fix: use python 3.13 in pre-commit hook (#782)

The pre-commit hook would not work after python was bumped from 3.12 to 3.13.

Also:
- enforce pre-commit check in CI/CD
- fix `.pre-commit-config.yaml` (exclude snapshot files)
- remove `yesqa` from `.pre-commit-config.yaml`, instead use `poetry run ruff check` or `poetry run ruff check --fix`
- fix existing files (that is, run the `pre-commit` hooks on the repository)

Author: leafty

.github/workflows/test_publish.yml

@@ -87,7 +87,9 @@ jobs:
       - name: Style checks
         uses: devcontainers/[email protected]
         with:
-          runCmd: make style_checks
+          runCmd: |
+            make style_checks
+            poetry run pre-commit run --all-files --show-diff-on-failure --hook-stage manual
           push: never
           skipContainerUserIdUpdate: false
           cacheFrom: ${{ needs.build-devcontainer.outputs.image_repository }}:${{ needs.build-devcontainer.outputs.image_tag }}

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 default_language_version:
-    python: python3.12
+  python: python3.13
 repos:
   - repo: local
     hooks:
@@ -8,6 +8,8 @@ repos:
         entry: make style_checks
         language: system
         pass_filenames: false
+        stages:
+          - pre-commit
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
@@ -18,11 +20,7 @@ repos:
       - id: check-toml
       - id: debug-statements
       - id: end-of-file-fixer
-        exclude: 'components/renku_data_services/message_queue/(avro_models|schemas)'
+        exclude: '(components/renku_data_services/message_queue/(avro_models|schemas))|(.ambr)'
       - id: mixed-line-ending
       - id: trailing-whitespace
-        exclude: 'components/renku_data_services/message_queue/(avro_models|schemas)'
-  - repo: https://github.com/asottile/yesqa
-    rev: v1.5.0
-    hooks:
-      - id: yesqa
+        exclude: '(components/renku_data_services/message_queue/(avro_models|schemas))|(.ambr)'

Makefile

@@ -94,7 +94,7 @@ style_checks: ${API_SPECS} ## Run linting and style checks
 	poetry check
 	poetry run mypy
 	poetry run ruff format --check
-	poetry run ruff check .
+	poetry run ruff check
 	poetry run bandit -c pyproject.toml -r .
 	poetry poly check
 	poetry poly libs

components/renku_data_services/base_models/__init__.py

@@ -1,3 +1,3 @@
 """Common models for all services."""
 
-from renku_data_services.base_models.core import *  # noqa: F401, F403
+from renku_data_services.base_models.core import *  # noqa: F403

components/renku_data_services/connected_services/db.py

@@ -63,7 +63,7 @@ async def get_oauth2_client(self, provider_id: str, user: base_models.APIUser) -
             client = result.one_or_none()
             if client is None:
                 raise errors.MissingResourceError(
-                    message=f"OAuth2 Client with id '{provider_id}' does not exist or you do not have access to it."  # noqa: E501
+                    message=f"OAuth2 Client with id '{provider_id}' does not exist or you do not have access to it."
                 )
             return client.dump(user_is_admin=user.is_admin)
 
@@ -302,7 +302,7 @@ async def get_oauth2_connection(self, connection_id: ULID, user: base_models.API
         """Get one OAuth2 connection from the database."""
         if not user.is_authenticated or user.id is None:
             raise errors.MissingResourceError(
-                message=f"OAuth2 connection with id '{connection_id}' does not exist or you do not have access to it."  # noqa: E501
+                message=f"OAuth2 connection with id '{connection_id}' does not exist or you do not have access to it."
             )
 
         async with self.session_maker() as session:
@@ -394,7 +394,7 @@ async def get_async_oauth2_client(
         """Get the AsyncOAuth2Client for the given connection_id and user."""
         if not user.is_authenticated or user.id is None:
             raise errors.MissingResourceError(
-                message=f"OAuth2 connection with id '{connection_id}' does not exist or you do not have access to it."  # noqa: E501
+                message=f"OAuth2 connection with id '{connection_id}' does not exist or you do not have access to it."
             )
 
         async with self.session_maker() as session:

components/renku_data_services/data_connectors/api.spec.yaml

@@ -855,7 +855,7 @@ components:
       description: Information about inaccessible data connector links
       type: object
       properties:
-        count: 
+        count:
           type: integer
           minimum: 0
           description: The number of data links the user does not have access to

components/renku_data_services/errors/__init__.py

@@ -1,3 +1,3 @@
 """Service errors component."""
 
-from renku_data_services.errors.errors import *  # noqa: F401, F403
+from renku_data_services.errors.errors import *  # noqa: F403

components/renku_data_services/migrations/core.py

@@ -15,7 +15,7 @@ def run_migrations_for_app(name: str, revision: str = "heads") -> None:
     """Perform migrations for app `name`.
 
     From: https://alembic.sqlalchemy.org/en/latest/cookbook.html#programmatic-api-use-connection-sharing-with-asyncio
-    """  # noqa: E501
+    """
     cfg = get_alembic_config(name)
     command.upgrade(cfg, revision)
 

components/renku_data_services/migrations/versions/450ae3930996_create_initial_global_environments.py

@@ -89,27 +89,27 @@ def upgrade() -> None:
             op.execute(
                 sa.text(
                     """INSERT INTO sessions.environments(
-                        id, 
+                        id,
                         name, description,
-                        created_by_id, 
-                        creation_date, 
-                        container_image, 
-                        default_url, 
+                        created_by_id,
+                        creation_date,
+                        container_image,
+                        default_url,
                         port,
                         working_directory,
                         mount_directory,
                         uid,
                         gid,
                         args,
                         command,
-                        environment_kind 
+                        environment_kind
                     )VALUES (
-                        generate_ulid(), 
-                        :name, 
-                        :description, 
-                        :created_by_id, 
-                        now(), 
-                        :container_image, 
+                        generate_ulid(),
+                        :name,
+                        :description,
+                        :created_by_id,
+                        now(),
+                        :container_image,
                         :default_url,
                         :port,
                         :working_directory,

projects/background_jobs/Dockerfile

@@ -22,7 +22,7 @@ RUN if $DEV_BUILD ; then \
     /home/renku/.local/bin/poetry export -o requirements.txt; \
   fi && \
   env/bin/pip install -r requirements.txt
-RUN /home/renku/.local/bin/poetry -C projects/background_jobs build-project -f wheel --custom-temp-path=/tmp 
+RUN /home/renku/.local/bin/poetry -C projects/background_jobs build-project -f wheel --custom-temp-path=/tmp
 RUN env/bin/pip --no-cache-dir install projects/background_jobs/dist/*.whl
 
 FROM python:3.13-slim-bookworm