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet2i, 2>& kernel)
+ {
+   const int32x2x2_t z = vzip_s32(kernel.packet[0], kernel.packet[1]);
+   kernel.packet[0] = z.val[0];
+   kernel.packet[1] = z.val[1];
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet4i, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet4i, 4>& kernel)
+ {
+   const int32x4x2_t tmp1 = vzipq_s32(kernel.packet[0], kernel.packet[1]);
+   const int32x4x2_t tmp2 = vzipq_s32(kernel.packet[2], kernel.packet[3]);
+@@ -3059,13 +3059,13 @@
+   kernel.packet[2] = vcombine_s32(vget_low_s32(tmp1.val[1]), vget_low_s32(tmp2.val[1]));
+   kernel.packet[3] = vcombine_s32(vget_high_s32(tmp1.val[1]), vget_high_s32(tmp2.val[1]));
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet2ui, 2>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet2ui, 2>& kernel)
+ {
+   const uint32x2x2_t z = vzip_u32(kernel.packet[0], kernel.packet[1]);
+   kernel.packet[0] = z.val[0];
+   kernel.packet[1] = z.val[1];
+ }
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet4ui, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet4ui, 4>& kernel)
+ {
+   const uint32x4x2_t tmp1 = vzipq_u32(kernel.packet[0], kernel.packet[1]);
+   const uint32x4x2_t tmp2 = vzipq_u32(kernel.packet[2], kernel.packet[3]);
+@@ -3075,7 +3075,7 @@
+   kernel.packet[2] = vcombine_u32(vget_low_u32(tmp1.val[1]), vget_low_u32(tmp2.val[1]));
+   kernel.packet[3] = vcombine_u32(vget_high_u32(tmp1.val[1]), vget_high_u32(tmp2.val[1]));
+ }
+-EIGEN_DEVICE_FUNC inline void
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void
+ ptranspose(PacketBlock<Packet2l, 2>& kernel)
+ {
+ #if EIGEN_ARCH_ARM64
+@@ -3094,7 +3094,7 @@
+   kernel.packet[1] = vcombine_s64(tmp[0][1], tmp[1][1]);
+ #endif
+ }
+-EIGEN_DEVICE_FUNC inline void
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void
+ ptranspose(PacketBlock<Packet2ul, 2>& kernel)
+ {
+ #if EIGEN_ARCH_ARM64
+@@ -3114,37 +3114,37 @@
+ #endif
+ }
+ 
+-template<> EIGEN_DEVICE_FUNC inline Packet2f pselect( const Packet2f& mask, const Packet2f& a, const Packet2f& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2f pselect( const Packet2f& mask, const Packet2f& a, const Packet2f& b)
+ { return vbsl_f32(vreinterpret_u32_f32(mask), a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet4f pselect(const Packet4f& mask, const Packet4f& a, const Packet4f& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4f pselect(const Packet4f& mask, const Packet4f& a, const Packet4f& b)
+ { return vbslq_f32(vreinterpretq_u32_f32(mask), a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet8c pselect(const Packet8c& mask, const Packet8c& a, const Packet8c& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8c pselect(const Packet8c& mask, const Packet8c& a, const Packet8c& b)
+ { return vbsl_s8(vreinterpret_u8_s8(mask), a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet16c pselect(const Packet16c& mask, const Packet16c& a, const Packet16c& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet16c pselect(const Packet16c& mask, const Packet16c& a, const Packet16c& b)
+ { return vbslq_s8(vreinterpretq_u8_s8(mask), a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet8uc pselect(const Packet8uc& mask, const Packet8uc& a, const Packet8uc& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8uc pselect(const Packet8uc& mask, const Packet8uc& a, const Packet8uc& b)
+ { return vbsl_u8(mask, a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet16uc pselect(const Packet16uc& mask, const Packet16uc& a, const Packet16uc& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet16uc pselect(const Packet16uc& mask, const Packet16uc& a, const Packet16uc& b)
+ { return vbslq_u8(mask, a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet4s pselect(const Packet4s& mask, const Packet4s& a, const Packet4s& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4s pselect(const Packet4s& mask, const Packet4s& a, const Packet4s& b)
+ { return vbsl_s16(vreinterpret_u16_s16(mask), a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet8s pselect(const Packet8s& mask, const Packet8s& a, const Packet8s& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8s pselect(const Packet8s& mask, const Packet8s& a, const Packet8s& b)
+ { return vbslq_s16(vreinterpretq_u16_s16(mask), a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet4us pselect(const Packet4us& mask, const Packet4us& a, const Packet4us& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4us pselect(const Packet4us& mask, const Packet4us& a, const Packet4us& b)
+ { return vbsl_u16(mask, a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet8us pselect(const Packet8us& mask, const Packet8us& a, const Packet8us& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8us pselect(const Packet8us& mask, const Packet8us& a, const Packet8us& b)
+ { return vbslq_u16(mask, a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet2i pselect(const Packet2i& mask, const Packet2i& a, const Packet2i& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2i pselect(const Packet2i& mask, const Packet2i& a, const Packet2i& b)
+ { return vbsl_s32(vreinterpret_u32_s32(mask), a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet4i pselect(const Packet4i& mask, const Packet4i& a, const Packet4i& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4i pselect(const Packet4i& mask, const Packet4i& a, const Packet4i& b)
+ { return vbslq_s32(vreinterpretq_u32_s32(mask), a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet2ui pselect(const Packet2ui& mask, const Packet2ui& a, const Packet2ui& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2ui pselect(const Packet2ui& mask, const Packet2ui& a, const Packet2ui& b)
+ { return vbsl_u32(mask, a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet4ui pselect(const Packet4ui& mask, const Packet4ui& a, const Packet4ui& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4ui pselect(const Packet4ui& mask, const Packet4ui& a, const Packet4ui& b)
+ { return vbslq_u32(mask, a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet2l pselect(const Packet2l& mask, const Packet2l& a, const Packet2l& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2l pselect(const Packet2l& mask, const Packet2l& a, const Packet2l& b)
+ { return vbslq_s64(vreinterpretq_u64_s64(mask), a, b); }
+-template<> EIGEN_DEVICE_FUNC inline Packet2ul pselect(const Packet2ul& mask, const Packet2ul& a, const Packet2ul& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2ul pselect(const Packet2ul& mask, const Packet2ul& a, const Packet2ul& b)
+ { return vbslq_u64(mask, a, b); }
+ 
+ /**
+@@ -3441,7 +3441,7 @@
+   return pandnot<Packet4us>(a, b);
+ }
+ 
+-template<> EIGEN_DEVICE_FUNC inline Packet4bf pselect(const Packet4bf& mask, const Packet4bf& a,
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4bf pselect(const Packet4bf& mask, const Packet4bf& a,
+                                                       const Packet4bf& b)
