traccuracy

traccuracy provides a suite of benchmarking functions that can be used to evaluate tracking solutions against ground truth annotations. It includes the standard metrics that are calculated by the Cell Tracking Challenge.

Learn more in the documentation.

Installation

pip install traccuracy

Development

For local development, clone the repo and install in editable mode.

git clone https://github.com/Janelia-Trackathon-2023/traccuracy.git
cd traccuracy
pip install -e .[dev]

Testing

Install testing requirements

pip install -e .[test]

Run tests

python -m pytest tests

Style

We utilize pre-commit with black (formatting) and ruff (linting). If you would like to run pre-commit locally:

pip install -e .[dev]
pre-commit install

Alternatively pre-commit.ci, will run and commit changes on any open PRs.

Releases

In order to deploy a new version, tag the commit with a version number and push it to github. This will trigger a github action that will build and deploy to PyPI. (see the "deploy" step in workflows/ci.yml). The version number is determined automatically based on the tag.

git tag -a v0.1.0 -m v0.1.0
git push --follow-tags

Documentation

Documentation is built with Sphinx using sphinx-autoapi to automatically generate API documentation at build time. Docs are hosted on ReadTheDocs and build automatically after each push to main. Documentation can be built locally by running the following:

# Install docs requirements
pip install -e .[docs]
# Run the build
sphinx-build docs/source docs/_build

You can view the documentation by opening docs/_build/index.html in your browser.