Migrate Jenkins workflow to Github Actions

.github/workflows/ci.yaml

@@ -6,70 +6,121 @@ on:
       - master
     tags:
       - "[0-9]+.[0-9]+.[0-9]+*"
-
   pull_request:
-
   workflow_dispatch:
 
 jobs:
-  test:
-    runs-on: ubuntu-22.04
+  unittest:
+    runs-on: arc-runner
+    env:
+      TOX_COMMAND: "tox --skip-missing-interpreters false"
+
     strategy:
       fail-fast: false
       matrix:
-        tox-env: [py38, py39, py310, py311, py312, docs, linters, package]
-        include:
-          - tox-env: py38
-            python-version: 3.8
-          - tox-env: py39
-            python-version: 3.9
-          - tox-env: py310
-            python-version: "3.10"
-          - tox-env: py311
-            python-version: "3.11"
-          - tox-env: py312
-            python-version: "3.12"
-          - tox-env: linters
-            python-version: "3.11"
-          - tox-env: package
-            python-version: "3.11"
+        toxenv: [py38, py39, py310, py311, py312, docs, linters, package]
 
     steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install Dependencies
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Assert PR is up-to-date
+        if: github.event_name == 'pull_request'
         run: |
-          python -m pip install --upgrade pip tox
+          git fetch origin ${{ github.base_ref }}
+          git_change_target_merge_base=$(git merge-base HEAD origin/${{ github.base_ref }})
+          git_change_target_sha=$(git rev-parse origin/${{ github.base_ref }})
+
+          if [[ "${git_change_target_merge_base}" != "${git_change_target_sha}" ]]; then
+            echo 'Pull request is not up-to-date!'
+            echo "Please, rebase your pull request on top of '${{ github.base_ref }}' (commit: ${git_change_target_sha})."
+            exit 1
+          fi
+
       - name: Run Tests
         run: >
-          tox -e ${{ matrix.tox-env }}
-      - name: Upload coverage to Codecov
-        if: matrix.tox-env == 'py38' || matrix.tox-env == 'py39' || matrix.tox-env == 'py310' || matrix.tox-env == 'py311' || matrix.tox-env == 'py312'
-        uses: codecov/codecov-action@v1
+          ${{ env.TOX_COMMAND }} -e ${{ matrix.toxenv }}
+
+  e2e:
+    runs-on: arc-runner
+    needs: unittest
+    env:
+      GENESIS_POSTGRESQL_NAME: resolwe-genialis
+      GENESIS_POSTGRESQL_USER: genialis-base
+      GENESIS_POSTGRESQL_PORT: 55434
+      GENESIS_REDIS_PORT: 56381
+      GENESIS_RESDK_PATH: ".."
+      GENESIS_REST_THROTTLING: '{"login": "100000/hour", "credentials": "100000/hour", "email": "100000/hour"}'
+
+    services:
+      postgres:
+        image: public.ecr.aws/docker/library/postgres:14
+        env:
+          POSTGRES_USER: genialis-base
+          POSTGRES_HOST_AUTH_METHOD: trust
+        ports:
+          - 55434:5432
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+
+      redis:
+        image: public.ecr.aws/docker/library/redis:7-alpine
+        ports:
+          - 56381:6379
+        options: >-
+          --health-cmd "redis-cli ping"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+
+    steps:
+      - name: Checkout resolwe-bio-py
+        uses: actions/checkout@v4
+
+      - name: Checkout genialis-base
+        uses: actions/checkout@v4
         with:
-          file: .coverage
+          repository: genialis/genialis-base
+          path: genialis-base
+          ssh-key: ${{ secrets.GHA_SSH_PRIVATE_KEY_GENIALIS_DEPLOY }}
 
-  build:
-    runs-on: ubuntu-22.04
+      - name: Run tests
+        run: |
+          cd genialis-base
 
-    needs: test
+          # Prepare frontend configuration
+          mkdir -p frontend/genjs/schema
+          echo '{}' > frontend/genjs/schema/configuration.json
 
-    if: "startsWith(github.ref, 'refs/tags')"
+          # Make sure `python` refers to the tox environment's Python
+          export PATH=`pwd`/.tox/py310-e2e-resdk/bin:$PATH
 
+          tox --skip-missing-interpreters false -e py310-e2e-resdk
+
+  build:
+    runs-on: arc-runner
+    needs: [unittest, e2e]
+    if: startsWith(github.ref, 'refs/tags')
+    env:
+      PYTHON: "python3.12"
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
+
       - name: Install build
-        run: python -m pip install --user build
+        run: ${{ env.PYTHON }} -m pip install --user build
+
       - name: Build a binary wheel and a source tarball
-        run: python -m build --sdist --wheel --outdir dist/ .
+        run: ${{ env.PYTHON }} -m build --sdist --wheel --outdir dist/ .
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          file: .coverage
+
       - name: Publish distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1.8
         with:
           password: ${{ secrets.pypi_password }}