fix new rubocop offences

.rubocop.yml

@@ -10,6 +10,8 @@ Style/ClassAndModuleChildren:
   Enabled: false
 
 # disable for now
+Lint/NestedMethodDefinition:
+  Enabled: false
 Style/ClassVars:
   Enabled: false
 Style/Documentation:

lib/commands/unipept.rb

@@ -55,7 +55,7 @@ def create_root_command
         option nil, :batch, 'specify the batch size', argument: :required, hidden: true
         option nil, :parallel, 'specify the number of parallel requests', argument: :required, hidden: true
         option :o, :output, 'write output to file', argument: :required
-        option :f, :format, "define the output format (available: #{Unipept::Formatter.available.join ', ' }) (default: #{Unipept::Formatter.default})", argument: :required
+        option :f, :format, "define the output format (available: #{Unipept::Formatter.available.join ', '}) (default: #{Unipept::Formatter.default})", argument: :required
 
         # Configuration options
         option nil, 'host', 'specify the server running the Unipept web service', argument: :required

lib/commands/unipept/config.rb

@@ -7,7 +7,7 @@ def run
 
       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

lib/formatters.rb

@@ -200,7 +200,7 @@ def footer
     def convert(data, _first)
       CSV.generate do |csv|
         data.each do |o|
-          csv << o.values.map { |v| v == ''  ? nil : v }
+          csv << o.values.map { |v| v == '' ? nil : v }
         end
       end
     end
@@ -217,13 +217,13 @@ def to_xml(name = nil)
 
     class ::Array
       def to_xml(array_name = :array, _item_name = :item)
-        %(<#{array_name}>) + map { |n|n.to_xml(:item) }.join + "</#{array_name}>"
+        %(<#{array_name}>) + map { |n| n.to_xml(:item) }.join + "</#{array_name}>"
       end
     end
 
     class ::Hash
       def to_xml(name = nil)
-        data = to_a.map { |k, v|v.to_xml(k) }.join
+        data = to_a.map { |k, v| v.to_xml(k) }.join
         name ? "<#{name}>#{data}</#{name}>" : data
       end
     end

test/commands/unipept/test_pept2prot.rb

@@ -43,9 +43,9 @@ def test_run_with_fasta_multiple_batches
       lines = out.each_line
       assert_equal('', err)
       assert(lines.next.start_with? 'fasta_header,peptide,uniprot_id,taxon_id')
-      assert(lines.select { |line| line.start_with? '>test,EGGAGSSTGQR,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>test,ENFVYIAK,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>tost,EGGAGSSTGQR,' }.size >= 1)
+      assert(lines.count { |line| line.start_with? '>test,EGGAGSSTGQR,' } >= 1)
+      assert(lines.count { |line| line.start_with? '>test,ENFVYIAK,' } >= 1)
+      assert(lines.count { |line| line.start_with? '>tost,EGGAGSSTGQR,' } >= 1)
     end
 
     def test_run_with_fasta_multiple_batches_json

test/commands/unipept/test_pept2taxa.rb

@@ -43,9 +43,9 @@ def test_run_with_fasta_multiple_batches
       lines = out.each_line
       assert_equal('', err)
       assert(lines.next.start_with? 'fasta_header,peptide,taxon_id,taxon_name,taxon_rank')
-      assert(lines.select { |line| line.start_with? '>test,EGGAGSSTGQR,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>test,ENFVYIAK,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>tost,EGGAGSSTGQR,' }.size >= 1)
+      assert(lines.count { |line| line.start_with? '>test,EGGAGSSTGQR,' } >= 1)
+      assert(lines.count { |line| line.start_with? '>test,ENFVYIAK,' } >= 1)
+      assert(lines.count { |line| line.start_with? '>tost,EGGAGSSTGQR,' } >= 1)
     end
 
     def test_run_with_fasta_multiple_batches_json

test/commands/unipept/test_taxonomy.rb

@@ -41,9 +41,9 @@ def test_run_with_fasta_multiple_batches
       lines = out.each_line
       assert_equal('', err)
       assert(lines.next.start_with? 'fasta_header,taxon_id,taxon_name,taxon_rank')
-      assert(lines.select { |line| line.start_with? '>test,1,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>test,216816,' }.size >= 1)
-      assert(lines.select { |line| line.start_with? '>tost,1,' }.size >= 1)
+      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)
     end
 
     def test_run_with_fasta_multiple_batches_json

test/test_retryable_typhoeus.rb

@@ -83,8 +83,8 @@ def test_failing_requests_finally_complete_with_error
 
     def new_request(extra_opts = {})
       ::RetryableTyphoeus::Request.new(
-          'stubbed.com',
-          request_options.merge(extra_opts)
+        'stubbed.com',
+        request_options.merge(extra_opts)
       )
     end