Merge pull request #5931 from RosettaCommons/JackMaguire/EnsureExclusivelySharedJump
JumpDownstreamSelector appears to have been making some assumptions about the foldtree that result in an inverted selection. The fix checks to see if the downstream residue from the jump is selected, and inverts the selection if not.
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Merge pull request #6001 from RosettaCommons/roccomoretti/xsd_loading
Don't load XSD citation info if we don't need it.
We don't need the citation info if we're just doing schema validation (it just adjusts the description, and doesn't effect the validity of the XML). Add a (default true) flag we can set to false to turn off generating and including the citation info string just for XML validation. (The XSD dump and the info tags still will include the citation info.)
This cleans up tracer output (e.g. it doesn't print warnings and setup noise from all of the Movers etc. which were previously being instantiated. It also avoids crashes due to mover instantiation issues.
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Merge pull request #5976 from RosettaCommons/vmullig/update_tools
Update tools submodule to reflect small tweak.
In the auto-generated docs, asterisks in citations were resulting in italics. I've updated the tools repo so that the script uses literal asterisks (with a backslash to avoid italics). This PR just updates the tools and documentation submodules to point to the latest master versions of these repos.
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Merge pull request #5962 from RosettaCommons/vmullig/fix_unit_test_breakage_from_packer_change
Fix unit test breakage, and restore skipping of final temperature jump in packing
This reverts pull request #5960 to restore pull request #5920, and fixes the unit test failure in the process.
TODO:
- [x] Fix failure in `AntibodySeqDesign:test_normal_tf_generation` unit test. --> A UTracer can simply be updated. The difference is likely a trajectory difference.
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Merge pull request #5915 from RosettaCommons/vmullig/restore_citations_in_docs
Revert the reversion to put citation info back into the docs
- [x] Add performance test that checks time to instantiate each mover, filter, etc. in sequence.
- [x] Identify high-cost movers, and fix these so that they can be instantiated without high cost.
- Done for some, and I've reduced the runtime by ~50% when instantiating all movers. Could still be better, though. The question is whether this is good enough.
- [x] Pull request #5916 must be merged before this one.
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Merge pull request #5960 from RosettaCommons/revert-5920-JackMaguire/PackerSkipTemp4
Revert "Skip final temperature raise in the default packer" temporarily, until unit test failure can be fixed.
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