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.
- checksums.yaml +7 -0
- data/.DS_Store +0 -0
- data/.env-example +12 -0
- data/.env.test +8 -0
- data/.github/workflows/docker-image.yml +63 -0
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- data/.gitignore +3 -0
- data/Gemfile +3 -0
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- data/LICENSE +21 -0
- data/README.md +190 -0
- data/Rakefile +13 -0
- data/bin/whedon +131 -0
- data/fixtures/latex_paper/paper.tex +0 -0
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- data/fixtures/paper/paper-single-author.md +24 -0
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- data/fixtures/paper/paper.bib +65 -0
- data/fixtures/paper/paper.html +14 -0
- data/fixtures/paper/paper.md +27 -0
- data/fixtures/paper/paper.pdf +0 -0
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- data/fixtures/test_paper/paper.bib +0 -0
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- data/fixtures/vcr_cassettes/joss-lookup.yml +58 -0
- data/fixtures/vcr_cassettes/review.yml +237 -0
- data/fixtures/vcr_cassettes/reviews.yml +270 -0
- data/lib/whedon/auditor.rb +39 -0
- data/lib/whedon/author.rb +81 -0
- data/lib/whedon/bibtex_parser.rb +103 -0
- data/lib/whedon/compilers.rb +379 -0
- data/lib/whedon/github.rb +12 -0
- data/lib/whedon/orcid_validator.rb +83 -0
- data/lib/whedon/processor.rb +178 -0
- data/lib/whedon/review.rb +25 -0
- data/lib/whedon/reviews.rb +29 -0
- data/lib/whedon/version.rb +3 -0
- data/lib/whedon.rb +387 -0
- data/paperdraft.Dockerfile +48 -0
- data/pkg/roboneuro-0.1.0.gem +0 -0
- data/resources/.DS_Store +0 -0
- data/resources/NeuroLibre/.DS_Store +0 -0
- data/resources/NeuroLibre/aas-logo.png +0 -0
- data/resources/NeuroLibre/apa.csl +1919 -0
- data/resources/NeuroLibre/defaults.yaml +14 -0
- data/resources/NeuroLibre/latex.template +541 -0
- data/resources/NeuroLibre/logo.png +0 -0
- data/resources/NeuroLibre/logo_link.png +0 -0
- data/resources/apa.csl +1919 -0
- data/resources/crossref.template +89 -0
- data/resources/docker-defaults.yaml +42 -0
- data/resources/docker-entrypoint.sh +37 -0
- data/resources/jats.csl +204 -0
- data/resources/jats.template +105 -0
- data/resources/jose/apa.csl +1919 -0
- data/resources/jose/defaults.yaml +14 -0
- data/resources/jose/latex.template +486 -0
- data/resources/jose/logo.png +0 -0
- data/resources/joss/aas-logo.png +0 -0
- data/resources/joss/apa.csl +1919 -0
- data/resources/joss/defaults.yaml +14 -0
- data/resources/joss/latex.template +525 -0
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- data/resources/latex.template +485 -0
- data/resources/time.lua +8 -0
- data/roboneuro.gemspec +39 -0
- data/spec/auditor_spec.rb +22 -0
- data/spec/author_spec.rb +17 -0
- data/spec/bibtex_spec.rb +31 -0
- data/spec/orcid_validator_spec.rb +33 -0
- data/spec/processor_spec.rb +66 -0
- data/spec/review_spec.rb +12 -0
- data/spec/reviews_spec.rb +18 -0
- data/spec/spec_helper.rb +22 -0
- data/spec/whedon_spec.rb +93 -0
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Application Skeleton: Generating Synthetic Applications for Infrastructure
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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
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author:** @zhaozhang (<a href=\"http://orcid.org/0000-0001-5921-0035\">Zhao
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Zhang</a>)\r\n**Repository:** <a href=\"https://github.com/applicationskeleton/Skeleton\"
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target =\"_blank\">https://github.com/applicationskeleton/Skeleton</a>\r\n**Version:**
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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
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=\"_blank\">http://dx.doi.org/10.5281/zenodo.13750</a>\r\n\r\n## Status\r\n\r\n[](http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6)\r\n\r\nStatus
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badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6\"><img
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src=\"http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6/status.svg\"></a>\r\nMarkdown:
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[]http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6\r\n```\r\n\r\n##
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Reviewer questions\r\n\r\n### General checks\r\n\r\n- [x] **Repository:**
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Is the source code for this software available at the <a target=\"_blank\"
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href=\"https://github.com/applicationskeleton/Skeleton\">repository url</a>?\r\n-
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[x] **License:** Does the repository contain a plain-text LICENSE file with
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the contents of an [OSI approved](https://opensource.org/licenses/alphabetical)
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software license?\r\n- [x] **Version:** Does the release version given match
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the GitHub release (v1.2)?\r\n- [x] **Archive:** Does the <a target=\"_blank\"
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href=\"http://dx.doi.org/10.5281/zenodo.13750\">software archive</a> resolve?\r\n\r\n###
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Functionality\r\n\r\n- [x] **Installation:** Does installation proceed as
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outlined in the documentation?\r\n- [x] **Functionality:** Have the functional
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claims of the software been confirmed?\r\n- [x] **Performance:** Have the
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performance claims of the software been confirmed?\r\n\r\n### Documentation\r\n\r\n-
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[x] **A statement of need:** Do the authors clearly state what problems the
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software is designed to solve and who the target audience is?\r\n- [x] **Installation
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instructions:** Is there a clearly-stated list of dependencies? Ideally these
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should be handled with an automated package management solution.\r\n- [x]
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(ideally to solve real-world analysis problems).\r\n- [x] **Functionality
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automated tests or manual steps described so that the function of the software
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for third parties wishing to 1) Contribute to the software 2) Report issues
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or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\nCompiled
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paper PDF: [paper.pdf](https://github.com/openjournals/joss-reviews/files/259667/paper.pdf)\r\n\r\n\r\n-
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[x] **Authors:** Does the `paper.md` file include a list of authors with their
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is?\r\n- [x] **References:** Do all archival references that should have a
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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}}'
