pr.yaml

name: Test Seurat workflow with CLI scripts

on: [pull_request]

jobs:
  setup:
    name: ${{ matrix.os }})
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"]
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - uses: actions/checkout@v2

      - name: Add workspace to path
        run: |
          echo "${GITHUB_WORKSPACE}" >> $GITHUB_PATH

      - uses: mamba-org/setup-micromamba@v1
        with:
          micromamba-version: '1.4.5-0'
          environment-file: test-environment.yml
          init-shell: >-
            bash
          cache-environment: true
          create-args: |
            python=${{ matrix.python-version }}
          post-cleanup: 'all'

      - name: Run tests
        shell: bash -el {0}
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
        run: |
          r-seurat-scripts-post-install-tests.sh