[med-svn] [Git][med-team/libbpp-phyl][master] 3 commits: New upstream version 2.4.1
Julien Y. Dutheil
gitlab at salsa.debian.org
Wed Aug 22 08:02:35 BST 2018
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl
Commits:
2d1077e7 by Julien Y. Dutheil at 2018-08-19T11:47:42Z
New upstream version 2.4.1
- - - - -
8727075f by Julien Y. Dutheil at 2018-08-19T11:47:45Z
Update upstream source from tag 'upstream/2.4.1'
Update to upstream version '2.4.1'
with Debian dir 5c4293258dee322f426609b9bfc198cd23ca79cd
- - - - -
4cd41b77 by Julien Y. Dutheil at 2018-08-19T21:15:15Z
Version 2.4.1.
Adresses: #906478
- - - - -
16 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-phyl.spec
- debian/changelog
- debian/control
- debian/libbpp-phyl12.symbols
- debian/patches/increase_test_tolerance.patch
- src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp
- src/Bpp/Phyl/Io/IoTree.h
- src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
- src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp
- src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h
- src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h
- src/Bpp/Phyl/Model/SubstitutionModelSet.h
- src/Bpp/Phyl/TreeTemplateTools.cpp
- test/test_likelihood_nh.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-phyl")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogenetics library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=====================================
Doxyfile
=====================================
--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-phyl
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 2.4.0
+PROJECT_NUMBER = 2.4.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
=====================================
bpp-phyl.spec
=====================================
--- a/bpp-phyl.spec
+++ b/bpp-phyl.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bpp-phyl
Name: bpp-phyl
-Version: 1.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -85,6 +85,8 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/include/*
%changelog
+* Mon Aug 13 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.4.1-1
+- Compatibility update gcc8
* Mon Mar 12 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.4.0-1
- Increased interface number
- Removed dynamic exceptions specifications.
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+libbpp-phyl (2.4.1-1) UNRELEASED; urgency=medium
+
+ * New upstream update.
+ * Ref: #906478
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Sun, 19 Aug 2018 21:36:23 +0200
+
libbpp-phyl (2.4.0-2) unstable; urgency=medium
[ Julien Dutheil ]
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper (>= 11~),
cmake,
d-shlibs (>= 0.82),
- libbpp-seq-dev (>= 2.4.0)
+ libbpp-seq-dev (>= 2.4.1)
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/libbpp-phyl
Vcs-Git: https://salsa.debian.org/med-team/libbpp-phyl.git
@@ -18,7 +18,7 @@ Architecture: any
Section: libdevel
Depends: libbpp-phyl12 (= ${binary:Version}),
${misc:Depends},
- libbpp-seq-dev (>= 2.4.0)
+ libbpp-seq-dev (>= 2.4.1)
Description: Bio++ Phylogenetic library development files
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.
