cairo: import spack.build_systems

.github/workflows/coverage.yml

@@ -29,7 +29,7 @@ jobs:
     - run: coverage xml
 
     - name: "Upload coverage report to CodeCov"
-      uses: codecov/codecov-action@1e68e06f1dbfde0e4cefc87efeba9e4643565303
+      uses: codecov/codecov-action@05f5a9cfad807516dbbef9929c4a42df3eb78766
       with:
         verbose: true
         fail_ci_if_error: false

.github/workflows/requirements/style/requirements.txt

@@ -2,6 +2,6 @@ black==24.10.0
 clingo==5.7.1
 flake8==7.1.1
 isort==5.13.2
-mypy==1.11.2
+mypy==1.8.0
 types-six==1.17.0.20241205
 vermin==1.6.0

.github/workflows/valid-style.yml

@@ -20,7 +20,7 @@ jobs:
     - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683
     - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
       with:
-        python-version: '3.13'
+        python-version: '3.11'
         cache: 'pip'
     - name: Install Python Packages
       run: |
@@ -39,7 +39,7 @@ jobs:
         fetch-depth: 0
     - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b
       with:
-        python-version: '3.13'
+        python-version: '3.11'
         cache: 'pip'
     - name: Install Python packages
       run: |
@@ -58,7 +58,7 @@ jobs:
     secrets: inherit
     with:
       with_coverage: ${{ inputs.with_coverage }}
-      python_version: '3.13'
+      python_version: '3.11'
   # Check that spack can bootstrap the development environment on Python 3.6 - RHEL8
   bootstrap-dev-rhel8:
     runs-on: ubuntu-latest

bin/spack

@@ -25,6 +25,7 @@ exit 1
 # The code above runs this file with our preferred python interpreter.
 
 import os
+import os.path
 import sys
 
 min_python3 = (3, 6)

etc/spack/defaults/packages.yaml

@@ -36,7 +36,7 @@ packages:
       go-or-gccgo-bootstrap: [go-bootstrap, gcc]
       iconv: [libiconv]
       ipp: [intel-oneapi-ipp]
-      java: [openjdk, jdk]
+      java: [openjdk, jdk, ibm-java]
       jpeg: [libjpeg-turbo, libjpeg]
       lapack: [openblas, amdlibflame]
       libc: [glibc, musl]
@@ -73,27 +73,15 @@ packages:
     permissions:
       read: world
       write: user
-  cray-fftw:
-    buildable: false
-  cray-libsci:
-    buildable: false
   cray-mpich:
     buildable: false
   cray-mvapich2:
     buildable: false
-  cray-pmi:
-    buildable: false
   egl:
     buildable: false
-  essl:
-    buildable: false
   fujitsu-mpi:
     buildable: false
-  fujitsu-ssl2:
-    buildable: false
   hpcx-mpi:
     buildable: false
-  mpt:
-    buildable: false
   spectrum-mpi:
     buildable: false

lib/spack/docs/bootstrapping.rst

@@ -170,7 +170,7 @@ bootstrapping.
    To register the mirror on the platform where it's supposed to be used run the following command(s):
      % spack bootstrap add --trust local-sources /opt/bootstrap/metadata/sources
      % spack bootstrap add --trust local-binaries /opt/bootstrap/metadata/binaries
-     % spack buildcache update-index /opt/bootstrap/bootstrap_cache
+
 
 This command needs to be run on a machine with internet access and the resulting folder
 has to be moved over to the air-gapped system. Once the local sources are added using the

lib/spack/docs/build_systems/custompackage.rst

@@ -56,13 +56,13 @@ If you look at the ``perl`` package, you'll see:
 
 .. code-block:: python
 
-   phases = ("configure", "build", "install")
+   phases = ["configure", "build", "install"]
 
 Similarly, ``cmake`` defines:
 
 .. code-block:: python
 
-   phases = ("bootstrap", "build", "install")
+   phases = ["bootstrap", "build", "install"]
 
 If we look at the ``cmake`` example, this tells Spack's ``PackageBase``
 class to run the ``bootstrap``, ``build``, and ``install`` functions

lib/spack/docs/developer_guide.rst

@@ -543,10 +543,10 @@ With either interpreter you can run a single command:
 
 .. code-block:: console
 
-   $ spack python -c 'from spack.concretize import concretize_one; concretize_one("python")'
+   $ spack python -c 'from spack.spec import Spec; Spec("python").concretized()'
    ...
 
-   $ spack python -i ipython -c 'from spack.concretize import concretize_one; concretize_one("python")'
+   $ spack python -i ipython -c 'from spack.spec import Spec; Spec("python").concretized()'
    Out[1]: ...
 
 or a file:

lib/spack/docs/module_file_support.rst

@@ -456,13 +456,14 @@ For instance, the following config options,
        tcl:
          all:
            suffixes:
-             ^python@3: 'python{^python.version.up_to_2}'
+             ^python@3: 'python{^python.version}'
              ^openblas: 'openblas'
 
-will add a ``python3.12`` to module names of packages compiled with Python 3.12, and similarly for
-all specs depending on ``python@3``. This is useful to know which version of Python a set of Python
-extensions is associated with. Likewise, the ``openblas`` string is attached to any program that
-has openblas in the spec, most likely via the ``+blas`` variant specification.
+will add a ``python-3.12.1`` version string to any packages compiled with
+Python matching the spec, ``python@3``. This is useful to know which
+version of Python a set of Python extensions is associated with. Likewise, the
+``openblas`` string is attached to any program that has openblas in the spec,
+most likely via the ``+blas`` variant specification.
 
 The most heavyweight solution to module naming is to change the entire
 naming convention for module files. This uses the projections format

lib/spack/docs/requirements.txt

@@ -4,7 +4,7 @@ sphinx_design==0.6.1
 sphinx-rtd-theme==3.0.2
 python-levenshtein==0.26.1
 docutils==0.21.2
-pygments==2.19.1
+pygments==2.18.0
 urllib3==2.3.0
 pytest==8.3.4
 isort==5.13.2

lib/spack/llnl/url.py

@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """URL primitives that just require Python standard library."""
 import itertools
-import os
+import os.path
 import re
 from typing import Optional, Set, Tuple
 from urllib.parse import urlsplit, urlunsplit

lib/spack/llnl/util/filesystem.py

@@ -75,6 +75,7 @@
     "install_tree",
     "is_exe",
     "join_path",
+    "last_modification_time_recursive",
     "library_extensions",
     "mkdirp",
     "partition_path",
@@ -1469,36 +1470,15 @@ def set_executable(path):
 
 
 @system_path_filter
-def recursive_mtime_greater_than(path: str, time: float) -> bool:
-    """Returns true if any file or dir recursively under `path` has mtime greater than `time`."""
-    # use bfs order to increase likelihood of early return
-    queue: Deque[str] = collections.deque([path])
-
-    if os.stat(path).st_mtime > time:
-        return True
-
-    while queue:
-        current = queue.popleft()
-
-        try:
-            entries = os.scandir(current)
-        except OSError:
-            continue
-
-        with entries:
-            for entry in entries:
-                try:
-                    st = entry.stat(follow_symlinks=False)
-                except OSError:
-                    continue
-
-                if st.st_mtime > time:
-                    return True
-
-                if entry.is_dir(follow_symlinks=False):
-                    queue.append(entry.path)
-
-    return False
+def last_modification_time_recursive(path):
+    path = os.path.abspath(path)
+    times = [os.stat(path).st_mtime]
+    times.extend(
+        os.lstat(os.path.join(root, name)).st_mtime
+        for root, dirs, files in os.walk(path)
+        for name in dirs + files
+    )
+    return max(times)
 
 
 @system_path_filter
@@ -1760,7 +1740,8 @@ def find(
 
 
 def _log_file_access_issue(e: OSError, path: str) -> None:
-    tty.debug(f"find must skip {path}: {e}")
+    errno_name = errno.errorcode.get(e.errno, "UNKNOWN")
+    tty.debug(f"find must skip {path}: {errno_name} {e}")
 
 
 def _file_id(s: os.stat_result) -> Tuple[int, int]:

lib/spack/spack/audit.py

@@ -1356,8 +1356,14 @@ def _test_detection_by_executable(pkgs, debug_log, error_cls):
 
             def _compare_extra_attribute(_expected, _detected, *, _spec):
                 result = []
+                # Check items are of the same type
+                if not isinstance(_detected, type(_expected)):
+                    _summary = f'{pkg_name}: error when trying to detect "{_expected}"'
+                    _details = [f"{_detected} was detected instead"]
+                    return [error_cls(summary=_summary, details=_details)]
+
                 # If they are string expected is a regex
-                if isinstance(_expected, str) and isinstance(_detected, str):
+                if isinstance(_expected, str):
                     try:
                         _regex = re.compile(_expected)
                     except re.error:
@@ -1373,7 +1379,7 @@ def _compare_extra_attribute(_expected, _detected, *, _spec):
                         _details = [f"{_detected} does not match the regex"]
                         return [error_cls(summary=_summary, details=_details)]
 
-                elif isinstance(_expected, dict) and isinstance(_detected, dict):
+                if isinstance(_expected, dict):
                     _not_detected = set(_expected.keys()) - set(_detected.keys())
                     if _not_detected:
                         _summary = f"{pkg_name}: cannot detect some attributes for spec {_spec}"
@@ -1388,10 +1394,6 @@ def _compare_extra_attribute(_expected, _detected, *, _spec):
                         result.extend(
                             _compare_extra_attribute(_expected[_key], _detected[_key], _spec=_spec)
                         )
-                else:
-                    _summary = f'{pkg_name}: error when trying to detect "{_expected}"'
-                    _details = [f"{_detected} was detected instead"]
-                    return [error_cls(summary=_summary, details=_details)]
 
                 return result
 

lib/spack/spack/binary_distribution.py

@@ -5,7 +5,6 @@
 import codecs
 import collections
 import concurrent.futures
-import contextlib
 import copy
 import hashlib
 import io
@@ -24,7 +23,7 @@
 import urllib.request
 import warnings
 from contextlib import closing
-from typing import IO, Callable, Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
+from typing import IO, Dict, Iterable, List, NamedTuple, Optional, Set, Tuple, Union
 
 import llnl.util.filesystem as fsys
 import llnl.util.lang
@@ -92,9 +91,6 @@
 CURRENT_BUILD_CACHE_LAYOUT_VERSION = 2
 
 
-INDEX_HASH_FILE = "index.json.hash"
-
-
 class BuildCacheDatabase(spack_db.Database):
     """A database for binary buildcaches.
 
@@ -506,7 +502,7 @@ def _fetch_and_cache_index(self, mirror_url, cache_entry={}):
         scheme = urllib.parse.urlparse(mirror_url).scheme
 
         if scheme != "oci" and not web_util.url_exists(
-            url_util.join(mirror_url, BUILD_CACHE_RELATIVE_PATH, spack_db.INDEX_JSON_FILE)
+            url_util.join(mirror_url, BUILD_CACHE_RELATIVE_PATH, "index.json")
         ):
             return False
 
@@ -595,18 +591,32 @@ def file_matches(f: IO[bytes], regex: llnl.util.lang.PatternBytes) -> bool:
         f.seek(0)
 
 
-def specs_to_relocate(spec: spack.spec.Spec) -> List[spack.spec.Spec]:
-    """Return the set of specs that may be referenced in the install prefix of the provided spec.
-    We currently include non-external transitive link and direct run dependencies."""
-    specs = [
+def deps_to_relocate(spec):
+    """Return the transitive link and direct run dependencies of the spec.
+
+    This is a special traversal for dependencies we need to consider when relocating a package.
+
+    Package binaries, scripts, and other files may refer to the prefixes of  dependencies, so
+    we need to rewrite those locations when dependencies are in a different place at install time
+    than they were at build time.
+
+    This traversal covers transitive link dependencies and direct run dependencies because:
+
+    1. Spack adds RPATHs for transitive link dependencies so that packages can find needed
+       dependency libraries.
+    2. Packages may call any of their *direct* run dependencies (and may bake their paths into
+       binaries or scripts), so we also need to search for run dependency prefixes when relocating.
+
+    This returns a deduplicated list of transitive link dependencies and direct run dependencies.
+    """
+    deps = [
         s
         for s in itertools.chain(
-            spec.traverse(root=True, deptype="link", order="breadth", key=traverse.by_dag_hash),
-            spec.dependencies(deptype="run"),
+            spec.traverse(root=True, deptype="link"), spec.dependencies(deptype="run")
         )
         if not s.external
     ]
-    return list(llnl.util.lang.dedupe(specs, key=lambda s: s.dag_hash()))
+    return llnl.util.lang.dedupe(deps, key=lambda s: s.dag_hash())
 
 
 def get_buildinfo_dict(spec):
@@ -620,7 +630,7 @@ def get_buildinfo_dict(spec):
         # "relocate_binaries": [],
         # "relocate_links": [],
         "hardlinks_deduped": True,
-        "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in specs_to_relocate(spec)},
+        "hash_to_prefix": {d.dag_hash(): str(d.prefix) for d in deps_to_relocate(spec)},
     }
 
 
@@ -673,24 +683,19 @@ def sign_specfile(key: str, specfile_path: str) -> str:
 
 
 def _read_specs_and_push_index(
-    file_list: List[str],
-    read_method: Callable,
-    cache_prefix: str,
-    db: BuildCacheDatabase,
-    temp_dir: str,
-    concurrency: int,
+    file_list, read_method, cache_prefix, db: BuildCacheDatabase, temp_dir, concurrency
 ):
     """Read all the specs listed in the provided list, using thread given thread parallelism,
         generate the index, and push it to the mirror.
 
     Args:
-        file_list: List of urls or file paths pointing at spec files to read
+        file_list (list(str)): List of urls or file paths pointing at spec files to read
         read_method: A function taking a single argument, either a url or a file path,
             and which reads the spec file at that location, and returns the spec.
-        cache_prefix: prefix of the build cache on s3 where index should be pushed.
+        cache_prefix (str): prefix of the build cache on s3 where index should be pushed.
         db: A spack database used for adding specs and then writing the index.
-        temp_dir: Location to write index.json and hash for pushing
-        concurrency: Number of parallel processes to use when fetching
+        temp_dir (str): Location to write index.json and hash for pushing
+        concurrency (int): Number of parallel processes to use when fetching
     """
     for file in file_list:
         contents = read_method(file)
@@ -708,7 +713,7 @@ def _read_specs_and_push_index(
 
     # Now generate the index, compute its hash, and push the two files to
     # the mirror.
-    index_json_path = os.path.join(temp_dir, spack_db.INDEX_JSON_FILE)
+    index_json_path = os.path.join(temp_dir, "index.json")
     with open(index_json_path, "w", encoding="utf-8") as f:
         db._write_to_file(f)
 
@@ -718,14 +723,14 @@ def _read_specs_and_push_index(
         index_hash = compute_hash(index_string)
 
     # Write the hash out to a local file
-    index_hash_path = os.path.join(temp_dir, INDEX_HASH_FILE)
+    index_hash_path = os.path.join(temp_dir, "index.json.hash")
     with open(index_hash_path, "w", encoding="utf-8") as f:
         f.write(index_hash)
 
     # Push the index itself
     web_util.push_to_url(
         index_json_path,
-        url_util.join(cache_prefix, spack_db.INDEX_JSON_FILE),
+        url_util.join(cache_prefix, "index.json"),
         keep_original=False,
         extra_args={"ContentType": "application/json", "CacheControl": "no-cache"},
     )
@@ -733,7 +738,7 @@ def _read_specs_and_push_index(
     # Push the hash
     web_util.push_to_url(
         index_hash_path,
-        url_util.join(cache_prefix, INDEX_HASH_FILE),
+        url_util.join(cache_prefix, "index.json.hash"),
         keep_original=False,
         extra_args={"ContentType": "text/plain", "CacheControl": "no-cache"},
     )
@@ -802,7 +807,7 @@ def url_read_method(url):
         try:
             _, _, spec_file = web_util.read_from_url(url)
             contents = codecs.getreader("utf-8")(spec_file).read()
-        except (web_util.SpackWebError, OSError) as e:
+        except web_util.SpackWebError as e:
             tty.error(f"Error reading specfile: {url}: {e}")
         return contents
 
@@ -870,12 +875,9 @@ def _url_generate_package_index(url: str, tmpdir: str, concurrency: int = 32):
     tty.debug(f"Retrieving spec descriptor files from {url} to build index")
 
     db = BuildCacheDatabase(tmpdir)
-    db._write()
 
     try:
-        _read_specs_and_push_index(
-            file_list, read_fn, url, db, str(db.database_directory), concurrency
-        )
+        _read_specs_and_push_index(file_list, read_fn, url, db, db.database_directory, concurrency)
     except Exception as e:
         raise GenerateIndexError(f"Encountered problem pushing package index to {url}: {e}") from e
 
@@ -1110,7 +1112,7 @@ def _exists_in_buildcache(spec: spack.spec.Spec, tmpdir: str, out_url: str) -> E
 
 
 def prefixes_to_relocate(spec):
-    prefixes = [s.prefix for s in specs_to_relocate(spec)]
+    prefixes = [s.prefix for s in deps_to_relocate(spec)]
     prefixes.append(spack.hooks.sbang.sbang_install_path())
     prefixes.append(str(spack.store.STORE.layout.root))
     return prefixes
@@ -1789,7 +1791,7 @@ def _oci_update_index(
         db.mark(spec, "in_buildcache", True)
 
     # Create the index.json file
-    index_json_path = os.path.join(tmpdir, spack_db.INDEX_JSON_FILE)
+    index_json_path = os.path.join(tmpdir, "index.json")
     with open(index_json_path, "w", encoding="utf-8") as f:
         db._write_to_file(f)
 
@@ -2010,7 +2012,7 @@ def fetch_url_to_mirror(url):
 
                 # Download the config = spec.json and the relevant tarball
                 try:
-                    manifest = json.load(response)
+                    manifest = json.loads(response.read())
                     spec_digest = spack.oci.image.Digest.from_string(manifest["config"]["digest"])
                     tarball_digest = spack.oci.image.Digest.from_string(
                         manifest["layers"][-1]["digest"]
@@ -2137,9 +2139,10 @@ def fetch_url_to_mirror(url):
 
 
 def dedupe_hardlinks_if_necessary(root, buildinfo):
-    """Updates a buildinfo dict for old archives that did not dedupe hardlinks. De-duping hardlinks
-    is necessary when relocating files in parallel and in-place. This means we must preserve inodes
-    when relocating."""
+    """Updates a buildinfo dict for old archives that did
+    not dedupe hardlinks. De-duping hardlinks is necessary
+    when relocating files in parallel and in-place. This
+    means we must preserve inodes when relocating."""
 
     # New archives don't need this.
     if buildinfo.get("hardlinks_deduped", False):
@@ -2168,48 +2171,65 @@ def dedupe_hardlinks_if_necessary(root, buildinfo):
         buildinfo[key] = new_list
 
 
-def relocate_package(spec: spack.spec.Spec) -> None:
-    """Relocate binaries and text files in the given spec prefix, based on its buildinfo file."""
-    spec_prefix = str(spec.prefix)
-    buildinfo = read_buildinfo_file(spec_prefix)
+def relocate_package(spec):
+    """
+    Relocate the given package
+    """
+    workdir = str(spec.prefix)
+    buildinfo = read_buildinfo_file(workdir)
+    new_layout_root = str(spack.store.STORE.layout.root)
+    new_prefix = str(spec.prefix)
+    new_rel_prefix = str(os.path.relpath(new_prefix, new_layout_root))
+    new_spack_prefix = str(spack.paths.prefix)
+
+    old_sbang_install_path = None
+    if "sbang_install_path" in buildinfo:
+        old_sbang_install_path = str(buildinfo["sbang_install_path"])
     old_layout_root = str(buildinfo["buildpath"])
+    old_spack_prefix = str(buildinfo.get("spackprefix"))
+    old_rel_prefix = buildinfo.get("relative_prefix")
+    old_prefix = os.path.join(old_layout_root, old_rel_prefix)
+    rel = buildinfo.get("relative_rpaths", False)
 
-    # Warn about old style tarballs created with the --rel flag (removed in Spack v0.20)
-    if buildinfo.get("relative_rpaths", False):
-        tty.warn(
-            f"Tarball for {spec} uses relative rpaths, which can cause library loading issues."
-        )
-
-    # In Spack 0.19 and older prefix_to_hash was the default and externals were not dropped, so
-    # prefixes were not unique.
+    # In the past prefix_to_hash was the default and externals were not dropped, so prefixes
+    # were not unique.
     if "hash_to_prefix" in buildinfo:
         hash_to_old_prefix = buildinfo["hash_to_prefix"]
     elif "prefix_to_hash" in buildinfo:
-        hash_to_old_prefix = {v: k for (k, v) in buildinfo["prefix_to_hash"].items()}
+        hash_to_old_prefix = dict((v, k) for (k, v) in buildinfo["prefix_to_hash"].items())
     else:
-        raise NewLayoutException(
-            "Package tarball was created from an install prefix with a different directory layout "
-            "and an older buildcache create implementation. It cannot be relocated."
-        )
+        hash_to_old_prefix = dict()
 
-    prefix_to_prefix: Dict[str, str] = {}
+    if old_rel_prefix != new_rel_prefix and not hash_to_old_prefix:
+        msg = "Package tarball was created from an install "
+        msg += "prefix with a different directory layout and an older "
+        msg += "buildcache create implementation. It cannot be relocated."
+        raise NewLayoutException(msg)
 
-    if "sbang_install_path" in buildinfo:
-        old_sbang_install_path = str(buildinfo["sbang_install_path"])
-        prefix_to_prefix[old_sbang_install_path] = spack.hooks.sbang.sbang_install_path()
+    # Spurious replacements (e.g. sbang) will cause issues with binaries
+    # For example, the new sbang can be longer than the old one.
+    # Hence 2 dictionaries are maintained here.
+    prefix_to_prefix_text = collections.OrderedDict()
+    prefix_to_prefix_bin = collections.OrderedDict()
 
-    # First match specific prefix paths. Possibly the *local* install prefix of some dependency is
-    # in an upstream, so we cannot assume the original spack store root can be mapped uniformly to
-    # the new spack store root.
+    if old_sbang_install_path:
+        install_path = spack.hooks.sbang.sbang_install_path()
+        prefix_to_prefix_text[old_sbang_install_path] = install_path
 
-    # If the spec is spliced, we need to handle the simultaneous mapping from the old install_tree
-    # to the new install_tree and from the build_spec to the spliced spec. Because foo.build_spec
-    # is foo for any non-spliced spec, we can simplify by checking for spliced-in nodes by checking
-    # for nodes not in the build_spec without any explicit check for whether the spec is spliced.
-    # An analog in this algorithm is any spec that shares a name or provides the same virtuals in
-    # the context of the relevant root spec. This ensures that the analog for a spec s is the spec
-    # that s replaced when we spliced.
-    relocation_specs = specs_to_relocate(spec)
+    # First match specific prefix paths. Possibly the *local* install prefix
+    # of some dependency is in an upstream, so we cannot assume the original
+    # spack store root can be mapped uniformly to the new spack store root.
+    #
+    # If the spec is spliced, we need to handle the simultaneous mapping
+    # from the old install_tree to the new install_tree and from the build_spec
+    # to the spliced spec.
+    # Because foo.build_spec is foo for any non-spliced spec, we can simplify
+    # by checking for spliced-in nodes by checking for nodes not in the build_spec
+    # without any explicit check for whether the spec is spliced.
+    # An analog in this algorithm is any spec that shares a name or provides the same virtuals
+    # in the context of the relevant root spec. This ensures that the analog for a spec s
+    # is the spec that s replaced when we spliced.
+    relocation_specs = deps_to_relocate(spec)
     build_spec_ids = set(id(s) for s in spec.build_spec.traverse(deptype=dt.ALL & ~dt.BUILD))
     for s in relocation_specs:
         analog = s
@@ -2228,66 +2248,98 @@ def relocate_package(spec: spack.spec.Spec) -> None:
         lookup_dag_hash = analog.dag_hash()
         if lookup_dag_hash in hash_to_old_prefix:
             old_dep_prefix = hash_to_old_prefix[lookup_dag_hash]
-            prefix_to_prefix[old_dep_prefix] = str(s.prefix)
+            prefix_to_prefix_bin[old_dep_prefix] = str(s.prefix)
+            prefix_to_prefix_text[old_dep_prefix] = str(s.prefix)
 
