diff --git a/.travis.yml b/.travis.yml
index 414104941..df908fdd8 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,7 +15,7 @@ addons:
     packages:
     - build-essential
     - cmake
-    - python
+    - python3
     - libboost-all-dev
     - libgsl-dev
     - libxerces-c-dev
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 92e1209de..0ade21b9e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,13 +2,7 @@
 # Copyright © 2005-2013 Swiss Tropical Institute and Liverpool School Of Tropical Medicine
 # Licence: GNU General Public Licence version 2 or later (see COPYING)
 
-cmake_minimum_required (VERSION 2.4)
-# We still (try to) support cmake 2.4, but cmake 2.8 policies also work:
-if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" GREATER 2.6)
-    cmake_policy(VERSION 2.8)
-elseif("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" GREATER 2.4)
-    cmake_policy(VERSION 2.6)
-endif("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" GREATER 2.6)
+cmake_minimum_required (VERSION 3.0)
 
 project (OpenMalaria CXX)
 
@@ -94,6 +88,11 @@ find_package (XSD)
 find_package (XERCESC)
 find_package (GSL)
 find_package (Z)
+find_package (Python)
+
+if (NOT PYTHON_EXECUTABLE)
+    message (SEND_ERROR "Unable to find a Python interpreter (required).")
+endif (NOT PYTHON_EXECUTABLE)
 
 
 # Find Boost:
diff --git a/FindPython.cmake b/FindPython.cmake
index 9c193304b..9aed8960e 100644
--- a/FindPython.cmake
+++ b/FindPython.cmake
@@ -4,7 +4,17 @@
 #
 # Defines PYTHON_EXECUTABLE. Doesn't abort if not found.
 
-find_program (PYTHON_EXECUTABLE python
+# We need Python 3.x which is now often the default version.
+# On Windows, install paths may help
+find_program (PYTHON_EXECUTABLE
+  NAMES python3 python3.exe python python.exe
+  PATHS
+    "C:\\Python37-x64" "C:\\Python37"
+    "C:\\Python36-x64" "C:\\Python36"
+    "C:\\Python35-x64" "C:\\Python35"
+    "C:\\Python34-x64" "C:\\Python34"
+    "C:\\Python33-x64" "C:\\Python33"
   DOC "Path to python (required).")
+message (STATUS "Found Python interpreter: ${PYTHON_EXECUTABLE}")
 
 mark_as_advanced (PYTHON_EXECUTABLE)
diff --git a/schema/CMakeLists.txt b/schema/CMakeLists.txt
index 2c92ef7d4..6930f34f5 100644
--- a/schema/CMakeLists.txt
+++ b/schema/CMakeLists.txt
@@ -2,8 +2,6 @@
 # Copyright © 2005-2011 Swiss Tropical Institute and Liverpool School Of Tropical Medicine
 # Licence: GNU General Public Licence version 2 or later (see COPYING)
 
-find_package (Python)
-
 set (SCHEMA_NAMES
   scenario
   demography
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 87f6384c0..dfe3ea090 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -2,8 +2,6 @@
 # Copyright © 2005-2009 Swiss Tropical Institute and Liverpool School Of Tropical Medicine
 # Licence: GNU General Public Licence version 2 or later (see COPYING)
 
-find_package (Python)
-
 # Testing via run.sh or run.py script:
 configure_file (
   ${CMAKE_CURRENT_SOURCE_DIR}/run.py
@@ -53,14 +51,11 @@ set (OM_BOXTEST_NAMES
 # tests with broken checkpointing:
 set (OM_BOXTEST_NC_NAMES)
 # Disabled due to "in-progress" work: (none)
+
 # Use python script.
-if (PYTHON_EXECUTABLE)
-  foreach (TEST_NAME ${OM_BOXTEST_NAMES})
+foreach (TEST_NAME ${OM_BOXTEST_NAMES})
     add_test (${TEST_NAME} ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/run.py ${TEST_NAME} -- --checkpoint)
-  endforeach (TEST_NAME)
-  foreach (TEST_NAME ${OM_BOXTEST_NC_NAMES})
+endforeach (TEST_NAME)
+foreach (TEST_NAME ${OM_BOXTEST_NC_NAMES})
     add_test (${TEST_NAME} ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/run.py -- ${TEST_NAME})
-  endforeach (TEST_NAME)
-else (PYTHON_EXECUTABLE)
-  message(WARNING "Tests are disabled (Python is needed to run them)")
-endif (PYTHON_EXECUTABLE)
+endforeach (TEST_NAME)
diff --git a/test/run.py b/test/run.py
index b0e5ba3b5..a854174f5 100755
--- a/test/run.py
+++ b/test/run.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # This file is part of OpenMalaria.
@@ -51,7 +51,7 @@ def __str__(self):
 testSrcDir="@CMAKE_CURRENT_SOURCE_DIR@"
 testBuildDir="@CMAKE_CURRENT_BINARY_DIR@"
 if not os.path.isdir(testSrcDir) or not os.path.isdir(testBuildDir):
-    print "Don't run this script directly; configure CMake then use the version in the CMake build dir."
+    print("Don't run this script directly; configure CMake then use the version in the CMake build dir.")
     sys.exit(-1)
 
