Merge branch 'develop' into woptim/extend-commit-fetch

The patches don't have a stable checksum.

lib/spack/spack/cmd/env.py

@@ -420,13 +420,6 @@ def actions():
 #
 def env_view_setup_parser(subparser):
     """manage a view associated with the environment"""
-    subparser.add_argument(
-        "-f",
-        "--force",
-        action="store_true",
-        dest="force",
-        help="regenerate even if regeneration cannot be done atomically",
-    )
     subparser.add_argument(
         "action", choices=ViewAction.actions(), help="action to take for the environment's view"
     )
@@ -440,7 +433,7 @@ def env_view(args):
 
     if env:
         if args.action == ViewAction.regenerate:
-            env.regenerate_views(force=args.force)
+            env.regenerate_views()
         elif args.action == ViewAction.enable:
             if args.view_path:
                 view_path = args.view_path

lib/spack/spack/environment/environment.py

@@ -38,7 +38,6 @@
 import spack.subprocess_context
 import spack.traverse
 import spack.user_environment as uenv
-import spack.util.atomic_update
 import spack.util.cpus
 import spack.util.environment
 import spack.util.hash
@@ -139,8 +138,6 @@ def default_manifest_yaml():
 default_view_name = "default"
 # Default behavior to link all packages into views (vs. only root packages)
 default_view_link = "all"
-# Default behavior to use exchange if possible and otherwise symlink for view updates
-default_update_method = ["exchange", "symlink"]
 
 
 def installed_specs():
@@ -409,7 +406,6 @@ def __init__(
         exclude=[],
         link=default_view_link,
         link_type="symlink",
-        update_method=default_update_method,
     ):
         self.base = base_path
         self.raw_root = root
@@ -419,7 +415,6 @@ def __init__(
         self.exclude = exclude
         self.link_type = view_func_parser(link_type)
         self.link = link
-        self.update_method = update_method
 
     def select_fn(self, spec):
         return any(spec.satisfies(s) for s in self.select)
@@ -436,7 +431,6 @@ def __eq__(self, other):
                 self.exclude == other.exclude,
                 self.link == other.link,
                 self.link_type == other.link_type,
-                self.update_method == other.update_method,
             ]
         )
 
@@ -457,8 +451,6 @@ def to_dict(self):
             ret["link_type"] = inverse_view_func_parser(self.link_type)
         if self.link != default_view_link:
             ret["link"] = self.link
-        if self.update_method != default_update_method:
-            ret["update_method"] = self.update_method
         return ret
 
     @staticmethod
@@ -471,39 +463,13 @@ def from_dict(base_path, d):
             d.get("exclude", []),
             d.get("link", default_view_link),
             d.get("link_type", "symlink"),
-            d.get("update_method", default_update_method),
         )
 
     @property
     def _current_root(self):
-        """
-        Return the directory in which the view has been constructed.
-
-        Query the view if it stores metadata on where it was constructed.
-
-        If the view us using symlinks for atomic updates, self.root is a link and we read the link
-        to find the real root directory.
-
-        If self.root is not a view with metadata and is not a link, the view has not been
-        constructed.
-        """
-        # Get the view as self.root even if it is actually a symlink
-        # We will not operate on this view object, only query metadata
-        # We don't want to pass a created_path to this view, so that we can read where it says it
-        # was created.
-        if not os.path.exists(self.root):
-            return None
-
-        view = self.view()
-        orig_path = view.metadata.get("created_path", None)
-        if orig_path:
-            return orig_path
-
-        # Backwards compat only applies for symlinked views
         if not os.path.islink(self.root):
             return None
 
-        # For backards compat, check link for symlink views if no "created_path"
         root = os.readlink(self.root)
         if os.path.isabs(root):
             return root
@@ -535,9 +501,11 @@ def get_projection_for_spec(self, spec):
         symlink.
         """
         view = self.view()
-        return view.get_projection_for_spec(spec)
+        view_path = view.get_projection_for_spec(spec)
+        rel_path = os.path.relpath(view_path, self._current_root)
+        return os.path.join(self.root, rel_path)
 
-    def view(self, new=None, created_path=False):
+    def view(self, new=None):
         """
         Generate the FilesystemView object for this ViewDescriptor
 
@@ -550,13 +518,8 @@ def view(self, new=None, created_path=False):
             new (str or None): If a string, create a FilesystemView
                 rooted at that path. Default None. This should only be used to
                 regenerate the view, and cannot be used to access specs.
-            created_path (bool): Pass metadata on the path the view was created in to the
-                underlying view implementation. Default False. This option should be enabled
-                when creating a view to add packages to, but not when creating a view object
-                to query an existing view.
         """
-        root = new if new else self.root
-
+        root = new if new else self._current_root
         if not root:
             # This can only be hit if we write a future bug
             msg = (
@@ -564,17 +527,13 @@ def view(self, new=None, created_path=False):
                 "View root is at %s" % self.root
             )
             raise SpackEnvironmentViewError(msg)
-
-        kwargs = {
-            "ignore_conflicts": True,
-            "projections": self.projections,
-            "link": self.link_type,
-            "final_destination": self.root,
-        }
-        if created_path:
-            kwargs["metadata"] = {"created_path": root}
-
-        return SimpleFilesystemView(root, spack.store.layout, **kwargs)
+        return SimpleFilesystemView(
+            root,
+            spack.store.layout,
+            ignore_conflicts=True,
+            projections=self.projections,
+            link=self.link_type,
+        )
 
     def __contains__(self, spec):
         """Is the spec described by the view descriptor
@@ -617,69 +576,7 @@ def specs_for_view(self, concretized_root_specs):
 
         return specs
 
-    def update_method_error_msg(self, methods):
-        """When methods are already determined invalid, construct error message for methods."""
-        msg = "View cannot be updated using specified update methods:"
-        if "exchange" in methods:
-            if not spack.util.atomic_update.renameat2():
-                msg += "\n  Operating system does not support 'exchange' atomic update method."
-                msg += f"\n    If the view {self.root} does not already exist on the filesystem,"
-                msg += " change its update_method to 'symlink' or 'auto'."
-                msg += f"\n    If the view at {self.root} exists already, either change the"
-                msg += " update_method and run `spack env view regenerate --force`"
-                msg += " or run on a newer OS."
-            else:
-                msg += f"\n  The view {self.root} cannot be updated with 'exchange' update method"
-                msg += " because it was originally constructed with the 'symlink' method."
-                msg += "\n    Either change the update method to 'symlink' or"
-                msg += " run `spack env view regenerate --force` for a non-atomic update."
-        if "symlink" in methods:
-            msg += f"\n  The view {self.root} cannot be updated with 'symlink' update method"
-            msg += " because it was originally constructed with the 'exchange' method."
-            msg += "\n    Either change the update method to 'exchange' or"
-            msg += " run `spack env view regenerate --force` for a non-atomic update."
-        return msg
-
-    def valid_update_method(self, method, force):
-        return getattr(self, f"valid_update_method_{method}")(force)
-
-    def valid_update_method_exchange(self, force):
-        if not spack.util.atomic_update.renameat2():
-            return False
-
-        # Ensure we don't swap symlink -> exchange if we have a symlink and symlink is an
-        # acceptable method. This is to avoid problems switching between OSs.
-        if os.path.islink(self.root):
-            if force:
-                os.unlink(self.root)
-            elif "symlink" in self.update_method:
-                return False
-
-        return True
-
-    def valid_update_method_symlink(self, force):
-        if os.path.exists(self.root):
-            if not os.path.islink(self.root):
-                if force:
-                    shutil.rmtree(self.root)
-                    return True
-                else:
-                    return False
-        return True
-
-    def update_method_to_use(self, force=False):
-        update_methods = self.update_method
-        if isinstance(update_methods, str):
-            update_methods = [update_methods]
-
-        for method in update_methods:
-            # Check whether we can use this method and return if we can
-            if self.valid_update_method(method, force):
-                return method
-
-        raise RuntimeError(self.update_method_error_msg(update_methods))
-
-    def regenerate(self, concretized_root_specs, force=False):
+    def regenerate(self, concretized_root_specs):
         specs = self.specs_for_view(concretized_root_specs)
 
         # To ensure there are no conflicts with packages being installed
@@ -700,39 +597,34 @@ def regenerate(self, concretized_root_specs, force=False):
             tty.debug("View at %s does not need regeneration." % self.root)
             return
 
-        # Check which atomic update method we need
-        update_method = self.update_method_to_use(force)
-
-        if update_method == "exchange" and os.path.isdir(new_root):
-            shutil.rmtree(new_root)
-
         _error_on_nonempty_view_dir(new_root)
 
         # construct view at new_root
         if specs:
             tty.msg("Updating view at {0}".format(self.root))
 
-        view = self.view(new=new_root, created_path=True)
+        view = self.view(new=new_root)
+
+        root_dirname = os.path.dirname(self.root)
+        tmp_symlink_name = os.path.join(root_dirname, "._view_link")
 
         # Create a new view
         try:
             fs.mkdirp(new_root)
             view.add_specs(*specs, with_dependencies=False)
-            if update_method == "exchange":
-                # Swap the view to the directory of the previous view if one exists so that
-                # the view that is swapped out will be named appropriately
-                if old_root:
-                    os.rename(new_root, old_root)
-                    exchange_location = old_root
-                else:
-                    exchange_location = new_root
-                spack.util.atomic_update.atomic_update_renameat2(exchange_location, self.root)
-            else:
-                spack.util.atomic_update.atomic_update_symlink(new_root, self.root)
+
+            # create symlink from tmp_symlink_name to new_root
+            if os.path.exists(tmp_symlink_name):
+                os.unlink(tmp_symlink_name)
+            symlink(new_root, tmp_symlink_name)
+
+            # mv symlink atomically over root symlink to old_root
+            fs.rename(tmp_symlink_name, self.root)
         except Exception as e:
             # Clean up new view and temporary symlink on any failure.
             try:
                 shutil.rmtree(new_root, ignore_errors=True)
+                os.unlink(tmp_symlink_name)
             except (IOError, OSError):
                 pass
 
@@ -1657,14 +1549,14 @@ def update_default_view(self, viewpath):
         else:
             self.views.pop(name, None)
 
