unipept 3.0.1 → 3.1.0

Sign up to get free protection for your applications and to get access to all the features.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA256:
3
- metadata.gz: 7ae25b4963b7859c29cacb41da52979f14d5c4c475bcf301b39c4b462484d491
4
- data.tar.gz: 9964dc3d83bb794673a067a9aac45cd638b6248230972c2ea02a13dab4beaba4
3
+ metadata.gz: 91451cf1d23535a5698b259a004df798959fb0116a0dc8ba11c17e2c4bbdcf23
4
+ data.tar.gz: 2b68c81a3d284b50e2d20f51cc2655dac736a649fbe1f743062bb32d38fce903
5
5
  SHA512:
6
- metadata.gz: de2af48a091dc98dc745c451433fa91fcb95ba056fe0fda4520a455568de93f7b60125e9e5c4bb4c27fc97c35d8464daf3c09c371b19e6bcb51f516af9b6eff9
7
- data.tar.gz: 3952e4ec06d8f64a0c536f3cb02fba11d6470fc63b0aaa6d4ba3dcbdb2c0f77ed02857559962ea2458f7642f59c2bb67276e7c5a0915745eda1ec0f445a1b1e9
6
+ metadata.gz: b7dfc8ec5d8d16ab448a2935eb8697252b360aa675021624a52383147ba07c93ef76a4396935bdee3e06a5ed968bf7c6afa180d2513ab0b118ace98af855c108
7
+ data.tar.gz: 616446c5da67f407c78cac0b051042c61dc7c25a15fd03c44656f1f347d3eabf841c4a4e80e0e17c4d2d54b1b4698578ca1a5d074fcbf0bf69d170abd8b503a5
@@ -0,0 +1,18 @@
1
+ // For format details, see https://aka.ms/devcontainer.json. For config options, see the
2
+ // README at: https://github.com/devcontainers/templates/tree/main/src/ruby
3
+ {
4
+ "name": "Ruby",
5
+ // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
6
+ "image": "mcr.microsoft.com/devcontainers/ruby:1-3.2-bookworm",
7
+ // Features to add to the dev container. More info: https://containers.dev/features.
8
+ // "features": {},
9
+ // Use 'forwardPorts' to make a list of ports inside the container available locally.
10
+ // "forwardPorts": [],
11
+ // Use 'postCreateCommand' to run commands after the container is created.
12
+ "postCreateCommand": "ruby --version",
13
+ "postStartCommand": "bundle install"
14
+ // Configure tool-specific properties.
15
+ // "customizations": {},
16
+ // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
17
+ // "remoteUser": "root"
18
+ }
@@ -7,7 +7,7 @@ jobs:
7
7
  runs-on: ubuntu-latest
8
8
  strategy:
9
9
  matrix:
10
- ruby: ["2.7", "3.0", "3.1"]
10
+ ruby: ["2.7", "3.0", "3.1", "3.2"]
11
11
  fail-fast: false
12
12
  name: Test Ruby ${{ matrix.ruby }}
13
13
  steps:
data/.rubocop.yml CHANGED
@@ -15,6 +15,8 @@ Style/FrozenStringLiteralComment:
15
15
  # disable for now
16
16
  Lint/NestedMethodDefinition:
17
17
  Enabled: false
18
+ Lint/Lint/RedundantStringCoercion:
19
+ Enabled: false
18
20
  Style/ClassVars:
19
21
  Enabled: false
20
22
  Style/Documentation:
@@ -0,0 +1,28 @@
1
+ {
2
+ "version": "2.0.0",
3
+ "tasks": [
4
+ {
5
+ "type": "rake",
6
+ "task": "test_style:autocorrect_all",
7
+ "group": "test",
8
+ "problemMatcher": [],
9
+ "label": "rake: test_style:autocorrect_all"
10
+ },
11
+ {
12
+ "type": "rake",
13
+ "task": "test",
14
+ "group": {
15
+ "kind": "test",
16
+ "isDefault": true
17
+ },
18
+ "problemMatcher": [],
19
+ "label": "rake: test"
20
+ },
21
+ {
22
+ "type": "shell",
23
+ "command": "bundle exec rake gemspec",
24
+ "label": "generate gemspec",
25
+ "problemMatcher": []
26
+ }
27
+ ]
28
+ }
data/Gemfile CHANGED
@@ -2,15 +2,15 @@ source 'http://rubygems.org'
