Apply autoformatting

Author: schlunma

esmvalcore/_main.py

@@ -1,4 +1,5 @@
 """Fix base classes for ICON on-the-fly CMORizer."""
+
 from __future__ import annotations
 
 import logging
@@ -27,10 +28,10 @@
 class IconFix(NativeDatasetFix):
     """Base class for all ICON fixes."""
 
-    CACHE_DIR = Path.home() / '.esmvaltool' / 'cache'
+    CACHE_DIR = Path.home() / ".esmvaltool" / "cache"
     CACHE_VALIDITY = 7 * 24 * 60 * 60  # [s]; = 1 week
     TIMEOUT = 5 * 60  # [s]; = 5 min
-    GRID_FILE_ATTR = 'grid_file_uri'
+    GRID_FILE_ATTR = "grid_file_uri"
 
     def __init__(self, *args, **kwargs):
         """Initialize ICON fix."""
@@ -65,7 +66,8 @@ def _create_mesh(self, cube: Cube) -> MeshXY:
         # 'vertex_of_cell'; since UGRID expects a different dimension ordering
         # we transpose the cube here)
         vertex_of_cell = horizontal_grid.extract_cube(
-            NameConstraint(var_name='vertex_of_cell'))
+            NameConstraint(var_name="vertex_of_cell")
+        )
         vertex_of_cell.transpose()
 
         # Extract start index used to name nodes from the the horizontal grid
@@ -74,8 +76,8 @@ def _create_mesh(self, cube: Cube) -> MeshXY:
 
         # Extract face coordinates from cube (in ICON jargon called 'cell
         # latitude' and 'cell longitude')
-        face_lat = cube.coord('latitude')
-        face_lon = cube.coord('longitude')
+        face_lat = cube.coord("latitude")
+        face_lon = cube.coord("longitude")
 
         # Extract node coordinates from horizontal grid
         (node_lat, node_lon) = self._get_node_coords(horizontal_grid)
@@ -87,11 +89,11 @@ def _create_mesh(self, cube: Cube) -> MeshXY:
 
         # Latitude: there might be slight numerical differences (-> check that
         # the differences are very small before fixing it)
-        close_kwargs = {'rtol': 1e-3, 'atol': 1e-5}
+        close_kwargs = {"rtol": 1e-3, "atol": 1e-5}
         if not np.allclose(
-                face_lat.bounds,
-                node_lat.points[conn_node_inds],
-                **close_kwargs,  # type: ignore
+            face_lat.bounds,
+            node_lat.points[conn_node_inds],
+            **close_kwargs,  # type: ignore
         ):
             logger.warning(
                 "Latitude bounds of the face coordinate ('clat_vertices' in "
@@ -127,15 +129,15 @@ def _create_mesh(self, cube: Cube) -> MeshXY:
         # Create mesh
         connectivity = Connectivity(
             indices=vertex_of_cell.data,
-            cf_role='face_node_connectivity',
+            cf_role="face_node_connectivity",
             start_index=start_index,
             location_axis=0,
         )
         mesh = MeshXY(
             topology_dimension=2,
-            node_coords_and_axes=[(node_lat, 'y'), (node_lon, 'x')],
+            node_coords_and_axes=[(node_lat, "y"), (node_lon, "x")],
             connectivities=[connectivity],
-            face_coords_and_axes=[(face_lat, 'y'), (face_lon, 'x')],
+            face_coords_and_axes=[(face_lat, "y"), (face_lon, "x")],
         )
 
         return mesh
@@ -146,7 +148,8 @@ def _get_grid_url(self, cube):
             raise ValueError(
                 f"Cube does not contain the attribute '{self.GRID_FILE_ATTR}' "
                 f"necessary to download the ICON horizontal grid file:\n"
-                f"{cube}")
+                f"{cube}"
+            )
         grid_url = cube.attributes[self.GRID_FILE_ATTR]
         parsed_url = urlparse(grid_url)
         grid_name = Path(parsed_url.path).name
@@ -162,21 +165,22 @@ def _get_node_coords(self, horizontal_grid):
 
