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<h3>
Maarten L. Hekkelman pushed to branch master
at <a href="https://salsa.debian.org/med-team/dssp">Debian Med / dssp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/dssp/-/commit/81d4273b3c7c3bb9f39c3653fef95fccc1056833">81d4273b</a></strong>
<div>
<span>by Maarten L. Hekkelman</span>
<i>at 2020-11-27T09:44:50+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update autopkgtest to use libcifpp-dev example file
</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
debian/README.test
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<li class="file-stats">
<a href="#76d0383397f94ee14a5b90916494163e242f2baf">
<span class="deleted-file">
−
debian/tests/1cbs.cif
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</a>
</li>
<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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</li>
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/dssp/-/commit/81d4273b3c7c3bb9f39c3653fef95fccc1056833#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</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">@@ -3,11 +3,11 @@ Notes on how this package can be tested.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">This</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">executing</span></span>
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"></span>
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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="php"> <span class="n" style="color: #333;">sh</span> <span class="n" style="color: #333;"><span class="idiff left right">installation</span></span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">test</span></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">
6
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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="LC6" class="line" lang="php"> <span class="n" style="color: #333;">sh</span> <span class="n" style="color: #333;"><span class="idiff left">run</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">unit</span></span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">test</span></span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_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">
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 old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"><span class="n" style="color: #333;">in</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">confirm</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">integrity</span><span class="mf" style="color: #099;">.</span></span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="php"></span>
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10
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<td class="diff-line-num new_line old" data-linenumber="10" 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="LC10" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Test</span> <span class="n" style="color: #333;">in</span> <span class="sb" style="color: #d14;">`<span class="idiff left right">installation</span>-test`</span> <span class="n" style="color: #333;">checks</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new old_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">
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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">
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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="LC10" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Test</span> <span class="n" style="color: #333;">in</span> <span class="sb" style="color: #d14;">`<span class="idiff left right">run-unit</span>-test`</span> <span class="n" style="color: #333;">checks</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span><span class="o" style="font-weight: 600;">:</span></span>
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11
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="php"></span>
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<td class="diff-line-num old_line" data-linenumber="12" 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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="php"><span class="mf" style="color: #099;">1.</span> <span class="n" style="color: #333;">runs</span> <span class="n" style="color: #333;">mkdssp</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">typical</span> <span class="no" style="color: #008080;">PDB</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">in</span> <span class="n" style="color: #333;">mmCIF</span> <span class="n" style="color: #333;">format</span></span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="php"><span class="n" style="color: #333;">creating</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">default</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">in</span> <span class="n" style="color: #333;">mmCIF</span> <span class="n" style="color: #333;">format</span><span class="mf" style="color: #099;">.</span></span>
</pre>
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<a href="https://salsa.debian.org/med-team/dssp/-/commit/81d4273b3c7c3bb9f39c3653fef95fccc1056833#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,26 +13,6 @@ Copyright: © 2012, Maarten L. Hekkelman <m.hekkelman@cmbi.ru.nl>,</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> © 2020 NKI/AVL, Netherlands Cancer Institute</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">License: BSD-2-Clause</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Files: debian/tests/1cbs.cif</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Copyright: © 2016, Kleywegt, G.J, Bergfors, T, Jones, T.A</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">License: PDB</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Comment: full protein structure in PDB format from RCSB PDB database</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> PDB ID: 1cbs, available at: http://www.rcsb.org</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="LC22" class="line" lang="plaintext">License: PDB</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> PDB File License - as described in RCSB PDB site - June 17, 2016</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> copyright restrictions and made fully and freely available for both</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> non-commercial and commercial use. Users of the data should attribute the</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> original authors of that structural data. By using the materials available in</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> the PDB archive, the user agrees to abide by the conditions described in the</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> PDB Advisory Notice (http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/pdb_advisory.html).</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> License's text is available on RCSB PDB database site (http://www.rcsb.org), on page named</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> "RCSB PDB Policies & References".</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> URL: http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/policies_references.html</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">License: BSD-2-Clause</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> .</span>
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<a href="https://salsa.debian.org/med-team/dssp/-/commit/81d4273b3c7c3bb9f39c3653fef95fccc1056833#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">debian/tests/<span class="idiff left right">installation</span>-test</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/<span class="idiff left right">run-unit</span>-test</span></pre>
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<a href="https://salsa.debian.org/med-team/dssp/-/commit/81d4273b3c7c3bb9f39c3653fef95fccc1056833#76d0383397f94ee14a5b90916494163e242f2baf"><strong>debian/tests/1cbs.cif</strong>
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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></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, libcifpp-dev</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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<a href="https://salsa.debian.org/med-team/dssp/-/commit/81d4273b3c7c3bb9f39c3653fef95fccc1056833#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -3,19 +3,18 @@ set -e</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</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;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"dssp"</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">testfile</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"/usr/share/doc/libcifpp-dev/examples/1cbs.cif.gz"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="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="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</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="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp </span>debian/tests/1cbs.cif <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</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="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># simply run mkdssp on 1cbs, should produce an output file</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell">mkdssp <span class="idiff left right">1cbs.cif</span> 1cbs-dssp.cif</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">mkdssp <span class="k" style="font-weight: 600;"><span class="idiff left">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">testfile</span></span><span class="k" style="font-weight: 600;"><span class="idiff right">}</span></span> 1cbs-dssp.cif</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> 1cbs-dssp.cif <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">mkdssp <span class="idiff left right">1cbs.cif</span> 1cbs-dssp.dssp</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">mkdssp <span class="k" style="font-weight: 600;"><span class="idiff left">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">testfile</span></span><span class="k" style="font-weight: 600;"><span class="idiff right">}</span></span> 1cbs-dssp.dssp</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> 1cbs-dssp.dssp <span class="o" style="font-weight: 600;">]</span></span></pre>
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