[Bioperl-l] New Jekyll theme at bioperl.github.io

[Peter Cock]

On Sat, Jan 9, 2016 at 7:03 AM, Brian Osborne <bosborne11 at verizon.net> wrote:
> Peter,
>
> It looks like you have a very nice plan to migrate this content that is
> close to - if not fully - automated. Good idea.
>
> Personally, the way I was thinking about the BioPerl Wiki was a bit
> different. The BioPerl Wiki is quite old, quite large, and a lot of its
> content is dated, or wrong, or now superfluous (e.g. each module in BioPerl
> has a Wiki page, which was written by code, and there are many Wiki pages
> about applications or terms or formats that are now handled by Wikipedia).
> So this migration, again my personal view, was an opportunity to remove a
> lot of content yet preserve what was truly useful. Also bear in mind that
> resources are very stretched at BioPerl, the less content we have to
> maintain, the better. So we hand selected the pages we wanted to migrate,
> and we also did some amount of editing of _each_ selected page, and
> consolidated pages. So that process gave us a set of some 150 GFM pages. No
> versions.

Fair enough - I'd have opted for a full automated conversion (to
capture the contributor history), and then done the clean up -
but the key thing is you've done this. Chatting with Chris Fields
there is certainly a lot of good stuff on the old BioPerl wiki which
would be better placed somewhere central (e.g. file formats on
wikipedia?).

> Then the question I puzzled over was “what look?” Check these out, if you
> want to get a sense of your Jekyll options:
>
> http://jekyllthemes.org
> https://github.com/jekyll/jekyll/wiki/sites
>
> There is necessarily some editing involved in the migration. Hopefully most
> of GFM does not have to be touched, (and the “front matter” section that
> Jekyll wants can be added by script to the GFM pages) but the migrators will
> have to look at the “topmost" pages (and maybe there’s just one of these,
> index.html or index.md).

Yes - and likely categories would work that way too.

> You also will want search capabilities in some of these sites. Some themes
> have it already, most of these above do not.

Interesting - I'd not looked at that at all.

> There also appears to be an issue around Google searching if sitemap.xml is
> not right, have not looked into this yet:
>
> http://gon.to/2015/03/03/f-percent-number-ck-github-pages-for-jekyll-why-i-decided-to-use-digital-ocean/
>
> Anyway, having said all of that, I can assist with the migration. What is
> the full list of Wikis? Is it something like this?
>
> [bosborne at ip-10-116-249-158 ~]$ ls /obf/websites/
> biodas.org           biopathways.org  bioruby.org  cgi.biodas.org
> helpdesk.open-bio.org  www.arareko.net
> biojava.org          bioperl.org      biosoap.org  cross-site-stuff
> lists.open-bio.org     www.open-bio.org
> biolib.open-bio.org  bioprolog.org    biosql.org   doc.bioperl.org
> news.open-bio.org
> biomoby.org          biopython.org    blipkit.org  emboss.open-bio.org
> obda.open-bio.org
>
> Some of these are not Wikis, like biomoby and open-bio.org.

BioMoby has some complicated stuff, but www.open-bio.org does
have a wiki (which I'm looking at as the first migration) and some
static HTML pages like old BOSC conferences (hopefully they
can be moved into GitHub as static HTML pages).

> And do we have owners for all of these? Are some of no interest?

Hopefully - migration is a good chance to verify all that.

> Finally, I think that each of these needs its own GitHub account
> in order to get a GitHub Pages site. Or were you thinking of only
> migrating some of these? A bunch of questions for OBF here.

Yes, but most of the active projects already have GitHub accounts.
We're looking at BioPerl (you), the main OBF wiki and Biopython
(me) as the first trial migrations to GitHub pages.

Regards,

Peter