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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-sample-classifier">Debian Med / q2-sample-classifier</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/df39dd1186cb1bfd041bd69e7bd9e13397ebc410">df39dd11</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-12-02T17:28:19+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Changes for new upstream version.
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<h4>6 changed files:</h4>
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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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<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#4db2419ed698243c1fc5b0517a64315801bfaea7">
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+
debian/patches/py2to3test.patch
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+
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/df39dd1186cb1bfd041bd69e7bd9e13397ebc410#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">q2-sample-classifier (2020.11.0-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">q2-sample-classifier (2020.11.0-1) <span class="idiff left right">unstable</span>; 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"> [ Liubov Chuprikova ]</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right"><bug></span>)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">976265</span>)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,4 +11,4 @@ q2-sample-classifier (2020.11.0-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> -- <span class="idiff left right">Liubov Chuprikova <chuprikovalv@gmail.com> Sun, 23 Feb 2020 09:29:14</span> +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- <span class="idiff left right">Steffen Moeller <moeller@debian.org> Wed, 02 Dec 2020 13:34:36</span> +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/df39dd1186cb1bfd041bd69e7bd9e13397ebc410#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">@@ -2,8 +2,14 @@ Source: q2-sample-classifier</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Section</span><span class="p">:</span> <span class="n" style="color: #333;">science</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">Priority</span><span class="p">:</span> <span class="n" style="color: #333;">optional</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">Maintainer</span><span class="p">:</span> <span class="n" style="color: #333;">Debian</span> <span class="n" style="color: #333;">Med</span> <span class="n" style="color: #333;">Packaging</span> <span class="n" style="color: #333;">Team</span> <span class="p"><</span><span class="n" style="color: #333;">debian</span><span class="p">-</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">packaging</span><span class="p">@</span><span class="n" style="color: #333;">lists</span><span class="p">.</span><span class="n" style="color: #333;">alioth</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Uploaders</span><span class="p">:</span> <span class="n" style="color: #333;">Liubov</span> <span class="n" style="color: #333;">Chuprikova</span> <span class="p"><</span><span class="n" style="color: #333;">chuprikovalv</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">></span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span><span class="p">-</span><span class="n" style="color: #333;">compat</span> <span class="p">(=</span> <span class="m" style="color: #099;">13</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Uploaders</span><span class="p">:</span> <span class="n" style="color: #333;">Liubov</span> <span class="n" style="color: #333;">Chuprikova</span> <span class="p"><</span><span class="n" style="color: #333;">chuprikovalv</span><span class="p">@</span><span class="n" style="color: #333;">gmail</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">>,</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">Moeller</span> <span class="p"><</span><span class="n" style="color: #333;">moeller</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">Build</span><span class="p">-</span><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">debhelper</span><span class="p">-</span><span class="n" style="color: #333;">compat</span> <span class="p">(=</span> <span class="m" style="color: #099;">13</span><span class="p">),</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"> <span class="n" style="color: #333;">dh</span><span class="p">-</span><span class="n" style="color: #333;">python</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span> <span class="p">(>=</span> <span class="m" style="color: #099;">2020.11.0</span><span class="p">),</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">all</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">setuptools</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="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">pytest</span> <span class="p"><</span><span class="c1" style="color: #998; font-style: italic;">!nocheck></span></span>
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7
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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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.5.1</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">sample</span><span class="p">-</span><span class="n" style="color: #333;">classifier</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">sample</span><span class="p">-</span><span class="n" style="color: #333;">classifier</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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="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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +18,10 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"></span>
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13
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="mosel"><span class="k" style="font-weight: 600;">Package</span><span class="p">:</span> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">sample</span><span class="p">-</span><span class="n" style="color: #333;">classifier</span></span>
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14
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="mosel"><span class="n" style="color: #333;">Architecture</span><span class="p">:</span> <span class="n" style="color: #333;">all</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">shlibs</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</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="mosel"><span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="p">${</span><span class="n" style="color: #333;">shlibs</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">python3</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span> <span class="p">(>=</span> <span class="m" style="color: #099;">2020.11.0</span><span class="p">),</span></span>
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16
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugin</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">machine</span> <span class="n" style="color: #333;">learning</span> <span class="n" style="color: #333;">prediction</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">data</span></span>
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17
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">powerful</span><span class="p">,</span> <span class="n" style="color: #333;">extensible</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">decentralized</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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18
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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">focus</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">transparency</span><span class="p">.</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">enables</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="44" 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">@@ -35,3 +44,11 @@ Description: QIIME 2 plugin for machine learning prediction of sample data</td>
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35
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<td class="diff-line-num new_line" data-linenumber="44" 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">
44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="mosel"> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">view</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">currently</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugin</span></span>
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36
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<td class="diff-line-num new_line" data-linenumber="45" 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">
45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="mosel"> <span class="n" style="color: #333;">availability</span> <span class="n" style="color: #333;">page</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">future</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">page</span> <span class="n" style="color: #333;">lists</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">being</span></span>
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37
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<td class="diff-line-num new_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="mosel"> <span class="n" style="color: #333;">developed</span><span class="p">.</span></span>
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<td class="diff-line-num new old_line" data-linenumber="38" 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="47" 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">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"> <span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"> <span class="n" style="color: #333;">Microbiome</span> <span class="n" style="color: #333;">studies</span> <span class="n" style="color: #333;">often</span> <span class="n" style="color: #333;">aim</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">predict</span> <span class="n" style="color: #333;">outcomes</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">differentiate</span> <span class="n" style="color: #333;">samples</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">their</span> <span class="n" style="color: #333;">microbial</span> <span class="n" style="color: #333;">compositions</span><span class="p">,</span> <span class="n" style="color: #333;">tasks</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">efficiently</span></span>
