LICENSE
README.md
pyproject.toml
setup.py
./pybrops/__init__.py
./pybrops/breed/__init__.py
./pybrops/breed/arch/BreedingEdge.py
./pybrops/breed/arch/BreedingGraph.py
./pybrops/breed/arch/BreedingNode.py
./pybrops/breed/arch/BreedingProgram.py
./pybrops/breed/arch/EmigrationOperator.py
./pybrops/breed/arch/GermplasmBank.py
./pybrops/breed/arch/ImmigrationOperator.py
./pybrops/breed/arch/RecurrentSelectionBreedingProgram.py
./pybrops/breed/arch/__init__.py
./pybrops/breed/op/__init__.py
./pybrops/breed/op/eval/EvaluationOperator.py
./pybrops/breed/op/eval/__init__.py
./pybrops/breed/op/init/InitializationOperator.py
./pybrops/breed/op/init/__init__.py
./pybrops/breed/op/log/Logbook.py
./pybrops/breed/op/log/__init__.py
./pybrops/breed/op/mate/MatingOperator.py
./pybrops/breed/op/mate/__init__.py
./pybrops/breed/op/psel/ParentSelectionOperator.py
./pybrops/breed/op/psel/__init__.py
./pybrops/breed/op/ssel/SurvivorSelectionOperator.py
./pybrops/breed/op/ssel/__init__.py
./pybrops/breed/prot/__init__.py
./pybrops/breed/prot/bv/BreedingValueProtocol.py
./pybrops/breed/prot/bv/MeanPhenotypicBreedingValue.py
./pybrops/breed/prot/bv/TrueBreedingValue.py
./pybrops/breed/prot/bv/__init__.py
./pybrops/breed/prot/gt/DenseUnphasedGenotyping.py
./pybrops/breed/prot/gt/GenotypingProtocol.py
./pybrops/breed/prot/gt/__init__.py
./pybrops/breed/prot/mate/FourWayCross.py
./pybrops/breed/prot/mate/FourWayDHCross.py
./pybrops/breed/prot/mate/MatingProtocol.py
./pybrops/breed/prot/mate/SelfCross.py
./pybrops/breed/prot/mate/ThreeWayCross.py
./pybrops/breed/prot/mate/ThreeWayDHCross.py
./pybrops/breed/prot/mate/TwoWayCross.py
./pybrops/breed/prot/mate/TwoWayDHCross.py
./pybrops/breed/prot/mate/__init__.py
./pybrops/breed/prot/mate/util.py
./pybrops/breed/prot/pt/G_E_Phenotyping.py
./pybrops/breed/prot/pt/PhenotypingProtocol.py
./pybrops/breed/prot/pt/TruePhenotyping.py
./pybrops/breed/prot/pt/__init__.py
./pybrops/breed/prot/sel/BinaryMateSelectionProtocol.py
./pybrops/breed/prot/sel/BinarySelectionProtocol.py
./pybrops/breed/prot/sel/EstimatedBreedingValueSelection.py
./pybrops/breed/prot/sel/ExpectedMaximumBreedingValueSelection.py
./pybrops/breed/prot/sel/FamilyEstimatedBreedingValueSelection.py
./pybrops/breed/prot/sel/GeneralizedWeightedGenomicEstimatedBreedingValueSelection.py
./pybrops/breed/prot/sel/GenomicEstimatedBreedingValueSelection.py
./pybrops/breed/prot/sel/GenotypeBuilderSelection.py
./pybrops/breed/prot/sel/IntegerMateSelectionProtocol.py
./pybrops/breed/prot/sel/IntegerSelectionProtocol.py
./pybrops/breed/prot/sel/L1NormGenomicSelection.py
./pybrops/breed/prot/sel/L2NormGenomicSelection.py
./pybrops/breed/prot/sel/MateSelectionProtocol.py
./pybrops/breed/prot/sel/MeanExpectedHeterozygositySelection.py
./pybrops/breed/prot/sel/MeanGenomicRelationshipSelection.py
