[Review Requested] Update Underway

content/00.front-matter.md

@@ -4,9 +4,14 @@
   Pandoc automatically inserts title from metadata.yaml, so it is not included in this template.
 ##}
 
-_A published version of this manuscript from 04 April 2018 is available at <https://doi.org/10.1098/rsif.2017.0387>.
-An effort is underway to update the manuscript.
-New authors and links to new sections are available in [GitHub Issue #959](https://github.com/greenelab/deep-review/issues/959)._
+<!-- include the Font Awesome library, per: https://fontawesome.com/start -->
+<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.7.2/css/all.css">
+[
+[]{.fas .fa-info-circle .fa-lg} **Update Underway**<br>
+A published version of this manuscript from 04 April 2018, termed Version 1.0, is available at <https://doi.org/10.1098/rsif.2017.0387>.
+A new effort is underway to update the manuscript to a Version 2.0 that is current as of the first half of 2020.
+New authors and links to new sections are available in [GitHub Issue #959](https://github.com/greenelab/deep-review/issues/959).
+]{.banner .lightred}
 
 {## Template to insert build date and source ##}
 <small><em>
@@ -25,12 +30,31 @@ on {{manubot.date}}.
 
 ## Authors
 
+### Version 2.0 Authors
+
+{% for author in manubot.authors %}
+  {% if author.v2 -%}
+    {% if author.orcid is defined -%}
+    [![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/{{author.orcid}})
+    {%- endif %}
+    {{author.name}}<sup>{{author.affiliation_numbers | join(',')}}♠{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}</sup>
+    {%- if not loop.last -%}, {%- endif -%}
+  {%- endif -%}
+{% endfor %}
+
+<sup>♠</sup> --- Author order for version 2.0 is currently arbitrary.<br>
+<sup>†</sup> --- To whom correspondence should be addressed: greenescientist@gmail.com (C.S.G.)
+
+### Version 1.0 Authors
+
 {% for author in manubot.authors %}
-{% if author.orcid is defined -%}
-[![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/{{author.orcid}})
-{%- endif %}
-{{author.name}}<sup>{{author.affiliation_numbers | join(',')}}{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}</sup>
-{%- if not loop.last -%}, {%- endif -%}
+  {% if author.v1 -%}
+    {% if author.orcid is defined -%}
+    [![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/{{author.orcid}})
+    {%- endif %}
+    {{author.name}}<sup>{{author.affiliation_numbers | join(',')}}{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}</sup>
+    {%- if not loop.last -%}, {%- endif -%}
+  {%- endif -%}
 {% endfor %}
 
 <sup>☯</sup> --- Author order was determined with a randomized algorithm<br>

content/08.methods.md

@@ -30,6 +30,37 @@ The ability to irrefutably prove manuscript existence at a past time could be im
 
 ### Author contributions
 
+#### Version 2.0
+
+We continued using the open repository on the GitHub version control platform ([`greenelab/deep-review`](https://github.com/greenelab/deep-review)) [@url:https://github.com/greenelab/deep-review], which was established to write the Version 1.0 manuscript.
+Drafted multiple sub-sections along with extensive editing, pull request reviews, or discussion:
+Drafted one or more sub-sections: .
+Revised specific sub-sections or supervised drafting one or more sub-sections: .
+Drafted sub-sections, edited the manuscript, reviewed pull requests, and coordinated co-authors: C.S.G.
+
+{% for v2, authors in manubot.authors | groupby('v2') %}
+  {% if v2 -%}
+    {{ v2 }}: {% for author in authors %}{{author.name}}{%- if not loop.last -%}, {%- endif -%}{% endfor %}
+  {%- endif -%}
+{% endfor %}
+
+<sup>♠</sup> --- Author order for version 2.0 is currently arbitrary.<br>
+<sup>†</sup> --- To whom correspondence should be addressed: greenescientist@gmail.com (C.S.G.)
+
+### Version 1.0 Authors
+
+{% for author in manubot.authors %}
+  {% if author.v1 is defined -%}
+    {% if author.orcid is defined -%}
+    [![ORCID icon](images/orcid.svg){height="11px" width="11px"}](https://orcid.org/{{author.orcid}})
+    {%- endif %}
+    {{author.name}}<sup>{{author.affiliation_numbers | join(',')}}{%- if author.symbol_str is defined -%},{{author.symbol_str}}{%- endif -%}</sup>
+    {%- if not loop.last -%}, {%- endif -%}
+  {%- endif -%}
+{% endfor %}
+
+#### Version 1.0
+
 We created an open repository on the GitHub version control platform ([`greenelab/deep-review`](https://github.com/greenelab/deep-review)) [@url:https://github.com/greenelab/deep-review].
 Here, we engaged with numerous authors from papers within and outside of the area.
 The manuscript was drafted via GitHub commits by {{authors | length}} individuals who met the ICMJE standards of authorship.
@@ -45,11 +76,11 @@ Drafted sub-sections, edited the manuscript, reviewed pull requests, and coordin
 
 ### Competing interests
 
-A.K. is on the Advisory Board of Deep Genomics Inc.
-E.F. is a full-time employee of GlaxoSmithKline.
-The remaining authors have no competing interests to declare.
-
-The authors last reviewed and approved this competing interests statement on May 26, 2017.
+|Author|Competing Interests|Last Reviewed|
+|---|---|---|
+{% for author in manubot.authors %}
+|{{author.name}}|{{author.coi.string}}|{{author.coi.lastapproved}}|
+{% endfor %}
 
 ### Acknowledgements