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[git/dials] master: Using dials.report in idials. Type "report" after each processing job to open report.json in default browser (840533f)
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Mon, 30 Nov 2015 17:09:30 +0000 |
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[git/dials] master: move dials.show_profiles -> dev (22f3738)
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Mon, 30 Nov 2015 17:00:27 +0000 |
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[git/dials] master: dials.show_models -> dials.show; now supports reflections.pickle (f67995d)
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Mon, 30 Nov 2015 16:58:33 +0000 |
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[git/dials] master: bug fix (fc59c1d)
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Mon, 30 Nov 2015 16:38:03 +0000 |
75 lines |
[git/dials] master: bug fix; fix indentation (44409f3)
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Mon, 30 Nov 2015 16:32:18 +0000 |
378 lines |
[git/dials] master: add unicode encoding to html header (ab0028d)
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Mon, 30 Nov 2015 15:50:49 +0000 |
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[git/dials] master: add units; print names of output files (b2a1685)
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Mon, 30 Nov 2015 15:14:52 +0000 |
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[git/dials] master: add scan-varying crystal model into dials.report (3b6ba9f)
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Mon, 30 Nov 2015 15:08:35 +0000 |
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[git/dials] master: output.html and output.json parameters to specify output filenames on command line (ff28f47)
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Mon, 30 Nov 2015 11:59:51 +0000 |
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[git/dials] master: bug fix for strong/indexed/refined.pickle (b82a912)
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Mon, 30 Nov 2015 11:50:07 +0000 |
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[git/dials] master: set zmin, zmax to 0, 1 respectively for correlation heatmaps (c2ede28)
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Mon, 30 Nov 2015 11:35:05 +0000 |
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[git/dials] master: dev.dials.analysis -> dials.report (6217aea)
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Mon, 30 Nov 2015 11:18:45 +0000 |
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[git/dials] master: centroid residuals xy/zy/xz plots: histogram2dcontour -> python histogram2d + plotly contour; disable scatter plot since they require all data saving for all reflections (5f739ff)
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Mon, 30 Nov 2015 11:11:56 +0000 |
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[git/dials] master: transpose in wrong place (10f93f8)
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Mon, 30 Nov 2015 10:15:50 +0000 |
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[git/dials] master: further reduce file sizes by plotting histogram as bar chart (3e12230)
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Mon, 30 Nov 2015 10:13:05 +0000 |
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[git/dials] master: histogram2d: compute histogram2d in python, plot as heatmap: significantly reduces file sizes (e198ffe)
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Mon, 30 Nov 2015 09:57:18 +0000 |
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[git/dials] master: respect pixels_per_bin parameter (44c212e)
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Sun, 29 Nov 2015 18:11:10 +0000 |
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[git/dials] master: calculate 1d histograms in python and plot as barchart (cc5e2c9)
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Sun, 29 Nov 2015 18:09:40 +0000 |
283 lines |
[git/dials] master: Fixed bugs (0b9c3c0)
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Sat, 28 Nov 2015 15:06:03 +0000 |
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[git/dials] master: don't waste valuable mb on whitespace (db0c7e8)
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Fri, 27 Nov 2015 16:39:38 +0000 |
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[git/dials] master: Friday afternoon (5f6ff31)
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Fri, 27 Nov 2015 16:24:53 +0000 |
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[git/dials] master: add intensity analysis plots (abc84b3)
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Fri, 27 Nov 2015 14:44:00 +0000 |
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[git/dials] master: add reference profile plots; group plots by analysis type in html report (041067d)
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Fri, 27 Nov 2015 14:44:00 +0000 |
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[git/dials] master: attempt to draw zerolines on density plots (f321131)
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Fri, 27 Nov 2015 14:44:00 +0000 |
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[git/dials] master: Added crude radial background algorith, (56513f9)
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Fri, 27 Nov 2015 12:48:57 +0000 |
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[git/dials] master: Added description to command and auto solution selection for bravis (168edf1)
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Fri, 27 Nov 2015 12:48:57 +0000 |
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[git/dials] master: fix axis labels (a6ded93)
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Fri, 27 Nov 2015 11:06:01 +0000 |
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[git/dials] master: centroid_differences_xy heatmap plots; finished all indexing/refinement plots (b5cd704)
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Fri, 27 Nov 2015 10:56:09 +0000 |
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[git/dials] master: add centroid residual scatter/density plots (780d750)
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Fri, 27 Nov 2015 10:22:52 +0000 |
