python-app.yml

name: Python package

on: [push, pull_request]

jobs:
  test:
    runs-on: macos-latest

    steps:
      - name: Checkout repository
        uses: actions/checkout@v2

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: "3.12.3" # Specify the version of Python to use

      - name: Cache conda
        uses: actions/cache@v2
        with:
          path: ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{ hashFiles('environment.yml') }}
          restore-keys: |
            ${{ runner.os }}-conda-

      - name: Install Miniconda
        shell: bash
        run: |
          wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
          bash miniconda.sh -b -p $HOME/miniconda
          source "$HOME/miniconda/etc/profile.d/conda.sh"
          conda config --set always_yes yes --set changeps1 no
          conda config --add pkgs_dirs ~/conda_pkgs_dir
          conda update -q conda

      - name: Add conda channels
        shell: bash
        run: |
          source "$HOME/miniconda/etc/profile.d/conda.sh"
          conda config --add channels conda-forge

      - name: Create and activate conda environment
        shell: bash
        run: |
          source "$HOME/miniconda/etc/profile.d/conda.sh"
          conda env create -f environment.yml
          conda activate protein-prediction
        env:
          CONDA_PKGS_DIRS: ~/conda_pkgs_dir

      - name: Check Python version
        shell: bash
        run: |
          source "$HOME/miniconda/etc/profile.d/conda.sh"
          conda activate protein-prediction
          python --version

      - name: Run tests
        shell: bash
        run: |
          source "$HOME/miniconda/etc/profile.d/conda.sh"
          conda activate protein-prediction
          pytest