Contributing to rtflite

Developer workflow

Setup

First off, install uv. rtflite uses uv to manage the Python package development environment.

If you have trouble installing the exact Python version pinned in the project, run

uv self update

to update your uv installation.

Branching

Clone the repository (if you have no direct access, replace the address with your forked repository address):

git clone https://github.com/pharmaverse/rtflite.git

Create a dedicated branch:

cd rtflite
git checkout -b my-branch

Dependencies

Restore the environment using uv sync. This will restore the exact versions of Python and dependency packages under the project's .venv/ directory:

uv sync --all-extras

Development

Open the project in VS Code:

code rtflite

Make changes to the codebase.

We use pytest for unit testing. To run tests and get an HTML preview of code coverage, open the VS Code terminal:

pytest
pytest tests/specific_test.py
pytest --cov=rtflite --cov-report=html:docs/coverage/

source .venv/bin/activate

Documentation

To preview the Zensical website locally:

zensical serve

To build the Zensical website locally into site/, run:

zensical build --clean

rtflite renders vignette-like articles under docs/articlesusing markdown-exec. This allows Zensical to render Python code chunks and their outputs when building the site. Check the markdown-exec documentation for possible code chunk options.

If you made changes to the .md files in the root directory, make sure to synchronize them to the Zensical website:

sh docs/scripts/sync.sh

Formatting

Use isort and ruff to sort imports and format Python code:

isort .
ruff format

Pull request

Add, commit, and push to remote, then send a pull request:

git add -A
git commit -m "Your commit message"
git push origin my-branch

Maintainer workflow

Updates

Update local uv version:

uv self update

Update uv.lock file regularly:

uv lock --upgrade
uv sync --all-extras

Python version

Pin a newer Python version in .python-version when appropriate:

uv python pin x.y.z

The latest Python release versions are often promptly supported by uv.

Publishing

Publish on PyPI (maintainer token required):

uv build
uv publish