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branch: master 「№61038」
Commited by: Vikram K. Mulligan
GitHub commit link: 「f55eb0d95436b5ad」 「№4361」
Difference from previous tested commit:  code diff
Commit date: 2019-11-13 23:36:10
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration.ubsan integration performance profile release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #4361 from RosettaCommons/vmullig/clang_analysis_issues_again Fixing a "not read" error flagged by clang analysis. I didn't hear back from @bioragul; will assume that this is fine.

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Test: linux.clang.unit

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branch: master 「№61037」
Commited by: Vikram K. Mulligan
GitHub commit link: 「e1e61459e6ead5a4」 「№4355」
Difference from previous tested commit:  code diff
Commit date: 2019-11-12 18:13:52
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy serialization integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release release.PyRosetta4.conda.Release release.source scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cofactor_binding_sites.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.loop_modeling_ccd_12res scientific.mhc_epitope_energy.debug scientific.mp_domain_assembly scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_ddG_of_mutation scientific.mp_f19_decoy_discrimination.debug scientific.mp_f19_sequence_recovery.debug scientific.mp_lipid_acc.debug scientific.mp_relax.debug scientific.mp_relax scientific.rna_denovo_favorites scientific.stepwise_rna_favorites.debug linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan util.apps

Merge pull request #4355 from RosettaCommons/vmullig/simplify_threadmanager_api Reduce mutex contention a bit by reducing reliance on std::shared_ptr in RosettaThreadManager classes. I was being overcautious with my ownership model, and unnecessarily using vectors of owning pointers of functions. This results in unnecessary locking of mutexes internal to `std::shared_ptr`, which can slow things down. Worse, I was _copying_ the owning pointers around, which results in new locking every time the reference count is incremented or decremented. (Even in the single-threaded build, unnecessarily passing around smart pointers is likely slowing things down a bit, since reference counts have to be incremented and decremented.) The vector object owns its contents and controls their destruction, so a vector of objects controlled by owning pointers is really unnecessary. This pull request refactors a bit so that the `RosettaThreadManager` now accepts a vector of function objects instead of a vector of owning pointers to function objects. TODO: - [x] Also switch the RosettaThreadAssignmentInfo object to be a stack-allocated object passed by reference, rather than a heap-allocated object passed by owning pointer. - [x] Check profile tests. Is there a performance benefit with packing in the single-threaded builds? (See the core_pack_pdig_current_default_sfxn performance test, which did show a slight drop in single-threaded execution when we switched to building a work vector and evaluating it). --> No big change. Maybe a small improvement. - [x] Does this improve performance scaling for multi-threaded interaction graph calculation? --> Not really. - [x] Does this rescue the scoring performance in the single-threaded build in PR #4342? --> No. Note, though, that the only slowdowns are with very fast-to-compute terms (_e.g._ chainbreak) or with an empty scorefunction. If there's any work to be done at all, the slowdown is negligible. - [x] Does this improve performance scaling for multi-threaded scoring in PR #4342? --> Not really.

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Test: gcc-9.gcc.python37.PyRosetta4.unit

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Test: linux.clang.code_quality.clang_analysis

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src/protocols/tcr/template_util.cc
Test: ubuntu.clang.code_quality.clang_tidy

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src/protocols/tcr/template_util.cc
Test: ubuntu.gcc.integration.addsan

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

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swm_general_polymer_sampler
Test: ubuntu.clang.python27.release.PyRosetta4.MinSizeRel

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Test: ubuntu.clang.python27.release.PyRosetta4.Release

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branch: master 「№61036」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「a984b21f93b91ded」 「№4354」
Difference from previous tested commit:  code diff
Commit date: 2019-11-11 17:26:33
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release release.PyRosetta4.conda.Release release.source scientific.FlexPepDock.debug scientific.FlexPepDock scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax.debug scientific.cartesian_relax scientific.ddg_ala_scan.debug scientific.dock_glycans scientific.docking.debug scientific.enzyme_design.debug scientific.ligand_docking.debug scientific.ligand_docking scientific.ligand_scoring_ranking.debug scientific.ligand_scoring_ranking scientific.loop_modeling_ccd_12res.debug scientific.loop_modeling_kic_fragments_12res.debug scientific.loop_modeling_ngk_12res.debug scientific.mp_symdock.debug scientific.protein_data_bank_diagnostic.cif scientific.sewing scientific.simple_cycpep_predict.debug scientific.simple_cycpep_predict scientific.stepwise_rna_favorites linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #4354 from RosettaCommons/aleaverfay/forward_kwargs_to_maybe_init Forward kwargs to maybe_init in pyrosertta distributed In pyrosetta::distributed initialization, pass the keyword arguments through to the maybe_init function.

