RubyGems - unipept - Versions diffs - 2.2.1 → 2.2.2 - Mend

unipept 2.2.1 → 2.2.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (39) hide show

checksums.yaml +4 -4
data/.github/dependabot.yml +9 -0
data/.github/workflows/ci.yml +6 -27
data/.rakeTasks +2 -2
data/.rubocop.yml +2 -0
data/.ruby-version +1 -1
data/CITATION.cff +30 -0
data/Gemfile +2 -2
data/Gemfile.lock +60 -41
data/README.md +2 -2
data/Rakefile +4 -4
data/VERSION +1 -1
data/lib/commands/prot2pept.rb +1 -2
data/lib/commands/unipept/api_runner.rb +7 -11
data/lib/commands/unipept/config.rb +1 -1
data/lib/commands/unipept/taxa2tree.rb +2 -2
data/lib/commands/uniprot.rb +4 -5
data/lib/configuration.rb +6 -7
data/lib/formatters.rb +7 -7
data/lib/server_message.rb +2 -4
data/test/commands/unipept/test_api_runner.rb +8 -7
data/test/commands/unipept/test_config.rb +1 -1
data/test/commands/unipept/test_pept2ec.rb +2 -2
data/test/commands/unipept/test_pept2funct.rb +2 -2
data/test/commands/unipept/test_pept2go.rb +2 -2
data/test/commands/unipept/test_pept2interpro.rb +2 -2
data/test/commands/unipept/test_pept2lca.rb +2 -2
data/test/commands/unipept/test_pept2prot.rb +2 -2
data/test/commands/unipept/test_pept2taxa.rb +2 -2
data/test/commands/unipept/test_peptinfo.rb +2 -2
data/test/commands/unipept/test_taxa2lca.rb +2 -2
data/test/commands/unipept/test_taxa2tree.rb +2 -2
data/test/commands/unipept/test_taxonomy.rb +2 -2
data/test/test_configuration.rb +1 -1
data/test/test_formatters.rb +5 -5
data/test/test_output_writer.rb +1 -1
data/test/test_server_message.rb +2 -2
data/unipept.gemspec +17 -21
metadata +11 -9

checksums.yaml CHANGED Viewed

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 920c619a2c620e0cd195ab1d2bfd4346f701ce53315787b599b128f6fdf43e0b
-  data.tar.gz: 44f6fb10ec0964a3b1f9005d7732c4d9b5ccb8b2984d5134922370faf9b9a0c9
+  metadata.gz: b8f3ce5867e19149483ab70e24d4cc5da97d8ba9e62e38491b714abc89078ee0
+  data.tar.gz: '09cfcdbc3608ee36a75825e7f7555add797b002e3abccc5caada703efc8d0b86'
 SHA512:
-  metadata.gz: b026faf39383b6cf737bda6ccdf7810cb820c1e1b4611a30a6edfdd31fd7123bca32b28b10963f30ec94bc4a4eaa2f38288c96fe8b5dff98e1dc42cba7d49d8b
-  data.tar.gz: a0f38cbca9c3355abee43ea433790dbd3a834da20ea384b3e90e50c1c52adb05b7df2ec180ce964f1550ced87eb1eb3b50003c2ee535cd189a7cf9be543f898f
+  metadata.gz: e29aa64adf5a502377c2fdedb63969d29fa6f8d517262d65ec0a99b40746bf0a1d3d5a26552dd25cd425008d0f8a0f4ed7bd69ec6786d77ef2c688ce0e5b7c5d
+  data.tar.gz: 9d6d08532a96fb85423a7843745df5fe75f125e6f7119f6ba2b76f525b75bd057aac7d27a0a5c1e6357df5aed0af42bb00a9fd260aa3be58f623dc75dc3da7b4

data/.github/dependabot.yml ADDED Viewed

@@ -0,0 +1,9 @@
+version: 2
+updates:
+- package-ecosystem: bundler
+  directory: "/"
+  schedule:
+    interval: monthly
+    time: "13:00"
+    timezone: Europe/Brussels
+  open-pull-requests-limit: 99

data/.github/workflows/ci.yml CHANGED Viewed

@@ -7,27 +7,16 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        ruby: ["2.4", "2.5", "2.6"]
+        ruby: ["2.7", "3.0", "3.1"]
       fail-fast: false
     name: Test Ruby ${{ matrix.ruby }}
     steps:
       - uses: actions/checkout@v1
       - name: Setup Ruby
-        uses: actions/setup-ruby@v1
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: ${{ matrix.ruby }}
-      - name: Cache Ruby dependencies
-        uses: actions/cache@v1
-        with:
-          path: vendor/bundle
-          key: ${{ runner.os }}-${{ matrix.ruby }}-gem-${{ hashFiles('**/Gemfile.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-${{ matrix.ruby }}-gem-
-      - name: Install dependencies
-        run: |
-          gem install bundler:1.17.2
-          bundle config path vendor/bundle
-          bundle install --jobs 4 --retry 3
+          bundler-cache: true
       - name: Test
         run: |
           bundle exec rake test
@@ -37,19 +26,9 @@ jobs:
     steps:
       - uses: actions/checkout@v1
       - name: Setup Ruby
-        uses: actions/setup-ruby@v1
-      - name: Cache Ruby dependencies
-        uses: actions/cache@v1
+        uses: ruby/setup-ruby@v1
         with:
-          path: vendor/bundle
-          key: ${{ runner.os }}-${{ matrix.ruby }}-gem-${{ hashFiles('**/Gemfile.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-${{ matrix.ruby }}-gem-
-      - name: Install dependencies
-        run: |
-          gem install bundler:1.17.2
-          bundle config path vendor/bundle
-          bundle install --jobs 4 --retry 3
+          bundler-cache: true
       - name: Test
         run: |
-          bundle exec rake test_style
+          bundle exec rake test_style

data/.rakeTasks CHANGED Viewed

@@ -1,7 +1,7 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="UTF-8"?>
 <Settings><!--This file was automatically generated by Ruby plugin.
 You are allowed to:
 1. Remove rake task
 2. Add existing rake tasks
 To add existing rake tasks automatically delete this file and reload the project.
---><RakeGroup description="" fullCmd="" taksId="rake"><RakeTask description="Build gem into pkg/" fullCmd="build" taksId="build" /><RakeTask description="Remove any temporary products" fullCmd="clean" taksId="clean" /><RakeTask description="Remove any generated files" fullCmd="clobber" taksId="clobber" /><RakeTask description="Remove RDoc HTML files" fullCmd="clobber_rdoc" taksId="clobber_rdoc" /><RakeTask description="Start IRB with all runtime dependencies loaded" fullCmd="console[script]" taksId="console[script]" /><RakeGroup description="" fullCmd="" taksId="gemcutter"><RakeTask description="Release gem to Gemcutter" fullCmd="gemcutter:release" taksId="release" /></RakeGroup><RakeTask description="Generate and validate gemspec" fullCmd="gemspec" taksId="gemspec" /><RakeGroup description="" fullCmd="" taksId="gemspec"><RakeTask description="Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)" fullCmd="gemspec:debug" taksId="debug" /><RakeTask description="Regenerate the gemspec on the filesystem" fullCmd="gemspec:generate" taksId="generate" /><RakeTask description="Regenerate and validate gemspec, and then commits and pushes to git" fullCmd="gemspec:release" taksId="release" /><RakeTask description="Validates the gemspec on the filesystem" fullCmd="gemspec:validate" taksId="validate" /></RakeGroup><RakeGroup description="" fullCmd="" taksId="git"><RakeTask description="Tag and push release to git" fullCmd="git:release" taksId="release" /></RakeGroup><RakeTask description="Build and install gem using `gem install`" fullCmd="install" taksId="install" /><RakeTask description="Build RDoc HTML files" fullCmd="rdoc" taksId="rdoc" /><RakeTask description="Release gem" fullCmd="release" taksId="release" /><RakeTask description="Rebuild RDoc HTML files" fullCmd="rerdoc" taksId="rerdoc" /><RakeTask description="Run RuboCop" fullCmd="test_style" taksId="test_style" /><RakeGroup description="" fullCmd="" taksId="test_style"><RakeTask description="Auto-correct RuboCop offenses" fullCmd="test_style:auto_correct" taksId="auto_correct" /></RakeGroup><RakeTask description="Displays the current version" fullCmd="version" taksId="version" /><RakeGroup description="" fullCmd="" taksId="version"><RakeGroup description="" fullCmd="" taksId="bump"><RakeTask description="Bump the major version by 1" fullCmd="version:bump:major" taksId="major" /><RakeTask description="Bump the a minor version by 1" fullCmd="version:bump:minor" taksId="minor" /><RakeTask description="Bump the patch version by 1" fullCmd="version:bump:patch" taksId="patch" /></RakeGroup><RakeTask description="Writes out an explicit version" fullCmd="version:write" taksId="write" /></RakeGroup><RakeTask description="" fullCmd="console" taksId="console" /><RakeTask description="" fullCmd="default" taksId="default" /><RakeTask description="" fullCmd="gemspec_required" taksId="gemspec_required" /><RakeTask description="" fullCmd="rdoc/created.rid" taksId="rdoc/created.rid" /><RakeTask description="" fullCmd="test" taksId="test" /><RakeTask description="" fullCmd="test_unit" taksId="test_unit" /><RakeTask description="" fullCmd="version_required" taksId="version_required" /></RakeGroup></Settings>
+--><RakeGroup description="" fullCmd="" taksId="rake"><RakeTask description="Build gem into pkg/" fullCmd="build" taksId="build" /><RakeTask description="Remove any temporary products" fullCmd="clean" taksId="clean" /><RakeTask description="Remove any generated files" fullCmd="clobber" taksId="clobber" /><RakeTask description="Remove RDoc HTML files" fullCmd="clobber_rdoc" taksId="clobber_rdoc" /><RakeTask description="Start IRB with all runtime dependencies loaded" fullCmd="console[script]" taksId="console[script]" /><RakeGroup description="" fullCmd="" taksId="gemcutter"><RakeTask description="Release gem to Gemcutter" fullCmd="gemcutter:release" taksId="release" /></RakeGroup><RakeTask description="Generate and validate gemspec" fullCmd="gemspec" taksId="gemspec" /><RakeGroup description="" fullCmd="" taksId="gemspec"><RakeTask description="Display the gemspec for debugging purposes, as juwelier knows it (not from the filesystem)" fullCmd="gemspec:debug" taksId="debug" /><RakeTask description="Regenerate the gemspec on the filesystem" fullCmd="gemspec:generate" taksId="generate" /><RakeTask description="Regenerate and validate gemspec, and then commits and pushes to git" fullCmd="gemspec:release" taksId="release" /><RakeTask description="Validates the gemspec on the filesystem" fullCmd="gemspec:validate" taksId="validate" /></RakeGroup><RakeGroup description="" fullCmd="" taksId="git"><RakeTask description="Tag and push release to git" fullCmd="git:release" taksId="release" /></RakeGroup><RakeTask description="Build and install gem using `gem install`" fullCmd="install" taksId="install" /><RakeTask description="Build RDoc HTML files" fullCmd="rdoc" taksId="rdoc" /><RakeTask description="Release gem" fullCmd="release" taksId="release" /><RakeTask description="Rebuild RDoc HTML files" fullCmd="rerdoc" taksId="rerdoc" /><RakeTask description="Run RuboCop" fullCmd="test_style" taksId="test_style" /><RakeGroup description="" fullCmd="" taksId="test_style"><RakeTask description="Auto-correct RuboCop offenses" fullCmd="test_style:auto_correct" taksId="auto_correct" /></RakeGroup><RakeTask description="Displays the current version" fullCmd="version" taksId="version" /><RakeGroup description="" fullCmd="" taksId="version"><RakeGroup description="" fullCmd="" taksId="bump"><RakeTask description="Bump the major version by 1" fullCmd="version:bump:major" taksId="major" /><RakeTask description="Bump the a minor version by 1" fullCmd="version:bump:minor" taksId="minor" /><RakeTask description="Bump the patch version by 1" fullCmd="version:bump:patch" taksId="patch" /></RakeGroup><RakeTask description="Writes out an explicit version" fullCmd="version:write" taksId="write" /></RakeGroup><RakeTask description="" fullCmd="console" taksId="console" /><RakeTask description="" fullCmd="default" taksId="default" /><RakeTask description="" fullCmd="gemspec_required" taksId="gemspec_required" /><RakeTask description="" fullCmd="rdoc/created.rid" taksId="rdoc/created.rid" /><RakeTask description="" fullCmd="test" taksId="test" /><RakeTask description="" fullCmd="test_unit" taksId="test_unit" /><RakeTask description="" fullCmd="version_required" taksId="version_required" /></RakeGroup></Settings>

