Working with MyST Documents

🛠 Throughout the tutorial, whenever you’re supposed to do something you will see a 🛠

node -v
>> v20.4.0

pip install mystmd

# Visit https://nodejs.org or:
conda install -c conda-forge 'nodejs>=20,<21'

conda install mystmd -c conda-forge

node -v
>> v20.4.0

npm install -g mystmd

git clone https://github.com/executablebooks/mystmd-quickstart.git
cd mystmd-quickstart

Start MyST 🚀¶

From the previous tutorial, you should already have created a myst.yml configuration file that is required to render your project. If you have not done that tutorial, type myst and follow the directions to start the server, otherwise:

🛠 Run myst start

If this is the first time you have run myst start, the theme will be installed (takes 15-30 seconds), and then bring up a local web-server that shows you a live preview of your documents as you are writing them! Every time you save a few milliseconds later the server will update.

📖 Built README.md in 33 ms.
📖 Built 01-paper.md in 30 ms.
📖 Built 02-notebook.ipynb in 6.94 ms.
📚 Built 3 pages for myst in 76 ms.

      ✨✨✨  Starting Book Theme  ✨✨✨

⚡️ Compiled in 510ms.

🔌 Server started on port 3000!  🥳 🎉

      👉  http://localhost:3000  👈

🛠 Open your web browser to http://localhost:3000^[1]

To fully explore myst start see the first quickstart tutorial on Working with MyST Websites. In this quickstart tutorial we will focus on creating printed documents! 📑

Use MyST Markdown! 🎉¶

Next we will improve the contents of the 01-paper.md, including the frontmatter, creating a “part” for the abstract, adding citations, figures, and cross-references.

Improve the frontmatter¶

🛠 Open 01-paper.md in a text editor

The start of the file includes information about the title, subtitle, author, affiliations and license. Unfortunately, this way of including this information is not easily machine-readable^[2], and focuses more on style/typography than on metadata.

# How to MyST, without being mystified 🧙

A tutorial to evolve markdown documents and notebooks into structured data

**Authors:** Rowan Cockett <sup>1,2</sup> \
**Affiliations:** <sup>1</sup> Executable Books, <sup>2</sup> Curvenote \
**License:** CC-BY

This will produce a document that looks like:

🛠 In 01-paper.md: Change the page frontmatter into a yaml block of data:

---
title: How to MyST, without being mystified 🧙
subject: Tutorial
subtitle: Evolve your markdown documents into structured data
short_title: How to MyST
authors:
  - name: Rowan Cockett
    affiliations:
      - Executable Books
      - Curvenote
    orcid: 0000-0002-7859-8394
    email: rowan@curvenote.com
license: CC-BY-4.0
keywords: myst, markdown, open-science
---

In this case, we are also adding additional metadata like an ORCID, as well as ensuring the license is an SPDX compatible code. Once these are added, the myst theme (in this case the book-theme template) can make it look pretty, this can also be customized by other themes, including $\LaTeX$ and Microsoft Word templates!

Add an abstract part¶

We will also add metadata about the “parts” of our document, for example, the abstract. This will be important when we export to PDF and also visually changes the book-theme.

🛠 In 01-paper.md: move the abstract into the frontmatter using a multiline YAML syntax abstract: |

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---
title: How to MyST, without being mystified 🧙
...
abstract: |
  We introduce, a set of open-source, community-driven ...
---

You can make other parts, like data_availability or acknowledgments or keypoints, templates will treat these differently and may require specific parts to fully render. See document parts for additional information.

Add a citation¶

🛠 In 01-paper.md: find the text citation for Bourne et al., 2012 (shown in red below), and change it to a doi based citation, as shown in green below:

- ... follow the FORCE11 recommendations (Bourne _et al._, 2012). Specifically:
+ ... follow the FORCE11 recommendations [](doi:10.4230/DAGMAN.1.1.41). Specifically:

1. rethink the unit and form of scholarly publication;
2. develop tools and technologies to better support the scholarly lifecycle; and
3. add data, software, and workflows as first-class research objects.

This will result in correct rendering of the citation (such as Bourne et al. (2012)), and automatic insertion into the references section.

🛠 In 01-paper.md: find the text citation for Head et al. (2021), and change it to:

[](doi:10.1145/3411764.3445648)

If you have replaced both of these citations, you can now safely remove the text-only, poorly formatted references section, as that is now auto generated for you!

🛠 In 01-paper.md: Remove the ## References section with the two references (leave the links!)

This will have created a References section at the bottom of the page automatically!

Add a figure directive¶

🛠 In 01-paper.md: replace the image and paragraph with a figure directive.

Replace:

![](./images/citations.png)
**Figure 1**: Citations are rendered with a popup directly inline.

with:

:::{figure} ./images/citations.png
:label: citations
Citations are rendered with a popup directly inline.
:::

🛠 If you are up for it, in 01-paper.md replace the rest of the images with figure directives!

Add a cross-reference¶

🛠 In 01-paper.md: replace the text “Figure 1” with a local link to the figure

- ... (see Figure 1).
+ ... (see [](#citations)).

The “Figure 1” text will be automatically filled in, for example, Figure 4.

Export Documents 📜¶

Next we will start to add information to be able to export to both PDF and Word documents!