     # Only then add the generic fallback of install prefix -> install prefix.
-    prefix_to_prefix[old_layout_root] = str(spack.store.STORE.layout.root)
+    prefix_to_prefix_text[old_prefix] = new_prefix
+    prefix_to_prefix_bin[old_prefix] = new_prefix
+    prefix_to_prefix_text[old_layout_root] = new_layout_root
+    prefix_to_prefix_bin[old_layout_root] = new_layout_root
 
-    # Delete identity mappings from prefix_to_prefix
-    prefix_to_prefix = {k: v for k, v in prefix_to_prefix.items() if k != v}
+    # This is vestigial code for the *old* location of sbang. Previously,
+    # sbang was a bash script, and it lived in the spack prefix. It is
+    # now a POSIX script that lives in the install prefix. Old packages
+    # will have the old sbang location in their shebangs.
+    orig_sbang = "#!/bin/bash {0}/bin/sbang".format(old_spack_prefix)
+    new_sbang = spack.hooks.sbang.sbang_shebang_line()
+    prefix_to_prefix_text[orig_sbang] = new_sbang
 
-    # If there's nothing to relocate, we're done.
-    if not prefix_to_prefix:
-        return
+    tty.debug("Relocating package from", "%s to %s." % (old_layout_root, new_layout_root))
 
-    for old, new in prefix_to_prefix.items():
-        tty.debug(f"Relocating: {old} => {new}.")
+    # Old archives maybe have hardlinks repeated.
+    dedupe_hardlinks_if_necessary(workdir, buildinfo)
 
-    # Old archives may have hardlinks repeated.
-    dedupe_hardlinks_if_necessary(spec_prefix, buildinfo)
+    def is_backup_file(file):
+        return file.endswith("~")
 
     # Text files containing the prefix text
-    textfiles = [os.path.join(spec_prefix, f) for f in buildinfo["relocate_textfiles"]]
-    binaries = [os.path.join(spec_prefix, f) for f in buildinfo.get("relocate_binaries")]
-    links = [os.path.join(spec_prefix, f) for f in buildinfo.get("relocate_links", [])]
+    text_names = list()
+    for filename in buildinfo["relocate_textfiles"]:
+        text_name = os.path.join(workdir, filename)
+        # Don't add backup files generated by filter_file during install step.
+        if not is_backup_file(text_name):
+            text_names.append(text_name)
 
-    platform = spack.platforms.by_name(spec.platform)
-    if "macho" in platform.binary_formats:
-        relocate.relocate_macho_binaries(binaries, prefix_to_prefix)
-    elif "elf" in platform.binary_formats:
-        relocate.relocate_elf_binaries(binaries, prefix_to_prefix)
+    # If we are not installing back to the same install tree do the relocation
+    if old_prefix != new_prefix:
+        files_to_relocate = [
+            os.path.join(workdir, filename) for filename in buildinfo.get("relocate_binaries")
+        ]
+        # If the buildcache was not created with relativized rpaths
+        # do the relocation of path in binaries
+        platform = spack.platforms.by_name(spec.platform)
+        if "macho" in platform.binary_formats:
+            relocate.relocate_macho_binaries(
+                files_to_relocate,
+                old_layout_root,
+                new_layout_root,
+                prefix_to_prefix_bin,
+                rel,
+                old_prefix,
+                new_prefix,
+            )
+        elif "elf" in platform.binary_formats and not rel:
+            # The new ELF dynamic section relocation logic only handles absolute to
+            # absolute relocation.
+            relocate.new_relocate_elf_binaries(files_to_relocate, prefix_to_prefix_bin)
+        elif "elf" in platform.binary_formats and rel:
+            relocate.relocate_elf_binaries(
+                files_to_relocate,
+                old_layout_root,
+                new_layout_root,
+                prefix_to_prefix_bin,
+                rel,
+                old_prefix,
+                new_prefix,
+            )
 
-    relocate.relocate_links(links, prefix_to_prefix)
-    relocate.relocate_text(textfiles, prefix_to_prefix)
-    changed_files = relocate.relocate_text_bin(binaries, prefix_to_prefix)
+        # Relocate links to the new install prefix
+        links = [os.path.join(workdir, f) for f in buildinfo.get("relocate_links", [])]
+        relocate.relocate_links(links, prefix_to_prefix_bin)
 
-    # Add ad-hoc signatures to patched macho files when on macOS.
-    if "macho" in platform.binary_formats and sys.platform == "darwin":
-        codesign = which("codesign")
-        if not codesign:
-            return
-        for binary in changed_files:
-            # preserve the original inode by running codesign on a copy
-            with fsys.edit_in_place_through_temporary_file(binary) as tmp_binary:
-                codesign("-fs-", tmp_binary)
+        # For all buildcaches
+        # relocate the install prefixes in text files including dependencies
+        relocate.relocate_text(text_names, prefix_to_prefix_text)
 
-    install_manifest = os.path.join(
-        spec.prefix,
-        spack.store.STORE.layout.metadata_dir,
-        spack.store.STORE.layout.manifest_file_name,
-    )
-    if not os.path.exists(install_manifest):
-        spec_id = spec.format("{name}/{hash:7}")
-        tty.warn("No manifest file in tarball for spec %s" % spec_id)
+        # relocate the install prefixes in binary files including dependencies
+        changed_files = relocate.relocate_text_bin(files_to_relocate, prefix_to_prefix_bin)
 
-    # overwrite old metadata with new
-    if spec.spliced:
-        # rewrite spec on disk
-        spack.store.STORE.layout.write_spec(spec, spack.store.STORE.layout.spec_file_path(spec))
+        # Add ad-hoc signatures to patched macho files when on macOS.
+        if "macho" in platform.binary_formats and sys.platform == "darwin":
+            codesign = which("codesign")
+            if not codesign:
+                return
+            for binary in changed_files:
+                # preserve the original inode by running codesign on a copy
+                with fsys.edit_in_place_through_temporary_file(binary) as tmp_binary:
+                    codesign("-fs-", tmp_binary)
 
-        # de-cache the install manifest
-        with contextlib.suppress(FileNotFoundError):
-            os.unlink(install_manifest)
+    # If we are installing back to the same location
+    # relocate the sbang location if the spack directory changed
+    else:
+        if old_spack_prefix != new_spack_prefix:
+            relocate.relocate_text(text_names, prefix_to_prefix_text)
 
 
 def _extract_inner_tarball(spec, filename, extract_to, signature_required: bool, remote_checksum):
@@ -2455,6 +2507,15 @@ def extract_tarball(spec, download_result, force=False, timer=timer.NULL_TIMER):
     except Exception as e:
         shutil.rmtree(spec.prefix, ignore_errors=True)
         raise e
+    else:
+        manifest_file = os.path.join(
+            spec.prefix,
+            spack.store.STORE.layout.metadata_dir,
+            spack.store.STORE.layout.manifest_file_name,
+        )
+        if not os.path.exists(manifest_file):
+            spec_id = spec.format("{name}/{hash:7}")
+            tty.warn("No manifest file in tarball for spec %s" % spec_id)
     finally:
         if tmpdir:
             shutil.rmtree(tmpdir, ignore_errors=True)
@@ -2559,6 +2620,10 @@ def install_root_node(
         tty.msg('Installing "{0}" from a buildcache'.format(spec.format()))
         extract_tarball(spec, download_result, force)
         spec.package.windows_establish_runtime_linkage()
+        if spec.spliced:  # overwrite old metadata with new
+            spack.store.STORE.layout.write_spec(
+                spec, spack.store.STORE.layout.spec_file_path(spec)
+            )
         spack.hooks.post_install(spec, False)
         spack.store.STORE.db.add(spec, allow_missing=allow_missing)
 
@@ -2596,14 +2661,11 @@ def try_direct_fetch(spec, mirrors=None):
         )
         try:
             _, _, fs = web_util.read_from_url(buildcache_fetch_url_signed_json)
-            specfile_contents = codecs.getreader("utf-8")(fs).read()
             specfile_is_signed = True
-        except (web_util.SpackWebError, OSError) as e1:
+        except web_util.SpackWebError as e1:
             try:
                 _, _, fs = web_util.read_from_url(buildcache_fetch_url_json)
-                specfile_contents = codecs.getreader("utf-8")(fs).read()
-                specfile_is_signed = False
-            except (web_util.SpackWebError, OSError) as e2:
+            except web_util.SpackWebError as e2:
                 tty.debug(
                     f"Did not find {specfile_name} on {buildcache_fetch_url_signed_json}",
                     e1,
@@ -2613,6 +2675,7 @@ def try_direct_fetch(spec, mirrors=None):
                     f"Did not find {specfile_name} on {buildcache_fetch_url_json}", e2, level=2
                 )
                 continue
+        specfile_contents = codecs.getreader("utf-8")(fs).read()
 
         # read the spec from the build cache file. All specs in build caches
         # are concrete (as they are built) so we need to mark this spec
@@ -2706,9 +2769,8 @@ def get_keys(install=False, trust=False, force=False, mirrors=None):
 
         try:
             _, _, json_file = web_util.read_from_url(keys_index)
-            json_index = sjson.load(json_file)
-        except (web_util.SpackWebError, OSError, ValueError) as url_err:
-            # TODO: avoid repeated request
+            json_index = sjson.load(codecs.getreader("utf-8")(json_file))
+        except web_util.SpackWebError as url_err:
             if web_util.url_exists(keys_index):
                 tty.error(
                     f"Unable to find public keys in {url_util.format(fetch_url)},"
@@ -2955,14 +3017,14 @@ def __init__(self, url, local_hash, urlopen=web_util.urlopen):
 
     def get_remote_hash(self):
         # Failure to fetch index.json.hash is not fatal
-        url_index_hash = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, INDEX_HASH_FILE)
+        url_index_hash = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, "index.json.hash")
         try:
             response = self.urlopen(urllib.request.Request(url_index_hash, headers=self.headers))
-            remote_hash = response.read(64)
-        except OSError:
+        except (TimeoutError, urllib.error.URLError):
             return None
 
         # Validate the hash
+        remote_hash = response.read(64)
         if not re.match(rb"[a-f\d]{64}$", remote_hash):
             return None
         return remote_hash.decode("utf-8")
@@ -2976,17 +3038,17 @@ def conditional_fetch(self) -> FetchIndexResult:
             return FetchIndexResult(etag=None, hash=None, data=None, fresh=True)
 
         # Otherwise, download index.json
-        url_index = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, spack_db.INDEX_JSON_FILE)
+        url_index = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, "index.json")
 
         try:
             response = self.urlopen(urllib.request.Request(url_index, headers=self.headers))
-        except OSError as e:
-            raise FetchIndexError(f"Could not fetch index from {url_index}", e) from e
+        except (TimeoutError, urllib.error.URLError) as e:
+            raise FetchIndexError("Could not fetch index from {}".format(url_index), e) from e
 
         try:
             result = codecs.getreader("utf-8")(response).read()
-        except (ValueError, OSError) as e:
-            raise FetchIndexError(f"Remote index {url_index} is invalid") from e
+        except ValueError as e:
+            raise FetchIndexError("Remote index {} is invalid".format(url_index), e) from e
 
         computed_hash = compute_hash(result)
 
@@ -3020,7 +3082,7 @@ def __init__(self, url, etag, urlopen=web_util.urlopen):
 
     def conditional_fetch(self) -> FetchIndexResult:
         # Just do a conditional fetch immediately
-        url = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, spack_db.INDEX_JSON_FILE)
+        url = url_util.join(self.url, BUILD_CACHE_RELATIVE_PATH, "index.json")
         headers = {"User-Agent": web_util.SPACK_USER_AGENT, "If-None-Match": f'"{self.etag}"'}
 
         try:
@@ -3030,12 +3092,12 @@ def conditional_fetch(self) -> FetchIndexResult:
                 # Not modified; that means fresh.
                 return FetchIndexResult(etag=None, hash=None, data=None, fresh=True)
             raise FetchIndexError(f"Could not fetch index {url}", e) from e
-        except OSError as e:  # URLError, socket.timeout, etc.
+        except (TimeoutError, urllib.error.URLError) as e:
             raise FetchIndexError(f"Could not fetch index {url}", e) from e
 
         try:
             result = codecs.getreader("utf-8")(response).read()
-        except (ValueError, OSError) as e:
+        except ValueError as e:
             raise FetchIndexError(f"Remote index {url} is invalid", e) from e
 
         headers = response.headers
@@ -3067,11 +3129,11 @@ def conditional_fetch(self) -> FetchIndexResult:
                     headers={"Accept": "application/vnd.oci.image.manifest.v1+json"},
                 )
             )
-        except OSError as e:
+        except (TimeoutError, urllib.error.URLError) as e:
             raise FetchIndexError(f"Could not fetch manifest from {url_manifest}", e) from e
 
         try:
-            manifest = json.load(response)
+            manifest = json.loads(response.read())
         except Exception as e:
             raise FetchIndexError(f"Remote index {url_manifest} is invalid", e) from e
 
@@ -3086,16 +3148,14 @@ def conditional_fetch(self) -> FetchIndexResult:
             return FetchIndexResult(etag=None, hash=None, data=None, fresh=True)
 
         # Otherwise fetch the blob / index.json
-        try:
-            response = self.urlopen(
-                urllib.request.Request(
-                    url=self.ref.blob_url(index_digest),
-                    headers={"Accept": "application/vnd.oci.image.layer.v1.tar+gzip"},
-                )
+        response = self.urlopen(
+            urllib.request.Request(
+                url=self.ref.blob_url(index_digest),
+                headers={"Accept": "application/vnd.oci.image.layer.v1.tar+gzip"},
             )
-            result = codecs.getreader("utf-8")(response).read()
-        except (OSError, ValueError) as e:
-            raise FetchIndexError(f"Remote index {url_manifest} is invalid", e) from e
+        )
+
+        result = codecs.getreader("utf-8")(response).read()
 
         # Make sure the blob we download has the advertised hash
         if compute_hash(result) != index_digest.digest:

lib/spack/spack/bootstrap/_common.py

@@ -5,14 +5,12 @@
 import fnmatch
 import glob
 import importlib
-import os
+import os.path
 import re
 import sys
 import sysconfig
 import warnings
-from typing import Optional, Sequence, Union
-
-from typing_extensions import TypedDict
+from typing import Dict, Optional, Sequence, Union
 
 import archspec.cpu
 
@@ -20,17 +18,13 @@
 from llnl.util import tty
 
 import spack.platforms
-import spack.spec
 import spack.store
 import spack.util.environment
 import spack.util.executable
 
 from .config import spec_for_current_python
 
-
-class QueryInfo(TypedDict, total=False):
-    spec: spack.spec.Spec
-    command: spack.util.executable.Executable
+QueryInfo = Dict[str, "spack.spec.Spec"]
 
 
 def _python_import(module: str) -> bool:
@@ -217,9 +211,7 @@ def _executables_in_store(
             ):
                 spack.util.environment.path_put_first("PATH", [bin_dir])
                 if query_info is not None:
-                    query_info["command"] = spack.util.executable.which(
-                        *executables, path=bin_dir, required=True
-                    )
+                    query_info["command"] = spack.util.executable.which(*executables, path=bin_dir)
                     query_info["spec"] = concrete_spec
                 return True
     return False

lib/spack/spack/bootstrap/clingo.py

@@ -27,9 +27,9 @@
 class ClingoBootstrapConcretizer:
     def __init__(self, configuration):
         self.host_platform = spack.platforms.host()
-        self.host_os = self.host_platform.default_operating_system()
+        self.host_os = self.host_platform.operating_system("frontend")
         self.host_target = archspec.cpu.host().family
-        self.host_architecture = spack.spec.ArchSpec.default_arch()
+        self.host_architecture = spack.spec.ArchSpec.frontend_arch()
         self.host_architecture.target = str(self.host_target)
         self.host_compiler = self._valid_compiler_or_raise()
         self.host_python = self.python_external_spec()

lib/spack/spack/bootstrap/config.py

@@ -4,7 +4,7 @@
 """Manage configuration swapping for bootstrapping purposes"""
 
 import contextlib
-import os
+import os.path
 import sys
 from typing import Any, Dict, Generator, MutableSequence, Sequence
 
@@ -141,7 +141,7 @@ def _bootstrap_config_scopes() -> Sequence["spack.config.ConfigScope"]:
 
 
 def _add_compilers_if_missing() -> None:
-    arch = spack.spec.ArchSpec.default_arch()
+    arch = spack.spec.ArchSpec.frontend_arch()
     if not spack.compilers.compilers_for_arch(arch):
         spack.compilers.find_compilers()
 

lib/spack/spack/bootstrap/core.py

@@ -25,6 +25,7 @@
 import functools
 import json
 import os
+import os.path
 import sys
 import uuid
 from typing import Any, Callable, Dict, List, Optional, Tuple
@@ -33,10 +34,8 @@
 from llnl.util.lang import GroupedExceptionHandler
 
 import spack.binary_distribution
-import spack.concretize
 import spack.config
 import spack.detection
-import spack.error
 import spack.mirrors.mirror
 import spack.platforms
 import spack.spec
@@ -45,17 +44,10 @@
 import spack.util.executable
 import spack.util.path
 import spack.util.spack_yaml
-import spack.util.url
 import spack.version
 from spack.installer import PackageInstaller
 
-from ._common import (
-    QueryInfo,
-    _executables_in_store,
-    _python_import,
-    _root_spec,
-    _try_import_from_store,
-)
+from ._common import _executables_in_store, _python_import, _root_spec, _try_import_from_store
 from .clingo import ClingoBootstrapConcretizer
 from .config import spack_python_interpreter, spec_for_current_python
 
@@ -97,12 +89,8 @@ def __init__(self, conf: ConfigDictionary) -> None:
         self.name = conf["name"]
         self.metadata_dir = spack.util.path.canonicalize_path(conf["metadata"])
 
-        # Check for relative paths, and turn them into absolute paths
-        # root is the metadata_dir
-        maybe_url = conf["info"]["url"]
-        if spack.util.url.is_path_instead_of_url(maybe_url) and not os.path.isabs(maybe_url):
-            maybe_url = os.path.join(self.metadata_dir, maybe_url)
-        self.url = spack.mirrors.mirror.Mirror(maybe_url).fetch_url
+        # Promote (relative) paths to file urls
+        self.url = spack.mirrors.mirror.Mirror(conf["info"]["url"]).fetch_url
 
     @property
     def mirror_scope(self) -> spack.config.InternalConfigScope:
@@ -146,7 +134,7 @@ class BuildcacheBootstrapper(Bootstrapper):
 
     def __init__(self, conf) -> None:
         super().__init__(conf)
-        self.last_search: Optional[QueryInfo] = None
+        self.last_search: Optional[ConfigDictionary] = None
         self.config_scope_name = f"bootstrap_buildcache-{uuid.uuid4()}"
 
     @staticmethod
@@ -223,14 +211,14 @@ def _install_and_test(
                 for _, pkg_hash, pkg_sha256 in item["binaries"]:
                     self._install_by_hash(pkg_hash, pkg_sha256, bincache_platform)
 
-                info: QueryInfo = {}
+                info: ConfigDictionary = {}
                 if test_fn(query_spec=abstract_spec, query_info=info):
                     self.last_search = info
                     return True
         return False
 
     def try_import(self, module: str, abstract_spec_str: str) -> bool:
-        info: QueryInfo
+        info: ConfigDictionary
         test_fn, info = functools.partial(_try_import_from_store, module), {}
         if test_fn(query_spec=abstract_spec_str, query_info=info):
             return True
@@ -243,7 +231,7 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
         return self._install_and_test(abstract_spec, bincache_platform, data, test_fn)
 
     def try_search_path(self, executables: Tuple[str], abstract_spec_str: str) -> bool:
-        info: QueryInfo
+        info: ConfigDictionary
         test_fn, info = functools.partial(_executables_in_store, executables), {}
         if test_fn(query_spec=abstract_spec_str, query_info=info):
             self.last_search = info
@@ -261,11 +249,11 @@ class SourceBootstrapper(Bootstrapper):
 
     def __init__(self, conf) -> None:
         super().__init__(conf)
-        self.last_search: Optional[QueryInfo] = None
+        self.last_search: Optional[ConfigDictionary] = None
         self.config_scope_name = f"bootstrap_source-{uuid.uuid4()}"
 
     def try_import(self, module: str, abstract_spec_str: str) -> bool:
-        info: QueryInfo = {}
+        info: ConfigDictionary = {}
         if _try_import_from_store(module, abstract_spec_str, query_info=info):
             self.last_search = info
             return True
@@ -282,10 +270,10 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
                 bootstrapper = ClingoBootstrapConcretizer(configuration=spack.config.CONFIG)
                 concrete_spec = bootstrapper.concretize()
             else:
-                abstract_spec = spack.spec.Spec(
+                concrete_spec = spack.spec.Spec(
                     abstract_spec_str + " ^" + spec_for_current_python()
                 )
-                concrete_spec = spack.concretize.concretize_one(abstract_spec)
+                concrete_spec.concretize()
 
         msg = "[BOOTSTRAP MODULE {0}] Try installing '{1}' from sources"
         tty.debug(msg.format(module, abstract_spec_str))
@@ -300,7 +288,7 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
         return False
 
     def try_search_path(self, executables: Tuple[str], abstract_spec_str: str) -> bool:
-        info: QueryInfo = {}
+        info: ConfigDictionary = {}
         if _executables_in_store(executables, abstract_spec_str, query_info=info):
             self.last_search = info
             return True
@@ -311,7 +299,7 @@ def try_search_path(self, executables: Tuple[str], abstract_spec_str: str) -> bo
         # might reduce compilation time by a fair amount
         _add_externals_if_missing()
 
-        concrete_spec = spack.concretize.concretize_one(abstract_spec_str)
+        concrete_spec = spack.spec.Spec(abstract_spec_str).concretized()
         msg = "[BOOTSTRAP] Try installing '{0}' from sources"
         tty.debug(msg.format(abstract_spec_str))
         with spack.config.override(self.mirror_scope):
@@ -328,9 +316,11 @@ def create_bootstrapper(conf: ConfigDictionary):
     return _bootstrap_methods[btype](conf)
 
 
-def source_is_enabled(conf: ConfigDictionary) -> bool:
-    """Returns true if the source is not enabled for bootstrapping"""
-    return spack.config.get("bootstrap:trusted").get(conf["name"], False)
+def source_is_enabled_or_raise(conf: ConfigDictionary):
+    """Raise ValueError if the source is not enabled for bootstrapping"""
+    trusted, name = spack.config.get("bootstrap:trusted"), conf["name"]
+    if not trusted.get(name, False):
+        raise ValueError("source is not trusted")
 
 
 def ensure_module_importable_or_raise(module: str, abstract_spec: Optional[str] = None):
@@ -360,23 +350,24 @@ def ensure_module_importable_or_raise(module: str, abstract_spec: Optional[str]
     exception_handler = GroupedExceptionHandler()
 
     for current_config in bootstrapping_sources():
-        if not source_is_enabled(current_config):
-            continue
         with exception_handler.forward(current_config["name"], Exception):
-            if create_bootstrapper(current_config).try_import(module, abstract_spec):
+            source_is_enabled_or_raise(current_config)
+            current_bootstrapper = create_bootstrapper(current_config)
+            if current_bootstrapper.try_import(module, abstract_spec):
                 return
 
+    assert exception_handler, (
+        f"expected at least one exception to have been raised at this point: "
+        f"while bootstrapping {module}"
+    )
     msg = f'cannot bootstrap the "{module}" Python module '
     if abstract_spec:
         msg += f'from spec "{abstract_spec}" '
-
-    if not exception_handler:
-        msg += ": no bootstrapping sources are enabled"
-    elif spack.error.debug or spack.error.SHOW_BACKTRACE:
+    if tty.is_debug():
         msg += exception_handler.grouped_message(with_tracebacks=True)
     else:
         msg += exception_handler.grouped_message(with_tracebacks=False)
-        msg += "\nRun `spack --backtrace ...` for more detailed errors"
+        msg += "\nRun `spack --debug ...` for more detailed errors"
     raise ImportError(msg)
 
 
@@ -414,9 +405,8 @@ def ensure_executables_in_path_or_raise(
     exception_handler = GroupedExceptionHandler()
 
     for current_config in bootstrapping_sources():
-        if not source_is_enabled(current_config):
-            continue
         with exception_handler.forward(current_config["name"], Exception):
+            source_is_enabled_or_raise(current_config)
             current_bootstrapper = create_bootstrapper(current_config)
             if current_bootstrapper.try_search_path(executables, abstract_spec):
                 # Additional environment variables needed
@@ -424,7 +414,6 @@ def ensure_executables_in_path_or_raise(
                     current_bootstrapper.last_search["spec"],
                     current_bootstrapper.last_search["command"],
                 )
-                assert cmd is not None, "expected an Executable"
                 cmd.add_default_envmod(
                     spack.user_environment.environment_modifications_for_specs(
                         concrete_spec, set_package_py_globals=False
@@ -432,17 +421,18 @@ def ensure_executables_in_path_or_raise(
                 )
                 return cmd
 