2
2
  # Add dependencies required to use your gem here.
3
3
 
4
4
  gem 'cri', '~>2.15.10'
5
- gem 'typhoeus', '~> 1.3.1'
5
+ gem 'typhoeus', '~> 1.4.0'
6
6
 
7
7
  # this is not explicitly used, but an older incompatible version comes bundled with ruby
8
- gem 'psych', '~> 4.0.3'
8
+ gem 'psych', '~> 5.1.0'
9
9
 
10
10
  group :development do
11
- gem 'minitest', '~> 5.14'
11
+ gem 'minitest', '~> 5.18'
12
12
  gem 'rake', '~> 13.0.1'
13
- gem 'rubocop', '~>1.11'
13
+ gem 'rubocop', '~>1.50'
14
14
  end
15
15
 
16
16
  group :release do
data/Gemfile.lock CHANGED
@@ -8,15 +8,16 @@ GEM
8
8
  cri (2.15.11)
9
9
  descendants_tracker (0.0.4)
10
10
  thread_safe (~> 0.3, >= 0.3.1)
11
- ethon (0.12.0)
12
- ffi (>= 1.3.0)
11
+ ethon (0.16.0)
12
+ ffi (>= 1.15.0)
13
13
  faraday (1.3.0)
14
14
  faraday-net_http (~> 1.0)
15
15
  multipart-post (>= 1.2, < 3)
16
16
  ruby2_keywords
17
17
  faraday-net_http (1.0.1)
18
- ffi (1.12.1)
19
- git (1.8.1)
18
+ ffi (1.15.5)
19
+ git (1.18.0)
20
+ addressable (~> 2.8)
20
21
  rchardet (~> 1.8)
21
22
  github_api (0.19.0)
22
23
  addressable (~> 2.4)
@@ -26,6 +27,7 @@ GEM
26
27
  oauth2 (~> 1.0)
27
28
  hashie (3.6.0)
28
29
  highline (2.0.3)
30
+ json (2.6.3)
29
31
  juwelier (2.4.9)
30
32
  builder
31
33
  bundler
@@ -42,53 +44,54 @@ GEM
42
44
  kamelcase (0.0.2)
43
45
  semver2 (~> 3)
44
46
  mini_portile2 (2.8.0)
45
- minitest (5.15.0)
47
+ minitest (5.18.1)
46
48
  multi_json (1.15.0)
47
49
  multi_xml (0.6.0)
48
50
  multipart-post (2.1.1)
49
- nokogiri (1.13.4)
51
+ nokogiri (1.13.10)
50
52
  mini_portile2 (~> 2.8.0)
51
53
  racc (~> 1.4)
52
- oauth2 (1.4.4)
53
- faraday (>= 0.8, < 2.0)
54
+ oauth2 (1.4.11)
55
+ faraday (>= 0.17.3, < 3.0)
54
56
  jwt (>= 1.0, < 3.0)
55
57
  multi_json (~> 1.3)
56
58
  multi_xml (~> 0.5)
57
- rack (>= 1.2, < 3)
58
- parallel (1.22.1)
59
- parser (3.1.1.0)
59
+ rack (>= 1.2, < 4)
60
+ parallel (1.23.0)
61
+ parser (3.2.2.1)
60
62
  ast (~> 2.4.1)
61
- psych (4.0.3)
63
+ psych (5.1.0)
62
64
  stringio
63
65
  public_suffix (4.0.6)
64
- racc (1.6.0)
65
- rack (2.2.3)
66
+ racc (1.6.1)
67
+ rack (3.0.7)
66
68
  rainbow (3.1.1)
67
69
  rake (13.0.6)
68
70
  rchardet (1.8.0)
69
71
  rdoc (6.4.0)
70
72
  psych (>= 4.0.0)
71
- regexp_parser (2.3.0)
73
+ regexp_parser (2.8.0)
72
74
  rexml (3.2.5)
73
- rubocop (1.27.0)
75
+ rubocop (1.50.2)
76
+ json (~> 2.3)
74
77
  parallel (~> 1.10)
75
- parser (>= 3.1.0.0)
78
+ parser (>= 3.2.0.0)
76
79
  rainbow (>= 2.2.2, < 4.0)
77
80
  regexp_parser (>= 1.8, < 3.0)
78
- rexml
79
- rubocop-ast (>= 1.16.0, < 2.0)
81
+ rexml (>= 3.2.5, < 4.0)
82
+ rubocop-ast (>= 1.28.0, < 2.0)
80
83
  ruby-progressbar (~> 1.7)
81
- unicode-display_width (>= 1.4.0, < 3.0)
82
- rubocop-ast (1.17.0)
83
- parser (>= 3.1.1.0)
84
- ruby-progressbar (1.11.0)
84
+ unicode-display_width (>= 2.4.0, < 3.0)
85
+ rubocop-ast (1.28.0)
86
+ parser (>= 3.2.1.0)
87
+ ruby-progressbar (1.13.0)
85
88
  ruby2_keywords (0.0.4)
86
89
  semver2 (3.4.2)
87
- stringio (3.0.1)
90
+ stringio (3.0.6)
88
91
  thread_safe (0.3.6)
89
- typhoeus (1.3.1)
92
+ typhoeus (1.4.0)
90
93
  ethon (>= 0.9.0)
