Merge pull request #117 from volkamerlab/update-black-formatting

Update black formatting

kissim/api/subset.py

@@ -141,7 +141,6 @@ def _subset_fingerprint_generator_data(fingerprint_generator, klifs_residue_ids)
     klifs_residue_ixs = [i - 1 for i in klifs_residue_ids]
 
     for id_, fp in fingerprint_generator.data.items():
-
         # Initialize new fingerprint
         fp_subset = Fingerprint()
         fp_subset.structure_klifs_id = fp.structure_klifs_id
@@ -151,7 +150,6 @@ def _subset_fingerprint_generator_data(fingerprint_generator, klifs_residue_ids)
 
         # Iterate over physiochemical and spatial features
         for feature_name1, features1 in fp.values_dict.items():
-
             fp_dict[feature_name1] = {}
 
             # Iterate over all physiochemical features
@@ -163,9 +161,7 @@ def _subset_fingerprint_generator_data(fingerprint_generator, klifs_residue_ids)
 
             # Iterate over all spatial features (includes distances and moments!)
             elif feature_name1 == "spatial":
-
                 for feature_name2, features2 in features1.items():
-
                     fp_dict[feature_name1][feature_name2] = {}
 
                     # Iterate over all distances

kissim/comparison/feature_distances.py

@@ -34,7 +34,6 @@ class FeatureDistances:
     """
 
     def __init__(self):
-
         self.structure_pair_ids = None
         self.kinase_pair_ids = None
         self.distances = None
@@ -54,7 +53,6 @@ def data(self):
         """
 
         if (self.distances is not None) and (self.bit_coverages is not None):
-
             feature_types = list(
                 chain.from_iterable(
                     [[key] * len(value) for key, value in DISTANCES_FEATURE_NAMES.items()]

kissim/comparison/feature_distances_generator.py

@@ -36,7 +36,6 @@ def __init__(self, **kwargs):
         self.structure_kinase_ids = None
 
     def __eq__(self, other):
-
         if isinstance(other, FeatureDistancesGenerator):
             return (
                 self.data.equals(other.data)
@@ -195,7 +194,6 @@ def _get_feature_distances(pair, fingerprints):
 
     @staticmethod
     def _feature_distances_list_to_df(feature_distances_list):
-
         structure_pair_ids_list = []
         kinase_pair_ids_list = []
         distances_list = []

kissim/comparison/fingerprint_distance.py

@@ -30,7 +30,6 @@ class FingerprintDistance:
     """
 
     def __init__(self):
-
         self.structure_pair_ids = None
         self.kinase_pair_ids = None
         self.distance = None

kissim/comparison/fingerprint_distance_generator.py

@@ -30,12 +30,10 @@ class FingerprintDistanceGenerator(BaseGenerator):
     """
 
     def __init__(self, *args, **kwargs):
-
         self.data = None
         self.structure_kinase_ids = None
 
     def __eq__(self, other):
-
         if isinstance(other, FingerprintDistanceGenerator):
             return (
                 self.data.equals(other.data)

kissim/comparison/tree.py

@@ -247,7 +247,6 @@ def _get_node_means(tree, matrix, node_means, leaf_mean):
 
     # Get mean only for nodes that are not a leaf
     if not tree.is_leaf():
-
         # Iterate over the nodes to the right and the left of the current node
         for left in [0, 1]:
             if left:

kissim/definitions.py

@@ -157,7 +157,6 @@
 DISTANCE_CUTOFFS = {}
 MOMENT_CUTOFFS = {}
 for how in ["fine", "coarse"]:
-
     DISTANCE_CUTOFFS[how] = pd.read_csv(
         PATH_DATA / f"min_max_distances_{how}.csv", index_col=[0, 1]
     )

kissim/encoding/features/exposure.py

@@ -48,7 +48,6 @@ class SolventExposureFeature(BaseFeature):
     """
 
     def __init__(self):
-
         self.name = None
         self._residue_ids = None
         self._residue_ixs = None

kissim/encoding/features/sco.py

@@ -49,7 +49,6 @@ class SideChainOrientationFeature(BaseFeature):
     """
 
     def __init__(self):
-
         self.name = None
         self._residue_ids = None
         self._residue_ixs = None

kissim/encoding/features/sitealign.py

@@ -45,7 +45,6 @@ class SiteAlignFeature(BaseFeature):
     """
 
     def __init__(self):
-
         self.name = None
         self._residue_ids = None
         self._residue_ixs = None

kissim/encoding/features/subpockets.py

@@ -37,7 +37,6 @@ class SubpocketsFeature(BaseFeature):
     """
 
     def __init__(self):
-
         self.name = None
         self._residue_ids = None
         self._residue_ixs = None

kissim/encoding/fingerprint_base.py

@@ -77,7 +77,6 @@ class FingerprintBase:
     """
 
     def __init__(self):
-
         # TODO add more structure metadata? e.g. bound ligand?
         self.structure_klifs_id = None
         self.kinase_name = None

kissim/encoding/fingerprint_generator_base.py

@@ -31,7 +31,6 @@ class FingerprintGeneratorBase:
     """
 