+ {
+   return pselect<Packet4us>(mask, a, b);
+@@ -3507,7 +3507,7 @@
+   return preverse<Packet4us>(a);
+ }
+ 
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet4bf, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet4bf, 4>& kernel)
+ {
+   PacketBlock<Packet4us, 4> k;
+   k.packet[0] = kernel.packet[0];
+@@ -3739,7 +3739,7 @@
+ template<> EIGEN_STRONG_INLINE void pstoreu<double>(double* to, const Packet2d& from)
+ { EIGEN_DEBUG_UNALIGNED_STORE vst1q_f64(to,from); }
+ 
+-template<> EIGEN_DEVICE_FUNC inline Packet2d pgather<double, Packet2d>(const double* from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2d pgather<double, Packet2d>(const double* from, Index stride)
+ {
+   Packet2d res = pset1<Packet2d>(0.0);
+   res = vld1q_lane_f64(from + 0*stride, res, 0);
+@@ -3747,7 +3747,7 @@
+   return res;
+ }
+ 
+-template<> EIGEN_DEVICE_FUNC inline void pscatter<double, Packet2d>(double* to, const Packet2d& from, Index stride)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<double, Packet2d>(double* to, const Packet2d& from, Index stride)
+ {
+   vst1q_lane_f64(to + stride*0, from, 0);
+   vst1q_lane_f64(to + stride*1, from, 1);
+@@ -3791,7 +3791,7 @@
+ { return vgetq_lane_f64(vpmaxq_f64(a,a), 0); }
+ 
+ 
+-EIGEN_DEVICE_FUNC inline void
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void
+ ptranspose(PacketBlock<Packet2d, 2>& kernel)
+ {
+   const float64x2_t tmp1 = vzip1q_f64(kernel.packet[0], kernel.packet[1]);
+@@ -3801,7 +3801,7 @@
+   kernel.packet[1] = tmp2;
+ }
+ 
+-template<> EIGEN_DEVICE_FUNC inline Packet2d pselect( const Packet2d& mask, const Packet2d& a, const Packet2d& b)
++template<> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet2d pselect( const Packet2d& mask, const Packet2d& a, const Packet2d& b)
+ { return vbslq_f64(vreinterpretq_u64_f64(mask), a, b); }
+ 
+ template<> EIGEN_STRONG_INLINE Packet2d pldexp<Packet2d>(const Packet2d& a, const Packet2d& exponent)
+@@ -3914,7 +3914,7 @@
+ };
+ 
+ template<>
+-EIGEN_DEVICE_FUNC Packet4hf predux_half_dowto4<Packet8hf>(const Packet8hf& a) {
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4hf predux_half_dowto4<Packet8hf>(const Packet8hf& a) {
+   return vadd_f16(vget_low_f16(a), vget_high_f16(a));
+ }
+ 
+@@ -4193,23 +4193,23 @@
+   return vcombine_f16(lo, hi);
+ }
+ 
+-EIGEN_DEVICE_FUNC inline Packet8hf pinsertfirst(const Packet8hf& a, Eigen::half b) { return vsetq_lane_f16(b.x, a, 0); }
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8hf pinsertfirst(const Packet8hf& a, Eigen::half b) { return vsetq_lane_f16(b.x, a, 0); }
+ 
+-EIGEN_DEVICE_FUNC inline Packet4hf pinsertfirst(const Packet4hf& a, Eigen::half b) { return vset_lane_f16(b.x, a, 0); }
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4hf pinsertfirst(const Packet4hf& a, Eigen::half b) { return vset_lane_f16(b.x, a, 0); }
+ 
+ template <>
+-EIGEN_DEVICE_FUNC inline Packet8hf pselect(const Packet8hf& mask, const Packet8hf& a, const Packet8hf& b) {
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8hf pselect(const Packet8hf& mask, const Packet8hf& a, const Packet8hf& b) {
+   return vbslq_f16(vreinterpretq_u16_f16(mask), a, b);
+ }
+ 
+ template <>
+-EIGEN_DEVICE_FUNC inline Packet4hf pselect(const Packet4hf& mask, const Packet4hf& a, const Packet4hf& b) {
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4hf pselect(const Packet4hf& mask, const Packet4hf& a, const Packet4hf& b) {
+   return vbsl_f16(vreinterpret_u16_f16(mask), a, b);
+ }
+ 
+-EIGEN_DEVICE_FUNC inline Packet8hf pinsertlast(const Packet8hf& a, Eigen::half b) { return vsetq_lane_f16(b.x, a, 7); }
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8hf pinsertlast(const Packet8hf& a, Eigen::half b) { return vsetq_lane_f16(b.x, a, 7); }
+ 
+-EIGEN_DEVICE_FUNC inline Packet4hf pinsertlast(const Packet4hf& a, Eigen::half b) { return vset_lane_f16(b.x, a, 3); }
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4hf pinsertlast(const Packet4hf& a, Eigen::half b) { return vset_lane_f16(b.x, a, 3); }
+ 
+ template <>
+ EIGEN_STRONG_INLINE void pstore<Eigen::half>(Eigen::half* to, const Packet8hf& from) {
+@@ -4232,7 +4232,7 @@
+ }
+ 
+ template <>
+-EIGEN_DEVICE_FUNC inline Packet8hf pgather<Eigen::half, Packet8hf>(const Eigen::half* from, Index stride) {
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet8hf pgather<Eigen::half, Packet8hf>(const Eigen::half* from, Index stride) {
+   Packet8hf res = pset1<Packet8hf>(Eigen::half(0.f));
+   res = vsetq_lane_f16(from[0 * stride].x, res, 0);
+   res = vsetq_lane_f16(from[1 * stride].x, res, 1);
+@@ -4246,7 +4246,7 @@
+ }
+ 
+ template <>
+-EIGEN_DEVICE_FUNC inline Packet4hf pgather<Eigen::half, Packet4hf>(const Eigen::half* from, Index stride) {
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet4hf pgather<Eigen::half, Packet4hf>(const Eigen::half* from, Index stride) {
+   Packet4hf res = pset1<Packet4hf>(Eigen::half(0.f));
+   res = vset_lane_f16(from[0 * stride].x, res, 0);
+   res = vset_lane_f16(from[1 * stride].x, res, 1);
+@@ -4256,7 +4256,7 @@
+ }
+ 
+ template <>
+-EIGEN_DEVICE_FUNC inline void pscatter<Eigen::half, Packet8hf>(Eigen::half* to, const Packet8hf& from, Index stride) {
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<Eigen::half, Packet8hf>(Eigen::half* to, const Packet8hf& from, Index stride) {
+   to[stride * 0].x = vgetq_lane_f16(from, 0);
+   to[stride * 1].x = vgetq_lane_f16(from, 1);
+   to[stride * 2].x = vgetq_lane_f16(from, 2);
+@@ -4268,7 +4268,7 @@
+ }
+ 
+ template <>
+-EIGEN_DEVICE_FUNC inline void pscatter<Eigen::half, Packet4hf>(Eigen::half* to, const Packet4hf& from, Index stride) {
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void pscatter<Eigen::half, Packet4hf>(Eigen::half* to, const Packet4hf& from, Index stride) {
+   to[stride * 0].x = vget_lane_f16(from, 0);
+   to[stride * 1].x = vget_lane_f16(from, 1);
+   to[stride * 2].x = vget_lane_f16(from, 2);
+@@ -4422,7 +4422,7 @@
+   return h;
+ }
+ 
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet8hf, 4>& kernel)
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet8hf, 4>& kernel)
+ {
+   EIGEN_ALIGN16 Eigen::half in[4][8];
+ 
+@@ -4451,7 +4451,7 @@
+   kernel.packet[3] = pload<Packet8hf>(out[3]);
+ }
+ 
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet4hf, 4>& kernel) {
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet4hf, 4>& kernel) {
+   EIGEN_ALIGN16 float16x4x4_t tmp_x4;
+   float16_t* tmp = (float16_t*)&kernel;
+   tmp_x4 = vld4_f16(tmp);
+@@ -4462,7 +4462,7 @@
+   kernel.packet[3] = tmp_x4.val[3];
+ }
+ 
+-EIGEN_DEVICE_FUNC inline void ptranspose(PacketBlock<Packet8hf, 8>& kernel) {
++EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void ptranspose(PacketBlock<Packet8hf, 8>& kernel) {
+   float16x8x2_t T_1[4];
+ 
+   T_1[0] = vuzpq_f16(kernel.packet[0], kernel.packet[1]);
+@@ -4498,3 +4498,4 @@
+ } // end namespace Eigen
+ 
+ #endif // EIGEN_PACKET_MATH_NEON_H
++

