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September 2017

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Subject	From	Date	Size
[git/cctbx] master: Fix bug read file (466491f77)	CCTBX Commit via DLS Jenkins	Fri, 29 Sep 2017 16:17:25 -0700	206 lines
[git/cctbx] master: add iotbx.fetch_pdb synonym (aa31ece0a)	CCTBX Commit via DLS Jenkins	Fri, 29 Sep 2017 09:56:11 +0100	72 lines
[git/cctbx] master: Fixed a bug in applying gain and pedestal introduced in refactor. The correct loop indices are now used. (deff7dc73)	CCTBX Commit via DLS Jenkins	Fri, 29 Sep 2017 09:55:28 +0100	122 lines
[git/cctbx] master: fixing density modification test and program (4ddd67ca0)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 14:41:39 -0700	222 lines
[git/cctbx] master: satisfying test (154e9ee7a)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 14:41:39 -0700	69 lines
[git/cctbx] master: Updated paths for Doxygen (711649707)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 14:32:48 -0700	196 lines
[git/cctbx] master: initialise Amber earlier (7d66e95ce)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 13:14:53 -0700	132 lines
[git/cctbx] master: Marking bad examples (df3b00099)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 12:55:45 -0700	140 lines
[git/cctbx] master: Refactored example (11898ad9b)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 12:55:23 -0700	175 lines
[git/cctbx] master: just changing API for mmtbx.model to hide xray_structure behind get and set functions (1997889dd)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 11:58:11 -0700	149 lines
[git/cctbx] master: better way (0970cdf35)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 11:58:11 -0700	84 lines
[git/cctbx] master: getters, setters, hiding mon_lib and ener_lib (177bc0e8a)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 11:58:11 -0700	217 lines
[git/cctbx] master: Bugfix for xtc_process. When using dispatch.integrate=False, do log the successfully indexed frames (438df88d1)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 11:19:29 -0700	83 lines
[git/cctbx] master: Fixes for XFEL GUI, transitioning from wxPython 2.8 to 3.0 (1be6fd6b3)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 11:19:29 -0700	378 lines
[git/cctbx] master: Change defaults for cxi.mpi_submit: use DIALS instead of LABELIT as default, use split_logs by default (c76659fb7)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 11:19:28 -0700	103 lines
[git/cctbx] master: pytest 3 compatibility fix (62441d3e7)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 09:41:57 +0100	78 lines
[git/cctbx] master: drop pypi package colorama from bootstrap (4621aaeda)	CCTBX Commit via DLS Jenkins	Thu, 28 Sep 2017 09:14:25 +0100	101 lines
[git/cctbx] master: fixed afitt (1938b3b9b)	CCTBX Commit via DLS Jenkins	Wed, 27 Sep 2017 14:01:16 -0700	80 lines
[git/cctbx] master: Add notes (32cf76c27)	CCTBX Commit via DLS Jenkins	Wed, 27 Sep 2017 13:47:59 -0700	78 lines
[git/cctbx] master: dummy fix (84a30b38f)	CCTBX Commit via DLS Jenkins	Wed, 27 Sep 2017 14:41:42 -0600	78 lines
[git/cctbx] master: dummy (706ca0048)	CCTBX Commit via DLS Jenkins	Wed, 27 Sep 2017 14:40:52 -0600	78 lines
[git/cctbx] master: remove unnecessary assertion (8098ec87b)	CCTBX Commit via DLS Jenkins	Wed, 27 Sep 2017 14:03:18 -0400	72 lines
[git/cctbx] master: local resolution estimate using model (d265d8e74)	CCTBX Commit via DLS Jenkins	Wed, 27 Sep 2017 12:36:53 -0400	226 lines
[git/cctbx] master: Raise a special error when DataBlock/ExperimentList validation fails (80cb8f74b)	CCTBX Commit via DLS Jenkins	Wed, 27 Sep 2017 10:48:51 +0100	241 lines
[git/cctbx] master: avoid import conflicts from shadowing python package name (71ef27bda)	CCTBX Commit via DLS Jenkins	Wed, 27 Sep 2017 07:56:21 +0100	446 lines
[git/cctbx] master: Test matplotlib (dd784c15e)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 23:43:17 -0700	179 lines
[git/cctbx] master: Placeholder for sigma-a calculation (7a42495b0)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 22:59:51 -0400	227 lines
