Merge pull request #223 from xylar/fix-flake8

Fix `flake8` lint in `geometric_features`

.github/workflows/build_workflow.yml

@@ -37,12 +37,20 @@ jobs:
         with:
           python-version: "3.10"
 
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        id: file_changes
+        uses: trilom/[email protected]
+        with:
+          output: ' '
+
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         # Run all pre-commit hooks on all the files.
         # Getting only staged files can be tricky in case a new PR is opened
         # since the action is run on a branch in detached head state
         name: Install and Run Pre-commit
         uses: pre-commit/[email protected]
+        with:
+          extra_args: --files ${{ steps.file_changes.outputs.files}}
 
   build:
     name: test geometric_features - python ${{ matrix.python-version }}

geometric_features/aggregation/__init__.py

@@ -58,11 +58,11 @@ def get_aggregator_by_name(region_group):
                                    'date': '20201123',
                                    'function': subbasins},
                'ISMIP6 Greenland Regions': {'prefix': 'ismip6GreenlandRegions',
-                                     'date': '20240510',
-                                     'function': ismip6_greenland},
-               'NASA Greenland Regions': {'prefix':'nasaGreenlandRegions',
-                                             'date':'20241017',
-                                             'function': nasa_greenland},
+                                            'date': '20240510',
+                                            'function': ismip6_greenland},
+               'NASA Greenland Regions': {'prefix': 'nasaGreenlandRegions',
+                                          'date': '20241017',
+                                          'function': nasa_greenland},
                'ISMIP6 Regions': {'prefix': 'ismip6Regions',
                                   'date': '20210201',
                                   'function': ismip6},
@@ -75,7 +75,7 @@ def get_aggregator_by_name(region_group):
                'Transport Transects': {'prefix': 'transportTransects',
                                        'date': '20210323',
                                        'function': transport},
-               'Arctic Transport Transects': {'prefix': 'arcticTransportTransects',
+               'Arctic Transport Transects': {'prefix': 'arcticTransportTransects',  # noqa: E501
                                               'date': '20220926',
                                               'function': arctic_transport}}
 

geometric_features/aggregation/landice/nasa_greenland_extended.py

@@ -1,6 +1,7 @@
 def nasa_greenland(gf):
     """
-    Aggregate NASA Greenland ice sheet basin regions extended to continental shelf.
+    Aggregate NASA Greenland ice sheet basin regions extended to continental
+    shelf.
 
     Parameters
     ----------

geometric_features/aggregation/seaice/historical_sea_ice.py

@@ -27,8 +27,8 @@ def qgreenland(gf):
                'May Historical Median Sea Ice Extent',
                'November Historical Median Sea Ice Extent',
                'October Historical Median Sea Ice Extent',
-               'September Historical Median Sea Ice Extent'
-              ]
+               'September Historical Median Sea Ice Extent']
+
     fc = gf.read(componentName='seaice', objectType='region',
                  featureNames=regions)
 

geometric_features/feature_collection.py

@@ -261,7 +261,7 @@ def difference(self, maskingFC, show_progress=False):
         featureCount = len(self.features)
         maskCount = len(maskingFC.features)
 
-        totalCount = featureCount*maskCount
+        totalCount = featureCount * maskCount
 
         if show_progress:
             print('Masking features...')
@@ -285,7 +285,7 @@ def difference(self, maskingFC, show_progress=False):
             masked = False
             for maskIndex, maskFeature in enumerate(maskingFC.features):
                 if show_progress:
-                    bar.update(maskIndex + featureIndex*maskCount)
+                    bar.update(maskIndex + featureIndex * maskCount)
                 maskShape = shapely.geometry.shape(maskFeature['geometry'])
                 if featureShape.intersects(maskShape):
                     masked = True
@@ -613,7 +613,8 @@ def _validate_feature(feature):
             raise KeyError(f'Feature {name} missing [{outerKey}] key')
         for innerKey in required[outerKey]:
             if innerKey not in feature[outerKey]:
-                raise KeyError(f'Feature {name} missing [{outerKey}][{innerKey}] key')
+                raise KeyError(
+                    f'Feature {name} missing [{outerKey}][{innerKey}] key')
 
     geomType = feature['geometry']['type']
     objectType = feature['properties']['object']
@@ -666,18 +667,18 @@ def _validate_feature(feature):
 
 def _split_geometry_crossing_antimeridian(geometry):
     def _to_polar(lon, lat):
-        phi = np.pi/180.*(np.mod(lon + 180., 360.) - 180.)
-        radius = np.pi/180.*(90. - sign*lat)
+        phi = np.pi / 180. * (np.mod(lon + 180., 360.) - 180.)
+        radius = np.pi / 180. * (90. - sign * lat)
 