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[git/dials] master: start work on dev.dials.analysis replacement for dials.analyse_output, outputs html file with javascript plts: very much a work in progress (currently only works with strong.pickle and indexed.pickle) (0b56cab)
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Thu, 26 Nov 2015 17:07:00 +0000 |
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[git/dials] master: update diamond-specific documentation page (1bc1e42)
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Thu, 26 Nov 2015 14:40:53 +0000 |
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[git/dials] master: Allow 4 digits for image no (f92ad79)
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Thu, 26 Nov 2015 14:10:14 +0000 |
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[git/dials] master: dials.export_mtz is now dials.export (da42f69)
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Wed, 25 Nov 2015 11:00:09 +0000 |
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[git/dials] master: I have vector d[a]/dp and d[b]/dp, and dalpha/d[a], dalpha/d[b]. This doesn't work though: dalpha/dp = d[a]/dp . dalpha/d[a] + d[b]/dp . dalpha/d[b]. Not sure why. Commit current state and come back to this later... (f86aca6)
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Wed, 25 Nov 2015 10:49:13 +0000 |
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[git/dials] master: add and test vector version of AngleDerivativeWrtVectorElts (301fde4)
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Wed, 25 Nov 2015 10:49:12 +0000 |
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[git/dials] master: test commit (6fb5952)
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Wed, 25 Nov 2015 10:19:05 +0000 |
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[git/dials] master: export_mtz now retired (bd61e29)
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Wed, 25 Nov 2015 08:23:53 +0000 |
78 lines |
[git/dials] master: Fixed identation in help message (f62baac)
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Tue, 24 Nov 2015 17:01:47 +0000 |
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[git/dials] master: gradients of real space cell angles for restraints still wrong though. More investigation required (65fe92e)
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Tue, 24 Nov 2015 16:57:03 +0000 |
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[git/dials] master: Gradients of real space cell dimensions seem reasonable for the current test, except for d[c]/dp5. This parameter is a scaled version of g5 = b*.c* (c8a2a50)
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Tue, 24 Nov 2015 16:57:03 +0000 |
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[git/dials] master: insert quick fix here, better fix to come (cc69b7f)
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Tue, 24 Nov 2015 16:57:03 +0000 |
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[git/dials] master: Updated documentation (0354e5a)
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Tue, 24 Nov 2015 16:53:45 +0000 |
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[git/dials] master: Added test etc (5a99e00)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Added documentation for create_profiole_model and added stuff I forgot to commit! (dcd6d11)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Removed find_overlaps (8b15d3a)
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Tue, 24 Nov 2015 16:39:45 +0000 |
792 lines |
[git/dials] master: Fixed some tests (5198eca)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Merged export_mtz, export_nxmx, export_mosflm, export_xds and export_spot_xds to a single script with a format=*mtz nxs mosflm xds option. (0731190)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Added apply_mask documentation and test (8aff1dc)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Added help string and documentation for predict (ca72fad)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Moved print_test_reflections to dev (df2793c)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Moved import_xds to dev (b4f85d4)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Moved a couple of programs to dev.dials (c2447cb)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Moved show_extensions to dev (9255b3d)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Removed old script (9f0232b)
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Tue, 24 Nov 2015 16:39:45 +0000 |
272 lines |
[git/dials] master: Removed dispatcher name (95003b3)
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Tue, 24 Nov 2015 16:39:45 +0000 |
74 lines |
[git/dials] master: Print help with no argd (5d5b0a9)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Added documentation for estimate gain and a test. Sorted run_tests.py and moved extract_shoeboxes to dev (ee08155)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Moved to dev (40f42a2)
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Tue, 24 Nov 2015 16:39:45 +0000 |
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[git/dials] master: Moved some compare scripts to dev (f0c45bc)
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Tue, 24 Nov 2015 16:39:44 +0000 |
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[git/dials] master: test commit 2 (2aac32d)
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Tue, 24 Nov 2015 15:07:40 +0000 |
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[git/dials] master: test commit (d40cad1)
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Tue, 24 Nov 2015 14:52:14 +0000 |
73 lines |
[git/dials] master: fix multi-lattice tutorial (91d9ed7)
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Tue, 24 Nov 2015 12:15:42 +0000 |
136 lines |
[git/dials] master: Confusion due to me mixing up columns and rows of matrix [O]. Doh (b3771cd)
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Tue, 24 Nov 2015 12:00:01 +0000 |
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[git/dials] master: d[O]/dp is correct even for oblique cell, so the problem is not there (a2cc9b9)
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Tue, 24 Nov 2015 11:48:58 +0000 |
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[git/dials] master: override setup_toolbar method so can remove unfunctioning icons (closes #1) (47dcc5c)
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Tue, 24 Nov 2015 09:24:06 +0000 |
