Chore: following suggestions from repo-review

.pre-commit-config.yaml

@@ -30,9 +30,9 @@ repos:
       - id: check-added-large-files
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.14.7'
+    rev: "v0.14.7"
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
@@ -51,28 +51,34 @@ repos:
           - boto3-stubs[essential]
         exclude: ^(diracx-client/src/diracx/client/_generated|diracx-[a-z]+/tests/|diracx-testing/|build|extensions/gubbins/gubbins-client/src/gubbins/client/_generated)
 
-  - repo: https://github.com/executablebooks/mdformat
+  - repo: https://github.com/hukkin/mdformat
     rev: 1.0.0
     hooks:
-    - id: mdformat
-      args: ["--number"]
-      additional_dependencies:
-      - mdformat-mkdocs
-      - mdformat-gfm
-      - mdformat-black
+      - id: mdformat
+        args: ["--number"]
+        additional_dependencies:
+          - mdformat-mkdocs
+          - mdformat-gfm
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
     hooks:
-    - id: codespell
-      args: ["-w"]
+      - id: codespell
+        args: ["-w"]
+
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.20.0
+    hooks:
+      - id: blacken-docs
+        additional_dependencies:
+          - black==22.12.0
 
   - repo: local
     hooks:
       - id: check-lollygag
         name: check for lollygag
         types: [python]
-        entry: '(?i)lollygag'
+        entry: "(?i)lollygag"
         language: pygrep
         files: ^diracx
 
@@ -83,4 +89,4 @@ repos:
         entry: pixi run -e default python .github/workflows/generate_pixi_tasks_doc.py
         language: system
         pass_filenames: false
-        files: ^pixi\.toml$|^pixi\.lock$   # only run if pixi files change
+        files: ^pixi\.toml$|^pixi\.lock$ # only run if pixi files change

diracx-client/src/diracx/client/patches/jobs/common.py

@@ -14,8 +14,8 @@
 
 import json
 from io import BytesIO, IOBase
-from typing import Any, IO, Dict, TypedDict, Union, Unpack, cast, Literal
-
+from typing import Any, IO, Dict, Union, Unpack, cast, Literal
+from typing_extensions import TypedDict
 from diracx.core.models import SearchSpec
 
 

diracx-core/src/diracx/core/s3.py

@@ -11,9 +11,10 @@
 
 import asyncio
 import base64
-from typing import TYPE_CHECKING, TypedDict, cast
+from typing import TYPE_CHECKING, cast
 
 from botocore.errorfactory import ClientError
+from typing_extensions import TypedDict
 
 from .models import ChecksumAlgorithm
 

diracx-db/src/diracx/db/os/utils.py

@@ -66,9 +66,12 @@ class BaseOSDB(metaclass=ABCMeta):
     MyDBClass = BaseOSDB.available_implementations(db_name)[0]
 
     db = MyDBClass(conn_params)
+    await db.init()
+
     async with db.client_context:
         async with db:
             # Do something with the OpenSearch client
+            pass
     ```
     """
 

diracx-db/src/diracx/db/sql/utils/base.py

@@ -84,6 +84,7 @@ class BaseSQLDB(metaclass=ABCMeta):
         async with db:
             # Do something in the first transaction
             # Commit will be called automatically
+            pass
 
         async with db:
             # This transaction will be rolled back due to the exception

docs/dev/explanations/components/api.md

@@ -18,7 +18,8 @@ from .utils import with_client
 
 
 @with_client
-async def create_sandbox(paths: list[Path], *, client: AsyncDiracClient) -> str: ...
+async def create_sandbox(paths: list[Path], *, client: AsyncDiracClient) -> str:
+    ...
 ```
 
 In this example, `paths` are the parameters of the API. The `@with_client` decorator allows the method to be called without manually managing the client:

docs/dev/explanations/components/cli.md

@@ -49,10 +49,11 @@ TODO: WRONG
     - To associate the command with `dirac`, import the module in `src/diracx/__init__.py`:
 
     ```python
-    from . import command
+    from . import my_command
+
     ...
 
-    app.add_typer(<command name>.app, name="<command name>")
+    app.add_typer(my_command.app, name="my_command")
     ```
 
 Users can then call the CLI:

docs/dev/explanations/components/routes.md

@@ -28,6 +28,8 @@ Example route definition:
 