[git/cctbx] master: cleanup (7c79ce9a7)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 14:13:48 -0700	151 lines
[git/cctbx] master: refactoring of pdb_atom_selection to use mmtbx.model (087d7c3af)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 13:10:23 -0700	214 lines
[git/cctbx] master: getter/setter (d0b92248f)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 13:09:58 -0700	90 lines
[git/cctbx] master: Better handling reprocessing (4916e343d)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 12:39:37 -0700	80 lines
[git/cctbx] master: rereading model when AC were cutted (2aaa1540a)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 08:53:40 -0700	119 lines
[git/cctbx] master: lazy fix. testing functionality that relies on random function (187cb32a1)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 08:53:40 -0700	74 lines
[git/cctbx] master: Nasty hacks which GW should revisit with JMP & ND to improve; for grid scans on eigers with complex depends-on stack (4969710db)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 16:32:24 +0100	119 lines
[git/cctbx] master: Ohai package management (ea7c2c051)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 16:27:14 +0100	245 lines
[git/cctbx] master: Make it clear that k_sol and b_sol are not applied in auto sharpening with map at present (8e79aea26)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 08:58:12 -0600	164 lines
[git/cctbx] master: Fix bug in segment_and_split with half-maps and no model (073be8f1d)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 08:14:05 -0600	102 lines
[git/cctbx] master: comment (88fcc2922)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 06:45:37 -0700	98 lines
[git/cctbx] master: make test skipping work. test still disabled though, #11 (1e223edec)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 13:44:21 +0100	86 lines
[git/cctbx] master: Allow uint32 & int32 as mask types (6f7f92baa)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 10:41:19 +0100	74 lines
[git/cctbx] master: Fixed indices for HDF5 files (36533b3a9)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 10:37:07 +0100	549 lines
[git/cctbx] master: Allow construction of an unpolarized beam (7b203e302)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 09:57:59 +0100	80 lines
[git/cctbx] master: unpolarized beam for various electron microscope formats (bc2747ca7)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 09:57:59 +0100	187 lines
[git/cctbx] master: reduce cython installation time from 96 seconds to 4 seconds (8f47ee232)	CCTBX Commit via DLS Jenkins	Tue, 26 Sep 2017 08:56:05 +0100	161 lines
[git/cctbx] master: Handle files. Code clean-up. (6469435fc)	CCTBX Commit via DLS Jenkins	Mon, 25 Sep 2017 18:05:54 -0700	780 lines
[git/cctbx] master: For dials/dials#453 only dials-assert if reader is not pointing at single file (00a8394c0)	CCTBX Commit via DLS Jenkins	Mon, 25 Sep 2017 13:05:18 +0100	81 lines
[git/cctbx] master: Update chain_comparison to ignore hetero and to include just unique chains in target if unique_only=True (3399d634d)	CCTBX Commit via DLS Jenkins	Sun, 24 Sep 2017 17:52:10 -0600	350 lines
[git/cctbx] master: Add quadratic interpolation with gradients (in progress, tests coming); add hooks to implement MLI target with uncertainties from experiment. (df5cf88e6)	CCTBX Commit via DLS Jenkins	Sat, 23 Sep 2017 09:39:42 -0700	94 lines
[git/cctbx] master: catch case where no mask is obtained (023cbc454)	CCTBX Commit via DLS Jenkins	Fri, 22 Sep 2017 17:13:44 -0600	78 lines
[git/cctbx] master: cleanup (54aad358b)	CCTBX Commit via DLS Jenkins	Fri, 22 Sep 2017 12:39:47 -0700	316 lines
[git/cctbx] master: adding monomer_parameters to the mmtbx.model to accomodate restraints by filename for now (phenix.refine accomodation). (2ee63fa58)	CCTBX Commit via DLS Jenkins	Fri, 22 Sep 2017 10:55:42 -0700	167 lines
[git/cctbx] master: Hopefully clearer error message (323d3e41f)	CCTBX Commit via DLS Jenkins	Fri, 22 Sep 2017 10:02:06 -0700	77 lines
[git/cctbx] master: Only look at first ncs group for point_group/helical symmetry (e0bd183bf)	CCTBX Commit via DLS Jenkins	Thu, 21 Sep 2017 20:46:08 -0600	76 lines
