part 2

 """

 Library of discrete time Epidemic models

@@ -49,8 +49,8 @@

     """

     Defines a library of discrete time population models

     """

-    @cython.locals(geocode='long', modtype='bytes', parallel='bint')

-    def __init__(self, geocode, modtype=b'', parallel=True):

+    @cython.locals(geocode='long', modtype='str', parallel='bint')

+    def __init__(self, geocode, modtype=u'', parallel=True):

         """

         defines which models a given site will use

         and set variable names accordingly.

@@ -78,9 +78,9 @@

         theta = int(nan_to_num(float(redisclient.get("{}:theta".format(self.geocode)))))

         npass = int(float(redisclient.get("{}:npass".format(self.geocode))))

         values = [float(i) for i in redisclient.lrange("{}:values".format(self.geocode), 0, -1)]

         return inits, simstep, totpop, theta, npass, bi, bp, values

@@ -106,7 +106,7 @@

             # self.parentGraph.epipath.append((self.parentGraph.simstep, self.geocode, self.infector))

             # TODO: have infector be stated in terms of geocodes

-@cython.locals(Type='bytes')

+@cython.locals(Type='str')

 def selectModel(Type):

     """

     Sets the model engine

@@ -157,7 +157,7 @@

             return CustomModel.Model

         return self

     def createModel(self, modtype='', name='model1', v=[], bi=None, bp=None):

@@ -105,7 +106,7 @@

         """

        # Init = init  # deprecated

         N = self.totpop

-        self.modtype = modtype

+        self.modtype = modtype.encode('utf-8')

@@ -109,11 +110,11 @@

         self.values = v

         self.bi = bi

         self.bp = bp

-        self.model = epimodels.Epimodel(self.geocode, modtype)

+        self.model = epimodels.Epimodel(self.geocode, self.modtype)

         self.vnames = epimodels.vnames[modtype]

         try:

             # self.ts = [[bi[vn.lower()] for vn in self.vnames]]

-            self.ts.append(list(bi.values()))  # This is fine since bi is an OrderedDict

+            self.ts.append(bi.values())  # This is fine since bi is an OrderedDict

         except KeyError as ke:

             if self.vnames == ['Exposed', 'Infectious', 'Susceptible']:

                 self.ts = [[bi[vn] for vn in ['e', 'i', 's']]]

@@ -1155,9 +1156,9 @@

         Length -- Length in kilometers of this route

         """

         self.dest = dest

         self.source = source

         self.sites = [source, dest]

@@ -1207,9 +1208,9 @@

         self.name = graph_name

         self.digraph = digraph

         self.site_dict = {} #geocode as keys

-        self.site_list = property(fget=lambda self: self.site_dict.values()) #only for backwards compatibility

+        self.site_list = property(fget=lambda self: list(self.site_dict.values())) #only for backwards compatibility

         self.edge_dict = {} #geocode tuple as key

-        self.edge_list = property(fget=lambda self: self.edge_dict.values()) #only for backwards compatibility

+        self.edge_list = property(fget=lambda self: list(self.edge_dict.values())) #only for backwards compatibility

         self.speed = 0 # speed of the transportation system

         self.simstep = 1 #current step in the simulation

         self.maxstep = 100 #maximum number of steps in the simulation

@@ -1251,7 +1252,7 @@

         """

         return sitenames

@@ -1512,9 +1512,9 @@

@@ -1512,7 +1512,7 @@

         dm = zeros((d, d), float)

         ap = zeros((d, d), float)

         i = 0

-        for sitei in g.iterkeys():

+        for sitei in g.keys():

             j = 0

-            for sitej in g.keys()[:i]: #calculates only the lower triangle

+            for sitej in list(g.keys())[:i]: #calculates only the lower triangle

             for sitej in g.keys()[:i]: #calculates only the lower triangle

                 sp = self.shortestPath(g, sitei, sitej)

                 lsp = self.getShortestPathLength(sitei, sp) #length of the shortestpath

                 self.shortPathList.append((sitei, sitej, sp, lsp))

@@ -1557,7 +1557,7 @@

             pass

         if not self.graphdict: #this generates site neighbors lists

             self.getGraphdict()

-        site_list = self.site_dict.values()

+        site_list = list(self.site_dict.values())

         nsites = len(self.site_dict)

         cm = zeros((nsites, nsites), float)

         for i, sitei in enumerate(site_list):

@@ -1636,7 +1636,7 @@

         The weight of all nodes in the graph (W(G)) is the summation

         of each node's order (o) multiplied by 2 for all orders above 1.