 # executable
@@ -106,7 +106,7 @@ def linkOrCopy (src, dest):
             # This can still fail: a VirtualBox guest is not allowed to create
             # links on a drive shared by the host
             os.symlink(os.path.abspath(src), dest)
-        except OSError,e:
+        except OSError as e:
             shutil.copy2(src, dest)
     else:
         shutil.copy2(src, dest)
@@ -133,13 +133,13 @@ def runScenario(options,omOptions,name):
         cmd=["xmllint","--noout","--schema",scenarioSchema,scenarioSrc]
         # alternative: ["xmlstarlet","val","-s",SCHEMA,scenarioSrc]
         if options.logging:
-            print "\033[0;32m  "+(" ".join(cmd))+"\033[0;00m"
+            print("\033[0;32m  "+(" ".join(cmd))+"\033[0;00m")
         return subprocess.call (cmd,cwd=testBuildDir)
     
     cmd=options.wrapArgs+[openMalariaExec,"--deprecation-warnings","--resource-path",os.path.abspath(testSrcDir),"--scenario",scenarioSrc]+omOptions
     
     if not options.run:
-        print "\033[0;32m  "+(" ".join(cmd))+"\033[0;00m"
+        print("\033[0;32m  "+(" ".join(cmd))+"\033[0;00m")
         return 0
     
     # Run from a temporary directory, so checkpoint files won't conflict
@@ -156,16 +156,16 @@ def runScenario(options,omOptions,name):
     linkOrCopy (scenarioSchema, scenario_xsd)
     
     if options.logging:
-        print time.strftime("\033[0;33m%a, %d %b %Y %H:%M:%S")+"\t\033[1;33m%s" % scenarioSrc
+        print(time.strftime("\033[0;33m%a, %d %b %Y %H:%M:%S")+"\t\033[1;33m%s" % scenarioSrc)
     
     startTime=lastTime=time.time()
     # While no output.txt file and cmd exits successfully:
     while (not os.path.isfile(outputFile)):
         if options.logging:
-            print "\033[0;32m  "+(" ".join(cmd))+"\033[0;00m"
+            print("\033[0;32m  "+(" ".join(cmd))+"\033[0;00m")
         ret=subprocess.call (cmd, shell=False, cwd=simDir)
         if ret != 0:
-            print "\033[1;31mNon-zero exit status: " + str(ret)
+            print("\033[1;31mNon-zero exit status: " + str(ret))
             break
         
         # check for output.txt.gz in place of output.txt and uncompress:
@@ -195,7 +195,7 @@ def runScenario(options,omOptions,name):
         lastTime=checkTime
     
     if ret == 0 and options.logging:
-        print "\033[0;33mDone in " + str(time.time()-startTime) + " seconds"
+        print("\033[0;33mDone in " + str(time.time()-startTime) + " seconds")
     
     if options.cleanup:
         os.remove(scenario_xsd)
@@ -218,7 +218,7 @@ def runScenario(options,omOptions,name):
                 ctsret,ctsident = compareCtsout.main (origCtsout, ctsoutFile)
             else:
                 ctsret,ctsident = 3,False
-                print "\033[1;31mNo original ctsout.txt to compare with."
+                print("\033[1;31mNo original ctsout.txt to compare with.")
             if ctsident and options.cleanup:
                 os.remove(ctsoutFile)
                 if os.path.isfile(newCtsout):
@@ -233,7 +233,7 @@ def runScenario(options,omOptions,name):
                 ret,ident = compareOutput.main (origOutput, outputFile, 0)
             else:
                 ret,ident = 3,False
-                print "\033[1;31mNo original output.txt to compare with."
+                print("\033[1;31mNo original output.txt to compare with.")
             if ident and options.cleanup:
                 os.remove(outputFile)
                 if os.path.isfile(newOutput):
@@ -243,12 +243,12 @@ def runScenario(options,omOptions,name):
             ret,ident = 1,False
             stderrFile=os.path.join(simDir,"stderr.txt")
             if os.path.isfile (stderrFile):
-                print "\033[1;31mNo output 'output.txt'; error messages:"
+                print("\033[1;31mNo output 'output.txt'; error messages:")
                 se = open(stderrFile)
                 se.read()
                 se.close()
             else:
-                print "\033[1;31mNo output 'output.txt'"
+                print("\033[1;31mNo output 'output.txt'")
         
         ret=max(ret,ctsret)
         ident=ident and ctsident
@@ -265,9 +265,9 @@ def runScenario(options,omOptions,name):
     try:
         os.rmdir(simDir)
     except OSError:
-        print "\033[0;31mDirectory %s not empty, so not deleted!" % simDir
+        print("\033[0;31mDirectory %s not empty, so not deleted!" % simDir)
     
-    print "\033[0;00m"
+    print("\033[0;00m")
     return ret
 
 def setWrapArgs(option, opt_str, value, parser, *args, **kwargs):
@@ -345,8 +345,8 @@ def main(args):
             retVal = r if retVal == 0 else retVal
         
         return retVal
-    except RunError,e:
-        print str(e)
+    except RunError as e:
+        print(str(e))
         return -1
 
 if __name__ == "__main__":
diff --git a/unittest/AgeGroupInterpolationSuite.py b/unittest/AgeGroupInterpolationSuite.py
index 5f0a99fb7..688df9bba 100755
--- a/unittest/AgeGroupInterpolationSuite.py
+++ b/unittest/AgeGroupInterpolationSuite.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # This file is part of OpenMalaria.
@@ -52,7 +52,7 @@ def set_age_groups(self,age_lower_bounds,values):
         self.v=[values[0]]
         self.v.extend(values)
         self.v.append(values[len(values)-1])
-        print "Lengths:",len(self.a),len(self.v)
+        print("Lengths:",len(self.a),len(self.v))
     
     def interpolate(self,t):
         i=0
@@ -141,9 +141,9 @@ def plot(self,subplot):
 # Generate sample data for unittest:
 x=[15.2,18.09,7.0, 2.5, 0.0,20.0,900.0,62.0]
 
