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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pdb2pqr">Debian Med / pdb2pqr</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/commit/96e7f41af8c8df4bf7f338a329bdd36f972f0172">96e7f41a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T16:36:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More Python3 issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/commit/78ddf6b666248328f1bcf0dec705fb0960d16515">78ddf6b6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T20:41:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some imports
</pre>
</li>
</ul>
<h4>1 changed file:</h4>
<ul>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/pdb2pqr/compare/382cbb2cf752593a6a1315a40ac77c8c556f7a82...78ddf6b666248328f1bcf0dec705fb0960d16515#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14560" 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">@@ -14560,6 +14560,15 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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14560
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<pre style="margin: 0;"> <span id="LC14560" class="line" lang="diff"> class TopologyResidue:</span>
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14561
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<td class="diff-line-num new_line" data-linenumber="14561" 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="LC14561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/utilities.py</span></span>
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<td class="diff-line-num new_line" data-linenumber="14562" 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">
14562
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<pre style="margin: 0;"> <span id="LC14562" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/utilities.py</span></span>
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<pre style="margin: 0;">+<span id="LC14563" class="line" lang="diff"><span class="p">@@ -53,7 +53,7 @@</span> import math</span>
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<td class="diff-line-num new new_line" data-linenumber="14564" 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="LC14564" class="line" lang="diff"> import os</span>
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<td class="diff-line-num new new_line" data-linenumber="14565" 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="LC14565" class="line" lang="diff"> from os.path import splitext </span>
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<td class="diff-line-num new new_line" data-linenumber="14566" 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="LC14566" class="line" lang="diff"> import sys</span>
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<td class="diff-line-num new new_line" data-linenumber="14567" 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="LC14567" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from aconf import INSTALLDIR, TMPDIR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14568" 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="LC14568" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .aconf import INSTALLDIR, TMPDIR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14569" 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="LC14569" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14570" class="line" lang="diff"> def startLogFile(jobName, fileName, logInput):</span>
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<pre style="margin: 0;">+<span id="LC14571" class="line" lang="diff"> with open('%s%s%s/%s' % (INSTALLDIR, TMPDIR, jobName, fileName), 'w') as f:</span>
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<pre style="margin: 0;"> <span id="LC14572" class="line" lang="diff"><span class="p">@@ -173,7 +173,7 @@</span> def sortDictByValue(inputdict):</span>
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<pre style="margin: 0;"> <span id="LC14573" class="line" lang="diff"> Returns</span>
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<pre style="margin: 0;"> <span id="LC14574" class="line" lang="diff"> items: The dictionary sorted by value (list)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14884" 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="diff-line-num unfold js-unfold new_line" data-linenumber="14893" 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">@@ -14884,3 +14893,25 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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<pre style="margin: 0;"> <span id="LC14893" class="line" lang="diff"> PyObject *ModuleDict = PyModule_GetDict(ThisModule); </span>
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<pre style="margin: 0;"> <span id="LC14894" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC14895" class="line" lang="diff"> // for correct handling of Numpy</span>
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<pre style="margin: 0;">+<span id="LC14896" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pdb2pqr.py.in</span></span>
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<pre style="margin: 0;">+<span id="LC14897" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pdb2pqr.py.in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14898" 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="LC14898" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span> __version__ = PDB2PQR_VERSION</span>
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<td class="diff-line-num new new_line" data-linenumber="14899" 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">
14899
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<pre style="margin: 0;">+<span id="LC14899" class="line" lang="diff"> if __name__ == "__main__":</span>
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<td class="diff-line-num new new_line" data-linenumber="14900" 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">
14900
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<pre style="margin: 0;">+<span id="LC14900" class="line" lang="diff"> """ Determine if called from command line or CGI """</span>
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<td class="diff-line-num new new_line" data-linenumber="14901" 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">
14901
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<pre style="margin: 0;">+<span id="LC14901" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="14902" 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">
14902
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<pre style="margin: 0;">+<span id="LC14902" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not os.environ.has_key("REQUEST_METHOD"):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14903" 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">
14903
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<pre style="margin: 0;">+<span id="LC14903" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if "REQUEST_METHOD" not in os.environ:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14904" 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">
14904
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<pre style="margin: 0;">+<span id="LC14904" class="line" lang="diff"> mainCommand(sys.argv)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14887" 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="14905" 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">
14905
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<pre style="margin: 0;">+<span id="LC14905" class="line" lang="diff"> else:</span>
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</td>
<td class="diff-line-num new new_line" data-linenumber="14906" 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">
14906
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<pre style="margin: 0;">+<span id="LC14906" class="line" lang="diff"> mainCGI()</span>
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<td class="diff-line-num new new_line" data-linenumber="14907" 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">
14907
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<pre style="margin: 0;">+<span id="LC14907" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/server.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14908" 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">
14908
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<pre style="margin: 0;">+<span id="LC14908" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/server.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14909" 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">
14909
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<pre style="margin: 0;">+<span id="LC14909" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span> import string</span>
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<td class="diff-line-num new new_line" data-linenumber="14910" 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">
14910
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<pre style="margin: 0;">+<span id="LC14910" class="line" lang="diff"> import os</span>
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<td class="diff-line-num new new_line" data-linenumber="14911" 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">
14911
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<pre style="margin: 0;">+<span id="LC14911" class="line" lang="diff"> import sys</span>
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<td class="diff-line-num new new_line" data-linenumber="14912" 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">
14912
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<pre style="margin: 0;">+<span id="LC14912" class="line" lang="diff"> import time</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14887" 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="14913" 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">
14913
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<pre style="margin: 0;">+<span id="LC14913" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from aconf import *</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14914" 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">
14914
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<pre style="margin: 0;">+<span id="LC14914" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .aconf import *</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14915" 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">
14915
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<pre style="margin: 0;">+<span id="LC14915" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14916" 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">
14916
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<pre style="margin: 0;">+<span id="LC14916" class="line" lang="diff"> # GLOBAL SERVER VARIABLES</span>
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<td class="diff-line-num new new_line" data-linenumber="14917" 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">
14917
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<pre style="margin: 0;">+<span id="LC14917" class="line" lang="diff"> #Currently this file is unused. TODO: Nuke it?</span></pre>
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