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January 2016

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Subject	From	Date	Size
[git/dials] master: For dials.combine_experiments, add ability to average the reference detector. (1c8c93c)	DIALS Commit via DLS Jenkins	Fri, 29 Jan 2016 17:26:34 -0800	288 lines
[git/dials] master: Use CalculateCellGradients within SingleUnitCellTie._calculate_uc_gradients (f9096cd)	DIALS Commit via DLS Jenkins	Fri, 29 Jan 2016 15:56:37 +0000	248 lines
[git/dials] master: New C++ class CalculateCellGradients to convert B and dB/dp into gradients of the real space cell (4b2184f)	DIALS Commit via DLS Jenkins	Fri, 29 Jan 2016 15:55:02 +0000	580 lines
[git/dials] master: also don't need the angles (f93d6d7)	DIALS Commit via DLS Jenkins	Fri, 29 Jan 2016 14:47:38 +0000	85 lines
[git/dials] master: remove unused variables (5c21ddd)	DIALS Commit via DLS Jenkins	Fri, 29 Jan 2016 14:32:27 +0000	78 lines
[git/dials] master: delete unused AngleDerivativeWrtVectorElts class (6518762)	DIALS Commit via DLS Jenkins	Thu, 28 Jan 2016 17:06:30 +0000	204 lines
[git/dials] master: use angle_derivative_wrt_vectors in SingleUnitCellTie (1cd557c)	DIALS Commit via DLS Jenkins	Thu, 28 Jan 2016 17:05:37 +0000	126 lines
[git/dials] master: now I can use more sensible names (5e11472)	DIALS Commit via DLS Jenkins	Thu, 28 Jan 2016 16:56:34 +0000	149 lines
[git/dials] master: Use C++ angle_derivative_wrt_vectors function within CrystalUnitCellParameterisation (129ce71)	DIALS Commit via DLS Jenkins	Thu, 28 Jan 2016 16:51:20 +0000	171 lines
[git/dials] master: add crystal IDs and slightly change format of ESD debug output (4ea9f62)	DIALS Commit via DLS Jenkins	Wed, 27 Jan 2016 15:57:22 +0000	123 lines
[git/dials] master: Do not add negative values when merging cbf files (5aeb14e)	DIALS Commit via DLS Jenkins	Wed, 27 Jan 2016 13:56:33 +0000	91 lines
[git/dials] master: Enable command line completion, show .json filename if written (19ea357)	DIALS Commit via DLS Jenkins	Wed, 27 Jan 2016 13:29:48 +0000	87 lines
[git/dials] master: Further fix for stills indexer. (6465bc4)	DIALS Commit via DLS Jenkins	Tue, 26 Jan 2016 14:55:40 -0800	87 lines
[git/dials] master: Fix for stills_index (53251e3)	DIALS Commit via DLS Jenkins	Tue, 26 Jan 2016 13:30:56 -0800	84 lines
[git/dials] master: prettify 'worst residuals' tables in the debug log (f12987a)	DIALS Commit via DLS Jenkins	Tue, 26 Jan 2016 11:54:04 +0000	291 lines
[git/dials] master: report number of experiments being refined in the log (b57d5ff)	DIALS Commit via DLS Jenkins	Tue, 26 Jan 2016 11:32:39 +0000	102 lines
[git/dials] master: also have to copy flag over here (ebbbccf)	DIALS Commit via DLS Jenkins	Tue, 26 Jan 2016 11:18:23 +0000	87 lines
[git/dials] master: set centroid_outlier flag in original indexed reflections (d5af485)	DIALS Commit via DLS Jenkins	Tue, 26 Jan 2016 10:51:32 +0000	88 lines
[git/dials] master: additional condition for #67 (a902c5a)	DIALS Commit via DLS Jenkins	Mon, 25 Jan 2016 20:36:45 +0000	74 lines
[git/dials] master: potential simple fix for #67, still to be tested against the problematic data (57c8131)	DIALS Commit via DLS Jenkins	Mon, 25 Jan 2016 19:58:15 +0000	79 lines
[git/dials] master: ascii_art: correctly support char and height keywords (147c103)	DIALS Commit via DLS Jenkins	Fri, 22 Jan 2016 15:09:59 +0000	200 lines
[git/dials] master: simplification of ascii art accompanying text suggested by @graeme-winter (4420938)	DIALS Commit via DLS Jenkins	Fri, 22 Jan 2016 14:12:32 +0000	118 lines