[git/cctbx] master: API: cs->crystal_symmetry (8bd12ebc0)	CCTBX Commit via DLS Jenkins	Thu, 21 Sep 2017 11:53:49 -0700	309 lines
[git/cctbx] master: Better names in mmtbx.model (6d4f492d3)	CCTBX Commit via DLS Jenkins	Thu, 21 Sep 2017 11:33:20 -0700	565 lines
[git/cctbx] master: some small rearrangements (04789e5ba)	CCTBX Commit via DLS Jenkins	Thu, 21 Sep 2017 10:08:40 -0700	149 lines
[git/cctbx] master: converting reprocess_pdb_hierarchy_inefficient to use self (3d8ba63da)	CCTBX Commit via DLS Jenkins	Wed, 20 Sep 2017 18:24:02 -0700	458 lines
[git/cctbx] master: image tracker upgrade (d16d95db2)	CCTBX Commit via DLS Jenkins	Wed, 20 Sep 2017 17:29:01 -0700	2050 lines
[git/cctbx] master: proper mmtbx.model usage in ensemble_ref (10eba1ad9)	CCTBX Commit via DLS Jenkins	Wed, 20 Sep 2017 15:49:49 -0700	508 lines
[git/cctbx] master: removing refinement_flags from mmtbx.model constructor (d4af59a01)	CCTBX Commit via DLS Jenkins	Wed, 20 Sep 2017 14:11:23 -0700	484 lines
Jenkins 5a cctbx Tests build 5037 Fixed	Jenkins Build Server (Diamond)	Wed, 20 Sep 2017 16:02:04 +0100	37 lines
Jenkins 5a cctbx Tests build 5036 Failure	Jenkins Build Server (Diamond)	Wed, 20 Sep 2017 15:20:47 +0100	154 lines
[git/cctbx] master: Catch rare case where there are many duplicate resolutions so kernel_width is too low (2f3230bc6)	CCTBX Commit via DLS Jenkins	Wed, 20 Sep 2017 08:18:04 -0600	95 lines
[git/cctbx] master: better default (8efdff985)	CCTBX Commit via DLS Jenkins	Tue, 19 Sep 2017 20:43:56 -0700	72 lines
[git/cctbx] master: Fast bugfixes to make model_idealization run (0b1bd768d)	CCTBX Commit via DLS Jenkins	Tue, 19 Sep 2017 19:54:09 -0700	214 lines
[git/cctbx] master: Fixing wrong output in statistics (386ebedf9)	CCTBX Commit via DLS Jenkins	Tue, 19 Sep 2017 19:54:09 -0700	79 lines
[git/cctbx] master: commenting out debug output (01e502915)	CCTBX Commit via DLS Jenkins	Tue, 19 Sep 2017 19:54:09 -0700	92 lines
[git/cctbx] master: new option (956e872bd)	CCTBX Commit via DLS Jenkins	Tue, 19 Sep 2017 19:54:09 -0700	130 lines
[git/cctbx] master: Follow up to removal of optik Rename --skip-phenix-dispatchers back to --skip_phenix_dispatchers Adjust usages of --skip_phenix_dispatchers, --enable_openmp_if_possible, --opt_resources and --clear_scons_memory to use underscores instead of dashes. (eef731000)	CCTBX Commit via DLS Jenkins	Tue, 19 Sep 2017 12:23:35 -0700	174 lines
[git/cctbx] master: libtbx: Rename skip_phenix_dispatchers option (c6d0be5e2)	CCTBX Commit via DLS Jenkins	Tue, 19 Sep 2017 13:57:18 +0100	86 lines
Jenkins 5a cctbx Tests build 5030 Fixed	Jenkins Build Server (Diamond)	Tue, 19 Sep 2017 10:02:47 +0100	37 lines
[git/cctbx] master: fix typo from May 2008 (0a9e8be3f)	CCTBX Commit via DLS Jenkins	Tue, 19 Sep 2017 09:56:59 +0100	77 lines
Jenkins 5a cctbx Tests build 5029 Unstable	Jenkins Build Server (Diamond)	Tue, 19 Sep 2017 09:50:24 +0100	98 lines
Jenkins 5a cctbx Tests build 5029 Unstable	Jenkins Build Server (Diamond)	Tue, 19 Sep 2017 09:50:23 +0100	40 lines
[git/cctbx] master: Replace optik library with optparse. (0da318d83)	CCTBX Commit via DLS Jenkins	Tue, 19 Sep 2017 08:02:50 +0100	86 lines
[git/cctbx] master: allow tolerances on point-group and helical symmetry to be changed in map_to_model (e84e92999)	CCTBX Commit via DLS Jenkins	Mon, 18 Sep 2017 23:51:46 -0600	256 lines
[git/cctbx] master: Fixing detector = None bug for HDF5 files (031e845f7)	CCTBX Commit via DLS Jenkins	Mon, 18 Sep 2017 11:10:08 +0100	109 lines
[git/cctbx] master: more ncs -> mmtbx.model (188b2d2ee)	CCTBX Commit via DLS Jenkins	Fri, 15 Sep 2017 17:50:36 -0700	649 lines
[git/cctbx] master: torsion_ncs -> mmtbx.model. adjusting test (3d1ce9a51)	CCTBX Commit via DLS Jenkins	Fri, 15 Sep 2017 16:26:01 -0700	343 lines
[git/cctbx] master: make getter (0ba26476b)	CCTBX Commit via DLS Jenkins	Fri, 15 Sep 2017 15:55:05 -0700	76 lines
[git/cctbx] master: better cif handling (45feb272d)	CCTBX Commit via DLS Jenkins	Fri, 15 Sep 2017 15:30:01 -0700	317 lines
