[SciPy-Dev] Cython as build dependency, file/dll size and current issues

Matthew Brett matthew.brett@gmail....
Thu Jul 5 13:57:26 CDT 2012


Hi,

On Thu, Jul 5, 2012 at 11:35 AM, Ralf Gommers
<ralf.gommers@googlemail.com> wrote:
>
>
> On Thu, Jul 5, 2012 at 8:31 PM, Matthew Brett <matthew.brett@gmail.com>
> wrote:
>>
>> Hi,
>>
>> On Thu, Jul 5, 2012 at 11:25 AM, Ralf Gommers
>> <ralf.gommers@googlemail.com> wrote:
>> > Hi all,
>> >
>> > On https://github.com/scipy/scipy/pull/261 the problem with large size
>> > of
>> > generated C files from Cython came up again, and Matthew suggested to
>> > add
>> > Cython as a build time dependency. He also pointed out that this was
>> > discussed before, with most people being in favor:
>> > http://mail.scipy.org/pipermail/scipy-dev/2009-November/013272.html
>> > http://mail.scipy.org/pipermail/scipy-dev/2009-November/013308.html
>> > We discussed the same issue on https://github.com/scipy/scipy/pull/211
>> > recently, and also the size of the binary.
>> >
>> > This is probably also the right moment to point out other recent Cython
>> > issues we've had:
>> > 1. A memoryview issue with Python 2.4, either a Cython or Numpy bug:
>> > https://github.com/numpy/numpy/pull/307
>> > 2. We had to manually patch the generated C files when using Cython
>> > 0.16, to
>> > make them work with MinGW: http://projects.scipy.org/scipy/ticket/1673
>> > 3. According to Ray, there's also an indexing bug in Cython 0.16 which
>> > requires to use 0.17-dev for https://github.com/scipy/scipy/pull/261
>> >
>> > I think it's clear that PR's like #261 above (Ray's ndimage.label
>> > rewrite)
>> > are in principle a good thing: faster and more general code which is
>> > easier
>> > to maintain. Now the question is what to do though. Here's some options
>> > that
>> > I see:
>> >
>> > a) Keep things as is for now. Accept large file/binary sizes. Manually
>> > patch
>> > the generated C if necessary.
>> > b) Keep things as is for now. Either go back to Cython 0.15, or bump
>> > required numpy version to latest dev version to not have to manually
>> > patch
>> > the generated C files.
>> > c) Keep things as they are now, without accepting too large file/binary
>> > sizes. To be defined what too large. Means we can't get the full
>> > benefits of
>> > fused types for example.
>> > d) Move to Cython as a build dependency. Write down the required
>> > versions
>> > and incompatibilities in the docs.
>> > e) Include a Cython version in the scipy git repo, patch it to solve the
>> > above issues 2 and 3 (and any other ones that come along).
>> > f) Some combination of the above.
>> > g) Any other options?
>>
>> Am I right in thinking that Cython 0.17dev will generate usable C
>> files without patching?
>
>
> Yes.

How about making Cython 0.17 a developer build-time dependency?

Meanwhile, making 'python setup.py sdist' dump the c files into the
source distribution?  Maybe with a nightly development snapshot pushed
up to sourceforge or similar?

That's what we are doing for dipy (the c files into the sdist):

https://github.com/nipy/dipy/blob/master/setup.py#L95
https://github.com/nipy/dipy/blob/master/cythexts.py

although a Bento way of doing that would probably be easier to maintain,

Cheers,

Matthew


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