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July 2023

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Subject	From	Date	Size
[git/cctbx_project] master: Update CHANGELOG.rst for 2023.7 release (60f07bc49c)	CCTBX commit	Mon, 31 Jul 2023 15:02:10 -0700	98 lines
[git/cctbx_project] tag 'v2023.7' created	CCTBX commit	Mon, 31 Jul 2023 15:02:10 -0700	40 lines
[git/cctbx_project] master: mmtbx: migrate omegalyze to run_program (1d35a23d5e)	CCTBX commit	Mon, 31 Jul 2023 14:06:02 -0700	124 lines
[git/cctbx_project] master: iotbx: add hide_parsing_output argument to run_program (2fb945f816)	CCTBX commit	Mon, 31 Jul 2023 13:59:30 -0700	175 lines
[git/cctbx_project] master: iotbx: clean clutter (3211c0869c)	CCTBX commit	Mon, 31 Jul 2023 13:58:37 -0700	102 lines
[git/cctbx_project] master: Add as_mmcif_string() to hierarchy; allow initialization of pdb_v3_cif_conversion with unique_values_dict (f51510d52b)	CCTBX commit	Mon, 31 Jul 2023 11:16:54 -0600	571 lines
[git/cctbx_project] master: Allow mrc files with cell angles of (0, 0, 0) and convert them to (90, 90, 90). Also print out error if symmetry cannot be interpreted (5793dbc466)	CCTBX commit	Mon, 31 Jul 2023 10:15:08 -0600	171 lines
[git/dxtbx] main: Fixes for EMBL beamlines at PETRA (#626) (64bcb324)	DXTBX commit	Mon, 31 Jul 2023 09:58:00 +0100	261 lines
[git/cctbx_project] master: Use HETNAM records to hold residue pdb_v3 conversions; try to use 3-char resname ending in tilde; allow special characters (46b4635656)	CCTBX commit	Fri, 28 Jul 2023 10:14:32 -0600	1633 lines
[git/cctbx_project] master: Add OK (cf47ad8cd3)	CCTBX commit	Fri, 28 Jul 2023 00:29:41 -0600	103 lines
[git/cctbx_project] master: Add method to remove origin shift and reset unit_cell_crystal_symmetry to match crystal_symmetry along with test (ae78d03c94)	CCTBX commit	Fri, 28 Jul 2023 00:28:35 -0600	313 lines
[git/cctbx_project] master: Revert addition of method to remove origin shift and unit_cell_crystal_symmetry (7481427ead)	CCTBX commit	Thu, 27 Jul 2023 14:41:42 -0700	211 lines
[git/cctbx_project] master: Add method to forget all about original unit call and origin in map_model_manager (4fce0a3424)	CCTBX commit	Thu, 27 Jul 2023 13:01:14 -0600	243 lines
[git/dxtbx] main: MNT: Update CMake modules path relative to script (0a068b56)	DXTBX commit	Thu, 27 Jul 2023 14:52:33 +0100	99 lines
[git/dxtbx] main: Make Imageset slices consistently index from 0 (69169ff5)	DXTBX commit	Wed, 26 Jul 2023 16:58:34 +0100	311 lines
[git/dxtbx] main: Check Registry against refl/expt files (#650) (e9b88d27)	DXTBX commit	Wed, 26 Jul 2023 13:41:57 +0000	129 lines
[git/dxtbx] main: FormatROD (#645) (180fac83)	DXTBX commit	Wed, 26 Jul 2023 14:17:57 +0100	1293 lines
[git/cctbx_project] master: CI: check disk space at the end (d500e12553)	CCTBX commit	Tue, 25 Jul 2023 18:47:30 -0700	94 lines
[git/cctbx_project] master: CI: free up disk space for XFEL CI (aac046d5c2)	CCTBX commit	Tue, 25 Jul 2023 16:45:09 -0700	165 lines
[git/cctbx_project] master: iotbx: clean clutter (eb3926f687)	CCTBX commit	Tue, 25 Jul 2023 14:22:11 -0700	132 lines
[git/cctbx_project] master: Moving N-terminal H3 addition to beginning of H placement (65849de48b)	CCTBX commit	Tue, 25 Jul 2023 11:02:52 -0700	809 lines
