[Biopython-dev] Ideas for Biopython 2.0

[Tiago Antão]

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 of modules you might end up with an up-to-date core and an out-of-date lone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 Antao
Scientific and HPC programmer
http://tiago.org
https://github.com/tiagoantao/
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