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3. Writing Markdown

In IPyPublish, all Markdown content is converted via Pandoc. Pandoc alllows for filters to be applied to the intermediary representation of the content, which IPyPublish supplies through a group of panflute filters, wrapped in a single ‘master’ filter; ipubpandoc. This filter extends the common markdown syntax to:

  • Correctly translate pieces of documentation written in other formats (such as using LaTeX commands like \cite or RST roles like :cite:)

  • Handle labelling and referencing of figures, tables and equations, and add additional formatting options.

ipubpandoc is detached from the rest of the notebook conversion process, and so can be used as a standalone process on any markdown content:

$ pandoc -f markdown -t html --filter ipubpandoc path/to/file.md

See also

The PDF representation of this notebook

Pandoc Markdown Conversion, for the notebook document level metadata options.

3.1. Converting Notebooks to RMarkdown

RMarkdown is a plain text representation of the workbook. Thanks to jupytext, we can easily convert an existing notebooks to RMarkdown (and back):

$ jupytext --to rmarkdown notebook.ipynb
$ jupytext --to notebook notebook.Rmd            # overwrite notebook.ipynb (remove outputs)
$ jupytext --to notebook --update notebook.Rmd   # update notebook.ipynb (preserve outputs)

Alternatively, simply create a notebook.Rmd, and add this to the top of the file:

---
jupyter:
  ipub:
    pandoc:
      convert_raw: true
      hide_raw: false
      at_notation: true
      use_numref: true
  jupytext:
    metadata_filter:
      notebook: ipub
    text_representation:
      extension: .Rmd
      format_name: rmarkdown
      format_version: '1.0'
      jupytext_version: 0.8.6
  kernelspec:
    display_name: Python 3
    language: python
    name: python3
---

Important

To preserve ipypublish notebook metadata, you must add: {"jupytext": {"metadata_filter": {"notebook": "ipub"}}} to your notebooks metadata before conversion.

Note

If a file with a .Rmd extension is supplied to nbpublish, it will automatically call jupytext and convert it. So it is possible to only ever write in the RMarkdown format!

3.2. Working with RMarkdown files

The recommended way to edit RMarkdown files is in Visual Studio Code, with the Markdown Preview Enhanced extension. Add this to your VS Code Settings:

{
    "files.associations": {
        "*.Rmd": "markdown"
    },
    "markdown-preview-enhanced.usePandocParser": true,
    "markdown-preview-enhanced.pandocArguments": "--filter=ipubpandoc",
    "markdown-preview-enhanced.enableScriptExecution": true
}

If you are using a Conda environment, you may also need to use:

{
    "markdown-preview-enhanced.pandocPath": "/anaconda/envs/myenv/bin/pandoc",
    "markdown-preview-enhanced.pandocArguments": "--filter=/anaconda/myenv/lsr/bin/ipubpandoc"
}

You will now be able to open a dynamic preview of your notebook, with executable code cells:

MPE Screenshot

Fig. 3.2.1 MPE Screenshot

[1]:
print(1)
1

See also

VS Code Extensions: Markdown Extended and markdownlint

3.3. Inter-Format Translation

ipubpandoc attempts to detect any segments of documentation written in LaTeX or Sphinx reStructuredText (and HTML citations), and convert them into a relevant panflute element.

Because of this we can write something like this:

- citations in @ notation [@zelenyak_molecular_2016; @kirkeminde_thermodynamic_2012]
- citations in rst notation :cite:`zelenyak_molecular_2016,kirkeminde_thermodynamic_2012`
- citations in latex notation \cite{zelenyak_molecular_2016,kirkeminde_thermodynamic_2012}
- citation in html notation <cite data-cite="kirkeminde_thermodynamic_2012">text</cite>

$$a = b + c$$ {#eqnlabel}

- a reference in @ notation =@eqnlabel {.capital}
- a reference in rst notation :eq:`eqnlabel`
- a reference in latex notation \eqref{eqnlabel}

.. note::

    a reference in latex notation within an RST directive \eqref{eqnlabel}

and it will be correctly resolved in the output document:

\begin{equation}a = b + c\end{equation}

Note

a reference in latex notation within an RST directive Eq. 3.3.1

Inter-format translation is turned on by default, but if you wish to turn it off, or hide it, simply add to the document metadata:

jupyter:
  ipub:
    pandoc:
      convert_raw: true
      hide_raw: false

3.4. Labelling, Formatting and Referencing Figures, Tables and Equations

ipubpandoc allows for figures, tables, equations and references to be supplied with an ‘attribute container’. This is a braced section to the side of the figures, equations, reference or table caption, that parses on additional information to the formatter, e.g. {#id .class-name attribute1=10}.

