Date: Sun, 30 Mar 2025 17:08:00 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 048dbfd0ede1 - main - =?utf-8?Q?science/dakota: update 6.17.0 =E2=86=92 6.21.0?= Message-ID: <202503301708.52UH80MI085773@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=048dbfd0ede1bd4eba658e7d3a749dd2fa1f3478 commit 048dbfd0ede1bd4eba658e7d3a749dd2fa1f3478 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2025-03-30 17:07:08 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2025-03-30 17:07:56 +0000 science/dakota: update 6.17.0 → 6.21.0 --- science/dakota/Makefile | 28 +-- science/dakota/distinfo | 6 +- science/dakota/files/fake-c++.sh | 4 + science/dakota/files/patch-CMakeLists.txt | 6 +- ...tilities_include_inline_keyed__registry.hpp.inl | 23 ++ science/dakota/files/patch-src_WorkdirHelper.cpp | 12 + science/dakota/files/patch-src_WorkdirHelper.hpp | 12 + .../files/patch-src_util_util__data__types.hpp | 12 + science/dakota/pkg-plist | 255 ++++++++++++++++++++- 9 files changed, 331 insertions(+), 27 deletions(-) diff --git a/science/dakota/Makefile b/science/dakota/Makefile index e250de6783ac..1ae5bc137bc7 100644 --- a/science/dakota/Makefile +++ b/science/dakota/Makefile @@ -1,20 +1,18 @@ PORTNAME= dakota -DISTVERSION= 6.17.0 -PORTREVISION= 12 +DISTVERSION= 6.21.0 CATEGORIES= science -MASTER_SITES= https://dakota.sandia.gov/sites/default/files/distributions/public/ -DISTNAME= ${PORTNAME}-${DISTVERSION}-release-public-src-cli +MASTER_SITES= https://github.com/snl-dakota/dakota/releases/download/v${DISTVERSION}/ +DISTNAME= ${PORTNAME}-${DISTVERSION}-public-src-cli DISTFILES= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Interface between analysis codes & iterative systems analysis methods -WWW= https://dakota.sandia.gov/ +WWW= https://dakota.sandia.gov \ + https://github.com/snl-dakota/dakota LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN= fails to build with boost-1.85+ - BUILD_DEPENDS= nanoflann>0:math/nanoflann LIB_DEPENDS= libblas.so:math/blas \ libboost_system.so:devel/boost-libs \ @@ -24,6 +22,7 @@ LIB_DEPENDS= libblas.so:math/blas \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ libicui18n.so:devel/icu \ + libkokkoscore.so:devel/kokkos \ liblapack.so:math/lapack \ libnlopt.so:math/nlopt \ libpng16.so:graphics/png \ @@ -44,6 +43,8 @@ SHEBANG_FILES= interfaces/Python/mpitile \ scripts/dprepro.perl \ test/dakota_test.perl +CXX= ${FILESDIR}/fake-c++.sh # change to c++14 + CMAKE_ON= HAVE_X_GRAPHICS # always enable graphics because w/out it a lot of unrelated files aren't installed due to bugs in the project CMAKE_ON+= Boost_NO_BOOST_CMAKE \ DAKOTA_GIT_checkout @@ -75,16 +76,9 @@ pre-configure: # MUQ_STANMATH_DIR is lost otherwise @${REINPLACE_CMD} 's|find_package(PkgConfig)|set(MUQ_STANMATH_DIR ${WRKSRC}/stanmath)|' ${WRKSRC}/packages/external/muq2/cmake/finds/FindSTANMATH.cmake post-install: - # remove eigen3 that Dakota installs - cd ${STAGEDIR}${PREFIX} && ${RM} -r include/eigen3 share/eigen3 - # remove cblas.h that Dakota installs - ${RM} ${STAGEDIR}${PREFIX}/include/cblas.h - # remove *.orig files - ${RM} ${STAGEDIR}${PREFIX}/include/colin/AppResponse.h.orig - # install libraries that it fails to install -.for l in libmuqSamplingAlgorithms.so libmuqModeling.so libmuqUtilities.so - ${INSTALL_LIB} ${BUILD_WRKSRC}/packages/external/muq2/lib/${l} ${STAGEDIR}${PREFIX}/lib -.endfor + # remove eigen3 that