pr.yaml

name: Galaxy Tool Linting and Tests for push and PR
on: [push, pull_request]
env:
  GALAXY_FORK: galaxyproject
  GALAXY_BRANCH: release_21.09
  MAX_CHUNKS: 4
  MAX_FILE_SIZE: 1M
concurrency:
  # group runs by PR, but keep runs on master 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: ['3.7']
    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: ${{ github.event.after }}'
    - name: Determine latest commit in the Galaxy repo
      id: get-galaxy-sha
      run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
    - name: Cache .planemo
      uses: actions/cache@v2
      id: cache-planemo
      with:
        path: ~/.planemo
        key: planemo_cache_py_${{ 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@v2
      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: ['3.7']
    steps:
    # checkout the repository
    # and use it as the current working directory
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
    - name: Planemo lint
      uses: galaxyproject/planemo-ci-action@v1
      id: lint
      with:
        mode: lint
        repository-list: ${{ needs.setup.outputs.repository-list }}
        tool-list: ${{ needs.setup.outputs.tool-list }}
    - uses: actions/upload-artifact@v2
      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: ${{ needs.setup.outputs.repository-list != '' }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ['3.7']
    steps:
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ 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@v2
      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: ['4.0.1']
    steps:
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: r-lib/actions/setup-r@master
      with:
        r-version: ${{ matrix.r-version }}
    - name: Cache R packages
      uses: actions/cache@v2
      with:
        path: ${{ env.R_LIBS_USER }}
        key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
    - name: Install non-R lintr dependencies
      run: sudo apt-get install libcurl4-openssl-dev
    - name: Install lintr
      run: |
        install.packages('remotes')
        remotes::install_cran("lintr")
      shell: Rscript {0}
    - name: Save repositories to file
      run: echo '${{ needs.setup.outputs.repository-list }}' > repository_list.txt
    - name: lintr
      run: |
        library(lintr)
        linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL)
        con <- file("repository_list.txt", "r")
        status <- 0
        while (TRUE) {
          repo <- readLines(con, n = 1)
          if (length(repo) == 0) {
             break
          }
          lnt <- lint_dir(repo, relative_path=T, linters=linters)
          if (length(lnt) > 0) {
            status <- 1
            for (l in lnt) {
              rel_path <- paste(repo, l$filename, sep="/")
              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), stderr())
              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), "rlint_report.txt", append=TRUE)
            }
          }
        }
        quit(status = status)
      shell: Rscript {0}
    - uses: actions/upload-artifact@v2
      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
    strategy:
      fail-fast: false
    steps:
    - uses: actions/checkout@v2
      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@v2
      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: ['3.7']
    services:
      postgres:
        image: postgres:11
        env:
          POSTGRES_USER: postgres
          POSTGRES_PASSWORD: postgres
          POSTGRES_DB: postgres
        ports:
          - 5432:5432
    steps:
    # checkout the repository
    # and use it as the current working directory
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
    - name: Cache .planemo
      uses: actions/cache@v2
      id: cache-planemo
      with:
        path: ~/.planemo
        key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
    - 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 }}
        chunk: ${{ matrix.chunk }}
        chunk-count: ${{ needs.setup.outputs.chunk-count }}
    - uses: actions/upload-artifact@v2
      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
#  SEEMS TO BE FAILING ON CONDA - UNABLE TO FIX
#  combine_outputs:
#    name: Combine chunked test results
#    needs: [setup, test]
#    if: ${{ needs.setup.outputs.repository-list != '' }}
#    runs-on: ubuntu-latest
#    strategy:
#      matrix:
#        python-version: ['3.7']
#    steps:
#    - uses: actions/download-artifact@v2
#      with:
#        path: artifacts
#    - uses: actions/setup-python@v1
#      with:
#        python-version: ${{ matrix.python-version }}
#    - name: Cache .cache/pip
#      uses: actions/cache@v2
#      id: cache-pip
#      with:
#        path: ~/.cache/pip
#        key: pip_cache_py_${{ 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
#    - uses: actions/upload-artifact@v2
#      with:
#        name: 'All tool test results'
#        path: upload
#    - name: Check outputs
#      uses: galaxyproject/planemo-ci-action@v1
#      id: check
#      with:
#        mode: check

  # deploy the tools to the toolsheds (first TTS for testing)
  deploy:
    name: Deploy
    needs: [setup, lint, flake8, lintr]
    if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'computational-metabolomics' }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.7']
    steps:
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ 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 }}

  determine-success:
    name: Check workflow success
    needs: [setup, lint, flake8, lintr, file_sizes]
    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