Reformat code with black

.github/workflows/lint.yml

@@ -0,0 +1,25 @@
+name: Linting
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.7", "3.10" ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install tox
+      - name: Check code quality with flake8
+        run: tox -e flake8

README.md

@@ -1002,3 +1002,11 @@ Generation of analogues of the specified molecule and unbiased library enumerati
 
 * ``enumerationInstance.getReconstructedMols(mol)`` - fragment provided molecule (should be RdKit molecule object and not smiles). Return two dictionary - *allSyntheticPathways* and *allSynthons* obtained during fragmentation.
 
+# Development
+
+This code is auto-formated with [`black`](https://github.com/psf/black) and [`isort`](https://pycqa.github.io/isort/) and checked with continuous integration to ensure code formatting has been properly applied. Please run the following in all pull requests:
+
+```shell
+$ pip install tox
+$ tox
+```

SyntOn_BBScaffoldGeneration.py

@@ -1,9 +1,13 @@
-import sys,os
+import os
+import sys
+
 from rdkit import Chem
+
 srcPath = os.path.split(os.path.realpath(__file__))[0]
 sys.path.insert(1, srcPath)
-from src.UsefulFunctions import *
 from src.SyntOn_BBs import *
+from src.UsefulFunctions import *
+
 
 def main(args):
     with open(args.output + "_Scaffolds.smi", "w") as out:
@@ -21,7 +25,9 @@ def main(args):
                         out.write(" " + scaffold + "\n")
                     else:
                         out.write(" linearMolecule\n")
-    scaffoldsCountSorted = {r: scaffoldsCount[r] for r in sorted(scaffoldsCount, key=scaffoldsCount.get, reverse=True)}
+    scaffoldsCountSorted = {
+        r: scaffoldsCount[r] for r in sorted(scaffoldsCount, key=scaffoldsCount.get, reverse=True)
+    }
     scaffoldsCount.clear()
     with open(args.output + "_scaffoldsCounts.smi", "w") as outCounts:
         for scaffold in scaffoldsCountSorted:
@@ -30,41 +36,49 @@ def main(args):
         cumSum = 0
         TotalCompNumb = sum(scaffoldsCountSorted.values())
         TotalScaffNumb = len(scaffoldsCountSorted)
-        for ind,scaff in enumerate(scaffoldsCountSorted):
+        for ind, scaff in enumerate(scaffoldsCountSorted):
             cumSum += scaffoldsCountSorted[scaff]
-            outCumPer.write(str(int(round((ind + 1) / TotalScaffNumb * 100))) + " " + str(
-                int(round(cumSum / TotalCompNumb * 100))) + "\n")
+            outCumPer.write(
+                str(int(round((ind + 1) / TotalScaffNumb * 100)))
+                + " "
+                + str(int(round(cumSum / TotalCompNumb * 100)))
+                + "\n"
+            )
     scaffoldsCountSorted.clear()
     scaffoldPlot(args.output + "_cumulativeprecentage.smi", args.output)
 
 
-
 def scaffoldPlot(cumPercentageFile, outName):
     from matplotlib import pyplot as plt
     from numpy import genfromtxt
-    Data = genfromtxt(cumPercentageFile, delimiter=' ', names=['x', 'y'])
+
+    Data = genfromtxt(cumPercentageFile, delimiter=" ", names=["x", "y"])
     fig, ax = plt.subplots()
-    ax.tick_params(axis='both', which='major', labelsize=12)
-    plt.plot(Data['x'], Data['y'], color="darkgreen")
+    ax.tick_params(axis="both", which="major", labelsize=12)
+    plt.plot(Data["x"], Data["y"], color="darkgreen")
     plt.ylim(ymin=0, ymax=100)
     plt.xlim(xmin=0, xmax=100)
-    plt.ylabel("Fraction of BBs, %", fontweight='bold', fontsize=14)
-    plt.xlabel("Fraction of scaffolds, %", fontweight='bold', fontsize=14)
-    plt.title("Cumulative Scaffold Frequency Plot", fontweight='bold', fontsize=14)
+    plt.ylabel("Fraction of BBs, %", fontweight="bold", fontsize=14)
+    plt.xlabel("Fraction of scaffolds, %", fontweight="bold", fontsize=14)
+    plt.title("Cumulative Scaffold Frequency Plot", fontweight="bold", fontsize=14)
     plt.savefig("Scaffolds_FreqPlot_" + outName + ".png")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import argparse
-    parser = argparse.ArgumentParser(description="BBs Scaffold analysis. Generates meaningful BBs scaffolds after removing ring-containing leaving and protective groups. Count scaffolds occurrence in the provided collection of BBs, and construct cumulative scaffold frequency plot.",
-                                     epilog="Code implementation:                Yuliana Zabolotna, Alexandre Varnek\n"
-                                            "                                    Laboratoire de Chémoinformatique, Université de Strasbourg.\n\n"
-                                            "Knowledge base (SMARTS library):    Dmitriy M.Volochnyuk, Sergey V.Ryabukhin, Kostiantyn Gavrylenko, Olexandre Oksiuta\n"
-                                            "                                    Institute of Organic Chemistry, National Academy of Sciences of Ukraine\n"
-                                            "                                    Kyiv National Taras Shevchenko University\n"
-                                            "2021 Strasbourg, Kiev",
-                                     prog="SyntOn_BBScaffoldGeneration", formatter_class=argparse.RawTextHelpFormatter)
+
+    parser = argparse.ArgumentParser(
+        description="BBs Scaffold analysis. Generates meaningful BBs scaffolds after removing ring-containing leaving and protective groups. Count scaffolds occurrence in the provided collection of BBs, and construct cumulative scaffold frequency plot.",
+        epilog="Code implementation:                Yuliana Zabolotna, Alexandre Varnek\n"
+        "                                    Laboratoire de Chémoinformatique, Université de Strasbourg.\n\n"
+        "Knowledge base (SMARTS library):    Dmitriy M.Volochnyuk, Sergey V.Ryabukhin, Kostiantyn Gavrylenko, Olexandre Oksiuta\n"
+        "                                    Institute of Organic Chemistry, National Academy of Sciences of Ukraine\n"
+        "                                    Kyiv National Taras Shevchenko University\n"
+        "2021 Strasbourg, Kiev",
+        prog="SyntOn_BBScaffoldGeneration",
+        formatter_class=argparse.RawTextHelpFormatter,
+    )
     parser.add_argument("-i", "--input", type=str, help="Input BBs file.")
     parser.add_argument("-o", "--output", type=str, help="Output files suffix name.")
     args = parser.parse_args()
-    main(args)
+    main(args)