dclab

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.

Intended Audience
- Science/Research
Operating System
- OS Independent
Programming Language
- Python :: 3
Topic
- Scientific/Engineering :: Visualization

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Release history Release notifications | RSS feed

2.18.0 yanked

Sep 11, 2024

Reason this release was yanked:

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This release

0.71.10

Jul 23, 2026

0.71.9

May 29, 2026

0.71.8

Apr 28, 2026

0.71.7

Apr 13, 2026

0.71.6

Apr 9, 2026

0.71.5

Apr 9, 2026

0.71.4

Apr 8, 2026

0.71.3

Mar 30, 2026

0.71.2

Mar 27, 2026

0.71.1

Mar 26, 2026

0.71.0

Mar 23, 2026

0.70.0

Mar 22, 2026

0.69.2

Mar 13, 2026

0.69.1

Mar 12, 2026

0.69.0

Mar 12, 2026

0.68.0

Feb 26, 2026

0.67.5

Feb 24, 2026

0.67.4

Feb 18, 2026

0.67.3

Jan 22, 2026

0.67.2

Nov 15, 2025

0.67.1

Nov 4, 2025

0.67.0

Aug 19, 2025

0.66.0

Jul 10, 2025

0.65.0

Jul 7, 2025

0.64.3

Jul 3, 2025

0.64.2

Jul 3, 2025

0.64.1

Jun 12, 2025

0.64.0

May 16, 2025

0.63.1

May 6, 2025

0.63.0

Apr 16, 2025

0.62.17

Apr 14, 2025

0.62.16

Mar 20, 2025

0.62.15

Feb 27, 2025

0.62.14

Feb 11, 2025

0.62.13

Feb 9, 2025

0.62.12

Feb 4, 2025

0.62.11

Jan 23, 2025

0.62.10

Jan 7, 2025

0.62.9

Jan 6, 2025

0.62.8

Jan 5, 2025

0.62.7

Dec 6, 2024

0.62.6

Oct 22, 2024

0.62.5

Oct 18, 2024

0.62.4

Oct 18, 2024

0.62.3

Oct 18, 2024

0.62.2

Oct 18, 2024

0.62.1

Oct 9, 2024

0.62.0

Oct 8, 2024

0.61.5

Oct 3, 2024

0.61.4

Sep 17, 2024

0.61.3

Sep 13, 2024

0.61.2 yanked

Sep 13, 2024

Reason this release was yanked:

empty environment variable caused TypeError

0.61.1

Sep 11, 2024

0.61.0

Sep 10, 2024

0.60.9

Jul 22, 2024

0.60.8

Jul 22, 2024

0.60.7

Jul 22, 2024

0.60.6

Jul 22, 2024

0.60.5

Jul 16, 2024

0.60.4

Jul 16, 2024

0.60.3

Jul 2, 2024

0.60.2

Jul 1, 2024

0.60.1

Jun 27, 2024

0.60.0

Jun 26, 2024

0.59.1

Jun 4, 2024

0.59.0

May 27, 2024

0.58.7

May 16, 2024

0.58.6

Apr 24, 2024

0.58.5

Apr 23, 2024

0.58.4

Apr 20, 2024

0.58.3

Apr 18, 2024

0.58.2

Apr 4, 2024

0.58.1

Apr 3, 2024

0.58.0

Apr 2, 2024

0.57.7

Feb 29, 2024

0.57.6

Feb 28, 2024

0.57.5

Feb 27, 2024

0.57.4

Feb 19, 2024

0.57.3

Jan 31, 2024

0.57.2

Jan 31, 2024

0.57.1

Jan 12, 2024

0.57.0

Jan 5, 2024

0.56.3

Jan 1, 2024

0.56.2

Jan 1, 2024

0.56.1

Jan 1, 2024

0.56.0

Dec 30, 2023

0.55.7

Nov 29, 2023

0.55.6

Nov 16, 2023

0.55.5

Nov 8, 2023

0.55.4

Nov 4, 2023

0.55.3

Nov 4, 2023

0.55.2

Nov 3, 2023

0.55.1

Nov 3, 2023

0.55.0

Nov 3, 2023

0.54.2

Oct 23, 2023

0.54.1

Oct 23, 2023

0.54.0

Oct 23, 2023

0.53.3

Oct 18, 2023

0.53.2 yanked

Oct 18, 2023

Reason this release was yanked:

invalid basin availability check

0.53.1

Oct 9, 2023

0.53.0

Oct 6, 2023

0.52.6

Oct 4, 2023

0.52.5

Oct 4, 2023

0.52.3

Oct 4, 2023

0.52.1

Oct 4, 2023

0.52.0

Aug 1, 2023

0.51.4

Jul 27, 2023

0.51.3

Jul 27, 2023

0.51.2

Jul 21, 2023

0.51.1

Jun 30, 2023

0.51.0

Jun 13, 2023

0.50.4

May 15, 2023

0.50.3

May 8, 2023

0.50.2

May 3, 2023

0.50.1

May 3, 2023

0.50.0

May 3, 2023

0.49.1

Apr 26, 2023

0.49.0

Apr 20, 2023

0.48.8

Apr 9, 2023

0.48.7

Apr 2, 2023

0.48.6

Apr 2, 2023

0.48.5

Apr 2, 2023

0.48.4

Mar 16, 2023

0.48.3 yanked

Mar 16, 2023

Reason this release was yanked:

Introduced wrong caching in HDF5 format

0.48.2

Mar 15, 2023

0.48.1

Feb 8, 2023

0.48.0 yanked

Feb 8, 2023

Reason this release was yanked:

Invalid caching with new Young's modulus viscosity model

0.47.8

Feb 1, 2023

0.47.7

Feb 1, 2023

0.47.6

Jan 30, 2023

0.47.5

Jan 23, 2023

0.47.4

Jan 10, 2023

0.47.3

Jan 4, 2023

0.47.2

Dec 6, 2022

0.47.1

Dec 2, 2022

0.47.0

Nov 25, 2022

0.46.6

Nov 23, 2022

0.46.5

Nov 16, 2022

0.46.4

Nov 11, 2022

0.46.3

Nov 7, 2022

0.46.2

Oct 19, 2022

0.46.1

Oct 14, 2022

0.46.0

Oct 6, 2022

0.45.0

Aug 25, 2022

0.44.0

Aug 16, 2022

0.43.1

Jul 18, 2022

0.43.0

Jun 21, 2022

0.42.3

Jun 17, 2022

0.42.2

May 18, 2022

0.42.1

May 18, 2022

0.42.0

May 3, 2022

0.41.0

Apr 20, 2022

0.40.0

Mar 14, 2022

0.39.18

Mar 14, 2022

0.39.17

Mar 1, 2022

0.39.16

Feb 28, 2022

0.39.15

Feb 10, 2022

0.39.14

Jan 31, 2022

0.39.13

Jan 27, 2022

0.39.12

Jan 27, 2022

0.39.11

Jan 25, 2022

0.39.10

Jan 25, 2022

0.39.9

Jan 12, 2022

0.39.8

Jan 11, 2022

0.39.7

Dec 19, 2021

0.39.6

Dec 16, 2021

0.39.5

Dec 16, 2021

0.39.4

Dec 16, 2021

0.39.3

Dec 10, 2021

0.39.2

Nov 26, 2021

0.39.1

Nov 25, 2021

0.39.0

Nov 24, 2021

0.38.2

Nov 9, 2021

0.38.1

Nov 9, 2021

0.38.0

Nov 8, 2021

0.37.3

Oct 30, 2021

0.37.2

Oct 27, 2021

0.37.1

Oct 25, 2021

0.37.0

Oct 24, 2021

0.36.1

Oct 19, 2021

0.36.0

Oct 18, 2021

0.35.8

Oct 14, 2021

0.35.7

Sep 15, 2021

0.35.6

Sep 8, 2021

0.35.5

Sep 7, 2021

0.35.4

Aug 24, 2021

0.35.3

Aug 24, 2021

0.35.2

Aug 24, 2021

0.35.1

Aug 24, 2021

0.35.0

Aug 23, 2021

0.34.6

Aug 22, 2021

0.34.5

Jul 8, 2021

0.34.4

Jul 3, 2021

0.34.3

Jul 1, 2021

0.34.2

Jun 18, 2021

0.34.1

Jun 4, 2021

0.34.0

May 20, 2021

0.33.3

Apr 8, 2021

0.33.2

Mar 29, 2021

0.33.1

Mar 19, 2021

0.33.0

Mar 18, 2021

0.32.5

Mar 7, 2021

0.32.4

Feb 17, 2021

0.32.3

Feb 1, 2021

0.32.2

Jan 29, 2021

0.32.1

Jan 28, 2021

0.32.0

Jan 18, 2021

0.31.4

Jan 4, 2021

0.31.3

Jan 4, 2021

0.31.2

Dec 3, 2020

0.31.1

Nov 13, 2020

0.31.0

Nov 11, 2020

