[Biopython-dev] Ideas for Biopython 2.0

[Mateusz Korycinski]

Dear All,

It's nice to hear that Biopython is still evolving, and Biopython 2.0 sounds really cool.

Would it be possible to get involved in this effort? I was looking around for a while to get more involved in Biopython, and ver 2.0 seems like a good opportunity to contribute and learn new things. Of course as I've only contributed so far very small bug fix I am not intending to be a part of decision-making group etc., just coding and implementing ideas.

Best regards,
Mateusz

Sent with [ProtonMail](https://protonmail.com) Secure Email.

-------- Original Message --------
Subject: Re: [Biopython-dev] Ideas for Biopython 2.0
Local Time: June 20, 2017 9:58 AM
UTC Time: June 20, 2017 7:58 AM
From: w.arindrarto at gmail.com
To: Peter Cock <p.j.a.cock at googlemail.com>, Tiago Antão <tiagoantao at gmail.com>
Biopython-Dev Mailing List <biopython-dev at biopython.org>

Dear Patrick, Peter, Tiago, and everyone,

Good to see this discussion being brought up again :) (and thank you Patrick for writing a thorough proposal).

On the big picture, I wholeheartedly agree that Bioptyhon 2.0 should adopt modern Python best practices, even if it requires a close to full rewrite. The Python scientific computing environment has progressed far beyond the time when Biopython was first written. Many scientific Python libraries are now mature and widely used that at least the thought of interop with them should be considered. This can be done, for example, making our data structures compatible with them (e.g. using numpy arrays) or by making our plotting functions (in Bio.Graphics, for example) compatible with them (e.g. using matplotlib or bokeh).

I don't have any strong preference for the new namespace (biopy.* or biopython.* is fine). But depending on how we structure the new modules, we may or may not need to share the namespace with the current Bio package, right? If we opt to do modularization ala biogems, only the core module is probably suitable for inclusion in the current Bio package. The rest would have their own repositories.

I did play around with a distributed package setup (https://github.com/bow/poc_biopy). There are two alternatives that I considered there. The first one, `poc_hook` uses an import hook so any non-core `biopy_*` package can be imported as `biopy.ext.*`. The second, `poc_pkgutil` one simply requires any non-core `biopy_*` package put their code inside `biopy.ext`. This was from about 3 years ago, however, so there may be better ways of doing this now.

But as Peter said, this is probably the one on which a consensus is hardest to build. In addition to that, we would need work to port existing packages to the new structure.

Now seems like a good time to attempt to do this, though :).

Cheers,
Bow

On Mon, Jun 19, 2017 at 10:43 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
Yep - that's what I meant :)

i.e. "biopython" (or "biopy" or ...") as a folder name meaning we'd
have for example "biopython/sequences/__init__.py`` which can
be import as "from biopython import sequences" etc.

The NumPy/SciPy like usage pattern for importing had crossed my
mind too - although if we try to minimise the top level automatic
imports I think that is less useful?

(By that I mean that for example people doing clustering would not
want the overhead of lots of sequence code being imported by default)

Peter

On Mon, Jun 19, 2017 at 3:47 PM, Tiago Antão <tiagoantao at gmail.com> wrote:
> Or even
> biopython.*
> and have a recommendation of
> import biopython as bp
> Tiago
>
> On 19 June 2017 at 08:45, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>
>> I am generally in agreement with your comments Tiago.
>>
>> Note as per my reply to Patrick, we can't use "bio" (lower case)
>> as this would be the same directory on disk as "Bio" (title case) on
>> Windows and most Macs which use a case-insensitive file system.
>> Thus suggestions like "biopy" and "biopython" instead.
>>
>> Peter
>>

_______________________________________________
Biopython-dev mailing list
Biopython-dev at mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/biopython-dev
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython-dev/attachments/20170620/158075c0/attachment.html>