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Tags: LS49-regression-nightly cctbx-ci cctbx-docs cctbx-nightly cctbxlite-nightly dials-nightly dials-nightly-regression labelit-nightly labelit-nightly-regression mpidialsregression-nightly phenix-docs phenix-externals phenix-nightly phenix-qrefine phenix-source py3-syntax-ci syntax-ci xfel-regression-nightly
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LS49-regression-nightly cctbx-ci cctbx-docs cctbx-nightly cctbxlite-nightly dials-nightly dials-nightly-regression labelit-nightly labelit-nightly-regression mpidialsregression-nightly phenix-docs phenix-externals phenix-nightly phenix-qrefine phenix-source py3-syntax-ci syntax-ci xfel-regression-nightly
Pavel
Mosaic bulk-solvent model: algorithms 2-4
  • cctbx-ci-ci: test ALL clutter failed -  stdio
terwill
clean clutter
Aaron Brewster
Py3 fix
Billy Poon
Remove unused import
Robert Oeffner
comment out Gabor's tests
Billy Poon
CI: fix path for CI branch
[skip ci]
terwill
Fix use of m.unit_cell_crystal_symmetry vs m.crystal_symmetry
terwill
Move all selections out of extract_box_around_model_and_map and into calling routines in preparation for simplification of extract_box_around_model_and_map. Note: no tests available for  __init__ method of box_build_refine_base
  • cctbx-ci-ci: test ALL clutter failed -  stdio
terwill
clean clutter
Pavel
Add alg 0 (gs)
Robert Oeffner
New regression tests for Phaser
terwill
Change test to use fixed model
terwill
remove unneeded parameters in preparation for using box.around_model in map_and_model
  • cctbx-ci-ci: test ALL clutter failed -  stdio
Nigel W. Moriarty
SF4-HIS link : bond only
Billy K. Poon
iotbx: reorganize map/model managers
- Moved <directory>/__init__.py to <directory>.py
- Replace write_real_map_file with write_map_with_map_manager function
  • cctbx-ci-ci: test ALL clutter failed -  stdio
terwill
Use customized_copy in map_manager to create new boxed map
  • cctbx-ci-ci: test ALL clutter failed -  stdio
terwill
allow deep_copy of map_manager with non-zero origin; use map symmetry in map_box if ignore_symmetry_conflicts=true and conflicts exist
Billy Poon
VS2017: remove std::swap call with template
- VS2017 does not accept calls to std::swap<T>
- https://developercommunity.visualstudio.com/content/problem/431904/vc-2017-stdswap-is-not-conforming.html
dcliebschner
cctbx documentation: add template html file
terwill
Change all uses of map_and_model to call with map_manager instead of map_data
Pavel
Change maptbx/box to to take only model and map_manager; separate instantiation and applying the box
Billy Poon
iotbx: only run test when chem_data is available
terwill
clean clutter
terwill
Clean cllutter and remove testing show_summary()
Ben Williams
Remove redundant parentheses and unused variables
terwill
Additional clean-up for map_manager and tst_map_manager. Allow origin shift to any origin
Billy Poon
CI: update pipelines
- Reduce timeout to 90 minutes
- Add CI for branches that batches builds
- Bump Xcode 11.4.1 to 11.5 on macOS 10.15
- Daily updates of build cache

[skip ci]
Pavel
CC
Oleg Sobolev
one more test
Pavel
Tests for mosaic solvent core algorithms
Aaron Brewster
Py3 fix
Oleg Sobolev
Proper label_seq_ids in struct_conn with test
terwill
clean clutter
Ben Williams
Add appropriate tests for merging anomalous data
Markus Gerstel
gltbx: use system libraries as fallback
When compiling with conda compilers in a conda environment the system
includes and libraries are not considered by default. This works fine
for 99% of the build, however libGL.so is not included in a conda
installation.

gltbx has a check whether libGL can be compiled against, and if it can't
then it won't be built. Here we add a fallback solution: if libGL can't
be compiled against AND we are using conda compilers AND we are on linux
then try explicitly to compile against system libraries. If this is not
successful then skip as before, otherwise build gltbx using the system
libraries.
terwill
Allow separate treatment for wrapping/not wrapping map information past cell boundaries
  • cctbx-ci-ci: test ALL clutter failed -  stdio
terwill
Retain original unit_cell information in boxed map_manager
Oleg Sobolev
Account for altlocs in get_label_seq_id procedure with tests
terwill
Refactor map_box.py to clarify functionality and prepare it for complete switch to use of model.manager and map_manager from use of pdb_hierarchy/xray_structure and map_data
  • cctbx-ci-ci: test ALL clutter failed -  stdio
terwill
Clarify deep_copy and customized_copy and simplify