[bip] Blog post on bioinformatics and Python

[Peter]

Peter wrote:
>> You can install Biopython without Numeric or Numpy installed - and it
>> will work fine, assuming you don't use the cluster library, PDB
>> parsing or the other numerical bits.  If all you care about is
>> sequences, BLAST and Entrez for example, you'll be fine.

Ryan replied:
> In my opinion, the whole point of a big all-in-one
> solves-all-my-problems library is that you install it, and then it
> solves all your problems. If parts of the library randomly fail (and
> it will appear random to someone who is not intimately familiar with
> the inner workings and structure of every element of the library) when
> "optional" dependencies are not installed, then those dependencies are
> not optional. ...
>
> When I install something and it doesn't clearly and loudly fail, then
> I expect everything to work. If BioPython can be installed without
> Numeric or Numpy when significant functionality depends on those
> libraries, then I do not think that is a feature, but a bug: the
> BioPython installation can silently fail.

When I said that you CAN install Biopython without Numeric/numpy, the
setup script does make it quite clear that you will be missing
functionality.  i.e. It can be described as an "optional" dependency,
conditional on what you want to use Biopython for.

Peter