[med-svn] [libbpp-core] 03/06: Merge tag 'upstream/2.2.0'
Andreas Tille
tille at debian.org
Fri Apr 8 20:01:37 UTC 2016
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tille pushed a commit to branch master
in repository libbpp-core.
commit eb5156a06dabee0a5c19a320698ecf826cdb294a
Merge: cfd17d4 39df58f
Author: Andreas Tille <tille at debian.org>
Date: Fri Apr 8 21:47:20 2016 +0200
Merge tag 'upstream/2.2.0'
Upstream version 2.2.0
CMakeLists.txt | 5 +-
ChangeLog | 13 +
Doxyfile | 2531 ++++++++++++--------
bpp-core.spec | 7 +-
debian/changelog | 7 +
debian/copyright | 6 +-
debian/postinst | 22 +-
debian/postrm | 26 +-
debian/prerm | 22 +-
debian/rules | 4 +-
debian/postinst => genIncludes.sh | 10 +-
src/Bpp/App/ApplicationTools.cpp | 126 +-
src/Bpp/App/ApplicationTools.h | 185 +-
src/Bpp/App/BppApplication.cpp | 11 +-
src/Bpp/App/BppApplication.h | 3 +-
src/Bpp/Exceptions.h | 1 +
src/Bpp/Graph/BasicONode.cpp | 4 +-
src/Bpp/Graph/BasicONode.h | 4 +-
src/Bpp/Graph/BasicTNode.cpp | 22 +-
src/Bpp/Graphics/AbstractGraphicDevice.h | 2 +-
src/Bpp/Graphics/ColorTools.cpp | 33 +-
src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp | 2 +-
src/Bpp/Graphics/Fig/XFigGraphicDevice.h | 2 +-
src/Bpp/Graphics/RgbColor.h | 8 +-
src/Bpp/Io/BppOParametrizableFormat.cpp | 76 +-
src/Bpp/Io/FileTools.cpp | 12 +-
src/Bpp/Io/OutputStream.h | 18 +-
src/Bpp/Numeric/AbstractParameterAliasable.cpp | 128 +-
src/Bpp/Numeric/AbstractParameterAliasable.h | 318 ++-
src/Bpp/Numeric/AbstractParametrizable.h | 17 +-
.../Numeric/AdaptiveKernelDensityEstimation.cpp | 2 +-
src/Bpp/Numeric/Constraints.h | 108 +-
src/Bpp/Numeric/DataTable.cpp | 504 ++--
src/Bpp/Numeric/DataTable.h | 809 ++++---
.../Function/ConjugateGradientMultiDimensions.cpp | 10 +-
.../Function/FivePointsNumericalDerivative.cpp | 35 +-
.../Function/FivePointsNumericalDerivative.h | 149 +-
src/Bpp/Numeric/Function/GoldenSectionSearch.cpp | 8 +-
src/Bpp/Numeric/Function/MetaOptimizer.h | 22 +-
.../Function/OneDimensionOptimizationTools.cpp | 284 +--
.../Function/OneDimensionOptimizationTools.h | 230 +-
.../Function/ReparametrizationFunctionWrapper.cpp | 4 +-
.../Function/ReparametrizationFunctionWrapper.h | 2 +-
.../Function/ThreePointsNumericalDerivative.cpp | 180 +-
.../Function/ThreePointsNumericalDerivative.h | 143 +-
.../Function/TwoPointsNumericalDerivative.cpp | 32 +-
.../Function/TwoPointsNumericalDerivative.h | 150 +-
.../Hmm/AbstractHmmTransitionMatrix.cpp} | 60 +-
src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h | 108 +
.../Hmm/AutoCorrelationTransitionMatrix.cpp | 113 +
.../Numeric/Hmm/AutoCorrelationTransitionMatrix.h | 118 +
src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp | 155 ++
src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h | 130 +
src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h | 133 +-
src/Bpp/Numeric/Hmm/HmmLikelihood.cpp | 90 +
src/Bpp/Numeric/Hmm/HmmLikelihood.h | 224 +-
