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October 2022

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Subject	From	Date	Size
[git/cctbx_project] master: Fix location of remainder_sequence_file (a0f6fba328)	CCTBX commit	Mon, 31 Oct 2022 16:03:53 -0600	92 lines
[git/cctbx_project] master: Remove py3 only expression (8294407ae8)	CCTBX commit	Mon, 31 Oct 2022 13:18:57 -0700	105 lines
[git/cctbx_project] master: Add new plot, delta_vs_azimuthal_angle (24cbad419e)	CCTBX commit	Mon, 31 Oct 2022 12:03:31 -0700	241 lines
[git/dxtbx] main: MNT: Revert prebuilt cctbx used by CI (7154bf3a)	DXTBX commit	Mon, 31 Oct 2022 16:19:10 +0000	93 lines
[git/dxtbx] main: Add VMXm to Eiger legacy dimensions list (#569) (8d2c2cc1)	DXTBX commit	Mon, 31 Oct 2022 15:29:56 +0000	134 lines
[git/dxtbx] main: MNT: Update prebuilt cctbx used by CI (e3fa7655)	DXTBX commit	Mon, 31 Oct 2022 12:12:58 +0000	87 lines
[git/cctbx_project] master: Sensible check on the array length. (94466e111e)	CCTBX commit	Sun, 30 Oct 2022 17:15:11 -0700	93 lines
[git/cctbx_project] master: Avoid branching in kokkos:add_background (a3c10f6336)	CCTBX commit	Sun, 30 Oct 2022 09:28:37 -0700	197 lines
[git/cctbx_project] master: Implement kokkos_gpu version of gpu test. (bf7087c67b)	CCTBX commit	Sun, 30 Oct 2022 09:28:37 -0700	281 lines
[git/cctbx_project] master: bugfix (ad8e4817e7)	CCTBX commit	Sun, 30 Oct 2022 09:28:37 -0700	100 lines
[git/cctbx_project] master: put constant expression outside of kokkos kernel (f06e824d68)	CCTBX commit	Sun, 30 Oct 2022 09:28:37 -0700	133 lines
[git/cctbx_project] master: Add source scaling to kokkos background override (7a6900f8d5)	CCTBX commit	Sun, 30 Oct 2022 09:28:37 -0700	179 lines
[git/cctbx_project] master: Always print the data counter. (637f8e82e8)	CCTBX commit	Sun, 30 Oct 2022 08:17:48 -0700	123 lines
[git/cctbx_project] master: DataManager: store user-selected labels in reflection data files (9161a379b5)	CCTBX commit	Fri, 28 Oct 2022 09:50:10 -0700	1140 lines
[git/cctbx_project] master: DataManager: add array_type for miller_array datatype (49cfea1285)	CCTBX commit	Fri, 28 Oct 2022 09:50:10 -0700	913 lines
[git/cctbx_project] master: DataManager: no longer export all data labels (0caf7ea69b)	CCTBX commit	Fri, 28 Oct 2022 09:50:10 -0700	1106 lines
[git/cctbx_project] master: DataManager: handle partial labels for reflection data files (7d92064e74)	CCTBX commit	Fri, 28 Oct 2022 09:50:10 -0700	184 lines
[git/cctbx_project] master: DataManager: reflection file server can use user selected labels (fde97eec4d)	CCTBX commit	Fri, 28 Oct 2022 09:50:10 -0700	322 lines
[git/cctbx_project] master: Remove an extra hierarchy level from SwissFEL JF16M NXmx files (20f34c33e6)	CCTBX commit	Fri, 28 Oct 2022 09:26:18 -0700	384 lines
[git/cctbx_project] master: Handle non-int run numbers (f7b1b05bdc)	CCTBX commit	Fri, 28 Oct 2022 09:18:25 -0700	99 lines
[git/cctbx_project] master: adopts standard mpi4py defaults and argument names (ed7ceaa94f)	CCTBX commit	Thu, 27 Oct 2022 14:31:44 -0700	165 lines
