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February 2021

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Subject	From	Date	Size
[git/cctbx_project] master: Add mpi4py as dependency for psana builds as it is no longer a dependency of psana itself (7bd198a2f8)	CCTBX commit	Fri, 26 Feb 2021 12:47:52 -0800	89 lines
[git/cctbx_project] master: A Python 3 fix for gltbx string rendering (#594) (6a1ad261be)	CCTBX commit	Fri, 26 Feb 2021 20:20:19 +0000	87 lines
[git/dxtbx] master: reads Nexus format with data beyond the signal (#303) (550a84a3)	DXTBX commit	Fri, 26 Feb 2021 10:18:05 -0600	566 lines
[git/dxtbx] master: numpy.float96 and numpy.float128 do not exist on all platforms. (#318) (4a348a64)	DXTBX commit	Fri, 26 Feb 2021 09:20:07 +0000	166 lines
[git/dxtbx] master: dxtbx is no longer supported on Python 2 (#320) (9e5d2b5d)	DXTBX commit	Fri, 26 Feb 2021 08:45:10 +0000	155 lines
[git/cctbx_project] master: Persist radiiscale and powerscale between sessions for different observation types (4930298f4b)	CCTBX commit	Fri, 26 Feb 2021 00:56:37 +0000	889 lines
[git/cctbx_project] master: A messy attempt for another option to do diff map (7aaa1d7cd2)	CCTBX commit	Wed, 24 Feb 2021 13:01:04 -0800	429 lines
[git/cctbx_project] master: Switch to using mmm (d58dae958e)	CCTBX commit	Wed, 24 Feb 2021 13:01:04 -0800	198 lines
[git/cctbx_project] master: clean clutter (ad688157ee)	CCTBX commit	Wed, 24 Feb 2021 09:43:58 -0800	64 lines
[git/cctbx_project] master: Allow changing hierarchy in split_models and merge_models (f8c01dea78)	CCTBX commit	Wed, 24 Feb 2021 09:20:47 -0800	574 lines
[git/cctbx_project] master: Update keywords (751300c2eb)	CCTBX commit	Wed, 24 Feb 2021 05:17:50 -0800	93 lines
[git/dxtbx] master: When decompressing CBF, count the elements (#313) (c4c38f43)	DXTBX commit	Wed, 24 Feb 2021 13:01:55 +0000	280 lines
[git/cctbx_project] master: cctbx only change (9e6d9c3cd9)	CCTBX commit	Tue, 23 Feb 2021 13:44:50 -0800	98 lines
[git/cctbx_project] master: clean clutter (3de456afcb)	CCTBX commit	Tue, 23 Feb 2021 12:25:38 -0800	66 lines
[git/cctbx_project] master: add get_density at model sites (88d116eccf)	CCTBX commit	Tue, 23 Feb 2021 11:03:52 -0800	569 lines
[git/dxtbx] master: Code cleanup for dangling file pointer investigation (#316) (c9530e86)	DXTBX commit	Tue, 23 Feb 2021 11:15:43 +0000	473 lines
[git/cctbx_project] master: Disable bare prints. This breaks phenix_regression/real_space_refine/tst_53.py (508843fe39)	CCTBX commit	Mon, 22 Feb 2021 10:45:11 -0800	103 lines
[git/dxtbx] master: Fix data-corruption error in CBF compression (#314) (d1f9583f)	DXTBX commit	Mon, 22 Feb 2021 16:14:03 +0000	443 lines
[git/dxtbx] master: Test fixes for Windows (#308) (af49159c)	DXTBX commit	Mon, 22 Feb 2021 08:41:56 +0000	309 lines
[git/cctbx_project] master: Tidying up "make new reflection data" GUI (c0f23a7692)	CCTBX commit	Mon, 22 Feb 2021 00:23:40 +0000	946 lines
[git/cctbx_project] master: Allow multiple chain types in hierarchy in get_sequence_from_pdb (a5004f2db2)	CCTBX commit	Sat, 20 Feb 2021 13:03:16 -0800	172 lines
[git/cctbx_project] master: fix for running remediator on commandline (c966140e48)	CCTBX commit	Fri, 19 Feb 2021 18:53:00 -0500	101 lines
