Dials

* dials.background: now allows masking prior to background calculation. Improved plots.
* dials.filter_reflections: create subsets of a reflection file based on user-specified criteria
* dials.export: command line interface change. Intensity choice for export given by option intensity, and exporting of partials now determined by options partiality_threshold and combine_partials.
* dials.scale: (for testing / evaluation) new program for scaling data from DIALS integration
* Behaviour change: DIALS commands will no longer read STDIN for parameters by default - you must specify that you want this behaviour e.g. cat some_params.phil | dials.import --phil=-. You may also pass filenames directly into the argument to get the identical behaviour e.g. --phil=some_params.phil (466)

* dials.report: Fix incorrect y-axis labels in plots
* xia2: Allow image= without range on Windows

* xia2: fix missing CIF information

* dials.export_bitmaps: Fix for still images, add output_file parameter
* Remove problematic format class from dxtbx
* Fix installation on newer Ubuntu versions

* Format fixes for Bruker Photon II images
* dials.show compatibility fixes
* xia2: gracefully handle invalid ranges with image=image_0001.cbf:start:end syntax
* xia2: disable currently unreliable check_indexing_symmetry feature

* Faster refinement for hierarchical multiple panel detectors by moving calculations to C++
* Scan-varying refinement of the goniometer setting matrix is now possible
* dials.plot_scan_varying_crystal changed to dials.plot_scan_varying_model. Now plots beam centre drift and error bars on scan-varying unit cell, if these have been recorded (414)
* Improvements to profile fitting in the presence of negative-valued pixels (537)
* 'DQE' renamed to 'QE' in across function names and in output data (544)
* Improved support for Bruker Photon II detectors
* New program `dials.cosym`: implementation of algorithms described in Gildea, R.J. & Winter, G. (2018). Acta Cryst. D74, https://doi.org/10.1107/S2059798318002978
* `dials.reindex`: bug fix when dealing with multi-sweep datasets (https://github.com/dials/dials/commit/40272998f75f2f283d6ccb690d0842e8ea545ebf)
* `dials.refine_bravais_settings`: bug fix for multi-sweep datasets if experimental models differ between experiments (554)