Use mypy and ruff from pixi environment

.circleci/config.yml

@@ -17,6 +17,20 @@ jobs:
       - run:
           name: Check dependencies are compatible
           command: pixi run --as-is pip check
+      - run:
+          name: Generate pre-commit cache key
+          command: date '+%Y-%W' | tee pre_commit_cache_key.txt
+      - restore_cache:
+          key: pre-commit-{{ .Branch }}-{{ checksum "pre_commit_cache_key.txt" }}
+      - run:
+          name: Check code quality
+          command: pixi run --as-is pre-commit run -a
+      - save_cache:
+          key: pre-commit-{{ .Branch }}-{{ checksum "pre_commit_cache_key.txt" }}
+          paths:
+            - ~/.cache/pre-commit
+            - ./.mypy_cache
+            - ./.ruff_cache
       - run:
           name: Run tests
           command: |

.github/dependabot.yml

@@ -14,6 +14,24 @@ updates:
       interval: "weekly"
     cooldown:
       default-days: 7
+    groups:
+      gha:
+        patterns:
+          - "*"
+    labels:
+      - dependencies
+      - github_actions
+      - automatedPR
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 7
+    groups:
+      pre-commit:
+        patterns:
+          - "*"
     labels:
       - dependencies
       - github_actions

.github/workflows/zizmor.yml

@@ -0,0 +1,23 @@
+name: GitHub Actions Security Analysis with zizmor 🌈
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["**"]
+
+permissions: {}
+
+jobs:
+  zizmor:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+        with:
+          persist-credentials: false
+
+      - name: Run zizmor 🌈
+        uses: zizmorcore/zizmor-action@192e21d79ab29983730a13d1382995c2307fbcaa # v0.5.7
+        with:
+          advanced-security: false

.pre-commit-config.yaml

@@ -25,20 +25,35 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.15.22"
+  - repo: local
     hooks:
       - id: ruff-check
-        args: [--fix]
+        name: ruff check
+        entry: "pixi run --locked ruff check --force-exclude --fix"
+        additional_dependencies: ['pixi']
+        language: python  # system
+        require_serial: true
+        types_or:
+          - python
+          - jupyter
       - id: ruff-format
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v2.3.0"
-    hooks:
+        name: ruff format
+        entry: "pixi run --locked ruff format --force-exclude"
+        additional_dependencies: ['pixi']
+        language: python  # system
+        require_serial: true
+        types_or:
+          - python
+          - jupyter
       - id: mypy
-        additional_dependencies:
-          - "types-PyYAML"
-          - "types-requests"
-          - "numpy"
+        name: mypy
+        entry: "pixi run --locked mypy"
+        additional_dependencies: ['pixi']
+        language: python  # system
+        types:
+          - python
+        pass_filenames: false
+        require_serial: true
   - repo: https://github.com/adrienverge/yamllint
     rev: "v1.38.0"
     hooks:
@@ -53,8 +68,3 @@ repos:
       - id: check-citation-file-format
       - id: check-github-workflows
       - id: check-circle-ci
-  - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.27.0
-    hooks:
-      - id: zizmor
-        args: [--fix=safe]

doc/contributing.rst

@@ -39,8 +39,8 @@ whenever you read it.
 
 It is recommended that you open a `draft pull
 request <https://github.blog/2019-02-14-introducing-draft-pull-requests/>`__
-early, as this will cause :ref:`CircleCI to run the unit tests <tests>`,
-:ref:`pre-commit.ci to analyse your code <code_quality>`, and
+early, as this will cause CircleCI to :ref:`run the tests <tests>` and
+:ref:`analyse the code <code_quality>`, and
 :ref:`readthedocs to build the documentation <documentation>`.
 It's also easier to get help from other developers if your code is visible in a
 pull request.
@@ -249,7 +249,7 @@ should be correct.
 Both `ruff`_ and `mypy`_ are automatically run by pre-commit.
 
 When you make a pull request, adherence to the Python development best practices
-is checked by `pre-commit.ci <https://results.pre-commit.ci/latest/github/ESMValGroup/ESMValCore/main>`_.
+is checked by running the pre-commit hooks on CircleCI.
 