[git/cctbx_project] master: Adjust assertion target due to changed OS on anaconda (40d0d74ada)	CCTBX commit	Fri, 19 Feb 2021 13:23:52 -0800	96 lines
[git/cctbx_project] master: Adjust assertion target due to changed OS on anaconda (0afaa1f51b)	CCTBX commit	Fri, 19 Feb 2021 12:26:42 -0800	98 lines
[git/cctbx_project] master: Adjust assertion target due to changed OS on anaconda (97e7862295)	CCTBX commit	Fri, 19 Feb 2021 12:20:27 -0800	170 lines
[git/cctbx_project] master: Adjust assertion target due to changed OS on anaconda (26628d914e)	CCTBX commit	Fri, 19 Feb 2021 11:32:29 -0800	104 lines
[git/dxtbx] master: Avoid crashes on Windows when printing unicode (#306) (57c4ed92)	DXTBX commit	Fri, 19 Feb 2021 12:52:38 +0000	1013 lines
[git/dxtbx] master: Skip failing test on Windows (#307) (3973110f)	DXTBX commit	Fri, 19 Feb 2021 12:25:57 +0000	105 lines
[git/cctbx_project] master: mmtbx: fix syntax warning (f2612df8b9)	CCTBX commit	Wed, 17 Feb 2021 19:58:36 -0800	98 lines
[git/cctbx_project] master: Better check for SS presence, more clear message. (ca7ced724c)	CCTBX commit	Wed, 17 Feb 2021 12:39:37 -0800	153 lines
[git/cctbx_project] master: Fix for potential crash when adding bad rotation operator (9663cf37df)	CCTBX commit	Wed, 17 Feb 2021 19:24:29 +0000	395 lines
[git/cctbx_project] master: fixed bugs with hydrogens not getting properly remediated; switch to chem components as source of H names (f7e4429fb3)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	489 lines
[git/cctbx_project] master: adding remediator test code files (6cdd8f2591)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	86 lines
[git/cctbx_project] master: adding remediator tests (6f9d7c6be0)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	116 lines
[git/cctbx_project] master: added check for chem_data (9c65856a55)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	96 lines
[git/cctbx_project] master: added addition debugging info to test code (74e273356e)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	135 lines
[git/cctbx_project] master: fixes to remediator for nucleic acids (1618161f75)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	646 lines
[git/cctbx_project] master: updated testing code (78f47d710c)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	132 lines
[git/cctbx_project] master: bug fix for H3T (03c07a23a4)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	179 lines
[git/cctbx_project] master: fixed regression folder paths for tst_remediator (bb0f85b235)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	155 lines
[git/cctbx_project] master: inital add of model object remediator function (a32aa91262)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	377 lines
[git/cctbx_project] master: added function to check if model object is v3 (9f4221f31a)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	346 lines
[git/cctbx_project] master: fix bug in command_line (2208922a28)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	92 lines
[git/cctbx_project] master: adding assert messages to tst_remediator (eb3b79cbf2)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	153 lines
[git/cctbx_project] master: clean up debugging file outputs, update comments (aadb24119c)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	172 lines
