Force cython to be used when building from source.

python/Makefile

@@ -15,6 +15,7 @@ all:
 	@echo Building python interface for PLUMED 
 	unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
           plumed_program_name=plumed \
+          plumed_force_cython=yes \
           plumed_version=$(VERSION) \
           plumed_include_dir=../src/wrapper \
           plumed_default_kernel="$$PWD/../src/lib/libplumedKernel.$(SOEXT)" \

src/lib/Makefile

@@ -314,6 +314,7 @@ ifdef python_bin
 	cd install/python && rm -fr *.so plumed.cpp build && \
           unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
           plumed_program_name=plumed \
+          plumed_force_cython=yes \
           plumed_version=$(VERSION) \
           plumed_include_dir=../../../wrapper \
           plumed_default_kernel="$(libdir)/lib$(program_name)Kernel.$(SOEXT)" \