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[git/cctbx] master: Trying mask_padding_fraction instead of adjusting fraction_of_max_mask_threshold. Problem addressed is the low res mask is a little too small. (260d154ae)
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Mon, 31 Dec 2018 08:39:56 -0700 |
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[git/cctbx] master: Reorganize conda-related checks (90534f797)
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Mon, 31 Dec 2018 09:17:40 +0100 |
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[git/cctbx] master: check helical symmetry only if necessary; set fraction_of_max_mask_threshold lower to increase size of mask for solvent content (22aff1ef5)
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Sun, 30 Dec 2018 15:44:34 -0800 |
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[git/cctbx] master: Using low_res mask for solvent content (068cd698c)
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Sun, 30 Dec 2018 13:31:49 -0800 |
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[git/cctbx] master: Minor update to Windows conda environments (94fdd78f2)
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Sun, 30 Dec 2018 01:57:36 -0800 |
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[git/cctbx] master: Fix typo in comment (f22c0e28a)
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Sun, 30 Dec 2018 09:09:00 +0100 |
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[git/cctbx] master: Minor update to macOS conda environments (7bee902e4)
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Sun, 30 Dec 2018 08:58:58 +0100 |
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[git/cctbx] master: Add MD5 hashes to linux conda environment list (ff8c35fdc)
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Sat, 29 Dec 2018 11:42:22 -0800 |
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[git/cctbx] master: Minor update to conda environment for linux (0ec6bce59)
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Sat, 29 Dec 2018 11:27:17 -0800 |
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[git/cctbx] master: Require user to specify how symmetry is to be defined if extract_unique is set in map_box (946ac6d56)
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Sat, 29 Dec 2018 06:14:30 -0800 |
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[git/cctbx] master: conda environment for macOS: (15a535f49)
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Fri, 28 Dec 2018 21:36:40 +0100 |
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[git/cctbx] master: minor format change (8619729de)
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Thu, 27 Dec 2018 09:47:08 -0700 |
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Jenkins CCTBX Branch Tests branch origin/ml_push Still Unstable
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Mon, 24 Dec 2018 11:13:36 +0000 |
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[git/cctbx] master: New use case requiring derivative of Fcalc w.r.t. fp and fpp. Longstanding implementation gives derivative of target function with respect to those parameters, however, it presupposes that a tight loop summing over Miller indicies can be performed within the C++ function call. Current code supports alternative uses where such a loop is not possible. Specifically, a loop over Bragg spot observations on separate images, where the slow loop is over MPI worker ranks on a distributed system. (e0aee10b2)
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Fri, 21 Dec 2018 14:37:17 -0800 |
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Jenkins CCTBX Branch Tests branch origin/ml_push Unstable
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Fri, 21 Dec 2018 22:36:00 +0000 |
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[git/cctbx] master: Slightly refined test. (0aeca42b8)
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Fri, 21 Dec 2018 13:43:59 -0800 |
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[git/cctbx] master: Turn off print of warning messages because they break 2 phenix.refine tests which do not expect the error messages (7f1e34976)
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Fri, 21 Dec 2018 13:35:12 -0800 |
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[git/cctbx] master: Allow control over printing error messages and stopping on read warnings (d9f88fc5f)
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Fri, 21 Dec 2018 12:39:18 -0800 |
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[git/cctbx] master: New function of GRM to accomodate shifting coordinates for us and external forcefields. (cc21afcf0)
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Fri, 21 Dec 2018 12:37:40 -0800 |
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[git/cctbx] master: Suppressing warnings output. Move imports out of the classes/functions. (ea7bf29a7)
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Fri, 21 Dec 2018 11:46:44 -0800 |
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[git/cctbx] master: Allow reading mrc files with no machine stamp (e7dcce465)
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Fri, 21 Dec 2018 06:37:38 -0800 |
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[git/cctbx] master: clean clutter (d50a1454e)
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Fri, 21 Dec 2018 06:35:49 -0700 |
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[git/cctbx] master: Moving all use of iotbx.ccp4_map to iotbx.mrcfile (9a650997a)
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Thu, 20 Dec 2018 20:14:59 -0800 |
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[git/cctbx] master: Add capability for writing output files with any axis order (2f0fef3cb)
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Thu, 20 Dec 2018 18:20:18 -0700 |
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Jenkins 5a cctbx Tests build 7688 Still Unstable
