Merge pull request #4378 from RosettaCommons/roccomoretti/more_residue_selector_switch
Convert a bunch of XML object to use ResidueSelectors internally.
Another spinoff of PR#2466, aiming at removing the pose dependence at parse time.
There's a number of objects which use pose in parse_my_tags() which can (and likely should) be converted to using /ResidueIndexDescriptors. (Note that I haven't changed the XML interface, just implemented the internals with ResidueSelectors/ResidueIndexDescriptors.)
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #4397 from RosettaCommons/roccomoretti/cppcheck_188_fixes
Some fixes for cppcheck 1.88
Sergey is looking to update some backends on the test server. This will involve updating the cppcheck version to 1.88.
That newer version catches more things. To avoid perma-failing on the cppcheck, we should address the new issues. I had already updated the known issues list with existing cppcheck 1.88 issues, but a few new ones have slipped through since. I've either just fixed them, or have updated the cppcheck suppression list to simply ignore a style test which doesn't quite match how we use Rosetta.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #4411 from RosettaCommons/roccomoretti/fix_release_script
Fix release script
I had changed the interface to generate_version_information() by adding an argument, but I missed an intermediate function. This should correct that (and future proof a bit, too).
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #4410 from RosettaCommons/roccomoretti/pre_talaris_HOH
Remove HOH from pre-talaris exclude_pdb_components_list\
The pre-talaris residue type set doesn't have an HOH type. As such, it shouldn't list the type in the exclude_pdb_component_list.txt file.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #4402 from RosettaCommons/roccomoretti/release_indication_in_version
Add backtrace to console output for developers
A desire was recently expressed to return the backtrace information to the console/tracer output for developers.
In order to provide this info for developers (for whom it may be useful) but not for users-at-large (for whom it probably isn't), this PR adds an additional version info feature for being a "public release". This will be true for the Academic and Commercial downloads of Rosetta, but will be false for any version of Rosetta directly compiled from Git. While the recently added -run:crash_to_console flag will control things if given, if the option is omitted, the behavior will be print the results on the console for git/developer releases, and to leave it out for the public releases.
In all cases, the ROSETTA_CRASH.log file is still generated.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #4406 from RosettaCommons/roccomoretti/fix_tests
Fix some broken-in-master tests.
This fixes some tests which are currently broken in master. (Except for those issues already addressed by #4404) In particular, it fixes the clang_tidy tests, as well as the glycan_anomers test.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #4231 from RosettaCommons/sergey/submodules
Adding tools, demos and documentation as submodules to main repository and fixing most of known scripts path to point to a new location. Rest of the scripts (and particularly all release scripts and clone scripts) will be fixed in a follow up PR.
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #4403 from RosettaCommons/JackMaguire/KillAtoPolarDesign
Renaming KillA2019 to PolarDesign2019
@Haddox found that KillA2019 doesn't actually Kill Alanines. In fact, it results in more alanines than MonomerDesign2019 (though nothing creates more alanines than "legacy", our old default until 8/2019). It also results in more polar residues, so the new name is PolarDesign2019.
This PR updates the database and integration tests to have the new name. Additionally, there is a check in FastRelax that will switch database queries for "KillA2019" with "PolarDesign2019". This protects us against poor advertising about the name change and allows users to keep the more fun name if they want (I probably will).
notify author
notify list [rosetta-logs@googlegroups.com]
Merge pull request #4367 from RosettaCommons/jadolfbr/thread_safe_sugar_bb
Make SugarBB Threadsafe
This PR addresses #2441 in association with @vmullig 's Scoring Threadsafety issue #4358 .
The changes include removal of step size option for the sampling data, and setup of the sampling data on construction of both the CHIEnergyFunction and OmegaPreferences functions - this is needed to keep threadsafety as Vikram pointed out in 2017 that we can't make either global object with the `safely_create_load_once_object_by_OP` if there are two+ versions that could be created.
notify author
notify list [rosetta-logs@googlegroups.com]