Dakota installs, see https://github.com/snl-dakota/dakota/issues/182 + @cd ${STAGEDIR}${PREFIX} && \ + ${RM} -r include/eigen3 share/eigen3 do-test: install # from Additional Test Suites @ https://dakota.sandia.gov/content/additional-test-suites (many tests are known to fail) ## minimal set of fast-running tests that should NOT FAIL (may DIFF, depending on platform / compiler) diff --git a/science/dakota/distinfo b/science/dakota/distinfo index 3a5ff0870e92..37406ed39d14 100644 --- a/science/dakota/distinfo +++ b/science/dakota/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1674268260 -SHA256 (dakota-6.17.0-release-public-src-cli.tar.gz) = a6045784426b75d4981efcc1f243a5cd74dfcf29d4572927d6162a82a12757c6 -SIZE (dakota-6.17.0-release-public-src-cli.tar.gz) = 142641074 +TIMESTAMP = 1743185006 +SHA256 (dakota-6.21.0-public-src-cli.tar.gz) = 7dcf9f93b7bc37a24dee3acda25be280c1a49774e22d53aa1e4b0a60df62ff97 +SIZE (dakota-6.21.0-public-src-cli.tar.gz) = 156415576 SHA256 (stan-dev-math-v2.18.0_GH0.tar.gz) = 53fbce2b28aea76695af7a91f51fdd356367153fc42b3573e2b91e6586eca91d SIZE (stan-dev-math-v2.18.0_GH0.tar.gz) = 17528084 diff --git a/science/dakota/files/fake-c++.sh b/science/dakota/files/fake-c++.sh new file mode 100755 index 000000000000..743abbb92474 --- /dev/null +++ b/science/dakota/files/fake-c++.sh @@ -0,0 +1,4 @@ +#!/bin/sh + + +c++ "$@" -std=c++14 diff --git a/science/dakota/files/patch-CMakeLists.txt b/science/dakota/files/patch-CMakeLists.txt index a86a5f282821..46fd92132cba 100644 --- a/science/dakota/files/patch-CMakeLists.txt +++ b/science/dakota/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2022-11-11 20:23:57 UTC +--- CMakeLists.txt.orig 2024-11-12 02:01:36 UTC +++ CMakeLists.txt -@@ -243,9 +243,11 @@ if(DAKOTA_MODULE_DAKOTA) +@@ -274,9 +274,11 @@ if(DAKOTA_MODULE_DAKOTA) endif() # Legacy examples @@ -14,7 +14,7 @@ add_subdirectory(dakota-examples) endif() -@@ -268,19 +270,23 @@ install(FILES INSTALL LICENSE COPYRIGHT README +@@ -299,19 +301,23 @@ install(FILES INSTALL LICENSE COPYRIGHT README DESTINATION ${DAKOTA_TOPFILES_INSTALL} ) diff --git a/science/dakota/files/patch-packages_external_JEGA_eddy_utilities_include_inline_keyed__registry.hpp.inl b/science/dakota/files/patch-packages_external_JEGA_eddy_utilities_include_inline_keyed__registry.hpp.inl new file mode 100644 index 000000000000..7316df24fc83 --- /dev/null +++ b/science/dakota/files/patch-packages_external_JEGA_eddy_utilities_include_inline_keyed__registry.hpp.inl @@ -0,0 +1,23 @@ +- https://github.com/snl-dakota/dakota/issues/178 + +--- packages/external/JEGA/eddy/utilities/include/inline/keyed_registry.hpp.inl.orig 2025-03-28 21:44:35 UTC ++++ packages/external/JEGA/eddy/utilities/include/inline/keyed_registry.hpp.inl +@@ -153,18 +153,6 @@ template<typename KeyType, typename ValueType> + } + + template<typename KeyType, typename ValueType> +-bool +-keyed_registry<KeyType, ValueType>::unregister( +- const KeyType& value +- ) +-{ +- typename container::iterator it(this->find(this->key)); +- if(it == this->_registry.end()) return false; +- this->_registry.erase(it); +- return true; +-} +- +-template<typename KeyType, typename ValueType> + typename keyed_registry<KeyType, ValueType>::const_iterator + keyed_registry<KeyType, ValueType>::find( + const KeyType& key diff --git a/science/dakota/files/patch-src_WorkdirHelper.cpp