DIALS core meeting 2021-07-29

[Previous meeting: 2021-07-15]

Previous Actions

• MG: Giving a typing intro lecture on 14th of July, 13:00 BST
• ND: conda-forge pycbf: Make new release to use dials-data directly for tests
• “Contiguous Nexus” cctbx/dxtbx#356
  • Non-draft state is pending checks against issues @dwpaley raised, and checking for non-contiguous cases [prev]
• dxtbx src/ layout [prev]
  • Action: Ask cctbxbb if anyone has knowledge or experience of re-export of dispatchers on windows
• Nonconventional P1 indexing [prev] - a possible problem with indexing nonstandard settings in P1
  • Action: Dan to try and demonstrate this on a simple/lysozyme example and file an issue

Agenda

dxtbx src/ layout

• Aaron has feedback from Billy; Two issues with current src/ layout
  • Modifies the conda-base folder - this is causing the windows problems
  • pip install fails on supercomputer bases when you cannot alter the base python that are read only
  • pip install --no-deps -e apparently contacts the internet - cannot do on
  • Until fixed will probably pin dials
  • All this applies to xia2 also

Mirror when stable

• Action occasionally fails - even when everything else passes - e.g. dff4fc1
• Sends an email to developer of most recent commit

• https://github.com/cctbx/cctbx_project/runs/3178538760?check_suite_focus=true

cbflib conda-forge package/pycbf

• Outstanding: 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. One possible solution is adding a special Format: dials/dials#366
• Still need to test with labelit/labelit_regression once the test suites actually work
  • All except one labelit tests are now working. On NKS todo list to fix.
• Progress on CBFlib 0.9.7?
  • No progress. HB probably busy with ACA.

flumpy – flex/numpy bridge

• Additional problem: cctbx/dxtbx#398 from_numpy currently fails if scitbx.array_family.flex has not already been imported. import fixed
• Additional issues seen:
  • cctbx/dxtbx#406 -Converting numpy arrays that don’t own their own data
  • cctbx/dxtbx#405 - Converting non-contiguous numpy arrays
    • scitbx arrays appears to have origin property that could be used for this? doesn’t appear possible. Throw helpful errors.

Next meeting

Thursday, August 12th, 4pm UK (BST), 8am PDT.