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December 2021

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Subject	From	Date	Size
[git/cctbx_project] master: CI: stop Python 3.6 builds (df4fd763f8)	CCTBX commit	Fri, 31 Dec 2021 12:21:02 -0800	163 lines
[git/cctbx_project] master: libtbx: update expected error messages for Python 3.10 (c5c59f9faf)	CCTBX commit	Fri, 31 Dec 2021 12:15:22 -0800	145 lines
[git/cctbx_project] master: libtbx: fix version in python library name for Windows (b17513ed74)	CCTBX commit	Fri, 31 Dec 2021 12:05:55 -0800	95 lines
[git/cctbx_project] master: gltbx: fix type name for Windows (8ab2d23100)	CCTBX commit	Fri, 31 Dec 2021 12:05:46 -0800	95 lines
[git/cctbx_project] master: CI: use patched version of Boost 1.74 for Python 3.10 (6d0d11bfc9)	CCTBX commit	Fri, 31 Dec 2021 12:05:23 -0800	366 lines
[git/cctbx_project] master: CI: start testing cctbxlite for Python 3.10 (777c37f862)	CCTBX commit	Fri, 31 Dec 2021 12:03:14 -0800	145 lines
[git/cctbx_project] master: temp fix for python3.8 for show_platform_info.py (unicode failure); catch target_completeness is None in simulate_low_res_data.py (needs to be fixed) (326d9d07a2)	CCTBX commit	Fri, 31 Dec 2021 10:50:08 -0800	220 lines
[git/cctbx_project] master: clean clutter (92791caba6)	CCTBX commit	Fri, 31 Dec 2021 08:27:09 -0800	61 lines
[git/cctbx_project] master: Allow OK in either python 3.8 or 2.7 for tst_box_around_molecule.py as difference is just order (b240370096)	CCTBX commit	Fri, 31 Dec 2021 08:09:29 -0800	184 lines
[git/cctbx_project] master: clean clutter (14f6bcedc9)	CCTBX commit	Fri, 31 Dec 2021 07:52:46 -0800	61 lines
[git/cctbx_project] master: Use standard random maps for consistency; fix error in refine_sharpening.py (951985a87e)	CCTBX commit	Fri, 31 Dec 2021 07:35:35 -0800	313 lines
[git/cctbx_project] master: Make note that iotbx/regression/tst_box_around_molecule.py fails in python 3 because the order of items in cif output changes (0de8d21f81)	CCTBX commit	Fri, 31 Dec 2021 06:08:15 -0800	98 lines
[git/cctbx_project] master: Remove try/except as there was no actual problem (cff7a5af56)	CCTBX commit	Fri, 31 Dec 2021 04:48:00 -0800	119 lines
[git/cctbx_project] master: clean clutter (ede913d22c)	CCTBX commit	Thu, 30 Dec 2021 20:18:29 -0800	61 lines
[git/cctbx_project] master: Mark python3 failures with XXX temp fix for python3 failure and temporarily set them to yield same result as python2.7 (0214ef9e18)	CCTBX commit	Thu, 30 Dec 2021 19:50:49 -0800	164 lines
[git/cctbx_project] master: Catch case where there are no pairs and it crashes...but not clear if None is the right result (eb4395ce81)	CCTBX commit	Thu, 30 Dec 2021 14:40:19 -0800	94 lines
[git/cctbx_project] master: CI: switch CentOS 8 to Rocky Linux 8 (0905ef5325)	CCTBX commit	Tue, 28 Dec 2021 14:45:48 -0800	163 lines
[git/cctbx_project] master: CI: bump Xcode 13.2 to 13.2.1 (460889b1ac)	CCTBX commit	Tue, 28 Dec 2021 10:40:38 -0800	93 lines
[git/cctbx_project] master: writing restraints from GRM support (c00b5ed882)	CCTBX commit	Thu, 23 Dec 2021 08:21:09 -0800	370 lines
[git/cctbx_project] master: better output and better variable names (8f37c3dcd0)	CCTBX commit	Thu, 23 Dec 2021 08:20:39 -0800	638 lines
[git/cctbx_project] master: small manips with log (34bbbdd646)	CCTBX commit	Tue, 21 Dec 2021 15:20:33 -0800	204 lines
[git/cctbx_project] master: adjust pip installs (fc77349cee)	CCTBX commit	Tue, 21 Dec 2021 13:32:10 -0800	92 lines
[git/cctbx_project] master: Updating Probe2 tests for new atom data and additional parameters (67b47bc625)	CCTBX commit	Tue, 21 Dec 2021 14:19:58 -0500	363 lines
