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CCTBX-COMMIT Archives


May 2019


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Jenkins 5a cctbx Tests build 8345 Unstable (1 message)
Jenkins 5a cctbx Tests build 8346 Fixed (1 message)
Jenkins 5a cctbx Tests build 8351 Unstable (1 message)
Jenkins 5a cctbx Tests build 8352 Fixed (1 message)
Jenkins 5a cctbx Tests build 8377 Unstable (1 message)
Jenkins 5a cctbx Tests build 8381 Fixed (1 message)
[git/cctbx] master: Add delay before loading file for update (0c9f39f9d) (1 message)
[git/cctbx] master: Add get_sites_frac method (1c6e68e97) (1 message)
[git/cctbx] master: add missing assert statements in tests (f9070af05) (1 message)
[git/cctbx] master: add pytest discovery to mmtbx/run_tests.py (bec02c711) (1 message)
[git/cctbx] master: Add restraints to mmCIF output from mmtbx.prepare_pdb_deposition (d9861bed3) (1 message)
[git/cctbx] master: added new test for mosaic spread functionality (334d037e8) (1 message)
[git/cctbx] master: added ReadMe (4fefcb2aa) (1 message)
[git/cctbx] master: allow optimization of molecule in extracting ncs au (961055df3) (1 message)
[git/cctbx] master: Automatic scaling of radii to ensure smallest radius is 0.25*largest radius (c5ca1309c) (1 message)
[git/cctbx] master: Avoid setting vdw radius to None in rare cases of unknown atom types (9839e81ba) (1 message)
[git/cctbx] master: Better NCS groups filtering. (0d61d621b) (1 message)
[git/cctbx] master: Bug fix for unknown miller array type FOM label formatting on colour gradient chart (130a6cd07) (1 message)
[git/cctbx] master: Bug fix: filter out noise (25738dc4a) (1 message)
[git/cctbx] master: bug fixes (57581855f) (1 message)
[git/cctbx] master: c++ implementation of convenience classes for manipulating TLS matrices and extracting Us. allows multi-dataset usage of TLS matrices. includes boost::python wrapper (mmtbx/tls/utils.py). includes associated tests in pytest. (b2331ec66) (1 message)
[git/cctbx] master: c++ implementation of decomposition of TLS matrices into physical motions (Urzhumtsev 2016; mmtbx/tls/analysis.py) with boost::python wrapper. incorporate c++ implementation of decomposition into mmtbx/tls/analysis.py. add to tests, checking against python implementation. (9c9ff218f) (1 message)
[git/cctbx] master: change pytest tests into libtbx tests. register in mmtbx.run_tests. (eee7382aa) (1 message)
[git/cctbx] master: changes for windows compatibility. change and/or to &&/||. (8bf8e6fa2) (1 message)
[git/cctbx] master: Clean clutter (59ba24436) (1 message)
[git/cctbx] master: clean clutter (trailing whitespace) (ce4e7d3b0) (1 message)
[git/cctbx] master: Clean clutter Print label of displayed miller array (ab1a63497) (1 message)
[git/cctbx] master: Comparama: more arrows, more color control. (20be6745a) (1 message)
[git/cctbx] master: conda: use warning instead of error (d83b77c69) (1 message)
[git/cctbx] master: convert 4-space indents to 2-space indents. (d60159532) (1 message)
[git/cctbx] master: DataManager: add default output filename and overwrite options (d87000681) (1 message)
[git/cctbx] master: DataManager: add default output filenames (ba89fd229) (1 message)
[git/cctbx] master: DataManager: unset stop_for_uknowns, no longer needed (bf8c7d7be) (1 message)
[git/cctbx] master: DataManager: update default filename functions (85f78d0ee) (1 message)
[git/cctbx] master: Find H bond code from Wensong. Needs more testing and optimization. (7d1634ae9) (1 message)
[git/cctbx] master: fix missing set of chain ID (7293edca6) (1 message)
[git/cctbx] master: fix mosaic domain initialization bug hopefully without breaking Sauter features (884b735a7) (1 message)
[git/cctbx] master: fix typo (5700dc6db) (1 message)
[git/cctbx] master: fix typo in mmtbx/tls/analysis.py (8cc18a3ab) (1 message)
[git/cctbx] master: fixing test. Order of setting variables matters in simtbx. whenever mosaic_spread_deg = 0 the mosaic_domains is automatically set to 1 (cc88a9b2b) (1 message)
[git/cctbx] master: Initialise member data in constructors rather than header files. Move function definitions to serparate cpp files rather than defining in header. Remove unnecessary includes. (3d8509456) (1 message)
[git/cctbx] master: LV: Stub for CCs. (6e2a1d2e3) (1 message)
[git/cctbx] master: Make sure gridding last is >= gridding first; set solvent fraction if not set, shift pdb_inp in segment_and_split_map (49251518a) (1 message)
[git/cctbx] master: Merge #316: Implement parts of mmtbx.TLS in C++ (2de01b24c) (1 message)
[git/cctbx] master: mmtbx.prepare_pdb_deposition: always construct geometry restraints manager (548c8633b) (1 message)
[git/cctbx] master: mmtbx.prepare_pdb_depostion: add PDB interpretation parameters for restraints and links (76a05b4da) (1 message)
[git/cctbx] master: mmtbx: fix extension name (19a1b2104) (1 message)
[git/cctbx] master: Move mmCIF output of sequence loops (85158210b) (1 message)
[git/cctbx] master: multiple fixes in nonsense space (d5997e85f) (1 message)
[git/cctbx] master: Parameters to fine-tune hbond angle sigmas. (c14114868) (1 message)
[git/cctbx] master: Partially Revert "Merge pull request #317 from msgpack_as_default" (57ca8299e) (1 message)
[git/cctbx] master: ProgramTemplate: handle case where DataManager is None (76c486f1f) (1 message)
[git/cctbx] master: python class with c++ optimiser for fitting an arbitrary combination of (tls) modes against refined Us from multiple datasets. includes boost::python wrapper and pytest tests. (8c3dcf438) (1 message)
[git/cctbx] master: Reapply f83b17271c30e8a7aefc59cb6dc09e6e1b78d51d to new location (1e37191b7) (1 message)
[git/cctbx] master: refactor mmtbx/tls/optimise_amplitudes (b84037627) (1 message)
[git/cctbx] master: Remove accidental commit of tmp files (4b35afc56) (1 message)
[git/cctbx] master: Remove unused import (98e178ce7) (1 message)
[git/cctbx] master: remove unused imports. add from __future__ import division. remove unused functions. fix typo in tests. (347e21b43) (1 message)
[git/cctbx] master: removed unused imports that I am actually using (ae48defa0) (1 message)
[git/cctbx] master: rename tests in mmtbx to follow libtbx convention (current naming is picked up by pytest discovery, with these tests being incompatible with pytest, causing subsquent failures). change documentation and import statements involving these test modules to compensate. (a53bb2af4) (1 message)
[git/cctbx] master: Return NaN if NaN submitted to roundoff() rather than crashing on Python3 (471dcb25d) (1 message)
[git/cctbx] master: sequence_cif: add all residues to _entity_poly_seq.mon_id (6795b490f) (1 message)
[git/cctbx] master: sequence_cif: update tests to use model class (a5833139f) (1 message)
[git/cctbx] master: Skip chain_type in extract_unique_part_of_hierarchy because it could be mixed (8365b54ca) (1 message)
[git/cctbx] master: Sort chains on resno and chain ID (bf61dbc6d) (1 message)
[git/cctbx] master: Tool to find reserved names (334ca5589) (1 message)
[git/cctbx] master: Update README.md (1b6a0061a) (1 message)
[git/cctbx_project] master: Add mtz output (c1bc1e3b9) (1 message)
[git/cctbx_project] master: Added NGL_HKLviewerGui.py (639c79ac0) (1 message)
[git/cctbx_project] master: Allowing phil input exclusively for controlling the viewer (09bf6336a) (1 message)
[git/cctbx_project] master: always build wxpython4 on macOS >= 10.14 (#240, #333) (e9d68f7d6) (1 message)
[git/cctbx_project] master: Avoid OSError when cctbx.python is run with uwsgi (9f48c8837) (1 message)
[git/cctbx_project] master: Bug fix for standalone GUI logging directories with lots of files instead of composite files (7a5a82607) (1 message)
[git/cctbx_project] master: Bugfix (8c8603f5f) (1 message)
[git/cctbx_project] master: Bugfix and better printout. (97e2e30866) (1 message)
[git/cctbx_project] master: Bugfixes for small cell processing using standalone GUI (4d232bbca) (1 message)
[git/cctbx_project] master: CCTBXParser: bug fix for constructing working_phil (c916ba716) (1 message)
[git/cctbx_project] master: conda: change channels for py36 to be the same as py27 (6af789668) (1 message)
[git/cctbx_project] master: conda: move dependencies to backup channel (04c8c4fe5b) (1 message)
[git/cctbx_project] master: conda: only set dispatcher environment variables when needed (23f2e1d25) (1 message)
[git/cctbx_project] master: configure: use installed scons, if available (71f4b84d7) (1 message)
[git/cctbx_project] master: corrected logic (cabb46b75) (1 message)
[git/cctbx_project] master: DataManager: add function for writing MTZ files (4e4391ef4b) (1 message)
[git/cctbx_project] master: Deactivate hbond vs clash for now. (2e04c08ae) (1 message)
[git/cctbx_project] master: Disable intensity histogram calculations, improve comments. (d4b777ee6) (1 message)
[git/cctbx_project] master: Don't compute min max values of arrays with nan values. Refactoring code to avoid excessive rebuilding of scenes and matching of miller arrays (cc717c4714) (1 message)
[git/cctbx_project] master: even more changes towards a gui (da8d4d767) (1 message)
