pr.yaml

name: Galaxy Tool Linting and Tests for push and PR
on:
  pull_request:
    paths-ignore:
      - 'deprecated/**'
      - 'docs/**'
      - '*'
  push:
    branches:
      - main
      - master
    paths-ignore:
      - 'deprecated/**'
      - 'docs/**'
      - '*'
env:
  GALAXY_FORK: galaxyproject
  GALAXY_BRANCH: release_24.1
  MAX_CHUNKS: 4
  MAX_FILE_SIZE: 1M
concurrency:
  # Group runs by PR, but keep runs on the default branch separate
  # because we do not want to cancel ToolShed uploads
  group: pr-${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && github.run_number || github.ref }}
  cancel-in-progress: true
jobs:
  # the setup job does two things:
  # 1. cache the pip cache and .planemo
  # 2. determine the list of changed repositories
  # it produces one artifact which contains
  # - a file with the latest SHA from the chosen branch of the Galaxy repo
  # - a file containing the list of changed repositories
  # which are needed in subsequent steps.
  setup:
    name: Setup cache and determine changed repositories
    runs-on: ubuntu-latest
    outputs:
      galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
      repository-list: ${{ steps.discover.outputs.repository-list }}
      tool-list: ${{ steps.discover.outputs.tool-list }}
      chunk-count: ${{ steps.discover.outputs.chunk-count }}
      chunk-list: ${{ steps.discover.outputs.chunk-list }}
      commit-range: ${{ steps.discover.outputs.commit-range }}
    strategy:
      matrix:
        python-version: ['3.10']
    steps:
    - name: Print github context properties
      run: |
        echo 'event: ${{ github.event_name }}'
        echo 'sha: ${{ github.sha }}'
        echo 'ref: ${{ github.ref }}'
        echo 'head_ref: ${{ github.head_ref }}'
        echo 'base_ref: ${{ github.base_ref }}'
        echo 'event.before: ${{ github.event.before }}'
        echo 'event.after: ${{ github.event.after }}'
        echo 'repository_owner: ${{ github.repository_owner }}'
    - name: Determine latest commit in the Galaxy repo
      id: get-galaxy-sha
      run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
    - uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v4
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
    - name: Cache .planemo
      uses: actions/cache@v4
      id: cache-planemo
      with:
        path: ~/.planemo
        key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
    # Install the `wheel` package so that when installing other packages which
    # are not available as wheels, pip will build a wheel for them, which can be cached.
    - name: Install wheel
      run: pip install wheel
    - name: Install flake8
      run: pip install flake8 flake8-import-order
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
    - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
      uses: galaxyproject/planemo-ci-action@v1
      id: discover
      with:
        create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }}
        galaxy-fork: ${{ env.GALAXY_FORK }}
        galaxy-branch: ${{ env.GALAXY_BRANCH }}
        max-chunks: ${{ env.MAX_CHUNKS }}
        python-version: ${{ matrix.python-version }}
    - name: Show commit range
      run: echo '${{ steps.discover.outputs.commit-range }}'
    - name: Show repository list
      run: echo '${{ steps.discover.outputs.repository-list }}'
    - name: Show tool list
      run: echo '${{ steps.discover.outputs.tool-list }}'
    - name: Show chunks
      run: |
        echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'

  # Planemo lint the changed repositories
  lint:
    name: Lint tool-list
    needs: setup
    if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ['3.10']
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v4
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}

    - name: Set fail level for pull request
      if: ${{ github.event_name == 'pull_request' }}
      run:
        echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
    - name: Set fail level for merge
      if: ${{ github.event_name != 'pull_request' }}
      run:
        echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
    - name: Planemo lint
      uses: galaxyproject/planemo-ci-action@v1
      id: lint
      with:
        mode: lint
        fail-level: ${{ env.FAIL_LEVEL }}
        repository-list: ${{ needs.setup.outputs.repository-list }}
        tool-list: ${{ needs.setup.outputs.tool-list }}
    - uses: actions/upload-artifact@v4
      if: ${{ failure() }}
      with:
        name: 'Tool linting output'
        path: lint_report.txt

  # flake8 of Python scripts in the changed repositories
  flake8:
    name: Lint Python scripts
    needs: setup
    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ['3.10']
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v4
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
    - name: Install flake8
      run: pip install flake8 flake8-import-order
    - name: Flake8
      run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
    - uses: actions/upload-artifact@v4
      if: ${{ failure() }}
      with:
        name: 'Python linting output'
        path: pylint_report.txt