             self.__heap.sort()  # builtin sort likely faster than O(n) heapify

         else:

             newPair = (val, key)

@@ -1953,7 +1953,7 @@

             heap[insertionPoint] = newPair

     def update(self, other):

-        for key in other.keys():

+        for key in list(other.keys()):

             self[key] = other[key]

     def setdefault(self, key, val):

--- epigrass.orig/Epigrass/primitives.py

+++ epigrass/Epigrass/primitives.py

@@ -9,7 +9,16 @@

+    gluNewQuadric, glColor4f, glPushMatrix, glTranslatef, glBegin, GL_POINTS,

+    glVertex3f, glEnd, glPopMatrix, GLU_FILL, glRotatef, gluQuadricDrawStyle,

+    gluDisk, gluPartialDisk, glEnable, GL_LINE_STIPPLE, glLineStipple,

+    glLineWidth, GL_LINE_LOOP, GL_QUADS, GL_POLYGON, GL_TRIANGLES, glDisable

+    glLineWidth, GL_LINE_LOOP, GL_QUADS, GL_POLYGON, GL_TRIANGLES, glDisable,

+    GLfloat, GL_LINES, glVertex2i, GLU_MAP1_TRIM_2, gluNewNurbsRenderer,

+    gluNurbsProperty, GLU_SAMPLING_TOLERANCE, GLU_DISPLAY_MODE, gluBeginCurve, 

+    gluNurbsCurve, GL_MAP1_VERTEX_3, gluEndCurve, GL_BLEND, glBlendFunc, 

                 return

         self.members = olist

     def getX(self) : 

@@ -458,7 +467,7 @@

     right = property(getRight, setRight)

     def setBottom(self,x):

-        self.rect = self.x, y-self.width*0.5, self.width, self.height

+        self.rect = self.x, self.y-self.width*0.5, self.width, self.height

     def getBottom(self): return self.rect[3]

     bottom = property(getBottom, setBottom)

@@ -506,7 +515,7 @@

         win.dispatch_events()

         mvmt = random.randint(-10, 10)

-        self.actionGML.setText(QtGui.QApplication.translate("MainWindow", "GML", None, QtGui.QApplication.UnicodeUTF8))

-        self.actionPajek.setText(QtGui.QApplication.translate("MainWindow", "Pajek", None, QtGui.QApplication.UnicodeUTF8))

-        self.actionYAML.setText(QtGui.QApplication.translate("MainWindow", "YAML", None, QtGui.QApplication.UnicodeUTF8))

-

-import epigrass_rc

-

-if __name__ == "__main__":

-    import sys

-    app = QtGui.QApplication(sys.argv)

-    MainWindow = QtGui.QMainWindow()

-    ui = Ui_MainWindow()

-    ui.setupUi(MainWindow)

-    MainWindow.show()

-    sys.exit(app.exec_())

+        self.dataPanel.setTabText(self.dataPanel.indexOf(self.Edges), _translate("MainWindow", "Edges"))

+        self.menuFile.setTitle(_translate("MainWindow", "&File"))

+        self.menu_Export.setTitle(_translate("MainWindow", "&Export"))

+        self.actionPajek.setText(_translate("MainWindow", "Pajek"))

+        self.actionYAML.setText(_translate("MainWindow", "YAML"))

 import epigrass_rc

-

-if __name__ == "__main__":

-    import sys

-    app = QtGui.QApplication(sys.argv)

-    MainWindow = QtGui.QMainWindow()

-    ui = Ui_MainWindow()

-    ui.setupUi(MainWindow)

-    MainWindow.show()

-    sys.exit(app.exec_())

-

+from . import epigrass_rc

--- epigrass.orig/Epigrass/dataObject.py

+++ epigrass/Epigrass/dataObject.py

@@ -62,13 +62,13 @@

-from PyQt4 import QtCore, QtGui

-from PyQt4.QtGui import QMainWindow

-from PyQt4.QtCore import pyqtSignature

+from PyQt5 import QtCore, QtGui

+from PyQt5.QtGui import QMainWindow

+from PyQt5 import QtCore, QtGui, QtWidgets

+from PyQt5.QtWidgets import QMainWindow

+from PyQt5.QtCore import pyqtSlot

 from types import MethodType

-from Ui_neteditor import Ui_MainWindow

         pass

-    @pyqtSignature("")

+    @pyqtSlot

+    @pyqtSlot()

     def on_edgeTable_itemSelectionChanged(self):

         """

         Slot documentation goes here.

