diff --git a/Engine/AppManager.h b/Engine/AppManager.h
index 14ac18a198..e10cbf97d1 100644
--- a/Engine/AppManager.h
+++ b/Engine/AppManager.h
@@ -44,7 +44,7 @@ CLANG_DIAG_ON(deprecated)
 #include <QtCore/QProcess>
 #include <QtCore/QMap>
 
-#if !defined(Q_MOC_RUN) && !defined(SBK_RUN)
+#if (!defined(Q_MOC_RUN) && !defined(SBK_RUN)) || defined(SBK2_GEN)
 #include <boost/scoped_ptr.hpp>
 #include <boost/shared_ptr.hpp>
 #include <boost/noncopyable.hpp>
diff --git a/Engine/Engine.pro b/Engine/Engine.pro
index 721f49d67f..95c763fb91 100644
--- a/Engine/Engine.pro
+++ b/Engine/Engine.pro
@@ -238,7 +238,6 @@ SOURCES += \
     NatronEngine/intparam_wrapper.cpp \
     NatronEngine/itembase_wrapper.cpp \
     NatronEngine/layer_wrapper.cpp \
-    NatronEngine/natron_namespace_wrapper.cpp \
     NatronEngine/natronengine_module_wrapper.cpp \
     NatronEngine/nodecreationproperty_wrapper.cpp \
     NatronEngine/outputfileparam_wrapper.cpp \
@@ -383,7 +382,6 @@ HEADERS += \
     PyParameter.h \
     PyRoto.h \
     PyTracker.h \
-    Pyside_Engine_Python.h \
     ReadNode.h \
     RectD.h \
     RectDSerialization.h \
diff --git a/Engine/ImagePlaneDesc.h b/Engine/ImagePlaneDesc.h
index 559207970f..d5747f2637 100644
--- a/Engine/ImagePlaneDesc.h
+++ b/Engine/ImagePlaneDesc.h
@@ -31,7 +31,7 @@
 #include <string>
 #include <vector>
 
-#if !defined(Q_MOC_RUN) && !defined(SBK_RUN)
+#if (!defined(Q_MOC_RUN) && !defined(SBK_RUN)) || defined(SBK2_GEN)
 GCC_DIAG_UNUSED_LOCAL_TYPEDEFS_OFF
 GCC_DIAG_OFF(unused-parameter)
 // /opt/local/include/boost/serialization/smart_cast.hpp:254:25: warning: unused parameter 'u' [-Wunused-parameter]
diff --git a/Engine/Knob.h b/Engine/Knob.h
index a90fa3c088..131afa9235 100644
--- a/Engine/Knob.h
+++ b/Engine/Knob.h
@@ -33,7 +33,7 @@
 #include <set>
 #include <map>
 
-#if !defined(Q_MOC_RUN) && !defined(SBK_RUN)
+#if (!defined(Q_MOC_RUN) && !defined(SBK_RUN)) || defined(SBK2_GEN)
 #include <boost/enable_shared_from_this.hpp>
 #include <boost/scoped_ptr.hpp>
 #endif
diff --git a/Engine/PySideCompat.cpp b/Engine/PySideCompat.cpp
index 0877733ebe..c56c9807aa 100644
--- a/Engine/PySideCompat.cpp
+++ b/Engine/PySideCompat.cpp
@@ -38,11 +38,17 @@
 CLANG_DIAG_OFF(mismatched-tags)
 GCC_DIAG_OFF(unused-parameter)
 GCC_DIAG_OFF(missing-field-initializers)
+#ifdef SBK2_GEN
+#include <basewrapper.h>
+#include <sbkconverter.h>
+#include <gilstate.h>
+#else
 #include <basewrapper.h>
 #include <conversions.h>
 #include <sbkconverter.h>
 #include <gilstate.h>
 #include <typeresolver.h>
+#endif
 #include <bindingmanager.h>
 CLANG_DIAG_ON(mismatched-tags)
 GCC_DIAG_ON(unused-parameter)
diff --git a/Engine/Pyside_Engine_Python.h b/Engine/Pyside_Engine_Python.h
index 2193eea4a2..432aea27bd 100644
--- a/Engine/Pyside_Engine_Python.h
+++ b/Engine/Pyside_Engine_Python.h
@@ -17,6 +17,9 @@
  * along with Natron.  If not, see <http://www.gnu.org/licenses/gpl-2.0.html>
  * ***** END LICENSE BLOCK ***** */
 
