[BioPython] [PopGen] a random Haplotype Sets generator

[Bruce Southey]

Tiago Antão wrote:
>> This is right: which word can I use, then?
>> HaplotypesSampler? RandomHaplotypesSpawner?
>> HaplotypesCreator?
>>     
>
> Considering that this is probably a small piece of code in the long
> run (correct me if I am wrong), I suggest creating
> Bio.PopGen.Utils.NameToBeDecided.py
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Hi,
I really don't mean to be negative, but you have certain 
responsibilities once you release code into the Biopython community. 
Part of my concern is that some of this is being overlooked especially 
in terms of the user of the code. I do see that simulation of SNPs is 
useful for users so it is important that it integrated correctly.

I think Michiel's recent comment in 'a sequence set object in biopython' 
thread is important here as well:

"Adding new classes to Biopython should be done very carefully ... once they're in, it's difficult to remove them again. In the past, removing classes that turned out to be less than ideal was a real headache."

While I have not looked at the code, my view is that must remain 
integrated into the PopGen module. I would expect that a user would some 
Biopython (PopGen) modules with some simulated SNPs. I would prefer that 
Biopython remains as much as possible a set of integrated tools rather 
than just a collection of tools. This is a clear example where if it is 
not totally integrated then I don't see the point in including it in 
Biopython.

The second aspect is that it must have a very stable API, similarly to 
Michiel's comment is that changing APIs after a release is also a pain 
especially if the module has been around a long time. Based on your 
first post, I would argue that you are not quite at this stage yet.

Bruce