Clean up following pre-commit

.bandit.yml

@@ -3,9 +3,9 @@ skips:
   - B101
   # Standard pseudo-random generators are not suitable for security/cryptographic purposes
   - B311
-  # Ignore warnings about importing subprocess  
-  - B404 
+  # Ignore warnings about importing subprocess
+  - B404
   # Ignore warnings about calling subprocess
-  - B603  
+  - B603
   # Ignore warnings about calling subprocess
-  - B607  
+  - B607

selector/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -24,4 +23,3 @@
 """Selector Package."""
 
 from selector.methods import *
-

selector/converter.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -22,10 +21,9 @@
 # --
 """Module for converting similarity measures to distance/dissimilarity measures."""
 
-import numpy as np
-
 from typing import Union
 
+import numpy as np
 
 __all__ = [
     "sim_to_dist",

selector/diversity.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -26,8 +25,8 @@
 import warnings
 
 import numpy as np
-from selector.similarity import tanimoto
 
+from selector.similarity import tanimoto
 
 __all__ = [
     "compute_diversity",

selector/methods/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #

selector/methods/base.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -22,11 +21,11 @@
 # --
 """Base class for diversity based subset selection."""
 
-import numpy as np
 import warnings
-
 from abc import ABC, abstractmethod
 
+import numpy as np
+
 __all__ = ["SelectionBase"]
 
 

selector/methods/distance.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -29,7 +28,6 @@ import scipy
 from selector.methods.base import SelectionBase
 from selector.methods.utils import optimize_radius
 
-
 __all__ = [
     "MaxMin",
     "MaxSum",

selector/methods/partition.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -29,9 +28,8 @@ import bitarray
 import numpy as np
 import scipy
 
-from selector.methods.base import SelectionBase
 from selector.diversity import compute_diversity
-
+from selector.methods.base import SelectionBase
 
 __all__ = [
     "GridPartition",

selector/methods/similarity.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -36,13 +35,13 @@ The ideas behind the similarity-based selection methods are described in the fol
 """
 
 import math
-from math import log
 import random
+from math import log
 from typing import List, Optional, Union
 
-from selector.methods.base import SelectionBase
 import numpy as np
 
+from selector.methods.base import SelectionBase
 
 __all__ = ["NSimilarity", "SimilarityIndex"]
 

selector/methods/tests/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #

selector/methods/tests/common.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -22,12 +21,11 @@
 # --
 """Common functions for test module."""
 
-import numpy as np
+from typing import Any, Tuple, Union
 
+import numpy as np
 from sklearn.datasets import make_blobs
 from sklearn.metrics import pairwise_distances
-from typing import Any, Tuple, Union
-
 
 __all__ = [
     "generate_synthetic_data",

selector/methods/tests/test_distance.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -23,12 +22,13 @@
 """Test selector/methods/distance.py."""
 
 
-from selector.methods.distance import MaxMin, MaxSum, OptiSim, DISE
 import numpy as np
+import pytest
 from numpy.testing import assert_equal, assert_raises
 from sklearn.metrics import pairwise_distances
+
+from selector.methods.distance import DISE, MaxMin, MaxSum, OptiSim
 from selector.methods.tests.common import generate_synthetic_data
-import pytest
 
 
 def test_maxmin():

selector/methods/tests/test_partition.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -23,13 +22,10 @@
 """Test Partition-Based Selection Methods."""
 
 import numpy as np
-from numpy.testing import assert_equal, assert_raises
 import pytest
+from numpy.testing import assert_equal, assert_raises
 
-from selector.methods.partition import (
-    GridPartition,
-    Medoid,
-)
+from selector.methods.partition import GridPartition, Medoid
 from selector.methods.tests.common import generate_synthetic_data
 
 

selector/methods/utils.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -26,7 +25,6 @@ import warnings
 
 import numpy as np
 
-
 __all__ = [
     "optimize_radius",
 ]

selector/similarity.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -22,10 +21,9 @@
 # --
 """Similarity Module."""
 
-import numpy as np
-
 from itertools import combinations_with_replacement
 
+import numpy as np
 
 __all__ = ["pairwise_similarity_bit", "tanimoto", "modified_tanimoto"]
 

selector/tests/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #

selector/tests/common.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #

selector/tests/test_converter.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -22,10 +21,10 @@
 # --
 """Test Converter Module."""
 
-import selector.converter as cv
 import numpy as np
 from numpy.testing import assert_almost_equal, assert_equal, assert_raises
 
+import selector.converter as cv
 
 # Tests for variations on input `x` for sim_to_dist()
 

selector/tests/test_diversity.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -23,21 +22,21 @@
 
 """Test Diversity Module."""
 
-import pytest
 import numpy as np
+import pytest
 from numpy.testing import assert_almost_equal, assert_equal, assert_raises, assert_warns
+
 from selector.diversity import (
     compute_diversity,
-    gini_coefficient,
     explicit_diversity_index,
+    gini_coefficient,
+    hypersphere_overlap_of_subset,
     logdet,
+    nearest_average_tanimoto,
     shannon_entropy,
-    hypersphere_overlap_of_subset,
     wdud,
-    nearest_average_tanimoto,
 )
 
-
 # each row is a feature and each column is a molecule
 sample1 = np.array([[4, 2, 6], [4, 9, 6], [2, 5, 0], [2, 0, 9], [5, 3, 0]])
 

selector/tests/test_similarity.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # The Selector library provides a set of tools for selecting a
 # subset of the dataset and computing diversity.
 #
@@ -26,11 +25,12 @@ import ast
 import csv
 
 import numpy as np
-from numpy.testing import assert_almost_equal, assert_equal, assert_raises
 import pkg_resources
 import pytest
-from selector.similarity import pairwise_similarity_bit, tanimoto, modified_tanimoto
+from numpy.testing import assert_almost_equal, assert_equal, assert_raises
+
 from selector.methods.similarity import NSimilarity, SimilarityIndex
+from selector.similarity import modified_tanimoto, pairwise_similarity_bit, tanimoto
 
 
 def test_pairwise_similarity_bit_raises():
@@ -1284,7 +1284,7 @@ def _get_selections_ref_dict():
     """
 
     file_path = get_data_file_path("ref_similarity_data.csv")
-    with open(file_path, mode="r", encoding="utf-8") as file:
+    with open(file_path, encoding="utf-8") as file:
         reader = csv.reader(file, delimiter=";")
         next(reader)  # skip header
         # initialize the dictionary