 #    app.setMainWidget(w)

--- epigrass.orig/Epigrass/report.py

+++ epigrass/Epigrass/report.py

@@ -2,7 +2,7 @@

@@ -2,7 +2,9 @@

 This module generates a report of the network simulation model

 using LaTeX.

 """

-import os, sys, commands, string, time, matplotlib, codecs

+import os, sys, subprocess, string, time, matplotlib, codecs

+from matplotlib.pyplot import close, savefig, bar, ylabel, xlabel, colorbar, title, pcolor, hist

+from numpy import mean

 #matplotlib.use("Agg")

 #from pylab import *

@@ -24,8 +24,8 @@

@@ -24,8 +26,8 @@

     """

     def __init__(self, simulation):

         self.workdir = os.getcwd()

         if pltx.startswith('which:'):

             self.latex = 0

         else:

@@ -348,12 +348,12 @@

@@ -348,12 +350,12 @@

         cuminc=[sum(incidence[:i]) for i in range(len(incidence))]

         infc = site.thetahist

         xlabel('Time')

         ylabel('Infectious individuous')

         savefig('inf.png')

@@ -382,7 +382,7 @@

@@ -382,7 +384,7 @@

         """

         epistats = self.sim.g.getEpistats()

         cumcities = [sum(epistats[1][:i]) for i in range(len(epistats[1]))]

         ylabel=('Number of infected cities')

         xlabel=('Time')

         savefig('sp.png')

@@ -439,7 +439,7 @@

@@ -439,7 +441,7 @@

         Path = Path.replace(' ','-')

         os.system('mkdir '+Path)

         os.chdir(Path)

         sitehead = r"""

                 \chapter{Site Specific Analyses}"

@@ -476,7 +476,7 @@

@@ -476,7 +478,7 @@

                     latexsrc += self.siteReport(site)

             latexsrc += tail

             timer = time.clock()-start

             if self.sim.gui:

                 self.sim.gui.textEdit1.insertParagraph('Time to generate Network report: %s seconds.'% timer,-1)

             self.savenBuild('Netreport',latexsrc)

@@ -489,7 +489,7 @@

@@ -489,7 +491,7 @@

                     latexsrc += self.genSiteEpi(site)

             latexsrc +=  tail

             timer = time.clock()-start

             if self.sim.gui:

                 self.sim.gui.textEdit1.insertParagraph('Time to generate epidemiological report: %s seconds.'% timer,-1)

             self.savenBuild('epireport',latexsrc)

@@ -508,7 +508,7 @@

@@ -508,7 +510,7 @@

                     latexsrc += self.genSiteEpi(site)

             latexsrc += tail

             timer = time.clock()-start

             if self.sim.gui:

                 self.sim.gui.textEdit1.insertParagraph('Time to generate full report: %s seconds.'% timer,-1)

             self.savenBuild('fullreport',latexsrc)

@@ -520,7 +520,7 @@

@@ -520,7 +522,7 @@

         if self.sim.gui:

             self.sim.gui.textEdit1.insertParagraph(string,-1)

         else:

         """

--- epigrass.orig/Epigrass/spread.py

+++ epigrass/Epigrass/spread.py

@@ -1,10 +1,6 @@

@@ -1,14 +1,8 @@

 #coding: utf8

 #spread display and analisys

 #

-#    from PyQt4.QtGui import *

-#except ImportError: 

-#    print "Please install PyQT 4"

 #from qt import *

-#from qt import *

 from xml.dom import minidom, Node

 import os, json

@@ -38,7 +34,7 @@

-from numpy import *

 import networkx as nx

 from networkx.readwrite import  json_graph

 import codecs

@@ -38,7 +32,7 @@

             infected = self.g.site_dict[n[1]]

             infectors = n[-1]

             self.nxg.add_node(n[1],name=infected.sitename,time=n[0])

                 self.nxg.add_edge(n[1],i.geocode,weight=float(c))

@@ -62,7 +58,7 @@

@@ -62,7 +56,7 @@

         Spread.writeENGML(f,tree) #calling as a class method

         f.write(']')

         f.close()

     writeGML = classmethod(writeGML)

     def writeENGML(self,fobj,tree):

@@ -72,10 +68,10 @@

@@ -72,10 +66,10 @@

         f=fobj

         #Create dictionary of node IDs, and eliminate possible node duplicates.

         nodes = dict([(i[1],n) for n,i in enumerate(tree)])