Following up on the discussion here, it would be good to document how to get reproducible results with UMAP.

I think we should consider changing random_state in the UMAP constructor to a seed (e.g. 42, like the new transform_seed default) so that UMAP is reproducible by default.

We should document that users can set `ran

Currently, the color palette is hardcoded in visuals.py:
https://github.com/MLWave/kepler-mapper/blob/0dfa7f736bd4218e8996888785b9d2adc63d5344/kmapper/visuals.py#L8-L15

and again in kmapper.js

https://github.com/MLWave/kepler-mapper/blob/0dfa7f736bd4218e8996888785b9d2adc63d5344/kmapper/static/kmapper.js#L25-L32

I'd like to see this

• duplication fixed and
• allow the palette

Test code:

from sklearn.datasets import load_digits
from gtda.homology import CubicalPersistence
from gtda.diagrams import PairwiseDistance

X, _ = load_digits(return_X_y=True) 
nb_samples = 100
CP = CubicalPersistence(homology_dimensions=(0, 1))
X_diag = CP.fit_transform(X[:nb_samples].reshape(nb_samples, 8, 8))
PD = PairwiseDistance(
    metric='bottleneck', metric_params={'delta'

Each project has a set of example scripts, it looks like Sphinx-gallery makes displaying rendering these examples look very nice.

In Representative Cocycles tutorial, this code block

result = ripser(x, coeff=17, do_cocycles=True)
diagrams = result['dgms']
cocycles = result['cocycles']
D = result['dm']

raises a KeyError: 'dm' since returned object doesn't have the key. The available keys are:

result.keys()
# ['dgms', 'cocycles', 'num_edges', 'dperm2all', 'idx_perm', 'r_cover']

It could be useful to have a way to clone a simplex tree, more efficiently than a loop on get_filtration doing inserts (we have a copy constructor in C++).

the python umap FAQ mentions a pure R version. you might submit a PR there to point to this pure Julia version too.

Magnus Botnan is running RIVET on OS X in dark mode and reports that the numbers in the GUI's text boxes (for example, for slope and offset) are shown as white; but that background for the boxes is also white, so that the numbers are invisible.

<img width="800" alt="Screen Shot 2020-01-19 at 12 22 43 PM" src="https://user-images.githubusercontent.com/12559620/72685271-76370e80-3ab6-11ea-8409-f1

Need to adjust documentation to reflect above fact. Potentially add parameter in permutation test function to allow user to pick their own distance function (takes persistent homology of two datasets as parameters, returns numeric).

Thanks to @kisungyou for bringing this to my attention.

So far we have to build docs locally and push them to gh-pages.

Wanted new behavior:

1. docs are updated automatically with each push of master

2. there remains a possobility to build docs locally in some gitignored folder for testing befor pushing

@rkwitt Research if u want to. i'll do the coding.