New Jekyll theme at bioperl.github.io

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New Jekyll theme at bioperl.github.io

Brian Osborne-2
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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Re: New Jekyll theme at bioperl.github.io

Peter Cock
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 <[hidden email]> 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.
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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Re: New Jekyll theme at bioperl.github.io

Mark A. Jensen
In reply to this post by Brian Osborne-2

Oooh, shiny!

On Fri, Jan 08, 2016 at 12:03 AM, Brian Osborne <[hidden email]> 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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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: New Jekyll theme at bioperl.github.io

Brian Osborne-2
Thank you Mark (I _think_ that was a complement anyway).

;-)

Forgot to mention, the old version had search, this one does not. This site must have search. I’ve already written code that creates JSON that can be searched (see _site/search.json), I have the old JS code that can search this JSON. I’ll probably get to this, but if anyone wants to fiddle with JS/CSS/HTML go for it.

The front page is too clogged, think I’ll move that “contribute” text down, or out. There’s a ridiculous amount of tweaking that goes into making a nice Web site ...

BIO

On Jan 8, 2016, at 9:37 AM, Mark A Jensen <[hidden email]> wrote:

Oooh, shiny!

On Fri, Jan 08, 2016 at 12:03 AM, Brian Osborne <[hidden email]> 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.
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l



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Re: New Jekyll theme at bioperl.github.io

Fields, Christopher J
In reply to this post by Brian Osborne-2
That’s pretty nice!  I almost think we could switch over; only true blocker is syntax highlighting (and IMHO that’s likely to be fixed on the Jekyll end).

-c

> On Jan 7, 2016, at 10:56 PM, Brian Osborne <[hidden email]> 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.
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: New Jekyll theme at bioperl.github.io

Fields, Christopher J
In reply to this post by Brian Osborne-2
Search would be very nice, yes.  If we could get that up I would almost say we can start redirecting the site over.  We’ll still need the old site running to migrate additional docs for the time being.

Also, re: tweaking the website, agreed, which is one reason I try very hard to not do or get involved with web site design :)

-c

On Jan 8, 2016, at 8:49 AM, Brian Osborne <[hidden email]> wrote:

Thank you Mark (I _think_ that was a complement anyway).

;-)

Forgot to mention, the old version had search, this one does not. This site must have search. I’ve already written code that creates JSON that can be searched (see _site/search.json), I have the old JS code that can search this JSON. I’ll probably get to this, but if anyone wants to fiddle with JS/CSS/HTML go for it.

The front page is too clogged, think I’ll move that “contribute” text down, or out. There’s a ridiculous amount of tweaking that goes into making a nice Web site ...

BIO

On Jan 8, 2016, at 9:37 AM, Mark A Jensen <[hidden email]> wrote:

Oooh, shiny!

On Fri, Jan 08, 2016 at 12:03 AM, Brian Osborne <[hidden email]> 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.
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: New Jekyll theme at bioperl.github.io

Brian Osborne-2
In reply to this post by Peter Cock
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:


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:


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@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 <[hidden email]> 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 <[hidden email]> 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.
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l

_______________________________________________
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[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: New Jekyll theme at bioperl.github.io

Peter Cock
On Sat, Jan 9, 2016 at 7:03 AM, Brian Osborne <[hidden email]> 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@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

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Re: New Jekyll theme at bioperl.github.io

Fields, Christopher J
BioJava and BioSQL would be the only other ones I can think of.  EMBOSS is static web content for the most part if I recall; is that hosted on the AWS server or is it a redirect?

chris

On Jan 10, 2016, at 2:26 AM, Peter Cock <[hidden email]> wrote:

On Sat, Jan 9, 2016 at 7:03 AM, Brian Osborne <[hidden email]> 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@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

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http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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Re: New Jekyll theme at bioperl.github.io

Brian Osborne-2
Chris and Peter,

A bit late with this, but you may have noticed: bioperl.github.bio now has search capability, it’s ready to take the bioperl.org address.

Peter, we talked about this a bit. Turns out it is not hard at all. Jekyll is file-based, no database there. There’s a Liquid template (/search.json) that’s used to convert all the HOWTO’s (and misc. other files, 111 pages in total) to JSON, in a single file (/_site/search.json). Then some simple JS (Jquery) searchs this file. The performance is good, on the other hand the JSON file is not large, 963 lines. 

There is remaining work upcoming. In May GitHub will disable all the Markdown converters except for kramdown, and we’re using redcarpet. I did some testing, it appears that our tables are not converted by kramdown, they will all have to be fixed. My guess is that this will be straightforward.

Thanks again,

Brian O.

On Jan 10, 2016, at 10:05 AM, Fields, Christopher J <[hidden email]> wrote:

BioJava and BioSQL would be the only other ones I can think of.  EMBOSS is static web content for the most part if I recall; is that hosted on the AWS server or is it a redirect?

chris

On Jan 10, 2016, at 2:26 AM, Peter Cock <[hidden email]> wrote:

On Sat, Jan 9, 2016 at 7:03 AM, Brian Osborne <[hidden email]> 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@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

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http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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Re: New Jekyll theme at bioperl.github.io

Peter Cock
Hi Brian,

Very timely - BioJava were just struggling with updating the wiki, and
Spencer is taking a look at the MediaWiki and OpenID plugins:

http://lists.open-bio.org/pipermail/open-bio-l/2016-March/001428.html
http://lists.open-bio.org/pipermail/open-bio-l/2016-March/001429.html
etc (and on root-l in private).

GitHub do try to give advance warning of changes, but using their
system will have downsides - here's quite negative example:
https://github.com/blog/1992-eight-lessons-learned-hacking-on-github-pages-for-six-months

One tiny issue: The search box on http://bioperl.github.io/ has a tiny
width (as is right aligned) under Firefox v44  - but a sensible size
(and left aligned) under Chrome and Safari.

Did you guys migrate all the generic things on the old wiki like the
file format pages to wikipedia or somewhere?

What are you doing about the static content outside the wiki? e.g.

http://bioperl.org/DIST/ <-- still important, or all on CRAN?
http://bioperl.org/SRC/ <-- looks like from pre-git days
http://bioperl.org/media/ <-- used in some documentation?

Those are the only things that came to mind before making the
DNS changes to point bioperl.org at bioperl.github.io

Note we'd want to check the @bioperl.org email addresses would
still be OK.

Regards,

Peter

On Fri, Mar 11, 2016 at 1:53 PM, Brian Osborne <[hidden email]> wrote:

> Chris and Peter,
>
> A bit late with this, but you may have noticed: bioperl.github.bio now has
> search capability, it’s ready to take the bioperl.org address.
>
> Peter, we talked about this a bit. Turns out it is not hard at all. Jekyll
> is file-based, no database there. There’s a Liquid template (/search.json)
> that’s used to convert all the HOWTO’s (and misc. other files, 111 pages in
> total) to JSON, in a single file (/_site/search.json). Then some simple JS
> (Jquery) searchs this file. The performance is good, on the other hand the
> JSON file is not large, 963 lines.
>
> There is remaining work upcoming. In May GitHub will disable all the
> Markdown converters except for kramdown, and we’re using redcarpet. I did
> some testing, it appears that our tables are not converted by kramdown, they
> will all have to be fixed. My guess is that this will be straightforward.
>
> Thanks again,
>
> Brian O.

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