[git/cctbx_project] master: add properties rank and size to mpiCommEmulator (541d349012)	CCTBX commit	Thu, 27 Oct 2022 10:54:09 -0700	95 lines
[git/cctbx_project] master: Avoid no data case failure (cef06acca9)	CCTBX commit	Thu, 27 Oct 2022 10:09:09 -0700	127 lines
[git/cctbx_project] master: Add arcticus to kokkos/SCons (adb5d8c070)	CCTBX commit	Thu, 27 Oct 2022 09:26:29 -0700	560 lines
[git/dxtbx] main: NXmx equipment component (#561) (b748a101)	DXTBX commit	Wed, 26 Oct 2022 20:51:59 +0000	916 lines
[git/cctbx_project] master: allow init. values in Alg4 (d9e19106a2)	CCTBX commit	Wed, 26 Oct 2022 13:21:20 -0700	322 lines
[git/cctbx_project] master: Further test fortification. (4c261aad01)	CCTBX commit	Wed, 26 Oct 2022 12:35:48 -0700	126 lines
[git/dxtbx] main: Nexus get_raw_data: stop taking redundant slices (#565) (a344a041)	DXTBX commit	Wed, 26 Oct 2022 17:22:19 +0000	153 lines
[git/cctbx_project] master: Kokkos update scons (#811) (de0e0f015c)	CCTBX commit	Tue, 25 Oct 2022 13:33:19 -0700	687 lines
[git/cctbx_project] master: allow toggling tooltips on/off for multiple datasets in table (cedcb62068)	CCTBX commit	Tue, 25 Oct 2022 20:46:48 +0200	246 lines
[git/cctbx_project] master: CI: use cached builds for XFEL CI branch (b6a6b15720)	CCTBX commit	Mon, 24 Oct 2022 16:52:49 -0700	270 lines
[git/cctbx_project] master: DataManager: add model_type argument for getting models (53b312fc11)	CCTBX commit	Mon, 24 Oct 2022 09:28:49 -0700	323 lines
[git/dxtbx] main: Suppress import error when deliberately catching errors (#567) (a5c227c6)	DXTBX commit	Mon, 24 Oct 2022 14:50:06 +0000	148 lines
[git/cctbx_project] master: Optionally omit values of some datasets from tooltips in the viewer. (2a7cb3e094)	CCTBX commit	Mon, 24 Oct 2022 16:09:49 +0200	306 lines
[git/cctbx_project] master: libtbx: modify updated PHIL for test (faa9879d6e)	CCTBX commit	Sun, 23 Oct 2022 10:34:04 -0700	93 lines
[git/cctbx_project] master: Remove old script (03d328bf7e)	CCTBX commit	Fri, 21 Oct 2022 14:53:33 -0700	116 lines
[git/cctbx_project] master: Only log stddev of correlations if n expts > 1 (db581e9ecd)	CCTBX commit	Fri, 21 Oct 2022 13:34:26 -0700	102 lines
[git/cctbx_project] master: Bug fix: To show tables of merged arrays ensure list of hkl indices for tabulation is a superset of all hkl indices and pad list of data values for tabulation with nan values where these are not matching hkl indices (1f610b2540)	CCTBX commit	Fri, 21 Oct 2022 09:46:25 +0100	334 lines
[git/cctbx_project] master: CI: retry Windows tests (2b33c65561)	CCTBX commit	Thu, 20 Oct 2022 22:28:58 -0700	139 lines
[git/cctbx_project] master: cctbx.xfel.powder_from_spots improvements (74593d588c)	CCTBX commit	Thu, 20 Oct 2022 16:30:18 -0700	501 lines
[git/cctbx_project] master: Update XFEL build instructions (#806) (2a82737499)	CCTBX commit	Thu, 20 Oct 2022 10:15:49 -0700	406 lines
[git/cctbx_project] master: Forgot to also store sigmas of newarray if these were defined (c21e61a7e7)	CCTBX commit	Thu, 20 Oct 2022 13:38:30 +0100	161 lines
[git/cctbx_project] master: Restore predecessor load balancing alg as global1 (94b6dc4ef1)	CCTBX commit	Thu, 20 Oct 2022 03:33:55 -0700	736 lines
