Update HEADER

HEADER

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

doc/conf.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of functions for transforming
-# a matrix to make it as similar as possible to a target matrix.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2017-2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

doc/getting_started.rst

@@ -1,3 +1,28 @@
+..
+    : # -*- coding: utf-8 -*-
+    : # The Selector library provides a set of tools for selecting a
+    : # subset of the dataset and computing diversity.
+    : #
+    : # Copyright (C) 2023 The QC-Devs Community
+    : #
+    : # This file is part of Selector.
+    : #
+    : # Selector is free software; you can redistribute it and/or
+    : # modify it under the terms of the GNU General Public License
+    : # as published by the Free Software Foundation; either version 3
+    : # of the License, or (at your option) any later version.
+    : #
+    : # Selector is distributed in the hope that it will be useful,
+    : # but WITHOUT ANY WARRANTY; without even the implied warranty of
+    : # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    : # GNU General Public License for more details.
+    : #
+    : # You should have received a copy of the GNU General Public License
+    : # along with this program; if not, see <http://www.gnu.org/licenses/>
+    : #
+    : # --
+    : --
+
 Getting Started
 ===============
 

doc/index.rst

@@ -1,3 +1,28 @@
+..
+    : # -*- coding: utf-8 -*-
+    : # The Selector library provides a set of tools for selecting a
+    : # subset of the dataset and computing diversity.
+    : #
+    : # Copyright (C) 2023 The QC-Devs Community
+    : #
+    : # This file is part of Selector.
+    : #
+    : # Selector is free software; you can redistribute it and/or
+    : # modify it under the terms of the GNU General Public License
+    : # as published by the Free Software Foundation; either version 3
+    : # of the License, or (at your option) any later version.
+    : #
+    : # Selector is distributed in the hope that it will be useful,
+    : # but WITHOUT ANY WARRANTY; without even the implied warranty of
+    : # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    : # GNU General Public License for more details.
+    : #
+    : # You should have received a copy of the GNU General Public License
+    : # along with this program; if not, see <http://www.gnu.org/licenses/>
+    : #
+    : # --
+    : --
+
 .. DiverseSelector documentation master file, created by
    sphinx-quickstart on Thu Mar 15 13:55:56 2018.
    You can adapt this file completely to your liking, but it should at least

selector/__init__.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

selector/_version.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -348,9 +348,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[
-        0
-    ].strip()
+    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
     pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
 
     return pieces

selector/converter.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

selector/distance.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

selector/diversity.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

selector/methods/__init__.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

selector/methods/base.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

selector/methods/dissimilarity.py

@@ -1,16 +1,17 @@
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

selector/methods/partition.py

@@ -1,16 +1,17 @@
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -19,7 +20,6 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
-
 """Module for Partition-Based Selection Methods."""
 
 import collections
@@ -29,7 +29,7 @@ import bitarray
 import scipy.spatial
 
 from selector.methods.base import SelectionBase
-from selector.diversity import compute_diversity, hypersphere_overlap_of_subset
+from selector.diversity import compute_diversity
 from selector.methods.utils import optimize_radius
 import numpy as np
 from scipy import spatial

selector/methods/similarity.py

@@ -1,16 +1,17 @@
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -19,7 +20,6 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
-
 """Module for Similarity-Based Selection Methods.
 
 This module contains the classes and functions for the similarity-based selection methods. To select

selector/methods/tests/__init__.py

@@ -0,0 +1,22 @@
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
+#
+# Copyright (C) 2023 The QC-Devs Community
+#
+# This file is part of Selector.
+#
+# Selector is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 3
+# of the License, or (at your option) any later version.
+#
+# Selector is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>
+#
+# --

selector/methods/tests/common.py

@@ -1,16 +1,17 @@
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

selector/methods/tests/test_dissimilarity.py

@@ -1,16 +1,17 @@
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -19,7 +20,6 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
-
 """Test Dissimilarity-Based Selection Methods."""
 
