bio-gem 1.2.0 → 1.2.1

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Files changed (7) hide show
  1. data/Gemfile.lock +4 -4
  2. data/README.rdoc +96 -27
  3. data/Rakefile +12 -0
  4. data/Tutorial.rdoc +1 -67
  5. data/VERSION +1 -1
  6. data/bio-gem.gemspec +15 -14
  7. metadata +24 -20
data/Gemfile.lock CHANGED
@@ -6,10 +6,10 @@ GEM
6
6
  bundler (~> 1.0)
7
7
  git (>= 1.2.5)
8
8
  rake
9
- json (1.6.1)
10
- rake (0.9.2)
11
- rcov (0.9.10)
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- rdoc (3.11)
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+ json (1.6.4)
10
+ rake (0.9.2.2)
11
+ rcov (0.9.11)
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+ rdoc (3.12)
13
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  json (~> 1.4)
14
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  shoulda (2.11.3)
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data/README.rdoc CHANGED
@@ -27,28 +27,109 @@ Also Biogem makes use of webservices. E.g.
27
27
  are two different services and you need to create different accounts for them
28
28
  if you already use GitHub.com you are set for using Biogem
29
29
 
30
- == Biogems Official Archive
30
+ == Installation
31
+
32
+ === Pre-requisites
33
+
34
+ * Ruby: Ruby: 1.9
35
+ * development and installation have been tested on 1.9.2, 1.9.3.
36
+
37
+ * RVM: RVM http://beginrescueend.com/ is optional, but suggested. Not only can you specify the Ruby interpreter version that works best with Biogem, RVM also allows multiple ruby interpreters in your home directory for testing purposes. When using RVM, make sure to compile with openssl support, e.g. on Debian
38
+ $ sudo apt-get install libssl-dev
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+ $ rvm install 1.9.3 --with-openssl-dir=$HOME/.rvm/usr
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+
41
+ * GitHub & RubyGems: In order to use Biogem to its fullest potential, you must create a regular GitHub http://github.com and RubyGems http://rubygems.org account. Why? Because for sharing and keeping track of source code we (currenlty) use github and for distributing the plugin we rely on RubyGems, the reference Ruby gem repository. To configure github and automate most of Biogem's tasks:
42
+ $ git config --global user.name "Firstname Lastname" Sets the name of the user for all git instances on the system
43
+ $ git config --global user.email "your_email@youremail.com"
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+ $ git config --global github.user "user_id"
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+ $ git config --global github.token "TOKEN ASSIGNED BY GITHUB"
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+
47
+ Note: another Ruby version management system used in BioRuby community is https://github.com/sstephenson/rbenv but for now we can not provide support for it.
48
+ ==== IMPORTANT NOTE
49
+ Rubygems will not let you install Biogem in an environment with a Ruby interpreter older than 1.9.X
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+
51
+ === Download
52
+
53
+ Install the Biogem toolset with
54
+
55
+ $ gem install bio-gem
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+
57
+ all the required dependencies will be downloaded and installed automatically.
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+
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+ $ gem install bio-gem
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+ Fetching: rake-0.9.2.2.gem (100%)
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+ Fetching: git-1.2.5.gem (100%)
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+ Fetching: jeweler-1.6.4.gem (100%)
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+ Fetching: json-1.6.4.gem (100%)
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+ Building native extensions. This could take a while...
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+ Fetching: rdoc-3.12.gem (100%)
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+ Depending on your version of ruby, you may need to install ruby rdoc/ri data:
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+ <= 1.8.6 : unsupported
68
+ = 1.8.7 : gem install rdoc-data; rdoc-data --install
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+ = 1.9.1 : gem install rdoc-data; rdoc-data --install
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+ >= 1.9.2 : nothing to do! Yay!
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+ Fetching: bio-gem-1.2.0.gem (100%)
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+ Successfully installed rake-0.9.2.2
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+ Successfully installed git-1.2.5
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+ Successfully installed jeweler-1.6.4
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+ Successfully installed json-1.6.4
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+ Successfully installed rdoc-3.12
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+ Successfully installed bio-gem-1.2.0
78
+ 6 gems installed
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+ Installing ri documentation for rake-0.9.2.2...
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+ Installing ri documentation for git-1.2.5...
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+ Installing ri documentation for jeweler-1.6.4...
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+ Installing ri documentation for json-1.6.4...
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+ Installing ri documentation for rdoc-3.12...
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+ Installing ri documentation for bio-gem-1.2.0...
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+ Installing RDoc documentation for rake-0.9.2.2...
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+ Installing RDoc documentation for git-1.2.5...
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+ Installing RDoc documentation for jeweler-1.6.4...
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+ Installing RDoc documentation for json-1.6.4...
89
+ Installing RDoc documentation for rdoc-3.12...
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+ Installing RDoc documentation for bio-gem-1.2.0...
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+
92
+ Note: the above list of dependencies is just an example and it may vary from your current installation.
93
+
94
+ == Browse the documentation
95
+
96
+ During the installation you may note how Rubygems install the documentation for you, for each library installed.
97
+ Is possible to access to all the documentations and API installed simply typing in the command line:
98
+ $ gem server
99
+ Server started at http://0.0.0.0:8808
100
+ Server started at http://[::ffff:0.0.0.0]:8808
101
+
102
+ To see Biogem documentation locally use this link:
103
+ http://localhost:8808/doc_root/bio-gem-1.2.0/rdoc/README_rdoc.html
104
+
105
+ Note: the above link must be update with your current version of Biogem
106
+
107
+ == Biogem Tutorial HowTo Develop a plugins
108
+
109
+ Please follow the guide reported in tutorial https://github.com/helios/bioruby-gem/blob/master/Tutorial.rdoc, which is the most up to date version.
110
+ You'll find out how to create:
111
+ * a simple plugin
112
+ * embed a database
113
+ * create a Biogem Engine to embed your gem into a Ruby on Rails web application
114
+ and much more
31
115
 
