[pre-commit.ci] pre-commit autoupdate (#2525)

Co-authored-by: Bouwe Andela <[email protected]>

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ exclude: |
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
       - id: check-ast
@@ -24,16 +24,16 @@ repos:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/adrienverge/yamllint
-    rev: 'v1.31.0'
+    rev: 'v1.35.1'
     hooks:
       - id: yamllint
   - repo: https://github.com/codespell-project/codespell
-    rev: 'v2.2.4'
+    rev: 'v2.3.0'
     hooks:
       - id: codespell
         additional_dependencies: [tomli]  # required for Python 3.10
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.10"
+    rev: "v0.6.8"
     hooks:
       - id: ruff
         args: [--fix]

CODE_OF_CONDUCT.md

@@ -6,7 +6,7 @@ In the interest of fostering an open and welcoming environment, we as
 contributors and maintainers pledge to making participation in our project and
 our community a harassment-free experience for everyone, regardless of age, body
 size, disability, ethnicity, sex characteristics, gender identity and expression,
-level of experience, education, socio-economic status, nationality, personal
+level of experience, education, socioeconomic status, nationality, personal
 appearance, race, religion, or sexual identity and orientation.
 
 ## Our Standards

doc/changelog.rst

@@ -1024,7 +1024,7 @@ Highlights
 ~~~~~~~~~~
 
 - ESMValCore now has the ability to automatically download missing data from ESGF. For details, see :ref:`Data Retrieval<data-retrieval>`.
-- ESMValCore now also can resume an earlier run. This is useful to re-use expensive preprocessor results. For details, see :ref:`Running<running>`.
+- ESMValCore now also can resume an earlier run. This is useful to reuse expensive preprocessor results. For details, see :ref:`Running<running>`.
 
 This release includes
 

doc/contributing.rst

@@ -101,7 +101,7 @@ Please keep the following considerations in mind when programming:
   code.
 - If you find yourself copy-pasting a piece of code and making minor changes
   to every copy, instead put the repeated bit of code in a function that you can
-  re-use, and provide the changed bits as function arguments.
+  reuse, and provide the changed bits as function arguments.
 - Be careful when changing existing unit tests to make your new feature work.
   You might be breaking existing features if you have to change existing tests.
 

doc/quickstart/find_data.rst

@@ -602,7 +602,7 @@ Key                  Description                            Default value if not
                                                             recipe if default DRS is used)
 ```special_attr``    A special attribute in the filename    No default
                      `ACCESS-ESM` raw data, it's related to
-                     frquency of raw data
+                     frequency of raw data
 ``sub_dataset``      Part of the ACCESS-ESM raw dataset     No default
                      root, need to specify if you want to
                      use the cmoriser

doc/quickstart/run.rst

@@ -93,14 +93,14 @@ Possible values are:
   - `default`: fail if there are any errors.
   - `strict`: fail if there are any warnings.
 
-To re-use pre-processed files from a previous run of the same recipe, you can
+To reuse pre-processed files from a previous run of the same recipe, you can
 use
 
 .. code:: bash
 
     esmvaltool run recipe_example.yml --resume_from ~/esmvaltool_output/recipe_python_20210930_123907
 
-Multiple directories can be specified for re-use, make sure to quote them:
+Multiple directories can be specified for reuse, make sure to quote them:
 
 .. code:: bash
 

esmvalcore/cmor/_fixes/cmip6/mcm_ua_1_0.py

@@ -26,7 +26,7 @@ class AllVars(Fix):
     def fix_metadata(self, cubes):
         """Fix metadata.
 
-        Remove unnecessary spaces in metadat and rename ``var_name`` of
+        Remove unnecessary spaces in metadata and rename ``var_name`` of
         latitude and longitude and fix longitude boundary description may be
         wrong (lons=[0, ..., 356.25]; on_bnds=[[-1.875, 1.875], ..., [354.375,
         360]]).

