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DIALS core meeting 2020-11-25

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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?

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?

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: Also built as manual feedstock, so available for install on conda-channel -c ndevenish cbflib. Limitations of approach:


cbflib_adaptbx dependency

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



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)

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.

Previous discussion outcomes:

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


renaming master branch → main

not discussed in this meeting

DIALS documentation build

not discussed in this meeting

Should the DIALS documentation build outside a cctbx environment?

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.

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.