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<h3>
Andreas Tille pushed to branch master
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/f59ed2eb09a7ba2ccf27880a3470a7c275c79742">f59ed2eb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-11T22:36:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.2.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/6d3829043c060f15a8c761d877f3ca3d0971ef0d">6d382904</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-11T22:36:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/3423d14e72295d6eb8775f581c4bae0e39abb704">3423d14e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-11T22:36:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.2.2'
Update to upstream version '0.2.2'
with Debian dir 32779528b613632d498a9901a1ab8d0fe1df32a2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/f7d8762407361be20ad044b477d7f12106a2a08c">f7d87624</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-11T22:36:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/dec5390fc74bb559c9a9eaa675594a3b490fab31">dec5390f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-11T22:36:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/2a5f781d32254957d49d6559cb378c583a48373e">2a5f781d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-11T22:36:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit.
Fixes: lintian: upstream-metadata-file-is-missing
See-also: https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pauvre/-/commit/7162608daed079f606cb85961af6ea4cbe43b227">7162608d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-11T22:40:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<span class="new-file">
+
debian/upstream/metadata
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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="#fb5bccee629bf474046d0f50a6714b171eba2311">
pauvre/custommargin.py
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<li class="file-stats">
<a href="#1273922d0ff5099f80cad189a5e0a96532add900">
pauvre/version.py
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<h4>Changes:</h4>
<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/python-pauvre/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227#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>
</pre>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: pauvre</span>
</pre>
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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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<td class="diff-line-num new_line old" 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: 0.2.<span class="idiff left right">1</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext">Version: 0.2.<span class="idiff left right">2</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="diff-line-num new_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="diff-line-num new_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>
</pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/python-pauvre/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![travis-ci</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/conchoecia/pauvre.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/conchoecia/pauvre) <span class="p">[</span><span class="nv" style="color: #008080;">![DOI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://zenodo.org/badge/112774670.svg</span><span class="p">)</span>](https://zenodo.org/badge/latestdoi/112774670)</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## <a name="started"></a>Getting Started</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## pauvre: a plotting package designed for nanopore and PacBio long reads</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown">pauvre custommargin -i custom.tsv --ycol length --xcol qual # Custom tsv input</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Table of Contents</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Getting Started</span><span class="p">](</span><span class="sx" style="color: #d14;">#started</span><span class="p">)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Users' Guide</span><span class="p">](</span><span class="sx" style="color: #d14;">#uguide</span><span class="p">)</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#installation</span><span class="p">)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Requirements</span><span class="p">](</span><span class="sx" style="color: #d14;">#reqs</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Install Instructions</span><span class="p">](</span><span class="sx" style="color: #d14;">#install</span><span class="p">)</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#usage</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">pauvre stats</span><span class="p">](</span><span class="sx" style="color: #d14;">#stats</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">pauvre marginplot</span><span class="p">](</span><span class="sx" style="color: #d14;">#marginplot</span><span class="p">)</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Basic Usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#marginbasic</span><span class="p">)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Plot Adjustments</span><span class="p">](</span><span class="sx" style="color: #d14;">#marginadjustments</span><span class="p">)</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Specialized Options</span><span class="p">](</span><span class="sx" style="color: #d14;">#marginspecialized</span><span class="p">)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Contributors</span><span class="p">](</span><span class="sx" style="color: #d14;">#contributors</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="markdown"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## <a name="uguide"></a>Users' Guide</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown">Pauvre is a plotting package originally designed to help QC the length and</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">quality distribution of Oxford Nanopore or PacBio reads. The main outputs</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">are marginplots. Now, <span class="sb" style="color: #d14;">`pauvre`</span> also hosts other additional data plotting</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">scripts.</span>
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5
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown">This package currently hosts f<span class="idiff left right">our</span> scripts for plotting and/or printing stats.</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown">This package currently hosts f<span class="idiff left right">ive</span> scripts for plotting and/or printing stats.</span>
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7
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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8
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="p">-</span> <span class="sb" style="color: #d14;">`pauvre marginplot`</span></span>
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9
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="p"> -</span> takes a fastq file as input and outputs a marginal histogram with a heatmap.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">-</span> <span class="sb" style="color: #d14;">`pauvre custommargin`</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p"> -</span> takes a tsv as input and outputs a marginal histogram with custom columns of your choice.</span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"><span class="p">-</span> <span class="sb" style="color: #d14;">`pauvre stats`</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="p"> -</span> Takes a fastq file as input and prints out a table of stats, including how many basepairs/reads there are for a length/mean quality cutoff.</span>
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12
