Merge branch 'dev' into 'main'

      - 'client/**'

      - 'doc/**'

      - 'lib/galaxy_test/selenium/**'

      - 'packages/**'

  pull_request:

    paths-ignore:

      - 'client/**'

      - 'doc/**'

      - 'lib/galaxy_test/selenium/**'

      - 'packages/**'

  schedule:

    # Run at midnight UTC every Tuesday

    - cron: '0 0 * * 2'

  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'

  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'

  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'

  GALAXY_TEST_REQUIRE_ALL_NEEDED_TOOLS: '1'

concurrency:

  group: ${{ github.workflow }}-${{ github.ref }}

  cancel-in-progress: true

      - uses: actions/setup-python@v5

        with:

          python-version: ${{ matrix.python-version }}

          cache: 'pip'

          cache-dependency-path: 'galaxy root/requirements.txt'

      - name: Get full Python version

        id: full-python-version

        shell: bash

        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT

      - name: Cache pip dir

        uses: actions/cache@v4

        with:

          path: ~/.cache/pip

          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}

      - name: Cache galaxy venv

        uses: actions/cache@v4

        with:

name: BioBlend Tests

on:

  pull_request:

    paths:

      - .github/workflows/bioblend.yaml

      - lib/galaxy/schema/**

      - lib/galaxy/webapps/galaxy/api/**

      - lib/galaxy/webapps/galaxy/services/**

  workflow_dispatch:

concurrency:

  group: ${{ github.workflow }}-${{ github.ref }}

  cancel-in-progress: true

jobs:

  test:

    runs-on: ubuntu-latest

    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:

        tox_env: [py313]

        galaxy_python_version: ["3.8"]

    steps:

      - name: Checkout Galaxy

        uses: actions/checkout@v4

        with:

          fetch-depth: 1

          path: galaxy

      - name: Checkout Bioblend

        uses: actions/checkout@v4

        with:

          repository: galaxyproject/bioblend

          path: bioblend

      - name: Cache pip dir

        uses: actions/cache@v4

        with:

          path: ~/.cache/pip

          key: pip-cache-${{ matrix.tox_env }}

      - 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'

      - name: Set up Python for Galaxy

        uses: actions/setup-python@v5

        with:

          python-version: ${{ matrix.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

          export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy

          ./bioblend/run_bioblend_tests.sh -g galaxy -v python${{ matrix.galaxy_python_version }} -e ${{ matrix.tox_env }}

      - name: The job has failed

        if: ${{ failure() }}

        run: |

          cat galaxy/*.log

  group: ${{ github.workflow }}-${{ github.ref }}

  cancel-in-progress: true

jobs:

  ghcrbuild:

    name: Build container image for GHCR

    runs-on: ubuntu-latest

    steps:

      - uses: actions/checkout@v4

      # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow

      - name: Set outputs

        id: commit

        run: echo "sha_short=$(git rev-parse --short HEAD)" >> $GITHUB_OUTPUT

      - name: Set branch name

        id: branch

        run: |

          if [[ "$GITHUB_REF" == "refs/tags/"* ]]; then

            echo "name=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT

          elif [[ "$GITHUB_REF" == "refs/heads/dev" ]]; then

            echo "name=dev" >> $GITHUB_OUTPUT

          elif [[ "$GITHUB_REF" == "refs/heads/release_"* ]]; then

            echo "name=${GITHUB_REF#refs/heads/release_}-auto" >> $GITHUB_OUTPUT

          fi

        shell: bash

      - name: Extract metadata for container image

        id: meta

        uses: docker/metadata-action@v4

        with:

          images: ghcr.io/${{ github.repository }}

          tags: |

            type=raw,value=${{steps.branch.outputs.name}}

      - name: Build args

        id: buildargs

        run: |

            echo "gitcommit=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT 

            echo "builddate=$(date -u +'%Y-%m-%dT%H:%M:%SZ')"

      - name: Set up Docker Buildx

        uses: docker/setup-buildx-action@v2

        with:

          platforms: linux/amd64

      - name: Login to GHCR

        uses: docker/login-action@v2

        with:

          registry: ghcr.io

          username: ${{ github.repository_owner }}

          password: ${{ secrets.GITHUB_TOKEN }}

      - name: Build and push container image to ghcr

        uses: docker/build-push-action@v4

        with:

          build-args: |

              GIT_COMMIT=${{ steps.buildargs.outputs.gitcommit }}

              BUILD_DATE=${{ steps.buildargs.outputs.builddate }}

              IMAGE_TAG=${{ steps.branch.outputs.name }}

          file: .k8s_ci.Dockerfile

          push: true

          context: .

          tags: ${{ steps.meta.outputs.tags }}

          labels: ${{ steps.meta.outputs.labels }}

          platforms: linux/amd64

  build:

    name: Build container image

    name: Build container image for Galaxy repos

    runs-on: ubuntu-latest

    if: github.repository_owner == 'galaxyproject'

    steps:

        uses: actions-hub/docker@master

        with:

          args: push galaxy/galaxy-min:${{ steps.branch.outputs.name }}

      - '.ci/check_test_class_names.sh'

      - 'lib/galaxy_test/**'

      - 'test/**'

concurrency:

  group: ${{ github.workflow }}-${{ github.ref }}

  cancel-in-progress: true

jobs:

  test:

    name: Test

      - uses: actions/setup-python@v5

        with:

          python-version: ${{ matrix.python-version }}

      - name: Cache pip dir

        uses: actions/cache@v4

        with:

          path: ~/.cache/pip

          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}

          cache: 'pip'

          cache-dependency-path: 'requirements.txt'

      - name: Install Python dependencies

        run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt

      - name: Run tests

    branches: [ dev ]

  schedule:

    - cron: '16 6 * * 0'

concurrency:

  group: ${{ github.workflow }}-${{ github.ref }}

  cancel-in-progress: true

jobs:

  analyze:

    name: Analyze