From email2ants at gmail.com  Wed Oct  5 10:57:44 2011
From: email2ants at gmail.com (Anthony Underwood)
Date: Wed, 5 Oct 2011 15:57:44 +0100
Subject: [BioRuby] BioRuby API
Message-ID: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>

 Hi all

Does anyone else find the new API docs more difficult to navigate than the old api?
It looks prettier but I find it harder to find what I'm after. OK frames may be very 1990s but in the case of the API having all the Methods and Classes in scrollable frames worked well.
Does anybody have 
any tips on how to navigate around?
a URL where the old form of presenting the API is still accessible?
the command to generate the old API locally?

Many thanks in advance

Anthony 


From ngoto at gen-info.osaka-u.ac.jp  Thu Oct  6 00:53:31 2011
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 6 Oct 2011 13:53:31 +0900
Subject: [BioRuby] BioRuby API
In-Reply-To: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>
References: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>
Message-ID: <20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>

Hi,

The change is due to the change of RDoc default html generator.
The new pages are generated by using RDoc bundled in Ruby 1.9.2,
with its default style.  Old style, which was the default of
older RDoc, seems to be no longer maintained by anyone, and
is dropped from current RDoc.

It is easy to generate API html pages locally.
"rake rdoc" in the top of bioruby source tree.
Old style pages may be generated by using Ruby 1.9.1-p431
(or Ruby 1.8.x with older version of RDoc).

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Wed, 5 Oct 2011 15:57:44 +0100
Anthony Underwood <email2ants at gmail.com> wrote:

>  Hi all
> 
> Does anyone else find the new API docs more difficult to navigate than the old api?
> It looks prettier but I find it harder to find what I'm after. OK frames may be very 1990s but in the case of the API having all the Methods and Classes in scrollable frames worked well.
> Does anybody have 
> any tips on how to navigate around?
> a URL where the old form of presenting the API is still accessible?
> the command to generate the old API locally?
> 
> Many thanks in advance
> 
> Anthony 
> 

From email2ants at gmail.com  Thu Oct  6 05:27:55 2011
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 6 Oct 2011 10:27:55 +0100
Subject: [BioRuby] BioRuby API
In-Reply-To: <20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>
References: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>
	<20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <C9F7A8C42A8B483BB6C652A68F2E46CA@gmail.com>

Hello Naohisa

Thanks for the advice. Thaks to rvm I have regenerated the 1.4.2 rdoc using rdoc version 2.2.1 (the last  version before the new 'darkfish' look beccame standard).
This is publically available at
http://www.hpa-bioinformatics.org.uk/bioruby-api/

Thanks again,

Anthony 


On Thursday, 6 October 2011 at 05:53, Naohisa GOTO wrote:

> Hi,
> 
> The change is due to the change of RDoc default html generator.
> The new pages are generated by using RDoc bundled in Ruby 1.9.2,
> with its default style. Old style, which was the default of
> older RDoc, seems to be no longer maintained by anyone, and
> is dropped from current RDoc.
> 
> It is easy to generate API html pages locally.
> "rake rdoc" in the top of bioruby source tree.
> Old style pages may be generated by using Ruby 1.9.1-p431
> (or Ruby 1.8.x with older version of RDoc).
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp (mailto:ngoto at gen-info.osaka-u.ac.jp) / ng at bioruby.org (mailto:ng at bioruby.org)
> 
> On Wed, 5 Oct 2011 15:57:44 +0100
> Anthony Underwood <email2ants at gmail.com (mailto:email2ants at gmail.com)> wrote:
> 
> >  Hi all
> > 
> > Does anyone else find the new API docs more difficult to navigate than the old api?
> > It looks prettier but I find it harder to find what I'm after. OK frames may be very 1990s but in the case of the API having all the Methods and Classes in scrollable frames worked well.
> > Does anybody have 
> > any tips on how to navigate around?
> > a URL where the old form of presenting the API is still accessible?
> > the command to generate the old API locally?
> > 
> > Many thanks in advance
> > 
> > Anthony 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org (mailto:BioRuby at lists.open-bio.org)
> http://lists.open-bio.org/mailman/listinfo/bioruby


From email2ants at gmail.com  Thu Oct  6 06:05:22 2011
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 6 Oct 2011 11:05:22 +0100
Subject: [BioRuby] BioRuby API
In-Reply-To: <20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>
References: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>
	<20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <E299887B420A4C6C89C890F923BB7E77@gmail.com>

I've also put up the same documentation but styled using YARD for those who prefer this stye:

http://www.hpa-bioinformatics.org.uk/bioruby-yard-api/ 


On Thursday, 6 October 2011 at 05:53, Naohisa GOTO wrote:

> Hi,
> 
> The change is due to the change of RDoc default html generator.
> The new pages are generated by using RDoc bundled in Ruby 1.9.2,
> with its default style. Old style, which was the default of
> older RDoc, seems to be no longer maintained by anyone, and
> is dropped from current RDoc.
> 
> It is easy to generate API html pages locally.
> "rake rdoc" in the top of bioruby source tree.
> Old style pages may be generated by using Ruby 1.9.1-p431
> (or Ruby 1.8.x with older version of RDoc).
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp (mailto:ngoto at gen-info.osaka-u.ac.jp) / ng at bioruby.org (mailto:ng at bioruby.org)
> 
> On Wed, 5 Oct 2011 15:57:44 +0100
> Anthony Underwood <email2ants at gmail.com (mailto:email2ants at gmail.com)> wrote:
> 
> >  Hi all
> > 
> > Does anyone else find the new API docs more difficult to navigate than the old api?
> > It looks prettier but I find it harder to find what I'm after. OK frames may be very 1990s but in the case of the API having all the Methods and Classes in scrollable frames worked well.
> > Does anybody have 
> > any tips on how to navigate around?
> > a URL where the old form of presenting the API is still accessible?
> > the command to generate the old API locally?
> > 
> > Many thanks in advance
> > 
> > Anthony 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org (mailto:BioRuby at lists.open-bio.org)
> http://lists.open-bio.org/mailman/listinfo/bioruby


From info at orbicule.com  Thu Oct  6 12:29:42 2011
From: info at orbicule.com (Peter Schols)
Date: Thu, 6 Oct 2011 18:29:42 +0200
Subject: [BioRuby] BioRuby API
Message-ID: <BF2E7988-96E2-4494-8D86-CBA0DF9246B1@orbicule.com>

Another interesting rdoc html generator is sdoc, maybe worth checking out for BioRuby:

https://github.com/voloko/sdoc

From email2ants at gmail.com  Thu Oct  6 15:16:20 2011
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 6 Oct 2011 20:16:20 +0100
Subject: [BioRuby] BioRuby API
In-Reply-To: <BF2E7988-96E2-4494-8D86-CBA0DF9246B1@orbicule.com>
References: <BF2E7988-96E2-4494-8D86-CBA0DF9246B1@orbicule.com>
Message-ID: <CAAZOFr9F4y-nuGowz=CeV_wJoYfab03upqmv_C+ug320ignJ8Q@mail.gmail.com>

Thanks for the info about sdoc Peter. I have generated documentation with
sdoc and put it live publicly at the following URL
http://www.hpa-bioinformatics.org.uk/bioruby-sdoc-api/

On 6 October 2011 17:29, Peter Schols <info at orbicule.com> wrote:

> Another interesting rdoc html generator is sdoc, maybe worth checking out
> for BioRuby:
>
> https://github.com/voloko/sdoc
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

From info at orbicule.com  Thu Oct  6 17:06:24 2011
From: info at orbicule.com (Peter Schols)
Date: Thu, 6 Oct 2011 23:06:24 +0200
Subject: [BioRuby] BioRuby API
In-Reply-To: <CAAZOFr9F4y-nuGowz=CeV_wJoYfab03upqmv_C+ug320ignJ8Q@mail.gmail.com>
References: <BF2E7988-96E2-4494-8D86-CBA0DF9246B1@orbicule.com>
	<CAAZOFr9F4y-nuGowz=CeV_wJoYfab03upqmv_C+ug320ignJ8Q@mail.gmail.com>
Message-ID: <61E4FDFC-AEAF-4F2C-8F04-3E424F01CD92@orbicule.com>

Fantastic, thanks!