[git/dials] master: ascii version of spot count per image plot (b45c83a)	DIALS Commit via DLS Jenkins	Fri, 22 Jan 2016 12:17:44 +0000	341 lines
[git/dials] master: Sync with get_raw_data changes in dxtbx. (7faaaf8)	DIALS Commit via DLS Jenkins	Wed, 20 Jan 2016 18:11:18 -0800	153 lines
[git/dials] master: enable command line completion for rlv (7863286)	DIALS Commit via DLS Jenkins	Wed, 20 Jan 2016 14:21:56 +0000	72 lines
[git/dials] master: Gracefully handle case (e.g. pseudosymmetry) where change of basis op results in non-integral miller indices (acc6e87)	DIALS Commit via DLS Jenkins	Wed, 20 Jan 2016 10:22:08 +0000	128 lines
[git/dials] master: Add a stills-specific indexer. (e9461c2)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 14:13:36 -0800	2216 lines
[git/dials] master: correct logic (c4f6d74)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 16:32:09 +0000	78 lines
[git/dials] master: bug fix for flagging unindexed reflections (40afbaa)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 16:07:42 +0000	79 lines
[git/dials] master: Make the format instance null before going into parallism. Then the format is reopened after the fork so that HDF5 doesn't break. NOTE THIS IS A STUPID HACK. WHY DOES HDF5 NOT ALLOW PARALLEL READS???? Fixes #35 (36f63d6)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 15:43:46 +0000	147 lines
[git/dials] master: make test fail gracefully if xia2_regression not properly configured (d825a5c)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 14:54:51 +0000	82 lines
[git/dials] master: Make it more obvious this column refers to the id in reflection table (2e11185)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 14:38:47 +0000	80 lines
[git/dials] master: Fixed profile fitting for scan varying profile model. Fixes #34 (882558d)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 13:18:26 +0000	198 lines
[git/dials] master: predict for all indexed reflections at end of indexing: closes #59 (92998e1)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 12:34:03 +0000	113 lines
[git/dials] master: More consistent formatting (1d2dbc4)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 08:40:34 +0000	73 lines
[git/dials] master: If len(crystals) == 1; info(crystal model); fixes #56 (a83c3a3)	DIALS Commit via DLS Jenkins	Tue, 19 Jan 2016 08:39:55 +0000	85 lines
[git/dials] master: Fixed simulate scripts (c231e81)	DIALS Commit via DLS Jenkins	Mon, 18 Jan 2016 13:29:48 +0000	414 lines
[git/dials] master: Fixed tests. Fixes #50 (18655c7)	DIALS Commit via DLS Jenkins	Mon, 18 Jan 2016 13:29:48 +0000	305 lines
[git/dials] master: bug fix (03a8e98)	DIALS Commit via DLS Jenkins	Mon, 18 Jan 2016 13:23:20 +0000	119 lines
[git/dials] master: default marker_size=5 (06f2cd8)	DIALS Commit via DLS Jenkins	Mon, 18 Jan 2016 13:09:07 +0000	74 lines
[git/dials] master: add buttons to choose which experiment ids to display in case of multiple lattices: closes #46 (453e4e0)	DIALS Commit via DLS Jenkins	Mon, 18 Jan 2016 13:01:37 +0000	201 lines
[git/dials] master: add possibility to select which experiment ids to display via command line (3c3b38f)	DIALS Commit via DLS Jenkins	Mon, 18 Jan 2016 11:32:31 +0000	105 lines
[git/dials] master: fix display of all/indexed/unindexed reflections (5b5a359)	DIALS Commit via DLS Jenkins	Mon, 18 Jan 2016 10:18:00 +0000	234 lines
[git/dials] master: increase default marker size (57e45d4)	DIALS Commit via DLS Jenkins	Fri, 15 Jan 2016 16:30:27 +0000	94 lines
[git/dials] master: display multiple lattices in different colours (a575f46)	DIALS Commit via DLS Jenkins	Fri, 15 Jan 2016 16:29:46 +0000	165 lines
