roboneuro 0.1.1

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 (83) hide show
  1. checksums.yaml +7 -0
  2. data/.DS_Store +0 -0
  3. data/.env-example +12 -0
  4. data/.env.test +8 -0
  5. data/.github/workflows/docker-image.yml +63 -0
  6. data/.github/workflows/tests.yml +28 -0
  7. data/.gitignore +3 -0
  8. data/Gemfile +3 -0
  9. data/Gemfile.lock +135 -0
  10. data/LICENSE +21 -0
  11. data/README.md +190 -0
  12. data/Rakefile +13 -0
  13. data/bin/whedon +131 -0
  14. data/fixtures/latex_paper/paper.tex +0 -0
  15. data/fixtures/paper/10.21105.jcon.00017.crossref.xml +88 -0
  16. data/fixtures/paper/crossref-metadata.yaml +34 -0
  17. data/fixtures/paper/paper-bib.md +27 -0
  18. data/fixtures/paper/paper-single-author.md +24 -0
  19. data/fixtures/paper/paper-with-harder-names.md +27 -0
  20. data/fixtures/paper/paper-with-missing-affiliations.md +21 -0
  21. data/fixtures/paper/paper.bib +65 -0
  22. data/fixtures/paper/paper.html +14 -0
  23. data/fixtures/paper/paper.md +27 -0
  24. data/fixtures/paper/paper.pdf +0 -0
  25. data/fixtures/paper/paper.xml +28 -0
  26. data/fixtures/paper/paper_with_missing_title.md +26 -0
  27. data/fixtures/review_body.txt +48 -0
  28. data/fixtures/test_paper/nested/paper.bib +0 -0
  29. data/fixtures/test_paper/nested/paper.md +0 -0
  30. data/fixtures/test_paper/paper.bib +0 -0
  31. data/fixtures/test_paper/paper.md +0 -0
  32. data/fixtures/vcr_cassettes/joss-lookup.yml +58 -0
  33. data/fixtures/vcr_cassettes/review.yml +237 -0
  34. data/fixtures/vcr_cassettes/reviews.yml +270 -0
  35. data/lib/whedon/auditor.rb +39 -0
  36. data/lib/whedon/author.rb +81 -0
  37. data/lib/whedon/bibtex_parser.rb +103 -0
  38. data/lib/whedon/compilers.rb +379 -0
  39. data/lib/whedon/github.rb +12 -0
  40. data/lib/whedon/orcid_validator.rb +83 -0
  41. data/lib/whedon/processor.rb +178 -0
  42. data/lib/whedon/review.rb +25 -0
  43. data/lib/whedon/reviews.rb +29 -0
  44. data/lib/whedon/version.rb +3 -0
  45. data/lib/whedon.rb +387 -0
  46. data/paperdraft.Dockerfile +48 -0
  47. data/pkg/roboneuro-0.1.0.gem +0 -0
  48. data/resources/.DS_Store +0 -0
  49. data/resources/NeuroLibre/.DS_Store +0 -0
  50. data/resources/NeuroLibre/aas-logo.png +0 -0
  51. data/resources/NeuroLibre/apa.csl +1919 -0
  52. data/resources/NeuroLibre/defaults.yaml +14 -0
  53. data/resources/NeuroLibre/latex.template +541 -0
  54. data/resources/NeuroLibre/logo.png +0 -0
  55. data/resources/NeuroLibre/logo_link.png +0 -0
  56. data/resources/apa.csl +1919 -0
  57. data/resources/crossref.template +89 -0
  58. data/resources/docker-defaults.yaml +42 -0
  59. data/resources/docker-entrypoint.sh +37 -0
  60. data/resources/jats.csl +204 -0
  61. data/resources/jats.template +105 -0
  62. data/resources/jose/apa.csl +1919 -0
  63. data/resources/jose/defaults.yaml +14 -0
  64. data/resources/jose/latex.template +486 -0
  65. data/resources/jose/logo.png +0 -0
  66. data/resources/joss/aas-logo.png +0 -0
  67. data/resources/joss/apa.csl +1919 -0
  68. data/resources/joss/defaults.yaml +14 -0
  69. data/resources/joss/latex.template +525 -0
  70. data/resources/joss/logo.png +0 -0
  71. data/resources/latex.template +485 -0
  72. data/resources/time.lua +8 -0
  73. data/roboneuro.gemspec +39 -0
  74. data/spec/auditor_spec.rb +22 -0
  75. data/spec/author_spec.rb +17 -0
  76. data/spec/bibtex_spec.rb +31 -0
  77. data/spec/orcid_validator_spec.rb +33 -0
  78. data/spec/processor_spec.rb +66 -0
  79. data/spec/review_spec.rb +12 -0
  80. data/spec/reviews_spec.rb +18 -0
  81. data/spec/spec_helper.rb +22 -0
  82. data/spec/whedon_spec.rb +93 -0
  83. metadata +386 -0
@@ -0,0 +1,237 @@
1
+ ---
2
+ http_interactions:
3
+ - request:
4
+ method: get
5
+ uri: https://api.github.com/repos/openjournals/joss-reviews/issues/17
6
+ body:
7
+ encoding: US-ASCII
8
+ string: ''
9
+ headers:
10
+ Accept:
11
+ - application/vnd.github.drax-preview+json
12
+ User-Agent:
13
+ - Octokit Ruby Gem 4.3.0
14
+ Content-Type:
15
+ - application/json
16
+ Authorization:
17
+ - token <GITHUB_TOKEN>
18
+ Accept-Encoding:
19
+ - gzip;q=1.0,deflate;q=0.6,identity;q=0.3
20
+ response:
21
+ status:
22
+ code: 200
23
+ message: OK
24
+ headers:
25
+ Server:
26
+ - GitHub.com
27
+ Date:
28
+ - Fri, 13 May 2016 23:54:24 GMT
29
+ Content-Type:
30
+ - application/json; charset=utf-8
31
+ Transfer-Encoding:
32
+ - chunked
33
+ Status:
34
+ - 200 OK
35
+ X-Ratelimit-Limit:
36
+ - '5000'
37
+ X-Ratelimit-Remaining:
38
+ - '4989'
39
+ X-Ratelimit-Reset:
40
+ - '1463184304'
41
+ Cache-Control:
42
+ - private, max-age=60, s-maxage=60
43
+ Vary:
44
+ - Accept, Authorization, Cookie, X-GitHub-OTP
45
+ - Accept-Encoding
46
+ Etag:
47
+ - W/"cf7856bd3095fcc0eab4ec74d7968540"
48
+ Last-Modified:
49
+ - Thu, 12 May 2016 12:36:22 GMT
50
+ X-Oauth-Scopes:
51
+ - notifications, repo
52
+ X-Accepted-Oauth-Scopes:
53
+ - repo
54
+ X-Github-Media-Type:
55
+ - github.drax-preview; format=json
56
+ Access-Control-Expose-Headers:
57
+ - ETag, Link, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset,
58
+ X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval
59
+ Access-Control-Allow-Origin:
60
+ - "*"
61
+ Content-Security-Policy:
62
+ - default-src 'none'
63
+ Strict-Transport-Security:
64
+ - max-age=31536000; includeSubdomains; preload
65
+ X-Content-Type-Options:
66
+ - nosniff
67
