main.yml

name: CI

on: [push, pull_request, workflow_dispatch]

env:
  MIN_COVERAGE_REQUIRED: 35


jobs:
  test:
    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
    runs-on: ubuntu-latest
    timeout-minutes: 10
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v3
      - name: Test outputs
        run: |
          python -m pip install .
          python -m pip install coverage
          bash run_test.sh
      - name: Test with old biopython
        run: |
          python -m pip install biopython==1.79
          bash run_test.sh
      - name: Coverage
        run: |
          coverage report
          test $(coverage report | grep TOTAL | awk '{ print $4 }' | tr -d "%") -ge $MIN_COVERAGE_REQUIRED

  #test_oldbio:
  #  if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
  #  runs-on: ubuntu-latest
  #  timeout-minutes: 10
  #  defaults:
  #    run:
  #      shell: bash -l {0}
#
#    steps:
#      - uses: actions/checkout@v3
#      - name: Test pipeline output
#        run: |
#          python -m pip install biopython==1.79
#          python -m pip install coverage
#          python -m pip install .
#          bash ./run_test.sh