 

selector/methods/tests/test_partition.py

@@ -1,16 +1,17 @@
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -19,7 +20,6 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
-
 """Test Partition-Based Selection Methods."""
 
 import numpy as np
@@ -92,16 +92,16 @@ def test_directed_sphere_on_line_with_larger_radius():
     # (0,0) as the reference point
     x = np.array(
         [
-          [0, 0],
-          [0, 1],
-          [0, 1.1],
-          [0, 1.2],
-          [0, 2],
-          [0, 3],
-          [0, 3.1],
-          [0, 3.2],
-          [0, 4],
-          [0, 5],
+            [0, 0],
+            [0, 1],
+            [0, 1.1],
+            [0, 1.2],
+            [0, 2],
+            [0, 3],
+            [0, 3.1],
+            [0, 3.2],
+            [0, 4],
+            [0, 5],
         ]
     )
     selector = DirectedSphereExclusion(r0=2.0, tol=0)
@@ -230,6 +230,7 @@ def test_raises_grid_partitioning():
     )  # Test number selected should be int
     assert_raises(TypeError, selector.select_from_cluster, grid, 5, [5.0])
 
+
 def test_medoid():
     """Testing Medoid class."""
     coords, _, _ = generate_synthetic_data(

selector/methods/utils.py

@@ -1,16 +1,17 @@
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -19,8 +20,8 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
-
 """Module for Selection Utilities."""
+
 import warnings
 
 import numpy as np

selector/tests/__init__.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -21,4 +21,4 @@
 #
 # --
 
-"""Testing Module for DiverseSelector."""
+"""Test Module."""

selector/tests/common.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -20,7 +20,6 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
-
 """Common functions for test module."""
 
 import numpy as np
@@ -50,11 +49,10 @@ def load_testing_mols(mol_type: str = "2d") -> list:
         The list of RDKit molecules.
     """
     if mol_type == "2d":
-        mols = [Chem.MolFromSmiles(smiles) for smiles in
-                ["OC(=O)[C@@H](N)Cc1[nH]cnc1",
-                 "OC(=O)C(=O)C",
-                 "CC(=O)OC1=CC=CC=C1C(=O)O"]
-                ]
+        mols = [
+            Chem.MolFromSmiles(smiles)
+            for smiles in ["OC(=O)[C@@H](N)Cc1[nH]cnc1", "OC(=O)C(=O)C", "CC(=O)OC1=CC=CC=C1C(=O)O"]
+        ]
     elif mol_type == "3d":
         with path("DiverseSelector.test.data", "drug_mols.sdf") as sdf_file:
             suppl = Chem.SDMolSupplier(str(sdf_file), removeHs=False)
@@ -130,7 +128,7 @@ def cosine(a, b):
     coeff : int
         cosine coefficient for molecule A and B.
     """
-    coeff = (sum(a * b)) / (((sum(a ** 2)) + (sum(b ** 2))) ** 0.5)
+    coeff = (sum(a * b)) / (((sum(a**2)) + (sum(b**2))) ** 0.5)
     return coeff
 
 
@@ -149,5 +147,5 @@ def dice(a, b):
     coeff : int
         dice coefficient for molecule A and B.
     """
-    coeff = (2 * (sum(a * b))) / ((sum(a ** 2)) + (sum(b ** 2)))
+    coeff = (2 * (sum(a * b))) / ((sum(a**2)) + (sum(b**2)))
     return coeff

selector/tests/test_converter.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -20,8 +20,7 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
-
-"""Testing for Converter.py."""
+"""Test Converter Module."""
 
 import selector.converter as cv
 import numpy as np

selector/tests/test_distance.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -20,8 +20,7 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
-
-"""Test distance.py Module."""
+"""Test Distance-Based Selection Methods."""
 
 
 from selector.distance import (
@@ -31,7 +30,7 @@ from selector.distance import (
 )
 
 import numpy as np
-from numpy.testing import assert_almost_equal, assert_equal, assert_raises
+from numpy.testing import assert_equal, assert_raises
 
 
 def test_pairwise_similarity_bit_raises():

selector/tests/test_diversity.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -21,7 +21,7 @@
 #
 # --
 
-"""Testing for the diversity algorithms in the diversity.py module."""
+"""Test Diversity Module."""
 
 import pytest
 import numpy as np

selector/tests/test_similarity.py

@@ -1,16 +1,17 @@
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
@@ -19,8 +20,7 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
-
-"""Test similarity-Based Selection Methods."""
+"""Test Similarity-Based Selection Methods."""
 
 import ast
 import csv

setup.py

@@ -1,17 +1,17 @@
 # -*- coding: utf-8 -*-
-# The DiverseSelector library provides a set of tools to select molecule
-# subset with maximum molecular diversity.
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
 #
-# Copyright (C) 2022 The QC-Devs Community
+# Copyright (C) 2023 The QC-Devs Community
 #
-# This file is part of DiverseSelector.
+# This file is part of Selector.
 #
-# DiverseSelector is free software; you can redistribute it and/or
+# Selector is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
 # as published by the Free Software Foundation; either version 3
 # of the License, or (at your option) any later version.
 #
-# DiverseSelector is distributed in the hope that it will be useful,
+# Selector is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.

