Feedback desired - What’s a good way to turn these into more closed-ended questions that are amenable for discussion and roadmapping?
PTM handling
How do we/which parts of the ff14SB PTM workflow do we deprecate once Rosemary comes out?
Suggestion: 6 month support window for old workflow after Rosemary release
Suggestion: We make no guarantee of support for any of the components of the early workflow once Rosemary comes out, but if there are API points that become widely used those may be upstreamed
How do we communicate the level of support of this workflow? Technical vs. Which features will need to remain supported in the longer run?How do we triage technical (“it doesn’t recognize my atom names”) vs. scientific (“these parameters don’t seem accurate”) support?
Suggestion: We say “the canonical AA parameters are 100% ff14SB, and the others are Sage with NAGL charges. They are philosophically compatible but use your judgement and report any issues to us”.
Should some sort of “react_molecule” method be permanently added to our public API to help stick small mols onto canonical proteins? Does this represent a shift towards supporting more system-preppy functions (eg,
Topology.solvate()etc.)? Alternatively, these API points could remain informal and live in jupyter notebooks/utils folders in one-off repos.How do we want to assess accuracy of PTM parameters? What guarantees do we make and how do we communicate them?
Docs
How confident are maintainers and users in the automated API docs?
Is everything you expect to be documented included?
Do you notice any errors?
Are maintainers confident they can control which items appear in the API docs?
Do users feel like they can find the documentation they need?
Are there any recurring frustrations with the API docs?
Are there any other recurring frustrations with documentation?
How do we want to prioritize improvements to the docs?
Additional type annotations
Docstring updates/corrections
New/updated software for automated API docs that might solve issues mentioned above
Virtual workshops
These are likely cancelled due to time constraints for the 2024-2025 roadmap year. Is this the right prioritization?
Which topics would be good to do workshops on for coming year?
Multi-vignette workshops vs. big single-topic workshops?