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branch: master 「№59879」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「1dee8ba273a92ec1」
Difference from previous tested commit:  code diff
Commit date: 2017-11-20 14:10:47
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2111 from RosettaCommons/aleaverfay/interleave_new_rotamers_in_rotset Aleaverfay/interleave new rotamers in rotset Adding a new way to append rotamers to a RotamerSet to reduce memory usage and running time when a large number of new rotamers need to be appended. The new functionality comes through the function RotamerSet::add_rotamer_into_existing_group and will figure out what existing residue-type group to add your rotamer to. If you already have a bunch of ARG rotamers and you add another, then the new rotamer will get slotted in at the end of the list of ARG rotamers, but in front of the set of SER rotamers (assuming you have SER rotamers). There are a number of places in the packer where the memory use scales quadratically with the number of different amino acid types, even if it scales linearly with the number of rotamers. Try avoiding calls to RotamerSet::add_rotamer. Expected integration test changes in the following integration tests which now have different rotamer orderings, and thus produce different outputs from the packer (and further downstream trajectory changes): - enzdes - inverse_rotamer_remodel - ligand_motif_design - motif_dna_packer_design



branch: master 「№59878」
Commited by: Vikram K. Mulligan
GitHub commit link: 「5c8b0f4a5d67a245」
Difference from previous tested commit:  code diff
Commit date: 2017-11-19 21:58:23
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration maintenance.documentation performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Beautifying Rosetta.



branch: master 「№59877」
Commited by: Andy Watkins
GitHub commit link: 「dded8767c1d02d1e」
Difference from previous tested commit:  code diff
Commit date: 2017-11-17 19:08:58
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics linux.clang.static.build.release static mac.clang.static.build.release linux.ui mac.ui beautification code_quality.clang_analysis serialization integration.addsan integration.mpi integration.release_debug integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan unit.valgrind

Merge pull request #2574 from RosettaCommons/everyday847/riboswitch_reconciliation More riboswitch-centric modifications

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Test: mac.clang.static.build.release

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Test: linux.gcc.code_quality.beautification

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/apps/public/darc/DARC.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/io/silent/RNA_SilentStruct.cc src/core/optimization/Minimizer.cc src/core/scoring/constraints/BigBinConstraint.cc src/core/scoring/constraints/ConstraintIO.cc src/core/scoring/methods/GaussianOverlapEnergy.cc src/core/scoring/power_diagram/PowerDiagram.cc src/protocols/antibody/ModelCDRH3.cc src/protocols/cartesian/md.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/frag_picker/scores/PhiPsiRmsd.cc src/protocols/frags/TorsionFragment.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/TMalign.cc src/protocols/legacy_sewing/sampling/LegacyMonteCarloAssemblyMover.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loops_main.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/moves/MoverStatus.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/util.cc src/protocols/noesy_assign/PeakFileFormat.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/PocketGrid.cc src/protocols/rna/denovo/fragments/FullAtomRNA_Fragments.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/sparta/Sparta.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/modeler/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/viewer/triangleIterator.cc src/utility/libsvm/Svm.cc test/core/conformation/UltraLightResidue.cxxtest.hh
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
input_and_output
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
rs_flexbbmoves test_energy_method_options
Test: mac.clang.integration

Failed sub-tests (click for more details):
rs_flexbbmoves test_energy_method_options


branch: master 「№59876」
Commited by: Vikram K. Mulligan
GitHub commit link: 「04eaa17e6be577df」
Difference from previous tested commit:  code diff
Commit date: 2017-11-17 18:05:05
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2730 from RosettaCommons/vmullig/rescountfilter_fix A few fixes to recent changes to the ResidueCountFilter Tasks: - [x] Add logic to avoid double-counting if multiple, overlapping properties are defined. - [x] Add logic to avoid double-counting if residue types AND residue properties are defined. - [x] Remove unnecessary `static` keyword and correct variable naming convention. - [x] Updating some Doxygen tags. - [x] Add unit test for ResidueCountFilter. - [x] Beauty. - [ ] Documentation. @hssnzdh2 @tjbrunette

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Test: linux.gcc.code_quality.beautification

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Test: mac.clang.integration

Failed sub-tests (click for more details):
rs_flexbbmoves test_energy_method_options


branch: master 「№59875」
Commited by: Sergey Lyskov
GitHub commit link: 「a995eac28418df1f」
Difference from previous tested commit:  code diff
Commit date: 2017-11-17 15:44:02
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2678 from RosettaCommons/sergey/f2 Refactoring Rosetta exceptions classes.

