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<h3>

Olivier Sallou pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/biomaj3-download">Debian Med / biomaj3-download</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/biomaj3-download/-/commit/35cf9f7ee5e23f6037c9135c869b119b4c9e6af6">35cf9f7e</a></strong>

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<span>by Olivier Sallou</span>

<i>at 2022-02-14T08:06:12+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.6</pre>

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<h4>4 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">

CHANGES.txt

</a>

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<li class="file-stats">

<a href="#d3ff2f83abc07542528c70838015fdc7df5bb541">

biomaj_download/download/interface.py

</a>

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

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<li class="file-stats">

<a href="#a5b5d0c7b9c558d9142a199ec517b633dd40faf5">

tests/biomaj_tests.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">

<a href="https://salsa.debian.org/med-team/biomaj3-download/-/commit/35cf9f7ee5e23f6037c9135c869b119b4c9e6af6#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.2.6:</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">  Disabled test with tenacity, compat.make_retry_state removed from lib</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">3.2.5:</span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  Fix regex handling for **/*</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">3.2.4:</span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">  #39 directhttp download issues</span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">    biomaj sends file name instead of file dict, workaround this</span>

</pre>

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<br>

</li>

<li id="d3ff2f83abc07542528c70838015fdc7df5bb541">

<a href="https://salsa.debian.org/med-team/biomaj3-download/-/commit/35cf9f7ee5e23f6037c9135c869b119b4c9e6af6#d3ff2f83abc07542528c70838015fdc7df5bb541"><strong>biomaj_download/download/interface.py</strong></a>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ import logging</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>

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<td class="new_line diff-line-num" data-linenumber="5" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="6" 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="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>import copy</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tenacity</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">simpleeval</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">simple_eval</span><span class="p">,</span> <span class="n" style="color: #333;">ast</span></span>

</pre>

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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">@@ -264,14 +264,15 @@ class DownloadInterface(object):</td>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Check that it is an instance of stop_base</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">stop_cond</span><span class="p">,</span> <span class="n" style="color: #333;">tenacity</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">.</span><span class="n" style="color: #333;">stop_base</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="n" style="color: #333;">stop_condition</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" doesn't yield a stop condition"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Disabled test, compat.make_retry_state removed from lib</span></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Test that this is a correct stop condition by calling it.</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># We use a deepcopy to be sure to not alter the object (even</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># if it seems that calling a wait policy doesn't modify it).</span></span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python">                    <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy</span><span class="p">.</span><span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">stop_cond</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python">                    <span class="n" style="color: #333;">s</span><span class="p">(</span><span class="n" style="color: #333;">tenacity</span><span class="p">.</span><span class="n" style="color: #333;">compat</span><span class="p">.</span><span class="n" style="color: #333;">make_retry_state</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="n" style="color: #333;">stop_condition</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" doesn't yield a stop condition"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>try:</span></span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>    s = copy.deepcopy(stop_cond)</span></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>    s(tenacity.compat.make_retry_state(0, 0))</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>except Exception:</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>    raise ValueError(stop_condition + " doesn't yield a stop condition")</span></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error while parsing stop condition: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="290" 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">...</td>

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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">@@ -290,14 +291,15 @@ class DownloadInterface(object):</td>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Check that it is an instance of wait_base</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">wait_pol</span><span class="p">,</span> <span class="n" style="color: #333;">tenacity</span><span class="p">.</span><span class="n" style="color: #333;">wait</span><span class="p">.</span><span class="n" style="color: #333;">wait_base</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="n" style="color: #333;">wait_policy</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" doesn't yield a wait policy"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Disabled test, compat.make_retry_state removed from lib</span></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Test that this is a correct wait policy by calling it.</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># We use a deepcopy to be sure to not alter the object (even</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># if it seems that calling a stop condition doesn't modify it).</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python">                    <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy</span><span class="p">.</span><span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">wait_pol</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python">                    <span class="n" style="color: #333;">w</span><span class="p">(</span><span class="n" style="color: #333;">tenacity</span><span class="p">.</span><span class="n" style="color: #333;">compat</span><span class="p">.</span><span class="n" style="color: #333;">make_retry_state</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="n" style="color: #333;">wait_policy</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" doesn't yield a wait policy"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>try:</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>    w = copy.deepcopy(wait_pol)</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>    w(tenacity.compat.make_retry_state(0, 0))</span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>except Exception:</span></span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>    raise ValueError(wait_policy + " doesn't yield a wait policy")</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error while parsing wait policy: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">e</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="377" 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">...</td>

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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">@@ -377,19 +379,13 @@ class DownloadInterface(object):</td>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python">                            <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python">                        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_append_file_to_download</span><span class="p">(</span><span class="n" style="color: #333;">rfile</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python">                        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">'Download:File:MatchRegExp:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python">                    <span class="k" style="font-weight: 600;">return</span></span>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>return</span></span>