-print "Age points:",x
-print "Piecewise constant:",[const.interpolate(t) for t in x]
-print "Linear interpolation:",[linear.interpolate(t) for t in x]
+print("Age points:",x)
+print("Piecewise constant:",[const.interpolate(t) for t in x])
+print("Linear interpolation:",[linear.interpolate(t) for t in x])
 
 
 # Third plot: CMF data
diff --git a/unittest/CMakeLists.txt b/unittest/CMakeLists.txt
index 668939066..968cc2aac 100644
--- a/unittest/CMakeLists.txt
+++ b/unittest/CMakeLists.txt
@@ -2,8 +2,6 @@
 # Copyright © 2005-2009 Swiss Tropical Institute and Liverpool School Of Tropical Medicine
 # Licence: GNU General Public Licence version 2 or later (see COPYING)
 
-find_package (Python)
-
 set (OM_CXXTEST_INTERPRETER ${PYTHON_EXECUTABLE})
 set (OM_CXXTEST_SCRIPT ${CMAKE_SOURCE_DIR}/contrib/cxxtest/bin/cxxtestgen)
 
@@ -50,18 +48,13 @@ set (OM_CXXTEST_HEADERS
   PkPdComplianceSuite.h
 )
 
-#Appears to be problems with this on windows...
-if (OM_CXXTEST_INTERPRETER)
-  add_custom_command (OUTPUT tests.cpp
-    COMMAND ${OM_CXXTEST_INTERPRETER} ${OM_CXXTEST_SCRIPT} ${OM_CXXTEST_OPTIONS} --runner=ParenPrinter -o ${CMAKE_CURRENT_BINARY_DIR}/tests.cpp ${OM_CXXTEST_HEADERS}
+add_custom_command (OUTPUT tests.cpp
+    COMMAND ${PYTHON_EXECUTABLE} ${OM_CXXTEST_SCRIPT} ${OM_CXXTEST_OPTIONS} --runner=ParenPrinter -o ${CMAKE_CURRENT_BINARY_DIR}/tests.cpp ${OM_CXXTEST_HEADERS}
     DEPENDS ${OM_CXXTEST_HEADERS}
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
     COMMENT "Generating unittest code with cxxtestgen"
     VERBATIM
-  )
-else (OM_CXXTEST_INTERPRETER)
-  message (SEND_ERROR "Unable to find python executable. Thus I can't build tests.cpp which is required to run the unittests.")
-endif (OM_CXXTEST_INTERPRETER)
+)
 