+//Defined to avoid including some headers when running shiboken which may crash shiboken (particularly boost headers)
+#define SBK_RUN
+
 #ifndef PYSIDE_ENGINE_PYTHON_H
 #define PYSIDE_ENGINE_PYTHON_H
 
@@ -33,10 +36,11 @@
  * Do not include it when compiling Natron.
  **/
 
-//Defined to avoid including some headers when running shiboken which may crash shiboken (particularly boost headers)
-#define SBK_RUN
-
+#ifdef SBK2_GEN
+#include <pyside2_global.h>
+#else
 #include <pyside_global.h>
+#endif
 #include <string>
 //Global
 #include <GlobalDefines.h>
diff --git a/Engine/typesystem_engine.xml b/Engine/typesystem_engine.xml
index 43f853b411..669c9d76f3 100644
--- a/Engine/typesystem_engine.xml
+++ b/Engine/typesystem_engine.xml
@@ -18,10 +18,13 @@
   - along with Natron.  If not, see <http://www.gnu.org/licenses/gpl-2.0.html>
    - ***** END LICENSE BLOCK ***** -->
 <typesystem package="NatronEngine">
-    
+
+    <inject-code class="native" position="beginning">
+        NATRON_NAMESPACE_USING NATRON_PYTHON_NAMESPACE_USING
+    </inject-code>
+
     <!--Load QtCore typesystem-->
     <load-typesystem name="typesystem_core.xml" generate="no" />
-    
     <!--Primitives-->
     <primitive-type name="bool"/>
     <primitive-type name="double"/>
@@ -209,8 +212,8 @@
         </conversion-rule>
     </container-type>
 
-     <!--Natron global enums-->
-    <namespace-type name="NATRON_NAMESPACE">
+     <!--Natron global enums
+    <namespace-type name="NATRON_NAMESPACE">-->
     <enum-type name="StatusEnum"/>
     <enum-type name="MergingFunctionEnum"/>
     <enum-type name="StandardButtonEnum" flags="StandardButtons"/>
@@ -225,7 +228,7 @@
     <enum-type name="OrientationEnum"/>
     <enum-type name="PlaybackModeEnum"/>
     <enum-type name="DisplayChannelsEnum"/>
-    </namespace-type>
+    <!--</namespace-type>-->
     
    
    <object-type name="RectI">
@@ -1506,6 +1509,7 @@
 
                     for (int j = 0; j &lt; subSize; ++j) {
                         PyObject* pyString = PyList_GET_ITEM(subList,j);
+                #if PY_VERSION_MAJOR &lt; 3
                         if ( PyString_Check(pyString) ) {
                             char* buf = PyString_AsString(pyString);
                             if (buf) {
@@ -1514,6 +1518,9 @@
                                 rowVec[j] = ret;
                                 }
                         } else if (PyUnicode_Check(pyString) ) {
+                #else
+                        if (PyUnicode_Check(pyString) ) {
+                #endif
                             PyObject* utf8pyobj = PyUnicode_AsUTF8String(pyString); // newRef
                             if (utf8pyobj) {
                                 char* cstr = PyBytes_AS_STRING(utf8pyobj); // Borrowed pointer
diff --git a/Global/Enums.h b/Global/Enums.h
index 7e76a8c6a1..3ec34bb7f8 100644
--- a/Global/Enums.h
+++ b/Global/Enums.h
@@ -28,7 +28,7 @@ CLANG_DIAG_OFF(deprecated)
 CLANG_DIAG_ON(deprecated)
 
 NATRON_NAMESPACE_ENTER
-#ifdef SBK_RUN
+#if defined(SBK_RUN) && !defined(SBK2_GEN)
 // shiboken doesn't generate SbkNatronEngine_StandardButtonEnum_as_number unless it is put in a class or namespace
 NATRON_NAMESPACE_EXIT
 namespace NATRON_NAMESPACE {
@@ -684,7 +684,7 @@ enum MergingFunctionEnum
 //typedef QFlags<StandardButtonEnum> StandardButtons;
 Q_DECLARE_FLAGS(StandardButtons, StandardButtonEnum)
 
-#ifdef SBK_RUN
+#if defined(SBK_RUN) && !defined(SBK2_GEN)
 }
 NATRON_NAMESPACE_ENTER
 #endif
diff --git a/Global/GlobalDefines.h b/Global/GlobalDefines.h
index 4929728224..30397bcc30 100644
--- a/Global/GlobalDefines.h
+++ b/Global/GlobalDefines.h
@@ -66,10 +66,10 @@ CLANG_DIAG_ON(deprecated)
 //#define foreach Q_FOREACH
 
