bootstrap: handle a new edge case of binary python packages with missing python-venv (#47094)

relevant for clingo installed without gcc-runtime and python-venv, which
is done for good reasons.

lib/spack/spack/binary_distribution.py

@@ -2562,7 +2562,13 @@ def _ensure_common_prefix(tar: tarfile.TarFile) -> str:
     return pkg_prefix
 
 
-def install_root_node(spec, unsigned=False, force=False, sha256=None):
+def install_root_node(
+    spec: spack.spec.Spec,
+    unsigned=False,
+    force: bool = False,
+    sha256: Optional[str] = None,
+    allow_missing: bool = False,
+) -> None:
     """Install the root node of a concrete spec from a buildcache.
 
     Checking the sha256 sum of a node before installation is usually needed only
@@ -2571,11 +2577,10 @@ def install_root_node(spec, unsigned=False, force=False, sha256=None):
 
     Args:
         spec: spec to be installed (note that only the root node will be installed)
-        unsigned (bool): if True allows installing unsigned binaries
+        unsigned: if True allows installing unsigned binaries
-        force (bool): force installation if the spec is already present in the
+        force: force installation if the spec is already present in the local store
-            local store
+        sha256: optional sha256 of the binary package, to be checked before installation
-        sha256 (str): optional sha256 of the binary package, to be checked
+        allow_missing: when true, allows installing a node with missing dependencies
-            before installation
     """
     # Early termination
     if spec.external or spec.virtual:
@@ -2613,7 +2618,7 @@ def install_root_node(spec, unsigned=False, force=False, sha256=None):
                 spec, spack.store.STORE.layout.spec_file_path(spec)
             )
         spack.hooks.post_install(spec, False)
-        spack.store.STORE.db.add(spec)
+        spack.store.STORE.db.add(spec, allow_missing=allow_missing)
 
 
 def install_single_spec(spec, unsigned=False, force=False):

lib/spack/spack/bootstrap/_common.py

@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 """Common basic functions used through the spack.bootstrap package"""
 import fnmatch
+import glob
 import importlib
 import os.path
 import re
@@ -60,10 +61,19 @@ def _try_import_from_store(
             python, *_ = candidate_spec.dependencies("python-venv")
         else:
             python, *_ = candidate_spec.dependencies("python")
+
+        # if python is installed, ask it for the layout
+        if python.installed:
             module_paths = [
                 os.path.join(candidate_spec.prefix, python.package.purelib),
                 os.path.join(candidate_spec.prefix, python.package.platlib),
             ]
+        # otherwise search for the site-packages directory
+        # (clingo from binaries with truncated python-venv runtime)
+        else:
+            module_paths = glob.glob(
+                os.path.join(candidate_spec.prefix, "lib", "python*", "site-packages")
+            )
         path_before = list(sys.path)
 
         # NOTE: try module_paths first and last, last allows an existing version in path

lib/spack/spack/bootstrap/core.py

@@ -175,7 +175,15 @@ def _install_by_hash(
             query = spack.binary_distribution.BinaryCacheQuery(all_architectures=True)
             for match in spack.store.find([f"/{pkg_hash}"], multiple=False, query_fn=query):
                 spack.binary_distribution.install_root_node(
-                    match, unsigned=True, force=True, sha256=pkg_sha256
+                    # allow_missing is true since when bootstrapping clingo we truncate runtime
+                    # deps such as gcc-runtime, since we link libstdc++ statically, and the other
+                    # further runtime deps are loaded by the Python interpreter. This just silences
+                    # warnings about missing dependencies.
+                    match,
+                    unsigned=True,
+                    force=True,
+                    sha256=pkg_sha256,
+                    allow_missing=True,
                 )
 
     def _install_and_test(

lib/spack/spack/database.py

@@ -1245,7 +1245,7 @@ def _add(
         self._data[key].explicit = explicit
 
     @_autospec
-    def add(self, spec: "spack.spec.Spec", *, explicit: bool = False) -> None:
+    def add(self, spec: "spack.spec.Spec", *, explicit: bool = False, allow_missing=False) -> None:
         """Add spec at path to database, locking and reading DB to sync.
 
         ``add()`` will lock and read from the DB on disk.
@@ -1254,7 +1254,7 @@ def add(self, spec: "spack.spec.Spec", *, explicit: bool = False) -> None:
         # TODO: ensure that spec is concrete?
         # Entire add is transactional.
         with self.write_transaction():
-            self._add(spec, explicit=explicit)
+            self._add(spec, explicit=explicit, allow_missing=allow_missing)
 
     def _get_matching_spec_key(self, spec: "spack.spec.Spec", **kwargs) -> str:
         """Get the exact spec OR get a single spec that matches."""