[git/dxtbx] main: Flumpy: Don't allow converting 1D vectors to vec2/3 (#648) (436a1b6a)	DXTBX commit	Tue, 25 Jul 2023 17:42:06 +0000	190 lines
[git/cctbx_project] master: Drop python 3.8 from XFEL CI (b5034cac07)	CCTBX commit	Tue, 25 Jul 2023 08:47:12 -0700	169 lines
[git/dxtbx] main: Easier override of panel geometry (#644) (930be095)	DXTBX commit	Tue, 25 Jul 2023 09:54:50 +0100	281 lines
[git/cctbx_project] master: Add methods for conversion between hierarchy and pdb_v3 compatible format, saving conversion information in REMARK records. Methods not applied anywhere. (da978d487b)	CCTBX commit	Mon, 24 Jul 2023 11:31:57 -0600	2291 lines
[git/cctbx_project] master: More flexible `cctbx.xfel.merge` file listing and validation (#889) (352071c118)	CCTBX commit	Sun, 23 Jul 2023 16:35:38 -0700	876 lines
[git/cctbx_project] master: add_complex_f_kb_scaled (a94d882f3a)	CCTBX commit	Sun, 23 Jul 2023 15:41:48 -0700	351 lines
[git/cctbx_project] master: Fix typo in doc string (542cbf8886)	CCTBX commit	Sun, 23 Jul 2023 11:05:11 -0600	95 lines
[git/cctbx_project] master: AttributeError bugfix in CCiso statistics. (#909) (2fe1f4d66e)	CCTBX commit	Sat, 22 Jul 2023 15:16:10 -0700	136 lines
[git/cctbx_project] master: better (8eaa2af71d)	CCTBX commit	Fri, 21 Jul 2023 17:18:51 -0700	111 lines
[git/cctbx_project] master: check for CCD file (5796079a07)	CCTBX commit	Fri, 21 Jul 2023 17:01:47 -0700	102 lines
[git/cctbx_project] master: bug fix of PHENIX_TEST (76f16ab692)	CCTBX commit	Fri, 21 Jul 2023 16:46:44 -0700	317 lines
[git/cctbx_project] master: clean clutter (7d5bd8b7d2)	CCTBX commit	Fri, 21 Jul 2023 16:00:48 -0700	117 lines
[git/cctbx_project] master: water b factors (233d0c79b5)	CCTBX commit	Fri, 21 Jul 2023 15:55:29 -0700	542 lines
[git/cctbx_project] master: initialize with the right type (perhaps isn't important) (74e342e097)	CCTBX commit	Fri, 21 Jul 2023 11:27:20 -0700	90 lines
[git/cctbx_project] master: switch back to using af::shared (890df45c43)	CCTBX commit	Fri, 21 Jul 2023 11:21:31 -0700	208 lines
[git/cctbx_project] master: start on a simple H restraints for hydrogenation (ca6be72066)	CCTBX commit	Thu, 20 Jul 2023 16:46:42 -0700	560 lines
[git/cctbx_project] master: fix so it runs (820b4a697d)	CCTBX commit	Thu, 20 Jul 2023 15:43:47 -0700	100 lines
[git/cctbx_project] master: Tricks to make it faster (a1ad4af750)	CCTBX commit	Thu, 20 Jul 2023 15:41:37 -0700	273 lines
[git/cctbx_project] master: added GLN to flipping (ef1ec0fc73)	CCTBX commit	Thu, 20 Jul 2023 14:20:08 -0700	267 lines
[git/cctbx_project] master: stubs for test method (f645135587)	CCTBX commit	Thu, 20 Jul 2023 13:29:50 -0700	140 lines
[git/cctbx_project] master: major reorg of QMR with the addition of NQ to H (4229f88cce)	CCTBX commit	Thu, 20 Jul 2023 12:06:55 -0700	2510 lines
[git/cctbx_project] master: simple updates (6a6dfb9424)	CCTBX commit	Thu, 20 Jul 2023 12:06:55 -0700	131 lines
[git/cctbx_project] master: First take. (ab383daac5)	CCTBX commit	Thu, 20 Jul 2023 11:18:05 -0700	1020 lines
