[Biopython-dev] Proposition for Biopython 2

Patrick Kunzmann padix.kleber at gmail.com
Wed Nov 15 08:40:44 UTC 2017

Dear Biopython community,

I decided to put the proposed Biopython 2 code base into an separate 
project for the time being. The main reason for this are the clarity 
issues that have bothered me lately: Although distinguishing Biopython 
and the proposed Biopython 2 would be easy on GitHub (different repos) 
and relatively easy on PyPI (version identifier), I think confusions 
could occur in other contexts (e.g. in the mailing list or 
StackOverflow). Therefore, the project is continued unter the name 
'Biotite'. The repository was moved into a separate GitHub organisation 
and can be found at https://github.com/biotite-dev/biotite . The project 
is still licensed under BSD 3-clause so potentially a project merge is 
still possible at a later point.

Best regards,

On 02.11.2017 11:42, Patrick Kunzmann wrote:
> Dear Biopython community,
> here I present you a proposition for a potential Biopython 2.x code 
> base. But first things first:
> A few months ago I proposed an endeavor to rewrite Biopython in order 
> to bring it onto modern scientific Python standards 
> (http://lists.open-bio.org/pipermail/biopython-dev/2017-June/021740.html). 
> Arguably, the consensus was that this is something that should be 
> done, but those changes would require almost a complete rewrite and 
> barely anyone has time for it. Therefore, I took the initiative some 
> time later and created an experimental repository for creating actual 
> Biopython 2 code 
> (https://github.com/padix-key/biopython2experimental). Unfortunately 
> it seems that the announcement mail for that did not reach the mailing 
> list, but went missing in the deep of the web. Anyway, the repository 
> is now at a presentable state. The corresponding HTML documentation 
> (including tutorial, API reference and install instructions) can be 
> found under 
> https://github.com/padix-key/biopython2/files/1437242/doc.zip . So far 
> it is not possible to install the package from PyPI, since it is not 
> the offical Biopython 2 package. Instead you have to install it 
> directly from the repo, if you want to test the package.
> The package contains basic types and operations for working with 
> structure and sequence data, offers biological database interaction 
> with RCSB and NCBI Entrez and provides seamless interfaces to external 
> software. Although the package aims to achieve similar area of 
> application as Biopython 1.x, it is a complete rewrite.
> The package is still in early development. I tried to incorporate the 
> ideas you and I brought up in the Biopython 2 discussion and still 
> everything is subject to changes in the discussion with you. I already 
> have some questions for discussion:
> 1. Should this package still be dual licensed? Since the BSD 3-Clause 
> and the Biopython license are quite similar, I would suggest licensing 
> Biopython 2 only under BSD 3-Clause for clarity. But I do not have a 
> strong opinion on that.
> 2. In our previous discussion some of you proposed putting only core 
> functionality into Biopython 2 and leaving specialized code 
> installable as plugins. This package does not contain a mechanism for 
> plugin packages, yet. I would rather suggest a 'recommended packages' 
> approach: Code that is based on Biopython 2 and tackles a general 
> biological problem would be linked in a 'Recommended packages' section 
> of the Biopython 2 documentation. In my opinion, direct plugins in the 
> Biopython 2 package requires some confusing namespace wizardry. 
> Recommended packages would achieve almost the same, with the slight 
> difference, that the user writes 'import recommendedpackage' rather 
> than 'import biopython.someplugin'.
> If this package is accepted by the community, I would like to hand 
> over repository ownership to the 'Biopython' organisation on GitHub 
> and I would like to continue and supervise its development as part of 
> the GitHub 'Biopython' organisation.
> Best regards,
> Patrick Kunzmann

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