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

@@ -17,6 +17,14 @@ class PyHorovod(PythonPackage, CudaPackage):
     maintainers = ['adamjstewart', 'aweits', 'tgaddair']
 
     version('master', branch='master', submodules=True)
+    version('0.25.0', tag='v0.25.0', submodules=True)
+    version('0.24.3', tag='v0.24.3', submodules=True)
+    version('0.24.2', tag='v0.24.2', submodules=True)
+    version('0.24.1', tag='v0.24.1', submodules=True)
+    version('0.24.0', tag='v0.24.0', submodules=True)
+    version('0.23.0', tag='v0.23.0', submodules=True)
+    version('0.22.1', tag='v0.22.1', submodules=True)
+    version('0.22.0', tag='v0.22.0', submodules=True)
     version('0.21.3', tag='v0.21.3', submodules=True)
     version('0.21.2', tag='v0.21.2', submodules=True)
     version('0.21.1', tag='v0.21.1', submodules=True)
@@ -43,7 +51,7 @@ class PyHorovod(PythonPackage, CudaPackage):
     # https://github.com/horovod/horovod/blob/master/docs/install.rst
     variant('frameworks', default='pytorch',
             description='Deep learning frameworks to build support for',
-            values=('tensorflow', 'pytorch', 'mxnet', 'keras', 'spark', 'ray'),
+            values=('tensorflow', 'keras', 'pytorch', 'mxnet', 'spark', 'ray'),
             multi=True)
     variant('controllers', default='mpi',
             description='Controllers to coordinate work between processes',
@@ -54,6 +62,11 @@ class PyHorovod(PythonPackage, CudaPackage):
     variant('cuda', default=True, description='Build with CUDA')
     variant('rocm', default=False, description='Build with ROCm')
 
+    # Build dependencies
+    depends_on('cmake@3.13:', type='build', when='@0.24:')
+    depends_on('cmake@2.8.12:', type='build', when='@0.20:')
+    depends_on('pkgconfig', type='build')
+
     # Required dependencies
     depends_on('python@3.6:',    type=('build', 'run'), when='@0.20:')
     depends_on('py-setuptools',  type='build')
@@ -66,38 +79,42 @@ class PyHorovod(PythonPackage, CudaPackage):
     # Framework dependencies
     depends_on('py-tensorflow@1.1.0:',  type=('build', 'link', 'run'), when='frameworks=tensorflow')
     depends_on('py-tensorflow@1.15:',   type=('build', 'link', 'run'), when='frameworks=tensorflow @0.20:')
-    depends_on('py-tensorflow-estimator', type=('build', 'run'), when='frameworks=tensorflow')
+    depends_on('py-tensorflow-estimator', type=('build', 'run'),       when='frameworks=tensorflow')
+    depends_on('py-keras@2.0.8,2.1.2:', type=('build', 'run'),         when='frameworks=keras')
     depends_on('py-torch@0.4.0:',       type=('build', 'link', 'run'), when='frameworks=pytorch')
     depends_on('py-torch@1.2:',         type=('build', 'link', 'run'), when='frameworks=pytorch @0.20:')
+    depends_on('py-torch@1.5:',         type=('build', 'link', 'run'), when='frameworks=pytorch @0.25:')
     depends_on('py-torchvision',        type=('build', 'run'),         when='frameworks=pytorch @:0.19.1')
     depends_on('py-cffi@1.4.0:',        type=('build', 'run'),         when='frameworks=pytorch')
+    depends_on('py-pytorch-lightning',  type=('build', 'run'),         when='frameworks=pytorch @0.22:0.23')
+    depends_on('py-pytorch-lightning@1.3.8', type=('build', 'run'),    when='frameworks=pytorch @0.24')
+    depends_on('py-pytorch-lightning@1.3.8:1.5.9', type=('build', 'run'), when='frameworks=pytorch @0.25:')
     depends_on('mxnet@1.4.1:+python',   type=('build', 'link', 'run'), when='frameworks=mxnet')
-    depends_on('py-keras@2.0.8,2.1.2:', type=('build', 'run'),         when='frameworks=keras')
-    depends_on('py-h5py@:2',        type=('build', 'run'),         when='frameworks=spark')
+    depends_on('py-h5py@:2',            type=('build', 'run'),         when='frameworks=spark @:0.23')
     depends_on('py-numpy',              type=('build', 'run'),         when='frameworks=spark')
     depends_on('py-petastorm@0.8.2',    type=('build', 'run'),         when='frameworks=spark @:0.19.1')
     depends_on('py-petastorm@0.9.0:',   type=('build', 'run'),         when='frameworks=spark @0.19.2:0.21.0')
     depends_on('py-petastorm@0.9.8:',   type=('build', 'run'),         when='frameworks=spark @0.21.1:')
+    depends_on('py-petastorm@0.11:',    type=('build', 'run'),         when='frameworks=spark @0.22:')
     depends_on('py-pyarrow@0.15.0:',    type=('build', 'run'),         when='frameworks=spark')
     depends_on('py-pyspark@2.3.2:',     type=('build', 'run'),         when='frameworks=spark ^python@:3.7')
     depends_on('py-pyspark@3.0.0:',     type=('build', 'run'),         when='frameworks=spark ^python@3.8:')
+    depends_on('py-fsspec',             type=('build', 'run'),         when='frameworks=spark @0.22.1:0.24.1')
+    depends_on('py-fsspec@2021.07:',    type=('build', 'run'),         when='frameworks=spark @0.24.2:')
     depends_on('py-ray',                type=('build', 'run'),         when='frameworks=ray')
-
-    # Build dependencies
-    depends_on('cmake@2.8.12:', type='build', when='@0.20:')
-    depends_on('pkgconfig', type='build')
+    depends_on('py-aioredis@:1',        type=('build', 'run'),         when='frameworks=ray @0.23:')
 
