ci.yml

name: Test and lint

on:
  pull_request:
    branches: ["main"]
  push:
    branches: ["main"]

jobs:
  build-and-test-qiime2-pathogenome-2024-10:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-13]

    steps:
    - uses: actions/checkout@v2

    - name: Set up Conda
      uses: conda-incubator/setup-miniconda@v3
      with:
        activate-environment: q2-amrfinderplus-qiime2-pathogenome-2024.10
        environment-file: environments/q2-amrfinderplus-qiime2-pathogenome-2024.10.yml
        auto-activate-base: false

    - name: Install plugin
      shell: bash -l {0}
      run: make install

    - name: Run tests
      shell: bash -l {0}
      run: make test

  lint:
    runs-on: ubuntu-latest
    steps:
    - name: checkout source
      uses: actions/checkout@v3

    - name: set up python 3.11
      uses: actions/setup-python@v4
      with:
        python-version: 3.11

    - name: install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install -q https://github.com/qiime2/q2lint/archive/master.zip
        pip install -q flake8

    - name: run flake8
      run: flake8

    - name: run q2lint
      run: q2lint