+    assert exception_handler, (
+        f"expected at least one exception to have been raised at this point: "
+        f"while bootstrapping {executables_str}"
+    )
     msg = f"cannot bootstrap any of the {executables_str} executables "
     if abstract_spec:
         msg += f'from spec "{abstract_spec}" '
-
-    if not exception_handler:
-        msg += ": no bootstrapping sources are enabled"
-    elif spack.error.debug or spack.error.SHOW_BACKTRACE:
+    if tty.is_debug():
         msg += exception_handler.grouped_message(with_tracebacks=True)
     else:
         msg += exception_handler.grouped_message(with_tracebacks=False)
-        msg += "\nRun `spack --backtrace ...` for more detailed errors"
+        msg += "\nRun `spack --debug ...` for more detailed errors"
     raise RuntimeError(msg)
 
 

lib/spack/spack/bootstrap/status.py

@@ -63,6 +63,7 @@ def _missing(name: str, purpose: str, system_only: bool = True) -> str:
 
 def _core_requirements() -> List[RequiredResponseType]:
     _core_system_exes = {
+        "make": _missing("make", "required to build software from sources"),
         "patch": _missing("patch", "required to patch source code before building"),
         "tar": _missing("tar", "required to manage code archives"),
         "gzip": _missing("gzip", "required to compress/decompress code archives"),

lib/spack/spack/build_environment.py

@@ -44,19 +44,7 @@
 from enum import Flag, auto
 from itertools import chain
 from multiprocessing.connection import Connection
-from typing import (
-    Callable,
-    Dict,
-    List,
-    Optional,
-    Sequence,
-    Set,
-    TextIO,
-    Tuple,
-    Type,
-    Union,
-    overload,
-)
+from typing import Callable, Dict, List, Optional, Set, Tuple
 
 import archspec.cpu
 
@@ -158,128 +146,48 @@ def get_effective_jobs(jobs, parallel=True, supports_jobserver=False):
 
 
 class MakeExecutable(Executable):
-    """Special callable executable object for make so the user can specify parallelism options
-    on a per-invocation basis.
+    """Special callable executable object for make so the user can specify
+    parallelism options on a per-invocation basis.  Specifying
+    'parallel' to the call will override whatever the package's
+    global setting is, so you can either default to true or false and
+    override particular calls. Specifying 'jobs_env' to a particular
+    call will name an environment variable which will be set to the
+    parallelism level (without affecting the normal invocation with
+    -j).
     """
 
-    def __init__(self, name: str, *, jobs: int, supports_jobserver: bool = True) -> None:
-        super().__init__(name)
+    def __init__(self, name, jobs, **kwargs):
+        supports_jobserver = kwargs.pop("supports_jobserver", True)
+        super().__init__(name, **kwargs)
         self.supports_jobserver = supports_jobserver
         self.jobs = jobs
 
-    @overload
-    def __call__(
-        self,
-        *args: str,
-        parallel: bool = ...,
-        jobs_env: Optional[str] = ...,
-        jobs_env_supports_jobserver: bool = ...,
-        fail_on_error: bool = ...,
-        ignore_errors: Union[int, Sequence[int]] = ...,
-        ignore_quotes: Optional[bool] = ...,
-        timeout: Optional[int] = ...,
-        env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
-        extra_env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
-        input: Optional[TextIO] = ...,
-        output: Union[Optional[TextIO], str] = ...,
-        error: Union[Optional[TextIO], str] = ...,
-        _dump_env: Optional[Dict[str, str]] = ...,
-    ) -> None: ...
-
-    @overload
-    def __call__(
-        self,
-        *args: str,
-        parallel: bool = ...,
-        jobs_env: Optional[str] = ...,
-        jobs_env_supports_jobserver: bool = ...,
-        fail_on_error: bool = ...,
-        ignore_errors: Union[int, Sequence[int]] = ...,
-        ignore_quotes: Optional[bool] = ...,
-        timeout: Optional[int] = ...,
-        env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
-        extra_env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
-        input: Optional[TextIO] = ...,
-        output: Union[Type[str], Callable] = ...,
-        error: Union[Optional[TextIO], str, Type[str], Callable] = ...,
-        _dump_env: Optional[Dict[str, str]] = ...,
-    ) -> str: ...
-
-    @overload
-    def __call__(
-        self,
-        *args: str,
-        parallel: bool = ...,
-        jobs_env: Optional[str] = ...,
-        jobs_env_supports_jobserver: bool = ...,
-        fail_on_error: bool = ...,
-        ignore_errors: Union[int, Sequence[int]] = ...,
-        ignore_quotes: Optional[bool] = ...,
-        timeout: Optional[int] = ...,
-        env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
-        extra_env: Optional[Union[Dict[str, str], EnvironmentModifications]] = ...,
-        input: Optional[TextIO] = ...,
-        output: Union[Optional[TextIO], str, Type[str], Callable] = ...,
-        error: Union[Type[str], Callable] = ...,
-        _dump_env: Optional[Dict[str, str]] = ...,
-    ) -> str: ...
-
-    def __call__(
-        self,
-        *args: str,
-        parallel: bool = True,
-        jobs_env: Optional[str] = None,
-        jobs_env_supports_jobserver: bool = False,
-        **kwargs,
-    ) -> Optional[str]:
-        """Runs this "make" executable in a subprocess.
-
-        Args:
-            parallel: if False, parallelism is disabled
-            jobs_env: environment variable that will be set to the current level of parallelism
-            jobs_env_supports_jobserver: whether the jobs env supports a job server
-
-        For all the other **kwargs, refer to the base class.
+    def __call__(self, *args, **kwargs):
+        """parallel, and jobs_env from kwargs are swallowed and used here;
+        remaining arguments are passed through to the superclass.
         """
+        parallel = kwargs.pop("parallel", True)
+        jobs_env = kwargs.pop("jobs_env", None)
+        jobs_env_supports_jobserver = kwargs.pop("jobs_env_supports_jobserver", False)
+
         jobs = get_effective_jobs(
             self.jobs, parallel=parallel, supports_jobserver=self.supports_jobserver
         )
         if jobs is not None:
-            args = (f"-j{jobs}",) + args
+            args = ("-j{0}".format(jobs),) + args
 
         if jobs_env:
-            # Caller wants us to set an environment variable to control the parallelism
+            # Caller wants us to set an environment variable to
+            # control the parallelism.
             jobs_env_jobs = get_effective_jobs(
                 self.jobs, parallel=parallel, supports_jobserver=jobs_env_supports_jobserver
             )
             if jobs_env_jobs is not None:
-                extra_env = kwargs.setdefault("extra_env", {})
-                extra_env.update({jobs_env: str(jobs_env_jobs)})
+                kwargs["extra_env"] = {jobs_env: str(jobs_env_jobs)}
 
         return super().__call__(*args, **kwargs)
 
 
-class UndeclaredDependencyError(spack.error.SpackError):
-    """Raised if a dependency is invoking an executable through a module global, without
-    declaring a dependency on it.
-    """
-
-
-class DeprecatedExecutable:
-    def __init__(self, pkg: str, exe: str, exe_pkg: str) -> None:
-        self.pkg = pkg
-        self.exe = exe
-        self.exe_pkg = exe_pkg
-
-    def __call__(self, *args, **kwargs):
-        raise UndeclaredDependencyError(
-            f"{self.pkg} is using {self.exe} without declaring a dependency on {self.exe_pkg}"
-        )
-
-    def add_default_env(self, key: str, value: str):
-        self.__call__()
-
-
 def clean_environment():
     # Stuff in here sanitizes the build environment to eliminate
     # anything the user has set that may interfere. We apply it immediately
@@ -301,13 +209,11 @@ def clean_environment():
     env.unset("CPLUS_INCLUDE_PATH")
     env.unset("OBJC_INCLUDE_PATH")
 
-    # prevent configure scripts from sourcing variables from config site file (AC_SITE_LOAD).
-    env.set("CONFIG_SITE", os.devnull)
     env.unset("CMAKE_PREFIX_PATH")
-
     env.unset("PYTHONPATH")
     env.unset("R_HOME")
     env.unset("R_ENVIRON")
+
     env.unset("LUA_PATH")
     env.unset("LUA_CPATH")
 
@@ -715,9 +621,10 @@ def set_package_py_globals(pkg, context: Context = Context.BUILD):
         module.std_meson_args = spack.build_systems.meson.MesonBuilder.std_args(pkg)
         module.std_pip_args = spack.build_systems.python.PythonPipBuilder.std_args(pkg)
 
-    module.make = DeprecatedExecutable(pkg.name, "make", "gmake")
-    module.gmake = DeprecatedExecutable(pkg.name, "gmake", "gmake")
-    module.ninja = DeprecatedExecutable(pkg.name, "ninja", "ninja")
+    # TODO: make these build deps that can be installed if not found.
+    module.make = MakeExecutable("make", jobs)
+    module.gmake = MakeExecutable("gmake", jobs)
+    module.ninja = MakeExecutable("ninja", jobs, supports_jobserver=False)
     # TODO: johnwparent: add package or builder support to define these build tools
     # for now there is no entrypoint for builders to define these on their
     # own

lib/spack/spack/build_systems/aspell_dict.py

@@ -6,9 +6,7 @@
 import llnl.util.filesystem as fs
 
 import spack.directives
-import spack.spec
 import spack.util.executable
-import spack.util.prefix
 
 from .autotools import AutotoolsBuilder, AutotoolsPackage
 
@@ -19,18 +17,19 @@ class AspellBuilder(AutotoolsBuilder):
     to the Aspell extensions.
     """
 
-    def configure(
-        self,
-        pkg: "AspellDictPackage",  # type: ignore[override]
-        spec: spack.spec.Spec,
-        prefix: spack.util.prefix.Prefix,
-    ):
+    def configure(self, pkg, spec, prefix):
         aspell = spec["aspell"].prefix.bin.aspell
         prezip = spec["aspell"].prefix.bin.prezip
         destdir = prefix
 
-        sh = spack.util.executable.Executable("/bin/sh")
-        sh("./configure", "--vars", f"ASPELL={aspell}", f"PREZIP={prezip}", f"DESTDIR={destdir}")
+        sh = spack.util.executable.which("sh")
+        sh(
+            "./configure",
+            "--vars",
+            "ASPELL={0}".format(aspell),
+            "PREZIP={0}".format(prezip),
+            "DESTDIR={0}".format(destdir),
+        )
 
 
 # Aspell dictionaries install their bits into their prefix.lib

lib/spack/spack/build_systems/autotools.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
+import os.path
 import stat
 import subprocess
 from typing import Callable, List, Optional, Set, Tuple, Union
@@ -355,13 +356,6 @@ def _do_patch_libtool_configure(self) -> None:
             )
             # Support Libtool 2.4.2 and older:
             x.filter(regex=r'^(\s*test \$p = "-R")(; then\s*)$', repl=r'\1 || test x-l = x"$p"\2')
-            # Configure scripts generated with libtool < 2.5.4 have a faulty test for the
-            # -single_module linker flag. A deprecation warning makes it think the default is
-            # -multi_module, triggering it to use problematic linker flags (such as ld -r). The
-            # linker default is `-single_module` from (ancient) macOS 10.4, so override by setting
-            # `lt_cv_apple_cc_single_mod=yes`. See the fix in libtool commit
-            # 82f7f52123e4e7e50721049f7fa6f9b870e09c9d.
-            x.filter("lt_cv_apple_cc_single_mod=no", "lt_cv_apple_cc_single_mod=yes", string=True)
 
     @spack.phase_callbacks.run_after("configure")
     def _do_patch_libtool(self) -> None:
@@ -533,7 +527,7 @@ def build_directory(self) -> str:
         return build_dir
 
     @spack.phase_callbacks.run_before("autoreconf")
-    def _delete_configure_to_force_update(self) -> None:
+    def delete_configure_to_force_update(self) -> None:
         if self.force_autoreconf:
             fs.force_remove(self.configure_abs_path)
 
@@ -546,7 +540,7 @@ def autoreconf_search_path_args(self) -> List[str]:
         return _autoreconf_search_path_args(self.spec)
 
     @spack.phase_callbacks.run_after("autoreconf")
-    def _set_configure_or_die(self) -> None:
+    def set_configure_or_die(self) -> None:
         """Ensure the presence of a "configure" script, or raise. If the "configure"
         is found, a module level attribute is set.
 
@@ -570,7 +564,10 @@ def configure_args(self) -> List[str]:
         return []
 
     def autoreconf(
-        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Not needed usually, configure should be already there"""
 
@@ -599,7 +596,10 @@ def autoreconf(
             self.pkg.module.autoreconf(*autoreconf_args)
 
     def configure(
-        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Run "configure", with the arguments specified by the builder and an
         appropriately set prefix.
@@ -612,7 +612,10 @@ def configure(
             pkg.module.configure(*options)
 
     def build(
-        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Run "make" on the build targets specified by the builder."""
         # See https://autotools.io/automake/silent.html
@@ -622,7 +625,10 @@ def build(
             pkg.module.make(*params)
 
     def install(
-        self, pkg: AutotoolsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Run "make" on the install targets specified by the builder."""
         with fs.working_dir(self.build_directory):
@@ -819,7 +825,7 @@ def installcheck(self) -> None:
             self.pkg._if_make_target_execute("installcheck")
 
     @spack.phase_callbacks.run_after("install")
-    def _remove_libtool_archives(self) -> None:
+    def remove_libtool_archives(self) -> None:
         """Remove all .la files in prefix sub-folders if the package sets
         ``install_libtool_archives`` to be False.
         """

lib/spack/spack/build_systems/cached_cmake.py

@@ -10,8 +10,6 @@
 import llnl.util.tty as tty
 
 import spack.phase_callbacks
-import spack.spec
-import spack.util.prefix
 
 from .cmake import CMakeBuilder, CMakePackage
 
@@ -295,13 +293,6 @@ def initconfig_hardware_entries(self):
                 entries.append(cmake_cache_string("AMDGPU_TARGETS", arch_str))
                 entries.append(cmake_cache_string("GPU_TARGETS", arch_str))
 
-            if spec.satisfies("%gcc"):
-                entries.append(
-                    cmake_cache_string(
-                        "CMAKE_HIP_FLAGS", f"--gcc-toolchain={self.pkg.compiler.prefix}"
-                    )
-                )
-
         return entries
 
     def std_initconfig_entries(self):
@@ -332,9 +323,7 @@ def initconfig_package_entries(self):
         """This method is to be overwritten by the package"""
         return []
 
-    def initconfig(
-        self, pkg: "CachedCMakePackage", spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def initconfig(self, pkg, spec, prefix):
         cache_entries = (
             self.std_initconfig_entries()
             + self.initconfig_compiler_entries()

lib/spack/spack/build_systems/cargo.py

@@ -7,8 +7,6 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, depends_on
 from spack.multimethod import when
 
@@ -83,16 +81,12 @@ def check_args(self):
     def setup_build_environment(self, env):
         env.set("CARGO_HOME", self.stage.path)
 
-    def build(
-        self, pkg: CargoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Runs ``cargo install`` in the source directory"""
         with fs.working_dir(self.build_directory):
             pkg.module.cargo("install", "--root", "out", "--path", ".", *self.build_args)
 
-    def install(
-        self, pkg: CargoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Copy build files into package prefix."""
         with fs.working_dir(self.build_directory):
             fs.install_tree("out", prefix)

lib/spack/spack/build_systems/cmake.py

@@ -454,7 +454,10 @@ def cmake_args(self) -> List[str]:
         return []
 
     def cmake(
-        self, pkg: CMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Runs ``cmake`` in the build directory"""
 
@@ -471,7 +474,10 @@ def cmake(
             pkg.module.cmake(*options)
 
     def build(
-        self, pkg: CMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Make the build targets"""
         with fs.working_dir(self.build_directory):
@@ -482,7 +488,10 @@ def build(
                 pkg.module.ninja(*self.build_targets)
 
     def install(
-        self, pkg: CMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Make the install targets"""
         with fs.working_dir(self.build_directory):

lib/spack/spack/build_systems/generic.py

@@ -7,8 +7,6 @@
 import spack.directives
 import spack.package_base
 import spack.phase_callbacks
-import spack.spec
-import spack.util.prefix
 
 from ._checks import BuilderWithDefaults, apply_macos_rpath_fixups, execute_install_time_tests
 
@@ -50,8 +48,3 @@ class GenericBuilder(BuilderWithDefaults):
 
     # unconditionally perform any post-install phase tests
     spack.phase_callbacks.run_after("install")(execute_install_time_tests)
-
-    def install(
-        self, pkg: Package, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
-        raise NotImplementedError

lib/spack/spack/build_systems/go.py

@@ -7,9 +7,7 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
-import spack.spec
-import spack.util.prefix
-from spack.directives import build_system, depends_on
+from spack.directives import build_system, extends
 from spack.multimethod import when
 
 from ._checks import BuilderWithDefaults, execute_install_time_tests
@@ -28,7 +26,9 @@ class GoPackage(spack.package_base.PackageBase):
     build_system("go")
 
     with when("build_system=go"):
-        depends_on("go", type="build")
+        # TODO: this seems like it should be depends_on, see
+        # setup_dependent_build_environment in go for why I kept it like this
+        extends("go@1.14:", type="build")
 
 
 @spack.builder.builder("go")
@@ -71,7 +71,6 @@ class GoBuilder(BuilderWithDefaults):
     def setup_build_environment(self, env):
         env.set("GO111MODULE", "on")
         env.set("GOTOOLCHAIN", "local")
-        env.set("GOPATH", fs.join_path(self.pkg.stage.path, "go"))
 
     @property
     def build_directory(self):
@@ -82,31 +81,19 @@ def build_directory(self):
     def build_args(self):
         """Arguments for ``go build``."""
         # Pass ldflags -s = --strip-all and -w = --no-warnings by default
-        return [
-            "-p",
-            str(self.pkg.module.make_jobs),
-            "-modcacherw",
-            "-ldflags",
-            "-s -w",
-            "-o",
-            f"{self.pkg.name}",
-        ]
+        return ["-modcacherw", "-ldflags", "-s -w", "-o", f"{self.pkg.name}"]
 
     @property
     def check_args(self):
         """Argument for ``go test`` during check phase"""
         return []
 
-    def build(
-        self, pkg: GoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Runs ``go build`` in the source directory"""
         with fs.working_dir(self.build_directory):
             pkg.module.go("build", *self.build_args)
 
-    def install(
-        self, pkg: GoPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Install built binaries into prefix bin."""
         with fs.working_dir(self.build_directory):
             fs.mkdirp(prefix.bin)

lib/spack/spack/build_systems/lua.py

@@ -7,9 +7,7 @@
 
 import spack.builder
 import spack.package_base
-import spack.spec
 import spack.util.executable
-import spack.util.prefix
 from spack.directives import build_system, depends_on, extends
 from spack.multimethod import when
 
@@ -57,9 +55,7 @@ class LuaBuilder(spack.builder.Builder):
     #: Names associated with package attributes in the old build-system format
     legacy_attributes = ()
 
-    def unpack(
-        self, pkg: LuaPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def unpack(self, pkg, spec, prefix):
         if os.path.splitext(pkg.stage.archive_file)[1] == ".rock":
             directory = pkg.luarocks("unpack", pkg.stage.archive_file, output=str)
             dirlines = directory.split("\n")
@@ -70,16 +66,15 @@ def unpack(
     def _generate_tree_line(name, prefix):
         return """{{ name = "{name}", root = "{prefix}" }};""".format(name=name, prefix=prefix)
 
-    def generate_luarocks_config(
-        self, pkg: LuaPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def generate_luarocks_config(self, pkg, spec, prefix):
         spec = self.pkg.spec
         table_entries = []
         for d in spec.traverse(deptype=("build", "run")):
             if d.package.extends(self.pkg.extendee_spec):
                 table_entries.append(self._generate_tree_line(d.name, d.prefix))
 
-        with open(self._luarocks_config_path(), "w", encoding="utf-8") as config:
+        path = self._luarocks_config_path()
+        with open(path, "w", encoding="utf-8") as config:
             config.write(
                 """
                 deps_mode="all"
@@ -90,26 +85,23 @@ def generate_luarocks_config(
                     "\n".join(table_entries)
                 )
             )
+        return path
 
-    def preprocess(
-        self, pkg: LuaPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def preprocess(self, pkg, spec, prefix):
         """Override this to preprocess source before building with luarocks"""
         pass
 
     def luarocks_args(self):
         return []
 
-    def install(
-        self, pkg: LuaPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         rock = "."
         specs = find(".", "*.rockspec", recursive=False)
         if specs:
             rock = specs[0]
         rocks_args = self.luarocks_args()
         rocks_args.append(rock)
-        pkg.luarocks("--tree=" + prefix, "make", *rocks_args)
+        self.pkg.luarocks("--tree=" + prefix, "make", *rocks_args)
 
     def _luarocks_config_path(self):
         return os.path.join(self.pkg.stage.source_path, "spack_luarocks.lua")

lib/spack/spack/build_systems/makefile.py

@@ -98,20 +98,29 @@ def build_directory(self) -> str:
         return self.pkg.stage.source_path
 
     def edit(
-        self, pkg: MakefilePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Edit the Makefile before calling make. The default is a no-op."""
         pass
 
     def build(
-        self, pkg: MakefilePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Run "make" on the build targets specified by the builder."""
         with fs.working_dir(self.build_directory):
             pkg.module.make(*self.build_targets)
 
     def install(
-        self, pkg: MakefilePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Run "make" on the install targets specified by the builder."""
         with fs.working_dir(self.build_directory):

lib/spack/spack/build_systems/maven.py

@@ -5,8 +5,6 @@
 
 import spack.builder
 import spack.package_base
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, depends_on
 from spack.multimethod import when
 from spack.util.executable import which
@@ -60,20 +58,16 @@ def build_args(self):
         """List of args to pass to build phase."""
         return []
 
-    def build(
-        self, pkg: MavenPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Compile code and package into a JAR file."""
         with fs.working_dir(self.build_directory):
-            mvn = which("mvn", required=True)
+            mvn = which("mvn")
             if self.pkg.run_tests:
                 mvn("verify", *self.build_args())
             else:
                 mvn("package", "-DskipTests", *self.build_args())
 
-    def install(
-        self, pkg: MavenPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Copy to installation prefix."""
         with fs.working_dir(self.build_directory):
             fs.install_tree(".", prefix)

lib/spack/spack/build_systems/meson.py

@@ -188,7 +188,10 @@ def meson_args(self) -> List[str]:
         return []
 
     def meson(
-        self, pkg: MesonPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Run ``meson`` in the build directory"""
         options = []
@@ -201,7 +204,10 @@ def meson(
             pkg.module.meson(*options)
 
     def build(
-        self, pkg: MesonPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Make the build targets"""
         options = ["-v"]
@@ -210,7 +216,10 @@ def build(
             pkg.module.ninja(*options)
 
     def install(
-        self, pkg: MesonPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
+        self,
+        pkg: spack.package_base.PackageBase,
+        spec: spack.spec.Spec,
+        prefix: spack.util.prefix.Prefix,
     ) -> None:
         """Make the install targets"""
         with fs.working_dir(self.build_directory):

lib/spack/spack/build_systems/msbuild.py

@@ -7,8 +7,6 @@
 
 import spack.builder
 import spack.package_base
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, conflicts
 
 from ._checks import BuilderWithDefaults
@@ -101,9 +99,7 @@ def msbuild_install_args(self):
         as `msbuild_args` by default."""
         return self.msbuild_args()
 
-    def build(
-        self, pkg: MSBuildPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Run "msbuild" on the build targets specified by the builder."""
         with fs.working_dir(self.build_directory):
             pkg.module.msbuild(
@@ -112,9 +108,7 @@ def build(
                 self.define_targets(*self.build_targets),
             )
 
-    def install(
-        self, pkg: MSBuildPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Run "msbuild" on the install targets specified by the builder.
         This is INSTALL by default"""
         with fs.working_dir(self.build_directory):

lib/spack/spack/build_systems/nmake.py

@@ -7,8 +7,6 @@
 
 import spack.builder
 import spack.package_base
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, conflicts
 
 from ._checks import BuilderWithDefaults
@@ -125,9 +123,7 @@ def nmake_install_args(self):
         Individual packages should override to specify NMake args to command line"""
         return []
 