[git/cctbx_project] master: Bugfix: removed python3.6-specific string formatting in weather.py (8c16323f20)	CCTBX commit	Wed, 19 Oct 2022 21:00:22 -0700	116 lines
[git/cctbx_project] master: Report quartiles with millisecond precision when creating the weather plot (1c98cdeaf8)	CCTBX commit	Wed, 19 Oct 2022 19:31:46 -0700	123 lines
[git/cctbx_project] master: added format option (6b36568af3)	CCTBX commit	Wed, 19 Oct 2022 18:58:28 -0700	221 lines
[git/cctbx_project] master: more details in print out (f253a59cc2)	CCTBX commit	Wed, 19 Oct 2022 18:58:28 -0700	102 lines
[git/cctbx_project] master: Rearrange filters to use the current filter user has chosen as default for next time user opens a file (d5b03cd457)	CCTBX commit	Thu, 20 Oct 2022 01:08:42 +0100	159 lines
[git/cctbx_project] master: Bug fix for submitting jobs with an empty queue. (f05a06a4a0)	CCTBX commit	Wed, 19 Oct 2022 16:14:25 -0700	97 lines
[git/cctbx_project] master: fixed bug that incorrectly displayed 1/resolution on the binning tab (a80e418f2e)	CCTBX commit	Wed, 19 Oct 2022 18:23:53 +0100	90 lines
[git/cctbx_project] master: Bug fix (missing atoms in super-sphere) (reported by Goska) (7ef9297d4c)	CCTBX commit	Tue, 18 Oct 2022 17:20:27 -0700	75 lines
[git/cctbx_project] master: Clean separation of cuda vs. kokkos_gpu contexts. (0c19d90aed)	CCTBX commit	Tue, 18 Oct 2022 11:40:46 -0700	2289 lines
[git/cctbx_project] master: Bug fix. Allow sorting columns properly when containing NaN values (89b77959ae)	CCTBX commit	Tue, 18 Oct 2022 15:43:56 +0100	168 lines
[git/dxtbx] main: Remove a vestigial test (#563) (e3c7acd8)	DXTBX commit	Tue, 18 Oct 2022 02:27:33 +0100	130 lines
[git/cctbx_project] master: Revert "iotbx: add convenience function for getting the master PHIL scope" (52ffb250bd)	CCTBX commit	Mon, 17 Oct 2022 17:53:11 -0700	159 lines
[git/cctbx_project] master: SwissFEL updates from P20231 (#804) (39d3dca926)	CCTBX commit	Mon, 17 Oct 2022 15:04:22 -0700	261 lines
[git/cctbx_project] master: Disable kokkos for Azure (no gpu on Azure) (7bda9cdf64)	CCTBX commit	Mon, 17 Oct 2022 13:39:25 -0700	90 lines
[git/cctbx_project] master: iotbx: add convenience function for getting the master PHIL scope (5581933f98)	CCTBX commit	Mon, 17 Oct 2022 12:51:15 -0700	149 lines
[git/cctbx_project] master: Allow creating merged reflection dataset. Don't interfere with user creating extra bins even if they are empty (3a7b6948ef)	CCTBX commit	Mon, 17 Oct 2022 17:26:01 +0100	216 lines
[git/cctbx_project] master: NCS search as part of PDB interpretation must be the last step in the whole procedure because any subsequent model manipulations (such as sort_atoms or flip_symmetric_amino_acids or similar) can alter the NCS selections (56b892f333)	CCTBX commit	Sat, 15 Oct 2022 19:06:52 -0700	149 lines
[git/cctbx_project] master: Additional unit test to tst_unified.py. (8c38ffedb8)	CCTBX commit	Sat, 15 Oct 2022 14:17:46 -0700	571 lines
[git/cctbx_project] master: Generalize tst_exafel_api to both cuda and kokkos (6800e88c06)	CCTBX commit	Sat, 15 Oct 2022 14:17:46 -0700	515 lines
