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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/macs">Debian Med / macs</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/macs/-/commit/9742008b9041cedd5248b29dc9dd957729e631c3">9742008b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-15T22:28:45+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Link properly with libm
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/macs/-/commit/2fe456747406999cd300b14cece0e4b9828fe3da">2fe45674</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-15T22:29:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/macs/-/commit/7777351466dcb086ca8538cc8e32a68e006641af">77773514</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-07-15T23:27:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not require pip
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/macs/-/commit/7094a0e3d3d54a6ca55bdb579793939672d3e742">7094a0e3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-07-15T23:33:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#98d07bcae64476e7ab7d5a1c498f6a0658c1a138">
<span class="new-file">
+
debian/patches/link-libm.patch
</span>
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<li class="file-stats">
<a href="#8bb5107b90075696512eacd5b0c9636f96bd71b7">
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+
debian/patches/no-pip.patch
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</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/macs/-/compare/6300ff53c5f264986c035d77a248117fe5d6339f...7094a0e3d3d54a6ca55bdb579793939672d3e742#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">macs (2.2.7.1-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Link properly with libm</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #965073</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</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"> -- Andreas Tille <tille@debian.org> Wed, 15 Jul 2020 23:27:39 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">macs (2.2.7.1-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Ensure that debian/rules clean always suceeds. Closes #958109</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/macs/-/compare/6300ff53c5f264986c035d77a248117fe5d6339f...7094a0e3d3d54a6ca55bdb579793939672d3e742#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Uploaders: Michael R. Crusoe <crusoe@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-all-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-numpy,</span>
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<li id="98d07bcae64476e7ab7d5a1c498f6a0658c1a138">
<a href="https://salsa.debian.org/med-team/macs/-/compare/6300ff53c5f264986c035d77a248117fe5d6339f...7094a0e3d3d54a6ca55bdb579793939672d3e742#98d07bcae64476e7ab7d5a1c498f6a0658c1a138"><strong>debian/patches/link-libm.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Date: Wed, 15 Jul 2020 18:16:54 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Aurelien Jarno <aurel32@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/965073</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Description: macs use the log() math function, but doesn't link link with libm.so.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> This causes the non-versioned __log_finite symbol to be used, which in</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> turn causes issues when glibc version is upgraded:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> https://ci.debian.net/data/autopkgtest/testing/amd64/m/macs/6261687/log.gz</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"> This patches is fixing this.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff">--- a/setup.py</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -59,8 +59,8 @@</span> def main():</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=extra_c_args),</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> #Extension("MACS2.Statistics", ["MACS2/Statistics.pyx"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),</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"> </span></pre>
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<li id="8bb5107b90075696512eacd5b0c9636f96bd71b7">
<a href="https://salsa.debian.org/med-team/macs/-/compare/6300ff53c5f264986c035d77a248117fe5d6339f...7094a0e3d3d54a6ca55bdb579793939672d3e742#8bb5107b90075696512eacd5b0c9636f96bd71b7"><strong>debian/patches/no-pip.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 15 Jul 2020 22:28:05 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Do not require pip</span></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">--- a/setup.py</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/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -27,21 +27,6 @@</span> def main():</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> cwd = os.path.abspath(os.path.dirname(__file__))</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"> # install required numpy</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;">- p = subprocess.call([sys.executable, "-m", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd)</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;">- if p != 0:</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;">- # Could be due to a too old pip version and build isolation, check that</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;">- try:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Note, pip may not be installed or not have been used</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import pip</span></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;">- if LooseVersion(pip.__version__) < LooseVersion('18.0.0'):</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise RuntimeError("Installing requirements failed. Possibly due "</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "to `pip` being too old, found version {}, "</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "needed is >= 18.0.0.".format(pip.__version__))</span></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;">- else:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise RuntimeError("Installing requirements failed!")</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except ImportError:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise RuntimeError("Installing requirement failed! `pip` has to be installed!")</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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="LC26" class="line" lang="diff"> from numpy import get_include as numpy_get_include</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> numpy_include_dir = [numpy_get_include()]</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/macs/-/compare/6300ff53c5f264986c035d77a248117fe5d6339f...7094a0e3d3d54a6ca55bdb579793939672d3e742#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">spelling</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">keep_debug</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">link-libm.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">no-pip.patch</span></pre>
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