body 0.1.0.pre1

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/COPYING

@@ -0,0 +1,3 @@
+skeleton is copyrighted free software by Popdevelop <contact@popdevelop.com>.
+You can redistribute it and/or modify it under either the terms of the GPL
+version 2 (see the file GPL).

data/GPL

@@ -0,0 +1,340 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+                       59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
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+
+  Finally, any free program is threatened constantly by software
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+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
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+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
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+
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+
+    c) Accompany it with the information you received as to the offer
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+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
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+
+If distribution of executable or object code is made by offering
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+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
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+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
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+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Library General
+Public License instead of this License.

data/Gemfile

@@ -0,0 +1,13 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

@@ -0,0 +1,20 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.9.2)
+    rcov (0.9.10)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.4)
+  rcov
+  shoulda

data/KNOWN_ISSUES.rdoc

@@ -0,0 +1,165 @@
+= KNOWN_ISSUES.rdoc - Known issues and bugs in skeleton
+Copyright:: Copyright (C) 2011 Sebastian Wallin, Johan Brissmyr, Johan Gyllenspetz, Joel Larsson <contact@popdevelop.com>
+License::   The Ruby License
+
+= Known issues and bugs in skeleton
+
+Below are known issues and bugs in skeleton. Patches to fix them are welcome.
+We hope they will be fixed in the future.
+
+Items marked with (WONT_FIX) tags would not be fixed within BioRuby because
+they are not BioRuby's issues and/or it is very difficult to fix them.
+
+== 1. Ruby version specific issues
+
+=== Ruby 1.9.1 or later
+
+Some classes/modules/methods still may not work or may return incorrect
+results in Ruby 1.9.1, especially those not covered by the unit tests.
+
+==== String encodings
+
+Currently, BioRuby do not care string encodings. In some cases,
+Encoding::CompatibilityError or "ArgumentError: invalid byte sequence in
+(encoding name)" may be raised.
+
+=== End-of-life Ruby versions
+
+==== Ruby 1.9.0
+
+(WONT_FIX) Ruby 1.9.0 is NOT supported because it isn't a stable release.
+Use Ruby 1.9.1 or later.
+
+==== Ruby 1.8.5 or earlier
+
+(WONT_FIX) Problems observed only with Ruby 1.8.5 or earlier will not be
+fixed. Note that Ruby 1.8.5 or earlier is no longer supported, as described
+in README.rdoc.
+
+==== Ruby 1.8.2 or earlier
+
+(WONT_FIX) In some cases, temporary files and directories may not be
+removed because of the lack of FileUtils.remove_entry_secure.
+
+=== Issues about SOAP/WSDL
+
+SOAP4R (SOAP and WSDL implementation) is no longer bundled with Ruby 1.9.
+In addition, because of the API changes in recent SOAP4R, some
+classes/modules using SOAP4R may not work.
+
+=== Problem with REXML DoS vulnerability patch before 09-Nov-2008
+
+(WONT_FIX) If you have applied a patch taken from
+http://www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/
+before 09 Nov 2008 12:40 +0900, because of the bug in the patch,
+parsing of Blast XML results with REXML parser may fail. The bug is already