[git/cctbx_project] master: In-depth unit tests for the Exascale API (2c2305b5c9)	CCTBX commit	Sat, 15 Oct 2022 14:17:46 -0700	1355 lines
[git/cctbx_project] master: Clean up. (d2c76a5357)	CCTBX commit	Sat, 15 Oct 2022 14:17:46 -0700	219 lines
[git/cctbx_project] master: Change whitelist argument for addresses to size_t. (c5f2228141)	CCTBX commit	Sat, 15 Oct 2022 14:17:46 -0700	734 lines
[git/cctbx_project] master: Implement unit tests for the whitelist mechanism. (6d24e36f3f)	CCTBX commit	Sat, 15 Oct 2022 14:17:46 -0700	826 lines
[git/cctbx_project] master: Use neutralize_scatterers if needed (de2aaf571f)	CCTBX commit	Sat, 15 Oct 2022 12:10:15 -0700	93 lines
[git/cctbx_project] master: Make sure xrs is removed in deep_copy of model (402399a3f9)	CCTBX commit	Sat, 15 Oct 2022 10:27:15 -0600	148 lines
[git/cctbx_project] master: Checking parameters to prevent user confusion. (513d3314d8)	CCTBX commit	Fri, 14 Oct 2022 14:46:58 -0700	417 lines
[git/cctbx_project] master: When creating new miller arrays allow user to amend their broken python code without having to use new column label (dbbb0dbb17)	CCTBX commit	Fri, 14 Oct 2022 17:05:34 +0100	172 lines
[git/cctbx_project] master: Bug fix: Ensure a new miller array can be created and displayed even if no miller array has been displayed since starting the HKLviewer (454fe4813a)	CCTBX commit	Fri, 14 Oct 2022 16:52:34 +0100	163 lines
[git/cctbx_project] master: Tidy up comment. (6875b1df3d)	CCTBX commit	Fri, 14 Oct 2022 09:29:22 +0100	99 lines
[git/cctbx_project] master: Attempt to make the test more stable (9062dc57ee)	CCTBX commit	Thu, 13 Oct 2022 16:27:48 -0700	114 lines
[git/cctbx_project] master: might be useful in the future to keep the pdb closer to input one (1bfe75febb)	CCTBX commit	Thu, 13 Oct 2022 15:28:56 -0700	96 lines
[git/cctbx_project] master: XFEL GUI, frame logging: don't use cache_commits during job startup (f2d3c1d4eb)	CCTBX commit	Thu, 13 Oct 2022 13:58:07 -0700	128 lines
[git/cctbx_project] master: XFEL GUI: don't require queue for slurm (5f62fe75da)	CCTBX commit	Thu, 13 Oct 2022 09:52:32 -0700	112 lines
[git/cctbx_project] master: libtbx_refresh runs with setuptools in "legacy_editable" mode (#802) (63510f58a3)	CCTBX commit	Thu, 13 Oct 2022 12:47:24 -0400	129 lines
[git/cctbx_project] master: libtbx: add "packages" entry to template setup.py (76db8ddf31)	CCTBX commit	Thu, 13 Oct 2022 00:48:45 -0700	102 lines
[git/cctbx_project] master: XFEL CI: increase timeout to 180 min (9eb3cdd7b3)	CCTBX commit	Wed, 12 Oct 2022 13:23:32 -0700	123 lines
[git/cctbx_project] master: Make sure we get the right python and pip (b80db8830a)	CCTBX commit	Wed, 12 Oct 2022 11:06:02 -0700	156 lines
[git/cctbx_project] master: removed print (fd2bf597d1)	CCTBX commit	Wed, 12 Oct 2022 10:18:05 -0700	161 lines
[git/cctbx_project] master: moved function to cctbx from qrefine (1a79502004)	CCTBX commit	Tue, 11 Oct 2022 17:41:09 -0700	124 lines
[git/cctbx_project] master: general improvements of QI including 6 HIS confs instead of 8 (5053d78ee7)	CCTBX commit	Tue, 11 Oct 2022 17:02:33 -0700	383 lines