[git/dials] master: only map_points_to_reciprocal_space if beam centre has changed (cba22ae)	DIALS Commit via DLS Jenkins	Fri, 15 Jan 2016 15:10:59 +0000	106 lines
[git/dials] master: min_cell_volume -> 25; catch ValueError from refinement in choose_best_orientation_matrix (6e1cd76)	DIALS Commit via DLS Jenkins	Fri, 15 Jan 2016 14:11:38 +0000	96 lines
[git/dials] master: add min_cell_volume=100; fixes #48 (7491648)	DIALS Commit via DLS Jenkins	Fri, 15 Jan 2016 14:00:53 +0000	102 lines
[git/dials] master: fixes #42 (d615adb)	DIALS Commit via DLS Jenkins	Fri, 15 Jan 2016 13:28:47 +0000	79 lines
[git/dials] master: 'fix' for #47 (412bb16)	DIALS Commit via DLS Jenkins	Fri, 15 Jan 2016 13:20:56 +0000	81 lines
[git/dials] master: ensure that all reflections with -ve id are flagged as not indexed (3a70d9e)	DIALS Commit via DLS Jenkins	Fri, 15 Jan 2016 12:01:36 +0000	100 lines
[git/dials] master: Added a script to interogate a selection of datablock files to decide which models might be shared between sweeps. (b4c08b1)	DIALS Commit via DLS Jenkins	Fri, 15 Jan 2016 11:05:10 +0000	459 lines
[git/dials] master: Added message in dials.integrate when you use an external mask. Fixes #44 (a692caf)	DIALS Commit via DLS Jenkins	Thu, 14 Jan 2016 14:54:42 +0000	88 lines
[git/dials] master: refactor report html code to make resuable elsewhere (7f3bab5)	DIALS Commit via DLS Jenkins	Thu, 14 Jan 2016 13:29:02 +0000	1205 lines
[git/dials] master: Remove test from scratch (d93fcc6)	DIALS Commit via DLS Jenkins	Wed, 13 Jan 2016 15:55:01 +0000	73 lines
[git/dials] master: Remove dangling SConscript reference (b62fb23)	DIALS Commit via DLS Jenkins	Wed, 13 Jan 2016 15:08:02 +0000	76 lines
[git/dials] master: Move /scratch and /doc/developer into dials_scratch. Put in a note so people know how to get them back (ad89f5a)	DIALS Commit via DLS Jenkins	Wed, 13 Jan 2016 13:18:22 +0000	1361 lines
[git/dials] master: temporarily disable cell doubling checks with known cell (b48de62)	DIALS Commit via DLS Jenkins	Tue, 12 Jan 2016 14:55:33 +0000	75 lines
[git/dials] master: check for unit cell doubling/tripling when provided with known unit cell (d1c6104)	DIALS Commit via DLS Jenkins	Tue, 12 Jan 2016 13:31:38 +0000	372 lines
[git/dials] master: Add option to force static model in export (0469d56)	DIALS Commit via DLS Jenkins	Tue, 12 Jan 2016 12:06:35 +0000	161 lines
[git/dials] master: Fixed test + clena clutter (b598de3)	DIALS Commit via DLS Jenkins	Tue, 12 Jan 2016 11:34:10 +0000	128 lines
[git/dials] master: Added checks in create_profile_model for indexed reflections etc as done in dials.integrate. Fixes #38 (e976eab)	DIALS Commit via DLS Jenkins	Tue, 12 Jan 2016 11:05:54 +0000	185 lines
[git/dials] master: Implement new refinery engine for SparseLevMar. (139e5f9)	DIALS Commit via DLS Jenkins	Mon, 11 Jan 2016 10:06:47 -0800	516 lines
[git/dials] master: Phil control option to pick a new refinery engine for SparseLevMar. (1fdb4fe)	DIALS Commit via DLS Jenkins	Mon, 11 Jan 2016 09:55:57 -0800	98 lines
[git/dials] master: update doc/sphinx README (2ee1850)	DIALS Commit via DLS Jenkins	Mon, 11 Jan 2016 17:14:49 +0000	251 lines
[git/dials] master: A parameterisation will not exist if all its parameters have been fixed (577d20f)	DIALS Commit via DLS Jenkins	Mon, 11 Jan 2016 16:35:35 +0000	91 lines
[git/dials] master: make gradients and curvatures flex.double once they are fully calculated, then treat them as such later (380ae18)	DIALS Commit via DLS Jenkins	Mon, 11 Jan 2016 14:25:41 +0000	131 lines