+fixed and new patch is available on the above URL. Note that some Linux
+distributions would have incorporated the patch in their manners, and may
+have the same problem.
+
+=== RubyGems 0.8.11 or earlier
+
+(WONT_FIX) With very old version of RubyGems, use 'require_gem' which was
+deprecated in RubyGems 0.9.0 and removed in RubyGems 1.0.1.
+
+  #!/usr/bin/env ruby
+  require 'rubygems'
+  require_gem 'bio'
+
+== 2. OS and/or architecture-dependent issues
+
+=== Microsoft Windows
+
+==== Text mode issues
+
+Following 4 tests failed on mswin32 (and maybe on mingw32 and bccwin32)
+because of the conversion of line feed codes in the text mode.
+
+* test_ended_pos and test_start_pos in test/unit/bio/io/test_flatfile.rb
+* test_pos in test/unit/bio/io/flatfile/test_buffer.rb
+* test_entry_pos in test/unit/bio/appl/blast/test_rpsblast.rb
+
+This indicates that br_bioflat.rb and Bio::FlatFileIndex may create
+incorrect indexes on mswin32, mingw32, and bccwin32. In addition,
+Bio::FlatFile may return incorrect data.
+
+==== String escaping of command-line arguments
+
+After BioRuby 1.4.1, in Ruby 1.9.X running on Windows, escaping of
+command-line arguments are processed by the Ruby interpreter. Before BioRuby
+1.4.0, the escaping is executed in Bio::Command#escape_shell_windows, and
+the behavior is different from the Ruby interpreter's one.
+
+Curreltly, due to the change, test/functional/bio/test_command.rb may fail
+on Windows with Ruby 1.9.X.
+
+==== Windows 95/98/98SE/ME
+
+(WONT_FIX) Some methods that call external programs may not work in
+Windows 95/98/98SE/ME because of the limitation of COMMAND.COM.
+
+=== OpenVMS, BeOS, OS/2, djgpp, Windows CE
+
+(WONT_FIX) BioRuby may not work on these platforms.
+
+== 3. Known issues and bugs in BioRuby
+
+=== Bio::Ensembl
+
+Due to the renewal of Ensembl web site, Bio::Ensembl does not work for
+the latest Ensembl. For a workaround, use an archive server. For example,
+"jul2008.archive.ensembl.org" seems to be the last server before the renewal.
+  human = Bio::Ensembl.new("Homo_sapiens", "jul2008.archive.ensembl.org")
+
+Alternatively, consider using Ruby Ensembl API.
+* http://github.com/jandot/ruby-ensembl-api
+
+=== Bio::DBGET and sample/dbget
+
+(WONT_FIX) Because the DBGET service have not been publically available for
+a long time, we give up support for Bio::DBGET and sample/dbget. Instead,
+using Bio::TogoWS or Bio::KEGG::API is recommended.
+
+=== Bio::NCBI::SOAP
+
+It seems that Bio::NCBI::SOAP (in lib/bio/io/ncbisoap.rb) does not work
+correctly, even running on Ruby 1.8.x. Instead, use Bio::NCBI::REST.
+
+=== Bio::KEGG::Taxonomy and sample/demo_kegg_taxonomy.rb
+
+Bio::KEGG::Taxonomy fails to parse current KEGG taxonomy data file probably
+because of the growth of the data size.
+
+=== Bio::SPTR
+
+Bio::SPTR should be updated to follow UniProtKB format changes described
+in http://www.uniprot.org/docs/sp_news.htm .
+
+== 4. Compatibility issues with other libraries/extensions
+
+=== ActiveRecord
+
+BioSQL support uses ActiveRecord, but the author of the document does not
+know which version is suitable.
+
+=== Ruby on Rails
+
+BioRuby Shell on Web uses Ruby on Rails, but the author of the document does
+not know which version is suitable.
+
+== 5. Historical descriptions
+
+=== CVS
+
+For historical purposes: the anonymous CVS was provided at 
+
+* http://cvs.bioruby.org/
+
+and could be obtained by the following procedure.
+
+  % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby login
+  CVS password: cvs (login with a password 'cvs' for the first time)
+  % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby co bioruby
+
+These may be closed without any prior notice.
+

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2011 Joel Larsson
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

@@ -0,0 +1,95 @@
+--
+= README.rdoc - README for skeleton
+Copyright:: Copyright (C) 2011 Sebastian Wallin, Johan Brissmyr, Johan Gyllenspetz, Joel Larsson <contact@popdevelop.com>
+License::   The Ruby License
+* The above statement is limited to this file. See below about Skeleton's
+  copyright and license.
+++
+
+= Skeleton
+
+Copyright (C) 2011 Sebastian Wallin, Johan Brissmyr, Johan Gyllenspetz, Joel Larsson <contact@popdevelop.com>
+
+Skeleton is an open source Ruby library for developing...
+
+== FOR MORE INFORMATION
+
+=== Documents in this distribution
+
+==== General information
+
+README.rdoc:: This file. General information and installation procedure.
+RELEASE_NOTES.rdoc:: News and important changes in this release.
+
+Issues are tracked on github at http://github.com/popdevelop/skeleton
+
+==== Tutorials, Examples and other useful information
+
+examples/:: Examples directory
+
+==== skeleton development
+
+README_DEV.rdoc:: Information for developers that want to contribute to the project, including coding styles and documentation guidelines.
+
+=== websites
+
+Authors website, day to day blog posts from our team
+* http://popdevelop.com
+
+Github, here you will find links to related resources including downloads, issue tracking, documentation etc.
+* http://github.com/popdevelop
+
+=== git
+
+If you need the latest development version, this is provided at
+
+* http://github.com/popdevelop/skeleton
+
+and can be obtained by the following procedure:
+
+  % git clone git://github.com/podevelop/skeleton.git
+
+== REQUIREMENTS
+
+* Ruby 1.8.6 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
+  * Ruby 1.8.7-p352 or later is recommended.
+
+== INSTALL
+
+=== INSTALL by using RubyGems (recommended)
+
+gem install skeleton
+
+=== INSTALL without RubyGems
+
+== USAGE
+
+You can load all skeleton classes just by requiring 'skeleton.rb'.  All the
+skeleton classes and modules are located under the module name 'skeleton' to
+separate the name space.
+
+  #!/usr/bin/env ruby
+  require 'skeleton'
+
+You can also read other documentation in the 'doc' directory.
+
+  doc/
+
+=== RubyGems on Ruby 1.8.x
+
+With RubyGems on Ruby 1.8.x, you may need to load 'rubygems' library before
+using 'skeleton'. This may not be needed, depending on settings of Ruby.
+
+  #!/usr/bin/env ruby
+  require 'rubygems'
+  require 'skeleton'
+
+== LICENSE
+
+skeleton can be freely distributed under the same terms as Ruby.
+See the file COPYING.
+
+== CONTACT
+
+Current staff of the skeleton project can be reached by sending e-mail
+to <contact@popdevelop.com>.

data/README_DEV.rdoc

@@ -0,0 +1,60 @@
+= README.DEV
+
+Copyright (C) 2011 Sebastian Wallin, Johan Brissmyr, Johan Gyllenspetz, Joel Larsson <contact@popdevelop.com>
+
+= HOW TO CONTRIBUTE TO THE skeleton PROJECT?
+
+There are many possible ways to contribute to the skeleton project,
+such as:
+
+* Send a bug report or write a bug fix patch
+* Add and correct documentation
+* Develop code for new features, etc.
+
+All of these are welcome!  However, this document describes the last option,
+how to contribute your code to the skeleton distribution.
+
+== Git
+
+skeleton is now under git source control at http://github.com/popdevelop/skeleton.
+There are two basic ways to contribute: with patches or pull requests.
+
+= CODING STYLE
+
+Please follow these guidelines, http://www.caliban.org/ruby/rubyguide.shtml#style
+
+== Indentation must not include evil tabs
+
+* Use 2 spaces for indentation.
+
+== Documentation should be written in the RDoc format in the source code
+
+The RDoc format is becoming the popular standard for Ruby documentation.
+
+Additional tutorial documentation and working examples are encouraged
+with your contribution. You may use the header part of the file for
+this purpose as demonstrated in the previous section.
+
+== Standard documentation
+
+Each file should start with a header, which covers the following topics:
+* copyright
+* license
+* description of the file (_not_ the classes; see below)
+* any references, if appropriate
+
+== Testing code should use 'test/unit'
+
+Unit tests should come with your modules by which you can assure what
+you meant to do with each method. The test code is useful to make
+maintenance easy and ensure stability.
+
+= NAMESPACE
+
+Your module should be located under the top-level module skeleton and put under
+the 'skeleton/lib/skeleton' directory.  The class/module names and the
+file names should be short and descriptive.
+
+= MAINTENANCE
+
+Finally, please maintain the code you've contributed.

data/RELEASE_NOTES.rdoc

@@ -0,0 +1,26 @@
+= skeleton x.x.x RELEASE NOTES
+
+Copyright:: Copyright (C) 2011 Sebastian Wallin, Johan Brissmyr, Johan Gyllenspetz, Joel Larsson <contact@popdevelop.com>
+License::   The Ruby License
+
+== New features
+
+=== New classes skeleton::fixme::fixme
+
+=== New classes skeleton::fixme::fixme
+
+== Bug fixes
+
+=== skeleton:fixme
+
+* First release, no bug fixes
+
+== Incompatible changes
+
+=== skeleton:fixme
+
+* First release, everything is compatible
+
+== Known issues
+
+Know issues are added and updated in the file KNOWN_ISSUES.rdoc::

data/Rakefile

@@ -0,0 +1,55 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+require './lib/body/version.rb'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "body"
+  gem.homepage = "http://github.com/tilljoel/body"
+  gem.license = "MIT"
+  gem.summary = %Q{testgem skeleton}
+  gem.description = %Q{longer description of your gem}
+  gem.email = "tilljoel@gmail.com"
+  gem.authors = ["Joel Larsson"]
+  gem.version = Body::Version::STRING
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "body #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/lib/body.rb

@@ -0,0 +1,35 @@
+require "body/version"
+#require 'body/base'
+
+module Body
+
+  # Document the responsibility of the class
+  #
+  # == Heading
+  #
+  # Formating the class description
+  #
+  # == Formatting
+  #
+  # Embody +parameters+ or +options+ in Teletype Text tags. You can also use
+  # *bold* or *italics* but must use HTML tags for <b>multiple words</b>,
+  # <i>like this</i> and <tt>like this</tt>.
+  class Arm
+    # Swings the arm, return
+    #
+    # === Params
+    #
+    # +speed+:: speed to swing with
+    # ==== Examples
+    #
+    #    arm = Arm.new()
+    #    arm.swing(10)
+    def swing(speed=10)
+      puts "Swining with speed #{speed}"
+      return speed
+    end
+
+  end
+
+end
+

data/lib/body/version.rb

@@ -0,0 +1,10 @@
+class Body
+  module Version
+    MAJOR = 0
+    MINOR = 1
+    PATCH = 0
+    BUILD = 'pre1'
+
+    STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
+  end
+end

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'body'
+
+class Test::Unit::TestCase
+end

data/test/test_body.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBody < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

@@ -0,0 +1,144 @@
+--- !ruby/object:Gem::Specification 
+name: body
+version: !ruby/object:Gem::Version 
+  hash: 1923831995
+  prerelease: 6
+  segments: 
+  - 0
+  - 1
+  - 0
+  - pre
+  - 1
+  version: 0.1.0.pre1
+platform: ruby
+authors: 
+- Joel Larsson
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-10-07 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  prerelease: false
+  version_requirements: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  requirement: *id001
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  prerelease: false
+  version_requirements: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 23
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  type: :development
+  requirement: *id002
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  prerelease: false
+  version_requirements: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 1
+        - 6
+        - 4
+        version: 1.6.4
+  type: :development
+  requirement: *id003
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  prerelease: false
+  version_requirements: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  requirement: *id004
+description: longer description of your gem
+email: tilljoel@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+- README_DEV.rdoc
+files: 
+- .document
+- COPYING
+- GPL
+- Gemfile
+- Gemfile.lock
+- KNOWN_ISSUES.rdoc
+- LICENSE.txt
+- README.rdoc
+- README_DEV.rdoc
+- RELEASE_NOTES.rdoc
+- Rakefile
+- lib/body.rb
+- lib/body/version.rb
+- test/helper.rb
+- test/test_body.rb
+homepage: http://github.com/tilljoel/body
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">"
+    - !ruby/object:Gem::Version 
+      hash: 25
+      segments: 
+      - 1
+      - 3
+      - 1
+      version: 1.3.1
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.6
+signing_key: 
+specification_version: 3
+summary: testgem skeleton
+test_files: []
+