unipept 1.3.0 → 1.4.0

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Files changed (8) hide show
  1. checksums.yaml +5 -5
  2. data/.ruby-version +1 -1
  3. data/Gemfile +3 -1
  4. data/Gemfile.lock +59 -57
  5. data/VERSION +1 -1
  6. data/lib/commands/uniprot.rb +1 -1
  7. data/unipept.gemspec +7 -7
  8. metadata +7 -8
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data/.ruby-version CHANGED
@@ -1 +1 @@
1
- 2.4.0
1
+ 2.6.0
data/Gemfile CHANGED
@@ -2,7 +2,9 @@ source 'http://rubygems.org'
2
2
  # Add dependencies required to use your gem here.
3
3
  # Example:
4
4
  # gem "activesupport", ">= 2.3.5"
5
- gem 'cri', '~> 2.7'
5
+
6
+ # for now, stay on version 2.11 because of a bug
7
+ gem 'cri', '2.11'
6
8
  gem 'typhoeus', '~> 1.1'
7
9
 
8
10
  group :development do
data/Gemfile.lock CHANGED
@@ -1,101 +1,103 @@
1
1
  GEM
2
2
  remote: http://rubygems.org/
3
3
  specs:
4
- addressable (2.5.0)
5
- public_suffix (~> 2.0, >= 2.0.2)
6
- ast (2.3.0)
4
+ addressable (2.4.0)
5
+ ast (2.4.0)
7
6
  builder (3.2.3)
8
7
  colored (1.2)
9
- coveralls (0.8.18)
8
+ coveralls (0.8.22)
10
9
  json (>= 1.8, < 3)
11
- simplecov (~> 0.12.0)
10
+ simplecov (~> 0.16.1)
12
11
  term-ansicolor (~> 1.3)
13
- thor (~> 0.19.1)
12
+ thor (~> 0.19.4)
14
13
  tins (~> 1.6)
15
- cri (2.7.1)
14
+ cri (2.11.0)
16
15
  colored (~> 1.2)
17
16
  descendants_tracker (0.0.4)
18
17
  thread_safe (~> 0.3, >= 0.3.1)
19
- docile (1.1.5)
20
- ethon (0.10.1)
18
+ docile (1.3.1)
19
+ ethon (0.12.0)
21
20
  ffi (>= 1.3.0)
22
21
  faraday (0.9.2)
23
22
  multipart-post (>= 1.2, < 3)
24
- ffi (1.9.17)
25
- git (1.3.0)
26
- github_api (0.11.3)
27
- addressable (~> 2.3)
28
- descendants_tracker (~> 0.0.1)
23
+ ffi (1.10.0)
24
+ git (1.5.0)
25
+ github_api (0.16.0)
26
+ addressable (~> 2.4.0)
27
+ descendants_tracker (~> 0.0.4)
29
28
  faraday (~> 0.8, < 0.10)
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- hashie (>= 1.2)
31
- multi_json (>= 1.7.5, < 2.0)
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- nokogiri (~> 1.6.0)
33
- oauth2
34
- hashie (3.4.6)
35
- highline (1.7.8)
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- jeweler (2.3.2)
29
+ hashie (>= 3.4)
30
+ mime-types (>= 1.16, < 3.0)
31
+ oauth2 (~> 1.0)
32
+ hashie (3.6.0)
33
+ highline (2.0.0)
34
+ jaro_winkler (1.5.2)
35
+ jeweler (2.3.9)
37
36
  builder
38
- bundler (>= 1.0)
37
+ bundler
39
38
  git (>= 1.2.5)
40
- github_api (~> 0.11.0)
39
+ github_api (~> 0.16.0)
41
40
  highline (>= 1.6.15)
42
41
  nokogiri (>= 1.5.10)
43
- psych (~> 2.2)
42
+ psych
44
43
  rake
45
44
  rdoc
46
45
  semver2
47
- json (2.0.3)
48
- jwt (1.5.6)
49
- mini_portile2 (2.1.0)
50
- minitest (5.10.1)
51
- multi_json (1.12.1)
46
+ json (2.1.0)
47
+ jwt (2.1.0)
48
+ mime-types (2.99.3)
49
+ mini_portile2 (2.4.0)
50
+ minitest (5.11.3)
51
+ multi_json (1.13.1)
52
52
  multi_xml (0.6.0)
53
53
  multipart-post (2.0.0)
54
- nokogiri (1.6.8.1)
55
- mini_portile2 (~> 2.1.0)
56
- oauth2 (1.3.0)
57
- faraday (>= 0.8, < 0.11)
58
- jwt (~> 1.0)
54
+ nokogiri (1.10.1)
55
+ mini_portile2 (~> 2.4.0)
56
+ oauth2 (1.4.1)
57
+ faraday (>= 0.8, < 0.16.0)
58
+ jwt (>= 1.0, < 3.0)
59
59
  multi_json (~> 1.3)
60
60
  multi_xml (~> 0.5)
61
61
  rack (>= 1.2, < 3)
62
- parser (2.3.3.1)
63
- ast (~> 2.2)
64
- powerpack (0.1.1)
65
- psych (2.2.2)
66
- public_suffix (2.0.5)
67
- rack (2.0.1)
68
- rainbow (2.2.1)
62
+ parallel (1.13.0)
63
+ parser (2.6.0.0)
64
+ ast (~> 2.4.0)
65
+ powerpack (0.1.2)
66
+ psych (3.1.0)
67
+ rack (2.0.6)
68
+ rainbow (3.0.0)
69
69
  rake (10.5.0)
70
- rdoc (5.0.0)
71
- rubocop (0.47.0)
72
- parser (>= 2.3.3.1, < 3.0)
70
+ rdoc (6.1.1)
71
+ rubocop (0.63.0)
72
+ jaro_winkler (~> 1.5.1)
73
+ parallel (~> 1.10)
74
+ parser (>= 2.5, != 2.5.1.1)
73
75
  powerpack (~> 0.1)
74
- rainbow (>= 1.99.1, < 3.0)
76
+ rainbow (>= 2.2.2, < 4.0)
75
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  ruby-progressbar (~> 1.7)
76
- unicode-display_width (~> 1.0, >= 1.0.1)
77
- ruby-progressbar (1.8.1)
78
+ unicode-display_width (~> 1.4.0)
79
+ ruby-progressbar (1.10.0)
78
80
  semver2 (3.4.2)
79
- simplecov (0.12.0)
80
- docile (~> 1.1.0)
81
+ simplecov (0.16.1)
82
+ docile (~> 1.1)
81
83
  json (>= 1.8, < 3)
82
84
  simplecov-html (~> 0.10.0)
83
- simplecov-html (0.10.0)
84
- term-ansicolor (1.4.0)
85
+ simplecov-html (0.10.2)
86
+ term-ansicolor (1.7.1)
85
87
  tins (~> 1.0)
86
88
  thor (0.19.4)
87
- thread_safe (0.3.5)
88
- tins (1.13.0)
89
- typhoeus (1.1.2)
89
+ thread_safe (0.3.6)
90
+ tins (1.20.2)
91
+ typhoeus (1.3.1)
90
92
  ethon (>= 0.9.0)
91
- unicode-display_width (1.1.3)
93
+ unicode-display_width (1.4.1)
92
94
 
