Contributing

Development Setup

1. Fork and clone the repository
2. Install backend: cd back-end && pip install -r requirements.txt
3. Install frontend: cd UI/DesktopPIPA && yarn install
4. Run backend: flask run --host 0.0.0.0 --port 5000
5. Run frontend: npx quasar dev

Running Tests

cd back-end
pip install pytest
python -m pytest tests/ -v

Project Structure

Pipa/
  back-end/
    app.py                  # Flask entry point
    blueprints/
      api.py                # REST API endpoints
      view.py               # Legacy HTML routes
    extensions/
      services.py           # Pipeline orchestrator
      services1/            # Individual service modules
        Service_Trimage.py  # Trimming
        Service_Assembly.py # Assembly
        Service_Predict.py  # Annotation tools
        Service_Report.py   # Report generation
    tests/                  # API tests
  UI/DesktopPIPA/
    src/
      components/tabs/      # Vue components (About, Software, Results)
      store/pipa/           # Vuex state management
      boot/axios.js         # HTTP client setup
    src-electron/           # Electron main process
  docs/                     # This documentation
  environment.yml           # Conda environment
  Dockerfile               # Container build
  docker-compose.yml       # Container orchestration

Adding a New Annotation Tool

1. Add the tool command to Service_Predict.py with a self._should_run("toolkey") guard
2. Add the tool key to ALL_TOOLS list in PredictService
3. Add a card for it in Software.vue defaultAnnotationTools array
4. Add the tool to environment.yml (Bioconda package name)
5. Document it in docs/user-guide/tools.md