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Library for real-time deformability cytometry (RT-DC)

Project description

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This is a Python library for the post-measurement analysis of real-time deformability cytometry (RT-DC) datasets; an essential part of Shape-Out.


The documentation, including the code reference and examples, is available at


pip install dclab[all]

For more options, please check out the documentation.

Information for developers


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.


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


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


We use flake8 to enforce coding style:

pip install flake8
flake8 --exclude dclab
flake8 docs
flake8 examples
flake8 tests

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.

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