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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/prottest">Debian Med / prottest</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/prottest/commit/f1fb44a908557ee288ec4d29227e816fbc72c504">f1fb44a9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-13T13:40:10+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">alter-sequence-statement has changed pathes - thanks for the patch to adapt this to Markus Koschany <apo@debian.org>
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<strong><a href="https://salsa.debian.org/med-team/prottest/commit/e32b766dcbcefde1c9c4a96012162c729886ea82">e32b766d</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-07-13T13:49:43+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not parse d/changelog
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<strong><a href="https://salsa.debian.org/med-team/prottest/commit/a59a1e3d14da53cd5a00c39cc605abd94b9770ac">a59a1e3d</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-07-13T13:53:08+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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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="#b046db5d67cd44a912573eea97ca4adb83390d97">
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+
debian/patches/alter-import.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/prottest/compare/8c6f1fa612c211d69c010afef04723765afe0598...a59a1e3d14da53cd5a00c39cc605abd94b9770ac#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">prottest (3.4.2+dfsg-3) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">prottest (3.4.2+dfsg-3) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></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="LC3" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.1.5</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * alter-sequence-statement has changed paths - thanks for the patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> to adapt this to Markus Koschany <apo@debian.org></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Do not parse d/changelog</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="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 11 Jul 2018 22:22:42</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Fri, 13 Jul 2018 13:49:49</span> +0200</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">prottest (3.4.2+dfsg-2) 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="b046db5d67cd44a912573eea97ca4adb83390d97">
<a href="https://salsa.debian.org/med-team/prottest/compare/8c6f1fa612c211d69c010afef04723765afe0598...a59a1e3d14da53cd5a00c39cc605abd94b9770ac#b046db5d67cd44a912573eea97ca4adb83390d97"><strong>debian/patches/alter-import.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Markus Koschany <apo@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Fri, 13 Jul 2018 13:05:25 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Subject: alter import</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> .../es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java | 8 ++++----</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> 1 file changed, 4 insertions(+), 4 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17,9 +17,9 @@ Foundation, Inc., 59 Temple Place, Suite</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> package es.uvigo.darwin.prottest.util.fileio;</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import converter.Converter;</span></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">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import converter.DefaultFactory;</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="gd" style="color: #000; background-color: #fdd;">-import converter.Factory;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import es.uvigo.ei.sing.alter.converter.Converter;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import es.uvigo.ei.sing.alter.converter.DefaultFactory;</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import es.uvigo.ei.sing.alter.converter.Factory;</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> import java.io.IOException;</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> import java.io.PrintWriter;</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> import java.io.PushbackReader;</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -44,7 +44,7 @@ import pal.tree.Tree;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> import pal.tree.TreeParseException;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> // TODO: Auto-generated Javadoc</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import parser.ParseException;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import es.uvigo.ei.sing.alter.parser.ParseException;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> * The Class AlignmentReader.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> */</span></pre>
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<a href="https://salsa.debian.org/med-team/prottest/compare/8c6f1fa612c211d69c010afef04723765afe0598...a59a1e3d14da53cd5a00c39cc605abd94b9770ac#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_packaged_phyml.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">build.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">alter-import.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/prottest/compare/8c6f1fa612c211d69c010afef04723765afe0598...a59a1e3d14da53cd5a00c39cc605abd94b9770ac#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">include /usr/share/dpkg/default.mk</span></span>
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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"># Uncomment this to turn on verbose mode.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">#export DH_VERBOSE=1</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">@@ -12,9 +12,9 @@ JAVA_HOME=/usr/lib/jvm/default-java</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_fixperms:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_fixperms</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> chmod -x debian/$(DEB<span class="idiff left right">PKGNAME)/etc/$(DEBPKGNAM</span>E)/*</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> find debian/$(DEB<span class="idiff left right">PKGNAME)/usr/share/doc/$(DEBPKGNAM</span>E)/examples -type f -exec chmod -x \{\} \;</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> find debian/$(DEB<span class="idiff left right">PKGNAME)/usr/share/$(DEBPKGNAM</span>E)/models -type f -exec chmod -x \{\} \;</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> chmod -x debian/$(DEB<span class="idiff left right">_SOURCE)/etc/$(DEB_SOURC</span>E)/*</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> find debian/$(DEB<span class="idiff left right">_SOURCE)/usr/share/doc/$(DEB_SOURC</span>E)/examples -type f -exec chmod -x \{\} \;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> find debian/$(DEB<span class="idiff left right">_SOURCE)/usr/share/$(DEB_SOURC</span>E)/models -type f -exec chmod -x \{\} \;</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">override_dh_installchangelogs:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> dh_installchangelogs src/main/resources/CHANGELOG</span>
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