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author:** @meyera (<a href=\"http://orcid.org/0000-0002-6944-2478\">Alexander
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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
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author:** @genomematt (<a href=\"http://orcid.org/0000-0001-6624-4698\">Matthew
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J Wakefield</a>)\r\n**Repository:** <a href=\"http://github.com/genomematt/xenomapper/\"
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[](http://joss.theoj.org/papers/7065e20e97ff4e44695b5e9fef7cdcd8)\r\n```\r\n\r\n##
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Reviewer questions\r\n\r\n### General checks\r\n\r\n- [ ] **Repository:**
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paper PDF: [10.21105.joss.00018.pdf](https://github.com/openjournals/joss-reviews/files/261671/10.21105.joss.00018.pdf)\r\n\r\n-
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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
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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:
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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
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VanderPlas</a>)\r\n**Repository:** <a href=\"http://github.com/jakevdp/mst_clustering\"
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target=\"_blank\">http://github.com/jakevdp/mst_clustering</a>\r\n**Version:**
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v1.0.0\r\n**Archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.50995\"
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target =\"_blank\">http://dx.doi.org/10.5281/zenodo.50995</a>\r\n\r\n## Status\r\n\r\n[](http://joss.theoj.org/papers/0b73d249cd34985b6fa1a5ad4f4f8014)\r\n\r\nStatus
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badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/0b73d249cd34985b6fa1a5ad4f4f8014\"><img
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[]http://joss.theoj.org/papers/0b73d249cd34985b6fa1a5ad4f4f8014\r\n```\r\n\r\n##
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Is the source code for this software available at the <a target=\"_blank\"
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href=\"http://github.com/jakevdp/mst_clustering\">repository url</a>?\r\n-
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software license?\r\n- [ ] **Version:** Does the release version given match
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the GitHub release (v1.0.0)?\r\n- [x] **Archive:** Does the <a target=\"_blank\"
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href=\"http://dx.doi.org/10.5281/zenodo.50995\">software archive</a> resolve?\r\n\r\n###
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outlined in the documentation?\r\n- [x] **Functionality:** Have the functional
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claims of the software been confirmed?\r\n- [x] **Performance:** Have the
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performance claims of the software been confirmed?\r\n\r\n### Documentation\r\n\r\n-
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[x] **A statement of need:** Do the authors clearly state what problems the
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(ideally to solve real-world analysis problems).\r\n- [x] **Functionality
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documentation:** Is the functionality of the software documented to a satisfactory
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automated tests or manual steps described so that the function of the software
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for third parties wishing to 1) Contribute to the software 2) Report issues
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or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\n-
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affiliations?\r\n- [x] **A statement of need:** Do the authors clearly state
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what problems the software is designed to solve and who the target audience
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is?\r\n- [ ] **References:** Do all archival references that should have a
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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:
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metricsgraphics: An R htmlwidget interface to the MetricsGraphics.js D3-based
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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
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author:** @hrbrmstr (<a href=\"http://orcid.org/0000-0001-5670-2640\">Bob
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Rudis</a>)\r\n**Repository:** <a href=\"https://github.com/hrbrmstr/metricsgraphics\"
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target=\"_blank\">https://github.com/hrbrmstr/metricsgraphics</a>\r\n**Version:**
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v0.9.1\r\n**Archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.50373\"
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target=\"_blank\">10.5281/zenodo.50373</a>\r\n\r\n## Status\r\n\r\n[](http://joss.theoj.org/papers/1677676c38bd118db5fe363a6eb3f88f)\r\n\r\nStatus
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badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/1677676c38bd118db5fe363a6eb3f88f\"><img
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[]http://joss.theoj.org/papers/1677676c38bd118db5fe363a6eb3f88f\r\n```\r\n\r\n##
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Is the source code for this software available at the <a target=\"_blank\"
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href=\"https://github.com/hrbrmstr/metricsgraphics\">repository url</a>?\r\n-
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the contents of an [OSI approved](https://opensource.org/licenses/alphabetical)
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software license?\r\n- [ ] **Version:** Does the release version given match
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the GitHub release (v0.9.1)?\r\n- [x] **Archive:** Does the <a target=\"_blank\"
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href=\"10.5281/zenodo.50373\">software archive</a> resolve?\r\n\r\n### Functionality\r\n\r\n-
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[x] **Performance:** Have the performance claims of the software been confirmed?\r\n\r\n###
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of dependencies? Ideally these should be handled with an automated package
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management solution.\r\n- [x] **Example usage:** Do the authors include examples
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software 2) Report issues or problems with the software 3) Seek support\r\n\r\n###
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and who the target audience is?\r\n- [x] **References:** Do all archival references
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that should have a DOI list one (e.g. papers, datasets, software)?\r\n"}]'
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# The Whedon::Auditor simply uses the regexes defined for a GitHub review issue
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