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Test: gcc-9.gcc.python37.PyRosetta4.unit

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/protocols/tcr/template_util.cc
Test: ubuntu.gcc.integration.addsan

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

Failed sub-tests (click for more details):
swm_general_polymer_sampler
Test: linux.clang.performance

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core_scoring_Score_100x_envsmooth
Test: ubuntu.clang.python27.release.PyRosetta4.MinSizeRel

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Test: ubuntu.clang.python27.release.PyRosetta4.Release

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Test: ubuntu.clang.python37.release.PyRosetta4.Release

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Test: linux.clang.scientific.dock_glycans

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branch: master 「№61035」
Commited by: Vikram K. Mulligan
GitHub commit link: 「87f9cd71cc056b1b」 「№4352」
Difference from previous tested commit:  code diff
Commit date: 2019-11-11 14:07:35
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release release.source scientific.ddg_ala_scan scientific.mp_dock.debug scientific.mp_dock scientific.mp_f19_energy_landscape scientific.mp_symdock linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release unit.ubsan util.apps

Merge pull request #4352 from RosettaCommons/vmullig/reduce_boost_dependency Reduce dependencies on Boost by switching to STL functions where feasible. Certain functions that were only defined in the Boost libraries are now part of the C++11 STL. These include `std::bind`, `std::function`, `std::cref`, and `std::ref`. This pull request aims to replace instances of `boost::bind`, `boost::function`, `boost::cref`, and `boost::ref` with their C++11 STL equivalents.

Vikram K. Mulligan 12 hours
Note: Sergey is working on a patch for the PyRosetta test failures introduced by this change. I have it from him that I shouldn't revert this right now.
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Test: gcc-9.gcc.python37.PyRosetta4.unit

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/protocols/tcr/template_util.cc
Test: ubuntu.clang.code_quality.clang_tidy

Failed sub-tests (click for more details):
src/protocols/tcr/template_util.cc
Test: ubuntu.clang.python27.release.PyRosetta4.MinSizeRel

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Test: ubuntu.clang.python35.release.PyRosetta4.MinSizeRel

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Test: ubuntu.clang.python36.release.PyRosetta4.MinSizeRel

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Test: ubuntu.clang.python37.release.PyRosetta4.MinSizeRel

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Test: ubuntu.clang.python27.release.PyRosetta4.Release

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Test: ubuntu.clang.python35.release.PyRosetta4.Release

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Test: ubuntu.clang.python36.release.PyRosetta4.Release

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Test: ubuntu.clang.python37.release.PyRosetta4.Release

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Test: linux.clang.scientific.mp_symdock

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branch: master 「№61034」
Commited by: Ragul Gowthaman
GitHub commit link: 「8ead6c9e84dc936f」 「№4329」
Difference from previous tested commit:  code diff
Commit date: 2019-11-11 13:38:55
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release release.source scientific.cofactor_binding_sites scientific.sewing.debug linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #4329 from RosettaCommons/bioragul/TCRmodel-updates TCRmodel bug fixes & minor updates

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Test: linux.gcc.python36.PyRosetta4.unit

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Test: linux.clang.code_quality.clang_analysis

Failed sub-tests (click for more details):
src/protocols/tcr/template_util.cc
Test: ubuntu.clang.code_quality.clang_tidy

Failed sub-tests (click for more details):
src/protocols/tcr/template_util.cc
Test: mac.clang.integration

Failed sub-tests (click for more details):
swm_general_polymer_sampler tcrmodel
Test: linux.gcc.unit.release