data/.rubocop.yml CHANGED Viewed

@@ -1,4 +1,6 @@
 AllCops:
+  TargetRubyVersion: 2.7
+  NewCops: enable
   Exclude:
     - 'unipept.gemspec'
     - 'vendor/**/*'

data/.ruby-version CHANGED Viewed

	@@ -1 +1 @@
1	- 2.6.6
1	+ 3.0.0

data/CITATION.cff ADDED Viewed

@@ -0,0 +1,30 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Verschaffelt"
+    given-names: "Pieter"
+  - family-names: "Van Thienen"
+    given-names: "Philippe"
+  - family-names: "Van Den Bossche"
+    given-names: "Tim"
+  - family-names: "Van der Jeugt"
+    given-names: "Felix"
+  - family-names: "De Tender"
+    given-names: "Caroline"
+  - family-names: "Martens"
+    given-names: "Lennart"
+  - family-names: "Dawyndt"
+    given-names: "Peter"
+  - family-names: "Mesuere"
+    given-names: "Bart"
+    orcid: "https://orcid.org/0000-0003-0610-3441"
+  doi: "10.1093/bioinformatics/btaa553"
+  journal: "Bioinformatics"
+  start: 4220
+  end: 4221
+  title: "Unipept CLI 2.0: adding support for visualizations and functional annotations"
+  issue: 14
+  volume: 36
+  year: 2020

data/Gemfile CHANGED Viewed

@@ -7,9 +7,9 @@ gem 'typhoeus', '~> 1.3.1'
 group :development do
   gem 'minitest', '~> 5.14'
   gem 'rake', '~> 13.0.1'
-  gem 'rubocop', '~>0.79.0'
+  gem 'rubocop', '~>1.11'
 end
 group :release do
-  gem 'jeweler'
+  gem 'juwelier'
 end