[git/cctbx] master: Better pdb output for mmtbx.model. Better failure report in tst_linking (7e970ff01)	CCTBX Commit via DLS Jenkins	Fri, 15 Sep 2017 14:21:14 -0700	329 lines
[git/cctbx] master: cleanup (329363afd)	CCTBX Commit via DLS Jenkins	Fri, 15 Sep 2017 12:34:44 -0700	117 lines
[git/cctbx] master: Switch load_model_and_data to use mmtbx.model. Copy setup_scattering_dictionaries to mmtbx.model, mark for deletion, switch phenix.refine to use it. Removing helpers 'pdb_file' and 'model_simple' from mmtbx.utils, refactoring code relied on them. (8ce84d46a)	CCTBX Commit via DLS Jenkins	Fri, 15 Sep 2017 12:09:34 -0700	1440 lines
[git/cctbx] master: Removing unused, custom-to-berkeley module. (21e37f4b7)	CCTBX Commit via DLS Jenkins	Fri, 15 Sep 2017 12:09:34 -0700	490 lines
[git/cctbx] master: bug fix for elderly I23 images where MultiAxisGoniometer does not exist (7c9d04bf4)	CCTBX Commit via DLS Jenkins	Fri, 15 Sep 2017 09:15:50 +0100	87 lines
[git/cctbx] master: Fixing path so the test would run again. (e660fc6a1)	CCTBX Commit via DLS Jenkins	Thu, 14 Sep 2017 12:00:00 -0700	74 lines
[git/cctbx] master: cleanup (d270ee041)	CCTBX Commit via DLS Jenkins	Thu, 14 Sep 2017 12:00:00 -0700	327 lines
[git/cctbx] master: Merge commit '0c13643' (dab14c201)	CCTBX Commit via DLS Jenkins	Thu, 14 Sep 2017 11:23:52 -0700	52 lines
[git/cctbx] master: Put titles on the XFEL UI unit cell plots with # xtals. (0c136439e)	CCTBX Commit via DLS Jenkins	Thu, 14 Sep 2017 11:16:17 -0700	242 lines
[git/cctbx] master: changing all_chain_proxies+xray_structure to mmtbx.model (2e413cbbb)	CCTBX Commit via DLS Jenkins	Wed, 13 Sep 2017 19:20:28 -0700	1111 lines
[git/cctbx] master: Turning model_vs_data, pdbtools, ensemble_refinement into using model to follow refactoring of mmtbx.get_atom_selections. (df1b28793)	CCTBX Commit via DLS Jenkins	Wed, 13 Sep 2017 19:20:28 -0700	88 lines
[git/cctbx] master: Allow alternate setting for icosahedral symmetry (758f04316)	CCTBX Commit via DLS Jenkins	Wed, 13 Sep 2017 13:53:10 -0600	858 lines
[git/cctbx] master: removed useless prints (98126bd4e)	CCTBX Commit via DLS Jenkins	Wed, 13 Sep 2017 11:35:09 -0700	78 lines
[git/cctbx] master: adjusted test to work on all machines (dbcc3741d)	CCTBX Commit via DLS Jenkins	Wed, 13 Sep 2017 11:15:12 -0700	143 lines
[git/cctbx] master: Temp disable strange test. (778a7ee52)	CCTBX Commit via DLS Jenkins	Wed, 13 Sep 2017 10:04:21 -0700	75 lines
[git/cctbx] master: HDF5 library update (ca39882d5)	CCTBX Commit via DLS Jenkins	Wed, 13 Sep 2017 08:52:33 +0100	95 lines
[git/cctbx] master: Merge branch 'master' into nigel (dad63a67c)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 16:52:41 -0700	56 lines
[git/cctbx] master: bugfix, testfix (1c0e4b6b2)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 16:52:15 -0700	193 lines
[git/cctbx] master: Add function to print out information about missing H atoms. (b17919d89)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 16:43:12 -0700	144 lines
[git/cctbx] master: Add test for H bound to two atoms. (6acc96d85)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 16:30:13 -0700	424 lines
[git/cctbx] master: PDBTools: updated to use phil scope for model filename (e84db3f59)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 15:55:11 -0700	160 lines
[git/cctbx] master: Splitting processing file and making grm in mmtbx.model (a6216e29f)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 15:51:55 -0700	496 lines
[git/cctbx] master: viewer selection (06617db85)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 15:43:25 -0700	623 lines
[git/cctbx] master: Add tests for custom restraints vs riding H. (b4a06f0cb)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 15:12:59 -0700	1247 lines
[git/cctbx] master: Safeguarding when ideal angles are missing. (38a899b08)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 15:06:03 -0700	174 lines
[git/cctbx] master: geometry minimisation error test (51b1d8a70)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 13:58:13 -0700	200 lines
[git/cctbx] master: test for superpose ideal (d2d5f80db)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 13:34:07 -0700	501 lines
[git/cctbx] master: multiple tests for superpose ideal (237720e12)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 13:32:55 -0700	219 lines
[git/cctbx] master: Add boost python class MosaicCrystalSauter2014. Extends Crystal class adding two values for mosaicity, the mosaic angle and the domain size. (ec079c603)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 13:10:24 -0700	857 lines
[git/cctbx] master: Add new crystal model MosaicCrystal, defining mosaicity with a single parameter. (d83f7ef5f)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 13:10:24 -0700	1975 lines
[git/cctbx] master: Hook up MosaicCrystalSauter2014. (a5f646bf2)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 13:10:24 -0700	779 lines
[git/cctbx] master: Rename MosaicCrystal to MosaicCrystalKabsch2010, since more are coming. (c4b946d91)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 13:10:24 -0700	782 lines
[git/cctbx] master: Bugfix in depickling (b44762bfb)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 13:10:24 -0700	79 lines
[git/cctbx] master: Export virtual functions defined by BeamBase into the BeamBase boost class. (4057b0017)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 12:23:30 -0700	387 lines
[git/cctbx] master: Add a FIXME (0ffd27f63)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 12:23:30 -0700	76 lines
[git/cctbx] master: Update ImageSet to use BeamBase instead of Beam (45d39ff7f)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 12:23:30 -0700	163 lines
[git/cctbx] master: Polymorphic refactor of Beam model step 2: change usages of Beam to BeamBase in the C++ code (51bb7c41b)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 12:23:30 -0700	569 lines
[git/cctbx] master: Derive Crystal from CrystalBase. (2b778ca89)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 12:23:30 -0700	578 lines
[git/cctbx] master: Polymorphic crystal model: add CrystalBase class with matching virtual functions (8ead9fce0)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 12:23:30 -0700	292 lines
[git/cctbx] master: Update usages of Crystal to CrystalBase as part of making Crystal polymorphic (f3376f86b)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 12:23:30 -0700	667 lines
[git/cctbx] master: Step 1 of making dxtbx Beam polymorphic: add virtual methods to BeamBase class. (ee17b130e)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 12:23:30 -0700	384 lines
[git/cctbx] master: minor PRIME GUI tweaks (d45df7367)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 11:59:50 -0700	77 lines
[git/cctbx] master: minor PRIME GUI updates (331b667a9)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 11:59:50 -0700	297 lines
[git/cctbx] master: Added and improved testing of links - now using ALL bond origin ID (e2d953ad5)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 10:10:56 -0700	585 lines
[git/cctbx] master: Merge branch 'dxtbx-refactor' (710eefb62)	CCTBX Commit via DLS Jenkins	Tue, 12 Sep 2017 09:01:49 +0100	53 lines
[git/cctbx] master: Origin_id=3 for user-supplied restraints via geometry_restraints.edits scope. With tests. (626098f04)	CCTBX Commit via DLS Jenkins	Mon, 11 Sep 2017 13:56:56 -0700	1022 lines
[git/cctbx] master: Complete postrefinement mpi (d512cd723)	CCTBX Commit via DLS Jenkins	Mon, 11 Sep 2017 12:16:12 -0700	584 lines
[git/cctbx] master: Did a clean clutter (83ec1e1f6)	CCTBX Commit via DLS Jenkins	Mon, 11 Sep 2017 12:01:06 +0100	69 lines
[git/cctbx] master: Fixing serialization bug (9043fc741)	CCTBX Commit via DLS Jenkins	Mon, 11 Sep 2017 11:58:22 +0100	125 lines
[git/cctbx] master: marking unstable (7a2305a51)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 17:31:57 -0700	78 lines
[git/cctbx] master: couple of small fixes (ca032dd28)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 16:18:12 -0700	107 lines
[git/cctbx] master: PRIME GUI tweaks (35d05bf0c)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 13:48:22 -0700	386 lines
[git/cctbx] master: Moving amber, affit and den restraints creation out of phenix.refine (8766cd78f)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 13:36:28 -0700	337 lines
