This is CrystFEL 0.10.00.10.0

10 files changed, 269 insertions, 380 deletions

diff --git a/AUTHORS b/AUTHORS
index 27d40acd..fe0966b8 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -103,3 +103,6 @@
 
 * Troy D. Hanson
   uthash (http://troydhanson.github.com/uthash/)
+
+* Philipp Middendorf <philipp.middendorf@desy.de>
+  Gitlab continuous integration
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 87ddfc23..78bcce10 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.6)
-set(CRYSTFEL_SHORT_VERSION 0.9.1)
+set(CRYSTFEL_SHORT_VERSION 0.10.0)
 set(CRYSTFEL_VERSION ${CRYSTFEL_SHORT_VERSION})
 set(CRYSTFEL_API_VERSION 14)
 project(crystfel VERSION ${CRYSTFEL_VERSION} LANGUAGES C)
diff --git a/ChangeLog b/ChangeLog
index df937a28..addf5ee2 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,5 +1,44 @@
+CrystFEL version 0.10.0, 16th August 2021
+-----------------------------------------
+
+- New GUI ('crystfel') added, replacing 'hdfsee' which has been removed
+- Added ZeroMQ interface for streaming data processing
+- Added Meson build system
+- get_hkl can now write XDS and MTZ directly
+- Removed geoptimiser
+- Removed wide-bandwidth features
+- Added 'parameter harvest files' to indexamajig and partialator
+- Better handling of static masks with multi-event files
+- Added 'FromFile' indexing
+- Added scripts/display-hdf5 and scripts/make-csplit
+- New DataTemplate API
+- New Stream API, allowing random access and better recreation of processing
+- Bug fix for asdf indexing, vastly increasing speed and success rate
+- Big speed improvement for TakeTwo
+- Speed improvement for detector pixel coordinate transformation
+- Speed improvement for UnitCell
+- Speed improvement for creation of bad pixel maps from bad regions
+- Fixed a large memory leak in cell_tool
+- Fix large number of "rejected" reflections
+- Support for units in geometry file distances (eg 'clen = 43 mm')
+- Support for wavelength and electron accelerating voltage in geometry file
+- Added detector_shift_x/y to geometry file
+- Added peak_list_type to geometry file
+- Added flag_{lessthan,morethan,equal} to geometry file
+- Added peak_list to geometry file (no more --hdf5-peaks)
+- Added requirement for fs/ss bad regions to name a panel
+- indexamajig: Added --no-image-data and --no-mask-data
+- partialator, process_hkl: Handle multiple input streams
+- partialator: Reject crystals with large profile radii
+- indexamajig: Added --wavelength-estimate and --camera-length-estimate
+- indexamajig: Added --max-indexer-threads
+- Figure of merit calculations moved to libcrystfel
+- Removed badrow culling
+- compare_hkl: Removed --intensity-shells
+
+
 CrystFEL version 0.9.1, 22nd June 2020
--------------------------------------
+--------------------------------------
 
 - indexamajig: Fixed default unit cell tolerance (was 1.5 rad, now 1.5 deg)
 - Fixed bug in unit cell reduction/comparison
diff --git a/announcement-0.10.0 b/announcement-0.10.0
new file mode 100644
index 00000000..75122e68
--- /dev/null
+++ b/announcement-0.10.0
@@ -0,0 +1,43 @@
+Dear CrystFEL users and interested crystallographers,
+
+CrystFEL version 0.10.0 has been released!
+
+This is a huge update to CrystFEL, adding a completely new graphical user
+interface (GUI) which makes it much easier to interact with your data, guiding
+you through the processing steps.  To give a preview of the GUI and help you
+get started, I've made a video tutorial to accompany this release:
+https://www.desy.de/~twhite/crystfel/presentations.html
+
+Electron diffraction is fully supported in this version of CrystFEL.  Amongst
+other things, you can now specify an electron accelerating voltage (instead of
+an X-ray photon energy) in the geometry file.  Combined with the 'diffractem'
+pre-processing software developed by the Max Planck Institute for the Structure
+and Dynamics of Matter, you have a complete solution for processing data from
+serial electron diffraction crystallography.  For more details, see:
+https://gitlab.desy.de/thomas.white/crystfel/-/blob/master/doc/articles/electrons.rst
+
+In addition, I've taken advantage of the extended quiet time to work on many
+internal parts of CrystFEL.  The most noticable benefit of this is that several
+parts of CrystFEL are now much faster.