Microsoft Word Documents¶

🛠 In the 01-paper.md add export: docx to the existing frontmatter section:

---
export: docx
---

🛠 Run myst build --docx

myst build --docx

The export process will run for any known files with docx specified in the export frontmatter. An equivalent command to export only this specific file is:
myst build 01-paper.md

📬 Performing exports:
   01-paper.md -> _build/exports/paper.docx
📖 Built 01-paper.md in 247 ms.
🔍 Querying template metadata from https://api.mystmd.org/templates/docx/myst/default
🐕 Fetching template from https://github.com/myst-templates/docx_default/archive/refs/heads/main.zip
💾 Saved template to path _build/templates/docx/myst/default
📄 Exported DOCX in 166 ms, copying to _build/exports/paper.docx

In this case, the default word template was used, resulting in a document formatted like this:

Next we will see how to change the template as well as how to add additional exports when working with $\LaTeX$ and PDF!

Exporting to PDF¶

To export to PDF, MyST currently requires $\LaTeX$ to be installed. See Scientific PDFs for more information about how to install $\LaTeX$.

First, we need to decide which template to export to, for this, we will use the myst templates command, and for example list all the two-column, PDF templates available.

🛠 List all two column PDF templates with:
myst templates list --pdf --tag two-column

arXiv (Two Column)       arxiv_two_column
Description: A two column arXiv compatible template
Tags: paper, two-column, preprint, arxiv, bioarxiv, eartharxiv

Volcanica                volcanica
Description: A template for submissions to the Volcanica journal
Tags: paper, journal, two-column, geoscience, earthscience

🛠 Then, list the specific information needed for a template:
myst templates list volcanica --pdf

Volcanica                volcanica
ID: tex/myst/volcanica
Version: 1.0.0
Authors: Volcanica
Description: A template for submissions to the Volcanica journal
Tags: paper, journal, two-column, geoscience, earthscience

Parts:
abstract (required) - No description
acknowledgments - No description
author_contributions - No description
data_availability - Links to data repositories, and/or a statement...

Options:
article_type (choice) - Details about different article types...

In addition basic information on the template, the template’s specific “parts” and “options” are shown. Some of these may be marked as (required) and be essential for the building the document correctly with the template.

🛠 In 01-paper.md create an exports list with docx and pdf formats.

---
exports:
  - format: docx
  - format: pdf
    template: volcanica
    article_type: Report
---

We have added a second export target for pdf and included additional information to specify the template, as well as set the article_type option, which is information we discovered when listing the template above! We also saw this template supports a number of “parts” including a required abstract part, but as we already added an abstract part earlier in this tutorial, we are good to go.

You can now build the exports with the following command:

🛠 Run myst build 01-paper.md

📬 Performing exports:
   01-paper.md -> _build/exports/paper.docx
   01-paper.md -> _build/exports/paper.pdf
🌠 Converting 3 GIF images to PNG using imagemagick
📖 Built 01-paper.md in 257 ms.
📄 Exported DOCX in 205 ms, copying to _build/exports/paper.docx
📑 Exported TeX in 5.11 ms, copying to _build/temp/myst8BVu1k/paper.tex
🖨 Rendering PDF to _build/temp/mystvUibhD/paper.pdf
📄 Exported PDF in 9.3 s, copying to _build/exports/paper.pdf

# on Mac OS
brew install imagemagick
# on Ubuntu
apt install imagemagick

You can now see your two-column PDF in a submission ready format for the journal (check the _build/exports folder). It is very easy to change the template to a different format -- just change the template: field in the frontmatter! Notice also that the PDF has converted dynamic images to a static alternative (e.g. GIFs are now PNGs).

Exporting to $\LaTeX$¶

If you would like to see the $\LaTeX$ source, you can look in the _build/temp directory, or you can update the

🛠 In 01-paper.md: replace format: pdf with format: tex. Specify the output location as a zip file.

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---
exports:
  - format: docx
  - format: tex
    template: volcanica
    article_type: Report
    output: arxiv.zip
---

🛠 Run myst build 01-paper.md

You should see these two additional lines:

📑 Exported TeX in 4.87 ms, copying to _build/exports/paper_tex/paper.tex
🤐 Zipping tex outputs to arxiv.zip

Without specifying the output: location, this will copy the unzipped contents into the _build/exports folder along with all other exports. Creating a zip file can be helpful when directly submitted to the arXiv or a journal!

Exporting to Markdown¶

🛠 In 01-paper.md create an exports list with docx, pdf and md formats.

---
exports:
  - format: docx
  - format: pdf
    template: volcanica
    article_type: Report
  - format: md
---

You can now build the exports with the following command:

🛠 Run myst build 01-paper.md

📬 Performing exports:
   01-paper.md -> _build/exports/paper.docx
   01-paper.md -> _build/exports/paper.pdf
   01-paper.md -> _build/exports/paper.md
🌠 Converting 3 GIF images to PNG using imagemagick
📖 Built 01-paper.md in 257 ms.
📄 Exported DOCX in 205 ms, copying to _build/exports/paper.docx
📑 Exported TeX in 5.11 ms, copying to _build/temp/myst8BVu1k/paper.tex
🖨 Rendering PDF to _build/temp/mystvUibhD/paper.pdf
📄 Exported PDF in 9.3 s, copying to _build/exports/paper.pdf
📄 Exported MD in 205 ms, copying to _build/exports/paper.md

Conclusion 🥳¶

That’s it for this quickstart tutorial!!

As next steps for specifically working with documents, we recommend looking at:

To learn more about the specifics of creating MyST websites: