Docs/fix errors - Githubissues

giotto-ai / giotto-tda

A high-performance topological machine learning toolbox in Python

https://giotto-ai.github.io/gtda-docs

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Docs/fix errors #488

Closed wreise closed 4 years ago

wreise commented 4 years ago

Reference issues/PRs

Types of changes

[x] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Description Fixes biblio and rst-references problems encountered when compiling docs. Fixes #408.

To do:

add entry for persistence_images,
integrate all the notebooks,

Screenshots (if appropriate)

Any other comments?

Checklist

[x] I have read the guidelines for contributing.
[x] My code follows the code style of this project. I used flake8 to check my Python changes.
[x] My change requires a change to the documentation.
[x] I have updated the documentation accordingly.
[ ] I have added tests to cover my changes.
[x] All new and existing tests passed. I used pytest to check this on Python tests.

ulupo commented 4 years ago

@wreise please, if you have time, could you take this opportunity to look for a fix for #408?

ulupo commented 4 years ago

@wreise I noticed the following concerning jupyter notebooks: in the classifying shapes and persistence homology of graphs notebooks, a gif is linked by means of the full URL https://raw.githubusercontent.com/giotto-ai/giotto-tda/master/examples/images/vietoris_rips_point_cloud.gif. This does not seem to display in GitHub (though URLs sending to Medium did in the past!). On the other hand, in #458 @lewtun uses the relative path images/time-delay-embedding.gif and this displays nicely in GitHub.

Ultimately, the final approach must be such that these GIFs are displayed in the API reference pages, but it would be a bonus if we can also display them in GitHub.

wreise commented 4 years ago

@wreise please, if you have time, could you take this opportunity to look for a fix for #408?

I don't know what helped, but, locally, i do not face the same issue anymore.

@wreise I noticed the following concerning jupyter notebooks: in the classifying shapes and persistence homology of graphs notebooks, a gif is linked by means of the full URL https://raw.githubusercontent.com/giotto-ai/giotto-tda/master/examples/images/vietoris_rips_point_cloud.gif. This does not seem to display in GitHub (though URLs sending to Medium did in the past!). On the other hand, in #458 @lewtun uses the relative path images/time-delay-embedding.gif and this displays nicely in GitHub.

I changed the urls, let's see if it works. On the other hand, i had to name the messages explicitly.

ulupo commented 4 years ago

Thanks @wreise!

On the other hand, i had to name the messages explicitly.

This is not great because those messages are displayed (remember "SegmentLocal"?). Why did it seem necessary?

wreise commented 4 years ago

This is not great because those messages are displayed (remember "SegmentLocal"?). Why did it seem necessary?

How could i have missed that :facepalm:. If you leave them empty, they are referenced automatically image1, image2 etc. While it should have been fixed in a previous release of sphinx, my experience was that the counter k in imagek restarts at 0, in a new notebook cell, and, for example, every image1 (first image in a cell) becomes replaced with the last image1 from the notebook.

Indeed, it looks ugly. What would you suggest?

ulupo commented 4 years ago

What happens if you put a single whitespace? I.e. ![ ](URL) instead of [](URL)?

wreise commented 4 years ago

What happens if you put a single whitespace? I.e. ![ ](URL) instead of [](URL)?

it doesn't work, no (even with a variable number of spaces)