Replace TravisCI with GitHub Actions

.github/workflows/cwl-tests.yml

@@ -0,0 +1,25 @@
+name: CWL wrapper tests
+# This workflow is triggered on pushes and PRs to the repository.
+on: [push, pull_request]
+
+jobs:
+  CwlTests:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out source-code repository
+      uses: actions/checkout@v2
+      with:
+        submodules: true
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Install cwltool
+      run: pip install cwltool
+
+    - name: CWL definition test
+      run: cwltool bionitio.cwl --fasta_file functional_tests/test_data/two_sequence.fasta

.github/workflows/docker.yml

@@ -0,0 +1,24 @@
+name: Docker Image
+# This workflow is triggered on pushes and package releases.
+on: [push, published]
+
+jobs:
+  BuildPushDocker:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out source-code repository
+      uses: actions/checkout@v2
+
+    - name: Push Docker image to GitHub Packages
+      uses: docker/build-push-action@v1
+      with:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+        registry: docker.pkg.github.com
+        repository: ${{github.repository}}/bionitio
+        tag_with_ref: true
+
+    - name: Functional Docker tests
+      run: docker run bionitio --entrypoint /bionitio/functional_tests/bionitio-test.sh -p bionitio -d /bionitio/functional_tests/test_data -v

.github/workflows/functional-tests.yml

@@ -0,0 +1,27 @@
+name: Functional tests
+# This workflow is triggered on pushes and PRs to the repository.
+on: [push, pull_request]
+
+jobs:
+  FuncTests:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out source-code repository
+      uses: actions/checkout@v2
+      with:
+        submodules: true
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Install python dependencies
+      run: |
+        pip install -r requirements-dev.txt
+        pip install .
+
+    - name: Run functional tests
+      run: functional_tests/bionitio-test.sh

.github/workflows/unit-tests.yml

@@ -0,0 +1,31 @@
+name: Unit tests
+# This workflow is triggered on pushes and PRs to the repository.
+on: [push, pull_request]
+
+jobs:
+  PythonTests:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - name: Check out source-code repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install python dependencies
+      run: |
+        pip install -r requirements-dev.txt
+        pip install .
+
+    - name: Run unit tests
+      run: python bionitio/bionitio_test.py
+
+    - name: Check program style
+      run: pylint -E bionitio/*.py