main.yml

name: CI Pipeline

on: [push]

jobs:
  build:
  
    runs-on: ubuntu-latest
    timeout-minutes: 60 
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2

      - name: setup python
        uses: actions/setup-python@v2
        with:
          python-version: 3.11 #install the python needed
      - name: Install dependencies
        run: |
            python -m pip install --upgrade pip
            pip install -r requirements-dev.txt
            pip install .
      # First download before tests as they make use of the downloaded files 
      - name: Download all files
        run: |
          python ci/download_all.py
      - name: Execute unittests
        run: |
          pytest ci/
      - name: Execute scGPT
        run: |
          python examples/run_scgpt.py
      - name: Execute Geneformer
        run: |
          python examples/run_geneformer.py
      - name: Execute UCE
        run: |
          python examples/run_uce.py