Peter

On 06 Oct 2011, at 21:16, Anthony Underwood wrote:

> Thanks for the info about sdoc Peter. I have generated documentation with sdoc and put it live publicly at the following URL 
> http://www.hpa-bioinformatics.org.uk/bioruby-sdoc-api/
> 
> On 6 October 2011 17:29, Peter Schols <info at orbicule.com> wrote:
> Another interesting rdoc html generator is sdoc, maybe worth checking out for BioRuby:
> 
> https://github.com/voloko/sdoc
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
> 



From pjotr.public14 at thebird.nl  Fri Oct 14 04:08:15 2011
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Fri, 14 Oct 2011 10:08:15 +0200
Subject: [BioRuby] biogems.info updated
In-Reply-To: <20110920165601.GA8933@thebird.nl>
References: <20110920165601.GA8933@thebird.nl>
Message-ID: <20111014080815.GA25807@thebird.nl>

Updated the site

   http://biogems.info/

Biogem status, meta-package info, and inviting links to source
tree and commits.

Shows how playful we are ;)

Pj.


From p.j.a.cock at googlemail.com  Mon Oct 31 19:09:52 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 31 Oct 2011 23:09:52 +0000
Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org
In-Reply-To: <CAA9RGEPRnbWRAwcaHtWS_eBAJzinuh9NZ_9hoi9vyV-rR7Ff2A@mail.gmail.com>
References: <CAKVJ-_6eMa0nYBMmsgJPet3fmpOTSwaDHgraOqxH_YEKF+szsg@mail.gmail.com>
	<CAA9RGEMcdZFmo_D04Rwf=bwd9_rY=+N_BnyjzvEmFSxCT+J7aw@mail.gmail.com>
	<CAKVJ-_63TyhETCPBkTW09ZPrhKKGyGh4qknO7EBEcAwQ=Krtmg@mail.gmail.com>
	<4EAEA028.1090906@bioteam.net>
	<CAKVJ-_5hXj+FrNXtPfB4FeDN3FqKtQBBFQR4EeQZ6Liuwet18A@mail.gmail.com>
	<4EAEA4D6.7090805@sonsorol.org>
	<CAKVJ-_4eOBd60sNy2wfFXygoeOd_QqBoPnxdm9LOGoQEHDS2fg@mail.gmail.com>
	<CAA9RGEM=XvbL3aU+2+G=x3MWEarOPfPSe=DT3LEZZTpb26ePDA@mail.gmail.com>
	<4EAEA6FA.3070100@bioteam.net>
	<CAA9RGEN0SLW8mRHipkSOVTSs7V3q+XHg1NdQ5L+bGTA6nZeTow@mail.gmail.com>
	<4EAEA99C.8020906@sonsorol.org>
	<CAA9RGEMqp0FyzgJCvihvqg0818+wsGFb2rnh3jA771mxECykwA@mail.gmail.com>
	<7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu>
	<CAA9RGEPRnbWRAwcaHtWS_eBAJzinuh9NZ_9hoi9vyV-rR7Ff2A@mail.gmail.com>
Message-ID: <CAKVJ-_4Kkwc-Ld+=J4qt1K_O33z=8b6YOu+2UQ9jXvNd8jgNvw@mail.gmail.com>

Hi all,

Excellent news below from Tiago regarding nightly test - let's
continue this discussion here on the BioRuby list as suggested.

As a quick introduction, Tiago is one of the Biopython developers
(he works on Population Genetics), and he setup most of our
nightly test infrastructure for Biopython using buildbot.

During the BioHackathon 2011 in Kyoto, Raoul asked me about
doing the same for BioRuby - and others like Pjotr are also
keen.

Let's work on the issues Tiago has identified (e.g. non-zero
return codes, option to disable network tests, etc) before
extending this to more build slaves, and to look at the gems.

