Extend black coverage

Related to #1620

parcels/_version.py

@@ -2,6 +2,13 @@
 import subprocess
 
 try:
-    version = subprocess.check_output(['git', '-C', os.path.dirname(__file__), 'describe', '--tags'], stderr=subprocess.PIPE).decode('ascii').strip()
+    version = (
+        subprocess.check_output(
+            ["git", "-C", os.path.dirname(__file__), "describe", "--tags"],
+            stderr=subprocess.PIPE,
+        )
+        .decode("ascii")
+        .strip()
+    )
 except:
     from parcels._version_setup import version as version  # noqa

parcels/interaction/neighborsearch/__init__.py

@@ -10,6 +10,10 @@
     KDTreeFlatNeighborSearch,
 )
 
-__all__ = ["HashFlatNeighborSearch", "HashSphericalNeighborSearch",
-           "BruteFlatNeighborSearch",
-           "BruteSphericalNeighborSearch", "KDTreeFlatNeighborSearch"]
+__all__ = [
+    "HashFlatNeighborSearch",
+    "HashSphericalNeighborSearch",
+    "BruteFlatNeighborSearch",
+    "BruteSphericalNeighborSearch",
+    "KDTreeFlatNeighborSearch",
+]

parcels/interaction/neighborsearch/distanceutils.py

@@ -7,20 +7,19 @@ def fast_distance(lat1, lon1, lat2, lon2):
     This is not the only possible implementation. It was taken from:
     https://www.mkompf.com/gps/distcalc.html
     """
-    g = np.sin(lat1)*np.sin(lat2)+np.cos(lat1)*np.cos(lat2)*np.cos(lon1-lon2)
+    g = np.sin(lat1) * np.sin(lat2) + np.cos(lat1) * np.cos(lat2) * np.cos(lon1 - lon2)
     return np.arccos(np.minimum(1, g))
 
 
-def spherical_distance(depth1_m, lat1_deg, lon1_deg, depth2_m, lat2_deg,
-                       lon2_deg):
+def spherical_distance(depth1_m, lat1_deg, lon1_deg, depth2_m, lat2_deg, lon2_deg):
     """Compute the arc distance, uses degrees as input."""
     R_earth = 6371000
-    lat1 = np.pi*lat1_deg/180
-    lon1 = np.pi*lon1_deg/180
-    lat2 = np.pi*lat2_deg/180
-    lon2 = np.pi*lon2_deg/180
+    lat1 = np.pi * lat1_deg / 180
+    lon1 = np.pi * lon1_deg / 180
+    lat2 = np.pi * lat2_deg / 180
+    lon2 = np.pi * lon2_deg / 180
 
-    horiz_dist = R_earth*fast_distance(lat1, lon1, lat2, lon2)
+    horiz_dist = R_earth * fast_distance(lat1, lon1, lat2, lon2)
 
-    vert_dist = np.abs(depth1_m-depth2_m)
+    vert_dist = np.abs(depth1_m - depth2_m)
     return (vert_dist, horiz_dist)

parcels/interaction/neighborsearch/kdtreeflat.py

@@ -7,12 +7,12 @@
 class KDTreeFlatNeighborSearch(BaseFlatNeighborSearch):
     def find_neighbors_by_coor(self, coor):
         coor = coor.reshape(3, 1)
-        corrected_coor = (coor/self.inter_dist).reshape(-1)
+        corrected_coor = (coor / self.inter_dist).reshape(-1)
         rel_idx = np.array(self._kdtree.query_ball_point(corrected_coor, r=1))
         neighbor_idx = self.active_idx[rel_idx]
         return neighbor_idx, np.vstack(self._distance(coor, neighbor_idx))
 
     def rebuild(self, values=None, active_mask=-1):
         super().rebuild(values, active_mask)
-        self._corrected_values = values[:, self._active_idx]/self.inter_dist
+        self._corrected_values = values[:, self._active_idx] / self.inter_dist
         self._kdtree = KDTree(self._corrected_values.T)

parcels/tools/loggers.py

@@ -1,8 +1,9 @@
 """Script to create a `logger` for Parcels."""
+
 import logging
 import sys
 