 YAML
 ~~~~

esmvalcore/_task.py

@@ -1006,7 +1006,7 @@ def _run_task(
 ) -> tuple[list[str], set[TrackedFile]]:
     """Run task and return the result."""
     if scheduler_address is None:
-        client = contextlib.nullcontext()
+        client: contextlib.AbstractContextManager = contextlib.nullcontext()
     else:
         client = Client(scheduler_address)
 

esmvalcore/cmor/_fixes/cordex/cordex_fixes.py

@@ -327,7 +327,7 @@ def _use_standard_lambert_conformal_grid(
         lon_coord.units = "degrees_east"
         lat_coord.units = "degrees_north"
         lon_coord.points, lat_coord.points = transformer.transform(
-            *np.meshgrid(x_coord.points, y_coord.points),
+            *np.meshgrid(x_coord.points, y_coord.points),  # type: ignore[call-overload]
             errcheck=True,
         )
 

esmvalcore/io/intake_esgf.py

@@ -186,7 +186,7 @@ def find_data(self, **facets: FacetValue) -> list[IntakeESGFDataset]:
             if not any(_isglob(v) for v in values)
         }
         # Translate "our" facets to ESGF facets and "our" values to ESGF values.
-        query = {
+        query: dict[str, Any] = {
             their_facet: [
                 self.values.get(our_facet, {}).get(v, v)
                 for v in non_glob_facets[our_facet]

esmvalcore/preprocessor/_area.py

@@ -16,6 +16,7 @@
 import numpy as np
 import shapely
 import shapely.ops
+import shapely.vectorized
 from dask import array as da
 from iris.coords import AuxCoord
 from iris.cube import CubeList
@@ -47,6 +48,8 @@
 
 logger = logging.getLogger(__name__)
 
+type ExtractShapeMethod = Literal["contains", "representative"]
+
 SHAPE_ID_KEYS: tuple[str, ...] = ("name", "NAME", "Name", "id", "ID")
 
 
@@ -597,7 +600,7 @@ def _get_masks_from_geometries(
     geometries: dict[str, dict],
     lon: np.ndarray,
     lat: np.ndarray,
-    method: str = "contains",
+    method: ExtractShapeMethod = "contains",
     decomposed: bool = False,
 ) -> dict[str, np.ndarray]:
     """Get cube masks from requested regions."""
@@ -643,7 +646,7 @@ def _get_bounds(
 def _get_single_mask(
     lon: np.ndarray,
     lat: np.ndarray,
-    method: str,
+    method: ExtractShapeMethod,
     geometry: dict,
 ) -> np.ndarray:
     """Get single mask from one region."""
@@ -750,7 +753,7 @@ def _update_shapefile_path(
 def extract_shape(
     cube: Cube,
     shapefile: str | Path,
-    method: str = "contains",
+    method: ExtractShapeMethod = "contains",
     crop: bool = True,
     decomposed: bool = False,
     ids: list | dict | None = None,

esmvalcore/preprocessor/_compare_with_refs.py

@@ -592,7 +592,7 @@ def _get_emd(
     arr: np.ndarray,
     ref_arr: np.ndarray,
     bin_centers: np.ndarray,
-) -> np.ndarray:
+) -> float | np.ma.core.MaskedConstant:
     """Calculate Earth mover's distance (non-lazy)."""
     if np.ma.is_masked(arr) or np.ma.is_masked(ref_arr):
         return np.ma.masked  # this is safe because PMFs will be masked arrays

esmvalcore/preprocessor/_io.py

@@ -25,7 +25,7 @@
 from esmvalcore.iris_helpers import dataset_to_iris
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
+    from collections.abc import Mapping, MutableMapping, Sequence
 
     from dask.delayed import Delayed
 
@@ -163,7 +163,7 @@ def load(
 def _load_zarr(
     file: str | Path,
     ignore_warnings: list[dict[str, Any]] | None = None,
-    backend_kwargs: dict[str, Any] | None = None,
+    backend_kwargs: Mapping[str, Any] | None = None,
 ) -> CubeList:
     # note on ``chunks`` kwarg to ``xr.open_dataset()``
     # docs.xarray.dev/en/stable/generated/xarray.open_dataset.html
@@ -177,7 +177,7 @@ def _load_zarr(
     # https://github.com/pp-mo/ncdata/issues/139
 
     time_coder = xr.coders.CFDatetimeCoder(use_cftime=True)
-    open_kwargs = {
+    open_kwargs: MutableMapping[str, Any] = {
         "consolidated": False,
         "decode_times": time_coder,
         "engine": "zarr",