32
- * http://biogems.info/
33
116
 
34
- == Biogem Tutorial
117
+ == Biogems Official Archive
35
118
 
36
- The latest version is on https://github.com/helios/bioruby-gem/blob/master/Tutorial.rdoc
119
+ * http://biogems.info
37
120
 
38
121
  == Contributing to Biogem
39
122
 
40
123
  The source code repositories for Biogem and http://biogems.info
41
- website are on github. If you want to contribute, feel free! Clone the
124
+ website are on github.
125
+ * https://github.com/helios/bioruby-gem
126
+ * https://github.com/pjotrp/biogems.info
127
+ If you want to contribute, feel free! Clone the
42
128
  project!
43
129
 
44
- === StepByStep
45
-
46
- Toshiaki Katayama wrote a step by step guide for a bio-foobar plugin @ http://bioruby.open-bio.org/wiki/BiogemInstallation.
47
-
48
130
  == BioRuby's Wiki Official Documentation
49
131
 
50
132
  * http://bioruby.open-bio.org/wiki/Plugins
51
- * http://biogems.info/ official collector for BioRuby plugins
52
133
 
53
134
  == Biogem options
54
135
 
@@ -57,17 +138,13 @@ Usage: biogem [options] reponame
57
138
  e.g. biogem the-perfect-gem
58
139
 
59
140
  --directory [DIRECTORY] specify the directory to generate into
60
-
61
- These options are for BioGem
62
-
63
- --meta create a meta package, just the Rakefile, Gemfile, Licence, Readme. This options takes the precedence over every other option.
141
+ These options are for BioGem
142
+ --meta create a meta package, just the Rakefile, Gemfile, Licence, Readme. This options takes the precedence over every other option.
64
143
  --with-bin create the bin directory and an executable template script called bioreponame
65
144
  --with-db create the database directory for a db application-library.
66
145
  --with-test-data create the data directory inside the test directory if the user need to set up a test with its own dataset
67
146
  --with-engine [NAMESPACE] create a Rails engine with the namespace given in input. Set default database creation
68
-
69
- These options are for Jeweler
70
-
147
+ These options are for Jeweler
71
148
  --rspec generate rspec code examples
72
149
  --shoulda generate shoulda tests
73
150
  --testunit generate test/unit tests
@@ -77,27 +154,19 @@ These options are for Jeweler
77
154
  --micronaut generate micronaut examples
78
155
  --riot generate riot tests
79
156
  --shindo generate shindo tests
80
-
81
157
  --[no-]bundler use bundler for managing dependencies
82
158
  --cucumber generate cucumber stories in addition to the other tests
83
-
84
159
  --reek generate rake task for reek
85
160
  --roodi generate rake task for roodi
86
-
87
161
  --summary [SUMMARY] specify the summary of the project
88
162
  --description [DESCRIPTION] specify a description of the project
89
-
90
163
  --user-name [USER_NAME] the user's name, ie that is credited in the LICENSE
91
164
  --user-email [USER_EMAIL] the user's email, ie that is credited in the Gem specification
92
-
93
- --github-username [GITHUB_USERNAME]
94
- name of the user on GitHub to set the project up under
95
- --github-token [GITHUB_TOKEN]
96
- GitHub token to use for interacting with the GitHub API
165
+ --github-username [GITHUB_USERNAME] name of the user on GitHub to set the project up under
166
+ --github-token [GITHUB_TOKEN] GitHub token to use for interacting with the GitHub API
97
167
  --git-remote [GIT_REMOTE] URI to set the git origin remote to
98
168
  --homepage [HOMEPAGE] the homepage for your project (defaults to the GitHub repo)
99
169
  --no-create-repo create the repository on GitHub
100
-
101
170
  --yard use yard for documentation
102
171
  --rdoc use rdoc for documentation
103
172
  -h, --help display this help and exit
data/Rakefile CHANGED
@@ -23,8 +23,20 @@ Jeweler::Tasks.new do |gem|
23
23
  # Include your dependencies below. Runtime dependencies are required when using your gem,
24
24
  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
25
25
  #gem.version='0.0.1'
26
+ gem.rdoc_options << '--main' << 'README' << '--line-numbers'
26
27
  gem.required_ruby_version = "~>1.9"
28
+ gem.extra_rdoc_files = ['LICENSE.txt', 'README.rdoc','Tutorial.rdoc']
27
29
  end
30
+
31
+
32
+
33
+ # # Ricordati ti aggiungere README e Tutorial
34
+ # # spec.extra_rdoc_files = ['README', 'doc/user-guide.txt']
35
+ #
36
+ # def extra_rdoc_files
37
+ # @extra_rdoc_files ||= []
38
+ # end
39
+ #
28
40
  Jeweler::RubygemsDotOrgTasks.new
29
41
 
