bio-gem 1.3.2 → 1.3.3

data/README.rdoc

@@ -188,7 +188,7 @@ e.g. biogem the-perfect-gem
         --github-token [GITHUB_TOKEN] GitHub token to use for interacting with the GitHub API
         --git-remote [GIT_REMOTE]    URI to set the git origin remote to
         --homepage [HOMEPAGE]        the homepage for your project (defaults to the GitHub repo)
-        --no-create-repo             create the repository on GitHub
+        --no-create-repo             dont't create the repository on GitHub
         --yard                       use yard for documentation
         --rdoc                       use rdoc for documentation
     -h, --help                       display this help and exit

data/Tutorial.rdoc

@@ -390,7 +390,7 @@ These options are for Jeweler
                                      GitHub token to use for interacting with the GitHub API
         --git-remote [GIT_REMOTE]    URI to set the git origin remote to
         --homepage [HOMEPAGE]        the homepage for your project (defaults to the GitHub repo)
-        --no-create-repo                create the repository on GitHub (repo is created by default)
+        --no-create-repo             don't create the repository on GitHub (repo is created by default)
 
         --yard                       use yard for documentation
         --rdoc                       use rdoc for documentation

data/VERSION

@@ -1 +1 @@
-1.3.2
+1.3.3

data/bin/biogem

@@ -11,6 +11,7 @@ require 'rake'
 orig_argv = ARGV.clone
 # application_exit[:exit] exists, application_exit[:options] it depends.
 application_exit = Bio::Gem::Generator::Application.run!(*ARGV)
+options = application_exit[:options]
 
 if (application_exit[:exit]==0)
   pwd = FileUtils.pwd
@@ -19,7 +20,17 @@ if (application_exit[:exit]==0)
 
   Bundler::CLI.start
   #TODO: call rake directly not from shell
-  # print "Note: if rake gives an error try running biogem from an installed gem instead\n"
+ 
+  if options[:testing_framework] == :rspec
+    # Don't remove the following warning, as it may be encountered by anyone running
+    # biogem from source (especially with the --with-rspec switch)!
+    print "
+    WARNING: if rake gives an (rspec) error try running biogem from a directly 
+             installed gem instead:
+     bundle exec rake install
+     biogem [options] 
+    "
+  end
   print "\trake version:write\n"
   sh "rake version:write"
   print "\trake gemspec\n"

data/bio-gem.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-gem"
-  s.version = "1.3.2"
+  s.version = "1.3.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Raoul J.P. Bonnal", "Pjotr Prins"]
-  s.date = "2012-03-20"
+  s.date = "2012-04-07"
   s.description = "Biogem is a software generator for those bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org .\n  The basic idea is to simplify and promote a modular approach to bioinformatics software development"
   s.email = "ilpuccio.febo@gmail.com"
   s.executables = ["biogem"]
@@ -40,6 +40,7 @@ Gem::Specification.new do |s|
     "lib/bio-gem/mod/jeweler.rb",
     "lib/bio-gem/mod/jeweler/github_mixin.rb",
     "lib/bio-gem/mod/jeweler/options.rb",
+    "lib/bio-gem/templates/README.md",
     "lib/bio-gem/templates/README.rdoc",
     "lib/bio-gem/templates/bin/bio-plugin",
     "lib/bio-gem/templates/database",

data/doc/biogem-hacking.md

@@ -38,14 +38,29 @@ sure to remove the bioruby-foo directory first
       rm -rf bioruby-foo 
 ```
 
-Recommended biogem switches are --with-bin and --rspec
+Recommended biogem switches are --with-bin and --rspec, e.g.
 
 ```sh
-      bundle exec ./bin/biogem --with-bin --rspec foo
+      bundle exec ./bin/biogem --with-bin --rspec --cucumber foo
+```
+
+For a foreign function interface use
+
+```sh
+      bundle exec ./bin/biogem --with-bin --rspec --cucumber --with-ffi foo
+```
+
+There are options for ActiveRecord, Ruby on Rails etc. Naturally, you can see
+all available options with
+
+```sh
+      bundle exec ./bin/biogem --help
 ```
 
 Note that we are running biogem here within bundler. This may cause a rakefile
-error after generating the plugin (nesting bundler is not a good idea). This can simply be fixed by running the rake by hand in the plugin directory after generation
+error after generating the plugin (nesting bundler is not a good idea). This
+can simply be fixed by running the rake by hand in the plugin directory after
+generation
 
 ```sh
       cd bioruby-foo
@@ -54,8 +69,8 @@ error after generating the plugin (nesting bundler is not a good idea). This can
       bundle exec rake gemspec
 ```
 
-Alternatively, install an updated version of biogem, and run biogem without
-bundler with
+Alternatively, install an updated version of biogem on your machine as a gem,
+and run biogem without bundler with
 
 ```sh
       bundle exec rake install

data/lib/bio-gem/generator/render.rb

@@ -62,6 +62,7 @@ module Biogem
       end 
       # Always do these
       output_template_in_target_generic 'README.rdoc'
+      output_template_in_target_generic 'README.md'
       output_template_in_target_generic_append 'gitignore', '.gitignore'
       output_template_in_target_generic_append 'travis.yml', '.travis.yml'
     end

data/lib/bio-gem/mod/jeweler/options.rb

@@ -160,7 +160,7 @@ class Jeweler
             self[:homepage] = homepage
           end
 
-          o.on('--no-create-repo', 'create the repository on GitHub') do
+          o.on('--no-create-repo', 'don\'t create the repository on GitHub') do
             self[:create_repo] = false
           end
 

data/lib/bio-gem/templates/README.md

@@ -0,0 +1,48 @@
+# <%= project_name %>
+
+[![Build Status](https://secure.travis-ci.org/<%= github_username %>/<%= github_repo_name %>.png)](http://travis-ci.org/<%= github_username %>/<%= github_repo_name %>)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install <%= project_name %>
+```
+
+## Usage
+
+```ruby
+    require '<%= project_name %>'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  <%= homepage %>
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#<%= project_name %>](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) <%= Time.now.year %> <%= user_name %>. See LICENSE.txt for further details.
+
+

data/lib/bio-gem/templates/README.rdoc

@@ -1,5 +1,9 @@
 = <%= project_name %>
 
+{<img
+src="https://secure.travis-ci.org/<%= github_username %>/<%= github_repo_name %>.png"
+/>}[http://travis-ci.org/#!/<%= github_username %>/<%= github_repo_name %>]
+
 Full description goes here
 
 Note: this software is under active development!
@@ -14,7 +18,7 @@ Note: this software is under active development!
 
 To use the library 
 
-        require '<%= project_name %>
+        require '<%= project_name %>'
 
 The API doc is online. For more code examples see also the test files in
 the source tree.
@@ -25,9 +29,15 @@ Information on the source tree, documentation, issues and how to contribute, see
 
   <%= homepage %>
 
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
 == Cite
 
-  If you use this software, please cite http://dx.doi.org/10.1093/bioinformatics/btq475
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
 
 == Biogems.info
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gem
 version: !ruby/object:Gem::Version
-  version: 1.3.2
+  version: 1.3.3
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-20 00:00:00.000000000 Z
+date: 2012-04-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2153251320 !ruby/object:Gem::Requirement
+  requirement: &2152113920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 1.0.21
   type: :runtime
   prerelease: false
-  version_requirements: *2153251320
+  version_requirements: *2152113920
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2153250800 !ruby/object:Gem::Requirement
+  requirement: &2152130740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2153250800
+  version_requirements: *2152130740
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2153250260 !ruby/object:Gem::Requirement
+  requirement: &2152146720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2153250260
+  version_requirements: *2152146720
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2153249360 !ruby/object:Gem::Requirement
+  requirement: &2152142220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,7 +55,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153249360
+  version_requirements: *2152142220
 description: ! "Biogem is a software generator for those bioinformaticans who want
   to start coding an application or a library for using/extending BioRuby core library
   and sharing it through rubygems.org .\n  The basic idea is to simplify and promote
@@ -90,6 +90,7 @@ files:
 - lib/bio-gem/mod/jeweler.rb
 - lib/bio-gem/mod/jeweler/github_mixin.rb
 - lib/bio-gem/mod/jeweler/options.rb
+- lib/bio-gem/templates/README.md
 - lib/bio-gem/templates/README.rdoc
 - lib/bio-gem/templates/bin/bio-plugin
 - lib/bio-gem/templates/database