This manuscript (permalink) was automatically generated from malariagen/manubot-test@5faeccc on June 23, 2020.

Authors

• John Doe
  XXXX-XXXX-XXXX-XXXX · johndoe · johndoe
  Department of Something, University of Whatever · Funded by Grant XXXXXXXX

• Jane Roe
  XXXX-XXXX-XXXX-XXXX · janeroe
  Department of Something, University of Whatever; Department of Whatever, University of Something

Abstract

This manuscript is a template (aka “rootstock”) for Manubot, a tool for writing scholarly manuscripts. Use this template as a starting point for your manuscript.

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.

Basic formatting

Bold text

Semi-bold text

Centered text

Right-aligned text

Italic text

Combined italics and bold

Strikethrough

1. Ordered list item
2. Ordered list item
   1. Sub-item
   2. Sub-item
      1. Sub-sub-item
3. Ordered list item
   1. Sub-item

• List item
• List item
• List item

subscript: H₂O is a liquid

superscript: 2¹⁰ is 1024.

unicode superscripts⁰¹²³⁴⁵⁶⁷⁸⁹

unicode subscripts₀₁₂₃₄₅₆₇₈₉

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 and version control.

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

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

Long link with lots of words and stuff and junk and bleep and blah and stuff and other stuff and more stuff yeah

Link with text

Link with hover text

Link by reference

Citations

Citation by DOI.¹

Citation by PubMed Central ID.²

Citation by PubMed ID.³

Citation by Wikidata ID.⁴

Citation by ISBN.⁵

Citation by URL.⁶

Citation by alias.⁷

Multiple citations can be put inside the same set of brackets.^1,5,7 Manubot plugins provide easier, more convenient visualization of and navigation between citations.^2,3,7,8

Citation tags (i.e. aliases) can be defined in their own paragraphs using Markdown’s reference link syntax:

Referencing figures, tables, equations

Figure 1

Figure 2

Figure 3

Figure 4

Table 1

Equation 1

Equation 2

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:

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

Tables

Equations

A LaTeX equation:

\[\int_0^\infty e^{-x^2} dx=\frac{\sqrt{\pi}}{2}\](1)

An equation too long to fit within page:

\[x = a + b + c + d + e + f + g + h + i + j + k + l + m + n + o + p + q + r + s + t + u + v + w + x + y + z + 1 + 2 + 3 + 4 + 5 + 6 + 7 + 8 + 9\](2)

Special

WARNING 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

Adding arbitrary HTML attributes to an element using Pandoc’s attribute syntax:

Adding arbitrary HTML attributes to an element with the Manubot attributes plugin (more flexible than Pandoc’s method in terms of which elements you can add attributes to):

Manubot Manubot Manubot Manubot Manubot. Manubot Manubot Manubot Manubot. Manubot Manubot Manubot. Manubot Manubot. Manubot.

Available background colors for text, images, code, banners, etc:

white lightgrey grey darkgrey black lightred lightyellow lightgreen lightblue lightpurple red orange yellow green blue purple

Using the Font Awesome icon set:

Light Grey Banner
useful for general information - manubot.org

Blue Banner
useful for important information - manubot.org

Light Red Banner
useful for warnings - manubot.org

Tables (misc. test)

At 6pt by wrapping in <div> with a style:

References (misc. test)

URL citation overridden by manual-references.json.⁹

Table from CSV hard-coded into Markdown content

Using the pantable Pandoc filter.

Table from CSV file source

• Using the pantable Pandoc filter with the include option, loading from content/csv/by_country.csv.
• Alignment has been specified: LRRRRRRR.
• ‘Samples By Country’ is the specified caption.
• dialect: unix is passed to csv.reader() by way of csv-kwargs
• include-encoding defaults to UTF-8

• See that column headings are carried onto the next page in PDF.
• See column headings are squashed/wrapped in HTML, perhaps decrease font size (e.g. wrapping in <div style="font-size:7pt">...</div>)
• See floats wrap
• See Year colum is so squashed that it’s vertical!
• Pantable uses Panflute, e.g. https://github.com/ickc/pantable/blob/master/pantable/csv_to_table_markdown.py
• If we needed to apply custom formatting during the build, e.g. to round those floats, we could probably write our own Pandoc filter.