93
95
  PLATFORMS
94
96
  ruby
95
97
 
96
98
  DEPENDENCIES
97
99
  coveralls (~> 0)
98
- cri (~> 2.7)
100
+ cri (= 2.11)
99
101
  jeweler
100
102
  minitest (~> 5.7)
101
103
  rake (~> 10.4)
@@ -103,4 +105,4 @@ DEPENDENCIES
103
105
  typhoeus (~> 1.1)
104
106
 
105
107
  BUNDLED WITH
106
- 1.13.7
108
+ 1.17.2
data/VERSION CHANGED
@@ -1 +1 @@
1
- 1.3.0
1
+ 1.4.0
data/lib/commands/uniprot.rb CHANGED
@@ -61,7 +61,7 @@ module Unipept::Commands
61
61
  get_uniprot_entry(accession, 'fasta').lines.map(&:chomp)[1..-1].join('')
62
62
  else
63
63
  # other format has been specified, just download and output
64
- resp = Typhoeus.get("http://www.uniprot.org/uniprot/#{accession}.#{format}")
64
+ resp = Typhoeus.get("https://www.uniprot.org/uniprot/#{accession}.#{format}")
65
65
  resp.response_body if resp.success?
66
66
  end
67
67
  end
data/unipept.gemspec CHANGED
@@ -2,16 +2,16 @@
2
2
  # DO NOT EDIT THIS FILE DIRECTLY
3
3
  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
4
4
  # -*- encoding: utf-8 -*-
5
- # stub: unipept 1.3.0 ruby lib
5
+ # stub: unipept 1.4.0 ruby lib
6
6
 
7
7
  Gem::Specification.new do |s|
8
8
  s.name = "unipept".freeze
9
- s.version = "1.3.0"
9
+ s.version = "1.4.0"
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 = ["Toon Willems".freeze, "Bart Mesuere".freeze, "Tom Naessens".freeze]
14
- s.date = "2017-01-28"
14
+ s.date = "2019-01-18"
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]
@@ -78,21 +78,21 @@ Gem::Specification.new do |s|
78
78
  s.homepage = "http://unipept.ugent.be".freeze
79
79
  s.licenses = ["MIT".freeze]
80
80
  s.required_ruby_version = Gem::Requirement.new(">= 2.0.0".freeze)
81
- s.rubygems_version = "2.6.8".freeze
81
+ s.rubygems_version = "3.0.1".freeze
82
82
  s.summary = "Command line interface to Unipept web services.".freeze
83
83
 
84
84
  if s.respond_to? :specification_version then
85
85
  s.specification_version = 4
86
86
 
87
87
  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
88
- s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.7"])
88
+ s.add_runtime_dependency(%q<cri>.freeze, ["= 2.11"])
89
89
  s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.1"])
90
90
  s.add_development_dependency(%q<rake>.freeze, ["~> 10.4"])
91
91
  s.add_development_dependency(%q<minitest>.freeze, ["~> 5.7"])
92
92
  s.add_development_dependency(%q<rubocop>.freeze, ["~> 0.32"])
93
93
  s.add_development_dependency(%q<coveralls>.freeze, ["~> 0"])
94
94
  else
95
- s.add_dependency(%q<cri>.freeze, ["~> 2.7"])
95
+ s.add_dependency(%q<cri>.freeze, ["= 2.11"])
96
96
  s.add_dependency(%q<typhoeus>.freeze, ["~> 1.1"])
97
97
  s.add_dependency(%q<rake>.freeze, ["~> 10.4"])
98
98
  s.add_dependency(%q<minitest>.freeze, ["~> 5.7"])
@@ -100,7 +100,7 @@ Gem::Specification.new do |s|
100
100
  s.add_dependency(%q<coveralls>.freeze, ["~> 0"])
101
101
  end
102
102
  else
103
- s.add_dependency(%q<cri>.freeze, ["~> 2.7"])
103
+ s.add_dependency(%q<cri>.freeze, ["= 2.11"])
104
104
  s.add_dependency(%q<typhoeus>.freeze, ["~> 1.1"])
105
105
  s.add_dependency(%q<rake>.freeze, ["~> 10.4"])
106
106
  s.add_dependency(%q<minitest>.freeze, ["~> 5.7"])
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: 1.3.0
4
+ version: 1.4.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Toon Willems
@@ -10,22 +10,22 @@ authors:
10
10
  autorequire:
11
11
  bindir: bin
12
12
  cert_chain: []
13
- date: 2017-01-28 00:00:00.000000000 Z
13
+ date: 2019-01-18 00:00:00.000000000 Z
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency
16
16
  name: cri
17
17
  requirement: !ruby/object:Gem::Requirement
18
18
  requirements:
19
- - - "~>"
19
+ - - '='
20
20
  - !ruby/object:Gem::Version
21
- version: '2.7'
21
+ version: '2.11'
22
22
  type: :runtime
23
23
  prerelease: false
24
24
  version_requirements: !ruby/object:Gem::Requirement
25
25
  requirements:
26
- - - "~>"
26
+ - - '='
27
27
  - !ruby/object:Gem::Version
28
- version: '2.7'
28
+ version: '2.11'
29
29
  - !ruby/object:Gem::Dependency
30
30
  name: typhoeus
31
31
  requirement: !ruby/object:Gem::Requirement
@@ -184,8 +184,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
184
184
  - !ruby/object:Gem::Version
185
185
  version: '0'
186
186
  requirements: []
187
- rubyforge_project:
188
- rubygems_version: 2.6.8
187
+ rubygems_version: 3.0.1
189
188
  signing_key:
190
189
  specification_version: 4
191
190
  summary: Command line interface to Unipept web services.