Regards,

Peter

2011/10/31 Tiago Ant?o <tiagoantao at gmail.com>:
> Dear All,
>
> It is a pleasure to report that a bare bones buildbot is now setup for
> bioruby. Some notes
> 1. You can find it here: http://testing.open-bio.org/bioruby/
> 2. It has just a single test slave, my machine
> 3. ruby setup.rb test is FAILING in two tests, but the script ends
> with exit code 0, thus not reporting an error. Would it be possible to
> end setup.rb test with a exit code noticing the error? Mode details
> here:
> http://testing.open-bio.org:8102/builders/Linux%2064%20-%20Ruby%201.8/builds/0/steps/compile/logs/stdio
>
> Please have a look. Comments appreciated. This is just a barebones
> version, we can then evolve to something else.
>
> Tiago
> PS - maybe technical discussions about bioruby setup should be moved
> elsewhere (e.g., not include the board and maybe include bioruby-dev)?


From p.j.a.cock at googlemail.com  Mon Oct 31 19:17:43 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 31 Oct 2011 23:17:43 +0000
Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org
In-Reply-To: <CAKVJ-_4Kkwc-Ld+=J4qt1K_O33z=8b6YOu+2UQ9jXvNd8jgNvw@mail.gmail.com>
References: <CAKVJ-_6eMa0nYBMmsgJPet3fmpOTSwaDHgraOqxH_YEKF+szsg@mail.gmail.com>
	<CAA9RGEMcdZFmo_D04Rwf=bwd9_rY=+N_BnyjzvEmFSxCT+J7aw@mail.gmail.com>
	<CAKVJ-_63TyhETCPBkTW09ZPrhKKGyGh4qknO7EBEcAwQ=Krtmg@mail.gmail.com>
	<4EAEA028.1090906@bioteam.net>
	<CAKVJ-_5hXj+FrNXtPfB4FeDN3FqKtQBBFQR4EeQZ6Liuwet18A@mail.gmail.com>
	<4EAEA4D6.7090805@sonsorol.org>
	<CAKVJ-_4eOBd60sNy2wfFXygoeOd_QqBoPnxdm9LOGoQEHDS2fg@mail.gmail.com>
	<CAA9RGEM=XvbL3aU+2+G=x3MWEarOPfPSe=DT3LEZZTpb26ePDA@mail.gmail.com>
	<4EAEA6FA.3070100@bioteam.net>
	<CAA9RGEN0SLW8mRHipkSOVTSs7V3q+XHg1NdQ5L+bGTA6nZeTow@mail.gmail.com>
	<4EAEA99C.8020906@sonsorol.org>
	<CAA9RGEMqp0FyzgJCvihvqg0818+wsGFb2rnh3jA771mxECykwA@mail.gmail.com>
	<7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu>
	<CAA9RGEPRnbWRAwcaHtWS_eBAJzinuh9NZ_9hoi9vyV-rR7Ff2A@mail.gmail.com>
	<CAKVJ-_4Kkwc-Ld+=J4qt1K_O33z=8b6YOu+2UQ9jXvNd8jgNvw@mail.gmail.com>
Message-ID: <CAKVJ-_733TTRp2hDoNwv1h3dyi73LPuYwc_K9T0S4K30dg1uKg@mail.gmail.com>

2011/10/31 Peter Cock <p.j.a.cock at googlemail.com>:
> Hi all,
>
> Excellent news below from Tiago regarding nightly test - let's
> continue this discussion here on the BioRuby list as suggested.
>
> As a quick introduction, Tiago is one of the Biopython developers
> (he works on Population Genetics), and he setup most of our
> nightly test infrastructure for Biopython using buildbot.
>
> During the BioHackathon 2011 in Kyoto, Raoul asked me about
> doing the same for BioRuby - and others like Pjotr are also
> keen.
>
> Let's work on the issues Tiago has identified (e.g. non-zero
> return codes, option to disable network tests, etc) before
> extending this to more build slaves, and to look at the gems.

