Merge pull request #71 from jensengroup/nathan/coverage

- add coverage.py to testing workflow
- use https://codecov.io/gh/jensengroup/propka

.github/workflows/python-package.yml

@@ -1,13 +1,13 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
+name: Tests
 
 on:
   push:
-    branches: [ master ]
+    branches: '**'
   pull_request:
-    branches: [ master ]
+    branches: '**'
 
 jobs:
   build:
@@ -27,6 +27,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools wheel
         pip install flake8 pytest
+        pip install coverage
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Lint with flake8
       run: |
@@ -34,7 +35,20 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+    - name: Test with pytest and coverage
       run: |
-        pip install pytest
-        python -m pytest
+        coverage run -m pytest
+        coverage report -m | tee coverage.txt
+        coverage html
+    - name: Upload coverage to https://codecov.io/gh/jensengroup/propka
+      run: bash <(curl -s https://codecov.io/bash)
+    - name: Store coverage text results
+      uses: actions/upload-artifact@v2
+      with:
+        name: coverage-text
+        path: coverage.txt
+    - name: Store coverage HTML results
+      uses: actions/upload-artifact@v2
+      with:
+        name: coverage-html
+        path: htmlcov/*

README.md

@@ -1,5 +1,7 @@
 # PROPKA 3
 
+![Tests](https://github.com/jensengroup/propka/workflows/Tests/badge.svg)
+
 PROPKA predicts the pKa values of ionizable groups in proteins
 (version 3.0) and protein-ligand complexes (version 3.1 and later)
 based on the 3D structure.