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

[Brian Osborne]

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.
 
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).

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

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

BIO



> On Jan 8, 2016, at 8:09 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 
> Hi Brian,
> 
> Since you've been working on the presentation end of this, and
> I've been working on the MediaWiki to Markdown history, we
> should try to combine efforts for the OBF wiki migrations?
> 
> https://github.com/peterjc/mediawiki_to_git_md
> 
> https://github.com/peterjc/peterjc.github.io (Bipython wiki)
> https://github.com/OBF/OBF.github.io (open-bio wiki)
> 
> If you don't have an XML dump for BioPerl, I can get you one.
> 
> Ideally we'd do the history preserving migration and then
> apply the styling fixes?
> 
> Peter
> 
> On Fri, Jan 8, 2016 at 1:56 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>> All,
>> 
>> I’ve switched from one of the default themes - dull - to a custom theme I derived from an existing site. Much better, but there are some issues:
>> 
>> - spacing between text blocks is a bit odd, in various places
>> - posts (news) do not yet work
>> - Perl code appears in blocks but without highlights
>> 
>> The last one is mysterious, it may be due to recent Jekyll versions and how they work or don’t work with the redcarpet MD -> HTML converter.
>> 
>> Check it out.
>> 
>> Brian O.
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>> Bioperl-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
> 
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