data/Gemfile.lock CHANGED Viewed

@@ -1,85 +1,104 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    addressable (2.4.0)
-    ast (2.4.0)
+    addressable (2.8.0)
+      public_suffix (>= 2.0.2, < 5.0)
+    ast (2.4.2)
     builder (3.2.4)
-    cri (2.15.10)
+    cri (2.15.11)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
     ethon (0.12.0)
       ffi (>= 1.3.0)
-    faraday (0.9.2)
+    faraday (1.3.0)
+      faraday-net_http (~> 1.0)
       multipart-post (>= 1.2, < 3)
+      ruby2_keywords
+    faraday-net_http (1.0.1)
     ffi (1.12.1)
-    git (1.5.0)
-    github_api (0.16.0)
-      addressable (~> 2.4.0)
+    git (1.8.1)
+      rchardet (~> 1.8)
+    github_api (0.19.0)
+      addressable (~> 2.4)
       descendants_tracker (~> 0.0.4)
-      faraday (~> 0.8, < 0.10)
-      hashie (>= 3.4)
-      mime-types (>= 1.16, < 3.0)
+      faraday (>= 0.8, < 2)
+      hashie (~> 3.5, >= 3.5.2)
       oauth2 (~> 1.0)
-    hashie (4.0.0)
+    hashie (3.6.0)
     highline (2.0.3)
-    jaro_winkler (1.5.4)
-    jeweler (2.3.9)
+    juwelier (2.4.9)
       builder
       bundler
-      git (>= 1.2.5)
-      github_api (~> 0.16.0)
-      highline (>= 1.6.15)
-      nokogiri (>= 1.5.10)
+      git
+      github_api
+      highline
+      kamelcase (~> 0)
+      nokogiri
       psych
       rake
       rdoc
       semver2
-    jwt (2.2.1)
-    mime-types (2.99.3)
-    mini_portile2 (2.4.0)
-    minitest (5.14.0)
-    multi_json (1.14.1)
+    jwt (2.2.2)
+    kamelcase (0.0.2)
+      semver2 (~> 3)
+    mini_portile2 (2.8.0)
+    minitest (5.15.0)
+    multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.1.1)
-    nokogiri (1.10.7)
-      mini_portile2 (~> 2.4.0)
-    oauth2 (1.4.2)
+    nokogiri (1.13.4)
+      mini_portile2 (~> 2.8.0)
+      racc (~> 1.4)
+    oauth2 (1.4.4)
       faraday (>= 0.8, < 2.0)
       jwt (>= 1.0, < 3.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
-    parallel (1.19.1)
-    parser (2.7.0.2)
-      ast (~> 2.4.0)
-    psych (3.1.0)
-    rack (2.1.1)
-    rainbow (3.0.0)
-    rake (13.0.1)
-    rdoc (6.2.1)
-    rubocop (0.79.0)
-      jaro_winkler (~> 1.5.1)
+    parallel (1.22.1)
+    parser (3.1.1.0)
+      ast (~> 2.4.1)
+    psych (4.0.3)
+      stringio
+    public_suffix (4.0.6)
+    racc (1.6.0)
+    rack (2.2.3)
+    rainbow (3.1.1)
+    rake (13.0.6)
+    rchardet (1.8.0)
+    rdoc (6.4.0)
+      psych (>= 4.0.0)
+    regexp_parser (2.3.0)
+    rexml (3.2.5)
+    rubocop (1.27.0)
       parallel (~> 1.10)
-      parser (>= 2.7.0.1)
+      parser (>= 3.1.0.0)
       rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.8, < 3.0)
+      rexml
+      rubocop-ast (>= 1.16.0, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 1.4.0, < 1.7)
-    ruby-progressbar (1.10.1)
+      unicode-display_width (>= 1.4.0, < 3.0)
+    rubocop-ast (1.17.0)
+      parser (>= 3.1.1.0)
+    ruby-progressbar (1.11.0)
+    ruby2_keywords (0.0.4)
     semver2 (3.4.2)
+    stringio (3.0.1)
     thread_safe (0.3.6)
     typhoeus (1.3.1)
       ethon (>= 0.9.0)
-    unicode-display_width (1.6.1)
+    unicode-display_width (2.1.0)
 PLATFORMS
   ruby
 DEPENDENCIES
   cri (~> 2.15.10)
-  jeweler
+  juwelier
   minitest (~> 5.14)
   rake (~> 13.0.1)
-  rubocop (~> 0.79.0)
+  rubocop (~> 1.11)
   typhoeus (~> 1.3.1)
 BUNDLED WITH

data/README.md CHANGED Viewed

@@ -7,11 +7,11 @@ Documentation about the web service can be found at [http://unipept.ugent.be/api
 ## Installation
-To use the Unipept CLI, Ruby version 1.9.3 or higher needs to be installed. You can check this by running `ruby -v` on the commandline:
+To use the Unipept CLI, Ruby version 2.6 or higher needs to be installed. You can check this by running `ruby -v` on the commandline:
 ```
 $ ruby -v
-ruby 2.2.2p95 (2015-04-13 revision 50295) [x86_64-darwin14]
+ruby 3.0.0p0 (2020-12-25 revision 95aff21468) [arm64-darwin21]
 ```
 More information on installing Ruby can be found at https://www.ruby-lang.org/en/installation/

data/Rakefile CHANGED Viewed

@@ -11,8 +11,8 @@ require 'rake'
 require 'rake/testtask'
 require 'rubocop/rake_task'
 begin
-  require 'jeweler'
-  Jeweler::Tasks.new do |gem|
+  require 'juwelier'
+  Juwelier::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]
@@ -26,9 +26,9 @@ begin
     EOS
     gem.email = 'unipept@ugent.be'
     gem.authors = ['Bart Mesuere', 'Pieter Verschaffelt', 'Toon Willems', 'Tom Naessens']
-    gem.required_ruby_version = '>= 2.0.0'
+    gem.required_ruby_version = '>= 2.6.0'
   end
-  Jeweler::RubygemsDotOrgTasks.new
+  Juwelier::RubygemsDotOrgTasks.new
 rescue LoadError
   # do nothing
 end

data/VERSION CHANGED Viewed

	@@ -1 +1 @@
1	- 2.2.1
1	+ 2.2.2

data/lib/commands/prot2pept.rb CHANGED Viewed

@@ -1,7 +1,6 @@
 module Unipept::Commands
   class Prot2pept
-    attr_reader :root_command
-    attr_reader :valid_formats
+    attr_reader :root_command, :valid_formats
     @root_command = Cri::Command.define do
       name 'prot2pept'