-    def build(
-        self, pkg: NMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Run "nmake" on the build targets specified by the builder."""
         opts = self.std_nmake_args
         opts += self.nmake_args()
@@ -136,9 +132,7 @@ def build(
         with fs.working_dir(self.build_directory):
             pkg.module.nmake(*opts, *self.build_targets, ignore_quotes=self.ignore_quotes)
 
-    def install(
-        self, pkg: NMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Run "nmake" on the install targets specified by the builder.
         This is INSTALL by default"""
         opts = self.std_nmake_args

lib/spack/spack/build_systems/octave.py

@@ -3,8 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import spack.builder
 import spack.package_base
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, extends
 from spack.multimethod import when
 
@@ -44,9 +42,7 @@ class OctaveBuilder(BuilderWithDefaults):
     #: Names associated with package attributes in the old build-system format
     legacy_attributes = ()
 
-    def install(
-        self, pkg: OctavePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Install the package from the archive file"""
         pkg.module.octave(
             "--quiet",

lib/spack/spack/build_systems/perl.py

@@ -10,8 +10,6 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, depends_on, extends
 from spack.install_test import SkipTest, test_part
 from spack.multimethod import when
@@ -151,9 +149,7 @@ def configure_args(self):
         """
         return []
 
-    def configure(
-        self, pkg: PerlPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def configure(self, pkg, spec, prefix):
         """Run Makefile.PL or Build.PL with arguments consisting of
         an appropriate installation base directory followed by the
         list returned by :py:meth:`~.PerlBuilder.configure_args`.
@@ -177,9 +173,7 @@ def fix_shebang(self):
             repl = "#!/usr/bin/env perl"
             filter_file(pattern, repl, "Build", backup=False)
 
-    def build(
-        self, pkg: PerlPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Builds a Perl package."""
         self.build_executable()
 
@@ -190,8 +184,6 @@ def check(self):
         """Runs built-in tests of a Perl package."""
         self.build_executable("test")
 
-    def install(
-        self, pkg: PerlPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Installs a Perl package."""
         self.build_executable("install")

lib/spack/spack/build_systems/python.py

@@ -28,7 +28,6 @@
 import spack.repo
 import spack.spec
 import spack.store
-import spack.util.prefix
 from spack.directives import build_system, depends_on, extends
 from spack.error import NoHeadersError, NoLibrariesError
 from spack.install_test import test_part
@@ -264,17 +263,16 @@ def update_external_dependencies(self, extendee_spec=None):
                     # Ensure architecture information is present
                     if not python.architecture:
                         host_platform = spack.platforms.host()
-                        host_os = host_platform.default_operating_system()
-                        host_target = host_platform.default_target()
+                        host_os = host_platform.operating_system("default_os")
+                        host_target = host_platform.target("default_target")
                         python.architecture = spack.spec.ArchSpec(
                             (str(host_platform), str(host_os), str(host_target))
                         )
                     else:
                         if not python.architecture.platform:
                             python.architecture.platform = spack.platforms.host()
-                        platform = spack.platforms.by_name(python.architecture.platform)
                         if not python.architecture.os:
-                            python.architecture.os = platform.default_operating_system()
+                            python.architecture.os = "default_os"
                         if not python.architecture.target:
                             python.architecture.target = archspec.cpu.host().family.name
 

lib/spack/spack/build_systems/qmake.py

@@ -6,8 +6,6 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, depends_on
 
 from ._checks import BuilderWithDefaults, execute_build_time_tests
@@ -29,7 +27,6 @@ class QMakePackage(spack.package_base.PackageBase):
     build_system("qmake")
 
     depends_on("qmake", type="build", when="build_system=qmake")
-    depends_on("gmake", type="build")
 
 
 @spack.builder.builder("qmake")
@@ -64,23 +61,17 @@ def qmake_args(self):
         """List of arguments passed to qmake."""
         return []
 
-    def qmake(
-        self, pkg: QMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def qmake(self, pkg, spec, prefix):
         """Run ``qmake`` to configure the project and generate a Makefile."""
         with working_dir(self.build_directory):
             pkg.module.qmake(*self.qmake_args())
 
-    def build(
-        self, pkg: QMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Make the build targets"""
         with working_dir(self.build_directory):
             pkg.module.make()
 
-    def install(
-        self, pkg: QMakePackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Make the install targets"""
         with working_dir(self.build_directory):
             pkg.module.make("install")

lib/spack/spack/build_systems/r.py

@@ -94,7 +94,7 @@ def list_url(cls):
         if cls.cran:
             return f"https://cloud.r-project.org/src/contrib/Archive/{cls.cran}/"
 
-    @lang.classproperty
-    def git(cls):
-        if cls.bioc:
-            return f"https://git.bioconductor.org/packages/{cls.bioc}"
+    @property
+    def git(self):
+        if self.bioc:
+            return f"https://git.bioconductor.org/packages/{self.bioc}"

lib/spack/spack/build_systems/racket.py

@@ -9,8 +9,6 @@
 import llnl.util.tty as tty
 
 import spack.builder
-import spack.spec
-import spack.util.prefix
 from spack.build_environment import SPACK_NO_PARALLEL_MAKE
 from spack.config import determine_number_of_jobs
 from spack.directives import build_system, extends, maintainers
@@ -76,22 +74,18 @@ def build_directory(self):
             ret = os.path.join(ret, self.subdirectory)
         return ret
 
-    def install(
-        self, pkg: RacketPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Install everything from build directory."""
         raco = Executable("raco")
         with fs.working_dir(self.build_directory):
-            parallel = pkg.parallel and (not env_flag(SPACK_NO_PARALLEL_MAKE))
-            name = pkg.racket_name
-            assert name is not None, "Racket package name is not set"
+            parallel = self.pkg.parallel and (not env_flag(SPACK_NO_PARALLEL_MAKE))
             args = [
                 "pkg",
                 "install",
                 "-t",
                 "dir",
                 "-n",
-                name,
+                self.pkg.racket_name,
                 "--deps",
                 "fail",
                 "--ignore-implies",
@@ -107,7 +101,8 @@ def install(
             except ProcessError:
                 args.insert(-2, "--skip-installed")
                 raco(*args)
-                tty.warn(
-                    f"Racket package {name} was already installed, uninstalling via "
+                msg = (
+                    "Racket package {0} was already installed, uninstalling via "
                     "Spack may make someone unhappy!"
                 )
+                tty.warn(msg.format(self.pkg.racket_name))

lib/spack/spack/build_systems/rocm.py

@@ -140,7 +140,7 @@ class ROCmPackage(PackageBase):
         when="+rocm",
     )
 
-    depends_on("llvm-amdgpu", type="build", when="+rocm")
+    depends_on("llvm-amdgpu", when="+rocm")
     depends_on("hsa-rocr-dev", when="+rocm")
     depends_on("hip +rocm", when="+rocm")
 

lib/spack/spack/build_systems/ruby.py

@@ -5,8 +5,6 @@
 
 import spack.builder
 import spack.package_base
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, extends, maintainers
 
 from ._checks import BuilderWithDefaults
@@ -44,9 +42,7 @@ class RubyBuilder(BuilderWithDefaults):
     #: Names associated with package attributes in the old build-system format
     legacy_attributes = ()
 
-    def build(
-        self, pkg: RubyPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Build a Ruby gem."""
 
         # ruby-rake provides both rake.gemspec and Rakefile, but only
@@ -62,9 +58,7 @@ def build(
             # Some Ruby packages only ship `*.gem` files, so nothing to build
             pass
 
-    def install(
-        self, pkg: RubyPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Install a Ruby gem.
 
         The ruby package sets ``GEM_HOME`` to tell gem where to install to."""

lib/spack/spack/build_systems/scons.py

@@ -4,8 +4,6 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, depends_on
 
 from ._checks import BuilderWithDefaults, execute_build_time_tests
@@ -61,9 +59,7 @@ def build_args(self, spec, prefix):
         """Arguments to pass to build."""
         return []
 
-    def build(
-        self, pkg: SConsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Build the package."""
         pkg.module.scons(*self.build_args(spec, prefix))
 
@@ -71,9 +67,7 @@ def install_args(self, spec, prefix):
         """Arguments to pass to install."""
         return []
 
-    def install(
-        self, pkg: SConsPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Install the package."""
         pkg.module.scons("install", *self.install_args(spec, prefix))
 

lib/spack/spack/build_systems/sip.py

@@ -11,8 +11,6 @@
 import spack.install_test
 import spack.package_base
 import spack.phase_callbacks
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, depends_on, extends
 from spack.multimethod import when
 from spack.util.executable import Executable
@@ -43,7 +41,6 @@ class SIPPackage(spack.package_base.PackageBase):
     with when("build_system=sip"):
         extends("python", type=("build", "link", "run"))
         depends_on("py-sip", type="build")
-        depends_on("gmake", type="build")
 
     @property
     def import_modules(self):
@@ -133,9 +130,7 @@ class SIPBuilder(BuilderWithDefaults):
 
     build_directory = "build"
 
-    def configure(
-        self, pkg: SIPPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def configure(self, pkg, spec, prefix):
         """Configure the package."""
 
         # https://www.riverbankcomputing.com/static/Docs/sip/command_line_tools.html
@@ -153,9 +148,7 @@ def configure_args(self):
         """Arguments to pass to configure."""
         return []
 
-    def build(
-        self, pkg: SIPPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Build the package."""
         args = self.build_args()
 
@@ -166,9 +159,7 @@ def build_args(self):
         """Arguments to pass to build."""
         return []
 
-    def install(
-        self, pkg: SIPPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Install the package."""
         args = self.install_args()
 

lib/spack/spack/build_systems/waf.py

@@ -6,8 +6,6 @@
 import spack.builder
 import spack.package_base
 import spack.phase_callbacks
-import spack.spec
-import spack.util.prefix
 from spack.directives import build_system, depends_on
 
 from ._checks import BuilderWithDefaults, execute_build_time_tests, execute_install_time_tests
@@ -99,9 +97,7 @@ def waf(self, *args, **kwargs):
         with working_dir(self.build_directory):
             self.python("waf", "-j{0}".format(jobs), *args, **kwargs)
 
-    def configure(
-        self, pkg: WafPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def configure(self, pkg, spec, prefix):
         """Configures the project."""
         args = ["--prefix={0}".format(self.pkg.prefix)]
         args += self.configure_args()
@@ -112,9 +108,7 @@ def configure_args(self):
         """Arguments to pass to configure."""
         return []
 
-    def build(
-        self, pkg: WafPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def build(self, pkg, spec, prefix):
         """Executes the build."""
         args = self.build_args()
 
@@ -124,9 +118,7 @@ def build_args(self):
         """Arguments to pass to build."""
         return []
 
-    def install(
-        self, pkg: WafPackage, spec: spack.spec.Spec, prefix: spack.util.prefix.Prefix
-    ) -> None:
+    def install(self, pkg, spec, prefix):
         """Installs the targets on the system."""
         args = self.install_args()
 

lib/spack/spack/ci/__init__.py

@@ -14,6 +14,7 @@
 import zipfile
 from collections import namedtuple
 from typing import Callable, Dict, List, Set
+from urllib.error import HTTPError, URLError
 from urllib.request import HTTPHandler, Request, build_opener
 
 import llnl.util.filesystem as fs
@@ -471,9 +472,12 @@ def generate_pipeline(env: ev.Environment, args) -> None:
     # Use all unpruned specs to populate the build group for this set
     cdash_config = cfg.get("cdash")
     if options.cdash_handler and options.cdash_handler.auth_token:
-        options.cdash_handler.populate_buildgroup(
-            [options.cdash_handler.build_name(s) for s in pipeline_specs]
-        )
+        try:
+            options.cdash_handler.populate_buildgroup(
+                [options.cdash_handler.build_name(s) for s in pipeline_specs]
+            )
+        except (SpackError, HTTPError, URLError, TimeoutError) as err:
+            tty.warn(f"Problem populating buildgroup: {err}")
     elif cdash_config:
         # warn only if there was actually a CDash configuration.
         tty.warn("Unable to populate buildgroup without CDash credentials")

lib/spack/spack/ci/common.py

@@ -1,21 +1,23 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
+import codecs
 import copy
 import json
 import os
 import re
+import ssl
 import sys
 import time
 from collections import deque
 from enum import Enum
 from typing import Dict, Generator, List, Optional, Set, Tuple
 from urllib.parse import quote, urlencode, urlparse
-from urllib.request import Request
+from urllib.request import HTTPHandler, HTTPSHandler, Request, build_opener
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
-from llnl.util.lang import memoized
+from llnl.util.lang import Singleton, memoized
 
 import spack.binary_distribution as bindist
 import spack.config as cfg
@@ -33,11 +35,32 @@
 from spack.reporters.cdash import SPACK_CDASH_TIMEOUT
 from spack.reporters.cdash import build_stamp as cdash_build_stamp
 
+
+def _urlopen():
+    error_handler = web_util.SpackHTTPDefaultErrorHandler()
+
+    # One opener with HTTPS ssl enabled
+    with_ssl = build_opener(
+        HTTPHandler(), HTTPSHandler(context=web_util.ssl_create_default_context()), error_handler
+    )
+
+    # One opener with HTTPS ssl disabled
+    without_ssl = build_opener(
+        HTTPHandler(), HTTPSHandler(context=ssl._create_unverified_context()), error_handler
+    )
+
+    # And dynamically dispatch based on the config:verify_ssl.
+    def dispatch_open(fullurl, data=None, timeout=None, verify_ssl=True):
+        opener = with_ssl if verify_ssl else without_ssl
+        timeout = timeout or cfg.get("config:connect_timeout", 1)
+        return opener.open(fullurl, data, timeout)
+
+    return dispatch_open
+
+
 IS_WINDOWS = sys.platform == "win32"
 SPACK_RESERVED_TAGS = ["public", "protected", "notary"]
-
-# this exists purely for testing purposes
-_urlopen = web_util.urlopen
+_dyn_mapping_urlopener = Singleton(_urlopen)
 
 
 def copy_files_to_artifacts(src, artifacts_dir):
@@ -256,25 +279,26 @@ def copy_test_results(self, source, dest):
         reports = fs.join_path(source, "*_Test*.xml")
         copy_files_to_artifacts(reports, dest)
 
-    def create_buildgroup(self, headers, url, group_name, group_type):
+    def create_buildgroup(self, opener, headers, url, group_name, group_type):
         data = {"newbuildgroup": group_name, "project": self.project, "type": group_type}
 
         enc_data = json.dumps(data).encode("utf-8")
 
         request = Request(url, data=enc_data, headers=headers)
 
-        try:
-            response_text = _urlopen(request, timeout=SPACK_CDASH_TIMEOUT).read()
-        except OSError as e:
-            tty.warn(f"Failed to create CDash buildgroup: {e}")
+        response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
+        response_code = response.getcode()
+
+        if response_code not in [200, 201]:
+            msg = f"Creating buildgroup failed (response code = {response_code})"
+            tty.warn(msg)
             return None
 
-        try:
-            response_json = json.loads(response_text)
-            return response_json["id"]
-        except (json.JSONDecodeError, KeyError) as e:
-            tty.warn(f"Failed to parse CDash response: {e}")
-            return None
+        response_text = response.read()
+        response_json = json.loads(response_text)
+        build_group_id = response_json["id"]
+
+        return build_group_id
 
     def populate_buildgroup(self, job_names):
         url = f"{self.url}/api/v1/buildgroup.php"
@@ -284,11 +308,16 @@ def populate_buildgroup(self, job_names):
             "Content-Type": "application/json",
         }
 
-        parent_group_id = self.create_buildgroup(headers, url, self.build_group, "Daily")
-        group_id = self.create_buildgroup(headers, url, f"Latest {self.build_group}", "Latest")
+        opener = build_opener(HTTPHandler)
+
+        parent_group_id = self.create_buildgroup(opener, headers, url, self.build_group, "Daily")
+        group_id = self.create_buildgroup(
+            opener, headers, url, f"Latest {self.build_group}", "Latest"
+        )
 
         if not parent_group_id or not group_id:
-            tty.warn(f"Failed to create or retrieve buildgroups for {self.build_group}")
+            msg = f"Failed to create or retrieve buildgroups for {self.build_group}"
+            tty.warn(msg)
             return
 
         data = {
@@ -300,12 +329,15 @@ def populate_buildgroup(self, job_names):
 
         enc_data = json.dumps(data).encode("utf-8")
 
-        request = Request(url, data=enc_data, headers=headers, method="PUT")
+        request = Request(url, data=enc_data, headers=headers)
+        request.get_method = lambda: "PUT"
 
-        try:
-            _urlopen(request, timeout=SPACK_CDASH_TIMEOUT)
-        except OSError as e:
-            tty.warn(f"Failed to populate CDash buildgroup: {e}")
+        response = opener.open(request, timeout=SPACK_CDASH_TIMEOUT)
+        response_code = response.getcode()
+
+        if response_code != 200:
+            msg = f"Error response code ({response_code}) in populate_buildgroup"
+            tty.warn(msg)
 
     def report_skipped(self, spec: spack.spec.Spec, report_dir: str, reason: Optional[str]):
         """Explicitly report skipping testing of a spec (e.g., it's CI
@@ -703,6 +735,9 @@ def _apply_section(dest, src):
                 for value in header.values():
                     value = os.path.expandvars(value)
 
+                verify_ssl = mapping.get("verify_ssl", spack.config.get("config:verify_ssl", True))
+                timeout = mapping.get("timeout", spack.config.get("config:connect_timeout", 1))
+
                 required = mapping.get("require", [])
                 allowed = mapping.get("allow", [])
                 ignored = mapping.get("ignore", [])
@@ -736,15 +771,19 @@ def job_query(job):
                         endpoint_url._replace(query=query).geturl(), headers=header, method="GET"
                     )
                     try:
-                        response = _urlopen(request)
-                        config = json.load(response)
+                        response = _dyn_mapping_urlopener(
+                            request, verify_ssl=verify_ssl, timeout=timeout
+                        )
                     except Exception as e:
                         # For now just ignore any errors from dynamic mapping and continue
                         # This is still experimental, and failures should not stop CI
                         # from running normally
-                        tty.warn(f"Failed to fetch dynamic mapping for query:\n\t{query}: {e}")
+                        tty.warn(f"Failed to fetch dynamic mapping for query:\n\t{query}")
+                        tty.warn(f"{e}")
                         continue
 
+                    config = json.load(codecs.getreader("utf-8")(response))
+
                     # Strip ignore keys
                     if ignored:
                         for key in ignored:

lib/spack/spack/cmd/__init__.py

@@ -202,7 +202,7 @@ def _concretize_spec_pairs(
     # Special case for concretizing a single spec
     if len(to_concretize) == 1:
         abstract, concrete = to_concretize[0]
-        return [concrete or spack.concretize.concretize_one(abstract, tests=tests)]
+        return [concrete or abstract.concretized(tests=tests)]
 
     # Special case if every spec is either concrete or has an abstract hash
     if all(
@@ -254,9 +254,9 @@ def matching_spec_from_env(spec):
     """
     env = ev.active_environment()
     if env:
-        return env.matching_spec(spec) or spack.concretize.concretize_one(spec)
+        return env.matching_spec(spec) or spec.concretized()
     else:
-        return spack.concretize.concretize_one(spec)
+        return spec.concretized()
 
 
 def matching_specs_from_env(specs):
@@ -297,7 +297,7 @@ def disambiguate_spec(
 
 def disambiguate_spec_from_hashes(
     spec: spack.spec.Spec,
-    hashes: Optional[List[str]],
+    hashes: List[str],
     local: bool = False,
     installed: Union[bool, InstallRecordStatus] = True,
     first: bool = False,

lib/spack/spack/cmd/arch.py

@@ -3,7 +3,6 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import collections
-import warnings
 
 import archspec.cpu
 
@@ -52,10 +51,10 @@ def setup_parser(subparser):
         "-t", "--target", action="store_true", default=False, help="print only the target"
     )
     parts2.add_argument(
-        "-f", "--frontend", action="store_true", default=False, help="print frontend (DEPRECATED)"
+        "-f", "--frontend", action="store_true", default=False, help="print frontend"
     )
     parts2.add_argument(
-        "-b", "--backend", action="store_true", default=False, help="print backend (DEPRECATED)"
+        "-b", "--backend", action="store_true", default=False, help="print backend"
     )
 
 
@@ -99,14 +98,15 @@ def arch(parser, args):
         display_targets(archspec.cpu.TARGETS)
         return
 
+    os_args, target_args = "default_os", "default_target"
     if args.frontend:
-        warnings.warn("the argument --frontend is deprecated, and will be removed in Spack v1.0")
+        os_args, target_args = "frontend", "frontend"
     elif args.backend:
-        warnings.warn("the argument --backend is deprecated, and will be removed in Spack v1.0")
+        os_args, target_args = "backend", "backend"
 
     host_platform = spack.platforms.host()
-    host_os = host_platform.default_operating_system()
-    host_target = host_platform.default_target()
+    host_os = host_platform.operating_system(os_args)
+    host_target = host_platform.target(target_args)
     if args.family:
         host_target = host_target.family
     elif args.generic:

lib/spack/spack/cmd/bootstrap.py

@@ -1,7 +1,7 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import os
+import os.path
 import shutil
 import sys
 import tempfile
@@ -14,9 +14,9 @@
 import spack.bootstrap
 import spack.bootstrap.config
 import spack.bootstrap.core
-import spack.concretize
 import spack.config
 import spack.mirrors.utils
+import spack.spec
 import spack.stage
 import spack.util.path
 import spack.util.spack_yaml
@@ -397,7 +397,7 @@ def _mirror(args):
         llnl.util.tty.msg(msg.format(spec_str, mirror_dir))
         # Suppress tty from the call below for terser messages
         llnl.util.tty.set_msg_enabled(False)
-        spec = spack.concretize.concretize_one(spec_str)
+        spec = spack.spec.Spec(spec_str).concretized()
         for node in spec.traverse():
             spack.mirrors.utils.create(mirror_dir, [node])
         llnl.util.tty.set_msg_enabled(True)
@@ -436,7 +436,6 @@ def write_metadata(subdir, metadata):
         shutil.copy(spack.util.path.canonicalize_path(GNUPG_JSON), abs_directory)
         shutil.copy(spack.util.path.canonicalize_path(PATCHELF_JSON), abs_directory)
         instructions += cmd.format("local-binaries", rel_directory)
-        instructions += "  % spack buildcache update-index <final-path>/bootstrap_cache\n"
     print(instructions)
 
 

lib/spack/spack/cmd/buildcache.py

@@ -16,7 +16,6 @@
 
 import spack.binary_distribution as bindist
 import spack.cmd
-import spack.concretize
 import spack.config
 import spack.deptypes as dt
 import spack.environment as ev
@@ -555,7 +554,8 @@ def check_fn(args: argparse.Namespace):
         tty.msg("No specs provided, exiting.")
         return
 
-    specs = [spack.concretize.concretize_one(s) for s in specs]
+    for spec in specs:
+        spec.concretize()
 
     # Next see if there are any configured binary mirrors
     configured_mirrors = spack.config.get("mirrors", scope=args.scope)
@@ -623,7 +623,7 @@ def save_specfile_fn(args):
     root = specs[0]
 
     if not root.concrete:
-        root = spack.concretize.concretize_one(root)
+        root.concretize()
 
     save_dependency_specfiles(
         root, args.specfile_dir, dependencies=spack.cmd.parse_specs(args.specs)

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

@@ -4,7 +4,7 @@
 
 
 import argparse
-import os
+import os.path
 import textwrap
 
 from llnl.util.lang import stable_partition

lib/spack/spack/cmd/containerize.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
+import os.path
 
 import llnl.util.tty
 

lib/spack/spack/cmd/debug.py

@@ -86,8 +86,8 @@ def create_db_tarball(args):
 
 def report(args):
     host_platform = spack.platforms.host()
-    host_os = host_platform.default_operating_system()
-    host_target = host_platform.default_target()
+    host_os = host_platform.operating_system("frontend")
+    host_target = host_platform.target("frontend")
     architecture = spack.spec.ArchSpec((str(host_platform), str(host_os), str(host_target)))
     print("* **Spack:**", spack.get_version())
     print("* **Python:**", platform.python_version())

lib/spack/spack/cmd/deprecate.py

@@ -18,7 +18,6 @@
 from llnl.util.symlink import symlink
 
 import spack.cmd
-import spack.concretize
 import spack.environment as ev
 import spack.installer
 import spack.store
@@ -104,7 +103,7 @@ def deprecate(parser, args):
     )
 
     if args.install:
-        deprecator = spack.concretize.concretize_one(specs[1])
+        deprecator = specs[1].concretized()
     else:
         deprecator = spack.cmd.disambiguate_spec(specs[1], env, local=True)
 

lib/spack/spack/cmd/dev_build.py

@@ -10,7 +10,6 @@
 import spack.build_environment
 import spack.cmd
 import spack.cmd.common.arguments
-import spack.concretize
 import spack.config
 import spack.repo
 from spack.cmd.common import arguments
@@ -114,8 +113,8 @@ def dev_build(self, args):
     source_path = os.path.abspath(source_path)
 