     # Controller dependencies
     depends_on('mpi', when='controllers=mpi')
-    # There does not appear to be a way to use an external Gloo installation
     depends_on('cmake', type='build', when='controllers=gloo')
     depends_on('libuv@1.26:', when='controllers=gloo platform=darwin')
 
     # Tensor Operations dependencies
     depends_on('nccl@2:', when='tensor_ops=nccl')
     depends_on('mpi', when='tensor_ops=mpi')
-    # There does not appear to be a way to use an external Gloo installation
     depends_on('cmake', type='build', when='tensor_ops=gloo')
+    depends_on('libuv@1.26:', when='tensor_ops=gloo platform=darwin')
+    depends_on('intel-oneapi-ccl', when='tensor_ops=ccl')
 
     conflicts('cuda_arch=none', when='+cuda',
               msg='Must specify CUDA compute capabilities of your GPU, see '
@@ -109,6 +126,11 @@ class PyHorovod(PythonPackage, CudaPackage):
     # https://github.com/horovod/horovod/pull/1835
     patch('fma.patch', when='@0.19.0:0.19.1')
 
+    # Patch vendored copy of eigen to fix build on aarch64
+    # https://github.com/horovod/horovod/issues/3605
+    # https://gitlab.com/libeigen/eigen/-/commit/fd1dcb6b45a2c797ad4c4d6cc7678ee70763b4ed
+    patch('eigen.patch', when='@0.21: target=aarch64:')
+
     @property
     def import_modules(self):
         modules = [
@@ -124,8 +146,7 @@ def import_modules(self):
 
         if 'frameworks=pytorch' in self.spec:
             modules.extend([
-                'horovod.torch', 'horovod.torch.mpi_lib',
-                'horovod.torch.elastic', 'horovod.torch.mpi_lib_impl'
+                'horovod.torch', 'horovod.torch.elastic'
             ])
 
         if 'frameworks=mxnet' in self.spec:
@@ -160,7 +181,7 @@ def setup_build_environment(self, env):
         # Build system
         env.set('PKG_CONFIG_EXECUTABLE',
                 self.spec['pkgconfig'].prefix.bin.join('pkg-config'))
-        if '^cmake' in self.spec:
+        if 'cmake' in self.spec:
             env.set('HOROVOD_CMAKE', self.spec['cmake'].command.path)
         env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
 
@@ -181,11 +202,11 @@ def setup_build_environment(self, env):
             env.set('HOROVOD_WITHOUT_MXNET', 1)
 
         # Controllers
-        if 'controllers=mpi' in self.spec:
+        if 'controllers=mpi' in self.spec or 'tensor_ops=mpi' in self.spec:
             env.set('HOROVOD_WITH_MPI', 1)
         else:
             env.set('HOROVOD_WITHOUT_MPI', 1)
-        if 'controllers=gloo' in self.spec:
+        if 'controllers=gloo' in self.spec or 'tensor_ops=gloo' in self.spec:
             env.set('HOROVOD_WITH_GLOO', 1)
         else:
             env.set('HOROVOD_WITHOUT_GLOO', 1)
@@ -220,4 +241,4 @@ def setup_build_environment(self, env):
 
     def test(self):
         super(PyHorovod, self).test()
-        run_test(self.prefix.bin.horovodrun, '--check-build')
+        self.run_test(self.prefix.bin.horovodrun, '--check-build')

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

@@ -14,6 +14,7 @@ class PyHttpstan(PythonPackage):
 
     maintainers = ['haralmha']
 
+    version('4.8.0', sha256='cadfce05d24ec2af50d71c5212c648cbee5684a7f98fedd3838e124e5a9b4962')
     version('4.7.2', sha256='94f6631d969cbd91d136194b074d02642d8c9e2a05674877a39059be87c5bf7b')
     version('4.6.1', sha256='703e5e04e60651e0004574bb9695827d759fd13eb0d6bd67f827c1bfa0a1fd31')
 

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

@@ -12,6 +12,7 @@ class PyKornia(PythonPackage):
     homepage = "https://www.kornia.org/"
     pypi     = "kornia/kornia-0.5.10.tar.gz"
 
+    version('0.6.6', sha256='e29f0f994e3bafec016b101a9a3e89c3751b4fe99ada3ac21d3febb47904faa4')
     version('0.6.5', sha256='14cbd8b4064b3d0fb5a8198d1b5fd9231bcd62b9039351641fca6b294b5069f0')
     version('0.6.4', sha256='ff60307a7244b315db43bfc4d4d6769094cf7d7494cf367c1d71a56343e2c50f')
     version('0.6.3', sha256='0b689b5a47f55f2b08f61e6731760542cc3e3c09c3f0498164b934a3aef0bab3')

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

@@ -2,6 +2,8 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 from spack.package import *
 
 
@@ -9,16 +11,32 @@ class PyMizani(PythonPackage):
     """Mizani is a scales package for graphics. It is based on Hadley Wickham's
     Scales package."""
 