I forgot to mention "Running BioRuby tests offline" has already
been filed as an issue, https://redmine.open-bio.org/issues/3293

Peter

From email2ants at gmail.com  Wed Oct  5 14:57:44 2011
From: email2ants at gmail.com (Anthony Underwood)
Date: Wed, 5 Oct 2011 15:57:44 +0100
Subject: [BioRuby] BioRuby API
Message-ID: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>

 Hi all

Does anyone else find the new API docs more difficult to navigate than the old api?
It looks prettier but I find it harder to find what I'm after. OK frames may be very 1990s but in the case of the API having all the Methods and Classes in scrollable frames worked well.
Does anybody have 
any tips on how to navigate around?
a URL where the old form of presenting the API is still accessible?
the command to generate the old API locally?

Many thanks in advance

Anthony 



From ngoto at gen-info.osaka-u.ac.jp  Thu Oct  6 04:53:31 2011
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Thu, 6 Oct 2011 13:53:31 +0900
Subject: [BioRuby] BioRuby API
In-Reply-To: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>
References: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>
Message-ID: <20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>

Hi,

The change is due to the change of RDoc default html generator.
The new pages are generated by using RDoc bundled in Ruby 1.9.2,
with its default style.  Old style, which was the default of
older RDoc, seems to be no longer maintained by anyone, and
is dropped from current RDoc.

It is easy to generate API html pages locally.
"rake rdoc" in the top of bioruby source tree.
Old style pages may be generated by using Ruby 1.9.1-p431
(or Ruby 1.8.x with older version of RDoc).

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Wed, 5 Oct 2011 15:57:44 +0100
Anthony Underwood <email2ants at gmail.com> wrote:

>  Hi all
> 
> Does anyone else find the new API docs more difficult to navigate than the old api?
> It looks prettier but I find it harder to find what I'm after. OK frames may be very 1990s but in the case of the API having all the Methods and Classes in scrollable frames worked well.
> Does anybody have 
> any tips on how to navigate around?
> a URL where the old form of presenting the API is still accessible?
> the command to generate the old API locally?
> 
> Many thanks in advance
> 
> Anthony 
> 


From email2ants at gmail.com  Thu Oct  6 09:27:55 2011
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 6 Oct 2011 10:27:55 +0100
Subject: [BioRuby] BioRuby API
In-Reply-To: <20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>
References: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>
	<20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <C9F7A8C42A8B483BB6C652A68F2E46CA@gmail.com>

Hello Naohisa

Thanks for the advice. Thaks to rvm I have regenerated the 1.4.2 rdoc using rdoc version 2.2.1 (the last  version before the new 'darkfish' look beccame standard).
This is publically available at
http://www.hpa-bioinformatics.org.uk/bioruby-api/

Thanks again,

Anthony 


On Thursday, 6 October 2011 at 05:53, Naohisa GOTO wrote:

> Hi,
> 
> The change is due to the change of RDoc default html generator.
> The new pages are generated by using RDoc bundled in Ruby 1.9.2,
> with its default style. Old style, which was the default of
> older RDoc, seems to be no longer maintained by anyone, and
> is dropped from current RDoc.
> 
> It is easy to generate API html pages locally.
> "rake rdoc" in the top of bioruby source tree.
> Old style pages may be generated by using Ruby 1.9.1-p431
> (or Ruby 1.8.x with older version of RDoc).
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp (mailto:ngoto at gen-info.osaka-u.ac.jp) / ng at bioruby.org (mailto:ng at bioruby.org)
> 
> On Wed, 5 Oct 2011 15:57:44 +0100
> Anthony Underwood <email2ants at gmail.com (mailto:email2ants at gmail.com)> wrote:
> 
> >  Hi all
> > 
> > Does anyone else find the new API docs more difficult to navigate than the old api?
> > It looks prettier but I find it harder to find what I'm after. OK frames may be very 1990s but in the case of the API having all the Methods and Classes in scrollable frames worked well.
> > Does anybody have 
> > any tips on how to navigate around?
> > a URL where the old form of presenting the API is still accessible?
> > the command to generate the old API locally?
> > 
> > Many thanks in advance
> > 
> > Anthony 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org (mailto:BioRuby at lists.open-bio.org)
> http://lists.open-bio.org/mailman/listinfo/bioruby



