test.yml

name: Run tests
on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  merge_group:
    types: [checks_requested]
    branches: [main]

# Cancel if a newer run is started
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

jobs:
  pre-commit:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v3
      - uses: pre-commit/action@v3.0.0
        # FIXME Flip this off once we get to less than a couple hundred. Adding
        # this so it will only run against changed files. It'll make it much
        # easier to fix these as they come up rather than everything at once.
        with:
          extra_args: ""

  prettier:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository
        uses: actions/checkout@v4

      - name: Install NodeJS
        uses: actions/setup-node@v4
        with:
          node-version: "20"

      - name: Install Prettier
        run: npm install -g prettier

      - name: Run Prettier --check
        run: prettier --check .

  editorconfig:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-node@v4
        with:
          node-version: "20"

      - name: Install editorconfig-checker
        run: npm install -g editorconfig-checker

      - name: Run ECLint check
        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)

  pytest-changes:
    name: pytest-changes
    runs-on: ubuntu-latest
    outputs:
      # Expose matched filters as job 'modules' output variable
      modules: ${{ steps.filter.outputs.changes }}
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 2 # To retrieve the preceding commit.

      # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented
      - uses: mirpedrol/paths-filter@main
        id: filter
        with:
          filters: "tests/config/pytest_modules.yml"
          token: ""

  nf-core-lint:
    runs-on: ubuntu-latest
    name: nf-core-lint
    needs: [pytest-changes]
    if: ${{ (needs.pytest-changes.outputs.modules != '[]') }}
    strategy:
      fail-fast: false
      matrix:
        tags:
          [
            "${{ fromJson(needs.pytest-changes.outputs.modules) }}"
          ]
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.11"

      - uses: actions/cache@v3
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Install pip
        run: python -m pip install --upgrade pip

      - uses: actions/setup-java@v3
        with:
          distribution: "temurin"
          java-version: "17"
      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v1

      - name: Install nf-core tools
        run: python -m pip install --upgrade --force-reinstall nf-core

      - name: Lint module ${{ matrix.tags }}
        run: nf-core modules --git-remote https://github.com/scilus/nf-scil.git lint ${{ matrix.tags }}
        if: ${{ !startsWith(matrix.tags, 'subworkflows/') }}

      - name: Remove substring from matrix.tags
        id: remove_substring
        run: echo subworkflow_names=$(echo "${{ matrix.tags }}" | sed 's/subworkflows\///g') >> $GITHUB_OUTPUT

      - name: Lint subworkflow ${{ matrix.tags }}
        run: nf-core subworkflows --git-remote https://github.com/scilus/nf-scil.git lint ${{steps.remove_substring.outputs.subworkflow_names}}
        if: ${{ startsWith(matrix.tags, 'subworkflows/') }}

  pytest:
    runs-on: ubuntu-latest
    name: pytest
    needs: [pytest-changes]
    if: needs.pytest-changes.outputs.modules != '[]'
    strategy:
      fail-fast: false
      matrix:
        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
        profile: ["docker", "singularity"]
        exclude:
          - tags: "nf-test"
    env:
      NXF_ANSI_LOG: false

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.11"

      - name: Install Python dependencies
        run: python -m pip install --upgrade pip pytest-workflow cryptography

      - uses: actions/setup-java@v3
        with:
          distribution: "temurin"
          java-version: "17"

      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v1

      - name: Setup apptainer
        if: matrix.profile == 'singularity'
        uses: eWaterCycle/setup-apptainer@main

      - name: Set up Singularity
        if: matrix.profile == 'singularity'
        run: |
          mkdir -p $NXF_SINGULARITY_CACHEDIR
          mkdir -p $NXF_SINGULARITY_LIBRARYDIR

      # Test the module
      - name: Run pytest-workflow
        # only use one thread for pytest-workflow to avoid race condition on conda cache.
        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes

      - name: Output log on failure
        if: failure()
        run: |
          sudo apt-get update > /dev/null
          sudo apt-get install bat > /dev/null
          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}

      - name: Setting global variables
        uses: actions/github-script@v6
        id: parsed
        with:
          script: |
            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
          result-encoding: string

      - name: Upload logs on failure
        if: failure()
        uses: actions/upload-artifact@v3
        with:
          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
          path: |
            /home/runner/pytest_workflow_*/*/.nextflow.log
            /home/runner/pytest_workflow_*/*/log.out
            /home/runner/pytest_workflow_*/*/log.err
            /home/runner/pytest_workflow_*/*/work
            !/home/runner/pytest_workflow_*/*/work/conda
            !/home/runner/pytest_workflow_*/*/work/singularity
            !${{ github.workspace }}/.singularity

  confirm-pass:
    runs-on: ubuntu-latest
    needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest]
    if: always()
    steps:
      - name: All tests ok
        if: ${{ success() || !contains(needs.*.result, 'failure') }}
        run: exit 0
      - name: One or more tests failed
        if: ${{ contains(needs.*.result, 'failure') }}
        run: exit 1

      - name: debug-print
        if: always()
        run: |
          echo "toJSON(needs) = ${{ toJSON(needs) }}"
          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"