[git/dials] master: move my scratch files into separate branch (0eb98c5)	DIALS Commit via DLS Jenkins	Mon, 11 Jan 2016 10:44:08 +0000	2233 lines
[git/dials] master: Clean clutter. (27d87d8)	DIALS Commit via DLS Jenkins	Mon, 11 Jan 2016 08:48:08 +0000	119 lines
[git/dials] master: Merge branch 'master' of github.com:dials/dials (e4b3401)	DIALS Commit via DLS Jenkins	Sat, 9 Jan 2016 15:50:27 -0800	373 lines
[git/dials] master: Clean clutter. (569c89d)	DIALS Commit via DLS Jenkins	Sat, 9 Jan 2016 15:19:05 -0800	119 lines
[git/dials] master: bug fix: put gradients in the right place for multiple crystals (097332f)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:44 +0000	106 lines
[git/dials] master: expose restrained refinement to AdaptLbfgs engines (595a382)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:44 +0000	119 lines
[git/dials] master: more testing (bfaef27)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:44 +0000	531 lines
[git/dials] master: return values as flex.double. Correct help string (9e20f83)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:43 +0000	108 lines
[git/dials] master: allow restrained refinement for AdaptLstbx engines (e1aa074)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:43 +0000	108 lines
[git/dials] master: allow specification of multiple experiments for a single set of tie_to_target.values (a347f74)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:43 +0000	191 lines
[git/dials] master: convert 0.0 to None here (2e7719e)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:43 +0000	73 lines
[git/dials] master: Target.compute_restraints_functional_gradients_and_curvatures might be the longest method name I've yet used. There are three return values, so it could be refactored. Anyway, this allows AdaptLbfgs-like engines to do restrained refinement (279f6fc)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:43 +0000	137 lines
[git/dials] master: tidying (32daffb)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:43 +0000	137 lines
[git/dials] master: correct help string: Nones do not work within floats (0b47229)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:43 +0000	85 lines
[git/dials] master: Do not calculate least squares quantities in the restraints. Leave this to the Target class (8efdd85)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:43 +0000	431 lines
[git/dials] master: Target.compute_restraints_residuals_and_gradients method (ef7493a)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 20:51:43 +0000	109 lines
[git/dials] master: Added directory option to import. Fixes #22 (3a66095)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 17:40:29 +0000	163 lines
[git/dials] master: select only non-negative experiment id in export_mtz (3e310b6)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 16:58:01 +0000	85 lines
[git/dials] master: Check the input datablock for beam and detector information. Raise a Sorry error if there is no information and add a useful error message. Fixes #32 (7f0578b)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 16:36:25 +0000	133 lines
[git/dials] master: Added the ability to propagate reflections passed in as reference spots which are not used because they are not indexed or have dodgy predictions etc. Enabled with output.include_bad_reference=True. Fixes #36 (35564d6)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 16:01:40 +0000	476 lines
[git/dials] master: Changed experiment iD from size_t to int to propagate unindexed reflections which have an id of -1 (4476506)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 16:01:40 +0000	225 lines