91
- unicode-display_width (2.1.0)
94
+ unicode-display_width (2.4.2)
92
95
 
93
96
  PLATFORMS
94
97
  ruby
@@ -96,11 +99,11 @@ PLATFORMS
96
99
  DEPENDENCIES
97
100
  cri (~> 2.15.10)
98
101
  juwelier
99
- minitest (~> 5.14)
100
- psych (~> 4.0.3)
102
+ minitest (~> 5.18)
103
+ psych (~> 5.1.0)
101
104
  rake (~> 13.0.1)
102
- rubocop (~> 1.11)
103
- typhoeus (~> 1.3.1)
105
+ rubocop (~> 1.50)
106
+ typhoeus (~> 1.4.0)
104
107
 
105
108
  BUNDLED WITH
106
- 1.17.2
109
+ 2.4.12
data/README.md CHANGED
@@ -7,7 +7,7 @@ Documentation about the web service can be found at [http://unipept.ugent.be/api
7
7
 
8
8
  ## Installation
9
9
 
10
- 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:
10
+ To use the Unipept CLI, Ruby version 2.7 or higher needs to be installed. You can check this by running `ruby -v` on the commandline:
11
11
 
12
12
  ```
13
13
  $ ruby -v
data/Rakefile CHANGED
@@ -25,8 +25,8 @@ begin
25
25
  commands for handling proteins using the command line.
26
26
  EOS
27
27
  gem.email = 'unipept@ugent.be'
28
- gem.authors = ['Bart Mesuere', 'Pieter Verschaffelt', 'Toon Willems', 'Tom Naessens']
29
- gem.required_ruby_version = '>= 2.6.0'
28
+ gem.authors = ['Bart Mesuere', 'Pieter Verschaffelt', 'Tibo Vande Moortele', 'Toon Willems', 'Tom Naessens']
29
+ gem.required_ruby_version = '>= 2.7.0'
30
30
  end
31
31
  Juwelier::RubygemsDotOrgTasks.new
32
32
  rescue LoadError
data/VERSION CHANGED
@@ -1 +1 @@
1
- 3.0.1
1
+ 3.1.0
@@ -0,0 +1,12 @@
1
+ require_relative 'api_runner'
2
+ module Unipept::Commands
3
+ class Protinfo < ApiRunner
4
+ def required_fields
5
+ ['protein']
6
+ end
7
+
8
+ def default_batch_size
9
+ 1000
10
+ end
11
+ end
12
+ end
@@ -17,6 +17,7 @@ require_relative 'unipept/pept2lca'
17
17
  require_relative 'unipept/pept2prot'
18
18
  require_relative 'unipept/pept2taxa'
19
19
  require_relative 'unipept/peptinfo'
20
+ require_relative 'unipept/protinfo'
20
21
  require_relative 'unipept/taxa2lca'
21
22
  require_relative 'unipept/taxonomy'
22
23
  require_relative 'unipept/taxa2tree'
@@ -33,6 +34,7 @@ module Unipept
33
34
  add_pept2interpro_command
34
35
  add_pept2lca_command
35
36
  add_peptinfo_command
37
+ add_protinfo_command
36
38
  add_taxa2lca_command
37
39
  add_pept2prot_command
38
40
  add_taxonomy_command
@@ -271,6 +273,28 @@ module Unipept
271
273
  end
272
274
  end
273
275
 
276
+ def add_protinfo_command
277
+ @root_command.define_command('protinfo') do
278
+ usage 'protinfo [options]'
279
+ summary 'Fetch functional and taxonomic information of UniProt ids'
280
+ description <<-EOS
281
+ For each UniProt id the unipept protinfo command retrieves from Unipept the functional information and the NCBI id. The command expects a list of UniProt ids that are passed
282
+
283
+ - as separate command line arguments
284
+
285
+ - in a text file that is passed as an argument to the -i option
286
+
287
+ - to standard input
288
+
289
+ The command will give priority to the first way tryptic peptides are passed, in the order as listed above. Text files and standard input should have one tryptic peptide per line.
