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

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

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.

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

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.

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.

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'

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.