     # Forces the build to run out of the source directory.
-    spec.constrain(f'dev_path="{source_path}"')
-    spec = spack.concretize.concretize_one(spec)
+    spec.constrain("dev_path=%s" % source_path)
+    spec.concretize()
 
     if spec.installed:
         tty.error("Already installed in %s" % spec.prefix)

lib/spack/spack/cmd/help.py

@@ -54,6 +54,10 @@
       @m{target=target}                 specific <target> processor
       @m{arch=platform-os-target}       shortcut for all three above
 
+    cross-compiling:
+      @m{os=backend} or @m{os=be}           build for compute node (backend)
+      @m{os=frontend} or @m{os=fe}          build for login node (frontend)
+
     dependencies:
       ^dependency [constraints]     specify constraints on dependencies
       ^@K{/hash}                        build with a specific installed

lib/spack/spack/cmd/install.py

@@ -13,7 +13,6 @@
 from llnl.util import lang, tty
 
 import spack.cmd
-import spack.concretize
 import spack.config
 import spack.environment as ev
 import spack.paths
@@ -451,7 +450,7 @@ def concrete_specs_from_file(args):
             else:
                 s = spack.spec.Spec.from_json(f)
 
-        concretized = spack.concretize.concretize_one(s)
+        concretized = s.concretized()
         if concretized.dag_hash() != s.dag_hash():
             msg = 'skipped invalid file "{0}". '
             msg += "The file does not contain a concrete spec."

lib/spack/spack/cmd/make_installer.py

@@ -7,9 +7,9 @@
 
 from llnl.path import convert_to_posix_path
 
-import spack.concretize
 import spack.paths
 import spack.util.executable
+from spack.spec import Spec
 
 description = "generate Windows installer"
 section = "admin"
@@ -65,7 +65,8 @@ def make_installer(parser, args):
     """
     if sys.platform == "win32":
         output_dir = args.output_dir
-        cmake_spec = spack.concretize.concretize_one("cmake")
+        cmake_spec = Spec("cmake")
+        cmake_spec.concretize()
         cmake_path = os.path.join(cmake_spec.prefix, "bin", "cmake.exe")
         cpack_path = os.path.join(cmake_spec.prefix, "bin", "cpack.exe")
         spack_source = args.spack_source

lib/spack/spack/cmd/mirror.py

@@ -492,7 +492,7 @@ def extend_with_additional_versions(specs, num_versions):
         mirror_specs = spack.mirrors.utils.get_all_versions(specs)
     else:
         mirror_specs = spack.mirrors.utils.get_matching_versions(specs, num_versions=num_versions)
-    mirror_specs = [spack.concretize.concretize_one(x) for x in mirror_specs]
+    mirror_specs = [x.concretized() for x in mirror_specs]
     return mirror_specs
 
 

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

@@ -5,7 +5,7 @@
 """Implementation details of the ``spack module`` command."""
 
 import collections
-import os
+import os.path
 import shutil
 import sys
 

lib/spack/spack/cmd/tutorial.py

@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os
+import os.path
 import shutil
 
 import llnl.util.tty as tty

lib/spack/spack/cmd/uninstall.py

@@ -144,7 +144,7 @@ def is_installed(spec):
         record = spack.store.STORE.db.query_local_by_spec_hash(spec.dag_hash())
         return record and record.installed
 
-    all_specs = traverse.traverse_nodes(
+    specs = traverse.traverse_nodes(
         specs,
         root=False,
         order="breadth",
@@ -155,7 +155,7 @@ def is_installed(spec):
     )
 
     with spack.store.STORE.db.read_transaction():
-        return [spec for spec in all_specs if is_installed(spec)]
+        return [spec for spec in specs if is_installed(spec)]
 
 
 def dependent_environments(

lib/spack/spack/cmd/unit_test.py

@@ -5,7 +5,7 @@
 import argparse
 import collections
 import io
-import os
+import os.path
 import re
 import sys
 

lib/spack/spack/compilers/__init__.py

@@ -801,17 +801,17 @@ def _extract_compiler_paths(spec: "spack.spec.Spec") -> Optional[Dict[str, str]]
     def _extract_os_and_target(spec: "spack.spec.Spec"):
         if not spec.architecture:
             host_platform = spack.platforms.host()
-            operating_system = host_platform.default_operating_system()
-            target = host_platform.default_target()
+            operating_system = host_platform.operating_system("default_os")
+            target = host_platform.target("default_target")
         else:
             target = spec.architecture.target
             if not target:
-                target = spack.platforms.host().default_target()
+                target = spack.platforms.host().target("default_target")
 
             operating_system = spec.os
             if not operating_system:
                 host_platform = spack.platforms.host()
-                operating_system = host_platform.default_operating_system()
+                operating_system = host_platform.operating_system("default_os")
         return operating_system, target
 
 

lib/spack/spack/concretize.py

@@ -37,12 +37,13 @@ def enable_compiler_existence_check():
 
 SpecPairInput = Tuple[Spec, Optional[Spec]]
 SpecPair = Tuple[Spec, Spec]
+SpecLike = Union[Spec, str]
 TestsType = Union[bool, Iterable[str]]
 
 
-def _concretize_specs_together(
-    abstract_specs: Sequence[Spec], tests: TestsType = False
-) -> List[Spec]:
+def concretize_specs_together(
+    abstract_specs: Sequence[SpecLike], tests: TestsType = False
+) -> Sequence[Spec]:
     """Given a number of specs as input, tries to concretize them together.
 
     Args:
@@ -50,10 +51,11 @@ def _concretize_specs_together(
         tests: list of package names for which to consider tests dependencies. If True, all nodes
             will have test dependencies. If False, test dependencies will be disregarded.
     """
-    from spack.solver.asp import Solver
+    import spack.solver.asp
 
     allow_deprecated = spack.config.get("config:deprecated", False)
-    result = Solver().solve(abstract_specs, tests=tests, allow_deprecated=allow_deprecated)
+    solver = spack.solver.asp.Solver()
+    result = solver.solve(abstract_specs, tests=tests, allow_deprecated=allow_deprecated)
     return [s.copy() for s in result.specs]
 
 
@@ -70,7 +72,7 @@ def concretize_together(
     """
     to_concretize = [concrete if concrete else abstract for abstract, concrete in spec_list]
     abstract_specs = [abstract for abstract, _ in spec_list]
-    concrete_specs = _concretize_specs_together(to_concretize, tests=tests)
+    concrete_specs = concretize_specs_together(to_concretize, tests=tests)
     return list(zip(abstract_specs, concrete_specs))
 
 
@@ -88,7 +90,7 @@ def concretize_together_when_possible(
         tests: list of package names for which to consider tests dependencies. If True, all nodes
             will have test dependencies. If False, test dependencies will be disregarded.
     """
-    from spack.solver.asp import Solver
+    import spack.solver.asp
 
     to_concretize = [concrete if concrete else abstract for abstract, concrete in spec_list]
     old_concrete_to_abstract = {
@@ -96,8 +98,9 @@ def concretize_together_when_possible(
     }
 
     result_by_user_spec = {}
+    solver = spack.solver.asp.Solver()
     allow_deprecated = spack.config.get("config:deprecated", False)
-    for result in Solver().solve_in_rounds(
+    for result in solver.solve_in_rounds(
         to_concretize, tests=tests, allow_deprecated=allow_deprecated
     ):
         result_by_user_spec.update(result.specs_by_input)
@@ -121,7 +124,7 @@ def concretize_separately(
         tests: list of package names for which to consider tests dependencies. If True, all nodes
             will have test dependencies. If False, test dependencies will be disregarded.
     """
-    from spack.bootstrap import ensure_bootstrap_configuration, ensure_clingo_importable_or_raise
+    import spack.bootstrap
 
     to_concretize = [abstract for abstract, concrete in spec_list if not concrete]
     args = [
@@ -131,8 +134,8 @@ def concretize_separately(
     ]
     ret = [(i, abstract) for i, abstract in enumerate(to_concretize) if abstract.concrete]
     # Ensure we don't try to bootstrap clingo in parallel
-    with ensure_bootstrap_configuration():
-        ensure_clingo_importable_or_raise()
+    with spack.bootstrap.ensure_bootstrap_configuration():
+        spack.bootstrap.ensure_clingo_importable_or_raise()
 
     # Ensure all the indexes have been built or updated, since
     # otherwise the processes in the pool may timeout on waiting
@@ -187,52 +190,10 @@ def _concretize_task(packed_arguments: Tuple[int, str, TestsType]) -> Tuple[int,
     index, spec_str, tests = packed_arguments
     with tty.SuppressOutput(msg_enabled=False):
         start = time.time()
-        spec = concretize_one(Spec(spec_str), tests=tests)
+        spec = Spec(spec_str).concretized(tests=tests)
         return index, spec, time.time() - start
 
 
-def concretize_one(spec: Union[str, Spec], tests: TestsType = False) -> Spec:
-    """Return a concretized copy of the given spec.
-
-    Args:
-        tests: if False disregard 'test' dependencies, if a list of names activate them for
-            the packages in the list, if True activate 'test' dependencies for all packages.
-    """
-    from spack.solver.asp import Solver, SpecBuilder
-
-    if isinstance(spec, str):
-        spec = Spec(spec)
-    spec = spec.lookup_hash()
-
-    if spec.concrete:
-        return spec.copy()
-
-    for node in spec.traverse():
-        if not node.name:
-            raise spack.error.SpecError(
-                f"Spec {node} has no name; cannot concretize an anonymous spec"
-            )
-
-    allow_deprecated = spack.config.get("config:deprecated", False)
-    result = Solver().solve([spec], tests=tests, allow_deprecated=allow_deprecated)
-
-    # take the best answer
-    opt, i, answer = min(result.answers)
-    name = spec.name
-    # TODO: Consolidate this code with similar code in solve.py
-    if spec.virtual:
-        providers = [s.name for s in answer.values() if s.package.provides(name)]
-        name = providers[0]
-
-    node = SpecBuilder.make_node(pkg=name)
-    assert (
-        node in answer
-    ), f"cannot find {name} in the list of specs {','.join([n.pkg for n in answer.keys()])}"
-
-    concretized = answer[node]
-    return concretized
-
-
 class UnavailableCompilerVersionError(spack.error.SpackError):
     """Raised when there is no available compiler that satisfies a
     compiler spec."""

lib/spack/spack/config.py

@@ -36,8 +36,6 @@
 import sys
 from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union
 
-import jsonschema
-
 from llnl.util import filesystem, lang, tty
 
 import spack.error
@@ -53,7 +51,6 @@
 import spack.schema.definitions
 import spack.schema.develop
 import spack.schema.env
-import spack.schema.env_vars
 import spack.schema.mirrors
 import spack.schema.modules
 import spack.schema.packages
@@ -71,7 +68,6 @@
     "compilers": spack.schema.compilers.schema,
     "concretizer": spack.schema.concretizer.schema,
     "definitions": spack.schema.definitions.schema,
-    "env_vars": spack.schema.env_vars.schema,
     "view": spack.schema.view.schema,
     "develop": spack.schema.develop.schema,
     "mirrors": spack.schema.mirrors.schema,
@@ -1052,6 +1048,8 @@ def validate(
     This leverages the line information (start_mark, end_mark) stored
     on Spack YAML structures.
     """
+    import jsonschema
+
     try:
         spack.schema.Validator(schema).validate(data)
     except jsonschema.ValidationError as e:

lib/spack/spack/container/__init__.py

@@ -6,8 +6,6 @@
 """
 import warnings
 
-import jsonschema
-
 import spack.environment as ev
 import spack.schema.env as env
 import spack.util.spack_yaml as syaml
@@ -32,6 +30,8 @@ def validate(configuration_file):
     Returns:
         A sanitized copy of the configuration stored in the input file
     """
+    import jsonschema
+
     with open(configuration_file, encoding="utf-8") as f:
         config = syaml.load(f)
 

lib/spack/spack/container/images.py

@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Manages the details on the images used in the various stages."""
 import json
-import os
+import os.path
 import shlex
 import sys
 

lib/spack/spack/container/writers.py

@@ -9,8 +9,6 @@
 from collections import namedtuple
 from typing import Optional
 
-import jsonschema
-
 import spack.environment as ev
 import spack.error
 import spack.schema.env
@@ -190,6 +188,8 @@ def paths(self):
     @tengine.context_property
     def manifest(self):
         """The spack.yaml file that should be used in the image"""
+        import jsonschema
+
         # Copy in the part of spack.yaml prescribed in the configuration file
         manifest = copy.deepcopy(self.config)
         manifest.pop("container")

lib/spack/spack/database.py

@@ -123,15 +123,6 @@
     "deprecated_for",
 )
 
-#: File where the database is written
-INDEX_JSON_FILE = "index.json"
-
-# Verifier file to check last modification of the DB
-_INDEX_VERIFIER_FILE = "index_verifier"
-
-# Lockfile for the database
-_LOCK_FILE = "lock"
-
 
 @llnl.util.lang.memoized
 def _getfqdn():
@@ -269,7 +260,7 @@ class ForbiddenLockError(SpackError):
 
 class ForbiddenLock:
     def __getattr__(self, name):
-        raise ForbiddenLockError(f"Cannot access attribute '{name}' of lock")
+        raise ForbiddenLockError("Cannot access attribute '{0}' of lock".format(name))
 
     def __reduce__(self):
         return ForbiddenLock, tuple()
@@ -428,25 +419,14 @@ class FailureTracker:
     the likelihood of collision very low with no cleanup required.
     """
 
-    #: root directory of the failure tracker
-    dir: pathlib.Path
-
-    #: File for locking particular concrete spec hashes
-    locker: SpecLocker
-
     def __init__(self, root_dir: Union[str, pathlib.Path], default_timeout: Optional[float]):
         #: Ensure a persistent location for dealing with parallel installation
         #: failures (e.g., across near-concurrent processes).
         self.dir = pathlib.Path(root_dir) / _DB_DIRNAME / "failures"
-        self.locker = SpecLocker(failures_lock_path(root_dir), default_timeout=default_timeout)
-
-    def _ensure_parent_directories(self) -> None:
-        """Ensure that parent directories of the FailureTracker exist.
-
-        Accesses the filesystem only once, the first time it's called on a given FailureTracker.
-        """
         self.dir.mkdir(parents=True, exist_ok=True)
 
+        self.locker = SpecLocker(failures_lock_path(root_dir), default_timeout=default_timeout)
+
     def clear(self, spec: "spack.spec.Spec", force: bool = False) -> None:
         """Removes any persistent and cached failure tracking for the spec.
 
@@ -489,18 +469,13 @@ def clear_all(self) -> None:
 
         tty.debug("Removing prefix failure tracking files")
         try:
-            marks = os.listdir(str(self.dir))
-        except FileNotFoundError:
-            return  # directory doesn't exist yet
+            for fail_mark in os.listdir(str(self.dir)):
+                try:
+                    (self.dir / fail_mark).unlink()
+                except OSError as exc:
+                    tty.warn(f"Unable to remove failure marking file {fail_mark}: {str(exc)}")
         except OSError as exc:
             tty.warn(f"Unable to remove failure marking files: {str(exc)}")
-            return
-
-        for fail_mark in marks:
-            try:
-                (self.dir / fail_mark).unlink()
-            except OSError as exc:
-                tty.warn(f"Unable to remove failure marking file {fail_mark}: {str(exc)}")
 
     def mark(self, spec: "spack.spec.Spec") -> lk.Lock:
         """Marks a spec as failing to install.
@@ -508,8 +483,6 @@ def mark(self, spec: "spack.spec.Spec") -> lk.Lock:
         Args:
             spec: spec that failed to install
         """
-        self._ensure_parent_directories()
-
         # Dump the spec to the failure file for (manual) debugging purposes
         path = self._path(spec)
         path.write_text(spec.to_json())
@@ -594,13 +567,17 @@ def __init__(
                 Relevant only if the repository is not an upstream.
         """
         self.root = root
-        self.database_directory = pathlib.Path(self.root) / _DB_DIRNAME
+        self.database_directory = os.path.join(self.root, _DB_DIRNAME)
         self.layout = layout
 
         # Set up layout of database files within the db dir
-        self._index_path = self.database_directory / INDEX_JSON_FILE
-        self._verifier_path = self.database_directory / _INDEX_VERIFIER_FILE
-        self._lock_path = self.database_directory / _LOCK_FILE
+        self._index_path = os.path.join(self.database_directory, "index.json")
+        self._verifier_path = os.path.join(self.database_directory, "index_verifier")
+        self._lock_path = os.path.join(self.database_directory, "lock")
+
+        # Create needed directories and files
+        if not is_upstream and not os.path.exists(self.database_directory):
+            fs.mkdirp(self.database_directory)
 
         self.is_upstream = is_upstream
         self.last_seen_verifier = ""
@@ -615,14 +592,14 @@ def __init__(
 
         # initialize rest of state.
         self.db_lock_timeout = lock_cfg.database_timeout
-        tty.debug(f"DATABASE LOCK TIMEOUT: {str(self.db_lock_timeout)}s")
+        tty.debug("DATABASE LOCK TIMEOUT: {0}s".format(str(self.db_lock_timeout)))
 
         self.lock: Union[ForbiddenLock, lk.Lock]
         if self.is_upstream:
             self.lock = ForbiddenLock()
         else:
             self.lock = lk.Lock(
-                str(self._lock_path),
+                self._lock_path,
                 default_timeout=self.db_lock_timeout,
                 desc="database",
                 enable=lock_cfg.enable,
@@ -639,11 +616,6 @@ def __init__(
         self._write_transaction_impl = lk.WriteTransaction
         self._read_transaction_impl = lk.ReadTransaction
 
-    def _ensure_parent_directories(self):
-        """Create the parent directory for the DB, if necessary."""
-        if not self.is_upstream:
-            self.database_directory.mkdir(parents=True, exist_ok=True)
-
     def write_transaction(self):
         """Get a write lock context manager for use in a `with` block."""
         return self._write_transaction_impl(self.lock, acquire=self._read, release=self._write)
@@ -658,8 +630,6 @@ def _write_to_file(self, stream):
 
         This function does not do any locking or transactions.
         """
-        self._ensure_parent_directories()
-
         # map from per-spec hash code to installation record.
         installs = dict(
             (k, v.to_dict(include_fields=self.record_fields)) for k, v in self._data.items()
@@ -789,7 +759,7 @@ def _read_from_file(self, filename):
         Does not do any locking.
         """
         try:
-            with open(str(filename), "r", encoding="utf-8") as f:
+            with open(filename, "r", encoding="utf-8") as f:
                 # In the future we may use a stream of JSON objects, hence `raw_decode` for compat.
                 fdata, _ = JSONDecoder().raw_decode(f.read())
         except Exception as e:
@@ -890,13 +860,11 @@ def reindex(self):
         if self.is_upstream:
             raise UpstreamDatabaseLockingError("Cannot reindex an upstream database")
 
-        self._ensure_parent_directories()
-
         # Special transaction to avoid recursive reindex calls and to
         # ignore errors if we need to rebuild a corrupt database.
         def _read_suppress_error():
             try:
-                if self._index_path.is_file():
+                if os.path.isfile(self._index_path):
                     self._read_from_file(self._index_path)
             except CorruptDatabaseError as e:
                 tty.warn(f"Reindexing corrupt database, error was: {e}")
@@ -1039,7 +1007,7 @@ def _check_ref_counts(self):
                     % (key, found, expected, self._index_path)
                 )
 
-    def _write(self, type=None, value=None, traceback=None):
+    def _write(self, type, value, traceback):
         """Write the in-memory database index to its file path.
 
         This is a helper function called by the WriteTransaction context
@@ -1050,8 +1018,6 @@ def _write(self, type=None, value=None, traceback=None):
 
         This routine does no locking.
         """
-        self._ensure_parent_directories()
-
         # Do not write if exceptions were raised
         if type is not None:
             # A failure interrupted a transaction, so we should record that
@@ -1060,16 +1026,16 @@ def _write(self, type=None, value=None, traceback=None):
             self._state_is_inconsistent = True
             return
 
-        temp_file = str(self._index_path) + (".%s.%s.temp" % (_getfqdn(), os.getpid()))
+        temp_file = self._index_path + (".%s.%s.temp" % (_getfqdn(), os.getpid()))
 
         # Write a temporary database file them move it into place
         try:
             with open(temp_file, "w", encoding="utf-8") as f:
                 self._write_to_file(f)
-            fs.rename(temp_file, str(self._index_path))
+            fs.rename(temp_file, self._index_path)
 
             if _use_uuid:
-                with self._verifier_path.open("w", encoding="utf-8") as f:
+                with open(self._verifier_path, "w", encoding="utf-8") as f:
                     new_verifier = str(uuid.uuid4())
                     f.write(new_verifier)
                     self.last_seen_verifier = new_verifier
@@ -1082,11 +1048,11 @@ def _write(self, type=None, value=None, traceback=None):
 
     def _read(self):
         """Re-read Database from the data in the set location. This does no locking."""
-        if self._index_path.is_file():
+        if os.path.isfile(self._index_path):
             current_verifier = ""
             if _use_uuid:
                 try:
-                    with self._verifier_path.open("r", encoding="utf-8") as f:
+                    with open(self._verifier_path, "r", encoding="utf-8") as f:
                         current_verifier = f.read()
                 except BaseException:
                     pass
@@ -1099,7 +1065,7 @@ def _read(self):
                 self._state_is_inconsistent = False
             return
         elif self.is_upstream:
-            tty.warn(f"upstream not found: {self._index_path}")
+            tty.warn("upstream not found: {0}".format(self._index_path))
 
     def _add(
         self,
@@ -1364,7 +1330,7 @@ def deprecate(self, spec: "spack.spec.Spec", deprecator: "spack.spec.Spec") -> N
     def installed_relatives(
         self,
         spec: "spack.spec.Spec",
-        direction: tr.DirectionType = "children",
+        direction: str = "children",
         transitive: bool = True,
         deptype: Union[dt.DepFlag, dt.DepTypes] = dt.ALL,
     ) -> Set["spack.spec.Spec"]:
@@ -1715,7 +1681,7 @@ def query(
             )
 
         results = list(local_results) + list(x for x in upstream_results if x not in local_results)
-        results.sort()  # type: ignore[call-overload]
+        results.sort()
         return results
 
     def query_one(

lib/spack/spack/detection/common.py

@@ -15,6 +15,7 @@
 import glob
 import itertools
 import os
+import os.path
 import pathlib
 import re
 import sys

lib/spack/spack/detection/path.py

@@ -7,6 +7,7 @@
 import collections
 import concurrent.futures
 import os
+import os.path
 import re
 import sys
 import traceback

lib/spack/spack/directives.py

@@ -32,7 +32,7 @@ class OpenMpi(Package):
 """
 import collections
 import collections.abc
-import os
+import os.path
 import re
 from typing import Any, Callable, List, Optional, Tuple, Type, Union
 

lib/spack/spack/environment/shell.py

@@ -10,7 +10,6 @@
 
 import spack.environment as ev
 import spack.repo
-import spack.schema.environment
 import spack.store
 from spack.util.environment import EnvironmentModifications
 
@@ -157,11 +156,6 @@ def activate(
     # MANPATH, PYTHONPATH, etc. All variables that end in PATH (case-sensitive)
     # become PATH variables.
     #
-
-    env_vars_yaml = env.manifest.configuration.get("env_vars", None)
-    if env_vars_yaml:
-        env_mods.extend(spack.schema.environment.parse(env_vars_yaml))
-
     try:
         if view and env.has_view(view):
             with spack.store.STORE.db.read_transaction():
@@ -195,10 +189,6 @@ def deactivate() -> EnvironmentModifications:
     if active is None:
         return env_mods
 