-    def regenerate_views(self, force=False):
+    def regenerate_views(self):
         if not self.views:
             tty.debug("Skip view update, this environment does not" " maintain a view")
             return
 
         concretized_root_specs = [s for _, s in self.concretized_specs()]
         for view in self.views.values():
-            view.regenerate(concretized_root_specs, force)
+            view.regenerate(concretized_root_specs)
 
     def check_views(self):
         """Checks if the environments default view can be activated."""

lib/spack/spack/fetch_strategy.py

@@ -862,6 +862,9 @@ def clone(self, dest=None, commit=None, branch=None, tag=None, bare=False):
                 )
 
             with working_dir(dest):
+                # By defaults, on all references are fetched by the clone
+                fetch_args = ["fetch", "origin", commit]
+                git(*fetch_args)
                 checkout_args = ["checkout", commit]
                 if not debug:
                     checkout_args.insert(1, "--quiet")

lib/spack/spack/filesystem_view.py

@@ -27,7 +27,7 @@
     SingleMergeConflictError,
     SourceMergeVisitor,
 )
-from llnl.util.symlink import islink, symlink
+from llnl.util.symlink import symlink
 from llnl.util.tty.color import colorize
 
 import spack.config
@@ -43,7 +43,6 @@
 
 
 _projections_path = ".spack/projections.yaml"
-_metadata_path = ".spack/metadata.yaml"
 
 
 def view_symlink(src, dst, **kwargs):
@@ -64,7 +63,7 @@ def view_copy(src, dst, view, spec=None):
 
     Use spec and view to generate relocations
     """
-    shutil.copy2(src, dst, follow_symlinks=False)
+    shutil.copy2(src, dst)
     if spec and not spec.external:
         # Not metadata, we have to relocate it
 
@@ -83,23 +82,18 @@ def view_copy(src, dst, view, spec=None):
         orig_sbang = "#!/bin/bash {0}/bin/sbang".format(spack.paths.spack_root)
         new_sbang = sbang.sbang_shebang_line()
 
-        root = view.final_destination
         prefix_to_projection = collections.OrderedDict(
-            {spec.prefix: os.path.join(root, view.get_relative_projection_for_spec(spec))}
+            {spec.prefix: view.get_projection_for_spec(spec)}
         )
 
         for dep in spec.traverse():
             if not dep.external:
-                prefix_to_projection[dep.prefix] = os.path.join(
-                    root, view.get_relative_projection_for_spec(dep)
-                )
+                prefix_to_projection[dep.prefix] = view.get_projection_for_spec(dep)
 
         if spack.relocate.is_binary(dst):
             spack.relocate.relocate_text_bin(binaries=[dst], prefixes=prefix_to_projection)
-        elif islink(dst):
-            spack.relocate.relocate_links(links=[dst], prefix_to_prefix=prefix_to_projection)
         else:
-            prefix_to_projection[spack.store.layout.root] = root
+            prefix_to_projection[spack.store.layout.root] = view._root
             prefix_to_projection[orig_sbang] = new_sbang
             spack.relocate.relocate_text(files=[dst], prefixes=prefix_to_projection)
         try:
@@ -156,13 +150,10 @@ def __init__(self, root, layout, **kwargs):
         self.layout = layout
 
         self.projections = kwargs.get("projections", {})
-        self.metadata = kwargs.get("metadata", {})
 
         self.ignore_conflicts = kwargs.get("ignore_conflicts", False)
         self.verbose = kwargs.get("verbose", False)
 
-        self.final_destination = kwargs.get("final_destination", self._root)
-
         # Setup link function to include view
         link_func = kwargs.get("link", view_symlink)
         self.link = ft.partial(link_func, view=self)
@@ -219,15 +210,12 @@ def remove_standalone(self, spec):
         """
         raise NotImplementedError
 
-    def get_relative_projection_for_spec(self, spec):
+    def get_projection_for_spec(self, spec):
         """
-        Get the relative projection in this view for a spec.
+        Get the projection in this view for a spec.
         """
         raise NotImplementedError
 
-    def get_projection_for_spec(self, spec):
-        return os.path.join(self._root, self.get_relative_projection_for_spec(spec))
-
     def get_all_specs(self):
         """
         Get all specs currently active in this view.
@@ -286,34 +274,8 @@ def __init__(self, root, layout, **kwargs):
                 msg += " which does not match projections passed manually."
                 raise ConflictingProjectionsError(msg)
 
-        self.metadata_path = os.path.join(self._root, _metadata_path)
-        if not self.metadata:
-            self.metadata = self.read_metadata()
-        elif not os.path.exists(self.metadata_path):
-            self.write_metadata()
-        else:
-            if self.metadata != self.read_metadata():
-                msg = f"View at {self._root} has metadata file"
-                msg += " which does not match metadata passed manually."
-                raise ConflictingMetadataError(msg)
-
         self._croot = colorize_root(self._root) + " "
 
-    def write_metadata(self):
-        if self.metadata:
-            mkdirp(os.path.dirname(self.metadata_path))
-            with open(self.metadata_path, "w") as f:
-                f.write(s_yaml.dump_config({"metadata": self.metadata}))
-
-    def read_metadata(self):
-        if os.path.exists(self.metadata_path):
-            with open(self.metadata_path, "r") as f:
-                # no schema as this is not user modified
-                metadata_data = s_yaml.load(f)
-                return metadata_data["metadata"]
-        else:
-            return {}
-
     def write_projections(self):
         if self.projections:
             mkdirp(os.path.dirname(self.projections_path))
@@ -524,9 +486,9 @@ def remove_standalone(self, spec):
         if self.verbose:
             tty.info(self._croot + "Removed package: %s" % colorize_spec(spec))
 
-    def get_relative_projection_for_spec(self, spec):
+    def get_projection_for_spec(self, spec):
         """
-        Return the relative projection for a spec in this view.
+        Return the projection for a spec in this view.
 
         Relies on the ordering of projections to avoid ambiguity.
         """
@@ -537,7 +499,9 @@ def get_relative_projection_for_spec(self, spec):
             locator_spec = spec.package.extendee_spec
 
         proj = spack.projections.get_projection(self.projections, locator_spec)
-        return spec.format(proj) if proj else ""
+        if proj:
+            return os.path.join(self._root, locator_spec.format(proj))
+        return self._root
 
     def get_all_specs(self):
         md_dirs = []
@@ -675,32 +639,6 @@ class SimpleFilesystemView(FilesystemView):
     def __init__(self, root, layout, **kwargs):
         super(SimpleFilesystemView, self).__init__(root, layout, **kwargs)
 
-        self.metadata_path = os.path.join(self._root, _metadata_path)
-        if not self.metadata:
-            self.metadata = self.read_metadata()
-        elif not os.path.exists(self.metadata_path):
-            self.write_metadata()
-        else:
-            if self.metadata != self.read_metadata():
-                msg = f"View at {self._root} has metadata file"
-                msg += " which does not match metadata passed manually."
-                raise ConflictingMetadataError(msg)
-
-    def write_metadata(self):
-        if self.metadata:
-            mkdirp(os.path.dirname(self.metadata_path))
-            with open(self.metadata_path, "w") as f:
-                f.write(s_yaml.dump_config({"metadata": self.metadata}))
-
-    def read_metadata(self):
-        if os.path.exists(self.metadata_path):
-            with open(self.metadata_path, "r") as f:
-                # no schema as this is not user modified
-                metadata_data = s_yaml.load(f)
-                return metadata_data["metadata"]
-        else:
-            return {}
-
     def _sanity_check_view_projection(self, specs):
         """A very common issue is that we end up with two specs of the same
         package, that project to the same prefix. We want to catch that as
@@ -827,13 +765,6 @@ def link_metadata(self, specs):
             self.link(os.path.join(src_root, src_relpath), os.path.join(self._root, dst_relpath))
 
     def get_relative_projection_for_spec(self, spec):
-        """
-        Return the relative projection for a spec in this view.
-
-        Relies on the ordering of projections to avoid ambiguity.
-        """
-        spec = spack.spec.Spec(spec)
-
         # Extensions are placed by their extendee, not by their own spec
         if spec.package.extendee_spec:
             spec = spec.package.extendee_spec
@@ -841,6 +772,22 @@ def get_relative_projection_for_spec(self, spec):
         p = spack.projections.get_projection(self.projections, spec)
         return spec.format(p) if p else ""
 
+    def get_projection_for_spec(self, spec):
+        """
+        Return the projection for a spec in this view.
+
+        Relies on the ordering of projections to avoid ambiguity.
+        """
+        spec = spack.spec.Spec(spec)
+
+        if spec.package.extendee_spec:
+            spec = spec.package.extendee_spec
+
+        proj = spack.projections.get_projection(self.projections, spec)
+        if proj:
+            return os.path.join(self._root, spec.format(proj))
+        return self._root
+
 
 #####################
 # utility functions #
@@ -902,7 +849,3 @@ def get_dependencies(specs):
 
 class ConflictingProjectionsError(SpackError):
     """Raised when a view has a projections file and is given one manually."""
-
-
-class ConflictingMetadataError(SpackError):
-    """Raised when a view has a metadata file and is given one manually."""

lib/spack/spack/schema/env.py

@@ -30,10 +30,6 @@
                         "type": "array",
                         "items": {"type": "array", "items": {"type": "string"}},
                     },
-                    "broadcast": {
-                        "type": "array",
-                        "items": {"type": "array", "items": {"type": "string"}},
-                    },
                     "exclude": {"type": "array", "items": {"type": "string"}},
                 },
             },
@@ -111,21 +107,6 @@
                                                 "type": "array",
                                                 "items": {"type": "string"},
                                             },
-                                            "update_method": {
-                                                "anyOf": [
-                                                    {
-                                                        "type": "string",
-                                                        "pattern": "(symlink|exchange)",
-                                                    },
-                                                    {
-                                                        "type": "array",
-                                                        "items": {
-                                                            "type": "string",
-                                                            "pattern": "(symlink|exchange)",
-                                                        },
-                                                    },
-                                                ]
-                                            },
                                             "projections": projections_scheme,
                                         },
                                     }

lib/spack/spack/spec_list.py

@@ -186,64 +186,41 @@ def _expand_matrix_constraints(matrix_config):
                 new_row.append([r])
         expanded_rows.append(new_row)
 
