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February 2018

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Subject	From	Date	Size
Jenkins 5b cctbx MacOS build 2187 Failure	DLS Jenkins	Wed, 28 Feb 2018 22:46:43 +0000	17 lines
[git/cctbx] master: Restore in-app version of matplotlib plots for runstats. (be154564d)	CCTBX commit	Wed, 28 Feb 2018 14:42:21 -0800	186 lines
[git/cctbx] master: changes to ramalyze to preserve model_id with results objects and allow ordered printing of all models in multimodel files (0c39cbac2)	CCTBX commit	Wed, 28 Feb 2018 17:22:15 -0500	179 lines
[git/cctbx] master: We still don't understand negative pixel values from this detector, but we have to expand the trusted range otherwise most reflections will be rejected in integration (c883b6436)	CCTBX commit	Wed, 28 Feb 2018 12:32:39 +0000	84 lines
[git/cctbx] master: removed more debug print(s) (ac3c7363e)	CCTBX commit	Tue, 27 Feb 2018 18:24:41 -0800	72 lines
[git/cctbx] master: removed unwanted debug print(s) (720e9c014)	CCTBX commit	Tue, 27 Feb 2018 18:21:47 -0800	71 lines
[git/cctbx] master: clustering from list of data (3d84a55f3)	CCTBX commit	Tue, 27 Feb 2018 18:07:39 -0800	151 lines
[git/cctbx] master: MOSFLM indexing in image tracker (da9cf2d76)	CCTBX commit	Tue, 27 Feb 2018 18:07:39 -0800	1587 lines
[git/cctbx] master: Xtriage GUI: round probability of finding substructure (b6bb7a1e3)	CCTBX commit	Tue, 27 Feb 2018 14:29:33 -0800	97 lines
[git/cctbx] master: Don't try to identify non-existing files (e1e199b40)	CCTBX commit	Tue, 27 Feb 2018 15:27:04 +0000	165 lines
[git/cctbx] master: Merge pull request #141 from cctbx/remove-indirection (6ff48ddc6)	CCTBX commit	Mon, 26 Feb 2018 17:08:32 -0800	55 lines
[git/cctbx] master: Xtriage: add traffic light for anomalous signal (fa281f5d9)	CCTBX commit	Mon, 26 Feb 2018 15:00:42 -0800	193 lines
[git/cctbx] master: Test for molprobity, will fail until the bug is fixed. (cbc42a1de)	CCTBX commit	Mon, 26 Feb 2018 12:47:10 -0800	273 lines
[git/cctbx] master: Update various dependencies (220f15385)	CCTBX commit	Mon, 26 Feb 2018 11:51:55 +0000	111 lines
[git/cctbx] master: Rewrite implementation of setting beam centre in the presence of a 2theta offset. The old method was (probably always) broken (e4caf8ae0)	CCTBX commit	Mon, 26 Feb 2018 10:52:02 +0000	495 lines
[git/cctbx] master: For a hierarchical detector set beam centre by just updating the root node (e05739ace)	CCTBX commit	Mon, 26 Feb 2018 09:41:09 +0000	160 lines
[git/cctbx] master: Do not ignore panel_id (1fe0be0f0)	CCTBX commit	Sun, 25 Feb 2018 01:19:22 +0000	122 lines
[git/cctbx] master: Internally beam centre is returned fast, slow. User parameter slow_fast_beam_centre is slow, fast because that is the order it is displayed in dials.image_viewer (7d2a1f049)	CCTBX commit	Sun, 25 Feb 2018 01:19:22 +0000	129 lines
[git/cctbx] master: Correctly handle fast and slow pixel size in case these ever differ (7e4996d10)	CCTBX commit	Sun, 25 Feb 2018 01:19:22 +0000	102 lines
[git/cctbx] master: Rework set_slow_fast_beam_centre_mm: avoid calculating old beam centre and work properly for multi-panel detectors (064096d00)	CCTBX commit	Sun, 25 Feb 2018 01:19:22 +0000	257 lines
[git/cctbx] master: Removing obsolete code and test. (4aeaa1f1c)	CCTBX commit	Fri, 23 Feb 2018 17:25:37 -0800	896 lines
[git/cctbx] master: deprecate unused helper function (ffa318278)	CCTBX commit	Fri, 23 Feb 2018 23:16:46 +0000	207 lines
[git/cctbx] master: fix broken test (6c8351613)	CCTBX commit	Fri, 23 Feb 2018 23:16:46 +0000	91 lines
[git/cctbx] master: Bugfix for nrgl split_by_chains(). Added test for this function. Enabled some more tests. Removed obsolete tests. (09f298769)	CCTBX commit	Fri, 23 Feb 2018 14:43:27 -0800	433 lines
[git/cctbx] master: add parameters so test would actually run (5b9d17262)	CCTBX commit	Fri, 23 Feb 2018 14:42:27 -0800	73 lines
[git/cctbx] master: Some nasty .ser files contain broken images. Can't do much about that, but at least report an image number when we fail to read a bad one (fde5af702)	CCTBX commit	Fri, 23 Feb 2018 18:24:48 +0000	115 lines
[git/cctbx] master: Use the first image to get expected image size. Allows reading of 2x2 binned images (8fd2127fb)	CCTBX commit	Fri, 23 Feb 2018 18:24:48 +0000	194 lines