[git/cctbx_project] master: fix invalid colours when colourdata has a nan value as first element. Towards consistent display of missing data (eaa2e4ff77) (1 message)
[git/cctbx_project] master: Fix longstanding bug with counting total number of lattices (ec3e4680c) (1 message)
[git/cctbx_project] master: Fix tls test on Windows (b56d5d9c8) (1 message)
[git/cctbx_project] master: Fixes for ignoring NaN values when generating colour and radii data. GUI changes (b6d0539e86) (1 message)
[git/cctbx_project] master: fixing some phil logic (61d1df1d9) (1 message)
[git/cctbx_project] master: further gui changes (92d84e5ec) (1 message)
[git/cctbx_project] master: getting rid of unused imports, bare excepts (835b8053a) (1 message)
[git/cctbx_project] master: gui bugfixes (d3c82f9b45) (1 message)
[git/cctbx_project] master: gui changes (aba929b4c) (1 message)
[git/cctbx_project] master: Handle mpack (384ace794) (1 message)
[git/cctbx_project] master: Hbonds: show method, cut-off values, cleanup. (4d058d31d) (1 message)
[git/cctbx_project] master: improved error message (ef07775d70) (1 message)
[git/cctbx_project] master: incremental gui development (cd3c9820b) (1 message)
[git/cctbx_project] master: IOTA and PRIME GUI bugfixes and tweaks (91f6f086eb) (1 message)
[git/cctbx_project] master: Ligand validation: adapt clashes code. Cleanup. Make test. (f5a6dda8d) (1 message)
[git/cctbx_project] master: Ligand validation: use new clashes class. Cleanup. (679086e6a) (1 message)
[git/cctbx_project] master: Make workers able to be ran standalone (abec745b8) (1 message)
[git/cctbx_project] master: Missing headers hint for macOS >= 10.14 (#240, #333) (d6f0f744b) (1 message)
[git/cctbx_project] master: more changes towards a gui (9cc60a331) (1 message)
[git/cctbx_project] master: more plotting bugfixes (036ad1652) (1 message)
[git/cctbx_project] master: NBO: break up results in sym related and macro_mol overlaps. (4100e16aa) (1 message)
[git/cctbx_project] master: NBO: check for monomer library. (8c96ab67d) (1 message)
[git/cctbx_project] master: NBO: cleanup and docstrings. (6567ccec3) (1 message)
[git/cctbx_project] master: NBO: Move clashes loop to function. Better docstring. (dd4d4674c) (1 message)
[git/cctbx_project] master: NBO: refactor tests to use model class. (5568470ad) (1 message)
[git/cctbx_project] master: NBO: refactor tests. (0cd11e38a) (1 message)
[git/cctbx_project] master: NBO: refactor the class (5f13bf983) (1 message)
[git/cctbx_project] master: NBO: refactoring, transfer test. (fa8ed2966) (1 message)
[git/cctbx_project] master: NBO: Remove unnecessary check. Activate test. (3859d4053) (1 message)
[git/cctbx_project] master: NBO: sort_clashes method, is_clashing method. Plus tests. (74c9d8edc) (1 message)
[git/cctbx_project] master: NBO: stub for new class. (e26864c29) (1 message)
[git/cctbx_project] master: NBO: transfer test. (b95f4c4e5) (1 message)
[git/cctbx_project] master: NBOs: No need for filenames in phil scope. (6229b6049) (1 message)
[git/cctbx_project] master: NBOs: refactor tests (5114803a8) (1 message)
[git/cctbx_project] master: needed to work with non-loop restraints (ef6265d77) (1 message)
[git/cctbx_project] master: Nonbonded overlaps: better phil parameter names and clean up of unused parameters. (57ea1f69b) (1 message)
[git/cctbx_project] master: Nonbonded overlaps: use model class, adapt tests, command line tool can read cif files. (a25541080) (1 message)
[git/cctbx_project] master: not importing numpy (dc4ad9b03e) (1 message)
[git/cctbx_project] master: Output more detailed intensity statistics, create new worker for output (09cb987a7) (1 message)
[git/cctbx_project] master: Output more detailed intensity statistics, create new worker for output, use os.path.join instead of '/'. (6bca89413) (1 message)
[git/cctbx_project] master: plotting bugfixes (dc3720bf2) (1 message)
[git/cctbx_project] master: Process nonbonded proxies: stub for Hbonds class (d66038eaa) (1 message)
[git/cctbx_project] master: ProgramTemplate: handle cases where the output PHIL scope may not exist (1a71792f7f) (1 message)
[git/cctbx_project] master: Reactivate flex. Dont trust findimports... (54516c0a7) (1 message)
[git/cctbx_project] master: Refactor nonbonded_overlaps: use program template. (91181a149) (1 message)
[git/cctbx_project] master: Remove bare printing (2b5e107fcd) (1 message)
[git/cctbx_project] master: Remove imports (90c04d77c) (1 message)
[git/cctbx_project] master: Reorder intensity statistics to odd, even, all. (3de3d86df) (1 message)
[git/cctbx_project] master: Resize main window to fit screen on application start if display size is too small (eeed4dc7c) (1 message)
[git/cctbx_project] master: Skip test if monomer library not present (2b19fb7b5) (1 message)
[git/cctbx_project] master: some more bugfixes (97f558692) (1 message)
[git/cctbx_project] master: Sort runs for run stats standalone (879d0cf25) (1 message)
[git/cctbx_project] master: spellcheck (5ec60685b) (1 message)
[git/cctbx_project] master: strange reason for test failure (83c4cabd2) (1 message)
[git/cctbx_project] master: stub for more detailed metal coordination filtering (27413a55e) (1 message)
[git/cctbx_project] master: switched cablam to using program template, fixed filename printing in oneline (84a0aca1c) (1 message)
[git/cctbx_project] master: switched cbetadev to use program template (b940da5e6) (1 message)
[git/cctbx_project] master: switched clashscore to use program template (0b402ba93) (1 message)
[git/cctbx_project] master: switched rotalyze to use program template (bc5c8598b) (1 message)
[git/cctbx_project] master: Towards allowing phil input exclusively for controlling the viewer (29f2d288c) (1 message)
[git/cctbx_project] master: Towards making sockets between NGLHKLviewerGui.py and cmdlinesframe.py (63de2e2f3) (1 message)
[git/cctbx_project] master: un-cluttering (6ad3b0cd3) (1 message)
[git/cctbx_project] master: un-cluttering (d9e7c78cc) (1 message)
[git/cctbx_project] master: Update boilerplate to save results (98a8762a1) (1 message)
[git/cctbx_project] master: update repository location (6e9db339f) (1 message)
[git/cctbx_project] master: Update test for sequence cif, stop _struct_ref_seq checks until cif output is reworked (c6852e7b9) (1 message)
[git/cctbx_project] master: Use import flex (6069c0e31) (1 message)
[git/cctbx_project] master: Use the center of mass (com) for the centroid definition for small cell. (ffe84f12a) (1 message)
[git/cctbx_project] master: yet even more changes towards a gui (34d260c2f) (1 message)
[git/dxtbx] master: Back out one of the unicode changes to make the tests pass again. (29943ce) (1 message)
[git/dxtbx] master: Clean clutter (043d9a1) (1 message)
[git/dxtbx] master: clean clutter (139877c) (1 message)
[git/dxtbx] master: Clean clutter (52bb9cb) (1 message)
[git/dxtbx] master: cleanup (c6b2624) (1 message)
[git/dxtbx] master: Combine all __future__ imports into one statement (8094491) (1 message)
[git/dxtbx] master: Consistent trusted_range for FormatSMVADSC etc. (5e6cbae) (1 message)
[git/dxtbx] master: Enable precommitbx nagging (099d878) (1 message)
[git/dxtbx] master: enable proper pre-commits for dxtbx (b47ddc2) (1 message)
[git/dxtbx] master: File refactoring (f1a5e55) (1 message)
[git/dxtbx] master: Fix DeprecationWarnings caused by dxtbx.ext move (f007bbc) (1 message)
[git/dxtbx] master: Fix format class hierarchy (1ee0d9c) (1 message)
[git/dxtbx] master: Fix test (b42f70b) (1 message)
[git/dxtbx] master: forward compatibility (510921d) (1 message)
[git/dxtbx] master: Horrible hack (ebe7369) (1 message)
[git/dxtbx] master: Invert FPE defaults for dxtbx (#28) (558119d) (1 message)
[git/dxtbx] master: Make error message slightly more useful (dca41d4) (1 message)
[git/dxtbx] master: map not subscriptable (c28cc4a) (1 message)
[git/dxtbx] master: Move dxtbx extensions from dxtbx.* to dxtbx.ext.* (a6773c6) (1 message)
[git/dxtbx] master: overload Crystal.set_unit_cell() to accept an actual unit_cell object (88b23ec) (1 message)
[git/dxtbx] master: pacify flake8 (c7f0162) (1 message)
[git/dxtbx] master: Py 2/3: handle strings in cbflib (5e69ff6) (1 message)
[git/dxtbx] master: Py2/3 metaclass (e987b8a) (1 message)
[git/dxtbx] master: Py2/3 more Unicode -> bytes in cbf land (0f31f2b) (1 message)
[git/dxtbx] master: Raise a Sorry when invalid image passed (56d9601) (1 message)
[git/dxtbx] master: refactoring: avoid 'unicode', simplify code (2547fbb) (1 message)
[git/dxtbx] master: Reject commits w/ merge conflicts or large files (db23201) (1 message)
[git/dxtbx] master: Rename serialize.load_path to resolve_path (#23) (2a9714d) (1 message)
[git/dxtbx] master: Reverse definitions of detector size (f0f3e1e) (1 message)
[git/dxtbx] master: Revert FormatSMVJHSim (692baf7) (1 message)
[git/dxtbx] master: Revert unicode cbf changes. (dbe6803) (1 message)
[git/dxtbx] master: Run flake8 only on pull requests (2ca91ad) (1 message)
[git/dxtbx] master: Run flake8 tests during testing stage (933a521) (1 message)
[git/dxtbx] master: split up test (4ee5585) (1 message)
[git/dxtbx] master: Use struct not numpy to unpack the bytestring. (#2) (19f630c) (1 message)

