GitHub workflows, RTD patch.

.github/workflows/python-package.yml

+name: build
+on:
+  push:
+    branches: 
+      - master
+  pull_request:
+    branches:
+      - master
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - 3.6
+          - 3.7
+          - 3.8
+          - 3.9
+    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 --upgrade pip
+          pip install flake8 pytest fake_open .
+      - name: Lint with flake8
+        run: |
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest

docs/conf.py

-from subprocess import call
-
-call('pip install ..', shell=True)
-
 from mutalyzer_backtranslate import _get_metadata
 
 
@@ -11,5 +7,5 @@ project = _get_metadata('Name')
 release = _get_metadata('Version')
 
 autoclass_content = 'both'
-extensions = ['sphinx.ext.autodoc']
+extensions = ['sphinx.ext.autodoc', 'sphinx_autodoc_typehints', 'sphinxarg.ext']
 master_doc = 'index'

docs/requirements.txt

+docutils==0.17.1
+sphinx-argparse
+sphinx-autodoc-typehints

mutalyzer_backtranslate/__init__.py

@@ -4,7 +4,7 @@ from .backtranslate import BackTranslate
 
 
 def _get_metadata(name):
-    pkg = get_distribution(__package__)
+    pkg = get_distribution('mutalyzer_backtranslate')
 
     for line in pkg.get_metadata_lines(pkg.PKG_INFO):
         if line.startswith('{}: '.format(name)):

mutalyzer_backtranslate/backtranslate.py

@@ -113,8 +113,9 @@ class BackTranslate(object):
                     substitutions_with_dna = self.with_dna(
                         codon, sample_amino_acid)
                     if (substitutions_with_dna and not
-                            cmp_subst(substitutions_without_dna,
-                            substitutions_with_dna) and
+                            cmp_subst(
+                                substitutions_without_dna,
+                                substitutions_with_dna) and
                             reference_amino_acid != sample_amino_acid):
                         substitutions.add(
                             (reference_amino_acid, sample_amino_acid))

mutalyzer_backtranslate/cli.py

@@ -78,8 +78,9 @@ def find_stops(input_handle, output_handle, offset, compact):
                 output_handle.write('{}\t{}\t{}\n'.format(
                     offset + (index * 3) + position,
                     list(stop_positions[position])[0][0],
-                    ','.join(map(lambda x: x[1],
-                    sorted(stop_positions[position])))))
+                    ','.join(map(
+                        lambda x: x[1],
+                        sorted(stop_positions[position])))))
 
 
 def main():
@@ -137,7 +138,7 @@ def main():
 
     try:
         args.func(
-            **dict((k, v) for k, v in vars(args).items() if k not in
-            ('func', 'subcommand')))
+            **dict((k, v) for k, v in vars(args).items() if k not in (
+                'func', 'subcommand')))
     except IOError as error:
         parser.error(error)

mutalyzer_backtranslate/util.py

@@ -6,7 +6,8 @@ def _three_to_one():
 
     :returns dict: Three letter to one letter amino acids table.
     """
-    return dict(list(map(lambda x: (str(x[0]), str(x[1])),
+    return dict(list(map(
+        lambda x: (str(x[0]), str(x[1])),
         IUPACData.protein_letters_3to1_extended.items())) + [('Ter', '*')])
 
 

setup.cfg

 [metadata]
 name = mutalyzer_backtranslate
-version = 0.1.3
+version = 0.1.4
 description = Functions for reverse translation.
 long_description = file: README.rst
 author = LUMC, Jeroen F.J. Laros
@@ -20,12 +20,23 @@ classifiers =
 [options]
 packages = find:
 install_requires =
-    biopython==1.76
-    python-Levenshtein==0.12.0
+    biopython>=1.76
+    python-Levenshtein>=0.12.0
 tests_require =
-    fake-open==0.0.1
-    pytest==4.0.1
+    fake-open>=0.0.1
+    pytest-cov>=2.10.0
+    pytest-pep8>=1.0.6
+    pytest>=4.0.1
 
 [options.entry_points]
 console_scripts =
     backtranslate = mutalyzer_backtranslate.cli:main
+
+[tool:pytest]
+pep8ignore = docs/conf.py ALL
+
+[coverage:report]
+exclude_lines = def main()
+
+[coverage:run]
+source = mutalyzer_backtranslate

tox.ini

-[tox]
-envlist = py35, py36
-
-[testenv]
-commands = py.test
-whitelist_externals = py.test