./pybrops/breed/prot/sel/MultiObjectiveGenomicSelection.py
./pybrops/breed/prot/sel/OptimalContributionSelection.py
./pybrops/breed/prot/sel/OptimalHaploidValueSelection.py
./pybrops/breed/prot/sel/OptimalPopulationValueSelection.py
./pybrops/breed/prot/sel/RandomSelection.py
./pybrops/breed/prot/sel/RealMateSelectionProtocol.py
./pybrops/breed/prot/sel/RealSelectionProtocol.py
./pybrops/breed/prot/sel/SelectionProtocol.py
./pybrops/breed/prot/sel/SubsetMateSelectionProtocol.py
./pybrops/breed/prot/sel/SubsetSelectionProtocol.py
./pybrops/breed/prot/sel/UnconstrainedGeneralized1NormGenomicSelection.py
./pybrops/breed/prot/sel/UnconstrainedMultiObjectiveGenomicMating.py
./pybrops/breed/prot/sel/UnconstrainedPopulationAlleleFrequencyDistanceSelection.py
./pybrops/breed/prot/sel/UnconstrainedPopulationAlleleUnavailabilitySelection.py
./pybrops/breed/prot/sel/UnconstrainedSelectionProtocol.py
./pybrops/breed/prot/sel/UsefulnessCriterionSelection.py
./pybrops/breed/prot/sel/WeightedGenomicSelection.py
./pybrops/breed/prot/sel/__init__.py
./pybrops/breed/prot/sel/targetfn.py
./pybrops/breed/prot/sel/transfn.py
./pybrops/breed/prot/sel/weightfn.py
./pybrops/breed/prot/sel/cfg/BinaryMateSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/BinarySelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/IntegerMateSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/IntegerSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/MateSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/RealMateSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/RealSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/SampledSelectionConfigurationMixin.py
./pybrops/breed/prot/sel/cfg/SelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/SimpleMateSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/SimpleSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/SubsetMateSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/SubsetSelectionConfiguration.py
./pybrops/breed/prot/sel/cfg/__init__.py
./pybrops/breed/prot/sel/prob/BinaryMateSelectionProblem.py
./pybrops/breed/prot/sel/prob/BinarySelectionProblem.py
./pybrops/breed/prot/sel/prob/EstimatedBreedingValueSelectionProblem.py
./pybrops/breed/prot/sel/prob/ExpectedMaximumBreedingValueSelectionProblem.py
./pybrops/breed/prot/sel/prob/FamilyEstimatedBreedingValueSelectionProblem.py
./pybrops/breed/prot/sel/prob/GeneralizedWeightedGenomicEstimatedBreedingValueSelectionProblem.py
./pybrops/breed/prot/sel/prob/GenomicEstimatedBreedingValueSelectionProblem.py
./pybrops/breed/prot/sel/prob/GenotypeBuilderSelectionProblem.py
./pybrops/breed/prot/sel/prob/IntegerMateSelectionProblem.py
./pybrops/breed/prot/sel/prob/IntegerSelectionProblem.py
./pybrops/breed/prot/sel/prob/L1NormGenomicSelectionProblem.py
./pybrops/breed/prot/sel/prob/L2NormGenomicSelectionProblem.py
