roboneuro 0.1.2 → 0.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 78096b7533c92f42eaf738db0ec575a6b41e28af65bd4352cd0187355a6cd509
-  data.tar.gz: 229efd4a36c74c79d4bd13b049d5fabc490755ba1cfd3c6b4975d7d3a679f6ee
+  metadata.gz: 8c5144858281c93c49bf4c84aa8fc29d298561539e10e3eb65adc45d0b60bc8f
+  data.tar.gz: a591afde7412ff24427f952ddb992ab6e2f629d78d4e1c8a46d0a2a1672ef79e
 SHA512:
-  metadata.gz: 1850c4dc81d2678265f2850d3b2e8eb1fe71bdfc88d0e948874ac803e7cd6f539a60c7d2a19a0401cba42e768b60a08d078bdd291320fb858f417f52fce822cd
-  data.tar.gz: 6bb0ccf1b8a1f58f3217505e05c548bc97efbe1f0151b397a0fabd8e6bd53be1e935ab16329933f27f218e7a369d131881ddd981b557eafe53822189c4548d8d
+  metadata.gz: 01177b8a7791aab9f2b583b711e7057bb3637befdd53ba22dc2a4756f51f1918976e810ff649fce96cd4d51e685eeb8ab29375072cd003fabb814b65905b436d
+  data.tar.gz: 87a1b4fda0aadf51fedc64c4dd34e8ad09411297a4301bc962cca173a726cdf7603fc28c607c6c07a331e797cdb5e35a8fd331358fe18a6f3e4caf1e2f7592d3

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    roboneuro (0.1.2)
+    roboneuro (0.1.3)
       bibtex-ruby (~> 6.0.0)
       dotenv
       github-linguist (~> 5.3)
@@ -102,7 +102,7 @@ GEM
       rspec-support (~> 3.10.0)
     rspec-support (3.10.2)
     ruby2_keywords (0.0.5)
-    rugged (1.4.2)
+    rugged (1.4.3)
     sawyer (0.8.2)
       addressable (>= 2.3.5)
       faraday (> 0.8, < 2.0)

data/README.md

@@ -14,6 +14,8 @@ Hopefully...
 
 [![Build Status](https://github.com/openjournals/whedon/actions/workflows/tests.yml/badge.svg)](https://github.com/openjournals/whedon/actions/workflows/tests.yml)
 
+[![Gem Version](https://badge.fury.io/rb/roboneuro.svg)](https://badge.fury.io/rb/roboneuro)
+
 ## Installation
 
 Depending on how Ruby is installed on your system there might slightly different steps be necessary. Note that Whedon is only tested for reasonably modern versions of Ruby (i.e. > 2.1) [Bundler](http://bundler.io/) is used to install dependencies.

data/fixtures/paper/paper-single-author.md

@@ -5,8 +5,8 @@ tags:
   - tags
   - for the paper
 authors:
- - name: Arfon M Smith
-   orcid: 0000-0002-3957-2474
+ - name: Agah Karakuzu
+   orcid: 0000-0001-7283-271X
    affiliation: "1,2"
 affiliations:
  - name: GitHub Inc.

data/fixtures/paper/paper.md

@@ -5,8 +5,8 @@ tags:
   - tags
   - for the paper
 authors:
- - name: Arfon M Smith
-   orcid: 0000-0002-3957-2474
+ - name: Agah Karakuzu
+   orcid: 0000-0001-7283-271X
    affiliation: "1,2"
  - name: Mickey Mouse
    orcid: 0000-0002-3957-2474

data/lib/whedon/compilers.rb

@@ -106,7 +106,6 @@ 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)
@@ -148,7 +147,6 @@ module Compilers
       "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,
@@ -178,7 +176,6 @@ module Compilers
     -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" \

data/lib/whedon/processor.rb

@@ -122,7 +122,9 @@ module Whedon
       joss_deposit
 
       puts "p=dat #{@review_issue_id};p.doi='#{paper.formatted_doi}';"\
-           "p.archive_doi=#{archive_doi};p.accepted_at=Time.now;"\
+           "p.repository_doi=#{repository_doi};p.accepted_at=Time.now;"\
+           "p.data_doi=#{data_doi};p.book_doi=#{book_doi};"\
+           "p.docker_doi=#{docker_doi};p.book_exec_url=#{book_exec_url};"\
            "p.citation_string='#{citation_string}';"\
            "p.authors='#{paper.authors_string}';p.title='#{paper.title}';"
     end
@@ -136,7 +138,11 @@ module Whedon
                   :id => paper.review_issue_id,
                   :metadata => Base64.encode64(paper.deposit_payload.to_json),
                   :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,
                   :citation_string => citation_string,
                   :title => paper.plain_title,
                   :secret => ENV['WHEDON_SECRET']

data/lib/whedon/version.rb

@@ -1,3 +1,3 @@
 module Whedon
-  VERSION = "0.1.2"
+  VERSION = "0.1.3"
 end

data/resources/NeuroLibre/defaults.yaml

@@ -4,9 +4,9 @@ csl: /usr/local/share/openjournals/NeuroLibre/apa.csl
 variables:
   joss_resource_url: 'N/A'
   journal_abbrev_title: 'NeuroLibre'
-  journal_alias: 'NeuroLibre'
+  journal_alias: 'neurolibre'
   journal_issn: '0000-0000'
-  journal_name: 'NeuroLibre Executable Preprint Server'
+  journal_name: 'NeuroLibre Reproducible Preprint Server'
   journal_url: 'https://neurolibre.org/'
 
 metadata:

data/resources/NeuroLibre/latex.template

@@ -431,29 +431,35 @@ $endif$
   %\hrule
   \sffamily\small
 
-  \href{$book_exec_url$}{\includegraphics[width=\marginparwidth]{$book_exec_icon$}}
-
-  \vspace{1mm}
+  \vspace{-4.5cm}
 
   {\bfseries DOI:} \href{https://doi.org/$formatted_doi$}{\color{red}{$formatted_doi$}}
 
   \vspace{2mm}
 
-  {\bfseries Jupyter Book}
+    {\bfseries Reproducible Preprint}
+  \begin{itemize}
+    \setlength\itemsep{0em}
+    \item \href{$book_exec_url$}{\color{red}{Jupyter Book}} \ExternalLink
+  \end{itemize}
+
+  \vspace{2mm}
+
+  {\bfseries Code}
   \begin{itemize}
     \setlength\itemsep{0em}
     \item \href{$review_issue_url$}{\color{red}{Technical Screening}} \ExternalLink
-    \item \href{$repository$}{\color{red}{Source}} \ExternalLink
+    \item \href{$repository$}{\color{red}{Submitted Repository}} \ExternalLink
   \end{itemize}
 
   \vspace{2mm}
 
-  {\bfseries Zenodo Archives}
+  {\bfseries Archives}
   \begin{itemize}
     \setlength\itemsep{0em}
     \item \href{$repository_doi$}{\color{red}{Repository}} \ExternalLink
     \item \href{$data_doi$}{\color{red}{Dataset}} \ExternalLink
-    \item \href{$book_doi$}{\color{red}{Built Book}} \ExternalLink
+    \item \href{$book_doi$}{\color{red}{Jupyter Book}} \ExternalLink
     \item \href{$docker_doi$}{\color{red}{Container}} \ExternalLink
   \end{itemize}
 

data/resources/crossref.template

@@ -7,14 +7,13 @@
       <depositor_name>NeuroLibre Admin</depositor_name>
       <email_address>roboneurolibre@gmail.com</email_address>
     </depositor>
-    <registrant>The Open Journal</registrant>
+    <registrant>Centre de Recherche de l'Institut Universitaire de Geriatrie de Montreal</registrant>
   </head>
   <body>
     <journal>
       <journal_metadata>
         <full_title>$journal_name$</full_title>
         <abbrev_title>$journal_abbrev_title$</abbrev_title>
-        <issn media_type="electronic">$journal_issn$</issn>
         <doi_data>
           <doi>10.55458/$journal_alias$</doi>
           <resource>$journal_url$</resource>
@@ -58,7 +57,7 @@
           </rel:related_item>
           <rel:related_item>
             <rel:description>Dataset archive</rel:description>
-            <rel:inter_work_relation relationship-type="hasPart" identifier-type="doi">$dataset_doi$</rel:inter_work_relation>
+            <rel:inter_work_relation relationship-type="hasPart" identifier-type="doi">$data_doi$</rel:inter_work_relation>
           </rel:related_item>
           <rel:related_item>
             <rel:description>Book archive</rel:description>

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: roboneuro
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.3
 platform: ruby
 authors:
 - Agah Karakuzu
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-04-12 00:00:00.000000000 Z
+date: 2022-04-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bibtex-ruby