notebooks/composing-recipes.ipynb

@@ -17,9 +17,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import yaml\n",
+    "\n",
     "from esmvalcore.config import CFG\n",
-    "from esmvalcore.dataset import Dataset, datasets_to_recipe\n",
-    "import yaml"
+    "from esmvalcore.dataset import Dataset, datasets_to_recipe"
    ]
   },
   {
@@ -38,7 +39,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "CFG['search_esgf'] = 'always'"
+    "CFG[\"search_esgf\"] = \"always\""
    ]
   },
   {
@@ -84,18 +85,18 @@
    ],
    "source": [
     "tas = Dataset(\n",
-    "    short_name='tas',\n",
-    "    mip='Amon',\n",
-    "    project='CMIP6',\n",
-    "    dataset='CanESM5-1',\n",
-    "    ensemble='r1i1p1f1',\n",
-    "    exp='historical',\n",
-    "    grid='gn',\n",
-    "    timerange='2000/2002',\n",
+    "    short_name=\"tas\",\n",
+    "    mip=\"Amon\",\n",
+    "    project=\"CMIP6\",\n",
+    "    dataset=\"CanESM5-1\",\n",
+    "    ensemble=\"r1i1p1f1\",\n",
+    "    exp=\"historical\",\n",
+    "    grid=\"gn\",\n",
+    "    timerange=\"2000/2002\",\n",
     ")\n",
-    "tas['diagnostic'] = 'diagnostic_name'\n",
+    "tas[\"diagnostic\"] = \"diagnostic_name\"\n",
     "\n",
-    "pr = tas.copy(short_name='pr')\n",
+    "pr = tas.copy(short_name=\"pr\")\n",
     "\n",
     "print(yaml.safe_dump(datasets_to_recipe([tas, pr])))"
    ]
@@ -127,14 +128,14 @@
    ],
    "source": [
     "dataset_template = Dataset(\n",
-    "    short_name='tas',\n",
-    "    mip='Amon',\n",
-    "    project='CMIP6',\n",
-    "    exp='historical',\n",
-    "    dataset='*',\n",
-    "    institute='*',\n",
-    "    ensemble='*',\n",
-    "    grid='*',\n",
+    "    short_name=\"tas\",\n",
+    "    mip=\"Amon\",\n",
+    "    project=\"CMIP6\",\n",
+    "    exp=\"historical\",\n",
+    "    dataset=\"*\",\n",
+    "    institute=\"*\",\n",
+    "    ensemble=\"*\",\n",
+    "    grid=\"*\",\n",
     ")\n",
     "datasets = list(dataset_template.from_files())\n",
     "len(datasets)"
@@ -584,7 +585,7 @@
    ],
    "source": [
     "for dataset in datasets:\n",
-    "    dataset.facets['diagnostic'] = 'diagnostic_name'\n",
+    "    dataset.facets[\"diagnostic\"] = \"diagnostic_name\"\n",
     "print(yaml.safe_dump(datasets_to_recipe(datasets)))"
    ]
   }

notebooks/discovering-data.ipynb

@@ -19,9 +19,8 @@
    "outputs": [],
    "source": [
     "from esmvalcore.config import CFG\n",
-    "from esmvalcore.dataset import Dataset, datasets_to_recipe\n",
-    "from esmvalcore.esgf import download\n",
-    "import yaml"
+    "from esmvalcore.dataset import Dataset\n",
+    "from esmvalcore.esgf import download"
    ]
   },
   {
@@ -40,7 +39,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "CFG['search_esgf'] = 'always'"
+    "CFG[\"search_esgf\"] = \"always\""
    ]
   },
   {
@@ -60,14 +59,14 @@
    "outputs": [],
    "source": [
     "dataset_template = Dataset(\n",
-    "    short_name='tas',\n",
-    "    mip='Amon',\n",
-    "    project='CMIP6',\n",
-    "    exp='historical',\n",
-    "    dataset='*',\n",
-    "    institute='*',\n",
-    "    ensemble='*',\n",
-    "    grid='*',\n",
+    "    short_name=\"tas\",\n",
+    "    mip=\"Amon\",\n",
+    "    project=\"CMIP6\",\n",
+    "    exp=\"historical\",\n",
+    "    dataset=\"*\",\n",
+    "    institute=\"*\",\n",
+    "    ensemble=\"*\",\n",
+    "    grid=\"*\",\n",
     ")"
    ]
   },
@@ -292,7 +291,7 @@
     }
    ],
    "source": [
-    "dataset.files[0].download(CFG['download_dir'])"
+    "dataset.files[0].download(CFG[\"download_dir\"])"
    ]
   },
   {
@@ -311,7 +310,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "download(dataset.files, CFG['download_dir'])"
+    "download(dataset.files, CFG[\"download_dir\"])"
    ]
   }
  ],

