[med-svn] [libbpp-core] branch upstream updated (39df58f -> d1b9141)
Andreas Tille
tille at debian.org
Thu Jun 1 14:03:22 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository libbpp-core.
from 39df58f Imported Upstream version 2.2.0
new d1b9141 New upstream version 2.3.0
The 1 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 | 46 -
debian/compat | 1 -
debian/control | 22 -
debian/copyright | 74 --
debian/docs | 0
debian/libbpp-core-dev.install | 3 -
debian/libbpp-core2.install | 1 -
debian/postinst | 57 -
debian/postrm | 59 -
debian/prerm | 41 -
debian/rules | 122 --
debian/source/format | 1 -
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 +++
129 files changed, 12714 insertions(+), 3605 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 100644 debian/changelog
delete mode 100644 debian/compat
delete mode 100644 debian/control
delete mode 100644 debian/copyright
delete mode 100644 debian/docs
delete mode 100644 debian/libbpp-core-dev.install
delete mode 100644 debian/libbpp-core2.install
delete mode 100755 debian/postinst
delete mode 100755 debian/postrm
delete mode 100755 debian/prerm
delete mode 100755 debian/rules
delete mode 100644 debian/source/format
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
More information about the debian-med-commit
mailing list