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Fri, 21 Dec 2018 01:14:55 +0000 |
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[git/cctbx] master: Add test file (a1c913a3b)
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Thu, 20 Dec 2018 17:10:37 -0800 |
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Jenkins 5a cctbx Tests build 7687 Still Unstable
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Fri, 21 Dec 2018 01:10:07 +0000 |
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[git/cctbx] master: Partial shift to mrcfile from ccp4_map (be2c4d69a)
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Thu, 20 Dec 2018 16:51:22 -0800 |
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[git/cctbx] master: corner wrapping, more tests (3a9df1729)
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Thu, 20 Dec 2018 16:45:39 -0800 |
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[git/cctbx] master: Refactoring, clean up output. (ac2f2e350)
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Thu, 20 Dec 2018 16:45:39 -0800 |
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[git/cctbx] master: Wrapping lines draft. (d87bb3c1b)
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Thu, 20 Dec 2018 16:45:39 -0800 |
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[git/cctbx] master: Moving testing functionality to standalone test (62c7829d5)
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Thu, 20 Dec 2018 16:45:39 -0800 |
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[git/cctbx] master: Implement Schrodinger hooks for refinement programs. (989582def)
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Thu, 20 Dec 2018 09:53:29 -0800 |
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[git/cctbx] master: Remove er_params for ensemble refinement. (86553b0db)
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Thu, 20 Dec 2018 09:53:29 -0800 |
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[git/cctbx] master: Use get_source method to identify geometry manager. (4be65d24a)
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Thu, 20 Dec 2018 09:53:29 -0800 |
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[git/cctbx] master: Fix typo geobox (1ad3fe055)
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Thu, 20 Dec 2018 09:53:29 -0800 |
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[git/cctbx] master: Import schrodinger module from SCHRODINGER distribution. (14095c0fd)
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Thu, 20 Dec 2018 09:53:29 -0800 |
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[git/cctbx] master: Clean up mrcfile reader/writer and its test (286cbd7b7)
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Thu, 20 Dec 2018 08:40:27 -0800 |
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[git/cctbx] master: Clean clutter (36e504758)
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Wed, 19 Dec 2018 20:41:42 -0700 |
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Jenkins 5a cctbx Tests build 7682 Still Unstable
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Thu, 20 Dec 2018 03:23:55 +0000 |
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[git/cctbx] master: Allow use of mrcfile but do not actually use it yet. Add tests verifying mrcfile gives same result as ccp4_map. To use just substitute ccp4_map with mrcfile in path (b855caac9)
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Wed, 19 Dec 2018 20:20:34 -0700 |
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[git/cctbx] master: Remove xfel/merging/application/merging (1c6dbb102)
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Wed, 19 Dec 2018 17:06:54 -0800 |
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[git/cctbx] master: Bugfixes and adopting more dials methods, such as index_reflections (81836e53d)
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Wed, 19 Dec 2018 16:55:23 -0800 |
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[git/cctbx] master: Multipanel bugfixes for small cell (1d0373604)
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Wed, 19 Dec 2018 16:55:23 -0800 |
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[git/cctbx] master: Clean all clutter. Should put us back to no clutter again. (5fdcc371d)
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Wed, 19 Dec 2018 16:49:54 -0800 |
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Jenkins 5a cctbx Tests build 7678 Still Unstable
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Wed, 19 Dec 2018 23:51:48 +0000 |
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[git/cctbx] master: Fix failure to apply shift in auto_sharpen from map_to_model (4cbe7882c)
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Wed, 19 Dec 2018 16:48:47 -0700 |
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[git/cctbx] master: common mode and gain updates for format class CSPAD (99e6fa705)
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Wed, 19 Dec 2018 06:07:00 -0800 |
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[git/cctbx] master: Fixing the cluster_two_merge_cs program based on work in LU50 and forcing it to use the client server MPI model (35ee79f24)
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Tue, 18 Dec 2018 16:19:40 -0800 |
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[git/cctbx] master: Clean clutter. (1258c91f1)
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Tue, 18 Dec 2018 14:26:30 -0800 |
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[git/cctbx] master: more skips in writing cif_link (6b99a3234)
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Tue, 18 Dec 2018 14:15:06 -0800 |
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[git/cctbx] master: added specific exclusion of origin ID in CDL update (7e480baeb)
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Tue, 18 Dec 2018 14:06:37 -0800 |
