pr.yaml

name: Galaxy Tool Linting and Tests for push and PR
on: [push, pull_request]
env:
  GALAXY_REPO: https://github.com/galaxyproject/galaxy
  GALAXY_RELEASE: release_24.0
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
    strategy:
      matrix:
        python-version: [3.11]
    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 }}'
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Determine latest galaxy commit
      run: echo "GALAXY_HEAD_SHA=$(git ls-remote ${{ env.GALAXY_REPO }} refs/heads/${{ env.GALAXY_RELEASE }} | cut -f1)" >> $GITHUB_ENV
    - name: Save latest galaxy commit to artifact file
      run: echo $GALAXY_HEAD_SHA > galaxy.sha
    - uses: actions/upload-artifact@v2
      with:
        name: Workflow artifacts
        path: galaxy.sha
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
    - name: Cache .planemo
      uses: actions/cache@v2
      id: cache-planemo
      with:
        path: ~/.planemo
        key: planemo_cache_py_${{ matrix.python-version }}_gxy1_$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 Planemo and flake8
      run: pip install planemo flake8 flake8-import-order
    - name: Fake a Planemo run to update cache
      if: steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true'
      run: |
        touch tool.xml
        PIP_QUIET=2 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE
    - uses: actions/checkout@v2
      with:
        fetch-depth: 0
    # The range of commits to check for changes is:
    # - `origin/master...` for all events happening on a feature branch
    # - for events on the master branch we compare against the sha before the event
    #   (note that this does not work for feature branch events since we want all
    #   commits on the feature branch and not just the commits of the last event)
    # - for pull requests we compare against the 1st ancestor, given the current
    #   HEAD is the merge between the PR branch and the base branch
    - name: Set commit range (push to the feature branch)
      if: github.ref != 'refs/heads/master' && github.event_name == 'push'
      run: |
        git fetch origin master
        echo "COMMIT_RANGE=origin/master..." >> $GITHUB_ENV
    - name: Set commit range (push to the master branch, e.g. merge)
      if: github.ref == 'refs/heads/master' && github.event_name == 'push'
      run: echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV
    - name: Set commit range (pull request)
      if: github.event_name == 'pull_request'
      run: echo "COMMIT_RANGE=HEAD~.." >> $GITHUB_ENV
    - name: Planemo ci_find_repos
      run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --exclude_from .tt_skip --output changed_repositories.list
    - name: Show repo list
      run: cat changed_repositories.list
    - uses: actions/upload-artifact@v2.0.1
      with:
        name: Workflow artifacts
        path: changed_repositories.list

  # Planemo lint the changed repositories
  lint:
    name: Lint tools
    needs: setup
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.11]
    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: ${{ matrix.python-version }}
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - name: Determine latest galaxy commit
      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
    - name: Install Planemo
      run: pip install planemo
    - name: Planemo lint
      run: |
        set -e
        while read -r DIR; do
            planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR";
        done < ../workflow_artifacts/changed_repositories.list

  # flake8 of Python scripts in the changed repositories
  flake8:
    name: Lint Python scripts
    needs: setup
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.11]
    steps:
    # checkout the repository to master
    # and use it as the current working directory
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - name: Determine latest galaxy commit
      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
    - name: Install flake8
      run: pip install flake8 flake8-import-order
    - name: Flake8
      run: |
        if [ -s ../workflow_artifacts/changed_repositories.list ]; then
            flake8 $(cat ../workflow_artifacts/changed_repositories.list)
        fi

  lintr:
    name: Lint R scripts
    needs: setup
    runs-on: ubuntu-latest
    strategy:
      matrix:
        r-version: [4.4.0]
    steps:
    # checkout the repository to master
    # and use it as the current working directory
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - uses: r-lib/actions/setup-r@master
      with:
        r-version: ${{ matrix.r-version }}
    - name: Cache R packages
      uses: actions/cache@v2
      with:
        path: ${{ env.R_LIBS_USER }}
        key: r_cache_1${{ 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", force=TRUE)
      shell: Rscript {0}
    - name: lintr
      run: |
        library(lintr)
        linters <- with_defaults(line_length_linter = NULL, 
                                 object_name_linter = NULL,
                                 object_usage_linter = NULL,
                                 cyclocomp_linter(complexity_limit = 25))
        con <- file("../workflow_artifacts/changed_repositories.list", "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())
            }
          }
        }
        quit(status = status)
      shell: Rscript {0}

