bio-logger 1.0.0 → 1.0.1

data/.travis.yml

@@ -0,0 +1,12 @@
+language: ruby
+rvm:
+  - 1.8.7
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -7,10 +7,11 @@ gem 'log4r', '>= 1.1.9'
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
+  gem "jeweler"
   gem "shoulda", ">= 0"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.5.2"
-  gem "rcov", ">= 0"
+  gem "bundler"
+  # gem "rcov", ">= 0"
   # gem "bio", ">= 1.4.1"
   gem "rspec", ">= 2.3.0"
+  gem "rdoc", ">= 3.12"
 end

data/Gemfile.lock

@@ -3,13 +3,16 @@ GEM
   specs:
     diff-lcs (1.1.2)
     git (1.2.5)
-    jeweler (1.5.2)
-      bundler (~> 1.0.0)
+    jeweler (1.8.3)
+      bundler (~> 1.0)
       git (>= 1.2.5)
       rake
+      rdoc
+    json (1.6.5)
     log4r (1.1.9)
-    rake (0.9.2)
-    rcov (0.9.9)
+    rake (0.9.2.2)
+    rdoc (3.12)
+      json (~> 1.4)
     rspec (2.6.0)
       rspec-core (~> 2.6.0)
       rspec-expectations (~> 2.6.0)
@@ -24,9 +27,9 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  bundler (~> 1.0.0)
-  jeweler (~> 1.5.2)
+  bundler
+  jeweler
   log4r (>= 1.1.9)
-  rcov
+  rdoc (>= 3.12)
   rspec (>= 2.3.0)
   shoulda

data/README.rdoc

@@ -1,7 +1,9 @@
+bio-logger is listed at http://biogems.info
+
 = bio-logger
 
 This is a plugin for nailing down problems with big data parsers,
-nowadays so common in bioinformatics, and sane handling of errors and
+so common in bioinformatics, and sane handling of errors and
 exceptions in different situations (log-act). 
 
 For example, using bio-logger, messages can be
@@ -164,6 +166,21 @@ For parsing command line options with the OptionParser:
   # Realize settings
   Bio::Log::CLI.configure('mylog')
 
+== Biogems
+
+The recommended way to use bio-logger from within a biogem is to setup a
+logger in lib/bio-gemname.rb (where you replace gemname with the name of your
+gem, of course) like so:
+
+  # bioruby-gemname/lib/bio-gemname.rb
+  require 'bio-logger'
+  Bio::Log::LoggerPlus.new('bio-gemname')
+
+Then the log can be written to anywhere within the biogem's code e.g.
+
+  log = Bio::Log::LoggerPlus['bio-gemname']
+  log.debug "a debug message"
+
 == Documentation
 
 The log4r documentation and source code can be used, as this Logger 

data/Rakefile

@@ -29,17 +29,18 @@ Jeweler::RubygemsDotOrgTasks.new
 require 'rake/testtask'
 Rake::TestTask.new(:test) do |test|
   test.libs << 'lib' << 'test'
-  test.pattern = 'test/**/test_*.rb'
+  # test.pattern = 'test/**/test_*.rb'
+  test.test_files = Dir.glob("test/**/test_*.rb")
   test.verbose = true
   Kernel.system('rspec spec/*.rb')
 end
 
-require 'rcov/rcovtask'
-Rcov::RcovTask.new do |test|
-  test.libs << '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
+# end
 