 # These files are needed to run various infection model tests:
 configure_file (${CMAKE_SOURCE_DIR}/test/autoRegressionParameters.csv ${CMAKE_CURRENT_BINARY_DIR} COPYONLY)
diff --git a/unittest/DecayFunctionSuite.py b/unittest/DecayFunctionSuite.py
index 49307157f..cb44c23af 100755
--- a/unittest/DecayFunctionSuite.py
+++ b/unittest/DecayFunctionSuite.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # This file is part of OpenMalaria.
diff --git a/util/WriteParamDocu.py b/util/WriteParamDocu.py
deleted file mode 100644
index a4a35ed09..000000000
--- a/util/WriteParamDocu.py
+++ /dev/null
@@ -1,134 +0,0 @@
-#!/usr/bin/env python2
-# -*- coding: utf-8 -*-
-"""
-This file is part of OpenMalaria.
-
-Copyright (C) 2005-2014 Swiss Tropical Institute
-
-OpenMalaria is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or (at
-your option) any later version.
-
-This program is distributed in the hope that it will be useful, but
-WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, write to the Free Software
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-"""
-"""
-Write parameter documenation to an Excel File. You may need to
-install http://www.python-excel.org/ xlwt, e.g.:
-apt-get install python-xlwt
-or download the windows installer
-"""
-
-from xlwt import Workbook
-from xlwt import easyxf
-from xml.etree.ElementTree import ElementTree
-
-import string
-import re
-
-appinfoOrder=['name','units','type','min','max','exposed','sweepable']
-docu_xf = easyxf('align: wrap on, vert centre')
-worksheets = {}
-
-def normalizeNewlines(string):
-    string=" ".join(string.split())
-    return re.sub(r'(\r\n|\r|\n)', ' ', string)
-
-def formatElement(el,path):
-    if (el.find("{http://www.w3.org/2001/XMLSchema}annotation") is not None):
-        splitPath=string.split(path,'/')
-        #set default component to "scenario", i.e. write to the "Scenario" worksheet below
-        component="scenario"
-        printPath=string.replace(path,"/"+component,"")
-        #update component if a know child element of scenario, i.e. write to another worksheet below
-        if (len(splitPath)>2):
-            if (splitPath[2] in worksheets):
-                component=splitPath[2]
-                printPath=string.replace(printPath,"/"+component,"")
-        sheet= worksheets[component][0]
-        row=worksheets[component][1]
-        sheet.write(row,0,string.lstrip(printPath,"/"))
-        annotation=el.find("{http://www.w3.org/2001/XMLSchema}annotation")
-        docuElem=annotation.find("{http://www.w3.org/2001/XMLSchema}documentation")
-        if (docuElem is not None):
-            docu=docuElem.text
-        else:
-            docu="TODO"
-        content=string.strip(docu)
-        sheet.write(row,1,normalizeNewlines(content),docu_xf)
-        appInfoElem=el.find("{http://www.w3.org/2001/XMLSchema}annotation").find("{http://www.w3.org/2001/XMLSchema}appinfo")
-        if (appInfoElem is not None):
-            appInfo=string.strip(appInfoElem.text)
-        else:
-            appInfo="name:TODO"
-        appInfoList=string.split(appInfo,";")[0:-1]
-        for keyValue in appInfoList:
-            splitPair=string.split(keyValue,":")
-            colIndex=appinfoOrder.index(string.strip(str(splitPair[0])))+2
-            sheet.write(row,colIndex,splitPair[1],docu_xf)
-        #update next row to be written in that sheet
-        worksheets[component][1]=worksheets[component][1]+1
-        
-def drillDown(el,path,isExtType):
-    name=el.get("name")
-    if (name and not isExtType):
-        path=path+"/"+name
-        formatElement(el,path)
-    for elem in el.getchildren():
-        drillDown(elem,path,False)
-    elType=el.get("type")
-    if (elType):
-        for typeDefinition in tree.findall("{http://www.w3.org/2001/XMLSchema}complexType"):
-            if (typeDefinition.get("name")==elType):
-                drillDown(typeDefinition,path,True)
-                break      
-
-def initWorksheets(elementName,sheetName):
-    sheet=book.add_sheet(sheetName)
-    worksheets[elementName]=[sheet,1]
-    sheet.col(0).width =10000
-    sheet.col(1).width =15000
-    sheet.col(2).width =6500
-    sheet.col(3).width =4300
-    sheet.col(4).width =4300
-    sheet.col(5).width =4500
-    sheet.col(6).width =4800
-    sheet.col(7).width =6000
-    sheet.col(8).width =5500
-    sheet.write(0,0,"Parameter name and path (in XML document)")
-    sheet.write(0,1,"Parameter documentation       ")
-    sheet.write(0,2,"Parameter name (in GUI)")
-    sheet.write(0,3,"Parameter units")
-    sheet.write(0,4,"Parameter type")
-    sheet.write(0,5,"Parameter min value")
-    sheet.write(0,6,"Parameter max value")
-    sheet.write(0,7,"Parameter exposed in GUI")
-    sheet.write(0,8,"Parameter is sweepable")
-    
-def main():
-    global tree,book
-    book = Workbook()
-    initWorksheets("scenario", "Scenario")
-    initWorksheets("demography", "Demography")
-    initWorksheets("monitoring", "Monitoring")
-    initWorksheets("interventions", "Interventions")
-    initWorksheets("healthSystem", "HealthSystem")
-    initWorksheets("entomology", "Entomology")
-    initWorksheets("pharmacology", "Pharmacology")
-    initWorksheets("model", "Model")
-    tree = ElementTree()
-    tree.parse("../schema/scenario_34.xsd")
-    #we know that the first element in the schema defines scenario
-    scenarioElement=tree.find("{http://www.w3.org/2001/XMLSchema}element")
-    drillDown(scenarioElement,"",False)
-    book.save('Documentation.xls')
-
-if __name__ == '__main__':
-    main()
diff --git a/util/approxEqual.py b/util/approxEqual.py
index 9233ca72f..624176b73 100755
--- a/util/approxEqual.py
+++ b/util/approxEqual.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is part of OpenMalaria.
@@ -86,39 +86,39 @@ class TestApproxEqual (unittest.TestCase):
     def testNaN (self):
         Inf = 1e10000
         NaN = Inf * 0.0
-        self.assert_ (not self.approxEqual6 (NaN, 1))
-        self.assert_ (not self.approxEqual6 (NaN, 0))
-        self.assert_ (not self.approxEqual6 (NaN, NaN))
-        self.assert_ (not self.approxEqual6 (NaN, Inf))
+        self.assertTrue (not self.approxEqual6 (NaN, 1))
+        self.assertTrue (not self.approxEqual6 (NaN, 0))
+        self.assertTrue (not self.approxEqual6 (NaN, NaN))
+        self.assertTrue (not self.approxEqual6 (NaN, Inf))
     
     def testInf (self):
         Inf = 1e10000
-        self.assert_ (not self.approxEqual6 (Inf, 1))
-        self.assert_ (not self.approxEqual6 (Inf, 0))
-        self.assert_ (not self.approxEqual6 (Inf, Inf))
-        self.assert_ (not self.approxEqual6 (Inf, -Inf))
+        self.assertTrue (not self.approxEqual6 (Inf, 1))
+        self.assertTrue (not self.approxEqual6 (Inf, 0))
+        self.assertTrue (not self.approxEqual6 (Inf, Inf))
+        self.assertTrue (not self.approxEqual6 (Inf, -Inf))
     
