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DIALS // knowledgebase

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[Previous meeting: 2021-07-29]

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]
- 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
- Dan: try and demonstrate this on a simple/lysozyme example and file an issue

Moving to 3.7 for all tests has exposed warnings that datablock is still being used in tests
Do we need to keep datablocks? The argument before was that since it’s only post-import, re-importing the images isn’t overly burdensome
- dials refers to datablocks in tests and documentation.
- Upgrading datablock DeprecationWarning to UserWarning worth doing?
- Would also suggest deprecating all other functions/classes in datablock.py
- 2020 LS49 paper apparently depends on datablocks quite heavily
  - Would need to be checked
- Make a roadmap plan for timescales to do this over - make a DC - long term plan - ~ 6 months

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
MG:
- Sounds like a bug in pip. Did you report this?
  - ND found a related issue
- Try installing with python setup.py develop. strace says no network interaction.
- Or, if you don’t care about editable installations, just drop the -e. According to strace this should also be fine.
Outcome: This is all resolved.

Action occasionally fails - even when everything else passes - e.g. dff4fc1
Sends an email to developer of most recent commit
MG: https://github.com/cctbx/cctbx_project/pull/646 should fix
Note: DIALS selects the python version to install using linux.txt with the conda option eg. conda-forge::python=3.7.*
Remove old environment files (PR #1865)

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?

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.
Had additional issue:
- ~~cctbx/dxtbx#415: Still some rogue size_t issues~~
All know/outstanding flumpy issues dealt with. Have started using e.g. dials/dials#1813 and reports are so far good.