[BioPython] Questions & suggestions

[Thomas Hamelryck]

On Friday 19 March 2004 18:37, Brad Chapman wrote:

> No, not that I know of. Honestly, I am not a big fan of
> BioPerl/Biopython comparisons just as I'm not a huge fan of
> Perl/Python comparisons 

I agree, but still, it would be handy to have a page that lists BioPerl and 
Biopython features so that people could decide what they want to use for a 
certain purpose. I'm not suggesting a 'BioPython is better than BioPerl 
page'. That is indeed pointless.

> As far as code goes -- if you have suggestions for modules that are
> no longer useful and we don't think can be fixed/updated easily
> please do suggest a plan of action. We can get a survey on whether
> others use these modules and then decide where to go. It's always a
> good idea to keep out cruft.

We could make a list of modules that will be potentially removed, post it to 
the biopython list, and then actually remove them when no-one objects. Is 
anybody using the two HMMs (HMM and MarkovModel) for instance? Or the 
support vector machine (SVM) and NeuralNetwork modules? The xKMeans, 
KNN and KMeans clustering modules also seem to be obsolete in view of Michiel 
de Hoons clustering module. 
 
> Yeah, I will also play around with that this weekend. But, I do
> think the number one priority on the doc front is extracting the
> Tutorial into smaller sections. If you want to help on that, it
> would be great. For instance, the PDB module could have it's own
> documentation section :-).

That's coming up!

I am very much in favor of automatically generated documentation. Each module 
should at least have 5-10 lines or so in api/Bio/index.html that describe 
what the module actually does! 
What are you thinking of using in the future? I must admit that the HappyDoc 
requirements for generating good and readable descriptions are a bit of a 
mystery to me.... Bio.PDB looks very ugly (my fault, probably). I'd sure like 
to improve that (especially since Bio.PDB is actually pretty well commented 
code).

In any case, thanks a lot for all the work you put into Biopython!

-Thomas