This is CrystFEL 0.9.10.9.1

4 files changed, 149 insertions, 2 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4b21e094..d51d5dc6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.6)
-set(CRYSTFEL_SHORT_VERSION 0.9.0)
+set(CRYSTFEL_SHORT_VERSION 0.9.1)
 set(CRYSTFEL_VERSION ${CRYSTFEL_SHORT_VERSION})
-set(CRYSTFEL_API_VERSION 12)
+set(CRYSTFEL_API_VERSION 13)
 project(crystfel VERSION ${CRYSTFEL_VERSION} LANGUAGES C)
 
 cmake_policy(SET CMP0074 NEW)
diff --git a/ChangeLog b/ChangeLog
index f67ecec8..df937a28 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,21 @@
+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
+- Improved the sigma estimate for very weak reflections
+- Fixed bug when indexing with rhombohedral R cells
+- indexamajig: Added --pinkIndexer-max-refinement-disbalance
+- Fixed two problems when reading metadata values from HDF5
+- partialator: Gracefully handle negative and NaN sigma values
+- scripts/transfer-geom: Now only writes coffset for panels which had
+  coffset values before
+- Fixed/improved pinkIndexer documentation and error messages
+- Fixed build with zlib < 1.2.3.5 (missing gzbuffer routine)
+- Fixed build with HDF5 >= 1.12
+- scripts/mtz2hkl, cif2hkl, hkl2hkl: Added missing header
+
+
 CrystFEL version 0.9.0, 6th February 2020
 -----------------------------------------
 
diff --git a/announcement-0.9.1 b/announcement-0.9.1
new file mode 100644
index 00000000..6ddda6cb
--- /dev/null
+++ b/announcement-0.9.1
@@ -0,0 +1,39 @@
+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/relnotes-0.9.1 b/relnotes-0.9.1
new file mode 100644
index 00000000..2d451cf0
--- /dev/null
+++ b/relnotes-0.9.1
@@ -0,0 +1,90 @@
+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.