Switch affiliations to a numbered list

Merges #236
Closes #230

Switch affiliations to a numbered list and add city / country to affiliations

As per PLOS Computational Biology request:

> Please modify the Affiliations section of your manuscript so that
all affiliations listed contain a Department, Institution, City,
and Country

content/00.front-matter.md

@@ -23,6 +23,7 @@ on {{date}}.
 
 ## Authors
 
+<!-- commented out for https://github.com/greenelab/meta-review/issues/230
 {## Template for listing authors ##}
 {% for author in authors %}
 + **{{author.name}}** {% if author.correspondence is defined and author.correspondence == true -%}^[✉](#correspondence)^{%- endif -%}<br>
@@ -52,3 +53,21 @@ on {{date}}.
 ✉ — correspondence preferred via [GitHub Issues](https://github.com/greenelab/meta-review/issues).
 Otherwise, address correspondence to <[email protected]> and <[email protected]>.
 :::
+-->
+
+{## Template for listing authors with numbered affiliations according to https://github.com/greenelab/meta-review/issues/230 ##}
+{% for author in authors %}
+{{author.name}}^{{author.affiliation_numbers | join(',')}}{% if author.correspondence is defined and author.correspondence == true -%}[*](#correspondence){%- endif -%}^
+{%- if not loop.last -%}, {%- endif -%}
+{% endfor %}
+
+
+{% for affiliation in affiliations %}
+{{affiliation.affiliation_number}}. {{affiliation.affiliation}}
+{%- endfor %}
+
+
+::: {#correspondence}
+\* — correspondence preferred via [GitHub Issues](https://github.com/greenelab/meta-review/issues).
+Otherwise, address correspondence to <[email protected]> and <[email protected]>.
+:::

content/metadata.yaml

@@ -23,7 +23,7 @@ author_info:
     twitter: dhimmel
     email: [email protected]
     affiliations:
-      - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
+      - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
     funders: G-2018-11163 and GBMF4552
     correspondence: true
     roles:
@@ -49,7 +49,7 @@ author_info:
     twitter: vincerubinetti
     email: [email protected]
     affiliations:
-      - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
+      - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
     funders: G-2018-11163 and GBMF4552
     roles:
       - Conceptualization: true
@@ -74,7 +74,7 @@ author_info:
     twitter: drslochower
     email: [email protected]
     affiliations:
-      - Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
+      - Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, San Diego, United States of America
     roles:
       - Conceptualization: true
       - Data curation: false
@@ -98,7 +98,7 @@ author_info:
     twitter: dongbohu
     email: [email protected]
     affiliations:
-      - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
+      - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
     funders: G-2018-11163 and GBMF4552
     roles:
       - Conceptualization: false
@@ -123,8 +123,8 @@ author_info:
     twitter: katatonikkat
     email: [email protected]
     affiliations:
-      - Department of Bioinformatics, University of Texas Southwestern Medical Center
-      - Bioinformatics Core Facility, University of Texas Southwestern Medical Center
+      - Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
+      - Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
     funders: CPRIT RP150596
     roles:
       - Conceptualization: false
@@ -149,7 +149,7 @@ author_info:
     twitter: GreeneScientist
     email: [email protected]
     affiliations:
-      - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
+      - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
     funders: G-2018-11163 and GBMF4552
     roles:
       - Conceptualization: true
@@ -174,8 +174,8 @@ author_info:
     twitter: anthonygitter
     email: [email protected]
     affiliations:
-      - Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison
-      - Morgridge Institute for Research
+      - Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
+      - Morgridge Institute for Research, Madison, Wisconsin, United States of America
     correspondence: true
     roles:
       - Conceptualization: true