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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-loompy">Debian Med / python-loompy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/34e1724d37e0e35e4b0ddda6d6dbb73594eb27bd">34e1724d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:16:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Simplify watch file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/5d565003abbee6805444adfef81a6dc890b86c55">5d565003</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:16:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/f0629e187c16c1d1f6d2fae3b8e72e699d5004cb">f0629e18</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:16:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/c182c2407f96dd24246c96c113464d326373a868">c182c240</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:17:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/58381f894d2e575bb0d30b51ef8e7d40579018ba">58381f89</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:17:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/e326c79fe0db261f12fc560a08deec7c07c756aa">e326c79f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:17:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes: lintian: file-contains-trailing-whitespace
See-also: https://lintian.debian.org/tags/file-contains-trailing-whitespace.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/0f67846593661b2abaa093c9c9df3b34fd1d188f">0f678465</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:17:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/fd186ffaf2bd6496d6d8731fea4d59ad904341ee">fd186ffa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:20:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cme fix dpkg-control
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/e67765690273b336e2bccf61d40e6e9d8b6271a4">e6776569</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:22:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends: python3-scipy, use nocheck
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/2a483a361e28eda42cd40e5f897cab929bb36d58">2a483a36</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:32:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Section: python
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/cf233cff1ec3839d3cebc0a6e859d4b5e404d232">cf233cff</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:33:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enhance description
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/1f236cd0f3b7ff6cab3bd764dc718dab8a1e49ca">1f236cd0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:34:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove ineffective file which is not needed anyway
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/9ff59a572c5574f3d249218aba1c53576a6fad95">9ff59a57</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:38:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-loompy/-/commit/0539abb613056f75be338c6f4f3fcb1454daf41e">0539abb6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-29T11:39:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Team upload to new
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
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</li>
<li class="file-stats">
<a href="#758e686dbc15a3673567c9e6db2f0b85cbd64dd7">
<span class="new-file">
+
debian/loompy.1
</span>
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</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
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</li>
<li class="file-stats">
<a href="#b772f74af996080140d44ec2db594d44a3e180ff">
<span class="deleted-file">
−
debian/python-loompy.docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
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</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
<hr>
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1
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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="plaintext">python-loompy (3.0.6+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="2" 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="1" 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="LC1" class="line" lang="plaintext">python-loompy (3.0.6+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="2" 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">
2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_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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<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">
3
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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="LC3" class="line" lang="plaintext"> * Team upload.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3" 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">
3
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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"> * Initial release (Closes: #934597)</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="4" 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">
4
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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC4" class="line" lang="plaintext"> Resubmitted with improved copyright. Thanks go to Thorsten.</span>
</pre>
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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">
5
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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"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6" 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">
6
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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> The new version (up from 2.x) has a build-dep on a Python module "numpy_groupies".</span>
</pre>
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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">
7
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<td class="diff-line-num new_line old" data-linenumber="6" 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"> This still needs to be packaged.</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="8" 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="6" 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="LC8" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Mon, 12 Aug 2019 13:14:47 +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sun, 29 Mar 2020 11:39:05 +0200</span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: python-loompy</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.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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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11), dh-python,</span>
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7
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<td class="diff-line-num new_line old" data-linenumber="4" 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"> python3-all, python3-setuptools,</span>
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8
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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC8" class="line" lang="plaintext"> python3-h5py,</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python3-numba,</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> python3-click</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.4.0</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Homepage: https://github.com/linnarsson-lab/loompy</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3-all,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-setuptools,</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="plaintext"> python3-h5py <!nocheck>,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-numba <!nocheck>,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-click <!nocheck>,</span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> python3-scipy <!nocheck>,</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> python3-numpy-groupies <!nocheck></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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13
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-loompy</span>
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14
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-loompy.git</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">#Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Homepage: https://github.com/linnarsson-lab/loompy</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">#install_requires=['h5py', 'numpy', 'scipy', 'setuptools', 'numba', 'click', "numpy-groupies"],</span>
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18
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Package: python3-loompy</span>
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19
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Depends: ${python3:Depends}, ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> python3-h5py,</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> python3-numpy,</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> python3-scipy,</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> python3-pandas,</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> python3-click</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> python3-h5py,</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> python3-scipy,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> python3-pandas,</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> python3-click,</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> python3-numpy-groupies</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Description: access loom formatted files for bioinformatics</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> Loom is an efficient file format for very large omics datasets,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> consisting of a main matrix, optional additional layers, a variable</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> number of row and column annotations. Loom also supports sparse</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> graphs. <span class="idiff left right">We use loom files</span> to store single-cell gene expression data:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> graphs. <span class="idiff left right"> Loom files are used</span> to store single-cell gene expression data:</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> the main matrix contains the actual expression values (one column per</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> cell, one row per gene); row and column annotations contain metadata</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> for genes and cells, such as Name, Chromosome, Position (for genes),</span>
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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/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><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="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>loompy</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<li id="758e686dbc15a3673567c9e6db2f0b85cbd64dd7">
<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#758e686dbc15a3673567c9e6db2f0b85cbd64dd7"><strong>debian/loompy.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH LOOMPY "1" "March 2020" "loompy 3.0.6" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">loompy \- access loom formatted files for bioinformatics</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B loompy</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,OPTIONS\/\fR] \fI\,COMMAND \/\fR[\fI\,ARGS\/\fR]...</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH OPTIONS</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.HP</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\fB\-\-show\-message\fR / \fB\-\-hide\-message\fR</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">\fB\-\-verbosity\fR [error|warning|info|debug]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-\-help\fR</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Show this message and exit.</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SS "Commands:"</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">fromfq</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.SH AUTHOR</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#b772f74af996080140d44ec2db594d44a3e180ff"><strong>debian/python-loompy.docs</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">README.Debian</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">README.source</span></pre>
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<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,4 +5,3 @@ export PYBUILD_NAME=loompy</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span></pre>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/linnarsson-lab/loompy/issues</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/linnarsson-lab/loompy/issues/new</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> - Name: OMICtools</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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">@@ -7,3 +9,5 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> Entry: loompy</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> - Name: bio.tools</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> Entry: NA</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Repository: https://github.com/linnarsson-lab/loompy.git</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Repository-Browse: https://github.com/linnarsson-lab/loompy</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/python-loompy/-/compare/8c17601b4f658320f183017bd1e65f6064b5092e...0539abb613056f75be338c6f4f3fcb1454daf41e#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">opts="dversionmangle=s/\+dfsg$//,uversionmangle=s/$/+dfsg/,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%python-loompy-$1.tar.gz%" \</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right"> https://github.com/linnarsson-lab/loompy/tags</span> \</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right"> (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate</span></span></pre>
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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"><span class="idiff left right">opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz"</span> \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right">https://github.com/linnarsson-lab/loompy/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@</span></span></pre>
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