Update content/02.delete-me.md to show formatting

Merges #169

content/02.delete-me.md

@@ -1,15 +1,259 @@
-## Manubot Rootstock Information
+This manuscript is a template (aka "rootstock") for [Manubot](https://manubot.org/ "Manubot"), a tool for writing scholarly manuscripts.
+Use this template as a starting point for your manuscript.
 
-**Note: Manubot instances should delete this file.**
+The rest of this document is a full list of formatting elements/features supported by Manubot.
+Compare the input (`.md` files in the `/content` directory) to the output you see below.
 
-The Manubot is a system for automating scholarly publishing.
-Content is written in [Pandoc Markdown](http://pandoc.org/MANUAL.html#pandocs-markdown) source files.
-See [`USAGE.md`](https://github.com/greenelab/manubot-rootstock/blob/master/USAGE.md) for more information on how to use the Manubot.
+## Basic formatting
 
-The Manubot project began with the [Deep Review](https://github.com/greenelab/deep-review), where it was used to compose a highly-collaborative review article [@doi:10.1098/rsif.2017.0387].
-Another example manuscript that was created with Manubot is:
+**Bold** __text__
 
-+ The Sci-Hub Coverage Study ([GitHub](https://github.com/greenelab/scihub-manuscript), [HTML manuscript](https://greenelab.github.io/scihub-manuscript/)) [@doi:10.7554/eLife.32822]
+[Semi-bold text]{.semibold}
 
