python-app.yml

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

name: Python application

on:
  push:
    branches: [ "refactoring" ]

permissions:
  contents: read

jobs:
  build:

    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python 3.10
      uses: actions/setup-python@v5
      with:
        python-version: "3.10"
    - name: Conda installation
      run: |
        mkdir -p ~/miniconda3
        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
        bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
        rm -rf ~/miniconda3/miniconda.sh
        ~/miniconda3/bin/conda init bash
        ~/miniconda3/bin/conda init zsh
    - name: Strainy Install 
      run: |
        #cd strainy
        ls
        git submodule update --init
        make -C submodules/Flye
        conda env create -f environment.yml -n strainy
    - name: Test strainy
      run: |
        conda run -n strainy ./strainy.py --gfa test_set/toy.gfa --fastq test_set/toy.fastq.gz --output out_strainy --mode hifi --threads 8