Revert "Add command for reading a json-based DB description (#24894)" (#29603)

This reverts commit 531b1c5c3dcc9bc7bec27e223608aed477e94dbd.

14 files changed, 41 insertions, 712 deletions

diff --git a/lib/spack/spack/cmd/external.py b/lib/spack/spack/cmd/external.py
index 1c9c4d33bc..7e73572028 100644
--- a/lib/spack/spack/cmd/external.py
+++ b/lib/spack/spack/cmd/external.py
@@ -5,7 +5,6 @@
 from __future__ import print_function
 
 import argparse
-import os
 import sys
 
 import llnl.util.tty as tty
@@ -14,7 +13,6 @@ import llnl.util.tty.colify as colify
 import spack
 import spack.cmd
 import spack.cmd.common.arguments
-import spack.cray_manifest as cray_manifest
 import spack.detection
 import spack.error
 import spack.util.environment
@@ -57,31 +55,11 @@ def setup_parser(subparser):
         'list', help='list detectable packages, by repository and name'
     )
 
-    read_cray_manifest = sp.add_parser(
-        'read-cray-manifest', help=(
-            "consume a Spack-compatible description of externally-installed "
-            "packages, including dependency relationships"
-        )
-    )
-    read_cray_manifest.add_argument(
-        '--file', default=None,
-        help="specify a location other than the default")
-    read_cray_manifest.add_argument(
-        '--directory', default=None,
-        help="specify a directory storing a group of manifest files")
-    read_cray_manifest.add_argument(
-        '--dry-run', action='store_true', default=False,
-        help="don't modify DB with files that are read")
-
 
 def external_find(args):
     # If the user didn't specify anything, search for build tools by default
     if not args.tags and not args.all and not args.packages:
         args.tags = ['core-packages', 'build-tools']
-        # If the user calls 'spack external find' with no arguments, and
-        # this system has a description of installed packages, then we should
-        # consume it automatically.
-        _collect_and_consume_cray_manifest_files()
 
     # If the user specified both --all and --tag, then --all has precedence
     if args.all and args.tags:
@@ -126,52 +104,6 @@ def external_find(args):
         tty.msg('No new external packages detected')
 
 
-def external_read_cray_manifest(args):
-    _collect_and_consume_cray_manifest_files(
-        manifest_file=args.file,
-        manifest_directory=args.directory,
-        dry_run=args.dry_run
-    )
-
-
-def _collect_and_consume_cray_manifest_files(
-        manifest_file=None, manifest_directory=None, dry_run=False):
-
-    manifest_files = []
-    if manifest_file:
-        manifest_files.append(manifest_file)
-
-    manifest_dirs = []
-    if manifest_directory:
-        manifest_dirs.append(manifest_directory)
-
-    if os.path.isdir(cray_manifest.default_path):
-        tty.debug(
-            "Cray manifest path {0} exists: collecting all files to read."
-            .format(cray_manifest.default_path))
-        manifest_dirs.append(cray_manifest.default_path)
-    else:
-        tty.debug("Default Cray manifest directory {0} does not exist."
-                  .format(cray_manifest.default_path))
-
-    for directory in manifest_dirs:
-        for fname in os.listdir(directory):
-            manifest_files.append(os.path.join(directory, fname))
-
-    if not manifest_files:
-        raise ValueError(
-            "--file/--directory not specified, and no manifest found at {0}"
-            .format(cray_manifest.default_path))
-
-    for path in manifest_files:
-        try:
-            cray_manifest.read(path, not dry_run)
-        except (AssertionError, spack.error.SpackError):
-            # TODO: the AssertionError comes from class_for_compiler_name
-            # and should be transformed into a SpackError
-            tty.warn("Failure reading manifest file: {0}".format(path))
-
-
 def external_list(args):
     # Trigger a read of all packages, might take a long time.
     list(spack.repo.path.all_packages())
@@ -183,6 +115,5 @@ def external_list(args):
 
 
 def external(parser, args):
-    action = {'find': external_find, 'list': external_list,
-              'read-cray-manifest': external_read_cray_manifest}
+    action = {'find': external_find, 'list': external_list}
     action[args.external_command](args)
diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index ce3d6f7dab..d82cb7eb3f 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -62,14 +62,9 @@ def setup_parser(subparser):
         '-a', '--all', action='store_true', dest='all',
         help="remove ALL installed packages that match each supplied spec"
     )
-    subparser.add_argument(
-        '--origin', dest='origin',
-        help="only remove DB records with the specified origin"
-    )
 
