increasing failure_threshold_execution_time in profile tests to prevent false positive signals

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Merge pull request #1417 from RosettaCommons/rfalford12/feature-reporter-code-template Code template for Features Reporter

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Refactoring PyRosetta generation procedure to make results more reproducible on different os/compiler/filesystems

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Merge pull request #1419 from RosettaCommons/vmullig/better_errors Add some more informative error messages

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Merge pull request #1416 from RosettaCommons/sergey/binder fixing PyRosetta SubClassing* tests

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Merge pull request #1413 from RosettaCommons/Cyrus/mergetarget Cyrus/mergetarget Four changes here: README.md: a minor informational change, originally meant to test these cross-fork PRs source/src/apps/pilot/smlewis/LoopAnalyzer.cc: bitrot repair in a disabled pilot app source/src/protocols/constraints_additional/BindingSiteConstraint.cc: adding comments gleaned from a deep SVN archaeology dive source/src/protocols/constraints_additional/BindingSiteConstraint.hh source/src/protocols/loops/loop_mover/perturb/LoopMover_KIC.cc: fixing a bug introduced by 543ed88 (a two year old refactoring) source/src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc No test changes expected. The only compiled code change prevents a crash, so this code path was perforce untested before.

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Just updated my old pilot app and merged with master

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Merge pull request #1408 from RosettaCommons/vmullig/fix_minimize Updating the minimize app to work the way the documentation will say it should: The minimize app didn't respect the -in:file:movemap flag. Now it does.

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Merge pull request #1399 from RosettaCommons/lqtza/antibody_fixes Minor antibody.cc, SnugDock, and prepack changes

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Merge pull request #1407 from RosettaCommons/rfalford12/fix-embedding-tr-error Rfalford12/fix embedding tr error This pull request tries to squash this error once and for all: "protocols.membrane.geometry.Embedding: WARNING: Message(s) above was printed in the end instead of proper place because this Tracer object has some contents left in inner buffer when destructor was called. Explicit call Tracer::flush() or end your IO with std::endl to disable this warning." Removed the offending TR << "\t"; lines from the embedding object. I also added code that calls embedding.show() to the mp_loadtime integration test as a check.

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Merge pull request #1405 from RosettaCommons/sergey/binder Adding PyRosetta4 tests

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Merge pull request #1315 from RosettaCommons/hssnzdh2/chirality_flip added a Mover for flipping chirality of a pose (mirror image)

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Merge pull request #1406 from RosettaCommons/JWLabonte/sugars/branching Glycosylation Fixes This merge corrects some database values related to the `LinkageConformerMover` and as such will change all integration tests using that `Mover`.

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Merge pull request #1404 from RosettaCommons/tlinsky/ss_sc_residue_selector Add residue_selector option to SecondaryStructureShapeComplementarityFilter

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Merge pull request #1403 from RosettaCommons/tlinsky/secstruct_filter_threshold Add threshold option to SecondaryStructureFilter

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Merge pull request #1400 from RosettaCommons/vmullig/cycpep_predict_tweaks Adding try/catch block to individual calls to SimpleCycpepPredictApplication in the MPI version, so that individual job failures don't bring down everything. There's an ultra-rare failure occurring one time in 100,000, so it only shows up in my production jobs (in which I usually have to mute all output, so I can't even see what's failing). It's REALLY irritating. I don't know how to track down and fix it, so I have to make sure that I can recover from whatever the error is when it happens.

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