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New Thread

Jenkins 5a cctbx Tests build 8345 Unstable

Jenkins 5a cctbx Tests build 8345 Unstable

DLS Jenkins

Thu, 16 May 2019 23:41:28 +0100

284 lines

New Thread

Jenkins 5a cctbx Tests build 8346 Fixed

Jenkins 5a cctbx Tests build 8346 Fixed

DLS Jenkins

Fri, 17 May 2019 00:09:16 +0100

43 lines

New Thread

Jenkins 5a cctbx Tests build 8351 Unstable

Jenkins 5a cctbx Tests build 8351 Unstable

DLS Jenkins

Fri, 17 May 2019 15:54:20 +0100

52 lines

New Thread

Jenkins 5a cctbx Tests build 8352 Fixed

Jenkins 5a cctbx Tests build 8352 Fixed

DLS Jenkins

Fri, 17 May 2019 16:28:00 +0100

43 lines

New Thread

Jenkins 5a cctbx Tests build 8377 Unstable

Jenkins 5a cctbx Tests build 8377 Unstable

DLS Jenkins

Wed, 22 May 2019 00:05:40 +0100

52 lines

New Thread

Jenkins 5a cctbx Tests build 8381 Fixed

Jenkins 5a cctbx Tests build 8381 Fixed

DLS Jenkins

Wed, 22 May 2019 11:01:31 +0100

42 lines

New Thread

[git/cctbx] master: Add delay before loading file for update (0c9f39f9d)

[git/cctbx] master: Add delay before loading file for update (0c9f39f9d)

CCTBX commit

Thu, 2 May 2019 22:34:08 -0700

84 lines

New Thread

[git/cctbx] master: Add get_sites_frac method (1c6e68e97)

[git/cctbx] master: Add get_sites_frac method (1c6e68e97)

CCTBX commit

Fri, 3 May 2019 15:48:44 +0800

84 lines

New Thread

[git/cctbx] master: add missing assert statements in tests (f9070af05)

[git/cctbx] master: add missing assert statements in tests (f9070af05)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

127 lines

New Thread

[git/cctbx] master: add pytest discovery to mmtbx/run_tests.py (bec02c711)

[git/cctbx] master: add pytest discovery to mmtbx/run_tests.py (bec02c711)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

95 lines

New Thread

[git/cctbx] master: Add restraints to mmCIF output from mmtbx.prepare_pdb_deposition (d9861bed3)

[git/cctbx] master: Add restraints to mmCIF output from mmtbx.prepare_pdb_deposition (d9861bed3)

CCTBX commit

Fri, 3 May 2019 14:41:55 -0700

110 lines

New Thread

[git/cctbx] master: added new test for mosaic spread functionality (334d037e8)

[git/cctbx] master: added new test for mosaic spread functionality (334d037e8)

CCTBX commit

Sun, 5 May 2019 08:44:26 -0700

344 lines

New Thread

[git/cctbx] master: added ReadMe (4fefcb2aa)

[git/cctbx] master: added ReadMe (4fefcb2aa)

CCTBX commit

Tue, 30 Apr 2019 23:24:29 +0100

309 lines

New Thread

[git/cctbx] master: allow optimization of molecule in extracting ncs au (961055df3)

[git/cctbx] master: allow optimization of molecule in extracting ncs au (961055df3)

CCTBX commit

Wed, 1 May 2019 17:02:06 -0600

382 lines

New Thread

[git/cctbx] master: Automatic scaling of radii to ensure smallest radius is 0.25*largest radius (c5ca1309c)

[git/cctbx] master: Automatic scaling of radii to ensure smallest radius is 0.25*largest radius (c5ca1309c)

CCTBX commit

Fri, 3 May 2019 17:56:44 +0100

282 lines

New Thread

[git/cctbx] master: Avoid setting vdw radius to None in rare cases of unknown atom types (9839e81ba)

[git/cctbx] master: Avoid setting vdw radius to None in rare cases of unknown atom types (9839e81ba)

CCTBX commit

Wed, 1 May 2019 09:57:45 +0800

127 lines

New Thread

[git/cctbx] master: Better NCS groups filtering. (0d61d621b)

[git/cctbx] master: Better NCS groups filtering. (0d61d621b)

CCTBX commit

Mon, 6 May 2019 13:27:57 -0700

168 lines

New Thread

[git/cctbx] master: Bug fix for unknown miller array type FOM label formatting on colour gradient chart (130a6cd07)

[git/cctbx] master: Bug fix for unknown miller array type FOM label formatting on colour gradient chart (130a6cd07)

CCTBX commit

Thu, 2 May 2019 18:07:26 +0100

548 lines

New Thread

[git/cctbx] master: Bug fix: filter out noise (25738dc4a)

[git/cctbx] master: Bug fix: filter out noise (25738dc4a)

CCTBX commit

Wed, 1 May 2019 20:20:07 +0800

121 lines

New Thread

[git/cctbx] master: bug fixes (57581855f)

[git/cctbx] master: bug fixes (57581855f)

CCTBX commit

Tue, 7 May 2019 19:05:39 +0100

269 lines

New Thread

[git/cctbx] master: c++ implementation of convenience classes for manipulating TLS matrices and extracting Us. allows multi-dataset usage of TLS matrices. includes boost::python wrapper (mmtbx/tls/utils.py). includes associated tests in pytest. (b2331ec66)

[git/cctbx] master: c++ implementation of convenience classes for manipulating TLS matrices and extracting Us. allows multi-dataset usage of TLS matrices. includes boost::python wrapper (mmtbx/tls/utils.py). includes associated tests in pytest. (b2331ec66)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

89 lines

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[git/cctbx] master: c++ implementation of decomposition of TLS matrices into physical motions (Urzhumtsev 2016; mmtbx/tls/analysis.py) with boost::python wrapper. incorporate c++ implementation of decomposition into mmtbx/tls/analysis.py. add to tests, checking against python implementation. (9c9ff218f)

[git/cctbx] master: c++ implementation of decomposition of TLS matrices into physical motions (Urzhumtsev 2016; mmtbx/tls/analysis.py) with boost::python wrapper. incorporate c++ implementation of decomposition into mmtbx/tls/analysis.py. add to tests, checking against python implementation. (9c9ff218f)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

95 lines

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[git/cctbx] master: change pytest tests into libtbx tests. register in mmtbx.run_tests. (eee7382aa)

[git/cctbx] master: change pytest tests into libtbx tests. register in mmtbx.run_tests. (eee7382aa)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

81 lines

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[git/cctbx] master: changes for windows compatibility. change and/or to &&/||. (8bf8e6fa2)

[git/cctbx] master: changes for windows compatibility. change and/or to &&/||. (8bf8e6fa2)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

586 lines

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[git/cctbx] master: Clean clutter (59ba24436)

[git/cctbx] master: Clean clutter (59ba24436)

CCTBX commit

Thu, 2 May 2019 09:28:25 -0700

85 lines

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[git/cctbx] master: clean clutter (trailing whitespace) (ce4e7d3b0)

[git/cctbx] master: clean clutter (trailing whitespace) (ce4e7d3b0)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

73 lines

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[git/cctbx] master: Clean clutter Print label of displayed miller array (ab1a63497)

[git/cctbx] master: Clean clutter Print label of displayed miller array (ab1a63497)

CCTBX commit

Wed, 1 May 2019 19:25:33 +0100

817 lines

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[git/cctbx] master: Comparama: more arrows, more color control. (20be6745a)

[git/cctbx] master: Comparama: more arrows, more color control. (20be6745a)

CCTBX commit

Fri, 3 May 2019 14:34:17 -0700

249 lines

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[git/cctbx] master: conda: use warning instead of error (d83b77c69)

[git/cctbx] master: conda: use warning instead of error (d83b77c69)

CCTBX commit

Mon, 6 May 2019 19:17:52 -0700

97 lines

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[git/cctbx] master: convert 4-space indents to 2-space indents. (d60159532)

[git/cctbx] master: convert 4-space indents to 2-space indents. (d60159532)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

108 lines

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[git/cctbx] master: DataManager: add default output filename and overwrite options (d87000681)

[git/cctbx] master: DataManager: add default output filename and overwrite options (d87000681)

CCTBX commit

Sat, 4 May 2019 17:44:13 -0700

1013 lines

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[git/cctbx] master: DataManager: add default output filenames (ba89fd229)

[git/cctbx] master: DataManager: add default output filenames (ba89fd229)

CCTBX commit

Sat, 4 May 2019 20:11:14 -0700

397 lines

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[git/cctbx] master: DataManager: unset stop_for_uknowns, no longer needed (bf8c7d7be)

[git/cctbx] master: DataManager: unset stop_for_uknowns, no longer needed (bf8c7d7be)

CCTBX commit

Fri, 3 May 2019 14:41:55 -0700

84 lines

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[git/cctbx] master: DataManager: update default filename functions (85f78d0ee)

[git/cctbx] master: DataManager: update default filename functions (85f78d0ee)

CCTBX commit

Sat, 4 May 2019 19:18:54 -0700

617 lines

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[git/cctbx] master: Find H bond code from Wensong. Needs more testing and optimization. (7d1634ae9)

[git/cctbx] master: Find H bond code from Wensong. Needs more testing and optimization. (7d1634ae9)

CCTBX commit

Sat, 4 May 2019 19:19:55 +0800

1861 lines

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[git/cctbx] master: fix missing set of chain ID (7293edca6)

[git/cctbx] master: fix missing set of chain ID (7293edca6)

CCTBX commit

Thu, 2 May 2019 05:03:49 -0700

116 lines

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[git/cctbx] master: fix mosaic domain initialization bug hopefully without breaking Sauter features (884b735a7)

[git/cctbx] master: fix mosaic domain initialization bug hopefully without breaking Sauter features (884b735a7)

CCTBX commit

Sun, 5 May 2019 08:44:26 -0700

271 lines

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[git/cctbx] master: fix typo (5700dc6db)

[git/cctbx] master: fix typo (5700dc6db)

CCTBX commit

Thu, 2 May 2019 05:45:59 -0700

88 lines

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[git/cctbx] master: fix typo in mmtbx/tls/analysis.py (8cc18a3ab)

[git/cctbx] master: fix typo in mmtbx/tls/analysis.py (8cc18a3ab)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

86 lines

New Thread

[git/cctbx] master: fixing test. Order of setting variables matters in simtbx. whenever mosaic_spread_deg = 0 the mosaic_domains is automatically set to 1 (cc88a9b2b)

[git/cctbx] master: fixing test. Order of setting variables matters in simtbx. whenever mosaic_spread_deg = 0 the mosaic_domains is automatically set to 1 (cc88a9b2b)

CCTBX commit

Sun, 5 May 2019 08:44:26 -0700

96 lines

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[git/cctbx] master: Initialise member data in constructors rather than header files. Move function definitions to serparate cpp files rather than defining in header. Remove unnecessary includes. (3d8509456)

[git/cctbx] master: Initialise member data in constructors rather than header files. Move function definitions to serparate cpp files rather than defining in header. Remove unnecessary includes. (3d8509456)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

103 lines

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[git/cctbx] master: LV: Stub for CCs. (6e2a1d2e3)

[git/cctbx] master: LV: Stub for CCs. (6e2a1d2e3)

CCTBX commit

Fri, 3 May 2019 10:44:29 -0700

849 lines

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[git/cctbx] master: Make sure gridding last is >= gridding first; set solvent fraction if not set, shift pdb_inp in segment_and_split_map (49251518a)

[git/cctbx] master: Make sure gridding last is >= gridding first; set solvent fraction if not set, shift pdb_inp in segment_and_split_map (49251518a)

CCTBX commit

Mon, 6 May 2019 10:42:55 -0700

214 lines

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[git/cctbx] master: Merge #316: Implement parts of mmtbx.TLS in C++ (2de01b24c)

[git/cctbx] master: Merge #316: Implement parts of mmtbx.TLS in C++ (2de01b24c)

CCTBX commit

Thu, 2 May 2019 11:49:07 +0100

171 lines

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[git/cctbx] master: mmtbx.prepare_pdb_deposition: always construct geometry restraints manager (548c8633b)

[git/cctbx] master: mmtbx.prepare_pdb_deposition: always construct geometry restraints manager (548c8633b)

CCTBX commit

Fri, 3 May 2019 14:41:55 -0700

93 lines

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[git/cctbx] master: mmtbx.prepare_pdb_depostion: add PDB interpretation parameters for restraints and links (76a05b4da)

[git/cctbx] master: mmtbx.prepare_pdb_depostion: add PDB interpretation parameters for restraints and links (76a05b4da)

CCTBX commit

Fri, 3 May 2019 14:41:55 -0700

118 lines

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[git/cctbx] master: mmtbx: fix extension name (19a1b2104)

[git/cctbx] master: mmtbx: fix extension name (19a1b2104)

CCTBX commit

Sat, 4 May 2019 17:28:30 -0700

82 lines

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[git/cctbx] master: Move mmCIF output of sequence loops (85158210b)

[git/cctbx] master: Move mmCIF output of sequence loops (85158210b)

CCTBX commit

Fri, 3 May 2019 14:41:55 -0700

3158 lines

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[git/cctbx] master: multiple fixes in nonsense space (d5997e85f)

[git/cctbx] master: multiple fixes in nonsense space (d5997e85f)

CCTBX commit

Sun, 5 May 2019 22:45:14 +0800

987 lines

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[git/cctbx] master: Parameters to fine-tune hbond angle sigmas. (c14114868)

[git/cctbx] master: Parameters to fine-tune hbond angle sigmas. (c14114868)

CCTBX commit

Mon, 6 May 2019 17:30:56 -0700

392 lines

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[git/cctbx] master: Partially Revert "Merge pull request #317 from msgpack_as_default" (57ca8299e)

[git/cctbx] master: Partially Revert "Merge pull request #317 from msgpack_as_default" (57ca8299e)

CCTBX commit

Thu, 2 May 2019 09:37:10 -0700

1565 lines

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[git/cctbx] master: ProgramTemplate: handle case where DataManager is None (76c486f1f)

[git/cctbx] master: ProgramTemplate: handle case where DataManager is None (76c486f1f)

CCTBX commit

Sat, 4 May 2019 17:59:37 -0700

113 lines

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[git/cctbx] master: python class with c++ optimiser for fitting an arbitrary combination of (tls) modes against refined Us from multiple datasets. includes boost::python wrapper and pytest tests. (8c3dcf438)

[git/cctbx] master: python class with c++ optimiser for fitting an arbitrary combination of (tls) modes against refined Us from multiple datasets. includes boost::python wrapper and pytest tests. (8c3dcf438)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

86 lines

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[git/cctbx] master: Reapply f83b17271c30e8a7aefc59cb6dc09e6e1b78d51d to new location (1e37191b7)

[git/cctbx] master: Reapply f83b17271c30e8a7aefc59cb6dc09e6e1b78d51d to new location (1e37191b7)

CCTBX commit

Fri, 3 May 2019 14:41:55 -0700

125 lines

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[git/cctbx] master: refactor mmtbx/tls/optimise_amplitudes (b84037627)

[git/cctbx] master: refactor mmtbx/tls/optimise_amplitudes (b84037627)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

778 lines

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[git/cctbx] master: Remove accidental commit of tmp files (4b35afc56)

[git/cctbx] master: Remove accidental commit of tmp files (4b35afc56)

CCTBX commit

Sat, 4 May 2019 19:20:50 +0800

580 lines

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[git/cctbx] master: Remove unused import (98e178ce7)

[git/cctbx] master: Remove unused import (98e178ce7)

CCTBX commit

Wed, 1 May 2019 18:29:54 -0600

84 lines

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[git/cctbx] master: remove unused imports. add from __future__ import division. remove unused functions. fix typo in tests. (347e21b43)