         """
         dual_area_cube = horizontal_grid.extract_cube(
-            NameConstraint(var_name='dual_area'))
-        node_lat = dual_area_cube.coord(var_name='vlat')
-        node_lon = dual_area_cube.coord(var_name='vlon')
+            NameConstraint(var_name="dual_area")
+        )
+        node_lat = dual_area_cube.coord(var_name="vlat")
+        node_lon = dual_area_cube.coord(var_name="vlon")
 
         # Fix metadata
         node_lat.bounds = None
         node_lon.bounds = None
-        node_lat.var_name = 'nlat'
-        node_lon.var_name = 'nlon'
-        node_lat.standard_name = 'latitude'
-        node_lon.standard_name = 'longitude'
-        node_lat.long_name = 'node latitude'
-        node_lon.long_name = 'node longitude'
-        node_lat.convert_units('degrees_north')
-        node_lon.convert_units('degrees_east')
+        node_lat.var_name = "nlat"
+        node_lon.var_name = "nlon"
+        node_lat.standard_name = "latitude"
+        node_lon.standard_name = "longitude"
+        node_lat.long_name = "node latitude"
+        node_lon.long_name = "node longitude"
+        node_lat.convert_units("degrees_north")
+        node_lon.convert_units("degrees_east")
 
         # Convert longitude to [0, 360]
         self._set_range_in_0_360(node_lon)
@@ -186,10 +190,10 @@ def _get_node_coords(self, horizontal_grid):
     def _get_path_from_facet(self, facet, description=None):
         """Try to get path from facet."""
         if description is None:
-            description = 'File'
+            description = "File"
         path = Path(os.path.expandvars(self.extra_facets[facet])).expanduser()
         if not path.is_file():
-            new_path = self.session['auxiliary_data_dir'] / path
+            new_path = self.session["auxiliary_data_dir"] / path
             if not new_path.is_file():
                 raise FileNotFoundError(
                     f"{description} '{path}' given by facet '{facet}' does "
@@ -238,8 +242,8 @@ def add_additional_cubes(self, cubes):
 
         """
         facets_to_consider = [
-            'zg_file',
-            'zghalf_file',
+            "zg_file",
+            "zghalf_file",
         ]
         for facet in facets_to_consider:
             if self.extra_facets.get(facet) is None:
@@ -254,7 +258,7 @@ def add_additional_cubes(self, cubes):
     def _get_grid_from_facet(self):
         """Get horizontal grid from user-defined facet `horizontal_grid`."""
         grid_path = self._get_path_from_facet(
-            'horizontal_grid', 'Horizontal grid file'
+            "horizontal_grid", "Horizontal grid file"
         )
         grid_name = grid_path.name
 
@@ -297,7 +301,7 @@ def _get_grid_from_cube_attr(self, cube: Cube) -> Cube:
     def _get_grid_from_rootpath(self, grid_name: str) -> CubeList | None:
         """Try to get grid from the ICON rootpath."""
         glob_patterns: list[Path] = []
-        for data_source in _get_data_sources('ICON'):
+        for data_source in _get_data_sources("ICON"):
             glob_patterns.extend(
                 data_source.get_glob_patterns(**self.extra_facets)
             )
@@ -334,8 +338,10 @@ def _get_downloaded_grid(self, grid_url: str, grid_name: str) -> CubeList:
                 logger.debug("Using cached ICON grid file '%s'", grid_path)
                 valid_cache = True
             else:
-                logger.debug("Existing cached ICON grid file '%s' is outdated",
-                             grid_path)
+                logger.debug(
+                    "Existing cached ICON grid file '%s' is outdated",
+                    grid_path,
+                )
 
