roboneuro 0.1.1 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3facccb4e09f68c233c0a386b6c9d35262ca140316c182026928c090a5a13e86
-  data.tar.gz: '00588aa4a555273fcb1bf62a78f0237167ab6c9d0e16d9b1c7ddeb4ee41eabb4'
+  metadata.gz: 78096b7533c92f42eaf738db0ec575a6b41e28af65bd4352cd0187355a6cd509
+  data.tar.gz: 229efd4a36c74c79d4bd13b049d5fabc490755ba1cfd3c6b4975d7d3a679f6ee
 SHA512:
-  metadata.gz: 88571deda0ffdccffd7a65a0756a9446b3ad1b52bcf397a53156062173d8a707ae03d2950d8e1ca78120487c752ac56084e44074fc47544bd91e1c58f22fef20
-  data.tar.gz: b543ab1f0436e2625cce9553bef99a549bb8b622d5639aee6225c0f87328a047f05266e5561dab649f061b7f2305c2bb1ee2f31147eaeca3d036929baa624342
+  metadata.gz: 1850c4dc81d2678265f2850d3b2e8eb1fe71bdfc88d0e948874ac803e7cd6f539a60c7d2a19a0401cba42e768b60a08d078bdd291320fb858f417f52fce822cd
+  data.tar.gz: 6bb0ccf1b8a1f58f3217505e05c548bc97efbe1f0151b397a0fabd8e6bd53be1e935ab16329933f27f218e7a369d131881ddd981b557eafe53822189c4548d8d

data/.gitignore

@@ -1,3 +1,4 @@
 .env
 tmp
-roboneuro*.gem
+roboneuro*.gem
+.DS_Store

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    roboneuro (0.1.1)
+    roboneuro (0.1.2)
       bibtex-ruby (~> 6.0.0)
       dotenv
       github-linguist (~> 5.3)

data/bin/whedon

@@ -42,7 +42,12 @@ class WhedonCli < Thor
   def prepare(issue_id, custom_path=nil, custom_branch=nil)
     review = Whedon::Review.new(issue_id)
     processor = Whedon::Processor.new(issue_id, review.issue_body, custom_path)
-    processor.archive_doi = 'PENDING'
+    processor.repository_doi = 'PENDING'
+    processor.data_doi = 'PENDING'
+    processor.book_doi = 'PENDING'
+    processor.docker_doi = 'PENDING'
+    processor.book_exec_url = 'PENDING'
+
 
     # Optionally set the path to work in
     path = custom_path ? custom_path : "tmp/#{issue_id}"

data/fixtures/review_body.txt

@@ -1,7 +1,11 @@
 **Submitting author:** @zhaozhang (<a href="http://orcid.org/0000-0001-5921-0035">Zhao Zhang</a>)
 **Repository:** <a href="https://github.com/applicationskeleton/Skeleton" target ="_blank">https://github.com/applicationskeleton/Skeleton</a>
 **Version:** v1.2
-**Archive:** <a href="http://dx.doi.org/10.5281/zenodo.13750" target ="_blank">http://dx.doi.org/10.5281/zenodo.13750</a>
+**Jupyter Book:** <a href="https://neurolibre.org" target ="_blank">https://neurolibre.org</a>
+**Repository archive:** <a href="http://dx.doi.org/10.5281/zenodo.13750" target ="_blank">http://dx.doi.org/10.5281/zenodo.13750</a>
+**Data archive:** <a href="http://dx.doi.org/10.5281/zenodo.13750" target ="_blank">http://dx.doi.org/10.5281/zenodo.13750</a>
+**Book archive:** <a href="http://dx.doi.org/10.5281/zenodo.13750" target ="_blank">http://dx.doi.org/10.5281/zenodo.13750</a>
+**Docker archive:** <a href="http://dx.doi.org/10.5281/zenodo.13750" target ="_blank">http://dx.doi.org/10.5281/zenodo.13750</a>
 