-    env_vars_yaml = active.manifest.configuration.get("env_vars", None)
-    if env_vars_yaml:
-        env_mods.extend(spack.schema.environment.parse(env_vars_yaml).reversed())
-
     active_view = os.getenv(ev.spack_env_view_var)
 
     if active_view and active.has_view(active_view):

lib/spack/spack/fetch_strategy.py

@@ -25,6 +25,7 @@
 import functools
 import http.client
 import os
+import os.path
 import re
 import shutil
 import urllib.error
@@ -320,15 +321,9 @@ def _fetch_urllib(self, url):
 
         request = urllib.request.Request(url, headers={"User-Agent": web_util.SPACK_USER_AGENT})
 
-        if os.path.lexists(save_file):
-            os.remove(save_file)
-
         try:
             response = web_util.urlopen(request)
-            tty.msg(f"Fetching {url}")
-            with open(save_file, "wb") as f:
-                shutil.copyfileobj(response, f)
-        except OSError as e:
+        except (TimeoutError, urllib.error.URLError) as e:
             # clean up archive on failure.
             if self.archive_file:
                 os.remove(self.archive_file)
@@ -336,6 +331,14 @@ def _fetch_urllib(self, url):
                 os.remove(save_file)
             raise FailedDownloadError(e) from e
 
+        tty.msg(f"Fetching {url}")
+
+        if os.path.lexists(save_file):
+            os.remove(save_file)
+
+        with open(save_file, "wb") as f:
+            shutil.copyfileobj(response, f)
+
         # Save the redirected URL for error messages. Sometimes we're redirected to an arbitrary
         # mirror that is broken, leading to spurious download failures. In that case it's helpful
         # for users to know which URL was actually fetched.
@@ -532,16 +535,11 @@ def __init__(self, *, url: str, checksum: Optional[str] = None, **kwargs):
     @_needs_stage
     def fetch(self):
         file = self.stage.save_filename
-
-        if os.path.lexists(file):
-            os.remove(file)
+        tty.msg(f"Fetching {self.url}")
 
         try:
             response = self._urlopen(self.url)
-            tty.msg(f"Fetching {self.url}")
-            with open(file, "wb") as f:
-                shutil.copyfileobj(response, f)
-        except OSError as e:
+        except (TimeoutError, urllib.error.URLError) as e:
             # clean up archive on failure.
             if self.archive_file:
                 os.remove(self.archive_file)
@@ -549,6 +547,12 @@ def fetch(self):
                 os.remove(file)
             raise FailedDownloadError(e) from e
 
+        if os.path.lexists(file):
+            os.remove(file)
+
+        with open(file, "wb") as f:
+            shutil.copyfileobj(response, f)
+
 
 class VCSFetchStrategy(FetchStrategy):
     """Superclass for version control system fetch strategies.

lib/spack/spack/filesystem_view.py

@@ -35,6 +35,7 @@
 
 import spack.config
 import spack.directory_layout
+import spack.paths
 import spack.projections
 import spack.relocate
 import spack.schema.projections
@@ -43,6 +44,7 @@
 import spack.util.spack_json as s_json
 import spack.util.spack_yaml as s_yaml
 from spack.error import SpackError
+from spack.hooks import sbang
 
 __all__ = ["FilesystemView", "YamlFilesystemView"]
 
@@ -89,10 +91,16 @@ def view_copy(
     if stat.S_ISLNK(src_stat.st_mode):
         spack.relocate.relocate_links(links=[dst], prefix_to_prefix=prefix_to_projection)
     elif spack.relocate.is_binary(dst):
-        spack.relocate.relocate_text_bin(binaries=[dst], prefix_to_prefix=prefix_to_projection)
+        spack.relocate.relocate_text_bin(binaries=[dst], prefixes=prefix_to_projection)
     else:
         prefix_to_projection[spack.store.STORE.layout.root] = view._root
-        spack.relocate.relocate_text(files=[dst], prefix_to_prefix=prefix_to_projection)
+
+        # This is vestigial code for the *old* location of sbang.
+        prefix_to_projection[f"#!/bin/bash {spack.paths.spack_root}/bin/sbang"] = (
+            sbang.sbang_shebang_line()
+        )
+
+        spack.relocate.relocate_text(files=[dst], prefixes=prefix_to_projection)
 
     # The os module on Windows does not have a chown function.
     if sys.platform != "win32":

lib/spack/spack/installer.py

@@ -275,7 +275,7 @@ def _do_fake_install(pkg: "spack.package_base.PackageBase") -> None:
     fs.mkdirp(pkg.prefix.bin)
     fs.touch(os.path.join(pkg.prefix.bin, command))
     if sys.platform != "win32":
-        chmod = which("chmod", required=True)
+        chmod = which("chmod")
         chmod("+x", os.path.join(pkg.prefix.bin, command))
 
     # Install fake header file
@@ -539,7 +539,7 @@ def dump_packages(spec: "spack.spec.Spec", path: str) -> None:
     # Note that we copy them in as they are in the *install* directory
     # NOT as they are in the repository, because we want a snapshot of
     # how *this* particular build was done.
-    for node in spec.traverse(deptype="all"):
+    for node in spec.traverse(deptype=all):
         if node is not spec:
             # Locate the dependency package in the install tree and find
             # its provenance information.

lib/spack/spack/main.py

@@ -14,6 +14,7 @@
 import io
 import operator
 import os
+import os.path
 import pstats
 import re
 import shlex
@@ -728,7 +729,7 @@ def _compatible_sys_types():
     with the current host.
     """
     host_platform = spack.platforms.host()
-    host_os = str(host_platform.default_operating_system())
+    host_os = str(host_platform.operating_system("default_os"))
     host_target = archspec.cpu.host()
     compatible_targets = [host_target] + host_target.ancestors
 

lib/spack/spack/mirrors/layout.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
+import os.path
 from typing import Optional
 
 import llnl.url

lib/spack/spack/mirrors/utils.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import os
+import os.path
 import traceback
 
 import llnl.util.tty as tty

lib/spack/spack/modules/common.py

@@ -31,7 +31,7 @@
 import copy
 import datetime
 import inspect
-import os
+import os.path
 import re
 import string
 from typing import List, Optional

lib/spack/spack/modules/lmod.py

@@ -4,7 +4,7 @@
 
 import collections
 import itertools
-import os
+import os.path
 from typing import Dict, List, Optional, Tuple
 
 import llnl.util.filesystem as fs

lib/spack/spack/modules/tcl.py

@@ -5,7 +5,7 @@
 """This module implements the classes necessary to generate Tcl
 non-hierarchical modules.
 """
-import os
+import os.path
 from typing import Dict, Optional, Tuple
 
 import spack.config

lib/spack/spack/oci/opener.py

@@ -7,7 +7,6 @@
 import base64
 import json
 import re
-import socket
 import time
 import urllib.error
 import urllib.parse
@@ -411,7 +410,7 @@ def wrapper(*args, **kwargs):
         for i in range(retries):
             try:
                 return f(*args, **kwargs)
-            except OSError as e:
+            except (urllib.error.URLError, TimeoutError) as e:
                 # Retry on internal server errors, and rate limit errors
                 # Potentially this could take into account the Retry-After header
                 # if registries support it
@@ -421,10 +420,9 @@ def wrapper(*args, **kwargs):
                         and (500 <= e.code < 600 or e.code == 429)
                     )
                     or (
-                        isinstance(e, urllib.error.URLError)
-                        and isinstance(e.reason, socket.timeout)
+                        isinstance(e, urllib.error.URLError) and isinstance(e.reason, TimeoutError)
                     )
-                    or isinstance(e, socket.timeout)
+                    or isinstance(e, TimeoutError)
                 ):
                     # Exponential backoff
                     sleep(2**i)

lib/spack/spack/operating_systems/_operating_system.py

@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import llnl.util.lang
 
+import spack.util.spack_yaml as syaml
+
 
 @llnl.util.lang.lazy_lexicographic_ordering
 class OperatingSystem:
@@ -40,4 +42,4 @@ def _cmp_iter(self):
         yield self.version
 
     def to_dict(self):
-        return {"name": self.name, "version": self.version}
+        return syaml.syaml_dict([("name", self.name), ("version", self.version)])

lib/spack/spack/package.py

@@ -3,52 +3,29 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 # flake8: noqa: F401
-"""spack.package defines the public API for Spack packages, by re-exporting useful symbols from
-other modules. Packages should import this module, instead of importing from spack.* directly
-to ensure forward compatibility with future versions of Spack."""
+"""spack.util.package is a set of useful build tools and directives for packages.
 
+Everything in this module is automatically imported into Spack package files.
+"""
 from os import chdir, environ, getcwd, makedirs, mkdir, remove, removedirs
 from shutil import move, rmtree
 
+from spack.error import InstallError, NoHeadersError, NoLibrariesError
+
+# Emulate some shell commands for convenience
+env = environ
+cd = chdir
+pwd = getcwd
+
 # import most common types used in packages
 from typing import Dict, List, Optional
 
-from llnl.util.filesystem import (
-    FileFilter,
-    FileList,
-    HeaderList,
-    LibraryList,
-    ancestor,
-    can_access,
-    change_sed_delimiter,
-    copy,
-    copy_tree,
-    filter_file,
-    find,
-    find_all_headers,
-    find_first,
-    find_headers,
-    find_libraries,
-    find_system_libraries,
-    force_remove,
-    force_symlink,
-    install,
-    install_tree,
-    is_exe,
-    join_path,
-    keep_modification_time,
-    library_extensions,
-    mkdirp,
-    remove_directory_contents,
-    remove_linked_tree,
-    rename,
-    set_executable,
-    set_install_permissions,
-    touch,
-    working_dir,
-)
+import llnl.util.filesystem
+from llnl.util.filesystem import *
 from llnl.util.symlink import symlink
 
+import spack.util.executable
+
 # These props will be overridden when the build env is set up.
 from spack.build_environment import MakeExecutable
 from spack.build_systems.aspell_dict import AspellDictPackage
@@ -99,24 +76,7 @@
 from spack.builder import BaseBuilder
 from spack.config import determine_number_of_jobs
 from spack.deptypes import ALL_TYPES as all_deptypes
-from spack.directives import (
-    build_system,
-    can_splice,
-    conditional,
-    conflicts,
-    depends_on,
-    extends,
-    license,
-    maintainers,
-    patch,
-    provides,
-    redistribute,
-    requires,
-    resource,
-    variant,
-    version,
-)
-from spack.error import InstallError, NoHeadersError, NoLibrariesError
+from spack.directives import *
 from spack.install_test import (
     SkipTest,
     cache_extra_test_sources,
@@ -126,36 +86,28 @@
     install_test_root,
     test_part,
 )
+from spack.installer import ExternalPackageError, InstallLockError, UpstreamPackageError
 from spack.mixins import filter_compiler_wrappers
 from spack.multimethod import default_args, when
-from spack.package_base import build_system_flags, env_flags, inject_flags, on_package_attributes
-from spack.package_completions import (
-    bash_completion_path,
-    fish_completion_path,
-    zsh_completion_path,
+from spack.package_base import (
+    DependencyConflictError,
+    build_system_flags,
+    env_flags,
+    flatten_dependencies,
+    inject_flags,
+    install_dependency_symlinks,
+    on_package_attributes,
 )
+from spack.package_completions import *
 from spack.phase_callbacks import run_after, run_before
-from spack.spec import Spec
-from spack.util.executable import Executable, ProcessError, which, which_string
+from spack.spec import InvalidSpecDetected, Spec
+from spack.util.executable import *
 from spack.util.filesystem import fix_darwin_install_name
 from spack.variant import any_combination_of, auto_or_any_combination_of, disjoint_sets
 from spack.version import Version, ver
 
-# Emulate some shell commands for convenience
-env = environ
-cd = chdir
-pwd = getcwd
-
-# These are just here for editor support; they may be set when the build env is set up.
-configure: Executable
-make_jobs: int
-make: MakeExecutable
-ninja: MakeExecutable
-python_include: str
-python_platlib: str
-python_purelib: str
-python: Executable
-spack_cc: str
-spack_cxx: str
-spack_f77: str
-spack_fc: str
+# These are just here for editor support; they will be replaced when the build env
+# is set up.
+make = MakeExecutable("make", jobs=1)
+ninja = MakeExecutable("ninja", jobs=1)
+configure = Executable(join_path(".", "configure"))

lib/spack/spack/package_base.py

@@ -30,6 +30,7 @@
 import llnl.util.filesystem as fsys
 import llnl.util.tty as tty
 from llnl.util.lang import classproperty, memoized
+from llnl.util.link_tree import LinkTree
 
 import spack.compilers
 import spack.config
@@ -766,9 +767,6 @@ def __init__(self, spec):
         self.win_rpath = fsys.WindowsSimulatedRPath(self)
         super().__init__()
 
-    def __getitem__(self, key: str) -> "PackageBase":
-        return self.spec[key].package
-
     @classmethod
     def dependency_names(cls):
         return _subkeys(cls.dependencies)
@@ -1098,14 +1096,14 @@ def update_external_dependencies(self, extendee_spec=None):
         """
         pass
 
-    def detect_dev_src_change(self) -> bool:
+    def detect_dev_src_change(self):
         """
         Method for checking for source code changes to trigger rebuild/reinstall
         """
         dev_path_var = self.spec.variants.get("dev_path", None)
         _, record = spack.store.STORE.db.query_by_spec_hash(self.spec.dag_hash())
-        assert dev_path_var and record, "dev_path variant and record must be present"
-        return fsys.recursive_mtime_greater_than(dev_path_var.value, record.installation_time)
+        mtime = fsys.last_modification_time_recursive(dev_path_var.value)
+        return mtime > record.installation_time
 
     def all_urls_for_version(self, version: StandardVersion) -> List[str]:
         """Return all URLs derived from version_urls(), url, urls, and
@@ -1818,6 +1816,12 @@ def _has_make_target(self, target):
         Returns:
             bool: True if 'target' is found, else False
         """
+        # Prevent altering LC_ALL for 'make' outside this function
+        make = copy.deepcopy(self.module.make)
+
+        # Use English locale for missing target message comparison
+        make.add_default_env("LC_ALL", "C")
+
         # Check if we have a Makefile
         for makefile in ["GNUmakefile", "Makefile", "makefile"]:
             if os.path.exists(makefile):
@@ -1826,12 +1830,6 @@ def _has_make_target(self, target):
             tty.debug("No Makefile found in the build directory")
             return False
 
-        # Prevent altering LC_ALL for 'make' outside this function
-        make = copy.deepcopy(self.module.make)
-
-        # Use English locale for missing target message comparison
-        make.add_default_env("LC_ALL", "C")
-
         # Check if 'target' is a valid target.
         #
         # `make -n target` performs a "dry run". It prints the commands that
@@ -2291,6 +2289,19 @@ def rpath_args(self):
 build_system_flags = PackageBase.build_system_flags
 
 
+def install_dependency_symlinks(pkg, spec, prefix):
+    """
+    Execute a dummy install and flatten dependencies.
+
+    This routine can be used in a ``package.py`` definition by setting
+    ``install = install_dependency_symlinks``.
+
+    This feature comes in handy for creating a common location for the
+    the installation of third-party libraries.
+    """
+    flatten_dependencies(spec, prefix)
+
+
 def use_cray_compiler_names():
     """Compiler names for builds that rely on cray compiler names."""
     os.environ["CC"] = "cc"
@@ -2299,6 +2310,23 @@ def use_cray_compiler_names():
     os.environ["F77"] = "ftn"
 
 
+def flatten_dependencies(spec, flat_dir):
+    """Make each dependency of spec present in dir via symlink."""
+    for dep in spec.traverse(root=False):
+        name = dep.name
+
+        dep_path = spack.store.STORE.layout.path_for_spec(dep)
+        dep_files = LinkTree(dep_path)
+
+        os.mkdir(flat_dir + "/" + name)
+
+        conflict = dep_files.find_conflict(flat_dir + "/" + name)
+        if conflict:
+            raise DependencyConflictError(conflict)
+
+        dep_files.merge(flat_dir + "/" + name)
+
+
 def possible_dependencies(
     *pkg_or_spec: Union[str, spack.spec.Spec, typing.Type[PackageBase]],
     transitive: bool = True,

lib/spack/spack/patch.py

@@ -4,9 +4,10 @@
 
 import hashlib
 import os
+import os.path
 import pathlib
 import sys
-from typing import Any, Dict, Optional, Set, Tuple, Type, Union
+from typing import Any, Dict, Optional, Tuple, Type, Union
 
 import llnl.util.filesystem
 from llnl.url import allowed_archive
@@ -503,38 +504,36 @@ def patch_for_package(self, sha256: str, pkg: "spack.package_base.PackageBase")
         patch_dict["sha256"] = sha256
         return from_dict(patch_dict, repository=self.repository)
 
-    def update_packages(self, pkgs_fullname: Set[str]) -> None:
+    def update_package(self, pkg_fullname: str) -> None:
         """Update the patch cache.
 
         Args:
             pkg_fullname: package to update.
         """
         # remove this package from any patch entries that reference it.
-        if self.index:
-            empty = []
-            for sha256, package_to_patch in self.index.items():
-                remove = []
-                for fullname, patch_dict in package_to_patch.items():
-                    if patch_dict["owner"] in pkgs_fullname:
-                        remove.append(fullname)
+        empty = []
+        for sha256, package_to_patch in self.index.items():
+            remove = []
+            for fullname, patch_dict in package_to_patch.items():
+                if patch_dict["owner"] == pkg_fullname:
+                    remove.append(fullname)
 
-                for fullname in remove:
-                    package_to_patch.pop(fullname)
+            for fullname in remove:
+                package_to_patch.pop(fullname)
 
-                if not package_to_patch:
-                    empty.append(sha256)
+            if not package_to_patch:
+                empty.append(sha256)
 
-            # remove any entries that are now empty
-            for sha256 in empty:
-                del self.index[sha256]
+        # remove any entries that are now empty
+        for sha256 in empty:
+            del self.index[sha256]
 
         # update the index with per-package patch indexes
-        for pkg_fullname in pkgs_fullname:
-            pkg_cls = self.repository.get_pkg_class(pkg_fullname)
-            partial_index = self._index_patches(pkg_cls, self.repository)
-            for sha256, package_to_patch in partial_index.items():
-                p2p = self.index.setdefault(sha256, {})
-                p2p.update(package_to_patch)
+        pkg_cls = self.repository.get_pkg_class(pkg_fullname)
+        partial_index = self._index_patches(pkg_cls, self.repository)
+        for sha256, package_to_patch in partial_index.items():
+            p2p = self.index.setdefault(sha256, {})
+            p2p.update(package_to_patch)
 
     def update(self, other: "PatchCache") -> None:
         """Update this cache with the contents of another.

lib/spack/spack/platforms/__init__.py

@@ -52,7 +52,8 @@ def use_platform(new_platform):
 
     import spack.config
 
-    assert isinstance(new_platform, Platform), f'"{new_platform}" must be an instance of Platform'
+    msg = '"{0}" must be an instance of Platform'
+    assert isinstance(new_platform, Platform), msg.format(new_platform)
 
     original_host_fn = host
 

lib/spack/spack/platforms/_platform.py

@@ -1,22 +1,42 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import warnings
 from typing import Optional
 
 import archspec.cpu
 
 import llnl.util.lang
 
+import spack.error
+
+
+class NoPlatformError(spack.error.SpackError):
+    def __init__(self):
+        msg = "Could not determine a platform for this machine"
+        super().__init__(msg)
+
 
 @llnl.util.lang.lazy_lexicographic_ordering
 class Platform:
     """Platform is an abstract class extended by subclasses.
 
+    To add a new type of platform (such as cray_xe), create a subclass and set all the
+    class attributes such as priority, front_target, back_target, front_os, back_os.
+
     Platform also contain a priority class attribute. A lower number signifies higher
     priority. These numbers are arbitrarily set and can be changed though often there
     isn't much need unless a new platform is added and the user wants that to be
     detected first.
+
+    Targets are created inside the platform subclasses. Most architecture (like linux,
+    and darwin) will have only one target family (x86_64) but in the case of Cray
+    machines, there is both a frontend and backend processor. The user can specify
+    which targets are present on front-end and back-end architecture.
+
+    Depending on the platform, operating systems are either autodetected or are
+    set. The user can set the frontend and backend operating setting by the class
+    attributes front_os and back_os. The operating system will be responsible for
+    compiler detection.
     """
 
     # Subclass sets number. Controls detection order
@@ -25,72 +45,82 @@ class Platform:
     #: binary formats used on this platform; used by relocation logic
     binary_formats = ["elf"]
 
-    default: str
-    default_os: str
+    front_end: Optional[str] = None
+    back_end: Optional[str] = None
+    default: Optional[str] = None  # The default back end target.
+
+    front_os: Optional[str] = None
+    back_os: Optional[str] = None
+    default_os: Optional[str] = None
 
     reserved_targets = ["default_target", "frontend", "fe", "backend", "be"]
     reserved_oss = ["default_os", "frontend", "fe", "backend", "be"]
-    deprecated_names = ["frontend", "fe", "backend", "be"]
 
     def __init__(self, name):
         self.targets = {}
         self.operating_sys = {}
         self.name = name
-        self._init_targets()
 
     def add_target(self, name: str, target: archspec.cpu.Microarchitecture) -> None:
+        """Used by the platform specific subclass to list available targets.
+        Raises an error if the platform specifies a name
+        that is reserved by spack as an alias.
+        """
         if name in Platform.reserved_targets:
-            msg = f"{name} is a spack reserved alias and cannot be the name of a target"
-            raise ValueError(msg)
+            msg = "{0} is a spack reserved alias and cannot be the name of a target"
+            raise ValueError(msg.format(name))
         self.targets[name] = target
 
-    def _init_targets(self):
-        self.default = archspec.cpu.host().name
+    def _add_archspec_targets(self):
         for name, microarchitecture in archspec.cpu.TARGETS.items():
             self.add_target(name, microarchitecture)
 
     def target(self, name):
+        """This is a getter method for the target dictionary
+        that handles defaulting based on the values provided by default,
+        front-end, and back-end. This can be overwritten
+        by a subclass for which we want to provide further aliasing options.
+        """
+        # TODO: Check if we can avoid using strings here
         name = str(name)
-        if name in Platform.deprecated_names:
-            warnings.warn(f"target={name} is deprecated, use target={self.default} instead")
-
-        if name in Platform.reserved_targets:
+        if name == "default_target":
             name = self.default
+        elif name == "frontend" or name == "fe":
+            name = self.front_end
+        elif name == "backend" or name == "be":
+            name = self.back_end
 
         return self.targets.get(name, None)
 
     def add_operating_system(self, name, os_class):
-        if name in Platform.reserved_oss + Platform.deprecated_names:
-            msg = f"{name} is a spack reserved alias and cannot be the name of an OS"
-            raise ValueError(msg)
+        """Add the operating_system class object into the
+        platform.operating_sys dictionary.
+        """
+        if name in Platform.reserved_oss:
+            msg = "{0} is a spack reserved alias and cannot be the name of an OS"
+            raise ValueError(msg.format(name))
         self.operating_sys[name] = os_class
 
-    def default_target(self):
-        return self.target(self.default)
-
-    def default_operating_system(self):
-        return self.operating_system(self.default_os)
-
     def operating_system(self, name):
-        if name in Platform.deprecated_names:
-            warnings.warn(f"os={name} is deprecated, use os={self.default_os} instead")
-
-        if name in Platform.reserved_oss:
+        if name == "default_os":
             name = self.default_os
+        if name == "frontend" or name == "fe":
+            name = self.front_os
+        if name == "backend" or name == "be":
+            name = self.back_os
 
         return self.operating_sys.get(name, None)
 
     def setup_platform_environment(self, pkg, env):
-        """Platform-specific build environment modifications.
-
-        This method is meant toi be overridden by subclasses, when needed.
+        """Subclass can override this method if it requires any
+        platform-specific build environment modifications.
         """
         pass
 
     @classmethod
     def detect(cls):
-        """Returns True if the host platform is detected to be the current Platform class,
-        False otherwise.
+        """Return True if the the host platform is detected to be the current
+        Platform class, False otherwise.
 