[git/cctbx] master: remove unused imports. add from __future__ import division. remove unused functions. fix typo in tests. (347e21b43)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

340 lines

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[git/cctbx] master: removed unused imports that I am actually using (ae48defa0)

[git/cctbx] master: removed unused imports that I am actually using (ae48defa0)

CCTBX commit

Sun, 5 May 2019 09:13:32 -0700

101 lines

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[git/cctbx] master: rename tests in mmtbx to follow libtbx convention (current naming is picked up by pytest discovery, with these tests being incompatible with pytest, causing subsquent failures). change documentation and import statements involving these test modules to compensate. (a53bb2af4)

[git/cctbx] master: rename tests in mmtbx to follow libtbx convention (current naming is picked up by pytest discovery, with these tests being incompatible with pytest, causing subsquent failures). change documentation and import statements involving these test modules to compensate. (a53bb2af4)

CCTBX commit

Wed, 1 May 2019 23:02:07 -0700

114 lines

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[git/cctbx] master: Return NaN if NaN submitted to roundoff() rather than crashing on Python3 (471dcb25d)

[git/cctbx] master: Return NaN if NaN submitted to roundoff() rather than crashing on Python3 (471dcb25d)

CCTBX commit

Fri, 3 May 2019 14:26:01 +0100

84 lines

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[git/cctbx] master: sequence_cif: add all residues to _entity_poly_seq.mon_id (6795b490f)

[git/cctbx] master: sequence_cif: add all residues to _entity_poly_seq.mon_id (6795b490f)

CCTBX commit

Fri, 3 May 2019 17:11:48 -0700

89 lines

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[git/cctbx] master: sequence_cif: update tests to use model class (a5833139f)

[git/cctbx] master: sequence_cif: update tests to use model class (a5833139f)

CCTBX commit

Fri, 3 May 2019 17:12:27 -0700

584 lines

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[git/cctbx] master: Skip chain_type in extract_unique_part_of_hierarchy because it could be mixed (8365b54ca)

[git/cctbx] master: Skip chain_type in extract_unique_part_of_hierarchy because it could be mixed (8365b54ca)

CCTBX commit

Wed, 1 May 2019 18:52:34 -0700

154 lines

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[git/cctbx] master: Sort chains on resno and chain ID (bf61dbc6d)

[git/cctbx] master: Sort chains on resno and chain ID (bf61dbc6d)

CCTBX commit

Thu, 2 May 2019 08:01:58 -0600

288 lines

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[git/cctbx] master: Tool to find reserved names (334ca5589)

[git/cctbx] master: Tool to find reserved names (334ca5589)

CCTBX commit

Fri, 3 May 2019 07:42:18 +0100

154 lines

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[git/cctbx] master: Update README.md (1b6a0061a)

[git/cctbx] master: Update README.md (1b6a0061a)

CCTBX commit

Thu, 2 May 2019 15:39:24 -0700

136 lines

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[git/cctbx_project] master: Add mtz output (c1bc1e3b9)

[git/cctbx_project] master: Add mtz output (c1bc1e3b9)

CCTBX commit

Thu, 9 May 2019 11:07:59 -0700

310 lines

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[git/cctbx_project] master: Added NGL_HKLviewerGui.py (639c79ac0)

[git/cctbx_project] master: Added NGL_HKLviewerGui.py (639c79ac0)

CCTBX commit

Mon, 20 May 2019 19:11:55 +0100

1005 lines

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[git/cctbx_project] master: Allowing phil input exclusively for controlling the viewer (09bf6336a)

[git/cctbx_project] master: Allowing phil input exclusively for controlling the viewer (09bf6336a)

CCTBX commit

Tue, 14 May 2019 18:07:22 +0100

726 lines

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[git/cctbx_project] master: always build wxpython4 on macOS >= 10.14 (#240, #333) (e9d68f7d6)

[git/cctbx_project] master: always build wxpython4 on macOS >= 10.14 (#240, #333) (e9d68f7d6)

CCTBX commit

Mon, 20 May 2019 09:31:13 +0100

113 lines

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[git/cctbx_project] master: Avoid OSError when cctbx.python is run with uwsgi (9f48c8837)

[git/cctbx_project] master: Avoid OSError when cctbx.python is run with uwsgi (9f48c8837)

CCTBX commit

Fri, 10 May 2019 13:09:31 -0700

93 lines

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[git/cctbx_project] master: Bug fix for standalone GUI logging directories with lots of files instead of composite files (7a5a82607)

[git/cctbx_project] master: Bug fix for standalone GUI logging directories with lots of files instead of composite files (7a5a82607)

CCTBX commit

Thu, 9 May 2019 07:01:58 +0900

285 lines

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[git/cctbx_project] master: Bugfix (8c8603f5f)

[git/cctbx_project] master: Bugfix (8c8603f5f)

CCTBX commit

Fri, 24 May 2019 15:20:27 -0700

129 lines

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[git/cctbx_project] master: Bugfix and better printout. (97e2e30866)

[git/cctbx_project] master: Bugfix and better printout. (97e2e30866)

CCTBX commit

Fri, 31 May 2019 11:09:29 -0700

330 lines

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[git/cctbx_project] master: Bugfixes for small cell processing using standalone GUI (4d232bbca)

[git/cctbx_project] master: Bugfixes for small cell processing using standalone GUI (4d232bbca)

CCTBX commit

Thu, 9 May 2019 02:09:39 +0900

154 lines

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[git/cctbx_project] master: CCTBXParser: bug fix for constructing working_phil (c916ba716)

[git/cctbx_project] master: CCTBXParser: bug fix for constructing working_phil (c916ba716)

CCTBX commit

Fri, 24 May 2019 12:51:22 -0700

89 lines

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[git/cctbx_project] master: conda: change channels for py36 to be the same as py27 (6af789668)

[git/cctbx_project] master: conda: change channels for py36 to be the same as py27 (6af789668)

CCTBX commit

Sun, 12 May 2019 22:53:04 -0700

160 lines

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[git/cctbx_project] master: conda: move dependencies to backup channel (04c8c4fe5b)

[git/cctbx_project] master: conda: move dependencies to backup channel (04c8c4fe5b)

CCTBX commit

Thu, 30 May 2019 23:32:48 -0700

100 lines

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[git/cctbx_project] master: conda: only set dispatcher environment variables when needed (23f2e1d25)

[git/cctbx_project] master: conda: only set dispatcher environment variables when needed (23f2e1d25)

CCTBX commit

Sun, 12 May 2019 19:26:35 -0700

162 lines

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[git/cctbx_project] master: configure: use installed scons, if available (71f4b84d7)

[git/cctbx_project] master: configure: use installed scons, if available (71f4b84d7)

CCTBX commit

Sun, 12 May 2019 20:08:16 -0700

106 lines

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[git/cctbx_project] master: corrected logic (cabb46b75)

[git/cctbx_project] master: corrected logic (cabb46b75)

CCTBX commit

Thu, 16 May 2019 15:32:02 -0700

92 lines

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[git/cctbx_project] master: DataManager: add function for writing MTZ files (4e4391ef4b)

[git/cctbx_project] master: DataManager: add function for writing MTZ files (4e4391ef4b)

CCTBX commit

Fri, 31 May 2019 15:14:49 -0700

277 lines

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[git/cctbx_project] master: Deactivate hbond vs clash for now. (2e04c08ae)

[git/cctbx_project] master: Deactivate hbond vs clash for now. (2e04c08ae)

CCTBX commit

Fri, 24 May 2019 17:18:29 -0700

93 lines

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[git/cctbx_project] master: Disable intensity histogram calculations, improve comments. (d4b777ee6)

[git/cctbx_project] master: Disable intensity histogram calculations, improve comments. (d4b777ee6)

CCTBX commit

Thu, 23 May 2019 11:18:55 -0700

658 lines

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[git/cctbx_project] master: Don't compute min max values of arrays with nan values. Refactoring code to avoid excessive rebuilding of scenes and matching of miller arrays (cc717c4714)

[git/cctbx_project] master: Don't compute min max values of arrays with nan values. Refactoring code to avoid excessive rebuilding of scenes and matching of miller arrays (cc717c4714)

CCTBX commit

Tue, 28 May 2019 17:28:21 +0100

1081 lines

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[git/cctbx_project] master: even more changes towards a gui (da8d4d767)

[git/cctbx_project] master: even more changes towards a gui (da8d4d767)

CCTBX commit

Fri, 17 May 2019 18:59:17 +0100

527 lines

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[git/cctbx_project] master: fix invalid colours when colourdata has a nan value as first element. Towards consistent display of missing data (eaa2e4ff77)

[git/cctbx_project] master: fix invalid colours when colourdata has a nan value as first element. Towards consistent display of missing data (eaa2e4ff77)

CCTBX commit

Thu, 30 May 2019 18:01:35 +0100

685 lines

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[git/cctbx_project] master: Fix longstanding bug with counting total number of lattices (ec3e4680c)

[git/cctbx_project] master: Fix longstanding bug with counting total number of lattices (ec3e4680c)

CCTBX commit

Thu, 9 May 2019 08:46:41 +0900

99 lines

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[git/cctbx_project] master: Fix tls test on Windows (b56d5d9c8)

[git/cctbx_project] master: Fix tls test on Windows (b56d5d9c8)

CCTBX commit

Fri, 10 May 2019 15:10:39 -0700

91 lines

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[git/cctbx_project] master: Fixes for ignoring NaN values when generating colour and radii data. GUI changes (b6d0539e86)

[git/cctbx_project] master: Fixes for ignoring NaN values when generating colour and radii data. GUI changes (b6d0539e86)

CCTBX commit

Wed, 29 May 2019 18:35:28 +0100

1285 lines

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[git/cctbx_project] master: fixing some phil logic (61d1df1d9)

[git/cctbx_project] master: fixing some phil logic (61d1df1d9)

CCTBX commit

Wed, 22 May 2019 17:38:13 +0100

623 lines

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[git/cctbx_project] master: further gui changes (92d84e5ec)

[git/cctbx_project] master: further gui changes (92d84e5ec)

CCTBX commit

Thu, 23 May 2019 17:55:56 +0100

943 lines

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[git/cctbx_project] master: getting rid of unused imports, bare excepts (835b8053a)

[git/cctbx_project] master: getting rid of unused imports, bare excepts (835b8053a)

CCTBX commit

Mon, 20 May 2019 22:51:21 +0100

178 lines

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[git/cctbx_project] master: gui bugfixes (d3c82f9b45)

[git/cctbx_project] master: gui bugfixes (d3c82f9b45)

CCTBX commit

Tue, 28 May 2019 18:30:44 -0700

930 lines

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[git/cctbx_project] master: gui changes (aba929b4c)

[git/cctbx_project] master: gui changes (aba929b4c)

CCTBX commit

Fri, 24 May 2019 19:22:14 +0100

587 lines

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[git/cctbx_project] master: Handle mpack (384ace794)

[git/cctbx_project] master: Handle mpack (384ace794)

CCTBX commit

Thu, 9 May 2019 08:50:58 -0700

110 lines

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[git/cctbx_project] master: Hbonds: show method, cut-off values, cleanup. (4d058d31d)

[git/cctbx_project] master: Hbonds: show method, cut-off values, cleanup. (4d058d31d)

CCTBX commit

Fri, 24 May 2019 15:08:38 -0700

807 lines

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[git/cctbx_project] master: improved error message (ef07775d70)

[git/cctbx_project] master: improved error message (ef07775d70)

CCTBX commit

Thu, 30 May 2019 09:40:32 -0700

132 lines

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[git/cctbx_project] master: incremental gui development (cd3c9820b)

[git/cctbx_project] master: incremental gui development (cd3c9820b)

CCTBX commit

Tue, 21 May 2019 17:31:58 +0100

1193 lines

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[git/cctbx_project] master: IOTA and PRIME GUI bugfixes and tweaks (91f6f086eb)

[git/cctbx_project] master: IOTA and PRIME GUI bugfixes and tweaks (91f6f086eb)

CCTBX commit

Thu, 30 May 2019 09:36:41 -0700

800 lines

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[git/cctbx_project] master: Ligand validation: adapt clashes code. Cleanup. Make test. (f5a6dda8d)

[git/cctbx_project] master: Ligand validation: adapt clashes code. Cleanup. Make test. (f5a6dda8d)

CCTBX commit

Tue, 21 May 2019 23:16:10 -0700

1220 lines

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[git/cctbx_project] master: Ligand validation: use new clashes class. Cleanup. (679086e6a)

[git/cctbx_project] master: Ligand validation: use new clashes class. Cleanup. (679086e6a)

CCTBX commit

Wed, 22 May 2019 20:47:45 -0700

812 lines

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[git/cctbx_project] master: Make workers able to be ran standalone (abec745b8)

[git/cctbx_project] master: Make workers able to be ran standalone (abec745b8)

CCTBX commit

Fri, 10 May 2019 08:47:05 -0700

453 lines

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[git/cctbx_project] master: Missing headers hint for macOS >= 10.14 (#240, #333) (d6f0f744b)

[git/cctbx_project] master: Missing headers hint for macOS >= 10.14 (#240, #333) (d6f0f744b)

CCTBX commit

Mon, 20 May 2019 09:31:13 +0100

99 lines

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[git/cctbx_project] master: more changes towards a gui (9cc60a331)

[git/cctbx_project] master: more changes towards a gui (9cc60a331)

CCTBX commit

Thu, 16 May 2019 18:17:38 +0100

973 lines

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[git/cctbx_project] master: more plotting bugfixes (036ad1652)

[git/cctbx_project] master: more plotting bugfixes (036ad1652)

CCTBX commit

Fri, 17 May 2019 16:59:26 -0700

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[git/cctbx_project] master: NBO: break up results in sym related and macro_mol overlaps. (4100e16aa)

[git/cctbx_project] master: NBO: break up results in sym related and macro_mol overlaps. (4100e16aa)

CCTBX commit

Sat, 18 May 2019 14:12:53 -0700

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[git/cctbx_project] master: NBO: check for monomer library. (8c96ab67d)

[git/cctbx_project] master: NBO: check for monomer library. (8c96ab67d)

CCTBX commit

Wed, 22 May 2019 21:38:30 -0700

127 lines

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[git/cctbx_project] master: NBO: cleanup and docstrings. (6567ccec3)

[git/cctbx_project] master: NBO: cleanup and docstrings. (6567ccec3)

CCTBX commit

Sat, 18 May 2019 23:24:01 -0700

407 lines

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[git/cctbx_project] master: NBO: Move clashes loop to function. Better docstring. (dd4d4674c)

[git/cctbx_project] master: NBO: Move clashes loop to function. Better docstring. (dd4d4674c)

CCTBX commit

Fri, 17 May 2019 11:20:03 -0700

506 lines

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[git/cctbx_project] master: NBO: refactor tests to use model class. (5568470ad)

[git/cctbx_project] master: NBO: refactor tests to use model class. (5568470ad)

CCTBX commit

Wed, 15 May 2019 12:33:45 -0700

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[git/cctbx_project] master: NBO: refactor tests. (0cd11e38a)

[git/cctbx_project] master: NBO: refactor tests. (0cd11e38a)

CCTBX commit

Sat, 18 May 2019 17:45:21 -0700

463 lines

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[git/cctbx_project] master: NBO: refactor the class (5f13bf983)

[git/cctbx_project] master: NBO: refactor the class (5f13bf983)

CCTBX commit

Thu, 16 May 2019 22:45:51 -0700

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[git/cctbx_project] master: NBO: refactoring, transfer test. (fa8ed2966)

[git/cctbx_project] master: NBO: refactoring, transfer test. (fa8ed2966)

CCTBX commit

Sat, 18 May 2019 13:13:48 -0700

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[git/cctbx_project] master: NBO: Remove unnecessary check. Activate test. (3859d4053)

[git/cctbx_project] master: NBO: Remove unnecessary check. Activate test. (3859d4053)

CCTBX commit

Tue, 21 May 2019 15:05:56 -0700

183 lines

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[git/cctbx_project] master: NBO: sort_clashes method, is_clashing method. Plus tests. (74c9d8edc)

[git/cctbx_project] master: NBO: sort_clashes method, is_clashing method. Plus tests. (74c9d8edc)

CCTBX commit

Mon, 20 May 2019 12:39:04 -0700

633 lines

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[git/cctbx_project] master: NBO: stub for new class. (e26864c29)

[git/cctbx_project] master: NBO: stub for new class. (e26864c29)

CCTBX commit

Wed, 15 May 2019 22:34:41 -0700

348 lines

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[git/cctbx_project] master: NBO: transfer test. (b95f4c4e5)

[git/cctbx_project] master: NBO: transfer test. (b95f4c4e5)

CCTBX commit

Fri, 17 May 2019 15:29:58 -0700

506 lines

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[git/cctbx_project] master: NBOs: No need for filenames in phil scope. (6229b6049)

[git/cctbx_project] master: NBOs: No need for filenames in phil scope. (6229b6049)

CCTBX commit

Tue, 14 May 2019 17:19:48 -0700

204 lines

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[git/cctbx_project] master: NBOs: refactor tests (5114803a8)

[git/cctbx_project] master: NBOs: refactor tests (5114803a8)

CCTBX commit

Sat, 18 May 2019 23:00:41 -0700

1629 lines

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[git/cctbx_project] master: needed to work with non-loop restraints (ef6265d77)

[git/cctbx_project] master: needed to work with non-loop restraints (ef6265d77)

CCTBX commit

Thu, 16 May 2019 15:19:29 -0700

87 lines

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[git/cctbx_project] master: Nonbonded overlaps: better phil parameter names and clean up of unused parameters. (57ea1f69b)

[git/cctbx_project] master: Nonbonded overlaps: better phil parameter names and clean up of unused parameters. (57ea1f69b)

