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: [ "master" ]
  pull_request:
    branches: [ "master" ]

permissions:
  contents: read

jobs:
  build:

    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3
    - name: Set up miniconda
      run: |
        wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
        bash Miniforge3-Linux-x86_64.sh -b
        ~/miniforge3/condabin/conda init
        source /home/runner/.bashrc
        conda config --add channels defaults
        conda config --add channels bioconda
        conda config --add channels conda-forge
        conda config --set channel_priority strict
    - name: install dependancies
      run: |
        /home/runner/miniforge3/bin/mamba install tb-profiler -y
        
    - name: Install dependencies
      run: |
        pip install --force-reinstall .
    - name: Run tests
      run: |
        cd tests
        /home/runner/miniforge3/bin/mamba install pytest -y
        pytest -x .