Xia2

========================

Bugfixes
--------

- Fix for missing ``SENSOR_THICKNESS=`` in XDS.INP generated for EIGER datasets introduced in 3.3.1 (`564 <https://github.com/xia2/xia2/issues/564>`_)

=======================

Bugfixes
--------

- Fix unicode logging errors on Windows (`558 <https://github.com/xia2/xia2/issues/558>`_)

=======================

From this release, xia2 version numbers `now follow <https://github.com/xia2/xia2/pull/528#issuecomment-716577121>`_ the DIALS release model.

Features
--------

- xia2 has been turned into a python package. This change includes major
refactoring work underneath the hood. (`528 <https://github.com/xia2/xia2/issues/528>`_)
- Updates to ``xia2.mmcif`` output to conform to the latest pdb dictionaries (v5).
``output.mmcif.pdb_version=`` option added (choices of ``v5``, ``v5_next``).
The default option ``v5_next`` includes output of unmerged reflection data. (`537 <https://github.com/xia2/xia2/issues/537>`_)
- ``xia2.html``: Add ``<dF/s(dF)>``-by-resolution plot if running xia with ``anomalous=True`` (`551 <https://github.com/xia2/xia2/issues/551>`_)


Bugfixes
--------

- ``xia2.multiplex``: pass ``dials.cosym`` parameter ``lattice_symmetry_max_delta=`` to ``dials.cosym``. (`544 <https://github.com/xia2/xia2/issues/544>`_)
- ``xia2.multiplex``: fix occasional error generating stereographic projections. (`546 <https://github.com/xia2/xia2/issues/546>`_)


Misc
----

- `533 <https://github.com/xia2/xia2/issues/533>`_, `#535 <https://github.com/xia2/xia2/issues/535>`_,
`538 <https://github.com/xia2/xia2/issues/538>`_, `#540 <https://github.com/xia2/xia2/issues/540>`_,
`541 <https://github.com/xia2/xia2/issues/541>`_, `#545 <https://github.com/xia2/xia2/issues/545>`_,
`547 <https://github.com/xia2/xia2/issues/547>`_, `#548 <https://github.com/xia2/xia2/issues/548>`_,
`552 <https://github.com/xia2/xia2/issues/552>`_.


xia2 (DIALS 3.2.1) (2020-11-09)
===============================

Features
--------

- ``xia2.multiplex``: Allow the user to override the default ``dials.scale``
parameter ``reflection_selection.method=``, to allow working around cases
where default can fail (`529 <https://github.com/xia2/xia2/issues/529>`_)
- ``xia2.merging_statistics``: Improved error handling (`531 <https://github.com/xia2/xia2/issues/531>`_)

Misc
----

- `530 <https://github.com/xia2/xia2/issues/530>`_

=======================================

Features
--------

- Add a radar plot to `xia2.multiplex` html report for comparison of merging
statistics between clusters. (`406 <https://github.com/xia2/xia2/issues/406>`_)
- Full matrix minimisation when using DIALS scaling is now Auto by default.
This will use full matrix for 4 sweeps or fewer, meaning that large data sets
now process much faster. (`428 <https://github.com/xia2/xia2/issues/428>`_)


Bugfixes
--------
- Temporary files are no longer left around during the dials scaling process (`497 <https://github.com/xia2/xia2/issues/497>`_)


Misc
----

- `514 <https://github.com/xia2/xia2/issues/514>`_, `#523 <https://github.com/xia2/xia2/issues/523>`_


xia2 (DIALS 3.1.4) (2020-10-12)
========================

Bugfixes
--------

- ``xia2.compare_merging_stats``: Fix occasionally incorrect axis ylimits (`517 <https://github.com/xia2/xia2/issues/517>`_)
- ``xia2.multiplex``: Fix corner case where reflections are present but not
used in refinement, leading to an error when selecting reflections with
``reflections.select_on_experiment_identifiers()`` (`524 <https://github.com/xia2/xia2/issues/524>`_)
- ``xia2.multiplex``: Fix error if one or more experiment has an image range
that doesn't overlap with the requested dose range. Instead, remove this
experiment from further analysis. (`525 <https://github.com/xia2/xia2/issues/525>`_)
- ``xia2.multiplex``: Gracefully handle failure of resolution estimation (`526 <https://github.com/xia2/xia2/issues/526>`_)
- Explicitly fail testing when the XDS licence has expired


xia2 (DIALS 3.1.1) (2020-09-01)
========================

Bugfixes
--------

- ``xia2.multiplex``: fix for dose parameter when scan doesn't start at 1 (`518 <https://github.com/xia2/xia2/issues/518>`_)
- ``xia2.html``: Fix crash on python 3.8 (`516 <https://github.com/xia2/xia2/issues/516>`_)

======================================

Features
--------

- xia2 now support Python 3.8 (`510 <https://github.com/xia2/xia2/issues/510>`_)
- Re-estimate resolution limit after deltacchalf filtering. Previously the
resolution limit of the filtered dataset would always be the same as the
unfiltered dataset. (`466 <https://github.com/xia2/xia2/issues/466>`_)
- Add support for dose_decay model for dials.scale (`467 <https://github.com/xia2/xia2/issues/467>`_)
- Report more useful error message if given an Eiger data file rather than a
master file, including suggestions of possible master files in the same
directory (`509 <https://github.com/xia2/xia2/issues/509>`_)
- Speed up ``xia2.compare_merging_stats`` (`502 <https://github.com/xia2/xia2/issues/502>`_)


Bugfixes
--------
- Work around changes to filenames output from dials.split_experiments (`478 <https://github.com/xia2/xia2/issues/478>`_)


Deprecations and Removals
-------------------------
- No longer create the ``xia2-files.txt`` file. The output now goes to ``xia2-debug.txt`` (`468 <https://github.com/xia2/xia2/issues/468>`_)


xia2 (DIALS 3.0.4) (2020-07-20)
===============================

Bugfixes
--------

- ``ispyb_xml``: Fix error reading PHIL files (`484 <https://github.com/xia2/xia2/issues/484>`_)
- When using ``read_image_headers=False``, ignore missing images outside of the
``start:end`` range specified on the command line (`491 <https://github.com/xia2/xia2/issues/491>`_)
- Improve treatment of reference instrument models when using ``reference_geometry=``.

Previously, a separate 'experiment list' (``.expt``) file was required
for each instrument model, but if any of the files contained multiple instrument
models (e.g. they had been created from multiple-sweep rotation data), xia2
could sometimes fail with a confusing message "no sweeps found".

Now, one can pass any number of ``.expt`` files with ``reference_geometry=``
arguments and each file may contain any number of instrument models. xia2
will sort out any duplicate models for you. (`485 <https://github.com/xia2/xia2/issues/485>`_)


xia2 (DIALS 3.0.3) (2020-07-06)
===============================

Bugfixes
--------

- Fix data from NSLS II with multiple triggers and one image per trigger (`475 <https://github.com/xia2/xia2/issues/475>`_)
- Gracefully handle xtriage errors when generating xia2 report. (`477 <https://github.com/xia2/xia2/issues/477>`_)
- xia2.compare_merging_stats: Plot the bin centres rather than bin d_min
values. This previously could lead to misleading apparent differences between
data sets with significantly different resolution limits. (`480 <https://github.com/xia2/xia2/issues/480>`_)
- Increase XDS COLSPOT minimum_pixels_per_spot from 1 to 2. The previous value may
have led to problems when spotfinding on images with many hot/warm pixels. (`472 <https://github.com/xia2/xia2/issues/472>`_)

xia2 (DIALS 3.0.1) (2020-06-11)
===============================

Bugfixes
--------

- Fix missing anomalous info in hkl data converted for shelx
- Compatibility with DIALS project_name changes

======================================

Features
--------

- Improve handling of diamond anvil cell data. When calling xia2 with `high_pressure.correction=True`:
- 'Dynamic shadowing' is enabled, to mask out the regions shadowed by the cell body.
- The minimum observation counts for profile modelling are relaxed — the defaults are unrealistic in the case of a small data set from a small-molecule material in a diamond anvil cell. In such cases, there are far fewer spots than the DIALS profile modelling expects, based on the norm in MX. This had been a frequent cause of frustration when processing small-molecule data with xia2.
- X-ray absorption in the diamond anvils is automatically corrected for using `dials.anvil_correction`. (`396 <https://github.com/xia2/xia2/issues/396>`_)
- New command-line interface for xia2.to_shelxcde utility to support SAD/MAD datasets. (`433 <https://github.com/xia2/xia2/issues/433>`_)
- - Include xtriage analysis in xia2.multiplex output
- xia2.multiplex now exports json file including xtriage results
- Include merging stats in multiplex json file (`443 <https://github.com/xia2/xia2/issues/443>`_)
- Add the option ``multi_sweep_refinement`` to the DIALS pipelines.
This performs the same indexing as ``multi_sweep_indexing`` and additionally refines all sweeps together, rather than refining each sweep individually.
When refining the sweeps together, the unit cell parameters of each sweep are restrained to the mean unit cell during the scan-static refinement.
This is achieved by setting the ``dials.refine`` option ``refinement.parameterisation.crystal.unit_cell.restraints.tie_to_group.sigmas=0.01,0.01,0.01,0.01,0.01,0.01``, but other values and ``tie_to_group``/``tie_to_target`` schemes of ``dials.refine`` may be invoked by passing suitable parameters.
See the various xia2 configuration parameters under ``dials.refine.restraints``, which are identical to the settings one can pass to ``dials.refine`` via its own parameter set ``refinement.parameterisation.crystal.unit_cell.restraints``.
As with the normal behaviour of xia2, the restraints do not apply to the scan-varying refinement step.

Since this is likely to be most useful for small-molecule chemical crystallography, the ``multi_sweep_refinement`` behaviour is made the default when ``small_molecule=True``. (`456 <https://github.com/xia2/xia2/issues/456>`_)


Bugfixes
--------

- Fixed printing of unit cells which are fixed by symmetry (89.9999999 -> 90.0) (`444 <https://github.com/xia2/xia2/issues/444>`_)
- Changed outlier rejection in 3dii pipeline - no longer throw out outliers by default, and if outlier rejection requested only perform this after assessing resolution limits. (`445 <https://github.com/xia2/xia2/issues/445>`_)
- Fix issue where missing images caused error: "can't convert negative value to unsigned int" (`463 <https://github.com/xia2/xia2/issues/463>`_)


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

- xia2 0.7 no longer supports Python 2 (`450 <https://github.com/xia2/xia2/issues/450>`_)
- Removed long-deprecated command line options -3dii / -dials and the like as well as the dials-full pipeline. (`452 <https://github.com/xia2/xia2/issues/452>`_)
- Remove xia2.chef: this is deprecated and replaced by dials.damage_analysis (`460 <https://github.com/xia2/xia2/issues/460>`_)


Misc
----

- `449 <https://github.com/xia2/xia2/issues/449>`_