-    # TODO someday: allow matrices inside `broadcast`
-    broadcast_rows = matrix_config.get("broadcast", [])
     excludes = matrix_config.get("exclude", [])  # only compute once
     sigil = matrix_config.get("sigil", "")
 
-    broadcast_constraints = list(itertools.product(*broadcast_rows))
-
     results = []
     for combo in itertools.product(*expanded_rows):
         # Construct a combined spec to test against excludes
         flat_combo = [constraint for constraint_list in combo for constraint in constraint_list]
         flat_combo = [Spec(x) for x in flat_combo]
 
-        # If no broadcast, this is [(,)].
-        # It will run once, as required, and apply no constraints
-        for broadcast_combo in broadcast_constraints:
-            final_combo = [_apply_broadcast(spec.copy(), broadcast_combo) for spec in flat_combo]
+        test_spec = flat_combo[0].copy()
+        for constraint in flat_combo[1:]:
+            test_spec.constrain(constraint)
 
-            # Check whether final spec is excluded
-            # requires constructing a spec from constraints
-            test_spec = final_combo[0].copy()
-            for constraint in final_combo[1:]:
-                test_spec.constrain(constraint)
+        # Abstract variants don't have normal satisfaction semantics
+        # Convert all variants to concrete types.
+        # This method is best effort, so all existing variants will be
+        # converted before any error is raised.
+        # Catch exceptions because we want to be able to operate on
+        # abstract specs without needing package information
+        try:
+            spack.variant.substitute_abstract_variants(test_spec)
+        except spack.variant.UnknownVariantError:
+            pass
+        if any(test_spec.satisfies(x) for x in excludes):
+            continue
 
-            # Abstract variants don't have normal satisfaction semantics
-            # Convert all variants to concrete types.
-            # This method is best effort, so all existing variants will be
-            # converted before any error is raised.
-            # Catch exceptions because we want to be able to operate on
-            # abstract specs without needing package information
-            try:
-                spack.variant.substitute_abstract_variants(test_spec)
-            except spack.variant.UnknownVariantError:
-                pass
+        if sigil:
+            flat_combo[0] = Spec(sigil + str(flat_combo[0]))
 
-            # actual exclusion check is here
-            if any(test_spec.satisfies(e) for e in excludes):
-                continue
-
-            # Apply sigil if applicable
-            if sigil:
-                final_combo[0] = Spec(sigil + str(final_combo[0]))
-
-            # Add to list of constraints
-            results.append(final_combo)
+        # Add to list of constraints
+        results.append(flat_combo)
 
     return results
 
 
-def _apply_broadcast(spec, constraints):
-    if constraints:
-        for node in spec.traverse():
-            if node.name:
-                for constraint in constraints:
-                    node.constrain(constraint)
-    return spec
-
-
 def _sigilify(item, sigil):
     if isinstance(item, dict):
         if sigil:

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

@@ -52,19 +52,6 @@
 
 sep = os.sep
 
-supports_renameat2 = bool(spack.util.atomic_update.renameat2())
-if supports_renameat2:
-    use_renameat2 = [True, False]
-else:
-    use_renameat2 = [False]
-
-
-@pytest.fixture(params=use_renameat2)
-def atomic_update_implementations(request, monkeypatch):
-    if request.param is False:
-        monkeypatch.setattr(spack.util.atomic_update, "_renameat2", None)
-    yield
-
 
 def check_mpileaks_and_deps_in_view(viewdir):
     """Check that the expected install directories exist."""
@@ -74,11 +61,9 @@ def check_mpileaks_and_deps_in_view(viewdir):
 
 def check_viewdir_removal(viewdir):
     """Check that the uninstall/removal worked."""
-    view_spack_dir = str(viewdir.join(".spack"))
-    if not os.path.exists(view_spack_dir):
-        return
-
-    assert all(f in ["projections.yaml", "metadata.yaml"] for f in os.listdir(view_spack_dir))
+    assert not os.path.exists(str(viewdir.join(".spack"))) or os.listdir(
+        str(viewdir.join(".spack"))
+    ) == ["projections.yaml"]
 
 
 def test_add():
@@ -612,9 +597,7 @@ def test_init_from_yaml(tmpdir):
 
 
 @pytest.mark.usefixtures("config")
-def test_env_view_external_prefix(
-    tmpdir_factory, mutable_database, mock_packages, atomic_update_implementations
-):
+def test_env_view_external_prefix(tmpdir_factory, mutable_database, mock_packages):
     fake_prefix = tmpdir_factory.mktemp("a-prefix")
     fake_bin = fake_prefix.join("bin")
     fake_bin.ensure(dir=True)
@@ -1195,9 +1178,7 @@ def test_store_different_build_deps(tmpdir):
         assert x_read["y"].dag_hash() != y_read.dag_hash()
 
 
-def test_env_updates_view_install(
-    tmpdir, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_updates_view_install(tmpdir, mock_stage, mock_fetch, install_mockery):
     view_dir = tmpdir.join("view")
     env("create", "--with-view=%s" % view_dir, "test")
     with ev.read("test"):
@@ -1207,9 +1188,7 @@ def test_env_updates_view_install(
     check_mpileaks_and_deps_in_view(view_dir)
 
 
-def test_env_view_fails(
-    tmpdir, mock_packages, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_view_fails(tmpdir, mock_packages, mock_stage, mock_fetch, install_mockery):
     # We currently ignore file-file conflicts for the prefix merge,
     # so in principle there will be no errors in this test. But
     # the .spack metadata dir is handled separately and is more strict.
@@ -1226,9 +1205,7 @@ def test_env_view_fails(
             install("--fake")
 
 
-def test_env_view_fails_dir_file(
-    tmpdir, mock_packages, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_view_fails_dir_file(tmpdir, mock_packages, mock_stage, mock_fetch, install_mockery):
     # This environment view fails to be created because a file
     # and a dir are in the same path. Test that it mentions the problematic path.
     view_dir = tmpdir.join("view")
@@ -1243,7 +1220,7 @@ def test_env_view_fails_dir_file(
 
 
 def test_env_view_succeeds_symlinked_dir_file(
-    tmpdir, mock_packages, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
+    tmpdir, mock_packages, mock_stage, mock_fetch, install_mockery
 ):
     # A symlinked dir and an ordinary dir merge happily
     view_dir = tmpdir.join("view")
@@ -1257,9 +1234,7 @@ def test_env_view_succeeds_symlinked_dir_file(
         assert os.path.exists(os.path.join(x_dir, "file_in_symlinked_dir"))
 
 
-def test_env_without_view_install(
-    tmpdir, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_without_view_install(tmpdir, mock_stage, mock_fetch, install_mockery):
     # Test enabling a view after installing specs
     env("create", "--without-view", "test")
 
@@ -1280,9 +1255,7 @@ def test_env_without_view_install(
     check_mpileaks_and_deps_in_view(view_dir)
 
 
-def test_env_config_view_default(
-    tmpdir, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_config_view_default(tmpdir, mock_stage, mock_fetch, install_mockery):
     # This config doesn't mention whether a view is enabled
     test_config = """\
 env:
@@ -1300,9 +1273,7 @@ def test_env_config_view_default(
     assert os.path.isdir(os.path.join(e.default_view.view()._root, ".spack", "mpileaks"))
 
 
-def test_env_updates_view_install_package(
-    tmpdir, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_updates_view_install_package(tmpdir, mock_stage, mock_fetch, install_mockery):
     view_dir = tmpdir.join("view")
     env("create", "--with-view=%s" % view_dir, "test")
     with ev.read("test"):
@@ -1311,9 +1282,7 @@ def test_env_updates_view_install_package(
     assert os.path.exists(str(view_dir.join(".spack/mpileaks")))
 
 
-def test_env_updates_view_add_concretize(
-    tmpdir, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_updates_view_add_concretize(tmpdir, mock_stage, mock_fetch, install_mockery):
     view_dir = tmpdir.join("view")
     env("create", "--with-view=%s" % view_dir, "test")
     install("--fake", "mpileaks")
@@ -1324,24 +1293,22 @@ def test_env_updates_view_add_concretize(
     check_mpileaks_and_deps_in_view(view_dir)
 
 
-def test_env_updates_view_uninstall(
-    tmpdir, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_updates_view_uninstall(tmpdir, mock_stage, mock_fetch, install_mockery):
     view_dir = tmpdir.join("view")
     env("create", "--with-view=%s" % view_dir, "test")
     with ev.read("test"):
-        print(install("--fake", "--add", "mpileaks"))
+        install("--fake", "--add", "mpileaks")
 
     check_mpileaks_and_deps_in_view(view_dir)
 
     with ev.read("test"):
-        print(uninstall("-ay"))
+        uninstall("-ay")
 
     check_viewdir_removal(view_dir)
 
 
 def test_env_updates_view_uninstall_referenced_elsewhere(
-    tmpdir, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
+    tmpdir, mock_stage, mock_fetch, install_mockery
 ):
     view_dir = tmpdir.join("view")
     env("create", "--with-view=%s" % view_dir, "test")
@@ -1358,14 +1325,10 @@ def test_env_updates_view_uninstall_referenced_elsewhere(
     check_viewdir_removal(view_dir)
 
 
-def test_env_updates_view_remove_concretize(
-    tmpdir, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_updates_view_remove_concretize(tmpdir, mock_stage, mock_fetch, install_mockery):
     view_dir = tmpdir.join("view")
-
     env("create", "--with-view=%s" % view_dir, "test")
     install("--fake", "mpileaks")
-
     with ev.read("test"):
         add("mpileaks")
         concretize()
@@ -1379,9 +1342,7 @@ def test_env_updates_view_remove_concretize(
     check_viewdir_removal(view_dir)
 
 
-def test_env_updates_view_force_remove(
-    tmpdir, mock_stage, mock_fetch, install_mockery, atomic_update_implementations
-):
+def test_env_updates_view_force_remove(tmpdir, mock_stage, mock_fetch, install_mockery):
     view_dir = tmpdir.join("view")
     env("create", "--with-view=%s" % view_dir, "test")
     with ev.read("test"):
@@ -1928,7 +1889,7 @@ def test_stack_definition_conditional_add_write(tmpdir):
 
 
 def test_stack_combinatorial_view(
-    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery, atomic_update_implementations
+    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery
 ):
     filename = str(tmpdir.join("spack.yaml"))
     viewdir = str(tmpdir.join("view"))
@@ -1963,9 +1924,7 @@ def test_stack_combinatorial_view(
             )
 
