rl-insulin-pump

Creating RL Agents for simglucose/PadovaT1D simulator.

Getting Started

Setup

1. Set up virtual environment

   python -m venv env
   source env/bin/activate  # On Windows: env\Scripts\activate

2. Install dependencies

   pip install -r requirements.txt

3. Install simglucose in editable mode:

   cd simglucose
   pip install -e . --config-settings editable_mode=compat
   cd ..

   Installing simglucose in editable mode within the project directory allows for direct imports and potential modifications to the source code. This gives us much greater control for customization and enables effective debugging.

4. Run scripts from root dir

   python -m src.main --cfg=<path to config file>

Run Tests

We use pytest for unit testing. Tests should be stored in the tests directory and should test basic functionality of any new helper functions added to the codebase. To run all tests:

cd tests
pytest -v --color=yes

Lint and format

We use pre-commit with ruff to check formatting and linting before commits are pushed. You can check this before making commits to the repository with the following:

pre-commit run --all-files

Project Directories

.
├── .github/                          # GitHub workflows for CI/CD tests
├── configs/                          # Training and evaluation configuration YAMLs
├── results/                          # Output from experiments: plots, logs, metrics, etc.
├── scripts/                          # Bash scripts for launching jobs, one-off experiments, etc.
│   ├── experiments/                  # Scripts and setups for running controlled experiments
│   └── watgpu/                       # WatGPU bash scripts
├── simglucose/                       # Custom fork of simglucose package
├── src/
│   ├── agents/                       # Creating, loading, and managing agents
│   ├── environments/				  # Custom Gym environments and reward functions
│   ├── training/                     # Orchestration of training, prediction, and evaluation
│   ├── utils/                        # Generic helper utilities
│   ├── __init__.py
│   └── main.py                       # Entry point for training/evaluation
├── tests/                            # Unit and integration tests
├── .gitignore
├── .pre-commit-config.yaml           # Pre-commit checks configuration
├── README.md
├── requirements.txt                  # Python package dependencies
└── setup.py                          # Install script to register `src` as a module

Managing the simglucose Fork

This repository includes simglucose as a git subtree. If you need to update or push changes to the simglucose fork, use the following commands in the root directory.

Pulling Updates from the Subtree

If the upstream simglucose repository has updates, you can pull them into the subtree:

git subtree pull --prefix=simglucose https://github.com/Blood-Glucose-Control/simglucose.git master --squash

Pushing Changes to the Subtree

To push changes made to simglucose back to the forked repository:

git subtree push --prefix=simglucose https://github.com/Blood-Glucose-Control/simglucose.git master