[Biopython] [Biopython-dev] Experimenting with migrating wiki to GitHub pages

Peter Cock p.j.a.cock at googlemail.com
Thu Apr 7 10:55:49 UTC 2016

Dear Biopythoneers,

In reference to my earlier email, the website migration has become more
urgent as the main biopython.org website is down until the AWS server
can be rebuilt:


BioPerl has already got a potential replacement home page up and
running using GitHub Pages, but this did not preserve the contribution


You may recall last year I started work on a migration from MediaWiki
to markdown using GitHub Pages?

https://github.com/peterjc/mediawiki_to_git_md [migration tool]

Andreas and the BioJava team started with my migration tool, and have
already raced ahead with adding styling on top to make something
quite impressive:

http://biojava.github.io/wiki/Main_Page [pretty]

In comparison right now the Biopython migration is currently very


I was hoping to fix some of the remaining issues in the conversion, in
particular the categories, but perhaps it is good enough already for the
Biopython wiki? (Some of these limitations would have been/are more
of a problem for the BioPerl wiki with many templates, and the main
OBF wiki with many wiki pages using subfolder slashes in their names):


Right now there are various things to do, including switching to the
kramdown markup engine and other tweaks for Jekyll 3.0 (which
Andreas has already done for BioJava):


After than I think it would be sensible to start adopting much of the
styling work pioneered by Andreas for the BioJava team?

Do we have any GitHub pages experts in the community?

In general, please have a look at the trial migration wiki pages
and if you see any glitches, please report them via:

and/or https://github.com/peterjc/mediawiki_to_git_md/issues

Thank you,


On Wed, Mar 4, 2015 at 4:46 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> I've got the basic wiki content converted in markdown and showing nicely
> (while preserving the wiki revisions and most of the contributors). Adding
> a theme for a pretty layout is a finishing touch. First, all the links and files
> need doing - definitely possible.
> A key question is will it be as easy for people to edit as the wiki is/was?
> Peter
> On Wed, Mar 4, 2015 at 4:22 PM, João Rodrigues
> <j.p.g.l.m.rodrigues at gmail.com> wrote:
>> Hi Peter, all,
>> I've used Jekyll + Github to create our lab webpage. Turns out to be an
>> amazingly simple solution and very collaborative as well. Nice thought of
>> moving the wiki to such a system.
>> A quick question: why not make a page from "scratch" ? Using a template and
>> converting the HTML to markdown seems pretty simple, it's just a matter of
>> agreeing on a layout.
>> Maybe I'm missing the point and you're doing this already..
>> Cheers,
>> João

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