Update mypy, fix its configuration

.github/workflows/ci.yml

@@ -15,11 +15,19 @@ jobs:
 
     steps:
       - uses: actions/checkout@v6
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.9"
-      - uses: pre-commit/[email protected]
+          version: 0.9.13
+          python-version: "3.11"
+          activate-environment: "true"
+
+      - name: Install dependencies from uv.lock
+        run: uv sync --locked
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
 
   tests:
     runs-on: ${{ matrix.os }}

.pre-commit-config.yaml

@@ -1,6 +1,7 @@
 ci:
-    autoupdate_schedule: monthly
+    autoupdate_schedule: quarterly
     autofix_prs: true
+    skip: [mypy]
 
 exclude: &exclude_files >
   (?x)^(
@@ -52,10 +53,14 @@ repos:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix, --show-fixes]
 
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+  - repo: local
     hooks:
-    - id: mypy
-      additional_dependencies:
-      - "sqlalchemy[mypy]==1.4.29"
-      files: ^(disk_objectstore/.*py)$
+      - id: mypy
+        name: mypy
+        entry: mypy
+        args: [--config-file=pyproject.toml, --pretty, disk_objectstore/]
+        language: python
+        types: [python]
+        require_serial: true
+        pass_filenames: false
+        files: ^(disk_objectstore/.*py)$

disk_objectstore/container.py

@@ -1021,9 +1021,10 @@ def count_objects(self) -> ObjectCount:
         In particular, it returns the number of loose objects,
         of packed objects, and the number of pack files."""
 
+        # TODO: Remove type: ignore! Do we need to handle number_packed==None?
         number_packed = self._get_operation_session().scalar(select(func.count()).select_from(Obj))
         return ObjectCount(
-            packed=number_packed,
+            packed=number_packed,  # type: ignore[arg-type]
             loose=sum(1 for _ in self._list_loose()),
             pack_files=sum(1 for _ in self._list_packs()),
         )
@@ -1095,7 +1096,8 @@ def get_total_size(self) -> TotalSize:
             total_size_loose += loose_path.stat().st_size
         retval['total_size_loose'] = total_size_loose
 
-        return TotalSize(**retval)
+        # TODO: Handle None?
+        return TotalSize(**retval)  # type: ignore[arg-type]
 
     @contextmanager
     def lock_pack(self, pack_id: str, allow_repack_pack: bool = False) -> Iterator[StreamWriteBytesType]:
@@ -2359,7 +2361,8 @@ def callback(self, action, value):
                 value={'total': total, 'description': f'Pack {pack_id}'},
             )
             # Update at most 400 times, avoiding to increase CPU usage; if the list is small: every object.
-            update_every = max(int(total / 400), 1)
+            # TODO: Handle total==None?
+            update_every = max(int(total / 400), 1)  # type: ignore[operator]
             # Counter of how many objects have been since since the last update.
             # A new callback will be performed when this value is > update_every.
             since_last_update = 0
@@ -2727,7 +2730,9 @@ def repack_pack(  # pylint: disable=too-many-branches,too-many-statements,too-ma
         # At this stage we just have a new pack -1 (_REPACK_PACK_ID) but it is never referenced.
         # Let us store the information in the DB.
         # We had already checked earlier that this at least one exists.
-        session.bulk_update_mappings(Obj, obj_dicts)
+        # TODO: error: Argument 1 to "bulk_update_mappings"
+        # of "Session" has incompatible type "type[Obj]"; expected "Mapper[Any]"
+        session.bulk_update_mappings(Obj, obj_dicts)  # type: ignore[arg-type]
         # I also commit.
         session.commit()
         # Clean up the cache

disk_objectstore/database.py

@@ -74,7 +74,7 @@ def do_begin(conn):  # pylint: disable=unused-variable
 
     # Bind the engine to the metadata of the Base class so that the
     # declaratives can be accessed through a DBSession instance
-    Base.metadata.bind = engine
+    Base.metadata.bind = engine  # type: ignore[attr-defined]
 
     # We set autoflush = False to avoid to lock the DB if just doing queries/reads
     session = sessionmaker(bind=engine, autoflush=False, autocommit=False, future=True)()

pyproject.toml

@@ -43,6 +43,10 @@ dev = [
     'pytest~=8.4',
     'pytest-benchmark~=5.2',
     'pytest-cov~=7.0',
+    'mypy~=1.19.0',
+    "sqlalchemy[mypy]>=1.4.22",
+    'types-psutil',
+    'types-tqdm',
 ]
 docs = [
     'jinja2<3.1',
@@ -144,6 +148,13 @@ scripts_are_modules = true
 warn_redundant_casts = true
 plugins = ['sqlalchemy.ext.mypy.plugin']
 
+[[tool.mypy.overrides]]
+ignore_missing_imports = true
+module = [
+  'profilehooks.*',
+  'memory_profiler.*',
+]
+
 [tool.tox]
 legacy_tox_ini = """
 [tox]