  lintr:
    name: Lint R scripts
    needs: setup
    if: ${{ needs.setup.outputs.repository-list != '' }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-20.04]
        r-version: ['release']
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 1
    - uses: r-lib/actions/setup-r@v2
      with:
        r-version: ${{ matrix.r-version }}
    - name: Cache R packages
      uses: actions/cache@v4
      with:
        path: ${{ env.R_LIBS_USER }}
        key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
    - name: Install packages
      uses: r-lib/actions/setup-r-dependencies@v2
      with:
        packages: |
          any::argparse 
          any::styler
    - name: lintr
      run: |
        set -eo pipefail
        echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
        git status
        git diff --exit-code | tee rlint_report.txt
    - uses: actions/upload-artifact@v4
      if: ${{ failure() }}
      with:
        name: 'R linting output'
        path: rlint_report.txt

  file_sizes:
    name: Check file sizes
    needs: setup
    if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
    - name: Check file sizes
      run: |
        touch file_size_report.txt
        git diff --diff-filter=d --name-only ${{ needs.setup.outputs.commit-range }} > git.diff
        while read line; do
          find "$line" -type f -size +${{ env.MAX_FILE_SIZE }} >> file_size_report.txt
        done < git.diff
        if [[ -s file_size_report.txt ]]; then
          echo "Files larger than ${{ env.MAX_FILE_SIZE }} found"
          cat file_size_report.txt
          exit 1
        fi
    - uses: actions/upload-artifact@v4
      if: ${{ failure() }}
      with:
        name: 'File size report'
        path: file_size_report.txt

  # Planemo test the changed repositories, each chunk creates an artifact
  # containing HTML and JSON reports for the executed tests
  test:
    name: Test tools
    needs: setup
    if: ${{ needs.setup.outputs.repository-list != '' }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
        python-version: ['3.10']
    services:
      postgres:
        image: postgres:11
        env:
          POSTGRES_USER: postgres
          POSTGRES_PASSWORD: postgres
          POSTGRES_DB: postgres
        ports:
          - 5432:5432
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v4
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
    - name: Cache .planemo
      uses: actions/cache@v4
      id: cache-planemo
      with:
        path: ~/.planemo
        key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
    - name: Get number of CPU cores
      uses: SimenB/github-actions-cpu-cores@v2
      id: cpu-cores
    - name: Clean dotnet folder for space
      run: rm -Rf /usr/share/dotnet

    # the following 2 steps are needed for testing the scripting tool
    - name: Install Apptainer's singularity
      uses: eWaterCycle/setup-apptainer@v2
    - name: Symlink singularity
      run: ln -s $(which apptainer) $(dirname apptainer)/singularity
    - name: Install containers
      run: |
        echo "${{ needs.setup.outputs.repository-list }}" > repository_list.txt
        if grep -q scripting repository_list.txt; then
          singularity pull --dir /tmp docker://continuumio/anaconda3
          singularity pull --dir /tmp docker://rocker/tidyverse
        fi
    
      # Set up the lambda-miner database
    - name: Create a database in the postgres for lambda-miner
      run: |
        PGPASSWORD=postgres psql -h localhost -U postgres -c "CREATE DATABASE lmdb;"
        PGPASSWORD=postgres psql -h localhost -U postgres -d lmdb -q -f ./.github/lambdaminer/build.sql
        sleep 10
        PGPASSWORD=postgres psql -h localhost -U postgres -d lmdb -c "SELECT * FROM public.instrument;"
        
    - name: Check if the OMERO folder changed before starting OMERO
      id: check_changes
      run: |
        if git diff --quiet HEAD^ HEAD -- ./tools/omero; then
            echo "changed=false" >> $GITHUB_ENV
        else
            echo "changed=true" >> $GITHUB_ENV
        fi
        
      # Start OMERO
    - name: Start OMERO
      if: env.changed == 'true'
      uses: sudo-bot/action-docker-compose@latest
      with:
        cli-args: "-f .github/omero-docker-compose.yml up -d"

      # Setup environment
    - name: Set up Python environment for omero-py
      if: env.changed == 'true'
      uses: actions/setup-python@v4
      with:
        python-version: '3.11.0'

      # Upload a dummy dataset in OMERO
    - name: Install dependencies and upload a OMERO dummy dataset
      if: env.changed == 'true'
      run: |
        echo "Waiting for OMERO to be ready..."
        sleep 60
        pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl
        pip install omero-py==5.19.4
        omero login -s localhost -u root -w omero -p 6064
        PID=$(omero obj new Project name='test_prj')
        DID=$(omero obj new Dataset name='test_dts')
        omero obj new ProjectDatasetLink parent=$PID child=$DID
        omero import -d $DID .github/dummy-dts-omero
        omero tag create --name test_tag --desc 'description of my_tag'
        omero tag link Image:1 1
        echo "Created the dummy dataset into OMERO"
        DID_HCS=$(omero obj new Dataset name='test_hcs_dts')
        omero import -d $DID_HCS .github/dummy-hcs-omero
        echo "Created the hcs dummy dataset into OMERO"

