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Revisions №61414

branch: master 「№61414」
Commited by: Vikram K. Mulligan
GitHub commit link: 「e3f2a694e904afc8」 「№4941」
Difference from previous tested commit:  code diff
Commit date: 2020-09-03 21:32:28
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 alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.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 build.ninja_debug graphics static mac.clang.static.build.release build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.source scientific.FlexPepDock.debug scientific.FlexPepDock scientific.antibody_grafting scientific.cofactor_binding_sites scientific.ddg_ala_scan scientific.mhc_epitope_energy scientific.mp_f19_ddG_of_mutation.debug scientific.mp_f19_sequence_recovery.debug scientific.mp_relax.debug scientific.peptide_pnear_vs_ic50.debug scientific.relax_cartesian.debug scientific.relax_cartesian scientific.relax_fast.debug scientific.relax_fast scientific.sewing 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 gcc-9.gcc.unit util.apps

Merge pull request #4941 from RosettaCommons/vmullig/tag_getOption_for_bool_strings Try to address cases in which a developer has provided a default value for a boolean as a string in parse_my_tag(). This code compiles correctly, but doesn't do what one expects: ```c++ bool myoption = tag->getOption<bool>( "myoption", "false" ); ``` The developer _expects_ that if the user doesn't specify the option "myoption", it will default to `false`. Unfortunately, the string literal `"false"` is sent to the `Tag::getOption<bool>( std::string const &, bool const )` function as a `char*`, which can be cast automatically to a bool. Any non-`nullptr` value gets interpreted as `true`, however, so the default is set to `true`. The general solution (since even if we fix all the instances currently in the codebase, this will creep back in) is to implement `Tag::getOption<bool>( std::string const &, char const * )`, which parses and interprets the default string and converts it to a `bool`. This PR does this. Thank you to @danielzaidman for bringing this issue to light!

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Test: mac.clang.python27.build.xcode

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Test: ubuntu.clang.code_quality.clang_tidy

Failed sub-tests (click for more details):
src/core/fragment/FragmentSetLoader.cc src/core/io/StructFileRepOptions.cc src/core/pack/task/operation/TaskOperations.cc src/core/simple_metrics/metrics/ResidueSummaryMetric.cc src/protocols/abinitio/abscript/FragmentJumpCM.cc src/protocols/calc_taskop_filters/MultipleSigmoidsFilter.cc src/protocols/calc_taskop_filters/OperatorFilter.cc src/protocols/calc_taskop_filters/SigmoidFilter.cc src/protocols/canonical_sampling/SimulatedTempering.cc src/protocols/chemically_conjugated_docking/UBQ_GTPaseMover.cc src/protocols/cutoutdomain/CutOutDomain.cc src/protocols/cyclic_peptide/DeclareBond.cc src/protocols/cyclic_peptide/PeptideStubMover.cc src/protocols/denovo_design/components/StructureData.cc src/protocols/dna_dock/PropagateClashCheckFilter.cc src/protocols/enzdes/EnzFilters.cc src/protocols/enzdes/PackRotamersMoverPartGreedy.cc src/protocols/evolution/NucleotideMutation.cc src/protocols/features/HBondFeatures.cc src/protocols/filters/BasicFilters.cc src/protocols/filters/ReplicateFilter.cc src/protocols/fldsgn/CircularPermutation.cc src/protocols/fldsgn/filters/InterlockingAromaFilter.cc src/protocols/fldsgn/filters/ParallelBetaPairingPreferenceFilter.cc src/protocols/fldsgn/filters/SecondaryStructureCountFilter.cc src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc src/protocols/grafting/simple_movers/KeepRegionMover.cc src/protocols/hbnet/HBNet.cc src/protocols/hbnet/HBNetStapleInterface.cc src/protocols/helical_bundle/BackboneGridSampler.cc src/protocols/helical_bundle/FitSimpleHelix.cc src/protocols/helical_bundle/MakeBundle.cc src/protocols/helical_bundle/PerturbBundle.cc src/protocols/hotspot_hashing/movers/PlaceProbeMover.cc src/protocols/hybridization/BackboneTorsionPerturbation.cc src/protocols/hybridization/BackboneTorsionSampler.cc src/protocols/hybridization/HybridizeProtocol.cc src/protocols/indexed_structure_store/movers/DirectSegmentLookupMover.cc src/protocols/ligand_docking/ProtLigEnsemble.cc src/protocols/loop_modeling/utilities/rosetta_scripts.cc src/protocols/loophash/LoopHashDiversifier.cc src/protocols/loophash/LoopHashMoverWrapper.cc src/protocols/loops/loops_definers/LoopsExplicitDefiner.cc src/protocols/matdes/ClashCheckFilter.cc src/protocols/matdes/GetRBDOFValues.cc src/protocols/matdes/OligomericAverageDegreeFilter.cc src/protocols/membrane/FlipMover.cc src/protocols/membrane/SpinAroundPartnerMover.cc src/protocols/minimization_packing/DisulfideOptimizationMover.cc src/protocols/multistage_rosetta_scripts/MRSJobQueen.cc src/protocols/ncbb/ResidueReplacementRebuildMover.cc src/protocols/parser/FragmentReader.cc src/protocols/pose_creation/RepeatPropagationMover.cc src/protocols/pose_length_moves/InsertResMover.cc src/protocols/protein_interface_design/filters/AverageDegreeFilter.cc src/protocols/protein_interface_design/filters/BoltzmannFilter.cc src/protocols/protein_interface_design/filters/DesignableResiduesFilter.cc src/protocols/protein_interface_design/filters/RmsdFilter.cc src/protocols/protein_interface_design/filters/StubScoreLoopsFilter.cc src/protocols/protein_interface_design/filters/TorsionFilter.cc src/protocols/protein_interface_design/movers/DockWithHotspotMover.cc src/protocols/protein_interface_design/movers/MapHotspot.cc src/protocols/protein_interface_design/movers/PlaceSimultaneouslyMover.cc src/protocols/protein_interface_design/movers/SetupHotspotConstraintsLoopsMover.cc src/protocols/protein_interface_design/movers/SetupHotspotConstraintsMover.cc src/protocols/protein_interface_design/movers/TryRotamers.cc src/protocols/relax/AtomCoordinateCstMover.cc src/protocols/relax/membrane/MPRangeRelaxMover.cc src/protocols/rna/denovo/movers/RNA_DeNovoProtocolMover.cc src/protocols/score_filters/ScoreCutoffFilter.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/seeded_abinitio/GrowPeptides.cc src/protocols/seeded_abinitio/SeedFoldTree.cc src/protocols/seeded_abinitio/SwapSegment.cc src/protocols/sewing/movers/AssemblyMover.cc src/protocols/sewing/requirements/ClashRequirement.cc src/protocols/sewing/requirements/DsspSpecificLengthRequirement.cc src/protocols/sewing/requirements/LengthInResiduesRequirement.cc src/protocols/sewing/requirements/LigandClashRequirement.cc src/protocols/sewing/requirements/SizeInSegmentsRequirement.cc src/protocols/simple_ddg/SSElementBisectddGFilter.cc src/protocols/simple_filters/DisulfideEntropyFilter.cc src/protocols/simple_filters/HelixHelixAngleFilter.cc src/protocols/simple_filters/MPSpanAngleFilter.cc src/protocols/simple_filters/NetChargeFilter.cc src/protocols/simple_filters/NonSequentialNeighborsFilter.cc src/protocols/simple_filters/PackStatFilter.cc src/protocols/simple_filters/ResidueSetChainEnergyFilter.cc src/protocols/simple_filters/SSElementMotifContactFilter.cc src/protocols/simple_filters/ShapeComplementarityFilter.cc src/protocols/simple_filters/SimpleMetricFilter.cc src/protocols/simple_filters/TaskAwareSASAFilter.cc src/protocols/simple_filters/TaskAwareScoreTypeFilter.cc src/protocols/simple_moves/AddChainMover.cc src/protocols/simple_moves/AlignChainMover.cc src/protocols/simple_moves/FavorSequenceProfile.cc src/protocols/simple_moves/SetTorsion.cc src/protocols/simple_moves/SuperimposeMover.cc src/protocols/simple_moves/asym_fold_and_dock/AsymFoldandDockMoveRbJumpMover.cc src/protocols/simple_moves/bin_transitions/InitializeByBins.cc src/protocols/simple_moves/bin_transitions/PerturbByBins.cc src/protocols/simple_task_operations/RestrictToInterface.cc src/protocols/splice/AlignEndsMover.cc src/protocols/splice/FindEndpointsOperation.cc src/protocols/splice/Splice.cc src/protocols/splice/SpliceIn.cc src/protocols/splice/SpliceInAntibody.cc src/protocols/splice/SpliceInTail.cc src/protocols/splice/SpliceOut.cc src/protocols/switches/GraftSwitchMover.cc src/protocols/task_operations/JointSequenceOperation.cc src/protocols/task_operations/ProteinInterfaceDesignOperation.cc src/protocols/task_operations/SelectBySASAOperation.cc src/protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.cc
Test: mac.clang.integration

