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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/mindthegap">Debian Med / mindthegap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/3d3c965d6d49c9f2bbaee361493abea636d058d7">3d3c965d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-11T07:04:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Architecture: all packages do not need ${shlibs:Depends}
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/e4c3a310c73a5fff8f0e31b9e079a7def095ed22">e4c3a310</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-11T07:05:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">There is no strict Depends relation from mindthegap - thus lowering the relation to Recommends - even Suggests is OK (may be users have some strange interest in using only the data - but well, that's pretty exotic). Please note: There was a missing ',' which is now not neede any more.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/a2d0228132a273ebadd63734b4997d36b96e68b8">a2d02281</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-11T07:07:43Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Silence lintian about short description: It should be no sentence!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/c79da8ace50396456c9cb54f42d0f5808803b02e">c79da8ac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-11T07:15:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends: dh-python to enable resolving
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/55fddb55fb00c7f4ccf2c32c7cdfdc30c336bcd7">55fddb55</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-11T07:16:10Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Close ITP bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/bd723bcd65e1b5b81906d5af58f517da81a81f6a">bd723bcd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-11T07:34:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Further means to get ${python3:Depends} resolved
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/e40ef62383e58100662a96fe9c7649c6a9d63a26">e40ef623</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-11T07:35:33Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unneeded boilerplate stuff from debian/rules; try enabling hardening options
</pre>
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<h4>3 changed files:</h4>
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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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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mindthegap/compare/e24d2fa2bf1113a7984b53ffaae8dae384cb8c0f...e40ef62383e58100662a96fe9c7649c6a9d63a26#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">mindthegap (2.2.0-1) 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"> * Initial release (Closes: #<span class="idiff left right"><bug></span>)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">931826</span>)</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"> -- Shayan Doust <hello@shayandoust.me> Tue, 02 Jul 2019 13:41:39 +0100</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mindthegap/compare/e24d2fa2bf1113a7984b53ffaae8dae384cb8c0f...e40ef62383e58100662a96fe9c7649c6a9d63a26#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<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">@@ -4,6 +4,8 @@ Uploaders: Shayan Doust <hello@shayandoust.me></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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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 (>= 12~),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> dh-sequence-python3,</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"> cmake,</span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libgatbcore-dev,</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"> libboost-dev,</span>
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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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +21,7 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> libgatbcore2</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Description: <span class="idiff left right">Performs detection and assembly of DNA insertion variants in NGS read datasets.</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Description: <span class="idiff left right">performs detection and assembly of DNA insertion variants in NGS read datasets</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> Designed to call insertions of any size, whether they are novel or</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> duplicated, homozygous or heterozygous in the donor genome. It takes as</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> input a set of reads and a reference genome. It outputs two sets of</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">@@ -32,11 +34,10 @@ Description: Performs detection and assembly of DNA insertion variants in NGS re</td>
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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">Package: mindthegap-examples</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> ${python3:Depends}</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"><span class="idiff left right"> </span> mindthegap</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">Description: <span class="idiff left right">Optional scripts and example resources for mindthegap.</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"><span class="idiff left right">Recommends:</span> mindthegap</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Description: <span class="idiff left right">optional scripts and example resources for mindthegap</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> Designed to call insertions of any size, whether they are novel or</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> duplicated, homozygous or heterozygous in the donor genome. it takes</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> as input a set of reads and a reference genome. It outputs two sets</span>
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<a href="https://salsa.debian.org/med-team/mindthegap/compare/e24d2fa2bf1113a7984b53ffaae8dae384cb8c0f...e40ef62383e58100662a96fe9c7649c6a9d63a26#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</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"># DH_VERBOSE := 1</span>
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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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8
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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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9
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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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13
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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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14
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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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15
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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="LC4" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"><span class="idiff left right"># </span>export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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">%:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">#override_dh_auto_test:</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"># do_stuff_for_testing</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC31" 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="LC32" class="line" lang="plaintext">#get-orig-source:</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> dh $@ --with python3</span></pre>
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