     def testZero (self):
-        self.assert_ (not self.approxEqual6 (0, 1e-6))
-        self.assert_ (    self.approxEqual6 (0, 1e-7))
+        self.assertTrue (not self.approxEqual6 (0, 1e-6))
+        self.assertTrue (    self.approxEqual6 (0, 1e-7))
     
     def testRegular (self):
-        self.assert_ (not self.approxEqual6 (1, 0))
-        self.assert_ (not self.approxEqual6 (1, 0.999999))
-        self.assert_ (    self.approxEqual6 (1, 0.9999995))
-        self.assert_ (not self.approxEqual6 (1000000, 999999))
-        self.assert_ (    self.approxEqual6 (1000000, 999999.5))
+        self.assertTrue (not self.approxEqual6 (1, 0))
+        self.assertTrue (not self.approxEqual6 (1, 0.999999))
+        self.assertTrue (    self.approxEqual6 (1, 0.9999995))
+        self.assertTrue (not self.approxEqual6 (1000000, 999999))
+        self.assertTrue (    self.approxEqual6 (1000000, 999999.5))
         # these are considered equal because of absolute precision limitation rather than relative:
-        self.assert_ (    self.approxEqual6 (0.000001, 0.0000005))
+        self.assertTrue (    self.approxEqual6 (0.000001, 0.0000005))
         # this is roughly on the verge of what isn't considered equal:
-        self.assert_ (not self.approxEqual6 (0.000001, 0.000002))
+        self.assertTrue (not self.approxEqual6 (0.000001, 0.000002))
         
         # if we only want to test relative precision:
         approxEqualRel = ApproxEqual(1e-6, 0)
-        self.assert_ (not approxEqualRel (0.000001, 0.000000999999))
-        self.assert_ (    approxEqualRel (0.000001, 0.0000009999995))
+        self.assertTrue (not approxEqualRel (0.000001, 0.000000999999))
+        self.assertTrue (    approxEqualRel (0.000001, 0.0000009999995))
         approxEqual = ApproxEqual(0, 1e-11)
-        self.assert_ (approxEqual (approxEqualRel.sumRelDiffs, 1.49999999994))
+        self.assertTrue (approxEqual (approxEqualRel.sumRelDiffs, 1.49999999994))
 
 
 if __name__ == '__main__':
diff --git a/util/assimilateForDBImport.py b/util/assimilateForDBImport.py
index 0b26ffe0e..d682715a9 100755
--- a/util/assimilateForDBImport.py
+++ b/util/assimilateForDBImport.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is part of OpenMalaria.
@@ -20,7 +20,6 @@
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 """
 
-import string
 import os.path
 import sys
 from optparse import OptionParser
@@ -52,16 +51,16 @@ def main(args):
         return 1
     
     sweeps,swArmIds = readSwArmIds(others[0])
-    sce_id_ind = next((i for i in xrange(len(sweeps)) if sweeps[i] == 'sce_id'), None)
+    sce_id_ind = next((i for i in range(len(sweeps)) if sweeps[i] == 'sce_id'), None)
     if sce_id_ind is None:
-        raise Exception, "unable to find column for sce_id!"
+        raise Exception("unable to find column for sce_id!")
     # sce_id_ind is zero-indexed and misses first column, so add 2:
-    print "Column for sce_id:",sce_id_ind+2
+    print(("Column for sce_id:",sce_id_ind+2))
     
     outFile=open(others[2],'w')
     resultDir=others[1]
     
-    for f,k in swArmIds.iteritems():
+    for f,k in list(swArmIds.items()):
         sce_id=k[sce_id_ind]
         lineStart=sce_id+'\t'
         resPath=os.path.join(resultDir,f+'.txt')
diff --git a/util/compareCtsout.py b/util/compareCtsout.py
index 376fdf263..f708da9db 100755
--- a/util/compareCtsout.py
+++ b/util/compareCtsout.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is part of OpenMalaria.
@@ -21,7 +21,6 @@
 """
 
 import sys
-import string
 from optparse import OptionParser
 from approxEqual import ApproxSame
 
@@ -64,21 +63,21 @@ def sumsApproxEq (fn1,fn2):
     t2,vec2=readSums(fn2)
     approxSame = ApproxSame(REL_PRECISION,ABS_PRECISION)
     if t1 != t2:
-        print "\033[1;31mColumns not equal:"
-        print t1
-        print t2
-        print "\033[0;0m",
+        print("\033[1;31mColumns not equal:")
+        print(t1)
+        print(t2)
+        print("\033[0;0m", end=' ')
         return False
     allApEq=True
     assert len(vec1)==len(vec2)
     for i in range(len(vec1)):
         if not approxSame(vec1[i],vec2[i]):
-            print "\033[0;31mSignificantly different:",t1[i],"; sums:",vec1[i],",",vec2[i]
+            print("\033[0;31mSignificantly different:",t1[i],"; sums:",vec1[i],",",vec2[i])
             allApEq=False
     if allApEq:
-        print "No significant differences (total relative diff: "+str(approxSame.getTotalRelDiff())+"), ok."
+        print("No significant differences (total relative diff: "+str(approxSame.getTotalRelDiff())+"), ok.")
     else:
-        print "\033[1;31mSome significant differences (total relative diff: "+str(approxSame.getTotalRelDiff())+ ")!\033[0;0m"
+        print("\033[1;31mSome significant differences (total relative diff: "+str(approxSame.getTotalRelDiff())+ ")!\033[0;0m")
     return allApEq
 
 def main(fn1,fn2):
@@ -88,19 +87,19 @@ def main(fn1,fn2):
         opt+=" --rel-prescision="+str(REL_PRECISION)
     if ABS_PRECISION!=1e-6:
         opt+=" --abs-prescision="+str(ABS_PRECISION)
-    print "\033[1;36m  compareCtsout.py"+opt+" "+fn1+" "+fn2+"\033[0;0m"
+    print("\033[1;36m  compareCtsout.py"+opt+" "+fn1+" "+fn2+"\033[0;0m")
     