[git/cctbx_project] master: atom_label_columns_formatter::format functions to work with extendedchain ids and resnames. Overall counts should work now. (418dfd3b7d)	CCTBX commit	Thu, 20 Jul 2023 11:18:05 -0700	743 lines
[git/cctbx_project] master: Cleanup, comments. (640e1a5e41)	CCTBX commit	Thu, 20 Jul 2023 11:18:05 -0700	185 lines
[git/cctbx_project] master: explicit int declation (b1c0c1b653)	CCTBX commit	Thu, 20 Jul 2023 06:00:42 -0700	93 lines
[git/cctbx_project] master: Avoid IndexError by ensuring number < len(d_star_sq_hkl) (53a94f7e12)	CCTBX commit	Wed, 19 Jul 2023 15:46:32 -0700	95 lines
[git/cctbx_project] master: Cleaner code (73156e8072)	CCTBX commit	Wed, 19 Jul 2023 15:46:32 -0700	96 lines
[git/cctbx_project] master: change python-igraph to igraph in error message (f9e7025dcb)	CCTBX commit	Wed, 19 Jul 2023 14:57:24 -0700	98 lines
[git/cctbx_project] master: Refactoring incorrect decoupling of selected hierarchy from original one (2a9cc327c0)	CCTBX commit	Wed, 19 Jul 2023 14:46:43 -0700	318 lines
[git/cctbx_project] master: Better test to serve as an example of selecting hierarchy. Passes now. (a732b95bcf)	CCTBX commit	Wed, 19 Jul 2023 10:15:08 -0700	334 lines
[git/cctbx_project] master: cctbx: fix syntax (70ad39e10e)	CCTBX commit	Wed, 19 Jul 2023 00:11:54 -0700	102 lines
[git/cctbx_project] master: LoFT - Local Fourier Transform: highly optimized FT for small regions of a map (most voxels of the map are assumed zero), and a test (a8fec10eb4)	CCTBX commit	Tue, 18 Jul 2023 16:23:03 -0700	1871 lines
[git/cctbx_project] master: Removing mmtbx_dssp as non-finished project (94346e80cc)	CCTBX commit	Tue, 18 Jul 2023 15:33:44 -0700	3350 lines
[git/cctbx_project] master: First stub for explicit local analytic FT (instead of standard FFT) (794d1566d3)	CCTBX commit	Mon, 17 Jul 2023 11:55:01 -0700	721 lines
[git/cctbx_project] master: For local mean intensity averaging, get sharpening B from sumfsqr, instead of from each value being averaged. The determination of the sharpening B for f1f2cos was poorly-conceived and unstable. (1a9c8f7a3d)	CCTBX commit	Mon, 17 Jul 2023 14:45:56 +0100	272 lines
[git/cctbx_project] master: more useful stdout for hopper (350d923f73)	CCTBX commit	Fri, 14 Jul 2023 08:16:47 -0500	326 lines
[git/cctbx_project] master: doc update (2445669614)	CCTBX commit	Fri, 14 Jul 2023 08:16:47 -0500	103 lines
[git/cctbx_project] master: rechecking stage 2 (598cf66f4d)	CCTBX commit	Fri, 14 Jul 2023 08:16:47 -0500	384 lines
[git/cctbx_project] master: updates (e8e1c0489b)	CCTBX commit	Fri, 14 Jul 2023 08:16:47 -0500	253 lines
[git/cctbx_project] master: iotbx: move test to expected failure list (634fe1b729)	CCTBX commit	Thu, 13 Jul 2023 16:08:33 -0700	107 lines
[git/cctbx_project] master: Failing test for discovered bug. (fba25cb3fe)	CCTBX commit	Thu, 13 Jul 2023 15:40:31 -0700	289 lines
[git/cctbx_project] master: Update hopper_utils.py (#906) (2b69ea3c2b)	CCTBX commit	Thu, 13 Jul 2023 13:22:29 -0700	153 lines
[git/cctbx_project] master: Add request to contact developers if external origin is not used. (bc3f047be1)	CCTBX commit	Thu, 13 Jul 2023 10:08:55 -0600	136 lines
[git/cctbx_project] master: Molprobity2 debug8 (#905) (50563d4df1)	CCTBX commit	Wed, 12 Jul 2023 18:07:18 -0400	629 lines