 task :default => :test
 

data/VERSION

@@ -1 +1 @@
-1.0.0
+1.0.1

data/bio-logger.gemspec

@@ -4,20 +4,21 @@
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = %q{bio-logger}
-  s.version = "1.0.0"
+  s.name = "bio-logger"
+  s.version = "1.0.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = [%q{Pjotr Prins}]
-  s.date = %q{2011-07-31}
-  s.description = %q{Log4r wrapper for BioRuby}
-  s.email = %q{pjotr.public01@thebird.nl}
+  s.authors = ["Pjotr Prins"]
+  s.date = "2012-04-02"
+  s.description = "Log4r wrapper for BioRuby"
+  s.email = "pjotr.public01@thebird.nl"
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
   ]
   s.files = [
     ".document",
+    ".travis.yml",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
@@ -37,43 +38,37 @@ Gem::Specification.new do |s|
     "test/helper.rb",
     "test/test_bio-logger.rb"
   ]
-  s.homepage = %q{https://github.com/pjotrp/bioruby-logger-plugin}
-  s.licenses = [%q{MIT}]
-  s.require_paths = [%q{lib}]
-  s.rubygems_version = %q{1.8.6}
-  s.summary = %q{Log4r wrapper with extra features for roles and sane error handling}
-  s.test_files = [
-    "spec/biologger_cli_spec.rb",
-    "spec/biologger_spec.rb",
-    "test/helper.rb",
-    "test/test_bio-logger.rb"
-  ]
+  s.homepage = "https://github.com/pjotrp/bioruby-logger-plugin"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.10"
+  s.summary = "Log4r wrapper with extra features for roles and sane error handling"
 
   if s.respond_to? :specification_version then
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<log4r>, [">= 1.1.9"])
+      s.add_development_dependency(%q<jeweler>, [">= 0"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, [">= 0"])
       s.add_development_dependency(%q<rspec>, [">= 2.3.0"])
+      s.add_development_dependency(%q<rdoc>, [">= 3.12"])
     else
       s.add_dependency(%q<log4r>, [">= 1.1.9"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
       s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bundler>, [">= 0"])
       s.add_dependency(%q<rspec>, [">= 2.3.0"])
+      s.add_dependency(%q<rdoc>, [">= 3.12"])
     end
   else
     s.add_dependency(%q<log4r>, [">= 1.1.9"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
     s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bundler>, [">= 0"])
     s.add_dependency(%q<rspec>, [">= 2.3.0"])
+    s.add_dependency(%q<rdoc>, [">= 3.12"])
   end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-logger
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-07-31 00:00:00.000000000Z
+date: 2012-04-02 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: log4r
-  requirement: &85295470 !ruby/object:Gem::Requirement
+  requirement: &20177980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.1.9
   type: :runtime
   prerelease: false
-  version_requirements: *85295470
+  version_requirements: *20177980
 - !ruby/object:Gem::Dependency
-  name: shoulda
-  requirement: &85289990 !ruby/object:Gem::Requirement
+  name: jeweler
+  requirement: &20177260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,51 +32,51 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *85289990
+  version_requirements: *20177260
 - !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: &85289160 !ruby/object:Gem::Requirement
+  name: shoulda
+  requirement: &20165560 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *85289160
+  version_requirements: *20165560
 - !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: &85288570 !ruby/object:Gem::Requirement
+  name: bundler
+  requirement: &20164820 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.5.2
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *85288570
+  version_requirements: *20164820
 - !ruby/object:Gem::Dependency
-  name: rcov
-  requirement: &85287930 !ruby/object:Gem::Requirement
+  name: rspec
+  requirement: &20164160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *85287930
+  version_requirements: *20164160
 - !ruby/object:Gem::Dependency
-  name: rspec
-  requirement: &85287260 !ruby/object:Gem::Requirement
+  name: rdoc
+  requirement: &20163380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 2.3.0
+        version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *85287260
+  version_requirements: *20163380
 description: Log4r wrapper for BioRuby
 email: pjotr.public01@thebird.nl
 executables: []
@@ -86,6 +86,7 @@ extra_rdoc_files:
 - README.rdoc
 files:
 - .document
+- .travis.yml
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -119,7 +120,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 915401137
+      hash: 1201955996654007073
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -128,12 +129,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.6
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: Log4r wrapper with extra features for roles and sane error handling
-test_files:
-- spec/biologger_cli_spec.rb
-- spec/biologger_spec.rb
-- test/helper.rb
-- test/test_bio-logger.rb
+test_files: []