[Biopython-dev] Building Gene Ontology support into Biopython

Giovanni Marco Dall'Olio dalloliogm at gmail.com
Mon Oct 19 09:46:43 UTC 2009

On Mon, Oct 19, 2009 at 10:55 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Mon, Oct 19, 2009 at 9:32 AM, Giovanni Marco Dall'Olio
> <dalloliogm at gmail.com> wrote:
> > On Sun, Oct 18, 2009 at 7:22 AM, Chris Lasher <chris.lasher at gmail.com
> >wrote:
> >
> >> 2) What is the Biopython stance on introducing third-party
> >> dependencies?
> >
> > The problem is that biopython is a monolitic packages - you have
> > to install it all or nothing.
> And why is that a problem? This is a serious question. NumPy
> is a build time dependency (due to the C code), but pure python
> dependencies like MySQLdb (or potentially NetworkX) can be
> installed after Biopython, if and when then are needed.

I didn't really mean to say it is a problem, I think it has some
disadvantages and some advantages, as everything :-)
Biopython now is  easier to install, because people can just download a
package or a module or use easy_install. and some common guidelines, like
how to write documentation, the SeqRecord system, make it easier to
maintain; but on the other hand, when you propose a new module you have to
pay attention to not adding new dependencies, which is something that the
bioConductor's developers don't have to care of.

Anyway, it is true that without a good system to download and install
packages automatically, BioConductor and CRAN would have been different.

> > Maybe in a future (it is just a tought) it would be better to
> > have it as a repository of packages, like BioConductor.
> If/when PyPI becomes the standard way to deal with Python packages
> and interdependencies, then that might be workable. But without some
> system like that in place, you'll only make installation harder.

I agree with that. By the way, I have heard that there is a lot of
discussion in python-dev mailing list about a package called 'distribute' (
http://packages.python.org/distribute/setuptools.html) which in the future
may replace setuptools while remaining compatible with it.
In fact, setuptools and easy_install have not been updated for a long time
now, let's see if with this something will improve soon....

> Out of
> interest, have you ever tried installing BioPerl (via CPAN)? There is
> a lot to be said for a single simple to install package as now.

No, I didn't.... but I am scared of perl in general :-)

>  Peter

Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it

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