[git/dials] master: dials.image_viewer: add text control to jump to arbitrary image number (5364c87)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 14:38:52 +0000	108 lines
[git/dials] master: Changed integration output to report low/high resolution bins as the outer bins in the resolution plot to be more like aimless/xia2 output rather than splitting dataset in half which some found confusing. Fixes #24 (55ee9b5)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 11:03:12 +0000	144 lines
[git/dials] master: override OnLeftUp method to avoid traceback on double-click (f4b08bf)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 10:31:53 +0000	83 lines
[git/dials] master: graceful fail without dials_regression (66a1f5d)	DIALS Commit via DLS Jenkins	Fri, 8 Jan 2016 10:01:26 +0000	83 lines
[git/dials] master: add to run_tests.py (0e7d5c6)	DIALS Commit via DLS Jenkins	Thu, 7 Jan 2016 16:12:41 +0000	94 lines
[git/dials] master: improve test (6319617)	DIALS Commit via DLS Jenkins	Thu, 7 Jan 2016 15:45:21 +0000	417 lines
[git/dials] master: remove debugging statements (2e0c118)	DIALS Commit via DLS Jenkins	Thu, 7 Jan 2016 15:44:46 +0000	202 lines
[git/dials] master: bug fix (38db260)	DIALS Commit via DLS Jenkins	Wed, 6 Jan 2016 18:19:36 +0000	80 lines
[git/dials] master: bug fix, RAD2DEG not applied properly in the test script (52a5bac)	DIALS Commit via DLS Jenkins	Wed, 6 Jan 2016 12:33:17 +0000	121 lines
[git/dials] master: continue work on a test of RestraintsParameterisation (bf75a95)	DIALS Commit via DLS Jenkins	Wed, 6 Jan 2016 12:33:17 +0000	393 lines
[git/dials] master: return angle derivatives in degrees not radians, as the target unit cell is provided in angstroms and degrees (aff5e87)	DIALS Commit via DLS Jenkins	Wed, 6 Jan 2016 12:33:16 +0000	148 lines
[git/dials] master: RestraintsParameterisation.get_values_and_gradients using sparse storage (5967ce7)	DIALS Commit via DLS Jenkins	Wed, 6 Jan 2016 12:33:16 +0000	160 lines
[git/dials] master: add values and gradients methods to SingleUnitCellTie (ad17e45)	DIALS Commit via DLS Jenkins	Wed, 6 Jan 2016 12:33:16 +0000	200 lines
[git/dials] master: plots of number of indexed reflections per image, distribution of unindexed reflections vs x/y, number of indexed reflections per lattice/per image (7fb6072)	DIALS Commit via DLS Jenkins	Tue, 5 Jan 2016 16:39:58 +0000	486 lines
[git/dials] master: include unindexed reflections in reflections output by dials.index (ca7d7cb)	DIALS Commit via DLS Jenkins	Tue, 5 Jan 2016 16:37:37 +0000	147 lines
[git/dials] master: fix dials.export syntax (c164435)	DIALS Commit via DLS Jenkins	Tue, 5 Jan 2016 16:35:19 +0000	127 lines
[git/dials] master: pass --long to git describe (35d3d72)	DIALS Commit via DLS Jenkins	Mon, 4 Jan 2016 14:30:42 +0000	82 lines
[git/dials] master: update default dials version to 1.0 (835a23a)	DIALS Commit via DLS Jenkins	Mon, 4 Jan 2016 14:22:45 +0000	74 lines
[git/dials] master: Fixed bug (2d6133e)	DIALS Commit via DLS Jenkins	Mon, 4 Jan 2016 10:04:40 +0000	100 lines
[git/dials] master: Rejigged a bit. Save state to json file. Fixes #19 (8a0dbb8)	DIALS Commit via DLS Jenkins	Mon, 4 Jan 2016 10:04:40 +0000	2806 lines
[git/dials] master: Allow export filename to be set Fixes #27 (0bbcbb5)	DIALS Commit via DLS Jenkins	Mon, 4 Jan 2016 10:04:40 +0000	117 lines
[git/dials] tag '1.0' created	DIALS Commit via DLS Jenkins	Fri, 18 Dec 2015 18:09:39 +0000	28 lines

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