         Derived classes are responsible for implementing this method.
         """
@@ -105,7 +135,11 @@ def __str__(self):
     def _cmp_iter(self):
         yield self.name
         yield self.default
+        yield self.front_end
+        yield self.back_end
         yield self.default_os
+        yield self.front_os
+        yield self.back_os
 
         def targets():
             for t in sorted(self.targets.values()):

lib/spack/spack/platforms/cray.py

@@ -1,7 +1,7 @@
 # Copyright Spack Project Developers. See COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
-import os
+import os.path
 
 
 def slingshot_network():

lib/spack/spack/platforms/darwin.py

@@ -4,6 +4,8 @@
 
 import platform as py_platform
 
+import archspec.cpu
+
 from spack.operating_systems.mac_os import MacOs
 from spack.version import Version
 
@@ -17,8 +19,18 @@ class Darwin(Platform):
 
     def __init__(self):
         super().__init__("darwin")
+        self._add_archspec_targets()
+
+        self.default = archspec.cpu.host().name
+        self.front_end = self.default
+        self.back_end = self.default
+
         mac_os = MacOs()
+
         self.default_os = str(mac_os)
+        self.front_os = str(mac_os)
+        self.back_os = str(mac_os)
+
         self.add_operating_system(str(mac_os), mac_os)
 
     @classmethod

lib/spack/spack/platforms/freebsd.py

@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import platform
 
+import archspec.cpu
+
 from spack.operating_systems.freebsd import FreeBSDOs
 
 from ._platform import Platform
@@ -13,8 +15,18 @@ class FreeBSD(Platform):
 
     def __init__(self):
         super().__init__("freebsd")
+
+        self._add_archspec_targets()
+
+        # Get specific default
+        self.default = archspec.cpu.host().name
+        self.front_end = self.default
+        self.back_end = self.default
+
         os = FreeBSDOs()
         self.default_os = str(os)
+        self.front_os = self.default_os
+        self.back_os = self.default_os
         self.add_operating_system(str(os), os)
 
     @classmethod

lib/spack/spack/platforms/linux.py

@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 import platform
 
+import archspec.cpu
+
 from spack.operating_systems.linux_distro import LinuxDistro
 
 from ._platform import Platform
@@ -13,8 +15,18 @@ class Linux(Platform):
 
     def __init__(self):
         super().__init__("linux")
+
+        self._add_archspec_targets()
+
+        # Get specific default
+        self.default = archspec.cpu.host().name
+        self.front_end = self.default
+        self.back_end = self.default
+
         linux_dist = LinuxDistro()
         self.default_os = str(linux_dist)
+        self.front_os = self.default_os
+        self.back_os = self.default_os
         self.add_operating_system(str(linux_dist), linux_dist)
 
     @classmethod

lib/spack/spack/platforms/test.py

@@ -16,19 +16,31 @@ class Test(Platform):
     if platform.system().lower() == "darwin":
         binary_formats = ["macho"]
 
+    if platform.machine() == "arm64":
+        front_end = "aarch64"
+        back_end = "m1"
+        default = "m1"
+    else:
+        front_end = "x86_64"
+        back_end = "core2"
+        default = "core2"
+
+    front_os = "redhat6"
+    back_os = "debian6"
     default_os = "debian6"
-    default = "m1" if platform.machine() == "arm64" else "core2"
 
     def __init__(self, name=None):
         name = name or "test"
         super().__init__(name)
-        self.add_operating_system("debian6", spack.operating_systems.OperatingSystem("debian", 6))
-        self.add_operating_system("redhat6", spack.operating_systems.OperatingSystem("redhat", 6))
+        self.add_target(self.default, archspec.cpu.TARGETS[self.default])
+        self.add_target(self.front_end, archspec.cpu.TARGETS[self.front_end])
 
-    def _init_targets(self):
-        targets = ("aarch64", "m1") if platform.machine() == "arm64" else ("x86_64", "core2")
-        for t in targets:
-            self.add_target(t, archspec.cpu.TARGETS[t])
+        self.add_operating_system(
+            self.default_os, spack.operating_systems.OperatingSystem("debian", 6)
+        )
+        self.add_operating_system(
+            self.front_os, spack.operating_systems.OperatingSystem("redhat", 6)
+        )
 
     @classmethod
     def detect(cls):

lib/spack/spack/platforms/windows.py

@@ -4,6 +4,8 @@
 
 import platform
 
+import archspec.cpu
+
 from spack.operating_systems.windows_os import WindowsOs
 
 from ._platform import Platform
@@ -14,8 +16,18 @@ class Windows(Platform):
 
     def __init__(self):
         super().__init__("windows")
+        self._add_archspec_targets()
+
+        self.default = archspec.cpu.host().name
+        self.front_end = self.default
+        self.back_end = self.default
+
         windows_os = WindowsOs()
+
         self.default_os = str(windows_os)
+        self.front_os = str(windows_os)
+        self.back_os = str(windows_os)
+
         self.add_operating_system(str(windows_os), windows_os)
 
     @classmethod

lib/spack/spack/provider_index.py

@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Classes and functions to manage providers of virtual dependencies"""
-from typing import Dict, Iterable, List, Optional, Set, Union
+from typing import Dict, List, Optional, Set
 
 import spack.error
 import spack.spec
@@ -26,7 +26,7 @@ class _IndexBase:
     #: Calling providers_for(spec) will find specs that provide a
     #: matching implementation of MPI. Derived class need to construct
     #: this attribute according to the semantics above.
-    providers: Dict[str, Dict["spack.spec.Spec", Set["spack.spec.Spec"]]]
+    providers: Dict[str, Dict[str, Set[str]]]
 
     def providers_for(self, virtual_spec):
         """Return a list of specs of all packages that provide virtual
@@ -99,56 +99,66 @@ def __init__(
         self.repository = repository
         self.restrict = restrict
         self.providers = {}
-        if specs:
-            self.update_packages(specs)
 
-    def update_packages(self, specs: Iterable[Union[str, "spack.spec.Spec"]]):
+        specs = specs or []
+        for spec in specs:
+            if not isinstance(spec, spack.spec.Spec):
+                spec = spack.spec.Spec(spec)
+
+            if self.repository.is_virtual_safe(spec.name):
+                continue
+
+            self.update(spec)
+
+    def update(self, spec):
         """Update the provider index with additional virtual specs.
 
         Args:
             spec: spec potentially providing additional virtual specs
         """
-        for spec in specs:
-            if not isinstance(spec, spack.spec.Spec):
-                spec = spack.spec.Spec(spec)
+        if not isinstance(spec, spack.spec.Spec):
+            spec = spack.spec.Spec(spec)
 
-            if not spec.name or self.repository.is_virtual_safe(spec.name):
-                # Only non-virtual packages with name can provide virtual specs.
-                continue
+        if not spec.name:
+            # Empty specs do not have a package
+            return
 
-            pkg_provided = self.repository.get_pkg_class(spec.name).provided
-            for provider_spec_readonly, provided_specs in pkg_provided.items():
-                for provided_spec in provided_specs:
-                    # TODO: fix this comment.
-                    # We want satisfaction other than flags
-                    provider_spec = provider_spec_readonly.copy()
-                    provider_spec.compiler_flags = spec.compiler_flags.copy()
+        msg = "cannot update an index passing the virtual spec '{}'".format(spec.name)
+        assert not self.repository.is_virtual_safe(spec.name), msg
 
-                    if spec.intersects(provider_spec, deps=False):
-                        provided_name = provided_spec.name
+        pkg_provided = self.repository.get_pkg_class(spec.name).provided
+        for provider_spec_readonly, provided_specs in pkg_provided.items():
+            for provided_spec in provided_specs:
+                # TODO: fix this comment.
+                # We want satisfaction other than flags
+                provider_spec = provider_spec_readonly.copy()
+                provider_spec.compiler_flags = spec.compiler_flags.copy()
 
-                        provider_map = self.providers.setdefault(provided_name, {})
-                        if provided_spec not in provider_map:
-                            provider_map[provided_spec] = set()
+                if spec.intersects(provider_spec, deps=False):
+                    provided_name = provided_spec.name
 
-                        if self.restrict:
-                            provider_set = provider_map[provided_spec]
+                    provider_map = self.providers.setdefault(provided_name, {})
+                    if provided_spec not in provider_map:
+                        provider_map[provided_spec] = set()
 
-                            # If this package existed in the index before,
-                            # need to take the old versions out, as they're
-                            # now more constrained.
-                            old = {s for s in provider_set if s.name == spec.name}
-                            provider_set.difference_update(old)
+                    if self.restrict:
+                        provider_set = provider_map[provided_spec]
 
-                            # Now add the new version.
-                            provider_set.add(spec)
+                        # If this package existed in the index before,
+                        # need to take the old versions out, as they're
+                        # now more constrained.
+                        old = set([s for s in provider_set if s.name == spec.name])
+                        provider_set.difference_update(old)
 
-                        else:
-                            # Before putting the spec in the map, constrain
-                            # it so that it provides what was asked for.
-                            constrained = spec.copy()
-                            constrained.constrain(provider_spec)
-                            provider_map[provided_spec].add(constrained)
+                        # Now add the new version.
+                        provider_set.add(spec)
+
+                    else:
+                        # Before putting the spec in the map, constrain
+                        # it so that it provides what was asked for.
+                        constrained = spec.copy()
+                        constrained.constrain(provider_spec)
+                        provider_map[provided_spec].add(constrained)
 
     def to_json(self, stream=None):
         """Dump a JSON representation of this object.
@@ -183,13 +193,14 @@ def merge(self, other):
 
                 spdict[provided_spec] = spdict[provided_spec].union(opdict[provided_spec])
 
-    def remove_providers(self, pkgs_fullname: Set[str]):
+    def remove_provider(self, pkg_name):
         """Remove a provider from the ProviderIndex."""
         empty_pkg_dict = []
         for pkg, pkg_dict in self.providers.items():
             empty_pset = []
             for provided, pset in pkg_dict.items():
-                pset.difference_update(pkgs_fullname)
+                same_name = set(p for p in pset if p.fullname == pkg_name)
+                pset.difference_update(same_name)
 
                 if not pset:
                     empty_pset.append(provided)

lib/spack/spack/relocate.py

@@ -6,7 +6,8 @@
 import os
 import re
 import sys
-from typing import Dict, Iterable, List, Optional
+from collections import OrderedDict
+from typing import List, Optional
 
 import macholib.mach_o
 import macholib.MachO
@@ -17,11 +18,28 @@
 from llnl.util.lang import memoized
 from llnl.util.symlink import readlink, symlink
 
+import spack.error
 import spack.store
 import spack.util.elf as elf
 import spack.util.executable as executable
 
-from .relocate_text import BinaryFilePrefixReplacer, PrefixToPrefix, TextFilePrefixReplacer
+from .relocate_text import BinaryFilePrefixReplacer, TextFilePrefixReplacer
+
+
+class InstallRootStringError(spack.error.SpackError):
+    def __init__(self, file_path, root_path):
+        """Signal that the relocated binary still has the original
+        Spack's store root string
+
+        Args:
+            file_path (str): path of the binary
+            root_path (str): original Spack's store root string
+        """
+        super().__init__(
+            "\n %s \ncontains string\n %s \n"
+            "after replacing it in rpaths.\n"
+            "Package should not be relocated.\n Use -a to override." % (file_path, root_path)
+        )
 
 
 @memoized
@@ -36,11 +54,144 @@ def _patchelf() -> Optional[executable.Executable]:
         return spack.bootstrap.ensure_patchelf_in_path_or_raise()
 
 
+def _elf_rpaths_for(path):
+    """Return the RPATHs for an executable or a library.
+
+    Args:
+        path (str): full path to the executable or library
+
+    Return:
+        RPATHs as a list of strings. Returns an empty array
+        on ELF parsing errors, or when the ELF file simply
+        has no rpaths.
+    """
+    return elf.get_rpaths(path) or []
+
+
+def _make_relative(reference_file, path_root, paths):
+    """Return a list where any path in ``paths`` that starts with
+    ``path_root`` is made relative to the directory in which the
+    reference file is stored.
+
+    After a path is made relative it is prefixed with the ``$ORIGIN``
+    string.
+
+    Args:
+        reference_file (str): file from which the reference directory
+            is computed
+        path_root (str): root of the relative paths
+        paths: (list) paths to be examined
+
+    Returns:
+        List of relative paths
+    """
+    start_directory = os.path.dirname(reference_file)
+    pattern = re.compile(path_root)
+    relative_paths = []
+
+    for path in paths:
+        if pattern.match(path):
+            rel = os.path.relpath(path, start=start_directory)
+            path = os.path.join("$ORIGIN", rel)
+
+        relative_paths.append(path)
+
+    return relative_paths
+
+
+def _normalize_relative_paths(start_path, relative_paths):
+    """Normalize the relative paths with respect to the original path name
+    of the file (``start_path``).
+
+    The paths that are passed to this function existed or were relevant
+    on another filesystem, so os.path.abspath cannot be used.
+
+    A relative path may contain the signifier $ORIGIN. Assuming that
+    ``start_path`` is absolute, this implies that the relative path
+    (relative to start_path) should be replaced with an absolute path.
+
+    Args:
+        start_path (str): path from which the starting directory
+            is extracted
+        relative_paths (str): list of relative paths as obtained by a
+            call to :ref:`_make_relative`
+
+    Returns:
+        List of normalized paths
+    """
+    normalized_paths = []
+    pattern = re.compile(re.escape("$ORIGIN"))
+    start_directory = os.path.dirname(start_path)
+
+    for path in relative_paths:
+        if path.startswith("$ORIGIN"):
+            sub = pattern.sub(start_directory, path)
+            path = os.path.normpath(sub)
+        normalized_paths.append(path)
+
+    return normalized_paths
+
+
 def _decode_macho_data(bytestring):
     return bytestring.rstrip(b"\x00").decode("ascii")
 
 
-def _macho_find_paths(orig_rpaths, deps, idpath, prefix_to_prefix):
+def macho_make_paths_relative(path_name, old_layout_root, rpaths, deps, idpath):
+    """
+    Return a dictionary mapping the original rpaths to the relativized rpaths.
+    This dictionary is used to replace paths in mach-o binaries.
+    Replace old_dir with relative path from dirname of path name
+    in rpaths and deps; idpath is replaced with @rpath/libname.
+    """
+    paths_to_paths = dict()
+    if idpath:
+        paths_to_paths[idpath] = os.path.join("@rpath", "%s" % os.path.basename(idpath))
+    for rpath in rpaths:
+        if re.match(old_layout_root, rpath):
+            rel = os.path.relpath(rpath, start=os.path.dirname(path_name))
+            paths_to_paths[rpath] = os.path.join("@loader_path", "%s" % rel)
+        else:
+            paths_to_paths[rpath] = rpath
+    for dep in deps:
+        if re.match(old_layout_root, dep):
+            rel = os.path.relpath(dep, start=os.path.dirname(path_name))
+            paths_to_paths[dep] = os.path.join("@loader_path", "%s" % rel)
+        else:
+            paths_to_paths[dep] = dep
+    return paths_to_paths
+
+
+def macho_make_paths_normal(orig_path_name, rpaths, deps, idpath):
+    """
+    Return a dictionary mapping the relativized rpaths to the original rpaths.
+    This dictionary is used to replace paths in mach-o binaries.
+    Replace '@loader_path' with the dirname of the origname path name
+    in rpaths and deps; idpath is replaced with the original path name
+    """
+    rel_to_orig = dict()
+    if idpath:
+        rel_to_orig[idpath] = orig_path_name
+
+    for rpath in rpaths:
+        if re.match("@loader_path", rpath):
+            norm = os.path.normpath(
+                re.sub(re.escape("@loader_path"), os.path.dirname(orig_path_name), rpath)
+            )
+            rel_to_orig[rpath] = norm
+        else:
+            rel_to_orig[rpath] = rpath
+    for dep in deps:
+        if re.match("@loader_path", dep):
+            norm = os.path.normpath(
+                re.sub(re.escape("@loader_path"), os.path.dirname(orig_path_name), dep)
+            )
+            rel_to_orig[dep] = norm
+        else:
+            rel_to_orig[dep] = dep
+    return rel_to_orig
+
+
+def macho_find_paths(orig_rpaths, deps, idpath, old_layout_root, prefix_to_prefix):
     """
     Inputs
     original rpaths from mach-o binaries
@@ -56,12 +207,13 @@ def _macho_find_paths(orig_rpaths, deps, idpath, prefix_to_prefix):
     # Sort from longest path to shortest, to ensure we try /foo/bar/baz before /foo/bar
     prefix_iteration_order = sorted(prefix_to_prefix, key=len, reverse=True)
     for orig_rpath in orig_rpaths:
-        for old_prefix in prefix_iteration_order:
-            new_prefix = prefix_to_prefix[old_prefix]
-            if orig_rpath.startswith(old_prefix):
-                new_rpath = re.sub(re.escape(old_prefix), new_prefix, orig_rpath)
-                paths_to_paths[orig_rpath] = new_rpath
-                break
+        if orig_rpath.startswith(old_layout_root):
+            for old_prefix in prefix_iteration_order:
+                new_prefix = prefix_to_prefix[old_prefix]
+                if orig_rpath.startswith(old_prefix):
+                    new_rpath = re.sub(re.escape(old_prefix), new_prefix, orig_rpath)
+                    paths_to_paths[orig_rpath] = new_rpath
+                    break
         else:
             paths_to_paths[orig_rpath] = orig_rpath
 
@@ -85,7 +237,7 @@ def _macho_find_paths(orig_rpaths, deps, idpath, prefix_to_prefix):
     return paths_to_paths
 
 
-def _modify_macho_object(cur_path, rpaths, deps, idpath, paths_to_paths):
+def modify_macho_object(cur_path, rpaths, deps, idpath, paths_to_paths):
     """
     This function is used to make machO buildcaches on macOS by
     replacing old paths with new paths using install_name_tool
@@ -128,7 +280,7 @@ def _modify_macho_object(cur_path, rpaths, deps, idpath, paths_to_paths):
             install_name_tool(*args, temp_path)
 
 
-def _macholib_get_paths(cur_path):
+def macholib_get_paths(cur_path):
     """Get rpaths, dependent libraries, and library id of mach-o objects."""
     headers = []
     try:
@@ -196,7 +348,9 @@ def _set_elf_rpaths_and_interpreter(
         return None
 
 
-def relocate_macho_binaries(path_names, prefix_to_prefix):
+def relocate_macho_binaries(
+    path_names, old_layout_root, new_layout_root, prefix_to_prefix, rel, old_prefix, new_prefix
+):
     """
     Use macholib python package to get the rpaths, depedent libraries
     and library identity for libraries from the MachO object. Modify them
@@ -209,26 +363,88 @@ def relocate_macho_binaries(path_names, prefix_to_prefix):
         # Corner case where macho object file ended up in the path name list
         if path_name.endswith(".o"):
             continue
-        # get the paths in the old prefix
-        rpaths, deps, idpath = _macholib_get_paths(path_name)
-        # get the mapping of paths in the old prerix to the new prefix
-        paths_to_paths = _macho_find_paths(rpaths, deps, idpath, prefix_to_prefix)
-        # replace the old paths with new paths
-        _modify_macho_object(path_name, rpaths, deps, idpath, paths_to_paths)
+        if rel:
+            # get the relativized paths
+            rpaths, deps, idpath = macholib_get_paths(path_name)
+            # get the file path name in the original prefix
+            orig_path_name = re.sub(re.escape(new_prefix), old_prefix, path_name)
+            # get the mapping of the relativized paths to the original
+            # normalized paths
+            rel_to_orig = macho_make_paths_normal(orig_path_name, rpaths, deps, idpath)
+            # replace the relativized paths with normalized paths
+            modify_macho_object(path_name, rpaths, deps, idpath, rel_to_orig)
+            # get the normalized paths in the mach-o binary
+            rpaths, deps, idpath = macholib_get_paths(path_name)
+            # get the mapping of paths in old prefix to path in new prefix
+            paths_to_paths = macho_find_paths(
+                rpaths, deps, idpath, old_layout_root, prefix_to_prefix
+            )
+            # replace the old paths with new paths
+            modify_macho_object(path_name, rpaths, deps, idpath, paths_to_paths)
+            # get the new normalized path in the mach-o binary
+            rpaths, deps, idpath = macholib_get_paths(path_name)
+            # get the mapping of paths to relative paths in the new prefix
+            paths_to_paths = macho_make_paths_relative(
+                path_name, new_layout_root, rpaths, deps, idpath
+            )
+            # replace the new paths with relativized paths in the new prefix
+            modify_macho_object(path_name, rpaths, deps, idpath, paths_to_paths)
+        else:
+            # get the paths in the old prefix
+            rpaths, deps, idpath = macholib_get_paths(path_name)
+            # get the mapping of paths in the old prerix to the new prefix
+            paths_to_paths = macho_find_paths(
+                rpaths, deps, idpath, old_layout_root, prefix_to_prefix
+            )
+            # replace the old paths with new paths
+            modify_macho_object(path_name, rpaths, deps, idpath, paths_to_paths)
 
 
-def relocate_elf_binaries(binaries: Iterable[str], prefix_to_prefix: Dict[str, str]) -> None:
-    """Take a list of binaries, and an ordered prefix to prefix mapping, and update the rpaths
-    accordingly."""
+def _transform_rpaths(orig_rpaths, orig_root, new_prefixes):
+    """Return an updated list of RPATHs where each entry in the original list
+    starting with the old root is relocated to another place according to the
+    mapping passed as argument.
+
+    Args:
+        orig_rpaths (list): list of the original RPATHs
+        orig_root (str): original root to be substituted
+        new_prefixes (dict): dictionary that maps the original prefixes to
+            where they should be relocated
+
+    Returns:
+        List of paths
+    """
+    new_rpaths = []
+    for orig_rpath in orig_rpaths:
+        # If the original RPATH doesn't start with the target root
+        # append it verbatim and proceed
+        if not orig_rpath.startswith(orig_root):
+            new_rpaths.append(orig_rpath)
+            continue
+
+        # Otherwise inspect the mapping and transform + append any prefix
+        # that starts with a registered key
+        # avoiding duplicates
+        for old_prefix, new_prefix in new_prefixes.items():
+            if orig_rpath.startswith(old_prefix):
+                new_rpath = re.sub(re.escape(old_prefix), new_prefix, orig_rpath)
+                if new_rpath not in new_rpaths:
+                    new_rpaths.append(new_rpath)
+    return new_rpaths
+
+
+def new_relocate_elf_binaries(binaries, prefix_to_prefix):
+    """Take a list of binaries, and an ordered dictionary of
+    prefix to prefix mapping, and update the rpaths accordingly."""
 