versioneer.py

@@ -1,3 +1,25 @@
+# -*- coding: utf-8 -*-
+# The Selector library provides a set of tools for selecting a
+# subset of the dataset and computing diversity.
+#
+# Copyright (C) 2023 The QC-Devs Community
+#
+# This file is part of Selector.
+#
+# Selector is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 3
+# of the License, or (at your option) any later version.
+#
+# Selector is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, see <http://www.gnu.org/licenses/>
+#
+# --
 
 # Version: 0.18
 
@@ -277,6 +299,7 @@ https://creativecommons.org/publicdomain/zero/1.0/ .
 """
 
 from __future__ import print_function
+
 try:
     import configparser
 except ImportError:
@@ -290,6 +313,7 @@ import sys
 
 # pylint: skip-file
 
+
 class VersioneerConfig:
     """Container for Versioneer configuration parameters."""
 
@@ -309,11 +333,13 @@ def get_root():
         setup_py = os.path.join(root, "setup.py")
         versioneer_py = os.path.join(root, "versioneer.py")
     if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
-        err = ("Versioneer was unable to run the project root directory. "
-               "Versioneer requires setup.py to be executed from "
-               "its immediate directory (like 'python setup.py COMMAND'), "
-               "or in a way that lets it use sys.argv[0] to find the root "
-               "(like 'python path/to/setup.py COMMAND').")
+        err = (
+            "Versioneer was unable to run the project root directory. "
+            "Versioneer requires setup.py to be executed from "
+            "its immediate directory (like 'python setup.py COMMAND'), "
+            "or in a way that lets it use sys.argv[0] to find the root "
+            "(like 'python path/to/setup.py COMMAND')."
+        )
         raise VersioneerBadRootError(err)
     try:
         # Certain runtime workflows (setup.py install/develop in a setuptools
@@ -326,8 +352,10 @@ def get_root():
         me_dir = os.path.normcase(os.path.splitext(me)[0])
         vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0])
         if me_dir != vsr_dir:
-            print("Warning: build in %s is using versioneer.py from %s"
-                  % (os.path.dirname(me), versioneer_py))
+            print(
+                "Warning: build in %s is using versioneer.py from %s"
+                % (os.path.dirname(me), versioneer_py)
+            )
     except NameError:
         pass
     return root
@@ -349,6 +377,7 @@ def get_config_from_root(root):
         if parser.has_option("versioneer", name):
             return parser.get("versioneer", name)
         return None
+
     cfg = VersioneerConfig()
     cfg.VCS = VCS
     cfg.style = get(parser, "style") or ""
@@ -373,17 +402,18 @@ HANDLERS = {}
 
 def register_vcs_handler(vcs, method):  # decorator
     """Decorator to mark a method as the handler for a particular VCS."""
+
     def decorate(f):
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:
             HANDLERS[vcs] = {}
         HANDLERS[vcs][method] = f
         return f
+
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
-                env=None):
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
     """Call the given command(s)."""
     assert isinstance(commands, list)
     p = None
@@ -391,10 +421,13 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
         try:
             dispcmd = str([c] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
-                                 stdout=subprocess.PIPE,
-                                 stderr=(subprocess.PIPE if hide_stderr
-                                         else None))
+            p = subprocess.Popen(
+                [c] + args,
+                cwd=cwd,
+                env=env,
+                stdout=subprocess.PIPE,
+                stderr=(subprocess.PIPE if hide_stderr else None),
+            )
             break
         except EnvironmentError:
             e = sys.exc_info()[1]
@@ -419,7 +452,9 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
     return stdout, p.returncode
 
 
-LONG_VERSION_PY['git'] = '''
+LONG_VERSION_PY[
+    "git"
+] = '''
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -994,7 +1029,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -1003,7 +1038,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r'\d', r)])
+        tags = set([r for r in refs if re.search(r"\d", r)])
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -1011,19 +1046,26 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix):]
+            r = ref[len(tag_prefix) :]
             if verbose:
                 print("picking %s" % r)
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None,
-                    "date": date}
+            return {
+                "version": r,
+                "full-revisionid": keywords["full"].strip(),
+                "dirty": False,
+                "error": None,
+                "date": date,
+            }
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags", "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": keywords["full"].strip(),
+        "dirty": False,
+        "error": "no suitable tags",
+        "date": None,
+    }
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
@@ -1038,8 +1080,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                          hide_stderr=True)
+    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -1047,10 +1088,11 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
-                                          "--always", "--long",
-                                          "--match", "%s*" % tag_prefix],
-                                   cwd=root)
+    describe_out, rc = run_command(
+        GITS,
+        ["describe", "--tags", "--dirty", "--always", "--long", "--match", "%s*" % tag_prefix],
+        cwd=root,
+    )
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
@@ -1073,17 +1115,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[:git_describe.rindex("-dirty")]
+        git_describe = git_describe[: git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
             # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%s'"
-                               % describe_out)
+            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
             return pieces
 
