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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-pauvre">Debian Med / python-pauvre</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc">5b36a488</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-02T10:04:18+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.2.1</pre>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#3a274887fec149e281cecbebbc37c26db5395ee6">
pauvre.egg-info/PKG-INFO
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<li class="file-stats">
<a href="#4c7f5e53b7de4c014112d1144434c514fd93a580">
pauvre.egg-info/requires.txt
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<li class="file-stats">
<a href="#34a1ac4288b33d60794567153f06469e0eb9e4ce">
pauvre.egg-info/top_level.txt
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<li class="file-stats">
<a href="#7a7dd78b6a64c19785bab01460ae92eb6462e744">
pauvre/marginplot.py
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</li>
<li class="file-stats">
<a href="#d75aa1dc6b4779e4e922c9871335a2afe0ab7c66">
pauvre/rcparams.py
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</li>
<li class="file-stats">
<a href="#dcbb81d4a478f46ac3fc36173a084bc38c38d499">
pauvre/redwood.py
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</li>
<li class="file-stats">
<a href="#1273922d0ff5099f80cad189a5e0a96532add900">
pauvre/version.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.2</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: pauvre</span>
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<td class="diff-line-num old old_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">1924</span></span>
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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="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">2.1</span></span>
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<td class="diff-line-num old_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext">Summary: Tools for plotting Oxford Nanopore and other long-read data.</span>
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<td class="diff-line-num old_line" 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="plaintext">Home-page: https://github.com/conchoecia/pauvre</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext">Author: Darrin Schultz</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: dts@ucsc.edu</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">GPLv3</span></span>
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<td class="diff-line-num new old_line" data-linenumber="9" 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="LC8" class="line" lang="plaintext">License: <span class="idiff left right">UNKNOWN</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Description: </span>
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<td class="diff-line-num old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> 'pauvre' is a package for plotting Oxford Nanopore and other long read data.</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> The name means 'poor' in French, a play on words to the oft-used 'pore' prefix</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="17" 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">@@ -17,10 +17,9 @@ Platform: UNKNOWN</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Classifier: Development Status :: 2 - Pre-Alpha</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext">Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)</span>
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<td class="diff-line-num old_line" data-linenumber="19" 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">
19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.5</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.6</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.7</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Classifier: Operating System :: POSIX :: Linux</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Classifier: Topic :: Scientific/Engineering :: Bio-Informatics</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Classifier: Intended Audience :: Science/Research</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">Requires: python (>3.0)</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Provides: pauvre</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Requires-Python: >=3</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,45 +24,6 @@ This package currently hosts four scripts for plotting and/or printing stats.</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"> genomes with the fewest crossings-over. Input is one <span class="sb" style="color: #d14;">`.gff`</span> file</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"> per circular genome and one directory of gene alignments.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Updates:</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown"><span class="p">-</span> 20200215 - v0.1.924 - Made some minor updates to work with python 3.7 and the latest version of pandas,</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"><span class="p">-</span> 20171130 - v0.1.86 - some changes by @wdecoster to integrate <span class="sb" style="color: #d14;">`pauvre`</span> into <span class="p">[</span><span class="nv" style="color: #008080;">nanoplot</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/wdecoster/NanoPlot</span><span class="p">)</span>,</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"> as well as some formatting changes that <span class="ge" style="font-style: italic;">*may*</span> make <span class="sb" style="color: #d14;">`pauvre`</span> work better with python2.7. Adding Travis-CI functionality.</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="p">-</span> 20171025 - v0.1.83 - added some changes to make marginplot interface</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"> with @wdecoster's <span class="p">[</span><span class="nv" style="color: #008080;">nanoPlot</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/wdecoster/NanoPlot</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"> package, and made <span class="sb" style="color: #d14;">`pauvre stats`</span> only output data tables for</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"> filtered reads. <span class="sb" style="color: #d14;">`pauvre stats`</span> also now has the <span class="sb" style="color: #d14;">`--filt_maxlen`</span>,</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"> <span class="sb" style="color: #d14;">`--filt_maxqual`</span>, <span class="sb" style="color: #d14;">`--filt_minlen`</span>, and <span class="sb" style="color: #d14;">`--filt_minqual`</span> options.</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"><span class="p">-</span> 20171018 - v0.1.8 - you can now filter reads and adjust the plotting viewing window.</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"> <span class="p">[</span><span class="nv" style="color: #008080;">See below for a demonstration.</span><span class="p">](</span><span class="sx" style="color: #d14;">#filter-reads-and-adjust-viewing-window</span><span class="p">)</span> I added the following options:</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"> --filt_maxlen FILT_MAXLEN</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"> This sets the max read length filter reads.</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"> --filt_maxqual FILT_MAXQUAL</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"> This sets the max mean read quality to filter reads.</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"> --filt_minlen FILT_MINLEN</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown"> This sets the min read length to filter reads.</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"> --filt_minqual FILT_MINQUAL</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"> This sets the min mean read quality to filter reads.</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"> --plot_maxlen PLOT_MAXLEN</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown"> Sets the maximum viewing area in the length dimension.</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown"> --plot_maxqual PLOT_MAXQUAL</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"> Sets the maximum viewing area in the quality</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"> dimension.</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown"> --plot_minlen PLOT_MINLEN</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown"> Sets the minimum viewing area in the length dimension.