Simple example that shows a compilation problem with Cython (see error.log for the error message), fixedTest.pyx shows a workaround. anotherTest.pyx is another failing example.

anotherTest.pyx

# This file also fails to compile with error error: redefinition of ‘std::vector<int, std::allocator<int> > __pyx_convert_vector_from_py_int(PyObject*)’. Note that it only fails when I have another definition without the fused type.

from libcpp.vector cimport vector

cdef extern from "test.h":
	cdef cppclass _TestClassInt "TestClass<int>":
		vector[double] toDouble(const vector[int] &items) except +

	cdef cppclass _TestClassChar "TestClass<char>":
		vector[double] toDouble(const vector[char] &items) except +

ctypedef fused CharInt:
	int
	char


cdef class TestClass:
	cdef _TestClassInt _thisInt

	def toDouble(self, vector[int] items):
		return self._thisInt.toDouble(items)

# This is actually what I want (with more useful code of course)
cdef class TestClass2:
	cdef _TestClassInt _thisInt
	cdef _TestClassChar _thisChar

	def toDouble(self, vector[CharInt] items):
		if CharInt is int:
			return self._thisInt.toDouble(items)
		else:
			return self._thisChar.toDouble(items)

error.log

running build_ext
building 'test' extension
gcc -pthread -Wno-unused-result -DNDEBUG -fmessage-length=0 -grecord-gcc-switches -fstack-protector -O2 -Wall -D_FORTIFY_SOURCE=2 -funwind-tables -fasynchronous-unwind-tables -g -fPIC -I/usr/include/python3.3m -c test.cpp -o build/temp.linux-x86_64-3.3/test.o
test.cpp: In function ‘PyObject* __pyx_convert_vector_to_py_double(const std::vector<double>&)’:
test.cpp:1142:18: error: redefinition of ‘PyObject* __pyx_convert_vector_to_py_double(const std::vector<double>&)’
 static PyObject *__pyx_convert_vector_to_py_double(const std::vector<double> &__pyx_v_v) {
                  ^
test.cpp:1086:18: error: ‘PyObject* __pyx_convert_vector_to_py_double(const std::vector<double>&)’ previously defined here
 static PyObject *__pyx_convert_vector_to_py_double(const std::vector<double> &__pyx_v_v) {
                  ^
error: command 'gcc' failed with exit status 1

fixedTest.pyx

from libcpp.vector cimport vector

cdef extern from "test.h":
        cdef cppclass _TestClassInt "TestClass<int>":
                vector[double] toDouble(const vector[int] &items) except +

cdef class TestClassInt:
        cdef _TestClassInt _this

        def toDouble(self, vector[int] items):
                return self._this.toDouble(items)

cdef extern from "test.h":
        cdef cppclass _TestClassChar "TestClass<char>":
                vector[double] toDouble(const vector[char] &items) except +

cdef class TestClassChar:
        cdef _TestClassChar _this

        def toDouble(self, vector[char] items):
                return self._this.toDouble(items)

setup.py

from distutils.core import setup
from setuptools import Extension
from Cython.Build import cythonize

setup(ext_modules = cythonize([Extension("*", ["*.pyx"], language = "c++")]))

test.h

#include <vector>

template<typename Item>
class TestClass {
public:
        std::vector<double> toDouble(const std::vector<Item> &items) {
                std::vector<double> result(items.size());
                for (size_t i = 0; i < items.size(); ++i) {
                        result[i] = (double)items[i];
                }
                return result;
        }
};

test.pyx

from libcpp.vector cimport vector

cdef extern from "test.h":
        cdef cppclass _TestClass "TestClass"[Item]:
                vector[double] toDouble(const vector[Item] &items) except +

cdef class TestClassInt:
        cdef _TestClass[int] _this

        def toDouble(self, vector[int] items):
                return self._this.toDouble(items)

cdef class TestClassChar:
        cdef _TestClass[char] _this

        def toDouble(self, vector[char] items):
                return self._this.toDouble(items)