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"><span class="p"> -</span> This is also automagically called when using <span class="sb" style="color: #d14;">`pauvre marginplot`</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="51" 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">@@ -24,7 +51,10 @@ This package currently hosts four scripts for plotting and/or printing stats.</td>
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<pre style="margin: 0;"> <span id="LC51" 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="LC52" class="line" lang="markdown"> per circular genome and one directory of gene alignments.</span>
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<pre style="margin: 0;"> <span id="LC53" 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="LC54" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## <a name="installation"></a>Installation</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### <a name="reqs"></a>Requirements</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC59" 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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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"><span class="p"> -</span> python 3.x</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="63" 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">@@ -33,8 +63,7 @@ This package currently hosts four scripts for plotting and/or printing stats.</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"><span class="p"> -</span> pandas</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="p"> -</span> pillow</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="LC36" class="line" lang="markdown"><span class="gh" style="color: #999;"># Installation</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### <a name="install">Install Instructions</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"><span class="p">-</span> Instructions to install on your mac or linux system. Not sure on</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"> Windows! Make sure <span class="ge" style="font-style: italic;">*python 3*</span> is the active environment before</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"> installing.</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">@@ -44,9 +73,9 @@ This package currently hosts four scripts for plotting and/or printing stats.</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"><span class="p">-</span> Or, install with pip</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`pip3 install pauvre`</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"><span class="gh" style="color: #999;">#<span class="idiff left right"> </span>Usage</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#<span class="idiff left right"># <a name="usage"><a/></span>Usage</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##<span class="idiff left right"> </span>`stats`</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##<span class="idiff left right"># <a name="stats"></a></span>`stats`</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"><span class="p"> -</span> generate basic statistics about the fastq file. For example, if I</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"> want to know the number of bases and reads with AT LEAST a PHRED</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"> score of 5 and AT LEAST a read length of 500, run the program as below</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">@@ -78,9 +107,9 @@ minLen Q0 Q5 Q10 Q15 Q17.5 Q20 Q21.5 Q25 Q25.5 Q30</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"> et cetera...</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##<span class="idiff left right"> </span>`marginplot`</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##<span class="idiff left right"># <a name="marginplot"></a></span>`marginplot`</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right"> Basic u</span>sage</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right"># <a name="marginbasic"></a>Basic U</span>sage</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"><span class="p">-</span> automatically calls <span class="sb" style="color: #d14;">`pauvre stats`</span> for each fastq file</span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"><span class="p">-</span> Make the default plot showing the 99th percentile of longest reads</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`pauvre marginplot --fastq miniDSMN15.fastq`</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">@@ -90,28 +119,27 @@ minLen Q0 Q5 Q10 Q15 Q17.5 Q20 Q21.5 Q25 Q25.5 Q30</td>
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90
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`pauvre marginplot --maxlen 4000 --maxqual 25 --lengthbin 50 --fileform pdf png --qualbin 0.5 --fastq miniDSMN15.fastq`</span></span>
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91
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"><span class="p"> -</span> !<span class="p">[</span><span class="nv" style="color: #008080;">example1</span><span class="p">](</span><span class="sx" style="color: #d14;">files/miniDSMN15.png</span><span class="p">)</span></span>
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Filter reads and adjust viewing window</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### <a name="marginadjustments"></a>Plot Adjustments</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"><span class="p">-</span> Filter out reads with a mean quality less than 5, and a length</span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"> less than 800. Zoom in to plot only mean quality of at least 4 and</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"> read length at least 500bp.</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`pauvre marginplot -f miniDSMN15.fastq --filt_minqual 5 --filt_minlen 800 -y --plot_minlen 500 --plot_minqual 4`</span></span>
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98
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="markdown"><span class="p"> -</span> !<span class="p">[</span><span class="nv" style="color: #008080;">test4</span><span class="p">](</span><span class="sx" style="color: #d14;">files/test4.png</span><span class="p">)</span></span>
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right"> </span>Specialized Options</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right"># <a name="marginspecialized"></a></span>Specialized Options</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="markdown"><span class="p">-</span> Plot ONT 1D data with a large tail</span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`pauvre marginplot --maxlen 100000 --maxqual 15 --lengthbin 500 <myfile>.fastq`</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="markdown"><span class="p">-</span> Get more resolution on lengths</span>
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105