+
+Some command-line parameters and geometry file directives have changed, but you
+should find that the error messages will direct you towards what needs to be
+updated.
+
+See the release notes and the ChangeLog for full details of the other
+improvements.
+
+Release notes for version 0.10.0:
+https://www.desy.de/~twhite/crystfel/relnotes-0.10.0
+
+Change log:
+https://www.desy.de/~twhite/crystfel/changes.html
+
+CrystFEL website:
+https://www.desy.de/~twhite/crystfel
+
+Thanks for all of your past and future feedback and contributions, and
+your continued use of CrystFEL.  As ever, please contact me directly if
+you would prefer to be unsubscribed from this mailing list.
+
+Tom
diff --git a/announcement-0.9.0 b/announcement-0.9.0
deleted file mode 100644
index 7915cece..00000000
--- a/announcement-0.9.0
+++ /dev/null
@@ -1,34 +0,0 @@
-Dear CrystFEL users and interested crystallographers,
-
-CrystFEL version 0.9.0 has been released!
-
-This release adds a new indexing method ("PinkIndexer") and improvements to
-reflection prediction which will enable data processing for wide bandwidth and
-electron diffraction experiments.
-
-A new core program has been added, "cell_tool", which can perform several
-useful tasks on unit cells such as transformation, finding indexing ambiguities
-and calculating power ring positions.
-
-There have been many other improvements across the whole suite.  Notably,
-CBFlib is no longer required by CrystFEL, manual resolution limits are no
-longer needed by ambigator, and "--no-cell-combinations" is no longer needed by
-indexamajig.
-
-See the release notes for more discussion of these improvements, and the
-ChangeLog for full details of the other improvements.
-
-Thanks for all of your past and future feedback and contributions, and
-your continued use of CrystFEL.  As ever, please contact me directly if
-you would prefer to be unsubscribed from this mailing list.
-
-CrystFEL website:
-https://www.desy.de/~twhite/crystfel
-
-Release notes for version 0.9.0:
-https://www.desy.de/~twhite/crystfel/relnotes-0.9.0
-
-CrystFEL tutorial:
-https://www.desy.de/~twhite/crystfel/tutorial
-
-Tom
diff --git a/announcement-0.9.1 b/announcement-0.9.1
deleted file mode 100644
index 6ddda6cb..00000000
--- a/announcement-0.9.1
+++ /dev/null
@@ -1,39 +0,0 @@
-Dear CrystFEL users and interested crystallographers,
-
-CrystFEL version 0.9.1 has been released!
-
-This is a maintenance and bug-fixing release which fixes a few problems which
-crept into version 0.9.0.  The most important fixes are:
-
-1. The unit cell comparision function, which was completely re-written for
-   CrystFEL 0.9.0, was updated to fix a mis-indexing problem with certain
-   types of unit cell.  This may increase indexing rate or fix wrong output
-   cells in those cases.
-
-2. The default unit cell angle tolerance, which was accidentally set to
-   1.5 radians in CrystFEL 0.9.0 as a result of the above changes,
-   was re-set to 1.5 degrees.
-
-3. Build compatability was added with very new HDF5 versions (>= 1.12) and
-   older versions of zlib (< 1.2.3.5).
-
-See the release notes and the ChangeLog for full details of the other
-improvements.
-
-Release notes for version 0.9.1:
-https://www.desy.de/~twhite/crystfel/relnotes-0.9.1
-
-Change log:
-https://www.desy.de/~twhite/crystfel/changes.html
-
-Thanks for all of your past and future feedback and contributions, and
-your continued use of CrystFEL.  As ever, please contact me directly if
-you would prefer to be unsubscribed from this mailing list.
-
-CrystFEL website:
-https://www.desy.de/~twhite/crystfel
-
-CrystFEL tutorial:
-https://www.desy.de/~twhite/crystfel/tutorial
-
-Tom
diff --git a/meson.build b/meson.build
index c4df5b42..acb33250 100644
--- a/meson.build
+++ b/meson.build
@@ -1,6 +1,6 @@
 # Meson file for CrystFEL
 project('crystfel', 'c',
-        version: '0.9.1',
+        version: '0.10.0',
         license: 'GPL3+',
         meson_version: '>=0.50.0',
         default_options: ['buildtype=debugoptimized'])
diff --git a/relnotes-0.10.0 b/relnotes-0.10.0
new file mode 100644
index 00000000..2ebeebe6
--- /dev/null
+++ b/relnotes-0.10.0
@@ -0,0 +1,181 @@
+CrystFEL - Data processing for serial crystallography
+-----------------------------------------------------
+
+Release notes for version 0.10.0
+
+Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
+                      a research centre of the Helmholtz Association.
+
+See AUTHORS as well as individual source code files for full details of contributors.
+
+CrystFEL is free software: you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+
+
+Overview
+--------
+
+The most important changes in this version of CrystFEL are:
+
+- New graphical user interface
+
+- Support for electron diffraction
+
+- Temporary removal of geoptimiser and pink beam support
+
+- Improved MTZ and XDS output
+
+- Big speed improvements
+
+- Improved options for bad pixel masking
+
+See below for information about each of these changes.
+
+In addition, there were many bug fixes and other improvements.  See the
+"ChangeLog" or the changes page on the CrystFEL website for details.
+
+
+New graphical user interface
+----------------------------
+
+This release adds a new graphical user interface to CrystFEL.  The old image
+viewer "hdfsee" has been removed entirely.  To start the GUI, simply run
+"crystfel" at the command line.  The GUI guides you through the stages of
+processing a dataset, from importing image data all the way to exporting
+merged data.  To help you get started, there is a video introduction:
+
+https://www.desy.de/~twhite/crystfel/presentations.html
+
+The "old" command-line way of processing data is still available.  The only
+difference is that you should now use the GUI to view the results graphically,
+instead of hdfsee and the old "check-near-bragg" and "check-peak-detection"
+programs.  Simply run the GUI, giving the stream filename as an argument, for
+example: "crystfel results-output.stream".
+
+
+Support for electron diffraction
+--------------------------------
+
+This release adds support for serial crystallography using electrons.  For more
+information, see doc/articles/electrons.rst in the CrystFEL distribution:
+https://gitlab.desy.de/thomas.white/crystfel/-/blob/master/doc/articles/electrons.rst
+
+
+Temporary removal of geoptimiser and pink beam support
+------------------------------------------------------
+
+A lot of internal re-organisation and cleaning-up has taken place in this
+release cycle.  Due to a lack of development resources, two things fell by the
+wayside in order to make the release in a reasonable timescale: this release
+does not include "geoptimiser", nor support for wide bandwidth ("pink-beam")
+diffraction.
+
+But don't worry!  The next release will include an improved replacement for
+geoptimiser.  For the time being, note that the data formats used by CrystFEL
+have not changed much, so an older CrystFEL version (e.g. 0.9.1) can still be
+used for fine-grained geometry refinement in almost all cases.
+
+If you previously installed CrystFEL 0.9.1, you should find that geoptimiser
+from the old installation is still present and working.  Therefore, you might
+not even notice the difference!
+
+Features for processing data acquired with wide bandwidth radiation will be
+developed further if there is demand.
+
+
+Improved MTZ and XDS output
+---------------------------
+
+This CrystFEL version can export directly to MTZ (CCP4) or XDS-ASCII format.