=====================================
debian/libbpp-phyl12.symbols
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/patches/increase_test_tolerance.patch
=====================================
--- a/debian/patches/increase_test_tolerance.patch
+++ b/debian/patches/increase_test_tolerance.patch
@@ -25,34 +25,3 @@ index b4cd485..c38a277 100644
throw Exception("Incorrect final value.");
}
-@@ -89,14 +89,14 @@ int main() {
- DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);
-
- size_t nsites = 1000;
-- unsigned int nrep = 20;
-+ unsigned int nrep = 5;
- size_t nmodels = modelSet->getNumberOfModels();
- vector<double> thetas(nmodels);
- vector<double> thetasEst1(nmodels);
- vector<double> thetasEst2(nmodels);
-
- for (size_t i = 0; i < nmodels; ++i) {
-- double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.99) + 0.005;
-+ double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.9) + 0.05;
- cout << "Theta" << i << " set to " << theta << endl;
- modelSet->setParameterValue("T92.theta_" + TextTools::toString(i + 1), theta);
- thetas[i] = theta;
-@@ -119,11 +119,11 @@ int main() {
- tl2.initialize();
-
- unsigned int c1 = OptimizationTools::optimizeNumericalParameters2(
-- &tl, tl.getParameters(), 0,
-+ &tl, tl.getSubstitutionModelParameters(), 0,
- 0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
-
- unsigned int c2 = OptimizationTools::optimizeNumericalParameters2(
-- &tl2, tl2.getParameters(), 0,
-+ &tl2, tl2.getSubstitutionModelParameters(), 0,
- 0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
-
- cout << c1 << ": " << tl.getValue() << "\t" << c2 << ": " << tl2.getValue() << endl;
=====================================
src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp
=====================================
--- a/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp
+++ b/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp
@@ -138,13 +138,14 @@ TransitionModel* BppOTransitionModelFormat::readTransitionModel(
}
delete nestedModel;
+
+ // update only for transition models
+ updateParameters_(model.get(), args);
+ if (parseArguments)
+ initialize_(*model, data);
}
else
model.reset(BppOSubstitutionModelFormat::read(alphabet, modelDescription, data, parseArguments));
- updateParameters_(model.get(), args);
- if (parseArguments)
- initialize_(*model, data);
-
return model.release();
}
=====================================
src/Bpp/Phyl/Io/IoTree.h
=====================================
--- a/src/Bpp/Phyl/Io/IoTree.h
+++ b/src/Bpp/Phyl/Io/IoTree.h
@@ -5,7 +5,7 @@
//
/*
-Copyright or © or Copr. CNRS, (November 16, 2004)
+Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.
@@ -170,7 +170,7 @@ class AbstractOTree:
write(tree, output);
output.close();
}
- catch (IOException e)
+ catch (IOException& e)
{
std::stringstream ss ;
ss << e.what() <<"\nProblem writing tree to file "<< path <<"\n Is the file path correct and do \
=====================================
src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
=====================================
--- a/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
+++ b/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
@@ -138,7 +138,7 @@ void DRASRTreeLikelihoodData::initLikelihoods(const Node* node, const SiteContai
{
seq = &sequences.getSequence(node->getName());
}
- catch (SequenceNotFoundException snfe)
+ catch (SequenceNotFoundException& snfe)
{
throw SequenceNotFoundException("DRASRTreeLikelihoodData::initTreelikelihoods. Leaf name in tree not found in site conainer: ", (node->getName()));
}
@@ -241,7 +241,7 @@ SitePatterns* DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(const Node* n
{
seq = &subSequences->getSequence(node->getName());
}
- catch (SequenceNotFoundException snfe)
+ catch (SequenceNotFoundException& snfe)
{
throw SequenceNotFoundException("HomogeneousTreeLikelihood::initTreelikelihoodsWithPatterns. Leaf name in tree not found in site conainer: ", (node->getName()));
}
=====================================
src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp
=====================================
--- a/src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp
+++ b/src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp
@@ -36,19 +36,23 @@
knowledge of the CeCILL license and that you accept its terms.
*/
-# include "AbstractCodonAAFitnessSubstitutionModel.h"
+#include "AbstractCodonAAFitnessSubstitutionModel.h"
+
+#include <Bpp/Seq/Alphabet/AlphabetTools.h>
+
using namespace bpp;
using namespace std;
+
/****************************************************************************************/
+
AbstractCodonAAFitnessSubstitutionModel::AbstractCodonAAFitnessSubstitutionModel(FrequenciesSet* pfitset, const GeneticCode* pgencode, const string& prefix):
- AbstractParameterAliasable(prefix), pfitset_(pfitset), pgencode_(pgencode), fitName_("")
+ AbstractParameterAliasable(prefix), pfitset_(pfitset), pgencode_(pgencode), fitName_(""), stateMap_(&pfitset->getStateMap())
{
- if (pfitset_->getAlphabet()->getAlphabetType()!="Proteic")
+ if (!AlphabetTools::isProteicAlphabet(pfitset_->getAlphabet()))
throw Exception("AbstractCodonAAFitnessSubstitutionModel::AbstractCodonAAFitnessSubstitutionModel need Proteic Fitness.");
- fitName_="fit_"+ pfitset_->getNamespace();
+ fitName_ = "fit_" + pfitset_->getNamespace();
pfitset_->setNamespace(prefix + fitName_);
- stateMap_=&pfitset_->getStateMap();
addParameters_(pfitset_->getParameters());
}
=====================================
src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h
=====================================
--- a/src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h
+++ b/src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h
@@ -90,7 +90,6 @@ namespace bpp
* @param pmodel shared_ptr to an amino_acid generator
* @param pgencode the genetic code
* @param prefix the Namespace
- * @param statemap the statemap
* @param paramSynRate is true iff synonymous rate is parameterised
* (default=false).
