python-app.yml

name: Python application with conda

on:
  push:
    branches: [ "main" ]
  pull_request:
    branches: [ "main" ]
  schedule:
    # min hours day(month) month day(week)
    - cron: "0 0 1 */3 *"  # quarterly

jobs:
  build:
    runs-on: ubuntu-latest
    container:
      image: continuumio/miniconda3  # Lightweight image with Miniconda

    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Cache Conda packages
        uses: actions/cache@v4
        id: conda-cache
        with:
          path: /home/runner/conda_pkgs_dir
          key: conda-${{ runner.os }}-${{ hashFiles('environment.yml') }}

      - name: Install Mamba for faster Conda operations    # fix for: [Errno 28] No space left on device
        run: |
          conda install -n base -c conda-forge mamba -y

      - name: Set up Conda environment using Mamba
        run: |
          mkdir -p /home/runner/conda_pkgs_dir  # Create a persistent cache location
          echo "CONDA_PKGS_DIRS=/home/runner/conda_pkgs_dir" >> $GITHUB_ENV
          mamba create -n selectzyme --file environment.yml -y
          source activate selectzyme
          python --version
          pip list
  
      - name: Install additional test dependencies
        run: |
          conda activate selectzyme
          conda install -y pytest pytest-cov
          pip list

      - name: Run tests with pytest
        shell: bash -l {0}  # Ensures the Conda environment is correctly sourced
        run: |
          conda activate selectzyme
          python -m pytest --cov=selectzyme/ -v tests/test_* -k 'not select and not gen_embedding and not TestML and not cuml and not cuda and not TestQdrantDB'  # exclude tests requiring GPU/cuda