./pybrops/breed/prot/sel/prob/MateSelectionProblem.py
./pybrops/breed/prot/sel/prob/MeanExpectedHeterozygositySelectionProblem.py
./pybrops/breed/prot/sel/prob/MeanGenomicRelationshipSelectionProblem.py
./pybrops/breed/prot/sel/prob/MultiObjectiveGenomicMatingProblem.py
./pybrops/breed/prot/sel/prob/MultiObjectiveGenomicSelectionProblem.py
./pybrops/breed/prot/sel/prob/OptimalContributionSelectionProblem.py
./pybrops/breed/prot/sel/prob/OptimalHaploidValueSelectionProblem.py
./pybrops/breed/prot/sel/prob/OptimalPopulationValueSelectionProblem.py
./pybrops/breed/prot/sel/prob/RandomSelectionProblem.py
./pybrops/breed/prot/sel/prob/RealLookAheadGeneralizedWeightedGenomicSelectionProblem.py
./pybrops/breed/prot/sel/prob/RealMateSelectionProblem.py
./pybrops/breed/prot/sel/prob/RealSelectionProblem.py
./pybrops/breed/prot/sel/prob/SelectionProblem.py
./pybrops/breed/prot/sel/prob/SubsetMateSelectionProblem.py
./pybrops/breed/prot/sel/prob/SubsetSelectionProblem.py
./pybrops/breed/prot/sel/prob/UsefulnessCriterionSelectionProblem.py
./pybrops/breed/prot/sel/prob/WeightedGenomicSelectionProblem.py
./pybrops/breed/prot/sel/prob/__init__.py
./pybrops/breed/prot/sel/prob/trans.py
./pybrops/breed/prot/sel/soln/BinaryMateSelectionSolution.py
./pybrops/breed/prot/sel/soln/BinarySelectionSolution.py
./pybrops/breed/prot/sel/soln/IntegerMateSelectionSolution.py
./pybrops/breed/prot/sel/soln/IntegerSelectionSolution.py
./pybrops/breed/prot/sel/soln/MateSelectionSolution.py
./pybrops/breed/prot/sel/soln/RealMateSelectionSolution.py
./pybrops/breed/prot/sel/soln/RealSelectionSolution.py
./pybrops/breed/prot/sel/soln/SelectionSolution.py
./pybrops/breed/prot/sel/soln/SubsetMateSelectionSolution.py
./pybrops/breed/prot/sel/soln/SubsetSelectionSolution.py
./pybrops/breed/prot/sel/soln/__init__.py
./pybrops/core/__init__.py
./pybrops/core/error/__init__.py
./pybrops/core/error/error_attr_python.py
./pybrops/core/error/error_generic_numpy.py
./pybrops/core/error/error_generic_python.py
./pybrops/core/error/error_io_python.py
./pybrops/core/error/error_type_h5py.py
./pybrops/core/error/error_type_numpy.py
./pybrops/core/error/error_type_pandas.py
./pybrops/core/error/error_type_python.py
./pybrops/core/error/error_value_h5py.py
./pybrops/core/error/error_value_numpy.py
./pybrops/core/error/error_value_pandas.py
./pybrops/core/error/error_value_python.py
./pybrops/core/io/CSVDictInputOutput.py
./pybrops/core/io/CSVInputOutput.py
./pybrops/core/io/DictInputOutput.py
./pybrops/core/io/HDF5InputOutput.py
./pybrops/core/io/NPYInputOutput.py
./pybrops/core/io/NPZInputOutput.py
./pybrops/core/io/NumPyInputOutput.py
./pybrops/core/io/PandasDictInputOutput.py
./pybrops/core/io/PandasInputOutput.py
./pybrops/core/io/__init__.py
./pybrops/core/mat/DenseMatrix.py
./pybrops/core/mat/DenseMutableMatrix.py
./pybrops/core/mat/DensePhasedMatrix.py