         # File is not present in cache or too old -> download it
         if not valid_cache:
@@ -347,12 +353,12 @@ def _get_downloaded_grid(self, grid_url: str, grid_name: str) -> CubeList:
                 tmp_path,
             )
             with requests.get(
-                    grid_url,
-                    stream=True,
-                    timeout=self.TIMEOUT,
+                grid_url,
+                stream=True,
+                timeout=self.TIMEOUT,
             ) as response:
                 response.raise_for_status()
-                with tmp_path.open('wb') as file:
+                with tmp_path.open("wb") as file:
                     copyfileobj(response.raw, file)
             shutil.move(tmp_path, grid_path)
             logger.info(
@@ -403,7 +409,7 @@ def get_horizontal_grid(self, cube):
             file.
 
         """
-        if self.extra_facets.get('horizontal_grid') is not None:
+        if self.extra_facets.get("horizontal_grid") is not None:
             grid = self._get_grid_from_facet()
         else:
             grid = self._get_grid_from_cube_attr(cube)
@@ -444,9 +450,9 @@ def get_mesh(self, cube):
         """
         # If specified by the user, use `horizontal_grid` facet to determine
         # grid name; otherwise, use the `grid_file_uri` attribute of the cube
-        if self.extra_facets.get('horizontal_grid') is not None:
+        if self.extra_facets.get("horizontal_grid") is not None:
             grid_path = self._get_path_from_facet(
-                'horizontal_grid', 'Horizontal grid file'
+                "horizontal_grid", "Horizontal grid file"
             )
             grid_name = grid_path.name
         else:
@@ -474,32 +480,33 @@ def _get_start_index(horizontal_grid):
 
         """
         vertex_index = horizontal_grid.extract_cube(
-            NameConstraint(var_name='vertex_index'))
+            NameConstraint(var_name="vertex_index")
+        )
         return np.int32(np.min(vertex_index.data))
 
     @staticmethod
     def _load_cubes(path: Path | str) -> CubeList:
         """Load cubes and ignore certain warnings."""
         with warnings.catch_warnings():
             warnings.filterwarnings(
-                'ignore',
+                "ignore",
                 message="Ignoring netCDF variable .* invalid units .*",
                 category=UserWarning,
-                module='iris',
+                module="iris",
             )  # iris < 3.8
             warnings.filterwarnings(
-                'ignore',
+                "ignore",
                 message="Ignoring invalid units .* on netCDF variable .*",
                 category=UserWarning,
-                module='iris',
+                module="iris",
             )  # iris >= 3.8
             warnings.filterwarnings(
-                'ignore',
+                "ignore",
                 message="Failed to create 'height' dimension coordinate: The "
-                        "'height' DimCoord bounds array must be strictly "
-                        "monotonic.",
+                "'height' DimCoord bounds array must be strictly "
+                "monotonic.",
                 category=UserWarning,
-                module='iris',
+                module="iris",
             )
             cubes = iris.load(path)
         return cubes

esmvalcore/_recipe/recipe.py

@@ -16,7 +16,7 @@
 from ._config_object import CFG, Config, Session
 
 __all__ = (
-    'CFG',
-    'Config',
-    'Session',
+    "CFG",
+    "Config",
+    "Session",
 )

esmvalcore/cmor/_fixes/icon/_base_fixes.py

@@ -1,4 +1,5 @@
 """Functions dealing with config-developer.yml and extra facets."""
+
 from __future__ import annotations
 
 import collections.abc
@@ -43,7 +44,7 @@ def _load_extra_facets(project, extra_facets_dir):
         config_file_paths = config_path.glob(f"{project.lower()}-*.yml")
         for config_file_path in sorted(config_file_paths):
             logger.debug("Loading extra facets from %s", config_file_path)
-            with config_file_path.open(encoding='utf-8') as config_file:
+            with config_file_path.open(encoding="utf-8") as config_file:
                 config_piece = yaml.safe_load(config_file)
             if config_piece:
                 _deep_update(config, config_piece)
@@ -54,7 +55,7 @@ def get_extra_facets(dataset, extra_facets_dir):
     """Read files with additional variable information ("extra facets")."""
     extra_facets_dir = tuple(extra_facets_dir)
     project_details = _load_extra_facets(
-        dataset.facets['project'],
+        dataset.facets["project"],
         extra_facets_dir,
     )
 