     # Read both files and combine into a map of key to pairs (v1, v2)
     try:
         if charEqual (fn1,fn2):
-            print "ctsout.txt files are identical"
+            print("ctsout.txt files are identical")
             return 0,True
         elif sumsApproxEq (fn1,fn2):
             return 0,False
         return 1,False
     # python 3000 syntax is "except IOError as e", backported to 2.6 but not always supported. Old syntax:
-    except IOError, e:
-        print str(e)
+    except IOError as e:
+        print(str(e))
         return 1,False
 
 # Test for options
@@ -131,6 +130,6 @@ def evalOptions (args):
     if (len(others) == 2):
         ret,ident = main (others[0],others[1])
     else:
-        print "Usage: "+sys.argv[0]+" logfile1 logfile2"
+        print("Usage: "+sys.argv[0]+" logfile1 logfile2")
         ret=-1
     sys.exit(ret)
diff --git a/util/compareOutput.py b/util/compareOutput.py
index db2fdf286..df058a0ff 100755
--- a/util/compareOutput.py
+++ b/util/compareOutput.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is part of OpenMalaria.
@@ -53,29 +53,29 @@ def main(fn1,fn2,maxDiffsToPrint=6):
         opt+=" --rel-prescision="+str(REL_PRECISION)
     if ABS_PRECISION!=1e-6:
         opt+=" --abs-prescision="+str(ABS_PRECISION)
-    print "\033[1;34m  compareOutput.py"+opt+" "+fn1+" "+fn2+" "+str(maxDiffsToPrint)+"\033[0;0m"
+    print(("\033[1;34m  compareOutput.py"+opt+" "+fn1+" "+fn2+" "+str(maxDiffsToPrint)+"\033[0;0m"))
     
     # Read both files and combine into a map of key to pairs (v1, v2)
     try:
         if charEqual (fn1,fn2):
-            print "output.txt files are identical"
+            print("output.txt files are identical")
             return 0,True
-        print "output.txt files aren't binary-equal"
+        print("output.txt files aren't binary-equal")
         
         values1=readEntries(fn1)
         values2=readEntries(fn2)
     # python 3000 syntax is "except IOError as e", backported to 2.6 but not always supported. Old syntax:
-    except IOError, e:
-        print str(e)
+    except IOError as e:
+        print((str(e)))
         return 1,False
     values=dict()
-    for (k,v1) in values1.iteritems():
+    for (k,v1) in list(values1.items()):
         v2=None
         if (k in values2):
             v2=values2[k]
             del values2[k]
         values[k] = (v1,v2)
-    for (k,v2) in values2.iteritems():
+    for (k,v2) in list(values2.items()):
         values[k] = (None,v2)
     
     # Go through all values:
@@ -91,7 +91,7 @@ def main(fn1,fn2,maxDiffsToPrint=6):
     perMeasureDiffAbsSum = dict()
     approxSame = ApproxSame(REL_PRECISION, ABS_PRECISION)
     
-    for (k,(v1,v2)) in values.iteritems():
+    for (k,(v1,v2)) in list(values.items()):
         if v1==None:
             numMissing1 += 1
         elif v2==None:
@@ -113,17 +113,17 @@ def main(fn1,fn2,maxDiffsToPrint=6):
         numPrinted += 1
         perMeasureNumDiff[k.a] = perMeasureNumDiff.get(k.a,0) + 1;
         if (numPrinted <= maxDiffsToPrint):
-            print "survey "+str(k.b)+", group "+str(k.c)+", measure "+str(k.a)+": "+str(v1)+" -> "+str(v2)
+            print(("survey "+str(k.b)+", group "+str(k.c)+", measure "+str(k.a)+": "+str(v1)+" -> "+str(v2)))
             if (numPrinted == maxDiffsToPrint):
-                print "[won't print any more line-by-line diffs]"
+                print("[won't print any more line-by-line diffs]")
     
     if (numMissing1 > 0) or (numMissing2 > 0):
-        print str(numMissing1) + " entries missing from first file, " + str(numMissing2) +" from second"
+        print((str(numMissing1) + " entries missing from first file, " + str(numMissing2) +" from second"))
         ret = 3
     