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branch: master 「№61033」
Commited by: Vikram K. Mulligan
GitHub commit link: 「7cd178fe05f3b176」 「№4353」
Difference from previous tested commit:  code diff
Commit date: 2019-11-10 03:53:03
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy serialization integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release release.PyRosetta4.conda.Release release.source scientific.antibody_grafting.debug scientific.antibody_grafting scientific.antibody_h3_modeling.debug scientific.antibody_h3_modeling scientific.antibody_snugdock.debug scientific.cartesian_relax.debug scientific.cofactor_binding_sites.debug scientific.dock_glycans.debug scientific.enzyme_design.debug scientific.enzyme_design scientific.fast_relax.debug scientific.fast_relax_5iter.debug scientific.fast_relax_5iter scientific.fast_relax scientific.ligand_scoring_ranking.debug scientific.ligand_scoring_ranking scientific.loop_modeling_kic_12res.debug scientific.loop_modeling_kic_fragments_12res.debug scientific.loop_modeling_ngk_12res.debug scientific.mhc_epitope_energy.debug scientific.mhc_epitope_energy scientific.mp_domain_assembly.debug scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_decoy_discrimination.debug scientific.mp_f19_energy_landscape.debug scientific.mp_lipid_acc.debug scientific.mp_lipid_acc scientific.mp_relax.debug scientific.mp_relax scientific.protein_data_bank_diagnostic.full scientific.rna_denovo_favorites.debug scientific.sewing linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan util.apps

Merge pull request #4353 from RosettaCommons/JackMaguire/fix_INCLUDED_core_scoring_util_methods_DumpTrajectoryEnergy_hh Fixing #ifdef and duplication #3575 copied a file but didn't update the ifdef include guards. The duplicate_header_guards test failed but was ignored because it blended in with a lot of other failed integration tests (presumably expected failures). This PR fixes the #ifdef duplication but there might be a bigger problem here. Was src/core/energy_methods/DumpTrajectoryEnergy.hh even supposed to make it into master? Its namespaces are incorrect and it's a perfect duplicate of src/core/scoring/util_methods/DumpTrajectoryEnergy.hh Tagging @vmullig because it was his PR, and @bcov77 because github credits this file to him.



branch: master 「№61032」
Commited by: Jack Maguire
GitHub commit link: 「cbb227abd9c8ea71」 「№4262」
Difference from previous tested commit:  code diff
Commit date: 2019-11-08 14:48:23
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy serialization integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release release.PyRosetta4.conda.Release release.source scientific.antibody_grafting.debug scientific.antibody_grafting scientific.cartesian_relax scientific.loop_modeling_kic_12res scientific.simple_cycpep_predict.debug linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan unit.valgrind util.apps

Merge pull request #4262 from RosettaCommons/JackMaguire/StrongTypeAliases Strong Sizes in JD3 `core::Size` is used frequently in JD3 (and Rosetta as a whole) to represent values that are conceptually different types but are all best represented with a simple `int`. Nobody should need to reinvent the `int` wheel every time we need a new integral type. `core::Size` is technically fine for all of these types but its ubiquitousness can lead to logic errors. The goal of this PR is to introduce distinct types for some common integral concepts in JD3. This will hopefully prevent bugs in JD3's already hard-to-understand framework. Here is a good example of this feature being added. Existing code: ```c++ StandardInnerLarvalJobOP create_inner_larval_job( core::Size nstruct, core::Size job_node, core::Size preliminary_job_node ) const; InnerLarvalJobOP create_and_init_inner_larval_job_from_preliminary( core::Size nstruct, core::Size prelim_job_node, core::Size job_node ) const; ``` These are two functions that JobQueen writers might replace with one another as drop-in replacements. If they do that, the compiler will not warn them that they need to _switch the 2nd and 3rd arguments_ because both arguments are core::Sizes. This logic error might not even be caught at runtime because `prelim_job_node` and `job_node` are often the same value for some JobQueens. The logic error might take months to reveal itself (like it did for MultistageRosettaScripts in #4238 ). New code: ```c++ StandardInnerLarvalJobOP create_inner_larval_job( core::Size nstruct, JobDagID job_node, PrelimJobNodeID preliminary_job_node ) const; InnerLarvalJobOP create_and_init_inner_larval_job_from_preliminary( core::Size nstruct, PrelimJobNodeID prelim_job_node, JobDagID job_node ) const; ``` This new code requires minimal boilerplate (thanks to Rocco's suggestions in #4237 ) and would immediately alert developers _at compile time_ when they are using values incorrectly. Performance hits will not be a concern because the compiler completely optimizes this feature away, even in debug mode (see godbolt links in #4237 ).