./pybrops/core/mat/DensePhasedTaxaVariantMatrix.py
./pybrops/core/mat/DenseSquareMatrix.py
./pybrops/core/mat/DenseSquareTaxaMatrix.py
./pybrops/core/mat/DenseSquareTaxaSquareTraitMatrix.py
./pybrops/core/mat/DenseSquareTaxaTraitMatrix.py
./pybrops/core/mat/DenseSquareTraitMatrix.py
./pybrops/core/mat/DenseTaxaMatrix.py
./pybrops/core/mat/DenseTaxaTraitMatrix.py
./pybrops/core/mat/DenseTaxaVariantMatrix.py
./pybrops/core/mat/DenseTraitMatrix.py
./pybrops/core/mat/DenseVariantMatrix.py
./pybrops/core/mat/GroupableMatrix.py
./pybrops/core/mat/Matrix.py
./pybrops/core/mat/MutableMatrix.py
./pybrops/core/mat/PhasedMatrix.py
./pybrops/core/mat/PhasedTaxaVariantMatrix.py
./pybrops/core/mat/PrunableMatrix.py
./pybrops/core/mat/SortableMatrix.py
./pybrops/core/mat/SquareMatrix.py
./pybrops/core/mat/SquareTaxaMatrix.py
./pybrops/core/mat/SquareTaxaSquareTraitMatrix.py
./pybrops/core/mat/SquareTaxaTraitMatrix.py
./pybrops/core/mat/SquareTraitMatrix.py
./pybrops/core/mat/TaxaMatrix.py
./pybrops/core/mat/TaxaTraitMatrix.py
./pybrops/core/mat/TaxaVariantMatrix.py
./pybrops/core/mat/TraitMatrix.py
./pybrops/core/mat/VariantMatrix.py
./pybrops/core/mat/__init__.py
./pybrops/core/mat/util.py
./pybrops/core/random/__init__.py
./pybrops/core/random/prng.py
./pybrops/core/random/sampling.py
./pybrops/core/util/__init__.py
./pybrops/core/util/arrayix.py
./pybrops/core/util/h5py.py
./pybrops/core/util/haplo.py
./pybrops/core/util/iterator.py
./pybrops/core/util/pareto.py
./pybrops/core/util/subroutines.py
./pybrops/model/__init__.py
./pybrops/model/gmod/AdditiveDominanceEpistaticLinearGenomicModel.py
./pybrops/model/gmod/AdditiveDominanceLinearGenomicModel.py
./pybrops/model/gmod/AdditiveLinearGenomicModel.py
./pybrops/model/gmod/CoancestryLinearGenomicModel.py
./pybrops/model/gmod/DenseAdditiveLinearGenomicModel.py
./pybrops/model/gmod/DenseLinearGenomicModel.py
./pybrops/model/gmod/GenomicModel.py
./pybrops/model/gmod/LinearGenomicModel.py
./pybrops/model/gmod/NonlinearGenomicModel.py
./pybrops/model/gmod/__init__.py
./pybrops/model/pcvmat/AdditiveProgenyGeneticCovarianceMatrix.py
./pybrops/model/pcvmat/AdditiveProgenyGenicCovarianceMatrix.py
./pybrops/model/pcvmat/DenseAdditiveProgenyGeneticCovarianceMatrix.py
./pybrops/model/pcvmat/DenseAdditiveProgenyGenicCovarianceMatrix.py
./pybrops/model/pcvmat/DenseDihybridDHAdditiveProgenyGeneticCovarianceMatrix.py
./pybrops/model/pcvmat/DenseDihybridDHAdditiveProgenyGenicCovarianceMatrix.py
./pybrops/model/pcvmat/DenseFourWayDHAdditiveProgenyGeneticCovarianceMatrix.py
./pybrops/model/pcvmat/DenseFourWayDHAdditiveProgenyGenicCovarianceMatrix.py
./pybrops/model/pcvmat/DenseProgenyGeneticCovarianceMatrix.py
./pybrops/model/pcvmat/DenseProgenyGenicCovarianceMatrix.py
./pybrops/model/pcvmat/DenseThreeWayDHAdditiveProgenyGeneticCovarianceMatrix.py