[git/cctbx] master: slow_fast_beam_centre parameter now shifts the detector origin instead of changing beam direction; unify slow_fast_beam_centre and mosflm_beam_centre implementation (3d9650163)	CCTBX commit	Fri, 23 Feb 2018 13:36:47 +0000	435 lines
[git/cctbx] master: LevMar minimizer for sdfac propagate and refine. (929f01036)	CCTBX commit	Thu, 22 Feb 2018 15:46:01 -0800	139 lines
[git/cctbx] master: cleaning clutter (6bc3e4e68)	CCTBX commit	Thu, 22 Feb 2018 13:54:30 -0800	48 lines
[git/cctbx] master: taking out test for cspad nexus file because the file is inconsistent with current nexus format (dc6f555ab)	CCTBX commit	Thu, 22 Feb 2018 13:42:05 -0800	119 lines
[git/cctbx] master: Refactoring atom_selection into template. Using customization for illustrative purposes and to preserve previous behavior. (2c49d1274)	CCTBX commit	Thu, 22 Feb 2018 13:39:00 -0800	672 lines
[git/cctbx] master: Changes to be consistent with the current nexus format. 1. Drop _F, _S vectors (including the depends_on list and transformations) 2. Use fast/slow_pixel_direction instead (single entry equal to pixel size) and use module_offset to position these vectors 3, Drop fast_pixel_size 4. Flatten module list (dbb0bf7bc)	CCTBX commit	Thu, 22 Feb 2018 11:13:52 -0800	368 lines
[git/cctbx] master: Model Viewer: updates for atom selection (1afb83496)	CCTBX commit	Thu, 22 Feb 2018 11:08:51 -0800	124 lines
[git/cctbx] master: move imports from lightweight functions to top of file (675920929)	CCTBX commit	Thu, 22 Feb 2018 11:35:39 +0000	156 lines
[git/cctbx] master: CCTBXParser: change some text formatting (653361a84)	CCTBX commit	Wed, 21 Feb 2018 16:38:37 -0800	115 lines
[git/cctbx] master: CCTBXParser: specifiy program name in citations (decf44910)	CCTBX commit	Wed, 21 Feb 2018 16:31:42 -0800	76 lines
[git/cctbx] master: CCTBXParser: add option for custom processing (6a418d014)	CCTBX commit	Wed, 21 Feb 2018 16:24:04 -0800	1011 lines
[git/cctbx] master: some more refactoring (8a9c64b27)	CCTBX commit	Wed, 21 Feb 2018 15:21:50 -0800	230 lines
[git/cctbx] master: Removing force from model.set_crystal_stymmetry(), fix affected, and bug related to nrgs None or []. Need strict policy here. (84886133e)	CCTBX commit	Wed, 21 Feb 2018 13:16:37 -0800	441 lines
[git/cctbx] master: Supposedly better procedure for RSR weight optimization for small structures. (cbf711d10)	CCTBX commit	Wed, 21 Feb 2018 13:15:29 -0800	106 lines
[git/cctbx] master: run processing in same address space and do not start another python instance (5e707e762)	CCTBX commit	Wed, 21 Feb 2018 16:00:55 +0000	74 lines
Jenkins 5a cctbx Tests build 6029 Fixed	DLS Jenkins	Wed, 21 Feb 2018 15:46:57 +0000	37 lines
[git/cctbx] master: Fixed bug (977629470)	CCTBX commit	Wed, 21 Feb 2018 15:41:06 +0000	79 lines
Jenkins 5a cctbx Tests build 6028 Failure	DLS Jenkins	Wed, 21 Feb 2018 15:02:00 +0000	363 lines
[git/cctbx] master: Added a simple px to mm strategy with an offset (4e6142098)	CCTBX commit	Wed, 21 Feb 2018 14:41:43 +0000	729 lines
[git/cctbx] master: clean clutter from reference code (84749d093)	CCTBX commit	Tue, 20 Feb 2018 22:00:32 -0800	74 lines
[git/cctbx] master: don't output SS errors in this tool. (3b08edb3b)	CCTBX commit	Tue, 20 Feb 2018 16:49:26 -0800	91 lines
[git/cctbx] master: some restrictions for mmtbx.model (b73a21a95)	CCTBX commit	Tue, 20 Feb 2018 16:14:47 -0800	267 lines
[git/cctbx] master: Make xfel builder not install mpi4py by default (5cfde1fc5)	CCTBX commit	Tue, 20 Feb 2018 13:15:17 -0800	76 lines
[git/cctbx] master: PhaserBuilder for building phaser only. Similar to CCTBXLiteBuilder but with even more base packages omitted (1d84059b3)	CCTBX commit	Tue, 20 Feb 2018 16:17:09 +0000	208 lines
[git/cctbx] master: abstracting away a common step of processing two maps and model (1ae8cce04)	CCTBX commit	Tue, 20 Feb 2018 00:35:25 -0800	2017 lines
[git/cctbx] master: printing bug fix; adjust what to compute based on d99 (no need to compute model-dependent stats if resolution is lower than 10 or so) (ac777da23)	CCTBX commit	Mon, 19 Feb 2018 14:38:18 -0800	524 lines
[git/cctbx] master: restore one import erroneously removed in 62baa44dc331f0db56f8fd8b8bf1807e7bbe5501 (33bbc2110)	CCTBX commit	Mon, 19 Feb 2018 14:30:00 +0000	73 lines
