[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -23,16 +23,16 @@ repos:
         args: [ '--pytest-test-first' ]
       - id: trailing-whitespace
   - repo: https://github.com/pappasam/toml-sort
-    rev: v0.24.3
+    rev: v0.24.4
     hooks:
       - id: toml-sort-fix
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.37.1
+    rev: v1.38.0
     hooks:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.10
+    rev: v0.15.9
     hooks:
       - id: ruff-check
         args: [ '--fix', '--show-fixes' ]
@@ -43,7 +43,7 @@ repos:
       - id: flake8
         args: [ '--config=.flake8' ]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.2
+    rev: 0.9.1
     hooks:
       - id: nbstripout
         files: ".ipynb"
@@ -59,7 +59,7 @@ repos:
       - id: rst-inline-touching-normal
       - id: text-unicode-replacement-char
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies: [ 'tomli' ]
@@ -73,7 +73,7 @@ repos:
     hooks:
       - id: gitleaks
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.0
+    rev: 0.37.1
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs

CI/requirements_ci.in

@@ -1,7 +1,7 @@
 bump-my-version==1.3.0
 exceptiongroup==1.3.1
 flit==3.12.0
-pip==25.3
+pip==26.0.1
 tomli==2.4.0
-tox==4.30.3
-tox-gh==1.5.0
+tox==4.52.0
+tox-gh==1.7.1