[git/cctbx_project] master: fixes to program template for remediator (d9aec45100)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	161 lines
[git/cctbx_project] master: bug fixes for remediator and nucleic acid structures (cab1ba123c)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	238 lines
[git/cctbx_project] master: remediator code cleanup (37edf310e0)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	214 lines
[git/cctbx_project] master: fix for remediator atom reordering, adding future import division (af1d3ede7e)	CCTBX commit	Wed, 17 Feb 2021 13:30:24 -0500	148 lines
[git/dxtbx] master: Slightly faster nexus (#293) (889861d1)	DXTBX commit	Wed, 17 Feb 2021 14:01:04 +0000	1016 lines
[git/cctbx_project] master: add clarification (366e026ef5)	CCTBX commit	Tue, 16 Feb 2021 16:28:10 -0800	88 lines
[git/cctbx_project] master: XFEL testing update (fed0f70521)	CCTBX commit	Tue, 16 Feb 2021 14:47:24 -0800	99 lines
[git/cctbx_project] master: XFEL LCLS build update (7b7d14aea1)	CCTBX commit	Tue, 16 Feb 2021 14:18:33 -0800	198 lines
[git/cctbx_project] master: Update instructions to include uc_metrics (5b6134bf72)	CCTBX commit	Tue, 16 Feb 2021 14:18:33 -0800	102 lines
[git/cctbx_project] master: Update README.md (d8eebfb3a6)	CCTBX commit	Tue, 16 Feb 2021 14:18:33 -0800	129 lines
[git/cctbx_project] master: Update XFEL LCLS build (a2bdc9e589)	CCTBX commit	Tue, 16 Feb 2021 14:18:33 -0800	129 lines
[git/cctbx_project] master: mmtbx: add check for None, file reading, and various fixes (b6e135d3d6)	CCTBX commit	Tue, 16 Feb 2021 10:36:05 -0800	205 lines
[git/cctbx_project] master: CI: pick Ubuntu version for data cache pipeline (f283e5b16e)	CCTBX commit	Mon, 15 Feb 2021 18:05:36 -0800	93 lines
[git/cctbx_project] master: explicit rotation around xyz axes, silence noisy messages from javascript (5feae1ca10)	CCTBX commit	Tue, 16 Feb 2021 01:17:37 +0000	89 lines
[git/dxtbx] master: DIALS 3.3.3 Changelog (daf2542a)	DXTBX commit	Mon, 15 Feb 2021 16:03:07 +0000	112 lines
[git/cctbx_project] master: allow checking reverse direction of matching segments (2bb6c8a954)	CCTBX commit	Mon, 15 Feb 2021 05:11:11 -0800	183 lines
[git/cctbx_project] master: boost_adaptbx: move file needed for Boost 1.70 (5447aa303c)	CCTBX commit	Sat, 13 Feb 2021 17:21:20 -0800	107 lines
[git/cctbx_project] master: Compute R using N lowest resolution reflections (b443b7dda3)	CCTBX commit	Sat, 13 Feb 2021 10:30:56 -0800	101 lines
[git/cctbx_project] master: Switch xfel_regression in Azure to point to new gitlab repo (d1a15e1eca)	CCTBX commit	Fri, 12 Feb 2021 19:38:16 -0800	271 lines
[git/cctbx_project] master: boost_adaptbx: updates for Boost 1.72 (1e82dbfd35)	CCTBX commit	Fri, 12 Feb 2021 18:13:33 -0800	146 lines
[git/cctbx_project] master: xfel_regression is now on gitlab. Update testing instructions. (09876f5715)	CCTBX commit	Fri, 12 Feb 2021 17:45:57 -0800	122 lines
[git/cctbx_project] master: moves padding function to util folder (50c4844e99)	CCTBX commit	Fri, 12 Feb 2021 13:52:05 -0800	206 lines
[git/cctbx_project] master: pre-pad gain and pedestal data (2fe1daf674)	CCTBX commit	Fri, 12 Feb 2021 13:52:05 -0800	298 lines
