2022-08-10 Mitchell/Wagner Check-in meeting notes

General updates

• JW – Do check ins

  • JM – Ok, will do

• JW – Coffee hour with me/MT/team one day a week? Tues/Thursday at 3 PM US Pacific?

  • Actually, there aren’t any days with overlap, so let’s not do this until the seasons change/time zones get more favorable.

• JW – Pushing on bespoke PR?

  • JM – I think it’s ready for review.

  • JW – I’ll take a quick look and encourage JHorton

  • (JW tests locally on min repro case, it successfully raises the error)

  • JW leaves nudging review:

• JW – Followup on mobley thread?

  • JM – Started writing “book” - Outlined 5 chapters, wrote 1.

• JW – Path toward finalizing toolkit showcase/toolkit examples for 0.11 release?

  • Want to make sure new stuff is in examples:

    • HierarchySchemes

    • from_polymer_pdb

  • JM opened PR with current status of new showcase

• JW – I made some performance improvements that may get the toolkit showcase running in an acceptable amount of time.

Todos

1. (high) refactor toolkit showcase to not use ParmEd/OMMFFs (from 2022-06-22 Mitchell/Wagner Check-in meeting notes )

2. (high) Resolve

3. (medium) Skunkworks notebook bespokefit integration

4. (medium) Centralized examples (from)

   1. (high) bespokefit protein-ligand or ligand-in-water example

5. (medium) Toolkit docs cleanup

6. (medium) Toolkit revised user guide (+-unifying/centralizing package user guides)

7. (medium) Come up with “milestones” for making first of three videos this year (like, “first video on covid spike protein and small molecule, filmed this day, edited in that range, etc…”)

8. (medium) bibtex blocks for website “how to cite” page on

9. (low) Propose policy for using GH citation machinery

10. (low) Check main website for broken links

11. (low) Conda env yamls for each release (automated inside of Toolkit’s single-file-installer action)