+ X-Frame-Options:
68
+ - deny
69
+ X-Xss-Protection:
70
+ - 1; mode=block
71
+ X-Served-By:
72
+ - c6c65e5196703428e7641f7d1e9bc353
73
+ X-Github-Request-Id:
74
+ - 46D006AD:1C0C0:898617:5736692F
75
+ body:
76
+ encoding: ASCII-8BIT
77
+ string: '{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/17","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/17/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/17/events","html_url":"https://github.com/openjournals/joss-reviews/issues/17","id":154275840,"number":17,"title":"Submission:
78
+ Application Skeleton: Generating Synthetic Applications for Infrastructure
79
+ Research","user":{"login":"whedon","id":18508068,"avatar_url":"https://avatars.githubusercontent.com/u/18508068?v=3","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/accepted","name":"accepted","color":"159818"},{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":24,"created_at":"2016-05-11T15:42:11Z","updated_at":"2016-05-12T12:36:22Z","closed_at":"2016-05-12T03:15:55Z","pull_request":{"url":null,"html_url":null,"diff_url":null,"patch_url":null},"body":"**Submitting
80
+ author:** @zhaozhang (<a href=\"http://orcid.org/0000-0001-5921-0035\">Zhao
81
+ Zhang</a>)\r\n**Repository:** <a href=\"https://github.com/applicationskeleton/Skeleton\"
82
+ target =\"_blank\">https://github.com/applicationskeleton/Skeleton</a>\r\n**Version:**
83
+ v1.2\r\n**Editor:** @arfon\r\n**Reviewers:** @jim, @bob\r\n**Archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.13750\" target
84
+ =\"_blank\">http://dx.doi.org/10.5281/zenodo.13750</a>\r\n\r\n## Status\r\n\r\n[![status](http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6/status.svg)](http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6)\r\n\r\nStatus
85
+ badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6\"><img
86
+ src=\"http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6/status.svg\"></a>\r\nMarkdown:
87
+ [![status](http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6/status.svg)]http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6\r\n```\r\n\r\n##
88
+ Reviewer questions\r\n\r\n### General checks\r\n\r\n- [x] **Repository:**
89
+ Is the source code for this software available at the <a target=\"_blank\"
90
+ href=\"https://github.com/applicationskeleton/Skeleton\">repository url</a>?\r\n-
91
+ [x] **License:** Does the repository contain a plain-text LICENSE file with
92
+ the contents of an [OSI approved](https://opensource.org/licenses/alphabetical)
93
+ software license?\r\n- [x] **Version:** Does the release version given match
94
+ the GitHub release (v1.2)?\r\n- [x] **Archive:** Does the <a target=\"_blank\"
95
+ href=\"http://dx.doi.org/10.5281/zenodo.13750\">software archive</a> resolve?\r\n\r\n###
96
+ Functionality\r\n\r\n- [x] **Installation:** Does installation proceed as
97
+ outlined in the documentation?\r\n- [x] **Functionality:** Have the functional
98
+ claims of the software been confirmed?\r\n- [x] **Performance:** Have the
99
+ performance claims of the software been confirmed?\r\n\r\n### Documentation\r\n\r\n-
100
+ [x] **A statement of need:** Do the authors clearly state what problems the
101
+ software is designed to solve and who the target audience is?\r\n- [x] **Installation
102
+ instructions:** Is there a clearly-stated list of dependencies? Ideally these
103
+ should be handled with an automated package management solution.\r\n- [x]
104
+ **Example usage:** Do the authors include examples of how to use the software
105
+ (ideally to solve real-world analysis problems).\r\n- [x] **Functionality
106
+ documentation:** Is the functionality of the software documented to a satisfactory
107
+ level (e.g. API method documentation)?\r\n- [x] **Automated tests:** Are there
108
+ automated tests or manual steps described so that the function of the software
109
+ can be verified?\r\n- [x] **Community guidelines:** Are there clear guidelines
110
+ for third parties wishing to 1) Contribute to the software 2) Report issues
111
+ or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\nCompiled
112
+ paper PDF: [paper.pdf](https://github.com/openjournals/joss-reviews/files/259667/paper.pdf)\r\n\r\n\r\n-
113
+ [x] **Authors:** Does the `paper.md` file include a list of authors with their
114
+ affiliations?\r\n- [x] **A statement of need:** Do the authors clearly state
115
+ what problems the software is designed to solve and who the target audience
116
+ is?\r\n- [x] **References:** Do all archival references that should have a
117
+ DOI list one (e.g. papers, datasets, software)?\r\n","closed_by":{"login":"arfon","id":4483,"avatar_url":"https://avatars.githubusercontent.com/u/4483?v=3","gravatar_id":"","url":"https://api.github.com/users/arfon","html_url":"https://github.com/arfon","followers_url":"https://api.github.com/users/arfon/followers","following_url":"https://api.github.com/users/arfon/following{/other_user}","gists_url":"https://api.github.com/users/arfon/gists{/gist_id}","starred_url":"https://api.github.com/users/arfon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arfon/subscriptions","organizations_url":"https://api.github.com/users/arfon/orgs","repos_url":"https://api.github.com/users/arfon/repos","events_url":"https://api.github.com/users/arfon/events{/privacy}","received_events_url":"https://api.github.com/users/arfon/received_events","type":"User","site_admin":true}}'