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[git/cctbx] master: angle edits now accept changes with test (cdab86344)
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Tue, 18 Dec 2018 12:59:16 -0800 |
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[git/cctbx] master: quick hack to get it started (74a3f4bbd)
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Tue, 18 Dec 2018 11:47:52 -0800 |
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[git/cctbx] master: proper case of stats output (6a4044e3d)
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Tue, 18 Dec 2018 10:47:50 -0800 |
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[git/cctbx] master: not writing some cif_links (9d6333d9c)
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Tue, 18 Dec 2018 10:47:50 -0800 |
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[git/cctbx] master: send qmmask back to amber.energies_sites to modify printing of Amber energies there (60768cb9a)
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Tue, 18 Dec 2018 13:32:34 -0500 |
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[git/cctbx] master: Adapt MPI merger to the "worker" architecture. (e35cf48a7)
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Mon, 17 Dec 2018 17:53:15 -0800 |
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[git/cctbx] master: Adapt MPI merger to the "worker" architecture. (780c97ab3)
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Mon, 17 Dec 2018 17:53:15 -0800 |
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[git/cctbx] master: Fixing corner-case in ccd, remove restraints for non-SS parts in SS idealization (c05bffaf0)
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Mon, 17 Dec 2018 17:10:55 -0800 |
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[git/cctbx] master: Fix split_boxes (6d0af4562)
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Mon, 17 Dec 2018 17:19:53 -0700 |
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[git/cctbx] master: chem_comp_atom not allowed in first block (a87637b9b)
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Mon, 17 Dec 2018 12:54:20 -0800 |
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[git/cctbx] master: more options (0651f128b)
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Mon, 17 Dec 2018 08:43:48 -0800 |
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[git/cctbx] master: Resulting from fix for https://github.com/cctbx/cctbx_project/issues/267 - need to propose default axis in McStas frame since will be subsequently rotated about 0, 1, 0 in mapping to imgCIF frame (a35197ff6)
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Mon, 17 Dec 2018 10:42:12 +0000 |
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[git/cctbx] master: Given data files do not have to contain _data_ to work; remove this constraint - must still have ?????? for XDS to work today though (a875d6bd5)
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Mon, 17 Dec 2018 09:30:45 +0000 |
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[git/cctbx] master: mpi_split_evaluator_run(), supports an LBFGS parameter optimization scenario where the target (functional and gradients) are significantly rate limiting, and moreover where the requisite terms of f and g can be load balanced by distributing the data over parallel evaluator instances, each of which can be handled by an MPI worker rank. Rank 0 then performs a simple MPI.reduce sum to obtain the full f and g. There has been no low-level redesign to support MPI. In particular, the ext.minimizer is run (wastefully) by every worker rank, using the same x parameters, f, and g. A simple working example is given. (d1aad6836)
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Sun, 16 Dec 2018 19:28:26 -0800 |
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[git/cctbx] master: start of pretty validation output (f7ce2366a)
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Sat, 15 Dec 2018 07:51:51 -0800 |
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[git/cctbx] master: adjusted tests for new validation output (098bc0e1f)
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Sat, 15 Dec 2018 07:51:51 -0800 |
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[git/cctbx] master: mmCIF improvements (e303e802a)
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Fri, 14 Dec 2018 15:42:30 -0800 |
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[git/cctbx] master: Allow setting origin based on another map (2a83a792f)
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Fri, 14 Dec 2018 15:26:51 -0800 |
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[git/cctbx] master: Allow setting origin based on another map (e3fb6e1a8)
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Fri, 14 Dec 2018 15:10:09 -0800 |
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[git/cctbx] master: removed outdated test (53a1deb82)
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Fri, 14 Dec 2018 14:52:19 -0800 |
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[git/cctbx] master: clean clutter (7c78f1f6b)
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Fri, 14 Dec 2018 14:20:52 -0800 |
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[git/cctbx] master: Proper parameter extraction and setting. (258190cd2)
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Fri, 14 Dec 2018 13:03:21 -0800 |
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Jenkins 5a cctbx Tests build 7652 Unstable
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Fri, 14 Dec 2018 19:42:51 +0000 |