[git/cctbx_project] master: Unpin setuptools following #797 (2b57e3e2bd)	CCTBX commit	Tue, 11 Oct 2022 12:15:40 -0400	89 lines
[git/cctbx_project] master: Stop importing pip, use subprocesses instead. Fixes #710 (#797) (8a0b852fd1)	CCTBX commit	Tue, 11 Oct 2022 12:10:08 -0400	393 lines
[git/cctbx_project] master: Don't fail if there is no structure factors in PDB. (108004a172)	CCTBX commit	Mon, 10 Oct 2022 14:58:16 -0700	100 lines
[git/cctbx_project] master: CI: network can also be flaky (1bf3be1f36)	CCTBX commit	Mon, 10 Oct 2022 10:22:33 -0700	193 lines
[git/cctbx_project] master: CI: retry occasionally flaky steps (43df757f0b)	CCTBX commit	Fri, 7 Oct 2022 15:26:49 -0700	236 lines
[git/cctbx_project] master: XFEL gui: cache database connections (#799) (cb972db4fa)	CCTBX commit	Fri, 7 Oct 2022 13:56:45 -0400	380 lines
[git/cctbx_project] master: Bug fix (964ff67818)	CCTBX commit	Fri, 7 Oct 2022 09:52:48 -0700	93 lines
[git/cctbx_project] master: Update tst_exafel_api for new function signature. (1af63a2441)	CCTBX commit	Thu, 6 Oct 2022 17:17:44 -0700	160 lines
[git/cctbx_project] master: Update the tst_exafel_api unit test. (3777006b16)	CCTBX commit	Thu, 6 Oct 2022 17:17:44 -0700	314 lines
[git/cctbx_project] master: Reconcile SMV and CBF writers in nanoBragg. (d0f4f8b369)	CCTBX commit	Thu, 6 Oct 2022 17:17:44 -0700	150 lines
[git/cctbx_project] master: intfile_scale parameter generalized in nanoBragg (e4579fd5ff)	CCTBX commit	Thu, 6 Oct 2022 17:17:44 -0700	380 lines
[git/cctbx_project] master: API maintenance on unit test for nanoBragg. (f5ef764ff8)	CCTBX commit	Thu, 6 Oct 2022 17:17:44 -0700	310 lines
[git/cctbx_project] master: Expose the intfile_scale in nanoBragg. (53e3810859)	CCTBX commit	Thu, 6 Oct 2022 17:17:44 -0700	255 lines
[git/cctbx_project] master: Switch to libsvm-official for libsvm Python interface (1a26e1bb6e)	CCTBX commit	Wed, 5 Oct 2022 14:13:21 -0700	177 lines
[git/cctbx_project] master: Mark failing test as expected fail (13986affd6)	CCTBX commit	Wed, 5 Oct 2022 09:06:43 -0700	111 lines
[git/cctbx_project] master: More notes for SS restraints. (5ed334b9d5)	CCTBX commit	Tue, 4 Oct 2022 16:37:10 -0700	145 lines
[git/cctbx_project] master: Add note on ss_by_chain (f954616896)	CCTBX commit	Tue, 4 Oct 2022 13:40:49 -0700	181 lines
[git/cctbx_project] master: CI: skip scitbx/suffixtree/test/tst_single.py on Weekly check (b11cbf2b50)	CCTBX commit	Mon, 3 Oct 2022 17:20:12 -0700	111 lines
[git/cctbx_project] master: Add a failing test for pdb_interpretation (HOP2 in DA) (41d7f1f9cf)	CCTBX commit	Mon, 3 Oct 2022 10:28:32 -0700	396 lines
[git/cctbx_project] master: Update CHANGELOG.rst for 2022.9 release (4b5f70e6b6)	CCTBX commit	Sat, 1 Oct 2022 13:31:40 -0700	102 lines
[git/cctbx_project] tag 'v2022.9' created	CCTBX commit	Sat, 1 Oct 2022 13:31:40 -0700	40 lines
[git/cctbx_project] master: libtbx: fix binary and source installers when /usr/bin/python is not available (00281bbad7)	CCTBX commit	Sat, 1 Oct 2022 13:00:47 -0700	163 lines

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October 2022

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