python-package.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: Python package

on:
  push:
    branches: [ "main" ]
  pull_request:
    branches: [ "main" ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v3
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install packagge
      run: |
        python -m pip install --upgrade pip pytest pytest-cov
        python -m pip install -e .

    - name: Create tasks needed for testing
      run: |
          python scripts/tasks_retrival/gene2gene_task_creation.py --allow-downloads True
          python scripts/tasks_retrival/Genecorpus_tasks_creation.py --allow-downloads True
          python scripts/tasks_retrival/HLA_task_creation.py --allow-downloads True
          python scripts/tasks_retrival/HPA_tasks_creation.py --allow-downloads True
          python scripts/tasks_retrival/humantfs_task_creation.py --allow-downloads True
          python scripts/tasks_retrival/Reactome_tasks_creation.py --use-local-files False

    - name: Test with pytest
      run: |
         python -m pytest -v --durations=40 --cov=gene_benchmark--cov-fail-under=70 gene_benchmark