 
-def test_stack_view_select(
-    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery, atomic_update_implementations
-):
+def test_stack_view_select(tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery):
     filename = str(tmpdir.join("spack.yaml"))
     viewdir = str(tmpdir.join("view"))
     with open(filename, "w") as f:
@@ -2005,9 +1964,7 @@ def test_stack_view_select(
                 )
 
 
-def test_stack_view_exclude(
-    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery, atomic_update_implementations
-):
+def test_stack_view_exclude(tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery):
     filename = str(tmpdir.join("spack.yaml"))
     viewdir = str(tmpdir.join("view"))
     with open(filename, "w") as f:
@@ -2048,7 +2005,7 @@ def test_stack_view_exclude(
 
 
 def test_stack_view_select_and_exclude(
-    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery, atomic_update_implementations
+    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery
 ):
     filename = str(tmpdir.join("spack.yaml"))
     viewdir = str(tmpdir.join("view"))
@@ -2090,9 +2047,7 @@ def test_stack_view_select_and_exclude(
                 )
 
 
-def test_view_link_roots(
-    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery, atomic_update_implementations
-):
+def test_view_link_roots(tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery):
     filename = str(tmpdir.join("spack.yaml"))
     viewdir = str(tmpdir.join("view"))
     with open(filename, "w") as f:
@@ -2136,9 +2091,7 @@ def test_view_link_roots(
                 )
 
 
-def test_view_link_run(
-    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery, atomic_update_implementations
-):
+def test_view_link_run(tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery):
     yaml = str(tmpdir.join("spack.yaml"))
     viewdir = str(tmpdir.join("view"))
     envdir = str(tmpdir)
@@ -2180,13 +2133,7 @@ def test_view_link_run(
 
 @pytest.mark.parametrize("link_type", ["hardlink", "copy", "symlink"])
 def test_view_link_type(
-    link_type,
-    tmpdir,
-    mock_fetch,
-    mock_packages,
-    mock_archive,
-    install_mockery,
-    atomic_update_implementations,
+    link_type, tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery
 ):
     filename = str(tmpdir.join("spack.yaml"))
     viewdir = str(tmpdir.join("view"))
@@ -2216,9 +2163,7 @@ def test_view_link_type(
             assert os.path.islink(file_to_test) == (link_type == "symlink")
 
 
-def test_view_link_all(
-    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery, atomic_update_implementations
-):
+def test_view_link_all(tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery):
     filename = str(tmpdir.join("spack.yaml"))
     viewdir = str(tmpdir.join("view"))
     with open(filename, "w") as f:
@@ -2329,7 +2274,7 @@ def test_stack_view_no_activate_without_default(
 
 
 def test_stack_view_multiple_views(
-    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery, atomic_update_implementations
+    tmpdir, mock_fetch, mock_packages, mock_archive, install_mockery
 ):
     filename = str(tmpdir.join("spack.yaml"))
     default_viewdir = str(tmpdir.join("default-view"))
@@ -2898,14 +2843,10 @@ def test_failed_view_cleanup(tmpdir, mock_stage, mock_fetch, install_mockery):
     assert os.path.samefile(resolved_view, view)
 
 
-def test_environment_view_target_already_exists(
-    tmpdir, mock_stage, mock_fetch, install_mockery, monkeypatch
-):
+def test_environment_view_target_already_exists(tmpdir, mock_stage, mock_fetch, install_mockery):
     """When creating a new view, Spack should check whether
     the new view dir already exists. If so, it should not be
     removed or modified."""
-    # Only works for symlinked atomic views
-    monkeypatch.setattr(spack.util.atomic_update, "_renameat2", None)
 
     # Create a new environment
     view = str(tmpdir.join("view"))
@@ -3298,103 +3239,3 @@ def test_environment_created_in_users_location(mutable_config, tmpdir):
     assert dir_name in out
     assert env_dir in ev.root(dir_name)
     assert os.path.isdir(os.path.join(env_dir, dir_name))
-
-
-@pytest.mark.parametrize("update_method", ["symlink", "exchange"])
-def test_view_update_mismatch(update_method, tmpdir, install_mockery, mock_fetch, monkeypatch):
-    root = str(tmpdir.join("root"))
-    if update_method == "symlink":
-        os.makedirs(root)
-        checker = "cannot be updated with 'symlink' update method"
-        forceable = True
-    else:
-        monkeypatch.setattr(spack.util.atomic_update, "_renameat2", None)
-        checker = "does not support 'exchange' atomic update method"
-        forceable = False
-
-    view = ev.environment.ViewDescriptor(
-        base_path=str(tmpdir), root=root, update_method=update_method
-    )
-
-    spec = spack.spec.Spec("libelf").concretized()
-    install("libelf")
-
-    with pytest.raises(RuntimeError, match=checker):
-        view.regenerate([spec])
-
-    if forceable:
-        view.regenerate([spec], force=True)
-        assert os.path.exists(view.root)
-
-
-@pytest.mark.parametrize("update_method", ["symlink", "exchange"])
-def test_view_update_fails(update_method, tmpdir, install_mockery, mock_fetch, monkeypatch):
-    root = str(tmpdir.join("root"))
-    view = ev.environment.ViewDescriptor(
-        base_path=str(tmpdir), root=root, update_method=update_method
-    )
-
-    spec = spack.spec.Spec("libelf").concretized()
-    install("libelf")
-
-    def raises(*args, **kwargs):
-        raise OSError
-
-    # The python symlink code fails by raising an error
-    monkeypatch.setattr(fs, "rename", raises)
-    # The c library call fails by a non-zero return code
-    monkeypatch.setattr(spack.util.atomic_update, "_renameat2", lambda x, y, z, v, w: 1)
-
-    with pytest.raises(OSError):
-        view.regenerate([spec])
-
-    assert not os.path.exists(view.root)
-    if update_method == "symlink":
-        link = os.path.join(str(tmpdir), "._root", "._tmp_symlink")
-        assert not os.path.lexists(link)
-
-
-@pytest.mark.parametrize("update_method", ["symlink", "exchange"])
-def test_view_update_unnecessary(update_method, tmpdir, install_mockery, mock_fetch, monkeypatch):
-    if update_method == "exchange" and not supports_renameat2:
-        pytest.skip("Testing on an OS that does not support the exchange update method")
-
-    root = str(tmpdir.join("root"))
-    view = ev.environment.ViewDescriptor(
-        base_path=str(tmpdir), root=root, update_method=update_method
-    )
-
-    libelf = spack.spec.Spec("libelf").concretized()
-    install("libelf")
-    libdwarf = spack.spec.Spec("libdwarf").concretized()
-    install("libdwarf")
-
-    # Create a "previous" view
-    # Wait after each view regeneration to ensure timestamps are different
-    view.regenerate([libelf])
-
-    # monkeypatch so that any attempt to actually regenerate the view fails
-    def raises(*args, **kwargs):
-        raise AssertionError
-
-    old_view = view.update_method_to_use
-    monkeypatch.setattr(view, "update_method_to_use", raises)
-
-    # regenerating the view is a no-op, so doesn't raise
-    # will raise if the view isn't identical
-    view.regenerate([libelf])
-    with pytest.raises(AssertionError):
-        view.regenerate([libelf, libdwarf])
-
-    # Create another view so there are multiple old views around
-    monkeypatch.setattr(view, "update_method_to_use", old_view)
-    view.regenerate([libelf, libdwarf])
-
-    # Redo the monkeypatch
-    monkeypatch.setattr(view, "update_method_to_use", raises)
-
-    # no raise for no-op regeneration
-    # raise when it's not a no-op
-    view.regenerate([libelf, libdwarf])
-    with pytest.raises(AssertionError):
-        view.regenerate([libelf])

lib/spack/spack/test/spec_list.py

@@ -214,17 +214,3 @@ def test_spec_list_constraints_with_structure(
         speclist = SpecList("specs", [matrix])
         assert len(speclist.specs) == 1
         assert libdwarf_spec in speclist.specs[0]
-
-    def test_spec_list_broadcast(self, mock_packages):
-        matrix = {
-            "matrix": [["mpileaks"], ["^callpath"]],
-            "broadcast": [["%gcc", "%clang"], ["+debug", "~debug"]],
-            "exclude": ["+debug%clang"],
-        }
-        speclist = SpecList("specs", [matrix])
-
-        assert len(speclist) == 3
-        for spec in speclist:
-            for node in spec.traverse():
-                assert node.compiler.name == spec.compiler.name
-                assert node.variants["debug"].value == spec.variants["debug"].value

lib/spack/spack/util/atomic_update.py

@@ -1,75 +0,0 @@
-# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import ctypes
-import os
-from typing import Optional
-
-import llnl.util.filesystem as fs
-from llnl.util.symlink import symlink
-
-# Magic numbers from linux headers
-RENAME_EXCHANGE = 2
-AT_FDCWD = -100
-
-# object for renameat2 not set
-# We use None for not found and notset for not set so that boolean checks work
-# properly in client code
-notset = object()
-_renameat2 = notset
-
-
-def set_renameat2():
-    libc: Optional[ctypes.CDLL] = None
-    try:
-        # CDLL(None) returns the python process
-        # python links against libc, so we can treat this as a libc handle
-        # we could also use CDLL("libc.so.6") but this is (irrelevantly) more future proof
-        libc = ctypes.CDLL(None)
-    except (OSError, TypeError):
-        # OSError if the call fails,
-        # TypeError on Windows
-        return None
-
-    return getattr(libc, "renameat2", None)
-
-
-def renameat2():
-    global _renameat2
-    if _renameat2 is notset:
-        _renameat2 = set_renameat2()
-    return _renameat2
-
-
-def atomic_update_renameat2(src, dest):
-    # Ensure a directory that is a symlink will not be read as symlink in libc
-    src = src.rstrip(os.path.sep)
-    dest = dest.rstrip(os.path.sep)
-
-    dest_exists = os.path.lexists(dest)
-    if not dest_exists:
-        fs.mkdirp(dest)
-    try:
-        rc = renameat2()(AT_FDCWD, src.encode(), AT_FDCWD, dest.encode(), RENAME_EXCHANGE)
-        if rc:
-            raise OSError(f"renameat2 failed to exchange {src} and {dest}")
-    except OSError:
-        if not dest_exists:
-            os.rmdir(dest)
-        raise
-
-
-def atomic_update_symlink(src, dest):
-    # Create temporary symlink to point to src
-    tmp_symlink_name = os.path.join(os.path.dirname(dest), "._tmp_symlink")
-    if os.path.exists(tmp_symlink_name):
-        os.unlink(tmp_symlink_name)
-    symlink(src, tmp_symlink_name)
-
-    # atomically mv the symlink to destpath (still points to srcpath)
-    try:
-        fs.rename(tmp_symlink_name, dest)
-    except OSError:
-        os.unlink(tmp_symlink_name)
-        raise

lib/spack/spack/util/environment.py

@@ -138,7 +138,7 @@ def dump_environment(path, environment=None):
     use_env = environment or os.environ
     hidden_vars = set(["PS1", "PWD", "OLDPWD", "TERM_SESSION_ID"])
 