         # tag
@@ -1092,10 +1133,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
-                               % (full_tag, tag_prefix))
+            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (full_tag, tag_prefix)
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -1106,13 +1146,11 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
-                                    cwd=root)
+        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
-                       cwd=root)[0].strip()
+    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
     pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
 
     return pieces
@@ -1168,16 +1206,22 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     for i in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {"version": dirname[len(parentdir_prefix):],
-                    "full-revisionid": None,
-                    "dirty": False, "error": None, "date": None}
+            return {
+                "version": dirname[len(parentdir_prefix) :],
+                "full-revisionid": None,
+                "dirty": False,
+                "error": None,
+                "date": None,
+            }
         else:
             rootdirs.append(root)
             root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print("Tried directories %s but none started with prefix %s" %
-              (str(rootdirs), parentdir_prefix))
+        print(
+            "Tried directories %s but none started with prefix %s"
+            % (str(rootdirs), parentdir_prefix)
+        )
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
@@ -1206,11 +1250,9 @@ def versions_from_file(filename):
             contents = f.read()
     except EnvironmentError:
         raise NotThisMethod("unable to read _version.py")
-    mo = re.search(r"version_json = '''\n(.*)'''  # END VERSION_JSON",
-                   contents, re.M | re.S)
+    mo = re.search(r"version_json = '''\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S)
     if not mo:
-        mo = re.search(r"version_json = '''\r\n(.*)'''  # END VERSION_JSON",
-                       contents, re.M | re.S)
+        mo = re.search(r"version_json = '''\r\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S)
     if not mo:
         raise NotThisMethod("no version_json in _version.py")
     return json.loads(mo.group(1))
@@ -1219,8 +1261,7 @@ def versions_from_file(filename):
 def write_to_version_file(filename, versions):
     """Write the given version number to the given _version.py file."""
     os.unlink(filename)
-    contents = json.dumps(versions, sort_keys=True,
-                          indent=1, separators=(",", ": "))
+    contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": "))
     with open(filename, "w") as f:
         f.write(SHORT_VERSION_PY % contents)
 
@@ -1252,8 +1293,7 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -1367,11 +1407,13 @@ def render_git_describe_long(pieces):
 def render(pieces, style):
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"],
-                "date": None}
+        return {
+            "version": "unknown",
+            "full-revisionid": pieces.get("long"),
+            "dirty": None,
+            "error": pieces["error"],
+            "date": None,
+        }
 
     if not style or style == "default":
         style = "pep440"  # the default
@@ -1391,9 +1433,13 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None,
-            "date": pieces.get("date")}
+    return {
+        "version": rendered,
+        "full-revisionid": pieces["long"],
+        "dirty": pieces["dirty"],
+        "error": None,
+        "date": pieces.get("date"),
+    }
 
 
 class VersioneerBadRootError(Exception):
@@ -1416,8 +1462,7 @@ def get_versions(verbose=False):
     handlers = HANDLERS.get(cfg.VCS)
     assert handlers, "unrecognized VCS '%s'" % cfg.VCS
     verbose = verbose or cfg.verbose
-    assert cfg.versionfile_source is not None, \
-        "please set versioneer.versionfile_source"
+    assert cfg.versionfile_source is not None, "please set versioneer.versionfile_source"
     assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
 
     versionfile_abs = os.path.join(root, cfg.versionfile_source)
@@ -1471,9 +1516,13 @@ def get_versions(verbose=False):
     if verbose:
         print("unable to compute version")
 
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None, "error": "unable to compute version",
-            "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": None,
+        "dirty": None,
+        "error": "unable to compute version",
+        "date": None,
+    }
 
 
 def get_version():
@@ -1522,6 +1571,7 @@ def get_cmdclass():
             print(" date: %s" % vers.get("date"))
             if vers["error"]:
                 print(" error: %s" % vers["error"])
+
     cmds["version"] = cmd_version
 