-    pypi = "mizani/mizani-0.7.3.tar.gz"
+    homepage = "https://mizani.readthedocs.io/en/latest"
+    pypi = "mizani/mizani-0.7.4.tar.gz"
 
-    version(
-        "0.7.3",
-        sha256="f521300bd29ca918fcd629bc8ab50fa04e41bdbe00f6bcf74055d3c6273770a4",
-    )
+    version('0.7.4', sha256='b84b923cd3b8b4c0421a750672e5a85ed2aa05e632bd37af8419d5bbf65c397c')
+    version('0.7.3', sha256='f521300bd29ca918fcd629bc8ab50fa04e41bdbe00f6bcf74055d3c6273770a4')
+    version('0.6.0', sha256='2cdba487ee54faf3e5bfe0903155a13ff13d27a2dae709f9432194915b4fb1cd')
 
-    depends_on('python@3.6:', type=('build', 'run'))
-    depends_on("py-matplotlib@3.1.1:", type=("build", "run"))
-    depends_on("py-numpy", type=("build", "run"))
+    # common requirements
     depends_on("py-palettable", type=("build", "run"))
-    depends_on("py-pandas@1.1.0:", type=("build", "run"))
-    depends_on("py-setuptools", type="build")
+
+    # variable requirements
+    depends_on('python@3.8:', type=('build', 'run'), when='@0.7.4:')
+    depends_on('python@3.6:', type=('build', 'run'), when='@0.6.0:')
+
+    depends_on("py-setuptools@42:", type="build", when='@0.7.4:')
+    depends_on("py-setuptools",     type="build", when='@0.6.0:')
+
+    depends_on("py-matplotlib@3.5.0:", type=("build", "run"), when='@0.7.4:')
+    depends_on("py-matplotlib@3.1.1:", type=("build", "run"), when='@0.6.0:')
+
+    depends_on("py-numpy@1.19.0:", type=("build", "run"), when='@0.7.4:')
+    depends_on("py-numpy",         type=("build", "run"), when='@0.6.0:')
+
+    depends_on("py-scipy@1.5.0:", type=("build", "run"), when='@0.7.4:')
+
+    depends_on("py-pandas@1.3.5:",  type=("build", "run"), when='@0.7.4:')
+    depends_on("py-pandas@1.1.0:",  type=("build", "run"), when='@0.7.2:')
+    depends_on("py-pandas@1.0.0:",  type=("build", "run"), when='@0.7.0:')
+    depends_on("py-pandas@0.25.0:", type=("build", "run"), when='@0.6.0:')

var/spack/repos/builtin/packages/py-pdoc3/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.package import *
+
+
+class PyPdoc3(PythonPackage):
+    """Auto-generate API documentation for Python projects."""
+
+    homepage = "https://pdoc3.github.io/pdoc/"
+    pypi     = "pdoc3/pdoc3-0.10.0.tar.gz"
+
+    version('0.10.0', sha256='5f22e7bcb969006738e1aa4219c75a32f34c2d62d46dc9d2fb2d3e0b0287e4b7')
+
+    depends_on('python@3.6:', type=('build', 'run'))
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools-git', type='build')
+    depends_on('py-setuptools-scm', type='build')
+
+    depends_on('py-mako', type=('build', 'run'))
+    depends_on('py-markdown@3.0:', type=('build', 'run'))

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

@@ -12,11 +12,13 @@ class PyPetastorm(PythonPackage):
     Tensorflow, Pytorch, and other Python-based ML training frameworks."""
 
     homepage = "https://github.com/uber/petastorm"
-    pypi = "petastorm/petastorm-0.8.2.tar.gz"
+    url = "https://github.com/uber/petastorm/archive/refs/tags/v0.11.4.tar.gz"
 
     maintainers = ['adamjstewart']
-    version('0.9.8', sha256='66009b7ad3f08b0485a748f12b2095a0d2470e04f0c63de43cd5b099f270c268')
-    version('0.8.2', sha256='7782c315e1ee8d15c7741e3eea41e77b9efce661cf58aa0220a801db64f52f91')
+
+    version('0.11.4', sha256='7090dfc86f110e641d95798bcc75f8b1ca14cd56ed3feef491baaa6849629e51')
+    version('0.9.8', sha256='571855224411b88b759ba5d48b288ad2ba09997ebd259292f72b9246144b8101')
+    version('0.8.2', sha256='1bf4f26ce0b14f7334c0c29868154f1e600021a044f7565a5ad766b5ecdde911')
 
     depends_on('python@3:', when='@0.9.8:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
@@ -33,3 +35,4 @@ class PyPetastorm(PythonPackage):
     depends_on('py-pyarrow@0.12.0:', type=('build', 'run'), when='@:0.8.2')
     depends_on('py-pyarrow@0.17.1:', type=('build', 'run'), when='@0.9.8:')
     depends_on('py-six@1.5.0:', type=('build', 'run'))
+    depends_on('py-fsspec', type=('build', 'run'), when='@0.11.4:')

var/spack/repos/builtin/packages/py-phydms/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.package import *
+
+
+class PyPhydms(PythonPackage):
+    """phydms enables phylogenetic analyses using deep mutational scanning data
+       to inform the substitution models. It implements Experimentally informed
+       codon models (ExpCM) for phylogenetic inference and the detection of
+       biologically interesting selection."""
+
+    homepage = "http://jbloomlab.github.io/phydms"
+    pypi     = "phydms/phydms-2.4.1.tar.gz"
+
+    version('2.4.1', sha256='04eb50bdb07907214050d19214d9bc8cf2002e24ca30fbe6e0f23f013d584d5c')
+
+    depends_on('python@3.5:',   type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-biopython@1.67:',   type=('build', 'run'))
+    depends_on('py-cython@0.28:',      type=('build', 'run'))
+    depends_on('py-numpy@1.16.5:',     type=('build', 'run'))
+    depends_on('py-scipy@0.18:',       type=('build', 'run'))
+    depends_on('py-matplotlib@2.0.2:', type=('build', 'run'))
+    depends_on('py-natsort@5.0.1:',    type=('build', 'run'))
+    depends_on('py-sympy@1.0:',        type=('build', 'run'))
+    depends_on('py-six@1.10:',         type=('build', 'run'))
+    depends_on('py-pandas@0.20.2:',    type=('build', 'run'))
+    depends_on('py-pyvolve@1.0.3:',    type=('build', 'run'))
+    depends_on('py-statsmodels@0.8:',  type=('build', 'run'))
+    depends_on('py-weblogo@3.4:3.5',   type=('build', 'run'))
+    depends_on('py-pypdf2@1.26:',      type=('build', 'run'))

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

@@ -17,6 +17,7 @@ class PyPip(Package):
 
     maintainers = ['adamjstewart']
 
