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<h3>
Joyce Zhou pushed to branch master
at <a href="https://salsa.debian.org/med-team/clearcut">Debian Med / clearcut</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/clearcut/commit/69db88ac329573e2ae2dd6b7b9f313d4637a0511">69db88ac</a></strong>
<div>
<span>by Joyce Zhou</span>
<i>at 2019-03-29T05:14:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add stdin test for proper input
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/clearcut/commit/7cb801e3151f047901deda8480ec53f4bba4a963">7cb801e3</a></strong>
<div>
<span>by Joyce Zhou</span>
<i>at 2019-03-29T05:15:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add stdin test for malformed input
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/clearcut/commit/b34ee2b51ecd6e51607b7bfb137cd718caecc8f5">b34ee2b5</a></strong>
<div>
<span>by Joyce Zhou</span>
<i>at 2019-03-29T05:18:18Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog timestamp
</pre>
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<h4>4 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="#1e46d9da32aaf01e72037ea0ae1253d51e8d0695">
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+
debian/tests/check-malformed
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/clearcut/compare/5ddc8b3fac55a560fe231633c2570d5c0dda5e53...b34ee2b51ecd6e51607b7bfb137cd718caecc8f5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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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">@@ -7,7 +7,7 @@ clearcut (1.0.9-4) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Add autopkgtest</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> Closes: #909711</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> -- Joyce Zhou <jyzhou15@uw.edu> Thu, 28 Mar 2019 <span class="idiff left right">09:01:31 +01</span>00</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Joyce Zhou <jyzhou15@uw.edu> Thu, 28 Mar 2019 <span class="idiff left right">22:16:52 -07</span>00</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">clearcut (1.0.9-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<li id="1e46d9da32aaf01e72037ea0ae1253d51e8d0695">
<a href="https://salsa.debian.org/med-team/clearcut/compare/5ddc8b3fac55a560fe231633c2570d5c0dda5e53...b34ee2b51ecd6e51607b7bfb137cd718caecc8f5#1e46d9da32aaf01e72037ea0ae1253d51e8d0695"><strong>debian/tests/check-malformed</strong></a>
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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="c" style="color: #998; font-style: italic;"># do not use set -e because we expect an error code</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">kg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"clearcut"</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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>
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<pre style="margin: 0;">+<span id="LC16" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># run clearcut with no args, passing in empty content.</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This should return nonzero (malformed input)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span> | clearcut</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exit</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$?</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-neq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/clearcut/compare/5ddc8b3fac55a560fe231633c2570d5c0dda5e53...b34ee2b51ecd6e51607b7bfb137cd718caecc8f5#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: @</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>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Tests: check-malformed</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/clearcut/compare/5ddc8b3fac55a560fe231633c2570d5c0dda5e53...b34ee2b51ecd6e51607b7bfb137cd718caecc8f5#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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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>
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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">@@ -19,5 +19,7 @@ cd "${AUTOPKGTEST_TMP}"</td>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell">clearcut <span class="nt" style="color: #000080;">--alignment</span> <span class="nt" style="color: #000080;">--DNA</span> <span class="nt" style="color: #000080;">--in</span><span class="o" style="font-weight: 600;">=</span>alignment1.dist <span class="nt" style="color: #000080;">--out</span><span class="o" style="font-weight: 600;">=</span>treefile.tre</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Compute tree from matrix</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell">clearcut <span class="nt" style="color: #000080;">--distance</span> <span class="nt" style="color: #000080;">--in</span><span class="o" style="font-weight: 600;">=</span>symmetric.dist <span class="nt" style="color: #000080;">--out</span><span class="o" style="font-weight: 600;">=</span>symmtree.tre</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run clearcut with properly formatted stdin input</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>lower_diag.dist | clearcut</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"test pass"</span></span></pre>
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