notebooks/loading-and-processing-data.ipynb

@@ -19,13 +19,13 @@
    "source": [
     "%matplotlib inline\n",
     "\n",
-    "import matplotlib.pyplot as plt\n",
     "import iris.quickplot\n",
+    "import matplotlib.pyplot as plt\n",
     "\n",
     "from esmvalcore.config import CFG\n",
     "from esmvalcore.dataset import Dataset\n",
-    "from esmvalcore.esgf import download, ESGFFile\n",
-    "from esmvalcore.preprocessor import area_statistics, annual_statistics"
+    "from esmvalcore.esgf import ESGFFile, download\n",
+    "from esmvalcore.preprocessor import annual_statistics, area_statistics"
    ]
   },
   {
@@ -43,7 +43,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "CFG['search_esgf'] = 'when_missing'"
+    "CFG[\"search_esgf\"] = \"when_missing\""
    ]
   },
   {
@@ -80,13 +80,13 @@
    ],
    "source": [
     "tas = Dataset(\n",
-    "    short_name='tas',\n",
-    "    mip='Amon',\n",
-    "    project='CMIP5',\n",
-    "    dataset='MPI-ESM-MR',\n",
-    "    ensemble='r1i1p1',\n",
-    "    exp='historical',\n",
-    "    timerange='1850/2000',\n",
+    "    short_name=\"tas\",\n",
+    "    mip=\"Amon\",\n",
+    "    project=\"CMIP5\",\n",
+    "    dataset=\"MPI-ESM-MR\",\n",
+    "    ensemble=\"r1i1p1\",\n",
+    "    exp=\"historical\",\n",
+    "    timerange=\"1850/2000\",\n",
     ")\n",
     "tas"
    ]
@@ -124,7 +124,7 @@
     }
    ],
    "source": [
-    "tas.add_supplementary(short_name='areacella', mip='fx', ensemble='r0i0p0')\n",
+    "tas.add_supplementary(short_name=\"areacella\", mip=\"fx\", ensemble=\"r0i0p0\")\n",
     "tas.supplementaries"
    ]
   },
@@ -247,7 +247,7 @@
     "for supplementary_ds in tas.supplementaries:\n",
     "    files.extend(supplementary_ds.files)\n",
     "files = [file for file in files if isinstance(file, ESGFFile)]\n",
-    "download(files, CFG['download_dir'])\n",
+    "download(files, CFG[\"download_dir\"])\n",
     "tas.find_files()\n",
     "print(tas.files)\n",
     "for supplementary_ds in tas.supplementaries:\n",
@@ -548,9 +548,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cube = area_statistics(cube, operator='mean')\n",
-    "cube = annual_statistics(cube, operator='mean')\n",
-    "cube.convert_units('degrees_C')"
+    "cube = area_statistics(cube, operator=\"mean\")\n",
+    "cube = annual_statistics(cube, operator=\"mean\")\n",
+    "cube.convert_units(\"degrees_C\")"
    ]
   },
   {

pyproject.toml

@@ -7,7 +7,7 @@ version_scheme = "release-branch-semver"
 
 [tool.codespell]
 skip = "*.ipynb,esmvalcore/config/extra_facets/ipslcm-mappings.yml"
-ignore-words-list = "vas,hist"
+ignore-words-list = "vas,hist,oce"
 
 [tool.pylint.main]
 jobs = 1  # Running more than one job in parallel crashes prospector.

tests/unit/preprocessor/_volume/test_volume.py

@@ -657,46 +657,42 @@ def test_volume_statistics_invalid_bounds(self):
 
         with self.assertRaises(ValueError) as err:
             volume_statistics(self.grid_invalid_z_bounds, "mean")
-        self.assertIn(
+        assert (
             "Z axis bounds shape found (3, 2, 2, 4). Bounds should be "
-            "2 in the last dimension to compute the thickness.",
-            str(err.exception),
-        )
+            "2 in the last dimension to compute the thickness."
+        ) in str(err.exception)
 
     def test_volume_statistics_invalid_units(self):
         """Test z-axis units cannot be converted to m"""
 
         with self.assertRaises(ValueError) as err:
             volume_statistics(self.grid_4d_sigma_space, "mean")
-        self.assertIn(
+        assert (
             "Cannot compute volume using the Z-axis. "
-            "Unable to convert from 'Unit('kg m-3')' to 'Unit('m')'.",
-            str(err.exception),
-        )
+            "Unable to convert from 'Unit('kg m-3')' to 'Unit('m')'."
+        ) in str(err.exception)
 
     def test_volume_statistics_z_axis_time_error(self):
         # Fails because depth z-axis coord depends on time dimensions
         # which would aggregate also along that dimension
         with self.assertRaises(ValueError) as err:
             volume_statistics(self.grid_4d_z, "mean")
-        self.assertIn(
+        assert (
             "X and Y axis coordinates depend on (2, 3) dimensions, "
             "while X, Y, and Z axis depends on (0, 1, 2, 3) dimensions. "
             "This may indicate Z axis depending on other dimension than "
-            "space that could provoke invalid aggregation...",
-            str(err.exception),
-        )
+            "space that could provoke invalid aggregation..."
+        ) in str(err.exception)
 
         grid_3d_no_x = self.grid_4d_z[..., 0]
         with self.assertRaises(ValueError) as err:
             volume_statistics(grid_3d_no_x, "mean")
-        self.assertIn(
+        assert (
             "X and Y axis coordinates depend on (2,) dimensions, "
             "while X, Y, and Z axis depends on (0, 1, 2) dimensions. "
             "This may indicate Z axis depending on other dimension than "
-            "space that could provoke invalid aggregation...",
-            str(err.exception),
-        )
+            "space that could provoke invalid aggregation..."
+        ) in str(err.exception)
 
     def test_volume_statistics_missing_axis(self):
         # x axis is missing
@@ -711,9 +707,7 @@ def test_volume_statistics_missing_axis(self):
         grid_no_z = self.grid_4d[:, 0]
         with self.assertRaises(ValueError) as err:
             volume_statistics(grid_no_z, "mean")
-        self.assertIn(
-            "Cannot compute volume with scalar Z-axis", str(err.exception)
-        )
+        assert "Cannot compute volume with scalar Z-axis" in str(err.exception)
 
     def test_volume_statistics_2d_depth(self):
         # Create new 2D depth coord