Merge branch 'main' into poetry-update

Author: tcompa

.pre-commit-config.yaml

@@ -1,25 +1,25 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v6.0.0
     hooks:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.1.0
+    rev: v3.15.0
     hooks:
     -   id: reorder-python-imports
 -   repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.12.1
     hooks:
     -   id: black
         args: [--line-length=79]
 -   repo: https://github.com/PyCQA/flake8
-    rev: 3.9.2
+    rev: 7.3.0
     hooks:
     -   id: flake8
         args: ["--ignore=E203,W503"]
 -   repo: https://github.com/PyCQA/bandit
-    rev: '1.7.4'
+    rev: '1.8.6'
     hooks:
     - id: bandit
       args: ["-x", "tests/*"]

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 # Unreleased
 
+* Bump versions of `pre-commit` tools (\#975).
+
 # 1.5.4
 * Tasks:
     * Catch `FileNotFoundError` in `apply_registration_to_image` task when race conditions with the reference cycle are hit (\#971).

docs/_tasks/generate_task_list.py

@@ -116,7 +116,7 @@
         homepage_url = package["homepage_url"]
         manifest_url = package["manifest_url"]
         description = package.get("description", None)
-        r = requests.get(manifest_url)
+        r = requests.get(manifest_url, timeout=100)
         if not r.status_code == 200:
             error_msg = f"Something wrong with the request to {manifest_url}"
             logger.error(f"{prefix} {error_msg}")

fractal_tasks_core/channels.py

@@ -420,7 +420,7 @@ def _get_new_unique_value(
 
 
 def update_omero_channels(
-    old_channels: list[dict[str, Any]]
+    old_channels: list[dict[str, Any]],
 ) -> list[dict[str, Any]]:
     """
     Make an existing list of Omero channels Fractal-compatible

fractal_tasks_core/dev/lib_descriptions.py

@@ -165,9 +165,11 @@ def _get_class_attrs_descriptions(
     docstring = ast.get_docstring(_class)
     parsed_docstring = docparse(docstring)
     descriptions = {
-        x.arg_name: _sanitize_description(x.description)
-        if x.description
-        else "Missing description"
+        x.arg_name: (
+            _sanitize_description(x.description)
+            if x.description
+            else "Missing description"
+        )
         for x in parsed_docstring.params
     }
     logging.info(f"[_get_class_attrs_descriptions] END ({class_name=})")

fractal_tasks_core/dev/lib_signature_constraints.py

@@ -81,7 +81,6 @@ def _validate_function_signature(function: Callable):
     """
     sig = signature(function)
     for param in sig.parameters.values():
-
         # CASE 1: Check that name is not forbidden
         if param.name in FORBIDDEN_PARAM_NAMES:
             raise ValueError(

fractal_tasks_core/pyramids.py

@@ -37,7 +37,6 @@ def build_pyramid(
     aggregation_function: Optional[Callable] = None,
     open_array_kwargs: Optional[Mapping] = None,
 ) -> None:
-
     """
     Starting from on-disk highest-resolution data, build and write to disk a
     pyramid with `(num_levels - 1)` coarsened levels.

fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py

@@ -143,7 +143,6 @@ def copy_ome_zarr_hcs_plate(
 
     # Generate parallelization list
     for zarr_url in zarr_urls:
-
         # Check if the zarr_url is valid
         if len(zarr_url.rstrip("/").split("/")) < 4:
             raise ValueError(

tests/data/fake_package_for_schema_experiments/new_args_schema.py

@@ -25,7 +25,6 @@
 
 
 if __name__ == "__main__":
-
     # Read manifest
     manifest_path = (
         Path(my_package.__file__).parent / "__FRACTAL_MANIFEST__.json"

tests/tasks/_validation.py

@@ -108,7 +108,6 @@ def validate_axes_and_coordinateTransformations(image_zarr: Path):
 def validate_labels_and_measurements(
     image_zarr: Path, *, label_name: str, table_name: str
 ):
-
     label_path = str(image_zarr / "labels" / label_name / "0")
     table_path = str(image_zarr / "tables" / table_name)
     debug(label_path)