 ## Status
 

data/fixtures/vcr_cassettes/review.yml

@@ -80,8 +80,12 @@ http_interactions:
         author:** @zhaozhang (<a href=\"http://orcid.org/0000-0001-5921-0035\">Zhao
         Zhang</a>)\r\n**Repository:** <a href=\"https://github.com/applicationskeleton/Skeleton\"
         target =\"_blank\">https://github.com/applicationskeleton/Skeleton</a>\r\n**Version:**
-        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
-        =\"_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
+        v1.2\r\n**Editor:** @arfon\r\n**Reviewers:** @jim, @bob\r\n**Repository archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.13750\" target
+        =\"_blank\">http://dx.doi.org/10.5281/zenodo.13750</a>r\n**Data archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.13750\" target
+        =\"_blank\">http://dx.doi.org/10.5281/zenodo.13750</a>r\n**Book archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.13750\" target
+        =\"_blank\">http://dx.doi.org/10.5281/zenodo.13750</a>r\n**Docker archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.13750\" target
+        =\"_blank\">http://dx.doi.org/10.5281/zenodo.13750</a>r\n**Jupyter Book:** <a href=\"https://neurolibre.org\" target
+        =\"_blank\">https://neurolibre.org</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
         badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6\"><img
         src=\"http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6/status.svg\"></a>\r\nMarkdown:
         [![status](http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6/status.svg)]http://joss.theoj.org/papers/6b34fdbf8215c1ecd4941afc8be7a7e6\r\n```\r\n\r\n##

data/lib/whedon/auditor.rb

@@ -14,6 +14,7 @@ module Whedon
       puts verify_version
       puts verify_repository
       puts verify_archive
+      puts verify_book
     end
 
     def verify_author
@@ -32,8 +33,16 @@ module Whedon
     end
 
     def verify_archive
-      archive = review_body[ARCHIVE_REGEX]
-      return "Archive: #{archive}" if archive
+      archive_repository = review_body[ARCHIVE_REPOSITORY_REGEX]
+      archive_data = review_body[ARCHIVE_DATA_REGEX]
+      archive_book = review_body[ARCHIVE_BOOK_REGEX]
+      archive_docker = review_body[ARCHIVE_DOCKER_REGEX]
+      return "Repository archive: #{archive_repository} Data archive: #{archive_data} Book archive: #{archive_book} Docker archive: #{archive_docker}" if archive_repository && archive_book && archive_data && archive_docker
+    end
+
+    def verify_book
+      book = review_body[BOOK_EXEC_REGEX]
+      return "Jupyter Book: #{book}"
     end
   end
 end

data/lib/whedon/compilers.rb

@@ -106,6 +106,7 @@ module Compilers
   def pdf_from_markdown(custom_branch=nil, draft=true, paper_issue=nil, paper_volume=nil, paper_year=nil)
     latex_template_path = "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/latex.template"
     csl_file = "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/apa.csl"
+    book_exec_icon = "#{Whedon.resources}/#{ENV['JOURNAL_ALIAS']}/logo_link.png"
 
     url = "#{ENV['JOURNAL_URL']}/papers/lookup/#{@review_issue_id}"
     response = RestClient.get(url)
@@ -142,7 +143,12 @@ module Compilers
 
     metadata = {
       "repository" => repository_address,
-      "archive_doi" => archive_doi,
+      "repository_doi" => repository_doi,
+      "data_doi" => data_doi,
+      "book_doi" => book_doi,
+      "docker_doi" => docker_doi,
+      "book_exec_url" => book_exec_url,
+      "book_exec_icon" => book_exec_icon,
       "paper_url" => paper.pdf_url,
       "journal_name" => ENV['JOURNAL_NAME'],
       "review_issue_url" => paper.review_issue_url,
@@ -167,7 +173,12 @@ module Compilers
 
