[med-svn] [libbpp-phyl] 03/03: DEP3
Andreas Tille
tille at debian.org
Fri Aug 25 12:04:15 UTC 2017
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tille pushed a commit to tag debian/2.3.1-10
in repository libbpp-phyl.
commit c8a90afef78be745275feb7e291006f702702037
Author: Andreas Tille <tille at debian.org>
Date: Wed Aug 23 23:55:44 2017 +0200
DEP3
---
debian/patches/remove_deprecated_warnings.patch | 22 +++++++---------------
debian/patches/test_likelihood_clock.patch | 14 ++++++++------
debian/patches/test_mapping.patch | 4 ++++
3 files changed, 19 insertions(+), 21 deletions(-)
diff --git a/debian/patches/remove_deprecated_warnings.patch b/debian/patches/remove_deprecated_warnings.patch
index d8f89f3..9809bb7 100644
--- a/debian/patches/remove_deprecated_warnings.patch
+++ b/debian/patches/remove_deprecated_warnings.patch
@@ -1,8 +1,10 @@
-diff --git a/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h b/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
-index cc1b85a..1bf7a5b 100644
+Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
+Date: Sun Jul 16 10:45:20 2017 +0200
+Description: Remove deprecated warnings
+
--- a/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
+++ b/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
-@@ -74,7 +74,7 @@ class AbstractNonHomogeneousTreeLikelihood:
+@@ -74,7 +74,7 @@ class AbstractNonHomogeneousTreeLikeliho
siteModelDescriptions_(), index_(0), nbModels_(modelSet->getNumberOfModels())
{
for (size_t i = 0; i < nbModels_; ++i)
@@ -11,11 +13,9 @@ index cc1b85a..1bf7a5b 100644
}
public:
-diff --git a/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp b/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
-index dafd301..ccf34e8 100644
--- a/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
+++ b/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
-@@ -142,7 +142,7 @@ void DRNonHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (
+@@ -142,7 +142,7 @@ void DRNonHomogeneousTreeLikelihood::set
data_ = PatternTools::getSequenceSubset(sites, *tree_->getRootNode());
if (verbose_)
ApplicationTools::displayTask("Initializing data structure");
@@ -24,11 +24,9 @@ index dafd301..ccf34e8 100644
// Which is a reasonable assumption as long as they share the same alphabet.
if (verbose_)
ApplicationTools::displayTaskDone();
-diff --git a/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp b/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
-index f736bf4..05a4c8c 100644
--- a/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
+++ b/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
-@@ -140,7 +140,7 @@ void RNonHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (E
+@@ -140,7 +140,7 @@ void RNonHomogeneousTreeLikelihood::setD
if (data_) delete data_;
data_ = PatternTools::getSequenceSubset(sites, *tree_->getRootNode());
if (verbose_) ApplicationTools::displayTask("Initializing data structure");
@@ -37,8 +35,6 @@ index f736bf4..05a4c8c 100644
//Which is a reasonable assumption as long as they share the same alphabet.
if (verbose_) ApplicationTools::displayTaskDone();
-diff --git a/src/Bpp/Phyl/Model/SubstitutionModelSet.h b/src/Bpp/Phyl/Model/SubstitutionModelSet.h
-index fbb6b3c..97a027b 100644
--- a/src/Bpp/Phyl/Model/SubstitutionModelSet.h
+++ b/src/Bpp/Phyl/Model/SubstitutionModelSet.h
@@ -247,7 +247,6 @@ public:
@@ -49,8 +45,6 @@ index fbb6b3c..97a027b 100644
const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException)
{
std::cerr << "#warning : SubstitutionModelSet::getModel function is deprecated in Bio++ 2.3.0. Replace it with SubstitutionModelSet::getSubstitutionModel." << std::endl;
-diff --git a/test/test_likelihood_nh.cpp b/test/test_likelihood_nh.cpp
-index b4cd485..1486b80 100644
--- a/test/test_likelihood_nh.cpp
+++ b/test/test_likelihood_nh.cpp
@@ -129,11 +129,11 @@ int main() {
@@ -69,8 +63,6 @@ index b4cd485..1486b80 100644
}
}
thetasEst1 /= static_cast<double>(nrep);
-diff --git a/test/test_simulations.cpp b/test/test_simulations.cpp
-index fa97a9c..f4fea6c 100644
--- a/test/test_simulations.cpp
+++ b/test/test_simulations.cpp
@@ -104,8 +104,8 @@ int main() {
diff --git a/debian/patches/test_likelihood_clock.patch b/debian/patches/test_likelihood_clock.patch
index 099ac82..7cdbeda 100644
--- a/debian/patches/test_likelihood_clock.patch
+++ b/debian/patches/test_likelihood_clock.patch
@@ -1,8 +1,10 @@
-diff --git a/test/test_likelihood_clock.cpp b/test/test_likelihood_clock.cpp
-index fa70e89..57e6943 100644
+Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
+Date: Sun Jul 16 10:45:20 2017 +0200
+Description: Relax test constraint
+
--- a/test/test_likelihood_clock.cpp
+++ b/test/test_likelihood_clock.cpp
-@@ -41,7 +41,7 @@ knowledge of the CeCILL license and that you accept its terms.
+@@ -41,7 +41,7 @@ knowledge of the CeCILL license and that
#include <Bpp/Seq/Alphabet/AlphabetTools.h>
#include <Bpp/Phyl/TreeTemplate.h>
#include <Bpp/Phyl/Model/Nucleotide/T92.h>
@@ -11,7 +13,7 @@ index fa70e89..57e6943 100644
#include <Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h>
#include <Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h>
#include <Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h>
-@@ -60,7 +60,7 @@ void fitModelH(SubstitutionModel* model, DiscreteDistribution* rdist, const Tree
+@@ -60,7 +60,7 @@ void fitModelH(SubstitutionModel* model,
ApplicationTools::displayResult("Test model", model->getName());
cout << setprecision(20) << tl.getValue() << endl;
ApplicationTools::displayResult("* initial likelihood", tl.getValue());
@@ -20,7 +22,7 @@ index fa70e89..57e6943 100644
throw Exception("Incorrect initial value.");
unique_ptr<OutputStream> messenger(new StlOutputStream(new ofstream("messages.txt", ios::out)));
unique_ptr<OutputStream> profiler(new StlOutputStream(new ofstream("profile.txt", ios::out)));
-@@ -69,7 +69,7 @@ void fitModelH(SubstitutionModel* model, DiscreteDistribution* rdist, const Tree
+@@ -69,7 +69,7 @@ void fitModelH(SubstitutionModel* model,
cout << setprecision(20) << tl.getValue() << endl;
ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue());
tl.getParameters().printParameters(cout);
@@ -29,7 +31,7 @@ index fa70e89..57e6943 100644
throw Exception("Incorrect final value.");
}
-@@ -92,7 +92,7 @@ void fitModelHClock(SubstitutionModel* model, DiscreteDistribution* rdist, const
+@@ -92,7 +92,7 @@ void fitModelHClock(SubstitutionModel* m
ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue());
tl.getParameters().printParameters(cout);
if (abs(tl.getValue() - finalValue) > 0.001)
diff --git a/debian/patches/test_mapping.patch b/debian/patches/test_mapping.patch
index 6da90ee..bd9f283 100644
--- a/debian/patches/test_mapping.patch
+++ b/debian/patches/test_mapping.patch
@@ -1,3 +1,7 @@
+Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
+Date: Sun Jul 16 10:45:20 2017 +0200
+Description: More sensible tests
+
--- a/test/test_mapping.cpp
+++ b/test/test_mapping.cpp
@@ -64,7 +64,8 @@ using namespace bpp;
--
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