unipept 1.3.0 → 1.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 6e803f0d77ccd06f8b983f3fac7d51ebc5c170e6
-  data.tar.gz: f30e852d61c6a69c250306148fc2fa1a064f63f7
+SHA256:
+  metadata.gz: 594507d190de8317807b00e739281a5a1a8d99de8b39193770f7510d491acb98
+  data.tar.gz: d137e5780251e56b16096d349763e2dad61072aec9986f5e739d81a15c329245
 SHA512:
-  metadata.gz: fb053972592c1c18b33304c6f39d7db8ebcfcb8dedf1ed99c53a9ad8d73121feff1b8f806c6b7f80bc75bab0c03e9ae272122020ab716093fd9d7a30e1a16c2f
-  data.tar.gz: 7664a300163ceed13732c7286b017e9e28e08ebfc39072b15321cce85d12db60d26de79a52f50f4d70aa2528f4e222e1b451fd3f027fa6072e293895dbe66799
+  metadata.gz: e0deb6a4677cedaedde87564b82d1ddb99993136d38149b2dc9b9d062e1119c0b5eb42512edde03c6195ccc97bdec0a857617a9c859f04b8075d1baf1ce486aa
+  data.tar.gz: ae2c359ba6591a83c00cd25b77ed741964f06ffc17f458a3541d3279ffc421fc2f28b00dc1f5f3fc5f20560792f03c87f3c2a221dab00e4e468f2ecbb42f45ee

data/.ruby-version

@@ -1 +1 @@
-2.4.0
+2.6.0

data/Gemfile

@@ -2,7 +2,9 @@ source 'http://rubygems.org'
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
-gem 'cri', '~> 2.7'
+
+# for now, stay on version 2.11 because of a bug
+gem 'cri', '2.11'
 gem 'typhoeus', '~> 1.1'
 
 group :development do

data/Gemfile.lock

@@ -1,101 +1,103 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    addressable (2.5.0)
-      public_suffix (~> 2.0, >= 2.0.2)
-    ast (2.3.0)
+    addressable (2.4.0)
+    ast (2.4.0)
     builder (3.2.3)
     colored (1.2)
-    coveralls (0.8.18)
+    coveralls (0.8.22)
       json (>= 1.8, < 3)
-      simplecov (~> 0.12.0)
+      simplecov (~> 0.16.1)
       term-ansicolor (~> 1.3)
-      thor (~> 0.19.1)
+      thor (~> 0.19.4)
       tins (~> 1.6)
-    cri (2.7.1)
+    cri (2.11.0)
       colored (~> 1.2)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
-    docile (1.1.5)
-    ethon (0.10.1)
+    docile (1.3.1)
+    ethon (0.12.0)
       ffi (>= 1.3.0)
     faraday (0.9.2)
       multipart-post (>= 1.2, < 3)
-    ffi (1.9.17)
-    git (1.3.0)
-    github_api (0.11.3)
-      addressable (~> 2.3)
-      descendants_tracker (~> 0.0.1)
+    ffi (1.10.0)
+    git (1.5.0)
+    github_api (0.16.0)
+      addressable (~> 2.4.0)
+      descendants_tracker (~> 0.0.4)
       faraday (~> 0.8, < 0.10)
-      hashie (>= 1.2)
-      multi_json (>= 1.7.5, < 2.0)
-      nokogiri (~> 1.6.0)
-      oauth2
-    hashie (3.4.6)
-    highline (1.7.8)
-    jeweler (2.3.2)
+      hashie (>= 3.4)
+      mime-types (>= 1.16, < 3.0)
+      oauth2 (~> 1.0)
+    hashie (3.6.0)
+    highline (2.0.0)
+    jaro_winkler (1.5.2)
+    jeweler (2.3.9)
       builder
-      bundler (>= 1.0)
+      bundler
       git (>= 1.2.5)
-      github_api (~> 0.11.0)
+      github_api (~> 0.16.0)
       highline (>= 1.6.15)
       nokogiri (>= 1.5.10)
-      psych (~> 2.2)
+      psych
       rake
       rdoc
       semver2
-    json (2.0.3)
-    jwt (1.5.6)
-    mini_portile2 (2.1.0)
-    minitest (5.10.1)
-    multi_json (1.12.1)
+    json (2.1.0)
+    jwt (2.1.0)
+    mime-types (2.99.3)
+    mini_portile2 (2.4.0)
+    minitest (5.11.3)
+    multi_json (1.13.1)
     multi_xml (0.6.0)
     multipart-post (2.0.0)
-    nokogiri (1.6.8.1)
-      mini_portile2 (~> 2.1.0)
-    oauth2 (1.3.0)
-      faraday (>= 0.8, < 0.11)
-      jwt (~> 1.0)
+    nokogiri (1.10.1)
+      mini_portile2 (~> 2.4.0)
+    oauth2 (1.4.1)
+      faraday (>= 0.8, < 0.16.0)
+      jwt (>= 1.0, < 3.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
-    parser (2.3.3.1)
-      ast (~> 2.2)
-    powerpack (0.1.1)
-    psych (2.2.2)
-    public_suffix (2.0.5)
-    rack (2.0.1)
-    rainbow (2.2.1)
+    parallel (1.13.0)
+    parser (2.6.0.0)
+      ast (~> 2.4.0)
+    powerpack (0.1.2)
+    psych (3.1.0)
+    rack (2.0.6)
+    rainbow (3.0.0)
     rake (10.5.0)
-    rdoc (5.0.0)
-    rubocop (0.47.0)
-      parser (>= 2.3.3.1, < 3.0)
+    rdoc (6.1.1)
+    rubocop (0.63.0)
+      jaro_winkler (~> 1.5.1)
+      parallel (~> 1.10)
+      parser (>= 2.5, != 2.5.1.1)
       powerpack (~> 0.1)
-      rainbow (>= 1.99.1, < 3.0)
+      rainbow (>= 2.2.2, < 4.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (~> 1.0, >= 1.0.1)
-    ruby-progressbar (1.8.1)
+      unicode-display_width (~> 1.4.0)
+    ruby-progressbar (1.10.0)
     semver2 (3.4.2)
-    simplecov (0.12.0)
-      docile (~> 1.1.0)
+    simplecov (0.16.1)
+      docile (~> 1.1)
       json (>= 1.8, < 3)
       simplecov-html (~> 0.10.0)
-    simplecov-html (0.10.0)
-    term-ansicolor (1.4.0)
+    simplecov-html (0.10.2)
+    term-ansicolor (1.7.1)
       tins (~> 1.0)
     thor (0.19.4)
-    thread_safe (0.3.5)
-    tins (1.13.0)
-    typhoeus (1.1.2)
+    thread_safe (0.3.6)
+    tins (1.20.2)
+    typhoeus (1.3.1)
       ethon (>= 0.9.0)
-    unicode-display_width (1.1.3)
+    unicode-display_width (1.4.1)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
   coveralls (~> 0)
-  cri (~> 2.7)
+  cri (= 2.11)
   jeweler
   minitest (~> 5.7)
   rake (~> 10.4)
@@ -103,4 +105,4 @@ DEPENDENCIES
   typhoeus (~> 1.1)
 