CCTBX commit

Tue, 14 May 2019 16:04:22 -0700

439 lines

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[git/cctbx_project] master: Nonbonded overlaps: use model class, adapt tests, command line tool can read cif files. (a25541080)

[git/cctbx_project] master: Nonbonded overlaps: use model class, adapt tests, command line tool can read cif files. (a25541080)

CCTBX commit

Tue, 14 May 2019 14:04:47 -0700

1745 lines

New Thread

[git/cctbx_project] master: not importing numpy (dc4ad9b03e)

[git/cctbx_project] master: not importing numpy (dc4ad9b03e)

CCTBX commit

Tue, 28 May 2019 20:31:50 +0100

95 lines

New Thread

[git/cctbx_project] master: Output more detailed intensity statistics, create new worker for output (09cb987a7)

[git/cctbx_project] master: Output more detailed intensity statistics, create new worker for output (09cb987a7)

CCTBX commit

Tue, 21 May 2019 17:26:31 -0700

1137 lines

New Thread

[git/cctbx_project] master: Output more detailed intensity statistics, create new worker for output, use os.path.join instead of '/'. (6bca89413)

[git/cctbx_project] master: Output more detailed intensity statistics, create new worker for output, use os.path.join instead of '/'. (6bca89413)

CCTBX commit

Tue, 21 May 2019 12:16:10 -0700

408 lines

New Thread

[git/cctbx_project] master: plotting bugfixes (dc3720bf2)

[git/cctbx_project] master: plotting bugfixes (dc3720bf2)

CCTBX commit

Thu, 16 May 2019 18:01:10 -0700

1845 lines

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[git/cctbx_project] master: Process nonbonded proxies: stub for Hbonds class (d66038eaa)

[git/cctbx_project] master: Process nonbonded proxies: stub for Hbonds class (d66038eaa)

CCTBX commit

Fri, 24 May 2019 13:21:50 -0700

411 lines

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[git/cctbx_project] master: ProgramTemplate: handle cases where the output PHIL scope may not exist (1a71792f7f)

[git/cctbx_project] master: ProgramTemplate: handle cases where the output PHIL scope may not exist (1a71792f7f)

CCTBX commit

Wed, 29 May 2019 15:21:39 -0700

125 lines

New Thread

[git/cctbx_project] master: Reactivate flex. Dont trust findimports... (54516c0a7)

[git/cctbx_project] master: Reactivate flex. Dont trust findimports... (54516c0a7)

CCTBX commit

Tue, 21 May 2019 23:29:35 -0700

87 lines

New Thread

[git/cctbx_project] master: Refactor nonbonded_overlaps: use program template. (91181a149)

[git/cctbx_project] master: Refactor nonbonded_overlaps: use program template. (91181a149)

CCTBX commit

Mon, 13 May 2019 13:02:27 -0700

1587 lines

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[git/cctbx_project] master: Remove bare printing (2b5e107fcd)

[git/cctbx_project] master: Remove bare printing (2b5e107fcd)

CCTBX commit

Fri, 31 May 2019 12:49:29 +0800

114 lines

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[git/cctbx_project] master: Remove imports (90c04d77c)

[git/cctbx_project] master: Remove imports (90c04d77c)

CCTBX commit

Wed, 22 May 2019 21:42:03 -0700

118 lines

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[git/cctbx_project] master: Reorder intensity statistics to odd, even, all. (3de3d86df)

[git/cctbx_project] master: Reorder intensity statistics to odd, even, all. (3de3d86df)

CCTBX commit

Thu, 23 May 2019 11:45:10 -0700

142 lines

New Thread

[git/cctbx_project] master: Resize main window to fit screen on application start if display size is too small (eeed4dc7c)

[git/cctbx_project] master: Resize main window to fit screen on application start if display size is too small (eeed4dc7c)

CCTBX commit

Thu, 9 May 2019 02:09:39 +0900

97 lines

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[git/cctbx_project] master: Skip test if monomer library not present (2b19fb7b5)

[git/cctbx_project] master: Skip test if monomer library not present (2b19fb7b5)

CCTBX commit

Wed, 22 May 2019 10:53:00 +0100

132 lines

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[git/cctbx_project] master: some more bugfixes (97f558692)

[git/cctbx_project] master: some more bugfixes (97f558692)

CCTBX commit

Mon, 20 May 2019 14:26:55 -0700

219 lines

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[git/cctbx_project] master: Sort runs for run stats standalone (879d0cf25)

[git/cctbx_project] master: Sort runs for run stats standalone (879d0cf25)

CCTBX commit

Wed, 8 May 2019 11:32:55 -0700

92 lines

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[git/cctbx_project] master: spellcheck (5ec60685b)

[git/cctbx_project] master: spellcheck (5ec60685b)

CCTBX commit

Thu, 23 May 2019 09:42:04 +0100

99 lines

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[git/cctbx_project] master: strange reason for test failure (83c4cabd2)

[git/cctbx_project] master: strange reason for test failure (83c4cabd2)

CCTBX commit

Thu, 16 May 2019 16:15:46 -0700

101 lines

New Thread

[git/cctbx_project] master: stub for more detailed metal coordination filtering (27413a55e)

[git/cctbx_project] master: stub for more detailed metal coordination filtering (27413a55e)

CCTBX commit

Thu, 16 May 2019 15:19:29 -0700

140 lines

New Thread

[git/cctbx_project] master: switched cablam to using program template, fixed filename printing in oneline (84a0aca1c)

[git/cctbx_project] master: switched cablam to using program template, fixed filename printing in oneline (84a0aca1c)

CCTBX commit

Thu, 23 May 2019 15:14:34 -0400

877 lines

New Thread

[git/cctbx_project] master: switched cbetadev to use program template (b940da5e6)

[git/cctbx_project] master: switched cbetadev to use program template (b940da5e6)

CCTBX commit

Thu, 23 May 2019 15:14:34 -0400

385 lines

New Thread

[git/cctbx_project] master: switched clashscore to use program template (0b402ba93)

[git/cctbx_project] master: switched clashscore to use program template (0b402ba93)

CCTBX commit

Thu, 23 May 2019 15:14:34 -0400

597 lines

New Thread

[git/cctbx_project] master: switched rotalyze to use program template (bc5c8598b)

[git/cctbx_project] master: switched rotalyze to use program template (bc5c8598b)

CCTBX commit

Thu, 23 May 2019 15:14:34 -0400

422 lines

New Thread

[git/cctbx_project] master: Towards allowing phil input exclusively for controlling the viewer (29f2d288c)

[git/cctbx_project] master: Towards allowing phil input exclusively for controlling the viewer (29f2d288c)

CCTBX commit

Mon, 13 May 2019 18:10:08 +0100

603 lines

New Thread

[git/cctbx_project] master: Towards making sockets between NGLHKLviewerGui.py and cmdlinesframe.py (63de2e2f3)

[git/cctbx_project] master: Towards making sockets between NGLHKLviewerGui.py and cmdlinesframe.py (63de2e2f3)

CCTBX commit

Wed, 15 May 2019 18:07:47 +0100

368 lines

New Thread

[git/cctbx_project] master: un-cluttering (6ad3b0cd3)

[git/cctbx_project] master: un-cluttering (6ad3b0cd3)

CCTBX commit

Tue, 14 May 2019 20:34:39 +0100

81 lines

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[git/cctbx_project] master: un-cluttering (d9e7c78cc)

[git/cctbx_project] master: un-cluttering (d9e7c78cc)

CCTBX commit

Mon, 13 May 2019 21:38:58 +0100

82 lines

New Thread

[git/cctbx_project] master: Update boilerplate to save results (98a8762a1)

[git/cctbx_project] master: Update boilerplate to save results (98a8762a1)

CCTBX commit

Fri, 10 May 2019 08:36:51 -0700

109 lines

New Thread

[git/cctbx_project] master: update repository location (6e9db339f)

[git/cctbx_project] master: update repository location (6e9db339f)

CCTBX commit

Tue, 14 May 2019 10:45:25 +0100

88 lines

New Thread

[git/cctbx_project] master: Update test for sequence cif, stop _struct_ref_seq checks until cif output is reworked (c6852e7b9)

[git/cctbx_project] master: Update test for sequence cif, stop _struct_ref_seq checks until cif output is reworked (c6852e7b9)

CCTBX commit

Wed, 15 May 2019 16:13:20 -0700

328 lines

New Thread

[git/cctbx_project] master: Use import flex (6069c0e31)

[git/cctbx_project] master: Use import flex (6069c0e31)

CCTBX commit

Tue, 14 May 2019 14:31:06 -0700

86 lines

New Thread

[git/cctbx_project] master: Use the center of mass (com) for the centroid definition for small cell. (ffe84f12a)

[git/cctbx_project] master: Use the center of mass (com) for the centroid definition for small cell. (ffe84f12a)

CCTBX commit

Thu, 9 May 2019 05:24:44 +0900

175 lines

New Thread

[git/cctbx_project] master: yet even more changes towards a gui (34d260c2f)

