Github actions for pytest & coveralls and for building and pushing to…

… Docker Hub (#219)

* switch from Travis CI to github actions - pytest and coveralls

* run action on ubuntu latest

* remove a command

* install conda software into the base environment

* simplify how sambamba is installed

* remove a comment

.github/workflows/docker_build_n_publish.yml

@@ -0,0 +1,20 @@
+name: Publish to Docker Hub
+
+on:
+ release:
+  types:
+   - created
+jobs:
+  docker-image-CI:
+   name: Docker Image CI
+   runs-on: ubuntu-latest
+   steps:
+    - name: Check out git repository
+      uses: actions/checkout@v2
+    - name: Publish to Registry
+      uses: elgohr/Publish-Docker-Github-Action@master
+      with:
+        name: clinicalgenomics/chanjo
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        tags: "latest,${{ github.event.release.tag_name }}"

.github/workflows/pytest_n_coveralls.yml

@@ -0,0 +1,26 @@
+name: Tests and coverage
+on: [pull_request]
+jobs:
+  Pytest_Coveralls:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@master
+      with:
+        python-version: 3.7
+    - name: Install Sambamba
+      run: |
+        brew install brewsci/bio/sambamba
+    - name: Install repo and its dependencies
+      run: |
+        pip install -r requirements.txt
+        pip install -r requirements-dev.txt
+        pip install -e .
+        pip install coveralls
+    - name: Run pytest and coveralls
+      run: |
+        pytest --cov=chanjo tests/
+        coveralls
+      env:
+        GITHUB_TOKEN: ${{ github.token }}

CHANGELOG.md

@@ -7,6 +7,8 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ### Added
 - User can pass on file with row separated gene IDs for coverage calculation
 - Dockerfile
+- Added the Docker image build and push triggered by new releases
+- Added githib action running pytest and coveralls
 
 ## [4.3.0] - 2020-02-05