github_tests.yml

name: Integration Tests & Code Style

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

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

    steps:
    - name: Checkout Repo
      uses: actions/checkout@v2
      with:
          lfs: true
    - name: Checkout LFS objects
      run: git lfs checkout

    - name: Set up Python
      uses: actions/setup-python@v2

    - name: Install dependencies
      run: |
        $CONDA/bin/conda env update --file environment.yml --name base

    - name: Lint with flake8
      run: |
        $CONDA/bin/flake8 src/marbel/

    - name: Run tests with pytest
      run: |
          $CONDA/bin/pytest tests --doctest-modules --cov=src/marbel --cov-report=xml

    - name: Convert coverage to lcov format
      run: |
        $CONDA/bin/coverage lcov

#    - name: Send coverage report to Coveralls
#      uses: coverallsapp/github-action@master
#      with:
#        github-token: ${{ secrets.GITHUB_TOKEN }}
#        path-to-lcov: "coverage.lcov"
  tests-functional:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
    - name: Checkout Repo
      uses: actions/checkout@v2
      with:
          lfs: true
    - name: Checkout LFS objects
      run: git lfs checkout
    - name: Set up Python
      uses: actions/setup-python@v2
    - name: Create conda env
      run: |
        conda create -n marbel python=3.10 r-base
    - name: Install the package
      run: |
        pip install -e .
    - name: Simulate reads
      run: |
        marbel --n-species 3 --n-orthogroups 10 --n-samples 2 4 --library-size 5000 --outdir run_spec10_orth200_samp5-10/
    # - name: Create conda env for testing, i.e. install skbio and pandas
    #   uses: conda-incubator/setup-miniconda@v3
    #   with:
    #     activate-environment: anaconda-client-env
    #     environment-file: tests/env_functional.yaml
    #     auto-activate-base: true
    # - name: debug
    #   run: |
    #     pwd
    - name: Create conda test-env
      run: |
        conda create -n marbel-test scikit-bio

    - name: Execute functional tests
      run: |
        conda info
        conda env list
        conda init
        eval "$(conda shell.bash hook)"
        conda activate marbel-tests
        echo $CONDA_PREFIX
        python tests/run_functional.py run_spec10_orth200_samp5-10/