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Test: ubuntu.gcc.integration.addsan

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

Failed sub-tests (click for more details):
swm_general_polymer_sampler
Test: mac.clang.scientific.antibody_grafting

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branch: master 「№61031」
Commited by: Vikram K. Mulligan
GitHub commit link: 「868bf3f9db0e20a0」 「№4345」
Difference from previous tested commit:  code diff
Commit date: 2019-11-08 13:01:12
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.PyRosetta4.Release release.source scientific.antibody_grafting linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #4345 from RosettaCommons/vmullig/make_FASTER_ig_threadsafe Add unit tests confirming that the FASTER interaction graph is threadsafe, and update test to use ref2015 instead of pre_talaris_2013_standard The FASTER interaction graph unit test fails stochastically in the multi-threaded build. This is likely due to a thread safety issue. This PR attempts to fix the issue. EDIT: The FASTER ig is, as far as I can tell, totally threadsafe. (This PR does add a pretty stringent test for this, computing the graph 100 times in threads and comparing each result to the graph computed in a single thread.) The score12 scorefunction, however, is not. I get concurrency issues ONLY when using score12, and these vanish with ref2015 (which is fully threadsafe). For now, I'm switching the FASTER ig unit test to use ref2015 instead of score12, though at some point I'll track down the concurrency issues in score12.



branch: master 「№61030」
Commited by: Vikram K. Mulligan
GitHub commit link: 「93f10bc3df39bbe5」 「№4350」
Difference from previous tested commit:  code diff
Commit date: 2019-11-07 18:14:42
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release release.source scientific.antibody_grafting.debug scientific.antibody_grafting scientific.docking scientific.loop_modeling_ccd_12res.debug scientific.loop_modeling_kic_fragments_12res scientific.loop_modeling_ngk_12res scientific.mp_f19_decoy_discrimination scientific.mp_f19_sequence_recovery linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #4350 from RosettaCommons/vmullig/fix_gcc_9_2_build Fixing gcc 9.2.0 compilation. A minor issue was introduced with the recent clang tidy clean-up. This PR replaces an explicitly-defined but trivial assignment operator with a default assignment operator to resolve the warning-as-error and to repair the build. @roccomoretti

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Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
swm_general_polymer_sampler
Test: linux.clang.profile

Failed sub-tests (click for more details):
rosie_ligand_dock
Test: linux.clang.scientific.mp_f19_sequence_recovery

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branch: master 「№61029」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「b470a6a0d47e4147」 「№4289」
Difference from previous tested commit:  code diff
Commit date: 2019-11-07 14:29:04
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #4289 from RosettaCommons/jadolfbr/den_map_fix Add setters and getters for LoadDensityMapMover for use in PyRosetta.

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Test: gcc-9.gcc.build.debug

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Test: linux.clang.profile

Failed sub-tests (click for more details):
rosie_ligand_dock


branch: master 「№61028」
Commited by: Ramya Rangan
GitHub commit link: 「0d7cf3210320e9e3」 「№4339」
Difference from previous tested commit:  code diff
Commit date: 2019-11-06 15:36:36
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #4339 from RosettaCommons/ramyarangan/segid_fix Ramyarangan/segid fix

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Test: gcc-9.gcc.build.debug

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branch: master 「№61027」
Commited by: Rocco Moretti
GitHub commit link: 「fa7471d5c03cfdb2」 「№4336」
Difference from previous tested commit:  code diff
Commit date: 2019-11-06 14:41:44
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #4336 from RosettaCommons/roccomoretti/clang_tidy_test_fixes2 Fix the `bugprone` series of clang-tidy tests. This PR enables testing for (and fixing the existing cases of) the series of "bugprone" tests which clang-tidy tests for. Mostly this was copy constructors which weren't calling their base class's copy constructor.



branch: master 「№61026」
Commited by: Sergey Lyskov
GitHub commit link: 「fc8ab401178f6f09」 「№4341」
Difference from previous tested commit:  code diff
Commit date: 2019-11-05 17:46:43
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release release.PyRosetta4.conda.Release release.source scientific.antibody_grafting.debug scientific.antibody_grafting linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release unit.ubsan util.apps

Merge pull request #4341 from RosettaCommons/benchmark Adding `--disable-new-dtags` linker option to default GCC settings, this should allow proper linking to Rosetta sqlite on Ubuntu.



branch: master 「№61025」
Commited by: Vikram K. Mulligan
GitHub commit link: 「94476f921d05cc5c」 「№4344」
Difference from previous tested commit:  code diff
Commit date: 2019-11-05 15:40:25
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck