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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/flye">Debian Med / flye</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/flye/-/commit/c221816bf964bd6eaca1d38d128328502a1ec2e7">c221816b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-05T18:18:37+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install files
</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="new-file">
+
debian/docs
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</a>
</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
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+
debian/install
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</li>
<li class="file-stats">
<a href="#ee54dc79014b3def963898e50c98877d46c6b27e">
debian/patches/use_debian_packaged_libs.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/flye/-/commit/c221816bf964bd6eaca1d38d128328502a1ec2e7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +19,7 @@ Homepage: https://github.com/fenderglass/Flye</td>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: flye</span>
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<td class="diff-line-num old_line" data-linenumber="20" 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">
20
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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext">Depends: ${shlibs:Depends},</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">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ${python3:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> ${misc:Depends}</span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
23
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: de novo assembler for single molecule sequencing reads using repeat graphs</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
24
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> Flye is a de novo assembler for single molecule sequencing reads, such</span>
</pre>
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<br>
</li>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/flye/-/commit/c221816bf964bd6eaca1d38d128328502a1ec2e7#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -11,7 +11,7 @@ Copyright: 2016-2019, The Regents of the University of California</td>
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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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Evgeny Polevikov</span>
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<td class="diff-line-num 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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">License: BSD-3-Clause</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Files: lib/interval_tree</span>
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<td class="diff-line-num new old_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="LC14" class="line" lang="plaintext">Files: lib/interval_tree<span class="idiff left right">/*</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Copyright: 2011 Erik Garrison</span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">License: MIT</span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> Permission is hereby granted, free of charge, to any person obtaining a copy of</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="32" 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">@@ -32,7 +32,7 @@ License: MIT</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</span>
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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> SOFTWARE.</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">Files: lib/libcuckoo</span>
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<td class="diff-line-num new old_line" data-linenumber="36" 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="LC35" class="line" lang="plaintext">Files: lib/libcuckoo<span class="idiff left right">/*</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Copyright: 2013, Carnegie Mellon University and Intel Corporation</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">License: Apache-2.0</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> Licensed under the Apache License, Version 2.0 (the "License");</span>
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<a href="https://salsa.debian.org/med-team/flye/-/commit/c221816bf964bd6eaca1d38d128328502a1ec2e7#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">docs/FAQ*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">docs/graph_example.png</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">docs/USAGE*</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">README*</span></pre>
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<a href="https://salsa.debian.org/med-team/flye/-/commit/c221816bf964bd6eaca1d38d128328502a1ec2e7#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bin usr</span></pre>
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<a href="https://salsa.debian.org/med-team/flye/-/commit/c221816bf964bd6eaca1d38d128328502a1ec2e7#ee54dc79014b3def963898e50c98877d46c6b27e"><strong>debian/patches/use_debian_packaged_libs.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">@@ -38,3 +38,14 @@ Description: use Debian packaged libminimap2 and liblemon</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm ${BIN_DIR}/flye-samtools</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f ${BIN_DIR}/flye-minimap2</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f ${BIN_DIR}/flye-samtools</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -55,7 +55,7 @@</span> class MakeInstall(SetuptoolsInstall):</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> build_dir = os.path.join(script_dir, "bin")</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> install_dir = self.install_scripts</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bin_files = ['flye-modules', 'flye-minimap2', 'flye-samtools']</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bin_files = ['flye-modules']</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> for file in bin_files:</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> if not os.path.isfile(os.path.join(build_dir, file)):</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> sys.exit('Error: binary not found: ' + file)</span></pre>
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<a href="https://salsa.debian.org/med-team/flye/-/commit/c221816bf964bd6eaca1d38d128328502a1ec2e7#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">@@ -4,28 +4,18 @@</td>
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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="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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">%:</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="LC12" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> dh_installchangelogs docs/NEWS.md</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># do_stuff_for_testing</span>
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27
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">#endif</span></pre>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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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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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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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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