main.yml

name: Sequence Processing Pipeline CI

# Controls when the action will run.
on:
  # Triggers the workflow on pull request and push events, only on the master
  # branch
  pull_request:
    branches: [ master ]
  push:
    branches: [ master ]

jobs:
  # name of job
  build:
    # The type of runner that the job will run on (available options are window/macOS/linux)
    runs-on: ubuntu-latest
    # we can add more versions of node.js in the future
    strategy:
      matrix:
        python-version: ['3.9']

    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      # first grab branch from github
      - uses: actions/checkout@v2
        with:
          persist-credentials: false
          fetch-depth: 0

      - uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: tester
          python-version: ${{ matrix.python-version }}
          conda-channels: anaconda, conda-forge, bioconda
          auto-update-conda: true

      - name: Main install
        shell: bash -l {0}
        run: |
          pip install -e ".[all]"

      - name: Python linter
        shell: bash -l {0}
        run: flake8 sequence_processing_pipeline/ setup.py
        
      - name: Run tests and measure coverage
        shell: bash -l {0}
        run: |
          nosetests --with-coverage --cover-inclusive --cover-package sequence_processing_pipeline

      - name: Coveralls
        uses: AndreMiras/coveralls-python-action@develop
        with:
          parallel: true
          flag-name: Unit Test

  coveralls_finish:
    needs: build
    runs-on: ubuntu-latest
    steps:
    - name: Coveralls Finished
      uses: AndreMiras/coveralls-python-action@develop
      with:
        github-token: ${{ secrets.github_token }}
        parallel-finished: true