[med-svn] [libbpp-phyl] 01/01: Patches improvements

[Julien Dutheil]

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jdutheil-guest pushed a commit to branch master
in repository libbpp-phyl.

commit 8bf832167dd7028ebdd698553b66f9e90bb37369
Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
Date:   Sun Jul 16 10:45:20 2017 +0200

    Patches improvements
    
    Still trying to get test_likelihood_clock passing on mips arch.
    Merged two patches that were somehow conflicting.
---
 debian/changelog                                   |  6 ++++++
 ...hreshold-for-application-to-a-broader-ran.patch | 22 ---------------------
 debian/patches/series                              |  1 -
 debian/patches/test_likelihood_clock.patch         | 23 +++++++++++++++-------
 debian/patches/test_mapping.patch                  |  2 --
 5 files changed, 22 insertions(+), 32 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 45a2971..2c699b5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+libbpp-phyl (2.3.1-8) unstable; urgency=medium
+
+  * another try to have test_likelihood_clock pass on mips architecture.
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr>  Sun, 16 Jul 2017 10:43:18 +0200
+
 libbpp-phyl (2.3.1-7) unstable; urgency=medium
 
   * Some tests redesign.
diff --git a/debian/patches/0001-Decreased-threshold-for-application-to-a-broader-ran.patch b/debian/patches/0001-Decreased-threshold-for-application-to-a-broader-ran.patch
deleted file mode 100644
index 9f46d12..0000000
--- a/debian/patches/0001-Decreased-threshold-for-application-to-a-broader-ran.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/test/test_likelihood_clock.cpp b/test/test_likelihood_clock.cpp
-index fa70e89..03f6f74 100644
---- a/test/test_likelihood_clock.cpp
-+++ b/test/test_likelihood_clock.cpp
-@@ -60,7 +60,7 @@ void fitModelH(SubstitutionModel* model, DiscreteDistribution* rdist, const Tree
-   ApplicationTools::displayResult("Test model", model->getName());
-   cout << setprecision(20) << tl.getValue() << endl;
-   ApplicationTools::displayResult("* initial likelihood", tl.getValue());
--  if (abs(tl.getValue() - initialValue) > 0.0001)
-+  if (abs(tl.getValue() - initialValue) > 0.001)
-     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
-   cout << setprecision(20) << tl.getValue() << endl;
-   ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue());
-   tl.getParameters().printParameters(cout);
--  if (abs(tl.getValue() - finalValue) > 0.0001)
-+  if (abs(tl.getValue() - finalValue) > 0.001)
-     throw Exception("Incorrect final value.");
- }
- 
diff --git a/debian/patches/series b/debian/patches/series
index 4c27f7d..95e0b27 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,4 @@
 relax_test_timeout.patch
-0001-Decreased-threshold-for-application-to-a-broader-ran.patch
 0002-Fixed-unit-tests-compilation-on-some-platforms.patch
 remove_deprecated_warnings.patch
 test_likelihood_clock.patch
diff --git a/debian/patches/test_likelihood_clock.patch b/debian/patches/test_likelihood_clock.patch
index 8d3ba01..099ac82 100644
--- a/debian/patches/test_likelihood_clock.patch
+++ b/debian/patches/test_likelihood_clock.patch
@@ -1,6 +1,8 @@
+diff --git a/test/test_likelihood_clock.cpp b/test/test_likelihood_clock.cpp
+index fa70e89..57e6943 100644
 --- a/test/test_likelihood_clock.cpp
 +++ b/test/test_likelihood_clock.cpp
-@@ -41,7 +41,7 @@ knowledge of the CeCILL license and that
+@@ -41,7 +41,7 @@ knowledge of the CeCILL license and that you accept its terms.
  #include <Bpp/Seq/Alphabet/AlphabetTools.h>
  #include <Bpp/Phyl/TreeTemplate.h>
  #include <Bpp/Phyl/Model/Nucleotide/T92.h>
@@ -9,22 +11,29 @@
  #include <Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h>
  #include <Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h>
  #include <Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h>
-@@ -82,7 +82,7 @@ void fitModelHClock(SubstitutionModel* m
+@@ -60,7 +60,7 @@ void fitModelH(SubstitutionModel* model, DiscreteDistribution* rdist, const Tree
    ApplicationTools::displayResult("Test model", model->getName());
    cout << setprecision(20) << tl.getValue() << endl;
    ApplicationTools::displayResult("* initial likelihood", tl.getValue());
--  if (abs(tl.getValue() - initialValue) > 0.001)
-+  if (abs(tl.getValue() - initialValue) > 0.0001)
+-  if (abs(tl.getValue() - initialValue) > 0.0001)
++  if (abs(tl.getValue() - initialValue) > 0.001)
      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)));
-@@ -91,8 +91,8 @@ void fitModelHClock(SubstitutionModel* m
+@@ -69,7 +69,7 @@ void fitModelH(SubstitutionModel* model, DiscreteDistribution* rdist, const Tree
    cout << setprecision(20) << tl.getValue() << endl;
    ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue());
    tl.getParameters().printParameters(cout);
--  if (abs(tl.getValue() - finalValue) > 0.001)
+-  if (abs(tl.getValue() - finalValue) > 0.0001)
++  if (abs(tl.getValue() - finalValue) > 0.001)
+     throw Exception("Incorrect final value.");
+ }
+ 
+@@ -92,7 +92,7 @@ void fitModelHClock(SubstitutionModel* model, DiscreteDistribution* rdist, const
+   ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue());
+   tl.getParameters().printParameters(cout);
+   if (abs(tl.getValue() - finalValue) > 0.001)
 -    throw Exception("Incorrect final value.");
-+  if (abs(tl.getValue() - finalValue) > 0.0001)
 +    throw Exception("Incorrect final value:" + TextTools::toString(tl.getValue()) + "<>" + TextTools::toString(finalValue));
  }
  
diff --git a/debian/patches/test_mapping.patch b/debian/patches/test_mapping.patch
index d3463d8..6da90ee 100644
--- a/debian/patches/test_mapping.patch
+++ b/debian/patches/test_mapping.patch
@@ -1,5 +1,3 @@
-diff --git a/test/test_mapping.cpp b/test/test_mapping.cpp
-index cb649d9..b74a24e 100644
 --- a/test/test_mapping.cpp
 +++ b/test/test_mapping.cpp
 @@ -64,7 +64,8 @@ using namespace bpp;

-- 
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