     def __init__(self):
-
         self.structure_klifs_ids = None
         self.klifs_session = None
         self.data = None

kissim/encoding/fingerprint_generator_normalized.py

@@ -28,7 +28,6 @@ class FingerprintGeneratorNormalized(FingerprintGeneratorBase):
     """
 
     def __init__(self):
-
         self.structure_klifs_ids = None
         self.klifs_session = None
         self.data = None

kissim/encoding/fingerprint_normalized.py

@@ -154,7 +154,6 @@ def _normalize_moments_bits(self, values_dict, fine_grained):
 
         if values_dict is not None:
             for subpocket_name, values in values_dict.items():
-
                 # This is truly ugly!
                 if fine_grained:
                     minimum = cutoffs[cutoffs.index.get_level_values("min_max") == "min"][

kissim/io/biopython.py

@@ -56,7 +56,6 @@ class PocketBioPython(PocketBase):
     """
 
     def __init__(self):
-
         self.name = None
         self._residue_ids = None
         self._residue_ixs = None

kissim/io/data.py

@@ -39,7 +39,6 @@ class KlifsToKissimData:
     """
 
     def __init__(self):
-
         self.klifs_session = None
         self.structure_klifs_id = None
         self.kinase_name = None

kissim/tests/api/test_api_compare.py

@@ -20,7 +20,6 @@
     ],
 )
 def test_compare(fingerprint_generator, output_path, feature_weights, n_cores):
-
     compare(fingerprint_generator, output_path, feature_weights, n_cores)
 
     if output_path is not None:

kissim/tests/api/test_api_encode.py

@@ -23,7 +23,6 @@
 def test_encode(
     structure_klifs_ids, fingerprints_json_filepath, local_klifs_download_path, n_cores
 ):
-
     with enter_temp_directory():
         fingerprint_generator = encode(
             structure_klifs_ids, fingerprints_json_filepath, local_klifs_download_path, n_cores

kissim/tests/api/test_api_outliers.py

@@ -32,7 +32,6 @@
 def test_outliers(
     fingerprints_path, distance_cutoff, fingerprints_wo_outliers_path, n_fingerprints_wo_outliers
 ):
-
     with enter_temp_directory():
         fingerprints = outliers(fingerprints_path, distance_cutoff, fingerprints_wo_outliers_path)
         assert isinstance(fingerprints, FingerprintGenerator)

kissim/tests/api/test_api_subset.py

@@ -47,9 +47,7 @@ def test_subset(
     fingerprints_subset_path,
     klifs_pocket_residue_subset,
 ):
-
     with enter_temp_directory():
-
         # Generate regular fingerprints
         fingerprints_path = Path(fingerprints_path)
         fingerprint_generator = FingerprintGenerator.from_structure_klifs_ids([12347, 3835])
@@ -73,7 +71,6 @@ def test_subset(
 
         # Test Fingerprint objects
         for fingerprint_id, fingerprint_subset in fingerprint_generator_subset.data.items():
-
             # Original fingerprint
             fingerprint = fingerprint_generator.data[fingerprint_id]
 
@@ -112,7 +109,6 @@ def test_subset(
 def test_subset_fingerprint_generator_data(
     structure_klifs_id, klifs_session, subset_residue_ids, fp_subset_sum
 ):
-
     fingerprint_generator = FingerprintGenerator.from_structure_klifs_ids(
         [structure_klifs_id], klifs_session
     )

kissim/tests/api/test_api_weights.py

@@ -23,7 +23,6 @@
     ],
 )
 def test_weights(feature_distances_path, feature_weights, fingerprint_distances_path):
-
     with enter_temp_directory():
         fingerprint_distances = weights(
             feature_distances_path, feature_weights, fingerprint_distances_path

kissim/tests/cli/test_cli_compare.py

@@ -37,7 +37,6 @@
     ],
 )
 def test_compare_from_cli(args):
-
     with enter_temp_directory():
         compare_from_cli(args)
 
@@ -139,7 +138,6 @@ def test_compare_from_cli(args):
     ],
 )
 def test_compare_from_cli_error(args, error):
-
     with enter_temp_directory():
         with pytest.raises(error):
             compare_from_cli(args)

kissim/tests/cli/test_cli_encode.py

@@ -49,7 +49,6 @@
     ],
 )
 def test_encode_from_cli(args):
-
     with enter_temp_directory():
         encode_from_cli(args)
 
