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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/35e1491b48ae739e590ba0ac59320dac09b3d558">35e1491b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T07:30:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Another fix suggested by Scott (thanks a lot)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pdb2pqr/commit/2497134056ff92e64a5953e1b8dea3179d5aa377">24971340</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T08:10:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some issues with C++ compatibility of Python3
</pre>
</li>
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<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/7df19812ecf8b2435338b691b6316451922ca930...2497134056ff92e64a5953e1b8dea3179d5aa377#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13728" 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">@@ -13728,7 +13728,8 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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13728
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<pre style="margin: 0;"> <span id="LC13728" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (k,v) in list(dict.items()):</span></span>
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13729
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<pre style="margin: 0;"> <span id="LC13729" class="line" lang="diff"> contents = contents.replace(k, v)</span>
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<pre style="margin: 0;"> <span id="LC13730" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">-<span id="LC13731" class="line" lang="diff"> f = open(targetfile, 'wb')</span>
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<pre style="margin: 0;">+<span id="LC13731" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f = open(targetfile, 'wb')</span></span>
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<pre style="margin: 0;">+<span id="LC13732" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = open(targetfile, 'w')</span></span>
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<pre style="margin: 0;"> <span id="LC13733" class="line" lang="diff"> f.write(contents)</span>
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<pre style="margin: 0;"> <span id="LC13734" class="line" lang="diff"> f.close()</span>
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<td class="diff-line-num new_line" data-linenumber="13735" 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="LC13735" class="line" lang="diff"> except:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14626" 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="14627" 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">@@ -14626,3 +14627,49 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100</td>
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<pre style="margin: 0;"> <span id="LC14627" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Alias('complete-test', testList)</span></span>
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<pre style="margin: 0;"> <span id="LC14628" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;"> <span id="LC14629" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Alias('complete-test', testList)</span></span>
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<pre style="margin: 0;">+<span id="LC14630" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pdb2pka/substruct/Algorithms.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC14631" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pdb2pka/substruct/Algorithms.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC14632" class="line" lang="diff"><span class="p">@@ -136,7 +136,7 @@</span> static PyObject *find_max_clique(PyObjec</span>
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<pre style="margin: 0;">+<span id="LC14633" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14634" class="line" lang="diff"> for (int i=0; i<cliq.size; i++) {</span>
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<pre style="margin: 0;">+<span id="LC14635" class="line" lang="diff"> cerr << cliq.vertex[i] << " ";</span>
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<pre style="margin: 0;">+<span id="LC14636" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PyList_Append(erg, PyInt_FromLong(cliq.vertex[i]));</span></span>
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<pre style="margin: 0;">+<span id="LC14637" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PyList_Append(erg, PyLong_FromLong(cliq.vertex[i]));</span></span>
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<pre style="margin: 0;">+<span id="LC14638" class="line" lang="diff"> }</span>
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14639
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<pre style="margin: 0;">+<span id="LC14639" class="line" lang="diff"> </span>
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14640
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<pre style="margin: 0;">+<span id="LC14640" class="line" lang="diff"> for(int i = 0; i < n; i++) {</span>
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14641
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<pre style="margin: 0;">+<span id="LC14641" class="line" lang="diff"><span class="p">@@ -242,7 +242,7 @@</span> static PyObject *find_cliques(PyObject *</span>
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14642
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<pre style="margin: 0;">+<span id="LC14642" class="line" lang="diff"> PyObject* cli = PyList_New(0);</span>
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14643
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<pre style="margin: 0;">+<span id="LC14643" class="line" lang="diff"> </span>
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14644
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<pre style="margin: 0;">+<span id="LC14644" class="line" lang="diff"> for (int j=0; j < collector.cliques[i].size; j++) {</span>
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14645
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<pre style="margin: 0;">+<span id="LC14645" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PyList_Append(cli, PyInt_FromLong(collector.cliques[i].vertex[j]));</span></span>
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14646
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<pre style="margin: 0;">+<span id="LC14646" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PyList_Append(cli, PyLong_FromLong(collector.cliques[i].vertex[j]));</span></span>
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14647
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<pre style="margin: 0;">+<span id="LC14647" class="line" lang="diff"> }</span>
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14648
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<pre style="margin: 0;">+<span id="LC14648" class="line" lang="diff"> </span>
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14649
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<pre style="margin: 0;">+<span id="LC14649" class="line" lang="diff"> PyList_Append(result, cli);</span>
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14650
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<pre style="margin: 0;">+<span id="LC14650" class="line" lang="diff"><span class="p">@@ -299,10 +299,24 @@</span> static PyMethodDef ModuleMethods[] = {</span>
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14651
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<pre style="margin: 0;">+<span id="LC14651" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC14652" class="line" lang="diff"> </span>
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14653
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<pre style="margin: 0;">+<span id="LC14653" class="line" lang="diff"> /*----------------------------------------------------------------------------*/</span>
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14654
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<pre style="margin: 0;">+<span id="LC14654" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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14655
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<pre style="margin: 0;">+<span id="LC14655" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Followed</span></span>
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14656
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<pre style="margin: 0;">+<span id="LC14656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// https://stackoverflow.com/questions/28305731/compiler-cant-find-py-initmodule-is-it-deprecated-and-if-so-what-should-i</span></span>
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14657
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<pre style="margin: 0;">+<span id="LC14657" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// to replace Py_InitModule</span></span>
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14658
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<pre style="margin: 0;">+<span id="LC14658" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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14659
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<pre style="margin: 0;">+<span id="LC14659" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static struct PyModuleDef cModMethods =</span></span>
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14660
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<pre style="margin: 0;">+<span id="LC14660" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+{</span></span>
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14661
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<pre style="margin: 0;">+<span id="LC14661" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PyModuleDef_HEAD_INIT,</span></span>
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14662
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<pre style="margin: 0;">+<span id="LC14662" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ MODULE_STR, /* name of module */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14663" 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">
14663
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<pre style="margin: 0;">+<span id="LC14663" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "", /* module documentation, may be NULL */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14664" 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">
14664
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<pre style="margin: 0;">+<span id="LC14664" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -1, /* size of per-interpreter state of the module, or -1 if the module keeps state in global variables. */</span></span>
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14665
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<pre style="margin: 0;">+<span id="LC14665" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ModuleMethods</span></span>
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14666
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<pre style="margin: 0;">+<span id="LC14666" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+};</span></span>
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14667
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<pre style="margin: 0;">+<span id="LC14667" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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14668
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<pre style="margin: 0;">+<span id="LC14668" class="line" lang="diff"> PyMODINIT_FUNC MODULE_INIT()</span>
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14669
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<pre style="margin: 0;">+<span id="LC14669" class="line" lang="diff"> {</span>
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14670
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<pre style="margin: 0;">+<span id="LC14670" class="line" lang="diff"> </span>
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14671
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<pre style="margin: 0;">+<span id="LC14671" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PyObject *ThisModule = Py_InitModule( MODULE_STR , ModuleMethods);</span></span>
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14672
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<pre style="margin: 0;">+<span id="LC14672" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PyObject *ThisModule = PyModule_Create(&cModMethods);</span></span>
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14673
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<pre style="margin: 0;">+<span id="LC14673" class="line" lang="diff"> PyObject *ModuleDict = PyModule_GetDict(ThisModule); </span>
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14674
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<pre style="margin: 0;">+<span id="LC14674" class="line" lang="diff"> </span>
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14675
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<pre style="margin: 0;">+<span id="LC14675" class="line" lang="diff"> // for correct handling of Numpy</span></pre>
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