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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-cogent">Debian Med / python-cogent</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/b4a4ef2055d49e14f711c8a753e883e713c934c9">b4a4ef20</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-06T09:40:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some typos
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/e1114c48e802080ece92029513e31c2186662ea8">e1114c48</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-06T09:54:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix privacy issue in doc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/01707a9f8930f2bca53ae83ae132bd0daaf64caf">01707a9f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-06T10:05:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop obsolete file debian/pyversions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/b0411300176d4de0f6e1cbfbd984221c63887d8e">b0411300</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-06T10:06:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix more spelling issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/4ddd312fd15f46bbf0b2a8cedcb8045e9d8a3c33">4ddd312f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-06T10:06:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop unneeded get-orig-source target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/0d01ff9af12969cbce878d98a67f8c327e5d5092">0d01ff9a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-06T10:08:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not parse d/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/bf8aa6a98dbfd0d6693e4d93fd8838ae32f92e71">bf8aa6a9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-06T10:33:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rename debian/tests/control to debian/tests/control.autodep8
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/cec8621c20f252f6af48cc96898486b0bf60eb5d">cec8621c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-06T11:09:53+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure test files will not end up in two packages, remove useless doctree files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc">e113d1c8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-06-06T11:16:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#f9ef23d9ffa9a1e60f7b065b61f85b8026e71baf">
debian/patches/ignore_numpy_test_issue.patch
</a>
</li>
<li class="file-stats">
<a href="#b46d29336084baa469c9a38cc2012f37c6a81b88">
<span class="new-file">
+
debian/patches/privacy.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#461c8e5572730bd4125e5ab1bc91f8044d4262ea">
debian/patches/raxml_unsupported_version.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#0bba138a5eaaa1a94aa68148bc14ebf3112f1e0d">
debian/patches/usr_bin_ls.patch
</a>
</li>
<li class="file-stats">
<a href="#2b6e3400065044f40b2fbc46bd83e14028d9fe80">
<span class="deleted-file">
−
debian/python-cogent-doc.docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#ddc828344fdd418e6bd51f5ccce232b39ae9d120">
<span class="new-file">
+
debian/python-cogent.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#fd69c370803e04887b202eb8e9f9d2fc535ec327">
<span class="deleted-file">
−
debian/pyversions
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#b4050d1f9b649372e9a774473db2bfeae3683f6d">
debian/tests/control
→
debian/tests/control.autodep8
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-cogent (1.9-12) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2" 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="1" 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">
1
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-cogent (1.9-12) <span class="idiff left right">unstable</span>; urgency=medium</span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Add registry data</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Testsuite: autopkgtest-pkg-python</span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="9" 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">@@ -9,8 +9,14 @@ python-cogent (1.9-12) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="9" 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">
9
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<td class="diff-line-num new_line" data-linenumber="9" 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">
9
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Standards-Version: 4.1.4</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Fix suite fails with latest matplotlib</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="diff-line-num 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">
11
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Closes: #899205</span>
</pre>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 05 Jun 2018 21:47:29 +0200</span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Fix privacy issue in doc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Drop obsolete file debian/pyversions</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Drop unneeded get-orig-source target</span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="15" 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="LC15" class="line" lang="plaintext"> * Do not parse d/changelog</span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="16" 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">
16
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Rename debian/tests/control to debian/tests/control.autodep8</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * Remove useless doctree files</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 06 Jun 2018 11:10:01 +0200</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">python-cogent (1.9-11) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#f9ef23d9ffa9a1e60f7b065b61f85b8026e71baf"><strong>debian/patches/ignore_numpy_test_issue.patch</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">@@ -7,10 +7,10 @@ Description: Skip test featuring wrong numpy usage</td>
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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"> TypeError: 'numpy.float64' object cannot be interpreted as an index</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"> The issue occured after upgrading from Numpy 1.11.2 to 1.12.0~b1 which</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> The issue occur<span class="idiff left right">r</span>ed after upgrading from Numpy 1.11.2 to 1.12.0~b1 which</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> has cause also other packages test suites failures. Since this version</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> of Cogent is in low maintenance mode it will probably not be adapted to</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> any new Numpy versions so skip<span class="idiff left right">ing two tests might be the most a</span>propriate</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> any new Numpy versions so skip<span class="idiff left right">ping two tests might be the most ap</span>propriate</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> step to deal with this issue</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/848746</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#b46d29336084baa469c9a38cc2012f37c6a81b88"><strong>debian/patches/privacy.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Tue, 05 Jun 2018 21:47:29 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Avoid insertion of Google phone home code</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/templates/layout.html</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/templates/layout.html</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,10 +1,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> {% extends "!layout.html" %}</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"><span class="gd" style="color: #000; background-color: #fdd;">-{% block extrahead %} </span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<script type="text/javascript" src="http://www.google.com/jsapi?key=ABQIAAAAbW_pA971hrPgosv-Msv7hRQZ4X-jPDmWcshBrz2j7-fJvuUABRTGWmdiw2G89JpgztGlFGG8hDxRAw"></script>\</span></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;">-<script type="text/javascript" src="{{ pathto("_static/google_feed.js",1)}}"></script></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-{% endblock %}</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> {% block sidebartoc %}</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> <div class="news"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> <table id="feed"><tr><td><h3><a href="http://pycogent.wordpress.com/">PyCogent News and Announcements</a></h3></td></span></pre>