Table from CSV file source with decreased font size

• Same as above, except wrapping in <div style="font-size:7pt">...</div>

• This font-size change is not honoured in some local renderings of the HTML, e.g. Datalab, but does work in others, e.g. GitHub Pages and opening a downloaded copy of index.html in a Chrome, although it always seems to work in the PDF.
• See that the Year column is very squashed, even with decreased font size, possibly because something has to give and no preference has been given.
  • Want some level of tighter control over table formatting, at the column level.
    • https://github.com/ickc/pantable supports a width argument: a list of relative width corresponding to the width of each columns

Table from CSV file source with decreased font size and specified column widths

• Same as above, except with column widths set to 0.125 (1 / 8) each.

Pantable docs suggest this syntax, perhaps for a different context, which will generate an error:

- width
    - 0.1
    - 0.2
    - 0.3
    - 0.4

Instead syntax like this (or equivalent) appears to work:

width: [0.125, 0.125, 0.125, 0.125, 0.125, 0.125, 0.125, 0.125]

Table from CSV file source with styles and specified column widths

• Same as above, except with styles set using the Manubot attributes plugin and Pandoc “divs”

Test figures from image sources

• May need to use secno=1 on all figures, e.g. {#fig:id secno=1} to avoid mislabelling/miscounting bug? https://github.com/tomduck/pandoc-fignos/issues/76

1) Separate figures with alt text (“captions”), no resizing, refs linked by default

5, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. 6, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• The “Figure {n}:” label before the alt text “captions”, e.g. Figure 6s: ROH Scatter Plot, is added automatically.
• Btw, {@fig:figure-test-1b} appears as {???}: when in “quotes”, e.g. “{???}”, which is unexpected, possibly a bug
• Curly brackets are to separate fig ref from adjacent non-whitespace strings, e.g. @fig:figure-test-1b- versus {@fig:figure-test-1b}-

2) Separate figures with no alt text (no “captions”), no resizing, refs linked by default

7, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. 8, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• The “Figure {n}:” label before the empty alt text “captions”, e.g. Figure 8:, is added automatically.
  • Want a way to override this label’s template
• The colon after the Figure 8:, which anticipates text, looks odd/confusing when there is no text. It looks like it applies to the content that follows after that label, but it doesn’t/shouldn’t.

3) Separate subfigures using Pandoc “divs”, with no alt text, no layout, no resizing

Figure 1

a, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. b, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• Pandoc divs let you group content under one Manubot figure reference, in this case two simple images (not Manubot figures in their own right)
• Putting the Markdown for the figures on separate paragraphs (as required by Pandoc) causes a vertical layout by default, which is undesirable here
• Figure references for 1a and 1b are just references/links to 1 plus manually managed suffixes
• Can switch off the link for figure references, e.g. @fig:figure-test3{nolink=True} gives 1 rather than 1
• The figure label was added in manually, i.e. **Figure @fig:figure-test3{nolink=True}**, otherwise there would be no visible label for this figure, even though it has a reference
• Note figure-test3 has reset to “1”, rather than 8 + 1. Bug? https://github.com/tomduck/pandoc-fignos/issues/76
  • Using secno=1 here, i.e. {#fig:figure-test3 secno=1} has made no difference, but perhaps need to use secno=1 on all figures in order to workaround. (?!)

4) Breaking of pandoc-fignos when figures are not in their own Markdown paragraph

??, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. ???{nolink=True}, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• See broken refs as “??” and ???{nolink=True}.
• Reports errors:
  • pandoc-fignos: Bad reference: @fig:figure-test4a.
  • Generating csl_item for 'figure-test3b' failed due to a NotImplementedError: Manubot does not know how to generate a csl_item for 'figure-test3b'

Pandoc requires:

![Stairway Plot](images/stairway_plot.svg){#fig:figure-test4a}

![ROH Scatter Plot](images/roh_scatter.svg){#fig:figure-test4b}

Instead of the above:

![Stairway Plot](images/stairway_plot.svg){#fig:figure-test4a}
![ROH Scatter Plot](images/roh_scatter.svg){#fig:figure-test4b}

• This constraint prevents figures from being placed next to eachother by a simple inline method (as above) without breaking the managed references.

