python-package-conda.yml

name: Python Package using Conda

on:
  push:
    branches:
    - main
    - release/*

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5

    steps:
    - uses: actions/checkout@v4

    - 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: Install dependencies
      run: |
        conda config --set solver classic
        conda update -n base -c defaults conda
        conda install phabox python=3.10  -c conda-forge -c bioconda -y
        conda install diamond=0.9 flake8 -c conda-forge -c bioconda 

    - name: Lint with flake8
      run: |
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

    - name: Test PhaBOX utilities
      run: |
        git clone https://github.com/KennthShang/PhaBOX.git
        cd PhaBOX
        python -m pip install .
        cd ..
        wget https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa
        wget https://github.com/KennthShang/PhaBOX/releases/download/v2/phabox_db_v2.zip
        unzip phabox_db_v2.zip > /dev/null
        phabox2 --task end_to_end --contigs example_contigs.fa -o end_to_end -d phabox_db_v2
        head end_to_end/final_prediction/final_prediction_summary.tsv
        phabox2 --task phamer --contigs example_contigs.fa -o phamer -d phabox_db_v2
        head phamer/final_prediction/phamer_prediction.tsv
        phabox2 --task phagcn --contigs example_contigs.fa -o phagcn -d phabox_db_v2
        head phagcn/final_prediction/phagcn_prediction.tsv
        phabox2 --task phatyp --contigs example_contigs.fa -o phatyp -d phabox_db_v2
        head phatyp/final_prediction/phatyp_prediction.tsv
        phabox2 --task cherry --contigs example_contigs.fa -o cherry -d phabox_db_v2
        head cherry/final_prediction/cherry_prediction.tsv
        phabox2 --task contamination --contigs example_contigs.fa -o contamination -d phabox_db_v2
        head contamination/final_prediction/contamination_prediction.tsv
        phabox2 --task votu --contigs example_contigs.fa -o votu -d phabox_db_v2 --mode AAI
        head votu/final_prediction/AAI_based_vOTU.tsv
        phabox2 --task votu --contigs example_contigs.fa -o votu -d phabox_db_v2 --mode ANI
        head votu/final_prediction/ANI_based_vOTU.tsv
        phabox2 --task tree --contigs example_contigs.fa -o tree -d phabox_db_v2 --msa Y --tree N
        head tree/final_prediction/combined_marker.msa