unipept 1.1.2 → 1.1.3

data/test/commands/unipept/test_taxa2lca.rb

@@ -22,14 +22,14 @@ module Unipept
           Commands::Unipept.run(%w(taxa2lca -h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
           Commands::Unipept.run(%w(taxa2lca --help))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
 
     def test_run
@@ -38,8 +38,8 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'taxon_id,taxon_name,taxon_rank')
-      assert(lines.next.start_with? '1678,Bifidobacterium,genus')
+      assert(lines.next.start_with?('taxon_id,taxon_name,taxon_rank'))
+      assert(lines.next.start_with?('1678,Bifidobacterium,genus'))
     end
 
     def test_run_xml
@@ -49,8 +49,8 @@ module Unipept
       lines = out.each_line
       output = lines.to_a.join('').chomp
       assert_equal('', err)
-      assert(output.start_with? '<results>')
-      assert(output.end_with? '</results>')
+      assert(output.start_with?('<results>'))
+      assert(output.end_with?('</results>'))
     end
 
     def test_run_json
@@ -60,8 +60,8 @@ module Unipept
       lines = out.each_line
       output = lines.to_a.join('').chomp
       assert_equal('', err)
-      assert(output.start_with? '[')
-      assert(output.end_with? ']')
+      assert(output.start_with?('['))
+      assert(output.end_with?(']'))
       assert(!output.include?('}{'))
       assert(!output.include?(']['))
     end

data/test/commands/unipept/test_taxonomy.rb

@@ -20,14 +20,14 @@ module Unipept
           Commands::Unipept.run(%w(taxonomy -h))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
 
       out, _err = capture_io_while do
         assert_raises SystemExit do
           Commands::Unipept.run(%w(taxonomy --help))
         end
       end
-      assert(out.include? 'show help for this command')
+      assert(out.include?('show help for this command'))
     end
 
     def test_run
@@ -36,8 +36,8 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'taxon_id,taxon_name,taxon_rank')
-      assert(lines.next.start_with? '1,root,no rank')
+      assert(lines.next.start_with?('taxon_id,taxon_name,taxon_rank'))
+      assert(lines.next.start_with?('1,root,no rank'))
     end
 
     def test_run_with_fasta_multiple_batches
@@ -46,7 +46,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'fasta_header,taxon_id,taxon_name,taxon_rank')
+      assert(lines.next.start_with?('fasta_header,taxon_id,taxon_name,taxon_rank'))
       assert(lines.count { |line| line.start_with? '>test,1,' } >= 1)
       assert(lines.count { |line| line.start_with? '>test,216816,' } >= 1)
       assert(lines.count { |line| line.start_with? '>tost,1,' } >= 1)
@@ -58,7 +58,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      assert(lines.next.start_with? 'fasta_header,taxon_id,taxon_name')
+      assert(lines.next.start_with?('fasta_header,taxon_id,taxon_name'))
       assert(lines.count { |line| line.start_with? '>test,1,' } >= 1)
       assert(lines.count { |line| line.start_with? '>test,216816,' } >= 1)
       assert(lines.count { |line| line.start_with? '>tost,1,' } >= 1)
@@ -71,10 +71,10 @@ module Unipept
       lines = out.each_line
       assert_equal('', err)
       output = lines.to_a.join('').chomp
-      assert(output.start_with? '[')
-      assert(output.end_with? ']')
+      assert(output.start_with?('['))
+      assert(output.end_with?(']'))
       assert(!output.include?('}{'))
-      assert(output.include? 'fasta_header')
+      assert(output.include?('fasta_header'))
     end
 
     def test_run_with_fasta_multiple_batches_xml
@@ -84,9 +84,9 @@ module Unipept
       lines = out.each_line
       assert_equal('', err)
       output = lines.to_a.join('').chomp
-      assert(output.start_with? '<results>')
-      assert(output.end_with? '</results>')
-      assert(output.include? '<fasta_header>')
+      assert(output.start_with?('<results>'))
+      assert(output.end_with?('</results>'))
+      assert(output.include?('<fasta_header>'))
     end
   end
 end

data/test/helper.rb

@@ -33,18 +33,18 @@ module Unipept
       FileUtils.rm_rf(@tmp_dir)
     end
 
-    def capture_io_with_input(input, &block)
+    def capture_io_with_input(input)
       capture_io_while do
         input = input.join("\n") if input.is_a? Array
         $stdin.write(input)
         $stdin.rewind
-        block.call
+        yield
       end
     end
 
-    def capture_io_while(&block)
+    def capture_io_while
       orig_io = capture_io
-      block.call
+      yield
       [$stdout.string, $stderr.string]
     ensure
       uncapture_io(*orig_io)

data/test/test_batch_iterator.rb

@@ -9,7 +9,7 @@ module Unipept
 
     def test_fasta
       iterator = BatchIterator.new(50)
-      assert(iterator.fasta? '> test')
+      assert(iterator.fasta?('> test'))
       assert(!(iterator.fasta? '< test'))
       assert(!(iterator.fasta? 'test'))
     end

data/test/test_formatters.rb

@@ -4,9 +4,9 @@ module Unipept
   class FormattersTestCase < Unipept::TestCase
     def test_available_formatters
       formatters = Formatter.available
-      assert(formatters.include? 'json')
-      assert(formatters.include? 'csv')
-      assert(formatters.include? 'xml')
+      assert(formatters.include?('json'))
+      assert(formatters.include?('csv'))
+      assert(formatters.include?('xml'))
     end
 
