DIALS core meeting 2022-03-31

Previous Actions

• (*) Removal of DataBlock [prev, prev]
  • Action: GW Make a PR/branch to remove this so that we can run things against it
    • Graeme will do this on 18th March
    • Behold \o/ cctbx/dxtbx#504
• (*) DXTBX/pycbf [prev]
  • ND: conda-forge pycbf: Make new release to use dials-data directly for tests
  • Nick: Add lots more attribution
• (*) Nick: dxtbx and read-only base
• Nick: Make sure that HKLviewer (prev) works at Diamond on module load
  • Attempted, installing pyside2 is easy, but fails after that (log)
  • Action ND: ask RO about this
• Aaron: Reduce zenodo dataset for contiguous nexus
  • Put on Dan Paley backburner also - time is short
  • On the Todo list now!
• ND to review: TOFBeam - A time-of-flight beam in dxtbx cctbx/dxtbx#492 (prev)
• Continue to discuss mac dispatcher issues (e.g. no GUI launch for image_viewer etc) in issues (cctbx/cctbx_project#739)
• std::string support for messagepack. This is used in XFEL module, should try to fix. dials/dials#1858.
  • Actually try to fix this
  • This is not going to happen before April at the earliest

Agenda

Dropping Data Blocks

https://github.com/cctbx/dxtbx/pull/504

• GW PR
• After PR/PRs, ASB to contact e.g. Mike Wall about this, too.
• GW thinks reasonable to merge when these concerns addressed

Still process

• Going to be a PR for “Diffbragg stage 1 refinement”
  • Uses pixel models of image to refine crystal using polychromotic spectra as per Mendez 2020 paper.
  • Implements an override in stills_process

ASB wants to put diffbrag stage 1 into dials.stills_process as a refinement engine. Depends on simtbx. This is very much dependent on GPU. Can use OMP etc.

• Derek Mendez going to send changes to Aaron

Add known_orientations to dials.stills_process

https://github.com/dials/dials/commit/eb7967fbd4be133b6f631af2ac14ac5e2697bca2

Pathlib changes

https://github.com/dials/dials/pull/2038

• Expecting this to be ready soon
• Is a big pull request
• Send out notice
• Action: GW to send out notice to dials-support

Deferred to next meeting

PyCBF

• Version 0.9.6.5 now out
• Added more attribution in dials/pycbf@b8d4f6 and conda-forge/pycbf-feedstock#10
• Now uses dials-data for testing data
• Added windows build: dials/pycbf#21 - somewhat scattered list of changes applied to CBFlib, at pycbf-build-time in 002_windows.patch
• Wheels live for multiple manylinux flavors, MacOS x86/arm, windows 64bit/32bit, for Pythons 3.6/3.7/3.8/3.9 live on pypi and, conda-forge mac/mac-arm/linux/windows 3.6/7/8/9/10.

DXTBX read-only base

• Read only base by default would be the ideal
• Turned out to be more involved
• Previously discussed downstream use cases and if DIALS needs to be included
  • PHENIX - depending on the readonly dxtbx stuff - until that is fixed DIALS will be pinned at 3.2 or similar. They also have a hard stop at Python 3.7, due to a slowly changing dependency.
• Defer for two meetings - pinning on DIALS 3.2/virtualenv script working around for now
• Issue cctbx/dxtbx#444
• Top Priority

Contiguous Nexus

• “Contiguous Nexus” cctbx/dxtbx#356
  • Non-draft state is pending checks against issues @dwpaley raised, and checking for non-contiguous cases [prev]
• AB wants this to be applied against new nexus writing
• RG: Probably useful to mock up an example in the nxmxtests
• Action: Aaron Reduce down zenodo dataset used in the issue (cctbx/dxtbx#93) so that we can include it in dials-data.
• Afterward: Coordinate with RG to make sure the ideas in this are integrated into new nexus reading

Next meeting

Thursday, April 14th, 4pm UK (BST), 8am PDT.