Jenkins 5a cctbx Tests build 6017 Fixed	DLS Jenkins	Mon, 19 Feb 2018 12:38:55 +0000	37 lines
[git/cctbx] master: Fix race condition in test. (e8562ac4a)	CCTBX commit	Mon, 19 Feb 2018 12:34:21 +0000	631 lines
Jenkins 5a cctbx Tests build 6016 Unstable	DLS Jenkins	Mon, 19 Feb 2018 12:07:36 +0000	46 lines
[git/cctbx] master: replace git repositories for hfd5_lz4 and bitshuffle by zip downloads (6b86aad3b)	CCTBX commit	Mon, 19 Feb 2018 11:58:15 +0000	118 lines
[git/cctbx] master: remove spurious libtbx dependencies (0afab790b)	CCTBX commit	Mon, 19 Feb 2018 11:32:24 +0000	747 lines
[git/cctbx] master: now fix the broken test (c2319e105)	CCTBX commit	Mon, 19 Feb 2018 11:32:19 +0000	77 lines
[git/cctbx] master: upgrade run_tests.py to run with libtbx.run_tests_parallel (8bd42a9d5)	CCTBX commit	Mon, 19 Feb 2018 11:28:30 +0000	104 lines
[git/cctbx] master: Actually fail the tests on errors, don't just swallow them and pretend everything is fine (36915ec5d)	CCTBX commit	Mon, 19 Feb 2018 11:28:30 +0000	195 lines
[git/cctbx] master: clean up imports (94280805a)	CCTBX commit	Sun, 18 Feb 2018 21:58:49 +0000	118 lines
[git/cctbx] master: Xtriage: use already defined variables for labels (d83e41949)	CCTBX commit	Sat, 17 Feb 2018 23:30:03 -0800	87 lines
[git/cctbx] master: Xtriage: update GUI output for anomalous data (e6373569a)	CCTBX commit	Sat, 17 Feb 2018 23:07:38 -0800	87 lines
[git/cctbx] master: imports... (bbd1f9d1f)	CCTBX commit	Fri, 16 Feb 2018 18:07:06 -0800	126 lines
[git/cctbx] master: Fixing affected places (32c5e5baa)	CCTBX commit	Fri, 16 Feb 2018 17:52:45 -0800	257 lines
[git/cctbx] master: Initial refactoring of ss_validation into program template (07f5833a7)	CCTBX commit	Fri, 16 Feb 2018 17:52:44 -0800	1984 lines
[git/cctbx] master: make it look like a class (b63e25fa2)	CCTBX commit	Fri, 16 Feb 2018 17:52:44 -0800	1266 lines
[git/cctbx] master: Xtriage: fix label in table (7ddc23ce6)	CCTBX commit	Fri, 16 Feb 2018 15:44:21 -0800	73 lines
[git/cctbx] master: Sdfac refine levmar fixes (906b3323a)	CCTBX commit	Fri, 16 Feb 2018 10:18:46 -0800	179 lines
[git/cctbx] master: Restore needed function for lbfgsb sdfac refine (45956ef79)	CCTBX commit	Fri, 16 Feb 2018 09:19:11 -0800	124 lines
[git/cctbx] master: Bugfix for when not using sdfac_refine (1d716f565)	CCTBX commit	Fri, 16 Feb 2018 08:40:30 -0800	83 lines
[git/cctbx] master: simtbx: fixed cell angle normalization bug (5b8cb8140)	CCTBX commit	Fri, 16 Feb 2018 08:35:25 -0800	87 lines
[git/cctbx] master: restored changed made by Sauter to work around matrix assignment bug fixed matrix assignment bug fixed core dump problem with background extraction fixed Brunger example to not use extracted background added "fast" option to Brunger example, so it runs in 24 seconds (4a904d43a)	CCTBX commit	Fri, 16 Feb 2018 08:35:25 -0800	2889 lines
[git/cctbx] master: Switch to useing tricubic interpolation by default instead of lineraly-interpolated differences (56ca51ac9)	CCTBX commit	Thu, 15 Feb 2018 13:39:42 -0800	80 lines
[git/cctbx] master: Changes required for: CryoEM-specific Comprehensive Validation program: pipeline of Mtriage+map_model_cc+(potentially)Molprobity (bf091c196)	CCTBX commit	Thu, 15 Feb 2018 11:18:40 -0800	1098 lines
[git/cctbx] master: remove dead code and unused imports (62baa44dc)	CCTBX commit	Thu, 15 Feb 2018 10:56:50 +0000	124 lines
[git/cctbx] master: use specific exception to say that something is not implemented (d5137cd37)	CCTBX commit	Thu, 15 Feb 2018 10:56:34 +0000	198 lines
[git/cctbx] master: fix function name typo (c8f963719)	CCTBX commit	Thu, 15 Feb 2018 10:35:11 +0000	193 lines
[git/cctbx] master: remove print (e7c63a1f2)	CCTBX commit	Thu, 15 Feb 2018 09:18:44 +0000	89 lines
[git/cctbx] master: fix parsing of dxtbx paper (3a4261621)	CCTBX commit	Thu, 15 Feb 2018 09:14:41 +0000	246 lines
[git/cctbx] master: DataManager: convert text to model (cb911912a)	CCTBX commit	Wed, 14 Feb 2018 14:52:13 -0800	666 lines
[git/cctbx] master: More fixes for sdfac propagate (fb140e3f2)	CCTBX commit	Wed, 14 Feb 2018 14:22:28 -0800	387 lines
[git/cctbx] master: default value and bugfix (cb94d489b)	CCTBX commit	Wed, 14 Feb 2018 12:55:06 -0800	104 lines
[git/cctbx] master: Allow py.path objects in dxtbx.load (6f262cff8)	CCTBX commit	Wed, 14 Feb 2018 19:05:28 +0000	105 lines
