binette_ci.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: Test Binette

on: [push] #to any branch

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.8] #["3.8", "3.9", "3.10"]

    steps:
    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
    - uses: actions/checkout@v3

    # # Setting up miniconda
    # - uses: conda-incubator/setup-miniconda@v2
    #   with:
    #     mamba-version: "*"
    #     python-version: ${{ matrix.python-version }}
    #     channels: conda-forge,bioconda,defaults
    #     activate-environment: test

    # - name: Set up test environment
    #   shell: bash -l {0}
    #   run: |
    #       mamba install -y binette

    # - name: check installation
    #   shell: bash -l {0}
    #   run: |
    #       python --version
    #       binette --version

    # - uses: actions/checkout@v3
    # - name: Set up Python ${{ matrix.python-version }}
    #   uses: actions/setup-python@v3
    #   with:
    #     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 mamba
    #   run: |
    #     conda install -c conda-forge mamba
    # - name: Install binette dependencies
    #   run: |
    #     mamba env update --file binette.yaml --name base

    # Setting up miniconda
    - uses: conda-incubator/setup-miniconda@v2
      with:
        mamba-version: "*"
        python-version: ${{ matrix.python-version }}
        channels: conda-forge,bioconda,defaults
        environment-file: binette.yaml
        activate-environment: binette
  
    - name: Install binette
      run: |
        pip install .
        binette -h

    - name: Lint with flake8
      run: |
        conda install flake8
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

    - name: Test with pytest
      run: |
        mamba install pytest
        pytestconda

    - name: Download test data
      uses: actions/checkout@v3
      with:
        repository: genotoul-bioinfo/Binette_TestData
        path: test_data

    - name: Run simple test case
      run: |
        cd test_data
        binette -b binning_results/* --contigs all_contigs.fna --checkm2_db checkm2_tiny_db/checkm2_tiny_db.dmnd  -v -o test_results

    - name: Compare results with expectation
      run: |
        cd test_data
        head  expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv
        python scripts/compare_results.py expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv