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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/python-team/packages/python-ncls">Debian Python Team / packages / python-ncls</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/python-team/packages/python-ncls/-/commit/3c6adc2bda756bb6a4475fdea596cea3db4f3157">3c6adc2b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-02T18:15:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move package to Debian Python Team
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/python-team/packages/python-ncls/-/commit/03f55351b7a705a35631f86c313333675a630d10">03f55351</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-02T18:16:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/python-team/packages/python-ncls/-/commit/7c6a01cdf3fda281f9f93299b4762e55639f9187">7c6a01cd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-02T18:16:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.0.63-hotfix+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/python-team/packages/python-ncls/-/commit/de2c1ffa53c58f574f939364b75a9306750653ef">de2c1ffa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-02T18:16:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.0.63-hotfix+ds'
Update to upstream version '0.0.63-hotfix+ds'
with Debian dir 0facbe0537228537b9efd8b861a37b590ba6446c</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/python-team/packages/python-ncls/-/commit/2f2ab8d91d7a0d0c0a5915ff316a19c802bc0711">2f2ab8d9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-02T18:18:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream has applied patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/python-team/packages/python-ncls/-/commit/9a78f4f047963a0282bf144f7eb91a2cdab5a6ff">9a78f4f0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-02T18:21:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="new-file">
+
.travis.yml
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#e947986004f151c5697e5c71062f5d92b301fe9e">
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−
debian/patches/fix-FTBFS.patch
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−
debian/patches/series
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<li class="file-stats">
<a href="#9f5513a7b12c629ad6d3563e589e4ea34bfd934e">
ncls/src/ncls.pyx
</a>
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</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/python-team/packages/python-ncls/-/compare/62c46f32c0f27cb7f57c41e0d6a3e097d2da429d...9a78f4f047963a0282bf144f7eb91a2cdab5a6ff#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install cython pytest</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># functionality is tested in the pyranges package</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">py.test tests/test_ncls.py && cd ~/ && python -c 'import ncls; print(ncls.__version__)'</span></span></pre>
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<a href="https://salsa.debian.org/python-team/packages/python-ncls/-/compare/62c46f32c0f27cb7f57c41e0d6a3e097d2da429d...9a78f4f047963a0282bf144f7eb91a2cdab5a6ff#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-ncls (0.0.63-hotfix+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Move package to Debian Python Team</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Upstream has applied patch</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> Sun, 02 Jan 2022 18:18:24 +0100</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">python-ncls (0.0.63+ds-1) unstable; urgency=medium</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"> * New upstream version 0.0.63+ds</span>
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<a href="https://salsa.debian.org/python-team/packages/python-ncls/-/compare/62c46f32c0f27cb7f57c41e0d6a3e097d2da429d...9a78f4f047963a0282bf144f7eb91a2cdab5a6ff#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: python-ncls</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Maintainer: Debian <span class="idiff left right">Med Packaging Team <debian-med-packaging@lists.alioth</span>.debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian <span class="idiff left right">Python Team <team+python@tracker</span>.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org>,</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Nilesh Patra <nilesh@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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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -13,8 +13,8 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-numpy <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python3-pytest <!nocheck></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Standards-Version: 4.6.0</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/<span class="idiff left right">med-team</span>/python-ncls</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/<span class="idiff left right">med-team</span>/python-ncls.git</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/<span class="idiff left right">python-team/packages</span>/python-ncls</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/<span class="idiff left right">python-team/packages</span>/python-ncls.git</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: https://github.com/biocore-ntnu/ncls</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<a href="https://salsa.debian.org/python-team/packages/python-ncls/-/compare/62c46f32c0f27cb7f57c41e0d6a3e097d2da429d...9a78f4f047963a0282bf144f7eb91a2cdab5a6ff#e947986004f151c5697e5c71062f5d92b301fe9e"><strong>debian/patches/fix-FTBFS.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From e813f99031ca37310ac91d16a1d3a64b517601d1 Mon Sep 17 00:00:00 2001</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">From: endre bakken stovner <endrebakkenstovner@endres-MacBook-Air.local></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Date: Tue, 2 Nov 2021 17:56:00 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH] hotfix</span></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>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> ncls/src/ncls.pyx | 4 ++--</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> 1 file changed, 2 insertions(+), 2 deletions(-)</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">diff --git a/ncls/src/ncls.pyx b/ncls/src/ncls.pyx</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">index 4c0233e..ba7d0d6 100644</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;">--- a/ncls/src/ncls.pyx</span></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/ncls/src/ncls.pyx</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -446,8 +446,8 @@</span> cdef class NCLS64:</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> @cython.boundscheck(False)</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> @cython.wraparound(False)</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> @cython.initializedcheck(False)</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;">- cpdef set_difference_helper(self, const int64_t [::1] starts, const int64_t [::1] ends, const int64_t [::1] indexes, const int64_t [::1] nhits,</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;">- const int64_t[::1] nhits):</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;">+ cpdef set_difference_helper(self, const int64_t [::1] starts, const int64_t [::1] ends, const int64_t [::1] indexes,</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;">+ const int64_t [::1] nhits):</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> cdef int i</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> cdef int nhit = 0</span></pre>
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<a href="https://salsa.debian.org/python-team/packages/python-ncls/-/compare/62c46f32c0f27cb7f57c41e0d6a3e097d2da429d...9a78f4f047963a0282bf144f7eb91a2cdab5a6ff#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">fix-FTBFS.patch</span></pre>
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<a href="https://salsa.debian.org/python-team/packages/python-ncls/-/compare/62c46f32c0f27cb7f57c41e0d6a3e097d2da429d...9a78f4f047963a0282bf144f7eb91a2cdab5a6ff#9f5513a7b12c629ad6d3563e589e4ea34bfd934e"><strong>ncls/src/ncls.pyx</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="446" 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">@@ -446,8 +446,8 @@ cdef class NCLS64:</td>
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446
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cython"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">cython</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">boundscheck</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cython"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">cython</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">wraparound</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cython"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">cython</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">initializedcheck</span><span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">set_difference_helper</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">indexes</span><span class="p">,</span><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">int64_t</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[::</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nhits</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span><span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">nhits</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cpdef</span> <span class="nf" style="color: #900; font-weight: 600;">set_difference_helper</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span> <span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">indexes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">int64_t</span><span class="idiff left right"> </span><span class="p">[::</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="n" style="color: #333;">nhits</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nhit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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