 ```python
 @router.post("/search", responses=EXAMPLE_RESPONSES)
+def search():
+    pass
 ```
 
 ## Dependency Injection
@@ -66,7 +68,8 @@ Usage example:
 
 ```python
 @router.get("/openid-configuration")
-async def get_openid_configuration(settings: AuthSettings): ...
+async def get_openid_configuration(settings: AuthSettings):
+    ...
 ```
 
 ### User Info
@@ -77,7 +80,12 @@ To retrieve information about the current user, depend on `AuthorizedUserInfo`.
 @router.get("/userinfo")
 async def userinfo(
     user_info: Annotated[AuthorizedUserInfo, Depends(verify_dirac_access_token)],
-): ...
+):
+    ...
+```
+
+```
+pass
 ```
 
 **TODO:** Consider avoiding the need to manually specify the annotation.
@@ -88,7 +96,8 @@ To extract information from the central DIRAC configuration:
 
 ```python
 @router.post("/summary")
-async def summary(config: Annotated[Config, Depends(ConfigSource.create)]): ...
+async def summary(config: Annotated[Config, Depends(ConfigSource.create)]):
+    ...
 ```
 
 The `Config` object is cached efficiently between requests and automatically refreshed. It is strongly typed and immutable for the duration of a request.
@@ -106,17 +115,18 @@ from diracx.routers.dependencies import JobDB, JobLoggingDB
 
 
 @router.delete("/{job_id}")
-async def delete_single_job(job_db: JobDB, job_logging_db: JobLoggingDB): ...
+async def delete_single_job(job_db: JobDB, job_logging_db: JobLoggingDB):
+    ...
 ```
 
 There are advanced and uncommon scenarios where committing a transaction is necessary even when returning an error response (e.g., revoking tokens in the database and returning an error to a potentially malicious user). In such cases, explicitly committing the transaction before raising an exception is crucial. Without this explicit commit, the intended changes would be rolled back along with the transaction, leading to unintended consequences:
 
 ```python
 from diracx.routers.dependencies import AuthDB
 
+
 @router.post("/token")
-async def token(auth_db: AuthDB, ...)
-    ...
+async def token(auth_db: AuthDB):
     if refresh_token_attributes["status"] == RefreshTokenStatus.REVOKED:
         # Revoke all the user tokens associated with the subject
         await auth_db.revoke_user_refresh_tokens(sub)
@@ -129,6 +139,8 @@ async def token(auth_db: AuthDB, ...)
         raise HTTPException(status_code=401)
 ```
 
+````
+
 Refer to the [SQLAlchemy documentation](https://docs.sqlalchemy.org/en/20/core/pooling.html) for more details.
 
 ### OpenSearch Databases
@@ -142,7 +154,8 @@ from diracx.routers.dependencies import JobParametersDB
 
 
 @router.post("/search", responses=EXAMPLE_RESPONSES)
-async def search(job_parameters_db: JobParametersDB): ...
+async def search(job_parameters_db: JobParametersDB):
+    ...
 ```
 
 ## Permission Management
@@ -183,7 +196,8 @@ from .access_policies import open_access
 
 @open_access
 @router.get("/")
-async def serve_config(): ...
+async def serve_config():
+    ...
 ```
 
 Implementing a new `AccessPolicy` is done by:
@@ -206,3 +220,4 @@ To ensure consistency, the following rules must be followed:
 - All routers must be tagged and the first tag becomes the name of the sub-client.
 - The name of the route becomes the name of the client method.
 - Uses of `fastapi.Form` must specify a `description`.
+````

docs/dev/reference/coding-conventions.md

@@ -32,7 +32,8 @@ import pytest
 
 
 @pytest.fixture
-def my_ficture(): ...
+def my_ficture():
+    ...
 ```
 
 </td>
@@ -44,7 +45,8 @@ from pytest import fixture
 
 
 @fixture
-def my_ficture(): ...
+def my_ficture():
+    ...
 ```
 
 </td>

docs/dev/reference/dependency-injection.md

@@ -81,7 +81,7 @@ For advanced scenarios requiring explicit transaction commits (e.g., revoking to
 
 ```python
 @router.post("/token")
-async def token(auth_db: AuthDB, ...):
+async def token(auth_db: AuthDB):
     if refresh_token_attributes["status"] == RefreshTokenStatus.REVOKED:
         # Revoke all the user tokens associated with the subject
         await auth_db.revoke_user_refresh_tokens(sub)