-    fd = os.open(path, os.O_WRONLY | os.O_CREAT, 0o600)
+    fd = os.open(path, os.O_WRONLY | os.O_CREAT | os.O_TRUNC, 0o600)
     with os.fdopen(fd, "w") as env_file:
         for var, val in sorted(use_env.items()):
             env_file.write(

lib/spack/spack/version.py

@@ -1336,6 +1336,10 @@ def lookup_ref(self, ref):
             # won't properly update the local rev-list)
             self.fetcher.git("fetch", "--tags", output=os.devnull, error=os.devnull)
 
+            # We need to do an attempt at fetching the commit in order to
+            # be sure to get it in case it comes from a PR in a fork.
+            self.fetcher.git("fetch", "origin", "%s" % ref, output=os.devnull, error=os.devnull)
+
             # Ensure ref is a commit object known to git
             # Note the brackets are literals, the ref replaces the format string
             try:

share/spack/spack-completion.bash

@@ -977,7 +977,7 @@ _spack_env_loads() {
 _spack_env_view() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -f --force"
+        SPACK_COMPREPLY="-h --help"
     else
         SPACK_COMPREPLY=""
     fi

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

@@ -723,17 +723,14 @@ def setup_dependent_package(self, module, dependent_spec):
         # Disable find package's config mode for versions of Boost that
         # didn't provide it. See https://github.com/spack/spack/issues/20169
         # and https://cmake.org/cmake/help/latest/module/FindBoost.html
-        #is_cmake = isinstance(dependent_spec.package, CMakePackage)
-        #if self.spec.satisfies("boost@:1.69.0") and is_cmake:
-        #    args_fn = type(dependent_spec.package).cmake_args
-        if self.spec.satisfies("boost@:1.69.0") and dependent_spec.satisfies("build_system=cmake"):
-            args_fn = type(dependent_spec.package.builder).cmake_args
+        is_cmake = isinstance(dependent_spec.package, CMakePackage)
+        if self.spec.satisfies("boost@:1.69.0") and is_cmake:
+            args_fn = type(dependent_spec.package).cmake_args
 
             def _cmake_args(self):
                 return ["-DBoost_NO_BOOST_CMAKE=ON"] + args_fn(self)
 
-            #type(dependent_spec.package).cmake_args = _cmake_args
-            type(dependent_spec.package.builder).cmake_args = _cmake_args
+            type(dependent_spec.package).cmake_args = _cmake_args
 
     def setup_dependent_build_environment(self, env, dependent_spec):
         if "+context" in self.spec and "context-impl" in self.spec.variants:

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

@@ -17,12 +17,38 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
 
     maintainers("sethrj")
 
-    version("0.2.0", sha256="12af28fda0e482a9eba89781b4ead445cf6f170bc1b8d88cc814e49b1ec09e9f")
-    version("0.1.4", sha256="ea82a03fc750a2a805f87afd9ac944109dd7537edb5c0c370f93d332d4cd47db")
-    version("0.1.3", sha256="992c49a48adba884fe3933c9624da5bf480ef0694809430ae98903f2c28cc881")
-    version("0.1.2", sha256="d123ea2e34267adba387d46bae8c9a1146a2e047f87f2ea5f823878c1684678d")
-    version("0.1.1", sha256="a1d58e29226e89a2330d69c40049d61e7c885cf991824e60ff8c9ccc95fc5ec6")
-    version("0.1.0", sha256="46692977b9b31d73662252cc122d7f016f94139475788bca7fdcb97279b93af8")
+    version("0.2.1", sha256="b3717b43f70dd0da848139da4171ca7a887bb6777908845b6d953d47b1f4db41")
+    version(
+        "0.2.0",
+        sha256="12af28fda0e482a9eba89781b4ead445cf6f170bc1b8d88cc814e49b1ec09e9f",
+        deprecated=True,
+    )
+    version("0.1.5", sha256="5e63b9ce7fcfe34a8938565b84453bce51fa6639d1ede13bb59d41de6431cef4")
+    version(
+        "0.1.4",
+        sha256="ea82a03fc750a2a805f87afd9ac944109dd7537edb5c0c370f93d332d4cd47db",
+        deprecated=True,
+    )
+    version(
+        "0.1.3",
+        sha256="992c49a48adba884fe3933c9624da5bf480ef0694809430ae98903f2c28cc881",
+        deprecated=True,
+    )
+    version(
+        "0.1.2",
+        sha256="d123ea2e34267adba387d46bae8c9a1146a2e047f87f2ea5f823878c1684678d",
+        deprecated=True,
+    )
+    version(
+        "0.1.1",
+        sha256="a1d58e29226e89a2330d69c40049d61e7c885cf991824e60ff8c9ccc95fc5ec6",
+        deprecated=True,
+    )
+    version(
+        "0.1.0",
+        sha256="46692977b9b31d73662252cc122d7f016f94139475788bca7fdcb97279b93af8",
+        deprecated=True,
+    )
 
     _cxxstd_values = ("14", "17")
 
@@ -49,7 +75,8 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("cmake@3.22:", type="build", when="+rocm")
 
     depends_on("nlohmann-json")
-    depends_on("geant4@10.6:", when="+geant4")
+    depends_on("geant4@10.7:11.0", when="@:0.2.0 +geant4")
+    depends_on("geant4@10.6:11.0", when="@0.2.1: +geant4")
     depends_on("hepmc3", when="+hepmc3")
     depends_on("root", when="+root")
     depends_on("swig", when="+swig")
@@ -68,6 +95,7 @@ class Celeritas(CMakePackage, CudaPackage, ROCmPackage):
     depends_on("vecgeom +gdml@1.1.17:", when="+vecgeom")
     depends_on("vecgeom +cuda", when="+vecgeom +cuda")
 
+    conflicts("cxxstd=14", when="@0.3:")
     conflicts("+rocm", when="+cuda", msg="AMD and NVIDIA accelerators are incompatible")
     conflicts("+rocm", when="+vecgeom", msg="HIP support is only available with ORANGE")
     conflicts("^vecgeom+shared@1.2.0", when="+vecgeom +cuda")

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

@@ -53,7 +53,6 @@ class Dyninst(CMakePackage):
     depends_on("boost@1.61.0:" + boost_libs, when="@10.1.0:")
     depends_on("boost@1.61.0:1.69" + boost_libs, when="@:10.0")
     depends_on("boost@1.67.0:" + boost_libs, when="@11.0.0:")
-    depends_on("boost@1.70.0:" + boost_libs, when="@12:")
 
     depends_on("libiberty+pic")
 
@@ -117,7 +116,7 @@ def cmake_args(self):
             "-DBoost_ROOT_DIR=%s" % spec["boost"].prefix,
             "-DElfUtils_ROOT_DIR=%s" % spec["elf"].prefix,
             "-DLibIberty_ROOT_DIR=%s" % spec["libiberty"].prefix,
-            "-DTBB_ROOT_DIR=%s" % spec["tbb"].prefix.tbb,
+            "-DTBB_ROOT_DIR=%s" % spec["tbb"].prefix,
             self.define("LibIberty_LIBRARIES", spec["libiberty"].libs),
         ]
 

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

@@ -199,8 +199,8 @@ def setup_build_environment(self, env):
             env.set("ESMF_CXX", spec["mpi"].mpicxx)
             env.set("ESMF_F90", spec["mpi"].mpifc)
         else:
-            os.environ["ESMF_CXX"] = os.environ["CXX"]
-            os.environ["ESMF_F90"] = os.environ["FC"]
+            env.set("ESMF_CXX", env["CXX"])
+            env.set("ESMF_F90", env["FC"])
 
         # This environment variable controls the build option.
         if "+debug" in spec:

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

@@ -116,6 +116,7 @@ def setup_build_environment(self, env):
         # internal Spack wrappers and fail.
         env.set("CC_FOR_TARGET", self.compiler.cc)
         env.set("CXX_FOR_TARGET", self.compiler.cxx)
+        env.set("GOMAXPROCS", make_jobs)
 
     def setup_dependent_package(self, module, dependent_spec):
         """Called before go modules' install() methods.