     def test_default_formatter
@@ -16,7 +16,7 @@ module Unipept
     def test_formatter_registration
       assert(!(Formatter.available.include? 'test'))
       Formatter.register(:test)
-      assert(Formatter.available.include? 'test')
+      assert(Formatter.available.include?('test'))
     end
 
     def test_new_for_format
@@ -73,6 +73,7 @@ module Unipept
       def f.integrate_fasta_headers(_a, _b)
         puts 'header'
       end
+
       def f.convert(_a, _b)
         'body'
       end

data/unipept.gemspec

@@ -2,19 +2,19 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 1.1.2 ruby lib
+# stub: unipept 1.1.3 ruby lib
 
 Gem::Specification.new do |s|
-  s.name = "unipept"
-  s.version = "1.1.2"
+  s.name = "unipept".freeze
+  s.version = "1.1.3"
 
-  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.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib".freeze]
+  s.authors = ["Toon Willems".freeze, "Bart Mesuere".freeze, "Tom Naessens".freeze]
   s.date = "2017-01-17"
-  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.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".freeze
+  s.email = "unipept@ugent.be".freeze
+  s.executables = ["unipept".freeze, "prot2pept".freeze, "peptfilter".freeze, "uniprot".freeze]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.md"
@@ -22,6 +22,7 @@ Gem::Specification.new do |s|
   s.files = [
     ".document",
     ".rubocop.yml",
+    ".ruby-version",
     ".travis.yml",
     "Gemfile",
     "Gemfile.lock",
@@ -74,40 +75,37 @@ Gem::Specification.new do |s|
     "test/test_server_message.rb",
     "unipept.gemspec"
   ]
-  s.homepage = "http://unipept.ugent.be"
-  s.licenses = ["MIT"]
-  s.required_ruby_version = Gem::Requirement.new(">= 2.0.0")
-  s.rubygems_version = "2.4.8"
-  s.summary = "Command line interface to Unipept web services."
+  s.homepage = "http://unipept.ugent.be".freeze
+  s.licenses = ["MIT".freeze]
+  s.required_ruby_version = Gem::Requirement.new(">= 2.0.0".freeze)
+  s.rubygems_version = "2.6.8".freeze
+  s.summary = "Command line interface to Unipept web services.".freeze
 
   if s.respond_to? :specification_version then
     s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<cri>, ["~> 2.7"])
-      s.add_runtime_dependency(%q<typhoeus>, ["= 0.7.2"])
-      s.add_development_dependency(%q<rake>, ["~> 10.4"])
-      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_runtime_dependency(%q<cri>.freeze, ["~> 2.7"])
+      s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.1"])
+      s.add_development_dependency(%q<rake>.freeze, ["~> 10.4"])
+      s.add_development_dependency(%q<minitest>.freeze, ["~> 5.7"])
+      s.add_development_dependency(%q<rubocop>.freeze, ["~> 0.32"])
+      s.add_development_dependency(%q<coveralls>.freeze, ["~> 0"])
     else
-      s.add_dependency(%q<cri>, ["~> 2.7"])
-      s.add_dependency(%q<typhoeus>, ["= 0.7.2"])
-      s.add_dependency(%q<rake>, ["~> 10.4"])
-      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<cri>.freeze, ["~> 2.7"])
+      s.add_dependency(%q<typhoeus>.freeze, ["~> 1.1"])
+      s.add_dependency(%q<rake>.freeze, ["~> 10.4"])
+      s.add_dependency(%q<minitest>.freeze, ["~> 5.7"])
+      s.add_dependency(%q<rubocop>.freeze, ["~> 0.32"])
+      s.add_dependency(%q<coveralls>.freeze, ["~> 0"])
     end
   else
-    s.add_dependency(%q<cri>, ["~> 2.7"])
-    s.add_dependency(%q<typhoeus>, ["= 0.7.2"])
-    s.add_dependency(%q<rake>, ["~> 10.4"])
-    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<cri>.freeze, ["~> 2.7"])
+    s.add_dependency(%q<typhoeus>.freeze, ["~> 1.1"])
+    s.add_dependency(%q<rake>.freeze, ["~> 10.4"])
+    s.add_dependency(%q<minitest>.freeze, ["~> 5.7"])
+    s.add_dependency(%q<rubocop>.freeze, ["~> 0.32"])
+    s.add_dependency(%q<coveralls>.freeze, ["~> 0"])
   end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.1.3
 platform: ruby
 authors:
 - Toon Willems
@@ -30,16 +30,16 @@ dependencies:
   name: typhoeus
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.7.2
+        version: '1.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.7.2
+        version: '1.1'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -82,20 +82,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.32'
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
@@ -111,9 +97,9 @@ dependencies:
       - !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.
+      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.
 email: unipept@ugent.be
 executables:
 - unipept
@@ -127,6 +113,7 @@ extra_rdoc_files:
 files:
 - ".document"
 - ".rubocop.yml"
+- ".ruby-version"
 - ".travis.yml"
 - Gemfile
 - Gemfile.lock
@@ -198,7 +185,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.8
+rubygems_version: 2.6.8
 signing_key: 
 specification_version: 4
 summary: Command line interface to Unipept web services.