Update and polish the sphinx docs

theochem / procrustes

Python library for finding the optimal transformation(s) that makes two matrices as close as possible to each other.

https://procrustes.qcdevs.org/

GNU General Public License v3.0

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Update and polish the sphinx docs #54

Closed FanwangM closed 3 years ago

FanwangM commented 3 years ago

This is a reminder for myself that a few things need to be fixed.

[x] Update the header
[x] Update contact information using QC-Dev community
[x] Update the footnote information in conf.py
[x] Update the equations and make it consistent with our manuscript.
[x] Update installation guide
[x] Update quick start example
[x] Add API rst file for kopt module
[ ] fix examples, following . This related to #26
[x] Update docstrings if necessary: equations, argument names, and default parameters. This relates to #25.
[x] Add RST file style checker

FarnazH commented 3 years ago

@fwmeng88 what do you want to change in the HEADER? There were updated in 06d2c283e58d83a34bb866e4c3638948be328c0d

Also, I am making changes to the docstrings (and equations), and to avoid conflicts, it's best not to change equations now. Then, we should make the paper's appendix consistent with the docstring.

I am also taking care of issue #25, as I messaged you.

FanwangM commented 3 years ago

The HEADER in the docs folder are not updated yet and I will fix it soon following 06d2c28. I will not touch the docstrings and other parts in the PY files for now until you tell me to.

This is just a reminder for me to double-check before the final release. I will only touch these files located in docs, not others.

Thanks for reminding the potential conflicts I may cause. @FarnazH

FarnazH commented 3 years ago

@fwmeng88 can you please add Table 1 and Equation 1 (from the paper) to the documentation (1st page)? We need to make the Procrustes method names clickable so they link to the API documentation. Thanks.

FanwangM commented 3 years ago

I will do it shortly.