     maxDiffSum=0.0
     maxAbsDiffSum=0.0
-    for (k.a,absDiff) in perMeasureDiffAbsSum.iteritems():
+    for (k.a,absDiff) in list(perMeasureDiffAbsSum.items()):
         if not (absDiff <= 1e-6):   # handle NANs
             # standard division throws on divide-by-zero, which I don't want
             def div(x,y):
@@ -139,15 +139,15 @@ def div(x,y):
             maxDiffSum=max(maxDiffSum,math.fabs(diffSum))
             absDiffSum=div(absDiff,sum1)
             maxAbsDiffSum=max(maxAbsDiffSum,absDiffSum)
-            print "for measure "+str(k.a)+":\tsum(1st file):"+str(sum1)+"\tsum(2nd file):"+str(sum2)+"\tdiff/sum: "+str(diffSum)+"\t(abs diff)/sum: "+str(absDiffSum)
+            print(("for measure "+str(k.a)+":\tsum(1st file):"+str(sum1)+"\tsum(2nd file):"+str(sum2)+"\tdiff/sum: "+str(diffSum)+"\t(abs diff)/sum: "+str(absDiffSum)))
     if maxDiffSum>0 or maxAbsDiffSum>0:
-        print "Max diff/sum:",maxDiffSum,"max (abs diff)/sum:",maxAbsDiffSum
+        print(("Max diff/sum:",maxDiffSum,"max (abs diff)/sum:",maxAbsDiffSum))
     
     if numDiffs == 0:
-        print "No significant differences (total relative diff: "+str(approxSame.getTotalRelDiff())+"), ok."
+        print(("No significant differences (total relative diff: "+str(approxSame.getTotalRelDiff())+"), ok."))
         return ret,False
     else:
-        print "\033[1;31m"+str(numDiffs)+" significant differences (total relative diff: "+str(approxSame.getTotalRelDiff())+ ")!\033[0;0m"
+        print(("\033[1;31m"+str(numDiffs)+" significant differences (total relative diff: "+str(approxSame.getTotalRelDiff())+ ")!\033[0;0m"))
         return 1,False
 
 # Test for options
@@ -179,6 +179,6 @@ def evalOptions (args):
     elif (len(others) == 2):
         ret,ident = main (others[0],others[1])
     else:
-        print "Usage: "+sys.argv[0]+" logfile1 logfile2 [max different lines to print]"
+        print(("Usage: "+sys.argv[0]+" logfile1 logfile2 [max different lines to print]"))
         ret=-1
     sys.exit(ret)
diff --git a/util/dataPlotter.py b/util/dataPlotter.py
index f195d4f44..53510a408 100644
--- a/util/dataPlotter.py
+++ b/util/dataPlotter.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # This file is part of OpenMalaria.
@@ -28,7 +28,6 @@
 #  data from a particular arm may be picked (all others ignored)
 #  data may be agglomerated using some expression involving the arm
 
-import string
 import os.path
 import sys
 from optparse import OptionParser
diff --git a/util/inlineSchema.py b/util/inlineSchema.py
index 392e68e67..a99f7c711 100755
--- a/util/inlineSchema.py
+++ b/util/inlineSchema.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is part of OpenMalaria.
@@ -35,7 +35,7 @@ def findIncludes(node,inlined,toInline):
         if node.nodeType==xd.Node.ELEMENT_NODE and node.tagName=="xs:include":
             incl=node.getAttribute("schemaLocation")
             if not os.path.isfile(incl):
-                raise Exception,"schema '{0}' not found".format(incl)
+                raise Exception("schema '{0}' not found".format(incl))
             if not incl in inlined:
                 if not incl in toInline:
                     #print "new include: {0}".format(incl)
@@ -49,7 +49,7 @@ def inlineSchema(sourcePath,destinationPath):
     doc=xd.parse(sourcePath)
     docElt=doc.documentElement
     if not (docElt.nodeType==xd.Node.ELEMENT_NODE and docElt.tagName=="xs:schema"):
-        raise Exception, "file {0} doesn't start with an elt of name xs:schema".format(sourcePath)
+        raise Exception("file {0} doesn't start with an elt of name xs:schema".format(sourcePath))
     
     inlined=set()
     toInline=set()
@@ -61,7 +61,7 @@ def inlineSchema(sourcePath,destinationPath):
         inclDoc=xd.parse(incl)
         iDElt=inclDoc.documentElement
         if not iDElt.nodeType==xd.Node.ELEMENT_NODE and iDElt.tagName=="xs:schema":
-            raise Exception, "file {0} doesn't start with an elt of name xs:schema".format(incl)
+            raise Exception("file {0} doesn't start with an elt of name xs:schema".format(incl))
         findIncludes(iDElt.firstChild,inlined,toInline)
         for child in iDElt.childNodes:
             docElt.appendChild(child.cloneNode(True))
@@ -82,7 +82,7 @@ def main(args):
         (options, others) = parser.parse_args(args=args[1:])
         if not len(others)==2:
             parser.print_usage()
-            raise Exception,"Expected 2 arguments"
+            raise Exception("Expected 2 arguments")
         
         inlineSchema(others[0],others[1])
     #except Exception,e:
diff --git a/util/readOutput.py b/util/readOutput.py
index 9356bd682..8a4e09076 100644
--- a/util/readOutput.py
+++ b/util/readOutput.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
 # This file is part of OpenMalaria.
@@ -19,7 +19,6 @@
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 
-import string
 import unittest
 
