dials.index: Handle possibility of krivy-gruber iteration limit exceeded exception

[jbeilstenedmands]

This is a rare but possible exception that can be raised by cctbx when performing niggli cell reduction, possibly only for higher symmetry cases, but is the second time I have seen this or had this reported

At the moment, it is uncaught and results in a stack trace e.g.:

  File "/dls_sw/apps/dials/dials-v3-12-1-2/modules/xia2/src/xia2/cli/ssx.py", line 69, in run
    run_xia2_ssx(cwd, params)
  File "/dls_sw/apps/dials/dials-v3-12-1-2/modules/xia2/src/xia2/Modules/SSX/util.py", line 21, in wrap_fn
    result = fn(*args, **kwargs)
  File "/dls_sw/apps/dials/dials-v3-12-1-2/modules/xia2/src/xia2/Modules/SSX/xia2_ssx.py", line 270, in run_xia2_ssx
    integrated_batch_directories = run_data_integration(
  File "/dls_sw/apps/dials/dials-v3-12-1-2/modules/xia2/src/xia2/Modules/SSX/data_integration_standard.py", line 756, in run_data_integration
    cumulative_determine_reference_geometry(
  File "/dls_sw/apps/dials/dials-v3-12-1-2/modules/xia2/src/xia2/Modules/SSX/data_integration_standard.py", line 513, in cumulative_determine_reference_geometry
    expts, refl, summary_this = ssx_index(working_directory, indexing_params)
  File "/dls_sw/apps/dials/dials-v3-12-1-2/modules/xia2/src/xia2/Modules/SSX/data_integration_programs.py", line 295, in ssx_index
    indexed_experiments, indexed_reflections, summary_data = index(
  File "/dls_sw/apps/dials/dials-v3-12-1-2/modules/dials/src/dials/algorithms/indexing/ssx/processing.py", line 442, in index
    indexed_experiments, indexed_reflections, results_summary = index_all_concurrent(
  File "/dls_sw/apps/dials/dials-v3-12-1-2/modules/dials/src/dials/algorithms/indexing/ssx/processing.py", line 262, in index_all_concurrent
    results: List[IndexingResult] = pool.map(
  File "/dls_sw/apps/dials/dials-v3-12-1-2/conda_base/lib/python3.9/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/dls_sw/apps/dials/dials-v3-12-1-2/conda_base/lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
cctbx.uctbx.reduction_base.iteration_limit_exceeded: Krivy-Gruber iteration limit exceeded (limit=1000).

This PR catches the exception and raises it as a DialsIndexError (as are other exceptions encountered in indexing), which is caught in the dials.index command line program.

[codecov]

Codecov Report

Merging #2332 (6a79357) into main (094ce52) will decrease coverage by 0.04%.
The diff coverage is 66.66%.

@@            Coverage Diff             @@
##             main    #2332      +/-   ##
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- Coverage   80.57%   80.53%   -0.04%     
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  Files         587      587              
  Lines       67276    67286      +10     
  Branches     8995     8995              
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- Hits        54205    54187      -18     
- Misses      10992    11020      +28     
  Partials     2079     2079