CI/requirements_ci.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.9
+# This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
 #    pip-compile --generate-hashes --output-file=CI/requirements_ci.txt CI/requirements_ci.in
@@ -19,10 +19,10 @@ bracex==2.5.post1 \
 bump-my-version==1.3.0 \
     --hash=sha256:3cdaa54588d2443a29303b77e7539417187952c3d22f87bfdd32c0fe6af2f570 \
     --hash=sha256:5780137a8d93378af3839798fcba01c7e6cb28dcc5aa5a7ab4d8507787f1995c
-    # via -r requirements_ci.in
-cachetools==6.1.0 \
-    --hash=sha256:1c7bb3cf9193deaf3508b7c5f2a79986c13ea38965c5adcff1f84519cf39163e \
-    --hash=sha256:b4c4f404392848db3ce7aac34950d17be4d864da4b8b66911008e430bc544587
+    # via -r CI/requirements_ci.in
+cachetools==7.0.5 \
+    --hash=sha256:0cd042c24377200c1dcd225f8b7b12b0ca53cc2c961b43757e774ebe190fd990 \
+    --hash=sha256:46bc8ebefbe485407621d0a4264b23c080cedd913921bad7ac3ed2f26c183114
     # via tox
 certifi==2025.1.31 \
     --hash=sha256:3d5da6925056f6f18f119200434a4780a94263f10d1c21d032a6f6b2baa20651 \
@@ -31,10 +31,6 @@ certifi==2025.1.31 \
     #   httpcore
     #   httpx
     #   requests
-chardet==5.2.0 \
-    --hash=sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7 \
-    --hash=sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970
-    # via tox
 charset-normalizer==3.4.1 \
     --hash=sha256:0167ddc8ab6508fe81860a57dd472b2ef4060e8d378f0cc555707126830f2537 \
     --hash=sha256:01732659ba9b5b873fc117534143e4feefecf3b2078b0a6a2e925271bb6f4cfa \
@@ -150,19 +146,18 @@ docutils==0.21.2 \
 exceptiongroup==1.3.1 \
     --hash=sha256:8b412432c6055b0b7d14c310000ae93352ed6754f70fa8f7c34141f91c4e3219 \
     --hash=sha256:a7a39a3bd276781e98394987d3a5701d0c4edffb633bb7a5144577f82c773598
+    # via -r CI/requirements_ci.in
+filelock==3.25.2 \
+    --hash=sha256:b64ece2b38f4ca29dd3e810287aa8c48182bbecd1ae6e9ae126c9b35f1382694 \
+    --hash=sha256:ca8afb0da15f229774c9ad1b455ed96e85a81373065fb10446672f64444ddf70
     # via
-    #   -r requirements_ci.in
-    #   anyio
-filelock==3.19.1 \
-    --hash=sha256:66eda1888b0171c998b35be2bcc0f6d75c388a7ce20c3f3f37aa8e96c2dddf58 \
-    --hash=sha256:d38e30481def20772f5baf097c122c3babc4fcdb7e14e57049eb9d88c6dc017d
-    # via
+    #   python-discovery
     #   tox
     #   virtualenv
 flit==3.12.0 \
     --hash=sha256:1c80f34dd96992e7758b40423d2809f48f640ca285d0b7821825e50745ec3740 \
     --hash=sha256:2b4e7171dc22881fa6adc2dbf083e5ecc72520be3cd7587d2a803da94d6ef431
-    # via -r requirements_ci.in
+    # via -r CI/requirements_ci.in
 flit-core==3.12.0 \
     --hash=sha256:18f63100d6f94385c6ed57a72073443e1a71a4acb4339491615d0f16d6ff01b2 \
     --hash=sha256:e7a0304069ea895172e3c7bb703292e992c5d1555dd1233ab7b5621b5b69e62c
@@ -194,16 +189,17 @@ mdurl==0.1.2 \
     --hash=sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8 \
     --hash=sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba
     # via markdown-it-py
-packaging==25.0 \
-    --hash=sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484 \
-    --hash=sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f
+packaging==26.0 \
+    --hash=sha256:00243ae351a257117b6a241061796684b084ed1c516a08c48a3f7e147a9d80b4 \
+    --hash=sha256:b36f1fef9334a5588b4166f8bcd26a14e521f2b55e6b9de3aaa80d3ff7a37529
     # via
     #   pyproject-api
     #   tox
-platformdirs==4.4.0 \
-    --hash=sha256:abd01743f24e5287cd7a5db3752faf1a2d65353f38ec26d98e25a6db65958c85 \
-    --hash=sha256:ca753cf4d81dc309bc67b0ea38fd15dc97bc30ce419a7f58d13eb3bf14c4febf
+platformdirs==4.9.4 \
+    --hash=sha256:1ec356301b7dc906d83f371c8f487070e99d3ccf9e501686456394622a01a934 \
+    --hash=sha256:68a9a4619a666ea6439f2ff250c12a853cd1cbd5158d258bd824a7df6be2f868
     # via
+    #   python-discovery
     #   tox
     #   virtualenv
 pluggy==1.6.0 \
@@ -330,10 +326,16 @@ pygments==2.19.1 \
     --hash=sha256:61c16d2a8576dc0649d9f39e089b5f02bcd27fba10d8fb4dcc28173f7a45151f \
     --hash=sha256:9ea1544ad55cecf4b8242fab6dd35a93bbce657034b0611ee383099054ab6d8c
     # via rich
-pyproject-api==1.9.1 \
-    --hash=sha256:43c9918f49daab37e302038fc1aed54a8c7a91a9fa935d00b9a485f37e0f5335 \
-    --hash=sha256:7d6238d92f8962773dd75b5f0c4a6a27cce092a14b623b811dba656f3b628948
+pyproject-api==1.10.0 \
+    --hash=sha256:40c6f2d82eebdc4afee61c773ed208c04c19db4c4a60d97f8d7be3ebc0bbb330 \
+    --hash=sha256:8757c41a79c0f4ab71b99abed52b97ecf66bd20b04fa59da43b5840bac105a09
     # via tox
+python-discovery==1.2.1 \
+    --hash=sha256:180c4d114bff1c32462537eac5d6a332b768242b76b69c0259c7d14b1b680c9e \
+    --hash=sha256:b6a957b24c1cd79252484d3566d1b49527581d46e789aaf43181005e56201502
+    # via
+    #   tox
+    #   virtualenv
 python-dotenv==1.0.1 \
     --hash=sha256:e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca \
     --hash=sha256:f7b63ef50f1b690dddf550d03497b66d609393b40b564ed0d674909a68ebf16a
@@ -408,28 +410,27 @@ tomli==2.4.0 \
     --hash=sha256:d20b797a5c1ad80c516e41bc1fb0443ddb5006e9aaa7bda2d71978346aeb9132 \
     --hash=sha256:d3d1654e11d724760cdb37a3d7691f0be9db5fbdaef59c9f532aabf87006dbaa \
     --hash=sha256:d878f2a6707cc9d53a1be1414bbb419e629c3d6e67f69230217bb663e76b5087
-    # via
-    #   -r requirements_ci.in
-    #   pyproject-api
-    #   tox
+    # via -r CI/requirements_ci.in
 tomli-w==1.2.0 \
     --hash=sha256:188306098d013b691fcadc011abd66727d3c414c571bb01b1a174ba8c983cf90 \
     --hash=sha256:2dd14fac5a47c27be9cd4c976af5a12d87fb1f0b4512f81d69cce3b35ae25021
-    # via flit
+    # via
+    #   flit
+    #   tox
 tomlkit==0.13.2 \
     --hash=sha256:7a974427f6e119197f670fbbbeae7bef749a6c14e793db934baefc1b5f03efde \
     --hash=sha256:fff5fe59a87295b278abd31bec92c15d9bc4a06885ab12bcea52c71119392e79
     # via bump-my-version
-tox==4.30.3 \
-    --hash=sha256:a9f17b4b2d0f74fe0d76207236925a119095011e5c2e661a133115a8061178c9 \
-    --hash=sha256:f3dd0735f1cd4e8fbea5a3661b77f517456b5f0031a6256432533900e34b90bf
+tox==4.52.0 \
+    --hash=sha256:6054abf5c8b61d58776fbec991f9bf0d34bb883862beb93d2fe55601ef3977c9 \
+    --hash=sha256:624d8ea4a8c6d5e8d168eedf0e318d736fb22e83ca83137d001ac65ffdec46fd
     # via
-    #   -r requirements_ci.in
+    #   -r CI/requirements_ci.in
     #   tox-gh
-tox-gh==1.5.0 \
-    --hash=sha256:bd4c56d1ebcde4ca2450fed347610a739614a7225945bdc89a67c8395eac9d63 \
-    --hash=sha256:fd7e8c826f4576a02af4737fd4b738817660b63898c161d6ee8f658c885f7fa1
-    # via -r requirements_ci.in
+tox-gh==1.7.1 \
+    --hash=sha256:4f4871ee4091b41464f2df9ab1fcedb14a48accdecbb60d53297301a9d8984c6 \
+    --hash=sha256:a82285b16a597516f9a24f20326b124ddc7924a8b70cb05a9192e1c53d7f701d
+    # via -r CI/requirements_ci.in
 typing-extensions==4.14.1 \
     --hash=sha256:38b39f4aeeab64884ce9f74c94263ef78f3c22467c8724005483154c26648d36 \
     --hash=sha256:d1e1e3b58374dc93031d6eda2420a48ea44a36c2b4766a4fdeb3710755731d76
@@ -438,17 +439,14 @@ typing-extensions==4.14.1 \
     #   exceptiongroup
     #   pydantic
     #   pydantic-core
-    #   rich
     #   rich-click
-    #   tox
-    #   virtualenv
 urllib3==2.6.3 \
     --hash=sha256:1b62b6884944a57dbe321509ab94fd4d3b307075e0c2eae991ac71ee15ad38ed \
     --hash=sha256:bf272323e553dfb2e87d9bfd225ca7b0f467b919d7bbd355436d3fd37cb0acd4
     # via requests
-virtualenv==20.36.1 \
-    --hash=sha256:575a8d6b124ef88f6f51d56d656132389f961062a9177016a50e4f507bbcc19f \
-    --hash=sha256:8befb5c81842c641f8ee658481e42641c68b5eab3521d8e092d18320902466ba
+virtualenv==21.2.0 \
+    --hash=sha256:1720dc3a62ef5b443092e3f499228599045d7fea4c79199770499df8becf9098 \
+    --hash=sha256:1bd755b504931164a5a496d217c014d098426cddc79363ad66ac78125f9d908f
     # via tox
 wcmatch==10.0 \
     --hash=sha256:0dd927072d03c0a6527a20d2e6ad5ba8d0380e60870c383bc533b71744df7b7a \