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<li id="461c8e5572730bd4125e5ab1bc91f8044d4262ea">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#461c8e5572730bd4125e5ab1bc91f8044d4262ea"><strong>debian/patches/raxml_unsupported_version.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Last-Update: Thu, 21 May 2015 08:47:01 +0200</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: The test is checking for an old ver<span class="idiff left right">is</span>on of raxml</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: The test is checking for an old ver<span class="idiff left right">si</span>on of raxml</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> for no good reason</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_app/test_raxml_v730.py</span></span>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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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">@@ -11,3 +11,4 @@ ignore_numpy_test_issue.patch</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">usr_bin_ls.patch</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">numpy_xor.patch</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">numpy-doctests.patch</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">privacy.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#0bba138a5eaaa1a94aa68148bc14ebf3112f1e0d"><strong>debian/patches/usr_bin_ls.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Last-Update: Fri, 16 Jun 2017 13:30:22 +0200</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Desription: ls will be moved from /bin/ls to /usr/bin/ls - lets skip</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Des<span class="idiff left right">c</span>ription: ls will be moved from /bin/ls to /usr/bin/ls - lets skip</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> this test which does not make real sense anyway.</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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_util/test_misc.py</span></span>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#2b6e3400065044f40b2fbc46bd83e14028d9fe80"><strong>debian/python-cogent-doc.docs</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">tests</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#ddc828344fdd418e6bd51f5ccce232b39ae9d120"><strong>debian/python-cogent.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">tests</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">python</span><span class="o" style="font-weight: 600;">-</span><span class="nx">cogent</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#fd69c370803e04887b202eb8e9f9d2fc535ec327"><strong>debian/pyversions</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.4-</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/71f105c54476f1f764723d3ec2eea36b9160c756...e113d1c8c87f9ca5d5152c1ce88ad8bdad8216bc#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">@@ -41,7 +41,8 @@ FAIL_ON_S390X_TESTS := test_maths.test_optimisers \</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"><span class="nv" style="color: teal;">FAIL_ON_MIPS_TESTS</span> <span class="o" style="font-weight: 600;">:=</span> test_seqsim.test_sequence_generators</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: teal;">PYBUILD_NAME</span><span class="o" style="font-weight: 600;">=</span>cogent</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="make"><span class="nv" style="color: teal;">PKG</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-n</span> <span class="s1" style="color: #d14;">'s/^Source: //p'</span><span class="nv" style="color: teal;">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">include</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">/usr/share/dpkg/default.mk</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="make"> dh <span class="nv" style="color: teal;">$@</span> <span class="nt" style="color: navy;">--with</span> python2 <span class="nt" style="color: navy;">--buildsystem</span><span class="o" style="font-weight: 600;">=</span>pybuild</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,7 +60,7 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="make"> dh_auto_build</span>
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60
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>doc<span class="p">;</span> <span class="nv" style="color: teal;">$(MAKE)</span> html</span>
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61
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># remove superfluous files and dirs</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="make"> <span class="nb" style="color: #0086b3;"><span class="idiff left">rm</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-f</span></span><span class="idiff right"> doc/_build/doctrees/COGENT_LICENSE.doctre</span>e</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="make"> <span class="idiff left">find doc/_build </span><span class="nt" style="color: navy;"><span class="idiff">-name</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"*.doctree*"</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff right">-delet</span>e</span></span>
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63
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> doc/_build/html/_sources/COGENT_LICENSE.txt</span>
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64
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> doc/_build/html/_static/jquery.js</span>
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65
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> doc/_build/html/_static/underscore.js</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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">@@ -74,7 +75,8 @@ override_dh_compress:</td>
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74
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="make"></span>
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75
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="make"><span class="nl">override_dh_installdocs</span><span class="o" style="font-weight: 600;">:</span></span>
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76
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="make"> dh_installdocs</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> debian/<span class="nv" style="color: teal;">$(PKG)</span>/usr/share/doc/<span class="nv" style="color: teal;">$(PKG)</span>/html/_sources</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> debian/<span class="nv" style="color: teal;">$(DEB_SOURCE)</span>/usr/share/doc/<span class="nv" style="color: teal;">$(DEB_SOURCE)</span>/html/_sources</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="make"> find debian <span class="nt" style="color: navy;">-name</span> doctrees <span class="nt" style="color: navy;">-type</span> d | xargs <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span></span>
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78
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="make"></span>
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79
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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="make"><span class="nl">override_dh_auto_test</span><span class="o" style="font-weight: 600;">:</span></span>
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80
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(,$(filter</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">nocheck,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(DEB_BUILD_OPTIONS)))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" 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="112" 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">@@ -110,8 +112,3 @@ endif</td>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mv</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py~</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">find</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-name</span> <span class="s2" style="color: #d14;">"*.pyc"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-delete</span></span>
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112
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span></pre>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="make"></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="make"><span class="nl">get-orig-source</span><span class="o" style="font-weight: 600;">:</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> ../tarballs</span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="make"> uscan <span class="nt" style="color: navy;">--verbose</span> <span class="nt" style="color: navy;">--force-download</span> <span class="nt" style="color: navy;">--destdir</span><span class="o" style="font-weight: 600;">=</span>../tarballs</span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="make"></span></pre>
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