Attribute containers are turned on by default, but if you wish to turn them off, simply add to the document metadata:

jupyter:
  ipub:
    pandoc:
      at_notation: false

Tip

Zero or more Space is generally allowed between the element and the attribute container.

3.4.1. Figures

Figures can have an identifier and a width or height. Additionally, placement will be used by LaTeX output.

![Image caption](_static/example.jpg){#fig:example width=50% placement='H'}

@fig:example
Image caption

Fig. 3.4.1 Image caption

3.4.2. Tables

Tables can have an identifier and relative widths (per column). Additionally, align will be used by LaTeX and HTML to set the alignment of the columns (l=left, r=right, c=center)

Table 3.4.1 Table caption

Column 1

Column 2

1

2

3.4.3. Equations

Equations can have an identifier and an env denoting the amsmath environment.

$$2x &=  8 \\ 3x + 9y &= -12$$ {#eqn:example2 env=align}
\begin{align}2x &= 8 \\ 3x + 9y &= -12\end{align}

Note

Labelled math must be ‘display math’, rather than inline, i.e. wrapped in double dollars.

3.4.4. References

Pandoc references are denoted by @, with an optional prefix, and multiple references can be wrapped in square brackets:

Citation [@zelenyak_molecular_2016; @kirkeminde_thermodynamic_2012]

Glossary Terms: %@gtkey2, &@akey2, &@symbol2

Citation [ZKT+16][KR12]

Glossary Terms: Name, MA, \(\pi\)

Note

Citations in sphinx are provided by the excellent sphinxcontrib-bibtex extension, and glossary referencing is provided by the equally good ipypublish.sphinx.gls

References can have attributes; latex (defining the LaTeX tag to use), rst (defining the RST role to use) and class .capital (defining if HTML naming is capitalized)

@fig:example {.capital latex=cref rst=numref}, [@eqnlabel;@eqn:example2] {latex=eqref rst=eq}

Fig. 3.4.1, Eq. 3.3.1 and Eq. 3.4.1

A number of prefixes are available, as shorthand’s to define attributes:

Table 3.4.2 Prefixes for reference attributes

prefix

attribute

“”

{latex=cite rst=cite}

“+”

{latex=cref rst=numref}

“!”

{latex=ref rst=ref}

“=”

{latex=eqref rst=eq}

“?”

{.capital latex=Cref rst=numref}

“&”

{latex=gls rst=gls}

“%”

{.capital latex=Gls rst=glsc}

?@fig:example, =[@eqnlabel;@eqn:example2]

Fig. 3.4.1, Eq. 3.3.1 and Eq. 3.4.1

Tip

Pandoc interprets (@label) as a numbered example, so instead use (@label{})

3.5. A Note on Implementation

To assign attributes to items, we use a preparation filter, to extract prefixes and attributes, and wrap the items in a Span containing them. For example:

$$a=1$$ {#a env=align}

will be transformed to:

<p>
<span id="a" class="labelled-Math" data-env="align">
<br />
<span class="math display">
<em>a</em> = 1
</span>
<br />
</span>
</p>

and

"+@label{ .class a=1} xyz *@label2* @label3{ .b}"

will be transformed to:

<p>
<span class="attribute-Cite class"
data-latex="cref" data-rst="numref" data-a="1">
<span class="citation" data-cites="label">
@label
</span></span>
xyz
<em><span class="citation" data-cites="label2">
@label2
</span></em>
<span class="attribute-Cite b">
<span class="citation" data-cites="label3">
@label3
</span></span>
</p>

Formatter filters, then look for these parent spans, to provide identifiers, classes and attributes.

Glossary

name

full description with latex

\(\pi\)

full description

MA

My Abbreviation

Bibliography

KR12(1,2,3,4,5)

Alec Kirkeminde and Shenqiang Ren. Thermodynamic control of iron pyrite nanocrystal synthesis with high photoactivity and stability. Journal of Materials Chemistry A, 1(1):49–54, 2012. doi:10.1039/C2TA00498D.

ZKT+16(1,2,3,4)

T. Yu Zelenyak, Kh T. Kholmurodov, A. R. Tameev, A. V. Vannikov, and P. P. Gladyshev. Molecular dynamics study of perovskite structures with modified interatomic interaction potentials. High Energy Chemistry, 50(5):400–405, 2016. doi:10.1134/S0018143916050209.