     # Transform to binary string
-    prefix_to_prefix_bin = {
-        k.encode("utf-8"): v.encode("utf-8") for k, v in prefix_to_prefix.items()
-    }
+    prefix_to_prefix = OrderedDict(
+        (k.encode("utf-8"), v.encode("utf-8")) for (k, v) in prefix_to_prefix.items()
+    )
 
     for path in binaries:
         try:
-            elf.substitute_rpath_and_pt_interp_in_place_or_raise(path, prefix_to_prefix_bin)
+            elf.substitute_rpath_and_pt_interp_in_place_or_raise(path, prefix_to_prefix)
         except elf.ElfCStringUpdatesFailed as e:
             # Fall back to `patchelf --set-rpath ... --set-interpreter ...`
             rpaths = e.rpath.new_value.decode("utf-8").split(":") if e.rpath else []
@@ -236,13 +452,105 @@ def relocate_elf_binaries(binaries: Iterable[str], prefix_to_prefix: Dict[str, s
             _set_elf_rpaths_and_interpreter(path, rpaths=rpaths, interpreter=interpreter)
 
 
-def _warn_if_link_cant_be_relocated(link: str, target: str):
+def relocate_elf_binaries(
+    binaries, orig_root, new_root, new_prefixes, rel, orig_prefix, new_prefix
+):
+    """Relocate the binaries passed as arguments by changing their RPATHs.
+
+    Use patchelf to get the original RPATHs and then replace them with
+    rpaths in the new directory layout.
+
+    New RPATHs are determined from a dictionary mapping the prefixes in the
+    old directory layout to the prefixes in the new directory layout if the
+    rpath was in the old layout root, i.e. system paths are not replaced.
+
+    Args:
+        binaries (list): list of binaries that might need relocation, located
+            in the new prefix
+        orig_root (str): original root to be substituted
+        new_root (str): new root to be used, only relevant for relative RPATHs
+        new_prefixes (dict): dictionary that maps the original prefixes to
+            where they should be relocated
+        rel (bool): True if the RPATHs are relative, False if they are absolute
+        orig_prefix (str): prefix where the executable was originally located
+        new_prefix (str): prefix where we want to relocate the executable
+    """
+    for new_binary in binaries:
+        orig_rpaths = _elf_rpaths_for(new_binary)
+        # TODO: Can we deduce `rel` from the original RPATHs?
+        if rel:
+            # Get the file path in the original prefix
+            orig_binary = re.sub(re.escape(new_prefix), orig_prefix, new_binary)
+
+            # Get the normalized RPATHs in the old prefix using the file path
+            # in the orig prefix
+            orig_norm_rpaths = _normalize_relative_paths(orig_binary, orig_rpaths)
+            # Get the normalize RPATHs in the new prefix
+            new_norm_rpaths = _transform_rpaths(orig_norm_rpaths, orig_root, new_prefixes)
+            # Get the relative RPATHs in the new prefix
+            new_rpaths = _make_relative(new_binary, new_root, new_norm_rpaths)
+            # check to see if relative rpaths are changed before rewriting
+            if sorted(new_rpaths) != sorted(orig_rpaths):
+                _set_elf_rpaths_and_interpreter(new_binary, new_rpaths)
+        else:
+            new_rpaths = _transform_rpaths(orig_rpaths, orig_root, new_prefixes)
+            _set_elf_rpaths_and_interpreter(new_binary, new_rpaths)
+
+
+def make_link_relative(new_links, orig_links):
+    """Compute the relative target from the original link and
+    make the new link relative.
+
+    Args:
+        new_links (list): new links to be made relative
+        orig_links (list): original links
+    """
+    for new_link, orig_link in zip(new_links, orig_links):
+        target = readlink(orig_link)
+        relative_target = os.path.relpath(target, os.path.dirname(orig_link))
+        os.unlink(new_link)
+        symlink(relative_target, new_link)
+
+
+def make_macho_binaries_relative(cur_path_names, orig_path_names, old_layout_root):
+    """
+    Replace old RPATHs with paths relative to old_dir in binary files
+    """
+    if not sys.platform == "darwin":
+        return
+
+    for cur_path, orig_path in zip(cur_path_names, orig_path_names):
+        (rpaths, deps, idpath) = macholib_get_paths(cur_path)
+        paths_to_paths = macho_make_paths_relative(
+            orig_path, old_layout_root, rpaths, deps, idpath
+        )
+        modify_macho_object(cur_path, rpaths, deps, idpath, paths_to_paths)
+
+
+def make_elf_binaries_relative(new_binaries, orig_binaries, orig_layout_root):
+    """Replace the original RPATHs in the new binaries making them
+    relative to the original layout root.
+
+    Args:
+        new_binaries (list): new binaries whose RPATHs is to be made relative
+        orig_binaries (list): original binaries
+        orig_layout_root (str): path to be used as a base for making
+            RPATHs relative
+    """
+    for new_binary, orig_binary in zip(new_binaries, orig_binaries):
+        orig_rpaths = _elf_rpaths_for(new_binary)
+        if orig_rpaths:
+            new_rpaths = _make_relative(orig_binary, orig_layout_root, orig_rpaths)
+            _set_elf_rpaths_and_interpreter(new_binary, new_rpaths)
+
+
+def warn_if_link_cant_be_relocated(link, target):
     if not os.path.isabs(target):
         return
-    tty.warn(f'Symbolic link at "{link}" to "{target}" cannot be relocated')
+    tty.warn('Symbolic link at "{}" to "{}" cannot be relocated'.format(link, target))
 
 
-def relocate_links(links: Iterable[str], prefix_to_prefix: Dict[str, str]) -> None:
+def relocate_links(links, prefix_to_prefix):
     """Relocate links to a new install prefix."""
     regex = re.compile("|".join(re.escape(p) for p in prefix_to_prefix.keys()))
     for link in links:
@@ -251,7 +559,7 @@ def relocate_links(links: Iterable[str], prefix_to_prefix: Dict[str, str]) -> No
 
         # No match.
         if match is None:
-            _warn_if_link_cant_be_relocated(link, old_target)
+            warn_if_link_cant_be_relocated(link, old_target)
             continue
 
         new_target = prefix_to_prefix[match.group()] + old_target[match.end() :]
@@ -259,32 +567,32 @@ def relocate_links(links: Iterable[str], prefix_to_prefix: Dict[str, str]) -> No
         symlink(new_target, link)
 
 
-def relocate_text(files: Iterable[str], prefix_to_prefix: PrefixToPrefix) -> None:
+def relocate_text(files, prefixes):
     """Relocate text file from the original installation prefix to the
     new prefix.
 
     Relocation also affects the the path in Spack's sbang script.
 
     Args:
-        files: Text files to be relocated
-        prefix_to_prefix: ordered prefix to prefix mapping
+        files (list): Text files to be relocated
+        prefixes (OrderedDict): String prefixes which need to be changed
     """
-    TextFilePrefixReplacer.from_strings_or_bytes(prefix_to_prefix).apply(files)
+    TextFilePrefixReplacer.from_strings_or_bytes(prefixes).apply(files)
 
 
-def relocate_text_bin(binaries: Iterable[str], prefix_to_prefix: PrefixToPrefix) -> List[str]:
+def relocate_text_bin(binaries, prefixes):
     """Replace null terminated path strings hard-coded into binaries.
 
     The new install prefix must be shorter than the original one.
 
     Args:
-        binaries: paths to binaries to be relocated
-        prefix_to_prefix: ordered prefix to prefix mapping
+        binaries (list): binaries to be relocated
+        prefixes (OrderedDict): String prefixes which need to be changed.
 
     Raises:
       spack.relocate_text.BinaryTextReplaceError: when the new path is longer than the old path
     """
-    return BinaryFilePrefixReplacer.from_strings_or_bytes(prefix_to_prefix).apply(binaries)
+    return BinaryFilePrefixReplacer.from_strings_or_bytes(prefixes).apply(binaries)
 
 
 def is_macho_magic(magic: bytes) -> bool:
@@ -321,7 +629,7 @@ def _exists_dir(dirname):
     return os.path.isdir(dirname)
 
 
-def is_macho_binary(path: str) -> bool:
+def is_macho_binary(path):
     try:
         with open(path, "rb") as f:
             return is_macho_magic(f.read(4))
@@ -345,7 +653,7 @@ def fixup_macos_rpath(root, filename):
         return False
 
     # Get Mach-O header commands
-    (rpath_list, deps, id_dylib) = _macholib_get_paths(abspath)
+    (rpath_list, deps, id_dylib) = macholib_get_paths(abspath)
 
     # Convert rpaths list to (name -> number of occurrences)
     add_rpaths = set()

lib/spack/spack/relocate_text.py

@@ -6,61 +6,64 @@
 paths inside text files and binaries."""
 
 import re
-from typing import IO, Dict, Iterable, List, Union
-
-from llnl.util.lang import PatternBytes
+from collections import OrderedDict
+from typing import Dict, Union
 
 import spack.error
 
 Prefix = Union[str, bytes]
-PrefixToPrefix = Union[Dict[str, str], Dict[bytes, bytes]]
 
 
 def encode_path(p: Prefix) -> bytes:
     return p if isinstance(p, bytes) else p.encode("utf-8")
 
 
-def _prefix_to_prefix_as_bytes(prefix_to_prefix: PrefixToPrefix) -> Dict[bytes, bytes]:
-    return {encode_path(k): encode_path(v) for (k, v) in prefix_to_prefix.items()}
+def _prefix_to_prefix_as_bytes(prefix_to_prefix) -> Dict[bytes, bytes]:
+    return OrderedDict((encode_path(k), encode_path(v)) for (k, v) in prefix_to_prefix.items())
 
 
-def utf8_path_to_binary_regex(prefix: str) -> PatternBytes:
+def utf8_path_to_binary_regex(prefix: str):
     """Create a binary regex that matches the input path in utf8"""
     prefix_bytes = re.escape(prefix).encode("utf-8")
     return re.compile(b"(?<![\\w\\-_/])([\\w\\-_]*?)%s([\\w\\-_/]*)" % prefix_bytes)
 
 
-def _byte_strings_to_single_binary_regex(prefixes: Iterable[bytes]) -> PatternBytes:
+def _byte_strings_to_single_binary_regex(prefixes):
     all_prefixes = b"|".join(re.escape(p) for p in prefixes)
     return re.compile(b"(?<![\\w\\-_/])([\\w\\-_]*?)(%s)([\\w\\-_/]*)" % all_prefixes)
 
 
-def utf8_paths_to_single_binary_regex(prefixes: Iterable[str]) -> PatternBytes:
+def utf8_paths_to_single_binary_regex(prefixes):
     """Create a (binary) regex that matches any input path in utf8"""
     return _byte_strings_to_single_binary_regex(p.encode("utf-8") for p in prefixes)
 
 
-def filter_identity_mappings(prefix_to_prefix: Dict[bytes, bytes]) -> Dict[bytes, bytes]:
+def filter_identity_mappings(prefix_to_prefix):
     """Drop mappings that are not changed."""
     # NOTE: we don't guard against the following case:
     # [/abc/def -> /abc/def, /abc -> /x] *will* be simplified to
     # [/abc -> /x], meaning that after this simplification /abc/def will be
     # mapped to /x/def instead of /abc/def. This should not be a problem.
-    return {k: v for k, v in prefix_to_prefix.items() if k != v}
+    return OrderedDict((k, v) for (k, v) in prefix_to_prefix.items() if k != v)
 
 
 class PrefixReplacer:
-    """Base class for applying a prefix to prefix map to a list of binaries or text files. Derived
-    classes implement _apply_to_file to do the actual work, which is different when it comes to
+    """Base class for applying a prefix to prefix map
+    to a list of binaries or text files.
+    Child classes implement _apply_to_file to do the
+    actual work, which is different when it comes to
     binaries and text files."""
 
-    def __init__(self, prefix_to_prefix: Dict[bytes, bytes]) -> None:
+    def __init__(self, prefix_to_prefix: Dict[bytes, bytes]):
         """
         Arguments:
-            prefix_to_prefix: An ordered mapping from prefix to prefix. The order is relevant to
-                support substring fallbacks, for example
-                ``[("/first/sub", "/x"), ("/first", "/y")]`` will ensure /first/sub is matched and
-                replaced before /first.
+
+            prefix_to_prefix (OrderedDict):
+
+                A ordered mapping from prefix to prefix. The order is
+                relevant to support substring fallbacks, for example
+                [("/first/sub", "/x"), ("/first", "/y")] will ensure
+                /first/sub is matched and replaced before /first.
         """
         self.prefix_to_prefix = filter_identity_mappings(prefix_to_prefix)
 
@@ -71,7 +74,7 @@ def is_noop(self) -> bool:
         or there are no prefixes to replace."""
         return not self.prefix_to_prefix
 
-    def apply(self, filenames: Iterable[str]) -> List[str]:
+    def apply(self, filenames: list):
         """Returns a list of files that were modified"""
         changed_files = []
         if self.is_noop:
@@ -81,20 +84,17 @@ def apply(self, filenames: Iterable[str]) -> List[str]:
                 changed_files.append(filename)
         return changed_files
 
-    def apply_to_filename(self, filename: str) -> bool:
+    def apply_to_filename(self, filename):
         if self.is_noop:
             return False
         with open(filename, "rb+") as f:
             return self.apply_to_file(f)
 
-    def apply_to_file(self, f: IO[bytes]) -> bool:
+    def apply_to_file(self, f):
         if self.is_noop:
             return False
         return self._apply_to_file(f)
 
-    def _apply_to_file(self, f: IO) -> bool:
-        raise NotImplementedError("Derived classes must implement this method")
-
 
 class TextFilePrefixReplacer(PrefixReplacer):
     """This class applies prefix to prefix mappings for relocation
@@ -112,11 +112,13 @@ def __init__(self, prefix_to_prefix: Dict[bytes, bytes]):
         self.regex = _byte_strings_to_single_binary_regex(self.prefix_to_prefix.keys())
 
     @classmethod
-    def from_strings_or_bytes(cls, prefix_to_prefix: PrefixToPrefix) -> "TextFilePrefixReplacer":
+    def from_strings_or_bytes(
+        cls, prefix_to_prefix: Dict[Prefix, Prefix]
+    ) -> "TextFilePrefixReplacer":
         """Create a TextFilePrefixReplacer from an ordered prefix to prefix map."""
         return cls(_prefix_to_prefix_as_bytes(prefix_to_prefix))
 
-    def _apply_to_file(self, f: IO) -> bool:
+    def _apply_to_file(self, f):
         """Text replacement implementation simply reads the entire file
         in memory and applies the combined regex."""
         replacement = lambda m: m.group(1) + self.prefix_to_prefix[m.group(2)] + m.group(3)
@@ -131,12 +133,12 @@ def _apply_to_file(self, f: IO) -> bool:
 
 
 class BinaryFilePrefixReplacer(PrefixReplacer):
-    def __init__(self, prefix_to_prefix: Dict[bytes, bytes], suffix_safety_size: int = 7) -> None:
+    def __init__(self, prefix_to_prefix, suffix_safety_size=7):
         """
-        prefix_to_prefix: Ordered dictionary where the keys are bytes representing the old prefixes
-            and the values are the new
-        suffix_safety_size: in case of null terminated strings, what size of the suffix should
-            remain to avoid aliasing issues?
+        prefix_to_prefix (OrderedDict): OrderedDictionary where the keys are
+            bytes representing the old prefixes and the values are the new
+        suffix_safety_size (int): in case of null terminated strings, what size
+            of the suffix should remain to avoid aliasing issues?
         """
         assert suffix_safety_size >= 0
         super().__init__(prefix_to_prefix)
@@ -144,18 +146,17 @@ def __init__(self, prefix_to_prefix: Dict[bytes, bytes], suffix_safety_size: int
         self.regex = self.binary_text_regex(self.prefix_to_prefix.keys(), suffix_safety_size)
 
     @classmethod
-    def binary_text_regex(
-        cls, binary_prefixes: Iterable[bytes], suffix_safety_size: int = 7
-    ) -> PatternBytes:
-        """Create a regex that looks for exact matches of prefixes, and also tries to match a
-        C-string type null terminator in a small lookahead window.
+    def binary_text_regex(cls, binary_prefixes, suffix_safety_size=7):
+        """
+        Create a regex that looks for exact matches of prefixes, and also tries to
+        match a C-string type null terminator in a small lookahead window.
 
         Arguments:
-            binary_prefixes: Iterable of byte strings of prefixes to match
-            suffix_safety_size: Sizeof the lookahed for null-terminated string.
+            binary_prefixes (list): List of byte strings of prefixes to match
+            suffix_safety_size (int): Sizeof the lookahed for null-terminated string.
+
+        Returns: compiled regex
         """
-        # Note: it's important not to use capture groups for the prefix, since it destroys
-        # performance due to common prefix optimization.
         return re.compile(
             b"("
             + b"|".join(re.escape(p) for p in binary_prefixes)
@@ -164,34 +165,36 @@ def binary_text_regex(
 
     @classmethod
     def from_strings_or_bytes(
-        cls, prefix_to_prefix: PrefixToPrefix, suffix_safety_size: int = 7
+        cls, prefix_to_prefix: Dict[Prefix, Prefix], suffix_safety_size: int = 7
     ) -> "BinaryFilePrefixReplacer":
         """Create a BinaryFilePrefixReplacer from an ordered prefix to prefix map.
 
         Arguments:
-            prefix_to_prefix: Ordered mapping of prefix to prefix.
-            suffix_safety_size: Number of bytes to retain at the end of a C-string to avoid binary
-                string-aliasing issues.
+            prefix_to_prefix (OrderedDict): Ordered mapping of prefix to prefix.
+            suffix_safety_size (int): Number of bytes to retain at the end of a C-string
+                to avoid binary string-aliasing issues.
         """
         return cls(_prefix_to_prefix_as_bytes(prefix_to_prefix), suffix_safety_size)
 
-    def _apply_to_file(self, f: IO[bytes]) -> bool:
+    def _apply_to_file(self, f):
         """
-        Given a file opened in rb+ mode, apply the string replacements as specified by an ordered
-        dictionary of prefix to prefix mappings. This method takes special care of null-terminated
-        C-strings. C-string constants are problematic because compilers and linkers optimize
-        readonly strings for space by aliasing those that share a common suffix (only suffix since
-        all of them are null terminated). See https://github.com/spack/spack/pull/31739 and
-        https://github.com/spack/spack/pull/32253 for details. Our logic matches the original
-        prefix with a ``suffix_safety_size + 1`` lookahead for null bytes. If no null terminator
-        is found, we simply pad with leading /, assuming that it's a long C-string; the full
-        C-string after replacement has a large suffix in common with its original value. If there
-        *is* a null terminator we can do the same as long as the replacement has a sufficiently
-        long common suffix with the original prefix. As a last resort when the replacement does
-        not have a long enough common suffix, we can try to shorten the string, but this only
-        works if the new length is sufficiently short (typically the case when going from large
-        padding -> normal path) If the replacement string is longer, or all of the above fails,
-        we error out.
+        Given a file opened in rb+ mode, apply the string replacements as
+        specified by an ordered dictionary of prefix to prefix mappings. This
+        method takes special care of null-terminated C-strings. C-string constants
+        are problematic because compilers and linkers optimize readonly strings for
+        space by aliasing those that share a common suffix (only suffix since all
+        of them are null terminated). See https://github.com/spack/spack/pull/31739
+        and https://github.com/spack/spack/pull/32253 for details. Our logic matches
+        the original prefix with a ``suffix_safety_size + 1`` lookahead for null bytes.
+        If no null terminator is found, we simply pad with leading /, assuming that
+        it's a long C-string; the full C-string after replacement has a large suffix
+        in common with its original value.
+        If there *is* a null terminator we can do the same as long as the replacement
+        has a sufficiently long common suffix with the original prefix.
+        As a last resort when the replacement does not have a long enough common suffix,
+        we can try to shorten the string, but this only works if the new length is
+        sufficiently short (typically the case when going from large padding -> normal path)
+        If the replacement string is longer, or all of the above fails, we error out.
 
         Arguments:
             f: file opened in rb+ mode
@@ -201,10 +204,11 @@ def _apply_to_file(self, f: IO[bytes]) -> bool:
         """
         assert f.tell() == 0
 
-        # We *could* read binary data in chunks to avoid loading all in memory, but it's nasty to
-        # deal with matches across boundaries, so let's stick to something simple.
+        # We *could* read binary data in chunks to avoid loading all in memory,
+        # but it's nasty to deal with matches across boundaries, so let's stick to
+        # something simple.
 
-        modified = False
+        modified = True
 
         for match in self.regex.finditer(f.read()):
             # The matching prefix (old) and its replacement (new)
@@ -214,7 +218,8 @@ def _apply_to_file(self, f: IO[bytes]) -> bool:
             # Did we find a trailing null within a N + 1 bytes window after the prefix?
             null_terminated = match.end(0) > match.end(1)
 
-            # Suffix string length, excluding the null byte. Only makes sense if null_terminated
+            # Suffix string length, excluding the null byte
+            # Only makes sense if null_terminated
             suffix_strlen = match.end(0) - match.end(1) - 1
 
             # How many bytes are we shrinking our string?
@@ -224,9 +229,9 @@ def _apply_to_file(self, f: IO[bytes]) -> bool:
             if bytes_shorter < 0:
                 raise CannotGrowString(old, new)
 
-            # If we don't know whether this is a null terminated C-string (we're looking only N + 1
-            # bytes ahead), or if it is and we have a common suffix, we can simply pad with leading
-            # dir separators.
+            # If we don't know whether this is a null terminated C-string (we're looking
+            # only N + 1 bytes ahead), or if it is and we have a common suffix, we can
+            # simply pad with leading dir separators.
             elif (
                 not null_terminated
                 or suffix_strlen >= self.suffix_safety_size  # == is enough, but let's be defensive
@@ -235,9 +240,9 @@ def _apply_to_file(self, f: IO[bytes]) -> bool:
             ):
                 replacement = b"/" * bytes_shorter + new
 
-            # If it *was* null terminated, all that matters is that we can leave N bytes of old
-            # suffix in place. Note that > is required since we also insert an additional null
-            # terminator.
+            # If it *was* null terminated, all that matters is that we can leave N bytes
+            # of old suffix in place. Note that > is required since we also insert an
+            # additional null terminator.
             elif bytes_shorter > self.suffix_safety_size:
                 replacement = new + match.group(2)  # includes the trailing null
 
@@ -252,6 +257,22 @@ def _apply_to_file(self, f: IO[bytes]) -> bool:
         return modified
 
 
+class BinaryStringReplacementError(spack.error.SpackError):
+    def __init__(self, file_path, old_len, new_len):
+        """The size of the file changed after binary path substitution
+
+        Args:
+            file_path (str): file with changing size
+            old_len (str): original length of the file
+            new_len (str): length of the file after substitution
+        """
+        super().__init__(
+            "Doing a binary string replacement in %s failed.\n"
+            "The size of the file changed from %s to %s\n"
+            "when it should have remanined the same." % (file_path, old_len, new_len)
+        )
+
+
 class BinaryTextReplaceError(spack.error.SpackError):
     def __init__(self, msg):
         msg += (
@@ -263,16 +284,17 @@ def __init__(self, msg):
 
 class CannotGrowString(BinaryTextReplaceError):
     def __init__(self, old, new):
-        return super().__init__(
-            f"Cannot replace {old!r} with {new!r} because the new prefix is longer."
-        )
+        msg = "Cannot replace {!r} with {!r} because the new prefix is longer.".format(old, new)
+        super().__init__(msg)
 
 
 class CannotShrinkCString(BinaryTextReplaceError):
     def __init__(self, old, new, full_old_string):
-        # Just interpolate binary string to not risk issues with invalid unicode, which would be
-        # really bad user experience: error in error. We have no clue if we actually deal with a
-        # real C-string nor what encoding it has.
-        super().__init__(
-            f"Cannot replace {old!r} with {new!r} in the C-string {full_old_string!r}."
+        # Just interpolate binary string to not risk issues with invalid
+        # unicode, which would be really bad user experience: error in error.
+        # We have no clue if we actually deal with a real C-string nor what
+        # encoding it has.
+        msg = "Cannot replace {!r} with {!r} in the C-string {!r}.".format(
+            old, new, full_old_string
         )
+        super().__init__(msg)

lib/spack/spack/repo.py

@@ -14,6 +14,7 @@
 import inspect
 import itertools
 import os
+import os.path
 import random
 import re
 import shutil
@@ -465,7 +466,7 @@ def read(self, stream):
         """Read this index from a provided file object."""
 
     @abc.abstractmethod
-    def update(self, pkgs_fullname: Set[str]):
+    def update(self, pkg_fullname):
         """Update the index in memory with information about a package."""
 
     @abc.abstractmethod
@@ -482,8 +483,8 @@ def _create(self):
     def read(self, stream):
         self.index = spack.tag.TagIndex.from_json(stream, self.repository)
 
-    def update(self, pkgs_fullname: Set[str]):
-        self.index.update_packages({p.split(".")[-1] for p in pkgs_fullname})
+    def update(self, pkg_fullname):
+        self.index.update_package(pkg_fullname.split(".")[-1])
 
     def write(self, stream):
         self.index.to_json(stream)
@@ -498,14 +499,15 @@ def _create(self):
     def read(self, stream):
         self.index = spack.provider_index.ProviderIndex.from_json(stream, self.repository)
 
-    def update(self, pkgs_fullname: Set[str]):
+    def update(self, pkg_fullname):
+        name = pkg_fullname.split(".")[-1]
         is_virtual = (
-            lambda name: not self.repository.exists(name)
-            or self.repository.get_pkg_class(name).virtual
+            not self.repository.exists(name) or self.repository.get_pkg_class(name).virtual
         )
-        non_virtual_pkgs_fullname = {p for p in pkgs_fullname if not is_virtual(p.split(".")[-1])}
-        self.index.remove_providers(non_virtual_pkgs_fullname)
-        self.index.update_packages(non_virtual_pkgs_fullname)
+        if is_virtual:
+            return
+        self.index.remove_provider(pkg_fullname)
+        self.index.update(pkg_fullname)
 
     def write(self, stream):
         self.index.to_json(stream)
@@ -530,8 +532,8 @@ def read(self, stream):
     def write(self, stream):
         self.index.to_json(stream)
 
-    def update(self, pkgs_fullname: Set[str]):
-        self.index.update_packages(pkgs_fullname)
+    def update(self, pkg_fullname):
+        self.index.update_package(pkg_fullname)
 
 
 class RepoIndex:
@@ -621,7 +623,9 @@ def _build_index(self, name: str, indexer: Indexer):
                 if new_index_mtime != index_mtime:
                     needs_update = self.checker.modified_since(new_index_mtime)
 
-                indexer.update({f"{self.namespace}.{pkg_name}" for pkg_name in needs_update})
+                for pkg_name in needs_update:
+                    indexer.update(f"{self.namespace}.{pkg_name}")
+
                 indexer.write(new)
 
         return indexer.index