 
-typedef boost::uint32_t U32;
-typedef boost::uint64_t U64;
-typedef boost::uint8_t U8;
-typedef boost::uint16_t U16;
+typedef std::uint32_t U32;
+typedef std::uint64_t U64;
+typedef std::uint8_t U8;
+typedef std::uint16_t U16;
 
 
 NATRON_NAMESPACE_ENTER
diff --git a/Global/Pyside_Shiboken2_Macros.h b/Global/Pyside_Shiboken2_Macros.h
new file mode 100644
index 0000000000..5c5d34b076
--- /dev/null
+++ b/Global/Pyside_Shiboken2_Macros.h
@@ -0,0 +1 @@
+#define SBK2_GEN
diff --git a/global.pri b/global.pri
index 96208f97e3..9d3a4d339f 100644
--- a/global.pri
+++ b/global.pri
@@ -41,8 +41,6 @@ run-without-python {
     # from <https://docs.python.org/3/c-api/intro.html#include-files>:
     # "Since Python may define some pre-processor definitions which affect the standard headers on some systems, you must include Python.h before any standard headers are included."
     CONFIG += python
-    QMAKE_CFLAGS += -include Python.h
-    QMAKE_CXXFLAGS += -include Python.h
     python3 {
       PYV=3
       PY_PKG_SUFFIX=-embed
diff --git a/tools/utils/runPostShiboken2.sh b/tools/utils/runPostShiboken2.sh
new file mode 100755
index 0000000000..b692d65243
--- /dev/null
+++ b/tools/utils/runPostShiboken2.sh
@@ -0,0 +1,88 @@
+#!/bin/sh
+# ***** BEGIN LICENSE BLOCK *****
+# This file is part of Natron <http://www.natron.fr/>,
+# Copyright (C) 2016 INRIA and Alexandre Gauthier
+#
+# Natron 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.
+#
+# Natron 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 Natron.  If not, see <http://www.gnu.org/licenses/gpl-2.0.html>
+# ***** END LICENSE BLOCK *****
+
+# exit if a command returns an error status
+set -e
+
+# PySide version override, add 2 for Qt5/PySide2
+PYV="${1:-2}"
+
+# To be run after shiboken to fix errors
+
+sed -e '/<destroylistener.h>/d' -i'.bak' Engine/NatronEngine/*.cpp
+sed -e '/<destroylistener.h>/d' -i'.bak' Gui/NatronGui/*.cpp
+sed -e "/SbkPySide${PYV}_QtCoreTypes;/d" -i'.bak' Gui/NatronGui/natrongui_module_wrapper.cpp
+sed -e "/SbkPySide${PYV}_QtCoreTypeConverters;/d" -i'.bak' Gui/NatronGui/natrongui_module_wrapper.cpp
+sed -e '/SbkNatronEngineTypes;/d' -i'.bak' Gui/NatronGui/natrongui_module_wrapper.cpp
+sed -e '/SbkNatronEngineTypeConverters;/d' -i'.bak' Gui/NatronGui/natrongui_module_wrapper.cpp
+sed -e 's/cleanTypesAttributes/cleanGuiTypesAttributes/g' -i'.bak' Gui/NatronGui/natrongui_module_wrapper.cpp
+sed -e '/Py_BEGIN_ALLOW_THREADS/d' -i'.bak' Engine/NatronEngine/*.cpp
+sed -e '/Py_BEGIN_ALLOW_THREADS/d' -i'.bak' Gui/NatronGui/*.cpp
+sed -e '/Py_END_ALLOW_THREADS/d' -i'.bak' Engine/NatronEngine/*.cpp
+sed -e '/Py_END_ALLOW_THREADS/d' -i'.bak' Gui/NatronGui/*.cpp
+
+# fix warnings
+sed -e 's@^#include <shiboken.h>$@#include "Global/Macros.h"\
+CLANG_DIAG_OFF(mismatched-tags)\
+GCC_DIAG_OFF(unused-parameter)\
+GCC_DIAG_OFF(missing-field-initializers)\
+GCC_DIAG_OFF(missing-declarations)\
+GCC_DIAG_OFF(uninitialized)\
+GCC_DIAG_UNUSED_LOCAL_TYPEDEFS_OFF\
+#include <shiboken.h> // produces many warnings@' -i'.bak' Engine/NatronEngine/*.cpp Gui/NatronGui/*.cpp
+
+sed -e 's@// inner classes@// inner classes\
+NATRON_NAMESPACE_USING NATRON_PYTHON_NAMESPACE_USING@' -i'.bak' Engine/NatronEngine/*.cpp Gui/NatronGui/*.cpp
+
+# replace NATRON_NAMESPACE with Natron for enums with flags (e.g. StandardButtonEnum)
+sed -e 's@"NatronEngine\.NATRON_NAMESPACE@"NatronEngine.Natron@g' -e 's@, NatronEngine\.NATRON_NAMESPACE@, NatronEngine.Natron@g' -e 's@"NatronGui\.NATRON_NAMESPACE@"NatronGui.Natron@g' -e 's@"NATRON_NAMESPACE@"Natron@g' -i'.bak' Engine/NatronEngine/*_wrapper.cpp
+
+# re-add the Natron namespace
+#sed -e 's@" ::\([^s][^t][^d]\)@ NATRON_NAMESPACE::\1@g' -i'.bak' Engine/NatronEngine/*.cpp Engine/NatronEngine/*.h Gui/NatronGui/*.cpp Gui/NatronGui/*.h
+
+sed -e '/AnimatedParam/ {:y;n;by};s@SbkType< ::\(.*\) >@SbkType<NATRON_NAMESPACE::\1 >@g' -i Engine/NatronEngine/natronengine_python.h
+sed -e 's@SbkType< ::@SbkType<NATRON_NAMESPACE::NATRON_PYTHON_NAMESPACE::@g' -e 's@SbkType<NATRON_NAMESPACE::QFlags<@SbkType< ::QFlags<NATRON_NAMESPACE::@g' -e's@NATRON_NAMESPACE::NATRON_PYTHON_NAMESPACE::Rect@NATRON_NAMESPACE::Rect@g' -i'.bak' Engine/NatronEngine/natronengine_python.h Gui/NatronGui/natrongui_python.h
+sed -e 's@^class @NATRON_NAMESPACE_ENTER NATRON_PYTHON_NAMESPACE_ENTER\
+class @g;T;{:y;/^};/! {n;by}};s@^};@};\
+NATRON_PYTHON_NAMESPACE_EXIT NATRON_NAMESPACE_EXIT@g'  -i'.bak' Engine/NatronEngine/*.h Gui/NatronGui/*.h
+
+# replace NATRON_NAMESPACE::NATRON_NAMESPACE with NATRON_NAMESPACE in the enums wrappers
+sed -e 's@NATRON_NAMESPACE::NATRON_PYTHON_NAMESPACE::NATRON_NAMESPACE@NATRON_NAMESPACE@g' -i'.bak' Engine/NatronEngine/natronengine_python.h Gui/NatronGui/natrongui_python.h
+
+sed -e 's@^#include <pysidemetafunction.h>$@CLANG_DIAG_OFF(header-guard)\
+#include <pysidemetafunction.h> // has wrong header guards in pyside 1.2.2@' -i'.bak' Engine/NatronEngine/*.cpp Gui/NatronGui/*.cpp
+
+sed -e 's@^#include <pyside'${PYV}'_qtcore_python.h>$@CLANG_DIAG_OFF(deprecated)\
+CLANG_DIAG_OFF(uninitialized)\
+CLANG_DIAG_OFF(keyword-macro)\
+#include <pyside'${PYV}'_qtcore_python.h> // produces warnings\
+CLANG_DIAG_ON(deprecated)\
+CLANG_DIAG_ON(uninitialized)\
+CLANG_DIAG_ON(keyword-macro)@' -i'.bak' Engine/NatronEngine/*.cpp Gui/NatronGui/*.cpp Engine/NatronEngine/*.h Gui/NatronGui/*.h
+
+sed -e 's@^#include <pyside'${PYV}'_qtgui_python.h>$@CLANG_DIAG_OFF(deprecated)\
+CLANG_DIAG_OFF(uninitialized)\
+CLANG_DIAG_OFF(keyword-macro)\
+#include <pyside'${PYV}'_qtgui_python.h> // produces warnings\
+CLANG_DIAG_ON(deprecated)\
+CLANG_DIAG_ON(uninitialized)\
+CLANG_DIAG_ON(keyword-macro)@' -i'.bak' Engine/NatronEngine/*.cpp Gui/NatronGui/*.cpp Engine/NatronEngine/*.h Gui/NatronGui/*.h
+
+# clean up
+rm Gui/NatronGui/*.bak Engine/NatronEngine/*.bak