 
-def find_matching_specs(env, specs, allow_multiple_matches=False, force=False,
-                        origin=None):
+def find_matching_specs(env, specs, allow_multiple_matches=False, force=False):
     """Returns a list of specs matching the not necessarily
        concretized specs given from cli
 
@@ -90,8 +85,8 @@ def find_matching_specs(env, specs, allow_multiple_matches=False, force=False,
     has_errors = False
     for spec in specs:
         install_query = [InstallStatuses.INSTALLED, InstallStatuses.DEPRECATED]
-        matching = spack.store.db.query_local(
-            spec, hashes=hashes, installed=install_query, origin=origin)
+        matching = spack.store.db.query_local(spec, hashes=hashes,
+                                              installed=install_query)
         # For each spec provided, make sure it refers to only one package.
         # Fail and ask user to be unambiguous if it doesn't
         if not allow_multiple_matches and len(matching) > 1:
@@ -245,8 +240,7 @@ def do_uninstall(env, specs, force):
 def get_uninstall_list(args, specs, env):
     # Gets the list of installed specs that match the ones give via cli
     # args.all takes care of the case where '-a' is given in the cli
-    uninstall_list = find_matching_specs(env, specs, args.all, args.force,
-                                         args.origin)
+    uninstall_list = find_matching_specs(env, specs, args.all, args.force)
 
     # Takes care of '-R'
     active_dpts, inactive_dpts = installed_dependents(uninstall_list, env)
diff --git a/lib/spack/spack/cray_manifest.py b/lib/spack/spack/cray_manifest.py
deleted file mode 100644
index c5a5c76ab4..0000000000
--- a/lib/spack/spack/cray_manifest.py
+++ /dev/null
@@ -1,162 +0,0 @@
-# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-import json
-
-import jsonschema
-import six
-
-import llnl.util.tty as tty
-
-import spack.cmd
-import spack.hash_types as hash_types
-from spack.schema.cray_manifest import schema as manifest_schema
-
-#: Cray systems can store a Spack-compatible description of system
-#: packages here.
-default_path = '/opt/cray/pe/cpe-descriptive-manifest/'
-
-
-def compiler_from_entry(entry):
-    compiler_name = entry['name']
-    paths = entry['executables']
-    version = entry['version']
-    arch = entry['arch']
-    operating_system = arch['os']
-    target = arch['target']
-
-    compiler_cls = spack.compilers.class_for_compiler_name(compiler_name)
-    spec = spack.spec.CompilerSpec(compiler_cls.name, version)
-    paths = [paths.get(x, None) for x in ('cc', 'cxx', 'f77', 'fc')]
-    return compiler_cls(
-        spec, operating_system, target, paths
-    )
-
-
-def spec_from_entry(entry):
-    arch_str = ""
-    if 'arch' in entry:
-        arch_format = "arch={platform}-{os}-{target}"
-        arch_str = arch_format.format(
-            platform=entry['arch']['platform'],
-            os=entry['arch']['platform_os'],
-            target=entry['arch']['target']['name']
-        )
-
-    compiler_str = ""
-    if 'compiler' in entry:
-        compiler_format  = "%{name}@{version}"
-        compiler_str = compiler_format.format(
-            name=entry['compiler']['name'],
-            version=entry['compiler']['version']
-        )
-
-    spec_format = "{name}@{version} {compiler} {arch}"
-    spec_str = spec_format.format(
-        name=entry['name'],
-        version=entry['version'],
-        compiler=compiler_str,
-        arch=arch_str
-    )
-
-    package = spack.repo.get(entry['name'])
-
-    if 'parameters' in entry:
-        variant_strs = list()
-        for name, value in entry['parameters'].items():
-            # TODO: also ensure that the variant value is valid?
-            if not (name in package.variants):
-                tty.debug("Omitting variant {0} for entry {1}/{2}"
-                          .format(name, entry['name'], entry['hash'][:7]))
-                continue
-
-            # Value could be a list (of strings), boolean, or string
-            if isinstance(value, six.string_types):
-                variant_strs.append('{0}={1}'.format(name, value))
-            else:
-                try:
-                    iter(value)
-                    variant_strs.append(
-                        '{0}={1}'.format(name, ','.join(value)))
-                    continue
-                except TypeError:
-                    # Not an iterable
-                    pass
-                # At this point not a string or collection, check for boolean
-                if value in [True, False]:
-                    bool_symbol = '+' if value else '~'
-                    variant_strs.append('{0}{1}'.format(bool_symbol, name))
-                else:
-                    raise ValueError(
-                        "Unexpected value for {0} ({1}): {2}".format(
-                            name, str(type(value)), str(value)
-                        )
-                    )
-        spec_str += ' ' + ' '.join(variant_strs)
-
-    spec, = spack.cmd.parse_specs(spec_str.split())
-
-    for ht in [hash_types.dag_hash, hash_types.build_hash,
-               hash_types.full_hash]:
-        setattr(spec, ht.attr, entry['hash'])
-
-    spec._concrete = True
-    spec._hashes_final = True
-    spec.external_path = entry['prefix']
-    spec.origin = 'external-db'
-    spack.spec.Spec.ensure_valid_variants(spec)
-
-    return spec
-
-
-def entries_to_specs(entries):
-    spec_dict = {}
-    for entry in entries:
-        try:
-            spec = spec_from_entry(entry)
-            spec_dict[spec._hash] = spec
-        except spack.repo.UnknownPackageError:
-            tty.debug("Omitting package {0}: no corresponding repo package"
-                      .format(entry['name']))
-        except spack.error.SpackError:
-            raise
-        except Exception:
-            tty.warn("Could not parse entry: " + str(entry))
-
-    for entry in filter(lambda x: 'dependencies' in x, entries):
-        dependencies = entry['dependencies']
-        for name, properties in dependencies.items():
-            dep_hash = properties['hash']
-            deptypes = properties['type']
-            if dep_hash in spec_dict:
-                if entry['hash'] not in spec_dict:
-                    continue
-                parent_spec = spec_dict[entry['hash']]
-                dep_spec = spec_dict[dep_hash]
-                parent_spec._add_dependency(dep_spec, deptypes)
-
-    return spec_dict
-
-
-def read(path, apply_updates):
-    with open(path, 'r') as json_file:
-        json_data = json.load(json_file)
-
-    jsonschema.validate(json_data, manifest_schema)
-
-    specs = entries_to_specs(json_data['specs'])
-    tty.debug("{0}: {1} specs read from manifest".format(
-        path,
-        str(len(specs))))
-    compilers = list(compiler_from_entry(x)
-                     for x in json_data['compilers'])
-    tty.debug("{0}: {1} compilers read from manifest".format(
-        path,
-        str(len(compilers))))
-    if apply_updates:
-        spack.compilers.add_compilers_to_config(
-            compilers, init_config=False)
-        for spec in specs.values():
-            spack.store.db.add(spec, directory_layout=None)
diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index 6a16a83e1c..3c7258728f 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -187,7 +187,6 @@ class InstallRecord(object):
             installation_time=None,
             deprecated_for=None,
             in_buildcache=False,
-            origin=None
     ):
         self.spec = spec
         self.path = str(path) if path else None
@@ -197,7 +196,6 @@ class InstallRecord(object):
         self.installation_time = installation_time or _now()
         self.deprecated_for = deprecated_for
         self.in_buildcache = in_buildcache
-        self.origin = origin
 
     def install_type_matches(self, installed):
         installed = InstallStatuses.canonicalize(installed)
@@ -219,9 +217,6 @@ class InstallRecord(object):
             else:
                 rec_dict.update({field_name: getattr(self, field_name)})
 
-        if self.origin:
-            rec_dict['origin'] = self.origin
-
         return rec_dict
 
     @classmethod
@@ -1136,10 +1131,6 @@ class Database(object):
                 'explicit': explicit,
                 'installation_time': installation_time
             }
-            # Commands other than 'spack install' may add specs to the DB,
-            # we can record the source of an installed Spec with 'origin'
-            if hasattr(spec, 'origin'):
-                extra_args['origin'] = spec.origin
             self._data[key] = InstallRecord(
                 new_spec, path, installed, ref_count=0, **extra_args
             )
@@ -1471,7 +1462,6 @@ class Database(object):
             end_date=None,
             hashes=None,
             in_buildcache=any,
-            origin=None
     ):
         """Run a query on the database."""
 
