Topological Data Analysis for Python🐍

Related tags

Sklearn Utilities topology mapper topological-data-analysis tda homology scikit-tda tda-python tda-libraries
Overview

DOI Pypi Downloads

Scikit-TDA is a home for Topological Data Analysis Python libraries intended for non-topologists.

This project aims to provide a curated library of TDA Python tools that are widely usable and easily approachable. It is structured so that each package can stand alone or be used as part of the scikit-tda bundle.

Documentation

For complete documentation please checkout scikit-tda.org.

Contact

If you would like to contribute, please reach out to us on github, twitter or on Slack.

Setup

To install all these libraries

    pip install scikit-tda

Citations

If you would like to cite Scikit-TDA, please use the following citation/bibtex

Saul, Nathaniel and Tralie, Chris. (2019). Scikit-TDA: Topological Data Analysis for Python. Zenodo. http://doi.org/10.5281/zenodo.2533369

@misc{scikittda2019,
  author       = {Nathaniel Saul, Chris Tralie},
  title        = {Scikit-TDA: Topological Data Analysis for Python},
  year         = 2019,
  doi          = {10.5281/zenodo.2533369},
  url          = {https://doi.org/10.5281/zenodo.2533369}
}

License

This package is licensed with the MIT license.

Contributing

Contributions are more than welcome! There are lots of opportunities for potential projects, so please get in touch if you would like to help out. Everything from code to notebooks to examples and documentation are all equally valuable so please don't feel you can't contribute. To contribute please fork the project make your changes and submit a pull request. We will do our best to work through any issues with you and get your code merged into the main branch.

Comments
  • error installing scikit-tda/ripser

    error installing scikit-tda/ripser

    Hi

    First of all, thanks for building this application. I've seen previous issues been posted before that were similar but I really wasn't able to figure it out. I get the following error trying to install scikit-tda:

