Contributing to tsbrowse

Contributing to tsbrowse#

All contributions, bug reports, documentation improvements and ideas are welcome. If you think there is anything missing, please open an issue or pull request on Github.

Requirements#

The packages needed for development are specified as optional dependencies in the pyproject.toml file. Install these using:

python3 -m venv env
source env/bin/activate
python3 -m pip install -e ".[dev]"

Alternatively, you can use uv for faster dependency management:

uv venv
source .venv/bin/activate
uv pip install -e ".[dev]"

Github workflow#

  1. Fork the tsbrowse github repository at https://github.com/tskit-dev/tsbrowse/ to create your own copy of the project.

  2. Clone a local copy:

$ git clone https://github.com/your-user-name/tsbrowse.git
$ cd tsbrowse
$ git remote add upstream https://github.com/tskit-dev/tsbrowse.git

This creates the directory tsbrowse and connects your repository to the upstream (main project) tsbrowse repository. 3. Install pre-commit hooks. These will be executed automatically on every commit, to ensure the code meets development requirements.

$ pre-commit install

  1. Run the test suite and make sure tests pass:

$ python3 -m pytest

  1. Create a topic branch and add commits:

$ git fetch upstream
$ git checkout upstream/main
$ git checkout -b topic_branch_name

  1. When you are ready to share your contribution, push changes to your fork:

$ git push origin branch-name

  1. Create a pull request on GitHub.

Documentation#

Tsbrowse documentation is written in markdown. These files are contained in the docs directory. To build the documentation, run make in the docs directory.

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