qiime_dev.yml

name: Test with qiime2-dev

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

jobs:
  test:

    strategy:
      fail-fast: false
      matrix:
        os:
            - image: "ubuntu-latest"
              short: "linux"
            - image: "macos-latest"
              short: "osx"
    runs-on: "${{matrix.os.image}}"

    steps:
    - uses: actions/checkout@v4
    - name: Setup conda
      uses: conda-incubator/setup-miniconda@v2
      with:
        miniforge-variant: Mambaforge
        miniforge-version: latest
        use-mamba: true
    - shell: bash -l {0}
      run: |
        conda info
        conda list
    - name: Install Qiime 2
      shell: bash -l {0}
      run: |
        wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-${{matrix.os.short}}-conda.yml
        mamba env create -n qiime2-dev --file qiime2-latest-py38-${{matrix.os.short}}-conda.yml
        rm qiime2-latest-py38-${{matrix.os.short}}-conda.yml
    - name: Install q2-micom
      shell: bash -l {0}
      run: |
        conda activate qiime2-dev
        mamba env update -n qiime2-dev -f q2-micom-${{matrix.os.short}}.yml
    - name: Install CPLEX
      shell: bash -l {0}
      run: |
        conda activate qiime2-dev
        mamba install -y -c ibmdecisionoptimization cplex
    - name: Lint with flake8
      shell: bash -l {0}
      run: |
        conda activate qiime2-dev
        pip install flake8
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --ignore=F203 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --ignore=F203 --exit-zero --statistics
    - name: Test with pytest
      shell: bash -l {0}
      run: |
        conda activate qiime2-dev
        pip install pytest pytest-benchmark pytest-cov
        pytest --benchmark-skip --cov=q2_micom --cov-report=xml