2023-06-28 Mitchell/Wagner Check-in meeting notes

General updates

• JW – Expect OFFTK 0.14 this week, mostly API deprecations.

• JW – Will begin work on QCSubmit shortly after this.

• JW – New science team hires (Alexandra and Brent) start Monday - We should smother them with attention. I’ll try to find a way to get them to spend an hour or two with you next week (on conda setup screenshares or something). Please grab any such opportunities if you can.

• JM - Examples PR in Toolkit/Interchange

  • JW – Please move lysozyme example to deprecated, we can think about deduplicating/redesigning the other later.

• JM - Fragmenter and QCSubmit examples have example notebooks

  • JM – Fragmenter example times out (takes more than 10 minutes)

    • JW – Fragmenter example is very polished but let’s leave it off the to-do list for now.

  • JM – QCSubmit example has some issue when run with RDKit backend. Some issue with image format/visualization

    • JW – Let’s also leave that one out for now, but could you leave an open PR on openff-docs to add those repos so I can work on them while you’re out?

    • JM – Can do.

Trello

Centralized examples

• JM – Could add “which repo did this come from” to examples

  • JW – Good idea

• JM – Could add warning to experimental notebooks to say that they’re experimental

  • JW – Good idea

• JM – Trajectories don’t work

  • JW – I vote we do nothing about this

  • JM – Agree

• JW – Could openff-docs itself hold some examples (thinking like the conformer_energies script+notebook)

  • JM – Yeah, that should be possible.

  • JW – Please leave a PR open for us trying this out

• JM – Once I merge this, there will be no way to have a separate rendered version for subsequent PRs. Though I could think about how to set that up in a subfolder of the rendered branch or something.

  • JW – For now, let’s try to set up the PR rendering automation in subfolders, and if that works, set up a quarterly calendar reminder to clear unused branches from the rendered page.

To dos

1. (high) Centralized examples (from)

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

   2. (high) convert all examples to Sage 2.1.0

2. (medium) Toolkit docs cleanup

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

4. (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…”)

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

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

7. (low) Check main website for broken links

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