[git/cctbx_project] master: small adjustment (0fe24a3ecb)	CCTBX commit	Tue, 21 Dec 2021 11:19:17 -0800	91 lines
[git/cctbx_project] master: don't need this dependencies anymore (9a5004a4b2)	CCTBX commit	Tue, 21 Dec 2021 10:55:49 -0800	91 lines
[git/cctbx_project] master: conda: update help text (1223376816)	CCTBX commit	Tue, 21 Dec 2021 10:54:12 -0800	101 lines
[git/cctbx_project] master: conda: add 3.9 to install_conda (6edb0553d1)	CCTBX commit	Tue, 21 Dec 2021 10:51:10 -0800	102 lines
[git/cctbx_project] master: Fixing Python-3 write and race conditions with subprocesses (6fb1bfbb47)	CCTBX commit	Mon, 20 Dec 2021 17:54:19 -0500	194 lines
[git/cctbx_project] master: Add new script (5ab8a0d0d4)	CCTBX commit	Mon, 20 Dec 2021 14:41:50 -0800	420 lines
[git/cctbx_project] master: Clean clutter (e87f16708c)	CCTBX commit	Mon, 20 Dec 2021 00:27:05 -0800	83 lines
[git/cctbx_project] master: added get_energy function (158ced2aad)	CCTBX commit	Sun, 19 Dec 2021 21:27:09 -0800	747 lines
[git/cctbx_project] master: Catch cases of one-atom models (ea99169ec1)	CCTBX commit	Sun, 19 Dec 2021 17:08:09 -0800	256 lines
[git/cctbx_project] master: Change mask gridding as described here: https://doi.org/10.1101/2021.12.09.471976 (2243cc9a24)	CCTBX commit	Sun, 19 Dec 2021 15:23:17 -0800	1449 lines
[git/cctbx_project] master: write optimised QM output correctly (73a1aa0f47)	CCTBX commit	Fri, 17 Dec 2021 16:19:17 -0800	638 lines
[git/cctbx_project] master: CCTBXParser: add argument to return JSON for run_program function (f0f1d2d468)	CCTBX commit	Fri, 17 Dec 2021 14:20:37 -0800	164 lines
[git/cctbx_project] master: updates diffBragg stage 1 (69ea163384)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	923 lines
[git/cctbx_project] master: modeling updates (f0e915b824)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	140 lines
[git/cctbx_project] master: save command line input, updates for skip hopper mode (296a84da79)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	185 lines
[git/cctbx_project] master: utils updates (01ce456dec)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	853 lines
[git/cctbx_project] master: adds comments for clarification (ea8783cb6a)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	154 lines
[git/cctbx_project] master: cleans clutters (be06c304d9)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	245 lines
[git/cctbx_project] master: updates various diffBragg features (112d328158)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	1277 lines
[git/cctbx_project] master: models structure factor intensity directly (35d0ba5399)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	680 lines
[git/cctbx_project] master: refines per ROI scale factors during stage 1 (c4736e4550)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	540 lines
[git/cctbx_project] master: refines multiple crystal models during stage 1 (ff98423f0b)	CCTBX commit	Fri, 17 Dec 2021 13:59:00 -0600	994 lines
[git/cctbx_project] master: Add additional debugging prints for cxi.make_dials_mask (ade0687066)	CCTBX commit	Fri, 17 Dec 2021 10:54:26 -0800	179 lines
[git/cctbx_project] master: CCTBXParser: add --json argument (a15e1d1db3)	CCTBX commit	Wed, 15 Dec 2021 23:54:10 -0800	165 lines
[git/cctbx_project] master: Molprobity2 improvements2 (#698) (3a75afe593)	CCTBX commit	Wed, 15 Dec 2021 15:46:12 -0500	2006 lines
[git/cctbx_project] master: Don't loose ligand info. (caf3c67d52)	CCTBX commit	Wed, 15 Dec 2021 11:26:56 -0800	89 lines