From email2ants at gmail.com  Thu Oct  6 10:05:22 2011
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 6 Oct 2011 11:05:22 +0100
Subject: [BioRuby] BioRuby API
In-Reply-To: <20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>
References: <D2DFB536ECDF4D4DB30288C93DB03128@gmail.com>
	<20111006045332.9A3581CBC51D@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <E299887B420A4C6C89C890F923BB7E77@gmail.com>

I've also put up the same documentation but styled using YARD for those who prefer this stye:

http://www.hpa-bioinformatics.org.uk/bioruby-yard-api/ 


On Thursday, 6 October 2011 at 05:53, Naohisa GOTO wrote:

> Hi,
> 
> The change is due to the change of RDoc default html generator.
> The new pages are generated by using RDoc bundled in Ruby 1.9.2,
> with its default style. Old style, which was the default of
> older RDoc, seems to be no longer maintained by anyone, and
> is dropped from current RDoc.
> 
> It is easy to generate API html pages locally.
> "rake rdoc" in the top of bioruby source tree.
> Old style pages may be generated by using Ruby 1.9.1-p431
> (or Ruby 1.8.x with older version of RDoc).
> 
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp (mailto:ngoto at gen-info.osaka-u.ac.jp) / ng at bioruby.org (mailto:ng at bioruby.org)
> 
> On Wed, 5 Oct 2011 15:57:44 +0100
> Anthony Underwood <email2ants at gmail.com (mailto:email2ants at gmail.com)> wrote:
> 
> >  Hi all
> > 
> > Does anyone else find the new API docs more difficult to navigate than the old api?
> > It looks prettier but I find it harder to find what I'm after. OK frames may be very 1990s but in the case of the API having all the Methods and Classes in scrollable frames worked well.
> > Does anybody have 
> > any tips on how to navigate around?
> > a URL where the old form of presenting the API is still accessible?
> > the command to generate the old API locally?
> > 
> > Many thanks in advance
> > 
> > Anthony 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org (mailto:BioRuby at lists.open-bio.org)
> http://lists.open-bio.org/mailman/listinfo/bioruby



From info at orbicule.com  Thu Oct  6 16:29:42 2011
From: info at orbicule.com (Peter Schols)
Date: Thu, 6 Oct 2011 18:29:42 +0200
Subject: [BioRuby] BioRuby API
Message-ID: <BF2E7988-96E2-4494-8D86-CBA0DF9246B1@orbicule.com>

Another interesting rdoc html generator is sdoc, maybe worth checking out for BioRuby:

https://github.com/voloko/sdoc


From email2ants at gmail.com  Thu Oct  6 19:16:20 2011
From: email2ants at gmail.com (Anthony Underwood)
Date: Thu, 6 Oct 2011 20:16:20 +0100
Subject: [BioRuby] BioRuby API
In-Reply-To: <BF2E7988-96E2-4494-8D86-CBA0DF9246B1@orbicule.com>
References: <BF2E7988-96E2-4494-8D86-CBA0DF9246B1@orbicule.com>
Message-ID: <CAAZOFr9F4y-nuGowz=CeV_wJoYfab03upqmv_C+ug320ignJ8Q@mail.gmail.com>

Thanks for the info about sdoc Peter. I have generated documentation with
sdoc and put it live publicly at the following URL
http://www.hpa-bioinformatics.org.uk/bioruby-sdoc-api/

On 6 October 2011 17:29, Peter Schols <info at orbicule.com> wrote:

> Another interesting rdoc html generator is sdoc, maybe worth checking out
> for BioRuby:
>
> https://github.com/voloko/sdoc
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>


From info at orbicule.com  Thu Oct  6 21:06:24 2011
From: info at orbicule.com (Peter Schols)
Date: Thu, 6 Oct 2011 23:06:24 +0200
Subject: [BioRuby] BioRuby API
In-Reply-To: <CAAZOFr9F4y-nuGowz=CeV_wJoYfab03upqmv_C+ug320ignJ8Q@mail.gmail.com>
References: <BF2E7988-96E2-4494-8D86-CBA0DF9246B1@orbicule.com>
	<CAAZOFr9F4y-nuGowz=CeV_wJoYfab03upqmv_C+ug320ignJ8Q@mail.gmail.com>
Message-ID: <61E4FDFC-AEAF-4F2C-8F04-3E424F01CD92@orbicule.com>

Fantastic, thanks!

