[Cython] Cannot cythonize subclasses of setuptools.extension._Extension

Tue Apr 19 05:48:41 EDT 2016

On Mon, Apr 18, 2016 at 6:56 PM, Manuel Nuno Melo
<manuel.nuno.melo at gmail.com> wrote:
> Ah, sorry Erik, you're absolutely right. I mixed my results a bit and must
> elaborate:
>
> 'setup_requires' on its own will indeed not generate the behavior I
> described.
>
> However, if you define the same dependency under 'setup_requires' AND
> 'install_requires', then you get the mess I mentioned. Essentially, when you
> reach 'install_requires' setuptools decides that the egg it has under .eggs
> suffices, and just links to it.
>
> This isn't an issue when depending on cython because it's really just a
> setup-time dependency. However, in our package we depend on numpy at both
> setup- and runtime, and therefore makes sense to have it under both
> 'requires' flags.
>
> This is why hooking in at the setup_requires step could be a potential
> workaround, if we could get it to do a full dependency install instead of
> local egg. I'm currently finishing up this approach.

Interesting.  This sounds to me like a regression, as I don't think it
used to do that.  This should probably be brought up on distutils-sig
or in the setuptools bug tracker, rather than spending a lot of time
hacking together a workaround or requiring changes specifically in
Cython (though I don't disagree that distutils.Extension should be
allowed in the first place).

IIRC it used to be that if the same package was specified in both
setup_requires and install_requires it would be built/installed twice.
This was recognized as inefficient, and that the copy installed in the
local .eggs directory satisfies an install_requires requirement it
should be copied from .eggs to the system site-packages (or whatever
the install target is).  I remember there at least being *discussion*
about that, but not sure what changes were made.

It sounds like in your case it's just adding Cython from your .eggs
into easy-install.pth which I agree is wrong.  If that's the case it
should be fixed in setuptools over all else.  I'll see if I can
reproduce it.  Jason Coombs who mantains setuptools is usually quick
to release bug fix versions if he gets a patch.