 class Keys:
@@ -71,14 +70,14 @@ def setUp(self):
         self.b1 = Multi3Keys(0,"abc",5);
         self.b2 = Multi3Keys(0,"abc",5);
     def testEq (self):
-        self.assert_ (self.a1.a == self.a2.a)
-        self.assert_ (self.a1 == self.a2)
-        self.assert_ (self.b1 == self.b2)
-        self.assert_ (self.a1 != self.a3)
+        self.assertTrue (self.a1.a == self.a2.a)
+        self.assertTrue (self.a1 == self.a2)
+        self.assertTrue (self.b1 == self.b2)
+        self.assertTrue (self.a1 != self.a3)
     def testHash (self):
-        self.assert_ (self.a1.__hash__() == self.a2.__hash__())
-        self.assert_ (self.a1.__hash__() != self.a3.__hash__()) # actually, hash collisions are possible
-        self.assert_ (self.b1.__hash__() == self.b2.__hash__())
+        self.assertTrue (self.a1.__hash__() == self.a2.__hash__())
+        self.assertTrue (self.a1.__hash__() != self.a3.__hash__()) # actually, hash collisions are possible
+        self.assertTrue (self.b1.__hash__() == self.b2.__hash__())
 
 def isAgeGroup(measure):
     if measure in set([7,9,21,25,26,28,29,31,32,33,34,35,36,39,40,47,48,49,50,51,54]):
@@ -123,11 +122,11 @@ def get(self,survey,group,cohort,genotype,f):
         except LookupError:
             return 1e1000 - 1e0000 # NaN
     def getGroups(self):
-        return range(0,self.nGroups)
+        return list(range(0,self.nGroups))
     def getCohorts(self):
-        return range(0,self.nCohorts)
+        return list(range(0,self.nCohorts))
     def getGenotypes(self):
-        return range(0,self.nGenotypes)
+        return list(range(0,self.nGenotypes))
 
 def stringIndexAllMatch(strs,ind,char):
     for s in strs:
@@ -153,7 +152,7 @@ def read(self,fileName,filterExpr,exprDebug):
         def filterFun(f,m,s,g,c,gt):
             r=eval(filterExpr)
             if exprDebug:
-                print "f="+str(f),"m="+str(m),"s="+str(s),"g="+str(g),"c="+str(c),"g="+str(g)+":",r
+                print(("f="+str(f),"m="+str(m),"s="+str(s),"g="+str(g),"c="+str(c),"g="+str(g)+":",r))
             return r
         aKS = Keys.SURVEY in self.aggregateKeys
         aKG = Keys.GROUP in self.aggregateKeys
@@ -168,10 +167,10 @@ def filterFun(f,m,s,g,c,gt):
         fileObj = open(fileName, 'r')
         nErrs=0
         for line in fileObj:
-            items=string.split(line)
+            items=line.split()
             if (len(items) != 4):
-                print "expected 4 items on line; found (following line):"
-                print line
+                print("expected 4 items on line; found (following line):")
+                print(line)
                 nErrs+=1
                 if nErrs>5:
                     raise Exception ("Too many errors reading "+fileName)
@@ -203,7 +202,7 @@ def filterFun(f,m,s,g,c,gt):
             self.values[m].add(s,g,c,gt,fID,robustFloat(items[3]))
     
     def getFiles(self):
-        return range(len(self.files))
+        return list(range(len(self.files)))
     def getFileName(self,n):
         return self.files[n]
     def getFileNames(self,replaceFN):
@@ -234,7 +233,7 @@ def getSurveys(self,m):
         if m==21:
             return [1]
         else:
-            return range(1,self.nSurveys+1)
+            return list(range(1,self.nSurveys+1))
     def getAllGroups(self):
         groups=set()
         for x in self.values:
@@ -282,10 +281,10 @@ def readEntries (fname):
     values=dict()
     fileObj = open(fname, 'r')
     for line in fileObj:
-        items=string.split(line)
+        items=line.split()
         if (len(items) != 4):
-            print "expected 4 items on line; found (following line):"
-            print line
+            print("expected 4 items on line; found (following line):")
+            print(line)
             continue
             
         key=Multi3Keys(int(items[2]),int(items[0]),int(items[1]))
diff --git a/util/resultAssimilator.py b/util/resultAssimilator.py
index 9fac27d8a..a990d6767 100755
--- a/util/resultAssimilator.py
+++ b/util/resultAssimilator.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is part of OpenMalaria.
@@ -20,7 +20,6 @@
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 """
 
-import string
 import os.path
 import sys
 from optparse import OptionParser
@@ -61,7 +60,7 @@ def main(args):
         outFile.write('\t')
     outFile.write('survey\tgroup\tmeasure\tvalue\n')
     
-    for f,k in swArmIds.iteritems():
+    for f,k in list(swArmIds.items()):
         lineStart=''
         for x in k:
             lineStart+=x+'\t'
diff --git a/util/update-header.py b/util/update-header.py
index 72e9e4fe3..c94692c60 100755
--- a/util/update-header.py
+++ b/util/update-header.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is part of OpenMalaria.
@@ -83,8 +83,8 @@ def update_source(filename, copyright):
     elif header in nonheaders:
         pass
     else:
-        print header
-        r=raw_input("Remove above header? (y/N): ")
+        print(header)
+        r=eval(input("Remove above header? (y/N): "))
         if r[0]=='y' or r[0]=='Y':
             oldheaders.add(header)
             fdata = fdata[len(header):]
@@ -92,7 +92,7 @@ def update_source(filename, copyright):
             nonheaders.add(header)
     
     if not (fdata.startswith(copyright)):
-        print "updating "+filename
+        print(("updating "+filename))
         fdata = copyright + fdata
         if (isUTF):
             file(filename,"w").write(utfstr+fdata)