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Test: linux.gcc.code_quality.beautification

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branch: master 「№59874」
Commited by: Vikram K. Mulligan
GitHub commit link: 「03bfcef676b9ba4e」
Difference from previous tested commit:  code diff
Commit date: 2017-11-16 16:42:24
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.Debug release.PyRosetta4.MinSizeRel release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Beautifying master.



branch: master 「№59873」
Commited by: TJ Brunette
GitHub commit link: 「f42d6af98f46edfd」
Difference from previous tested commit:  code diff
Commit date: 2017-11-16 14:14:14
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2723 from RosettaCommons/hssnzdh2/rescount adding an option to count properties in ResidueCountFilter

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Test: linux.gcc.code_quality.beautification

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Test: mac.clang.integration

Failed sub-tests (click for more details):
rs_flexbbmoves test_energy_method_options


branch: master 「№59872」
Commited by: Rocco Moretti
GitHub commit link: 「174064d29df073f7」
Difference from previous tested commit:  code diff
Commit date: 2017-11-16 12:42:02
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2668 from RosettaCommons/roccomoretti/first_use_tracer_2 Change how we do `thread_local` tracers Having a large number of static thread_local Tracer objects causes issues with stack usage with multithreading. This PR separates the static portion of Tracers from the main, thread_local, part (now called TracerImpl), and adds a behind-the-scenes construct-on-first-use linkage between the two. **What does this mean for the average Rosetta Developer?** Not much. I attempted to make this invisible to normal Tracer use. The only change for most people is now you need to omit the THREAD_LOCAL from the Tracer definition. (You'll likely you'll get a compiler error if you forget, and there's also an integration test to check.)



branch: master 「№59871」
Commited by: Jack Maguire
GitHub commit link: 「7df3eabf9f62ec1a」
Difference from previous tested commit:  code diff
Commit date: 2017-11-16 12:23:58
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2716 from RosettaCommons/JackMaguire/atom_level_HBondGraph2 Fixing HBNet Integration Tests

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Test: linux.gcc.code_quality.beautification

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branch: master 「№59870」
Commited by: Rhiju Das
GitHub commit link: 「33951edddf31c03c」
Difference from previous tested commit:  code diff
Commit date: 2017-11-16 00:23:54
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2578 from RosettaCommons/rhiju/ribodraw RiboDraw stuff (rna_motif expansion)

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Test: linux.gcc.code_quality.beautification

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branch: master 「№59869」
Commited by: Andy Watkins
GitHub commit link: 「a83c2abc6f96b901」
Difference from previous tested commit:  code diff
Commit date: 2017-11-15 23:44:19
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2691 from RosettaCommons/everyday847/stepwise_performance Some stepwise performance benefits

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Test: linux.gcc.code_quality.beautification

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branch: master 「№59868」
Commited by: Sergey Lyskov
GitHub commit link: 「1b0845bfd90c8ee9」
Difference from previous tested commit:  code diff
Commit date: 2017-11-15 23:38:49
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2720 from RosettaCommons/benchmark fixing unicode conversion issues

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Test: linux.clang.build.cppcheck

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branch: master 「№59867」
Commited by: Jason Klima
GitHub commit link: 「38ed7a54e2e70fa1」
Difference from previous tested commit:  code diff
Commit date: 2017-11-14 20:19:21
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile ubuntu.clang.python27.release.PyRosetta4.Debug ubuntu.clang.python36.release.PyRosetta4.Debug release.PyRosetta4.MinSizeRel linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.ubsan

Merge pull request #2725 from RosettaCommons/klimaj/reformat Reformatting RosettaScripts

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Test: linux.clang.build.cppcheck

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Test: linux.gcc.performance

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branch: master 「№59866」
Commited by: Andy Watkins
GitHub commit link: 「b2483eb03190cc18」
Difference from previous tested commit:  code diff
Commit date: 2017-11-14 18:26:04
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.addsan integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Merge pull request #2714 from RosettaCommons/everyday847/ignore_energy_method_addition Ignore extraneous output from EnergyMethod option addition

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Test: linux.clang.build.cppcheck

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branch: master 「№59865」
Commited by: Andy Watkins
GitHub commit link: 「f62e0975cea31291」
Difference from previous tested commit:  code diff
Commit date: 2017-11-14 10:40:17
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan

Merge pull request #2717 from RosettaCommons/everyday847/cleanup Fix FragmentHomologyExclusion segfault

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Test: linux.clang.build.cppcheck

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branch: master 「№59864」
Commited by: Sergey Lyskov
GitHub commit link: 「7e01283cc220c42b」
Difference from previous tested commit:  code diff
Commit date: 2017-11-13 13:49:18
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit mac.PyRosetta.unit cppcheck mysql postgres mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui beautification serialization integration.mpi integration.release_debug integration.ubsan integration performance profile ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

fixing build

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Test: linux.clang.build.levels

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Test: linux.gcc.mpi.serialization.integration.mpi

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Test: ubuntu.gcc.integration.ubsan

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Test: linux.gcc.performance

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