@@ -1500,9 +1490,6 @@ class Database(object):
             if hashes is not None and rec.spec.dag_hash() not in hashes:
                 continue
 
-            if origin and not (origin == rec.origin):
-                continue
-
             if not rec.install_type_matches(installed):
                 continue
 
diff --git a/lib/spack/spack/schema/cray_manifest.py b/lib/spack/spack/schema/cray_manifest.py
deleted file mode 100644
index 0bde78612f..0000000000
--- a/lib/spack/spack/schema/cray_manifest.py
+++ /dev/null
@@ -1,130 +0,0 @@
-# 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)
-
-"""Schema for Cray descriptive manifest: this describes a set of
-   installed packages on the system and also specifies dependency
-   relationships between them (so this provides more information than
-   external entries in packages configuration).
-
-   This does not specify a configuration - it is an input format
-   that is consumed and transformed into Spack DB records.
-"""
-
-schema = {
-    "$schema": "http://json-schema.org/schema#",
-    "title": "CPE manifest schema",
-    "type": "object",
-    "additionalProperties": False,
-    "properties": {
-        "_meta": {
-            "type": "object",
-            "additionalProperties": False,
-            "properties": {
-                "file-type": {"type": "string", "minLength": 1},
-                "version": {"type": "string", "minLength": 1},
-                "system-type": {"type": "string", "minLength": 1}
-            }
-        },
-        "compilers": {
-            "type": "array",
-            "items": {
-                "type": "object",
-                "additionalProperties": False,
-                "properties": {
-                    "name": {"type": "string", "minLength": 1},
-                    "version": {"type": "string", "minLength": 1},
-                    "prefix": {"type": "string", "minLength": 1},
-                    "executables": {
-                        "type": "object",
-                        "additionalProperties": False,
-                        "properties": {
-                            "cc": {"type": "string", "minLength": 1},
-                            "cxx": {"type": "string", "minLength": 1},
-                            "fc": {"type": "string", "minLength": 1}
-                        }
-                    },
-                    "arch": {
-                        "type": "object",
-                        "required": ["os", "target"],
-                        "additionalProperties": False,
-                        "properties": {
-                            "os": {"type": "string", "minLength": 1},
-                            "target": {"type": "string", "minLength": 1}
-                        }
-                    }
-                }
-            }
-        },
-        "specs": {
-            "type": "array",
-            "items": {
-                "type": "object",
-                "required": [
-                    "name",
-                    "version",
-                    "arch",
-                    "compiler",
-                    "prefix",
-                    "hash"],
-                "additionalProperties": False,
-                "properties": {
-                    "name": {"type": "string", "minLength": 1},
-                    "version": {"type": "string", "minLength": 1},
-                    "arch": {
-                        "type": "object",
-                        "required": ["platform", "platform_os", "target"],
-                        "additioanlProperties": False,
-                        "properties": {
-                            "platform": {"type": "string", "minLength": 1},
-                            "platform_os": {"type": "string", "minLength": 1},
-                            "target": {
-                                "type": "object",
-                                "additionalProperties": False,
-                                "required": ["name"],
-                                "properties": {
-                                    "name": {"type": "string", "minLength": 1}
-                                }
-                            }
-                        }
-                    },
-                    "compiler": {
-                        "type": "object",
-                        "required": ["name", "version"],
-                        "additionalProperties": False,
-                        "properties": {
-                            "name": {"type": "string", "minLength": 1},
-                            "version": {"type": "string", "minLength": 1}
-                        }
-                    },
-                    "dependencies": {
-                        "type": "object",
-                        "patternProperties": {
-                            "\\w[\\w-]*": {
-                                "type": "object",
-                                "required": ["hash"],
-                                "additionalProperties": False,
-                                "properties": {
-                                    "hash": {"type": "string", "minLength": 1},
-                                    "type": {
-                                        "type": "array",
-                                        "items": {
-                                            "type": "string", "minLength": 1}
-                                    }
-                                }
-                            }
-                        }
-                    },
-                    "prefix": {
-                        "type": "string", "minLength": 1},
-                    "rpm": {"type": "string", "minLength": 1},
-                    "hash": {"type": "string", "minLength": 1},
-                    "parameters": {
-                        "type": "object",
-                    }
-                }
-            }
-        }
-    }
-}
diff --git a/lib/spack/spack/solver/asp.py b/lib/spack/spack/solver/asp.py
index 85a3c28b4c..89c9108fc1 100644
--- a/lib/spack/spack/solver/asp.py
+++ b/lib/spack/spack/solver/asp.py
@@ -1505,12 +1505,9 @@ class SpackSolverSetup(object):
                     continue
 
                 if strict and s.compiler not in cspecs:
-                    if not s.concrete:
-                        raise spack.concretize.UnavailableCompilerVersionError(
-                            s.compiler
-                        )
-                    # Allow unknown compilers to exist if the associated spec
-                    # is already built
+                    raise spack.concretize.UnavailableCompilerVersionError(
+                        s.compiler
+                    )
                 else:
                     cspecs.add(s.compiler)
                     self.gen.fact(fn.allow_compiler(
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 468c781b28..b4c778ee76 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -2911,7 +2911,7 @@ class Spec(object):
                 if a list of names activate them for the packages in the list,
                 if True activate 'test' dependencies for all packages.
         """
-        clone = self.copy()
+        clone = self.copy(caches=True)
         clone.concretize(tests=tests)
         return clone
 
@@ -3210,8 +3210,8 @@ class Spec(object):
                 "Attempting to normalize anonymous spec")
 
         # Set _normal and _concrete to False when forced
-        if force and not self._concrete:
-            self._normal = False
+        if force:
+            self._mark_concrete(False)
 
         if self._normal:
             return False
@@ -3680,7 +3680,7 @@ class Spec(object):
 
         return patches
 
-    def _dup(self, other, deps=True, cleardeps=True):
+    def _dup(self, other, deps=True, cleardeps=True, caches=None):
         """Copy the spec other into self.  This is an overwriting
         copy. It does not copy any dependents (parents), but by default
         copies dependencies.
@@ -3695,6 +3695,10 @@ class Spec(object):
             cleardeps (bool): if True clears the dependencies of ``self``,
                 before possibly copying the dependencies of ``other`` onto
                 ``self``
+            caches (bool or None): preserve cached fields such as
+                ``_normal``, ``_hash``, and ``_dunder_hash``. By
+                default this is ``False`` if DAG structure would be
+                changed by the copy, ``True`` if it's an exact copy.
 
         Returns:
             True if ``self`` changed because of the copy operation,
@@ -3745,6 +3749,12 @@ class Spec(object):
         self.extra_attributes = other.extra_attributes
         self.namespace = other.namespace
 
+        # Cached fields are results of expensive operations.
+        # If we preserved the original structure, we can copy them
+        # safely. If not, they need to be recomputed.
+        if caches is None:
+            caches = (deps is True or deps == dp.all_deptypes)
+
         # If we copy dependencies, preserve DAG structure in the new spec
         if deps:
             # If caller restricted deptypes to be copied, adjust that here.
@@ -3752,31 +3762,29 @@ class Spec(object):
             deptypes = dp.all_deptypes
             if isinstance(deps, (tuple, list)):
                 deptypes = deps
-            self._dup_deps(other, deptypes)
+            self._dup_deps(other, deptypes, caches)
 
         self._concrete = other._concrete
         self._hashes_final = other._hashes_final
 
-        if self._concrete:
+        if caches:
             self._hash = other._hash
             self._build_hash = other._build_hash
             self._dunder_hash = other._dunder_hash
-            self._normal = True
+            self._normal = other._normal
             self._full_hash = other._full_hash
             self._package_hash = other._package_hash
         else:
             self._hash = None
             self._build_hash = None
             self._dunder_hash = None
-            # Note, we could use other._normal if we are copying all deps, but
-            # always set it False here to avoid the complexity of checking
             self._normal = False
             self._full_hash = None
             self._package_hash = None
 
         return changed
 
-    def _dup_deps(self, other, deptypes):
+    def _dup_deps(self, other, deptypes, caches):
         def spid(spec):
             return id(spec)
 
@@ -3787,11 +3795,11 @@ class Spec(object):
 
             if spid(edge.parent) not in new_specs:
                 new_specs[spid(edge.parent)] = edge.parent.copy(
-                    deps=False
+                    deps=False, caches=caches
                 )
 
             if spid(edge.spec) not in new_specs:
-                new_specs[spid(edge.spec)] = edge.spec.copy(deps=False)
+                new_specs[spid(edge.spec)] = edge.spec.copy(deps=False, caches=caches)
 
             new_specs[spid(edge.parent)].add_dependency_edge(
                 new_specs[spid(edge.spec)], edge.deptypes
@@ -4627,19 +4635,22 @@ class Spec(object):
         # _dependents of these specs should not be trusted.
         # Variants may also be ignored here for now...
 
