python-package-conda.yml

# configuration derived from q2-katharoseq
name: Python Package using Conda

on: [push]

jobs:
  build-linux:
    runs-on: ${{ matrix.os }}
    strategy:
      max-parallel: 5
      matrix:
        os: ["ubuntu-latest", "macos-latest"]

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - uses: conda-incubator/setup-miniconda@v2
      with:
        auto-update-conda: true
        python-version: ${{ matrix.python-version }}
    - name: Add conda to system path
      run: |
        # $CONDA is an environment variable pointing to the root of the miniconda directory
        echo $CONDA/bin >> $GITHUB_PATH
    - name: Install QIIME 2 ${{ matrix.os }}
      if: matrix.os == 'macos-latest'
      shell: bash -l {0}
      run: |
        wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-osx-conda.yml
        conda env create -q -n test-env --file qiime2-latest-py38-osx-conda.yml
    - name: Install QIIME 2 ${{ matrix.os }}
      if: matrix.os == 'ubuntu-latest'
      shell: bash -l {0}
      run: |
        wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml
        conda env create -q -n test-env --file qiime2-latest-py38-linux-conda.yml
    - name: Install q2-greengenes2
      shell: bash -l {0}
      run: |
        source activate test-env
        conda install flake8 pytest
        pip install -e . 
    - name: Lint with flake8
      shell: bash -l {0}
      run: |
        source activate test-env
        flake8 q2_gg2
    - name: Test with pytest
      shell: bash -l {0}
      run: |
        source activate test-env
        pytest

  lint:
    runs-on: ubuntu-latest
    steps:
    - name: flake8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - name: install dependencies
      shell: bash -l {0}
      run: |
        python -m pip install --upgrade pip
    - name: Check out repository code
      uses: actions/checkout@v2
    - name: lint
      shell: bash -l {0}
      run: |
        pip install -q flake8
        flake8 q2_gg2