290
+ EOS
291
+
292
+ option :s, :select, 'select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used.', argument: :required, multiple: true
293
+
294
+ runner Commands::Protinfo
295
+ end
296
+ end
297
+
274
298
  def add_taxa2lca_command
275
299
  @root_command.define_command('taxa2lca') do
276
300
  usage 'taxa2lca [options]'
@@ -60,7 +60,7 @@ module Unipept::Commands
60
60
  get_uniprot_entry(accession, 'fasta').lines.map(&:chomp)[1..].join
61
61
  else
62
62
  # other format has been specified, just download and output
63
- resp = Typhoeus.get("https://www.uniprot.org/uniprot/#{accession}.#{format}")
63
+ resp = Typhoeus.get("https://rest.uniprot.org/uniprotkb/#{accession}.#{format}")
64
64
  resp.response_body if resp.success?
65
65
  end
66
66
  end
@@ -0,0 +1,45 @@
1
+ require_relative '../../../lib/commands'
2
+
3
+ module Unipept
4
+ class UnipeptProtinfoTestCase < Unipept::TestCase
5
+ def test_default_batch_size
6
+ command = Cri::Command.define { name 'protinfo' }
7
+ protinfo = Commands::Protinfo.new({ host: 'http://api.unipept.ugent.be' }, [], command)
8
+ assert_equal(1000, protinfo.default_batch_size)
9
+ end
10
+
11
+ def test_required_fields
12
+ command = Cri::Command.define { name 'protinfo' }
13
+ protinfo = Commands::Protinfo.new({ host: 'http://api.unipept.ugent.be' }, [], command)
14
+ assert_equal(['protein'], protinfo.required_fields)
15
+ end
16
+
17
+ def test_argument_batch_size
18
+ command = Cri::Command.define { name 'protinfo' }
19
+ protinfo = Commands::Protinfo.new({ host: 'http://api.unipept.ugent.be', batch: '123' }, [], command)
20
+ assert_equal(123, protinfo.batch_size)
21
+ end
22
+
23
+ def test_batch_size
24
+ command = Cri::Command.define { name 'protinfo' }
25
+ protinfo = Commands::Protinfo.new({ host: 'http://api.unipept.ugent.be' }, [], command)
26
+ assert_equal(1000, protinfo.batch_size)
27
+ end
28
+
29
+ def test_help
30
+ out, _err = capture_io_while do
31
+ assert_raises SystemExit do
32
+ Commands::Unipept.run(%w[protinfo -h])
33
+ end
34
+ end
35
+ assert(out.include?('show help for this command'))
36
+
37
+ out, _err = capture_io_while do
38
+ assert_raises SystemExit do
39
+ Commands::Unipept.run(%w[protinfo --help])
40
+ end
41
+ end
42
+ assert(out.include?('show help for this command'))
43
+ end
44
+ end
45
+ end
data/test/helper.rb CHANGED
@@ -85,4 +85,4 @@ module Unipept
85
85
  end
86
86
 
87
87
  # Unexpected system exit is unexpected
88
- ::MiniTest::Unit::TestCase::PASSTHROUGH_EXCEPTIONS.delete(SystemExit)
88
+ MiniTest::Unit::TestCase::PASSTHROUGH_EXCEPTIONS.delete(SystemExit)
data/unipept.gemspec CHANGED
@@ -1,17 +1,17 @@
1
1
  # Generated by juwelier
2
2
  # DO NOT EDIT THIS FILE DIRECTLY
3
- # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
3
+ # Instead, edit Juwelier::Tasks in rakefile, and run 'rake gemspec'
4
4
  # -*- encoding: utf-8 -*-
5
- # stub: unipept 3.0.1 ruby lib
5
+ # stub: unipept 3.1.0 ruby lib
6
6
 
7
7
  Gem::Specification.new do |s|
8
8
  s.name = "unipept".freeze
9
- s.version = "3.0.1"
9
+ s.version = "3.1.0"
10
10
 
11
11
  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
12
12
  s.require_paths = ["lib".freeze]
13
13
  s.authors = ["Bart Mesuere".freeze, "Pieter Verschaffelt".freeze, "Toon Willems".freeze, "Tom Naessens".freeze]
14
- s.date = "2022-04-27"
14
+ s.date = "2023-07-24"
15
15
  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
16
16
  s.email = "unipept@ugent.be".freeze
17
17