[git/cctbx] master: scrap git commit hooks, #91 (84d890fed)	CCTBX commit	Wed, 14 Feb 2018 14:41:28 +0000	194 lines
Jenkins 5b cctbx MacOS build 2128 Fixed	DLS Jenkins	Wed, 14 Feb 2018 10:49:11 +0000	37 lines
Jenkins 5b cctbx MacOS build 2127 Failure	DLS Jenkins	Wed, 14 Feb 2018 00:21:34 +0000	138 lines
[git/cctbx] master: bug fix in variable name (7a0687d29)	CCTBX commit	Tue, 13 Feb 2018 15:28:30 -0800	80 lines
[git/cctbx] master: MolProbity: re-enable probe file output (66edcfcff)	CCTBX commit	Tue, 13 Feb 2018 15:16:59 -0800	356 lines
[git/cctbx] master: Moving hierarchy creation into appropriate place to mimic what is happening with PDB. Now we can compare iotbx.pdb.input() and construct_hierarchy() runtimes correctly for PDB and mmCIF. (3bdfe2207)	CCTBX commit	Tue, 13 Feb 2018 11:34:59 -0800	178 lines
[git/cctbx] master: DataManager: post-process model with pdb_interpretation (9c91afc2f)	CCTBX commit	Tue, 13 Feb 2018 10:50:19 -0800	256 lines
Jenkins 5b cctbx MacOS build 2122 Fixed	DLS Jenkins	Tue, 13 Feb 2018 08:29:16 +0000	37 lines
[git/cctbx] master: Provide interpolation options to real-space lbfgs minimizer; remove potentially unstable (and low-value anyway!) checks in interpolation tests. (937d4eac3)	CCTBX commit	Mon, 12 Feb 2018 18:39:31 -0800	672 lines
[git/cctbx] master: not used parameter (9992ded56)	CCTBX commit	Mon, 12 Feb 2018 17:54:11 -0800	75 lines
Jenkins 5b cctbx MacOS build 2121 Unstable	DLS Jenkins	Mon, 12 Feb 2018 23:56:21 +0000	32 lines
[git/cctbx] master: Xtriage: bug fix and backwards compatibility (b4ba6dbb1)	CCTBX commit	Mon, 12 Feb 2018 15:38:30 -0800	132 lines
[git/cctbx] master: Raising Sorry when selections are not correct. (d58d1a7c5)	CCTBX commit	Mon, 12 Feb 2018 12:03:31 -0800	100 lines
[git/cctbx] master: image modification bugfix (3a0e012e4)	CCTBX commit	Mon, 12 Feb 2018 12:00:34 -0800	674 lines
Jenkins 5b cctbx MacOS build 2119 Fixed	DLS Jenkins	Mon, 12 Feb 2018 19:18:26 +0000	37 lines
Jenkins 5a cctbx Tests build 5978 Fixed	DLS Jenkins	Mon, 12 Feb 2018 18:23:42 +0000	37 lines
[git/cctbx] master: Merge pull request #136 from cctbx/mpi_build (7bd053c0d)	CCTBX commit	Mon, 12 Feb 2018 10:14:22 -0800	61 lines
Jenkins 5b cctbx MacOS build 2118 Unstable	DLS Jenkins	Mon, 12 Feb 2018 17:25:37 +0000	34 lines
Jenkins 5a cctbx Tests build 5977 Unstable	DLS Jenkins	Mon, 12 Feb 2018 17:13:57 +0000	32 lines
[git/cctbx] master: Check for divide by zero (9c5ede35a)	CCTBX commit	Mon, 12 Feb 2018 09:07:13 -0800	130 lines
[git/cctbx] master: Fix formatting disaster; do not create processed pdb file object because it is not needed here. (aeeb1ed79)	CCTBX commit	Mon, 12 Feb 2018 08:41:17 -0800	106 lines
Jenkins 5a cctbx Tests build 5975 Fixed	DLS Jenkins	Mon, 12 Feb 2018 14:17:48 +0000	36 lines
[git/cctbx] master: libtbx: Remove some old test supression code (3a3825e5d)	CCTBX commit	Mon, 12 Feb 2018 14:04:21 +0000	151 lines
[git/cctbx] master: Let's see if this is better.. (412ed3383)	CCTBX commit	Sun, 11 Feb 2018 23:42:27 -0800	179 lines
[git/cctbx] master: use larger tolerance (0b81ca799)	CCTBX commit	Sat, 10 Feb 2018 16:14:51 -0800	97 lines
[git/cctbx] master: add future (b8a255a5e)	CCTBX commit	Sat, 10 Feb 2018 16:12:43 -0800	64 lines
Jenkins 5a cctbx Tests build 5969 Unstable	DLS Jenkins	Sun, 11 Feb 2018 00:02:56 +0000	34 lines
[git/cctbx] master: removed (1fe9f335e)	CCTBX commit	Sat, 10 Feb 2018 15:55:55 -0800	1373 lines
[git/cctbx] master: Bug fix in quadratic interpolation. Add tricubic interpolation with analytic gradients. Add thorough tests. (ce5d5a160)	CCTBX commit	Sat, 10 Feb 2018 15:55:54 -0800	2421 lines
[git/cctbx] master: catch case where too few anom diffs to use anomalous info (28a390ef8)	CCTBX commit	Fri, 9 Feb 2018 21:04:16 -0800	101 lines
[git/cctbx] master: clean clutter (acfe51395)	CCTBX commit	Fri, 9 Feb 2018 18:02:55 -0800	48 lines
[git/cctbx] master: Add plan_sad_experiment analysis to xtriage (fada459c9)	CCTBX commit	Fri, 9 Feb 2018 18:53:22 -0700	482 lines
[git/cctbx] master: Shortcut euristics for ncs search. Phil parameter for it disabled by default for now. (839d365e6)	CCTBX commit	Fri, 9 Feb 2018 17:38:24 -0800	469 lines
[git/cctbx] master: Put all parameters into phil scope and use it consistently everywhere - iotbx.ncs.input. (1f52b4a21)	CCTBX commit	Fri, 9 Feb 2018 17:38:24 -0800	1260 lines
[git/cctbx] master: List all builders with -h (d2a69db9b)	CCTBX commit	Fri, 9 Feb 2018 16:50:13 -0800	144 lines
[git/cctbx] master: Add new builder, cctbxlite, which skips dxtbx, hdf5 and cbflib. (158cdaa62)	CCTBX commit	Fri, 9 Feb 2018 16:32:11 -0800	253 lines
[git/cctbx] master: More speedup for sdfac propagate and refine (b0b4980fa)	CCTBX commit	Fri, 9 Feb 2018 15:13:38 -0800	454 lines
[git/cctbx] master: Bug fixes and corrected derivatives for sdfac propagate and refine. Finite differences and analytical derivatives now match. (ff7ab813d)	CCTBX commit	Fri, 9 Feb 2018 12:06:59 -0800	483 lines
[git/cctbx] master: Moving sequence alignment to C++ (53a54735b)	CCTBX commit	Thu, 8 Feb 2018 19:10:03 -0800	1282 lines
[git/cctbx] master: Draft implementation of refine_propagated_errors in cxi.merge (314c56a05)	CCTBX commit	Thu, 8 Feb 2018 17:00:07 -0800	596 lines
[git/cctbx] master: Tidying and refactor, prepping for refinement of propagated error terms (e400cceb1)	CCTBX commit	Thu, 8 Feb 2018 17:00:06 -0800	680 lines
[git/cctbx] master: Refactor, splitting parameter intialization into separate function (4f6198fe5)	CCTBX commit	Thu, 8 Feb 2018 17:00:06 -0800	585 lines
[git/cctbx] master: Fix minor typo in help (0ccf878b0)	CCTBX commit	Thu, 8 Feb 2018 09:54:05 -0700	81 lines
[git/cctbx] master: Convenience function required for Lunus. (3d453037a)	CCTBX commit	Wed, 7 Feb 2018 18:48:11 -0500	85 lines
[git/cctbx] master: changing help message for --mpi-build (7b240f0d2)	CCTBX commit	Wed, 7 Feb 2018 15:34:36 -0800	86 lines
[git/cctbx] master: Moving alignment into separate directory. (8626298db)	CCTBX commit	Wed, 7 Feb 2018 15:33:02 -0800	76 lines
[git/cctbx] master: Move tests to proper place (1d9ca5ac0)	CCTBX commit	Wed, 7 Feb 2018 15:33:02 -0800	710 lines
[git/cctbx] master: Remove strange unused global var (fbe6a307d)	CCTBX commit	Wed, 7 Feb 2018 15:33:02 -0800	72 lines
[git/cctbx] master: DataManager: improve handling of inheritance * Automatically add datatype of parent class(es) * Extra check to ensure datatypes are correct (aed77a854)	CCTBX commit	Wed, 7 Feb 2018 15:19:30 -0800	140 lines
[git/cctbx] master: Make iotbx depend on dxtbx, but only if dxtbx is explicitly configured. (0340a7e06)	CCTBX commit	Wed, 7 Feb 2018 14:46:47 -0800	79 lines
[git/cctbx] master: Remove expensive check that was not triggered for the last 2 years. (57db004d4)	CCTBX commit	Wed, 7 Feb 2018 14:26:40 -0800	122 lines
[git/cctbx] master: XFEL build should always have MPI; other softwares have an option (162f2bd4b)	CCTBX commit	Wed, 7 Feb 2018 13:22:29 -0800	173 lines
[git/cctbx] master: some refactoring (470ccd5f0)	CCTBX commit	Wed, 7 Feb 2018 13:20:50 -0800	106 lines
[git/cctbx] master: bugfix to previous commit (fa71333d9)	CCTBX commit	Wed, 7 Feb 2018 13:20:50 -0800	92 lines
[git/cctbx] master: Speed up this function 4x for 150Mb pdb file. Overall runtime of ncs search dropped 390->230 seconds (179e56f40)	CCTBX commit	Wed, 7 Feb 2018 13:20:50 -0800	128 lines
[git/cctbx] master: Fix minor case where no ncs present (ccc94fe5a)	CCTBX commit	Wed, 7 Feb 2018 13:20:17 -0800	81 lines
[git/cctbx] master: Adding options to build XFEL with MPI capability (199eaf642)	CCTBX commit	Wed, 7 Feb 2018 12:14:54 -0800	281 lines
[git/cctbx] master: Safeguarding, fix failing test. (03c52589e)	CCTBX commit	Wed, 7 Feb 2018 11:25:02 -0800	71 lines
[git/cctbx] master: Refactoring function so that it does not change passed arguments. Thanks Tom for pointing out that changed r is used in the second line, so my proposed change was not equivalent. (30cac1f25)	CCTBX commit	Wed, 7 Feb 2018 11:25:02 -0800	99 lines
[git/cctbx] master: Remove extra comment (3029511d2)	CCTBX commit	Wed, 7 Feb 2018 11:24:43 -0800	71 lines
[git/cctbx] master: DataManager: add support for real maps * Generalize CCTBXParser handling of different datatypes * Add real_map datatype to DataManager (50ad5c04f)	CCTBX commit	Wed, 7 Feb 2018 11:21:52 -0800	498 lines
[git/cctbx] master: Fix reference (3d2b26fa6)	CCTBX commit	Wed, 7 Feb 2018 11:16:55 -0800	74 lines
[git/cctbx] master: Add trumpet plot from Sauter 2015 (2fc55c7ed)	CCTBX commit	Wed, 7 Feb 2018 10:58:17 -0800	159 lines
[git/cctbx] master: add clutter (026680ea2)	CCTBX commit	Wed, 7 Feb 2018 18:22:34 +0000	80 lines
[git/cctbx] master: Bootstrap fallback: Tell curl to follow redirects (612ab761b)	CCTBX commit	Wed, 7 Feb 2018 17:42:32 +0000	103 lines
[git/cctbx] master: bug fix (f5e78599a)	CCTBX commit	Wed, 7 Feb 2018 16:30:21 +0000	77 lines
[git/cctbx] master: Get total memory also on Windows (40afc602c)	CCTBX commit	Wed, 7 Feb 2018 15:30:19 +0000	85 lines
[git/cctbx] master: Add extra format class for 516*516 pixel SMV images from a Timepix detector, based on patches supplied by Viktor Bengtsson (e6fc8cc3b)	CCTBX commit	Wed, 7 Feb 2018 14:56:54 +0000	725 lines
[git/cctbx] master: Reuse chains_info, get sort() out of my_selection. (498f99a89)	CCTBX commit	Tue, 6 Feb 2018 18:39:52 -0800	204 lines
[git/cctbx] master: Use my_selection in one more function. More speedup. (7dc050da8)	CCTBX commit	Tue, 6 Feb 2018 18:27:03 -0800	174 lines
[git/cctbx] master: Getting rid of the last select() in ncs_search. Amazing speedup outlined in the comment. (2160b77d8)	CCTBX commit	Tue, 6 Feb 2018 17:38:49 -0800	356 lines
[git/cctbx] master: Remove accidentally included debug code (33146606a)	CCTBX commit	Wed, 7 Feb 2018 00:23:46 +0000	78 lines
[git/cctbx] master: dxtbx: Slightly improve format-reading error messages (0970a2d38)	CCTBX commit	Tue, 6 Feb 2018 18:50:44 +0000	160 lines
[git/cctbx] master: Change max_drop_eps from 1e-5 to 1e-10 for lbfgs implementation of sdfac_refine (367ee5f6a)	CCTBX commit	Tue, 6 Feb 2018 09:17:06 -0800	90 lines
[git/cctbx] master: Add missed __future__ imports (be7950086)	CCTBX commit	Tue, 6 Feb 2018 14:26:06 +0000	100 lines
[git/cctbx] master: dxtbx: add batch_offset to scan model (in the manner of MTZ batch number column) (#132) (65e45c957)	CCTBX commit	Tue, 6 Feb 2018 13:02:55 +0000	1020 lines
[git/cctbx] master: dxtbx file cache: Avoid invalid state when open fails (ddfcbb50a)	CCTBX commit	Tue, 6 Feb 2018 11:50:27 +0000	251 lines
[git/cctbx] master: unused imports (7ad536797)	CCTBX commit	Mon, 5 Feb 2018 19:33:18 -0800	93 lines
[git/cctbx] master: create self.nrgl on the fly when filtering user-supplied ncs_groups. (25e34c73b)	CCTBX commit	Mon, 5 Feb 2018 19:29:10 -0800	660 lines
[git/cctbx] master: get rid of NCS_groups_container and Transfom classes, streamline ncs search procedure. (098638b0d)	CCTBX commit	Mon, 5 Feb 2018 18:45:27 -0800	1114 lines
[git/cctbx] master: Some editing, clean clutter, rmsd in NCS_copy (43cfaef47)	CCTBX commit	Mon, 5 Feb 2018 17:43:07 -0800	1164 lines
[git/cctbx] master: Change title for documentation to "CCTBX Developer documentation" (ac39bc3a6)	CCTBX commit	Mon, 5 Feb 2018 17:03:31 -0800	74 lines
[git/cctbx] master: Update Sphinx documentation to have more tours and newsletters (81d03dd21)	CCTBX commit	Mon, 5 Feb 2018 16:46:55 -0800	258 lines
[git/cctbx] master: Remove unused code (9825306fa)	CCTBX commit	Mon, 5 Feb 2018 16:45:43 -0800	470 lines
[git/cctbx] master: More trash removed. (d495d00ce)	CCTBX commit	Mon, 5 Feb 2018 16:40:02 -0800	740 lines
[git/cctbx] master: Replace function with just 1 line. (e3d5b777b)	CCTBX commit	Mon, 5 Feb 2018 16:40:02 -0800	212 lines
[git/cctbx] master: libtbx.find_unused_imports_crude (9a5b81808)	CCTBX commit	Mon, 5 Feb 2018 16:18:32 -0800	77 lines
[git/cctbx] master: Significant refactoring in Mtriage and relevant functions to improve runtime and memory efficiency. (7e121a61b)	CCTBX commit	Mon, 5 Feb 2018 16:16:00 -0800	100 lines
[git/cctbx] master: remove extra dictionaries and respective source code from iotbx.ncs.input. Ajdust tests. __eq__ functionality in nrgl for testing purposes (d942d4b49)	CCTBX commit	Mon, 5 Feb 2018 15:45:38 -0800	93 lines
[git/cctbx] master: Update Sphinx documentation with tutorials from SourceForge (8b17d828b)	CCTBX commit	Mon, 5 Feb 2018 14:26:44 -0800	94 lines
[git/cctbx] master: Update Sphinx documentation for mailing list (8bc4a9a21)	CCTBX commit	Mon, 5 Feb 2018 13:57:24 -0800	78 lines
[git/cctbx] master: Update PHIL documentation for Sphinx (8fa062ab8)	CCTBX commit	Mon, 5 Feb 2018 13:33:33 -0800	93 lines
[git/cctbx] master: Update links in documentation for PHIL and add examples (11736c226)	CCTBX commit	Mon, 5 Feb 2018 13:01:10 -0800	1079 lines