./pybrops/model/pcvmat/DenseThreeWayDHAdditiveProgenyGenicCovarianceMatrix.py
./pybrops/model/pcvmat/DenseTwoWayDHAdditiveProgenyGeneticCovarianceMatrix.py
./pybrops/model/pcvmat/DenseTwoWayDHAdditiveProgenyGenicCovarianceMatrix.py
./pybrops/model/pcvmat/ProgenyGeneticCovarianceMatrix.py
./pybrops/model/pcvmat/ProgenyGenicCovarianceMatrix.py
./pybrops/model/pcvmat/__init__.py
./pybrops/model/vmat/AdditiveGeneticVarianceMatrix.py
./pybrops/model/vmat/AdditiveGenicVarianceMatrix.py
./pybrops/model/vmat/DenseAdditiveGeneticVarianceMatrix.py
./pybrops/model/vmat/DenseAdditiveGenicVarianceMatrix.py
./pybrops/model/vmat/DenseDihybridDHAdditiveGeneticVarianceMatrix.py
./pybrops/model/vmat/DenseDihybridDHAdditiveGenicVarianceMatrix.py
./pybrops/model/vmat/DenseFourWayDHAdditiveGeneticVarianceMatrix.py
./pybrops/model/vmat/DenseFourWayDHAdditiveGenicVarianceMatrix.py
./pybrops/model/vmat/DenseGeneticVarianceMatrix.py
./pybrops/model/vmat/DenseGenicVarianceMatrix.py
./pybrops/model/vmat/DenseThreeWayDHAdditiveGeneticVarianceMatrix.py
./pybrops/model/vmat/DenseThreeWayDHAdditiveGenicVarianceMatrix.py
./pybrops/model/vmat/DenseTwoWayDHAdditiveGeneticVarianceMatrix.py
./pybrops/model/vmat/DenseTwoWayDHAdditiveGenicVarianceMatrix.py
./pybrops/model/vmat/GeneticVarianceMatrix.py
./pybrops/model/vmat/GenicVarianceMatrix.py
./pybrops/model/vmat/__init__.py
./pybrops/model/vmat/util.py
./pybrops/model/vmat/fcty/AdditiveGeneticVarianceMatrixFactory.py
./pybrops/model/vmat/fcty/AdditiveGenicVarianceMatrixFactory.py
./pybrops/model/vmat/fcty/DenseDihybridDHAdditiveGeneticVarianceMatrixFactory.py
./pybrops/model/vmat/fcty/DenseFourWayDHAdditiveGeneticVarianceMatrixFactory.py
./pybrops/model/vmat/fcty/DenseThreeWayDHAdditiveGeneticVarianceMatrixFactory.py
./pybrops/model/vmat/fcty/DenseTwoWayDHAdditiveGeneticVarianceMatrixFactory.py
./pybrops/model/vmat/fcty/DenseTwoWayDHAdditiveGenicVarianceMatrixFactory.py
./pybrops/model/vmat/fcty/GeneticVarianceMatrixFactory.py
./pybrops/model/vmat/fcty/GenicVarianceMatrixFactory.py
./pybrops/model/vmat/fcty/__init__.py
./pybrops/opt/__init__.py
./pybrops/opt/algo/BinaryGeneticAlgorithm.py
./pybrops/opt/algo/BinaryOptimizationAlgorithm.py
./pybrops/opt/algo/IntegerGeneticAlgorithm.py
./pybrops/opt/algo/IntegerOptimizationAlgorithm.py
./pybrops/opt/algo/NSGA2BinaryGeneticAlgorithm.py
./pybrops/opt/algo/NSGA2IntegerGeneticAlgorithm.py
./pybrops/opt/algo/NSGA2RealGeneticAlgorithm.py
./pybrops/opt/algo/NSGA2SubsetGeneticAlgorithm.py
./pybrops/opt/algo/OptimizationAlgorithm.py
./pybrops/opt/algo/RealGeneticAlgorithm.py
./pybrops/opt/algo/RealOptimizationAlgorithm.py
./pybrops/opt/algo/SortingSteepestDescentSubsetHillClimber.py
./pybrops/opt/algo/SortingSubsetOptimizationAlgorithm.py
./pybrops/opt/algo/SteepestDescentSubsetHillClimber.py
./pybrops/opt/algo/SubsetGeneticAlgorithm.py