118
+ http_version:
119
+ recorded_at: Fri, 13 May 2016 23:54:24 GMT
120
+ - request:
121
+ method: get
122
+ uri: https://api.github.com/repos/openjournals/joss-reviews/issues/17
123
+ body:
124
+ encoding: US-ASCII
125
+ string: ''
126
+ headers:
127
+ Accept:
128
+ - application/vnd.github.drax-preview+json
129
+ User-Agent:
130
+ - Octokit Ruby Gem 4.3.0
131
+ Content-Type:
132
+ - application/json
133
+ Authorization:
134
+ - token <GITHUB_TOKEN>
135
+ Accept-Encoding:
136
+ - gzip;q=1.0,deflate;q=0.6,identity;q=0.3
137
+ response:
138
+ status:
139
+ code: 200
140
+ message: OK
141
+ headers:
142
+ Server:
143
+ - GitHub.com
144
+ Date:
145
+ - Fri, 13 May 2016 23:54:24 GMT
146
+ Content-Type:
147
+ - application/json; charset=utf-8
148
+ Transfer-Encoding:
149
+ - chunked
150
+ Status:
151
+ - 200 OK
152
+ X-Ratelimit-Limit:
153
+ - '5000'
154
+ X-Ratelimit-Remaining:
155
+ - '4988'
156
+ X-Ratelimit-Reset:
157
+ - '1463184304'
158
+ Cache-Control:
159
+ - private, max-age=60, s-maxage=60
160
+ Vary:
161
+ - Accept, Authorization, Cookie, X-GitHub-OTP
162
+ - Accept-Encoding
163
+ Etag:
164
+ - W/"cf7856bd3095fcc0eab4ec74d7968540"
165
+ Last-Modified:
166
+ - Thu, 12 May 2016 12:36:22 GMT
167
+ X-Oauth-Scopes:
168
+ - notifications, repo
169
+ X-Accepted-Oauth-Scopes:
170
+ - repo
171
+ X-Github-Media-Type:
172
+ - github.drax-preview; format=json
173
+ Access-Control-Expose-Headers:
174
+ - ETag, Link, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset,
175
+ X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval
176
+ Access-Control-Allow-Origin:
177
+ - "*"
178
+ Content-Security-Policy:
179
+ - default-src 'none'
180
+ Strict-Transport-Security:
181
+ - max-age=31536000; includeSubdomains; preload
182
+ X-Content-Type-Options:
183
+ - nosniff
184
+ X-Frame-Options:
185
+ - deny
186
+ X-Xss-Protection:
187
+ - 1; mode=block
188
+ X-Served-By:
189
+ - bd82876e9bf04990f289ba22f246ee9b
190
+ X-Github-Request-Id:
191
+ - 46D006AD:1C0C3:160CA65:57366930
192
+ body:
193
+ encoding: ASCII-8BIT
194
+ string: '{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/17","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/17/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/17/events","html_url":"https://github.com/openjournals/joss-reviews/issues/17","id":154275840,"number":17,"title":"Submission:
195
+ Application Skeleton: Generating Synthetic Applications for Infrastructure
196
+ Research","user":{"login":"whedon","id":18508068,"avatar_url":"https://avatars.githubusercontent.com/u/18508068?v=3","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/accepted","name":"accepted","color":"159818"},{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":24,"created_at":"2016-05-11T15:42:11Z","updated_at":"2016-05-12T12:36:22Z","closed_at":"2016-05-12T03:15:55Z","pull_request":{"url":null,"html_url":null,"diff_url":null,"patch_url":null},"body":"**Submitting
197
+ author:** @zhaozhang (<a href=\"http://orcid.org/0000-0001-5921-0035\">Zhao
198
+ Zhang</a>)\r\n**Repository:** <a href=\"https://github.com/applicationskeleton/Skeleton\"
199
+ target =\"_blank\">https://github.com/applicationskeleton/Skeleton</a>\r\n**Version:**
200
+ v1.2\r\n**Archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.13750\" target
201
+ =\"_blank\">http://dx.doi.org/10.5281/zenodo.13750</a>\r\n\r\n## Status\r\n\r\n[![status](http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6/status.svg)](http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6)\r\n\r\nStatus
202
+ badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6\"><img
203
+ src=\"http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6/status.svg\"></a>\r\nMarkdown:
204
+ [![status](http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6/status.svg)]http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6\r\n```\r\n\r\n##
205
+ Reviewer questions\r\n\r\n### General checks\r\n\r\n- [x] **Repository:**
206
+ Is the source code for this software available at the <a target=\"_blank\"
207
+ href=\"https://github.com/applicationskeleton/Skeleton\">repository url</a>?\r\n-
208
+ [x] **License:** Does the repository contain a plain-text LICENSE file with
209
+ the contents of an [OSI approved](https://opensource.org/licenses/alphabetical)
210
+ software license?\r\n- [x] **Version:** Does the release version given match
211
+ the GitHub release (v1.2)?\r\n- [x] **Archive:** Does the <a target=\"_blank\"
212
+ href=\"http://dx.doi.org/10.5281/zenodo.13750\">software archive</a> resolve?\r\n\r\n###
213
+ Functionality\r\n\r\n- [x] **Installation:** Does installation proceed as
214
+ outlined in the documentation?\r\n- [x] **Functionality:** Have the functional
215
+ claims of the software been confirmed?\r\n- [x] **Performance:** Have the
216
+ performance claims of the software been confirmed?\r\n\r\n### Documentation\r\n\r\n-
217
+ [x] **A statement of need:** Do the authors clearly state what problems the
218
+ software is designed to solve and who the target audience is?\r\n- [x] **Installation
219
+ instructions:** Is there a clearly-stated list of dependencies? Ideally these
220
+ should be handled with an automated package management solution.\r\n- [x]
221
+ **Example usage:** Do the authors include examples of how to use the software
222