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[git/cctbx] master: tst_pdb_as_cif works with new pdb_as_cif (8ab5a6117)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: moved writing restraints to mmCIF from all_chains to model (f5c1a2015)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: smarter writing of struct conn loop (7dac9b2fa)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: added new pdb_as_cif (2c119fcf0)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: fixed more tests (5cb1563c9)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: adjustments for geo output (a75b565dd)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: removed self._cif for standard links (bdae31b56)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: need to refresh the bond pair proxies (d8e681151)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: fixed metal coordination test (ad5168368)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: Final fixes for origin ID (12e925e33)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: started to remove self._cif ... (610cded25)
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Fri, 14 Dec 2018 11:38:39 -0800 |
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[git/cctbx] master: small bugs fixes and a start on parallelity (e4a2868da)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: Getting very close (837db1160)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: completed adding parallelities (cf276fe63)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: add struct_conn output to model via restraints manager (4f1fb6547)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: start of new origin ids and struct_conn mmCIF fields (2ad8fb7a9)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: tidy print statements (63309e61f)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: small change to print correct number of dihedral types (1501bf9c6)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: Added chiral and planes to different origin_id (4ca0b9184)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: added trans peptide to origin_ids (6bbb1f11c)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: checkpoint (6752d5128)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: ALPHA2-6 does not works normal glyco route because of ring oxygen function (5000190f5)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: adjusting tests for origin_ids (0e50e3566)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: tst_geometry_restraints_2 fix. (08f6a1566)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: another easy model (a0cac6ea4)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: tst_grm fix (b518c9c86)
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Fri, 14 Dec 2018 11:38:38 -0800 |
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[git/cctbx] master: Improve output format (5dc51d82e)
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Fri, 14 Dec 2018 11:32:04 -0800 |
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[git/cctbx] master: minor bugfixes (f42d1c3fd)
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Thu, 13 Dec 2018 17:50:03 -0800 |
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[git/cctbx] master: some logistics to break arrows. Not implemented yet. (ec6b61bfb)
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Thu, 13 Dec 2018 15:39:12 -0800 |
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[git/cctbx] master: First take on drawing arrows (fe9a247e7)
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Thu, 13 Dec 2018 15:39:12 -0800 |
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[git/cctbx] master: Decoupling making plots and writing them on disc (ddfd569bd)
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Thu, 13 Dec 2018 15:39:12 -0800 |
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[git/cctbx] master: better results handling (de47cd195)
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Thu, 13 Dec 2018 15:39:12 -0800 |
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[git/cctbx] master: First stub of comparing ramachandran validation (8d4e9289c)
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Thu, 13 Dec 2018 15:39:12 -0800 |
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[git/cctbx] master: Moving output outside computing function. More parameters. (390a83e9d)
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Thu, 13 Dec 2018 15:39:12 -0800 |
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[git/cctbx] master: Putative fix for #267 (8ce75c61a)
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Thu, 13 Dec 2018 21:27:34 +0000 |
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[git/cctbx] master: Set up backup method for estimation of solvent content based on SD map > 0.05 (adjustable) of max (41ea92b15)
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Thu, 13 Dec 2018 14:11:45 -0700 |
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[git/cctbx] master: Add keyword to scale map (63950e1c4)
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Wed, 12 Dec 2018 12:44:41 -0700 |
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[git/cctbx] master: Prioritize probe from cctbx (e6cb6120e)
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Wed, 12 Dec 2018 10:19:14 -0800 |
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Jenkins 5b cctbx MacOS build 3305 Fixed
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[git/cctbx] master: fix for small EIGERs (ba61eeb34)
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Jenkins 5b cctbx MacOS build 3304 Still Failing
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[git/cctbx] master: use stpmax (1d1fb72e5)
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Jenkins 5b cctbx MacOS build 3303 Still Failing
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[git/cctbx] master: Bugfix for ImageSetLazy (5485fc3a8)
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Tue, 11 Dec 2018 14:17:50 -0800 |
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[git/cctbx] master: minor bugfixes (07d475994)
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Tue, 11 Dec 2018 11:07:13 -0800 |
