bananomia 0.1.0 → 0.1.2

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 (12) hide show
  1. checksums.yaml +4 -4
  2. data/.github/workflows/main.yml +5 -2
  3. data/.gitignore +3 -1
  4. data/CHANGELOG.md +15 -0
  5. data/LICENSE.txt +6 -9
  6. data/README.md +6 -4
  7. data/bananomia.gemspec +6 -11
  8. data/lib/bananomia/error.rb +1 -1
  9. data/lib/bananomia/request.rb +1 -1
  10. data/lib/bananomia/version.rb +1 -1
  11. metadata +45 -46
  12. data/Gemfile.lock +0 -53
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data/.github/workflows/main.yml CHANGED
@@ -5,12 +5,15 @@ on: [push,pull_request]
5
5
  jobs:
6
6
  build:
7
7
  runs-on: ubuntu-latest
8
+ strategy:
9
+ matrix:
10
+ ruby-version: ['3.3.4', '4.0.0']
8
11
  steps:
9
12
  - uses: actions/checkout@v2
10
- - name: Set up Ruby
13
+ - name: Set up Ruby ${{ matrix.ruby-version }}
11
14
  uses: ruby/setup-ruby@v1
12
15
  with:
13
- ruby-version: 3.1.3
16
+ ruby-version: ${{ matrix.ruby-version }}
14
17
  bundler-cache: true
15
18
  - name: Run the default task
16
19
  run: bundle exec rake
data/.gitignore CHANGED
@@ -6,4 +6,6 @@
6
6
  /doc/
7
7
  /pkg/
8
8
  /spec/reports/
9
- /tmp/
9
+ /tmp/
10
+ /logo
11
+ Gemfile.lock
data/CHANGELOG.md CHANGED
@@ -1,5 +1,20 @@
1
1
  ## [Unreleased]
2
2
 
3
+ ## [0.1.2] - 2026-06-17
4
+ - Allow Ruby 4.0.0:
5
+ - Relaxed `required_ruby_version` to `>= 2.5.0, < 5.0`
6
+ - Added Ruby 4.0.0 to the CI matrix
7
+ - Bumped `faraday-follow_redirects` upper bound to allow 0.5+ (which lifts the Ruby < 4 cap)
8
+ - Dropped the `bundler` development dependency
9
+ - Added `irb` development dependency (no longer in stdlib)
10
+ - Fixed `Bananomia.search_occurrences` (and other endpoints) being blocked by Bionomia's Cloudflare bot mitigation by requesting strictly `Accept: application/ld+json` instead of `application/ld+json,*/*`
11
+ - Updated license from NCSA to MIT
12
+
13
+ ## [0.1.1] - 2024-09-11
14
+ - Updated documentation
15
+ - Removed Gemfile.lock
16
+ - Bumped development depency versions to avoid CVE-2024-43398
17
+
3
18
  ## [0.1.0] - 2022-01-20
4
19
 
5
20
  - Initial release
data/LICENSE.txt CHANGED
@@ -1,13 +1,10 @@
1
- Copyright © 2023 Species File Group. All rights reserved.
1
+ The MIT License (MIT)
2
2
 
3
- Developed by: Species File Group
4
- Illinois Natural History Survey
5
- https://github.com/SpeciesFileGroup/bananomia
3
+ Copyright © 2024 Species File Group
6
4
 
7
- Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
8
6
 
9
- Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers.
10
- Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution.
11
- Neither the names of <Name of Development Group, Name of Institution>, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission.
7
+ The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
8
+
9
+ THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
12
10
 
13
- THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
data/README.md CHANGED
@@ -1,6 +1,8 @@
1
1
  # Bananomia
2
2
 
3
- This is a Ruby wrapper on the [Bionomia](https://bionomia.net) API. Code follow the spirit/approach of the Gem [serrano](https://github.com/sckott/serrano), and indeed much of the wrapping utility is copied 1:1 from that repo, thanks [@sckott](https://github.com/sckott).
3
+ ![Bananomia logo](https://github.com/SpeciesFileGroup/bananomia/assets/8573609/cb3f07e6-081f-4187-a11f-3aa1f8b24106)
4
+
5
+ Bananomia is a Ruby wrapper on the [Bionomia](https://bionomia.net) API. Code follow the spirit/approach of the Gem [serrano](https://github.com/sckott/serrano), and indeed much of the wrapping utility is copied 1:1 from that repo, thanks [@sckott](https://github.com/sckott).
4
6
 
5
7
  ## Installation
6
8
 
@@ -105,7 +107,7 @@ Bananomia.occurrence('477976412') # => JSON-LD object
105
107
 
106
108
  Parse authorships with names separated by `;` and each authorship set separated by `\r\n`:
107
109
  ```ruby
108
- Bananomia.parse(names: 'Henry Robert Nicollon des Abbayes; Groom Q\r\nMrs. John Errol Chandos Aberdeen') # => MultiJson object
110
+ Bananomia.parse('Henry Robert Nicollon des Abbayes; Groom Q\r\nMrs. John Errol Chandos Aberdeen') # => MultiJson object
109
111
  ```
110
112
 
111
113
  ---
@@ -114,7 +116,7 @@ Bananomia.parse(names: 'Henry Robert Nicollon des Abbayes; Groom Q\r\nMrs. John
114
116
 
115
117
  After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake test` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
116
118
 
117
- To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and the created tag, and push the `.gem` file to [rubygems.org](https://rubygems.org).
119
+ To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, update the `CHANGELOG.md`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and the created tag, and push the `.gem` file to [rubygems.org](https://rubygems.org).
118
120
 
119
121
  ## Contributing
120
122
 
@@ -122,7 +124,7 @@ Bug reports and pull requests are welcome on GitHub at https://github.com/Specie
122
124
 
123
125
  ## License
124
126
 
125
- The gem is available as open source under the terms of the [NCSA/Illinois](https://github.com/SpeciesFileGroup/bananomia/blob/main/LICENSE.txt) license. You can learn more about the NCSA license on [Wikipedia](https://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License) and compare it with other open source licenses at the [Open Source Initiative](https://opensource.org/license/uoi-ncsa-php/).
127
+ The gem is available as open source under the terms of the [MIT license](https://github.com/SpeciesFileGroup/bananomia/blob/main/LICENSE.txt). You can learn more about the MIT license on [Wikipedia](https://en.wikipedia.org/wiki/MIT_License) and compare it with other open source licenses at the [Open Source Initiative](https://opensource.org/license/mit/).
126
128
 
127
129
  ## Code of Conduct
128
130
 
data/bananomia.gemspec CHANGED
@@ -11,8 +11,8 @@ Gem::Specification.new do |s|
11
11
  s.summary = "Bionomia Client"
12
12
  s.description = "Bananomia is a low-level wrapper around the Bionomia API."
13
13
  s.homepage = "https://github.com/SpeciesFileGroup/bananomia"
14
- s.license = "NCSA"
15
- s.required_ruby_version = ">= 2.4.0"
14
+ s.license = "MIT"
15
+ s.required_ruby_version = [">= 2.5.0", "< 5.0"]
16
16
 
17
17
  # s.metadata["allowed_push_host"] = "TODO: Set to 'https://mygemserver.com'"
18
18
 
@@ -32,23 +32,18 @@ Gem::Specification.new do |s|
32
32
  # Uncomment to register a new dependency of your gem
33
33
  # s.add_dependency "example-gem", "~> 1.0"
34
34
 
35
- s.add_development_dependency "bundler", "~> 2.1", ">= 2.1.4"
36
- # s.add_development_dependency "codecov", "~> 0.5.0"
37
- # s.add_development_dependency "json", "~> 2.3", ">= 2.3.1"
38
35
  s.add_development_dependency "rake", "~> 13.0", ">= 13.0.1"
39
- # s.add_development_dependency "standard", "~> 1.0"
40
- # s.add_development_dependency "simplecov", "~> 0.21.2"
41
36
  s.add_development_dependency "test-unit", "~> 3.3", ">= 3.3.6"
42
37
  s.add_development_dependency "vcr", "~> 6.0"
43
38
  s.add_development_dependency "webmock", "~> 3.18"
39
+ s.add_development_dependency "rexml", "~> 3.3", ">= 3.3.6"
40
+ s.add_development_dependency "irb", "~> 1.0"
41
+ # s.add_development_dependency "byebug"
44
42
 
45
43
  s.add_runtime_dependency "faraday", "~> 2.2"
46
- s.add_runtime_dependency "faraday-follow_redirects", ">= 0.1", "< 0.4"
44
+ s.add_runtime_dependency "faraday-follow_redirects", ">= 0.1", "< 0.6"
47
45
  s.add_runtime_dependency "multi_json", "~> 1.15"
48
46
 
49
- # TODO: comment out
50
- s.add_development_dependency "byebug"
51
-
52
47
  # s.add_runtime_dependency "thor", "~> 1.0", ">= 1.0.1"
53
48
 
54
49
  # For more information and examples about making a new gem, checkout our
data/lib/bananomia/error.rb CHANGED
@@ -21,4 +21,4 @@ module Bananomia
21
21
 
22
22
  # Raised when Bionomia returns the HTTP status code 504
23
23
  class GatewayTimeout < Error; end
24
- end
24
+ end
data/lib/bananomia/request.rb CHANGED
@@ -64,7 +64,7 @@ module Bananomia
64
64
  end
65
65
  end
66
66
 
67
- conn.headers['Accept'] = 'application/ld+json,*/*'
67
+ conn.headers['Accept'] = 'application/ld+json'
68
68
  conn.headers[:user_agent] = make_user_agent
69
69
  conn.headers["X-USER-AGENT"] = make_user_agent
70
70
 
data/lib/bananomia/version.rb CHANGED
@@ -1,5 +1,5 @@
1
1
  # frozen_string_literal: true
2
2
 
3
3
  module Bananomia
4
- VERSION = "0.1.0"
4
+ VERSION = "0.1.2"
5
5
  end
metadata CHANGED
@@ -1,35 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bananomia
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.1.0
4
+ version: 0.1.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - Geoff Ower, Matt Yoder
8
- autorequire:
9
8
  bindir: exe
10
9
  cert_chain: []
11
- date: 2023-08-30 00:00:00.000000000 Z
10
+ date: 1980-01-02 00:00:00.000000000 Z
12
11
  dependencies:
13
- - !ruby/object:Gem::Dependency
14
- name: bundler
15
- requirement: !ruby/object:Gem::Requirement
16
- requirements:
17
- - - "~>"
18
- - !ruby/object:Gem::Version
19
- version: '2.1'
20
- - - ">="
21
- - !ruby/object:Gem::Version
22
- version: 2.1.4
23
- type: :development
24
- prerelease: false
25
- version_requirements: !ruby/object:Gem::Requirement
26
- requirements:
27
- - - "~>"
28
- - !ruby/object:Gem::Version
29
- version: '2.1'
30
- - - ">="
31
- - !ruby/object:Gem::Version
32
- version: 2.1.4
33
12
  - !ruby/object:Gem::Dependency
34
13
  name: rake
35
14
  requirement: !ruby/object:Gem::Requirement
@@ -98,6 +77,40 @@ dependencies:
98
77
  - - "~>"
99
78
  - !ruby/object:Gem::Version
100
79
  version: '3.18'
80
+ - !ruby/object:Gem::Dependency
81
+ name: rexml
82
+ requirement: !ruby/object:Gem::Requirement
83
+ requirements:
84
+ - - "~>"
85
+ - !ruby/object:Gem::Version
86
+ version: '3.3'
87
+ - - ">="
88
+ - !ruby/object:Gem::Version
89
+ version: 3.3.6
90
+ type: :development
91
+ prerelease: false
92
+ version_requirements: !ruby/object:Gem::Requirement
93
+ requirements:
94
+ - - "~>"
95
+ - !ruby/object:Gem::Version
96
+ version: '3.3'
97
+ - - ">="
98
+ - !ruby/object:Gem::Version
99
+ version: 3.3.6
100
+ - !ruby/object:Gem::Dependency
101
+ name: irb
102
+ requirement: !ruby/object:Gem::Requirement
103
+ requirements:
104
+ - - "~>"
105
+ - !ruby/object:Gem::Version
106
+ version: '1.0'
107
+ type: :development
108
+ prerelease: false
109
+ version_requirements: !ruby/object:Gem::Requirement
110
+ requirements:
111
+ - - "~>"
112
+ - !ruby/object:Gem::Version
113
+ version: '1.0'
101
114
  - !ruby/object:Gem::Dependency
102
115
  name: faraday
103
116
  requirement: !ruby/object:Gem::Requirement
@@ -121,7 +134,7 @@ dependencies:
121
134
  version: '0.1'
122
135
  - - "<"
123
136
  - !ruby/object:Gem::Version
124
- version: '0.4'
137
+ version: '0.6'
125
138
  type: :runtime
126
139
  prerelease: false
127
140
  version_requirements: !ruby/object:Gem::Requirement
@@ -131,7 +144,7 @@ dependencies:
131
144
  version: '0.1'
132
145
  - - "<"
133
146
  - !ruby/object:Gem::Version
134
- version: '0.4'
147
+ version: '0.6'
135
148
  - !ruby/object:Gem::Dependency
136
149
  name: multi_json
137
150
  requirement: !ruby/object:Gem::Requirement
@@ -146,20 +159,6 @@ dependencies:
146
159
  - - "~>"
147
160
  - !ruby/object:Gem::Version
148
161
  version: '1.15'
149
- - !ruby/object:Gem::Dependency
150
- name: byebug
151
- requirement: !ruby/object:Gem::Requirement
152
- requirements:
153
- - - ">="
154
- - !ruby/object:Gem::Version
155
- version: '0'
156
- type: :development
157
- prerelease: false
158
- version_requirements: !ruby/object:Gem::Requirement
159
- requirements:
160
- - - ">="
161
- - !ruby/object:Gem::Version
162
- version: '0'
163
162
  description: Bananomia is a low-level wrapper around the Bionomia API.
164
163
  email:
165
164
  - gdower@illinois.edu
@@ -172,7 +171,6 @@ files:
172
171
  - CHANGELOG.md
173
172
  - CODE_OF_CONDUCT.md
174
173
  - Gemfile
175
- - Gemfile.lock
176
174
  - LICENSE.txt
177
175
  - README.md
178
176
  - Rakefile
@@ -188,12 +186,11 @@ files:
188
186
  - lib/bananomia/version.rb
189
187
  homepage: https://github.com/SpeciesFileGroup/bananomia
190
188
  licenses:
191
- - NCSA
189
+ - MIT
192
190
  metadata:
193
191
  homepage_uri: https://github.com/SpeciesFileGroup/bananomia
194
192
  source_code_uri: https://github.com/SpeciesFileGroup/bananomia
195
- changelog_uri: https://github.com/SpeciesFileGroup/bananomia/releases/tag/v0.1.0
196
- post_install_message:
193
+ changelog_uri: https://github.com/SpeciesFileGroup/bananomia/releases/tag/v0.1.2
197
194
  rdoc_options: []
198
195
  require_paths:
199
196
  - lib
@@ -201,15 +198,17 @@ required_ruby_version: !ruby/object:Gem::Requirement
201
198
  requirements:
202
199
  - - ">="
203
200
  - !ruby/object:Gem::Version
204
- version: 2.4.0
201
+ version: 2.5.0
202
+ - - "<"
203
+ - !ruby/object:Gem::Version
204
+ version: '5.0'
205
205
  required_rubygems_version: !ruby/object:Gem::Requirement
206
206
  requirements:
207
207
  - - ">="
208
208
  - !ruby/object:Gem::Version
209
209
  version: '0'
210
210
  requirements: []
211
- rubygems_version: 3.4.10
212
- signing_key:
211
+ rubygems_version: 4.0.3
213
212
  specification_version: 4
214
213
  summary: Bionomia Client
215
214
  test_files: []
data/Gemfile.lock DELETED
@@ -1,53 +0,0 @@
1
- PATH
2
- remote: .
3
- specs:
4
- bananomia (0.1.0)
5
- faraday (~> 2.2)
6
- faraday-follow_redirects (>= 0.1, < 0.4)
7
- multi_json (~> 1.15)
8
-
9
- GEM
10
- remote: https://rubygems.org/
11
- specs:
12
- addressable (2.8.1)
13
- public_suffix (>= 2.0.2, < 6.0)
14
- byebug (11.1.3)
15
- crack (0.4.5)
16
- rexml
17
- faraday (2.7.10)
18
- faraday-net_http (>= 2.0, < 3.1)
19
- ruby2_keywords (>= 0.0.4)
20
- faraday-follow_redirects (0.3.0)
21
- faraday (>= 1, < 3)
22
- faraday-net_http (3.0.2)
23
- hashdiff (1.0.1)
24
- minitest (5.15.0)
25
- multi_json (1.15.0)
26
- power_assert (2.0.1)
27
- public_suffix (5.0.1)
28
- rake (13.0.6)
29
- rexml (3.2.5)
30
- ruby2_keywords (0.0.5)
31
- test-unit (3.5.3)
32
- power_assert
33
- vcr (6.0.0)
34
- webmock (3.18.1)
35
- addressable (>= 2.8.0)
36
- crack (>= 0.3.2)
37
- hashdiff (>= 0.4.0, < 2.0.0)
38
-
39
- PLATFORMS
40
- x86_64-linux
41
-
42
- DEPENDENCIES
43
- bananomia!
44
- bundler (~> 2.1, >= 2.1.4)
45
- byebug
46
- minitest (~> 5.0)
47
- rake (~> 13.0)
48
- test-unit (~> 3.3, >= 3.3.6)
49
- vcr (~> 6.0)
50
- webmock (~> 3.18)
51
-
52
- BUNDLED WITH
53
- 2.3.24