debian/patches/2to3.patch

@@ -13728,7 +13728,8 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
 +        for (k,v) in list(dict.items()):
              contents = contents.replace(k, v)
      try:
-         f = open(targetfile, 'wb')
+-        f = open(targetfile, 'wb')
++        f = open(targetfile, 'w')
          f.write(contents)
          f.close()
      except:
@@ -14626,3 +14627,49 @@ Last-Update: Thu, 12 Dec 2019 15:41:47 +0100
 -Alias('complete-test', testList)
 \ No newline at end of file
 +Alias('complete-test', testList)
+--- a/pdb2pka/substruct/Algorithms.cpp
++++ b/pdb2pka/substruct/Algorithms.cpp
+@@ -136,7 +136,7 @@ static PyObject *find_max_clique(PyObjec
+ 
+   for (int i=0; i<cliq.size; i++) {
+     cerr << cliq.vertex[i] << " ";
+-    PyList_Append(erg, PyInt_FromLong(cliq.vertex[i]));
++    PyList_Append(erg, PyLong_FromLong(cliq.vertex[i]));
+   }
+   
+   for(int i = 0; i < n; i++) {
+@@ -242,7 +242,7 @@ static PyObject *find_cliques(PyObject *
+     PyObject* cli = PyList_New(0);
+ 
+     for (int j=0; j < collector.cliques[i].size; j++) {
+-      PyList_Append(cli, PyInt_FromLong(collector.cliques[i].vertex[j]));
++      PyList_Append(cli, PyLong_FromLong(collector.cliques[i].vertex[j]));
+     }
+ 
+     PyList_Append(result, cli);
+@@ -299,10 +299,24 @@ static PyMethodDef ModuleMethods[] =   {
+ };
+ 
+ /*----------------------------------------------------------------------------*/
++
++// Followed
++//   https://stackoverflow.com/questions/28305731/compiler-cant-find-py-initmodule-is-it-deprecated-and-if-so-what-should-i
++// to replace Py_InitModule
++
++static struct PyModuleDef cModMethods =
++{
++    PyModuleDef_HEAD_INIT,
++    MODULE_STR,  /* name of module */
++    "",          /* module documentation, may be NULL */
++    -1,          /* size of per-interpreter state of the module, or -1 if the module keeps state in global variables. */
++    ModuleMethods
++};
++
+ PyMODINIT_FUNC MODULE_INIT()
+ {
+     
+-    PyObject *ThisModule = Py_InitModule( MODULE_STR , ModuleMethods);
++    PyObject *ThisModule = PyModule_Create(&cModMethods);
+     PyObject *ModuleDict = PyModule_GetDict(ThisModule);  
+ 
+     // for correct handling of Numpy