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DC-analysis / dclab

Python library for the post-measurement analysis of real-time deformability cytometry (RT-DC) data sets
https://dclab.readthedocs.io
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|dclab|

|PyPI Version| |Build Status| |Coverage Status| |Docs Status|

This is a Python library for the post-measurement analysis of real-time deformability cytometry (RT-DC) datasets; an essential part of Shape-Out <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut2>__.

Documentation

The documentation, including the code reference and examples, is available at dclab.readthedocs.io <https://dclab.readthedocs.io/en/stable/>__.

Installation

::

pip install dclab[all]

For more options, please check out the documentation <https://dclab.readthedocs.io/en/latest/sec_getting_started.html#installation>__.

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 <https://github.com/DC-analysis/dclab/blob/master/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 <https://www.sphinx-doc.org>`_. 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

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.

.. |dclab| image:: https://raw.github.com/DC-analysis/dclab/master/docs/logo/dclab.png
.. |PyPI Version| image:: https://img.shields.io/pypi/v/dclab.svg
   :target: https://pypi.python.org/pypi/dclab
.. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/DC-analysis/dclab/check.yml
   :target: https://github.com/DC-analysis/dclab/actions?query=workflow%3AChecks
.. |Coverage Status| image:: https://img.shields.io/codecov/c/github/DC-analysis/dclab/master.svg
   :target: https://codecov.io/gh/DC-analysis/dclab
.. |Docs Status| image:: https://readthedocs.org/projects/dclab/badge/?version=latest
   :target: https://readthedocs.org/projects/dclab/builds/