b/science/dakota/files/patch-src_WorkdirHelper.cpp new file mode 100644 index 000000000000..09c38b92c034 --- /dev/null +++ b/science/dakota/files/patch-src_WorkdirHelper.cpp @@ -0,0 +1,12 @@ +- https://github.com/snl-dakota/dakota/pull/181 + +--- src/WorkdirHelper.cpp.orig 2025-03-30 08:18:38 UTC ++++ src/WorkdirHelper.cpp +@@ -11,6 +11,7 @@ + #include "dakota_data_util.hpp" // for strcontains + #include "dakota_global_defs.hpp" + #include <boost/array.hpp> ++#include <boost/filesystem/exception.hpp> + #include <boost/tokenizer.hpp> + #include <cassert> + diff --git a/science/dakota/files/patch-src_WorkdirHelper.hpp b/science/dakota/files/patch-src_WorkdirHelper.hpp new file mode 100644 index 000000000000..3b4a404cb809 --- /dev/null +++ b/science/dakota/files/patch-src_WorkdirHelper.hpp @@ -0,0 +1,12 @@ +- https://github.com/snl-dakota/dakota/pull/179 + +--- src/WorkdirHelper.hpp.orig 2025-03-30 07:11:51 UTC ++++ src/WorkdirHelper.hpp +@@ -17,6 +17,7 @@ + #include <boost/regex.hpp> + #include <boost/iterator/filter_iterator.hpp> + ++#include <boost/filesystem/directory.hpp> + #include <boost/filesystem/operations.hpp> + #include <boost/filesystem/path.hpp> + namespace bfs = boost::filesystem; diff --git a/science/dakota/files/patch-src_util_util__data__types.hpp b/science/dakota/files/patch-src_util_util__data__types.hpp new file mode 100644 index 000000000000..8992762c2be1 --- /dev/null +++ b/science/dakota/files/patch-src_util_util__data__types.hpp @@ -0,0 +1,12 @@ +- https://github.com/snl-dakota/dakota/issues/180 + +--- src/util/util_data_types.hpp.orig 2025-03-30 07:57:31 UTC ++++ src/util/util_data_types.hpp +@@ -21,6 +21,7 @@ + #include <boost/serialization/array.hpp> + #include <boost/serialization/serialization.hpp> + #define EIGEN_MATRIX_PLUGIN "util_eigen_plugins.hpp" ++#undef Success // https://github.com/snl-dakota/dakota/issues/180 + #include "Eigen/Dense" + + /// dakota (lowercase) namespace for new %Dakota modules diff --git a/science/dakota/pkg-plist b/science/dakota/pkg-plist index 1f0347e2ed67..6462bd1b85e3 100644 --- a/science/dakota/pkg-plist +++ b/science/dakota/pkg-plist @@ -39,7 +39,9 @@ include/AllOperators.hpp.inl include/Appl_Data.h include/Appl_Data_NPSOL.h include/ApplicationInterface.hpp +include/ApproximationFieldInterface.hpp include/ApproximationInterface.hpp +include/ApreproParametersFileWriter.hpp include/AsciiDataWriter.h include/AverageFitnessTrackerConverger.hpp include/AverageFitnessTrackerConverger.hpp.inl @@ -135,6 +137,7 @@ include/DakotaApproximation.hpp include/DakotaBuildInfo.hpp include/DakotaConstraints.hpp include/DakotaEnvironment.hpp +include/DakotaFieldApproximation.hpp include/DakotaGraphics.hpp include/DakotaInterface.hpp include/DakotaInterfaceAPI.hpp @@ -149,6 +152,7 @@ include/DakotaResponse.hpp include/DakotaSurrogates.hpp include/DakotaSurrogatesGP.hpp include/DakotaSurrogatesPoly.hpp +include/DakotaSurrogatesPython.hpp include/DakotaTPLDataTransfer.hpp include/DakotaTraitsBase.hpp include/DakotaVariables.hpp @@ -191,6 +195,7 @@ include/DesignVariableNatureBase.hpp include/DesignVariableNatureBase.hpp.inl include/DesignVariableTypeBase.hpp include/DesignVariableTypeBase.hpp.inl +include/DigitalNet.hpp include/DirectApplicInterface.hpp include/DiscrepancyCalculator.hpp include/DiscrepancyCorrection.hpp @@ -355,7 +360,6 @@ include/HermiteOrthogPolynomial.hpp include/HierarchInterpPolyApproximation.hpp