[Biopython-dev] Ideas for Biopython 2.0

[Iddo Friedberg]

> 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.

I would be very careful with putting efforts into a deliberate code rewrite
for the sake of it, as (1) bp is not really anyone's day job  and (2) a
major danger in rewrites is that they may break back-compatibility, either
with code (beyond the 3.x fork move which is inevitable), or, more
insidiously, through modified output. Note that bp is a component in a
large number of operation bioinformatics software out there, and we have a
responsibility to the people using it.



On Tue, Jun 20, 2017 at 2:58 AM, Wibowo Arindrarto <w.arindrarto at gmail.com>
wrote:

> 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
>> >>
>>
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>
>
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-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
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