Add BioBlend tests

.github/workflows/bioblend.yaml

@@ -0,0 +1,128 @@
+name: Tests
+on:
+  pull_request:
+    paths:
+      - "lib/galaxy/webapps/galaxy/api/**"
+  workflow_dispatch:
+
+concurrency:
+  group: test-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    services:
+      postgres:
+        image: postgres
+        # Provide the password for postgres
+        env:
+          POSTGRES_PASSWORD: postgres
+        # Set health checks to wait until postgres has started
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        tox_env: [py38]
+        galaxy_version:
+          - dev
+          - release_24.1
+          - release_24.0
+          - release_23.2
+          - release_23.1
+          - release_23.0
+          - release_22.05
+          - release_22.01
+          - release_21.09
+          - release_21.05
+          - release_21.01
+          - release_20.09
+          - release_20.05
+          - release_20.01
+          - release_19.09
+          - release_19.05
+        include:
+          - os: ubuntu-latest
+            tox_env: py313
+            galaxy_version: dev
+          # Cannot test on macOS because service containers are not supported
+          # yet: https://github.community/t/github-actions-services-available-on-others-vms/16916
+          # - os: macos-latest
+          #   tox_env: py38
+          #   galaxy_version: dev
+    steps:
+      - run: git clone https://github.com/galaxyproject/bioblend
+      - name: Cache pip dir
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.tox_env }}-${{ matrix.galaxy_version }}
+      - name: Calculate Python version for BioBlend from tox_env
+        id: get_bioblend_python_version
+        run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT
+      - name: Set up Python for BioBlend
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
+      - name: Install tox
+        run: |
+          python3 -m pip install --upgrade pip setuptools
+          python3 -m pip install 'tox>=1.8.0' 'virtualenv>=20.0.14'
+      - name: Determine Python version for Galaxy
+        id: get_galaxy_python_version
+        run: |
+          case ${{ matrix.galaxy_version }} in
+            release_19.05 | release_19.09 | release_20.0? )
+              # The minimum Python version supported by the 19.05 and 19.09
+              # releases is 2.7, but virtualenv dropped support for creating
+              # Python <3.7 environments in v20.22.0 .
+              # The minimum Python version supported by the 20.0* releases is
+              # 3.5, but the setup-python GitHub action dropped support for
+              # Python 3.5 and 3.6 on Ubuntu 22.04, see
+              # https://github.com/actions/setup-python/issues/544#issuecomment-1332535877
+              galaxy_python_version=3.7
+              ;;
+            release_21.0? )
+              # The minimum Python supported version by these releases is 3.6,
+              # but same as above.
+              galaxy_python_version=3.7
+              ;;
+            release_22.0? | release_23.? )
+              galaxy_python_version=3.7
+              ;;
+            release_24.? | dev )
+              galaxy_python_version=3.8
+              ;;
+          esac
+          echo "galaxy_python_version=$galaxy_python_version" >> $GITHUB_OUTPUT
+      - name: Set up Python for Galaxy
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }}
+      - name: Run tests
+        env:
+          PGPASSWORD: postgres
+          PGPORT: 5432
+          PGHOST: localhost
+        run: |
+          # Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
+          createdb -U postgres galaxy
+          # Run ToolShed tests only once per Python version
+          if [ "${{ matrix.galaxy_version }}" = 'dev' ]; then
+              export BIOBLEND_TOOLSHED_URL=https://testtoolshed.g2.bx.psu.edu/
+          fi
+          # Install Galaxy
+          GALAXY_DIR=galaxy-${{ matrix.galaxy_version }}
+          git clone --depth=1 -b ${{ matrix.galaxy_version }} https://github.com/galaxyproject/galaxy $GALAXY_DIR
+          export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
+          ./bioblend/run_bioblend_tests.sh -g $GALAXY_DIR -v python${{ steps.get_galaxy_python_version.outputs.galaxy_python_version }} -e ${{ matrix.tox_env }}
+      - name: The job has failed
+        if: ${{ failure() }}
+        run: |
+          cat galaxy-${{ matrix.galaxy_version }}/*.log