         # nudge points at +/- 180 out of the way so they don't intersect the
         # testing wedge
         phi = np.sign(phi) * \
-            np.where(np.abs(phi) > np.pi - 1.5*epsilon,
-                     np.pi - 1.5*epsilon, np.abs(phi))
+            np.where(np.abs(phi) > np.pi - 1.5 * epsilon,
+                     np.pi - 1.5 * epsilon, np.abs(phi))
         # radius = np.where(radius < 1.5*epsilon, 1.5*epsilon, radius)
 
-        x = radius*np.sin(phi)
-        y = radius*np.cos(phi)
+        x = radius * np.sin(phi)
+        y = radius * np.cos(phi)
         if isinstance(lon, list):
             x = x.tolist()
             y = y.tolist()
@@ -688,17 +689,17 @@ def _to_polar(lon, lat):
         return x, y
 
     def _from_polar(x, y):
-        radius = np.sqrt(np.array(x)**2+np.array(y)**2)
+        radius = np.sqrt(np.array(x)**2 + np.array(y)**2)
         phi = np.arctan2(x, y)
 
         # close up the tiny gap
-        radius = np.where(radius < 2*epsilon, 0., radius)
+        radius = np.where(radius < 2 * epsilon, 0., radius)
         phi = np.sign(phi) * \
-            np.where(np.abs(phi) > np.pi - 2*epsilon,
+            np.where(np.abs(phi) > np.pi - 2 * epsilon,
                      np.pi, np.abs(phi))
 
-        lon = 180./np.pi*phi
-        lat = sign*(90. - 180./np.pi*radius)
+        lon = 180. / np.pi * phi
+        lat = sign * (90. - 180. / np.pi * radius)
 
         if isinstance(x, list):
             lon = lon.tolist()
@@ -717,8 +718,8 @@ def _from_polar(x, y):
                                                   (epsilon, -np.pi)])
 
     featureShape = shapely.geometry.shape(geometry)
-    sign = (2.*(0.5*(featureShape.bounds[1] + featureShape.bounds[3]) >= 0.) -
-            1.)
+    sign_mask = featureShape.bounds[1] + featureShape.bounds[3] >= 0.
+    sign = 2. * sign_mask - 1.
     polarShape = shapely.ops.transform(_to_polar, featureShape)
 
     if not polarShape.intersects(antimeridianWedge):

geometric_features/plot.py

@@ -83,17 +83,17 @@ def subdivide_line_string(lineString, periodic=False):
             coords.append(coords[0])
 
         outCoords = [coords[0]]
-        for iVert in range(len(coords)-1):
+        for iVert in range(len(coords) - 1):
             segment = shapely.geometry.LineString([coords[iVert],
-                                                   coords[iVert+1]])
+                                                   coords[iVert + 1]])
             if segment.length < maxLength:
-                outCoords.append(coords[iVert+1])
+                outCoords.append(coords[iVert + 1])
             else:
                 # we need to subdivide this segment
-                subsegment_count = int(np.ceil(segment.length/maxLength))
+                subsegment_count = int(np.ceil(segment.length / maxLength))
                 for index in range(subsegment_count):
                     point = segment.interpolate(
-                        float(index+1)/float(subsegment_count),
+                        float(index + 1) / float(subsegment_count),
                         normalized=True)
                     outCoords.append(point.coords[0])
 
@@ -126,7 +126,8 @@ def subdivide_line_string(lineString, periodic=False):
     elif geomtype == 'Point':
         newGeometry = geometry
     else:
-        print(f"Warning: subdividing geometry type {geomtype} is not supported.")
+        print(
+            f"Warning: subdividing geometry type {geomtype} is not supported.")
         newGeometry = geometry
 
     return newGeometry

geometric_features/test/test_aggregation.py

@@ -1,5 +1,3 @@
-import pytest
-
 from geometric_features import GeometricFeatures
 from geometric_features.aggregation import (antarctic, arctic_ocean,
                                             arctic_seaice, arctic_transport,
@@ -8,18 +6,19 @@
                                             ismip6_greenland, moc,
                                             nasa_greenland, qgreenland_seaice,
                                             subbasins, transport)
-from geometric_features.test import TestCase, loaddatadir
+from geometric_features.test import TestCase
 