[git/cctbx_project] master: libtbx: handle warnings from "xcodebuild -version" (ce9b565af4)	CCTBX commit	Wed, 15 Dec 2021 11:02:37 -0800	100 lines
[git/cctbx_project] master: Allow specification of crystal_symmetry in add_crystal_symmetry_if_necessary (72317fc0f0)	CCTBX commit	Wed, 15 Dec 2021 11:01:17 -0800	130 lines
[git/cctbx_project] master: small bug fix (982d7f47b2)	CCTBX commit	Tue, 14 Dec 2021 13:19:59 -0800	99 lines
[git/cctbx_project] master: improving QMR (5627529f44)	CCTBX commit	Tue, 14 Dec 2021 09:22:49 -0800	678 lines
[git/dxtbx] main: Tighten up specificity of FormatTIFF (#457) (ebba6d03)	DXTBX commit	Tue, 14 Dec 2021 16:40:41 +0000	142 lines
[git/cctbx_project] master: CI: bump Xcode 13.1 to 13.2 (719a6429f9)	CCTBX commit	Mon, 13 Dec 2021 22:26:02 -0800	93 lines
[git/cctbx_project] master: mmCIF: support outputting of multi-model files with test. (466cde3a36)	CCTBX commit	Mon, 13 Dec 2021 15:54:49 -0800	678 lines
[git/cctbx_project] master: adjust to changes elsewhere (2bf7f4af55)	CCTBX commit	Mon, 13 Dec 2021 12:53:29 -0800	91 lines
[git/cctbx_project] master: Add convenience functions (0e4585795f)	CCTBX commit	Mon, 13 Dec 2021 12:51:29 -0800	100 lines
[git/cctbx_project] master: Raise Sorry when found duplicated loop or tag while reading CIF. Note that constructing cif programmatically should not be affected. Should fix issue #662 (ef17235100)	CCTBX commit	Mon, 13 Dec 2021 12:11:09 -0800	403 lines
[git/cctbx_project] master: Catch None in self.resolution() (a8407094dc)	CCTBX commit	Sun, 12 Dec 2021 09:28:23 -0700	134 lines
[git/cctbx_project] master: Clean up mosaic code before putting in production (cf5c856caf)	CCTBX commit	Fri, 10 Dec 2021 17:55:55 -0800	1018 lines
[git/cctbx_project] master: Assert chain IDs are not blank (4fd901429a)	CCTBX commit	Fri, 10 Dec 2021 17:55:55 -0800	87 lines
[git/cctbx_project] master: CI: switch macOS 10.14 to 10.15 (3d002b947d)	CCTBX commit	Fri, 10 Dec 2021 15:03:49 -0800	121 lines
[git/cctbx_project] master: conda: add win selector to devenv (59bbd3db7e)	CCTBX commit	Fri, 10 Dec 2021 11:40:07 -0800	109 lines
[git/cctbx_project] master: conda: enable wxpython for osx-arm64 in devenv for cctbxlite (8cb554e530)	CCTBX commit	Wed, 8 Dec 2021 22:56:21 -0800	94 lines
[git/cctbx_project] master: Bug fix: incorrect phil parameter names (555d3c7b83)	CCTBX commit	Wed, 8 Dec 2021 23:52:49 +0000	121 lines
[git/cctbx_project] master: Merge branch 'HKLviewerChimerax' (1b8fd07996)	CCTBX commit	Wed, 8 Dec 2021 14:46:44 +0000	86 lines
[git/cctbx_project] master: de-clutter (e67842876f)	CCTBX commit	Wed, 8 Dec 2021 14:44:04 +0000	61 lines
[git/cctbx_project] master: fixes for updating dialog size with new font size (dc693cb39c)	CCTBX commit	Wed, 8 Dec 2021 14:27:08 +0000	331 lines
[git/dxtbx] main: Fix problems with image pedestal in FormatSMVJHSim (#456) (14a0cee4)	DXTBX commit	Wed, 8 Dec 2021 09:18:33 +0000	178 lines
[git/cctbx_project] master: Updated interface for gpu instance holder (5f97a17f80)	CCTBX commit	Tue, 7 Dec 2021 20:22:59 -0800	411 lines
[git/cctbx_project] master: Updated interface for exascale Structure Factors (15636e6357)	CCTBX commit	Tue, 7 Dec 2021 20:22:59 -0800	328 lines
[git/cctbx_project] master: Updated interface for exascale Detector object. (9e9db63edd)	CCTBX commit	Tue, 7 Dec 2021 20:22:59 -0800	989 lines
[git/cctbx_project] master: Both CUDA and Kokkos interfaces accept deviceID (27c96c37b1)	CCTBX commit	Tue, 7 Dec 2021 20:22:59 -0800	430 lines