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`pauvre marginplot --maxlen 100000 --lengthbin 5 <myfile>.fastq`</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="markdown"></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Transparency</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="markdown"><span class="p">-</span> Turn off transparency if you just want a white background</span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`pauvre marginplot --transparent False <myfile>.fastq`</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown"><span class="p"> -</span> Note: transparency is the default behavior</span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="markdown"><span class="p"> -</span> !<span class="p">[</span><span class="nv" style="color: #008080;">transparency</span><span class="p">](</span><span class="sx" style="color: #d14;">files/transparency.001.jpeg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown"><span class="gh" style="color: #999;">#<span class="idiff left right"> </span>Contributors</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#<span class="idiff left right"># <a name="contributors"></a></span>Contributors</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="markdown">@conchoecia (Darrin Schultz)</span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown">@mebbert (Mark Ebbert)</span>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pauvre (0.2.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</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"> -- Andreas Tille <tille@debian.org> Thu, 11 Jun 2020 22:36:46 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">python-pauvre (0.2.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Initial release (Closes: #958951)</span>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,7 +3,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -18,6 +18,7 @@ Standards-Version: 4.5.0</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-pauvre</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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-pauvre.git</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Homepage: https://github.com/conchoecia/pauvre</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Package: python3-pauvre</span>
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<td class="diff-line-num old_line" 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="LC24" class="line" lang="plaintext">Architecture: all</span>
</pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/python-pauvre/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">---</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Database: https://github.com/conchoecia/pauvre/issues</span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Bug-Submit: https://github.com/conchoecia/pauvre/issues/new</span></pre>
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<li id="3a274887fec149e281cecbebbc37c26db5395ee6">
<a href="https://salsa.debian.org/med-team/python-pauvre/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227#3a274887fec149e281cecbebbc37c26db5395ee6"><strong>pauvre.egg-info/PKG-INFO</strong></a>
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1
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1
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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="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<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">
3
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<td class="diff-line-num new_line old" 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: 0.2.<span class="idiff left right">1</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3
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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: 0.2.<span class="idiff left right">2</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">
4
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<td class="diff-line-num new_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>
</pre>
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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="diff-line-num new_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">
5
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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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<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">
6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Darrin Schultz</span>
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<li id="fb5bccee629bf474046d0f50a6714b171eba2311">
<a href="https://salsa.debian.org/med-team/python-pauvre/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227#fb5bccee629bf474046d0f50a6714b171eba2311"><strong>pauvre/custommargin.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" 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">@@ -30,6 +30,7 @@ import pandas as pd</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">opath</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sys</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">stderr</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pauvre.functions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_images</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pauvre.marginplot</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">generate_panel</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pauvre.stats</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">stats</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pauvre.rcparams</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">rc</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</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">@@ -38,44 +39,6 @@ import logging</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># logging</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</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="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_panel</span><span class="p">(</span><span class="n" style="color: #333;">panel_left</span><span class="p">,</span> <span class="n" style="color: #333;">panel_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">panel_width</span><span class="p">,</span> <span class="n" style="color: #333;">panel_height</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">axis_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'both'</span><span class="p">,</span> <span class="n" style="color: #333;">which_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'both'</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;">bottom_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'on'</span><span class="p">,</span> <span class="n" style="color: #333;">label_bottom_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'on'</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;">left_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'on'</span><span class="p">,</span> <span class="n" style="color: #333;">label_left_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'on'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">right_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'off'</span><span class="p">,</span> <span class="n" style="color: #333;">label_right_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'off'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">top_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'off'</span><span class="p">,</span> <span class="n" style="color: #333;">label_top_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'off'</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;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> Setting default panel tick parameters. Some of these are the defaults</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> for matplotlib anyway, but specifying them for readability. Here are</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> options and defaults for the parameters used below:</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> axis : {'x', 'y', 'both'}; which axis to modify; default = 'both'</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> which : {'major', 'minor', 'both'}; which ticks to modify;</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> default = 'major'</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> bottom, top, left, right : bool or {'on', 'off'}; ticks on or off;</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> labelbottom, labeltop, labelleft, labelright : bool or {'on', 'off'}</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># create the panel</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">panel_rectangle</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">panel_left</span><span class="p">,</span> <span class="n" style="color: #333;">panel_bottom</span><span class="p">,</span> <span class="n" style="color: #333;">panel_width</span><span class="p">,</span> <span class="n" style="color: #333;">panel_height</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">panel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="n" style="color: #333;">axes</span><span class="p">(</span><span class="n" style="color: #333;">panel_rectangle</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Set tick parameters</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">panel</span><span class="p">.