*/
=====================================
src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h
=====================================
--- a/src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h
+++ b/src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h
@@ -93,7 +93,6 @@ namespace bpp
*
* @param pgencode the genetic code
* @param prefix the Namespace
- * @param statemap the statemap
*/
AbstractCodonBGCSubstitutionModel(
const GeneticCode* pgencode,
=====================================
src/Bpp/Phyl/Model/SubstitutionModelSet.h
=====================================
--- a/src/Bpp/Phyl/Model/SubstitutionModelSet.h
+++ b/src/Bpp/Phyl/Model/SubstitutionModelSet.h
@@ -269,7 +269,7 @@ public:
{
try
{
- return dynamic_cast<const SubstitutionModel*>(getModel(i));
+ return &dynamic_cast<const SubstitutionModel&>(*getModel(i));
}
catch (std::bad_cast& bc)
{
@@ -282,7 +282,7 @@ public:
{
try
{
- return dynamic_cast<SubstitutionModel*>(getModel(i));
+ return &dynamic_cast<SubstitutionModel&>(*getModel(i));
}
catch (std::bad_cast& bc)
{
=====================================
src/Bpp/Phyl/TreeTemplateTools.cpp
=====================================
--- a/src/Bpp/Phyl/TreeTemplateTools.cpp
+++ b/src/Bpp/Phyl/TreeTemplateTools.cpp
@@ -241,7 +241,7 @@ TreeTemplateTools::Element TreeTemplateTools::getElement(const string& elt)
}
}
}
- catch (exception e)
+ catch (exception& e)
{
throw IOException("Bad tree description: " + elt);
}
=====================================
test/test_likelihood_nh.cpp
=====================================
--- a/test/test_likelihood_nh.cpp
+++ b/test/test_likelihood_nh.cpp
@@ -89,14 +89,14 @@ int main() {
DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);
size_t nsites = 1000;
- unsigned int nrep = 20;
+ unsigned int nrep = 3;
size_t nmodels = modelSet->getNumberOfModels();
vector<double> thetas(nmodels);
vector<double> thetasEst1(nmodels);
vector<double> thetasEst2(nmodels);
for (size_t i = 0; i < nmodels; ++i) {
- double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.99) + 0.005;
+ double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.9) + 0.05;
cout << "Theta" << i << " set to " << theta << endl;
modelSet->setParameterValue("T92.theta_" + TextTools::toString(i + 1), theta);
thetas[i] = theta;
@@ -119,11 +119,11 @@ int main() {
tl2.initialize();
unsigned int c1 = OptimizationTools::optimizeNumericalParameters2(
- &tl, tl.getParameters(), 0,
+ &tl, tl.getSubstitutionModelParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
unsigned int c2 = OptimizationTools::optimizeNumericalParameters2(
- &tl2, tl2.getParameters(), 0,
+ &tl2, tl2.getSubstitutionModelParameters(), 0,
0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);
cout << c1 << ": " << tl.getValue() << "\t" << c2 << ": " << tl2.getValue() << endl;
View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/compare/1758b136bedd42110dcc4e27c7938ae5d511223e...4cd41b77b3ad9393a60b72e546099dc60b441f57
--
View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/compare/1758b136bedd42110dcc4e27c7938ae5d511223e...4cd41b77b3ad9393a60b72e546099dc60b441f57
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