[git/cctbx_project] master: virtual dataset that points to the raw (9d9ddd96b6)	CCTBX commit	Fri, 12 Feb 2021 13:52:05 -0800	322 lines
[git/cctbx_project] master: Add pedestal and gain maps to swissfel jungfrau data (367598b89d)	CCTBX commit	Fri, 12 Feb 2021 13:52:05 -0800	144 lines
[git/cctbx_project] master: Validate H: fix test (atom sorting) (a0450cb476)	CCTBX commit	Thu, 11 Feb 2021 19:28:16 -0800	213 lines
[git/cctbx_project] master: Update the psana + cctbx.xfel build instructions and environment file, and add testing instructions (cefad8803f)	CCTBX commit	Thu, 11 Feb 2021 15:01:05 -0800	230 lines
[git/cctbx_project] master: Performance optimizations for cctbx::miller::match_indices (#589) (8214d1eae3)	CCTBX commit	Thu, 11 Feb 2021 13:54:03 -0800	866 lines
[git/dxtbx] master: Initial support for Timepix 2M detector (#298) (218a0bce)	DXTBX commit	Thu, 11 Feb 2021 15:35:47 +0000	221 lines
[git/cctbx_project] master: Fix failure to set lower_bounds_list and upper_bounds_list (32d4c515c2)	CCTBX commit	Thu, 11 Feb 2021 06:45:27 -0800	118 lines
[git/cctbx_project] master: de-cluttered (1587b82558)	CCTBX commit	Thu, 11 Feb 2021 00:16:59 +0000	64 lines
[git/cctbx_project] master: Change xfel-ci azure builder (non-psana task) to centos 7 (58d345ef96)	CCTBX commit	Wed, 10 Feb 2021 14:43:29 -0800	125 lines
[git/cctbx_project] master: textwidget on statusbar (25e9260bde)	CCTBX commit	Wed, 10 Feb 2021 13:08:56 +0000	286 lines
[git/cctbx_project] master: xia2 renamed 'master' to 'main', cf. xia2/xia2#557 (bb2fe0593c)	CCTBX commit	Wed, 10 Feb 2021 11:22:02 +0000	94 lines
[git/dxtbx] master: Add utility function to get URL scheme (#301) (1c4b528a)	DXTBX commit	Wed, 10 Feb 2021 10:52:13 +0000	420 lines
[git/cctbx_project] master: Make d_max and d_min the right way round (#588) (d214d863a3)	CCTBX commit	Wed, 10 Feb 2021 09:44:29 +0000	122 lines
[git/cctbx_project] master: Dynamically updating HKL direction normal to screen of reflections in statusbar during mouse rotation. Bug fixes (e3b8370563)	CCTBX commit	Wed, 10 Feb 2021 01:12:33 +0000	611 lines
[git/cctbx_project] master: 10% speedup of pdb_interpretation by reusing sorted non-bonded proxies. There is one more to optimize in linking_mixins.py. (df08761130)	CCTBX commit	Tue, 9 Feb 2021 14:44:53 -0800	289 lines
[git/dxtbx] master: Clean clutter (f8c11d4e)	DXTBX commit	Mon, 8 Feb 2021 11:44:02 +0000	113 lines
[git/cctbx_project] master: missed one line (10a8633af3)	CCTBX commit	Fri, 5 Feb 2021 16:48:42 -0800	89 lines
[git/cctbx_project] master: fixed chemical components CIF parser to correctly return floats appropriately (c10252088b)	CCTBX commit	Fri, 5 Feb 2021 16:14:07 -0800	256 lines
[git/cctbx_project] master: Make sure map to sf is always p1 (495b565bc1)	CCTBX commit	Fri, 5 Feb 2021 15:58:00 -0800	176 lines
[git/cctbx_project] master: use map_manager instead of map_to_sf (ab3a7cae2d)	CCTBX commit	Fri, 5 Feb 2021 15:31:50 -0700	321 lines
[git/cctbx_project] master: Refactor as prep for using program template (65e8ee48c7)	CCTBX commit	Fri, 5 Feb 2021 13:56:01 -0800	712 lines
[git/cctbx_project] master: bug fixes dealing with nan data in miller arrays, inconsistent sceneids (fa4160032f)	CCTBX commit	Fri, 5 Feb 2021 19:27:21 +0000	506 lines
