runTest.yml

name: runTest

on: [push]

jobs:
  test-python-app:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
    - name: Set up Python 3.10
      uses: actions/setup-python@v3
      with:
        python-version: '3.10'
    - 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: create environment 4 yacht
      uses: conda-incubator/setup-miniconda@v2
      with:
        auto-activate-base: false
        activate-environment: yacht
        environment-file: env/yacht_env.yaml
    - name: Install dependencies
      run: |
        pip install certifi==2023.7.22
        pip install scipy==1.11.2
        pip install numpy==1.25
        pip install wget==3.2
        pip install pandas
        pip install sourmash
        pip install loguru
    - name: make training data
      run: python make_training_data_from_sketches.py --ref_file 'tests/testdata/20_genomes_sketches.zip' --ksize 31 --out_prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95                                
    - name: run YACHT
      run: python run_YACHT.py --ref_matrix 'gtdb_ani_thresh_0.95_ref_matrix_processed.npz' --ksize 31 --sample_file 'tests/testdata/sample.sig' --ani_thresh 0.95 --significance 0.99 --min_coverage 1 --outfile 'yacht_results.csv'