[git/cctbx] master: This is reverting change made couple days ago. This fixes Tom's test in test_find_ncs/tst_find_ncs.py related to correct deep_copy of ncs.ncs.ncs object. As one can see, this function actually will damage passed r and t matrices. (860edb5b2)	CCTBX commit	Mon, 5 Feb 2018 12:13:21 -0800	232 lines
[git/cctbx] master: Better check for bad values (039e4d093)	CCTBX commit	Mon, 5 Feb 2018 09:21:29 -0800	104 lines
[git/cctbx] master: Fixed test (3b7cd555c)	CCTBX commit	Mon, 5 Feb 2018 13:33:19 +0000	105 lines
[git/cctbx] master: Bugfix: stop crashing the XFEL UI from the RunStats tab. (6f6410ec0)	CCTBX commit	Sun, 4 Feb 2018 03:37:52 -0800	258 lines
[git/cctbx] master: More resizing to eliminate one set of scroll bars in the Trials tab. (f71e987d9)	CCTBX commit	Fri, 2 Feb 2018 21:46:20 -0800	108 lines
[git/cctbx] master: Resize excessively smallified things after wxpython update. (5aa4531df)	CCTBX commit	Fri, 2 Feb 2018 21:26:26 -0800	117 lines
[git/cctbx] master: switching string output of iotbx.ncs.input to use self.nrgl. (be9fdc58b)	CCTBX commit	Fri, 2 Feb 2018 20:09:31 -0800	853 lines
[git/cctbx] master: make nrgl have str selections (bd3ad779c)	CCTBX commit	Fri, 2 Feb 2018 18:55:52 -0800	362 lines
[git/cctbx] master: Rewritten get_ncs_info_as_spec to use ncs_restraints_group_list (79eb18783)	CCTBX commit	Fri, 2 Feb 2018 17:46:16 -0800	881 lines
[git/cctbx] master: Bugfix for zunderion. Plus test. (2281e4f3d)	CCTBX commit	Fri, 2 Feb 2018 16:31:46 -0800	588 lines
[git/cctbx] master: Removing another function (fb9e5eb4a)	CCTBX commit	Fri, 2 Feb 2018 15:33:17 -0800	348 lines
[git/cctbx] master: Attempt to create ncs_restraints_group_list in appropriate functions. (4a65e22a4)	CCTBX commit	Fri, 2 Feb 2018 15:33:17 -0800	1205 lines
[git/cctbx] master: fix typo (96c811fe4)	CCTBX commit	Fri, 2 Feb 2018 13:32:08 -0800	94 lines
[git/cctbx] master: clean clutter (aa6b92568)	CCTBX commit	Fri, 2 Feb 2018 14:02:25 -0700	48 lines
[git/cctbx] master: allow extraction of point-group symmetry (1c0faf49b)	CCTBX commit	Fri, 2 Feb 2018 12:47:25 -0800	391 lines
Jenkins 5a cctbx Tests build 5899 Fixed	DLS Jenkins	Fri, 2 Feb 2018 14:21:44 +0000	37 lines
[git/cctbx] master: add used imports, remove unused imports (752590bc3)	CCTBX commit	Fri, 2 Feb 2018 14:20:48 +0000	183 lines
[git/cctbx] master: add if __name__ == '__main__' (2cf51ec7e)	CCTBX commit	Fri, 2 Feb 2018 14:18:27 +0000	75 lines
[git/cctbx] master: fixing missed test (9592f7929)	CCTBX commit	Fri, 2 Feb 2018 14:16:52 +0000	82 lines
Jenkins 5a cctbx Tests build 5898 Unstable	DLS Jenkins	Fri, 2 Feb 2018 14:11:58 +0000	35 lines
[git/cctbx] master: Remove Python 2.1-compatible 'property' replacement (1f6ea3494)	CCTBX commit	Fri, 2 Feb 2018 14:04:15 +0000	920 lines
[git/cctbx] master: Remove SCons references to sources that have never existed (5ad8dac48)	CCTBX commit	Fri, 2 Feb 2018 14:00:59 +0000	131 lines
[git/cctbx] master: Be my guest if you do not want deprecation warnings. (2808b9413)	CCTBX commit	Fri, 2 Feb 2018 10:27:43 +0000	88 lines
[git/cctbx] master: remove indirection (40b8ea861)	CCTBX commit	Fri, 2 Feb 2018 10:27:20 +0000	320 lines
[git/cctbx] master: Update OrderedSet container. Apparently fixes a memory leak (bfe3025fe)	CCTBX commit	Fri, 2 Feb 2018 10:06:23 +0000	239 lines
[git/cctbx] master: Removing self.ncs_atom_selection, self.ncs_selection_str, self.ncs_chain_selection, self.selection_ids from iotbx.ncs.input. (0bf727b03)	CCTBX commit	Thu, 1 Feb 2018 18:28:34 -0800	671 lines
[git/cctbx] master: Removed object vars (990186ee6)	CCTBX commit	Thu, 1 Feb 2018 18:16:22 -0800	95 lines
[git/cctbx] master: Removing self.total_asu_length from iotbx.pdb.input (d4f526fac)	CCTBX commit	Thu, 1 Feb 2018 17:27:18 -0800	587 lines
[git/cctbx] master: Cleanup, remove self.found_ncs_transforms (a48ed6bd0)	CCTBX commit	Thu, 1 Feb 2018 17:00:08 -0800	520 lines
[git/cctbx] master: Cleanup args as well (a7b3ad28f)	CCTBX commit	Thu, 1 Feb 2018 16:11:16 -0800	106 lines
[git/cctbx] master: ProgramTemplate: clearer separation for output PHIL * output PHIL scope parameters in ProgramTemplate should not be changed, only added to * CCTBXParser pulls output PHIL scope directly from ProgramTemplate, not a subclass of ProgramTemplate (673eb3b55)	CCTBX commit	Thu, 1 Feb 2018 15:44:26 -0800	214 lines
