I think this is a result of a recent change to Pyrex that has been merged into Cython.
If a directory contains an __init__.py or __init__.pyx file, it’s now assumed to be a package directory. So, for example, if you have a directory structure:
foo/
__init__.py
shrubbing.pxd
shrubbing.pyx
then the shrubbing module is assumed to belong to a package called ‘foo’, and its fully qualified module name is ‘foo.shrubbing’.
So when Pyrex wants to find out whether there is a .pxd file for shrubbing, it looks for one corresponding to a module called foo.shrubbing. It does this by searching the include path for a top-level package directory called ‘foo’ containing a file called ‘shrubbing.pxd’.
However, if foo is the current directory you’re running the compiler from, and you haven’t added foo to the include path using a -I option, then it won’t be on the include path, and the .pxd won’t be found.
What to do about this depends on whether you really intend the module to reside in a package.
If you intend shrubbing to be a top-level module, you will have to move it somewhere else where there is no __init__.* file.
If you do intend it to reside in a package, then there are two alternatives:
cd to the directory containing foo and compile from there:
cd ..; cython foo/shrubbing.pyx
arrange for the directory containing foo to be passed as a -I option, e.g.:
cython -I .. shrubbing.pyx
Arguably this behaviour is not very desirable, and I’ll see if I can do something about it.