[BioRuby-cvs] bioruby README.DEV,1.5,1.6

Sun Nov 13 20:34:15 EST 2005

Update of /home/repository/bioruby/bioruby
In directory pub.open-bio.org:/tmp/cvs-serv25531

Modified Files:
	README.DEV 
Log Message:
* Corrections contributed by Trevor Wennbolm

Index: README.DEV
===================================================================
RCS file: /home/repository/bioruby/bioruby/README.DEV,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** README.DEV	8 Nov 2005 06:42:54 -0000	1.5
--- README.DEV	14 Nov 2005 01:34:12 -0000	1.6
***************
*** 8,51 ****

  There are many possible ways to contribute to the BioRuby project,
! such as

  * Join the discussion on the BioRuby mailing list
! * Send a bug report, write a bug fix patch
! * Add and correcting documentations
! * Development codes for new features etc.
! 
! and all of these are welcome!

! However, here we describe on the last option -- how to contribute and
! include your codes to the BioRuby distribution.

  We would like to include your contribution as long as the scope of
  your module meets the field of bioinformatics.

! == Licence

! If you wish your module to be included in the BioRuby distribution,
! you need to agree that your module is licensed under the GNU's LGPL
! as the BioRuby chosen LGPL for its license.

  == Coding style

! You need to follow the typical coding styles of the BioRuby modules:

  === Use the following naming conventions

! * CamelCase for module and class names,
! * '_'-separated lowercase names for method names,
! * '_'-separated lowercase names for variable names, and
! * all uppercase names for constants.

  === Indentation must not include tabs

  * Use 2 spaces for indentation.
! * Don't replace spaces at the line head to tabs.

  === Comments

! Don't use =begin and =end block for comments.  If you need to add
  comments, include it in the RDoc documentation.

--- 8,49 ----

  There are many possible ways to contribute to the BioRuby project,
! such as:

  * Join the discussion on the BioRuby mailing list
! * 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!  This document describes the last option,
! how to contribute your code to the BioRuby distribution.

  We would like to include your contribution as long as the scope of
  your module meets the field of bioinformatics.

! == License

! If you would like your module to be included in the BioRuby
! distribution, please license your module under GNU's LGPL for
! compatibility with the BioRuby project.

  == Coding style

! You will need to follow the typical coding styles of the BioRuby modules:

  === Use the following naming conventions

! * CamelCase for module and class names
! * '_'-separated_lowercase for method names
! * '_'-separated_lowercase for variable names
! * all UPPERCASE for constants

  === Indentation must not include tabs

  * Use 2 spaces for indentation.
! * Don't replace spaces to tabs.

  === Comments

! Don't use =begin and =end blocks for comments.  If you need to add
  comments, include it in the RDoc documentation.

***************
*** 55,62 ****
    # = bio/db/hoge.rb - Hoge database parser
    #
!   # Copyright::	Copyright (C) 2001, 2005
!   #		Bio R. Hacker <brh at example.org>,
!   #		Chem R. Hacker <crh at example.org>
!   # Lisence::	LGPL
    #
    # $Id$
--- 53,60 ----
    # = bio/db/hoge.rb - Hoge database parser
    #
!   # Copyright::    Copyright (C) 2001, 2005
!   #        Bio R. Hacker <brh at example.org>,
!   #        Chem R. Hacker <crh at example.org>
!   # License::    LGPL
    #
    # $Id$
***************
*** 75,79 ****
    # == References
    #
!   # * Hoge F. et al., The Hoge database, Nucleic. Acid. Res. 123:100--123 (2030)
    #
    # * http://hoge.db/
--- 73,78 ----
    # == References
    #
!   # * Hoge F. et al., The Hoge database, Nucleic. Acid. Res. 
! 123:100--123 (2030)
    #
    # * http://hoge.db/
***************
*** 93,97 ****
    #  You should have received a copy of the GNU Lesser General Public
    #  License along with this library; if not, write to the Free Software
!   #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
    #
    #
--- 92,97 ----
    #  You should have received a copy of the GNU Lesser General Public
    #  License along with this library; if not, write to the Free Software
!   #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 
! 02111-1307  USA
    #
    #
***************
*** 99,134 ****
  === Documentation should be written in the RDoc format in the source code

! The RDoc format is becoming de facto standard for the Ruby documentation.
! So, we are now in transition from the RD format which we have been used
! to the RDoc format in API documentations.

! Additional tutorial documents and some working examples are also
! welcome when you contribute your codes.  You may also able to use
! the header part of the file for this purpose as shown in the previous
! section.

  === Testing code should use 'test/unit'

! Unit test should come with your modules by which you can assure what
! you meant to do with each method.  The test code is also able to make
! your maintainance procedure easy and stable.

  === Using autoload

! To make fast start up, we replaced most of 'require' to 'autoload'
! since the BioRuby version 0.7.  During this change, we have found
  some tips:

! You sholud not separate a same namespace into several files.

  * For example, if you have separated definitions of the Bio::Foo
!   class in two files (e.g. 'bio/foo.rb' and 'bio/bar.rb'), you
!   need to resolve the dependency of them (including the order of
!   loading these two files) by yourself.

! * It is not the case that you have a definition of Bio::Foo in
!   'bio/foo.rb' and a definition of Bio::Foo::Bar in 'bio/bar.rb'.
!   In this case, you just need to add following line in the
!   'bio/foo.rb' file.

      autoload :Bar, 'bio/foo/bar'
--- 99,133 ----
  === Documentation should be written in the RDoc format in the source code

! The RDoc format is becoming the popular standard for Ruby documentation.
! We are now in transition from the previously used RD format to the RDoc
! format in API 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.

  === 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.

  === Using autoload

! To quicken the initial load time we have replaced most of 'require' to 
! 'autoload'
! since BioRuby version 0.7.  During this change, we have found
  some tips:

! You should not separate the same namespace into several files.

  * For example, if you have separated definitions of the Bio::Foo
!   class into two files (e.g. 'bio/foo.rb' and 'bio/bar.rb'), you
!   need to resolve the dependencies (including the load order)
!   yourself.

! * If you have a defined Bio::Foo in 'bio/foo.rb' and a defined
!   Bio::Foo::Bar in 'bio/foo/bar.rb' add the following line in the
!   'bio/foo.rb' file:

      autoload :Bar, 'bio/foo/bar'
***************
*** 150,158 ****
      autoload :Foo, 'bio/foo'

!   to make autoload can be written in 1 line.

  == Name space

! Your module should be located under the module Bio and put under
  the 'bioruby/lib/bio' directory.  The class/module names and the
  file names should be short and descriptive.
--- 149,157 ----
      autoload :Foo, 'bio/foo'

!   so autoload can be written in 1 line.

  == Name space

! Your module should be located under the top-level module Bio and put under
  the 'bioruby/lib/bio' directory.  The class/module names and the
  file names should be short and descriptive.
***************
*** 167,177 ****
    bio/util/  -- utilities and algorithms for bioinformatics

! If your module doesn't match to any of the above, please propose
  an appropriate directory name when you contribute.

  == Maintainance

! Finally, please keep maintain the code your contrubuted.  The BioRuby
! staff is willing to give you CVS privilege if needed.

  =end
--- 166,177 ----
    bio/util/  -- utilities and algorithms for bioinformatics

! If your module doesn't match any of the above, please propose
  an appropriate directory name when you contribute.

  == Maintainance

! Finally, please maintain the code you've contrubuted.  The BioRuby
! staff is willing to give you CVS privileges if needed.

  =end
+ 