DIALS core meeting 2021-01-14

Previous Actions

• MG+ND: write a proposal for ‘overall architecture discussion’ and ‘new installer’
  • MG+ND: Come up with a proposal to move away from all code being in header files and consolidate into a single library
• ND: update CONTRIBUTING in a (separate) pull request to include a soft-imposition of stable master, dials#1353.
  • MG to look into and see if we can make a reasonable change otherwise we can drop it
• MG: organise a typing intro lecture.
• cbflib conda-forge package
  • ND to prepare an agenda for the HDRMX meeting
  • ASB to organise a side-meeting next to the HDRMX workshop
  • ASB to explore what should happen to cbflib maintenance in the future
  • GW: Unlikely to happen in the next couple of weeks. In March there is an HDRMX workshop, potentially we could add a peripheral meeting there.
• ND to set up a cbflib_adaptbx pull request for MAR detector fixes. Verify with labelit_regression.
• GW: write dxtbx rewrite project proposal.
  • Forked dxtbx, created a dx2 repository at https://github.com/graeme-winter/dx2/ and explored the terrain.
  • Python 3.6 as baseline

Agenda

Aaron’s PR Requests

Aaron requested that a slew of pull requests be reviewed by the next meeting after 2020-11-25:

dxtbx:

• Allow certain classes to be labeled as ‘abstract’ (#255)
• Deprecate h5rawdata and use Format.ignore() in the Registry (#261)
• Make FormatHDF5SaclaMPCCD lazy (#227)

Dials:

• Redo test to support new h5 file parsing behavior in dxtbx (#1499)
• dials.import: individually select models from reference expt (#1371)
• Multiple stills view (#1463)
  • too large to review here; but has been in use for a number of months
  • [DLS] Are going to look at this and merge by next core meeting - if not done by then, then it goes straight in pending news etc
• Add is_stills parameter to the spotfinder API to allow dials.stills_process to work with scans (#1508)
  • MG to refactor the test
  • merge, with proviso to please add a ticket that we will review this as part of the dx2 work
  • ND to add a newsfragment, ASB to merge

renaming master branch → main

• As of January 2021 Github has started rolling out their seamless branch rename
• Agreed to migrate to main. Turn this into dxtbx/dials/xia2 issues and move once GitHub provides a migration path. Use xia2 as a test-bed and move dials and dxtbx two weeks later.
• These tickets have been created as xia2/xia2#557, dials/dials#1546, and cctbx/dxtbx#281
• Plan is to deliberately break master, then migrate, then revert the breakage, so that anyone stuck on master will notice right away.
• TBD: define breakage-message

DIALS documentation build

Should the DIALS documentation build outside a cctbx environment?

• Currently you can only build the DIALS documentation inside a cctbx environment. This means a remote documentation build needs to build cctbx first, so we can’t easily run the documentation build on every commit. When things break they are difficult to fix. We can’t use readthedocs.
• MG: I believe the main obstacles are three cctbx Sphinx plugins that may need to be extracted or removed from DIALS documentation, and some phil parsing logic.
  • MG: the cctbx conda-forge package may be useful here
• GW & ND: It would be nice. At this time we don’t have the time.
• Outcome: wontfix

move the active dxtbx repository into the DIALS organisation

Having the main repository in cctbx_project has a few distinct disadvantages. The most annoying is the eternal fight against the lockdown bot, but we also don’t get LGTM output.

• This predates the dx2 discussion. dx2 will live in the DIALS organisation.
• Outcome: Leave this as it is.

pandas

XFEL package may introduce a pandas dependency. Want to use dials.cosym + XFEL data + MPI, pandas proved useful for bookkeeping.

General enthusiasm noted.

dials.index: create new experiments

not discussed in this meeting

dials.index should (or should not) create new experiments with crystals in rather than modifying in place existing experiments as proposed in this issue

Next meeting

Thursday, January 28th, 4pm UK time, 8am PDT.