This is an automated email from the git hooks/post-receive script. tille pushed a change to branch master in repository libbpp-core.
from 78725db Upload to unstable new 1c707a8 Point to Github new 68716b5 New upstream version new d1b9141 New upstream version 2.3.0 new ed3f251 Updated version 2.3.0 from 'upstream/2.3.0' new c3362aa Update patches The 5 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: .gitignore | 15 + AUTHORS.txt | 3 + CMakeLists.txt | 137 +- CTestConfig.cmake | 13 + ChangeLog | 8 + Doxyfile | 420 +++--- INSTALL.txt | 19 +- bpp-core.spec | 104 +- cmake/doc-cmake-for-developpers.cmake | 240 ++++ cmake/project-template-for-users.cmake | 106 ++ debian/changelog | 7 + debian/patches/gcc-6.patch | 4 +- debian/patches/unforce-cxxflags.patch | 18 +- debian/watch | 5 +- genIncludes.sh | 35 - package.cmake.in | 25 + src/Bpp/App/ApplicationTools.cpp | 39 - src/Bpp/App/ApplicationTools.h | 41 +- src/Bpp/App/NumCalcApplicationTools.cpp | 1 + src/Bpp/BppBoolean.h | 7 +- src/Bpp/BppString.h | 7 +- src/Bpp/BppVector.h | 7 +- src/Bpp/Clonable.h | 32 +- src/Bpp/Exceptions.cpp | 6 - src/Bpp/Exceptions.h | 7 +- src/Bpp/Graph/AssociationDAGraphImplObserver.h | 406 ++++++ src/Bpp/Graph/AssociationDAGraphObserver.h | 256 ++++ src/Bpp/Graph/AssociationGraphImplObserver.h | 1332 ++++++++++++++++++++ src/Bpp/Graph/AssociationGraphObserver.h | 483 +++++++ src/Bpp/Graph/AssociationTreeGraphImplObserver.h | 397 ++++++ src/Bpp/Graph/AssociationTreeGraphObserver.h | 255 ++++ src/Bpp/Graph/BasicONode.h | 61 - src/Bpp/Graph/BasicTNode.cpp | 208 --- src/Bpp/Graph/BasicTNode.h | 160 --- src/Bpp/Graph/DAGraph.h | 174 +++ src/Bpp/Graph/DAGraphImpl.h | 525 ++++++++ src/Bpp/Graph/GlobalGraph.cpp | 990 +++++++++++++++ src/Bpp/Graph/GlobalGraph.h | 956 ++++++++++++++ src/Bpp/Graph/Graph.h | 582 +++++++++ .../GraphObserver.h} | 80 +- src/Bpp/Graph/ONode.h | 170 --- src/Bpp/Graph/TNode.h | 129 -- src/Bpp/Graph/TreeGraph.h | 201 +++ src/Bpp/Graph/TreeGraphImpl.h | 593 +++++++++ src/Bpp/Graph/UNode.h | 123 -- src/Bpp/Graphics/Font/Font.h | 7 +- src/Bpp/Graphics/Font/FontManager.h | 1 + src/Bpp/Graphics/RgbColor.h | 7 +- src/Bpp/Io/BppODiscreteDistributionFormat.cpp | 19 +- src/Bpp/Io/OutputStream.h | 10 +- src/Bpp/Numeric/AbstractParameterAliasable.cpp | 206 ++- src/Bpp/Numeric/AbstractParameterAliasable.h | 443 +++---- src/Bpp/Numeric/AbstractParametrizable.h | 95 +- src/Bpp/Numeric/AutoParameter.cpp | 134 +- src/Bpp/Numeric/DataTable.h | 3 +- src/Bpp/Numeric/DataTableExceptions.h | 175 --- .../Numeric/Function/AbstractNumericalDerivative.h | 51 +- src/Bpp/Numeric/Function/BrentOneDimension.cpp | 2 + .../Function/ConjugateGradientMultiDimensions.cpp | 6 + src/Bpp/Numeric/Function/DownhillSimplexMethod.h | 7 +- src/Bpp/Numeric/Function/Functions.h | 22 +- src/Bpp/Numeric/Function/MetaOptimizer.h | 4 - .../Function/OneDimensionOptimizationTools.cpp | 8 + .../Numeric/Function/Operators/BinaryOperator.h | 168 +++ .../Numeric/Function/Operators/ComputationTree.cpp | 213 ++++ .../Numeric/Function/Operators/ComputationTree.h | 113 ++ .../Operators/ConstantOperator.h} | 73 +- .../Numeric/Function/Operators/FunctionOperator.h | 133 ++ src/Bpp/Numeric/Function/Operators/MathOperator.h | 138 ++ .../StatTest.h => Function/Operators/Operator.h} | 46 +- .../Numeric/Function/OptimizationStopCondition.h | 14 +- src/Bpp/Numeric/Function/Optimizer.h | 4 - .../Function/ReparametrizationFunctionWrapper.h | 12 - .../Function/ThreePointsNumericalDerivative.cpp | 6 +- .../Numeric/Hmm/AbstractHmmTransitionMatrix.cpp | 45 + src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h | 12 + .../Hmm/AutoCorrelationTransitionMatrix.cpp | 2 +- src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp | 19 +- src/Bpp/Numeric/Hmm/HmmLikelihood.h | 9 +- src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp | 165 ++- src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h | 139 +- .../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp | 9 + .../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h | 39 +- src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp | 68 +- src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h | 25 +- src/Bpp/Numeric/Matrix/Matrix.h | 9 +- src/Bpp/Numeric/Matrix/MatrixTools.h | 211 ++-- src/Bpp/Numeric/Number.h | 1 + src/Bpp/Numeric/Parameter.h | 21 +- src/Bpp/Numeric/ParameterAliasable.h | 10 +- src/Bpp/Numeric/ParameterList.cpp | 158 ++- src/Bpp/Numeric/ParameterList.h | 52 +- src/Bpp/Numeric/ParametrizableCollection.h | 26 + src/Bpp/Numeric/Prob/DiscreteDistribution.h | 2 - src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp | 18 +- src/Bpp/Numeric/Prob/GammaDiscreteDistribution.h | 17 +- .../Numeric/Prob/MixtureOfDiscreteDistributions.h | 4 - .../Numeric/Prob/MultipleDiscreteDistribution.h | 2 - src/Bpp/Numeric/Prob/Simplex.cpp | 6 +- src/Bpp/Numeric/Prob/Simplex.h | 7 +- src/Bpp/Numeric/Random/RandomTools.cpp | 19 - src/Bpp/Numeric/Random/RandomTools.h | 15 +- src/Bpp/Numeric/Range.h | 24 + src/Bpp/Numeric/Stat/ContingencyTableTest.h | 7 +- src/Bpp/Numeric/Stat/Mva/CorrespondenceAnalysis.h | 11 +- src/Bpp/Numeric/Stat/Mva/DualityDiagram.h | 7 +- src/Bpp/Numeric/Table.h | 1222 ++++++++++++++++++ src/Bpp/Numeric/TableExceptions.h | 175 +++ src/Bpp/Numeric/VectorTools.h | 95 +- src/Bpp/Text/KeyvalTools.cpp | 76 +- src/Bpp/Text/KeyvalTools.h | 23 +- src/Bpp/Text/StringTokenizer.cpp | 6 - src/Bpp/Text/StringTokenizer.h | 6 +- src/Bpp/Text/TextTools.cpp | 18 +- src/Bpp/Text/TextTools.h | 762 +++++------ src/Bpp/{Graph/BasicONode.cpp => Version.h} | 19 +- src/CMakeLists.txt | 257 +--- test/CMakeLists.txt | 120 +- test/test_dAGraphObs.cpp | 159 +++ test/test_graphObs.cpp | 144 +++ test/test_treeGraphObs.cpp | 178 +++ 121 files changed, 12735 insertions(+), 3191 deletions(-) create mode 100644 .gitignore create mode 100644 CTestConfig.cmake create mode 100644 cmake/doc-cmake-for-developpers.cmake create mode 100644 cmake/project-template-for-users.cmake delete mode 100755 genIncludes.sh create mode 100644 package.cmake.in create mode 100644 src/Bpp/Graph/AssociationDAGraphImplObserver.h create mode 100644 src/Bpp/Graph/AssociationDAGraphObserver.h create mode 100644 src/Bpp/Graph/AssociationGraphImplObserver.h create mode 100644 src/Bpp/Graph/AssociationGraphObserver.h create mode 100644 src/Bpp/Graph/AssociationTreeGraphImplObserver.h create mode 100644 src/Bpp/Graph/AssociationTreeGraphObserver.h delete mode 100644 src/Bpp/Graph/BasicONode.h delete mode 100644 src/Bpp/Graph/BasicTNode.cpp delete mode 100644 src/Bpp/Graph/BasicTNode.h create mode 100644 src/Bpp/Graph/DAGraph.h create mode 100644 src/Bpp/Graph/DAGraphImpl.h create mode 100644 src/Bpp/Graph/GlobalGraph.cpp create mode 100644 src/Bpp/Graph/GlobalGraph.h create mode 100644 src/Bpp/Graph/Graph.h copy src/Bpp/{Numeric/Prob/ExponentialDiscreteDistribution.cpp => Graph/GraphObserver.h} (53%) delete mode 100644 src/Bpp/Graph/ONode.h delete mode 100644 src/Bpp/Graph/TNode.h create mode 100644 src/Bpp/Graph/TreeGraph.h create mode 100644 src/Bpp/Graph/TreeGraphImpl.h delete mode 100644 src/Bpp/Graph/UNode.h delete mode 100644 src/Bpp/Numeric/DataTableExceptions.h create mode 100644 src/Bpp/Numeric/Function/Operators/BinaryOperator.h create mode 100644 src/Bpp/Numeric/Function/Operators/ComputationTree.cpp create mode 100644 src/Bpp/Numeric/Function/Operators/ComputationTree.h copy src/Bpp/Numeric/{Stat/StatTest.h => Function/Operators/ConstantOperator.h} (63%) create mode 100644 src/Bpp/Numeric/Function/Operators/FunctionOperator.h create mode 100644 src/Bpp/Numeric/Function/Operators/MathOperator.h copy src/Bpp/Numeric/{Stat/StatTest.h => Function/Operators/Operator.h} (72%) create mode 100644 src/Bpp/Numeric/Table.h create mode 100644 src/Bpp/Numeric/TableExceptions.h rename src/Bpp/{Graph/BasicONode.cpp => Version.h} (86%) create mode 100644 test/test_dAGraphObs.cpp create mode 100644 test/test_graphObs.cpp create mode 100644 test/test_treeGraphObs.cpp -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-core.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit