"cimported module has no attribute" when compiling Cython code

[m-dz]

After running the standard python setup.py install I got a series of errors:

cythoning hdbscan/_hdbscan_boruvka.pyx to hdbscan\_hdbscan_boruvka.c

Error compiling Cython file:
------------------------------------------------------------
...
# Fused type for certain operations
ctypedef fused DITYPE_t:
    ITYPE_t
    DTYPE_t

ITYPE = np.intp
         ^
------------------------------------------------------------

hdbscan\dist_metrics.pxd:22:10: cimported module has no attribute 'intp'

Error compiling Cython file:
------------------------------------------------------------
...
    ITYPE_t
    DTYPE_t

ITYPE = np.intp

DTYPE = np.double
         ^
------------------------------------------------------------

hdbscan\dist_metrics.pxd:24:10: cimported module has no attribute 'double'

Fixed by uninstalling Cython v. 0.27.3 and installing Cython v. 0.25.2, I will report there as well, but maybe it's worth to amend requirements.txt here as well?

Edit: system info: Win 10 64 bits, Python 2.7.14, up to date master of hdbscan.

[m-dz]

Discussed here: https://github.com/cython/cython/issues/1738

[m-dz]

It's strange as in _hdbscan_boruvka.pyx you are both importing and cimporting numpy, so this should not happen.

[lmcinnes]

Thanks, I was unaware of these apparent Cython changes. They will involve a lot of changes across the codebase :-( Worse still is the issue of backwards compatability.

[m-dz]

It still should work though as you have both (c)imports in place in this particular file (I was lucky enough to compile all using Cython 0.25.2 and then work only on boruvka after updating to 0.27.3).

[robertwb]

The "backwards incompatable" change in #1738 is that what was a runtime error (using an unimported module) becomes a compile time error instead.

[robertwb]

FWIW, it looks like _hdbscan_boruvka.pyx has been correctly importing and cimporting numpy for years now. I just tried building master with the latest Cython and could not reproduce the issue.

[m-dz]

Maybe it is system/Python version related then? I will try one more time.

Edit: @robertwb , I have checked on a different computer, same issue. Win 8.1, Python 2.7.14, pip-installed Cython 0.27.3. all working after installing Cython 0.25.2.

[trevorboydsmith]

i experience a similar issue with missing "np.intp" and "np.float64" causing compiler errors.

i tried cython 0.29.x. then 0.27.x. then with 0.25.2 i was successful.

i am using

• platform: centos 7
• scipy version 0.12.x from yum repo
• numpy version 1.7.x from yum repo
• python 2.7.x from yum repo
• scikit-learn 0.18.2 tarball

(i am using 0.18.2 scikit-learn because it's reqs still mostly fit with centos7)