     `cd #{paper.directory} && pandoc \
     -V repository="#{repository_address}" \
-    -V archive_doi="#{archive_doi}" \
+    -V repository_doi="#{repository_doi}" \
+    -V data_doi="#{data_doi}" \
+    -V book_doi="#{book_doi}" \
+    -V docker_doi="#{docker_doi}" \
+    -V book_exec_url="#{book_exec_url}" \
+    -V book_exec_icon="#{book_exec_icon}" \
     -V review_issue_url="#{paper.review_issue_url}" \
     -V editor_url="#{editor_url}" \
     -V graphics="true" \
@@ -182,7 +193,7 @@ module Compilers
     if File.exists?("#{paper.directory}/#{paper.filename_doi}.pdf")
       puts "#{paper.directory}/#{paper.filename_doi}.pdf"
     else
-      abort("Looks like we failed to compile the PDF")
+      abort("Looks like we failed to compile the PDF :/")
     end
   end
 
@@ -280,7 +291,11 @@ module Compilers
       "timestamp" => Time.now.strftime('%Y%m%d%H%M%S'),
       "doi_batch_id" => generate_doi_batch_id,
       "formatted_doi" => paper.formatted_doi,
-      "archive_doi" => archive_doi,
+      "repository_doi" => repository_doi,
+      "data_doi" => data_doi,
+      "book_doi" => book_doi,
+      "docker_doi" => docker_doi,
+      "book_exec_url" => book_exec_url,
       "review_issue_url" => paper.review_issue_url,
       "paper_url" => paper.pdf_url,
       "joss_resource_url" => paper.joss_resource_url,

data/lib/whedon/processor.rb

@@ -12,7 +12,11 @@ module Whedon
     attr_accessor :review_issue_id
     attr_accessor :review_body
     attr_accessor :repository_address
-    attr_accessor :archive_doi
+    attr_accessor :repository_doi
+    attr_accessor :data_doi
+    attr_accessor :book_exec_url
+    attr_accessor :book_doi
+    attr_accessor :docker_doi
     attr_accessor :paper_path
     attr_accessor :xml_path
     attr_accessor :doi_batch_id
@@ -26,7 +30,11 @@ module Whedon
       @review_issue_id = review_issue_id
       @review_body = review_body
       @repository_address = review_body[REPO_REGEX]
-      @archive_doi = review_body[ARCHIVE_REGEX]
+      @repository_doi = review_body[ARCHIVE_REPOSITORY_REGEX]
+      @data_doi = review_body[ARCHIVE_DATA_REGEX]
+      @book_doi = review_body[ARCHIVE_BOOK_REGEX]
+      @docker_doi = review_body[ARCHIVE_DOCKER_REGEX]
+      @book_exec_url = review_body[BOOK_EXEC_REGEX]
       @custom_path = custom_path
       # Probably a much nicer way to do this...
       @current_year = ENV["CURRENT_YEAR"].nil? ? Time.new.year : ENV["CURRENT_YEAR"]

data/lib/whedon/version.rb

@@ -1,3 +1,3 @@
 module Whedon
-  VERSION = "0.1.1"
+  VERSION = "0.1.2"
 end

data/lib/whedon.rb

@@ -32,7 +32,12 @@ module Whedon
   AUTHOR_REGEX = /(?<=\*\*Submitting author:\*\*\s)(\S+)/
   REPO_REGEX = /(?<=\*\*Repository:\*\*.<a\shref=)"(.*?)"/
   VERSION_REGEX = /(?<=\*\*Version:\*\*\s)(\S+)/
-  ARCHIVE_REGEX = /(?<=\*\*Archive:\*\*.<a\shref=)"(.*?)"/
+  ARCHIVE_REPOSITORY_REGEX = /(?<=\*\*Repository archive:\*\*.<a\shref=)"(.*?)"/
+  ARCHIVE_DATA_REGEX = /(?<=\*\*Data archive:\*\*.<a\shref=)"(.*?)"/
+  ARCHIVE_BOOK_REGEX = /(?<=\*\*Book archive:\*\*.<a\shref=)"(.*?)"/
+  ARCHIVE_DOCKER_REGEX = /(?<=\*\*Docker archive:\*\*.<a\shref=)"(.*?)"/
+  BOOK_EXEC_REGEX = /(?<=\*\*Jupyter Book:\*\*.<a\shref=)"(.*?)"/
+
 