Erik

> On Mon, Apr 18, 2016 at 11:16 AM, Erik Bray <erik.m.bray at gmail.com> wrote:
>>
>> On Sat, Apr 16, 2016 at 1:29 PM, Manuel Nuno Melo
>> <manuel.nuno.melo at gmail.com> wrote:
>> > Hi Erik,
>> > Please post your solution; I'm curious to see it.
>>
>> Will do in a bit. I need to see if I can distill it somewhat from its
>> original context so that it can be better understood.
>>
>> > Currently, we're also using setup_requires but are moving away from it
>> > because of two main issues:
>> >
>> > 1- there's no flexibility to hook into it via setuptools.Distribution
>> > subclassing (unless you rewrite the entire __init__);
>>
>> I don't really think that's a big issue but maybe you've encountered
>> some reason that it is.
>> The worse thing about it is the general chicken-egg problem that you
>> need to call setup() to get your setup_requires, but you may need some
>> packages pulled in from setup_requires in order to do anything useful
>> with setup().
>>
>> d2to1 [1] solves this problem quite well, but unfortunately
>> development on it is stalled for the time being.  Another alternative
>> that can work quite well is some version of Daniel Holth's
>> "setup-requires" hack [2].
>>
>> > 2- (and more serious) setuptools installs setup_requires dependencies in
>> > the
>> > local directory, not as a system-wide install.
>>
>> That's a feature, not a bug.  Build requirements for a package might
>> be in conflict with the versions of those same requirements you have
>> already installed.  It also prevents things from being installed that
>> are *not* required at runtime.  It makes it easier for projects to pin
>> a little more strictly to their known-working build requirements,
>> without the constraints imposed by supporting a wider range of runtime
>> requirements.
>>
>> > Even worse, it then puts a
>> > path link to the current directory under the system-wide
>> > easy_install.pth.
>> > This means that if you install from the source directory via 'sudo
>> > ./setup.py install', you get a Cython egg downloaded into that
>> > directory,
>> > and its path added to sys.path (!!). Needless to say this can break in
>> > many
>> > nasty ways...
>>
>> Huh??  I'm not sure we're talking about the same thing now.  The local
>> .eggs cache directory created for setup_requires downloads most
>> certainly does not get added to easy_install.pth.  Are you sure you're
>> not thinking of `setup.py develop`?
>>
>> [1] https://pypi.python.org/pypi/d2to1
>> [2] https://bitbucket.org/dholth/setup-requires/src
>>
>> > On Sat, Apr 16, 2016 at 1:10 PM, Erik Bray <erik.m.bray at gmail.com>
>> > wrote:
>> >>
>> >> On Apr 14, 2016 21:07, "Manuel Nuno Melo" <manuel.nuno.melo at gmail.com>
>> >> wrote:
>> >> >
>> >> > Our need to control cythonization comes from the fact that we
>> >> > implement
>> >> > cython as a lazy and optional dependency. Lazy in the sense that we
>> >> > delay as
>> >> > much as possible cythonization so that setuptools or pip have time to
>> >> > install cython, if needed. Optional because we distribute both .pyx
>> >> > and
>> >> > cythonized .c files, and decide on which to use based on user flags.
>> >> >
>> >> > We, therefore, need an Extension class that only cythonizes if we
>> >> > decide
>> >> > to.
>> >> >
>> >> > Thanks for the feedback,
>> >> > Manel
>> >>
>> >> I have a solution for exactly this in astropy_helpers which makes it
>> >> possible, for example, to pull in Cython via setup_requires, but only
>> >> if
>> >> it's needed.
>> >>
>> >> Remind me on Monday and I can point out how it works.
>> >>
>> >> > On Apr 14, 2016 8:17 PM, "Matthew Brett" <matthew.brett at gmail.com>
>> >> > wrote:
>> >> > >
>> >> > > On Thu, Apr 14, 2016 at 6:08 AM, Erik Bray <erik.m.bray at gmail.com>
>> >> > > wrote:
>> >> > > > On Wed, Apr 13, 2016 at 9:35 PM, Manuel Nuno Melo
>> >> > > > <manuel.nuno.melo at gmail.com> wrote:
>> >> > > >> Hello devs,
>> >> > > >>
>> >> > > >> I'm developing the setup.py for a scientific package, MDAnalysis
>> >> > > >> (see PR
>> >> > > >> #799). We depend on distutils and setuptool. Namely, we use
>> >> > > >> setuptools.extension.Extension class for our extensions.
>> >> > > >>
>> >> > > >> Some older versions of setuptools (<18.0) do filename
>> >> > > >> cythonization
>> >> > > >> themselves upon initialization of the Extension object.
>> >> > > >>
>> >> > > >> Because we want to control name cythonization ourselves I try to
>> >> > > >> directly
>> >> > > >> use distutils.extension.Extension, which has none of setuptools'
>> >> > > >> cythonization. However, this doesn't work because setuptools
>> >> > > >> patches
>> >> > > >> distutils, so that distutils.extension.Extension effectively
>> >> > > >> becomes
>> >> > > >> setuptools.extension.Extension.
>> >> > > >
>> >> > > > I'm wondering what it is specifically you need to do in your
>> >> > > > subclass--might it still be possible to do with a subclass of the
>> >> > > > setuptools Extension?  Not saying I disagree with the overall
>> >> > > > idea,
>> >> > > > but I also wonder if there isn't a better way.
>> >> > >
>> >> > > I know this is a terrible and ugly hack, but the projects I work in
>> >> > > have a 'fake_pyrex' directory, that fools setuptools into thinking
>> >> > > that 'pyrex' is installed, and therefore prevents it from doing the
>> >> > > .pyx -> .c filename conversions in the extension:
>> >> > >
>> >> > > https://github.com/regreg/regreg/blob/master/setup.py#L33
>> >> > >
>> >> > > Cheers,
>> >> > >
>> >> > > Matthew
>> >> > > _______________________________________________
>> >> > > cython-devel mailing list
>> >> > > cython-devel at python.org
>> >> > > https://mail.python.org/mailman/listinfo/cython-devel
>> >> >
>> >> >
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>> >>
>> >>
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