+    version('22.1.2', sha256='a3edacb89022ef5258bf61852728bf866632a394da837ca49eb4303635835f17', expand=False)
     version('21.3.1', sha256='deaf32dcd9ab821e359cd8330786bcd077604b5c5730c0b096eda46f95c24a2d', expand=False)
     version('21.1.2', sha256='f8ea1baa693b61c8ad1c1d8715e59ab2b93cd3c4769bacab84afcc4279e7a70e', expand=False)
     version('20.2',   sha256='d75f1fc98262dabf74656245c509213a5d0f52137e40e8f8ed5cc256ddd02923', expand=False)
@@ -28,6 +29,7 @@ class PyPip(Package):
     version('9.0.1',  sha256='690b762c0a8460c303c089d5d0be034fb15a5ea2b75bdf565f40421f542fefb0', expand=False)
 
     extends('python')
+    depends_on('python@3.7:', when='@22:', type=('build', 'run'))
     depends_on('python@3.6:', when='@21:', type=('build', 'run'))
     depends_on('python@2.7:2.8,3.5:', when='@19.2:', type=('build', 'run'))
     depends_on('python@2.7:2.8,3.4:', when='@18:', type=('build', 'run'))

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

@@ -2,6 +2,8 @@
 # Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 from spack.package import *
 
 
@@ -10,20 +12,46 @@ class PyPlotnine(PythonPackage):
     based on ggplot2. The grammar allows users to compose plots by explicitly
     mapping data to the visual objects that make up the plot."""
 
-    pypi = "plotnine/plotnine-0.8.0.tar.gz"
+    homepage = "https://plotnine.readthedocs.io/en/stable"
+    pypi     = "plotnine/plotnine-0.8.0.tar.gz"
 
-    version(
-        "0.8.0",
-        sha256="39de59edcc28106761b65238647d0b1f6212ea7f3a78f8be0b846616db969276",
-    )
+    version('0.9.0', sha256='0e89a93015f3c71d6844ac7aa9fb0da09b908f5f7dfa7dd5d68a5ca32b2ebcea')
+    version('0.8.0', sha256='39de59edcc28106761b65238647d0b1f6212ea7f3a78f8be0b846616db969276')
+    version('0.7.1', sha256='02f2b0435dae2e917198c5367fd97b010445d64d9888c6b7e755d3cdfe7ad057')
+    version('0.7.0', sha256='8ee67cbf010ccea32670760e930b7b02177030a89ccdf85e35d156a96ce36cd3')
+    version('0.6.0', sha256='aae2c8164abb209ef4f28cab01132d23f6879fcf8d492657487359e1241459e5')
 
-    depends_on('python@3.6:', type=('build', 'run'))
-    depends_on("py-descartes@1.1.0:", type=("build", "run"))
-    depends_on("py-matplotlib@3.1.1:", type=("build", "run"))
-    depends_on("py-mizani@0.7.3:", type=("build", "run"))
-    depends_on("py-numpy@1.19.0:", type=("build", "run"))
-    depends_on("py-pandas@1.1.0:", type=("build", "run"))
-    depends_on("py-patsy@0.5.1:", type=("build", "run"))
-    depends_on("py-scipy@1.5.0:", type=("build", "run"))
-    depends_on("py-setuptools", type="build")
-    depends_on("py-statsmodels@0.12.1:", type=("build", "run"))
+    depends_on('python@3.8:',                 type=('build', 'run'), when='@0.9.0:')
+    depends_on('python@3.6:',                 type=('build', 'run'), when='@0.6.0:')
+
+    depends_on("py-setuptools@59:",           type="build", when='@0.9.0:')
+    depends_on("py-setuptools",               type="build", when='@0.6.0:')
+
+    depends_on("py-setuptools-scm@6.4:+toml", type="build", when='@0.9.0:')
+
+    depends_on("py-descartes@1.1.0:",         type=("build", "run"), when='@:0.8.0')
+
+    depends_on("py-matplotlib@3.5.0:",        type=("build", "run"), when='@0.9.0:')
+    depends_on("py-matplotlib@3.1.1:",        type=("build", "run"), when='@0.6.0:')
+
+    depends_on("py-mizani@0.7.3:",            type=("build", "run"), when='@0.8.0:')
+    depends_on("py-mizani@0.6.0:",            type=("build", "run"), when='@0.6.0:')
+
+    depends_on("py-numpy@1.19.0:",            type=("build", "run"), when='@0.8.0:')
+    depends_on("py-numpy@1.16.0:",            type=("build", "run"), when='@0.6.0:')
+
+    depends_on("py-pandas@1.3.5:",            type=("build", "run"), when='@0.9.0:')
+    depends_on("py-pandas@1.1.0:",            type=("build", "run"), when='@0.7.1:')
+    depends_on("py-pandas@1.0.3:",            type=("build", "run"), when='@0.7.0:')
+    depends_on("py-pandas@0.25.0:",           type=("build", "run"), when='@0.6.0:')
+
+    depends_on("py-patsy@0.5.1:",             type=("build", "run"), when='@0.7.0:')
+    depends_on("py-patsy@0.4.1:",             type=("build", "run"), when='@0.6.0:')
+
+    depends_on("py-scipy@1.5.0:",             type=("build", "run"), when='@0.8.0:')
+    depends_on("py-scipy@1.2.0:",             type=("build", "run"), when='@0.6.0:')
+
+    depends_on("py-statsmodels@0.13.2:",      type=("build", "run"), when='@0.9.0:')
+    depends_on("py-statsmodels@0.12.1:",      type=("build", "run"), when='@0.8.0:')
+    depends_on("py-statsmodels@0.11.1:",      type=("build", "run"), when='@0.7.0:')
+    depends_on("py-statsmodels@0.9.0:",       type=("build", "run"), when='@0.6.0:')

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

@@ -54,7 +54,7 @@ class PyPyarrow(PythonPackage, CudaPackage):
         depends_on('arrow+cuda' + v, when='+cuda' + v)
         depends_on('arrow+orc' + v, when='+orc' + v)
 
-    patch('for_aarch64.patch', when='target=aarch64:')
+    patch('for_aarch64.patch', when='@0 target=aarch64:')
 
     def install_options(self, spec, prefix):
         args = []

var/spack/repos/builtin/packages/py-pypdf2/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.package import *
+
+
+class PyPypdf2(PythonPackage):
+    """PyPDF2 is a free and open source pure-python PDF library capable of
+       splitting, merging, cropping, and transforming the pages of PDF files.
+       It can also add custom data, viewing options, and passwords to PDF files.
+       PyPDF2 can retrieve text and metadata from PDFs as well."""
+
+    homepage = "https://pypdf2.readthedocs.io/en/latest/"
+    pypi     = "PyPDF2/PyPDF2-2.5.0.tar.gz"
+
+    version('2.5.0',  sha256='5802b1f40fa79be1b5ab9edc95a4e7f7e73399589db4f0e66ca831f449e7a2cd')
+    version('1.26.0', sha256='e28f902f2f0a1603ea95ebe21dff311ef09be3d0f0ef29a3e44a932729564385')
+
+    depends_on('python@3.6:',          type=('build', 'run'), when='@2.0.0:')
+    depends_on('py-setuptools',        type='build')
+    depends_on('py-typing-extensions', type=('build', 'run'), when='@2.0.0:^python@:3.9')

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

@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+
 from spack.package import *
 
 
@@ -14,13 +15,22 @@ class PyPystan(PythonPackage):
 
     maintainers = ['haralmha']
 
-    version('3.4.0', sha256='325e2fb0ab804555c05a603e0c9152ab11fcc3af01f3e9a9ff9fe9954b93184f')
+    version('3.5.0',    sha256='078571d071a5b7c0af59206d4994a0979f4ac4b61f4a720b640c44fe35514929')
+    version('3.4.0',    sha256='325e2fb0ab804555c05a603e0c9152ab11fcc3af01f3e9a9ff9fe9954b93184f')
+    version('2.19.1.1', sha256='fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038')
+    version('2.19.0.0', sha256='b85301b960d5991918b40bd64a4e9321813657a9fc028e0f39edce7220a309eb')
 
-    depends_on('python@3.8:3', type=('build', 'run'))
-    depends_on('py-setuptools', type=('build', 'run'))
-    depends_on('py-poetry-core@1.0.0:', type='build')
-    depends_on('py-aiohttp@3.6:3', type=('build', 'run'))
-    depends_on('py-httpstan@4.7', type=('build', 'run'))
-    depends_on('py-pysimdjson@3.2:3', type=('build', 'run'))
-    depends_on('py-numpy@1.19:1', type=('build', 'run'))
-    depends_on('py-clikit@0.6', type=('build', 'run'))
+    # common requirements
+    depends_on('py-setuptools',         type=('build', 'run'))
+    depends_on('py-poetry-core@1.0.0:', type=('build', 'run'))
+
+    # variable requirements
+    depends_on('python@3.8:3',                  type=('build', 'run'), when='@3.4.0:')
+    depends_on('py-aiohttp@3.6:3',              type=('build', 'run'), when='@3.4.0:')
+    depends_on('py-httpstan@4.8',               type=('build', 'run'), when='@3.5.0:')
+    depends_on('py-httpstan@4.7',               type=('build', 'run'), when='@3.4')
+    depends_on('py-pysimdjson@3.2:3',           type=('build', 'run'), when='@3.4.0:')
+    depends_on('py-numpy@1.19:1',               type=('build', 'run'), when='@3.4.0:')
+    depends_on('py-numpy@1.7:',                 type=('build', 'run'), when='@2.19.0.0:')
+    depends_on('py-clikit@0.6',                 type=('build', 'run'), when='@3.4.0:')
+    depends_on('py-cython@0.22:0.23.2,0.25.2:', type=('build', 'run'), when='@:2.19.1.1')

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

@@ -0,0 +1,25 @@
+# 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.package import *
+
+
+class PyPyvolve(PythonPackage):
+    """Pyvolve is an open-source Python module for simulating sequences
+       along a phylogenetic tree according to continuous-time Markov models
+       of sequence evolution"""
+
+    homepage = "https://github.com/sjspielman/pyvolve"
+    pypi     = "Pyvolve/Pyvolve-1.1.0.tar.gz"
+
+    version('1.1.0', sha256='850aae6213a95c3f8c438ef7cdab33f4dafe8ef305b6fa85bbea1a9e7484c787')
+    version('1.0.3', sha256='725d5851f24b3b4564970a999bad8e2e90782cf81a07c3a3370c492a956d9d51')
+
+    depends_on('py-setuptools',    type='build')
+    depends_on('py-biopython',     type=('build', 'run'))
+    depends_on('py-numpy@1.20.0:', type=('build', 'run'), when='@1.1.0:')
+    depends_on('py-numpy@1.7:',    type=('build', 'run'), when='@1.0.3:')
+    depends_on('py-scipy',         type=('build', 'run'))

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

@@ -12,6 +12,7 @@ class PyStatsmodels(PythonPackage):
     homepage = "https://www.statsmodels.org"
     pypi = "statsmodels/statsmodels-0.8.0.tar.gz"
 
+    version('0.13.2', sha256='77dc292c9939c036a476f1770f9d08976b05437daa229928da73231147cde7d4')
     version('0.13.1', sha256='006ec8d896d238873af8178d5475203844f2c391194ed8d42ddac37f5ff77a69')
     version('0.13.0', sha256='f2efc02011b7240a9e851acd76ab81150a07d35c97021cb0517887539a328f8a')
     version('0.12.2', sha256='8ad7a7ae7cdd929095684118e3b05836c0ccb08b6a01fe984159475d174a1b10')
@@ -53,6 +54,7 @@ class PyStatsmodels(PythonPackage):
     depends_on('py-scipy@0.18:',       type=('build', 'run'), when='@0.10.1:')
     depends_on('py-scipy@1.2:',        type=('build', 'run'), when='@0.12.0:')
     depends_on('py-scipy@1.3:',        type=('build', 'run'), when='@0.13.0:')
+    depends_on('py-packaging@21.3:',   type=('build', 'run'), when='@0.13.2:')
     depends_on('py-matplotlib@1.3:',   type=('build', 'run'), when='@0.8.0 +plotting')
 
     depends_on('py-pytest', type='test')

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

@@ -31,7 +31,7 @@ class PyTensorflowHub(Package):
     depends_on('py-protobuf@3.8.0:',   type=('build', 'run'))
 
     patch("https://github.com/tensorflow/hub/commit/049192a7edd3e80eebf1735b93f57c7965381bdb.patch?full_index=1",
-          sha256="a825b2dd96d8f1ff1aaf2e4c9e2cbb52d3d75609909fce960e1cfa681040c4c3",
+          sha256="c8b59d17511a8ebd2a58717723b9b77514a12b43bb2e6acec6d0c1062df6e457",
           when="@:0.12")
 
     def install(self, spec, prefix):

var/spack/repos/builtin/packages/py-typing-extensions/package.py

@@ -15,6 +15,7 @@ class PyTypingExtensions(PythonPackage):
     homepage = "https://github.com/python/typing/tree/master/typing_extensions"
     pypi = "typing_extensions/typing_extensions-3.7.4.tar.gz"
 
+    version('4.3.0', sha256='e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6')
     version('4.2.0', sha256='f1c24655a0da0d1b67f07e17a5e6b2a105894e6824b92096378bb3668ef02376')
     version('4.1.1', sha256='1a9462dcc3347a79b1f1c0271fbe79e844580bb598bafa1ed208b94da3cdcd42')
     version('3.10.0.2', sha256='49f75d16ff11f1cd258e1b988ccff82a3ca5570217d7ad8c5f48205dd99a677e')