[git/cctbx] master: Cleanup and reenable test (8836675a3)	CCTBX commit	Thu, 1 Feb 2018 15:22:39 -0800	563 lines
[git/cctbx] master: Actually removing commented out code (1aadef12f)	CCTBX commit	Thu, 1 Feb 2018 15:22:39 -0800	2425 lines
[git/cctbx] master: Cleanup and enabling test (3a220c8a5)	CCTBX commit	Thu, 1 Feb 2018 15:22:39 -0800	621 lines
[git/cctbx] master: Cleanup (e88bda6b2)	CCTBX commit	Thu, 1 Feb 2018 15:22:39 -0800	826 lines
[git/cctbx] master: fixed bug in setting wavelength fixed bug in writing CBF setting up for demo of indexing problems (88833e2cf)	CCTBX commit	Thu, 1 Feb 2018 14:45:41 -0800	160 lines
[git/cctbx] master: CCTBXParser: fix typo (5a30a3cbf)	CCTBX commit	Thu, 1 Feb 2018 13:54:34 -0800	82 lines
[git/cctbx] master: DataManager: standardize outputting files * Add standard output.overwrite PHIL parameter to ProgramTemplate * Add --overwrite option to CCTBXParser for overwriting files * output.overwrite will be automatically included in master phil scope for program * PHIL file output in CCTBXParser uses DataManager function so that IOError handling is standardized * Update mmtb.prepare_pdb_deposition to have standard output.overwrite parameter (2cd5a0c46)	CCTBX commit	Thu, 1 Feb 2018 13:40:36 -0800	421 lines
[git/cctbx] master: Move plot_group to a callable function (2b755a5d2)	CCTBX commit	Thu, 1 Feb 2018 12:55:17 -0800	328 lines
Jenkins 5a cctbx Tests build 5885 Fixed	DLS Jenkins	Thu, 1 Feb 2018 19:04:23 +0000	37 lines
Jenkins 5a cctbx Tests build 5884 Still Failing	DLS Jenkins	Thu, 1 Feb 2018 18:55:48 +0000	170 lines
[git/cctbx] master: bug fix for linux build (48ee232ff)	CCTBX commit	Thu, 1 Feb 2018 18:55:31 +0000	186 lines
[git/cctbx] master: fix typo (f9bc45734)	CCTBX commit	Thu, 1 Feb 2018 11:54:37 -0700	76 lines
Re: [git/cctbx] master: Allow compiling standalone statically linked executable of Phaser on Windows and MinGW platforms requires: static linking of some boost libraries, additional preprocessor defines for Windows build, additional library specified for rstbx build (29fc06f71)	Graeme Winter	Thu, 1 Feb 2018 18:51:58 +0000	260 lines
Jenkins 5a cctbx Tests build 5883 Still Failing	DLS Jenkins	Thu, 1 Feb 2018 18:49:48 +0000	166 lines
[git/cctbx] master: Refactor and enable ncs test. (1c6ecb393)	CCTBX commit	Thu, 1 Feb 2018 10:48:35 -0800	266 lines
Jenkins 5a cctbx Tests build 5882 Failure	DLS Jenkins	Thu, 1 Feb 2018 18:08:46 +0000	162 lines
[git/cctbx] master: Allow compiling standalone statically linked executable of Phaser on Windows and MinGW platforms requires: static linking of some boost libraries, additional preprocessor defines for Windows build, additional library specified for rstbx build (29fc06f71)	CCTBX commit	Thu, 1 Feb 2018 18:07:49 +0000	240 lines
[git/cctbx] master: Issue warning if map is low-resolution (b1705a2da)	CCTBX commit	Thu, 1 Feb 2018 09:02:24 -0700	101 lines
[git/cctbx] master: DataManager: add restraint support and abort with unrecognized PHIL (9589e2013)	CCTBX commit	Wed, 31 Jan 2018 17:51:19 -0800	161 lines
[git/cctbx] master: imports (a9e0327e9)	CCTBX commit	Wed, 31 Jan 2018 17:29:12 -0800	68 lines
[git/cctbx] master: Reuse ASC, chain id generator from central location (417f3a1fa)	CCTBX commit	Wed, 31 Jan 2018 17:11:00 -0800	225 lines
[git/cctbx] master: Moving test to appropriate location (8e9dc6703)	CCTBX commit	Wed, 31 Jan 2018 17:11:00 -0800	354 lines
[git/cctbx] master: moving domain creation into simple_ncs_from_pdb (76cc37015)	CCTBX commit	Wed, 31 Jan 2018 17:11:00 -0800	188 lines
[git/cctbx] master: cleaned 'end of line' clutter (2e7b53afb)	CCTBX commit	Wed, 31 Jan 2018 16:44:13 -0800	48 lines
[git/cctbx] master: DataManager: add datatype for restraints (85a3db36e)	CCTBX commit	Wed, 31 Jan 2018 16:34:03 -0800	268 lines
[git/cctbx] master: fixed indexing error handling (021b534bf)	CCTBX commit	Wed, 31 Jan 2018 16:25:59 -0800	225 lines
[git/cctbx] master: error handling bugfix (ef2d1df2d)	CCTBX commit	Wed, 31 Jan 2018 16:25:59 -0800	102 lines
[git/cctbx] master: UI bugfixes (f75598197)	CCTBX commit	Wed, 31 Jan 2018 16:25:59 -0800	830 lines
[git/cctbx] master: fixed file type identification bug (c69a4f708)	CCTBX commit	Wed, 31 Jan 2018 16:25:59 -0800	141 lines

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