From 7ac4db618cbed4380b5904d301016f8a9678011a Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Tue, 14 Apr 2020 16:45:44 -0500 Subject: [PATCH 1/7] Enable automatic section numbering --- build/pandoc-defaults/common.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/build/pandoc-defaults/common.yaml b/build/pandoc-defaults/common.yaml index 12c0c3438..9387f4bdc 100644 --- a/build/pandoc-defaults/common.yaml +++ b/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 +13,4 @@ wrap: preserve metadata: csl: build/assets/style.csl link-citations: true +number-sections: true From eb555bdba6d6941cd317bf17c4a4b98a35761b59 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Tue, 14 Apr 2020 17:02:46 -0500 Subject: [PATCH 2/7] Offset top level section numbers --- build/pandoc-defaults/common.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/build/pandoc-defaults/common.yaml b/build/pandoc-defaults/common.yaml index 9387f4bdc..74b0fd1fb 100644 --- a/build/pandoc-defaults/common.yaml +++ b/build/pandoc-defaults/common.yaml @@ -14,3 +14,5 @@ metadata: csl: build/assets/style.csl link-citations: true number-sections: true +# a list of offsets at each heading level +number-offset: [1,0,0,0,0,0] From 02b1c8658c8660cad2471ac27746fdfaa3338aeb Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Tue, 14 Apr 2020 17:07:41 -0500 Subject: [PATCH 3/7] Shift header levels --- build/pandoc-defaults/common.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/build/pandoc-defaults/common.yaml b/build/pandoc-defaults/common.yaml index 74b0fd1fb..84f0bcf4a 100644 --- a/build/pandoc-defaults/common.yaml +++ b/build/pandoc-defaults/common.yaml @@ -16,3 +16,5 @@ metadata: number-sections: true # a list of offsets at each heading level number-offset: [1,0,0,0,0,0] +# offset Manubot's use of level-1 headings for the title only +shift-heading-level-by: -1 From 684a9feeaa276e41e094f6c639ee081dd1a3032d Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Tue, 14 Apr 2020 17:27:28 -0500 Subject: [PATCH 4/7] Continue tweaking section numbers --- build/pandoc-defaults/common.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/build/pandoc-defaults/common.yaml b/build/pandoc-defaults/common.yaml index 84f0bcf4a..5b0e75d5c 100644 --- a/build/pandoc-defaults/common.yaml +++ b/build/pandoc-defaults/common.yaml @@ -15,6 +15,4 @@ metadata: link-citations: true number-sections: true # a list of offsets at each heading level -number-offset: [1,0,0,0,0,0] -# offset Manubot's use of level-1 headings for the title only -shift-heading-level-by: -1 +number-offset: 1,0,0,0,0,0 From 577f7b60d949cfa5c2651cecb1987d9f4fda8393 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Tue, 14 Apr 2020 17:39:15 -0500 Subject: [PATCH 5/7] Test unnumbered sections --- build/pandoc-defaults/common.yaml | 2 +- content/00.front-matter.md | 2 +- content/01.abstract.md | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/build/pandoc-defaults/common.yaml b/build/pandoc-defaults/common.yaml index 5b0e75d5c..74b0fd1fb 100644 --- a/build/pandoc-defaults/common.yaml +++ b/build/pandoc-defaults/common.yaml @@ -15,4 +15,4 @@ metadata: link-citations: true number-sections: true # a list of offsets at each heading level -number-offset: 1,0,0,0,0,0 +number-offset: [1,0,0,0,0,0] diff --git a/content/00.front-matter.md b/content/00.front-matter.md index 7369f43c0..cab906e98 100644 --- a/content/00.front-matter.md +++ b/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 %} diff --git a/content/01.abstract.md b/content/01.abstract.md index 0e4eb906e..180db95c0 100644 --- a/content/01.abstract.md +++ b/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. @@ -8,7 +8,7 @@ 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 foundational 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) From 5925cdb2303ea7ee0cf584ce3a8182ee98fc929d Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Thu, 16 Apr 2020 11:29:22 -0500 Subject: [PATCH 6/7] Explore shifted header levels again --- build/pandoc-defaults/common.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/build/pandoc-defaults/common.yaml b/build/pandoc-defaults/common.yaml index 74b0fd1fb..0f0a505e7 100644 --- a/build/pandoc-defaults/common.yaml +++ b/build/pandoc-defaults/common.yaml @@ -15,4 +15,6 @@ metadata: link-citations: true number-sections: true # a list of offsets at each heading level -number-offset: [1,0,0,0,0,0] +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 From 1d44ab68f0f3f88cbc9fb4de97f348c0a611ea78 Mon Sep 17 00:00:00 2001 From: Anthony Gitter Date: Thu, 16 Apr 2020 12:21:39 -0500 Subject: [PATCH 7/7] Only center title h1 header --- build/themes/default.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build/themes/default.html b/build/themes/default.html index 26675bdfd..2bac10bac 100644 --- a/build/themes/default.html +++ b/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") */