lilio developer documentation

If you’re looking for user documentation, go here.

Development install

For a full development enviroment run the commands below.

Note that this is optional: if you already have hatch in your main environment, this setup is not needed, as you can use the hatch environments to run all commands.

# Create a virtual environment, e.g. with
python3 -m venv env_name

# activate virtual environment
source env_name/bin/activate
# Or on windows:
#  env_name/Scripts/Activate.ps1

# make sure to have a recent version of pip and hatch
python3 -m pip install --upgrade pip hatch

# (from the project root directory)
# install lilio as an editable package
python3 -m pip install --no-cache-dir --editable .
# install development dependencies
python3 -m pip install --no-cache-dir --editable .[dev]

Afterwards check that the install directory is present in the PATH environment variable.

Running the tests

Lilio uses pytest for unit testing. Running tests has been configured using hatch, and can be started by running:

hatch run test

In addition to just running the tests to see if they pass, they can be used for coverage statistics, i.e. to determine how much of the package’s code is actually executed during tests. Inside the package directory, run:

hatch run coverage

This runs tests and prints the results to the command line, as well as storing the result in a coverage.xml file (for analysis by, e.g. SonarCloud).

Running linters locally

For linting and code style we use ruff. We additionally use mypy to check the type hints. All tools can simply be run by doing:

hatch run lint

To comply with formatting you can run:

hatch run format

Generating the documentation

To generate the documentation, simply run the following command. This will also test the documentation code snippets. Note that you might need to install pandoc to be able to generate the documentation.

hatch run docs:build

The documentation will be in docs/_build/html.

You can also make use of the sphinx-autobuild plugin to show a live preview of the documentation, which can make developing the documentation a bit easier.


Bumping the version across all files is done with bumpversion, e.g.

bumpversion major
bumpversion minor
bumpversion patch

Making a release

This section describes how to make a release in 3 parts: preparation, release and validation.


  1. Update the file

  2. Verify that the information in CITATION.cff is correct

  3. Make sure the version has been updated.

  4. Run the unit tests with hatch run test

Making the GitHub release

Make a release and tag on This will:

  • trigger Zenodo into making a snapshot of your repository and sticking a DOI on it.

  • start a GitHub action that builds and uploads the new version to PyPI.

    • Which should trigger conda-forge to update the package as well.


After making the release, you should check that:

  1. The Zenodo page is updated

  2. The publishing action ran successfully, and that pip install lilio installs the new version.

  3. The conda-forge package is updated, and can be installed using conda.