[git/cctbx_project] master: Set external_origin to (0, 0, 0) after using it (9c5ce6ffd0)	CCTBX commit	Tue, 11 Jul 2023 15:34:24 -0600	95 lines
[git/cctbx_project] master: Print warning messages if external_origin is not on a grid point (769099baa3)	CCTBX commit	Tue, 11 Jul 2023 14:58:37 -0600	220 lines
[git/cctbx_project] master: Update test for XDS files with sigmas; apply external_origin to map files at time of shift_origin (b6389a39f8)	CCTBX commit	Tue, 11 Jul 2023 13:28:43 -0700	549 lines
[git/cctbx_project] master: Ignore XDS ascii values with sigma < 0 (769e5338a5)	CCTBX commit	Tue, 11 Jul 2023 12:37:51 -0600	108 lines
[git/cctbx_project] master: Changes to make sure external_origin is tuple of real numbers. (d659efbb80)	CCTBX commit	Tue, 11 Jul 2023 09:47:39 +0100	130 lines
[git/cctbx_project] master: Tidy external_origin check to properly handle case where it is None. (b524c98715)	CCTBX commit	Tue, 11 Jul 2023 09:41:05 +0100	113 lines
[git/cctbx_project] master: initialize self.external_origin (53986b484f)	CCTBX commit	Mon, 10 Jul 2023 17:17:15 -0600	89 lines
[git/cctbx_project] master: libtbx: update under_base to handle installed locations (b65cee5157)	CCTBX commit	Mon, 10 Jul 2023 13:08:48 -0700	117 lines
[git/cctbx_project] master: Remove option to specify half-maps with non-standard map_ids, which was not used. Reject map files that specify non-zero origin with external_origin (.mrc file ORIGIN field) instead of with grid units. These are converted in em_placement_script.py before calling this procedure. The same correction could be done here, but it would be better to put the method into maptbx first. (0a3b7bfefc)	CCTBX commit	Mon, 10 Jul 2023 16:57:43 +0100	261 lines
[git/cctbx_project] master: catch helical symmetry (5f87fec2b3)	CCTBX commit	Sun, 9 Jul 2023 17:59:51 -0600	128 lines
[git/cctbx_project] master: catch missing param (385f671177)	CCTBX commit	Sun, 9 Jul 2023 11:09:45 -0600	95 lines
[git/cctbx_project] master: Check for 1 grid unit center offset (05d04c6841)	CCTBX commit	Sun, 9 Jul 2023 06:31:24 -0600	604 lines
[git/cctbx_project] master: Fix for keep_existing (2c6d274fc9)	CCTBX commit	Sat, 8 Jul 2023 11:25:01 -0700	96 lines
[git/cctbx_project] master: Option to keep existing water (12fcf49cb6)	CCTBX commit	Fri, 7 Jul 2023 17:14:16 -0700	300 lines
[git/cctbx_project] master: Further converting to std::string for flexible length of chain ids and resnames. (4be1c01329)	CCTBX commit	Fri, 7 Jul 2023 15:01:02 -0700	386 lines
[git/cctbx_project] master: Fix bug in merging_statistics.as_cif_block function (eda696f7aa)	CCTBX commit	Wed, 5 Jul 2023 21:30:45 -0700	124 lines
[git/cctbx_project] master: Bug fix when scripting HKLviewer from python prompt (a1928f5fb4)	CCTBX commit	Tue, 4 Jul 2023 18:22:03 +0100	164 lines
[git/cctbx_project] master: Use `mpl.plt.get_cmap` instead of deprecated `mpl.cm.get_cmap` (#897) (c33daa3b14)	CCTBX commit	Mon, 3 Jul 2023 14:50:42 -0700	258 lines
[git/cctbx_project] master: Raise sorry instead of crash. This functionality is exposed to users and StopIteration is not catched (5d16fcf40a)	CCTBX commit	Mon, 3 Jul 2023 11:35:28 -0700	102 lines

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