@@ -85,6 +84,5 @@ def test_encode_from_cli(args):
     ],
 )
 def test_encode_from_cli_error(args, error):
-
     with pytest.raises(error):
         encode_from_cli(args)

kissim/tests/comparison/test_feature_distances.py

@@ -206,7 +206,6 @@ def test_from_fingerprints(self, fingerprint_generator):
         ],
     )
     def test_from_dict(self, feature_distances_dict):
-
         feature_distances_calculated = FeatureDistances._from_dict(feature_distances_dict)
         assert isinstance(feature_distances_calculated, FeatureDistances)
         assert isinstance(feature_distances_calculated.structure_pair_ids, tuple)

kissim/tests/comparison/test_feature_distances_generator.py

@@ -69,7 +69,6 @@ def test_from_fingerprints(
         ],
     )
     def test_from_structure_klifs_ids(self, structure_klifs_ids, klifs_session, n_cores):
-
         # Test FeatureDistancesGenerator class attributes
         feature_distances_generator = FeatureDistancesGenerator.from_structure_klifs_ids(
             structure_klifs_ids, klifs_session, n_cores
@@ -85,38 +84,31 @@ def test_from_structure_klifs_ids(self, structure_klifs_ids, klifs_session, n_co
         [[["pdbA", "kinaseA"], ["pdbB", "kinaseA"], ["pdbC", "kinaseB"]]],
     )
     def test_structure_kinase_ids(self, feature_distances_generator, structure_kinase_ids):
-
         assert feature_distances_generator._structure_kinase_ids == structure_kinase_ids
 
     @pytest.mark.parametrize(
         "structure_pair_ids", [[["pdbA", "pdbB"], ["pdbA", "pdbC"], ["pdbB", "pdbC"]]]
     )
     def test_structure_pair_ids(self, feature_distances_generator, structure_pair_ids):
-
         assert feature_distances_generator.structure_pair_ids == structure_pair_ids
 
     @pytest.mark.parametrize(
         "kinase_pair_ids",
         [[["kinaseA", "kinaseA"], ["kinaseA", "kinaseB"], ["kinaseA", "kinaseB"]]],
     )
     def test_kinase_pair_ids(self, feature_distances_generator, kinase_pair_ids):
-
         assert feature_distances_generator.kinase_pair_ids == kinase_pair_ids
 
     @pytest.mark.parametrize("structure_ids", [["pdbA", "pdbB", "pdbC"]])
     def test_structure_ids(self, feature_distances_generator, structure_ids):
-
         assert feature_distances_generator.structure_ids == structure_ids
 
     @pytest.mark.parametrize("kinase_ids", [["kinaseA", "kinaseB"]])
     def test_kinase_ids(self, feature_distances_generator, kinase_ids):
-
         assert feature_distances_generator.kinase_ids == kinase_ids
 
     def test_to_from_csv(self, feature_distances_generator):
-
         with enter_temp_directory():
-
             filepath = Path("test.csv.bz2")
 
             feature_distances_generator.to_csv(filepath)

kissim/tests/comparison/test_fingerprint_distance.py

@@ -76,7 +76,6 @@ def test_from_feature_distances(self, feature_distances, feature_weights, distan
         ],
     )
     def test_calculate_weighted_sum(self, values, weights, calculated_weighted_sum):
-
         fingerprint_distance = FingerprintDistance()
         calculated_weighted_sum_calculated = fingerprint_distance._calculate_weighted_sum(
             values, weights
@@ -97,7 +96,6 @@ def test_calculate_weighted_sum(self, values, weights, calculated_weighted_sum):
         ],
     )
     def test_calculate_weighted_sum_raises(self, values, weights):
-
         with pytest.raises(ValueError):
             fingerprint_distance = FingerprintDistance()
             fingerprint_distance._calculate_weighted_sum(values, weights)
@@ -122,7 +120,6 @@ def test_calculate_weighted_sum_raises(self, values, weights):
     def test_remove_nan_distances_and_recalibrate_weights(
         self, distances, weights, distances_wo_nan, weights_wo_nan_recalibrated
     ):
-
         fingerprint_distance = FingerprintDistance()
         (
             distances_wo_nan_calculated,

kissim/tests/comparison/test_tree.py

@@ -65,9 +65,7 @@ def test_from_file(
     node_means,
     tree_string,
 ):
-
     with enter_temp_directory():
-
         tree_nodes_calculated, node_means_calculated = tree.from_file(
             distance_matrix_path, tree_path, annotation_path, clustering_method, similarity
         )
@@ -76,7 +74,6 @@ def test_from_file(
         assert node_means == pytest.approx(node_means_calculated, abs=1e-6)
 
         if tree_path:
-
             tree_path = Path(tree_path)
             # Tree file there?
             assert tree_path.exists()
@@ -86,7 +83,6 @@ def test_from_file(
             tree_path.unlink()
 
         if annotation_path:
-
             annotation_path = Path(annotation_path)
             # Annotation file there?
             assert annotation_path.exists()

kissim/tests/encoding/test_fingerprint.py

@@ -179,7 +179,6 @@ def test_to_from_json(self, structure_klifs_id):
         json_filepath = Path("fingerprint.json")
 
         with enter_temp_directory():
-
             # Save json file
             fingerprint.to_json(json_filepath)
             assert json_filepath.exists()

kissim/tests/encoding/test_fingerprint_generator.py

@@ -94,7 +94,6 @@ def test_to_from_json(self, structure_klifs_ids, values_array_sum):
         json_filepath = Path("fingerprints.json")
 
         with enter_temp_directory():
-
             # Save json file
             fingerprints.to_json(json_filepath)
             assert json_filepath.exists()