+        # Keep all cached hashes because we will invalidate the ones that need
+        # invalidating later, and we don't want to invalidate unnecessarily
+
         if transitive:
-            self_nodes = dict((s.name, s.copy(deps=False))
+            self_nodes = dict((s.name, s.copy(deps=False, caches=True))
                               for s in self.traverse(root=True)
                               if s.name not in other)
-            other_nodes = dict((s.name, s.copy(deps=False))
+            other_nodes = dict((s.name, s.copy(deps=False, caches=True))
                                for s in other.traverse(root=True))
         else:
             # If we're not doing a transitive splice, then we only want the
             # root of other.
-            self_nodes = dict((s.name, s.copy(deps=False))
+            self_nodes = dict((s.name, s.copy(deps=False, caches=True))
                               for s in self.traverse(root=True)
                               if s.name != other.name)
-            other_nodes = {other.name: other.copy(deps=False)}
+            other_nodes = {other.name: other.copy(deps=False, caches=True)}
 
         nodes = other_nodes.copy()
         nodes.update(self_nodes)
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index d5c7177e41..c946898076 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -788,16 +788,7 @@ def database(mock_store, mock_packages, config):
 
 
 @pytest.fixture(scope='function')
-def database_mutable_config(mock_store, mock_packages, mutable_config,
-                            monkeypatch):
-    """This activates the mock store, packages, AND config."""
-    with spack.store.use_store(str(mock_store)) as store:
-        yield store.db
-        store.db.last_seen_verifier = ''
-
-
-@pytest.fixture(scope='function')
-def mutable_database(database_mutable_config, _store_dir_and_cache):
+def mutable_database(database, _store_dir_and_cache):
     """Writeable version of the fixture, restored to its initial state
     after each test.
     """
@@ -805,7 +796,7 @@ def mutable_database(database_mutable_config, _store_dir_and_cache):
     store_path, store_cache = _store_dir_and_cache
     store_path.join('.spack-db').chmod(mode=0o755, rec=1)
 
