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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-deeptoolsintervals">Debian Med / python-deeptoolsintervals</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/commit/7df663a7f7f0493f6293f7c51146fd96eed804a3">7df663a7</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-21T18:14:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add a very simple autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/commit/28feb4673bed14c0185cced4b62c6044a7d63266">28feb467</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-21T18:14:29+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install relevant test file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/commit/7c020addd769dc9c441fc9f53d1393b379f78d08">7c020add</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-21T18:14:55+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Compat version: 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/commit/3e392ed1f091c0f130e08fcfabc86cef125b2d27">3e392ed1</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-21T18:15:18+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add "Rules-Requires-Root:no"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/commit/d76f8699db2ce639c34827b7d4ba42bf024eef0a">d76f8699</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-21T18:16:17+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Hardening flags
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="new-file">
+
debian/examples
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
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</li>
<li class="file-stats">
<a href="#b71aedf894ace3e472595814c71bbde706a49f13">
<span class="new-file">
+
debian/tests/sample_test.py
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/compare/e36773556abf1dada9be7ff9dba173ed1e00c2cb...d76f8699db2ce639c34827b7d4ba42bf024eef0a#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">@@ -4,7 +4,7 @@ Uploaders: Steffen Moeller <moeller@debian.org></td>
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<td class="diff-line-num 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">
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<td class="diff-line-num 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num old_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">
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<td class="diff-line-num 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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="6" 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="LC6" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num old old_line" data-linenumber="7" 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="7" 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="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="7" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<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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<td class="diff-line-num old_line" data-linenumber="8" 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="8" 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="LC8" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-all-dev,</span>
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<td class="diff-line-num old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-setuptools,</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>
<td class="diff-line-num unfold js-unfold new_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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,7 @@ Standards-Version: 4.5.0</td>
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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">Vcs-Browser: https://salsa.debian.org/med-team/python-deeptoolsintervals</span>
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<td class="diff-line-num old_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-deeptoolsintervals.git</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext">Homepage: https://github.com/deeptools/deeptools_intervals/</span>
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<td class="diff-line-num new old_line" data-linenumber="16" 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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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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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"></span>
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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext">Package: python3-deeptoolsintervals</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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">
18
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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">Architecture: any</span>
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<li id="9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/compare/e36773556abf1dada9be7ff9dba173ed1e00c2cb...d76f8699db2ce639c34827b7d4ba42bf024eef0a#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/sample_test.py</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/compare/e36773556abf1dada9be7ff9dba173ed1e00c2cb...d76f8699db2ce639c34827b7d4ba42bf024eef0a#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">export DH_VERBOSE = 1</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export PYBUILD_NAME=deeptoolsintervals</span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">%:</span>
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<a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/compare/e36773556abf1dada9be7ff9dba173ed1e00c2cb...d76f8699db2ce639c34827b7d4ba42bf024eef0a#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, python3-all, python3-pytest</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/compare/e36773556abf1dada9be7ff9dba173ed1e00c2cb...d76f8699db2ce639c34827b7d4ba42bf024eef0a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>deeptoolsintervals</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/lib/python3/dist-packages/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/python3-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Run sample test ....'</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span></pre>
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<li id="b71aedf894ace3e472595814c71bbde706a49f13">
<a href="https://salsa.debian.org/med-team/python-deeptoolsintervals/-/compare/e36773556abf1dada9be7ff9dba173ed1e00c2cb...d76f8699db2ce639c34827b7d4ba42bf024eef0a#b71aedf894ace3e472595814c71bbde706a49f13"><strong>debian/tests/sample_test.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">deeptoolsintervals</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GTF</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">deeptoolsintervals</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Enrichment</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Very basic test to check functionality</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_functionality</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"> <span class="n" style="color: #333;">gtf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GTF</span><span class="p">([</span><span class="s" style="color: #d14;">"GRCh38.84.2.gtf.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GRCh38.84.bed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GRCh38.84.gtf.gz"</span><span class="p">],</span> <span class="n" style="color: #333;">keepExons</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">list_labels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gtf</span><span class="p">.</span><span class="n" style="color: #333;">labels</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">list_labels</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">list_labels</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'GRCh38.84.2.gtf.gz'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GRCh38.84.bed'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GRCh38.84.gtf.gz'</span><span class="p">,</span> <span class="s" style="color: #d14;">'group 1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'group 1_r1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'group 2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'group 3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'group2'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">gtf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GTF</span><span class="p">(</span><span class="s" style="color: #d14;">"GRCh38.84.gtf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;">keepExons</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">gtf</span><span class="p">.</span><span class="n" style="color: #333;">findOverlaps</span><span class="p">(</span><span class="s" style="color: #d14;">"chr1"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">20000</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">11800</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">gtf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Enrichment</span><span class="p">(</span><span class="s" style="color: #d14;">"GRCh38.84.gtf.gz"</span><span class="p">,</span> <span class="n" style="color: #333;">keepExons</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">attributeKey</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gene_biotype"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">overlap_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">gtf</span><span class="p">.</span><span class="n" style="color: #333;">findOverlaps</span><span class="p">(</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="p">[(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2000000</span><span class="p">)]))</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">overlap_result</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">overlap_result</span> <span class="o" style="font-weight: 600;">==</span> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'group 1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'group 2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'lincRNA'</span><span class="p">,</span> <span class="s" style="color: #d14;">'miRNA'</span><span class="p">,</span> <span class="s" style="color: #d14;">'processed_pseudogene'</span><span class="p">,</span> <span class="s" style="color: #d14;">'protein_coding'</span><span class="p">,</span> <span class="s" style="color: #d14;">'transcribed_unprocessed_pseudogene'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unprocessed_pseudogene'</span><span class="p">])</span></span></pre>
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