    `(base) MacBook-Pro-van-Tom:~ Tom$ pip3 --version
pip 21.0.1 from /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip (python 3.9)
(base) MacBook-Pro-van-Tom:~ Tom$ pip3 install scikit-tda
Collecting scikit-tda
  Using cached scikit_tda-0.1.0-py3-none-any.whl (2.9 kB)
Collecting cechmate
  Using cached cechmate-0.1.0-py3-none-any.whl (23 kB)
Collecting phat
  Using cached phat-1.5.0a.tar.gz (4.7 MB)
WARNING: Discarding https://files.pythonhosted.org/packages/43/82/c14de81dc2953a71a060f72f2bc34c41996307956b162751f2a47e2c78f7/phat-1.5.0a.tar.gz#sha256=51e7fe5e05adf5c7e0895765572fff05b979731234251f13011610d71d4980ab (from https://pypi.org/simple/phat/). Requested phat from https://files.pythonhosted.org/packages/43/82/c14de81dc2953a71a060f72f2bc34c41996307956b162751f2a47e2c78f7/phat-1.5.0a.tar.gz#sha256=51e7fe5e05adf5c7e0895765572fff05b979731234251f13011610d71d4980ab (from scikit-tda) has inconsistent version: filename has '1.5.0a0', but metadata has '1.5.0'
Collecting scikit-tda
  Using cached scikit_tda-0.0.3-py3-none-any.whl (2.6 kB)
Collecting ripser
  Using cached ripser-0.6.0.tar.gz (71 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting Cython
  Using cached Cython-0.29.22-py2.py3-none-any.whl (980 kB)
Collecting tadasets
  Using cached tadasets-0.0.4-py3-none-any.whl (7.1 kB)
Collecting persim
  Using cached persim-0.2.0-py3-none-any.whl (31 kB)
Collecting scikit-learn
  Using cached scikit_learn-0.24.1-cp39-cp39-macosx_10_13_x86_64.whl (7.3 MB)
Collecting numba
  Using cached numba-0.51.2.tar.gz (2.1 MB)
Collecting scipy
  Using cached scipy-1.6.1-cp39-cp39-macosx_10_9_x86_64.whl (30.9 MB)
Collecting kmapper
  Using cached kmapper-1.4.1-py3-none-any.whl (95 kB)
Collecting umap-learn
  Using cached umap_learn-0.5.1-py3-none-any.whl
Collecting matplotlib
  Using cached matplotlib-3.3.4-cp39-cp39-macosx_10_9_x86_64.whl (8.5 MB)
Collecting pillow
  Using cached Pillow-8.1.0-cp39-cp39-macosx_10_10_x86_64.whl (2.2 MB)
Collecting numpy
  Using cached numpy-1.20.1-cp39-cp39-macosx_10_9_x86_64.whl (16.1 MB)
Collecting Jinja2
  Using cached Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
Collecting MarkupSafe>=0.23
  Using cached MarkupSafe-1.1.1-cp39-cp39-macosx_10_9_x86_64.whl (16 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3
  Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting python-dateutil>=2.1
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting cycler>=0.10
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting kiwisolver>=1.0.1
  Using cached kiwisolver-1.3.1-cp39-cp39-macosx_10_9_x86_64.whl (61 kB)
Collecting six
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting llvmlite<0.35,>=0.34.0.dev0
  Using cached llvmlite-0.34.0.tar.gz (107 kB)
Requirement already satisfied: setuptools in /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from numba->scikit-tda) (49.2.1)
Collecting deprecated
  Using cached Deprecated-1.2.11-py2.py3-none-any.whl (9.1 kB)
Collecting joblib
  Using cached joblib-1.0.1-py3-none-any.whl (303 kB)
Collecting hopcroftkarp
  Using cached hopcroftkarp-1.2.5-py2.py3-none-any.whl
Collecting wrapt<2,>=1.10
  Using cached wrapt-1.12.1-py3-none-any.whl
Collecting threadpoolctl>=2.0.0
  Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB)
Collecting pynndescent>=0.5
  Using cached pynndescent-0.5.2-py3-none-any.whl
Using legacy 'setup.py install' for numba, since package 'wheel' is not installed.
Using legacy 'setup.py install' for llvmlite, since package 'wheel' is not installed.
Building wheels for collected packages: ripser
  Building wheel for ripser (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9 /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /var/folders/mf/t7pnn0d50j19hqjm70yjbbbw0000gn/T/tmpfheg2jtg
       cwd: /private/var/folders/mf/t7pnn0d50j19hqjm70yjbbbw0000gn/T/pip-install-ikgb1occ/ripser_b696215e91084205a9847d1f777061bc
  Complete output (16 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.9-universal2-3.9
  creating build/lib.macosx-10.9-universal2-3.9/ripser
  copying ripser/_version.py -> build/lib.macosx-10.9-universal2-3.9/ripser
  copying ripser/__init__.py -> build/lib.macosx-10.9-universal2-3.9/ripser
  copying ripser/ripser.py -> build/lib.macosx-10.9-universal2-3.9/ripser
  running build_ext
  building 'pyRipser' extension
  creating build/temp.macosx-10.9-universal2-3.9
  creating build/temp.macosx-10.9-universal2-3.9/ripser
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -DUSE_COEFFICIENTS=1 -DNDEBUG=1 -DASSEMBLE_REDUCTION_MATRIX=1 -I./ripser -I/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9 -I/private/var/folders/mf/t7pnn0d50j19hqjm70yjbbbw0000gn/T/pip-build-env-a0nbkw5b/overlay/lib/python3.9/site-packages/numpy/core/include -c ripser/pyRipser.cpp -o build/temp.macosx-10.9-universal2-3.9/ripser/pyRipser.o -Ofast -D_hypot=hypot -std=c++11 -mmacosx-version-min=10.9
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  error: command '/usr/bin/gcc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for ripser
Failed to build ripser
ERROR: Could not build wheels for ripser which use PEP 517 and cannot be installed directly
`

    Since I read the previous similar issues. I have tried to install previous versions of pip (19.0.0.1, 20.0) and different versions of python (3.6, 3.7, 3.8. 3.9). I have tried installing it on the root and in virtual environments (anaconda, pycharm). I have tried to disable pep517 with the following command python -m pip install --no-use-pep517 ripser

    I really don't know what to do at this point. I must say that I am pretty unfamiliar with git. Any help would be appreciated.

