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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/microbegps">Debian Med / microbegps</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/microbegps/commit/dd2de3d5738e1e9db3125634dca98c11194f980a">dd2de3d5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T14:25:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/microbegps/commit/18ffadf31dc183b6b7fea8bc8a8df9d5c032437b">18ffadf3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T14:56:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix linking of data dir
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/microbegps/commit/12da5071a42b1cb647a3a038c9e06c9521d2d457">12da5071</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T14:56:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/microbegps/commit/5913289309544debac195fac51dd7f1bb457bee1">59132893</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T14:56:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/microbegps/commit/8a3a44091bfe66651cda5d5d437985bf2e223172">8a3a4409</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T14:56:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/microbegps/commit/481aa88e394c435da735a0747b2854f26c8fa473">481aa88e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T14:56:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in debian/watch.
Fixes lintian: debian-watch-uses-insecure-uri
See https://lintian.debian.org/tags/debian-watch-uses-insecure-uri.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/microbegps/commit/6210c0d9c0f3926f63cb5c8e01f342590c903d55">6210c0d9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T14:56:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Archive.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/microbegps/commit/c456bd2a0ead992c8bf434f1bf8cf1a64408970c">c456bd2a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-05T15:00:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">microbegps (1.0.0-4) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #937043</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * Secure URI in copyright format</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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"> * Use secure URI in debian/watch.</span>
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<td class="diff-line-num new new_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="LC9" class="line" lang="plaintext"> * Set upstream metadata fields: Archive.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 05 Sep 2019 16:56:54 +0200</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext">microbegps (1.0.0-3) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * debhelper 11</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c#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">@@ -3,12 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python-setuptools,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> python<span class="idiff left right">-</span>qt4</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-setuptools,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python<span class="idiff left right">3-py</span>qt4</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.0</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/microbegps</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/microbegps.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: http://sourceforge.net/projects/microbegps/</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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">@@ -16,9 +16,9 @@ Homepage: http://sourceforge.net/projects/microbegps/</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Package: microbegps</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> python-matplotlib-venn,</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> python<span class="idiff left right">-</span>qt4</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> ${python<span class="idiff left right">3</span>:Depends},</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-matplotlib-venn,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python<span class="idiff left right">3-py</span>qt4</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Description: explorative taxonomic profiling tool for metagenomic data</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> MicrobeGPS is a bioinformatics tool for the analysis of metagenomic</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> sequencing data. The goal is to profile the composition of metagenomic</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: MicrobeGPS</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: Martin S. Lindner <LindnerM@rki.de></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: http://sourceforge.net/projects/microbegps/files/</span>
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<a href="https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/937043</span></span>
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1
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 06 May 2015 15:53:45 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Patch created by 2to3 to run with Python3</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Thu, 05 Sep 2019 16:17:31 +0200</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/README</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -52,7 +52,7 @@</span> Installation</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> * Source distribution</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> Download the MicrobeGPS source file from the project home page. This method</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- requires you to have Python (>= 2.7), PyQt4 and pip installed. To install </span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ requires you to have Python3 (>= 3.3), PyQt4 and pip installed. To install </span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> MicrobeGPS, run the following command from your command line:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> > pip install MicrobeGPS-X.X.tax.gz</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> Now you can run the program by typing MicrobeGPS on the command line.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -61,9 +61,9 @@</span> Installation</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> Check out a current development snapshot from the MicrobeGPS project page.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> Navigate to the MicrobeGPS directory. Now you can directly run MicrobeGPS </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> from the command line with:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- > python run.py</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ > python3 run.py</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> Install MicrobeGPS using the provided setup.py script:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- > python setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ > python3 setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> Now you can run the program by typing MicrobeGPS on the command line.</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -77,13 +77,13 @@</span> If you want to use the source distributi</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> following dependencies.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> Software:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * Python (2.7)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * Python3 (3.3)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> Python packages:</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> * setuptools (1.3)</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> * PyQt4 (4.9)</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-The following Python packages must be installed manually, if the tool is not</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-installed as a python egg or via the setup.py script:</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+The following Python3 packages must be installed manually, if the tool is not</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+installed as a python3 egg or via the setup.py script:</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> * numpy (1.8.0)</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> * scipy (0.13.0)</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> * matplotlib (1.3.1)</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/microbegps/__init__.py</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/microbegps/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -1,3 +1,3 @@</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __version__ import __version__,__url__</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .__version__ import __version__,__url__</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> #__version__='1.0.0'</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> #__url__='https://sourceforge.net/p/microbegps'</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/microbegps/gps.py</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/microbegps/gps.py</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"><span class="p">@@ -5,11 +5,11 @@</span> Analysis tools used by MicrobeGPS</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="236" 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">@@ -236,6 +285,15 @@ Description: Patch created by 2to3 to run with Python3</td>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="diff"> pool.close()</span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="diff"> #GpsTools.calculate_valcov(p.ref_table,printer)</span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="diff"> def custom_filt2(ref):</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="p">@@ -879,7 +879,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> self.load_modules()</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> def load_modules(self):</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """ Loads all python modules located in 'modules'. This function was </span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ """ Loads all python3 modules located in 'modules'. This function was </span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> inspired by Luca Invernizzi on http://stackoverflow.com/a/8556471"""</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> modules_d = dict()</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> for importer, mod_name, _ in pkgutil.iter_modules(modules.__path__):</span>
