PCA tutorial projection example fails with ValueError

[orbeckst]

Describe the bug
Example in PCA https://userguide.mdanalysis.org/dev/examples/analysis/reduced_dimensions/pca.html#Visualising-projections-into-a-reduced-dimensional-space fails.

Reporter: https://groups.google.com/g/mdnalysis-discussion/c/hM_p0JDY2hQ/m/CPlxf2MZCgAJ

To Reproduce
Steps to reproduce the behavior: Follow tutorial until

pc1 = pc.p_components[:, 0]
trans1 = transformed[:, 0]
projected = np.outer(trans1, pc1) + pc.mean

Expected behavior
projected is computed

Actual behavior
Fails with

Input In [22], in <module>
----> 1 projected = np.outer(trans1, pc1) + pc.mean

ValueError: operands could not be broadcast together with shapes (98,2565) (855,3)

Fix

projected = np.outer(trans1, pc1) + pc.mean.flatten()

[orbeckst]

I am trying to load this notebook directly with jupyter-lab (Jupyter Server 1.13.3) and get an error

File Load Error for pca.ipynb
Unreadable Notebook: ~/MDAnalysis/UserGuide/doc/source/examples/analysis/reduced_dimensions/pca.ipynb NotJSONError('Notebook does not appear to be JSON: \'{\\n "cells": [\\n {\\n "cell_type": "m...')

(The diffusion notebook in the same directory loads fine.)

[orbeckst]

Loading also fails with Jupyter Notebook 6.4.7

Error loading notebook

Unreadable Notebook: ~/MDAnalysis/UserGuide/doc/source/examples/analysis/reduced_dimensions/pca.ipynb NotJSONError('Notebook does not appear to be JSON: \'{\\n "cells": [\\n {\\n "cell_type": "m...')

[orbeckst]

I'd like to actually fix this issue but don't know how to proceed if I cannot even load it. I pulled the master branch or should I use develop?

[orbeckst]

Working from develop works...

[lilyminium]

Sorry, I missed this. I have no idea how or why but a closing brace was missing. You can see it here: https://github.com/MDAnalysis/UserGuide/pull/185/files#diff-1834d90511e206f517d291636dc4e135a63d87a7d2ca9d8cd5979df102defe02R8168

Edit: line 8168 in pca.ipynb, or where it should be in master is line 8239.

[lilyminium]

Closed in #184