It's pretty awesome that Sphinx will work with Cython code files (.pyx) but there are currently a few wrinkles:
- You need to rerun the cython compiler before the documentation changes take since sphinx reads this off the compiled library
- Function signatures are omitted in the documentation and the compiler directive
# cython: embedsignature=Truedoes not work either. The workaround is to repeat the signature as the first line of the docstring
def merge_variants(c1, c2): """ merge_variants(c1, c2) ... rest of docstring ... """