 
-@pytest.mark.usefixtures('loaddatadir')
 class TestAggregation(TestCase):
 
     def test_get_aggregator_by_name(self):
         gf = GeometricFeatures()
-        names = ['Antarctic Regions', 'Arctic Ocean Regions', 'ISMIP6 Greenland Regions',
-                 'NASA Greenland Regions', 'Arctic Sea Ice Regions', 'Ocean Basins',
-                 'Ice Shelves', 'Ocean Subbasins', 'ISMIP6 Regions', 'MOC Basins', 'Historical Sea Ice',
-                 'Transport Transects', 'Arctic Transport Transects']
+        names = ['Antarctic Regions', 'Arctic Ocean Regions',
+                 'ISMIP6 Greenland Regions', 'NASA Greenland Regions',
+                 'Arctic Sea Ice Regions', 'Ocean Basins', 'Ice Shelves',
+                 'Ocean Subbasins', 'ISMIP6 Regions', 'MOC Basins',
+                 'Historical Sea Ice', 'Transport Transects',
+                 'Arctic Transport Transects']
 
         for name in names:
             function, prefix, date = get_aggregator_by_name(name)

geometric_features/test/test_feature_collection.py

@@ -7,7 +7,7 @@
 
 from geometric_features import (FeatureCollection, GeometricFeatures,
                                 read_feature_collection)
-from geometric_features.test import TestCase, loaddatadir
+from geometric_features.test import TestCase, loaddatadir  # noqa: F401
 
 
 @pytest.mark.usefixtures('loaddatadir')
@@ -393,7 +393,7 @@ def test_plot(self):
 
         projection = 'cyl'
 
-        fig = fc.plot(projection, maxLength=4.0, figsize=(12,12),
+        fig = fc.plot(projection, maxLength=4.0, figsize=(12, 12),
                       colors=colors, dpi=200)
 
         dest_filename = str(self.datadir.join('plot.png'))

geometric_features/test/test_features_and_tags.py

@@ -1,13 +1,10 @@
 import difflib
 import os
 
-import pytest
-
-from geometric_features.test import TestCase, loaddatadir
+from geometric_features.test import TestCase
 from geometric_features.utils import write_feature_names_and_tags
 
 
-@pytest.mark.usefixtures('loaddatadir')
 class TestFeaturesAndTags(TestCase):
 
     def test_features_and_tags(self):
@@ -36,5 +33,5 @@ def test_features_and_tags(self):
 
         if count != 0:
             raise ValueError(
-                'Unexpected differences in geometric_features/features_and_tags.json '
-                'compared with the results of geometric_features.utils.write_feature_names_and_tags()')
+                'Unexpected differences in geometric_features/features_and_tags.json '  # noqa: E501
+                'compared with the results of geometric_features.utils.write_feature_names_and_tags()')  # noqa: E501

geometric_features/test/test_geometric_features.py

@@ -3,7 +3,7 @@
 import pytest
 
 from geometric_features import GeometricFeatures
-from geometric_features.test import TestCase, loaddatadir
+from geometric_features.test import TestCase, loaddatadir  # noqa: F401
 
 
 @pytest.mark.usefixtures('loaddatadir')
@@ -138,5 +138,5 @@ def test_split(self, component='ocean', object_type='region',
         for feature in fc.features:
             name = feature['properties']['name']
             subdir = name.replace(' ', '_')
-            path = f'{self.datadir}/{component}/{object_type}/{subdir}/{object_type}.geojson'
+            path = f'{self.datadir}/{component}/{object_type}/{subdir}/{object_type}.geojson'  # noqa: E501
             assert os.path.exists(path)

geometric_features/utils.py

@@ -64,5 +64,5 @@ def provenance_command():
     call = ' '.join(sys.argv)
     host = socket.gethostname()
     sep = ' : '
-    provstr = sep.join([curtime,  host, user, cwd, call]) + ';'
+    provstr = sep.join([curtime, host, user, cwd, call]) + ';'
     return provstr