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]"
Install testing requirements
pip install -e ".[test]"
Run tests
python -m pytest tests
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.
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 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]"
# Change into docs directory
cd docs
# Run the build
sphinx-build source _build
Note that running documentation locally requires Pandoc to be installed as well - https://pandoc.org/installing.html.
You can view the documentation by opening docs/_build/index.html in your browser.
Executable code blocks can be added to rst files using .. jupyter-execute::. In order to get these code cells to run, assume that sphinx-build is being called from the docs/source directory and append to sys.path if necessary.