c_numpy.pxd missing?

[Oliver Beckstein]

Hi,

I want to rebuild cython files (in particular, distances.pxd) with 

   python setup.py build

but I got the error that c_numpy.pxd is missing. This "used to work" but I don't remember what package I'd need for this to be picked up. According to Google, we used to ship such a file in the past with MDAnalysis. Other projects seem to also include a version, see  https://www.google.com/#q=c_numpy.pxd and there seems an outdated example at http://scipy-cookbook.readthedocs.org/items/Pyrex_and_NumPy.html

Thanks,

Oliver

Error compiling Cython file:

------------------------------------------------------------

...

Serial versions of all distance calculations

"""

cimport cython

cimport c_numpy

       ^

------------------------------------------------------------

MDAnalysis/lib/distances.pyx:26:8: 'c_numpy.pxd' not found

[Oliver Beckstein]

Well, apparently we still had our version, in package/include/c_numpy.pxd.

I did a

cp include/c_numpy.pxd MDAnalysis/lib/include/

and now it works. However, this file seems to be the source of these warnings

/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

so we might want to look into

1. modernizing c_numpy.pxd
2. figuring out where it really has to live

Oliver

[Hai Nguyen]

I think `cimport c_numpy` should be `cimport numpy`

http://docs.cython.org/src/tutorial/numpy.html#adding-types

Hai

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[Hai Nguyen]

I don't see the benefit of using `cimport numpy` over using cython memory view.

Advantage of memory view:

- don't need numpy at compiling time

- you can still use numpy at running time or use any type of array supporting buffer protocol.

Hai

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[Max Linke]

On 11/11/2015 08:53 PM, Oliver Beckstein wrote:
> so we might want to look into
>

> 1. modernizing c_numpy.pxd
> 2. figuring out where it really has to live

Why do we even have that module? I never needed it in my own cython
code. Never since I started to use cython (something like 2-3 years ago)

>
> Oliver
>
>
>>
>

[Richard Gowers]

Yeah I moved that back in this issue https://github.com/MDAnalysis/mdanalysis/issues/444

We used to have a few copies of that header file so I moved it into a common directory.

And yeah, I think using that file is outdated, so as long as we don't kill compat with old versions of numpy we could move to the new solution.

[Oliver Beckstein]

On 11 Nov, 2015, at 13:12, Max Linke wrote:

> Why do we even have that module? I never needed it in my own cython code. Never since I started to use cython (something like 2-3 years ago)

I removed it as part of PR #529.

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[Oliver Beckstein]

On 11 Nov, 2015, at 12:55, Hai Nguyen wrote:

> I don't see the benefit of using `cimport numpy` over using cython memory view.

Fair enough.

PR?

>
> Advantage of memory view:
>
> - don't need numpy at compiling time
> - you can still use numpy at running time or use any type of array supporting buffer protocol.
>

[Hai Nguyen]

On Wed, Nov 11, 2015 at 5:10 PM, Oliver Beckstein <orbe...@gmail.com> wrote:

On 11 Nov, 2015, at 12:55, Hai Nguyen wrote:

> I don't see the benefit of using `cimport numpy` over using cython memory view.

Fair enough.

 

PR?

I will wait for someone to clean up the distance*.pyx codes. I am not sure why he/she duplicated lot of code in each file.

Hai 

>
> Advantage of memory view:
>
> - don't need numpy at compiling time
> - you can still use numpy at running time or use any type of array supporting buffer protocol.
>

--
Oliver Beckstein * orbe...@gmx.net
skype: orbeckst  * orbe...@gmail.com

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