+Export to MTZ and XDS format can also be done via the "Export" function of the
+new CrystFEL GUI.  Alternatively, use get_hkl to convert the file, for example:
+
+$ get_hkl -i my-data.hkl -o my-data.mtz --output-format=mtz -p my-data.cell
+
+This replaces the old "create-mtz" and "create-xscale" scripts, and the
+resulting files are more consistent with the expectations of other software.
+
+
+Big speed improvements
+----------------------
+
+Several significant speed improvements have been made.  In particular, these
+affect 'asdf' and 'TakeTwo' indexing, unit cell transformations and loading
+image data.  You should notice a greatly reduced number of "timeouts" during
+indexing.
+
+
+Improved options for bad pixel masking
+--------------------------------------
+
+More ways to mask bad pixels have been added.  You can now use one or more of
+the following directives in the geometry file to flag pixels with values lower
+than, equal or more than a given value: "flag_lessthan", "flag_morethan",
+"flag_equal".
+
+In addition, this version of CrystFEL is better able to handle the situation
+where a single bad pixel mask applies to multiple frames in a "multi-event"
+data file.  For example: with data in HDF5 format, if the location of the bad
+pixel mask contains fewer "placeholder" characters ("%") than the image data,
+only the required number of placeholders will be filled in when calculating the
+location of the mask.  This means that you can do something like this:
+
+data = /data/image/%/frames/%/pixel_values
+mask = /data/image/%/bad_pixel_mask
+
+In this case, one "bad_pixel_mask" would apply to everything under each set of
+"frames".
+
+
+API changes
+-----------
+
+The following changes have been made to the libcrystfel API.
+
+Additions:
+	- DataTemplate API (data_template_*, see datatemplate.h)
+	- Figure of merit API (fom_*, see fom.h)
+	- Stream API (stream_*, see stream.h)
+	- Image API (image_*, see image.h)
+	- 'struct detgeom' and associated API (detgeom_*)
+	- str_peaksearch and parse_peaksearch
+	- intcontext_new, integrate_rings_once, intcontext_free
+	- write_to_mtz, write_to_xds, libcrystfel_can_write_mtz
+	- parse_indexing_methods
+	- base_indexer_str
+	- default_method_options
+	- cell_print_oneline
+	- has_unique_axis
+	- lowest_reflection
+	- colscale_lookup (replaces 'render_scale')
+	- crystal_copy_deep
+	- Miscellaneous utility functions: compare_double, safe_strdup,
+	  load_entire_file, file_exists, filename_extension,
+	  set_log_message_func, el_v_to_lambda, CLEAR_BIT, convert_int,
+	  convert_float, ELECTRON_MASS
+
+Removals:
+	- 'struct detector' and associated API
+	- 'struct event' and associated API
+	- 'struct hdfile' and associated API (hdf5-file.h)
+	- 'struct beam_params'
+	- All direct interfaces to indexing engines, e.g. xds_prepare
+	- render_scale (renamed to colscale_lookup)
+	- stderr_lock
+	- {get,set}_panel (replaced by {get,set}_panel_number)
+	- INDEXING_DEBUG (use INDEXING_FILE instead)
+
+Changes:
+	- cell_get_* and cell_has_parameters (changes to 'const' qualifiers)
+	- struct image: removed 'parent', 'p', 'rx,ry,rz', added 'pn'
+	- estimate_peak_resolution (added 'det' arg)
+	- setup_indexing (added lots of new args)
diff --git a/relnotes-0.9.0 b/relnotes-0.9.0
deleted file mode 100644
index 43c5f147..00000000
--- a/relnotes-0.9.0
+++ /dev/null
@@ -1,214 +0,0 @@
-CrystFEL - Data processing for serial crystallography
------------------------------------------------------
-
-Release notes for version 0.9.0
-
-Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
-                      a research centre of the Helmholtz Association.
