unipept 1.0.0 → 1.0.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -11,5 +11,5 @@ group :development do
   gem 'minitest', '~> 5.7'
   gem 'rubocop', '~>0.32'
   gem 'jeweler', '~> 2.0'
-  gem 'coveralls', require: false
+  gem 'coveralls', '~> 0', require: false
 end

data/Gemfile.lock

@@ -103,7 +103,7 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  coveralls
+  coveralls (~> 0)
   cri (~> 2.7)
   jeweler (~> 2.0)
   minitest (~> 5.7)

data/README.md

@@ -6,7 +6,7 @@
 [![Code Climate](https://codeclimate.com/github/unipept/unipept-cli/badges/gpa.svg)](https://codeclimate.com/github/unipept/unipept-cli)
 
 Unipept-cli offers a command line interface to the [Unipept](http://unipept.ugent.be) web service.
-Documentation about the web service can be found at [http://unipept.ugent.be/apidocs](http://unipept.ugent.be/apidocs).
+Documentation about the web service can be found at [http://unipept.ugent.be/apidocs](http://unipept.ugent.be/apidocs), documentation about the command line tools at [http://unipept.ugent.be/clidocs](http://unipept.ugent.be/clidocs).
 
 ## Installation
 
@@ -14,7 +14,7 @@ To use the Unipept CLI, Ruby version 1.9.3 or higher needs to be installed. You
 
 ```
 $ ruby -v
-ruby 2.1.6p336 (2015-04-13 revision 50298) [x86_64-darwin14.0]
+ruby 2.2.2p95 (2015-04-13 revision 50295) [x86_64-darwin14]
 ```
 
 More information on installing Ruby can be found at https://www.ruby-lang.org/en/installation/
@@ -23,8 +23,8 @@ The Unipept CLI is available as a *gem*. This means it can easily be installed w
 
 ```bash
 $ gem install unipept
-Successfully installed unipept-0.10.0
-Parsing documentation for unipept-0.10.0
+Successfully installed unipept-1.0.1
+Parsing documentation for unipept-1.0.1
 Done installing documentation for unipept after 0 seconds
 1 gem installed
 ```
@@ -33,7 +33,7 @@ After successful installation, the unipept command should be available:
 
 ```bash
 $ unipept -v
-0.10.0
+1.0.1
 ```
 
 The help can be accessed by running `unipept -h`.

data/Rakefile

@@ -18,13 +18,13 @@ Jeweler::Tasks.new do |gem|
   # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
   gem.name = 'unipept'
   gem.executables = %w(unipept prot2pept peptfilter uniprot)
-  gem.homepage = 'https://github.com/unipept/unipept-cli/'
+  gem.homepage = 'http://unipept.ugent.be'
   gem.license = 'MIT'
   gem.summary = 'Command line interface to Unipept web services.'
   gem.description = <<-EOS
   Command line interface to the Unipept (http://unipept.ugent.be) web services
-  (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility commands for
-  handling proteins using the command line.
+  (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
+  commands for handling proteins using the command line.
   EOS
   gem.email = 'unipept@ugent.be'
   gem.authors = ['Toon Willems', 'Bart Mesuere', 'Tom Naessens']

data/VERSION

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

data/lib/commands/peptfilter.rb

@@ -20,7 +20,8 @@ module Unipept::Commands
         puts cmd.help
         exit 0
       end
-      run do |opts, _args, _cmd|
+      run do |opts, args, _cmd|
+        abort "error: peptfilter doesn't support input as arguments. Use standard input instead." unless args.empty?
         minlen = opts.fetch(:minlen, '5').to_i
         maxlen = opts.fetch(:maxlen, '50').to_i
         lacks = opts.fetch(:lacks, '').chars.to_a
@@ -38,8 +39,6 @@ module Unipept::Commands
       end
     end
 