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239
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="diff"><span class="p">@@ -892,7 +892,7 @@</span> class GPSAnalyzer(QtGui.QMainWindow):</span>
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240
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="diff"> self.pr('<b><font color="DarkRed">Failed loading module %s</font></b><br>Message: <i>%s</i>'%(mod_name,e.message)) </span>
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241
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="diff"> self.modules = modules_d</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -394,14 +452,13 @@ Description: Patch created by 2to3 to run with Python3</td>
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394
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="diff"> assert type(settings) == dict</span>
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395
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="diff"> try:</span>
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396
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454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="diff"> sgroups = settings['candidates']</span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/microbegps/__init__.py</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/microbegps/__init__.py</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="diff"><span class="p">@@ -1,3 +1,3 @@</span></span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __version__ import __version__,__url__</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .__version__ import __version__,__url__</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="diff"> #__version__='1.0.0'</span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="diff"> #__url__='https://sourceforge.net/p/microbegps'</span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="p">@@ -1739,4 +1739,4 @@</span> def main():</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> app.exec_() </span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> </span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"> if __name__ == '__main__':</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- main()</span></span>
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404
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460
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ main()</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/microbegps/modules/composition_analysis.py</span></span>
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406
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/microbegps/modules/composition_analysis.py</span></span>
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464
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="diff"><span class="p">@@ -79,15 +79,15 @@</span> class GPSModule:</span>
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<a href="https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right"># </span>2to3.patch</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -2,13 +2,16 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">export DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export PYBUILD_NAME=microbegps</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">INTERPRETER=python<span class="idiff left right">2.7</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">INTERPRETER=python<span class="idiff left right">3</span></span>
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6
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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">%:</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2</span> --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">3</span> --buildsystem=pybuild</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> mkdir -p debian/$(PYBUILD_NAME)/usr/share/$(PYBUILD_NAME)</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> mv debian/$(PYBUILD_NAME)/usr/lib/$(INTERPRETER)/dist-packages/microbegps/data debian/$(PYBUILD_NAME)/usr/share/$(PYBUILD_NAME)</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> ln -s ../../../../share/$(PYBUILD_NAME)/data debian/$(PYBUILD_NAME)/usr/lib/$(INTERPRETER)/dist-packages/microbegps/</span></pre>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> mv debian/$(PYBUILD_NAME)/usr/lib/$(INTERPRETER)*/dist-packages/microbegps/data debian/$(PYBUILD_NAME)/usr/share/$(PYBUILD_NAME)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">override_dh_link:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> dh_link</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> dh_link /usr/share/$(PYBUILD_NAME)/data /usr/lib/$(INTERPRETER)/dist-packages/$(PYBUILD_NAME)/data</span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right"> - Author: </span> Martin S. Lindner and Bernhard Y. Renard</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right"> </span>Title: Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right"> </span>Journal: PLoS One</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>Year: 2015</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>Volume: 10</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right"> </span>Number: 2</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>Pages: e0117711</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>DOI: 10.1371/journal.pone.0117711</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>PMID: 25643362</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117711</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right"> </span>eprint: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0117711&representation=PDF</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">- Author:</span> Martin S. Lindner and Bernhard Y. Renard</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Journal: PLoS One</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Year: 2015</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Volume: 10</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Number: 2</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Pages: e0117711</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> DOI: 10.1371/journal.pone.0117711</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> PMID: 25643362</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117711</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> eprint: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0117711&representation=PDF</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> - Name: OMICtools</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> Entry: OMICS_17085</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> - Name: bio.tools</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> Entry: MicrobeGPS</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> - Name: SciCrunch</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> Entry: NA</span></pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">- Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Entry: OMICS_17085</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">- Name: bio.tools</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Entry: MicrobeGPS</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">- Name: SciCrunch</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Entry: NA</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Archive: SourceForge</span></pre>
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<a href="https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=3</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">http://sf.net/microbegps/MicrobeGPS-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">http<span class="idiff left right">s</span>://sf.net/microbegps/MicrobeGPS-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))</span></pre>
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