github_tests.yml

name: integration tests & code style

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build-linux:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout Repo
      uses: actions/checkout@v3
    - name: Set up Python
      uses: actions/setup-python@v3
    - name: setup conda
      uses: conda-incubator/setup-miniconda@v2
      with:
        # This uses *miniforge*, rather than *minicond*. The primary difference
        # is that the defaults channel is not enabled at all
        miniforge-version: latest
        # These properties enable the use of mamba, which is much faster and far
        # less error prone than conda while being completely compatible with the
        # conda CLI
        use-mamba: true
        mamba-version: "*"
        environment-file: environment.yml
        python-version: "3.10"
    - name: Lint with flake8
      # Bash shells do not use ~/.profile or ~/.bashrc so these shells need to
      # be explicitely declared as shell: bash -el {0} on steps that need to be
      # properly activated (or use a default shell). This is because bash shells
      # are executed with bash --noprofile --norc -eo pipefail {0} thus ignoring
      # updated on bash profile files made by conda init bash. See Github
      # Actions Documentation and thread.
      shell: bash -el {0}
      run: |
        flake8 phylofiller/
    - name: run python tests
      shell: bash -el {0}
      run: |
        nosetests phylofiller --with-doctest --with-coverage
    - name: convert coverage
      shell: bash -el {0}
      run: |
        coverage lcov
    - name: send coverage report
      uses: coverallsapp/github-action@master
      with:
        github-token: ${{ secrets.GITHUB_TOKEN }}
        path-to-lcov: "coverage.lcov"