From ngoto at gen-info.osaka-u.ac.jp  Wed Sep  2 09:15:46 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 2 Sep 2009 22:15:46 +0900
Subject: [BioRuby] BioRuby 1.3.1 is released
Message-ID: <20090902131547.9F26E1CBC433@idnmail.gen-info.osaka-u.ac.jp>

Hi all,

We are pleased to announce the release of BioRuby 1.3.1.

The archive is available at:
  http://bioruby.org/archive/bioruby-1.3.1.tar.gz

Web page:
  http://bioruby.org/
  http://bioruby.open-bio.org/
API documentation:
  http://bioruby.org/rdoc/
Bug report:
  http://rubyforge.org/projects/bioruby/

We also put RubyGems pacakge at RubyForge as always.
You can easily install by using RubyGems.
 % sudo gem install bio

You can also obtain bioruby gem file from bioruby.org.
  http://bioruby.org/archive/gems/bio-1.3.1.gem

Here is a brief summary of changes.

 * Refactoring of BioSQL support.
 * Bio::PubMed bug fixes.
 * Bio::NCBI::REST bug fixes.
 * Bio::GCG::Msf bug fixes.
 * Bio::Fasta::Report bug fixes and added support for multiple query
   sequences.
 * Bio::Sim4::Report bug fixes.
 * Added unit tests for Bio::GCG::Msf and Bio::Sim4::Report.
 * License of BioRuby is clarified.

In addition, many changes have been made, mainly bug fixes.
For more information, you can see ChangeLog at

http://github.com/bioruby/bioruby/blob/e731c6e52bc9a672e4546eeca4f2d2d968bdba09/ChangeLog

Hope you enjoy.

P.S.
In the next major release (maybe 1.4.0), PhyloXML, Chromatogram, and
many other new functions developed in GitHub will be merged.


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

From andrew.j.grimm at gmail.com  Sat Sep  5 23:48:05 2009
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Sun, 6 Sep 2009 13:48:05 +1000
Subject: [BioRuby] Gem production of bioruby forks
Message-ID: <b9140daa0909052048m2c85c71ak9c8ec38bea49d4df@mail.gmail.com>

Is it ok if I ask github to create a bioruby gem based on my fork
(agrimm/bioruby), or should nobody other than the core developers do
this, to avoid too many different gems being created?

Thanks,

Andrew

From ngoto at gen-info.osaka-u.ac.jp  Mon Sep 14 09:10:57 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 14 Sep 2009 22:10:57 +0900
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
Message-ID: <20090914131057.D9A051CBC459@idnmail.gen-info.osaka-u.ac.jp>

Hi Diana,

On Mon, 10 Aug 2009 15:54:55 -0400
Diana Jaunzeikare <rozziite at gmail.com> wrote:

> * Testing. added more unit tests (now writer has 9 tests, 26 assertions;
> parser: 40 tests, 134 assertions)

test/unit/bio/db/test_phyloxml_writer.rb failed with libxml-ruby 1.1.3.
There are possibly 3 reasons.

1. Incompatible changes to XML::Document#save in libxml-ruby 0.9.6.
The method now takes options as a hash. The following patch fixes the bug.

======================================================================
--- a/lib/bio/db/phyloxml/phyloxml_writer.rb
+++ b/lib/bio/db/phyloxml/phyloxml_writer.rb
@@ -92,5 +92,5 @@ module Bio
       #@doc.encoding = XML::Encoding::UTF_8
 
-      @doc.save(@filename, true)
+      @doc.save(@filename, :indent => true)
       end
 
@@ -126,5 +126,5 @@ module Bio
             [:objarr, 'property', 'properties']] )
 
-        @doc.save(@filename, @indent)
+        @doc.save(@filename, :indent => @indent)
       end #writer#write
 
@@ -150,5 +150,5 @@ module Bio
           @root << other_obj.to_xml
         end
-        @doc.save(@filename, @indent)
+        @doc.save(@filename, :indent => @indent)
       end
 
======================================================================

2. TypeError raised in the following tests.

test_made_up_xml_file(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'

test_phyloxml_examples_file(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'

test_phyloxml_examples_sequence_relation(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'

test_phyloxml_examples_tree2(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'

test_phyloxml_examples_tree4(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'

etc.

The following patch fixes the error, but I'm not sure it is correct.

