[bip] Blog post on bioinformatics and Python

[Peter]

Andrew Perry wrote:
> The problem I have at the moment is when I go to use a Biopython
> module, I have no idea if this is going to a be a well maintained and
> nicely working "core" part, or a deprecated, half implemented, 'slightly
> broken' or experimental/extra piece.

Well if its actually deprecated, when you do an "import" you'll get a
warning.  I've also started sticking "DEPRECATED" or "OBSOLETE" in the
doc strings so they show up in the help and on
http://biopython.org/DIST/docs/api/

We've tried not to add "experimental" bits to Biopython, but there are
still some of *old* unloved and possibly slightly broken bits... the
last year or so has seen a gradual "spring clean" going on.

> I've also noticed that a lot of potentially useful code has disappeared
> from Biopython over the years (wasn't there a HMMER module at one
> point, or did it never make it in ?). That is a good thing if it was really
> broken and unmaintained, but once it's gone from the mainline
>distribution, it becomes a case of 'out of sight out of mind'.

As I recall, all the recent deprecations have been unmaintained code,
which have been either identified as obsolete (e.g. parsers for file
formats no longer used, or web APIs which are no longer available), in
need of significant work (e.g. dependent on a third party library
which has changed in a non-backwards compatible way), or in some cases
a duplication of functionality elsewhere in Biopython which is better
maintained or documented.

In the case of an HMMER parser, I don't believe we have one in
Biopython, but code to do this would be worthwhile.

> Yes, maybe we could go back to earier CVS revisions to find it .. but
> if it was mostly working and living in an "experimental" package, then
> there is more chance of someone finding it and fixing it.

If it was "mostly working" its less likely to have been deprecated and
dropped in the first place - but I take your point that an
"experimental" package would be a useful staging post for new code.

Peter wrote:
>>Would having official Biopython (or BioPerl etc) hosted debian (etc)
>>packages help here?  In theory you could add this to your list of
>>repositories and then automatically get official Biopython releases.

Andrew Perry's reply:
> That's a great idea. I may even be tempted to volunteer to maintain
> that, if I can get over the learning curve and get started doing proper
> Debian python packaging.

Now that could be worth following up.  We would have to ask the OBF
about the hosting side, and try and get the existing Biopython debian
packagers input.  Please come over to the biopthon (dev) mailing list
to talk about it.

Peter