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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/python-cogent">Debian Med / python-cogent</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/5a08aa71dd92bccc8f69ecbdc7d7199d45807190">5a08aa71</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-02-25T16:39:46+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More tolerant tests on i386 and armel (patches provided by upstream)

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/1b6213e55ca627295cacf7e94545b0016ee62db2">1b6213e5</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-02-25T16:42:48+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch does not apply - just ignored here

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/4e093643b88099b9e1847fc6bd1aee446fae9480">4e093643</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-02-25T16:51:06+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-cogent/-/commit/b92f93b10ea3f06f3845d2a706e3508e9441632c">b92f93b1</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-02-25T19:51:57+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>5 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#6624b2fdbd825ce0eaa060246bdc1184625056cc">

<span class="new-file">

+

debian/patches/3bc0a8a413cb82ec6a3e86beaa0e2e71ad8ed3fb.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#613deecdce0bea1b1f43de8f67c113f2df661c9a">

<span class="new-file">

+

debian/patches/9ea740ee6a936895f68af59537fd6171803aa7e6.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">

<span class="new-file">

+

debian/salsa-ci.yml

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/79f8f0c02b7274895792e150fd99403bfe2df308...b92f93b10ea3f06f3845d2a706e3508e9441632c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-cogent (2020.2.7a+dfsg-2) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * More tolerant tests on i386 and armel (patches provided by upstream)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * Add salsa-ci file (routine-update)</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Tue, 25 Feb 2020 16:51:08 +0100</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre>

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1

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">python-cogent (2020.2.7a+dfsg-1) unstable; urgency=medium</span>

</pre>

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2

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9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

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3

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * Solve one issue in test suite i386 / armel (other issue seems to be</span>

</pre>

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<br>

</li>

<li id="6624b2fdbd825ce0eaa060246bdc1184625056cc">

<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/79f8f0c02b7274895792e150fd99403bfe2df308...b92f93b10ea3f06f3845d2a706e3508e9441632c#6624b2fdbd825ce0eaa060246bdc1184625056cc"><strong>debian/patches/3bc0a8a413cb82ec6a3e86beaa0e2e71ad8ed3fb.patch</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 9ea740ee6a936895f68af59537fd6171803aa7e6 Mon Sep 17 00:00:00 2001</span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Gavin Huttley <Gavin.Huttley@anu.edu.au></span></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Thu, 20 Feb 2020 08:25:55 +1100</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/950474</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Subject: [PATCH] TST: tweak the atol values for evaluating jsd/jsm cases that</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> produce 0, addresses #534</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Remark: Patch does not apply - just ignored here</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">[CHANGED] the i386, armel CPUs have lower floating point precision. I've increased</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">    the asbolute tolerance in the testing (for these functions only) to 4x machine</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">    precision. This "may" fix the reported issue.</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">---</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> tests/test_maths/test_measure.py | 20 +++++++++++++++++---</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 1 file changed, 17 insertions(+), 3 deletions(-)</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff">diff --git a/tests/test_maths/test_measure.py b/tests/test_maths/test_measure.py</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gh" style="color: #999;">index b2b64d81..f4c9f159 100644</span></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;">--- a/tests/test_maths/test_measure.py</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;">+++ b/tests/test_maths/test_measure.py</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> from unittest import TestCase, main</span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from numpy import diag_indices, dot</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from numpy import diag_indices, dot, finfo, float64</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> from numpy.random import random</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> from numpy.testing import assert_allclose</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="p">@@ -111,6 +111,11 @@</span> def test_paralinear_continuous_time_validate(self):</span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </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"> class TestJensenShannon(TestCase):</span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    # the following value is 4x machine precision, used to handle</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;">+    # architectures that have lower precision and do not produce 0.0 from</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    # numerical calcs involved in jsd/jsm</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    atol = 4 * finfo(float64).eps</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff">     def test_jsd_validation(self):</span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff">         """jsd fails with malformed