</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"> --plot_minqual PLOT_MINQUAL</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown"> Sets the minimum viewing area in the quality</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown"> dimension.</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"><span class="p">-</span> 20171014 - uploading information on <span class="sb" style="color: #d14;">`pauvre redwood`</span> and <span class="sb" style="color: #d14;">`pauvre synteny`</span> usage.</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown"><span class="p">-</span> 20171012 - made <span class="sb" style="color: #d14;">`pauvre stats`</span> more consistently produce useful histograms.</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown"> <span class="sb" style="color: #d14;">`pauvre stats`</span> now also calculates some statistics for different size ranges.</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown"><span class="p">-</span> 20170529 - added automatic scaling to the input fastq file. It</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"> scales to show the highest read quality and the top 99th percentile</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"> of reads by length.</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"><span class="gh" style="color: #999;"># Requirements</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"><span class="p">-</span> You must have the following installed on your system to install this software:</span>
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<br>
</li>
<li id="3a274887fec149e281cecbebbc37c26db5395ee6">
<a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc#3a274887fec149e281cecbebbc37c26db5395ee6"><strong>pauvre.egg-info/PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.2</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: pauvre</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">1924</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Tools for plotting Oxford Nanopore and other long-read data.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/conchoecia/pauvre</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Darrin Schultz</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: dts@ucsc.edu</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">GPLv3</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">UNKNOWN</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Description: </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> 'pauvre' is a package for plotting Oxford Nanopore and other long read data.</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> The name means 'poor' in French, a play on words to the oft-used 'pore' prefix</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="17" 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">@@ -17,10 +17,9 @@ Platform: UNKNOWN</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Classifier: Development Status :: 2 - Pre-Alpha</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.5</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.6</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Classifier: Programming Language :: Python :: 3.7</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Classifier: Operating System :: POSIX :: Linux</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Classifier: Topic :: Scientific/Engineering :: Bio-Informatics</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Classifier: Intended Audience :: Science/Research</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">Requires: python (>3.0)</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Provides: pauvre</span>
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<td class="diff-line-num old_line" 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="LC25" class="line" lang="plaintext">Requires-Python: >=3</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">@@ -3,4 +3,4 @@ biopython>=1.68</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">pandas>=0.20.1</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">numpy>=1.12.1</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">scipy</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">s<span class="idiff left right">k</span>learn</span></pre>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">s<span class="idiff left right">cikit-</span>learn</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc#34a1ac4288b33d60794567153f06469e0eb9e4ce"><strong>pauvre.egg-info/top_level.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">pauvre</span></pre>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">scripts</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc#7a7dd78b6a64c19785bab01460ae92eb6462e744"><strong>pauvre/marginplot.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -378,9 +378,7 @@ def margin_plot(df, **kwargs):</td>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">min_plot_qual</span><span class="p">,</span> <span class="n" style="color: #333;">max_plot_qual</span><span class="p">,</span> <span class="n" style="color: #333;">min_plot_length</span><span class="p">,</span> <span class="n" style="color: #333;">max_plot_length</span><span class="p">),</span></span>
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Print image(s)</span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"BASENAME"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"path"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">file_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"BASENAME"</span><span class="p">]</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"BASENAME"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"BASENAME"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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384
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">file_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opath</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">opath</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"fastq"</span><span class="p">]))[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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385
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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386
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">file_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"BASENAME"</span><span class="p">]</span></span>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc#d75aa1dc6b4779e4e922c9871335a2afe0ab7c66"><strong>pauvre/rcparams.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,21 +5,24 @@ from matplotlib import rcParams</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">update_rcParams</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This mpl style is from the UCSC BME163 class.</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">rcParams</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">({</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"> <span class="s" style="color: #d14;">'font.size'</span> <span class="p">:</span> <span class="mf" style="color: #099;">8.0</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="s" style="color: #d14;">'font.sans-serif'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'Arial'</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.major.size'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.major.width'</span> <span class="p">:</span> <span class="mf" style="color: #099;">0.75</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.labelsize'</span> <span class="p">:</span> <span class="mf" style="color: #099;">8.0</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.direction'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'out'</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.major.size'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.major.width'</span> <span class="p">:</span> <span class="mf" style="color: #099;">0.75</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.labelsize'</span> <span class="p">:</span> <span class="mf" style="color: #099;">8.0</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.direction'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'out'</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.major.pad'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.minor.pad'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.major.pad'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.minor.pad'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'savefig.dpi'</span> <span class="p">:</span> <span class="mi" style="color: #099;">601</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'axes.linewidth'</span> <span class="p">:</span> <span class="mf" style="color: #099;">0.75</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'text.usetex'</span> <span class="p">:</span> <span class="bp" style="color: #999;">False</span> <span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'text.latex.unicode'</span> <span class="p">:</span> <span class="bp" style="color: #999;">False</span> <span class="p">})</span></span></pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="s" style="color: #d14;">'font.size'</span> <span class="p">:</span> <span class="mf" style="color: #099;">8.0</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="s" style="color: #d14;">'font.sans-serif'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'Arial'</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.major.size'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.major.width'</span> <span class="p">:</span> <span class="mf" style="color: #099;">0.75</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.labelsize'</span> <span class="p">:</span> <span class="mf" style="color: #099;">8.0</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.direction'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'out'</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.major.size'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.major.width'</span> <span class="p">:</span> <span class="mf" style="color: #099;">0.75</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.labelsize'</span> <span class="p">:</span> <span class="mf" style="color: #099;">8.0</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.direction'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'out'</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.major.pad'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'xtick.minor.pad'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.major.pad'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'ytick.minor.pad'</span> <span class="p">:</span> <span class="mi" style="color: #099;">2</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'savefig.dpi'</span> <span class="p">:</span> <span class="mi" style="color: #099;">601</span> <span class="p">,</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'axes.linewidth'</span> <span class="p">:</span> <span class="mf" style="color: #099;">0.75</span> <span class="p">,</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'text.usetex'</span> <span class="p">:</span> <span class="bp" style="color: #999;">False</span> <span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"image.composite_image"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span> <span class="p">,</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">"pdf.fonttype"</span> <span class="p">:</span> <span class="mi" style="color: #099;">42</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">"ps.fonttype"</span> <span class="p">:</span> <span class="mi" style="color: #099;">42</span> <span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc#dcbb81d4a478f46ac3fc36173a084bc38c38d499"><strong>pauvre/redwood.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="703" 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">@@ -703,7 +703,7 @@ def redwood(args):</td>
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703
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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704
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704
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">)</span></span>
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705
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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Print image(s)</span></span>
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="python"> <span class="n" style="color: #333;">ifargs</span><span class="p">.</span><span class="n" style="color: #333;">BASENAME</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="idiff left right"> </span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">BASENAME</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="python"> <span class="n" style="color: #333;">file_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"redwood"</span></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"> <span class="n" style="color: #333;">file_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">BASENAME</span></span>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc#1273922d0ff5099f80cad189a5e0a96532add900"><strong>pauvre/version.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.1924"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.2.1"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/5b36a488dc50b5083d1db52a8b0c306cd9ecffbc#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># pauvre<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># pauvre</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2016-2020 Darrin T. Schultz.</span></span>
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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></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This file is part of pauvre.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" 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">@@ -28,11 +28,9 @@ from setuptools import setup, find_packages</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">version_py</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="s" style="color: #d14;">'pauvre'</span><span class="p">,</span> <span class="s" style="color: #d14;">'version.py'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">version_py</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'='</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">).</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'pauvre'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'python (>3.0)'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">version</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Tools for plotting Oxford Nanopore and other long-read data.'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"""</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,7 +40,6 @@ setup(name='pauvre',</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> python 2. You can visit the gitub page for more detailed information here:</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> https://github.com/conchoecia/pauvre</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/conchoecia/pauvre'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Darrin Schultz'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'dts@ucsc.edu'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,14 +47,13 @@ setup(name='pauvre',</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">'Development Status :: 2 - Pre-Alpha'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">'License :: OSI Approved :: GNU General Public License v3 (GPLv3)'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3.5'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3.6'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">'Operating System :: POSIX :: Linux'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">'Topic :: Scientific/Engineering :: Bio-Informatics'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">'Intended Audience :: Science/Research'</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">'Intended Audience :: Science/Research'</span><span class="p"><span class="idiff left right">,</span></span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'GPLv3'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">provides</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'pauvre'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">'scripts'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">python_requires</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'>=3'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">"matplotlib >= 2.0.2"</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,7 +61,7 @@ setup(name='pauvre',</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">"pandas >= 0.20.1"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">"numpy >= 1.12.1"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">"scipy"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="s" style="color: #d14;">"s<span class="idiff left right">klearn"</span></span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">"s<span class="idiff left">cikit-learn"</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="s" style="color: #d14;">'console_scripts'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'pauvre=pauvre.pauvre_main:main'</span><span class="p">],</span></span>
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