[Biopython-dev] numpy setup-time dependency workaround

[Manuel Nuno Melo]

Yes, I understand that the limited install might be desirable under some
circumstances.
Maybe adding some argument-parsing capabilities to setup.py so that one
could invoke
./setup.py install --nonumpy
(pip could be made to also accept flags to this end with --install-option
="--nonumpy")
Python implementations where C-compiled code isn't supported would just
silently ignore the flags and skip any numpy-related stuff.

My point here is that a user wouldn't have to actively preinstall numpy.
"pip install biopython" would just work.

What do you think?
Manel

On Fri, Oct 23, 2015 at 5:12 PM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> Hi Manuel,
>
> The numpy specific hacks in Biopython's setup.py are a bit
> of a pain, yes.
>
> In my view, the main reason we have a "soft" dependency on
> NumPy is that we also want to be able to use Biopython on
> other Python implementations where NumPy is not available,
> e.g. Jython and PyPy (we need to check how their NumPyPy
> work is getting on, it may cover some of our usage now).
>
> In practice, even if the traditional Python implementation (in C)
> is used, there are times when it is helpful to be able to install
> most of Biopython without NumPy - for example virtual machine
> images for testing etc.
>
> In practise, maybe we should remove this special case an
> for the traditional Python implementation (in C) insist that
> numpy is already installed?
>
> (Modularising Biopython would be another practical solution
> to the partial NumPy dependency, but vastly more work)
>
> Peter
>
> On Fri, Oct 23, 2015 at 2:56 PM, Manuel Nuno Melo
> <manuel.nuno.melo at gmail.com> wrote:
> > Dear biopython devs,
> >
> > I recently implemented in MDAnalysis a distutils/setuptools workaround
> > (https://github.com/MDAnalysis/mdanalysis/pull/499) to the numpy
> > dependency-at-setuptime problem, and I think biopython might benefit from
> > it.
> >
> > The problem is that in setup.py distutils' setup() must be provided a
> list
> > of Extension objects, which in turn must contain the list of directories
> in
> > which to look for include files (namely, numpy's).
> >
> > If numpy isn't installed the Extensions objects can't be instantiated. If
> > numpy is specified as a setup-time dependency it will get installed when
> > setup() is called, but the instantiation of the Extensions happens before
> > the call to setup(). We get a cyclic dependency in that we need to know
> the
> > path to the numpy install before calling the function that will install
> > numpy.
> >
> > My solution was to subclass Extension to have a managed include_dirs
> > attribute which only probes for numpy at install-time. Since by then
> setup()
> > has had time to install numpy, all works fine.
> >
> > I believe a similar workaround could work well for biopython (although it
> > might involve setting numpy as as hard requirement, or at least asking
> the
> > user beforehand whether to install it).
> >
> > Of course, it would also benefit us at MDAnalysis since we could then
> > cleanly depend on biopython without worrying whether its install is
> > numpy-complete or not.
> >
> > I'll be glad with helping with the implementation, if you think it's
> worthy.
> >
> > Cheers,
> > Manel
> >
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>
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