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[git/dials] master: Fixed comment (dd8f759)
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Mon, 23 Nov 2015 17:48:59 +0000 |
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[git/dials] master: Added "models" command to show models at each step in the processing (1e5e4bb)
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Mon, 23 Nov 2015 17:40:17 +0000 |
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[git/dials] master: Added placeholder for report and results (7c2b509)
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Mon, 23 Nov 2015 17:26:57 +0000 |
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[git/dials] master: Fixed type. Added discover_better_experimental_model to iDials. Also added access to shell commands (a06d4ac)
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Mon, 23 Nov 2015 17:26:57 +0000 |
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[git/dials] master: Investigating expressions for gradients needed for restraints of unit cell angles (121a3bf)
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Mon, 23 Nov 2015 16:54:58 +0000 |
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[git/dials] master: remove temporary testing lines (d94b406)
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Mon, 23 Nov 2015 12:36:03 +0000 |
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[git/dials] master: Added tab completion for setting parameters, filenames for loading phil files and for setting parameters with the imperative mode commands. Still no import filename completion though (ed5d1de)
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Mon, 23 Nov 2015 12:15:08 +0000 |
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[git/dials] master: Changed refine_bs to refine_bravais_settings and added import from directory and filename glob match (fc8d8fd)
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Mon, 23 Nov 2015 11:33:44 +0000 |
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[git/dials] master: Added some documentation (262b4da)
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Fri, 20 Nov 2015 18:16:47 +0000 |
221 lines |
[git/dials] master: Fixed tests (25ff294)
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Fri, 20 Nov 2015 17:47:17 +0000 |
280 lines |
[git/dials] master: Fixed some stuff, and added test for idials (5dde56f)
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Fri, 20 Nov 2015 16:00:55 +0000 |
312 lines |
[git/dials] master: Added live output as well as file output (9dd786e)
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Fri, 20 Nov 2015 16:00:54 +0000 |
368 lines |
[git/dials] master: Enable phil file == None in integrate and save mtz to working directory in idials (85fb110)
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Fri, 20 Nov 2015 16:00:54 +0000 |
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[git/dials] master: Live output, better exception handling and added refine_bravais_settings and reindex (08faa60)
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Fri, 20 Nov 2015 16:00:54 +0000 |
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[git/dials] master: Added stuff to make it easier to call programs in idials (6707691)
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Fri, 20 Nov 2015 16:00:54 +0000 |
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[git/dials] master: Fixed in case where output directory already exists (ec19d0a)
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Fri, 20 Nov 2015 16:00:54 +0000 |
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[git/dials] master: Cope properly with input override; was broken (8b38156)
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Fri, 20 Nov 2015 09:28:55 +0000 |
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[git/dials] master: Cope with long symops (cfa7bf6)
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Fri, 20 Nov 2015 09:28:25 +0000 |
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[git/dials] master: only output peaks.pdb in debug mode (c65b0cd)
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Thu, 19 Nov 2015 14:21:10 +0000 |
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[git/dials] master: Imperative mode added and tab completion for change modes explicitly (1212221)
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Thu, 19 Nov 2015 12:33:34 +0000 |
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[git/dials] master: clean up and remove now superseded max_cell logic (84d9c63)
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Thu, 19 Nov 2015 12:31:11 +0000 |
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[git/dials] master: clean up (ed7844a)
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Thu, 19 Nov 2015 12:04:32 +0000 |
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[git/dials] master: export_mtz fix for image numbering starting at zero: pointless really does not like it when BATCH starts at zero (7515adf)
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Thu, 19 Nov 2015 12:00:47 +0000 |
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[git/dials] master: Set log filenames as phil parameters (d00a5eb)
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Thu, 19 Nov 2015 09:46:29 +0000 |
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[git/dials] master: iDIALS: interactive dials - first go (525b257)
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Thu, 19 Nov 2015 09:46:29 +0000 |
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[git/dials] master: Toy command line interpreter (79d96ab)
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Thu, 19 Nov 2015 08:43:42 +0000 |
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[git/dials] master: Typo fix (6ca84f3)
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Thu, 19 Nov 2015 07:23:55 +0000 |
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[git/dials] master: Code to allow dump of intensities to file for plotting (12e367a)
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Thu, 19 Nov 2015 07:03:59 +0000 |
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[git/dials] master: Remove reflections with -ve summed intensity from input also (f478a62)
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Wed, 18 Nov 2015 16:23:24 +0000 |
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[git/dials] master: Remove reflections with -ve variance from input (743066c)