</span><span class="n" style="color: #333;">tick_params</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">axis_tick_param</span><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;">which</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">which_tick_param</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">bottom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bottom_tick_param</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">labelbottom</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label_bottom_tick_param</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">left_tick_param</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">labelleft</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label_left_tick_param</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">right</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">right_tick_param</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">labelright</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label_right_tick_param</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">top_tick_param</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">labeltop</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">label_top_tick_param</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">panel</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_generate_histogram_bin_patches</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="p">,</span> <span class="n" style="color: #333;">bin_values</span><span class="p">,</span> <span class="n" style="color: #333;">horizontal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"""This helper method generates the histogram that is added to the panel.</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></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">@@ -271,19 +234,19 @@ def custommargin(df, **kwargs):</td>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" - Setting panel options."</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC235" 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;">"Y_AXES"</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_spine</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_tick</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'on'</span></span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'on'</span></span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_tick</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">True</span></span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">True</span></span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">x_left_spine</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">x_left_tick</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'on'</span></span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">x_left_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'on'</span></span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">x_left_tick</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">True</span></span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">x_left_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">True</span></span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">x_y_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Count'</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_spine</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_tick</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'off'</span></span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'off'</span></span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_tick</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">False</span></span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">y_bottom_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">False</span></span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">x_left_spine</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">x_left_tick</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'off'</span></span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">x_left_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'off'</span></span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">x_left_tick</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">False</span></span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">x_left_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">False</span></span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">x_y_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">panels</span> <span class="o" style="font-weight: 600;">=</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">@@ -336,12 +299,12 @@ def custommargin(df, **kwargs):</td>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">legend_panel_height</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">heat_map_panel_height</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">fig_height</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">legend_panel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">generate_panel</span><span class="p">(</span><span class="n" style="color: #333;">legend_panel_left</span><span class="p">,</span> <span class="n" style="color: #333;">legend_panel_bottom</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">legend_panel_width</span><span class="p">,</span> <span class="n" style="color: #333;">legend_panel_height</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">bottom_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'off'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">label_bottom_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'off'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">left_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'off'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">label_left_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'off'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">right_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'on'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">label_right_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'on'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">bottom_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">False</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">label_bottom_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">False</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">left_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">False</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">label_left_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">False</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">right_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">True</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">label_right_tick_param</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">True</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">panels</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">legend_panel</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/python-pauvre/-/compare/fbc74f864c27fd7d2889e2a3cf977aeb685440bd...7162608daed079f606cb85961af6ea4cbe43b227#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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2
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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;">"0.2.<span class="idiff left right">1</span>"</span></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;">"0.2.<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span></pre>
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