  # Planemo test the changed repositories, each chunk creates an artifact
  # containing HTML and JSON reports for the executed tests
  test:
    name: Test tools
    # This job runs on Linux
    runs-on: ubuntu-latest
    needs: setup
    strategy:
      fail-fast: false
      matrix:
        chunk: [0]
        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: ${{ matrix.python-version }}
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - name: Determine latest galaxy commit
      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
    - name: Cache .planemo
      uses: actions/cache@v2
      id: cache-planemo
      with:
        path: ~/.planemo
        key: planemo_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
    - name: Install Planemo
      run: pip install planemo
    - name: Planemo ci_find_tools
      run: |
        touch changed_repositories_chunk.list changed_tools_chunk.list
        if [ -s ../workflow_artifacts/changed_repositories.list ]; then
            if [ $(wc -l < ../workflow_artifacts/changed_repositories.list) -eq 1 ]; then
                planemo ci_find_tools --chunk_count 1 --chunk ${{ matrix.chunk }} \
                               --output changed_tools_chunk.list \
                               $(cat ../workflow_artifacts/changed_repositories.list)
            else
                planemo ci_find_repos --chunk_count 1 --chunk ${{ matrix.chunk }} \
                               --output changed_repositories_chunk.list \
                               $(cat ../workflow_artifacts/changed_repositories.list)
            fi
        fi
    - name: Show changed tools/repositories chunk list
      run: cat changed_tools_chunk.list changed_repositories_chunk.list
    - name: Planemo test tools
      run: |
        if grep -lqf .tt_biocontainer_skip changed_tools_chunk.list changed_repositories_chunk.list; then
                PLANEMO_OPTIONS=""
        else
                PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
        fi
        if [ -s changed_tools_chunk.list ]; then
            PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json tool_test_output.json $(cat changed_tools_chunk.list) || true
            docker system prune --all --force --volumes || true
        elif [ -s changed_repositories_chunk.list ]; then
            while read -r DIR; do
                if [[ "$DIR" =~ ^data_managers.* ]]; then
                    TESTPATH=$(planemo ci_find_tools "$DIR")
                else
                    TESTPATH="$DIR"
                fi
                PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE --galaxy_python_version ${{ matrix.python-version }} --test_output_json "$DIR"/tool_test_output.json "$TESTPATH" || true
                docker system prune --all --force --volumes || true
            done < changed_repositories_chunk.list
        else
            echo '{"tests":[]}' > tool_test_output.json
        fi
    - name: Merge tool_test_output.json files
      run: find . -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
    - name: Create tool_test_output.html
      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
    - name: Copy artifacts into place
      run: |
        mkdir upload
        mv tool_test_output.json tool_test_output.html upload/
    - uses: actions/upload-artifact@v2.0.1
      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: test
    strategy:
      matrix:
        python-version: [3.7]
    # This job runs on Linux
    runs-on: ubuntu-latest
    steps:
    - uses: actions/download-artifact@v2
      with:
        path: artifacts
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Determine latest galaxy commit
      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy1_$GALAXY_HEAD_SHA
    - name: Install Planemo
      run: pip install planemo
    - name: Install jq
      run: sudo apt-get install jq
    - name: Combine outputs
      run: find artifacts/ -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
    - name: Create tool_test_output.html
      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
    - name: Copy artifacts into place
      run: |
        mkdir upload
        mv tool_test_output.json tool_test_output.html upload/
    - uses: actions/upload-artifact@v2.0.1
      with:
        name: 'All tool test results'
        path: upload
    - name: Check status of combined status
      run: |
        if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then
            echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
            exit 1
        fi

  # deploy the tools to the toolsheds (first TTS for testing)
  deploy:
    name: Deploy
    needs: [lint,flake8,lintr,combine_outputs]
    strategy:
      matrix:
        python-version: [3.7]
    runs-on: ubuntu-latest
    if: github.ref == 'refs/heads/master' && github.repository_owner == 'computational-metabolomics'
    steps:
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - name: Determine latest galaxy commit
      run: echo "GALAXY_HEAD_SHA=$(cat ../workflow_artifacts/galaxy.sha)" >> $GITHUB_ENV
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_$GALAXY_HEAD_SHA
    - name: Install Planemo
      run: pip install planemo
    - name: Deploy on testtoolshed
      env:
        SHED_KEY: ${{ secrets.tts_api_key }}
      run: |
        while read -r DIR; do
            planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
        done < ../workflow_artifacts/changed_repositories.list
      continue-on-error: true
    - name: Deploy on toolshed
      env:
        SHED_KEY: ${{ secrets.ts_api_key }}
      run: |
        while read -r DIR; do
            planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
        done < ../workflow_artifacts/changed_repositories.list