[git/cctbx_project] master: catch case where incoming model has shift_cart but map does not by automatically shifting model to match map at the start (92af807f6d)	CCTBX commit	Fri, 5 Feb 2021 12:07:40 -0700	152 lines
[git/cctbx_project] master: Function to make HL from phases (f1a589bbd9)	CCTBX commit	Fri, 5 Feb 2021 09:32:56 -0800	157 lines
[git/dxtbx] master: Fix bit rot for DM4 format. (#297) (3990b1e9)	DXTBX commit	Fri, 5 Feb 2021 15:24:11 +0000	165 lines
[git/cctbx_project] master: Fix the crash when ncs_search.enabled=False and ncs.type=constraints (08b8e83bb3)	CCTBX commit	Wed, 3 Feb 2021 16:23:50 -0800	96 lines
[git/cctbx_project] master: crys3d: switch under_root to under_dist (fab979cc4a)	CCTBX commit	Wed, 3 Feb 2021 15:22:56 -0800	109 lines
[git/cctbx_project] master: enable hyperlinks in textlabel (02acb4c171)	CCTBX commit	Wed, 3 Feb 2021 23:03:27 +0000	115 lines
[git/cctbx_project] master: changed url (1932983e3d)	CCTBX commit	Wed, 3 Feb 2021 23:03:27 +0000	323 lines
[git/cctbx_project] master: Merge pull request #583 from cctbx/bioinformatics_python3 (3367abd1c7)	CCTBX commit	Wed, 3 Feb 2021 15:22:17 +0000	71 lines
[git/cctbx_project] master: Called libtbx.clean_clutter on the __init__.py to remove extra spaces (6ecf515e55)	CCTBX commit	Wed, 3 Feb 2021 07:31:49 +0000	66 lines
[git/cctbx_project] master: Update __init__.py (f7539ed79a)	CCTBX commit	Wed, 3 Feb 2021 07:25:56 +0000	144 lines
[git/cctbx_project] master: Update __init__.py (cfc026e2bc)	CCTBX commit	Wed, 3 Feb 2021 07:16:16 +0000	69 lines
[git/cctbx_project] master: box_around_molecule: final cleanup (b30566ca57)	CCTBX commit	Tue, 2 Feb 2021 21:37:55 -0800	190 lines
[git/dxtbx] master: Fix missing SENSOR_THICKNESS= for EIGER (#296) (db6f00ed)	DXTBX commit	Tue, 2 Feb 2021 16:31:42 +0000	132 lines
[git/cctbx_project] master: Update __init__.py (d148405d18)	CCTBX commit	Tue, 2 Feb 2021 10:04:29 +0000	157 lines
[git/cctbx_project] tag 'v2021.1' created	CCTBX commit	Mon, 1 Feb 2021 19:01:53 -0800	40 lines
[git/cctbx_project] master: Update CHANGELOG.rst for 2020.1 release (27531c4f1c)	CCTBX commit	Mon, 1 Feb 2021 19:01:53 -0800	90 lines
[git/cctbx_project] master: Minor fix for evaluate sheet topology (c41501777b)	CCTBX commit	Mon, 1 Feb 2021 16:12:32 -0800	153 lines
[git/dxtbx] master: DIALS 3.3.2 Changelog (6a30dac0)	DXTBX commit	Mon, 1 Feb 2021 19:42:17 +0000	176 lines
[git/cctbx_project] master: libtbx: Add information fields to ProgramTemplate (ef411b2fde)	CCTBX commit	Mon, 1 Feb 2021 09:40:30 -0800	217 lines
[git/cctbx_project] master: iotbx: DataManager write functions return the output filename (109aef7b9b)	CCTBX commit	Mon, 1 Feb 2021 09:40:30 -0800	571 lines
[git/cctbx_project] master: Optionally evalulate beta sheet topology (542286938c)	CCTBX commit	Mon, 1 Feb 2021 05:53:10 -0700	643 lines
[git/dxtbx] master: Remove code that cannot be hit (#291) (211ab56a)	DXTBX commit	Mon, 1 Feb 2021 12:19:24 +0000	124 lines
[git/dxtbx] master: Bug fix: if eiger then EIGER not PILATUS (#292) (836fe085)	DXTBX commit	Mon, 1 Feb 2021 10:48:13 +0000	154 lines

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February 2021

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