Setting up MedModels#

MedModels leverages a combination of Python and Rust code. To contribute effectively, you’ll need to set up a development environment that supports both languages.

Requirements:

Using the Makefile:

MedModels utilizes a Makefile to manage development tasks. Here’s a breakdown of the available commands and their functionalities:

  • install: Sets up the virtual environment and installs the project in editable mode (meaning changes to the code are reflected without needing to reinstall).

  • install-dev: Similar to install, but additionally installs development dependencies needed for running tests, linting, code formatting and the documentation.

  • install-tests: Similar to install, but additionally installs development dependencies needed for running tests.

  • install-docs: Similar to install, but additionally installs development dependencies needed for building the docs.

  • build-dev: Builds the Rust crate and installs it as a python module (using maturin develop).

  • test: Runs both Python (using pytest) and Rust unit tests (using cargo test).

  • docs Builds the docs using sphinx.

  • docs-serve Builds docs and live serves them to the localhost.

  • docs-clean Removes all locally generated documentation files.

  • lint: Runs code linters for both Python (using ruff) and Rust (using cargo clippy).

  • format: Formats Python code (using ruff) and Rust code (using rustfmt).

  • clean: Removes the virtual environment, cache directories, build artifacts, and other temporary files.