-
-Authors:
-  Thomas White <taw@physics.org>
-  Richard Kirian <rkirian@asu.edu>
-  Kenneth Beyerlein <kenneth.beyerlein@desy.de>
-  Andrew Aquila <andrew.aquila@cfel.de>
-  Andrew Martin <andrew.martin@desy.de>
-  Lorenzo Galli <lorenzo.galli@desy.de>
-  Chun Hong Yoon <chun.hong.yoon@desy.de>
-  Karol Nass <karol.nass@desy.de>
-  Nadia Zatsepin <nadia.zatsepin@asu.edu>
-  Anton Barty <anton.barty@desy.de>
-  Cornelius Gati <cornelius.gati@desy.de>
-  Fedor Chervinskii <fedor.chervinskii@gmail.com>
-  Alexandra Tolstikova <alexandra.tolstikova@desy.de>
-  Wolfgang Brehm <wolfgang.brehm@gmail.com>
-  Valerio Mariani <valerio.mariani@desy.de>
-  Parker de Waal <Parker.deWaal@vai.org>
-  Takanori Nakane <nakane.t@gmail.com>
-  Keitaro Yamashita <k.yamashita@spring8.or.jp>
-  Oleksandr Yefanov <oleksandr.yefanov@cfel.de>
-  Steve Aplin <steve.aplin@desy.de>
-  Helen Ginn <helen@strubi.ox.ac.uk>
-  Thomas Grant <tgrant@hwi.buffalo.edu>
-  Mamoru Suzuki <mamoru.suzuki@protein.osaka-u.ac.jp>
-  Nicolas Riebesel <nicolas.riebesel@tuhh.de>
-  Yaroslav Gevorkov <yaroslav.gevorkov@desy.de>
-  Omri Mor <omor1@asu.edu>
-
-CrystFEL is free software: you can redistribute it and/or modify it under the
-terms of the GNU General Public License as published by the Free Software
-Foundation, either version 3 of the License, or (at your option) any later
-version.
-
-CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE.  See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
-
-
-Overview
---------
-
-The most important new features in this version of CrystFEL are:
-
-- Features for wide bandwidth and electron diffraction processing
-
-- Introduction of cell_tool
-
-- New unit cell comparison algorithm (eliminating --no-cell-combinations)
-
-- CBF files now handled natively (CBFlib not required)
-
-- Resolution limits no longer needed for ambigator
-
-See below for information about each of these features.
-
-In addition, there were many bug fixes and other improvements.  See the
-"ChangeLog" or the changes page on the CrystFEL website for details.
-
-
-Features for wide bandwidth and electron diffraction processing
----------------------------------------------------------------
-
-A new indexing method has been added: PinkIndexer.  This is a new indexing
-algorithm which can index wide bandwidth data as well as flat Ewald sphere
-(i.e. electron diffraction) data.  For more information, see:
-Gevorkov et al., Acta Cryst. A72 (2020) doi:10.1107/S2053273319015559
-
-To accompany the new indexing algorithm, the reflection position calculation
-("prediction") has also been improved.  The results should be better for all
-types of data, particularly at low resolution.
-
-Further improvements for wide bandwidth and electron data are planned for future
-releases of CrystFEL.
-
-
-Introduction of cell_tool
--------------------------
-
-A new CrystFEL core program has been added: cell_tool.  This program can perform
-a variety of operations on unit cell files, similar to how get_hkl can do things
-with reflection data files.  The tasks include: finding indexing ambiguities,
-turning a centered cell into a primitive one, calculating power ring positions,
-comparing unit cells, transforming unit cells, and working out all the possible
-cell choices for centered monoclinic cells.
-
-
-New unit cell comparison algorithm
-----------------------------------
-
-The way that indexamajig compares indexing results to your target cell has been
-improved.  Previously,  the option --no-cell-combinations was needed for certain
-unit cells.  This is no longer the case, and the new comparison should be more
-reliable in all cases.
-
-
-CBF files now handled natively
-------------------------------
-
-The CBF library (CBFlib) is no longer used in CrystFEL.  Most common types of
-CBF file can now be read directly by CrystFEL.  If you find a CBF file that
-cannot be read, please get in touch so we can fix it.