-    yield database_mutable_config
+    yield database
 
     # Restore the initial state by copying the content of the cache back into
     # the store and making the database read-only
diff --git a/lib/spack/spack/test/cray_manifest.py b/lib/spack/spack/test/cray_manifest.py
deleted file mode 100644
index c551f12f27..0000000000
--- a/lib/spack/spack/test/cray_manifest.py
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-import json
-
-import pytest
-
-import spack
-import spack.cray_manifest as cray_manifest
-from spack.cray_manifest import compiler_from_entry, entries_to_specs
-
-example_x_json_str = """\
-{
-  "name": "packagex",
-  "hash": "hash-of-x",
-  "prefix": "/path/to/packagex-install/",
-  "version": "1.0",
-  "arch": {
-    "platform": "linux",
-    "platform_os": "centos8",
-    "target": {
-      "name": "haswell"
-    }
-  },
-  "compiler": {
-    "name": "gcc",
-    "version": "10.2.0"
-  },
-  "dependencies": {
-    "packagey": {
-      "hash": "hash-of-y",
-      "type": ["link"]
-    }
-  },
-  "parameters": {
-    "precision": ["double", "float"]
-  }
-}
-"""
-
-
-example_compiler_entry = """\
-{
-  "name": "gcc",
-  "prefix": "/path/to/compiler/",
-  "version": "7.5.0",
-  "arch": {
-    "os": "centos8",
-    "target": "x86_64"
-  },
-  "executables": {
-    "cc": "/path/to/compiler/cc",
-    "cxx": "/path/to/compiler/cxx",
-    "fc": "/path/to/compiler/fc"
-  }
-}
-"""
-
-
-class JsonSpecEntry(object):
-    def __init__(self, name, hash, prefix, version, arch, compiler,
-                 dependencies, parameters):
-        self.name = name
-        self.hash = hash
-        self.prefix = prefix
-        self.version = version
-        self.arch = arch
-        self.compiler = compiler
-        self.dependencies = dependencies
-        self.parameters = parameters
-
-    def to_dict(self):
-        return {
-            'name': self.name,
-            'hash': self.hash,
-            'prefix': self.prefix,
-            'version': self.version,
-            'arch': self.arch,
-            'compiler': self.compiler,
-            'dependencies': self.dependencies,
-            'parameters': self.parameters
-        }
-
-    def as_dependency(self, deptypes):
-        return (self.name,
-                {'hash': self.hash,
-                 'type': list(deptypes)})
-
-
-class JsonArchEntry(object):
-    def __init__(self, platform, os, target):
-        self.platform = platform
-        self.os = os
-        self.target = target
-
-    def to_dict(self):
-        return {
-            'platform': self.platform,
-            'platform_os': self.os,
-            'target': {
-                'name': self.target
-            }
-        }
-
-
-class JsonCompilerEntry(object):
-    def __init__(self, name, version):
-        self.name = name
-        self.version = version
-
-    def to_dict(self):
-        return {
-            'name': self.name,
-            'version': self.version
-        }
-
-
-_common_arch = JsonArchEntry(
-    platform='linux',
-    os='centos8',
-    target='haswell'
-).to_dict()
-
-
-_common_compiler = JsonCompilerEntry(
-    name='gcc',
-    version='10.2.0'
-).to_dict()
-
-
-def test_compatibility():
-    """Make sure that JsonSpecEntry outputs the expected JSON structure
-       by comparing it with JSON parsed from an example string. This
-       ensures that the testing objects like JsonSpecEntry produce the
-       same JSON structure as the expected file format.
-    """
-    y = JsonSpecEntry(
-        name='packagey',
-        hash='hash-of-y',
-        prefix='/path/to/packagey-install/',
-        version='1.0',
-        arch=_common_arch,
-        compiler=_common_compiler,
-        dependencies={},
-        parameters={}
-    )
-
-    x = JsonSpecEntry(
-        name='packagex',
-        hash='hash-of-x',
-        prefix='/path/to/packagex-install/',
-        version='1.0',
-        arch=_common_arch,
-        compiler=_common_compiler,
-        dependencies=dict([y.as_dependency(deptypes=['link'])]),
-        parameters={'precision': ['double', 'float']}
-    )
-
-    x_from_entry = x.to_dict()
-    x_from_str = json.loads(example_x_json_str)
-    assert x_from_entry == x_from_str
-
-
-def test_compiler_from_entry():
-    compiler_data = json.loads(example_compiler_entry)
-    compiler_from_entry(compiler_data)
-
-
-def generate_openmpi_entries():
-    """Generate two example JSON entries that refer to an OpenMPI
-       installation and a hwloc dependency.
-    """
-    # The hashes need to be padded with 'a' at the end to align with 8-byte
-    # boundaries (for base-32 decoding)
-    hwloc = JsonSpecEntry(
-        name='hwloc',
-        hash='hwlocfakehashaaa',
-        prefix='/path/to/hwloc-install/',
-        version='2.0.3',
-        arch=_common_arch,
-        compiler=_common_compiler,
-        dependencies={},
-        parameters={}
-    )
-
-    # This includes a variant which is guaranteed not to appear in the
-    # OpenMPI package: we need to make sure we can use such package
-    # descriptions.
-    openmpi = JsonSpecEntry(
-        name='openmpi',
-        hash='openmpifakehasha',
-        prefix='/path/to/openmpi-install/',
-        version='4.1.0',
-        arch=_common_arch,
-        compiler=_common_compiler,
-        dependencies=dict([hwloc.as_dependency(deptypes=['link'])]),
-        parameters={
-            'internal-hwloc': False,
-            'fabrics': ['psm'],
-            'missing_variant': True
-        }
-    )
-
-    return [openmpi, hwloc]
-
-
-def test_spec_conversion():
-    """Given JSON entries, check that we can form a set of Specs
-       including dependency references.
-    """
-    entries = list(x.to_dict() for x in generate_openmpi_entries())
-    specs = entries_to_specs(entries)
-    openmpi_spec, = list(x for x in specs.values() if x.name == 'openmpi')
-    assert openmpi_spec['hwloc']
-
-
-def _example_db():
-    return {
-        'specs': list(x.to_dict() for x in generate_openmpi_entries()),
-        'compilers': []
-    }
-
-
-def test_read_cray_manifest(
-        tmpdir, mutable_config, mock_packages, mutable_database):
-    """Check that (a) we can read the cray manifest and add it to the Spack
-       Database and (b) we can concretize specs based on that.
-    """
-    if spack.config.get('config:concretizer') == 'clingo':
-        pytest.skip("The ASP-based concretizer currently doesn't support"
-                    " dependency hash references - see #22613")
-
-    with tmpdir.as_cwd():
-        test_db_fname = 'external-db.json'
-        with open(test_db_fname, 'w') as db_file:
-            json.dump(_example_db(), db_file)
-        cray_manifest.read(test_db_fname, True)
-        query_specs = spack.store.db.query('openmpi')
-        assert any(x.dag_hash() == 'openmpifakehasha' for x in query_specs)
-
-        concretized_specs = spack.cmd.parse_specs(
-            'depends-on-openmpi %gcc@4.5.0 arch=test-redhat6-x86_64'
-            ' ^/openmpifakehasha'.split(),
-            concretize=True)
-        assert concretized_specs[0]['hwloc'].dag_hash() == 'hwlocfakehashaaa'
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index aea298b2d0..046ff7aad2 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -599,6 +599,8 @@ class TestSpecDag(object):
 
