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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>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2b47de610eda7c3e4c3bcf4a7ee0f6f60993c3b7">2b47de61</a></strong>
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<span>by Julien Y. Dutheil</span>
<i>at 2018-04-30T17:48:26+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fixing failing test on some archs.
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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+
debian/patches/increase_test_tolerance.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2b47de610eda7c3e4c3bcf4a7ee0f6f60993c3b7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libbpp-phyl (2.4.0-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Increases likelihood test tolerance.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Julien Dutheil <julien.dutheil@univ-montp2.fr> Mon, 30 Apr 2018 16:58:46 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">libbpp-phyl (2.4.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> [ Julien Dutheil ]</span>
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<li id="c1aa55833744d018e2b2e675fe64f344c1f95249">
<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2b47de610eda7c3e4c3bcf4a7ee0f6f60993c3b7#c1aa55833744d018e2b2e675fe64f344c1f95249"><strong>debian/patches/increase_test_tolerance.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" 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="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">index b4cd485..b8358d1 100644</span></span>
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<pre style="margin: 0;">+<span id="LC3" 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="LC4" 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="LC5" 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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> tl.initialize();</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> cout << setprecision(20) << tl.getValue() << endl;</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ApplicationTools::displayResult("* initial likelihood", tl.getValue());</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (abs(tl.getValue() - initialValue) > 0.0001)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (abs(tl.getValue() - initialValue) > 0.01)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> throw Exception("Incorrect initial value.");</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> OptimizationTools::optimizeTreeScale(&tl);</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> ApplicationTools::displayResult("* likelihood after tree scale", tl.getValue());</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- OptimizationTools::optimizeNumericalParameters2(&tl, tl.getParameters(), 0, 0.000001, 10000, 0, 0);</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ OptimizationTools::optimizeNumericalParameters2(&tl, tl.getParameters(), 0, 0.0001, 10000, 0, 0);</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> cout << setprecision(20) << tl.getValue() << endl;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue());</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (abs(tl.getValue() - finalValue) > 0.0001)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (abs(tl.getValue() - finalValue) > 0.01)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> throw Exception("Incorrect final value.");</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/libbpp-phyl/commit/2b47de610eda7c3e4c3bcf4a7ee0f6f60993c3b7#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">increase_test_tolerance.patch</span></pre>
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