+ (ideally to solve real-world analysis problems).\r\n- [x] **Functionality
223
+ documentation:** Is the functionality of the software documented to a satisfactory
224
+ level (e.g. API method documentation)?\r\n- [x] **Automated tests:** Are there
225
+ automated tests or manual steps described so that the function of the software
226
+ can be verified?\r\n- [x] **Community guidelines:** Are there clear guidelines
227
+ for third parties wishing to 1) Contribute to the software 2) Report issues
228
+ or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\nCompiled
229
+ paper PDF: [paper.pdf](https://github.com/openjournals/joss-reviews/files/259667/paper.pdf)\r\n\r\n\r\n-
230
+ [x] **Authors:** Does the `paper.md` file include a list of authors with their
231
+ affiliations?\r\n- [x] **A statement of need:** Do the authors clearly state
232
+ what problems the software is designed to solve and who the target audience
233
+ is?\r\n- [x] **References:** Do all archival references that should have a
234
+ DOI list one (e.g. papers, datasets, software)?\r\n","closed_by":{"login":"arfon","id":4483,"avatar_url":"https://avatars.githubusercontent.com/u/4483?v=3","gravatar_id":"","url":"https://api.github.com/users/arfon","html_url":"https://github.com/arfon","followers_url":"https://api.github.com/users/arfon/followers","following_url":"https://api.github.com/users/arfon/following{/other_user}","gists_url":"https://api.github.com/users/arfon/gists{/gist_id}","starred_url":"https://api.github.com/users/arfon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arfon/subscriptions","organizations_url":"https://api.github.com/users/arfon/orgs","repos_url":"https://api.github.com/users/arfon/repos","events_url":"https://api.github.com/users/arfon/events{/privacy}","received_events_url":"https://api.github.com/users/arfon/received_events","type":"User","site_admin":true}}'
235
+ http_version:
236
+ recorded_at: Fri, 13 May 2016 23:54:24 GMT
237
+ recorded_with: VCR 2.9.3
@@ -0,0 +1,270 @@
1
+ ---
2
+ http_interactions:
3
+ - request:
4
+ method: get
5
+ uri: https://api.github.com/repos/openjournals/joss-reviews/issues
6
+ body:
7
+ encoding: US-ASCII
8
+ string: ''
9
+ headers:
10
+ Accept:
11
+ - application/vnd.github.drax-preview+json
12
+ User-Agent:
13
+ - Octokit Ruby Gem 4.3.0
14
+ Content-Type:
15
+ - application/json
16
+ Authorization:
17
+ - token <GITHUB_TOKEN>
18
+ Accept-Encoding:
19
+ - gzip;q=1.0,deflate;q=0.6,identity;q=0.3
20
+ response:
21
+ status:
22
+ code: 200
23
+ message: OK
24
+ headers:
25
+ Server:
26
+ - GitHub.com
27
+ Date:
28
+ - Fri, 13 May 2016 23:47:37 GMT
29
+ Content-Type:
30
+ - application/json; charset=utf-8
31
+ Transfer-Encoding:
32
+ - chunked
33
+ Status:
34
+ - 200 OK
35
+ X-Ratelimit-Limit:
36
+ - '5000'
37
+ X-Ratelimit-Remaining:
38
+ - '4991'
39
+ X-Ratelimit-Reset:
40
+ - '1463184304'
41
+ Cache-Control:
42
+ - private, max-age=60, s-maxage=60
43
+ Vary:
44
+ - Accept, Authorization, Cookie, X-GitHub-OTP
45
+ - Accept-Encoding
46
+ Etag:
47
+ - W/"79a7e069c386ef28d985c99982628e2c"
48
+ X-Oauth-Scopes:
49
+ - notifications, repo
50
+ X-Accepted-Oauth-Scopes:
51
+ - repo
52
+ X-Github-Media-Type:
53
+ - github.drax-preview; format=json
54
+ Access-Control-Expose-Headers:
55
+ - ETag, Link, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset,
56
+ X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval
57
+ Access-Control-Allow-Origin:
58
+ - "*"
59
+ Content-Security-Policy:
60
+ - default-src 'none'
61
+ Strict-Transport-Security:
62
+ - max-age=31536000; includeSubdomains; preload
63
+ X-Content-Type-Options:
64
+ - nosniff
65
+ X-Frame-Options:
66
+ - deny
67
+ X-Xss-Protection:
68
+ - 1; mode=block
69
+ X-Served-By:
70
+ - 173530fed4bbeb1e264b2ed22e8b5c20
71
+ X-Github-Request-Id:
72
+ - 46D006AD:B213:160A668:57366799
73
+ body:
74
+ encoding: ASCII-8BIT
75
+ string: '[{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/19","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/19/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/19/events","html_url":"https://github.com/openjournals/joss-reviews/issues/19","id":154513135,"number":19,"title":"Submission:
76
+ riskscorer - automating risk calculation in clinical practice and research","user":{"login":"whedon","id":18508068,"avatar_url":"https://avatars.githubusercontent.com/u/18508068?v=3","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-05-12T15:33:08Z","updated_at":"2016-05-13T22:53:14Z","closed_at":null,"pull_request":{"url":null,"html_url":null,"diff_url":null,"patch_url":null},"body":"**Submitting
77
+ author:** @meyera (<a href=\"http://orcid.org/0000-0002-6944-2478\">Alexander
78
+ Meyer</a>)\r\n**Repository:** <a href=\"https://github.com/meyera/riskscorer\"
79
+ target =\"_blank\">https://github.com/meyera/riskscorer</a>\r\n**Version:**
80
+ v0.2.0\r\n**Archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.51342\"
81
+ target =\"_blank\">http://dx.doi.org/10.5281/zenodo.51342</a>\r\n\r\n## Status\r\n\r\n[![status](http://joss.theoj.org/papers/b6fca2486948af8ebd56fc31fc7277c3/status.svg)](http://joss.theoj.org/papers/b6fca2486948af8ebd56fc31fc7277c3)\r\n\r\nStatus
82
+ badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/b6fca2486948af8ebd56fc31fc7277c3\"><img
83
+ src=\"http://joss.theoj.org/papers/b6fca2486948af8ebd56fc31fc7277c3/status.svg\"></a>\r\nMarkdown:
84
+ [![status](http://joss.theoj.org/papers/b6fca2486948af8ebd56fc31fc7277c3/status.svg)](http://joss.theoj.org/papers/b6fca2486948af8ebd56fc31fc7277c3)\r\n```\r\n\r\n##
85
+ Reviewer questions\r\n\r\n### General checks\r\n\r\n- [ ] **Repository:**
86
+ Is the source code for this software available at the <a target=\"_blank\"
87
+ href=\"https://github.com/meyera/riskscorer\">repository url</a>?\r\n- [ ]
88
+ **License:** Does the repository contain a plain-text LICENSE file with the
89
+ contents of an [OSI approved](https://opensource.org/licenses/alphabetical)
90
+ software license?\r\n- [ ] **Version:** Does the release version given match
91
+ the GitHub release (v0.2.0)?\r\n- [ ] **Archive:** Does the <a target=\"_blank\"
92
+ href=\"http://dx.doi.org/10.5281/zenodo.51342\">software archive</a> resolve?\r\n\r\n###
93
+ Functionality\r\n\r\n- [ ] **Installation:** Does installation proceed as
94
+ outlined in the documentation?\r\n- [ ] **Functionality:** Have the functional
95
+ claims of the software been confirmed?\r\n- [ ] **Performance:** Have the
96
+ performance claims of the software been confirmed?\r\n\r\n### Documentation\r\n\r\n-
97
+ [ ] **A statement of need:** Do the authors clearly state what problems the
98
+ software is designed to solve and who the target audience is?\r\n- [ ] **Installation
99
+ instructions:** Is there a clearly-stated list of dependencies? Ideally these
100
+ should be handled with an automated package management solution.\r\n- [ ]
101
+ **Example usage:** Do the authors include examples of how to use the software
102
+ (ideally to solve real-world analysis problems).\r\n- [ ] **Functionality
103
+ documentation:** Is the functionality of the software documented to a satisfactory
104
+ level (e.g. API method documentation)?\r\n- [ ] **Automated tests:** Are there
105
+ automated tests or manual steps described so that the function of the software
106
+ can be verified?\r\n- [ ] **Community guidelines:** Are there clear guidelines
107
+ for third parties wishing to 1) Contribute to the software 2) Report issues
108
+ or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\nCompiled
109
+ paper PDF: [10.21105.joss.00019.pdf](https://github.com/openjournals/joss-reviews/files/261684/10.21105.joss.00019.pdf)\r\n\r\n-
110
+ [ ] **Authors:** Does the `paper.md` file include a list of authors with their
111
+ affiliations?\r\n- [ ] **A statement of need:** Do the authors clearly state
112
+ what problems the software is designed to solve and who the target audience
113
+ is?\r\n- [ ] **References:** Do all archival references that should have a
114
+ DOI list one (e.g. papers, datasets, software)?\r\n"},{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/18","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/18/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/18/events","html_url":"https://github.com/openjournals/joss-reviews/issues/18","id":154512370,"number":18,"title":"Submission:
115
+ Xenomapper - short read mapping in a mixed species context","user":{"login":"whedon","id":18508068,"avatar_url":"https://avatars.githubusercontent.com/u/18508068?v=3","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-05-12T15:30:11Z","updated_at":"2016-05-12T15:32:11Z","closed_at":null,"pull_request":{"url":null,"html_url":null,"diff_url":null,"patch_url":null},"body":"**Submitting
116
+ author:** @genomematt (<a href=\"http://orcid.org/0000-0001-6624-4698\">Matthew
117
+ J Wakefield</a>)\r\n**Repository:** <a href=\"http://github.com/genomematt/xenomapper/\"
118
+ target =\"_blank\">http://github.com/genomematt/xenomapper/</a>\r\n**Version:**
119
+ v1.0.0\r\n**Archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.51337\"
120
+ target =\"_blank\">10.5281/zenodo.51337</a>\r\n\r\n## Status\r\n\r\n[![status](http://joss.theoj.org/papers/7065e20e97ff4e44695b5e9fef7cdcd8/status.svg)](http://joss.theoj.org/papers/7065e20e97ff4e44695b5e9fef7cdcd8)\r\n\r\nStatus
121
+ badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/7065e20e97ff4e44695b5e9fef7cdcd8\"><img
122
+ src=\"http://joss.theoj.org/papers/7065e20e97ff4e44695b5e9fef7cdcd8/status.svg\"></a>\r\nMarkdown:
123
+ [![status](http://joss.theoj.org/papers/7065e20e97ff4e44695b5e9fef7cdcd8/status.svg)](http://joss.theoj.org/papers/7065e20e97ff4e44695b5e9fef7cdcd8)\r\n```\r\n\r\n##
124
+ Reviewer questions\r\n\r\n### General checks\r\n\r\n- [ ] **Repository:**
125
+ Is the source code for this software available at the <a target=\"_blank\"
126
+ href=\"http://github.com/genomematt/xenomapper/\">repository url</a>?\r\n-
127
+ [ ] **License:** Does the repository contain a plain-text LICENSE file with
128
+ the contents of an [OSI approved](https://opensource.org/licenses/alphabetical)
129
+ software license?\r\n- [ ] **Version:** Does the release version given match
130
+ the GitHub release (v1.0.0)?\r\n- [ ] **Archive:** Does the <a target=\"_blank\"
131
+ href=\"http://dx.doi.org/10.5281/zenodo.51337\">software archive</a> resolve?\r\n\r\n###
132
+ Functionality\r\n\r\n- [ ] **Installation:** Does installation proceed as
133
+ outlined in the documentation?\r\n- [ ] **Functionality:** Have the functional
134
+ claims of the software been confirmed?\r\n- [ ] **Performance:** Have the
135
+ performance claims of the software been confirmed?\r\n\r\n### Documentation\r\n\r\n-