-If you notice a problem with Manubot, it's best to submit an upstream fix to the appropriate repository:
-[`greenelab/manubot-rootstock`](https://github.com/greenelab/manubot-rootstock) for the git repository stub or [`greenelab/manubot`](https://github.com/greenelab/manubot) for the Python package.
+[Centered text]{.center}
+
+[Right-aligned text]{.right}
+
+*Italic* _text_
+
+Combined *italics and __bold__*
+
+~~Strikethrough~~
+
+1. Ordered list item
+2. Ordered list item
+    a. Sub-item
+    b. Sub-item
+        i. Sub-sub-item
+3. Ordered list item
+    a. Sub-item
+
+- List item
+- List item
+- List item
+
+superscript<sup>2</sup>
+
+subscript<sub>2n+1</sub>
+
+[unicode superscripts](https://www.google.com/search?q=superscript+generator)⁰¹²³⁴⁵⁶⁷⁸⁹
+
+[unicode subscripts](https://www.google.com/search?q=superscript+generator)₀₁₂₃₄₅₆₇₈₉
+
+A long paragraph of text.
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
+Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
+Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur.
+Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+
+
+Putting each sentence on its own line has numerous benefits with regard to [editing](https://asciidoctor.org/docs/asciidoc-recommended-practices/#one-sentence-per-line) and [version control](https://rhodesmill.org/brandon/2012/one-sentence-per-line/).
+
+Line break without starting a new paragraph by putting  
+two spaces at end of line.
+
+## Document organization
+
+Document section headings:
+
+# Heading 1
+
+## Heading 2
+
+### Heading 3
+
+#### Heading 4
+
+### A heading centered on its own printed page{.center .page_center}
+
+<!-- an arbitrary comment. visible in input, but not visible in output. -->
+
+Horizontal rule:
+
+---
+
+`Heading 1`'s are recommended to be reserved for the title of the manuscript.
+
+`Heading 2`'s are recommended for broad sections such as *Abstract*, *Methods*, *Conclusion*, etc.
+
+`Heading 3`'s and `Heading 4`'s are recommended for sub-sections.
+
+## Links
+
+Bare URL link: <https://manubot.org>
+
+[Link with text](https://manubot.org)
+
+[Link with hover text](https://manubot.org "Manubot Homepage")
+
+[Link by reference][manubot homepage]
+
+[Manubot Homepage]: https://manubot.org
+
+## Citations
+
+Citation by DOI [@doi:10.7554/eLife.32822].
+
+Citation by PubMed Central ID [@pmcid:PMC6103790].
+
+Citation by PubMed ID [@pmid:30718888].
+
+Citation by Wikidata ID [@wikidata:Q56458321].
+
+Citation by ISBN [@isbn:9780262517638].
+
+Citation by URL [@url:https://github.com/manubot/rootstock].
+
+Citation by tag [@tag:deep-review].
+
+Multiple citations can be put inside the same set of brackets [@doi:10.7554/eLife.32822; @tag:deep-review; @isbn:9780262517638].
+Manubot plugins provide easier, more convenient visualization of and navigation between citations [@url:https://greenelab.github.io/meta-review; @pmid:30718888; @pmcid:PMC6103790; @tag:deep-review].
+
+## Referencing figures, tables, equations
+
+Figure @fig:square-image
+
+Figure @fig:wide-image
+
+Figure @fig:tall-image
+
+Figure @fig:vector-image
+
+Table @tbl:bowling-scores
+
+Equation @eq:regular-equation
+
+Equation @eq:long-equation
+
+## Quotes and code
+
+> Quoted text
+
+
+> Quoted block of text
+>
+> Two roads diverged in a wood, and I—  
+> I took the one less traveled by,  
+> And that has made all the difference.
+
+
+Code `in the middle` of normal text, aka `inline code`.
+
+Code block with Python syntax highlighting:
+
+```python
+from manubot.cite.doi import expand_short_doi
+
+def test_expand_short_doi():
+    doi = expand_short_doi("10/c3bp")
+    # a string too long to fit within page:
+    assert doi == "10.25313/2524-2695-2018-3-vliyanie-enhansera-copia-i-insulyatora-gypsy-na-sintez-ernk-modifikatsii-hromatina-i-svyazyvanie-insulyatornyh-belkov-vtransfetsirovannyh-geneticheskih-konstruktsiyah"
+```
+
+Code block with no syntax highlighting:
+
+```
+Exporting HTML manuscript
+Exporting DOCX manuscript
+Exporting PDF manuscript
+```
+
+## Figures
+
+![
+**A square image at actual size and with a bottom caption.**
+Loaded from the latest version of image on GitHub.
+](https://raw.githubusercontent.com/greenelab/manubot-resources/master/test/square.png "Square image"){#fig:square-image}
+
+![
+**An image too wide to fit within page at full size.**
+Loaded from a specific (hashed) version of the image on GitHub.
+](https://raw.githubusercontent.com/manubot/resources/bfd6afcd9f47d7da34362e62a005d86e85aef25a/test/wide.png "Wide image"){#fig:wide-image}
+
+![
+**A tall image with a specified height.**
+Loaded from a specific (hashed) version of the image on GitHub.
+](https://raw.githubusercontent.com/manubot/resources/bfd6afcd9f47d7da34362e62a005d86e85aef25a/test/tall.png "Tall image"){#fig:tall-image height=3in}
+
+![
+**A vector `.svg` image loaded from GitHub.**
+The parameter `sanitize=true` is necessary to properly load SVGs hosted via GitHub URLs.
+White background specified to serve as a backdrop for transparent sections of the image.
+](https://raw.githubusercontent.com/manubot/resources/master/test/vector.svg?sanitize=true "Vector image"){#fig:vector-image height=2.5in .white}
+
+## Tables
+
+| *Bowling Scores* | Jane          | John          | Alice         | Bob           |
+|:-----------------|:-------------:|:-------------:|:-------------:|:-------------:|
+| Game 1 | 150 | 187 | 210 | 105 |
+| Game 2 |  98 | 202 | 197 | 102 |
+| Game 3 | 123 | 180 | 238 | 134 |
+
+Table: A table with a top caption and specified relative column widths.
+{#tbl:bowling-scores}
+
+|         | Digits 1-33                        | Digits 34-66                      | Digits 67-99                      | Ref.                        |
+|:--------|:-----------------------------------|:----------------------------------|:----------------------------------|:----------------------------|
+| pi | 3.14159265358979323846264338327950 | 288419716939937510582097494459230 | 781640628620899862803482534211706 | [`piday.org`](https://www.piday.org/million/) |
+| e  | 2.71828182845904523536028747135266 | 249775724709369995957496696762772 | 407663035354759457138217852516642 | [`nasa.gov`](https://apod.nasa.gov/htmltest/gifcity/e.2mil) |
+
+Table: A table too wide to fit within page.
+{#tbl:constant-digits}
+
+## Equations
+
+A LaTeX equation:
+
+$$\int_0^\infty e^{-x^2} dx=\frac{\sqrt{\pi}}{2}$$ {#eq:regular-equation}
+
+An equation too long to fit within page:
+
+$$x = a + b + c + d + e + f + g + h + i + j + k + l + m + n + o + p + q + r + s + t + u + v + w + x + y + z + 1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9$$ {#eq:long-equation}
+
+## Special
+
+<i class="fas fa-exclamation-triangle"></i> [WARNING]{.semibold} _The following features are only supported and intended for `.html` and `.pdf` exports._
+_Journals are not likely to support them, and they may not display correctly when converted to other formats such as `.docx`._
+
+[Link styled as a button](https://manubot.org "Manubot Homepage"){.button}
+
+Available background colors for text, images, code, banners, etc:  
+
+`white`{.white}
+`lightgrey`{.lightgrey}
+`grey`{.grey}
+`darkgrey`{.darkgrey}
+`black`{.black}
+`lightred`{.lightred}
+`lightyellow`{.lightyellow}
+`lightgreen`{.lightgreen}
+`lightblue`{.lightblue}
+`lightpurple`{.lightpurple}
+`red`{.red}
+`orange`{.orange}
+`yellow`{.yellow}
+`green`{.green}
+`blue`{.blue}
+`purple`{.purple}
+
+Using the [Font Awesome](https://fontawesome.com/) icon set:
+
+<!-- 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">
+
+<i class="fas fa-check"></i> <i class="fas fa-question"></i> <i class="fas fa-star"></i> <i class="fas fa-bell"></i> <i class="fas fa-times-circle"></i> <i class="fas fa-ellipsis-h"></i>
+
+[
+<i class="fas fa-scroll fa-lg"></i> **Light Grey Banner**<br>
+useful for *general information* - [manubot.org](https://manubot.org/)
+]{.banner .lightgrey}
+
+[
+<i class="fas fa-info-circle fa-lg"></i> **Blue Banner**<br>
+useful for *important information* - [manubot.org](https://manubot.org/)
+]{.banner .lightblue}
+
+[
+<i class="fas fa-ban fa-lg"></i> **Light Red Banner**<br>
+useful for *warnings* - [manubot.org](https://manubot.org/)
+]{.banner .lightred}

content/citation-tags.tsv

@@ -1,2 +1,2 @@
 tag	citation
-deep_review	doi:10.1101/142760
+deep-review	doi:10.1098/rsif.2017.0387

content/metadata.yaml

@@ -1,5 +1,5 @@
 ---
-title: "Manubot Rootstock: Manuscript Title"
+title: "Manuscript Title"
 keywords:
   - markdown
   - publishing