-__all__ = ['logger', 'XarrayDecodedFilter']
+__all__ = ["logger", "XarrayDecodedFilter"]
 
 warning_once_level = 25
 info_once_level = 26
@@ -53,4 +54,4 @@ class XarrayDecodedFilter(logging.Filter):
     """Filters the warning_once from fieldfilebuffer when cf_decoding fails."""
 
     def filter(self, record):
-        return 'Filling values might be wrongly parsed' not in record.getMessage()
+        return "Filling values might be wrongly parsed" not in record.getMessage()

pyproject.toml

@@ -104,38 +104,17 @@ convention = "numpy"
 [tool.ruff.format]
 # List of files to ignore formatting (ordered by ascending line count)
 exclude = [
-  "parcels/interaction/__init__.py",
-  "parcels/compilation/__init__.py",
-  "parcels/application_kernels/__init__.py",
-  "parcels/tools/__init__.py",
-  "parcels/_version.py",
-  "tests/test_converters.py",
-  "parcels/__init__.py",
-  "parcels/interaction/neighborsearch/bruteforce.py",
-  "parcels/interaction/neighborsearch/kdtreeflat.py",
-  "tests/test_data/fieldset_nemo.py",
-  "tests/test_examples.py",
-  "parcels/interaction/neighborsearch/__init__.py",
-  "tests/test_data/fieldset_nemo_error.py",
-  "parcels/interaction/neighborsearch/distanceutils.py",
-  "parcels/tools/global_statics.py",
   "tests/test_mpirun.py",
-  "parcels/tools/loggers.py",
+  "parcels/tools/global_statics.py",
   "tests/test_tools.py",
-  "docs/examples/example_brownian.py",
-  "docs/examples/example_mitgcm.py",
   "parcels/gridset.py",
   "parcels/tools/timer.py",
-  "docs/examples/example_ofam.py",
   "parcels/application_kernels/TEOSseawaterdensity.py",
   "tests/test_particles.py",
-  "docs/examples/example_radial_rotation.py",
   "parcels/application_kernels/interaction.py",
   "parcels/application_kernels/advectiondiffusion.py",
-  "docs/examples/example_decaying_moving_eddy.py",
   "parcels/tools/statuscodes.py",
   "tests/test_data/create_testfields.py",
-  "docs/examples/example_nemo_curvilinear.py",
   "tests/test_diffusion.py",
   "parcels/tools/exampledata_utils.py",
   "parcels/tools/interpolation_utils.py",
@@ -148,15 +127,11 @@ exclude = [
   "parcels/tools/converters.py",
   "parcels/application_kernels/advection.py",
   "parcels/particlefile.py",
-  "docs/examples/example_stommel.py",
   "parcels/compilation/codecompiler.py",
   "parcels/particle.py",
   "tests/test_interaction.py",
-  "docs/examples/example_peninsula.py",
   "tests/test_particlefile.py",
-  "docs/examples/example_globcurrent.py",
   "parcels/application_kernels/EOSseawaterproperties.py",
-  "docs/examples/example_moving_eddies.py",
   "tests/test_kernel_execution.py",
   "tests/test_particlesets.py",
   "parcels/particledata.py",
@@ -166,7 +141,6 @@ exclude = [
   "tests/test_advection.py",
   "parcels/kernel.py",
   "parcels/fieldfilebuffer.py",
-  "docs/examples/example_dask_chunk_OCMs.py",
   "tests/test_fieldset_sampling.py",
   "parcels/compilation/codegenerator.py",
   "tests/test_grids.py",

tests/test_converters.py

@@ -10,5 +10,5 @@ def test_TimeConverter():
         date = getattr(cftime, cf_datetime)(1990, 1, 1)
         assert TimeConverter(date).calendar == date.calendar
     assert TimeConverter(None).calendar is None
-    date_datetime64 = np.datetime64('2001-01-01T12:00')
+    date_datetime64 = np.datetime64("2001-01-01T12:00")
     assert TimeConverter(date_datetime64).calendar == "np_datetime64"

tests/test_data/fieldset_nemo.py

@@ -6,13 +6,19 @@
 def create_fieldset(indices=None):
     data_path = os.path.join(os.path.dirname(__file__))
 