data/lib/commands/unipept/api_runner.rb CHANGED Viewed

@@ -2,18 +2,14 @@ require_relative '../../retryable_typhoeus'
 module Unipept
   class Commands::ApiRunner < Cri::CommandRunner
-    attr_reader :configuration
-    attr_reader :url
-    attr_reader :user_agent
+    attr_reader :configuration, :url, :user_agent
     def initialize(args, opts, cmd)
       super
       @configuration = Unipept::Configuration.new
       @host = host
-      @user_agent = 'Unipept CLI - unipept ' + Unipept::VERSION
+      @user_agent = "Unipept CLI - unipept #{Unipept::VERSION}"
       @url = "#{@host}/api/v1/#{cmd.name}.json"
       @fasta = false
     end
@@ -39,7 +35,7 @@ module Unipept
     # - if none of the previous are given, uses stdin
     def input_iterator
       return arguments.each unless arguments.empty?
-      return IO.foreach(options[:input]) if options[:input]
+      return File.foreach(options[:input]) if options[:input]
       $stdin.each_line
     end
@@ -148,7 +144,7 @@ module Unipept
     def save_error(message)
       path = error_file_path
       FileUtils.mkdir_p File.dirname(path)
-      File.open(path, 'w') { |f| f.write message }
+      File.write(path, message)
       warn "API request failed! log can be found in #{path}"
     end
@@ -173,7 +169,7 @@ module Unipept
       lambda do
         unless result.empty?
-          output_writer.write_line formatter.header(result, fasta_mapper) if batch_id.zero? && !options[:"no-header"]
+          output_writer.write_line formatter.header(result, fasta_mapper) if batch_id.zero? && !options[:'no-header']
           output_writer.write_line formatter.format(result, fasta_mapper, batch_id.zero?)
         end
       end
@@ -183,7 +179,7 @@ module Unipept
       if response.timed_out?
         -> { save_error('request timed out, continuing anyway, but results might be incomplete') }
       elsif response.code.zero?
-        -> { save_error('could not get an http response, continuing anyway, but results might be incomplete' + response.return_message) }
+        -> { save_error("could not get an http response, continuing anyway, but results might be incomplete#{response.return_message}") }
       else
         -> { save_error("Got #{response.code}: #{response.response_body}\nRequest headers: #{response.request.options}\nRequest body:\n#{response.request.encoded_body}\n\n") }
       end
@@ -212,7 +208,7 @@ module Unipept
           if %w[ec go ipr].include? k
             v.each do |item|
               item.each do |field_name, field_value|
-                new_field_name = %w[ec_number go_term ipr_code].include?(field_name) ? field_name : k + '_' + field_name
+                new_field_name = %w[ec_number go_term ipr_code].include?(field_name) ? field_name : "#{k}_#{field_name}"
                 output_row[new_field_name] = [] unless output_row.key? new_field_name
                 output_row[new_field_name] << field_value
               end

data/lib/commands/unipept/config.rb CHANGED Viewed

@@ -7,7 +7,7 @@ module Unipept
       if arguments.size == 2
         set_config(key, value)
-        puts key + ' was set to ' + value
+        puts "#{key} was set to #{value}"
       else
         puts get_config(key)
       end

data/lib/commands/unipept/taxa2tree.rb CHANGED Viewed

@@ -34,7 +34,7 @@ module Unipept::Commands
     def input_iterator
       return arguments.each unless arguments.empty?
-      return IO.foreach(options[:input]) if options[:input]
+      return File.foreach(options[:input]) if options[:input]
       @stdin_contents.each
     end
@@ -57,7 +57,7 @@ module Unipept::Commands
           splitted[1] = splitted[1].to_i
           splitted
         end
-        data = Hash[data]
+        data = data.to_h
       else
         data = Hash.new 0
         input.each do |i|

data/lib/commands/uniprot.rb CHANGED Viewed

@@ -2,8 +2,7 @@ require 'typhoeus'
 module Unipept::Commands
   class Uniprot
-    attr_reader :root_command
-    attr_reader :valid_formats
+    attr_reader :root_command, :valid_formats
     valid_formats = Set.new %w[fasta txt xml rdf gff sequence]
     @root_command = Cri::Command.define do
@@ -21,7 +20,7 @@ module Unipept::Commands
       The uniprot command yields just the protein sequences as a default, but can return several formats.
       EOS
-      required :f, :format, 'specify output format (available: ' + valid_formats.to_a.join(', ') + ') (default: sequence)'
+      required :f, :format, "specify output format (available: #{valid_formats.to_a.join(', ')}) (default: sequence)"
       flag :h, :help, 'show help for this command' do |_value, cmd|
         puts cmd.help
         exit 0
@@ -29,7 +28,7 @@ module Unipept::Commands
       run do |opts, args, _cmd|
         format = opts.fetch(:format, 'sequence')
         unless valid_formats.include? format
-          warn format + ' is not a valid output format. Available formats are: ' + valid_formats.to_a.join(', ')
+          warn "#{format} is not a valid output format. Available formats are: #{valid_formats.to_a.join(', ')}"
           exit 1
         end
         iterator = args.empty? ? $stdin.each_line : args
@@ -58,7 +57,7 @@ module Unipept::Commands
     # @return [String] The requested UniProt entry in the requested format
     def self.get_uniprot_entry(accession, format)
       if format == 'sequence'
-        get_uniprot_entry(accession, 'fasta').lines.map(&:chomp)[1..-1].join('')
+        get_uniprot_entry(accession, 'fasta').lines.map(&:chomp)[1..].join
       else
         # other format has been specified, just download and output
         resp = Typhoeus.get("https://www.uniprot.org/uniprot/#{accession}.#{format}")

data/lib/configuration.rb CHANGED Viewed

@@ -2,8 +2,7 @@ require 'yaml'
 module Unipept
   class Configuration
-    attr_reader :config
-    attr_reader :file_name
+    attr_reader :config, :file_name
     # Creates a new config object, based on a given YAML file. If no filename
     # given, '.unipeptrc' in the home dir of the user will be used.
@@ -14,17 +13,17 @@ module Unipept
     # config from
     def initialize(file = nil)
       @file_name = file || File.join(Dir.home, '.unipeptrc')
-      @config = if !File.exist? file_name
-                  {}
+      @config = if File.exist? file_name
+                  YAML.load_file file_name, permitted_classes: [Time]
                 else
-                  YAML.load_file file_name
+                  {}
                 end
     end
     # Saves the config to disk. If the file doesn't exist yet, a new one will be
     # created
     def save
-      File.open(file_name, 'w') { |f| f.write config.to_yaml }
+      File.write(file_name, config.to_yaml)
     end
     # Deletes a key
@@ -39,7 +38,7 @@ module Unipept
     # forwards =[] to the internal config hash
     def []=(*args)
-      config.[]=(*args)
+      config.[]=(*args) # rubocop:disable Layout/SpaceBeforeBrackets
     end
   end
 end

data/lib/formatters.rb CHANGED Viewed

@@ -156,7 +156,7 @@ module Unipept
     # @return [String] The converted input data in the JSON format
     def convert(data, first)
       output = data.map(&:to_json).join(',')
-      first ? output : ',' + output
+      first ? output : ",#{output}"
     end
   end
@@ -178,7 +178,7 @@ module Unipept
       # First we look for items for both ec numbers, go terms and ipr codes that are fully filled in.
       data.each do |row|
-        non_empty_items.keys.each do |annotation_type|
+        non_empty_items.each_key do |annotation_type|
           non_empty_items[annotation_type] = row if row[annotation_type] && !row[annotation_type].empty?
         end
       end
@@ -195,7 +195,7 @@ module Unipept
         idx = keys.index(annotation_type)
         keys.delete_at(idx)
-        keys.insert(idx, *non_empty_item[annotation_type].first.keys.map { |el| %w[ec_number go_term ipr_code].include?(el) ? el : annotation_type + '_' + el })
+        keys.insert(idx, *non_empty_item[annotation_type].first.keys.map { |el| %w[ec_number go_term ipr_code].include?(el) ? el : "#{annotation_type}_#{el}" })
         $keys_length = *non_empty_item[annotation_type].first.keys.length # rubocop:disable Style/GlobalVars
       end
@@ -243,8 +243,8 @@ module Unipept
           o.each do |k, v|
             if %w[ec go ipr].include? k
               if v && !v.empty?
-                v.first.keys.each do |key|
-                  row[key == 'protein_count' ? k + '_protein_count' : key] = (v.map { |el| el[key] }).join(' ').strip
+                v.first.each_key do |key|
+                  row[key == 'protein_count' ? "#{k}_protein_count" : key] = (v.map { |el| el[key] }).join(' ').strip
                 end
               else
                 row[k] = row.concat(Array.new($keys_length[0], nil)) # rubocop:disable Style/GlobalVars
@@ -304,7 +304,7 @@ module Unipept
     #
     # @return [String] The converted input data in the XML format
     def convert(data, _first)
-      data.map { |row| '<result>' + row.to_xml + '</result>' }.join('')
+      data.map { |row| "<result>#{row.to_xml}</result>" }.join
     end
   end
@@ -405,7 +405,7 @@ module Unipept
     #
     # @return [String] The converted input data in the Blast format
     def convert(data, _first)
-      data[0]['gist'].sub!('https://gist.github.com/', 'https://bl.ocks.org/') + "\n"
+      "#{data[0]['gist'].sub!('https://gist.github.com/', 'https://bl.ocks.org/')}\n"
     end
   end
 end

data/lib/server_message.rb CHANGED Viewed

@@ -4,9 +4,7 @@ require_relative 'configuration'
 module Unipept
   class ServerMessage
-    attr_reader :message_url
-    attr_reader :configuration
+    attr_reader :message_url, :configuration
     def initialize(host)
       @message_url = "#{host}/api/v1/messages.json"
@@ -34,7 +32,7 @@ module Unipept
     # ago.
     def recently_fetched?
       last_fetched = @configuration['last_fetch_date']
-      !last_fetched.nil? && (last_fetched + 60 * 60 * 24) > Time.now
+      !last_fetched.nil? && (last_fetched + (60 * 60 * 24)) > Time.now
     end
     # Updates the last checked timestamp

data/test/commands/unipept/test_api_runner.rb CHANGED Viewed

@@ -67,8 +67,8 @@ module Unipept
     end
     def test_input_iterator_file
-      File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
-      runner = new_runner('test',  host: 'https://param_host', input: 'input_file')
+      File.write('input_file', %w[a b c].join("\n"))
+      runner = new_runner('test', host: 'https://param_host', input: 'input_file')
       output = []
       runner.input_iterator.each { |el| output << el.chomp }
       assert_equal(%w[a b c], output)
@@ -84,7 +84,7 @@ module Unipept
     end
     def test_input_iterator_arguments_priority
-      File.open('input_file', 'w') { |file| file.write(%w[1 2 3].join("\n")) }
+      File.write('input_file', %w[1 2 3].join("\n"))
       runner = new_runner('test', { host: 'https://param_host', input: 'input_file' }, %w[a b c])
       output = []
       _out, _err = capture_io_with_input(%w[1 2 3]) do
@@ -94,8 +94,8 @@ module Unipept
     end
     def test_input_iterator_file_priority
-      File.open('input_file', 'w') { |file| file.write(%w[a b c].join("\n")) }
-      runner = new_runner('test',  host: 'https://param_host', input: 'input_file')
+      File.write('input_file', %w[a b c].join("\n"))
+      runner = new_runner('test', host: 'https://param_host', input: 'input_file')
       output = []
       _out, _err = capture_io_with_input(%w[1 2 3]) do
         runner.input_iterator.each { |el| output << el.chomp }
@@ -280,7 +280,7 @@ module Unipept
           runner.save_error('error message')
         end
         assert(err.start_with?('API request failed! log can be found in'))
-        assert_equal('error message', IO.foreach('errordir/error.log').next.chomp)
+        assert_equal('error message', File.foreach('errordir/error.log').next.chomp)
       end
     end
@@ -319,7 +319,7 @@ module Unipept
     end
     def test_success_no_header_option_handle_response
-      runner = new_runner('test', Hash[:host, 'test', :'no-header', true])
+      runner = new_runner('test', { host: 'test', 'no-header': true })
       response = new_response(success: true, response_body: '[{"key1":"value1","key2":"value1"},{"key1":"value2","key2":"value2"}]')
       lambda = runner.handle_response(response, 0, nil)
       assert(lambda.lambda?)
@@ -409,6 +409,7 @@ module Unipept
     def new_response(values)
       response = Class.new do
         def initialize(values)
+          super()
           @values = values
         end