  s.executables = ["unipept".freeze, "prot2pept".freeze, "peptfilter".freeze, "uniprot".freeze]
@@ -20,12 +20,14 @@ Gem::Specification.new do |s|
20
20
  "README.md"
21
21
  ]
22
22
  s.files = [
23
+ ".devcontainer/devcontainer.json",
23
24
  ".document",
24
25
  ".github/dependabot.yml",
25
26
  ".github/workflows/ci.yml",
26
27
  ".rakeTasks",
27
28
  ".rubocop.yml",
28
29
  ".ruby-version",
30
+ ".vscode/tasks.json",
29
31
  "CITATION.cff",
30
32
  "Gemfile",
31
33
  "Gemfile.lock",
@@ -53,6 +55,7 @@ Gem::Specification.new do |s|
53
55
  "lib/commands/unipept/pept2prot.rb",
54
56
  "lib/commands/unipept/pept2taxa.rb",
55
57
  "lib/commands/unipept/peptinfo.rb",
58
+ "lib/commands/unipept/protinfo.rb",
56
59
  "lib/commands/unipept/taxa2lca.rb",
57
60
  "lib/commands/unipept/taxa2tree.rb",
58
61
  "lib/commands/unipept/taxonomy.rb",
@@ -78,6 +81,7 @@ Gem::Specification.new do |s|
78
81
  "test/commands/unipept/test_pept2prot.rb",
79
82
  "test/commands/unipept/test_pept2taxa.rb",
80
83
  "test/commands/unipept/test_peptinfo.rb",
84
+ "test/commands/unipept/test_protinfo.rb",
81
85
  "test/commands/unipept/test_taxa2lca.rb",
82
86
  "test/commands/unipept/test_taxa2tree.rb",
83
87
  "test/commands/unipept/test_taxonomy.rb",
@@ -105,27 +109,16 @@ Gem::Specification.new do |s|
105
109
  s.homepage = "http://unipept.ugent.be".freeze
106
110
  s.licenses = ["MIT".freeze]
107
111
  s.required_ruby_version = Gem::Requirement.new(">= 2.6.0".freeze)
108
- s.rubygems_version = "3.2.15".freeze
112
+ s.rubygems_version = "3.4.10".freeze
109
113
  s.summary = "Command line interface to Unipept web services.".freeze
110
114
 
111
- if s.respond_to? :specification_version then
112
- s.specification_version = 4
113
- end
115
+ s.specification_version = 4
114
116
 
115
- if s.respond_to? :add_runtime_dependency then
116
- s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.15.10"])
117
- s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
118
- s.add_runtime_dependency(%q<psych>.freeze, ["~> 4.0.3"])
119
- s.add_development_dependency(%q<minitest>.freeze, ["~> 5.14"])
120
- s.add_development_dependency(%q<rake>.freeze, ["~> 13.0.1"])
121
- s.add_development_dependency(%q<rubocop>.freeze, ["~> 1.11"])
122
- else
123
- s.add_dependency(%q<cri>.freeze, ["~> 2.15.10"])
124
- s.add_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
125
- s.add_dependency(%q<psych>.freeze, ["~> 4.0.3"])
126
- s.add_dependency(%q<minitest>.freeze, ["~> 5.14"])
127
- s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
128
- s.add_dependency(%q<rubocop>.freeze, ["~> 1.11"])
129
- end
117
+ s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.15.10"])
118
+ s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.4.0"])
119
+ s.add_runtime_dependency(%q<psych>.freeze, ["~> 5.1.0"])
120
+ s.add_development_dependency(%q<minitest>.freeze, ["~> 5.18"])
121
+ s.add_development_dependency(%q<rake>.freeze, ["~> 13.0.1"])
122
+ s.add_development_dependency(%q<rubocop>.freeze, ["~> 1.50"])
130
123
  end
131
124
 
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: unipept
3
3
  version: !ruby/object:Gem::Version
4
- version: 3.0.1
4
+ version: 3.1.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Bart Mesuere
@@ -11,7 +11,7 @@ authors:
11
11
  autorequire:
12
12
  bindir: bin
13
13
  cert_chain: []
14
- date: 2022-04-27 00:00:00.000000000 Z
14
+ date: 2023-07-24 00:00:00.000000000 Z
15
15
  dependencies:
16
16
  - !ruby/object:Gem::Dependency
