Xia2

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Features
--------

- xia2 now has coloured output by default.
You can disable this by setting the environment variable NO_COLOR. (`267 <https://github.com/xia2/xia2/issues/267>`_)
- The DIALS pipeline now generates .sca output files again (`384 <https://github.com/xia2/xia2/issues/384>`_)
- Prescale data before dials.symmetry when in multi_sweep_indexing mode

This mirrors the behaviour of the CCP4ScalerA by prescaling the data
with KB scaling to ensure that all experiments are on the same scale
before running dials.symmetry. This should lead to more reliable
results from the symmetry analysis in multi_sweep_indexing mode. (`395 <https://github.com/xia2/xia2/issues/395>`_)
- Switch the default plugin for reading HDF5 files with XDS to DURIN (`400 <https://github.com/xia2/xia2/issues/400>`_)
- The error output file xia2.error has been renamed xia2-error.txt (`407 <https://github.com/xia2/xia2/issues/407>`_)


Bugfixes
--------

- Export DANO when running cctbx French & Wilson procedure (`399 <https://github.com/xia2/xia2/issues/399>`_)
- If .nxs and _master.h5 files reference the same underlying data files on disk,
do not process both, only process _master files. Fixes longstanding annoyance. (`408 <https://github.com/xia2/xia2/issues/408>`_)
- Made image reading in xia2.overload more general, means screen19 now works with
Eiger detectors (`412 <https://github.com/xia2/xia2/issues/412>`_)
- Fix bug for space_group= option in combination with the dials pipeline where
output mtz files would be in the Laue group, rather than the space group. (`420 <https://github.com/xia2/xia2/issues/420>`_)
- Remove the check that HDF5 data files are in place for master files, since this
implicitly assumes that the data are written following DECTRIS manner. (`401 <https://github.com/xia2/xia2/issues/401>`_)

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Features
--------

- Perform systematic absence analysis in multiplex

- Run dials.symmetry in systematic-absences-only mode after scaling to determine
full space group in xia2.multiplex
- Set laue_group= to skip Laue group determination by dials.cosym
- Set space_group= to skip both Laue group determination by dials.cosym and
systematic absences analysis by dials.symmetry (`355 <https://github.com/xia2/xia2/issues/355>`_)
- Use cctbx-based French/Wilson procedure in place of ctruncate.
Set truncate=ctruncate to use ctruncate instead. (`377 <https://github.com/xia2/xia2/issues/377>`_)
- Generate integrated.mtz files for dials pipeline, saved in Datafiles (`385 <https://github.com/xia2/xia2/issues/385>`_)


Bugfixes
--------

- Don't raise error if anomalous probability plot fails (`357 <https://github.com/xia2/xia2/issues/357>`_)
- Ensure that integration results are copied to DataFiles. In some circumstances,
when re-indexing/integrating the data, they were inadvertently missed (`379 <https://github.com/xia2/xia2/issues/379>`_) (`#379 <https://github.com/xia2/xia2/issues/379>`_)
- Fix for running dials.symmetry in multi_sweep_indexing mode (`390 <https://github.com/xia2/xia2/issues/390>`_)


Deprecations and Removals
-------------------------

- Retire mosflm/2d pipeline and related features (`222 <https://github.com/xia2/xia2/issues/222>`_)
- -journal.txt output files are no longer created.
Any output goes into the debug logfile instead. (`267 <https://github.com/xia2/xia2/issues/267>`_)
- Retire command dev.xia2.pea_in_box (`348 <https://github.com/xia2/xia2/issues/348>`_)
- Retire xdssum indexer (`351 <https://github.com/xia2/xia2/issues/351>`_)
- Retire labelit/labelitii indexer and related features (`367 <https://github.com/xia2/xia2/issues/367>`_)


Misc
----

- `342 <https://github.com/xia2/xia2/issues/342>`_, `#370 <https://github.com/xia2/xia2/issues/370>`_

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Features
--------

- Change the default pipeline (dials) to use DIALS for scaling instead of AIMLESS

Scaling with AIMLESS is still available by running xia2 with ``pipeline=dials-aimless`` (`301 <https://github.com/xia2/xia2/issues/301>`_)
- Reduce the number of calls to dials.export for performance improvement.

The integrated.mtz (unscaled) no longer appears in the Logfiles but can
be generated from the corresponding .refl and .expt files (`329 <https://github.com/xia2/xia2/issues/329>`_)
- Reduce the total sweep range for searching for the correct beam centre.

After 180 degrees no new information is provided so restrict the range if
the total number of reflections is > 20,000 (only 10,000 randomly selected
refections are used for this calculation anyway). (`249 <https://github.com/xia2/xia2/issues/249>`_)