[git/cctbx_project] master: yet even more changes towards a gui (34d260c2f)

CCTBX commit

Mon, 20 May 2019 19:09:39 +0100

385 lines

New Thread

[git/dxtbx] master: Back out one of the unicode changes to make the tests pass again. (29943ce)

[git/dxtbx] master: Back out one of the unicode changes to make the tests pass again. (29943ce)

DXTBX commit

Thu, 16 May 2019 15:56:38 -0700

91 lines

New Thread

[git/dxtbx] master: Clean clutter (043d9a1)

[git/dxtbx] master: Clean clutter (043d9a1)

DXTBX commit

Sun, 26 May 2019 05:10:26 +0100

127 lines

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[git/dxtbx] master: clean clutter (139877c)

[git/dxtbx] master: clean clutter (139877c)

DXTBX commit

Thu, 16 May 2019 16:05:03 +0100

180 lines

New Thread

[git/dxtbx] master: Clean clutter (52bb9cb)

[git/dxtbx] master: Clean clutter (52bb9cb)

DXTBX commit

Sun, 5 May 2019 05:10:21 +0100

119 lines

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[git/dxtbx] master: cleanup (c6b2624)

[git/dxtbx] master: cleanup (c6b2624)

DXTBX commit

Mon, 13 May 2019 08:00:41 +0100

109 lines

New Thread

[git/dxtbx] master: Combine all __future__ imports into one statement (8094491)

[git/dxtbx] master: Combine all __future__ imports into one statement (8094491)

DXTBX commit

Thu, 2 May 2019 15:06:24 +0100

112 lines

New Thread

[git/dxtbx] master: Consistent trusted_range for FormatSMVADSC etc. (5e6cbae)

[git/dxtbx] master: Consistent trusted_range for FormatSMVADSC etc. (5e6cbae)

DXTBX commit

Wed, 8 May 2019 13:56:01 +0100

673 lines

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[git/dxtbx] master: Enable precommitbx nagging (099d878)

[git/dxtbx] master: Enable precommitbx nagging (099d878)

DXTBX commit

Fri, 24 May 2019 21:57:53 +0100

90 lines

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[git/dxtbx] master: enable proper pre-commits for dxtbx (b47ddc2)

[git/dxtbx] master: enable proper pre-commits for dxtbx (b47ddc2)

DXTBX commit

Fri, 3 May 2019 12:39:55 +0100

143 lines

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[git/dxtbx] master: File refactoring (f1a5e55)

[git/dxtbx] master: File refactoring (f1a5e55)

DXTBX commit

Thu, 16 May 2019 16:31:25 +0100

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[git/dxtbx] master: Fix DeprecationWarnings caused by dxtbx.ext move (f007bbc)

[git/dxtbx] master: Fix DeprecationWarnings caused by dxtbx.ext move (f007bbc)

DXTBX commit

Wed, 29 May 2019 19:51:45 +0100

498 lines

New Thread

[git/dxtbx] master: Fix format class hierarchy (1ee0d9c)

[git/dxtbx] master: Fix format class hierarchy (1ee0d9c)

DXTBX commit

Thu, 30 May 2019 07:53:57 +0100

118 lines

New Thread

[git/dxtbx] master: Fix test (b42f70b)

[git/dxtbx] master: Fix test (b42f70b)

DXTBX commit

Wed, 29 May 2019 19:41:47 +0100

93 lines

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[git/dxtbx] master: forward compatibility (510921d)

[git/dxtbx] master: forward compatibility (510921d)

DXTBX commit

Thu, 16 May 2019 11:00:54 +0100

168 lines

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[git/dxtbx] master: Horrible hack (ebe7369)

[git/dxtbx] master: Horrible hack (ebe7369)

DXTBX commit

Fri, 17 May 2019 16:19:26 +0100

106 lines

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[git/dxtbx] master: Invert FPE defaults for dxtbx (#28) (558119d)

[git/dxtbx] master: Invert FPE defaults for dxtbx (#28) (558119d)

DXTBX commit

Wed, 29 May 2019 13:08:01 +0100

131 lines

New Thread

[git/dxtbx] master: Make error message slightly more useful (dca41d4)

[git/dxtbx] master: Make error message slightly more useful (dca41d4)

DXTBX commit

Fri, 17 May 2019 12:03:30 +0100

130 lines

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[git/dxtbx] master: map not subscriptable (c28cc4a)

[git/dxtbx] master: map not subscriptable (c28cc4a)

DXTBX commit

Thu, 16 May 2019 16:08:46 +0100

88 lines

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[git/dxtbx] master: Move dxtbx extensions from dxtbx.* to dxtbx.ext.* (a6773c6)

[git/dxtbx] master: Move dxtbx extensions from dxtbx.* to dxtbx.ext.* (a6773c6)

DXTBX commit

Wed, 29 May 2019 14:41:26 +0100

195 lines

New Thread

[git/dxtbx] master: overload Crystal.set_unit_cell() to accept an actual unit_cell object (88b23ec)

[git/dxtbx] master: overload Crystal.set_unit_cell() to accept an actual unit_cell object (88b23ec)

DXTBX commit

Tue, 21 May 2019 13:28:08 +0100

235 lines

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[git/dxtbx] master: pacify flake8 (c7f0162)

[git/dxtbx] master: pacify flake8 (c7f0162)

DXTBX commit

Thu, 30 May 2019 07:53:57 +0100

114 lines

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[git/dxtbx] master: Py 2/3: handle strings in cbflib (5e69ff6)

[git/dxtbx] master: Py 2/3: handle strings in cbflib (5e69ff6)

DXTBX commit

Thu, 16 May 2019 15:29:24 -0700

1812 lines

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[git/dxtbx] master: Py2/3 metaclass (e987b8a)

[git/dxtbx] master: Py2/3 metaclass (e987b8a)

DXTBX commit

Thu, 16 May 2019 10:39:25 -0700

133 lines

New Thread

[git/dxtbx] master: Py2/3 more Unicode -> bytes in cbf land (0f31f2b)

[git/dxtbx] master: Py2/3 more Unicode -> bytes in cbf land (0f31f2b)

DXTBX commit

Thu, 16 May 2019 16:36:30 -0700

1572 lines

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[git/dxtbx] master: Raise a Sorry when invalid image passed (56d9601)

[git/dxtbx] master: Raise a Sorry when invalid image passed (56d9601)

DXTBX commit

Fri, 10 May 2019 04:27:02 +0100

281 lines

New Thread

[git/dxtbx] master: refactoring: avoid 'unicode', simplify code (2547fbb)

[git/dxtbx] master: refactoring: avoid 'unicode', simplify code (2547fbb)

DXTBX commit

Thu, 16 May 2019 22:57:52 +0100

168 lines

New Thread

[git/dxtbx] master: Reject commits w/ merge conflicts or large files (db23201)

[git/dxtbx] master: Reject commits w/ merge conflicts or large files (db23201)

DXTBX commit

Wed, 15 May 2019 11:58:05 +0100

83 lines

New Thread

[git/dxtbx] master: Rename serialize.load_path to resolve_path (#23) (2a9714d)

[git/dxtbx] master: Rename serialize.load_path to resolve_path (#23) (2a9714d)

DXTBX commit

Tue, 28 May 2019 11:44:17 +0100

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[git/dxtbx] master: Reverse definitions of detector size (f0f3e1e)

[git/dxtbx] master: Reverse definitions of detector size (f0f3e1e)

DXTBX commit

Fri, 17 May 2019 15:40:32 +0100

140 lines

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[git/dxtbx] master: Revert FormatSMVJHSim (692baf7)

[git/dxtbx] master: Revert FormatSMVJHSim (692baf7)

DXTBX commit

Fri, 10 May 2019 09:39:45 +0100

117 lines

New Thread

[git/dxtbx] master: Revert unicode cbf changes. (dbe6803)

[git/dxtbx] master: Revert unicode cbf changes. (dbe6803)

DXTBX commit

Fri, 17 May 2019 09:27:34 -0700

183 lines

New Thread

[git/dxtbx] master: Run flake8 only on pull requests (2ca91ad)

[git/dxtbx] master: Run flake8 only on pull requests (2ca91ad)

DXTBX commit

Wed, 29 May 2019 21:39:33 +0100

97 lines

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[git/dxtbx] master: Run flake8 tests during testing stage (933a521)

[git/dxtbx] master: Run flake8 tests during testing stage (933a521)

DXTBX commit

Wed, 29 May 2019 21:35:29 +0100

161 lines

New Thread

[git/dxtbx] master: split up test (4ee5585)

[git/dxtbx] master: split up test (4ee5585)

DXTBX commit

Tue, 21 May 2019 13:28:08 +0100

87 lines

New Thread

[git/dxtbx] master: Use struct not numpy to unpack the bytestring. (#2) (19f630c)

[git/dxtbx] master: Use struct not numpy to unpack the bytestring. (#2) (19f630c)

DXTBX commit

Wed, 22 May 2019 12:13:42 +0100

195 lines

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