[Biojava-dev] ongoing release - mediawiki woes

[Peter Cock]

On Fri, Mar 11, 2016 at 5:03 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi,
>
> Jose and I worked on the release today. Everything went well with Maven
> Central, and the code is already available from there.  However it turns out
> that the MediaWiki instance on biojava.org is fundamentally broken and it is
> almost impossible to login (both Google and Yahoo open id login are broken).
> I managed to login just by chance (long story). I am in the process of
> updating the wiki pages. We will finalize and write the announce email
> tomorrow (Friday).
>
> The bottom line is, we will need to migrate away from MediaWiki soon, since
> it is not maintainable. I suggest we move to GitHub markdown pages.
> https://help.github.com/articles/using-a-custom-domain-with-github-pages/
>
> Andreas

Hello Andreas & the BioJava developers,

I said much of this directly on root-l, but it is worth stating openly as
for any migration more eyes are especially welcome. I have deliberately
CC'd the cross-project open-bio-l mailing list (a public list) plus also
root-l (our closed mailing list for SysAdmin stuff).

Brian Osborne has been driving the BioPerl Wiki migration to GitHub
pages, using pandoc to migrate to markdown, with a lot of fine tuning:

http://bioperl.github.io/
https://github.com/bioperl/bioperl.github.io

Presumably at some point www.bioperl.org will point there instead, perhaps
after all the non-BioPerl content like file format pages has been moved to
wikipedia or elsewhere - anyone curious can follow up on the BioPerl-l
mailing list.

Before that I had started looking at migrating MediaWiki to GitHub pages
using pandoc for the markdown conversion while preserving the history:

https://github.com/peterjc/mediawiki_to_git_md/

There are a few niggles like dealing with categories and sub-folders
messing up the URL mapping, which meant this isn't yet good enough
to use for the www.open-bio.org wiki (most of the BOSC URLs break),
nor for the www.bioperl.org wiki (lots of templates and other advanced
features) but looks more promising for the simpler biopython.org wiki.

https://OBF.github.io
https://github.com/OBF/OBF.github.io

https://biopython.github.io
https://github.com/biopython/biopython.github.io

Once the migration is working nicely preserving functional content,
I plan to copy all the nice styling work from Brian to make the pages
look nice.

If you would like to try this migration script on the BioJava wiki, please
let me know - You'll need the XML dump from MediaWiki which Andreas
can probably get - if not I could, or another root-l mailing list volunteer.

Regards,

Peter
Biopython developer, OBF secretary, BOSC co-chair, etc.