./pybrops/opt/algo/SubsetOptimizationAlgorithm.py
./pybrops/opt/algo/UnconstrainedNSGA2SetGeneticAlgorithm.py
./pybrops/opt/algo/UnconstrainedOptimizationAlgorithm.py
./pybrops/opt/algo/UnconstrainedSetGeneticAlgorithm.py
./pybrops/opt/algo/UnconstrainedSteepestAscentSetHillClimber.py
./pybrops/opt/algo/__init__.py
./pybrops/opt/algo/pymoo_addon.py
./pybrops/opt/prob/BinaryProblem.py
./pybrops/opt/prob/FunctionWeight.py
./pybrops/opt/prob/IntegerProblem.py
./pybrops/opt/prob/Problem.py
./pybrops/opt/prob/RealProblem.py
./pybrops/opt/prob/SubsetProblem.py
./pybrops/opt/prob/__init__.py
./pybrops/opt/soln/BinarySolution.py
./pybrops/opt/soln/IntegerSolution.py
./pybrops/opt/soln/RealSolution.py
./pybrops/opt/soln/Solution.py
./pybrops/opt/soln/SubsetSolution.py
./pybrops/opt/soln/__init__.py
./pybrops/popgen/__init__.py
./pybrops/popgen/bvmat/BreedingValueMatrix.py
./pybrops/popgen/bvmat/DenseBreedingValueMatrix.py
./pybrops/popgen/bvmat/DenseEstimatedBreedingValueMatrix.py
./pybrops/popgen/bvmat/DenseGenomicEstimatedBreedingValueMatrix.py
./pybrops/popgen/bvmat/__init__.py
./pybrops/popgen/cmat/CoancestryMatrix.py
./pybrops/popgen/cmat/DenseCoancestryMatrix.py
./pybrops/popgen/cmat/DenseGeneralizedWeightedCoancestryMatrix.py
./pybrops/popgen/cmat/DenseMolecularCoancestryMatrix.py
./pybrops/popgen/cmat/DenseVanRadenCoancestryMatrix.py
./pybrops/popgen/cmat/DenseYangCoancestryMatrix.py
./pybrops/popgen/cmat/__init__.py
./pybrops/popgen/cmat/fcty/CoancestryMatrixFactory.py
./pybrops/popgen/cmat/fcty/DenseCoancestryMatrixFactory.py
./pybrops/popgen/cmat/fcty/DenseGeneralizedWeightedCoancestryMatrixFactory.py
./pybrops/popgen/cmat/fcty/DenseMolecularCoancestryMatrixFactory.py
./pybrops/popgen/cmat/fcty/DenseVanRadenCoancestryMatrixFactory.py
./pybrops/popgen/cmat/fcty/DenseYangCoancestryMatrixFactory.py
./pybrops/popgen/cmat/fcty/__init__.py
./pybrops/popgen/gmap/DenseGeneticMappableMatrix.py
./pybrops/popgen/gmap/ExtendedGeneticMap.py
./pybrops/popgen/gmap/GeneticMap.py
./pybrops/popgen/gmap/GeneticMapFunction.py
./pybrops/popgen/gmap/GeneticMappableMatrix.py
./pybrops/popgen/gmap/HaldaneMapFunction.py
./pybrops/popgen/gmap/KosambiMapFunction.py
./pybrops/popgen/gmap/StandardGeneticMap.py
./pybrops/popgen/gmap/__init__.py
./pybrops/popgen/gmap/util.py
./pybrops/popgen/gmat/DenseGenotypeMatrix.py
./pybrops/popgen/gmat/DensePhasedGenotypeMatrix.py
./pybrops/popgen/gmat/GenotypeMatrix.py
./pybrops/popgen/gmat/HaplotypeMatrix.py
./pybrops/popgen/gmat/PhasedGenotypeMatrix.py
./pybrops/popgen/gmat/PhasedHaplotypeMatrix.py
./pybrops/popgen/gmat/__init__.py
./pybrops/test/__init__.py
./pybrops/test/assert_numpy.py
./pybrops/test/assert_python.py
pybrops.egg-info/PKG-INFO
pybrops.egg-info/SOURCES.txt
pybrops.egg-info/dependency_links.txt
pybrops.egg-info/requires.txt
pybrops.egg-info/top_level.txt