30
42
  require 'rake/testtask'
data/Tutorial.rdoc CHANGED
@@ -1,67 +1,5 @@
1
1
  = Biogem Tutorial
2
2
 
3
- The latest version of this document is on https://github.com/helios/bioruby-gem/blob/master/Tutorial.rdoc
4
-
5
- == Installation
6
-
7
- === Pre-requisites
8
-
9
- * Ruby: at least 1.9.x, current tested version is 1.9.2, moving to 1.9.3
10
-
11
- * RVM: RVM http://beginrescueend.com/ is optional, but suggested. Not only can you specify the Ruby interpreter version that works best with Biogem, RVM also allows multiple ruby interpreters in your home directory for testing purposes. When using RVM, make sure to compile with openssl support, e.g. on Debian
12
-
13
- $ sudo apt-get install libssl-dev
14
- $ rvm install 1.9.3 --with-openssl-dir=$HOME/.rvm/usr
15
-
16
- * GitHub & RubyGems: In order to use Biogem to its fullest potential, you must create a regular GitHub http://github.com and RubyGems http://rubygems.org account. Why? Because for sharing and keeping track of source code we (currenlty) use github and for distributing the plugin we rely on RubyGems, the reference Ruby gem repository. To configure github and automate most of Biogem's tasks:
17
-
18
- $ git config --global user.name "Firstname Lastname" Sets the name of the user for all git instances on the system
19
- $ git config --global user.email "your_email@youremail.com"
20
- $ git config --global github.user "user_id"
21
- $ git config --global github.token "TOKEN ASSIGNED BY GITHUB"
22
-
23
- Note: another Ruby version management system used in BioRuby community is https://github.com/sstephenson/rbenv but for now we can not provide support for it.
24
-
25
- === Download
26
-
27
- Install the Biogem toolset with
28
-
29
- $ gem install bio-gem
30
-
31
- all the required dependencies will be downloaded and installed automatically.
32
-
33
- Fetching: bundler-1.0.21.gem (100%)
34
- Fetching: git-1.2.5.gem (100%)
35
- Fetching: jeweler-1.6.4.gem (100%)
36
- Fetching: json-1.6.3.gem (100%)
37
- Building native extensions. This could take a while...
38
- Fetching: rdoc-3.11.gem (100%)
39
- Depending on your version of ruby, you may need to install ruby rdoc/ri data:
40
- <= 1.8.6 : unsupported
41
- = 1.8.7 : gem install rdoc-data; rdoc-data --install
42
- = 1.9.1 : gem install rdoc-data; rdoc-data --install
43
- >= 1.9.2 : nothing to do! Yay!
44
- Fetching: bio-gem-1.1.2.gem (100%)
45
- Successfully installed bundler-1.0.21
46
- Successfully installed git-1.2.5
47
- Successfully installed jeweler-1.6.4
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- Successfully installed json-1.6.3
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- Successfully installed rdoc-3.11
50
- Successfully installed bio-gem-1.1.2
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- 6 gems installed
52
- Installing ri documentation for bundler-1.0.21...
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- Installing ri documentation for git-1.2.5...
54
- Installing ri documentation for jeweler-1.6.4...
55
- Installing ri documentation for json-1.6.3...
56
- Installing ri documentation for rdoc-3.11...
57
- Installing ri documentation for bio-gem-1.1.2...
58
- Installing RDoc documentation for bundler-1.0.21...
59
- Installing RDoc documentation for git-1.2.5...
60
- Installing RDoc documentation for jeweler-1.6.4...
61
- Installing RDoc documentation for json-1.6.3...
62
- Installing RDoc documentation for rdoc-3.11...
63
- Installing RDoc documentation for bio-gem-1.1.2...
64
-
65
3
  == Create your first BioRuby Plugin
66
4
 
67
5
  === Standard
@@ -514,13 +452,9 @@ which guarantees that all the called programs/tasks will be executed inside the
514
452
 
515
453
  * http://bioruby.open-bio.org/wiki/Plugins
516
454
 
517
- === StepByStep
518
-
519
- Toshiaki Katayama wrote a step by step guide for a bio-foobar plugin @ http://bioruby.open-bio.org/wiki/BiogemInstallation; note this information could be older than this.
520
-
521
455
  == Biogem Official Plugin Archive
522
456
 
523
- * http://biogems.info/
457
+ * http://biogems.info
524
458
 
525
459
  == TODO
526
460
 
data/VERSION CHANGED
@@ -1 +1 @@
1
- 1.2.0
1
+ 1.2.1
data/bio-gem.gemspec CHANGED
@@ -4,19 +4,19 @@
4
4
  # -*- encoding: utf-8 -*-
5
5
 
6
6
  Gem::Specification.new do |s|
7
- s.name = %q{bio-gem}
8
- s.version = "1.2.0"
7
+ s.name = "bio-gem"
8
+ s.version = "1.2.1"
9
9
 
10
10
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
- s.authors = [%q{Raoul J.P. Bonnal}]
12
- s.date = %q{2012-01-04}
13
- s.description = %q{BioGem is a scaffold 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 .
14
- The basic idea is to simplify and promote a modular approach to the BioRuby package.}
15
- s.email = %q{ilpuccio.febo@gmail.com}
16
- s.executables = [%q{biogem}]
11
+ s.authors = ["Raoul J.P. Bonnal"]
12
+ s.date = "2012-01-05"
13
+ s.description = "BioGem is a scaffold 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 the BioRuby package."
14
+ s.email = "ilpuccio.febo@gmail.com"
15
+ s.executables = ["biogem"]
17
16
  s.extra_rdoc_files = [
18
17
  "LICENSE.txt",
19
- "README.rdoc"
18
+ "README.rdoc",
19
+ "Tutorial.rdoc"
20
20
  ]
21
21
  s.files = [
22
22
  ".document",
@@ -53,12 +53,13 @@ Gem::Specification.new do |s|
53
53
  "test/helper.rb",
54
54
  "test/test_bio-gem.rb"
55
55
  ]
56
- s.homepage = %q{http://github.com/helios/bioruby-gem}
57
- s.licenses = [%q{MIT}]
58
- s.require_paths = [%q{lib}]
56
+ s.homepage = "http://github.com/helios/bioruby-gem"
57
+ s.licenses = ["MIT"]
58
+ s.rdoc_options = ["--main", "README", "--line-numbers"]
59
+ s.require_paths = ["lib"]
59
60
  s.required_ruby_version = Gem::Requirement.new("~> 1.9")
60
- s.rubygems_version = %q{1.8.6}
61
- s.summary = %q{BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package}
61
+ s.rubygems_version = "1.8.10"
62
+ s.summary = "BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package"
62
63
 
63
64
  if s.respond_to? :specification_version then
64
65
  s.specification_version = 3
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-gem
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.2.0
4
+ version: 1.2.1
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -9,11 +9,11 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2012-01-04 00:00:00.000000000Z
12
+ date: 2012-01-05 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: bundler
16
- requirement: &2154411360 !ruby/object:Gem::Requirement
16
+ requirement: &2164563920 !ruby/object:Gem::Requirement
17
17
  none: false
18
18
  requirements:
19
19
  - - ~>
@@ -21,10 +21,10 @@ dependencies:
21
21
  version: 1.0.18
22
22
  type: :runtime
23
23
  prerelease: false
24
- version_requirements: *2154411360
24
+ version_requirements: *2164563920
25
25
  - !ruby/object:Gem::Dependency
26
26
  name: jeweler
27
- requirement: &2154410260 !ruby/object:Gem::Requirement
27
+ requirement: &2164579040 !ruby/object:Gem::Requirement
28
28
  none: false
29
29
  requirements:
30
30
  - - ~>
@@ -32,10 +32,10 @@ dependencies:
32
32
  version: 1.6.4
33
33
  type: :runtime
34
34
  prerelease: false
35
- version_requirements: *2154410260
35
+ version_requirements: *2164579040
36
36
  - !ruby/object:Gem::Dependency
37
37
  name: rdoc
38
- requirement: &2154399520 !ruby/object:Gem::Requirement
38
+ requirement: &2164578060 !ruby/object:Gem::Requirement
39
39
  none: false
40
40
  requirements:
41
41
  - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
43
43
  version: '0'
44
44
  type: :runtime
45
45
  prerelease: false
46
- version_requirements: *2154399520
46
+ version_requirements: *2164578060
47
47
  - !ruby/object:Gem::Dependency
48
48
  name: shoulda
49
- requirement: &2154398380 !ruby/object:Gem::Requirement
49
+ requirement: &2164576000 !ruby/object:Gem::Requirement
50
50
  none: false
51
51
  requirements:
52
52
  - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
54
54
  version: '0'
55
55
  type: :development
56
56
  prerelease: false
57
- version_requirements: *2154398380
57
+ version_requirements: *2164576000
58
58
  - !ruby/object:Gem::Dependency
59
59
  name: bundler
60
- requirement: &2154395340 !ruby/object:Gem::Requirement
60
+ requirement: &2164574520 !ruby/object:Gem::Requirement
61
61
  none: false
62
62
  requirements:
63
63
  - - ~>
@@ -65,10 +65,10 @@ dependencies:
65
65
  version: 1.0.18
66
66
  type: :development
67
67
  prerelease: false
68
- version_requirements: *2154395340
68
+ version_requirements: *2164574520
69
69
  - !ruby/object:Gem::Dependency
70
70
  name: jeweler
71
- requirement: &2154393980 !ruby/object:Gem::Requirement
71
+ requirement: &2164573360 !ruby/object:Gem::Requirement
72
72
  none: false
73
73
  requirements:
74
74
  - - ~>
@@ -76,10 +76,10 @@ dependencies:
76
76
  version: 1.6.4
77
77
  type: :development
78
78
  prerelease: false
79
- version_requirements: *2154393980
79
+ version_requirements: *2164573360
80
80
  - !ruby/object:Gem::Dependency
81
81
  name: rcov
82
- requirement: &2154392880 !ruby/object:Gem::Requirement
82
+ requirement: &2164572440 !ruby/object:Gem::Requirement
83
83
  none: false
84
84
  requirements:
85
85
  - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
87
87
  version: '0'
88
88
  type: :development
89
89
  prerelease: false
90
- version_requirements: *2154392880
90
+ version_requirements: *2164572440
91
91
  - !ruby/object:Gem::Dependency
92
92
  name: rdoc
93
- requirement: &2154391820 !ruby/object:Gem::Requirement
93
+ requirement: &2164571480 !ruby/object:Gem::Requirement
94
94
  none: false
95
95
  requirements:
96
96
  - - ! '>='
@@ -98,7 +98,7 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
101
- version_requirements: *2154391820
101
+ version_requirements: *2164571480
102
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  description: ! "BioGem is a scaffold generator for those Bioinformaticans who want
103
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  to start coding an application or a library for using/extending BioRuby core library
104
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  and sharing it through rubygems.org .\n The basic idea is to simplify and promote
@@ -110,6 +110,7 @@ extensions: []
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  extra_rdoc_files:
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  - LICENSE.txt
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  - README.rdoc
113
+ - Tutorial.rdoc
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  files:
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  - .document
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  - Gemfile
@@ -148,7 +149,10 @@ homepage: http://github.com/helios/bioruby-gem
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  licenses:
149
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  - MIT
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  post_install_message:
151
- rdoc_options: []
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+ rdoc_options:
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+ - --main
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+ - README
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+ - --line-numbers
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  require_paths:
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  - lib
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  required_ruby_version: !ruby/object:Gem::Requirement
@@ -165,7 +169,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 1.8.6
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+ rubygems_version: 1.8.10
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  signing_key:
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  specification_version: 3
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  summary: BioGem helps Bioinformaticians start developing plugins/modules for BioRuby