[git/cctbx_project] master: Updated interface for Exascale API. (47143bc2fa)	CCTBX commit	Tue, 7 Dec 2021 20:22:59 -0800	914 lines
[git/cctbx_project] master: Exascale API is polymorphic (f94c05b3e8)	CCTBX commit	Tue, 7 Dec 2021 20:22:59 -0800	108 lines
[git/cctbx_project] master: ORCA bug fix (f4a5453020)	CCTBX commit	Tue, 7 Dec 2021 16:19:40 -0800	131 lines
[git/cctbx_project] master: general tidy and more parameter option for QM restraints (9347bca0f9)	CCTBX commit	Tue, 7 Dec 2021 15:21:50 -0800	802 lines
[git/cctbx_project] master: Update CONTRIBUTING.md (bb5051f059)	CCTBX commit	Tue, 7 Dec 2021 14:13:04 -0800	209 lines
[git/cctbx_project] master: add HKLviewer.settings menu to chimerax, use str() to cope with nan values (997c7df242)	CCTBX commit	Mon, 6 Dec 2021 15:06:11 +0000	314 lines
[git/cctbx_project] master: bug fix (77f6f06b9d)	CCTBX commit	Sun, 5 Dec 2021 23:16:27 +0000	146 lines
[git/cctbx_project] master: Towards streaming reflection data from Isolde to HKLviewer in ChimeraX (45c746f051)	CCTBX commit	Sun, 5 Dec 2021 20:21:00 +0000	409 lines
[git/cctbx_project] master: Rename "cuda" suffix in functions to "kokkos" (312021daea)	CCTBX commit	Sat, 4 Dec 2021 14:10:42 -0800	1056 lines
[git/cctbx_project] master: Port "energy_channels_from_kokkos_amplitudes_cuda" (119d055039)	CCTBX commit	Sat, 4 Dec 2021 14:10:42 -0800	2583 lines
[git/cctbx_project] master: Fix no 'sinpi' function for __host__ (a0ca25a781)	CCTBX commit	Sat, 4 Dec 2021 14:10:42 -0800	91 lines
[git/cctbx_project] master: Catch stdout and stderr for every rank. (d4b824d811)	CCTBX commit	Sat, 4 Dec 2021 11:46:22 -0800	123 lines
[git/cctbx_project] master: Edits to support gamma_miller_units option. Also some debugging (7775136648)	CCTBX commit	Fri, 3 Dec 2021 19:14:19 -0600	462 lines
[git/cctbx_project] master: Set up diffuse refinement in hopper_utils.py (e9745ff0a9)	CCTBX commit	Fri, 3 Dec 2021 19:14:19 -0600	130 lines
[git/cctbx_project] master: Extend gamma_miller_units to GPU code (d3d7f20a34)	CCTBX commit	Fri, 3 Dec 2021 19:14:19 -0600	434 lines
[git/cctbx_project] master: In progress: Streaming reflection data from Isolde to HKLviewer in ChimeraX (e4af8de805)	CCTBX commit	Sat, 4 Dec 2021 00:43:31 +0000	761 lines
[git/cctbx_project] master: more robust code for QI QM restraints (7fd8d47b77)	CCTBX commit	Thu, 2 Dec 2021 12:33:22 -0800	424 lines
[git/cctbx_project] master: conda: update devenv (be44f141ae)	CCTBX commit	Wed, 1 Dec 2021 23:55:07 -0800	98 lines
[git/cctbx_project] master: small changes (799f3c7041)	CCTBX commit	Wed, 1 Dec 2021 15:46:20 -0800	134 lines
[git/cctbx_project] master: updated modified for Glyco (f27f474c04)	CCTBX commit	Wed, 1 Dec 2021 15:44:44 -0800	4454 lines
[git/cctbx_project] master: COPIED code to conformer (8ab90f3c04)	CCTBX commit	Wed, 1 Dec 2021 15:43:37 -0800	153 lines
[git/cctbx_project] master: adjustment to FASTA output (fd78bc4c7d)	CCTBX commit	Wed, 1 Dec 2021 14:02:15 -0800	154 lines
[git/cctbx_project] master: adding modifieds that have ? for parent (05ced45e3a)	CCTBX commit	Wed, 1 Dec 2021 12:03:14 -0800	81 lines
[git/cctbx_project] tag 'v2021.11' created	CCTBX commit	Tue, 30 Nov 2021 23:01:48 -0800	40 lines
[git/cctbx_project] master: Update CHANGELOG.rst for 2021.11 release (cfd0495307)	CCTBX commit	Tue, 30 Nov 2021 23:01:48 -0800	103 lines
[git/cctbx_project] master: Allow keeping just best chain in chain_comparison matching (fbf757ec84)	CCTBX commit	Tue, 30 Nov 2021 16:21:15 -0800	203 lines

CCTBX-COMMIT Archives

December 2021

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