Development Setup

Setup

Each project is a standalone PyTorch repository. Clone the one you want to work on and follow that repository's environment file. DeepLens requires Python 3.12.

Project	Repository	Editable install
DeepLens	vccimaging/DeepLens	pip install -e ".[dev]"
End2endImaging	vccimaging/End2endImaging	pip install -r requirements.txt

# Clone the project (DeepLens shown; substitute End2endImaging as needed)
git clone https://github.com/vccimaging/DeepLens.git
cd DeepLens

# Create and activate the conda environment
conda env create -f environment.yml -n deeplens_env
conda activate deeplens_env

# Install in editable mode with development extras
pip install -e ".[dev]"

Workflow

1. Fork the repository and clone your fork.
2. Create a branch from main: git checkout -b fix/short-description.
3. Make your changes, keeping commits focused and well-described.

4. Lint and format changed Python files with Ruff:

   ruff check --fix path/to/changed.py
   ruff format path/to/changed.py
   

   Before review, run the repository-wide gates: ruff check . and ruff format --check .. Do not apply --unsafe-fixes without reviewing each proposed change.

5. Add tests for new behaviour and run the suite:

   pytest test/ -v
   # with coverage (use the project's package name)
   pytest test/ --cov=deeplens --cov-report=term-missing      # DeepLens
   pytest test/ --cov=end2end_imaging --cov-report=term-missing  # End2endImaging
   

6. Open a pull request against main (see the PR guidelines).