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Wed, 18 Nov 2015 16:18:32 +0000 |
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[git/dials] master: Allow n bins to be set - properly (7825d9d)
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Wed, 18 Nov 2015 15:44:33 +0000 |
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[git/dials] master: Allow n bins to be set (1205375)
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Wed, 18 Nov 2015 15:37:09 +0000 |
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[git/dials] master: n_bins should be passed (5712977)
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Wed, 18 Nov 2015 14:43:31 +0000 |
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[git/dials] master: experimental option to normalise intensities before calculating cc's in rbs and cis (761b747)
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Wed, 18 Nov 2015 14:16:44 +0000 |
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[git/dials] master: larger default max_cell_step_size=45 now that separating entering/exiting reflections in nearest neighbour analysis (141a7cc)
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Wed, 18 Nov 2015 13:57:47 +0000 |
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[git/dials] master: new default outlier.separate_panels=Auto (1a60248)
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Wed, 18 Nov 2015 13:04:26 +0000 |
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[git/dials] master: update link to mac installer (10.11 -> 10.11.1) (4e1650a)
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Wed, 18 Nov 2015 11:37:17 +0000 |
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[git/dials] master: use tukey instead of mcd as default outlier.algorithm for rotation images in indexing: faster and more appropriate at this stage (438df26)
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Wed, 18 Nov 2015 10:43:54 +0000 |
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[git/dials] master: separate entering and exiting reflections in nearest neighbour analysis to avoid overlaps between multiple observations of the same reflection (664c3b7)
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Tue, 17 Nov 2015 17:20:30 +0000 |
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[git/dials] master: max_cell determination: filter out resolution bins with much higher counts than rest (a2bc48f)
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Tue, 17 Nov 2015 15:30:49 +0000 |
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[git/dials] master: user configurable max_cell_step_size parameter (6b4c538)
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Tue, 17 Nov 2015 15:16:24 +0000 |
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[git/dials] master: correct term is location function (e77b960)
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Tue, 17 Nov 2015 14:43:28 +0000 |
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[git/dials] master: Do not use magic numbers (a0ac1d5)
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Tue, 17 Nov 2015 14:41:05 +0000 |
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[git/dials] master: separate spot count by experiment id (e0a846f)
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Tue, 17 Nov 2015 14:10:02 +0000 |
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[git/dials] master: Allow automatic relaxation of max_cell if set to automatic and no solution found with initial estimate (f61d605)
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Tue, 17 Nov 2015 14:05:46 +0000 |
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[git/dials] master: Do not create versioned copies of dispatchers during installation (2c34c9d)
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Tue, 17 Nov 2015 09:21:38 +0000 |
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[git/dials] master: fix reverse phi option in rlv (7e7020b)
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Tue, 17 Nov 2015 09:20:23 +0000 |
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[git/dials] master: Working on SingleUnitCellTie class. Testing analytical derivatives vs FD and looks ok. (a6f8fb6)
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Mon, 16 Nov 2015 15:25:08 +0000 |
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[git/dials] master: Can't use pipe and exit code propagation at the same time (63a55d4)
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Mon, 16 Nov 2015 10:13:10 +0000 |
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[git/dials] master: copy stderr and stdout into log files (2df2d7c)
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Mon, 16 Nov 2015 10:05:37 +0000 |
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[git/dials] master: Start work on RestraintsParameterisation (bc902e2)
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Fri, 13 Nov 2015 16:25:28 +0000 |
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[git/dials] master: Add phil interface for restraints (45f9dbb)
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Fri, 13 Nov 2015 16:25:28 +0000 |
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[git/dials] master: check in WIP restraints (cf61aa6)
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Fri, 13 Nov 2015 16:25:28 +0000 |
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[git/dials] master: Making a start on a restraints framework (8ac8394)
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Fri, 13 Nov 2015 16:25:27 +0000 |
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[git/dials] master: PHIL interface for restraints (f42a646)
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Fri, 13 Nov 2015 16:25:27 +0000 |
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[git/dials] master: Added prefix option (9464d81)
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Fri, 13 Nov 2015 15:11:57 +0000 |
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[git/dials] master: Enable command line completion for dials.find_spots (1672592)
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Fri, 13 Nov 2015 13:06:05 +0000 |
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[git/dials] master: bug fix: only pass non-zero miller indices to detect_non_primitive_basis() (25cda7e)