Failed sub-tests (click for more details):
database_md5 residue_energy_breakdown
Test: linux.clang.performance

Failed sub-tests (click for more details):
core_scoring_Score_100x_envsmooth
Test: linux.gcc.unit

Failed sub-tests (click for more details):
core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_cart_bonded core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_atr core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_dun core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_elec core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_rep core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_sol core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_hbonds core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_omega core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_p_aa_pp core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_pro_close core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_rama core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_rama_prepro core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_talaris2014 core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_yhh_planarity core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_beta_nov15 core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_cart_bonded core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_fa_atr core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_fa_dun core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_fa_elec core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_fa_rep core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_fa_sol core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_hbonds core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_lk_ball_wtd core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_omega core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_p_aa_pp core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_pro_close core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_rama core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_rama_prepro core:CyclicGeometry_betanov15_TwoChainTests:test_cyclic_permutation_yhh_planarity core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_beta core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_cart_bonded core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_atr core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_dun_rot core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_elec core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_intra_elec core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_sol core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_hbonds core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_hxl_tors core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_lk_ball core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_lk_ball_iso core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_omega core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_rama core:SequenceSymmetricAnnealerTests:test_chain_similarity_after_packing core:SequenceSymmetricAnnealerTests:test_chain_similarity_after_packing_cli core:SequenceSymmetricAnnealerTests:test_chain_similarity_with_virtual_root core:SequenceSymmetricAnnealerTests:test_recover_symmetry core:SequenceSymmetricAnnealerTests:test_residue_selectors core:SequenceSymmetricAnnealerTests:test_unequal_chain_lengths protocols:MRSJobQueenTests:test_MRSJobQueen_with_good_input protocols:MRSJobQueenTests:test_incorrect_attribute_value protocols:MRSJobQueenTests:test_not_enough_job_results_for_next_node protocols:MRSJobQueenTests:test_tag_for_nonmover_nonfilter protocols:MRSJobQueenTests:test_typo_in_score_function protocols:MoverFactoryTests:test_MoverFactory_all_Mover_all_attributes_have_descriptions protocols:MoverFactoryTests:test_MoverFactory_all_Mover_complexTypes_have_descriptions protocols:MoverFactoryTests:test_all_movers_define_valid_xsds