Xia2

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

Features
--------

- ``xia2.multiplex``
- Add ``absorption_level=`` parameter to set the corresponding parameter in dials.scale. If
unspecified, decisions about absorption correction will be deferred to ``dials.scale``. This
means that for large sweeps (>60°), absorption correction will now be turned on automatically. (`603 <https://github.com/xia2/xia2/issues/603>`_)
- Add dano/sigdano by resolution plots to html report (`604 <https://github.com/xia2/xia2/issues/604>`_)
- Also output reflections in scalepack format (`607 <https://github.com/xia2/xia2/issues/607>`_)
- Enable sharing of an absorption correction for scaling with dials, with the option ``share.absorption=True`` (`614 <https://github.com/xia2/xia2/issues/614>`_)


Bugfixes
--------

- Separate data by I+/I- in merged .sca file produced by the dials pipeline (`606 <https://github.com/xia2/xia2/issues/606>`_)
- ``xia2.compare_merging_stats``: Print input files in deterministic order (`612 <https://github.com/xia2/xia2/issues/612>`_)
- ``xia2.compare_merging_stats``: fix crash when setting ``anomalous=True`` (`613 <https://github.com/xia2/xia2/issues/613>`_)


Misc
----

- `596 <https://github.com/xia2/xia2/issues/596>`_, `#597 <https://github.com/xia2/xia2/issues/597>`_, `#598 <https://github.com/xia2/xia2/issues/598>`_, `#608 <https://github.com/xia2/xia2/issues/608>`_, `#609 <https://github.com/xia2/xia2/issues/609>`_

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

Features
--------

- Separate anomalous pairs when scaling with ``dials.scale`` if ``anomalous=True``. The ``anomalous=`` parameter has also been added to ``xia2.multiplex``. (`539 <https://github.com/xia2/xia2/issues/539>`_)
- Add new ``surface_weight=`` parameter, to control the ``dials.scale`` absorption correction. (`584 <https://github.com/xia2/xia2/issues/584>`_)
- Add ``error_model_grouping=`` option to allow refining of an individual or grouped error model in dials. (`585 <https://github.com/xia2/xia2/issues/585>`_)
- Added ``absorption_level=[low|medium|high]`` option for control of the absorption correction, when using ``dials.scale``. (`592 <https://github.com/xia2/xia2/issues/592>`_)


Bugfixes
--------

- Prevent unintended output when checking version of ``pointless`` (`586 <https://github.com/xia2/xia2/issues/586>`_)
- Fix documentation section on resolution estimation (`593 <https://github.com/xia2/xia2/issues/593>`_)


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

- Removed python test files from the xia2 package installation, slightly reducing the package size. (`587 <https://github.com/xia2/xia2/issues/587>`_)
- Remove leftover Travis CI-related files (`588 <https://github.com/xia2/xia2/issues/588>`_)


Misc
----

- `582 <https://github.com/xia2/xia2/issues/582>`_

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

Bugfixes
--------

- Fix reading of split HKL files output from XSCALE (`579 <https://github.com/xia2/xia2/issues/579>`_)

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

Features
--------

- ``xia2.multiplex``: Use resolution cutoff determined during scaling for cluster analysis (`576 <https://github.com/xia2/xia2/issues/576>`_)


Bugfixes
--------

- ``xia2.multiplex``: Fix cos-angle clustering varying between runs (`576 <https://github.com/xia2/xia2/issues/576>`_)

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

- Fix tests affected by changes to profile fitting in `dials/dials1297 <https://github.com/dials/dials/pull/1297>` (`#569 <https://github.com/xia2/xia2/issues/569>`_)
- The main development branch of xia2 was renamed from 'master' to 'main'. (`561 <https://github.com/xia2/xia2/issues/561>`_)

Misc
----

- `550 <https://github.com/xia2/xia2/issues/550>`_, `#554 <https://github.com/xia2/xia2/issues/554>`_, `#555 <https://github.com/xia2/xia2/issues/555>`_, `#556 <https://github.com/xia2/xia2/issues/556>`_, `#565 <https://github.com/xia2/xia2/issues/565>`_, `#568 <https://github.com/xia2/xia2/issues/568>`_, `#572 <https://github.com/xia2/xia2/issues/572>`_, `#573 <https://github.com/xia2/xia2/issues/573>`_, `#574 <https://github.com/xia2/xia2/issues/574>`_, `#575 <https://github.com/xia2/xia2/issues/575>`_

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

Bugfixes
--------

- Fix ``type object has no attribute 'ignore'`` error (`570 <https://github.com/xia2/xia2/issues/570>`_)