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

@@ -14,6 +14,7 @@ class Hdf5VolCache(CMakePackage):
     maintainers("hyoklee", "lrknox")
 
     version("default", branch="develop")
+    version("v1.1", tag="v1.1")
     version("v1.0", tag="v1.0")
 
     depends_on("hdf5-vol-async")

var/spack/repos/builtin/packages/hpctoolkit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch

@@ -0,0 +1,91 @@
+From 411d62544717873432c49ef45c7cb99cc5de2fb8 Mon Sep 17 00:00:00 2001
+From: "Mark W. Krentel" <krentel@rice.edu>
+Date: Thu, 15 Dec 2022 16:43:43 -0600
+Subject: [PATCH] Add a temporary hack to allow both ROCM 5.2/5.3 to build
+ cleanly.
+
+There were some corner cases (build 5.3 pieces from spack and feed
+into autotools) that didn't work.  After the next release, I will want
+to rework ROCM configure more extensively.
+---
+ configure    | 21 +++++++++++++--------
+ configure.ac | 17 +++++++++++------
+ 2 files changed, 24 insertions(+), 14 deletions(-)
+
+diff --git a/configure b/configure
+index 1760e678e8..814376b3bd 100755
+--- a/configure
++++ b/configure
+@@ -23891,10 +23891,13 @@ $as_echo "$as_me: found $ROCM/rocprofiler/lib/librocprofiler64.so" >&6;}
+     fi
+ 
+     # HSA
+-    if test -f "$ROCM/include/hsa/hsa.h" ; then
+-      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM/include/hsa/hsa.h" >&5
+-$as_echo "$as_me: found $ROCM/include/hsa/hsa.h" >&6;}
+-      ROCM_HSA_IFLAGS="-I$ROCM/include/hsa"
++    # FIXME: as of rocm 5.2/5.3, this was not fully switched over,
++    # so temporarily use both paths.
++    if test -f "$ROCM/include/hsa/hsa.h" || test -f "$ROCM/include/hsa.h"
++    then
++      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM: hsa.h" >&5
++$as_echo "$as_me: found $ROCM: hsa.h" >&6;}
++      ROCM_HSA_IFLAGS="-I$ROCM/include -I$ROCM/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM/hsa"
+       found=yes
+     fi
+@@ -24020,10 +24023,12 @@ case "$ROCM_HSA" in
+     require_rocm=yes
+     found=no
+ 
+-    if test -f "$ROCM_HSA/include/hsa/hsa.h" ; then
+-      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM_HSA/include/hsa/hsa.h" >&5
+-$as_echo "$as_me: found $ROCM_HSA/include/hsa/hsa.h" >&6;}
+-      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include/hsa"
++    # FIXME: again, temporarily use both paths
++    if test -f "$ROCM_HSA/include/hsa/hsa.h" || test -f "$ROCM_HSA/include/hsa.h"
++    then
++      { $as_echo "$as_me:${as_lineno-$LINENO}: found $ROCM_HSA: hsa.h" >&5
++$as_echo "$as_me: found $ROCM_HSA: hsa.h" >&6;}
++      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include -I$ROCM_HSA/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM_HSA"
+       found=yes
+     fi
+diff --git a/configure.ac b/configure.ac
+index a14b15835f..9d5ed46134 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -4885,9 +4885,12 @@ case "$ROCM" in
+     fi
+ 
+     # HSA
+-    if test -f "$ROCM/include/hsa/hsa.h" ; then
+-      AC_MSG_NOTICE([found $ROCM/include/hsa/hsa.h])
+-      ROCM_HSA_IFLAGS="-I$ROCM/include/hsa"
++    # FIXME: as of rocm 5.2/5.3, this was not fully switched over,
++    # so temporarily use both paths.
++    if test -f "$ROCM/include/hsa/hsa.h" || test -f "$ROCM/include/hsa.h"
++    then
++      AC_MSG_NOTICE([found $ROCM: hsa.h])
++      ROCM_HSA_IFLAGS="-I$ROCM/include -I$ROCM/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM/hsa"
+       found=yes
+     fi
+@@ -5002,9 +5005,11 @@ case "$ROCM_HSA" in
+     require_rocm=yes
+     found=no
+ 
+-    if test -f "$ROCM_HSA/include/hsa/hsa.h" ; then
+-      AC_MSG_NOTICE([found $ROCM_HSA/include/hsa/hsa.h])
+-      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include/hsa"
++    # FIXME: again, temporarily use both paths
++    if test -f "$ROCM_HSA/include/hsa/hsa.h" || test -f "$ROCM_HSA/include/hsa.h"
++    then
++      AC_MSG_NOTICE([found $ROCM_HSA: hsa.h])
++      ROCM_HSA_IFLAGS="-I$ROCM_HSA/include -I$ROCM_HSA/include/hsa"
+       ROCM_HSA_INC_MESG="$ROCM_HSA"
+       found=yes
+     fi
+-- 
+GitLab
+

var/spack/repos/builtin/packages/hpctoolkit/511afd95b01d743edc5940c84e0079f462b2c23e.patch

@@ -0,0 +1,130 @@
+From 511afd95b01d743edc5940c84e0079f462b2c23e Mon Sep 17 00:00:00 2001
+From: "Mark W. Krentel" <krentel@rice.edu>
+Date: Tue, 18 May 2021 14:54:41 -0500
+Subject: [PATCH] Cleanup some usage for gcc/g++ 11.x (#413)
+
+1. Change epsilon to hpc_epsilon in prof/Metric header files.  This
+ conflicted with using epsilon in some STL template libraries.
+
+ 2. Add const to some comparison operators that are used in some STL
+ maps.
+---
+ src/lib/banal/Struct-Inline.hpp   | 6 +++---
+ src/lib/prof/Metric-AExpr.cpp     | 4 ++--
+ src/lib/prof/Metric-AExpr.hpp     | 2 +-
+ src/lib/prof/Metric-AExprIncr.hpp | 6 +++---
+ src/lib/support/StringTable.hpp   | 2 +-
+ 5 files changed, 10 insertions(+), 10 deletions(-)
+
+diff --git a/src/lib/banal/Struct-Inline.hpp b/src/lib/banal/Struct-Inline.hpp
+index ffb93355fd..0099ad112d 100644
+--- a/src/lib/banal/Struct-Inline.hpp
++++ b/src/lib/banal/Struct-Inline.hpp
+@@ -150,14 +150,14 @@ public:
+     pretty_index = strTab.str2index(node.getPrettyName());
+   }
+ 
+-  bool operator == (const FLPIndex rhs)
++  bool operator == (const FLPIndex rhs) const
+   {
+     return file_index == rhs.file_index
+       && line_num == rhs.line_num
+       && pretty_index == rhs.pretty_index;
+   }
+ 
+-  bool operator != (const FLPIndex rhs)
++  bool operator != (const FLPIndex rhs) const
+   {
+     return ! (*this == rhs);
+   }
+@@ -167,7 +167,7 @@ public:
+ // Compare (file, line, proc) indices lexigraphically.
+ class FLPCompare {
+ public:
+-  bool operator() (const FLPIndex t1, const FLPIndex t2)
++  bool operator() (const FLPIndex t1, const FLPIndex t2) const
+   {
+     if (t1.file_index < t2.file_index) { return true; }
+     if (t1.file_index > t2.file_index) { return false; }
+diff --git a/src/lib/prof/Metric-AExpr.cpp b/src/lib/prof/Metric-AExpr.cpp
+index 2ce43e6d39..5b32ff67d1 100644
+--- a/src/lib/prof/Metric-AExpr.cpp
++++ b/src/lib/prof/Metric-AExpr.cpp
+@@ -483,7 +483,7 @@ CoefVar::eval(const Metric::IData& mdata) const
+   double sdev = sqrt(v_m.first); // always non-negative
+   double mean = v_m.second;
+   double z = 0.0;
+-  if (mean > epsilon) {
++  if (mean > hpc_epsilon) {
+     z = sdev / mean;
+   }
+ 
+@@ -522,7 +522,7 @@ RStdDev::eval(const Metric::IData& mdata) const
+   double sdev = sqrt(v_m.first); // always non-negative
+   double mean = v_m.second;
+   double z = 0.0;
+-  if (mean > epsilon) {
++  if (mean > hpc_epsilon) {
+     z = (sdev / mean) * 100;
+   }
+ 
+diff --git a/src/lib/prof/Metric-AExpr.hpp b/src/lib/prof/Metric-AExpr.hpp
+index 56359cc9df..d75189f763 100644
+--- a/src/lib/prof/Metric-AExpr.hpp
++++ b/src/lib/prof/Metric-AExpr.hpp
+@@ -97,7 +97,7 @@
+ 
+ //****************************************************************************
+ 
+-#define epsilon  (0.000001)
++#define hpc_epsilon  (0.000001)
+ 
+ namespace Prof {
+ 
+diff --git a/src/lib/prof/Metric-AExprIncr.hpp b/src/lib/prof/Metric-AExprIncr.hpp
+index f1b38d7f74..d0c0feb7e6 100644
+--- a/src/lib/prof/Metric-AExprIncr.hpp
++++ b/src/lib/prof/Metric-AExprIncr.hpp
+@@ -97,7 +97,7 @@
+ 
+ //****************************************************************************
+ 
+-#define epsilon  (0.000001)
++#define hpc_epsilon  (0.000001)
+ 
+ namespace Prof {
+ 
+@@ -841,7 +841,7 @@ public:
+     double sdev = finalizeStdDev(mdata);
+     double mean = accumVar(1, mdata);
+     double z = 0.0;
+-    if (mean > epsilon) {
++    if (mean > hpc_epsilon) {
+       z = sdev / mean;
+     }
+     accumVar(0, mdata) = z;
+@@ -927,7 +927,7 @@ public:
+     double sdev = finalizeStdDev(mdata);
+     double mean = accumVar(1, mdata);
+     double z = 0.0;
+-    if (mean > epsilon) {
++    if (mean > hpc_epsilon) {
+       z = (sdev / mean) * 100;
+     }
+     accumVar(0, mdata) = z;
+diff --git a/src/lib/support/StringTable.hpp b/src/lib/support/StringTable.hpp
+index 9930bc5649..36ce5b7fa9 100644
+--- a/src/lib/support/StringTable.hpp
++++ b/src/lib/support/StringTable.hpp
+@@ -75,7 +75,7 @@ namespace HPC {
+ // compare the strings, not the pointers
+ class StringCompare {
+ public:
+-  bool operator() (const std::string *s1, const std::string *s2)
++  bool operator() (const std::string *s1, const std::string *s2) const
+   {
+     return *s1 < *s2;
+   }
+-- 
+GitLab
+

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

@@ -162,17 +162,11 @@ class Hpctoolkit(AutotoolsPackage):
     # Fix the build for old revs with gcc 10.x.
     patch("gcc10-enum.patch", when="@2020.01.01:2020.08 %gcc@10.0:")
 
-    patch(
-        "https://gitlab.com/hpctoolkit/hpctoolkit/-/commit/511afd95b01d743edc5940c84e0079f462b2c23e.patch",
-        sha256="8da18df88a80847c092da8d0892de51ea2bf2523124148b6305ab8717707d897",
-        when="@2019.08.01:2021.03 %gcc@11.0:",
-    )
+    patch("511afd95b01d743edc5940c84e0079f462b2c23e.patch", when="@2019.08.01:2021.03 %gcc@11.0:")
 