   class Paper
     include GitHub
@@ -176,7 +181,10 @@ module Whedon
       %w(title tags languages).each { |var| payload['paper'][var] = self.send(var) }
       payload['paper']['authors'] = authors.collect { |a| a.to_h }
       payload['paper']['doi'] = formatted_doi
-      payload['paper']['archive_doi'] = review_issue_body[ARCHIVE_REGEX].gsub('"', '')
+      payload['paper']['repository_doi'] = review_issue_body[ARCHIVE_REPOSITORY_REGEX].gsub('"', '')
+      payload['paper']['data_doi'] = review_issue_body[ARCHIVE_DATA_REGEX].gsub('"', '')
+      payload['paper']['book_doi'] = review_issue_body[ARCHIVE_BOOK_REGEX].gsub('"', '')
+      payload['paper']['docker_doi'] = review_issue_body[ARCHIVE_DOCKER_REGEX].gsub('"', '')
       payload['paper']['repository_address'] = review_issue_body[REPO_REGEX].gsub('"', '')
       payload['paper']['editor'] = "@#{editor}"
       payload['paper']['reviewers'] = reviewers.collect(&:strip)

data/paperdraft.Dockerfile

@@ -1,7 +1,11 @@
 FROM pandoc/latex:2.11.2
 
 # Update tlmgr
-RUN tlmgr update --self
+RUN tlmgr repository add ftp://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/tlnet-final; \
+    tlmgr repository list; \
+    tlmgr repository remove http://mirror.ctan.org/systems/texlive/tlnet; \
+    tlmgr option repository ftp://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/tlnet-final; \
+    tlmgr update --self
 
 # Install additional LaTeX packages
 RUN tlmgr install \

data/resources/NeuroLibre/latex.template

@@ -431,7 +431,7 @@ $endif$
   %\hrule
   \sffamily\small
 
-  \href{{$book_exec_url$}}{\includegraphics[width=\marginparwidth]{$book_exec_icon$}}
+  \href{$book_exec_url$}{\includegraphics[width=\marginparwidth]{$book_exec_icon$}}
 
   \vspace{1mm}
 

data/spec/auditor_spec.rb

@@ -17,6 +17,11 @@ describe Whedon::Auditor do
   end
 
   it "knows how to find the archive from the issue body" do
-    expect(subject.verify_archive).to eql("Archive: \"http://dx.doi.org/10.5281/zenodo.13750\"")
+    expect(subject.verify_archive).to eql("Repository archive: \"http://dx.doi.org/10.5281/zenodo.13750\" Data archive: \"http://dx.doi.org/10.5281/zenodo.13750\" Book archive: \"http://dx.doi.org/10.5281/zenodo.13750\" Docker archive: \"http://dx.doi.org/10.5281/zenodo.13750\"")
+  end
+
+  it "knows how to find the Jupyter Book from the issue body" do
+    expect(subject.verify_book).to eql("Jupyter Book: \"https://neurolibre.org\"")
   end
 end
+

data/spec/whedon_spec.rb

@@ -85,7 +85,7 @@ describe Whedon do
 
   it "should know how to generate the deposit_payload" do
     VCR.use_cassette('review') do
-      %w{title tags languages authors doi archive_doi repository_address editor reviewers}.each do |attribute|
+      %w{title tags languages authors doi repository_doi data_doi book_doi docker_doi repository_address editor reviewers}.each do |attribute|
         expect(paper_with_harder_names.deposit_payload['paper'][attribute].nil?).to be_falsey
       end
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: roboneuro
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - Agah Karakuzu
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-04-11 00:00:00.000000000 Z
+date: 2022-04-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bibtex-ruby
@@ -270,7 +270,6 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- ".DS_Store"
 - ".env-example"
 - ".env.test"
 - ".github/workflows/docker-image.yml"
@@ -316,8 +315,6 @@ files:
 - lib/whedon/version.rb
 - paperdraft.Dockerfile
 - pkg/roboneuro-0.1.0.gem
-- resources/.DS_Store
-- resources/NeuroLibre/.DS_Store
 - resources/NeuroLibre/aas-logo.png
 - resources/NeuroLibre/apa.csl
 - resources/NeuroLibre/defaults.yaml