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Fri, 13 Nov 2015 11:49:33 +0000 |
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[git/dials] master: add d_min option to dials.image_viewer (a8f2c4a)
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Fri, 13 Nov 2015 09:29:01 +0000 |
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[git/dials] master: write all options into debug file (aa00ca8)
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Fri, 13 Nov 2015 08:57:58 +0000 |
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[git/dials] master: Replace the remaining associative array with explicit function. Add some comments and completion of boolean parameters. (db34f17)
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Fri, 13 Nov 2015 08:55:29 +0000 |
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[git/dials] master: Typo fix (b919334)
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Fri, 13 Nov 2015 08:26:03 +0000 |
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[git/dials] master: Add explicit dependency of the autocompletion cache on the generating and using code (8703091)
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Thu, 12 Nov 2015 16:21:05 +0000 |
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[git/dials] master: Replace one associative array with explicit function. This should be more reliable on different platforms (42dae4d)
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Thu, 12 Nov 2015 15:26:20 +0000 |
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[git/dials] master: Removed unused import spitting out lots of warnings (4bc4deb)
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Wed, 11 Nov 2015 16:05:33 +0000 |
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[git/dials] master: Removed typename from non-template clas (f8d5937)
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Wed, 11 Nov 2015 16:02:49 +0000 |
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[git/dials] master: Use a different data structure for overlaps to reduce memory usage. (98bd7cc)
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Wed, 11 Nov 2015 15:52:00 +0000 |
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[git/dials] master: Added example usage showing dials.import directory input (90019db)
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Wed, 11 Nov 2015 15:52:00 +0000 |
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[git/dials] master: Making it more obvious that dials.import can take paths as well (35bb870)
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DIALS Commit via DLS Jenkins |
Wed, 11 Nov 2015 11:22:39 +0000 |
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[git/dials] master: use Nick's labelit algorithm for detection and correcion of non-primitive basis (2760ef8)
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DIALS Commit via DLS Jenkins |
Mon, 9 Nov 2015 15:25:50 +0000 |
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[git/dials] master: Added generate mask documentation (768a4ef)
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DIALS Commit via DLS Jenkins |
Mon, 9 Nov 2015 11:31:37 +0000 |
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[git/dials] master: Updated help strings in generate_mask and integrate (7f042c5)
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DIALS Commit via DLS Jenkins |
Mon, 9 Nov 2015 10:27:56 +0000 |
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[git/dials] master: check that server has read access to file (a270f8a)
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DIALS Commit via DLS Jenkins |
Mon, 9 Nov 2015 09:23:21 +0000 |
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[git/dials] master: Change centroid to use background subtracted signal pixels (d7d1714)
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DIALS Commit via DLS Jenkins |
Fri, 6 Nov 2015 15:57:59 +0000 |
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[git/dials] master: bug fix: inspite of axis label indicating to the contrary, rmsd/mean phi residuals were plotted in radians (0e4b147)
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DIALS Commit via DLS Jenkins |
Fri, 6 Nov 2015 11:42:48 +0000 |
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[git/dials] master: use all reflections in indexing for fft1d by default (478051f)
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DIALS Commit via DLS Jenkins |
Wed, 4 Nov 2015 18:07:05 +0000 |
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[git/dials] master: remove dials.show_isig_rmsd as no longer needed by xia2 (c7c53bc)
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DIALS Commit via DLS Jenkins |
Wed, 4 Nov 2015 16:20:55 +0000 |
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[git/dials] master: Changed list of tables/arrays to dictionaries (e58120c)
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DIALS Commit via DLS Jenkins |
Wed, 4 Nov 2015 14:56:11 +0000 |
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[git/dials] master: Added a couple of helper functions (50e8a70)
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DIALS Commit via DLS Jenkins |
Wed, 4 Nov 2015 14:01:16 +0000 |
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[git/dials] master: Added XY RMSD to the integration report (106d1be)
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DIALS Commit via DLS Jenkins |
Wed, 4 Nov 2015 14:01:16 +0000 |
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[git/dials] master: Allow control of verbosity (default False). (c5abd93)
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DIALS Commit via DLS Jenkins |
Tue, 3 Nov 2015 19:54:17 +0000 |
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[git/dials] master: experiment_id -> crystal_id (4582b78)
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DIALS Commit via DLS Jenkins |
Mon, 2 Nov 2015 15:47:03 +0000 |
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[git/dials] master: add rbs tests for multi-sweep and multi-crystal input (abf0253)
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DIALS Commit via DLS Jenkins |
Mon, 2 Nov 2015 15:47:03 +0000 |
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[git/dials] master: Do not build autocompletion hints on Windows (8b78113)
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DIALS Commit via DLS Jenkins |
Mon, 2 Nov 2015 14:19:35 +0000 |
94 lines |