Peter

On 06 Oct 2011, at 21:16, Anthony Underwood wrote:

> Thanks for the info about sdoc Peter. I have generated documentation with sdoc and put it live publicly at the following URL 
> http://www.hpa-bioinformatics.org.uk/bioruby-sdoc-api/
> 
> On 6 October 2011 17:29, Peter Schols <info at orbicule.com> wrote:
> Another interesting rdoc html generator is sdoc, maybe worth checking out for BioRuby:
> 
> https://github.com/voloko/sdoc
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
> 




From pjotr.public14 at thebird.nl  Fri Oct 14 08:08:15 2011
From: pjotr.public14 at thebird.nl (Pjotr Prins)
Date: Fri, 14 Oct 2011 10:08:15 +0200
Subject: [BioRuby] biogems.info updated
In-Reply-To: <20110920165601.GA8933@thebird.nl>
References: <20110920165601.GA8933@thebird.nl>
Message-ID: <20111014080815.GA25807@thebird.nl>

Updated the site

   http://biogems.info/

Biogem status, meta-package info, and inviting links to source
tree and commits.

Shows how playful we are ;)

Pj.



From p.j.a.cock at googlemail.com  Mon Oct 31 23:09:52 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 31 Oct 2011 23:09:52 +0000
Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org
In-Reply-To: <CAA9RGEPRnbWRAwcaHtWS_eBAJzinuh9NZ_9hoi9vyV-rR7Ff2A@mail.gmail.com>
References: <CAKVJ-_6eMa0nYBMmsgJPet3fmpOTSwaDHgraOqxH_YEKF+szsg@mail.gmail.com>
	<CAA9RGEMcdZFmo_D04Rwf=bwd9_rY=+N_BnyjzvEmFSxCT+J7aw@mail.gmail.com>
	<CAKVJ-_63TyhETCPBkTW09ZPrhKKGyGh4qknO7EBEcAwQ=Krtmg@mail.gmail.com>
	<4EAEA028.1090906@bioteam.net>
	<CAKVJ-_5hXj+FrNXtPfB4FeDN3FqKtQBBFQR4EeQZ6Liuwet18A@mail.gmail.com>
	<4EAEA4D6.7090805@sonsorol.org>
	<CAKVJ-_4eOBd60sNy2wfFXygoeOd_QqBoPnxdm9LOGoQEHDS2fg@mail.gmail.com>
	<CAA9RGEM=XvbL3aU+2+G=x3MWEarOPfPSe=DT3LEZZTpb26ePDA@mail.gmail.com>
	<4EAEA6FA.3070100@bioteam.net>
	<CAA9RGEN0SLW8mRHipkSOVTSs7V3q+XHg1NdQ5L+bGTA6nZeTow@mail.gmail.com>
	<4EAEA99C.8020906@sonsorol.org>
	<CAA9RGEMqp0FyzgJCvihvqg0818+wsGFb2rnh3jA771mxECykwA@mail.gmail.com>
	<7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu>
	<CAA9RGEPRnbWRAwcaHtWS_eBAJzinuh9NZ_9hoi9vyV-rR7Ff2A@mail.gmail.com>
Message-ID: <CAKVJ-_4Kkwc-Ld+=J4qt1K_O33z=8b6YOu+2UQ9jXvNd8jgNvw@mail.gmail.com>

Hi all,

Excellent news below from Tiago regarding nightly test - let's
continue this discussion here on the BioRuby list as suggested.

As a quick introduction, Tiago is one of the Biopython developers
(he works on Population Genetics), and he setup most of our
nightly test infrastructure for Biopython using buildbot.

During the BioHackathon 2011 in Kyoto, Raoul asked me about
doing the same for BioRuby - and others like Pjotr are also
keen.

Let's work on the issues Tiago has identified (e.g. non-zero
return codes, option to disable network tests, etc) before
extending this to more build slaves, and to look at the gems.