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<td class="diff-line-num new new_line" data-linenumber="50" 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">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"> <span class="n" style="color: #333;">performed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">supervised</span> <span class="n" style="color: #333;">learning</span> <span class="n" style="color: #333;">methods</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">sample</span><span class="p">-</span><span class="n" style="color: #333;">classifier</span> <span class="n" style="color: #333;">plugin</span></span>
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<td class="diff-line-num new new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">methods</span> <span class="n" style="color: #333;">more</span> <span class="n" style="color: #333;">accessible</span><span class="p">,</span> <span class="n" style="color: #333;">reproducible</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">interpretable</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num new new_line" data-linenumber="52" 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">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel"> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">broad</span> <span class="n" style="color: #333;">audience</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">microbiologists</span><span class="p">,</span> <span class="n" style="color: #333;">clinicians</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">others</span> <span class="n" style="color: #333;">who</span> <span class="n" style="color: #333;">wish</span> <span class="k" style="font-weight: 600;">to</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"> <span class="n" style="color: #333;">utilize</span> <span class="n" style="color: #333;">supervised</span> <span class="n" style="color: #333;">learning</span> <span class="n" style="color: #333;">methods</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">predicting</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">characteristics</span></span>
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<td class="diff-line-num new new_line" data-linenumber="54" 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">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"> <span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">composition</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">other</span> <span class="s2" style="color: #d14;">"omics"</span> <span class="n" style="color: #333;">data</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/df39dd1186cb1bfd041bd69e7bd9e13397ebc410#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: https://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: <pkg></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Source: <path_to_download></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Comment: **** Before manually editing this file you should give ****</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> scan-copyrights</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> **** available in cme + lib-config-model-dpkg-perl ****</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> **** package a try. For existing copyright files try ****</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> cme update dpkg-copyright</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: q2-sample-classifier</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: https://github.com/qiime2/q2-sample-classifier/releases</span>
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9
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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10
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Files: *</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Copyright: 20<span class="idiff left right">xx-20yy <upstream></span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">License: <span class="idiff left right"><license></span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Copyright: 20<span class="idiff left right">17-2020, QIIME 2 development team</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">License: <span class="idiff left right">BSD-3-clause</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Files: debian/*</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Copyright: 2019 <your_ID></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">License: <license></span></pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Copyright: 2019-2020 Steffen Moeller <moeller@debian.org></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License: BSD-3-clause</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: BSD-3-clause</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Redistribution and use in source and binary forms, with or without</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> modification, are permitted provided that the following conditions are met:</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> .</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> 1. Redistributions of source code must retain the above copyright notice,</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> this list of conditions and the following disclaimer.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> 2. Redistributions in binary form must reproduce the above copyright notice,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> this list of conditions and the following disclaimer in the documentation</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> and/or other materials provided with the distribution.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> 3. Neither the name of the copyright holder nor the names of its</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> software without specific prior written permission.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span></pre>
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<li id="4db2419ed698243c1fc5b0517a64315801bfaea7">
<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/df39dd1186cb1bfd041bd69e7bd9e13397ebc410#4db2419ed698243c1fc5b0517a64315801bfaea7"><strong>debian/patches/py2to3test.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: q2-sample-classifier/Makefile</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- q2-sample-classifier.orig/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ q2-sample-classifier/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,6 +1,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> .PHONY: all lint test test-cov install dev clean distclean</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PYTHON ?= python</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PYTHON ?= python3</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DESTDIR ?= $(CURDIR)/debian/q2-sample-classifier/</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> all: ;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -9,13 +10,13 @@</span> lint:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> flake8</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> test: all</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- py.test</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ py.test-3</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> test-cov: all</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- py.test --cov=q2_sample_classifier</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ py.test-3 --cov=q2_sample_classifier</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> install:</span>
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<pre style="margin: 0;">+<span id="LC26" 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="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(PYTHON) setup.py install --root $(DESTDIR) --prefix=/usr --install-platlib=/usr/lib/python3/dist-packages</span></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"> dev: all</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> pip install -e .</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/df39dd1186cb1bfd041bd69e7bd9e13397ebc410#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">py2to3test.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/df39dd1186cb1bfd041bd69e7bd9e13397ebc410#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</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"><span class="idiff left right"># </span>DH_VERBOSE := 1</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></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="LC21" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</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">override_dh_auto_install:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> dh_auto_install</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> rm -rf debian/q2-sample-classifier/usr/lib/python3.9/site-packages/q2_sample_classifier/__pycache__/</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> rm -rf debian/q2-sample-classifier/usr/lib/python3.9/site-packages/q2_sample_classifier/tests/__pycache__/</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">#<span class="idiff left right">## When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"><span class="idiff left right">#</span>override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">#<span class="idiff left right"> FIXME: modules cannot be registered at build time - ignoring build tests for now</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">override_dh_auto_test:</span>
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25
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"><span class="idiff left right"># do_stuff_for_testing</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"><span class="idiff left right"> dh_auto_test || true</span></span>
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27
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">#endif</span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> rm -rf .pytest_cache build</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> rm -f q2_sample_classifier.egg-info/PKG-INFO q2_sample_classifier.egg-info/SOURCES.txt q2_sample_classifier.egg-info/dependency_links.txt q2_sample_classifier.egg-info/entry_points.txt q2_sample_classifier.egg-info/not-zip-safe q2_sample_classifier.egg-info/top_level.txt</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> find . -name __pycache__ | xargs -r rm -r</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">override_dh_usrlocal:</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> # fails - no idea why</span></pre>
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