-    @root_command.add_command(Cri::Command.new_basic_help)
-
     # Invokes the peptfilter command-line tool with the given arguments.
     #
     # @param [Array<String>] args An array of command-line arguments

data/test/commands/test_peptfilter.rb

@@ -151,6 +151,16 @@ module Unipept
       assert_equal(">\nAALTER\n>", out.chomp)
     end
 
+    def test_no_input
+      out, err = capture_io_while do
+        assert_raises SystemExit do
+          Commands::Peptfilter.run(%w(some argument))
+        end
+      end
+      assert_equal('', out.chomp)
+      assert_equal("error: peptfilter doesn't support input as arguments. Use standard input instead.", err.chomp)
+    end
+
     def test_normal_input
       out, _err = capture_io_with_input(['A', 'A' * 11, 'AAAAB', 'BBBBB', 'CCCCC', 'CCCCCA']) do
         Commands::Peptfilter.run(%w(--minlen 4 --maxlen 10 --lacks B --contains A))

data/unipept.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 1.0.0 ruby lib
+# stub: unipept 1.0.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept"
-  s.version = "1.0.0"
+  s.version = "1.0.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
-  s.date = "2015-07-14"
-  s.description = "  Command line interface to the Unipept (http://unipept.ugent.be) web services\n  (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility commands for\n  handling proteins using the command line.\n"
+  s.date = "2015-07-31"
+  s.description = "  Command line interface to the Unipept (http://unipept.ugent.be) web services\n  (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility\n  commands for handling proteins using the command line.\n"
   s.email = "unipept@ugent.be"
   s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]
   s.extra_rdoc_files = [
@@ -74,7 +74,7 @@ Gem::Specification.new do |s|
     "test/test_server_message.rb",
     "unipept.gemspec"
   ]
-  s.homepage = "https://github.com/unipept/unipept-cli/"
+  s.homepage = "http://unipept.ugent.be"
   s.licenses = ["MIT"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.3")
   s.rubygems_version = "2.4.8"
@@ -90,7 +90,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<minitest>, ["~> 5.7"])
       s.add_development_dependency(%q<rubocop>, ["~> 0.32"])
       s.add_development_dependency(%q<jeweler>, ["~> 2.0"])
-      s.add_development_dependency(%q<coveralls>, [">= 0"])
+      s.add_development_dependency(%q<coveralls>, ["~> 0"])
     else
       s.add_dependency(%q<cri>, ["~> 2.7"])
       s.add_dependency(%q<typhoeus>, ["= 0.7.2"])
@@ -98,7 +98,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<minitest>, ["~> 5.7"])
       s.add_dependency(%q<rubocop>, ["~> 0.32"])
       s.add_dependency(%q<jeweler>, ["~> 2.0"])
-      s.add_dependency(%q<coveralls>, [">= 0"])
+      s.add_dependency(%q<coveralls>, ["~> 0"])
     end
   else
     s.add_dependency(%q<cri>, ["~> 2.7"])
@@ -107,7 +107,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<minitest>, ["~> 5.7"])
     s.add_dependency(%q<rubocop>, ["~> 0.32"])
     s.add_dependency(%q<jeweler>, ["~> 2.0"])
-    s.add_dependency(%q<coveralls>, [">= 0"])
+    s.add_dependency(%q<coveralls>, ["~> 0"])
   end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.1
 platform: ruby
 authors:
 - Toon Willems
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-14 00:00:00.000000000 Z
+date: 2015-07-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri
@@ -100,20 +100,20 @@ dependencies:
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '0'
 description: |2
     Command line interface to the Unipept (http://unipept.ugent.be) web services
-    (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility commands for
-    handling proteins using the command line.
+    (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
+    commands for handling proteins using the command line.
 email: unipept@ugent.be
 executables:
 - unipept
@@ -178,7 +178,7 @@ files:
 - test/test_retryable_typhoeus.rb
 - test/test_server_message.rb
 - unipept.gemspec
-homepage: https://github.com/unipept/unipept-cli/
+homepage: http://unipept.ugent.be
 licenses:
 - MIT
 metadata: {}