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">direlt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dir_list</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python">                    <span class="n" style="color: #333;">subdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">direlt</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">'Download:File:Subdir:Check:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="386" 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="LC386" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'**/*'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python">                        <span class="p">(</span><span class="n" style="color: #333;">subfile_list</span><span class="p">,</span> <span class="n" style="color: #333;">subdirs_list</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">subdir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python">                        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">([</span><span class="n" style="color: #333;">pattern</span><span class="p">],</span> <span class="n" style="color: #333;">subfile_list</span><span class="p">,</span> <span class="n" style="color: #333;">subdirs_list</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">subdir</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python">                        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rfile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">file_list</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pattern</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'**/*'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">,</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]):</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python">                                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python">                                    <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python">                                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_append_file_to_download</span><span class="p">(</span><span class="n" style="color: #333;">rfile</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python">                                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">'Download:File:MatchRegExp:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rfile</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="393" 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="LC389" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="394" 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="LC390" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">subdirs_pattern</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">subdir</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="395" 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="LC391" class="line" lang="python">                            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">'Download:File:Subdir:Match:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">subdir</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/biomaj3-download/-/commit/35cf9f7ee5e23f6037c9135c869b119b4c9e6af6#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</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 class="diff-line-num unfold js-unfold old_line" data-linenumber="22" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,7 @@ config = {</td>

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<td class="old_line diff-line-num" data-linenumber="22" 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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<td class="new_line diff-line-num" data-linenumber="22" 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="LC22" class="line" lang="python">    <span class="s" style="color: #d14;">'url'</span><span class="p">:</span> <span class="s" style="color: #d14;">'http://biomaj.genouest.org'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="23" 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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<td class="new_line diff-line-num" data-linenumber="23" 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="LC23" class="line" lang="python">    <span class="s" style="color: #d14;">'download_url'</span><span class="p">:</span> <span class="s" style="color: #d14;">'http://biomaj.genouest.org'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="24" 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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<td class="new_line diff-line-num" data-linenumber="24" 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="LC24" class="line" lang="python">    <span class="s" style="color: #d14;">'author_email'</span><span class="p">:</span> <span class="s" style="color: #d14;">'olivier.sallou@irisa.fr'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python">    <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.2.<span class="idiff left right">4</span>'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="26" 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="new_line diff-line-num new" data-linenumber="25" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">    <span class="s" style="color: #d14;">'version'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3.2.<span class="idiff left right">6</span>'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" 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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<td class="new_line diff-line-num" data-linenumber="26" 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="LC26" class="line" lang="python">    <span class="s" style="color: #d14;">'classifiers'</span><span class="p">:</span> <span class="p">[</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="27" 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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<td class="new_line diff-line-num" data-linenumber="27" 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="LC27" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># How mature is this project? Common values are</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#   3 - Alpha</span></span>

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<li id="a5b5d0c7b9c558d9142a199ec517b633dd40faf5">

<a href="https://salsa.debian.org/med-team/biomaj3-download/-/commit/35cf9f7ee5e23f6037c9135c869b119b4c9e6af6#a5b5d0c7b9c558d9142a199ec517b633dd40faf5"><strong>tests/biomaj_tests.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="190" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -190,8 +190,8 @@ class TestDownloadInterface(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Test some garbage</span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python">    <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">stop_condition</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"stop_after_attempts"</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># no param</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">downloader</span><span class="p">.</span><span class="n" style="color: #333;">set_options</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python">    <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">stop_condition</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1 & 1"</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># not a stop_condition</span></span>

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<td class="new_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python">    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">downloader</span><span class="p">.</span><span class="n" style="color: #333;">set_options</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="195" 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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<td class="new_line diff-line-num new" data-linenumber="193" 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="LC193" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>d = dict(stop_condition="1 & 1")  # not a stop_condition</span></span>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>self.assertRaises(ValueError, downloader.set_options, d)</span></span>

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<td class="new_line diff-line-num" data-linenumber="195" 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="LC195" class="line" lang="python">    <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">stop_condition</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"stop_after_attempts(5) & 1"</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># not a stop_condition</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">downloader</span><span class="p">.</span><span class="n" style="color: #333;">set_options</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="197" 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="LC197" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Test some garbage</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="199" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="199" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -199,8 +199,8 @@ class TestDownloadInterface(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python">    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">downloader</span><span class="p">.</span><span class="n" style="color: #333;">set_options</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="200" 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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<td class="new_line diff-line-num" data-linenumber="200" 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="LC200" class="line" lang="python">    <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">wait_policy</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"I love python"</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># not a wait_condition</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python">    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">downloader</span><span class="p">.</span><span class="n" style="color: #333;">set_options</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python">    <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">wait_policy</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"wait_random(5) + 3"</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># not a wait_condition</span></span>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python">    <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">downloader</span><span class="p">.</span><span class="n" style="color: #333;">set_options</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="202" 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="LC202" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>d = dict(wait_policy="wait_random(5) + 3")  # not a wait_condition</span></span>

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<td class="new_line diff-line-num new" data-linenumber="203" 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="LC203" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>self.assertRaises(ValueError, downloader.set_options, d)</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Test operators</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python">    <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">stop_condition</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"stop_never | stop_after_attempt(5)"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python">             <span class="n" style="color: #333;">wait_policy</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"wait_none + wait_random(1, 2)"</span><span class="p">)</span></span>

</pre>

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