     # we override "build_py" in both distutils and setuptools
@@ -1554,14 +1604,15 @@ def get_cmdclass():
             # now locate _version.py in the new build/ directory and replace
             # it with an updated value
             if cfg.versionfile_build:
-                target_versionfile = os.path.join(self.build_lib,
-                                                  cfg.versionfile_build)
+                target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build)
                 print("UPDATING %s" % target_versionfile)
                 write_to_version_file(target_versionfile, versions)
+
     cmds["build_py"] = cmd_build_py
 
     if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
         from cx_Freeze.dist import build_exe as _build_exe
+
         # nczeczulin reports that py2exe won't like the pep440-style string
         # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g.
         # setup(console=[{
@@ -1582,17 +1633,21 @@ def get_cmdclass():
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(LONG %
-                            {"DOLLAR": "$",
-                             "STYLE": cfg.style,
-                             "TAG_PREFIX": cfg.tag_prefix,
-                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                             })
+                    f.write(
+                        LONG
+                        % {
+                            "DOLLAR": "$",
+                            "STYLE": cfg.style,
+                            "TAG_PREFIX": cfg.tag_prefix,
+                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        }
+                    )
+
         cmds["build_exe"] = cmd_build_exe
         del cmds["build_py"]
 
-    if 'py2exe' in sys.modules:  # py2exe enabled?
+    if "py2exe" in sys.modules:  # py2exe enabled?
         try:
             from py2exe.distutils_buildexe import py2exe as _py2exe  # py3
         except ImportError:
@@ -1611,13 +1666,17 @@ def get_cmdclass():
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(LONG %
-                            {"DOLLAR": "$",
-                             "STYLE": cfg.style,
-                             "TAG_PREFIX": cfg.tag_prefix,
-                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                             })
+                    f.write(
+                        LONG
+                        % {
+                            "DOLLAR": "$",
+                            "STYLE": cfg.style,
+                            "TAG_PREFIX": cfg.tag_prefix,
+                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        }
+                    )
+
         cmds["py2exe"] = cmd_py2exe
 
     # we override different "sdist" commands for both environments
@@ -1644,8 +1703,8 @@ def get_cmdclass():
             # updated value
             target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
             print("UPDATING %s" % target_versionfile)
-            write_to_version_file(target_versionfile,
-                                  self._versioneer_generated_versions)
+            write_to_version_file(target_versionfile, self._versioneer_generated_versions)
+
     cmds["sdist"] = cmd_sdist
 
     return cmds
@@ -1700,11 +1759,9 @@ def do_setup():
     root = get_root()
     try:
         cfg = get_config_from_root(root)
-    except (EnvironmentError, configparser.NoSectionError,
-            configparser.NoOptionError) as e:
+    except (EnvironmentError, configparser.NoSectionError, configparser.NoOptionError) as e:
         if isinstance(e, (EnvironmentError, configparser.NoSectionError)):
-            print("Adding sample versioneer config to setup.cfg",
-                  file=sys.stderr)
+            print("Adding sample versioneer config to setup.cfg", file=sys.stderr)
             with open(os.path.join(root, "setup.cfg"), "a") as f:
                 f.write(SAMPLE_CONFIG)
         print(CONFIG_ERROR, file=sys.stderr)
@@ -1713,15 +1770,18 @@ def do_setup():
     print(" creating %s" % cfg.versionfile_source)
     with open(cfg.versionfile_source, "w") as f:
         LONG = LONG_VERSION_PY[cfg.VCS]
-        f.write(LONG % {"DOLLAR": "$",
-                        "STYLE": cfg.style,
-                        "TAG_PREFIX": cfg.tag_prefix,
-                        "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                        "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                        })
-
-    ipy = os.path.join(os.path.dirname(cfg.versionfile_source),
-                       "__init__.py")
+        f.write(
+            LONG
+            % {
+                "DOLLAR": "$",
+                "STYLE": cfg.style,
+                "TAG_PREFIX": cfg.tag_prefix,
+                "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                "VERSIONFILE_SOURCE": cfg.versionfile_source,
+            }
+        )
+
+    ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py")
     if os.path.exists(ipy):
         try:
             with open(ipy, "r") as f:
@@ -1763,8 +1823,7 @@ def do_setup():
     else:
         print(" 'versioneer.py' already in MANIFEST.in")
     if cfg.versionfile_source not in simple_includes:
-        print(" appending versionfile_source ('%s') to MANIFEST.in" %
-              cfg.versionfile_source)
+        print(" appending versionfile_source ('%s') to MANIFEST.in" % cfg.versionfile_source)
         with open(manifest_in, "a") as f:
             f.write("include %s\n" % cfg.versionfile_source)
     else: