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DIALS core meeting 2020-11-05


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DC1 – per-module

As previously agreed we now have a pull request demonstrating DC1 for xia2 in

Open questions that need deciding:

cctbx conda-forge package

We want to evaluate moving the dxtbx/DIALS Azure builds to build on top of the cctbx conda-forge package.

Consequences: We will get faster builds and clearer API boundaries and versioning, however it also means that we start treating cctbx as a software package. This restricts dxtbx/DIALS code to only use functionality that is part of the relevant cctbx release. From time to time, when cctbx releases new versions, we would update our dependencies, which would then allow the use of new cctbx features.

RG raised concerns after the last meeting, so left on agenda for further discussion.

dxtbxxfel dependencies

not discussed in this meeting

This discussion has now moved into dxtbx#239.

NIAC Nexus

not discussed in this meeting

This discussion has now moved into #1474.

Pull request When file indices are provided,…

ASB: This is dxtbx#210. The FormatSaclaHDF5 class isn’t lazy, which led to that problem. Will fix this in a separate PR, but the PR above is still a good PR independently of that.

In discussion we identified a new potential issue. We need to ensure during deserialisation this loop isn’t hit for classes that don’t have scans and goniometers.

Definition of trusted_range

Discuss PR Definition of trusted_range (dxtbx#182)

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

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

dxtbx json/msgpack performance

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 declared is 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.

renaming master branch → main

DIALS documentation build

Should the DIALS documentation build outside a cctbx environment?

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.

Next meeting

November 19th, 4pm UK time, 8am PDT.