======================================================================
--- a/lib/bio/db/phyloxml/phyloxml_elements.rb
+++ b/lib/bio/db/phyloxml/phyloxml_elements.rb
@@ -278,5 +278,5 @@ module PhyloXML
       if branch_length != nil       
         if write_branch_length_as_subelement
-          clade << XML::Node.new('branch_length', branch_length)
+          clade << XML::Node.new('branch_length', branch_length.to_s)
         else
           clade["branch_length"] = branch_length.to_s
@@ -379,5 +379,5 @@ module PhyloXML
           raise "Type is a required attribute for confidence."
         else
-          confidence = XML::Node.new('confidence', @value.to_f)
+          confidence = XML::Node.new('confidence', @value.to_s)
           confidence["type"] = @type          
           return confidence
======================================================================

3. The file "ncbi_taxonomy_mollusca_short.xml" specified in test_init
does not exist. Putting the file, or changing the file name can fix
the problem.


Thanks,

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

From rozziite at gmail.com  Fri Sep 18 22:08:52 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Fri, 18 Sep 2009 22:08:52 -0400
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <20090914131057.D9A051CBC459@idnmail.gen-info.osaka-u.ac.jp>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com> 
	<20090914131057.D9A051CBC459@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <4057d3bf0909181908p30437671jd5db672f3d621e97@mail.gmail.com>

Hi Naohisa,

Thanks for the patches. I didn't realized that I had old version of
libxml-ruby on my computer. I got the newest 1.1.3 and made the code
compatible with it. I also added  the ncbi_mollusca_short.xml test file.
All changes are pushed to github.

Diana

On Mon, Sep 14, 2009 at 9:10 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi Diana,
>
> On Mon, 10 Aug 2009 15:54:55 -0400
> Diana Jaunzeikare <rozziite at gmail.com> wrote:
>
> > * Testing. added more unit tests (now writer has 9 tests, 26 assertions;
> > parser: 40 tests, 134 assertions)
>
> test/unit/bio/db/test_phyloxml_writer.rb failed with libxml-ruby 1.1.3.
> There are possibly 3 reasons.
>
> 1. Incompatible changes to XML::Document#save in libxml-ruby 0.9.6.
> The method now takes options as a hash. The following patch fixes the bug.
>
> ======================================================================
> --- a/lib/bio/db/phyloxml/phyloxml_writer.rb
> +++ b/lib/bio/db/phyloxml/phyloxml_writer.rb
> @@ -92,5 +92,5 @@ module Bio
>       #@doc.encoding = XML::Encoding::UTF_8
>
> -      @doc.save(@filename, true)
> +      @doc.save(@filename, :indent => true)
>       end
>
> @@ -126,5 +126,5 @@ module Bio
>             [:objarr, 'property', 'properties']] )
>
> -        @doc.save(@filename, @indent)
> +        @doc.save(@filename, :indent => @indent)
>       end #writer#write
>
> @@ -150,5 +150,5 @@ module Bio
>           @root << other_obj.to_xml
>         end
> -        @doc.save(@filename, @indent)
> +        @doc.save(@filename, :indent => @indent)
>       end
>
> ======================================================================
>
> 2. TypeError raised in the following tests.
>
> test_made_up_xml_file(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'
>
> test_phyloxml_examples_file(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'
>
> test_phyloxml_examples_sequence_relation(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'
>
> test_phyloxml_examples_tree2(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'
>
> test_phyloxml_examples_tree4(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'
>
> etc.
>
> The following patch fixes the error, but I'm not sure it is correct.
>
> ======================================================================
> --- a/lib/bio/db/phyloxml/phyloxml_elements.rb
> +++ b/lib/bio/db/phyloxml/phyloxml_elements.rb
> @@ -278,5 +278,5 @@ module PhyloXML
>       if branch_length != nil
>         if write_branch_length_as_subelement
> -          clade << XML::Node.new('branch_length', branch_length)
> +          clade << XML::Node.new('branch_length', branch_length.to_s)
>         else
>           clade["branch_length"] = branch_length.to_s
> @@ -379,5 +379,5 @@ module PhyloXML
>           raise "Type is a required attribute for confidence."
>         else
> -          confidence = XML::Node.new('confidence', @value.to_f)
> +          confidence = XML::Node.new('confidence', @value.to_s)
>           confidence["type"] = @type
>           return confidence
> ======================================================================
>
> 3. The file "ncbi_taxonomy_mollusca_short.xml" specified in test_init
> does not exist. Putting the file, or changing the file name can fix
> the problem.
>
>
> Thanks,
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>

From ngoto at gen-info.osaka-u.ac.jp  Wed Sep  2 13:15:46 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Wed, 2 Sep 2009 22:15:46 +0900
Subject: [BioRuby] BioRuby 1.3.1 is released
Message-ID: <20090902131547.9F26E1CBC433@idnmail.gen-info.osaka-u.ac.jp>

Hi all,

We are pleased to announce the release of BioRuby 1.3.1.

