2022_02_14 Core devs

General updates

Individual updates

• JW

  • I’ll be out next Monday

  • Vsite test cases - Working on defining full input space that exercises all vsite inputs, should be able to condense this down into minimal input space for tests

  • Dedicated all of thursday to closing PRs, closed 3. I’m not sure that we can realistically ever close all of those at this rate.

    • DD – Can other folks take over some PR reviews?

    • JW – Some of the issues are pretty complex, not sure that everyone is well-suited to review, but we can handle it case by case

    • MT – I’ve opened lots of PRs recently, This is a narrow window of time to bring in API breaking changes. The volume of PRs from me may decrease a little moving forward

  • Worked with DN on project planning/all hands presentation. He’s picking up info really quickly.

    • DN – Thanks. I’ll be pinging other members of the team to get more feedback on the organization. Please let me know if any diagrams are wrong or things are missing.

  • Working on biopolymer release - Still doing import/export tests for residues and chains. OpenMM is the hardest

• DD

  • Protein-Ligand Benchmarks

    • first working group meeting is tomorrow; will be preparing agenda today based on discussions with Jeff and Diego on what we need from the working group upfront

      • JW – Do we want to prepare for this before the actual meeting?

      • DD – I was going to prepare an agenda myself, I’m happy to involve you in the agenda setting process. This is a kickoff meeting

      • DN – I won’t follow the deep technical details, but I’ll be involved at the process/planning level

      • JW – I’d like to make sure that we frame this project in a way that puts DN and/or I in a position to guard DD’s focus and prevent changes from coming in at the wrong time.

      • DN – I’m planning to keep track of approvals/decisions, the backlog, and to keep the board of directors informed of what’s happening.

  • QCArchive

    • new QCFractal release is out; aiming to deploy new prod environments today to PRP and Lilac

      • thanks Pavan for the review!

    • worked with Ben on hardware solutions for QCArchive to meet both MolSSI's and OpenFF's needs; also worked with him on technical bits for datasets in next version

      • We’d like users of QCPortal to attend the next few weeks' QC* calls, since Ben will be asking for feedback before the release

  • Partner Benchmark

    • merged a few PRs on openff-benchmark; need to cut a new release this week after Lorenzo gives review on openff-benchmark#100

  • CLI tooling

    • spun up work on openff-gopt; this is more background work, not urgent but want to use it as a testbed for CLI ideas

• MT

  • Not-fully-cheminformatics-valid molecule infrastructure

  • Units refactor and elements refactors merged

  • Small releases for units and utilities packages

  • Bugfixes for HJ

  • Virtual sites hell

  • Bespokefit conda package

• CC

  • Out Friday (Feb 18) to Wednesday (Feb 23) for Biophysical Society meeting

  • Submitted TorsionDrives for scanning sidechain dihedrals for capped 1-mers (PR here) - thanks PB for review!

    • Blocked in exec-lifecycle by mamba failure

    • PB - related to python version in GitHub Actions

  • Continued work on LiveCoMS review

  • This week, I will start preparing a spec for biopolymer benchmarks: more details about ShiftX installation and input, sources of Karplus parameters, expected changes in Evaluator

    • CC - Most of it would be post-processing of trajectories, so minimal changes in core code of evaluator.

    • MT - Sounds good. Yeah, SB is the main dev who knows about the architecture of evaluator and can direct on where things need to go.

• PB

  • Fitting experiments related to impropers, and another starting from a different initial set of parameters (modified seminario angles and bonds) instead of previous forcefield parameters.

  • Some qca tasks, comms and PR reviews.