src/Bpp/Numeric/Hmm/HmmStateAlphabet.h | 140 +-
src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h | 73 +-
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp | 325 ++-
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h | 325 ++-
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp | 7 +-
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h | 41 +-
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp | 298 ++-
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h | 324 ++-
src/Bpp/Numeric/Matrix/EigenValue.h | 364 +--
src/Bpp/Numeric/Matrix/Matrix.h | 114 +-
src/Bpp/Numeric/Matrix/MatrixTools.h | 2032 ++++++++--------
src/Bpp/Numeric/NumConstants.h | 2 +-
src/Bpp/Numeric/Number.h | 144 +-
src/Bpp/Numeric/Parameter.h | 1 -
src/Bpp/Numeric/ParameterAliasable.h | 118 +-
src/Bpp/Numeric/ParameterList.cpp | 66 +-
src/Bpp/Numeric/ParameterList.h | 21 +-
src/Bpp/Numeric/ParametrizableCollection.h | 356 +++
.../Numeric/Prob/AbstractDiscreteDistribution.cpp | 4 +-
src/Bpp/Numeric/Prob/ConstantDistribution.cpp | 12 +-
src/Bpp/Numeric/Prob/ConstantDistribution.h | 3 +-
.../Prob/InvariantMixedDiscreteDistribution.h | 256 +-
.../Numeric/Prob/SimpleDiscreteDistribution.cpp | 4 +-
src/Bpp/Numeric/Prob/Simplex.cpp | 165 +-
src/Bpp/Numeric/Prob/Simplex.h | 140 +-
src/Bpp/Numeric/Random/RandomTools.cpp | 9 +-
src/Bpp/Numeric/Random/RandomTools.h | 21 +-
src/Bpp/Numeric/Range.h | 4 +-
src/Bpp/Numeric/TransformedParameter.h | 12 +-
src/Bpp/Numeric/VectorTools.h | 1 +
src/Bpp/Text/KeyvalTools.cpp | 2 +
src/Bpp/Text/NestedStringTokenizer.cpp | 110 +-
src/Bpp/Text/NestedStringTokenizer.h | 116 +-
src/Bpp/Text/StringTokenizer.cpp | 2 +-
src/Bpp/Text/StringTokenizer.h | 160 +-
src/Bpp/Text/TextTools.cpp | 29 +-
src/Bpp/Text/TextTools.h | 7 +-
src/Bpp/Utils/AttributesTools.cpp | 229 +-
src/Bpp/Utils/AttributesTools.h | 304 ++-
src/CMakeLists.txt | 8 +
test/CMakeLists.txt | 12 +-
test/test_derivative1.cpp | 12 +-
test/test_reparametrization.cpp | 98 +
test/test_simplex.cpp | 117 +
100 files changed, 8945 insertions(+), 5071 deletions(-)
diff --cc debian/changelog
index b7a106d,d84c97f..e501bc5
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,11 -1,11 +1,18 @@@
-libbpp-core (2.2.0-1) unstable; urgency=low
+libbpp-core (2.1.0-2) UNRELEASED; urgency=medium
++ [ Andreas Tille ]
+ * Moved to Debian Med Git
+ * Better description
+ * Team maintenance in Debian Med team
+ * wrote watch file
+
++ [ Julien Dutheil ]
+ * Reparametrization wrapper debugged
+ * Improved and rationalized display of warning messages
+ * Possibility to set random seed in applications
+ * Code checked for compilation with CLang.
+
- -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Wed, 17 Sep 2014 14:00:00 +0100
+ -- Andreas Tille <tille at debian.org> Thu, 07 Apr 2016 09:19:57 +0200
libbpp-core (2.1.0-1) unstable; urgency=low
--
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