DIALS core meeting 2021-06-17

Previous Actions

• MG: giving a typing intro lecture on 14th of July, 13:00 BST
• dx2 proposal
  • MG to put in a PR to create a proposal in the proposal-space
  • MG+ND: Come up with a proposal to move away from all code being in header files and consolidate into a single library
• cbflib conda-forge/pycbf packaging
  • Aaron: Look into labelit regression tests
  • MG: Add HJB as repository owner
• DIALS deprecations
  • cctbx/dxtbx#371 can go in
  • xtc_process needs minor work before dials/dials#1731
• Accept DC-3 to follow NEP-29
  • Python 3.6 will be supported on development branch until DIALS 3.6.0 is released, at which point 3.7 will become the minimum supported version of python.
  • Python 3.7 will be dropped on Dec 26, 2021, which means that DIALS 3.8.* will be the last release to support Python 3.7 as a minimum.
• Delete master branches from dials/dxtbx
• Switch to hdf5plugin as the HDF5 plugin provider
  • dxtbx#373 and dials#1733 merged. Developers will have to update this manually.
• scitbx flex “ABI” issue
  • resolved by conda-forge pulling package in question

Agenda

Azure tests broken on dxtbx/xia2 [Fixed]

• cctbx/dxtbx#383 Merged.
• xia2/xia2#601 fix incoming via dials/dials#1752
• Cause is mismatch between cctbx in modules/ and version in conda_base/lib/python3.X/site-packages/ - having a second copy of cctbx_project appears to be limitation of libtbx build system\
• Look into adding check for version shear in libtbx.SConscript - Make ticket (Action: Nick)

cbflib conda-forge package/pycbf

• Version: 0.9.6.3 - fixes some distribution issues. .4 coming soon to use released dials-data datasets
• dxtbx#368 for optional usage in dxtbx, no binary dependence on cbflib/_adaptbx if present.
  • Still stray issue with dataset SPring8_ADSC_SN916 being the only one requiring FormatCBFFull.
• Still need to test with labelit/labelit_regression once the test suites actually work
  • GW needs to review https://github.com/cctbx/dxtbx/pull/369 (merged)
  • All except one labelit tests are now working. On NKS todo list to fix.

Status checks before merging

We had two cases recently where pull requests were merged too eagerly (dials#1699, dials#1729). We now have a status indicating build step. Should we set it so that the pull request build has to complete before merging? We can then also enable automatic merging once the build passes.

Outcome: Turn it on, and evaluate in a month.

Update to Python 3.9 as default environment

dials#1735 will make 3.9 the default for new environments. You can still pick 3.6 – 3.8 by specifying a version manually.

Outcome: No objection to merging. Make it so.

src/ layout for dxtbx

cctbx/dxtbx#382, currently blocked by https://github.com/cctbx/dxtbx/issues/383. This is now affecting other people, dials/dials#1749.

Outcome:

• Check cctbx bootstrap, xfel builder Check phenix builder (needs --cci-user)
• Check dials bootstrap builder
• Barring extra problems happy to make this change
• Migration for libtbx entry point case in libtbx_refresh.py
• Will need a developer ‘this is how you update your environment’ bulletin

Enable pathlib objects for dials-data

dials/data#275 will be merged soon. This deprecates the default py.path return objects, and adds an option to the dials-data fixture that allows returning py.path or pathlib objects.

(Currently blocked by xia2/xia2#597, which is blocked by cctbx/dxtbx#381, which is blocked by cctbx/dxtbx#383)

Outcome: Make this happen once blockers are out of the way.

flumpy – flex/numpy bridge

• cctbx/dxtbx#377
• Tests blocked by cctbx/cctbx_project@ab8949 making it into release (cctbx v2021.6)

Enthusiastically received.

Next meeting

Thursday, July 1st, 4pm UK (BST), 8am PDT.