-
-
-Resolution limits no longer needed for ambigator
-------------------------------------------------
-
-Previously, a careful choice of resolution bounds (--highres and --lowres) was
-needed for good results with ambigator.  Now, the reflections will be compared
-and correlated in three resolution bins (>10, 10-2.5 and <2.5 Angstroms).  For
-most datasets, this allows ambiguities to be resolved easily without any manual
-adjustment.  You can still override this and use your own resolution limits,
-if you need to.
-
-
-API changes
------------
-
-The following changes have been made to the libcrystfel API.
-
-New functions:
-	- cell_print_full
-	- compare_cell_parameters
-	- compare_cell_parameters_and_orientation
-	- compare_permuted_cell_parameters_and_orientation
-	- compare_derivative_cell_parameters
-	- compare_reindexed_cell_parameters
-	- cell_get_G6
-	- cell_transform_gsl_direct
-	- cell_transform_rational
-	- cell_transform_rational_inverse
-	- cell_transform_intmat
-	- cell_transform_intmat_inverse
-	- crystal_get_image_const
-	- get_detector_geometry_from_string
-	- write_detector_geometry_3
-	- multi_event_geometry
-	- parse_polarisation
-	- indexing_methods
-	- intmat_size
-	- intmat_zero
-	- intmat_create_3x3
-	- transform_indices
-	- intmat_times_intmat
-	- indexing_peak_check
-	- pinkIndexer_prepare/cleanup/probe/run_pinkIndexer
-	- rtnl_zero
-	- rtnl
-	- rtnl_as_double
-	- rtnl_mul/div/add/sub/cmp/abs
-	- rtnl_list
-	- rtnl_mtx_new/copy/get/set/free/print/dev
-	- rtnl_mtx_from_intmat
-	- rtnl_mtx_is_identity/perm
-	- intmat_from_rtnl_mtx
-	- rtnl_mtx_identity
-	- rtnlmtx_times_rtnlmtx
-	- rtnlmtx_times_intmat
-	- intmat_times_rtnlmtx
-	- transform_fractional_coords_rtnl
-	- transform_fractional_coords_rtnl_inverse
-	- spectrum_new/free/load
-	- spectrum_set_gaussians
-	- spectrum_get_gaussian
-	- spectrum_get_num_gaussians
-	- spectrum_set_pdf
-	- spectrum_get_range
-	- spectrum_get_density_at_k
-	- spectrum_generate_tophat/gaussian/sase/twocolour
-	- free_stuff_from_stream
-	- stream_geometry_file
-	- parse_symmetry_operation
-	- parse_cell_transformation
-	- mean_variance
-
-Removed functions:
-	- cell_transform
-	- cell_transform_inverse
-	- tfn_identity/from_intmat/combine/print/inverse/vector/free
-	- transform_cell_gsl  [use cell_transform_ functions instead]
-	- match_cell
-	- match_cell_ab
-	- compare_cells  [use compare_*_cell_parmeters functions instead]
-	- intmat_intvec_mult
-	- intmat_intmat_mult  [use intmat_times_intmat instead]
-
-Changed function prototypes:
-	- uncenter_cell
-	- cell_get_parameters/cartesian/reciprocal  [const added]
-	- panel_number  [const added]
-	- polarisation_correction  [uses new 'polarisation' structure]
-	- setup_indexing
-	- intmat_copy  [const added]
-	- taketwo_prepare/index
-
-Changed structure/enum definitions:
-	- UnitCellTransformation  [removed, use IntegerMatrix/RationalMatrix instead]
-	- struct rigid_group  [removed unused panel position deltas]
-	- PartialityModel  [added PMODEL_OFFSET and PMODEL_GGPM]
-	- struct spectrum/struct sample  [removed, use Spectrum instead]
-	- struct image  [removed num_peaks and num_saturated_peaks]
-	- IndexingMethod  [added INDEXING_PINKINDEXER]
-	- IndexingFlags  [removed _CHECK_CELL_COMBINATIONS/AXES, added _CHECK_CELL]
-	- IntegrationMethod  [removed INTEGRATION_RESCUT]
diff --git a/relnotes-0.9.1 b/relnotes-0.9.1
deleted file mode 100644
index 2d451cf0..00000000
--- a/relnotes-0.9.1
+++ /dev/null
@@ -1,90 +0,0 @@
-CrystFEL - Data processing for serial crystallography
------------------------------------------------------
-
-Release notes for version 0.9.1
-
-Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
-                      a research centre of the Helmholtz Association.