data"""</span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff">         freqs1 = random(5)</span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -164,7 +169,8 @@</span> def test_jsd_validation(self):</span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff">             jsd(normalised_freqs1, freqs2, validate=True)  # invalid freqs2</span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff">     def test_jsd(self):</span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """case1 is testing if the jsd between two identical distributions is 0.0"""</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        """evaluate jsd between identical, and non-identical distributions"""</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        # case1 is testing if the jsd between two identical distributions is 0.0</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff">         case1 = [</span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff">             [0.0, 0.0, 0.0],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff">             [0.0, 0.0, 0.0],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -176,6 +182,7 @@</span> def test_jsd(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff">                 jsd(case1[0], case1[1], validate=True),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff">                 0.0,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff">                 err_msg="Testing case1 for jsd failed",</span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff">             )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff">             case1[0][index] = 0.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff">             case1[1][index] = 0.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -185,6 +192,7 @@</span> def test_jsd(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff">             jsd(case2[0], case2[1], validate=True),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff">             0.7655022032053593,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff">             err_msg="Testing case2 for jsd failed",</span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff">         )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff">         # case3 is testing the numerical output of jsd between two distant distributions</span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff">         case3 = [[1.0, 0.0], [1 / 2, 1 / 2]]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -192,6 +200,7 @@</span> def test_jsd(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff">             jsd(case3[0], case3[1], validate=True),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff">             0.3112781244591328,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff">             err_msg="Testing case3 for jsd failed",</span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff">         )</span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff">         # case4 - the jsd between two identical uniform distributions is 0.0</span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff">         case4 = [</span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="p">@@ -202,10 +211,11 @@</span> def test_jsd(self):</span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff">             jsd(case4[0], case4[1], validate=True),</span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff">             0.0,</span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff">             err_msg="Testing case4 for jsd failed",</span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff">         )</span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff">     def test_jsm(self):</span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """case1 is testing if the jsm between two identical distributions is 0.0"""</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        """evaluate jsm between identical, and non-identical distributions"""</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff">         case1 = [</span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff">             [0.0, 0.0, 0.0],</span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff">             [0.0, 0.0, 0.0],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -217,6 +227,7 @@</span> def test_jsm(self):</span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff">                 jsm(case1[0], case1[1], validate=True),</span>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff">                 0.0,</span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff">                 err_msg="Testing case1 for jsm failed",</span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff">             )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff">             case1[0][index] = 0.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff">             case1[1][index] = 0.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -226,6 +237,7 @@</span> def test_jsm(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff">             jsm(case2[0], case2[1], validate=True),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff">             0.8749298275892526,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff">             err_msg="Testing case2 for jsm failed",</span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff">         )</span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff">         # case3 is testing the numerical output of jsm between two random distributions</span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff">         case3 = [[1.0, 0.0], [1 / 2, 1 / 2]]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -233,6 +245,7 @@</span> def test_jsm(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff">             jsm(case3[0], case3[1], validate=True),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff">             0.5579230452841438,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff">             err_msg="Testing case3 for jsm failed",</span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff">         )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff">         # case4 is testing if the jsm between two identical uniform distributions is 0.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff">         case4 = [</span>