136
+ [ ] **A statement of need:** Do the authors clearly state what problems the
137
+ software is designed to solve and who the target audience is?\r\n- [ ] **Installation
138
+ instructions:** Is there a clearly-stated list of dependencies? Ideally these
139
+ should be handled with an automated package management solution.\r\n- [ ]
140
+ **Example usage:** Do the authors include examples of how to use the software
141
+ (ideally to solve real-world analysis problems).\r\n- [ ] **Functionality
142
+ documentation:** Is the functionality of the software documented to a satisfactory
143
+ level (e.g. API method documentation)?\r\n- [ ] **Automated tests:** Are there
144
+ automated tests or manual steps described so that the function of the software
145
+ can be verified?\r\n- [ ] **Community guidelines:** Are there clear guidelines
146
+ for third parties wishing to 1) Contribute to the software 2) Report issues
147
+ or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\nCompiled
148
+ paper PDF: [10.21105.joss.00018.pdf](https://github.com/openjournals/joss-reviews/files/261671/10.21105.joss.00018.pdf)\r\n\r\n-
149
+ [ ] **Authors:** Does the `paper.md` file include a list of authors with their
150
+ affiliations?\r\n- [ ] **A statement of need:** Do the authors clearly state
151
+ what problems the software is designed to solve and who the target audience
152
+ is?\r\n- [ ] **References:** Do all archival references that should have a
153
+ DOI list one (e.g. papers, datasets, software)?\r\n"},{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/16","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/16/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/16/events","html_url":"https://github.com/openjournals/joss-reviews/issues/16","id":153815019,"number":16,"title":"Submission:
154
+ R3D2: Relativistic Reactive Riemann problem solver for Deflagrations and Detonations","user":{"login":"whedon","id":18508068,"avatar_url":"https://avatars.githubusercontent.com/u/18508068?v=3","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04"}],"state":"open","locked":false,"assignee":{"login":"kyleniemeyer","id":190432,"avatar_url":"https://avatars.githubusercontent.com/u/190432?v=3","gravatar_id":"","url":"https://api.github.com/users/kyleniemeyer","html_url":"https://github.com/kyleniemeyer","followers_url":"https://api.github.com/users/kyleniemeyer/followers","following_url":"https://api.github.com/users/kyleniemeyer/following{/other_user}","gists_url":"https://api.github.com/users/kyleniemeyer/gists{/gist_id}","starred_url":"https://api.github.com/users/kyleniemeyer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kyleniemeyer/subscriptions","organizations_url":"https://api.github.com/users/kyleniemeyer/orgs","repos_url":"https://api.github.com/users/kyleniemeyer/repos","events_url":"https://api.github.com/users/kyleniemeyer/events{/privacy}","received_events_url":"https://api.github.com/users/kyleniemeyer/received_events","type":"User","site_admin":false},"milestone":null,"comments":4,"created_at":"2016-05-09T16:22:44Z","updated_at":"2016-05-12T09:20:23Z","closed_at":null,"pull_request":{"url":null,"html_url":null,"diff_url":null,"patch_url":null},"body":"**Submitting
155
+ author:** @harpolea (<a href=\"http://orcid.org/0000-0002-1530-781X\">Alice
156
+ Harpole</a>)\r\n**Repository:** <a href=\"https://github.com/harpolea/r3d2\"
157
+ target =\"_blank\">https://github.com/harpolea/r3d2</a>\r\n**Version:** v1.0\r\n**Archive:**
158
+ <a href=\"http://dx.doi.org/10.5281/zenodo.51096\" target =\"_blank\">http://dx.doi.org/10.5281/zenodo.51096</a>\r\n\r\n##
159
+ Status\r\n\r\n[![status](http://joss.theoj.org/papers/99f57be50022ae8b2eecdd1d28b05766/status.svg)](http://joss.theoj.org/papers/99f57be50022ae8b2eecdd1d28b05766)\r\n\r\nStatus
160
+ badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/99f57be50022ae8b2eecdd1d28b05766\"><img
161
+ src=\"http://joss.theoj.org/papers/99f57be50022ae8b2eecdd1d28b05766/status.svg\"></a>\r\nMarkdown:
162
+ [![status](http://joss.theoj.org/papers/99f57be50022ae8b2eecdd1d28b05766/status.svg)]http://joss.theoj.org/papers/99f57be50022ae8b2eecdd1d28b05766\r\n```\r\n\r\n##
163
+ Reviewer questions\r\n\r\n### General checks\r\n\r\n- [x] **Repository:**
164
+ Is the source code for this software available at the <a target=\"_blank\"
165
+ href=\"https://github.com/harpolea/r3d2\">repository url</a>?\r\n- [ ] **License:**
166
+ Does the repository contain a plain-text LICENSE file with the contents of
167
+ an [OSI approved](https://opensource.org/licenses/alphabetical) software license?\r\n-
168
+ [x] **Version:** Does the release version given match the GitHub release (v1.0)?\r\n-
169
+ [x] **Archive:** Does the <a target=\"_blank\" href=\"http://dx.doi.org/10.5281/zenodo.51096\">software
170
+ archive</a> resolve?\r\n\r\n### Functionality\r\n\r\n- [ ] **Installation:**
171
+ Does installation proceed as outlined in the documentation?\r\n- [ ] **Functionality:**
172
+ Have the functional claims of the software been confirmed?\r\n- [ ] **Performance:**
173
+ Have the performance claims of the software been confirmed?\r\n\r\n### Documentation\r\n\r\n-
174
+ [ ] **A statement of need:** Do the authors clearly state what problems the
175
+ software is designed to solve and who the target audience is?\r\n- [ ] **Installation
