Configure PRODIGY pipeline for WES execution with S3 and Harbor

.github/workflows/ci.yml

@@ -0,0 +1,49 @@
+name: ci
+
+on: push
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - run: pip install '.[dev]'
+
+      - name: check types
+        run: mypy .
+
+      - name: run unittests
+        run: >-
+          pytest 
+          -m "not integration"
+          --cov
+          --cov-report xml:coverage.xml
+          --cov-append
+          -vv
+          --hypothesis-show-statistics
+
+      - name: run integration tests
+        run: >-
+          pytest 
+          -m integration
+          --cov
+          --cov-report xml:coverage.xml
+          --cov-append
+          -vv
+          --hypothesis-show-statistics
+
+      - name: Run codacy-coverage-reporter
+        uses: codacy/codacy-coverage-reporter-action@v1
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+          coverage-reports: coverage.xml