Initial commit: FlowDock pipeline configured for WES execution

.github/workflows/test.yml

@@ -0,0 +1,139 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, "release/*", "dev"]
+
+jobs:
+  run_tests_ubuntu:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    timeout-minutes: 20
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          conda env create -f environment.yml
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install sh
+
+      - name: List dependencies
+        run: |
+          python -m pip list
+
+      - name: Run pytest
+        run: |
+          pytest -v
+
+  run_tests_macos:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["macos-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    timeout-minutes: 20
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          conda env create -f environment.yml
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install sh
+
+      - name: List dependencies
+        run: |
+          python -m pip list
+
+      - name: Run pytest
+        run: |
+          pytest -v
+
+  run_tests_windows:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["windows-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    timeout-minutes: 20
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          conda env create -f environment.yml
+          python -m pip install --upgrade pip
+          pip install pytest
+
+      - name: List dependencies
+        run: |
+          python -m pip list
+
+      - name: Run pytest
+        run: |
+          pytest -v
+
+  # upload code coverage report
+  code-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          conda env create -f environment.yml
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install pytest-cov[toml]
+          pip install sh
+
+      - name: Run tests and collect coverage
+        run: pytest --cov flowdock # NEEDS TO BE UPDATED WHEN CHANGING THE NAME OF "src" FOLDER
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3