5) Separate figures with HTML table-based layout, with tags, no alt text, no resizing

a, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. b, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• If the HTML contains any preceding whitespace in the markup, e.g. indentation, you will see broken HTML markup
• HTML table-based layout could be used to place the figures next to each other while still meeting the Pandoc separate-paragraph rule, but it’s a bit of a hack
• Table cell borders removed using <td style="border: none">
• Manubot shows a figure label for each figure, even when no alt/caption text. Here the figure label/number is overidden usign specified “tags”
• Tags can be used to override the automatic managed figure number, e.g. here @fig:figure-test5a is labelled as “a” instead of an automatically incremented figure number. In other words, normally the figure label would be a number, which would be incremented automatically, except for bug/feature: https://github.com/tomduck/pandoc-fignos/issues/76, but here we have overridden that figure label.
• Again, the colon after the figure label, which anticipates text, looks odd/confusing when there is no text. It looks like it applies to the content that follows after that label, but it doesn’t/shouldn’t.

6) Breaking of separate figures with Markdown table-based layout, no alt text, no resizing

??, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. ??, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• See broken figure references as “??”, and no figure labels under the figures, compared to (5)
  • Generates errors pandoc-fignos: Bad reference: @fig:figure-test6a. and pandoc-fignos: Bad reference: @fig:figure-test6b.
• Want to remove visible table cell borders
• Markdown table-based layout cannot be used to place the figures next to each other without breaking the Pandoc separate-paragraph rule

7) Separate figures using images inline (not Manubot figures), no resizing

a, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. b, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• images can be used to simulate figures, at the cost of all the figure management features of Manubot (assuming the features worked as intended)
• references for figures would have to be managed manually. A figure reference has not been added here, and would have to be added and maintained manually (outside of Manubot’s system, by hard-coding the figure identifier/label, e.g. Figure 1, in the Markdown)

8) Separate figures using images inline (not Manubot figures), resized to 3in and 4in width, rearranged

a, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. b, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• Labels a and b in the description are manually coded (these are not Manubot-managed figures, only Markdown images)
• See that subfigure b appears before (left of) subfigure a, intentionally swapped around
• See that the b label is larger than the a label, because the whole b image has been made larger than a, intentionally
• embedding subfigure labels in the image means that image resizing and rearranging is frustrated
  • new images would need to be generated with new labels, or the SVG code modified by hand

9) Separate figures using images (not Manubot figures) with HTML table-based layout, resized to 3in and 4in width

If the labels were not embedded in the image, the labels would naturally need be added to the Markdown in some way, perhaps as figure “captions”.

Imagine that the two images below did not contain their a and b labels in their top-left corners:

Figure 42

a, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. b, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• This is similar to (1), except with the layout approach of (5)
• The a and b in the descriptions are taken from the Manubot figure tag labels, specified in Markdown.
• The label Figure 42 was added manually. Only the subfigure identifiers/labels are managed by Manubot. There is no “Manubot figure 42”, so that label would have to be managed/maintained manually.

10) Single figure with subfigures as labelled images in a HTML table-based layout

Imagine that the following two images do not contain labels a and b in their top-left corners:

Figure 1

a

b

1a, Stairway plot of changes in population size over time. Absolute values of time and Ne are shown on alternative axes as a range of values, assuming lower and upper limits for the mutation rate μ as 2.8 × 10−9 and 5.5 × 10−9, respectively, and t = 11 generations per year. ka, thousand years ago. 1b, Runs of homozygosity (ROH) in individual mosquitoes, highlighting recent inbreeding in Kenyan (grey) and colony (black) mosquitoes. G, Ghana; K, Kisumu; M, Mali; P, Pimperena.

• This is similar to (3), except with the layout approach of (5)
• The label Figure 1 was added manually, but the 1 part is automatic.
• The subfigure labels a and b outside the image were added manually.
• In the description, the 1 part (of 1a and 1b) is automatic, whereas the “a” and “b” parts are added manually, i.e. hard-coded in the Markdown.

Test plotly

• See that the plot shows in HTML rendering (and is interactive) but it does not show in the PDF rendering (as a static image).

Foo bar baz

test 123

References