[ase-users] Opinion about potentially adding Cython as a dependency

[Jens Jørgen Mortensen]

Den 10-10-2017 kl. 16:32 skrev Gaël Donval via ase-users:
> Dear Ask,
>> Dear Gaël,
>>
>> 2017-10-10 12:52 GMT+02:00 Gaël Donval via ase-users
>> <ase-users at listserv.fysik.dtu.dk>:
>>> Dear list,
>>>
>>> I am currently working on some geometrical code that I will
>>> ultimately
>>> propose adding to ASE. I am currently using Cython to speed up what
>>> needs speeding up and, to a more limited extent, I also use it to
>>> very
>>> conveniently generate bindings to C.
>>>
>>> The question is: would anyone see using Cython as a problem?
>>>
>>> I know that the fewer dependencies, the better. However Cython is
>>> almost as ubiquitous as Scipy nowadays in Python's scientific
>>> stack.
>>>
>>> The only real drawbacks I can think of (and I can read about on the
>>> internet) are pain points on Windows and incompatibility with
>>> different
>>> Python implementations (e.g. PyPy). However, with pip wheels,
>>> Windows
>>> is a non problem (most Python distributions on Windows now also
>>> include
>>> Cython by default so manual compilation is far from the pain it
>>> used to
>>> be) and ASE/GPAW do not support PyPy anyway because of all the C
>>> dependencies.
>>>
>>> Note that I am *not* proposing to convert any existing code to
>>> Cython
>>> nor to use Cython by default. I am talking about specific cases
>>> which
>>> would currently be handled by writing pure C code.
>> There are already a few cases where performance becomes an issue, so
>> this is worth thinking about.  Can Cython be an optional dependency?
> Yes it can and at two different levels:
>
>      1) *Provide fallback functions* Nothing would really prevent us from
>      providing two different versions of hot functions and degrade to
>      pure Python ones upon import if needed. However this would require
>      to keep function APIs in sync in two different places.
>
>      On the bright side, the slow and hopefully correct Python function
>      could be used as a reference in unit tests: these would rarely be
>      changed and most of the optimisation would occur in the Cython ones
>      instead.
>
>      2) *Provide C/C++ files* Ultimately, Cython generates a bunch of C
>      files containing Cython-defined code + everything needed to create a
>      native Python module. Directly using those C files (thus not
>      requiring Cython itself) is just a matter of tracking them in git!
>      :) That kind of optional Cython support can be reflected in setup.py
>      directly (look for USE_CYTHON    ):
>
>      https://gist.github.com/ctokheim/6c34dc1d672afca0676a#setuppy-and-disutils
>
> (note however that a C compiler is still needed).

I would like "pip install ase" to always just work, and for that I think 
we would need 1).  Alternatively, we should provide wheels for all 
architectures (manylinux1, win32, macosx, ...), but I don't think we 
have the resources to do that.

PS: You can always start with the slow Python version.

Jens Jørgen

>
> Regards,
> Gaël
>
>> Best regards
>> Ask
>>
>>> Best regards,
>>> Gaël
>>>
>>>
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