         assert orig == copy
         assert orig.eq_dag(copy)
+        assert orig._normal == copy._normal
+        assert orig._concrete == copy._concrete
 
         # ensure no shared nodes bt/w orig and copy.
         orig_ids = set(id(s) for s in orig.traverse())
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 7bbb3ba211..9e4586abbb 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -1017,7 +1017,7 @@ _spack_external() {
     then
         SPACK_COMPREPLY="-h --help"
     else
-        SPACK_COMPREPLY="find list read-cray-manifest"
+        SPACK_COMPREPLY="find list"
     fi
 }
 
@@ -1034,10 +1034,6 @@ _spack_external_list() {
     SPACK_COMPREPLY="-h --help"
 }
 
-_spack_external_read_cray_manifest() {
-    SPACK_COMPREPLY="-h --help --file --directory --dry-run"
-}
-
 _spack_fetch() {
     if $list_options
     then
@@ -1795,7 +1791,7 @@ _spack_undevelop() {
 _spack_uninstall() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -f --force -R --dependents -y --yes-to-all -a --all --origin"
+        SPACK_COMPREPLY="-h --help -f --force -R --dependents -y --yes-to-all -a --all"
     else
         _installed_packages
     fi
diff --git a/var/spack/repos/builtin.mock/packages/depends-on-openmpi/package.py b/var/spack/repos/builtin.mock/packages/depends-on-openmpi/package.py
deleted file mode 100644
index ff3ee9057c..0000000000
--- a/var/spack/repos/builtin.mock/packages/depends-on-openmpi/package.py
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class DependsOnOpenmpi(Package):
-    """For testing concretization of packages that use
-       `spack external read-cray-manifest`"""
-
-    depends_on('openmpi')
-
-    version('1.0')
-    version('0.9')
diff --git a/var/spack/repos/builtin.mock/packages/hwloc/package.py b/var/spack/repos/builtin.mock/packages/hwloc/package.py
deleted file mode 100644
index 2cd984f438..0000000000
--- a/var/spack/repos/builtin.mock/packages/hwloc/package.py
+++ /dev/null
@@ -1,10 +0,0 @@
-# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Hwloc(Package):
-    version('2.0.3')
diff --git a/var/spack/repos/builtin.mock/packages/openmpi/package.py b/var/spack/repos/builtin.mock/packages/openmpi/package.py
deleted file mode 100644
index 0d02c314a6..0000000000
--- a/var/spack/repos/builtin.mock/packages/openmpi/package.py
+++ /dev/null
@@ -1,15 +0,0 @@
-# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
-#
-# SPDX-License-Identifier: (Apache-2.0 OR MIT)
-
-from spack import *
-
-
-class Openmpi(Package):
-    version('4.1.1')
-
-    variant('internal-hwloc', default=False)
-    variant('fabrics', values=any_combination_of('psm', 'mxm'))
-
-    depends_on('hwloc', when="~internal-hwloc")