     # Update configure for rocm 5.3.0
     patch(
-        "https://gitlab.com/hpctoolkit/hpctoolkit/-/commit/411d62544717873432c49ef45c7cb99cc5de2fb8.patch",
-        sha256="484045891a665cdba3b0f141540c89f0d691ed32c5912ef62a93670d44c2786c",
-        when="@2022.04:2022.10 +rocm ^hip@5.3.0:",
+        "411d62544717873432c49ef45c7cb99cc5de2fb8.patch", when="@2022.04:2022.10 +rocm ^hip@5.3.0:"
     )
 
     # Change python to python3 for some old revs that use a script

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

@@ -740,8 +740,7 @@ def post_install(self):
                 install_tree("clang/bindings/python", python_platlib)
 
         with working_dir(self.build_directory):
-            if not os.path.exists(join_path(self.prefix, 'libexec', 'llvm')):
-                install_tree("bin", join_path(self.prefix, "libexec", "llvm"))
+            install_tree("bin", join_path(self.prefix, "libexec", "llvm"))
 
     def llvm_config(self, *args, **kwargs):
         lc = Executable(self.prefix.bin.join("llvm-config"))

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

@@ -124,10 +124,7 @@ class NetcdfC(AutotoolsPackage):
     # Starting version 4.4.0, it became possible to disable parallel I/O even
     # if HDF5 supports it. For previous versions of the library we need
     # HDF5 without mpi support to disable parallel I/O:
-    #depends_on("hdf5~mpi", when="@:4.3~mpi")
-    # While it may be possible to do this, it messes with concretizing large environments with
-    # both ~mpi and +mpi builds of hdf5
-    depends_on("hdf5~mpi", when="~mpi")
+    depends_on("hdf5~mpi", when="@:4.3~mpi")
 
     # We need HDF5 with mpi support to enable parallel I/O.
     depends_on("hdf5+mpi", when="+mpi")

var/spack/repos/builtin/packages/ompss-2/package.py

@@ -31,6 +31,8 @@ class Ompss2(Package):
     depends_on("python", type="build")
     depends_on("cmake", type="build")
     depends_on("extrae", when="+extrae")
+    depends_on("boost@1.59.0:")
+    depends_on("numactl")
 
     resource(
         name="jemalloc",
@@ -105,6 +107,8 @@ def install_nanos6(self, spec, prefix):
             "--prefix=%s" % prefix,
             "--with-jemalloc=%s" % prefix,
             "--with-hwloc=%s" % spec["hwloc"].prefix,
+            "--with-boost=%s" % spec["boost"].prefix,
+            "--with-libnuma=%s" % spec["numactl"].prefix,
             "--disable-stats-instrumentation",
             "--disable-verbose-instrumentation",
             "--disable-lint-instrumentation",

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

@@ -42,10 +42,13 @@ class Openmpi(AutotoolsPackage, CudaPackage):
 
     # Current
     version(
-        "4.1.4", sha256="92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d"
-    )  # libmpi.so.40.30.4
+        "4.1.5", sha256="a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3"
+    )  # libmpi.so.40.30.5
 
     # Still supported
+    version(
+        "4.1.4", sha256="92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d"
+    )  # libmpi.so.40.30.4
     version(
         "4.1.3", sha256="3d81d04c54efb55d3871a465ffb098d8d72c1f48ff1cbaf2580eb058567c0a3b"
     )  # libmpi.so.40.30.3

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

@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyNbqa(PythonPackage):
+    """Run any standard Python code quality tool on a Jupyter Notebook."""
+
+    homepage = "https://github.com/nbQA-dev/nbQA"
+    pypi = "nbqa/nbqa-1.6.3.tar.gz"
+
+    version("1.6.3", sha256="5394a29fc6d27b9a950c0a36d2d9de25de980be9acfe2a3f3aea0d27b5f7fec1")
+
+    depends_on("python@3.8:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-ipython@7.8:", type=("build", "run"))
+    depends_on("py-tokenize-rt@3.2:", type=("build", "run"))
+    depends_on("py-tomli", type=("build", "run"))

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

@@ -18,7 +18,7 @@ class PyWarpx(PythonPackage):
     """
 
     homepage = "https://ecp-warpx.github.io"
-    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.01.tar.gz"
+    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.02.tar.gz"
     git = "https://github.com/ECP-WarpX/WarpX.git"
 
     maintainers("ax3l", "dpgrote", "RemiLehe")
@@ -27,6 +27,7 @@ class PyWarpx(PythonPackage):
 
     # NOTE: if you update the versions here, also see warpx
     version("develop", branch="development")
+    version("23.02", sha256="a6c63ebc38cbd224422259a814be501ac79a3b734dab7f59500b6957cddaaac1")
     version("23.01", sha256="e853d01c20ea00c8ddedfa82a31a11d9d91a7f418d37d7f064cf8a241ea4da0c")
     version("22.12", sha256="96019902cd6ea444a1ae515e8853048e9074822c168021e4ec1687adc72ef062")
     version("22.11", sha256="528f65958f2f9e60a094e54eede698e871ccefc89fa103fe2a6f22e4a059515e")
@@ -53,6 +54,7 @@ class PyWarpx(PythonPackage):
     variant("mpi", default=True, description="Enable MPI support")
 
     for v in [
+        "23.02",
         "23.01",
         "22.12",
         "22.11",

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

@@ -0,0 +1,27 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RArrangements(RPackage):
+    """Fast Generators and Iterators for Permutations, Combinations, Integer
+    Partitions and Compositions.
+
+    Fast generators and iterators for permutations, combinations, integer
+    partitions and compositions. The arrangements are in lexicographical order
+    and generated iteratively in a memory efficient manner. It has been
+    demonstrated that 'arrangements' outperforms most existing packages of
+    similar kind. Benchmarks could be found at
+    <https://randy3k.github.io/arrangements/articles/benchmark.html>."""
+
+    cran = "arrangements"
+
+    version("1.1.9", sha256="e9b5dcb185ec9b28201b196384b04a8d5a15f4ddb9e0b0b2a0c718635ff7345b")
+
+    depends_on("r@3.4.0:", type=("build", "run"))
+    depends_on("r-gmp", type=("build", "run"))
+    depends_on("r-r6", type=("build", "run"))
+    depends_on("gmp@4.2.3:")

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

@@ -0,0 +1,28 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RGoogleauthr(RPackage):
+    """Authenticate and Create Google APIs.
+
+    Create R functions that interact with OAuth2 Google APIs
+    <https://developers.google.com/apis-explorer/> easily, with auto-refresh
+    and Shiny compatibility."""
+
+    cran = "googleAuthR"
+
+    version("2.0.0", sha256="ba504baf3bde2e1b3e988bee7602df5765cc6ca542cf0ab76a782c4e60966feb")
+
+    depends_on("r@3.3.0:", type=("build", "run"))
+    depends_on("r-assertthat", type=("build", "run"))
+    depends_on("r-cli", type=("build", "run"))
+    depends_on("r-digest", type=("build", "run"))
+    depends_on("r-gargle@1.2.0:", type=("build", "run"))
+    depends_on("r-httr@1.4.0:", type=("build", "run"))
+    depends_on("r-jsonlite@1.6:", type=("build", "run"))
+    depends_on("r-memoise@1.1.0:", type=("build", "run"))
+    depends_on("r-rlang", type=("build", "run"))

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

@@ -0,0 +1,26 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RIeugwasr(RPackage):
+    """R Interface to the OpenGWAS Database API.
+
+    R interface to the OpenGWAS database API. Includes a wrapper
+    to make generic calls to the API, plus convenience functions for
+    specific queries."""
+
+    homepage = "https://github.com/MRCIEU/ieugwasr"
+    url = "https://github.com/MRCIEU/ieugwasr/archive/refs/tags/0.1.5.tar.gz"
+
+    version("0.1.5", sha256="8d900d5a780f23836c80191f9635fbf48a0ca94f828452948c0f445e3217f422")
+
+    depends_on("r@3.6.0:", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-googleauthr", type=("build", "run"))
+    depends_on("r-dplyr", type=("build", "run"))
+    depends_on("r-httr", type=("build", "run"))
+    depends_on("r-jsonlite", type=("build", "run"))

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

@@ -0,0 +1,29 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RIterpc(RPackage):
+    """Efficient Iterator for Permutations and Combinations.
+
+    Iterator for generating permutations and combinations. They can be either
+    drawn with or without replacement, or with distinct/ non-distinct items
+    (multiset). The generated sequences are in lexicographical order
+    (dictionary order). The algorithms to generate permutations and
+    combinations are memory efficient. These iterative algorithms enable users
+    to process all sequences without putting all results in the memory at the
+    same time. The algorithms are written in C/C++ for faster performance.
+    Note: 'iterpc' is no longer being maintained. Users are recommended to
+    switch to 'arrangements'."""
+
+    cran = "iterpc"
+
+    version("0.4.2", sha256="38bd464042a27536f676e889263eb2c257a431b59083f58cb54473f42ba2071b")
+
+    depends_on("r@3.0.0:", type=("build", "run"))
+    depends_on("r-iterators", type=("build", "run"))
+    depends_on("r-gmp@0.5-12:", type=("build", "run"))
+    depends_on("r-arrangements@1.0.0:", type=("build", "run"))

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

@@ -0,0 +1,32 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMendelianrandomization(RPackage):
+    """Mendelian Randomization Package.
+
+    Encodes several methods for performing Mendelian randomization analyses
+    with summarized data. Summarized data on genetic associations with the
+    exposure and with the outcome can be obtained from large consortia. These
+    data can be used for obtaining causal estimates using instrumental variable
+    methods."""
+
+    cran = "MendelianRandomization"
+
+    version("0.7.0", sha256="cad7cc1b6964fc7d299864378694c5fd947caa83796a1958e581299796b854c7")
+
+    depends_on("r@3.0.1:", type=("build", "run"))
+    depends_on("r-knitr", type=("build", "run"))
+    depends_on("r-rmarkdown", type=("build", "run"))
+    depends_on("r-plotly@3.6.0:", type=("build", "run"))
+    depends_on("r-ggplot2@1.0.1:", type=("build", "run"))
+    depends_on("r-robustbase@0.92-6:", type=("build", "run"))
+    depends_on("r-matrix@1.2:", type=("build", "run"))
+    depends_on("r-iterpc@0.3:", type=("build", "run"))
+    depends_on("r-quantreg@5.01:", type=("build", "run"))
+    depends_on("r-rjson", type=("build", "run"))
+    depends_on("r-glmnet", type=("build", "run"))