Regards,

Peter

2011/10/31 Tiago Ant?o <tiagoantao at gmail.com>:
> Dear All,
>
> It is a pleasure to report that a bare bones buildbot is now setup for
> bioruby. Some notes
> 1. You can find it here: http://testing.open-bio.org/bioruby/
> 2. It has just a single test slave, my machine
> 3. ruby setup.rb test is FAILING in two tests, but the script ends
> with exit code 0, thus not reporting an error. Would it be possible to
> end setup.rb test with a exit code noticing the error? Mode details
> here:
> http://testing.open-bio.org:8102/builders/Linux%2064%20-%20Ruby%201.8/builds/0/steps/compile/logs/stdio
>
> Please have a look. Comments appreciated. This is just a barebones
> version, we can then evolve to something else.
>
> Tiago
> PS - maybe technical discussions about bioruby setup should be moved
> elsewhere (e.g., not include the board and maybe include bioruby-dev)?



From p.j.a.cock at googlemail.com  Mon Oct 31 23:17:43 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 31 Oct 2011 23:17:43 +0000
Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org
In-Reply-To: <CAKVJ-_4Kkwc-Ld+=J4qt1K_O33z=8b6YOu+2UQ9jXvNd8jgNvw@mail.gmail.com>
References: <CAKVJ-_6eMa0nYBMmsgJPet3fmpOTSwaDHgraOqxH_YEKF+szsg@mail.gmail.com>
	<CAA9RGEMcdZFmo_D04Rwf=bwd9_rY=+N_BnyjzvEmFSxCT+J7aw@mail.gmail.com>
	<CAKVJ-_63TyhETCPBkTW09ZPrhKKGyGh4qknO7EBEcAwQ=Krtmg@mail.gmail.com>
	<4EAEA028.1090906@bioteam.net>
	<CAKVJ-_5hXj+FrNXtPfB4FeDN3FqKtQBBFQR4EeQZ6Liuwet18A@mail.gmail.com>
	<4EAEA4D6.7090805@sonsorol.org>
	<CAKVJ-_4eOBd60sNy2wfFXygoeOd_QqBoPnxdm9LOGoQEHDS2fg@mail.gmail.com>
	<CAA9RGEM=XvbL3aU+2+G=x3MWEarOPfPSe=DT3LEZZTpb26ePDA@mail.gmail.com>
	<4EAEA6FA.3070100@bioteam.net>
	<CAA9RGEN0SLW8mRHipkSOVTSs7V3q+XHg1NdQ5L+bGTA6nZeTow@mail.gmail.com>
	<4EAEA99C.8020906@sonsorol.org>
	<CAA9RGEMqp0FyzgJCvihvqg0818+wsGFb2rnh3jA771mxECykwA@mail.gmail.com>
	<7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu>
	<CAA9RGEPRnbWRAwcaHtWS_eBAJzinuh9NZ_9hoi9vyV-rR7Ff2A@mail.gmail.com>
	<CAKVJ-_4Kkwc-Ld+=J4qt1K_O33z=8b6YOu+2UQ9jXvNd8jgNvw@mail.gmail.com>
Message-ID: <CAKVJ-_733TTRp2hDoNwv1h3dyi73LPuYwc_K9T0S4K30dg1uKg@mail.gmail.com>

2011/10/31 Peter Cock <p.j.a.cock at googlemail.com>:
> Hi all,
>
> Excellent news below from Tiago regarding nightly test - let's
> continue this discussion here on the BioRuby list as suggested.
>
> As a quick introduction, Tiago is one of the Biopython developers
> (he works on Population Genetics), and he setup most of our
> nightly test infrastructure for Biopython using buildbot.
>
> During the BioHackathon 2011 in Kyoto, Raoul asked me about
> doing the same for BioRuby - and others like Pjotr are also
> keen.
>
> Let's work on the issues Tiago has identified (e.g. non-zero
> return codes, option to disable network tests, etc) before
> extending this to more build slaves, and to look at the gems.

I forgot to mention "Running BioRuby tests offline" has already
been filed as an issue, https://redmine.open-bio.org/issues/3293

Peter