<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Peter,<div class=""><br class=""></div><div class="">It looks like you have a very nice plan to migrate this content that is close to - if not fully - automated. Good idea.</div><div class=""><br class=""></div><div class="">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.</div><div class=""> </div><div class="">Then the question I puzzled over was “what look?” Check these out, if you want to get a sense of your Jekyll options:</div><div class=""><br class=""></div><div class=""><a href="http://jekyllthemes.org" class="">http://jekyllthemes.org</a></div><div class=""><a href="https://github.com/jekyll/jekyll/wiki/sites" class="">https://github.com/jekyll/jekyll/wiki/sites</a></div><div class=""><br class=""></div><div class="">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).</div><div class=""><br class=""></div><div class="">You also will want search capabilities in some of these sites. Some themes have it already, most of these above do not.</div><div class=""><br class=""></div><div class="">There also appears to be an issue around Google searching if sitemap.xml is not right, have not looked into this yet:</div><div class=""><br class=""></div><div class=""><a href="http://gon.to/2015/03/03/f-percent-number-ck-github-pages-for-jekyll-why-i-decided-to-use-digital-ocean/" class="">http://gon.to/2015/03/03/f-percent-number-ck-github-pages-for-jekyll-why-i-decided-to-use-digital-ocean/</a></div><div class=""><br class=""></div><div class="">Anyway, having said all of that, I can assist with the migration. What is the full list of Wikis? Is it something like this?</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: Courier; background-color: rgb(179, 187, 255);" class="">[bosborne@ip-10-116-249-158 ~]$ ls /obf/websites/</div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: Courier; color: rgb(0, 91, 250); background-color: rgb(179, 187, 255);" class=""><a href="http://biodas.org" class="">biodas.org</a><span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>biopathways.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>bioruby.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>cgi.biodas.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>helpdesk.open-bio.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>www.arareko.net</div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: Courier; color: rgb(0, 91, 250); background-color: rgb(179, 187, 255);" class=""><a href="http://biojava.org" class="">biojava.org</a><span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>bioperl.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>biosoap.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>cross-site-stuff<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>lists.open-bio.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>www.open-bio.org</div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: Courier; color: rgb(0, 91, 250); background-color: rgb(179, 187, 255);" class=""><a href="http://biolib.open-bio.org" class="">biolib.open-bio.org</a><span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>bioprolog.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>biosql.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>doc.bioperl.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>news.open-bio.org</div><div style="margin: 0px; font-size: 14px; line-height: normal; font-family: Courier; color: rgb(0, 91, 250); background-color: rgb(179, 187, 255);" class=""><a href="http://biomoby.org" class="">biomoby.org</a><span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>biopython.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>blipkit.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>emboss.open-bio.org<span style="font-variant-ligatures: no-common-ligatures; color: #000000" class=""> </span>obda.open-bio.org</div></div><div class=""><br class=""></div><div class="">Some of these are not Wikis, like biomoby and <a href="http://open-bio.org" class="">open-bio.org</a>. 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.</div><div class=""><br class=""></div><div class="">BIO</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 8, 2016, at 8:09 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" class="">p.j.a.cock@googlemail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Brian,<br class=""><br class="">Since you've been working on the presentation end of this, and<br class="">I've been working on the MediaWiki to Markdown history, we<br class="">should try to combine efforts for the OBF wiki migrations?<br class=""><br class=""><a href="https://github.com/peterjc/mediawiki_to_git_md" class="">https://github.com/peterjc/mediawiki_to_git_md</a><br class=""><br class="">https://github.com/peterjc/peterjc.github.io (Bipython wiki)<br class="">https://github.com/OBF/OBF.github.io (open-bio wiki)<br class=""><br class="">If you don't have an XML dump for BioPerl, I can get you one.<br class=""><br class="">Ideally we'd do the history preserving migration and then<br class="">apply the styling fixes?<br class=""><br class="">Peter<br class=""><br class="">On Fri, Jan 8, 2016 at 1:56 PM, Brian Osborne <bosborne11@verizon.net> wrote:<br class=""><blockquote type="cite" class="">All,<br class=""><br class="">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:<br class=""><br class="">- spacing between text blocks is a bit odd, in various places<br class="">- posts (news) do not yet work<br class="">- Perl code appears in blocks but without highlights<br class=""><br class="">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.<br class=""><br class="">Check it out.<br class=""><br class="">Brian O.<br class="">_______________________________________________<br class="">Bioperl-l mailing list<br class="">Bioperl-l@mailman.open-bio.org<br class="">http://mailman.open-bio.org/mailman/listinfo/bioperl-l<br class=""></blockquote><br class="">_______________________________________________<br class="">Bioperl-l mailing list<br class="">Bioperl-l@mailman.open-bio.org<br class="">http://mailman.open-bio.org/mailman/listinfo/bioperl-l</div></div></blockquote></div><br class=""></div></body></html>