20230116 developer call notes

[hammer]

Pre-notes

• Notes from previous meeting

PRs

• sgkit#975 Initial gene-ε implementation
• sgkit#995 [WIP] Deduplicate dosage variables

Issues

• sgkit#980 Implement G123 selection statistic
• sgkit#984 Release 0.6.0
  • sgkit#994 Generic approach to converting between kinship and relationship estimates
• sgkit-publication

Notes

Attendees

1. Jeff Hammerbacher
2. Tom White
3. Jerome Kelleher
4. Ben Jeffery

Discussion

• sgkit-publication
  • Tool for the paper?
    • Google docs + paper pile?
    • Manubot? https://github.com/manubot/manubot
    • Quarto? https://quarto.org/
    • JK: manubot installs
    • TW: let’s try that
  • TW: I will start on popgen example
  • BJ: tsinfer example
• BJ would like to derive arrays and write them to disk w/o touch existing data
  • TW: capability of Xarray?
  • JH: Stack Overflow Adding new Xarray DataArray to an existing Zarr store without re-writing the whole dataset?
  • JH: region and append_dim keywords in to_zarr?
• sgkit#994 Generic approach to converting between kinship and relationship estimates
  • Tim wants to get this done before the release
  • JK: since we haven’t released these methods yet, let’s hold for the refactor so we don’t need to worry about backwards compatibility
  • License discussion: cf. Can I bundle MIT licensed components in a Apache 2.0 licensed project?
• sgkit#995 [WIP] Deduplicate dosage variables
  • Not tied to release, but Tim M is working on it