Add code coverage

.github/workflows/pythonapp.yml

@@ -3,7 +3,11 @@
 
 name: build
 
-on: [pull_request]
+on:
+  pull_request:
+  push:
+    branches:
+      - master
 
 jobs:
   build:
@@ -21,7 +25,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov
+        pip install flake8 pytest coveralls
         pip install .
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Lint with flake8
@@ -32,11 +36,34 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest tests/ --doctest-modules --cov=challengeutils --cov-report=html
-    - name: Upload pytest test results
-      uses: actions/upload-artifact@master
-      with:
-        name: pytest-results-${{ matrix.python-version }}
-        path: htmlcov
-      # Use always() to always run this step to publish test results when there are test failures
-      if: ${{ always() }}
+        pytest tests
+    # - name: Upload pytest test results
+    #   uses: actions/upload-artifact@master
+    #   with:
+    #     name: pytest-results-${{ matrix.python-version }}
+    #     path: htmlcov
+    #   # Use always() to always run this step to publish test results when there are test failures
+    #   if: ${{ always() }}
+    - name: Prepare environment for coveralls
+      run: |
+        echo "PYTHON_ENV=$(echo py${{ matrix.python-version }} | tr -d .)" >> $GITHUB_ENV
+    - name: Coveralls Parallel
+      env:
+        COVERALLS_FLAG_NAME: ${{ env.PYTHON_ENV }}
+        COVERALLS_PARALLEL: true
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        coverage run --source=challengeutils --omit=challengeutils/__main__.py -m pytest tests/
+        coveralls --service=github
+
+  finish-coveralls:
+    needs: build
+    runs-on: ubuntu-latest
+    container: python:3-slim
+    steps:
+    - name: Finish Coveralls Parallel
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip3 install --upgrade coveralls
+        coveralls --finish

README.md

@@ -1,6 +1,7 @@
 # Sage Bionetworks Challenge Utilities
 
-[![Get challengeutils from PyPI](https://img.shields.io/pypi/v/challengeutils.svg?style=for-the-badge&logo=appveyor)](https://pypi.python.org/pypi/challengeutils) [![Docker Automated](https://img.shields.io/docker/automated/sagebionetworks/challengeutils.svg?style=for-the-badge&logo=appveyor)](https://hub.docker.com/r/sagebionetworks/challengeutils/) [![Docker Pull](https://img.shields.io/docker/pulls/sagebionetworks/challengeutils.svg?style=for-the-badge&logo=appveyor)](https://hub.docker.com/r/sagebionetworks/challengeutils/)
+[![Get challengeutils from PyPI](https://img.shields.io/pypi/v/challengeutils.svg?style=for-the-badge&logo=pypi)](https://pypi.python.org/pypi/challengeutils) [![Docker Automated](https://img.shields.io/docker/automated/sagebionetworks/challengeutils.svg?style=for-the-badge&logo=docker)](https://hub.docker.com/r/sagebionetworks/challengeutils/) [![Docker Pull](https://img.shields.io/docker/pulls/sagebionetworks/challengeutils.svg?style=for-the-badge&logo=docker)](https://hub.docker.com/r/sagebionetworks/challengeutils/) [![Coverage Status](https://img.shields.io/coveralls/github/Sage-Bionetworks/challengeutils.svg?&style=for-the-badge&label=coverage&logo=Coveralls)](https://coveralls.io/github/Sage-Bionetworks/challengeutils)
+
 
 `challengeutils` is a set of tools and commands that provides an interface for managing crowd-sourced challenges administered on [Synapse](https://www.synapse.org), including but not limited to, [DREAM Challenges](http://dreamchallenges.org/).  Its main purpose is to ease the process of creating, monitoring, and ending a challenge, as well as provide useful functions for post-competition analysis. _This package is being actively developed and maintained by DREAM and Informatics & Biocomputing (IBC), Computational Oncology Group at Sage Bionetworks._