data/test/commands/unipept/test_config.rb CHANGED Viewed

@@ -44,7 +44,7 @@ module Unipept
       out, _err = capture_io_while do
         Commands::Unipept.run(['config', 'test', value])
       end
-      assert_equal('test was set to ' + value, out.chomp)
+      assert_equal("test was set to #{value}", out.chomp)
       assert_equal(value, Unipept::Configuration.new['test'])
     end

data/test/commands/unipept/test_pept2ec.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2funct.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2go.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2interpro.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2lca.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2prot.rb CHANGED Viewed

@@ -88,7 +88,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -101,7 +101,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_pept2taxa.rb CHANGED Viewed

@@ -70,7 +70,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -83,7 +83,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_peptinfo.rb CHANGED Viewed

@@ -87,7 +87,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -100,7 +100,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/commands/unipept/test_taxa2lca.rb CHANGED Viewed

@@ -47,7 +47,7 @@ module Unipept
         Commands::Unipept.run(%w[taxa2lca --host http://api.unipept.ugent.be --format xml 216816 1680])
       end
       lines = out.each_line
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert_equal('', err)
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
@@ -58,7 +58,7 @@ module Unipept
         Commands::Unipept.run(%w[taxa2lca --host http://api.unipept.ugent.be --format json 216816 1680])
       end
       lines = out.each_line
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert_equal('', err)
       assert(output.start_with?('['))
       assert(output.end_with?(']'))

data/test/commands/unipept/test_taxa2tree.rb CHANGED Viewed

@@ -36,7 +36,7 @@ module Unipept
       Commands::Unipept.run(%w[taxa2tree --host http://api.unipept.ugent.be 78 57 89 28 67])
     end
     lines = out.each_line
-    output = lines.to_a.join('').chomp
+    output = lines.to_a.join.chomp
     assert_equal('', err)
     assert(output.start_with?('{'))
@@ -60,7 +60,7 @@ module Unipept
     end
     lines = out.each_line
     assert_equal('', err)
-    output = lines.to_a.join('').chomp
+    output = lines.to_a.join.chomp
     assert(output.start_with?('<!DOCTYPE html>'))
     assert(output.end_with?('</html>'))
     assert(output.include?('</body>'))

data/test/commands/unipept/test_taxonomy.rb CHANGED Viewed

@@ -70,7 +70,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('['))
       assert(output.end_with?(']'))
       assert(!output.include?('}{'))
@@ -83,7 +83,7 @@ module Unipept
       end
       lines = out.each_line
       assert_equal('', err)
-      output = lines.to_a.join('').chomp
+      output = lines.to_a.join.chomp
       assert(output.start_with?('<results>'))
       assert(output.end_with?('</results>'))
       assert(output.include?('<fasta_header>'))

data/test/test_configuration.rb CHANGED Viewed

@@ -9,7 +9,7 @@ module Unipept
     def test_load_with_file
       hash = { 'key' => 'value' }
-      File.open('new_file', 'w') { |f| f.write hash.to_yaml }
+      File.write('new_file', hash.to_yaml)
       config = Configuration.new('new_file')
       assert_equal(hash, config.config)
     end

data/test/test_formatters.rb CHANGED Viewed

@@ -114,7 +114,7 @@ module Unipept
     def test_convert
       assert_equal(TestObject.as_json, formatter.convert([TestObject.test_object], true))
-      assert_equal(',' + TestObject.as_json, formatter.convert([TestObject.test_object], false))
+      assert_equal(",#{TestObject.as_json}", formatter.convert([TestObject.test_object], false))
     end
     def test_format_with_fasta
@@ -159,7 +159,7 @@ module Unipept
       fasta = [['peptide', '>test']]
       object = [TestObject.test_object, TestObject.test_object]
       assert_equal(TestObject.as_csv_header, formatter.header(object))
-      assert_equal('fasta_header,' + TestObject.as_csv_header, formatter.header(object, fasta))
+      assert_equal("fasta_header,#{TestObject.as_csv_header}", formatter.header(object, fasta))
     end
     def test_footer
@@ -180,7 +180,7 @@ module Unipept
     def test_format_with_fasta
       fasta = [['>test', '5']]
       object = [TestObject.test_object, TestObject.test_object]
-      csv = ['>test,' + TestObject.as_csv, '>test,' + TestObject.as_csv, ''].join("\n")
+      csv = [">test,#{TestObject.as_csv}", ">test,#{TestObject.as_csv}", ''].join("\n")
       assert_equal(csv, formatter.format(object, fasta, false))
     end
   end
@@ -203,7 +203,7 @@ module Unipept
     end
     def test_convert
-      xml = '<result>' + TestObject.as_xml + '</result>'
+      xml = "<result>#{TestObject.as_xml}</result>"
       assert_equal(xml, formatter.convert([TestObject.test_object], true))
       assert_equal(xml, formatter.convert([TestObject.test_object], false))
     end
@@ -211,7 +211,7 @@ module Unipept
     def test_format_with_fasta
       fasta = [['>test', '5']]
       output = formatter.format([TestObject.test_object], fasta, false)
-      xml = '<result><fasta_header>>test</fasta_header>' + TestObject.as_xml + '</result>'
+      xml = "<result><fasta_header>>test</fasta_header>#{TestObject.as_xml}</result>"
       assert_equal(xml, output)
     end
   end

data/test/test_output_writer.rb CHANGED Viewed

@@ -23,7 +23,7 @@ module Unipept
         writer.output.flush
       end
       assert_equal('', out)
-      assert_equal('hello world', IO.foreach('output_file').next.chomp)
+      assert_equal('hello world', File.foreach('output_file').next.chomp)
     end
   end
 end

data/test/test_server_message.rb CHANGED Viewed

@@ -79,13 +79,13 @@ module Unipept
     def test_old_recently_fetched
       server = ServerMessage.new('http://api.unipept.ugent.be')
-      server.configuration['last_fetch_date'] = Time.now - 60 * 60 * 25
+      server.configuration['last_fetch_date'] = Time.now - (60 * 60 * 25)
       assert(!server.recently_fetched?)
     end
     def test_recently_recently_fetched
       server = ServerMessage.new('http://api.unipept.ugent.be')
-      server.configuration['last_fetch_date'] = Time.now - 60 * 60 * 1
+      server.configuration['last_fetch_date'] = Time.now - (60 * 60 * 1)
       assert(server.recently_fetched?)
     end
   end

data/unipept.gemspec CHANGED Viewed

@@ -1,17 +1,17 @@
-# Generated by jeweler
+# Generated by juwelier
 # DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: unipept 2.2.1 ruby lib
+# stub: unipept 2.2.2 ruby lib
 Gem::Specification.new do |s|
   s.name = "unipept".freeze
-  s.version = "2.2.1"
+  s.version = "2.2.2"
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Bart Mesuere".freeze, "Pieter Verschaffelt".freeze, "Toon Willems".freeze, "Tom Naessens".freeze]
-  s.date = "2020-04-27"
+  s.date = "2022-04-13"
   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]
@@ -21,10 +21,12 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".document",
+    ".github/dependabot.yml",
     ".github/workflows/ci.yml",
     ".rakeTasks",
     ".rubocop.yml",
     ".ruby-version",
+    "CITATION.cff",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
@@ -102,32 +104,26 @@ 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 = "3.0.3".freeze
+  s.required_ruby_version = Gem::Requirement.new(">= 2.6.0".freeze)
+  s.rubygems_version = "3.1.4".freeze
   s.summary = "Command line interface to Unipept web services.".freeze
   if s.respond_to? :specification_version then
     s.specification_version = 4
+  end
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.15.10"])
-      s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
-      s.add_development_dependency(%q<minitest>.freeze, ["~> 5.14"])
-      s.add_development_dependency(%q<rake>.freeze, ["~> 13.0.1"])
-      s.add_development_dependency(%q<rubocop>.freeze, ["~> 0.79.0"])
-    else
-      s.add_dependency(%q<cri>.freeze, ["~> 2.15.10"])
-      s.add_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
-      s.add_dependency(%q<minitest>.freeze, ["~> 5.14"])
-      s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
-      s.add_dependency(%q<rubocop>.freeze, ["~> 0.79.0"])
-    end
+  if s.respond_to? :add_runtime_dependency then
+    s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.15.10"])
+    s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
+    s.add_development_dependency(%q<minitest>.freeze, ["~> 5.14"])
+    s.add_development_dependency(%q<rake>.freeze, ["~> 13.0.1"])
+    s.add_development_dependency(%q<rubocop>.freeze, ["~> 1.11"])
   else
     s.add_dependency(%q<cri>.freeze, ["~> 2.15.10"])
     s.add_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
     s.add_dependency(%q<minitest>.freeze, ["~> 5.14"])
     s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
-    s.add_dependency(%q<rubocop>.freeze, ["~> 0.79.0"])
+    s.add_dependency(%q<rubocop>.freeze, ["~> 1.11"])
   end
 end

metadata CHANGED Viewed

@@ -1,17 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: unipept
 version: !ruby/object:Gem::Version
-  version: 2.2.1
+  version: 2.2.2
 platform: ruby
 authors:
 - Bart Mesuere
 - Pieter Verschaffelt
 - Toon Willems
 - Tom Naessens
-autorequire:
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-04-27 00:00:00.000000000 Z
+date: 2022-04-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cri
@@ -75,14 +75,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.79.0
+        version: '1.11'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.79.0
+        version: '1.11'
 description: |2
       Command line interface to the Unipept (http://unipept.ugent.be) web services
       (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
@@ -99,10 +99,12 @@ extra_rdoc_files:
 - README.md
 files:
 - ".document"
+- ".github/dependabot.yml"
 - ".github/workflows/ci.yml"
 - ".rakeTasks"
 - ".rubocop.yml"
 - ".ruby-version"
+- CITATION.cff
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -181,7 +183,7 @@ homepage: http://unipept.ugent.be
 licenses:
 - MIT
 metadata: {}
-post_install_message:
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -189,15 +191,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.0.0
+      version: 2.6.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
-signing_key:
+rubygems_version: 3.1.4
+signing_key:
 specification_version: 4
 summary: Command line interface to Unipept web services.
 test_files: []