env: continue to mark non-roots as implicitly installed on partial env installs (#47183)

Fixes a change in behavior/bug in
70412612c7, where partial environment
installs would mark the selected spec as explicitly installed, even if
it was not a root of the environment.

The desired behavior is that roots by definition are the to be
explicitly installed specs. The specs on the `spack -e ... install x`
command line are just filters for partial installs, so leave them
implicitly installed if they aren't roots.

lib/spack/spack/environment/environment.py

@@ -1936,17 +1936,16 @@ def install_specs(self, specs: Optional[List[Spec]] = None, **install_args):
         specs = specs if specs is not None else roots
 
         # Extend the set of specs to overwrite with modified dev specs and their parents
-        overwrite: Set[str] = set()
-        overwrite.update(install_args.get("overwrite", []), self._dev_specs_that_need_overwrite())
-        install_args["overwrite"] = overwrite
+        install_args["overwrite"] = {
+            *install_args.get("overwrite", ()),
+            *self._dev_specs_that_need_overwrite(),
+        }
 
-        explicit: Set[str] = set()
-        explicit.update(
-            install_args.get("explicit", []),
-            (s.dag_hash() for s in specs),
-            (s.dag_hash() for s in roots),
-        )
-        install_args["explicit"] = explicit
+        # Only environment roots are marked explicit
+        install_args["explicit"] = {
+            *install_args.get("explicit", ()),
+            *(s.dag_hash() for s in roots),
+        }
 
         PackageInstaller([spec.package for spec in specs], install_args).install()
 

lib/spack/spack/test/env.py

@@ -843,3 +843,17 @@ def test_root_version_weights_for_old_versions(mutable_mock_env_path, mock_packa
 
     assert bowtie.satisfies("@=1.3.0")
     assert gcc.satisfies("@=1.0")
+
+
+def test_only_roots_are_explicitly_installed(tmp_path, mock_packages, config, temporary_store):
+    """When installing specific non-root specs from an environment, we continue to mark them
+    as implicitly installed. What makes installs explicit is that they are root of the env."""
+    env = ev.create_in_dir(tmp_path)
+    env.add("mpileaks")
+    env.concretize()
+    mpileaks = env.concrete_roots()[0]
+    callpath = mpileaks["callpath"]
+    env.install_specs([callpath], fake=True)
+    assert callpath in temporary_store.db.query(explicit=False)
+    env.install_specs([mpileaks], fake=True)
+    assert temporary_store.db.query(explicit=True) == [mpileaks]