[git/cctbx] master: Turn off writing of debug maps (f9efb363e)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 12:00:19 -0600	136 lines
[git/cctbx] master: Fix bug in setting soft_mask in segment_and_split_map introduced recently (72f986fe8)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 11:54:29 -0600	223 lines
[git/cctbx] master: PDBTools: phil update (cba1518a0)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 10:35:49 -0700	161 lines
[git/cctbx] master: Fixing segfault on pickle (5038fb27f)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 14:38:22 +0100	98 lines
[git/cctbx] master: Make indices a list from flex.size_t before jsonifying (bedcaddbf)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 13:38:30 +0100	81 lines
[git/cctbx] master: Merge branch dxtbx-refactor into 'master' (3cf5c93c7)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 12:24:12 +0100	72 lines
[git/cctbx] master: Fixed an issue with iteration and also setting indices (d19225705)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 12:14:46 +0100	357 lines
[git/cctbx] master: Remove excess print (653c4e16a)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 09:26:55 +0100	71 lines
[git/cctbx] master: Putative fix for dials/dials#434 (7038becb2)	CCTBX Commit via DLS Jenkins	Fri, 8 Sep 2017 09:26:55 +0100	176 lines
[git/cctbx] master: moving GRM producing to mmtbx.model in phenix.refine (b8ace59a2)	CCTBX Commit via DLS Jenkins	Thu, 7 Sep 2017 17:48:21 -0700	422 lines
[git/cctbx] master: PRIME GUI tweaks (7ef2d417d)	CCTBX Commit via DLS Jenkins	Thu, 7 Sep 2017 16:12:36 -0700	1188 lines
[git/cctbx] master: Client-server in psana rax mode (3ef2acafc)	CCTBX Commit via DLS Jenkins	Thu, 7 Sep 2017 15:20:03 -0700	323 lines
[git/cctbx] master: Add mpi ts log. Update psana event offset class name. (4fefe9f86)	CCTBX Commit via DLS Jenkins	Thu, 7 Sep 2017 15:20:03 -0700	109 lines
[git/cctbx] master: Raise Sorry when process_percent is used in client-server mode. (a7039c657)	CCTBX Commit via DLS Jenkins	Thu, 7 Sep 2017 15:20:03 -0700	87 lines
[git/cctbx] master: Merge branch 'master' into dxtbx-refactor (456a4130f)	CCTBX Commit via DLS Jenkins	Thu, 7 Sep 2017 15:10:25 +0100	176 lines
[git/cctbx] master: Use PIP builder for Jinja and test related packages. (aaa5badeb)	CCTBX Commit via DLS Jenkins	Thu, 7 Sep 2017 12:29:21 +0100	305 lines
[git/cctbx] master: cleanup (038ea94f1)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 18:12:31 -0700	201 lines
[git/cctbx] master: bugs (b92cdc1a3)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 18:11:46 -0700	118 lines
[git/cctbx] master: refactoring __init__ in mmtbx.model to make it more linear (fc6c8b337)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 17:45:43 -0700	473 lines
[git/cctbx] master: get rid of xray_structure_initial (41d299bc5)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 17:12:26 -0700	257 lines
[git/cctbx] master: more init cleanup in mmtbx.model (c4fd1940b)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 17:02:04 -0700	415 lines
[git/cctbx] master: cleaning up mmtbx.model:__init__ (6f9f4f3f1)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 15:58:22 -0700	233 lines
[git/cctbx] master: Remove soft_mask_in_density_select parameter that is not used (51c6e8bb6)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 16:45:07 -0600	183 lines
[git/cctbx] master: Add capability to keep map size and apply soft mask and/or model mask (72d72c42a)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 16:34:54 -0600	248 lines
[git/cctbx] master: cleanup (db80a3b1d)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 14:51:19 -0700	189 lines
[git/cctbx] master: Slight refactoring of IAS in mmtbx.model (651185c7b)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 14:47:50 -0700	1513 lines
[git/cctbx] master: cleanup (97923eb4f)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 12:40:01 -0700	161 lines
[git/cctbx] master: Get rid of wilson_b in mmtbx.model (c7788b635)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 12:19:00 -0700	367 lines