-
-Authors:
-  Thomas White <taw@physics.org>
-  Richard Kirian <rkirian@asu.edu>
-  Kenneth Beyerlein <kenneth.beyerlein@desy.de>
-  Andrew Aquila <andrew.aquila@cfel.de>
-  Andrew Martin <andrew.martin@desy.de>
-  Lorenzo Galli <lorenzo.galli@desy.de>
-  Chun Hong Yoon <chun.hong.yoon@desy.de>
-  Karol Nass <karol.nass@desy.de>
-  Nadia Zatsepin <nadia.zatsepin@asu.edu>
-  Anton Barty <anton.barty@desy.de>
-  Cornelius Gati <cornelius.gati@desy.de>
-  Fedor Chervinskii <fedor.chervinskii@gmail.com>
-  Alexandra Tolstikova <alexandra.tolstikova@desy.de>
-  Wolfgang Brehm <wolfgang.brehm@gmail.com>
-  Valerio Mariani <valerio.mariani@desy.de>
-  Parker de Waal <Parker.deWaal@vai.org>
-  Takanori Nakane <nakane.t@gmail.com>
-  Keitaro Yamashita <k.yamashita@spring8.or.jp>
-  Oleksandr Yefanov <oleksandr.yefanov@cfel.de>
-  Steve Aplin <steve.aplin@desy.de>
-  Helen Ginn <helen@strubi.ox.ac.uk>
-  Thomas Grant <tgrant@hwi.buffalo.edu>
-  Mamoru Suzuki <mamoru.suzuki@protein.osaka-u.ac.jp>
-  Nicolas Riebesel <nicolas.riebesel@tuhh.de>
-  Yaroslav Gevorkov <yaroslav.gevorkov@desy.de>
-  Omri Mor <omor1@asu.edu>
-
-CrystFEL is free software: you can redistribute it and/or modify it under the
-terms of the GNU General Public License as published by the Free Software
-Foundation, either version 3 of the License, or (at your option) any later
-version.
-
-CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE.  See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
-
-
-Overview
---------
-
-This is a maintenance and bug-fixing release which fixes a few issues which
-crept into CrystFEL 0.9.0.  Here are the detils, in roughly decreasing
-order of importance:
-
-1. The unit cell comparision function, which was completely re-written for
-   CrystFEL 0.9.0, was updated to fix a mis-indexing problem with certain
-   types of unit cell.  This may increase indexing rate or fix wrong output
-   cells in those cases.
-
-2. The default unit cell angle tolerance, which was accidentally set to
-   1.5 radians in CrystFEL 0.9.0, was re-set to 1.5 degrees.
-
-3. Build compatability was added with very new HDF5 versions (>= 1.12) and
-   older versions of zlib (< 1.2.3.5).
-
-4. A problem was fixed in indexamajig when reading metadata from certain
-   HDF5 structures (arrays of fixed length strings).
-
-5. The sigma(I) estimates for very weakly negative (unmerged) reflections
-   were improved.
-
-6. PinkIndexer logic fixes and documentation improvements, and addition of
-   "--pinkIndexer-max-refinement-disbalance" option to indexamajig.
-
-7. General documentation improvements.
-
-For your convenience, the announcement and release notes for the previous
-version (CrystFEL 0.9.0) have been included with version 0.9.1.  If you're
-upgrading from CrystFEL 0.8.0, you should check those files as well.
-As always, you can find more details in the "ChangeLog" or the changes page
-on the CrystFEL website.
-
-
-API changes
------------
-
-"maxRefinementDisbalance" was added to "struct pinkIndexer_options".
-No other API changes.