0.30.1

Nov 4, 2020

0.30.0

Nov 4, 2020

0.29.1

Oct 8, 2020

0.29.0

Oct 8, 2020

0.28.0

Sep 18, 2020

0.27.11

Aug 4, 2020

0.27.10

Jul 27, 2020

0.27.9

Jul 27, 2020

0.27.8

Jul 23, 2020

0.27.7

Jul 16, 2020

0.27.6

Jun 8, 2020

0.27.5

May 25, 2020

0.27.4

May 25, 2020

0.27.3

May 25, 2020

0.27.2

May 25, 2020

0.27.1

May 25, 2020

0.27.0

May 25, 2020

0.26.2

May 19, 2020

0.26.1

May 12, 2020

0.26.0

May 5, 2020

0.25.0

Apr 27, 2020

0.24.8

Apr 26, 2020

0.24.7

Apr 23, 2020

0.24.6

Apr 22, 2020

0.24.5

Apr 22, 2020

0.24.4

Apr 22, 2020

0.24.2

Apr 21, 2020

0.24.1

Apr 21, 2020

0.24.0

Apr 20, 2020

0.23.0

Apr 6, 2020

0.22.7

Mar 27, 2020

0.22.6

Mar 24, 2020

0.22.5

Mar 23, 2020

0.22.4

Mar 22, 2020

0.22.3

Mar 18, 2020

0.22.2

Mar 16, 2020

0.22.1

Mar 9, 2020

0.22.0

Mar 5, 2020

0.21.2

Feb 13, 2020

0.21.1

Feb 13, 2020

0.21.0

Feb 13, 2020

0.20.8

Feb 12, 2020

0.20.7

Feb 10, 2020

0.20.6

Feb 9, 2020

0.20.5

Feb 9, 2020

0.20.4

Feb 7, 2020

0.20.3

Jan 8, 2020

0.20.2

Jan 8, 2020

0.20.1

Dec 20, 2019

0.20.0

Dec 13, 2019

0.19.1

Dec 6, 2019

0.19.0

Dec 5, 2019

0.18.2 yanked

Sep 13, 2024

Reason this release was yanked:

invalid tag

0.18.0

Nov 13, 2019

0.17.1

Nov 6, 2019

0.17.0

Nov 6, 2019

0.16.1

Nov 4, 2019

0.16.0

Oct 25, 2019

0.15.0

Oct 21, 2019

0.14.8

Oct 8, 2019

0.14.7

Sep 4, 2019

0.14.6

Aug 17, 2019

0.14.5

Aug 13, 2019

0.14.4

Aug 12, 2019

0.14.3

Aug 7, 2019

0.14.2

Aug 1, 2019

0.14.1

Aug 1, 2019

0.14.0

Jul 31, 2019

0.13.0

Jul 30, 2019

0.12.0

Jul 12, 2019

0.11.1

Jun 28, 2019

0.11.0

Jun 20, 2019

0.10.5

May 23, 2019

0.10.4

May 23, 2019

0.10.3

May 13, 2019

0.10.2

May 13, 2019

0.10.1

Apr 11, 2019

0.10.0

Apr 10, 2019

0.9.1

Feb 26, 2019

0.9.0

Jan 15, 2019

0.8.0

Nov 20, 2018

0.7.0

Oct 11, 2018

0.6.3

Aug 18, 2018

0.6.2

Jul 21, 2018

0.6.1

Jul 21, 2018

0.6.0

Jul 20, 2018

0.5.2

Jun 8, 2018

0.5.1

May 18, 2018

0.5.0

May 15, 2018

0.4.0

Apr 17, 2018

0.3.3

Mar 27, 2018

0.3.2

Feb 23, 2018

0.3.1

Dec 30, 2017

0.3.0

Nov 18, 2017

0.2.9

Oct 13, 2017

0.2.8

Oct 12, 2017

0.2.7

Sep 8, 2017

0.2.6

Jul 31, 2017

0.2.5

Jul 11, 2017

0.2.4

Jun 22, 2017

0.2.3

Apr 5, 2017

0.2.2

Mar 14, 2017

0.2.1

Feb 13, 2017

0.2.0

Dec 16, 2016

0.1.8

Sep 6, 2016

0.1.7

Jun 7, 2016

0.1.6

Apr 28, 2016

0.1.5

Nov 24, 2015

0.1.4

Nov 13, 2015

0.1.3

Nov 12, 2015

0.1.2

Sep 7, 2015

0.1.1

Jun 14, 2015

0.1.0

Jun 13, 2015

dclab 0.71.10

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PEP8

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2 maintainers

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