clisops/core/regrid.py

@@ -583,20 +583,20 @@ def _apply_lsm(self, mask: str | None = None) -> bool:
 
         Parameters
         ----------
-        self: Grid
+        self : Grid
             The Grid object to which the mask will be applied.
-        mask: str, optional
+        mask : str, optional
             Whether to mask "ocean" cells or "land" cells. The default is None.
 
-        Raises
-        ------
-        Warning
-            If mask is specified but not found in dataset.
-
         Returns
         -------
         bool
             Whether self.lsm was assigned to a 2D-mask in form of a xr.DataArray or not.
+
+        Raises
+        ------
+        UserWarning
+            If mask is specified but not found in dataset.
         """
         if any(maskvar in self.ds for maskvar in ["sftlf", "lsm"]) and mask is not None:
             if "sftlf" in self.ds:

clisops/ops/base_operation.py

@@ -189,6 +189,10 @@ def _remove_redundant_coordinates_attr(ds):
         """
         Remove the coordinate attribute added by xarray.
 
+        See Also
+        --------
+        https://github.com/roocs/clisops/issues/224
+
         Examples
         --------
         If you have a dataset with a time_bnds variable that has a coordinate attribute:
@@ -202,11 +206,6 @@ def _remove_redundant_coordinates_attr(ds):
         .. code-block:: shell
 
             Warning (cdf_set_var): Inconsistent variable definition for time_bnds!
-
-        See Also
-        --------
-        https://github.com/roocs/clisops/issues/224
-
         """
         if isinstance(ds, xr.Dataset):
             var_list = list(ds.coords) + list(ds.data_vars)

tests/test_dataset_utils.py

@@ -457,9 +457,12 @@ def test_determine_lon_lat_range_unstructured(mini_esgf_data):
 def test_determine_lon_lat_range_regular_lat_lon(mini_esgf_data):
     """Test the function determine_lon_lat_range for regular lat lon grids."""
     with xr.open_mfdataset(mini_esgf_data["CMIP5_TAS"], decode_times=xr.coders.CFDatetimeCoder(use_cftime=True)) as ds:
-        ds.lat.values[1] = -999.0
+        # Deal with immutable numpy arrays
+        lat = ds.lat.values.copy()
+        lat[1] = -999.0
+        ds_copy = ds.assign_coords(lat=lat)
         with pytest.warns(UserWarning, match="fix is not possible for regular"):
-            clidu.determine_lon_lat_range(ds, "lon", "lat", "lon_bnds", "lat_bnds", apply_fix=True)
+            clidu.determine_lon_lat_range(ds_copy, "lon", "lat", "lon_bnds", "lat_bnds", apply_fix=True)
 
 
 def test_crosses_0_meridian(mini_esgf_data):