The archive is available at:
  http://bioruby.org/archive/bioruby-1.3.1.tar.gz

Web page:
  http://bioruby.org/
  http://bioruby.open-bio.org/
API documentation:
  http://bioruby.org/rdoc/
Bug report:
  http://rubyforge.org/projects/bioruby/

We also put RubyGems pacakge at RubyForge as always.
You can easily install by using RubyGems.
 % sudo gem install bio

You can also obtain bioruby gem file from bioruby.org.
  http://bioruby.org/archive/gems/bio-1.3.1.gem

Here is a brief summary of changes.

 * Refactoring of BioSQL support.
 * Bio::PubMed bug fixes.
 * Bio::NCBI::REST bug fixes.
 * Bio::GCG::Msf bug fixes.
 * Bio::Fasta::Report bug fixes and added support for multiple query
   sequences.
 * Bio::Sim4::Report bug fixes.
 * Added unit tests for Bio::GCG::Msf and Bio::Sim4::Report.
 * License of BioRuby is clarified.

In addition, many changes have been made, mainly bug fixes.
For more information, you can see ChangeLog at

http://github.com/bioruby/bioruby/blob/e731c6e52bc9a672e4546eeca4f2d2d968bdba09/ChangeLog

Hope you enjoy.

P.S.
In the next major release (maybe 1.4.0), PhyloXML, Chromatogram, and
many other new functions developed in GitHub will be merged.


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


From andrew.j.grimm at gmail.com  Sun Sep  6 03:48:05 2009
From: andrew.j.grimm at gmail.com (Andrew Grimm)
Date: Sun, 6 Sep 2009 13:48:05 +1000
Subject: [BioRuby] Gem production of bioruby forks
Message-ID: <b9140daa0909052048m2c85c71ak9c8ec38bea49d4df@mail.gmail.com>

Is it ok if I ask github to create a bioruby gem based on my fork
(agrimm/bioruby), or should nobody other than the core developers do
this, to avoid too many different gems being created?

Thanks,

Andrew


From ngoto at gen-info.osaka-u.ac.jp  Mon Sep 14 13:10:57 2009
From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO)
Date: Mon, 14 Sep 2009 22:10:57 +0900
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com>
Message-ID: <20090914131057.D9A051CBC459@idnmail.gen-info.osaka-u.ac.jp>

Hi Diana,

On Mon, 10 Aug 2009 15:54:55 -0400
Diana Jaunzeikare <rozziite at gmail.com> wrote:

> * Testing. added more unit tests (now writer has 9 tests, 26 assertions;
> parser: 40 tests, 134 assertions)

test/unit/bio/db/test_phyloxml_writer.rb failed with libxml-ruby 1.1.3.
There are possibly 3 reasons.

1. Incompatible changes to XML::Document#save in libxml-ruby 0.9.6.
The method now takes options as a hash. The following patch fixes the bug.

======================================================================
--- a/lib/bio/db/phyloxml/phyloxml_writer.rb
+++ b/lib/bio/db/phyloxml/phyloxml_writer.rb
@@ -92,5 +92,5 @@ module Bio
       #@doc.encoding = XML::Encoding::UTF_8
 
-      @doc.save(@filename, true)
+      @doc.save(@filename, :indent => true)
       end
 
@@ -126,5 +126,5 @@ module Bio
             [:objarr, 'property', 'properties']] )
 
-        @doc.save(@filename, @indent)
+        @doc.save(@filename, :indent => @indent)
       end #writer#write
 
@@ -150,5 +150,5 @@ module Bio
           @root << other_obj.to_xml
         end
-        @doc.save(@filename, @indent)
+        @doc.save(@filename, :indent => @indent)
       end
 
======================================================================

2. TypeError raised in the following tests.

test_made_up_xml_file(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'

test_phyloxml_examples_file(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'

test_phyloxml_examples_sequence_relation(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'

test_phyloxml_examples_tree2(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'

test_phyloxml_examples_tree4(Bio::TestPhyloXMLWriter):
TypeError: wrong argument type Float (expected String)
    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'

etc.

The following patch fixes the error, but I'm not sure it is correct.

======================================================================
--- a/lib/bio/db/phyloxml/phyloxml_elements.rb
+++ b/lib/bio/db/phyloxml/phyloxml_elements.rb
@@ -278,5 +278,5 @@ module PhyloXML
       if branch_length != nil       
         if write_branch_length_as_subelement
-          clade << XML::Node.new('branch_length', branch_length)
+          clade << XML::Node.new('branch_length', branch_length.to_s)
         else
           clade["branch_length"] = branch_length.to_s
@@ -379,5 +379,5 @@ module PhyloXML
           raise "Type is a required attribute for confidence."
         else
-          confidence = XML::Node.new('confidence', @value.to_f)
+          confidence = XML::Node.new('confidence', @value.to_s)
           confidence["type"] = @type          
           return confidence
======================================================================

3. The file "ncbi_taxonomy_mollusca_short.xml" specified in test_init
does not exist. Putting the file, or changing the file name can fix
the problem.


Thanks,

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


From rozziite at gmail.com  Sat Sep 19 02:08:52 2009
From: rozziite at gmail.com (Diana Jaunzeikare)
Date: Fri, 18 Sep 2009 22:08:52 -0400
Subject: [BioRuby] GSOC: Bioruby PhyloXML update 12
In-Reply-To: <20090914131057.D9A051CBC459@idnmail.gen-info.osaka-u.ac.jp>
References: <4057d3bf0908101254l6d2b793aibed738981a79680a@mail.gmail.com> 
	<20090914131057.D9A051CBC459@idnmail.gen-info.osaka-u.ac.jp>
Message-ID: <4057d3bf0909181908p30437671jd5db672f3d621e97@mail.gmail.com>

Hi Naohisa,

Thanks for the patches. I didn't realized that I had old version of
libxml-ruby on my computer. I got the newest 1.1.3 and made the code
compatible with it. I also added  the ncbi_mollusca_short.xml test file.
All changes are pushed to github.

Diana

On Mon, Sep 14, 2009 at 9:10 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi Diana,
>
> On Mon, 10 Aug 2009 15:54:55 -0400
> Diana Jaunzeikare <rozziite at gmail.com> wrote:
>
> > * Testing. added more unit tests (now writer has 9 tests, 26 assertions;
> > parser: 40 tests, 134 assertions)
>
> test/unit/bio/db/test_phyloxml_writer.rb failed with libxml-ruby 1.1.3.
> There are possibly 3 reasons.
>
> 1. Incompatible changes to XML::Document#save in libxml-ruby 0.9.6.
> The method now takes options as a hash. The following patch fixes the bug.
>
> ======================================================================
> --- a/lib/bio/db/phyloxml/phyloxml_writer.rb
> +++ b/lib/bio/db/phyloxml/phyloxml_writer.rb
> @@ -92,5 +92,5 @@ module Bio
>       #@doc.encoding = XML::Encoding::UTF_8
>
> -      @doc.save(@filename, true)
> +      @doc.save(@filename, :indent => true)
>       end
>
> @@ -126,5 +126,5 @@ module Bio
>             [:objarr, 'property', 'properties']] )
>
> -        @doc.save(@filename, @indent)
> +        @doc.save(@filename, :indent => @indent)
>       end #writer#write
>
> @@ -150,5 +150,5 @@ module Bio
>           @root << other_obj.to_xml
>         end
> -        @doc.save(@filename, @indent)
> +        @doc.save(@filename, :indent => @indent)
>       end
>
> ======================================================================
>
> 2. TypeError raised in the following tests.
>
> test_made_up_xml_file(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'
>
> test_phyloxml_examples_file(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'
>
> test_phyloxml_examples_sequence_relation(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'
>
> test_phyloxml_examples_tree2(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'
>
> test_phyloxml_examples_tree4(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'
>
> etc.
>
> The following patch fixes the error, but I'm not sure it is correct.
>
> ======================================================================
> --- a/lib/bio/db/phyloxml/phyloxml_elements.rb
> +++ b/lib/bio/db/phyloxml/phyloxml_elements.rb
> @@ -278,5 +278,5 @@ module PhyloXML
>       if branch_length != nil
>         if write_branch_length_as_subelement
> -          clade << XML::Node.new('branch_length', branch_length)
> +          clade << XML::Node.new('branch_length', branch_length.to_s)
>         else
>           clade["branch_length"] = branch_length.to_s
> @@ -379,5 +379,5 @@ module PhyloXML
>           raise "Type is a required attribute for confidence."
>         else
> -          confidence = XML::Node.new('confidence', @value.to_f)
> +          confidence = XML::Node.new('confidence', @value.to_s)
>           confidence["type"] = @type
>           return confidence
> ======================================================================
>
> 3. The file "ncbi_taxonomy_mollusca_short.xml" specified in test_init
> does not exist. Putting the file, or changing the file name can fix
> the problem.
>
>
> Thanks,
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>