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Jenkins 5b cctbx MacOS build 3301 Still Failing
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Jenkins 5b cctbx MacOS build 3300 Failure
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[git/cctbx] master: decluttered (c8df4138b)
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Tue, 11 Dec 2018 09:59:13 -0800 |
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[git/cctbx] master: Add keyword for wrapping = True/False in cctbx_maptbx_ext.mask (was True always previously) (498ea097f)
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Tue, 11 Dec 2018 10:53:30 -0700 |
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[git/cctbx] master: minor bugfix (9d6fcaea9)
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Mon, 10 Dec 2018 17:26:45 -0800 |
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[git/cctbx] master: Update run_tests (4661428fe)
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Mon, 10 Dec 2018 15:56:35 -0800 |
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[git/cctbx] master: This test was created because cif_as_mtz failed to correctly group the arrays of pdb entries 5pti and 5rsa. The reason was incorrectly formatted sf.cif file in the PDB (space group info was missing for the second array). The two entries were corrected after contacting pdb and cif_as_mtz now works correctly. The test can thus be deleted. (34ce3b859)
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Mon, 10 Dec 2018 15:42:19 -0800 |
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[git/cctbx] master: Two obvious bug fixes (950e03547)
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Mon, 10 Dec 2018 14:34:00 -0800 |
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Jenkins 5a cctbx Tests build 7631 Fixed
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[git/cctbx] master: Add backwards compatibility for --use_conda flag (1f2fbe394)
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[git/cctbx] master: Add .vscode to .gitignore list (91e73d79f)
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Jenkins 5a cctbx Tests build 7629 Failure
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[git/cctbx] master: Add --use_conda flag for configuration (4fc187976)
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[git/cctbx] master: Bugfix for submitting custom jobs (876c025cc)
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Fri, 7 Dec 2018 15:01:40 -0800 |
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[git/cctbx] master: Fully support custom dispatches for the xfel gui (a3ed02131)
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Fri, 7 Dec 2018 09:58:51 -0800 |
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[git/cctbx] master: C++ 11 compatibility, fable. (f1dfa0b92)
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Thu, 6 Dec 2018 15:03:44 -0800 |
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[git/cctbx] master: simple_compilation.py support for c++11 standard on gcc (c480eb113)
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Thu, 6 Dec 2018 14:30:10 -0800 |
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[git/cctbx] master: Update README (41606c9f5)
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Thu, 6 Dec 2018 13:27:56 -0800 |
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[git/cctbx] master: verbose works with None for atoms (9cb16f7e2)
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[git/cctbx] master: Add Windows environments based on cctbx_dependencies metapackage (ba01ffcdc)
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Wed, 5 Dec 2018 12:48:06 -0800 |
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[git/cctbx] master: Update macOS environments based on cctbx_dependencies metapackage (3cef70ca5)
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Wed, 5 Dec 2018 11:11:24 -0800 |
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[git/cctbx] master: Update linux environments based on cctbx_dependencies metapackage (34ac303fd)
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Wed, 5 Dec 2018 11:02:01 -0800 |
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[git/cctbx] master: Fix bug reading images. (17f0a2480)
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Tue, 4 Dec 2018 16:30:28 -0800 |
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[git/cctbx] master: Aligning numbers better (a005506a0)
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[git/cctbx] master: Change platform check so that .bat files are created for Python 3 on Windows (dd5285b6b)
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Tue, 4 Dec 2018 14:07:12 -0800 |
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[git/cctbx] master: Properly mark percentage and use correct format, specifically for cbeta outliers. With test. (587c7a0e5)
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Tue, 4 Dec 2018 13:23:35 -0800 |
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[git/cctbx] master: mrcfile not used by PhaserBuilder (b40d5321f)
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Tue, 4 Dec 2018 12:45:25 +0000 |
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[git/cctbx] master: Add linux conda environments based on cctbx_dependencies metapackage (8f399fa48)
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Mon, 3 Dec 2018 15:56:34 -0800 |
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[git/cctbx] master: Fix problem where button is clipped. (c94b2a6ca)
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[git/cctbx] master: Bug fix and add main function (e83cc909a)
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[git/cctbx] master: Move matplotlib import for compute clusters without it (e9b006b31)
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[git/cctbx] master: Bfactors for residues around ligand. (e80576a1b)
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