</pre>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="p">@@ -243,6 +256,7 @@</span> def test_jsm(self):</span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff">             jsm(case4[0], case4[1], validate=True),</span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff">             0.0,</span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff">             err_msg="Testing case4 for jsm failed",</span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff">         )</span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span></pre>

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<br>

</li>

<li id="613deecdce0bea1b1f43de8f67c113f2df661c9a">

<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/79f8f0c02b7274895792e150fd99403bfe2df308...b92f93b10ea3f06f3845d2a706e3508e9441632c#613deecdce0bea1b1f43de8f67c113f2df661c9a"><strong>debian/patches/9ea740ee6a936895f68af59537fd6171803aa7e6.patch</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From 9ea740ee6a936895f68af59537fd6171803aa7e6 Mon Sep 17 00:00:00 2001</span></span>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Gavin Huttley <Gavin.Huttley@anu.edu.au></span></span>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Thu, 20 Feb 2020 08:25:55 +1100</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/950474</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Subject: [PATCH] TST: tweak the atol values for evaluating jsd/jsm cases that</span></span>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> produce 0, addresses #534</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">[CHANGED] the i386, armel CPUs have lower floating point precision. I've increased</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">    the asbolute tolerance in the testing (for these functions only) to 4x machine</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">    precision. This "may" fix the reported issue.</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> tests/test_maths/test_measure.py | 20 +++++++++++++++++---</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 1 file changed, 17 insertions(+), 3 deletions(-)</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff">diff --git a/tests/test_maths/test_measure.py b/tests/test_maths/test_measure.py</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">index b2b64d81..f4c9f159 100644</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_maths/test_measure.py</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_maths/test_measure.py</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> from unittest import TestCase, main</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 class="gd" style="color: #000; background-color: #fdd;">-from numpy import diag_indices, dot</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from numpy import diag_indices, dot, finfo, float64</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> from numpy.random import random</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> from numpy.testing import assert_allclose</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 class="p">@@ -111,6 +111,11 @@</span> def test_paralinear_continuous_time_validate(self):</span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> class TestJensenShannon(TestCase):</span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    # the following value is 4x machine precision, used to handle</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    # architectures that have lower precision and do not produce 0.0 from</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;">+    # numerical calcs involved in jsd/jsm</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    atol = 4 * finfo(float64).eps</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff">     def test_jsd_validation(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff">         """jsd fails with malformed data"""</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff">         freqs1 = random(5)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -164,7 +169,8 @@</span> def test_jsd_validation(self):</span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff">             jsd(normalised_freqs1, freqs2, validate=True)  # invalid freqs2</span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff">     def test_jsd(self):</span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """case1 is testing if the jsd between two identical distributions is 0.0"""</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        """evaluate jsd between identical, and non-identical distributions"""</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        # case1 is testing if the jsd between two identical distributions is 0.0</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff">         case1 = [</span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff">             [0.0, 0.0, 0.0],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff">             [0.0, 0.0, 0.0],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -176,6 +182,7 @@</span> def test_jsd(self):</span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff">                 jsd(case1[0], case1[1], validate=True),</span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff">                 0.0,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff">                 err_msg="Testing case1 for jsd failed",</span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff">             )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff">             case1[0][index] = 0.0</span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff">             case1[1][index] = 0.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -185,6 +192,7 @@</span> def test_jsd(self):</span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff">             jsd(case2[0], case2[1], validate=True),</span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff">             0.7655022032053593,</span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff">             err_msg="Testing case2 for jsd failed",</span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff">         )</span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff">         # case3 is testing the numerical output of jsd between two distant distributions</span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff">         case3 = [[1.0, 0.0], [1 / 2, 1 / 2]]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -192,6 +200,7 @@</span> def test_jsd(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff">             jsd(case3[0], case3[1], validate=True),</span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff">             0.3112781244591328,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff">             err_msg="Testing case3 for jsd failed",</span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff">         )</span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff">         # case4 - the jsd between two identical uniform distributions is 0.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff">         case4 = [</span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -202,10 +211,11 @@</span> def test_jsd(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff">             jsd(case4[0], case4[1], validate=True),</span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff">             0.0,</span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff">             err_msg="Testing case4 for jsd failed",</span>

</pre>

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77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff">         )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff">     def test_jsm(self):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """case1 is testing if the jsm between two identical distributions is 0.0"""</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        """evaluate jsm between identical, and non-identical distributions"""</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff">         case1 = [</span>

</pre>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff">             [0.0, 0.0, 0.0],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff">             [0.0, 0.0, 0.0],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="p">@@ -217,6 +227,7 @@</span> def test_jsm(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff">                 jsm(case1[0], case1[1], validate=True),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff">                 0.0,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff">                 err_msg="Testing case1 for jsm failed",</span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff">             )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff">             case1[0][index] = 0.0</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff">             case1[1][index] = 0.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="p">@@ -226,6 +237,7 @@</span> def test_jsm(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff">             jsm(case2[0], case2[1], validate=True),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff">             0.8749298275892526,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff">             err_msg="Testing case2 for jsm failed",</span>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff">         )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff">         # case3 is testing the numerical output of jsm between two random distributions</span>

</pre>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff">         case3 = [[1.0, 0.0], [1 / 2, 1 / 2]]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="p">@@ -233,6 +245,7 @@</span> def test_jsm(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff">             jsm(case3[0], case3[1], validate=True),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff">             0.5579230452841438,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff">             err_msg="Testing case3 for jsm failed",</span>

</pre>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff">         )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff">         # case4 is testing if the jsm between two identical uniform distributions is 0.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff">         case4 = [</span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="p">@@ -243,6 +256,7 @@</span> def test_jsm(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff">             jsm(case4[0], case4[1], validate=True),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff">             0.0,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff">             err_msg="Testing case4 for jsm failed",</span>

</pre>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            atol=self.atol,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff">         )</span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> </span></pre>

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<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/79f8f0c02b7274895792e150fd99403bfe2df308...b92f93b10ea3f06f3845d2a706e3508e9441632c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

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1

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1

</td>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">sphinx.patch</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_interpreter.patch</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">96ab670d76f88a188286017602c1c47463be5037.patch</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">9ea740ee6a936895f68af59537fd6171803aa7e6.patch</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># 3bc0a8a413cb82ec6a3e86beaa0e2e71ad8ed3fb.patch</span></pre>

</td>

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</table>

<br>

</li>

<li id="b1dbf22e88351ec0d5d1d1a7f53295504b480e61">

<a href="https://salsa.debian.org/med-team/python-cogent/-/compare/79f8f0c02b7274895792e150fd99403bfe2df308...b92f93b10ea3f06f3845d2a706e3508e9441632c#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>

</td>

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