This is a Python library for the post-measurement analysis of real-time deformability cytometry (RT-DC) datasets; an essential part of the DC Cosmos ( DCscope, DCOR, DCOR-Aid, DCTag, DCKit, ).

Documentation

The documentation, including the code reference and examples, is available at dclab.readthedocs.io.

Installation

pip install dclab[all]

For more options, please check out the documentation.

Information for developers

Contributing

The main branch for developing dclab is master. If you want to make small changes like one-liners, documentation, or default values in the configuration, you may work on the master branch. If you want to change more, please (fork dclab and) create a separate branch, e.g. my_new_feature_dev, and create a pull-request once you are done making your changes. Please make sure to edit the Changelog.

Very important: Please always try to use

git pull --rebase

instead of:

git pull

to prevent non-linearities in the commit history.

Tests

dclab is tested using pytest. If you have the time, please write test methods for your code and put them in the tests directory. To run the tests, install pytest and run:

pytest tests

Docs

The docs are built with sphinx. Please make sure they compile when you change them (this also includes function doc strings):

cd docs
pip install -r requirements.txt
sphinx-build . _build  # open "index.html" in the "_build" directory

PEP8

We use flake8 to enforce coding style:

pip install flake8
flake8 --exclude _version.py dclab
flake8 docs
flake8 examples
flake8 tests

Type Hinting

For type hinting and docstring styling, try to keep the Code Reference readable in the documentation website. If in doubt just ask, or look at the examples in the codebase.

• Simple type combintions such as float or str | pathlib.Path should be included as type hints, but do not need to be included in the docstring parameter description.
• More involved type hints can have extra information in the docstring. For example for numpy arrays, npt.NDArray[np.bool] doesn't render in a readable way in the Code Reference, and doesn't include shape. Therefore, you can also keep the docstring parameter description with the shape and dtype information e.g., binary ndarray of shape (M, N).

Incrementing version

Dclab gets its version from the latest git tag. If you think that a new version should be published, create a tag on the master branch (if you have the necessary permissions to do so):

git tag -a "0.1.3"
git push --tags origin

Appveyor and GitHub Actions will then automatically build source package and wheels and publish them on PyPI.