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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libedlib">Debian Med / libedlib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/commit/d0a9904c3ca3981b44719517927e879512065ae4">d0a9904c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-11T10:08:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add Python3 bindings
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libedlib/commit/91091344f9685d5d5099858ebcc91b3fcae2e6fb">91091344</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-11T12:12:21Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try hard to enforce buildsystem=pybuild over cmake but failed
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#c5b12eedcbfaeb489795a3c470454f1eea540ffb">
<span class="new-file">
+
debian/patches/cython3.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libedlib/compare/aad52a1b3d59da7b059605e9dc78456291a83e36...91091344f9685d5d5099858ebcc91b3fcae2e6fb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">libedlib (1.2.3-4) UNRELEASED; 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"> * Make sure the executable is found in test</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add Python3 bindings</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="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Sun, 21 Oct 2018 08:05:00 +02</span>00</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Tue, 11 Dec 2018 09:52:41 +01</span>00</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">libedlib (1.2.3-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libedlib/compare/aad52a1b3d59da7b059605e9dc78456291a83e36...91091344f9685d5d5099858ebcc91b3fcae2e6fb#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,8 +5,12 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> d-shlibs,</span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> rename</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> rename,</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> cython3,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-dev,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-setuptools</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Standards-Version: 4.2.1</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/libedlib</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/libedlib.git</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">@@ -103,3 +107,36 @@ Description: edlib sequence alignment tool using edit distance</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"> * It can easily handle small or very large sequences, even when finding</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> alignment path, while consuming very little memory.</span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> * Super fast thanks to Myers's bit-vector algorithm.</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">Package: python3-edlib</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> ${python3:Depends}</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">Description: library for sequence alignment using edit distance (Python3 module)</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> A lightweight and super fast C/C++ library for sequence alignment using</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> edit distance.</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> Calculating edit distance of two strings is as simple as:</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> edlibAlign("hello", 5, "world!", 6,</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> edlibDefaultAlignConfig()).editDistance;</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> Features</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> * Calculates edit distance (Levehnstein distance).</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> * It can find optimal alignment path (instructions how to transform</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> first sequence into the second sequence).</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> * It can find just the start and/or end locations of alignment path -</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> can be useful when speed is more important than having exact</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> alignment path.</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> * Supports multiple alignment methods: global(NW), prefix(SHW) and</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> infix(HW), each of them useful for different scenarios.</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> * You can extend character equality definition, enabling you to e.g.</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> have wildcard characters, to have case insensitive alignment or to</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> work with degenerate nucleotides.</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> * It can easily handle small or very large sequences, even when finding</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> alignment path, while consuming very little memory.</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> * Super fast thanks to Myers's bit-vector algorithm.</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> .</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> This package contains the Python3 module.</span></pre>
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<li id="c5b12eedcbfaeb489795a3c470454f1eea540ffb">
<a href="https://salsa.debian.org/med-team/libedlib/compare/aad52a1b3d59da7b059605e9dc78456291a83e36...91091344f9685d5d5099858ebcc91b3fcae2e6fb#c5b12eedcbfaeb489795a3c470454f1eea540ffb"><strong>debian/patches/cython3.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: Tue, 11 Dec 2018 09:52:41 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Use Cython3/Python3</span>
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4
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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/bindings/python/Makefile</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/bindings/python/Makefile</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;">@@ -7,15 +7,15 @@ edlib: ../../edlib</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> cp -R ../../edlib .</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"> pyedlib.bycython.cpp: edlib.pyx cedlib.pxd</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;">- cython --cplus edlib.pyx -o edlib.bycython.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cython3 --cplus edlib.pyx -o edlib.bycython.cpp</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> #######################################</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> ############## COMMANDS ###############</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> build: ${FILES}</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py build_ext -i</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py build_ext -i</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> sdist: ${FILES}</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py sdist</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py sdist</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> publish: clean sdist</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> twine upload dist/*</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/libedlib/compare/aad52a1b3d59da7b059605e9dc78456291a83e36...91091344f9685d5d5099858ebcc91b3fcae2e6fb#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">soversion.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">do_not_build_hello_example.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">cython3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/libedlib/compare/aad52a1b3d59da7b059605e9dc78456291a83e36...91091344f9685d5d5099858ebcc91b3fcae2e6fb#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,15 +2,27 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<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"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">export PYBUILD_NAME = edlib</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">DEB_CMAKE_EXTRA_FLAGS = -DCMAKE_BUILD_TYPE=Release</span>
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8
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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9
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --buildsystem=pybuild</span></span>
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11
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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12
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">override_dh_auto_configure:</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> dh_auto_configure -- $(DEB_CMAKE_EXTRA_FLAGS)</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> dh_auto_configure --buildsystem=cmake -- $(DEB_CMAKE_EXTRA_FLAGS)</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">override_dh_auto_build:</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dh_auto_build --buildsystem=cmake</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> # $(MAKE) --directory=bindings/python</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> dh_auto_build -O--buildsystem=pybuild -O--source-directory=bindings/python</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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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">override_dh_auto_install:</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> dh_auto_install --buildsystem=cmake</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"># $(MAKE) install --directory=bindings/python</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> dh_auto_install --buildsystem=pybuild -O--source-directory=bindings/python</span>
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14
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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15
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">override_dh_install:</span>
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16
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> dh_install</span>
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