[med-svn] [libbpp-core] branch master updated (78725db -> c3362aa)
Andreas Tille
tille at debian.org
Thu Jun 1 14:03:21 UTC 2017
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
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