176
+ instructions:** Is there a clearly-stated list of dependencies? Ideally these
177
+ should be handled with an automated package management solution.\r\n- [ ]
178
+ **Example usage:** Do the authors include examples of how to use the software
179
+ (ideally to solve real-world analysis problems).\r\n- [ ] **Functionality
180
+ documentation:** Is the functionality of the software documented to a satisfactory
181
+ level (e.g. API method documentation)?\r\n- [ ] **Automated tests:** Are there
182
+ automated tests or manual steps described so that the function of the software
183
+ can be verified?\r\n- [ ] **Community guidelines:** Are there clear guidelines
184
+ for third parties wishing to 1) Contribute to the software 2) Report issues
185
+ or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\nCompiled
186
+ paper PDF: [paper.pdf](https://github.com/openjournals/joss-reviews/files/255410/paper.pdf)\r\n\r\n\r\n-
187
+ [ ] **Authors:** Does the `paper.md` file include a list of authors with their
188
+ affiliations?\r\n- [ ] **A statement of need:** Do the authors clearly state
189
+ what problems the software is designed to solve and who the target audience
190
+ is?\r\n- [ ] **References:** Do all archival references that should have a
191
+ DOI list one (e.g. papers, datasets, software)?\r\n\r\n"},{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/12","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/12/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/12/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/12/events","html_url":"https://github.com/openjournals/joss-reviews/issues/12","id":153160519,"number":12,"title":"Submission:
192
+ mst_clustering: Clustering via Minimum Spanning Trees","user":{"login":"whedon","id":18508068,"avatar_url":"https://avatars.githubusercontent.com/u/18508068?v=3","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":15,"created_at":"2016-05-05T03:16:01Z","updated_at":"2016-05-13T21:01:42Z","closed_at":null,"pull_request":{"url":null,"html_url":null,"diff_url":null,"patch_url":null},"body":"**Submitting
193
+ author:** @jakevdp (<a href=\"http://orcid.org/0000-0002-9623-3401\">Jacob
194
+ VanderPlas</a>)\r\n**Repository:** <a href=\"http://github.com/jakevdp/mst_clustering\"
195
+ target=\"_blank\">http://github.com/jakevdp/mst_clustering</a>\r\n**Version:**
196
+ v1.0.0\r\n**Archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.50995\"
197
+ target =\"_blank\">http://dx.doi.org/10.5281/zenodo.50995</a>\r\n\r\n## Status\r\n\r\n[![status](http://joss.theoj.org/papers/0b73d249cd34985b6fa1a5ad4f4f8014/status.svg)](http://joss.theoj.org/papers/0b73d249cd34985b6fa1a5ad4f4f8014)\r\n\r\nStatus
198
+ badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/0b73d249cd34985b6fa1a5ad4f4f8014\"><img
199
+ src=\"http://joss.theoj.org/papers/0b73d249cd34985b6fa1a5ad4f4f8014/status.svg\"></a>\r\nMarkdown:
200
+ [![status](http://joss.theoj.org/papers/0b73d249cd34985b6fa1a5ad4f4f8014/status.svg)]http://joss.theoj.org/papers/0b73d249cd34985b6fa1a5ad4f4f8014\r\n```\r\n\r\n##
201
+ Reviewer questions\r\n\r\n### General checks\r\n\r\n- [x] **Repository:**
202
+ Is the source code for this software available at the <a target=\"_blank\"
203
+ href=\"http://github.com/jakevdp/mst_clustering\">repository url</a>?\r\n-
204
+ [x] **License:** Does the repository contain a plain-text LICENSE file with
205
+ the contents of an [OSI approved](https://opensource.org/licenses/alphabetical)
206
+ software license?\r\n- [ ] **Version:** Does the release version given match
207
+ the GitHub release (v1.0.0)?\r\n- [x] **Archive:** Does the <a target=\"_blank\"
208
+ href=\"http://dx.doi.org/10.5281/zenodo.50995\">software archive</a> resolve?\r\n\r\n###
209
+ Functionality\r\n\r\n- [x] **Installation:** Does installation proceed as
210
+ outlined in the documentation?\r\n- [x] **Functionality:** Have the functional
211
+ claims of the software been confirmed?\r\n- [x] **Performance:** Have the
212
+ performance claims of the software been confirmed?\r\n\r\n### Documentation\r\n\r\n-
213
+ [x] **A statement of need:** Do the authors clearly state what problems the
214
+ software is designed to solve and who the target audience is?\r\n- [x] **Installation
215
+ instructions:** Is there a clearly-stated list of dependencies? Ideally these
216
+ should be handled with an automated package management solution.\r\n- [x]
217
+ **Example usage:** Do the authors include examples of how to use the software
218
+ (ideally to solve real-world analysis problems).\r\n- [x] **Functionality
219
+ documentation:** Is the functionality of the software documented to a satisfactory
220
+ level (e.g. API method documentation)?\r\n- [x] **Automated tests:** Are there
221
+ automated tests or manual steps described so that the function of the software
222
+ can be verified?\r\n- [ ] **Community guidelines:** Are there clear guidelines
223
+ for third parties wishing to 1) Contribute to the software 2) Report issues
224
+ or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\n-
225
+ [x] **Authors:** Does the `paper.md` file include a list of authors with their
226
+ affiliations?\r\n- [x] **A statement of need:** Do the authors clearly state
227
+ what problems the software is designed to solve and who the target audience
228