    # download or create large test data via script
    - name: Create test data
      run: |
          set -x
          pip install planemo > /dev/null
          echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
          mapfile -t REPO_ARRAY < repository_list.txt
          planemo ci_find_tools --chunk_count "${{ needs.setup.outputs.chunk-count }}" --chunk "${{ matrix.chunk }}" --output tool_list_chunk.txt "${REPO_ARRAY[@]}"
          cat tool_list_chunk.txt | sed 's@/[^/]*$@@' | sort -i > repository_list_chunk.txt
          while read repo
          do
              echo "executing test-data.sh for $repo"
              if [ -x $repo/test-data.sh ]; then
                  cd $repo
                  ./test-data.sh
              fi
          done < repository_list_chunk.txt

    - name: Planemo test
      uses: galaxyproject/planemo-ci-action@v1
      id: test
      with:
        mode: test
        repository-list: ${{ needs.setup.outputs.repository-list }}
        galaxy-fork: ${{ env.GALAXY_FORK }}
        galaxy-branch: ${{ env.GALAXY_BRANCH }}
        additional-planemo-options: --docker_run_extra_arguments '--add-host=host.docker.internal:host-gateway'
        chunk: ${{ matrix.chunk }}
        chunk-count: ${{ needs.setup.outputs.chunk-count }}
        galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
        # Limit each test to 15 minutes
        test_timeout: 1800
    - uses: actions/upload-artifact@v4
      with:
        name: 'Tool test output ${{ matrix.chunk }}'
        path: upload

  # - combine the results of the test chunks (which will never fail due
  #   to `|| true`) and create a global test report as json and html which
  #   is provided as artifact
  # - check if any tool test actually failed (by lookup in the combined json)
  #   and fail this step if this is the case
  combine_outputs:
    name: Combine chunked test results
    needs: [setup, test]
    if: ${{ always() && needs.setup.outputs.repository-list != '' }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.10']
    steps:
    - uses: actions/download-artifact@v4
      with:
        path: artifacts
    - uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v4
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
    - name: Combine outputs
      uses: galaxyproject/planemo-ci-action@v1
      id: combine
      with:
        mode: combine
        html-report: true
        markdown-report: true
    - uses: actions/upload-artifact@v4
      with:
        name: 'All tool test results'
        path: upload
    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
    - name: Check outputs
      uses: galaxyproject/planemo-ci-action@v1
      id: check
      with:
        mode: check
    - name: Check if all test chunks succeeded
      run: |
        NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l)
        if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
          exit 1
        fi

  # deploy the tools to the toolsheds (first TTS for testing)
  deploy:
    name: Deploy
    needs: [setup, lint, combine_outputs]
    if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'Helmholtz-UFZ' }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.10']
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v4
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
    - name: Deploy on testtoolshed
      uses: galaxyproject/planemo-ci-action@v1
      with:
        mode: deploy
        repository-list: ${{ needs.setup.outputs.repository-list }}
        shed-target: testtoolshed
        shed-key: ${{ secrets.TTS_API_KEY }}
      continue-on-error: true
    - name: Deploy on toolshed
      uses: galaxyproject/planemo-ci-action@v1
      with:
        mode: deploy
        repository-list: ${{ needs.setup.outputs.repository-list }}
        shed-target: toolshed
        shed-key: ${{ secrets.TS_API_KEY }}

  deploy-report:
    name: Report deploy status
    needs: [deploy]
    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'Helmholtz-UFZ' }}
    runs-on: ubuntu-latest
    steps:
    # report to the PR if deployment failed
    - name: Get PR object
      uses: 8BitJonny/gh-get-current-pr@2.2.0
      id: getpr
      with:
        sha: ${{ github.event.after }}
    - name: Create comment
      uses: peter-evans/create-or-update-comment@v4
      with:
        token: ${{ secrets.PAT }}
        issue-number: ${{ steps.getpr.outputs.number }}
        body: |
          Attention: deployment ${{ needs.deploy.result }}!

          https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}

  determine-success:
    name: Check workflow success
    needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs]
    if: ${{ always() && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/main' }}
    runs-on: ubuntu-latest
    steps:
    - name: Check tool lint status
      if: ${{ needs.lint.result != 'success' && needs.flake8.result != 'skipped' }}
      run: exit 1
    - name: Indicate Python script lint status
      if: ${{ needs.flake8.result != 'success' && needs.flake8.result != 'skipped' }}
      run: exit 1
    - name: Indicate R script lint status
      if: ${{ needs.lintr.result != 'success' && needs.lintr.result != 'skipped' }}
      run: exit 1
    - name: Indicate file size check status
      if: ${{ needs.file_sizes.result != 'success' && needs.file_sizes.result != 'skipped' }}
      run: exit 1
    - name: Check tool test status
      if: ${{ needs.combine_outputs.result != 'success' && needs.combine_outputs.result != 'skipped' }}
      run: exit 1