[git/cctbx] master: Catch case with alt conf (1c8b13352)	CCTBX Commit via DLS Jenkins	Wed, 6 Sep 2017 09:26:53 -0600	81 lines
[git/cctbx] master: adjusted PRIME GUI to read new stat file (66bf000b0)	CCTBX Commit via DLS Jenkins	Tue, 5 Sep 2017 17:26:37 -0700	155 lines
[git/cctbx] master: turned off recovery path update (03c964e6a)	CCTBX Commit via DLS Jenkins	Tue, 5 Sep 2017 13:41:58 -0700	532 lines
[git/cctbx] master: recover dialog bugfix (72f2e14a7)	CCTBX Commit via DLS Jenkins	Tue, 5 Sep 2017 11:29:31 -0700	112 lines
[git/cctbx] master: Parameter validation for LABELIT backend in addition to DIALS backend for cctbx.xfel GUI (9c4ede1d0)	CCTBX Commit via DLS Jenkins	Tue, 5 Sep 2017 09:52:54 -0700	187 lines
[git/cctbx] master: Fix bug in apply_soft_mask for case where mask is everywhere and to fix background value (889a4d568)	CCTBX Commit via DLS Jenkins	Mon, 4 Sep 2017 13:11:05 -0600	173 lines
[git/cctbx] master: Fixing problem that can occur if largest region is more than empty area (3535366d3)	CCTBX Commit via DLS Jenkins	Mon, 4 Sep 2017 12:51:57 -0600	106 lines
[git/cctbx] master: Refactor slightly before fixing problem that can occur if largest region is more than empty area (d0c85543e)	CCTBX Commit via DLS Jenkins	Mon, 4 Sep 2017 12:39:48 -0600	142 lines
[git/cctbx] master: Refactor slightly (c4ecb8df2)	CCTBX Commit via DLS Jenkins	Sun, 3 Sep 2017 10:02:40 -0600	128 lines
[git/cctbx] master: Update default to density_select_in_auto_sharpen=True (384097ed3)	CCTBX Commit via DLS Jenkins	Sat, 2 Sep 2017 20:33:58 -0600	204 lines
[git/cctbx] master: Set default for discard_if_worse=None and use full target in chain-comparison (aa10942ad)	CCTBX Commit via DLS Jenkins	Sat, 2 Sep 2017 16:32:13 -0600	245 lines
[git/cctbx] master: Set default for discard_if_worse=None (02dc59bd6)	CCTBX Commit via DLS Jenkins	Sat, 2 Sep 2017 16:21:56 -0600	152 lines
[git/cctbx] master: Add option for density_select_in_auto_sharpen (25b0a8343)	CCTBX Commit via DLS Jenkins	Sat, 2 Sep 2017 10:40:13 -0600	817 lines
[git/cctbx] master: pdbtools (a9e8064e1)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 19:55:12 -0700	127 lines
[git/cctbx] master: . (f440b30e4)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 19:26:43 -0700	78 lines
[git/cctbx] master: more changes due to pdbtool (79ca52699)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 18:52:18 -0700	82 lines
[git/cctbx] master: more fixes due to phenix.pdbtools refactoring (b9add99c2)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 17:59:55 -0700	568 lines
[git/cctbx] master: bug fix (c059f12be)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 16:47:32 -0700	254 lines
[git/cctbx] master: bug fix (4bee49e76)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 16:28:09 -0700	93 lines
[git/cctbx] master: phenix.pdbtools: massive refactoring; many functions moved to pdb.hierarchy; separate CL-specific code from actual calculations; add more tests; remove dependency on phenix_regression/pdb. THIS WILL BREAK GUI (Model tools)git add iotbx/pdb/hierarchy.py iotbx/pdb/tst_hierarchy.py mmtbx/command_line/pdbtools.py mmtbx/pdbtools.py mmtbx/regression/tst_pdbtools.py! (7b15a9fba)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 15:53:20 -0700	80 lines
[git/cctbx] master: Bugfix: Can't select the cbf default with the LABELIT backend (6afe7b80d)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 15:18:12 -0700	94 lines
[git/cctbx] master: recover moved projects (b1713dc22)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 14:58:17 -0700	1169 lines
[git/cctbx] master: remove compile from Q\|R bot (6f668775f)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 10:51:30 -0700	73 lines
[git/cctbx] master: Fixes to get dials tests to run (09793c32a)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 17:16:28 +0100	342 lines
[git/cctbx] master: Merge branch 'master' into dxtbx-refactor (d57789149)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 15:56:38 +0100	236 lines
[git/cctbx] master: Made all models pointers so we can set None (fe41239bd)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 15:52:56 +0100	1073 lines
