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<h3>
Julien Y. Dutheil pushed to branch master
at <a href="https://salsa.debian.org/med-team/libbpp-phyl">Debian Med / libbpp-phyl</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/e988691e2c0107969c54b6d74dd4cedd7c8f53f3">e988691e</a></strong>
<div>
<span>by Julien Y. Dutheil</span>
<i>at 2018-05-01T15:53:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improved failing test.
Merged with reduce time patch.
</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#c1aa55833744d018e2b2e675fe64f344c1f95249">
debian/patches/increase_test_tolerance.patch
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</li>
<li class="file-stats">
<a href="#95aaf53e4a28a1610dd98adc3b2ce909079bf0c3">
<span class="deleted-file">
−
debian/patches/reduce_test_time.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="c1aa55833744d018e2b2e675fe64f344c1f95249">
<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/e988691e2c0107969c54b6d74dd4cedd7c8f53f3#c1aa55833744d018e2b2e675fe64f344c1f95249"><strong>debian/patches/increase_test_tolerance.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Description: By increasing tolerance of test boundaries the package should</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> build on all architectures</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/test/test_likelihood_nh.cpp b/test/test_likelihood_nh.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">index b4cd485..<span class="idiff left right">b8358d1</span> 100644</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">index b4cd485..<span class="idiff left right">c38a277</span> 100644</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_likelihood_nh.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_likelihood_nh.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -59,14 +59,14 @@ void fitModelNH(SubstitutionModelSet* model, DiscreteDistribution* rdist, const</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,3 +25,34 @@ index b4cd485..b8358d1 100644</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> throw Exception("Incorrect final value.");</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -89,14 +89,14 @@ int main() {</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> size_t nsites = 1000;</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- unsigned int nrep = 20;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ unsigned int nrep = 5;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> size_t nmodels = modelSet->getNumberOfModels();</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> vector<double> thetas(nmodels);</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> vector<double> thetasEst1(nmodels);</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> vector<double> thetasEst2(nmodels);</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> for (size_t i = 0; i < nmodels; ++i) {</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.99) + 0.005;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.9) + 0.05;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> cout << "Theta" << i << " set to " << theta << endl; </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> modelSet->setParameterValue("T92.theta_" + TextTools::toString(i + 1), theta);</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> thetas[i] = theta;</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -119,11 +119,11 @@ int main() {</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> tl2.initialize();</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> unsigned int c1 = OptimizationTools::optimizeNumericalParameters2(</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- &tl, tl.getParameters(), 0,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ &tl, tl.getSubstitutionModelParameters(), 0,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> 0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> unsigned int c2 = OptimizationTools::optimizeNumericalParameters2(</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- &tl2, tl2.getParameters(), 0,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ &tl2, tl2.getSubstitutionModelParameters(), 0,</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> 0.0001, 10000, messenger, profiler, false, false, 1, OptimizationTools::OPTIMIZATION_NEWTON);</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> cout << c1 << ": " << tl.getValue() << "\t" << c2 << ": " << tl2.getValue() << endl;</span></pre>
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<li id="95aaf53e4a28a1610dd98adc3b2ce909079bf0c3">
<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/e988691e2c0107969c54b6d74dd4cedd7c8f53f3#95aaf53e4a28a1610dd98adc3b2ce909079bf0c3"><strong>debian/patches/reduce_test_time.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Julien Y. Dutheil</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: 2018-02-11 21:18:30 +0100</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: Reduce number of iterations to reduce test time</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/test/test_likelihood_nh.cpp b/test/test_likelihood_nh.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">index b4cd485..97431aa 100644</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_likelihood_nh.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_likelihood_nh.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -89,7 +89,7 @@ int main() {</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> size_t nsites = 1000;</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- unsigned int nrep = 20;</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ unsigned int nrep = 3;</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> size_t nmodels = modelSet->getNumberOfModels();</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> vector<double> thetas(nmodels);</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> vector<double> thetasEst1(nmodels);</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">unforce-cxxflags.patch</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">reduce_test_time.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">increase_test_tolerance.patch</span></pre>
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