Type-hint imperatively-mapped RepositoryMetadata columns

RepositoryMetadata stays imperatively mapped because a declaratively
mapped class cannot have a `metadata` column attribute (it collides with
DeclarativeBase.metadata, see PR #12064). The downside has been that
mypy can't see any of the column attributes, forcing every caller to
either ignore [attr-defined] or work around it with setattr.

Add Mapped[X] annotations on the class — they're inert at runtime (the
mapper still installs InstrumentedAttribute descriptors via
map_imperatively) and only feed the type checker. JSON columns
(`metadata`, `tool_versions`) are typed as Mapped[Any] rather than
Optional, matching existing caller assumptions that they're populated
when accessed.

Drops three now-obsolete `# type: ignore[has-type]` /
`# type: ignore[attr-defined]` comments. mypy error count on the
affected toolshed files goes from 62 to 53 with no new failures.

lib/tool_shed/metadata/repository_metadata_manager.py

@@ -1087,7 +1087,7 @@ def get_repository_metadata(session, repository_id):
     stmt = (
         select(RepositoryMetadata)
         .where(RepositoryMetadata.repository_id == repository_id)
-        .order_by(RepositoryMetadata.changeset_revision, RepositoryMetadata.update_time.desc())  # type: ignore[attr-defined]  # mapped attribute
+        .order_by(RepositoryMetadata.changeset_revision, RepositoryMetadata.update_time.desc())
     )
     return session.scalars(stmt)
 

lib/tool_shed/webapp/model/__init__.py

@@ -387,13 +387,14 @@ class Repository(Base, Dictifiable):
     user = relationship("User", back_populates="active_repositories")
     downloadable_revisions = relationship(
         "RepositoryMetadata",
-        primaryjoin=lambda: (Repository.id == RepositoryMetadata.repository_id) & (RepositoryMetadata.downloadable == true()),  # type: ignore[has-type]
+        primaryjoin=lambda: (Repository.id == RepositoryMetadata.repository_id)
+        & (RepositoryMetadata.downloadable == true()),
         viewonly=True,
-        order_by=lambda: desc(RepositoryMetadata.update_time),  # type: ignore[attr-defined]
+        order_by=lambda: desc(RepositoryMetadata.update_time),
     )
     metadata_revisions = relationship(
         "RepositoryMetadata",
-        order_by=lambda: desc(RepositoryMetadata.update_time),  # type: ignore[attr-defined]
+        order_by=lambda: desc(RepositoryMetadata.update_time),
         back_populates="repository",
     )
     roles = relationship("RepositoryRoleAssociation", back_populates="repository")
@@ -702,10 +703,26 @@ class Tag(Base):
 
 
 class RepositoryMetadata(Dictifiable):
-    repository: "Repository"
+    # Annotations only — runtime attributes are installed by
+    # mapper_registry.map_imperatively below.
+    id: Mapped[Optional[int]]
+    create_time: Mapped[Optional[datetime]]
+    update_time: Mapped[Optional[datetime]]
+    repository_id: Mapped[Optional[int]]
+    changeset_revision: Mapped[Optional[str]]
+    numeric_revision: Mapped[Optional[int]]
+    metadata: Mapped[Any]
+    tool_versions: Mapped[Any]
+    malicious: Mapped[Optional[bool]]
+    downloadable: Mapped[Optional[bool]]
+    missing_test_components: Mapped[Optional[bool]]
+    has_repository_dependencies: Mapped[Optional[bool]]
+    includes_datatypes: Mapped[Optional[bool]]
+    includes_tools: Mapped[Optional[bool]]
+    includes_tool_dependencies: Mapped[Optional[bool]]
+    includes_workflows: Mapped[Optional[bool]]
+    repository: Mapped["Repository"]
 
-    # Once the class has been mapped, all Column items in this table will be available
-    # as instrumented class attributes on RepositoryMetadata.
     table = Table(
         "repository_metadata",
         mapper_registry.metadata,

test/unit/tool_shed/test_shed_index.py

@@ -91,12 +91,10 @@ def test_get_repositories_for_indexing_orders_by_last_revision_create_time(shed_
     base = datetime(2026, 1, 1, 12, 0, 0)
     rm_a = RepositoryMetadata(repository_id=repo_a.id, changeset_revision="a", downloadable=True)
     rm_b = RepositoryMetadata(repository_id=repo_b.id, changeset_revision="b", downloadable=True)
-    # setattr — RepositoryMetadata is imperatively mapped, so create_time /
-    # update_time aren't visible to the static type checker.
-    setattr(rm_a, "create_time", base)
-    setattr(rm_a, "update_time", base)
-    setattr(rm_b, "create_time", base + timedelta(hours=1))
-    setattr(rm_b, "update_time", base + timedelta(hours=1))
+    rm_a.create_time = base
+    rm_a.update_time = base
+    rm_b.create_time = base + timedelta(hours=1)
+    rm_b.update_time = base + timedelta(hours=1)
     session.add_all([rm_a, rm_b])
     # Make repo_a's row look "recently updated" — under the old ORDER BY this
     # surfaced repo_a first even though repo_b has the newer downloadable