[git/cctbx] master: Fixed some bits so that all dxtbx tests now pass (f0f325035)	CCTBX Commit via DLS Jenkins	Fri, 1 Sep 2017 13:12:13 +0100	2620 lines
[git/cctbx] master: more parameters for GRM construction in mmtbx.model. (6f42e36b7)	CCTBX Commit via DLS Jenkins	Thu, 31 Aug 2017 17:24:00 -0700	130 lines
[git/cctbx] master: safeguarding mmtbx.model, the old way constructor. (f8e2ea4a9)	CCTBX Commit via DLS Jenkins	Thu, 31 Aug 2017 16:28:59 -0700	77 lines
[git/cctbx] master: Added pickle support to c++ classes. (525bbe3a6)	CCTBX Commit via DLS Jenkins	Thu, 31 Aug 2017 17:15:17 +0100	1443 lines
[git/cctbx] master: Sweep tests all pass along with nexus tests (f4e8bfefb)	CCTBX Commit via DLS Jenkins	Thu, 31 Aug 2017 13:23:19 +0100	1017 lines
[git/cctbx] master: ImageSet tests now passing (e14846dc6)	CCTBX Commit via DLS Jenkins	Thu, 31 Aug 2017 10:58:51 +0100	2212 lines
[git/cctbx] master: Added a test for ImageSetData class (06a852af7)	CCTBX Commit via DLS Jenkins	Sat, 26 Aug 2017 12:20:46 +0530	991 lines
[git/cctbx] master: Added test for external lookup (b3fb840c8)	CCTBX Commit via DLS Jenkins	Fri, 25 Aug 2017 16:38:55 +0530	159 lines
[git/cctbx] master: Testing ImageTile and ImageBuffer (923089196)	CCTBX Commit via DLS Jenkins	Fri, 25 Aug 2017 16:24:01 +0530	197 lines
[git/cctbx] master: Moved export of imageset to dxtbx_imageset_ext Testing ImageTile class (84be43263)	CCTBX Commit via DLS Jenkins	Fri, 25 Aug 2017 16:16:52 +0530	1292 lines
[git/cctbx] master: Merge branch 'master' into dxtbx-refactor (50039f064)	CCTBX Commit via DLS Jenkins	Fri, 25 Aug 2017 15:22:27 +0530	60 lines
[git/cctbx] master: Added some comments and convert mask (29ecd747a)	CCTBX Commit via DLS Jenkins	Fri, 25 Aug 2017 12:22:17 +0530	433 lines
[git/cctbx] master: Fixed compilation error (635f827a7)	CCTBX Commit via DLS Jenkins	Fri, 25 Aug 2017 12:14:14 +0530	329 lines
[git/cctbx] master: Update indices when setting scan in sweep (e115288ed)	CCTBX Commit via DLS Jenkins	Fri, 25 Aug 2017 11:41:08 +0530	114 lines
[git/cctbx] master: Merge branch 'master' into dxtbx-refactor (123d8a047)	CCTBX Commit via DLS Jenkins	Fri, 25 Aug 2017 11:28:20 +0530	702 lines
[git/cctbx] master: Using boost python objects for reader and masker (386da139b)	CCTBX Commit via DLS Jenkins	Fri, 25 Aug 2017 11:25:52 +0530	315 lines
[git/cctbx] master: Use shared ptrs for models (25594b226)	CCTBX Commit via DLS Jenkins	Thu, 24 Aug 2017 18:45:54 +0530	811 lines
[git/cctbx] master: Storing models as shared ptrs to allow each image beam/detector etc to point to sweep model if necessary plus allows goniometer and scan to be absent (7e5c1ca1c)	CCTBX Commit via DLS Jenkins	Wed, 23 Aug 2017 23:06:55 +0530	978 lines
[git/cctbx] master: Some changes to imageset.py (2e9a3aa87)	CCTBX Commit via DLS Jenkins	Mon, 21 Aug 2017 22:24:36 +0530	48 lines
[git/cctbx] master: Tidied up a bit (1cb802d18)	CCTBX Commit via DLS Jenkins	Mon, 21 Aug 2017 22:24:12 +0530	765 lines
[git/cctbx] master: Tidied up image class and did a clean clutter (2768edfc4)	CCTBX Commit via DLS Jenkins	Mon, 21 Aug 2017 15:40:34 +0530	313 lines
[git/cctbx] master: Modified image tile data structures (b3adb755c)	CCTBX Commit via DLS Jenkins	Mon, 21 Aug 2017 15:34:26 +0530	2010 lines
[git/cctbx] master: Using format/image.h (d3d15cce8)	CCTBX Commit via DLS Jenkins	Mon, 21 Aug 2017 13:15:18 +0530	993 lines
[git/cctbx] master: Restructred image class slightly (6c5968107)	CCTBX Commit via DLS Jenkins	Mon, 21 Aug 2017 12:48:11 +0530	739 lines
[git/cctbx] master: Renamed some header files and separated image class from image reader class (57763d711)	CCTBX Commit via DLS Jenkins	Mon, 21 Aug 2017 12:11:39 +0530	87 lines
[git/cctbx] master: Merge branch 'master' into dxtbx-refactor (a99cd2e5a)	CCTBX Commit via DLS Jenkins	Mon, 21 Aug 2017 11:51:13 +0530	306 lines
[git/cctbx] master: Implementing imageset in c++, first commit - it compiles. (627b595a1)	CCTBX Commit via DLS Jenkins	Mon, 21 Aug 2017 11:50:00 +0530	69 lines

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