    KR

    opened by thjnmcdonald 4
  • error for windows installation

    error for windows installation

    how to install on windows? can you put it to conda forge then instalation will be easy like http://gudhi.gforge.inria.fr/ conda install -c conda-forge gudhi

    opened by Sandy4321 3
  • Most docs customization to an installable sphinx extension.

    Most docs customization to an installable sphinx extension.

    Code in docs/_static, docs/_templates, and docs/theme_settings.py should be packaged into a sphinx extension.

    This will make it easier to sync documentation configurations across all the scikit-tda packages.

    opened by sauln 2
  • Plotting the cocycles of dim.3, modifying the PlotCocycle2D code

    Plotting the cocycles of dim.3, modifying the PlotCocycle2D code

    Hello, I am able to apply the codes of the "Representative Cocycles" page on python successfully. However, I am more interested in having the cycles (cocycles) of dim.3 barcodes. Is there a possibility to help me in modifying the code that plots the cocycles. i.e. the function plotCocycle2D(D, X, cocycle, thresh) to accept a 3D point cloud and plot its cocycles of dim.3. I would highly appreciate it. I have tried but unfortunately, it did not work out for me. Many thanks in advance

    opened by NadaSaleh1991 0
  • A

    A "Getting Started" section of the documentation would be helpful.

    In addition to the promised tutorials for this software package, a short "Getting Started" section would help me understand how to use this software package.

    opened by galenseilis 1
  • 1-dimensional persistence diagram of image data

    1-dimensional persistence diagram of image data

    Hi,

    Is there a way to create 1-dimensional persistence diagram using sublevelset filtration or lower star filtration on image data? I think it is not possible to construct 1D PD with lower_star_img. Currently, I am able to construct 0D PD using lower_star_img, but I can't find a way to make 1D PDs. Any help would be greatly appreciated.

    Thank you.

    opened by AshleyChraya 2
  • help needed with installation error - Requested phat has different version

    help needed with installation error - Requested phat has different version

    Hi, when I downloaded scikit-tda, I got the error that "Requested phat has different version". May I know what I should do from here? The error message is as follows.

    pip install scikit-tda Collecting scikit-tda Downloading scikit_tda-0.1.0-py3-none-any.whl (2.9 kB) Requirement already satisfied: numpy in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (1.19.2) Requirement already satisfied: scikit-learn in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (0.23.2) Requirement already satisfied: Cython in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (0.29.21) Requirement already satisfied: scipy in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (1.6.0) Requirement already satisfied: pillow in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (8.1.0) Requirement already satisfied: matplotlib in ./opt/anaconda3/lib/python3.7/site-packages (from scikit-tda) (3.3.4) Collecting cechmate Downloading cechmate-0.1.0-py3-none-any.whl (23 kB) Collecting phat Downloading phat-1.5.0a.tar.gz (4.7 MB) |████████████████████████████████| 4.7 MB 2.6 MB/s ERROR: Requested phat from https://files.pythonhosted.org/packages/43/82/c14de81dc2953a71a060f72f2bc34c41996307956b162751f2a47e2c78f7/phat-1.5.0a.tar.gz#sha256=51e7fe5e05adf5c7e0895765572fff05b979731234251f13011610d71d4980ab (from scikit-tda) has different version in metadata: '1.5.0'

    opened by c-siu 12
  • Persistence diagram for a clique complex

    Persistence diagram for a clique complex

    Hi everybody,

    I have seen a ton of codes to compute a persistence diagram when the input data is a point cloud. Is there a way to compute the persistence diagram for a filtration of a clique complex if the input data is a weighted graph? It cannot be done with the Ripser library right? Any code would be very much appreciated.

    Thank you.

    opened by Nilsmiz 1
Releases(v1.0.0)
Owner
Scikit-TDA
Topological Data Analysis for the Python ecosystem.
Scikit-TDA
GitHub https://scikit-tda.org
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