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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/edtsurf">Debian Med / edtsurf</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/edtsurf/-/commit/d6172ddafc6d276e4ae0e1cb4a76e3b2879595e6">d6172dda</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-06T12:44:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add test data and references
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/edtsurf/-/commit/462b10c1e5579aca5144fe566173b6f8419f8bf6">462b10c1</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-06T12:44:43+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make a new binary package for examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/edtsurf/-/commit/8795824ea5625eb741fd20b6dc035bd53858b5cb">8795824e</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-06T12:52:06+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch to fix return values
EDTSurf returns 1 on successful execution which breaks autopkgtests
It seems safe to make this change purely by looking at the code and
I can't find any documentation about EDTSurf anywhere
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/edtsurf/-/commit/2ceafcc5852e57c773b29a8c3fcbb9b6de27628c">2ceafcc5</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-06T12:52:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/edtsurf/-/commit/154ac84fa80a0ba4edda1cf0e0ef55e4e1efb495">154ac84f</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-06T12:52:33+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/edtsurf/-/commit/99f2ccaf581796527955dd9906481fbfb311d00e">99f2ccaf</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-06T12:52:41+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add Pranav Ballaney to Uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/edtsurf/-/commit/96f64ced72b012732dacd52f1b3417012d507aff">96f64ced</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-06T12:53:15+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="new-file">
+
debian/docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#4bf7e15af03379cc328050ac22940ef421eb20f8">
<span class="new-file">
+
debian/edtsurf-examples.install
</span>
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</li>
<li class="file-stats">
<a href="#0c7131605b0d8001202c06d1293d1dfdb4f59107">
<span class="new-file">
+
debian/patches/fix_return_values.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#a2a565aa25c2bf10949e3702636a59d9f1110a11">
<span class="new-file">
+
debian/tests/README.test_data
</span>
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</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
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</li>
<li class="file-stats">
<a href="#4291f4a24232ded4c6d194d206e618d64a7b1ae5">
<span class="new-file">
+
debian/tests/data/4we2.pdb.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#e86405cb9a0a88c0fa346861534b87f645851360">
<span class="new-file">
+
debian/tests/ref/4we2-cav.pdb.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#ea7ca86e74176290d5798615a1694e608de710e5">
<span class="new-file">
+
debian/tests/ref/4we2.ply.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/edtsurf/-/compare/57c9f964fda8f3f14670cf992fe3363466a3169f...96f64ced72b012732dacd52f1b3417012d507aff#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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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="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
</pre>
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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="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/edtsurf/-/compare/57c9f964fda8f3f14670cf992fe3363466a3169f...96f64ced72b012732dacd52f1b3417012d507aff#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">edtsurf (0.2009-7) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Add test data and references</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> * Make a new binary package for examples</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Patch to fix return values</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * Add autopkgtests</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="plaintext"> * Install docs</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Add Pranav Ballaney to Uploaders</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"> -- Pranav Ballaney <ballaneypranav@gmail.com> Mon, 06 Jul 2020 12:52:53 +0530</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">edtsurf (0.2009-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<a href="https://salsa.debian.org/med-team/edtsurf/-/compare/57c9f964fda8f3f14670cf992fe3363466a3169f...96f64ced72b012732dacd52f1b3417012d507aff#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: edtsurf</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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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Pranav Ballaney <ballaneypranav@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~)</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,10 +15,23 @@ Package: edtsurf</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Suggests: meshlab</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Suggests: meshlab<span class="idiff left right">, edtsurf-examples</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Description: triangulated mesh surfaces for protein structures</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> EDTSurf is a open source program to construct triangulated surfaces</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> for macromolecules. It generates three major macromolecular surfaces:</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> van der Waals surface, solvent-accessible surface and molecular surface</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> (solvent-excluded surface). EDTsurf also identifies cavities which are</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> inside of macromolecules.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Package: edtsurf-examples</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Enhances: edtsurf</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Description: triangulated mesh surfaces for protein structures</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> EDTSurf is a open source program to construct triangulated surfaces</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> for macromolecules. It generates three major macromolecular surfaces:</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> van der Waals surface, solvent-accessible surface and molecular surface</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> (solvent-excluded surface). EDTsurf also identifies cavities which are</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> inside of macromolecules.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> This packages contains some examples for EDTSurf.</span></pre>
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<a href="https://salsa.debian.org/med-team/edtsurf/-/compare/57c9f964fda8f3f14670cf992fe3363466a3169f...96f64ced72b012732dacd52f1b3417012d507aff#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/README*</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<a href="https://salsa.debian.org/med-team/edtsurf/-/compare/57c9f964fda8f3f14670cf992fe3363466a3169f...96f64ced72b012732dacd52f1b3417012d507aff#4bf7e15af03379cc328050ac22940ef421eb20f8"><strong>debian/edtsurf-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">data</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">edtsurf</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ref</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">edtsurf</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/edtsurf/-/compare/57c9f964fda8f3f14670cf992fe3363466a3169f...96f64ced72b012732dacd52f1b3417012d507aff#0c7131605b0d8001202c06d1293d1dfdb4f59107"><strong>debian/patches/fix_return_values.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/EDTSurf.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/EDTSurf.cpp</span></span>
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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -36,7 +36,7 @@</span> int main(int argc, char** argv)</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> printf("output1: outname.ply\n");</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> printf("output2: outname.asa\n");</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> printf("output3: outname-cav.pdb\n");</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="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return 0;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> for(i=0;i<7;i++)</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="diff"> {</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="diff"><span class="p">@@ -376,7 +376,7 @@</span> int main(int argc, char** argv)</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> fprintf(file,"%4d %4d %c %7.3f\n",i+1,pp.bb[i].resind,pp.bb[i].resid,tsum);</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> fclose(file);</span>
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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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return 1;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 0;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> //additional functions below</span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> pps.checkEuler();</span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -413,6 +413,6 @@</span> int main(int argc, char** argv)</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> sprintf(filename,"%s.asa",tpname);</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> pps.outsas(pp.numbb,pp.bb,pp.proseq,filename);</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return 1;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 0;</span></span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> } </span>
</pre>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/edtsurf/-/compare/57c9f964fda8f3f14670cf992fe3363466a3169f...96f64ced72b012732dacd52f1b3417012d507aff#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">CFLAGS_missing_in_Makefile.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix-use-of-unsigned-char.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">fix_return_values.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/edtsurf/-/compare/57c9f964fda8f3f14670cf992fe3363466a3169f...96f64ced72b012732dacd52f1b3417012d507aff#a2a565aa25c2bf10949e3702636a59d9f1110a11"><strong>debian/tests/README.test_data</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">data/4we2.pdb was obtained from https://www.rcsb.org/structure/4WE2</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ref/* files were obtained by running 4we2.pdb through EDTSurf as shown in Test 1 in run-unit-test</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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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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<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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<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;">pkg</span><span class="o" style="font-weight: 600;">=</span>edtsurf</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="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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<pre style="margin: 0;">+<span id="LC7" 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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<pre style="margin: 0;">+<span id="LC8" 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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<pre style="margin: 0;">+<span id="LC9" 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="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</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;">ls</span> <span class="nt" style="color: #000080;">-R</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>data</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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25
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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="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 1</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">EDTSurf <span class="nt" style="color: #000080;">-i</span> 4we2.pdb</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>hello</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">diff data/4we2.ply ref/4we2.ply</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>hello2</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">diff data/4we2-cav.pdb ref/4we2-cav.pdb</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>data</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 2</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">EDTSurf <span class="nt" style="color: #000080;">-i</span> 4we2.pdb <span class="nt" style="color: #000080;">-t</span> 2 <span class="nt" style="color: #000080;">-o</span> 4we2-vcmc-ms</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 3</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">EDTSurf <span class="nt" style="color: #000080;">-i</span> 4we2.pdb <span class="nt" style="color: #000080;">-s</span> 1 <span class="nt" style="color: #000080;">-t</span> 1 <span class="nt" style="color: #000080;">-o</span> 4we2-mc-vws</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 4</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell">EDTSurf <span class="nt" style="color: #000080;">-i</span> 4we2.pdb <span class="nt" style="color: #000080;">-s</span> 2 <span class="nt" style="color: #000080;">-t</span> 2 <span class="nt" style="color: #000080;">-c</span> 3 <span class="nt" style="color: #000080;">-o</span> 4we2-sas-vcmc-chain</span>
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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="50" 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">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"></span></pre>
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