DIALS core meeting 2020-11-25

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: organise a typing intro lecture.
• GW: move cbflib_adaptbx’s compress and uncompress functions into dxtbx in a PR.
  • broke building on Mac completely, and looked like it broke building on Linux but may have been a coincidence. ND looking at it.
  • Now merged as dxtbx#238
• MG to set up dxtbx/dials Azure builds against cctbx conda-forge package
• MG to finish up DC1 pull request for xia2
• DP to merge dxtbx#210

Agenda

dxtbx/dials Azure builds against cctbx conda-forge package

Ready in dxtbx#262, based on cctbx release 2020.10. This adds a single linux build in addition to the currently 2 (uncached) linux and macos builds.

Build times are significantly reduced: about 2 minutes environment setup, 2 minutes build time, 4 minutes test time, for 8 minutes in total. An uncached linux build otherwise takes >30 minutes.

Go / no go decision?

• cctbx can do approximately weekly point releases to include bugfixes
• Let’s do this.

xia2 DC1

Ready in xia2#528.

This changes the repository to source layout (files that used to be in / are moved to /src/xia2).

Full description of changes in xia2#528#comment, including the release versioning process.

Go / no go decision?

• ND to review
• followed by ‘let’s do this’.

reduce package

Concerns on impact of the new reduce package (cctbx#567) on DIALS releases

BKP: license file issue is acknowledged and being worked on. reduce code is older than cctbx.

MG: CCIBuilder is possibly not the best place to add this?

BKP: Will review

ASB: We are using DIALSBuilder and base builds.

Outcome: We should be fine whether or not reduce is distributed via the cctbx conda-forge package.

cbflib conda-forge package

Have merged in ND’s working branch to repo for pull: https://github.com/conda-forge/staged-recipes/pull/12742. Also built as manual feedstock, so available for install on conda-channel -c ndevenish cbflib. Limitations of approach:

• Windows not working yes, various compile errors including C99-related
• Fortran build seems to error on macOS - hdf5 only builds static libs?
• Builds off master by replacing CMakeLists.txt, but currently pointed to yayahjb/cbflib#19 for python 3 behavioural issues

Actions:

• ND to set up an agenda for a code-review meeting
• ASB to set up a meeting with HJB, BKP, ASB, ND
• ASB to explore what should happen to cbflib maintenance in the future

cbflib_adaptbx dependency

ND has a few changes to fix the MAR detector without cbflib_adaptbx dependency cctbx/dxtbx#264

Actions:

• ND to set up a pull request from that
  • ASB: Make sure to run labelit_regression tests on that

dials-data-files

Aaron would like to add a set of files: Add first 4 frames of cxidb entry 33 from Takanori Nakane

MG merged this PR.

The upcoming PR to dials-data is welcome. This might not work directly because of Travis CI policy changes. MG will sort it if there are technical issues.

Definition of trusted_range

not discussed in this meeting

Discuss PR Definition of trusted_range (dxtbx#182)

image_range vs. array_range baked in off-by-one errors

not discussed in this meeting

Discuss image_range vs. array_range baked in off-by-one errors (dxtbx#186)

• DW made a proposal and started work on that, but it proved messy
• There is a new, simpler, proposal but this version kills off the image_range concept rather than array_range
• Discuss, again, what we want here and whether the new proposal is useful

dxtbx json/msgpack performance

not discussed in this meeting

ASB reports json being problematic when importing e.g. 50,000 experiments, as everything is stored in a single file, so everything needs to be read at once.

• GW: cf. Load before heat death (dxtbx#118). At the core of it are bad design choices in dxtbx.
• Future discussion topics:
  1. treatment of large serial datasets
  2. using an HDF5 backend for reflection files
  3. dials#1407 specific proposal
• ASB: I want check_format to go away.

Previous discussion outcomes:

• ASB:
  • General consensus that this is needed.
  • Make models and store them
  • Load them in parallel with minimal memory requirements
  • Version all models and rewind them
    • This needs a lot of thought and at this time we don’t have agreement here.
  • Not need to copy data like shoeboxes when they aren’t being changed, operate by reference

Remove tntbx dependency

Appears not to be used anywhere outside of cctbx_project/xfel, but xfel does not declare it as a dependency. xfel only uses the svd() function. Maybe change xfel to use numpy.linalg.svd instead and drop tntbx entirely?

Peter Zwart: My favorite SVD tools lives in scipy.sparse.linalg.svds. This routine allows calculation of the top K vectors in an SVD, it is a massive time saver if you know the rank of the matrix. The code works for dense as well as sparse matrices.

ASB: This seems to be obsolete code. I think if you dropped the dependency from DIALS it wouldn’t hurt us

Action:

• remove tntbx from bootstrap -> dials#1507

renaming master branch → main

not discussed in this meeting

• Nothing much will happen on this any time soon - either way we’ll wait for GitHub support on this one
• General assent that this is useful
• since 1st of October new GitHub repositories have main as the default
• proposed outcome: Agree 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.

DIALS documentation build

not discussed in this meeting

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

move the active dxtbx repository into the DIALS organisation

not discussed in this meeting

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.

• proposed outcome: move the active dxtbx repository into the DIALS organisation. Do it in such a way that the impact on existing installations, issues, pull requests is minimal.

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

Wednesday, December 9th, 4pm UK time, 8am PDT.

Ring-fenced to discuss pull requests with the word ‘range’ and/or ‘lazy’ in the subject, and performance issues baked into dxtbx.