@@ -76,10 +77,11 @@ def pattern_filter(patterns, name):
         return [pat for pat in patterns if fnmatch.fnmatchcase(name, pat)]
 
     extra_facets = {}
-    for dataset_ in pattern_filter(project_details, dataset['dataset']):
-        for mip_ in pattern_filter(project_details[dataset_], dataset['mip']):
-            for var in pattern_filter(project_details[dataset_][mip_],
-                                      dataset['short_name']):
+    for dataset_ in pattern_filter(project_details, dataset["dataset"]):
+        for mip_ in pattern_filter(project_details[dataset_], dataset["mip"]):
+            for var in pattern_filter(
+                project_details[dataset_][mip_], dataset["short_name"]
+            ):
                 facets = project_details[dataset_][mip_][var]
                 extra_facets.update(facets)
 
@@ -88,23 +90,25 @@ def pattern_filter(patterns, name):
 
 def load_config_developer(cfg_file):
     """Read the developer's configuration file."""
-    with open(cfg_file, 'r', encoding='utf-8') as file:
+    with open(cfg_file, "r", encoding="utf-8") as file:
         cfg = yaml.safe_load(file)
 
-    if 'obs4mips' in cfg:
+    if "obs4mips" in cfg:
         logger.warning(
             "Correcting capitalization, project 'obs4mips'"
-            " should be written as 'obs4MIPs' in %s", cfg_file)
-        cfg['obs4MIPs'] = cfg.pop('obs4mips')
+            " should be written as 'obs4MIPs' in %s",
+            cfg_file,
+        )
+        cfg["obs4MIPs"] = cfg.pop("obs4mips")
 
     for project, settings in cfg.items():
-        for site, drs in settings.get('input_dir', {}).items():
+        for site, drs in settings.get("input_dir", {}).items():
             # Since v2.8, 'version' can be used instead of 'latestversion'
             if isinstance(drs, list):
-                drs = [d.replace('{latestversion}', '{version}') for d in drs]
+                drs = [d.replace("{latestversion}", "{version}") for d in drs]
             else:
-                drs = drs.replace('{latestversion}', '{version}')
-            settings['input_dir'][site] = drs
+                drs = drs.replace("{latestversion}", "{version}")
+            settings["input_dir"][site] = drs
         CFG[project] = settings
 
     read_cmor_tables(cfg_file)
@@ -119,8 +123,8 @@ def get_project_config(project):
 
 def get_institutes(variable):
     """Return the institutes given the dataset name in CMIP6."""
-    dataset = variable['dataset']
-    project = variable['project']
+    dataset = variable["dataset"]
+    project = variable["project"]
     try:
         return CMOR_TABLES[project].institutes[dataset]
     except (KeyError, AttributeError):
@@ -129,9 +133,9 @@ def get_institutes(variable):
 
 def get_activity(variable):
     """Return the activity given the experiment name in CMIP6."""
-    project = variable['project']
+    project = variable["project"]
     try:
-        exp = variable['exp']
+        exp = variable["exp"]
         if isinstance(exp, list):
             return [CMOR_TABLES[project].activities[value][0] for value in exp]
         return CMOR_TABLES[project].activities[exp][0]
@@ -144,8 +148,8 @@ def get_ignored_warnings(project: FacetValue, step: str) -> None | list:
     if project not in CFG:
         return None
     project_cfg = CFG[project]
-    if 'ignore_warnings' not in project_cfg:
+    if "ignore_warnings" not in project_cfg:
         return None
-    if step not in project_cfg['ignore_warnings']:
+    if step not in project_cfg["ignore_warnings"]:
         return None
-    return project_cfg['ignore_warnings'][step]
+    return project_cfg["ignore_warnings"][step]