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MDAnalysis / membrane-curvature

MDAnalysis tool to calculate membrane curvature.
https://membrane-curvature.readthedocs.io/
GNU General Public License v3.0
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Fixed plots in documentation pages (transposed arrays). #89

Closed ojeda-e closed 1 year ago

ojeda-e commented 2 years ago

Description

This PR fixes #88.

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Status

codecov[bot] commented 2 years ago

Codecov Report

Merging #89 (84733c4) into main (ab0d652) will not change coverage. The diff coverage is n/a.

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ojeda-e commented 1 year ago

I added a warning in the visualization.rst page and the two tutorials. All plots included in these files were updated. NGL widgets are functional and working as expected.

To clarify why I ran this tutorial with MDAnalysis 2.1.0 and Python 3.7: I find an error when building docs with in Python 3.8+. I am working with v4.3.2 and higher. The error reads as 

Notebook error:
JSONDecodeError in cphtml/doctrees/nbsphinx/source/pages/Curvature_membrane_protein_nopr_all_atom.ipynb:
Expecting value: line 1 column 1 (char 0)
make: *** [html] Error 2

I tried to fix it but honestly, I couldn't find a way to build docs with Python 3.8+ and MDA 2.2.0+. I need to modernize some lines in Sphinx but that will be a separate issue and probably I will end up moving notebooks to pages with iPython.

@orbeckst would you please help me to review PR? Hopefully, I didn't miss anything. Thanks!