 BUNDLED WITH
-   1.13.7
+   1.17.2

data/VERSION

@@ -1 +1 @@
-1.3.0
+1.4.0

data/lib/commands/uniprot.rb

@@ -61,7 +61,7 @@ module Unipept::Commands
         get_uniprot_entry(accession, 'fasta').lines.map(&:chomp)[1..-1].join('')
       else
         # other format has been specified, just download and output
-        resp = Typhoeus.get("http://www.uniprot.org/uniprot/#{accession}.#{format}")
+        resp = Typhoeus.get("https://www.uniprot.org/uniprot/#{accession}.#{format}")
         resp.response_body if resp.success?
       end
     end

data/unipept.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 1.3.0 ruby lib
+# stub: unipept 1.4.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "unipept".freeze
-  s.version = "1.3.0"
+  s.version = "1.4.0"
 
   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 = "2017-01-28"
+  s.date = "2019-01-18"
   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]
@@ -78,21 +78,21 @@ Gem::Specification.new do |s|
   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.rubygems_version = "3.0.1".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>.freeze, ["~> 2.7"])
+      s.add_runtime_dependency(%q<cri>.freeze, ["= 2.11"])
       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>.freeze, ["~> 2.7"])
+      s.add_dependency(%q<cri>.freeze, ["= 2.11"])
       s.add_dependency(%q<typhoeus>.freeze, ["~> 1.1"])
       s.add_dependency(%q<rake>.freeze, ["~> 10.4"])
       s.add_dependency(%q<minitest>.freeze, ["~> 5.7"])
@@ -100,7 +100,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<coveralls>.freeze, ["~> 0"])
     end
   else
-    s.add_dependency(%q<cri>.freeze, ["~> 2.7"])
+    s.add_dependency(%q<cri>.freeze, ["= 2.11"])
     s.add_dependency(%q<typhoeus>.freeze, ["~> 1.1"])
     s.add_dependency(%q<rake>.freeze, ["~> 10.4"])
     s.add_dependency(%q<minitest>.freeze, ["~> 5.7"])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 1.3.0
+  version: 1.4.0
 platform: ruby
 authors:
 - Toon Willems
@@ -10,22 +10,22 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-01-28 00:00:00.000000000 Z
+date: 2019-01-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: '2.7'
+        version: '2.11'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - '='
       - !ruby/object:Gem::Version
-        version: '2.7'
+        version: '2.11'
 - !ruby/object:Gem::Dependency
   name: typhoeus
   requirement: !ruby/object:Gem::Requirement
@@ -184,8 +184,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.8
+rubygems_version: 3.0.1
 signing_key: 
 specification_version: 4
 summary: Command line interface to Unipept web services.