Merge pull request #892 from RosettaCommons/everyday847/modified_rna_readin
1. cppcheck test failure has been fixed by my most recent commit
2. integration test changes stem from three sources: PDB or silent i/o now retaining segment IDs, the addition of the 0TD NCAA, and the 15 that inconsistently break these days.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #896 from RosettaCommons/dougrenfrew/remove_generated_sewing_options
Remove sewing options file. This and all other generated files, should be automatically generated by a script and not under version control. I suspect it was checked in by accident, possibly before the git transition.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #890 from RosettaCommons/kimdn/dn
[SEWING update]
* Integration test
Change of results of 'continuous_sewing_hasher' and
'discontinuous_sewing_hasher' during pull request are expected ones.
* sewing_hasher update
- Even three_secondary_structure_based models have better defined model_file_name
- Even three_secondary_structure_based models can specify between
'hash_tag_only_terminal_Es' and 'hash_between_any_HEs'
- Unit test input file name updated
* ModelTrimmer update
- user can give 'leave_models_by_ss_num' and 'model_should_have_this_num_of_ss' option
* EnumerateAssemblyMover update
- name change (ExhaustiveAssemblyMover -> EnumerateAssemblyMover)
- now EnumerateAssemblyMover spits 'path info' like MonteCarloAssemblyMover does
- now EnumerateAssemblyMover can use min_assembly_score cutoff like MonteCarloAssemblyMover can
* AssemblyConstraintsMover update
- newly added 'native_pro_bonus'
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #887 from RosettaCommons/aleaverfay/more_rlts
Added four new ResidueLevelTaskOperations to expand the utility of the ResidueSelectors.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #893 from RosettaCommons/vmullig/fix_sewing_hasher_tests
Fixing app_exception_handling AGAIN.
This is the danger of letting an integration test sit around in a broken state: when people check in additional code that ALSO breaks what the integration test is meant to test, they don't know that they've done something wrong. Because Rhiju's gaussian_chain_func_test was causing app_exception_handling to fail, two more apps slipped in under the radar without try/catch blocks.
The struc_set_fragment_picker app, which was newly-added, had no try/catch block. Fixed now in this pull request.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #891 from RosettaCommons/vmullig/fix_sewing_hasher_tests
Still trying to fix app_exception_handling test.
Problems remain in Rhiju's gaussian_chain_func_test pilot app. Fixed now, I think.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #888 from RosettaCommons/vmullig/fix_sewing_hasher_tests
Fix failing integration tests
This fixes the app_exception_handling, continuous_sewing_hasher, and discontinuous_sewing_hasher integration tests:
- app_exception_handling is fixed by adding try/catch blocks in the gaussian_chain_test and ModelTrimmer pilot apps. Please don't add a pilot app to pilot_apps.src.settings.all unless you have its functionality enclosed in a try/catch block.
- The sewing_hasher integration tests are fixed by removing datestamps from sewing_hasher.cc. If you write an integration test, don't have it write out the date on which it was run. This WILL cause a daily failure.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #886 from RosettaCommons/vmullig/fix_setup_for_symmetry
Minor tweak to MakeBundle mover
Tweaking MakeBundle to clear the PDBInfo of the input pose if it exists (since it won't be accurate any more once the new geometry is added).
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #881 from RosettaCommons/rhiju/general_bps
Rhiju/general bps
Adding 'base pair step' moves that allow efficient sampling of RNA structures in FARNA if you know which residues for noncanonical pairs. Includes database file additions (not too big after gzipping!).
some integration.release_debug tests on linux change -- this appears to be due to testing on the different linux servers, as the integration tests (on mac clangrelease) look OK.
notify author
notify list [rosetta-logs@googlegroups.com]