[Biopython-dev] Ideas for Biopython 2.0

Thu Jun 29 00:54:16 UTC 2017

> It can see plenty of issues where it could help. In my specific case all the PopGen code is stopped for 10 years because I would need to write very fast code (say in> Cython). This would be an extension module, not a core module because it would impart a very big dependency on the system.
I would suggest to first check how far numpy can help to speed up the code. If there are still some parts that need very fast code, you could write it as a C extension. That avoids the dependency on Cython. I'd be happy to help you with the C code.

> Modules would allow a core with very strict policies and dependencies _but_ extensions that could be way more relaxed.> It would also lower the barrier of entry for new content. Everyone could publish an extension. If the extension would survive time (which most do not - creating a 
> maintenance burden in the core) then it could eventually be made a core extension. Now the policy in practice is to add very little innovation out of the fear that it will 
> become stagnant and not-supported by the main author (say after publication). An extension system would accommodate both innovation whereas preserving the core 
> quality. 

But do you need Biopython for that? A module that may not be supported after publication could exist outside of Biopython.

> Currently we have a gigantic monolith that in practice imposes very conservative technologies and changes. I suspect that is why we do not see anything really exciting> with Biopython for the better part of the last decade,
I agree that we have been way too conservative in improving Biopython. This is just as much (or even more so) a problem with core parts of Biopython, e.g. with Seq objects and alphabets. But this is just a matter of choice: We can just decide to be less conservative.
Best,-Michiel.

    On Thursday, June 29, 2017 12:06 AM, Tiago Antão <tiagoantao at gmail.com> wrote:

 It can see plenty of issues where it could help. In my specific case all the PopGen code is stopped for 10 years because I would need to write very fast code (say in Cython). This would be an extension module, not a core module because it would impart a very big dependency on the system.
Modules would allow a core with very strict policies and dependencies _but_ extensions that could be way more relaxed.
It would also lower the barrier of entry for new content. Everyone could publish an extension. If the extension would survive time (which most do not - creating a maintenance burden in the core) then it could eventually be made a core extension. Now the policy in practice is to add very little innovation out of the fear that it will become stagnant and not-supported by the main author (say after publication). An extension system would accommodate both innovation whereas preserving the core quality. 

Currently we have a gigantic monolith that in practice imposes very conservative technologies and changes. I suspect that is why we do not see anything really exciting with Biopython for the better part of the last decade,
On 28 June 2017 at 04:25, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

I agree with Joao here. I don't see an immediate and overriding problem that modularity would solve, and I can see many drawbacks.
Best,-Michiel 

    On Monday, June 26, 2017 11:03 AM, João Rodrigues <j.p.g.l.m.rodrigues at gmail.com > wrote:

 Copied from the other thread where I mistakenly posted:

I think we should focus on other topics such as modularity. What do the proponents of the said modularity say about it? What are its advantages? I personally think a big disadvantage is that with one package install you get a wide array of tools for a variety of subjects. With a constellation of modules you might end up with an up-to-date core and an out-of-date lone module somewhere, which makes things much much harder not only to maintain but also to debug in case of issues. 

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-- 
Tiago AntaoScientific and HPC programmerhttp://tiago.orghttps://github.com/tiagoantao/

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