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

@@ -0,0 +1,33 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMeta(RPackage):
+    """General Package for Meta-Analysis.
+
+    User-friendly general package providing standard methods for meta-analysis
+    and supporting Schwarzer, Carpenter, and Rücker
+    <doi:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - common
+    effect and random effects meta-analysis; - several plots (forest, funnel,
+    Galbraith / radial, L'Abbe, Baujat, bubble); - three-level meta-analysis
+    model; - generalised linear mixed model; - Hartung-Knapp method for random
+    effects model; - Kenward-Roger method for random effects model; -
+    prediction interval; - statistical tests for funnel plot asymmetry; -
+    trim-and-fill method to evaluate bias in meta-analysis; - meta-regression;
+    - cumulative meta-analysis and leave-one-out meta-analysis; - import data
+    from 'RevMan 5'; - produce forest plot summarising several (subgroup)
+    meta-analyses."""
+
+    cran = "meta"
+
+    version("6.2-0", sha256="8ec8fb412996bbe17d3ca073f15c191a77bad486b08f39d7b8c2d07360ad5781")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-metafor@3.0-0:", type=("build", "run"))
+    depends_on("r-lme4", type=("build", "run"))
+    depends_on("r-compquadform", type=("build", "run"))
+    depends_on("r-xml2", type=("build", "run"))

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

@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMetadat(RPackage):
+    """Meta-Analysis Datasets.
+
+    A collection of meta-analysis datasets for teaching purposes,
+    illustrating/testing meta-analytic methods, and validating published
+    analyses."""
+
+    cran = "metadat"
+
+    version("1.2-0", sha256="f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-mathjaxr", type=("build", "run"))

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

@@ -0,0 +1,39 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMetafor(RPackage):
+    """Meta-Analysis Package for R.
+
+    A comprehensive collection of functions for conducting meta-analyses in R.
+    The package includes functions to calculate various effect sizes or outcome
+    measures, fit equal-, fixed-, random-, and mixed-effects models to such
+    data, carry out moderator and meta-regression analyses, and create various
+    types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe,
+    Baujat, bubble, and GOSH plots). For meta-analyses of binomial and
+    person-time data, the package also provides functions that implement
+    specialized methods, including the Mantel-Haenszel method, Peto's method,
+    and a variety of suitable generalized linear (mixed-effects) models (i.e.,
+    mixed-effects logistic and Poisson regression models). Finally, the package
+    provides functionality for fitting meta-analytic multivariate/multilevel
+    models that account for non-independent sampling errors and/or true effects
+    (e.g., due to the inclusion of multiple treatment studies, multiple
+    endpoints, or other forms of clustering). Network meta-analyses and
+    meta-analyses accounting for known correlation structures (e.g., due to
+    phylogenetic relatedness) can also be conducted. An introduction to the
+    package can be found in Viechtbauer (2010) <doi:10.18637/jss.v036.i03>."""
+
+    cran = "metafor"
+
+    version("3.8-1", sha256="d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514")
+
+    depends_on("r@4.0.0:", type=("build", "run"))
+    depends_on("r-matrix", type=("build", "run"))
+    depends_on("r-metadat", type=("build", "run"))
+    depends_on("r-nlme", type=("build", "run"))
+    depends_on("r-mathjaxr", type=("build", "run"))
+    depends_on("r-pbapply", type=("build", "run"))

var/spack/repos/builtin/packages/r-mr-raps/package.py

@@ -0,0 +1,24 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMrRaps(RPackage):
+    """Two Sample Mendelian Randomization using Robust Adjusted Profile Score.
+
+    Mendelian randomization is a method of identifying and estimating a
+    confounded causal effect using genetic instrumental variables. This
+    packages implements methods for two-sample Mendelian randomization with
+    summary statistics by using Robust Adjusted Profile Score (RAPS).
+    References: Qingyuan Zhao, Jingshu Wang, Jack Bowden, Dylan S. Small.
+    Statistical inference in two-sample summary-data Mendelian randomization
+    using robust adjusted profile score. <arXiv:1801.09652>."""
+
+    cran = "mr.raps"
+
+    version("0.2", sha256="c899f6143dac99e1232ff0a8d9f5fe099d4f69960782e6843db5b0d7f4f63b19")
+
+    depends_on("r-nortest", type=("build", "run"))

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

@@ -0,0 +1,19 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMrinstruments(RPackage):
+    """Data sources for genetic instruments to be used in MR.
+
+    Datasets of eQTLs, GWAS catalogs, etc."""
+
+    homepage = "https://github.com/MRCIEU/MRInstruments"
+    url = "https://github.com/MRCIEU/MRInstruments/archive/refs/tags/0.3.3.tar.gz"
+
+    version("0.3.3", sha256="4ddbaf6335133e8f7baef469d6bc1f89212462b9f4062c9e4ddda37b12eb3486")
+
+    depends_on("r@2.10:", type=("build", "run"))

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

@@ -0,0 +1,18 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMrmix(RPackage):
+    """Mendelian Randomization Analysis Using Mixture Models (MRMix).
+
+    This package gives robust estimation of causal effects by conducting
+    Mendelian randomization analysis using a mixture model approach."""
+
+    homepage = "https://github.com/gqi/MRMix"
+    git = "https://github.com/gqi/MRMix"
+
+    version("0.1.0", commit="56afdb2bc96760842405396f5d3f02e60e305039")

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

@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RMrpresso(RPackage):
+    """Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier
+    (MR-PRESSO) test.
+
+    MR-PRESSO (Mendelian Randomization Pleiotropy RESidual Sum and Outlier) is
+    a framework that allows for the evaluation of pleiotropy in
+    multi-instrument Mendelian Randomization utilizing genome-wide summary
+    association statistics."""
+
+    homepage = "https://github.com/rondolab/MR-PRESSO"
+    git = "https://github.com/rondolab/MR-PRESSO"
+
+    version("1.0", commit="cece763b47e59763a7916974de43c7cb93843e41")

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

@@ -0,0 +1,23 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RRadialmr(RPackage):
+    """RadialMR.
+
+    A package for implementing radial inverse variance weighted and MR-Egger
+    methods."""
+
+    homepage = "https://github.com/WSpiller/RadialMR"
+    git = "https://github.com/WSpiller/RadialMR"
+
+    version("1.0", commit="d63d3fc8270836ab441b9e14a5ba3eeb2795d7cb")
+
+    depends_on("r@3.5.0:", type=("build", "run"))
+    depends_on("r-ggplot2", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-plotly", type=("build", "run"))

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

@@ -0,0 +1,51 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RTwosamplemr(RPackage):
+    """Two Sample MR functions and interface to MR Base database.
+
+    A package for performing Mendelian randomization using GWAS summary data.
+    It uses the IEU GWAS database to obtain data automatically, and a wide
+    range of methods to run the analysis. You can use the MR-Base web app to
+    try out a limited range of the functionality in this package, but for any
+    serious work we strongly recommend using this R package."""
+
+    homepage = "https://mrcieu.github.io/TwoSampleMR/"
+    url = "https://github.com/MRCIEU/TwoSampleMR/archive/refs/tags/v0.5.6.tar.gz"
+
+    version("0.5.6", sha256="c63eb008ab7ed08a6f30ccbf0c299beb31b2f5835e5e2aa1b59c5e4fe284a30c")
+
+    depends_on("r@3.6.0:", type=("build", "run"))
+    depends_on("r-ieugwasr@0.1.5:", type=("build", "run"))
+    depends_on("r-ggplot2", type=("build", "run"))
+    depends_on("r-gridextra", type=("build", "run"))
+    depends_on("r-cowplot", type=("build", "run"))
+    depends_on("r-plyr", type=("build", "run"))
+    depends_on("r-reshape2", type=("build", "run"))
+    depends_on("r-stringr", type=("build", "run"))
+    depends_on("r-knitr", type=("build", "run"))
+    depends_on("r-markdown", type=("build", "run"))
+    depends_on("r-gtable", type=("build", "run"))
+    depends_on("r-rmarkdown", type=("build", "run"))
+    depends_on("r-mendelianrandomization", type=("build", "run"))
+    depends_on("r-dplyr", type=("build", "run"))
+    depends_on("r-mr-raps", type=("build", "run"))
+    depends_on("r-psych", type=("build", "run"))
+    depends_on("r-magrittr", type=("build", "run"))
+    depends_on("r-car", type=("build", "run"))
+    depends_on("r-randomforest", type=("build", "run"))
+    depends_on("r-meta", type=("build", "run"))
+    depends_on("r-data-table", type=("build", "run"))
+    depends_on("r-mrpresso", type=("build", "run"))
+    depends_on("r-mrinstruments", type=("build", "run"))
+    depends_on("r-radialmr", type=("build", "run"))
+    depends_on("r-mrmix", type=("build", "run"))
+    depends_on("r-glmnet", type=("build", "run"))
+    depends_on("r-lattice", type=("build", "run"))
+    depends_on("r-pbapply", type=("build", "run"))
+    depends_on("r-mass", type=("build", "run"))

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

@@ -17,7 +17,7 @@ class Warpx(CMakePackage):
     """
 
     homepage = "https://ecp-warpx.github.io"
-    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.01.tar.gz"
+    url = "https://github.com/ECP-WarpX/WarpX/archive/refs/tags/23.02.tar.gz"
     git = "https://github.com/ECP-WarpX/WarpX.git"
 
     maintainers("ax3l", "dpgrote", "MaxThevenet", "RemiLehe")
@@ -25,6 +25,7 @@ class Warpx(CMakePackage):
 
     # NOTE: if you update the versions here, also see py-warpx
     version("develop", branch="development")
+    version("23.02", sha256="a6c63ebc38cbd224422259a814be501ac79a3b734dab7f59500b6957cddaaac1")
     version("23.01", sha256="e853d01c20ea00c8ddedfa82a31a11d9d91a7f418d37d7f064cf8a241ea4da0c")
     version("22.12", sha256="96019902cd6ea444a1ae515e8853048e9074822c168021e4ec1687adc72ef062")
     version("22.11", sha256="528f65958f2f9e60a094e54eede698e871ccefc89fa103fe2a6f22e4a059515e")