include/HierarchSparseGridDriver.hpp include/HierarchSurrBasedLocalMinimizer.hpp -include/HierarchSurrModel.hpp include/HistogramBinRandomVariable.hpp include/HypergeometricRandomVariable.hpp include/IncrementalSparseGridDriver.hpp @@ -375,12 +379,18 @@ include/IteratorScheduler.hpp include/JEGAConfig.hpp include/JEGAOptimizer.hpp include/JEGATypes.hpp +include/JSONParametersFileWriter.hpp +include/JSONResultsFileReader.hpp +include/JSONResultsParser.hpp include/JacobiOrthogPolynomial.hpp include/KarhunenLoeveInverseTransformation.hpp include/KrawtchoukOrthogPolynomial.hpp include/LARSolver.hpp +include/LDDriver.hpp +include/LDDriverAdapter.hpp include/LHS.h include/LHSDriver.hpp +include/LHSDriverAdapter.hpp include/LRUDesignCache.hpp include/LRUDesignCache.hpp.inl include/LSQCrossValidationIterator.hpp @@ -409,6 +419,7 @@ include/Logger.hpp.inl include/Logging.hpp include/LognormalRandomVariable.hpp include/LoguniformRandomVariable.hpp +include/LowDiscrepancySequence.hpp include/MAlgorithmConfig.hpp include/MBasicParameterDatabaseImpl.hpp include/MConfig.hpp @@ -432,6 +443,222 @@ include/MParameterDatabase.hpp include/MProblemConfig.hpp include/MSolution.hpp include/MStreamHijacker.hpp +include/MUQ/Approximation/ForwardUQ.h +include/MUQ/Approximation/GaussianProcesses/ConcatenateKernel.h +include/MUQ/Approximation/GaussianProcesses/ConstantKernel.h +include/MUQ/Approximation/GaussianProcesses/CovarianceKernels.h +include/MUQ/Approximation/GaussianProcesses/GaussianProcess.h +include/MUQ/Approximation/GaussianProcesses/KarhunenLoeveBase.h +include/MUQ/Approximation/GaussianProcesses/KarhunenLoeveExpansion.h +include/MUQ/Approximation/GaussianProcesses/KarhunenLoeveFactory.h +include/MUQ/Approximation/GaussianProcesses/KernelBase.h +include/MUQ/Approximation/GaussianProcesses/KernelImpl.h +include/MUQ/Approximation/GaussianProcesses/LinearKernel.h +include/MUQ/Approximation/GaussianProcesses/LinearTransformKernel.h +include/MUQ/Approximation/GaussianProcesses/MaternKernel.h +include/MUQ/Approximation/GaussianProcesses/ObservationInformation.h +include/MUQ/Approximation/GaussianProcesses/PeriodicKernel.h +include/MUQ/Approximation/GaussianProcesses/ProductKernel.h +include/MUQ/Approximation/GaussianProcesses/SeparableKarhunenLoeve.h +include/MUQ/Approximation/GaussianProcesses/SquaredExpKernel.h +include/MUQ/Approximation/GaussianProcesses/StateSpaceGP.h +include/MUQ/Approximation/GaussianProcesses/SumKernel.h +include/MUQ/Approximation/GaussianProcesses/WhiteNoiseKernel.h +include/MUQ/Approximation/PolynomialChaos/AdaptiveSmolyakPCE.h +include/MUQ/Approximation/PolynomialChaos/PCEFactory.h +include/MUQ/Approximation/PolynomialChaos/PolynomialChaosExpansion.h +include/MUQ/Approximation/PolynomialChaos/SmolyakEstimator.h +include/MUQ/Approximation/Polynomials/BasisExpansion.h +include/MUQ/Approximation/Polynomials/HermiteFunction.h +include/MUQ/Approximation/Polynomials/IndexedScalarBasis.h +include/MUQ/Approximation/Polynomials/Jacobi.h +include/MUQ/Approximation/Polynomials/Laguerre.h +include/MUQ/Approximation/Polynomials/Legendre.h +include/MUQ/Approximation/Polynomials/Monomial.h +include/MUQ/Approximation/Polynomials/MonotoneExpansion.h +include/MUQ/Approximation/Polynomials/OrthogonalPolynomial.h +include/MUQ/Approximation/Polynomials/PhysicistHermite.h +include/MUQ/Approximation/Polynomials/ProbabilistHermite.h +include/MUQ/Approximation/Quadrature/AdaptiveSmolyakQuadrature.h +include/MUQ/Approximation/Quadrature/ClenshawCurtisQuadrature.h +include/MUQ/Approximation/Quadrature/ExponentialGrowthQuadrature.h +include/MUQ/Approximation/Quadrature/FullTensorQuadrature.h +include/MUQ/Approximation/Quadrature/GaussPattersonQuadrature.h +include/MUQ/Approximation/Quadrature/GaussQuadrature.h +include/MUQ/Approximation/Quadrature/Quadrature.h +include/MUQ/Approximation/Quadrature/SmolyakQuadrature.h +include/MUQ/Approximation/Regression/LocalRegression.h +include/MUQ/Approximation/Regression/Regression.h +include/MUQ/Approximation/TemplatedArrayUtilities.h +include/MUQ/Inference/Filtering/KalmanFilter.h +include/MUQ/Inference/Filtering/KalmanSmoother.h +include/MUQ/Modeling/CombineVectors.h +include/MUQ/Modeling/ConstantPiece.h +include/MUQ/Modeling/ConstantVector.h +include/MUQ/Modeling/CwiseOperators/CwiseUnaryOperator.h +include/MUQ/Modeling/Distributions/Density.h +include/MUQ/Modeling/Distributions/DensityProduct.h +include/MUQ/Modeling/Distributions/Distribution.h +include/MUQ/Modeling/Distributions/Gamma.h +include/MUQ/Modeling/Distributions/Gaussian.h +include/MUQ/Modeling/Distributions/GaussianBase.h +include/MUQ/Modeling/Distributions/InverseGamma.h +include/MUQ/Modeling/Distributions/MixtureDistribution.h +include/MUQ/Modeling/Distributions/PyDistribution.h +include/MUQ/Modeling/Distributions/RandomVariable.h +include/MUQ/Modeling/Distributions/UniformBox.h +include/MUQ/Modeling/Dolfin/FenicsPiece.h +include/MUQ/Modeling/Dolfin/SwigExtract.h +include/MUQ/Modeling/Flann/FlannCache.h +include/MUQ/Modeling/GradientPiece.h +include/MUQ/Modeling/IdentityPiece.h +include/MUQ/Modeling/JacobianPiece.h +include/MUQ/Modeling/LinearAlgebra/AffineOperator.h +include/MUQ/Modeling/LinearAlgebra/AnyAlgebra.h +include/MUQ/Modeling/LinearAlgebra/AnyAlgebra2.h +include/MUQ/Modeling/LinearAlgebra/AnyVec.h +include/MUQ/Modeling/LinearAlgebra/BlockDiagonalOperator.h +include/MUQ/Modeling/LinearAlgebra/BlockRowOperator.h +include/MUQ/Modeling/LinearAlgebra/CompanionMatrix.h +include/MUQ/Modeling/LinearAlgebra/ConcatenateOperator.h +include/MUQ/Modeling/LinearAlgebra/DiagonalOperator.h +include/MUQ/Modeling/LinearAlgebra/EigenLinearOperator.h +include/MUQ/Modeling/LinearAlgebra/EigenMatrixAlgebra.h +include/MUQ/Modeling/LinearAlgebra/EigenVectorAlgebra.h +include/MUQ/Modeling/LinearAlgebra/GaussNewtonOperator.h +include/MUQ/Modeling/LinearAlgebra/GaussianOperator.h +include/MUQ/Modeling/LinearAlgebra/GeneralizedEigenSolver.h +include/MUQ/Modeling/LinearAlgebra/HessianOperator.h +include/MUQ/Modeling/LinearAlgebra/IdentityOperator.h +include/MUQ/Modeling/LinearAlgebra/KroneckerProductOperator.h +include/MUQ/Modeling/LinearAlgebra/LOBPCG.h +include/MUQ/Modeling/LinearAlgebra/LinearOperator.h +include/MUQ/Modeling/LinearAlgebra/LyapunovSolver.h +include/MUQ/Modeling/LinearAlgebra/ProductOperator.h +include/MUQ/Modeling/LinearAlgebra/ScalarAlgebra.h +include/MUQ/Modeling/LinearAlgebra/SliceOperator.h +include/MUQ/Modeling/LinearAlgebra/StochasticEigenSolver.h +include/MUQ/Modeling/LinearAlgebra/SumOperator.h +include/MUQ/Modeling/LinearAlgebra/SundialsAlgebra.h +include/MUQ/Modeling/LinearAlgebra/ZeroOperator.h +include/MUQ/Modeling/LinearSDE.h +include/MUQ/Modeling/ModGraphPiece.h +include/MUQ/Modeling/ModPiece.h +include/MUQ/Modeling/Modeling.h +include/MUQ/Modeling/MultiLogisticLikelihood.h +include/MUQ/Modeling/NodeNameFinder.h +include/MUQ/Modeling/ODE.h +include/MUQ/Modeling/ODEData.h +include/MUQ/Modeling/OneStepCachePiece.h +include/MUQ/Modeling/ProductPiece.h +include/MUQ/Modeling/PyModPiece.h +include/MUQ/Modeling/Python/PyAny.h +include/MUQ/Modeling/ReplicateOperator.h +include/MUQ/Modeling/RootfindingIVP.h +include/MUQ/Modeling/ScaleVector.h +include/MUQ/Modeling/SplitVector.h +include/MUQ/Modeling/SumPiece.h +include/MUQ/Modeling/UMBridge/UMBridgeModPiece.h +include/MUQ/Modeling/UMBridge/UMBridgeModPieceServer.h +include/MUQ/Modeling/UMBridge/httplib.h +include/MUQ/Modeling/UMBridge/json.h +include/MUQ/Modeling/UMBridge/umbridge.h +include/MUQ/Modeling/WorkGraph.h +include/MUQ/Modeling/WorkGraphEdge.h +include/MUQ/Modeling/WorkGraphNode.h +include/MUQ/Modeling/WorkGraphPiece.h +include/MUQ/Modeling/WorkPiece.h +include/MUQ/Optimization/CostFunction.h +include/MUQ/Optimization/ModPieceCostFunction.h +include/MUQ/Optimization/NLoptOptimizer.h +include/MUQ/Optimization/NewtonTrust.h +include/MUQ/Optimization/Optimizer.h +include/MUQ/SamplingAlgorithms/AMProposal.h +include/MUQ/SamplingAlgorithms/AbstractSamplingProblem.h +include/MUQ/SamplingAlgorithms/ConcatenatingInterpolation.h +include/MUQ/SamplingAlgorithms/CrankNicolsonProposal.h +include/MUQ/SamplingAlgorithms/DILIKernel.h +include/MUQ/SamplingAlgorithms/DRKernel.h +include/MUQ/SamplingAlgorithms/DefaultComponentFactory.h +include/MUQ/SamplingAlgorithms/Diagnostics.h +include/MUQ/SamplingAlgorithms/DistributedCollection.h +include/MUQ/SamplingAlgorithms/DummyKernel.h +include/MUQ/SamplingAlgorithms/ExpensiveSamplingProblem.h +include/MUQ/SamplingAlgorithms/GMHKernel.h +include/MUQ/SamplingAlgorithms/GreedyMLMCMC.h +include/MUQ/SamplingAlgorithms/ISKernel.h +include/MUQ/SamplingAlgorithms/ImportanceSampling.h +include/MUQ/SamplingAlgorithms/IndependenceProposal.h +include/MUQ/SamplingAlgorithms/InfMALAProposal.h +include/MUQ/SamplingAlgorithms/InferenceProblem.h +include/MUQ/SamplingAlgorithms/InverseGammaProposal.h +include/MUQ/SamplingAlgorithms/MALAProposal.h +include/MUQ/SamplingAlgorithms/MCKernel.h +include/MUQ/SamplingAlgorithms/MCMCFactory.h +include/MUQ/SamplingAlgorithms/MCMCProposal.h +include/MUQ/SamplingAlgorithms/MHKernel.h +include/MUQ/SamplingAlgorithms/MHProposal.h +include/MUQ/SamplingAlgorithms/MIComponentFactory.h +include/MUQ/SamplingAlgorithms/MIDummyKernel.h +include/MUQ/SamplingAlgorithms/MIInterpolation.h +include/MUQ/SamplingAlgorithms/MIKernel.h +include/MUQ/SamplingAlgorithms/MIMCMC.h +include/MUQ/SamplingAlgorithms/MIMCMCBox.h +include/MUQ/SamplingAlgorithms/MarkovChain.h +include/MUQ/SamplingAlgorithms/MixtureProposal.h +include/MUQ/SamplingAlgorithms/MonteCarlo.h +include/MUQ/SamplingAlgorithms/MultiIndexEstimator.h +include/MUQ/SamplingAlgorithms/ParallelAMProposal.h +include/MUQ/SamplingAlgorithms/ParallelAbstractSamplingProblem.h +include/MUQ/SamplingAlgorithms/ParallelFixedSamplesMIMCMC.h +include/MUQ/SamplingAlgorithms/ParallelFlags.h +include/MUQ/SamplingAlgorithms/ParallelMIComponentFactory.h +include/MUQ/SamplingAlgorithms/ParallelMIMCMCBox.h +include/MUQ/SamplingAlgorithms/ParallelMIMCMCWorker.h +include/MUQ/SamplingAlgorithms/ParallelTempering.h +include/MUQ/SamplingAlgorithms/ParallelizableMIComponentFactory.h +include/MUQ/SamplingAlgorithms/Phonebook.h +include/MUQ/SamplingAlgorithms/RemoteMIProposal.h +include/MUQ/SamplingAlgorithms/SLMCMC.h +include/MUQ/SamplingAlgorithms/SampleCollection.h +include/MUQ/SamplingAlgorithms/SampleEstimator.h +include/MUQ/SamplingAlgorithms/Sampling.h +include/MUQ/SamplingAlgorithms/SamplingAlgorithm.h +include/MUQ/SamplingAlgorithms/SamplingProblem.h +include/MUQ/SamplingAlgorithms/SamplingState.h +include/MUQ/SamplingAlgorithms/SaveSchedulerBase.h +include/MUQ/SamplingAlgorithms/SingleChainMCMC.h +include/MUQ/SamplingAlgorithms/SubsamplingMIProposal.h +include/MUQ/SamplingAlgorithms/ThinScheduler.h +include/MUQ/SamplingAlgorithms/TransitionKernel.h +include/MUQ/SamplingAlgorithms/sMMALAProposal.h +include/MUQ/Utilities/AnyHelpers.h +include/MUQ/Utilities/Cereal/BoostAnySerializer.h +include/MUQ/Utilities/Cereal/MultiIndexSerializer.h +include/MUQ/Utilities/Demangler.h +include/MUQ/Utilities/EigenUtilities.h +include/MUQ/Utilities/Exceptions.h +include/MUQ/Utilities/HDF5/AnyWriter.h +include/MUQ/Utilities/HDF5/Attributes.h +include/MUQ/Utilities/HDF5/BlockDataset.h +include/MUQ/Utilities/HDF5/H5Object.h +include/MUQ/Utilities/HDF5/HDF5File.h +include/MUQ/Utilities/HDF5/HDF5Types.h +include/MUQ/Utilities/HDF5/PathTools.h +include/MUQ/Utilities/LinearAlgebra/LinearOperator.h +include/MUQ/Utilities/MultiIndices/MultiIndex.h +include/MUQ/Utilities/MultiIndices/MultiIndexFactory.h +include/MUQ/Utilities/MultiIndices/MultiIndexLimiter.h +include/MUQ/Utilities/MultiIndices/MultiIndexSet.h +include/MUQ/Utilities/OTF2Tracer.h +include/MUQ/Utilities/PyDictConversion.h +include/MUQ/Utilities/RandomGenerator.h +include/MUQ/Utilities/RegisterClassName.h +include/MUQ/Utilities/StringUtilities.h +include/MUQ/Utilities/VariadicMacros.h +include/MUQ/Utilities/VectorSlice.h +include/MUQ/Utilities/WaitBar.h +include/MUQ/config.h include/MainEffectAnalyzer.h include/MainEffectsAnalyzer.h include/MainEffectsAnalyzer3.h @@ -522,13 +749,13 @@ include/NonDAdaptiveSampling.hpp include/NonDBayesCalibration.hpp include/NonDC3FunctionTrain.hpp include/NonDCalibration.hpp -include/NonDControlVariateSampling.hpp include/NonDCubature.hpp include/NonDDREAMBayesCalibration.hpp include/NonDEnsembleSampling.hpp include/NonDExpansion.hpp include/NonDGPImpSampling.hpp include/NonDGPMSABayesCalibration.hpp +include/NonDGenACVSampling.hpp include/NonDGlobalEvidence.hpp include/NonDGlobalInterval.hpp include/NonDGlobalReliability.hpp @@ -546,6 +773,7 @@ include/NonDLocalReliability.hpp include/NonDLocalSingleInterval.hpp include/NonDMUQBayesCalibration.hpp include/NonDMultifidelitySampling.hpp +include/NonDMultilevBLUESampling.hpp include/NonDMultilevControlVarSampling.hpp include/NonDMultilevelFunctionTrain.hpp include/NonDMultilevelPolynomialChaos.hpp @@ -565,7 +793,6 @@ include/NonDSurrogateExpansion.hpp include/NonDWASABIBayesCalibration.hpp include/NonDuplicatingRouletteWheelSelector.hpp include/NonDuplicatingRouletteWheelSelector.hpp.inl -include/NonHierarchSurrModel.hpp include/NonLinearConstraint.h include/NonLinearConstraintNature.hpp include/NonLinearConstraintNature.hpp.inl @@ -659,6 +886,7 @@ include/ParamStudy.hpp include/ParameterDatabase.hpp include/ParameterExtractor.hpp include/ParameterExtractor.hpp.inl +include/ParametersFileWriter.hpp include/PecosApproximation.hpp include/PenaltyFitnessAssessorBase.hpp include/PenaltyFitnessAssessorBase.hpp.inl @@ -1093,6 +1321,7 @@ include/RandomUniqueInitializer.hpp include/RandomUniqueInitializer.hpp.inl include/RandomVariable.hpp include/RangeVariable.hpp +include/Rank1Lattice.hpp include/RealDesignVariableType.hpp include/RealDesignVariableType.hpp.inl include/RecastModel.hpp @@ -1108,6 +1337,7 @@ include/RestartVersion.hpp include/ResultsDBAny.hpp include/ResultsDBBase.hpp include/ResultsDBHDF5.hpp +include/ResultsFileReader.hpp include/ResultsManager.hpp include/RichExtrapVerification.hpp include/RosenblattTransformation.hpp @@ -1122,6 +1352,7 @@ include/SOGA.hpp.inl include/SOGAOperatorGroup.hpp include/SOGAOperatorGroup.hpp.inl include/SOLBase.hpp +include/SamplerDriver.hpp include/SamplingInverseTransformation.hpp include/ScalingModel.hpp include/ScalingOptions.hpp @@ -1165,6 +1396,8 @@ include/StandardMainLoop.hpp include/StandardMainLoop.hpp.inl include/StandardOperatorGroup.hpp include/StandardOperatorGroup.hpp.inl +include/StandardParametersFileWriter.hpp +include/StandardResultsFileReader.hpp include/Statistics.h include/StdDeviation.h include/SubspaceModel.hpp @@ -1593,6 +1826,7 @@ include/config.hpp include/cougaar_levels.hpp include/current_function.hpp include/dak_f90_config.h +include/dakota_bit_utils.hpp include/dakota_c3_include.hpp include/dakota_data_io.hpp include/dakota_data_types.hpp @@ -1607,7 +1841,6 @@ include/dakota_results_types.hpp include/dakota_stat_util.hpp include/dakota_system_defs.hpp include/dakota_tabular_io.hpp -include/dakota_windows.h include/ddace_fortran.h include/decorator_log.hpp include/default_types.hpp @@ -1656,6 +1889,7 @@ include/list_log.hpp include/log4j_levels.hpp include/log_gateways.hpp include/logs.hpp +include/low_discrepancy_data.hpp include/macros.hpp include/math_tools.hpp include/menu.h @@ -1805,6 +2039,7 @@ include/thread_pool.hpp.inl include/threadsafe.hpp include/tinystr.h include/tinyxml.h +include/tolerance_intervals.hpp include/ts_list.hpp include/ts_list.hpp.inl include/ts_map.hpp @@ -1822,6 +2057,7 @@ include/util_data_types.hpp include/util_eigen_plugins.hpp include/util_math_tools.hpp include/util_metrics.hpp +include/util_windows.hpp include/utilib/AbstractHashTable.h include/utilib/AbstractHeap.h include/utilib/AbstractSplayTree.h @@ -1947,6 +2183,8 @@ include/xtndeclare.h include/xtndispatch.h include/xtnset.h lib/cmake/Dakota/DakotaConfig.cmake +lib/cmake/Dakota/DakotaDepends-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/Dakota/DakotaDepends.cmake lib/cmake/Dakota/DakotaTargets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/Dakota/DakotaTargets.cmake lib/cmake/Dakota/DakotaVersion.cmake @@ -2586,6 +2824,15 @@ lib/libutilities.so %%DATADIR%%/Python/dakota/interfacing/interfacing.py %%DATADIR%%/Python/dakota/interfacing/parallel.py %%DATADIR%%/Python/dakota/interfacing/slurm.py +%%DATADIR%%/Python/muq/Approximation/__init__.py +%%DATADIR%%/Python/muq/Inference/__init__.py +%%DATADIR%%/Python/muq/Modeling/__init__.py +%%DATADIR%%/Python/muq/Optimization/__init__.py +%%DATADIR%%/Python/muq/SamplingAlgorithms/__init__.py +%%DATADIR%%/Python/muq/Utilities/__init__.py +%%DATADIR%%/Python/muq/__init__.py +%%DATADIR%%/Python/muq/pymuqModeling/PDEModPiece.py +%%DATADIR%%/Python/muq/pymuqModeling/__init__.py %%DATADIR%%/README %%DATADIR%%/VERSION %%DATADIR%%/examples/hopspack/1-var-bnds-only/example1_params.txthome | help
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