DIALS core meeting 2024-05-30

Previous Actions

• ND Investigate getting psana tests running on the DIALS xfel-regression testing
• ND: Investigate using stable-nightly conda builds of cctbx (e.g. cctbx tests) longer term
• JBE: H5 on-disk experiment: review practicalities of using this & welcome people looking at James’s work above. round trip example files could be useful - exists in dials.export.

Agenda

OptionParser

• Dials east has reserved time to look into removing some of the limitations on this. Graeme notes: https://github.com/dials/dials/pull/1265
  • Set for Tues 21st
  • https://github.com/dials/dials/compare/main…new-argument-parser branch, Ben not cleaned for review yet

JBE Demos

• Previously [prev]:
  • Draft PR https://github.com/dials/dials/pull/2567
  • GW suggested making a special release in order to test this changeset at DLS (in new year).
    • Wait until PR notes addressed, then build this as a test release for wider consumption
  • Not been touched much since NY
  • Keeps coming up as something that would be useful
• James has rebased this, updated tests, Rick and Kevin feel OK with this => need to pick up some PR comments
• Hope to merge in near future (next month)
• Aaron points to notes
• Previous Actions: Still relevant?
  • AB: Run this against Xfel-regression tests: AB pls can you run this James?
  • ND: Make test release using these branches
• Few more issues outstanding
• 3.19 out now so good time to merge testing - providing xfel-regression works
• Paper taking next two weeks (pick up next time)

XFEL-Regression

• Previous boost problem causing test failures - squashed.
• Now back to:

  PackagesNotFoundError: The following packages are not available from current channels:
  
  - hdf5[version='<1.13.*']
  

---

• Digging in, have found separate problems:
• Something weirdly wrong with pipelines, failures that aren’t recognised
  • https://dev.azure.com/azure-dials/dials/_build/results?buildId=13914&view=logs&j=f1969cb6-27fc-501b-a53f-82c2e07f83cb&t=52a3e45b-bad8-5b1d-ad31-3233c5cd5eb2
• Action: ND have a look and see what is going on
  • ND has not done this yet

Making ellipsoid integrated data work with cctbx.xfel.merge

• JBE: I had prepared this, but now I’m not sure this is the best approach, discuss: https://github.com/dials/dials/pull/2661

Discussion of how to handle the difference between partiality and so on between the DIALS ellipsoid model / xfel.merge postrefine was discussed: since the intensities are modified “it’s complicated.” Need to make sure not to correct for partiality twice. Per-image scale factors are computed before postrefinement but Wilson B is only optimised during postrefinement - so this is meaningfully different from how dials.scale works.

Conclusion: share custom script

MetaCIF

• Ability to add extra metadata that is merged into the output shelx file in dials.export
  • Discussion about xia2.to_shelx and xia2 exporting metadata
  • Graeme points out xia2 CIF handling in https://github.com/xia2/xia2/blob/main/src/xia2/Handlers/CIF.py
• Dan is not here today. Pick up next week. (if available).

AOB?

CBFlib

• HJB in process of updating for HDF5 1.14.4
• We’re on 1.14.3
• dials/cbflib has been updated to latest and should be picked up when DIALS 3.20 is released. Some extra work to switch the release scripts to use cbflib/main instead of cbflib/master.

Next meeting

Thursday, June 13th, 4pm (BST), 8am (PDT)