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

@@ -11,9 +11,11 @@ class PyWeblogo(PythonPackage):
     sequence logos as easy and painless as possible."""
 
     homepage = "http://weblogo.threeplusone.com"
-    pypi = "weblogo/weblogo-3.6.0.tar.gz"
+    pypi     = "weblogo/weblogo-3.6.0.tar.gz"
 
-    version('3.6.0', sha256='af5a9f065581f18d71bd7c22b160c1e443932f22cab992d439d3dc8757c80a85')
+    version('3.6.0',  sha256='af5a9f065581f18d71bd7c22b160c1e443932f22cab992d439d3dc8757c80a85')
+    version('3.5.0',  sha256='84e39ee7c4f70efea55d6a92b3efdc4d2602b3d32a793f98865bca35e6bd1133')
+    version('3.4',    sha256='1fb661df47252064dd6d59d3c340b24d87bebe9048ca9ada904ac1e95669e08f')
 
     depends_on('py-setuptools', type='build')
     depends_on('ghostscript', type=('build', 'run'))

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

@@ -42,7 +42,7 @@ def post_install(self):
             join_path(spec['gdk-pixbuf'].prefix.lib, 'girepository-1.0'),
             join_path(spec['gtkplus'].prefix.lib, 'girepository-1.0'),
             join_path(spec['harfbuzz'].prefix.lib, 'girepository-1.0'))
-        dst = join_path(python_platlib, 'xdot', '__init__.py')
+        dst = join_path(python_purelib, 'xdot', '__init__.py')
         filter_file("import sys",
                     "import sys\nimport os\nos.environ['GI_TYPELIB_PATH']" +
                     " = '%s'" % repo_paths, dst)

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

@@ -45,3 +45,9 @@ def libs(self):
         else:
             return find_libraries('libqhull', self.prefix,
                                   shared=True, recursive=True)
+
+    @run_after('install')
+    def darwin_fix(self):
+        # The shared library is not installed correctly on Darwin; fix this
+        if self.spec.satisfies('platform=darwin'):
+            fix_darwin_install_name(self.prefix.lib)

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

@@ -85,23 +85,18 @@ def check(self):
         depends_on('llvm-amdgpu@' + ver,  type='build',  when='@' + ver)
         depends_on('rocminfo@' + ver,     type='build',  when='@' + ver)
 
-    for ver in ['3.5.0', '3.7.0', '3.8.0', '3.9.0']:
-        depends_on('rocm-smi@' + ver, type='build', when='@' + ver)
-
-    for ver in ['4.0.0', '4.1.0', '4.2.0', '4.3.0', '4.3.1', '4.5.0', '4.5.2',
-                '5.0.0', '5.0.2', '5.1.0', '5.1.3']:
-        depends_on('rocm-smi-lib@' + ver, type='build', when='@' + ver)
-
-    # This is the default library format since 3.7.0
-    depends_on('msgpack-c@3:', when='@3.7:')
-
     depends_on('python@3.6:', type='build')
-    depends_on('py-virtualenv', type='build')
-    depends_on('perl-file-which', type='build')
-    depends_on('py-pyyaml', type='build')
-    depends_on('py-wheel', type='build')
-    depends_on('py-msgpack', type='build')
-    depends_on('py-pip', type='build')
+
+    with when('+tensile'):
+        # default library format since 3.7.0
+        depends_on('msgpack-c@3:', when='@3.7:')
+
+        depends_on('py-virtualenv', type='build')
+        depends_on('perl-file-which', type='build')
+        depends_on('py-pyyaml', type='build')
+        depends_on('py-wheel', type='build')
+        depends_on('py-msgpack', type='build')
+        depends_on('py-pip', type='build')
 
     for t_version, t_commit in [
         ('@3.5.0',  'f842a1a4427624eff6cbddb2405c36dec9a210cd'),

var/spack/repos/builtin/packages/simmetrix-simmodsuite/package.py

@@ -235,6 +235,7 @@ class SimmetrixSimmodsuite(Package):
     variant('paralleladapt', default=False, description='enable parallel adaptation')
 
     depends_on('mpi')
+    depends_on('rpc')
 
     oslib = 'x64_rhel7_gcc48'
 

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

@@ -12,6 +12,7 @@ class Snappy(CMakePackage):
     homepage = "https://github.com/google/snappy"
     url      = "https://github.com/google/snappy/archive/1.1.8.tar.gz"
 
+    version('1.1.9', sha256='75c1fbb3d618dd3a0483bff0e26d0a92b495bbe5059c8b4f1c962b478b6e06e7')
     version('1.1.8', sha256='16b677f07832a612b0836178db7f374e414f94657c138e6993cbfc5dcc58651f')
     version('1.1.7', sha256='3dfa02e873ff51a11ee02b9ca391807f0c8ea0529a4924afa645fbf97163f9d4')
 
@@ -20,13 +21,14 @@ class Snappy(CMakePackage):
 
     depends_on('googletest', type='test')
 
-    patch('link_gtest.patch')
+    patch('link_gtest.patch', when='@:1.1.8')
 
     def cmake_args(self):
         return [
             self.define('CMAKE_INSTALL_LIBDIR', self.prefix.lib),
             self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
             self.define('SNAPPY_BUILD_TESTS', self.run_tests),
+            self.define('SNAPPY_BUILD_BENCHMARKS', 'OFF'),
         ]
 
     def flag_handler(self, name, flags):

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

@@ -17,6 +17,7 @@ class Tamaas(SConsPackage):
     maintainers = ["prs513rosewood"]
 
     version("master", branch="master")
+    version("2.5.0.post1", sha256="28e52dc5b8a5f77588c73a6ef396c44c6a8e9d77e3e4929a4ab07232dc9bc565")
     version("2.4.0", sha256="38edba588ff3a6643523c28fb391e001dbafa9d0e58053b9e080eda70f8c71c9")
     version("2.3.1", sha256="7d63e374cbc7b5b93578ece7be5c084d1c2f0dbe1d57c4f0c8abd5ff5fff9ab0")
     version("2.3.0", sha256="0529e015c6cb5bbabaea5dce6efc5ec0f2aa76c00541f0d90ad0e2e3060a4520")
@@ -61,6 +62,7 @@ def build_args(self, spec, prefix):
             "real_type=double",
             "integer_type=int",
             "build_tests=False",
+            "doc_builders=none",
             "prefix={}".format(prefix),
             "BOOST_ROOT={}".format(spec['boost'].prefix),
             "THRUST_ROOT={}".format(spec['thrust'].prefix),