Enable automatic section numbering

build/pandoc-defaults/common.yaml

@@ -1,4 +1,6 @@
 # Pandoc --defaults shared between Manubot output formats.
+# See documentation at https://github.com/jgm/pandoc/issues/5990
+# and https://pandoc.org/MANUAL.html#default-files
 from: markdown
 input-file: output/manuscript.md
 filters:
@@ -11,3 +13,8 @@ wrap: preserve
 metadata:
   csl: build/assets/style.csl
   link-citations: true
+number-sections: true
+# a list of offsets at each heading level
+number-offset: [0,0,0,0,0,0]
+# offset Manubot's use of level-1 headings for the title only
+shift-heading-level-by: -1

build/themes/default.html

@@ -70,7 +70,6 @@
     /* biggest heading */
     h1 {
         margin: 40px 0;
-        text-align: center;
     }
 
     /* second biggest heading */
@@ -87,6 +86,7 @@
     /* manuscript title */
     header > h1 {
         margin: 0;
+        text-align: center;
     }
 
     /* manuscript title caption text (ie "automatically generated on") */

content/00.front-matter.md

@@ -32,7 +32,7 @@ If you are interested in guidelines on testing, therapies, or other issues relat
 Instead, you should collect information from your local health department, the [CDC's guidance](https://www.cdc.gov/coronavirus/2019-ncov/index.html), or your own government.
 ]{.banner .lightred}
 
-## Authors
+## Authors {.unnumbered}
 
 {## Template for listing authors ##}
 {% for author in manubot.authors %}

content/01.abstract.md

@@ -1,4 +1,4 @@
-## Abstract {.page_break_before} 
+## Abstract {.page_break_before .unnumbered}
 Since late 2019, Coronavirus disease 2019 (COVID-19) has spread around the world, resulting in the declaration of a pandemic by the World Health Organization (WHO).
 This infectious disease is caused by the newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
 Research on the virus SARS-CoV-2 and the disease it causes is emerging rapidly through global scientific efforts.
@@ -10,7 +10,7 @@ We present information about the virus in the context of what is known about rel
 A broad scientific effort to understand this pandemic and related viruses and diseases will be fundamental to efforts to predict possible interventions.
 This text is an evolving and collaborative document that seeks to incorporate the ever-expanding body of information related to SARS-CoV-2 and COVID-19.
 
-## Where to Contribute
+## Where to Contribute {.unnumbered}
 Introduce Yourself (GitHub Issue) [https://github.com/greenelab/covid19-review/issues/17](https://github.com/greenelab/covid19-review/issues/17)
 
 Community Chat (Gitter Room) [https://gitter.im/covid19-review/community](https://gitter.im/covid19-review/community)