2021-06-09 Mitchell/Behara/Wagner Check in

QC interface demo/cheat sheet

• JW will link video here

  • https://drive.google.com/file/d/160f82BhWWTNiP2IqGS5XEI2CeK915erV/view?usp=sharing

• PB will send notebook to JW and JM

• Do we want a QC interface example at all? What would it do that a QCSubmit example wouldn’t?

  • Write to SDF with energy as metadata?

• JM – A lot of the examples in the OpenFF toolkit are interdependent/redundant, and this confusion can hurt discoverability. What if we put them all in one place?

  • JW – I’d be worried about maintenance in that case. If examples are bundled with packages, then if the package in unmaintained, the the examples are implicitly unmaintained. But if they were grouped, it would be easy for things to fall out of date.

  • JM – Could centralize examples, and have a central maintainer for them.

  • JW – I think it’s good to have each package maintainer responsible for their own examples.

• This notebook is very strong. We should make it a QCSubmit example after the next release.

General discussion

• Cookbook of “all the different ways to make a molecule”

• Some way to convey info like FF-related objects and their converters

• JM – There have been a lot of mistakes slipping into docstrings (using markdown instead of rST). I’ve fixed many of them in molecule.py, but we should check the docs render as part of PR reviews.

  • JW – I’ll make sure to check new docstrings in future PRs

• JM – Also, there’s duplication of method listings in the docs. This is because autodoc and numpydoc are both running

• Theme review

• FF modification example tests failing

• PRs

  • FF modification notebook

    • Something’s out of sync with forcefield.get_partial_charges – Will need to fiddle with git to make it work.

  • Lots of little changes

    • Approved

  • Material theme

    • JM – I think we should have a dedicated theme repo. This will let us maintain it in a single place, and keep it consistent and up to date with things we need to fix.

    • JW – Would this prevent people from compiling docs offline?

      • JM – People already need to get things from online to compile docs (like sphinx and the current theme)

    • JM – The monospace font can be configured to be more readable

    • JM – If we put this into a central repo, each repo that uses the theme will need to have its own icon.

    • JM – If we made this a dedicated package, each package that switches to use it would just need to update the conf.py htmk_theme_options dict, html_theme, and possible html_sidebars (depending on the repo)

    • JW – I’m worried about what we’ll do if this breaks and nobody arund knows CSS

      • JM – You’re currently in that situation, where bootstrap is essentially unmaintained, a bunch of stuff is broken, and nobody knows how to fix it.

    • Made