With IPython 0.13.2 and Cython 0.18 I can compile cells with %%cython magic just find. However, the -a to output the annotated output stopped working after I upgraded. I get
UsageError: unrecognized arguments: -a
What version of IPython were you running before? I believe the annotate (-a) feature was added to the development branch after 0.13 (meaning it won't be in the 0.13.x releases).
I must have gotten confused and were running a newer version before then.
I just upgraded to git master (1.0dev) but cython magic seems to not work at all anymore:
File "", line 2
SyntaxError: invalid syntax
Did the syntax change perhaps?
cell magics are currently broken in 1.0dev