-    filenames = {'U': {'lon': os.path.join(data_path, 'mask_nemo_cross_180lon.nc'),
-                       'lat': os.path.join(data_path, 'mask_nemo_cross_180lon.nc'),
-                       'data': os.path.join(data_path, 'Uu_eastward_nemo_cross_180lon.nc')},
-                 'V': {'lon': os.path.join(data_path, 'mask_nemo_cross_180lon.nc'),
-                       'lat': os.path.join(data_path, 'mask_nemo_cross_180lon.nc'),
-                       'data': os.path.join(data_path, 'Vv_eastward_nemo_cross_180lon.nc')}}
-    variables = {'U': 'U', 'V': 'V'}
-    dimensions = {'lon': 'glamf', 'lat': 'gphif', 'time': 'time_counter'}
+    filenames = {
+        "U": {
+            "lon": os.path.join(data_path, "mask_nemo_cross_180lon.nc"),
+            "lat": os.path.join(data_path, "mask_nemo_cross_180lon.nc"),
+            "data": os.path.join(data_path, "Uu_eastward_nemo_cross_180lon.nc"),
+        },
+        "V": {
+            "lon": os.path.join(data_path, "mask_nemo_cross_180lon.nc"),
+            "lat": os.path.join(data_path, "mask_nemo_cross_180lon.nc"),
+            "data": os.path.join(data_path, "Vv_eastward_nemo_cross_180lon.nc"),
+        },
+    }
+    variables = {"U": "U", "V": "V"}
+    dimensions = {"lon": "glamf", "lat": "gphif", "time": "time_counter"}
     indices = indices or {}
     return parcels.FieldSet.from_nemo(filenames, variables, dimensions, indices=indices)

tests/test_data/fieldset_nemo_error.py

@@ -6,14 +6,20 @@
 def random_function_name():
     data_path = os.path.join(os.path.dirname(__file__))
 
-    filenames = {'U': {'lon': os.path.join(data_path, 'mask_nemo_cross_180lon.nc'),
-                       'lat': os.path.join(data_path, 'mask_nemo_cross_180lon.nc'),
-                       'data': os.path.join(data_path, 'Uu_eastward_nemo_cross_180lon.nc')},
-                 'V': {'lon': os.path.join(data_path, 'mask_nemo_cross_180lon.nc'),
-                       'lat': os.path.join(data_path, 'mask_nemo_cross_180lon.nc'),
-                       'data': os.path.join(data_path, 'Vv_eastward_nemo_cross_180lon.nc')}}
-    variables = {'U': 'U', 'V': 'V'}
-    dimensions = {'lon': 'glamf', 'lat': 'gphif', 'time': 'time_counter'}
+    filenames = {
+        "U": {
+            "lon": os.path.join(data_path, "mask_nemo_cross_180lon.nc"),
+            "lat": os.path.join(data_path, "mask_nemo_cross_180lon.nc"),
+            "data": os.path.join(data_path, "Uu_eastward_nemo_cross_180lon.nc"),
+        },
+        "V": {
+            "lon": os.path.join(data_path, "mask_nemo_cross_180lon.nc"),
+            "lat": os.path.join(data_path, "mask_nemo_cross_180lon.nc"),
+            "data": os.path.join(data_path, "Vv_eastward_nemo_cross_180lon.nc"),
+        },
+    }
+    variables = {"U": "U", "V": "V"}
+    dimensions = {"lon": "glamf", "lat": "gphif", "time": "time_counter"}
     return parcels.FieldSet.from_nemo(filenames, variables, dimensions)