+ is?\r\n- [ ] **References:** Do all archival references that should have a
229
+ DOI list one (e.g. papers, datasets, software)?\r\n"},{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/10","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/10/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/10/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/10/events","html_url":"https://github.com/openjournals/joss-reviews/issues/10","id":153024367,"number":10,"title":"Submission:
230
+ metricsgraphics: An R htmlwidget interface to the MetricsGraphics.js D3-based
231
+ visualization library","user":{"login":"whedon","id":18508068,"avatar_url":"https://avatars.githubusercontent.com/u/18508068?v=3","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":11,"created_at":"2016-05-04T14:22:32Z","updated_at":"2016-05-07T22:47:02Z","closed_at":null,"pull_request":{"url":null,"html_url":null,"diff_url":null,"patch_url":null},"body":"**Submitting
232
+ author:** @hrbrmstr (<a href=\"http://orcid.org/0000-0001-5670-2640\">Bob
233
+ Rudis</a>)\r\n**Repository:** <a href=\"https://github.com/hrbrmstr/metricsgraphics\"
234
+ target=\"_blank\">https://github.com/hrbrmstr/metricsgraphics</a>\r\n**Version:**
235
+ v0.9.1\r\n**Archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.50373\"
236
+ target=\"_blank\">10.5281/zenodo.50373</a>\r\n\r\n## Status\r\n\r\n[![status](http://joss.theoj.org/papers/1677676c38bd118db5fe363a6eb3f88f/status.svg)](http://joss.theoj.org/papers/1677676c38bd118db5fe363a6eb3f88f)\r\n\r\nStatus
237
+ badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/1677676c38bd118db5fe363a6eb3f88f\"><img
238
+ src=\"http://joss.theoj.org/papers/1677676c38bd118db5fe363a6eb3f88f/status.svg\"></a>\r\nMarkdown:
239
+ [![status](http://joss.theoj.org/papers/1677676c38bd118db5fe363a6eb3f88f/status.svg)]http://joss.theoj.org/papers/1677676c38bd118db5fe363a6eb3f88f\r\n```\r\n\r\n##
240
+ Reviewer questions\r\n\r\n### General checks\r\n\r\n- [x] **Repository:**
241
+ Is the source code for this software available at the <a target=\"_blank\"
242
+ href=\"https://github.com/hrbrmstr/metricsgraphics\">repository url</a>?\r\n-
243
+ [ ] **License:** Does the repository contain a plain-text LICENSE file with
244
+ the contents of an [OSI approved](https://opensource.org/licenses/alphabetical)
245
+ software license?\r\n- [ ] **Version:** Does the release version given match
246
+ the GitHub release (v0.9.1)?\r\n- [x] **Archive:** Does the <a target=\"_blank\"
247
+ href=\"10.5281/zenodo.50373\">software archive</a> resolve?\r\n\r\n### Functionality\r\n\r\n-
248
+ [x] **Installation:** Does installation proceed as outlined in the documentation?\r\n-
249
+ [x] **Functionality:** Have the functional claims of the software been confirmed?\r\n-
250
+ [x] **Performance:** Have the performance claims of the software been confirmed?\r\n\r\n###
251
+ Documentation\r\n\r\n- [x] **A statement of need:** Do the authors clearly
252
+ state what problems the software is designed to solve and who the target audience
253
+ is?\r\n- [x] **Installation instructions:** Is there a clearly-stated list
254
+ of dependencies? Ideally these should be handled with an automated package
255
+ management solution.\r\n- [x] **Example usage:** Do the authors include examples
256
+ of how to use the software (ideally to solve real-world analysis problems).\r\n-
257
+ [x] **Functionality documentation:** Is the functionality of the software
258
+ documented to a satisfactory level (e.g. API method documentation)?\r\n- [x]
259
+ **Automated tests:** Are there automated tests or manual steps described so
260
+ that the function of the software can be verified?\r\n- [ ] **Community guidelines:**
261
+ Are there clear guidelines for third parties wishing to 1) Contribute to the
262
+ software 2) Report issues or problems with the software 3) Seek support\r\n\r\n###
263
+ Software paper\r\n\r\n- [x] **Authors:** Does the `paper.md` file include
264
+ a list of authors with their affiliations?\r\n- [x] **A statement of need:**
265
+ Do the authors clearly state what problems the software is designed to solve
266
+ and who the target audience is?\r\n- [x] **References:** Do all archival references
267
+ that should have a DOI list one (e.g. papers, datasets, software)?\r\n"}]'
268
+ http_version:
269
+ recorded_at: Fri, 13 May 2016 23:47:37 GMT
270
+ recorded_with: VCR 2.9.3
@@ -0,0 +1,39 @@
1
+ # The Whedon::Auditor simply uses the regexes defined for a GitHub review issue
2
+ # body and prints them out.
3
+
4
+ module Whedon
5
+ class Auditor
6
+ attr_accessor :review_body
7
+
8
+ def initialize(review_body)
9
+ @review_body = review_body
10
+ end
11
+
12
+ def audit
13
+ puts verify_author
14
+ puts verify_version
15
+ puts verify_repository
16
+ puts verify_archive
17
+ end
18
+
19
+ def verify_author
20
+ author = review_body[AUTHOR_REGEX]
21
+ return "Author: #{author}" if author
22
+ end
23
+
24
+ def verify_version
25
+ version = review_body[VERSION_REGEX]
26
+ return "Version: #{version}" if version
27
+ end
28
+
29
+ def verify_repository
30
+ repository_address = review_body[REPO_REGEX]
31
+ return "Repository: #{repository_address}" if repository_address
32
+ end
33
+
34
+ def verify_archive
35
+ archive = review_body[ARCHIVE_REGEX]
36
+ return "Archive: #{archive}" if archive
37
+ end
38
+ end
39
+ end