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mosdef-hub / foyer

A package for atom-typing as well as applying and disseminating forcefields
https://foyer.mosdef.org
MIT License
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Update foyer documentation #415

Closed rsdefever closed 3 years ago

rsdefever commented 3 years ago

PR Summary:

This PR overhauls the organization of the foyer documentation and adds a few new sections. Let me know what you think! Let's tear it up and make it better 👍.

I think I'm reasonably happy with the organization, but I think the topic guides could be sharpened up/expanded upon some.

Closes #407.

codecov[bot] commented 3 years ago

Codecov Report

Merging #415 (2dff070) into master (c8e789b) will not change coverage. The diff coverage is n/a.

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  Coverage   73.84%   73.84%           
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  Files          17       17           
  Lines        1839     1839           
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  Hits         1358     1358           
  Misses        481      481
rsdefever commented 3 years ago

@umesh-timalsina I think I broke the fancy footer when I reorganized things. If you could have a glance when you have a chance that would be great.

rsdefever commented 3 years ago

I might suggest giving "Paper Examples" 1 and 2 more descriptive names. Maybe they could be combined with "Usage Examples"?

Yes! I agree. Those were vestiges from the previous organization...I didn't want to make the changes too dramatic at first but this is a good point and I will take a closer look.

rsdefever commented 3 years ago

@umesh-timalsina I think I broke the fancy footer when I reorganized things. If you could have a glance when you have a chance that would be great.

bump @umesh-timalsina

rsdefever commented 3 years ago

This organization is such an improvement! I might suggest giving "Paper Examples" 1 and 2 more descriptive names. Maybe they could be combined with "Usage Examples"?

Thanks for the suggestion! I have renamed the examples, but left them flagged as coming from the paper.

I think we should re-work the first couple of examples since they are so similar to the paper examples. Also, we use this (IMO) weird workflow where we pass the force field to the .save() function in mbuild, which seems to convolute the mbuild-foyer distinction.

justinGilmer commented 3 years ago

And whoops, it does seem like the fancy footer is missing.

rsdefever commented 3 years ago

@justinGilmer I vote we get these changes merged into the docs and then open an issue to update some of the examples. The paper examples will obviously stay the same.