17
17
  name: cri
@@ -33,42 +33,42 @@ dependencies:
33
33
  requirements:
34
34
  - - "~>"
35
35
  - !ruby/object:Gem::Version
36
- version: 1.3.1
36
+ version: 1.4.0
37
37
  type: :runtime
38
38
  prerelease: false
39
39
  version_requirements: !ruby/object:Gem::Requirement
40
40
  requirements:
41
41
  - - "~>"
42
42
  - !ruby/object:Gem::Version
43
- version: 1.3.1
43
+ version: 1.4.0
44
44
  - !ruby/object:Gem::Dependency
45
45
  name: psych
46
46
  requirement: !ruby/object:Gem::Requirement
47
47
  requirements:
48
48
  - - "~>"
49
49
  - !ruby/object:Gem::Version
50
- version: 4.0.3
50
+ version: 5.1.0
51
51
  type: :runtime
52
52
  prerelease: false
53
53
  version_requirements: !ruby/object:Gem::Requirement
54
54
  requirements:
55
55
  - - "~>"
56
56
  - !ruby/object:Gem::Version
57
- version: 4.0.3
57
+ version: 5.1.0
58
58
  - !ruby/object:Gem::Dependency
59
59
  name: minitest
60
60
  requirement: !ruby/object:Gem::Requirement
61
61
  requirements:
62
62
  - - "~>"
63
63
  - !ruby/object:Gem::Version
64
- version: '5.14'
64
+ version: '5.18'
65
65
  type: :development
66
66
  prerelease: false
67
67
  version_requirements: !ruby/object:Gem::Requirement
68
68
  requirements:
69
69
  - - "~>"
70
70
  - !ruby/object:Gem::Version
71
- version: '5.14'
71
+ version: '5.18'
72
72
  - !ruby/object:Gem::Dependency
73
73
  name: rake
74
74
  requirement: !ruby/object:Gem::Requirement
@@ -89,14 +89,14 @@ dependencies:
89
89
  requirements:
90
90
  - - "~>"
91
91
  - !ruby/object:Gem::Version
92
- version: '1.11'
92
+ version: '1.50'
93
93
  type: :development
94
94
  prerelease: false
95
95
  version_requirements: !ruby/object:Gem::Requirement
96
96
  requirements:
97
97
  - - "~>"
98
98
  - !ruby/object:Gem::Version
99
- version: '1.11'
99
+ version: '1.50'
100
100
  description: |2
101
101
  Command line interface to the Unipept (http://unipept.ugent.be) web services
102
102
  (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
@@ -112,12 +112,14 @@ extra_rdoc_files:
112
112
  - LICENSE.txt
113
113
  - README.md
114
114
  files:
115
+ - ".devcontainer/devcontainer.json"
115
116
  - ".document"
116
117
  - ".github/dependabot.yml"
117
118
  - ".github/workflows/ci.yml"
118
119
  - ".rakeTasks"
119
120
  - ".rubocop.yml"
120
121
  - ".ruby-version"
122
+ - ".vscode/tasks.json"
121
123
  - CITATION.cff
122
124
  - Gemfile
123
125
  - Gemfile.lock
@@ -145,6 +147,7 @@ files:
145
147
  - lib/commands/unipept/pept2prot.rb
146
148
  - lib/commands/unipept/pept2taxa.rb
147
149
  - lib/commands/unipept/peptinfo.rb
150
+ - lib/commands/unipept/protinfo.rb
148
151
  - lib/commands/unipept/taxa2lca.rb
149
152
  - lib/commands/unipept/taxa2tree.rb
150
153
  - lib/commands/unipept/taxonomy.rb
@@ -170,6 +173,7 @@ files:
170
173
  - test/commands/unipept/test_pept2prot.rb
171
174
  - test/commands/unipept/test_pept2taxa.rb
172
175
  - test/commands/unipept/test_peptinfo.rb
176
+ - test/commands/unipept/test_protinfo.rb
173
177
  - test/commands/unipept/test_taxa2lca.rb
174
178
  - test/commands/unipept/test_taxa2tree.rb
175
179
  - test/commands/unipept/test_taxonomy.rb
@@ -212,7 +216,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
212
216
  - !ruby/object:Gem::Version
213
217
  version: '0'
214
218
  requirements: []
215
- rubygems_version: 3.2.15
219
+ rubygems_version: 3.4.10
216
220
  signing_key:
217
221
  specification_version: 4
218
222
  summary: Command line interface to Unipept web services.