Markdown

Scientific Computing

Prof. Calvin

Why Markdown?

What is Markdown (.md)?

• A way of writing text and styling text that can be read with or without a markdown editor.
• A lightweight alternative to HTML.
• Probably the foremost standard for documentation in scientific computing.

Different “.md”

• Markdown is a fairly open standard, and not all Markdown is exactly the same, but tends to follow common rules.
• I will teach GitHub Markdown, a major but not the only standard.
• These slides are generated in Quarto Markdown, an extension of the standard.
• Dillinger and Obsidian are popular Markdown platforms.

What is the relation to GitHub?

• By convention, every GitHub repository should come with a README.md file.
• By default, GitHub will style this and display it on the main repository page.
• This is how you should communicate to anyone who discovers your code or is looking for your code what the code does.

Conceptualizing

• Suppose you are describing some code, like tax.py
  • You may wish to link to primary source documents on tax policy.
  • You may wish to create paragraphs, unnumbered and numbered lists.
  • You may wish to embed images, code snippets.
  • You may wish to use rich bold or italic text.

Problem Solving

• Markdown
  • Uses existing, common typographical characters
  • Corresponds to widely standardized HTML
  • Is human-readable without being rendered in HTML
• Can be:
  • Written in any text editor.
  • Authored in a dedicated Markdown editor.

Stepping Back

• git was made to solve this exact problem!
• The world leading scientific computing operating system, Linux, was being developed remotely via volunteers.
• They used millions of lines of code in complex file structures.
• They had to have a way to keep track of everything!

We will

• Introduce Markdown syntax:
  • Style text
  • Link to resources
• Use “Markdown” to:
  • Document our code with Markdown

Documentation

• Previously, we learned about comments.
  • Lines in code that do not affect what the code does, but help human users understand it.
• Often we document repositories with README files.
  • Often as README.md, a “Markdown” file.
• We introduce Markdown.

Text

A note

• These slides are written in Markdown.
• I’ll show the Markdown in a left column and how it is rendered. on the right.
• If you wish to follow along, the most obvious way is https://dillinger.io/

Text

• The most natural thing to do in a README.md is simply write text.

Unremarkable text.

Unremakrable text.

Bold

• Enclose text in double **, double __ or HTML style <b> to bold text.

We can make text **bold**.

We can make text __bold__.

We can make text <b>bold</b>.

We can make text bold.

We can make text bold.

We can make text bold.

Italic

• Enclose text in single *, single _ or HTML style <i> to italicize text.

We can make text *italic*.

We can make text _italic_.

We can make text <i>italic</i>.

We can make text italic.

We can make text italic.

We can make text italic.

Strikethrough

• Very helpful to show what not to do.

We can make text ~strikethrough~ sometimes.

We can make text ~~strikethrough~~.

We can make text <s>strikethrough</s>.

We can make text _{strikethrough} sometimes.

We can make text strikethrough.

We can make text strikethrough.

Nesting

• As a rule, formatting can be nested but not overlapped.

__Bold__, *italic*, or ***both***.

__Bold, *nested,*__ or *italic*.

__Can't be *overlapped__, however*.

Bold, italic, or both.

Bold, nested, or italic.

__Can’t be *overlapped__, however*.

Sub/superscript

• In scientific publication, we often require subscripts and superscripts.

Squaring *x* as *x*<sup>2</sup> or *x*^2^

Denoting a Helium-3 isotope as He<sub>3</sub> or He~3~.

Squaring x as x² or x²

Denoting a Helium-3 isotope as He₃ or He₃.

When .md fails

• A number of of formatting options require the heavier-weight HTML tags.

Underlining is <u>rarely</u> used.

Some editors support ==.md== or <mark>HTML</mark> highlighting.

Underlining is rarely used.

Some editors support ==.md== or HTML highlighting.

Quotes

Blockquotes

• Quotes are used frequently in Markdown, for various reasons.
• When quoting another writer, or a source, often use blockquotes:

> Veni, vidi, vici.

<blockquote>Oṃ maṇi padme hūm̐</blockquote>

Veni, vidi, vici.

Oṃ maṇi padme hūm̐

Unicode

• We note Markdown generally supports unicode characters as well as anything else does - usually exactly as well as your browser.

> ॐ मणि पद्मे हूँ

ॐ मणि पद्मे हूँ

Backticks

• The backtick character ` (near ~) has special meaning in Markdown.

Single back for `print('hi')`

Use triple backtick for:

```
for i in range(10):
    print(i*i)
```

Single back for print('hi')

Use triple backtick for:

for i in range(10):
    print(i*i)

Syntax Highlighting

• Often we want codeblocks to have highlighting as we see in a code editor.
• Specify the file extension immediately after the opening triple backtick.

```py
def ten_sqs():
    for i in range(10):
        print(i*i)
    return
```

def ten_sqs():
    for i in range(10):
        print(i*i)
    return

• In Quarto Markdown, this also changes background (this is non-standard).

Lists

Better than sentences

• As a rule, it’s a good idea to break text up.
• Note that * or - work and linebreaks don’t break the list.

- Use lists.
- Be concise.

* Use bullets.
* Save space.

• Use lists.

• Be concise.

• Use bullets.

• Save space.

Nesting

• Lists can be nested via indentiation with whitespace.

- Lists are great!
  - Easy to read.
    - Either as markdown or text!
  - Easy to type.
- Try them out! 

• Lists are great!
  • Easy to read.
    • Either as markdown or text!
  • Easy to type.
• Try them out!

Numbering

• Lists are numbered automatically.

1. One
1. Two
1. Three
1. Four
   1. Four and half
1. Five

• There is no graceful way to start a list at zero.

1. One
2. Two
3. Three
4. Four
   1. Four and half
5. Five

Task lists

• You can also make “task lists”.
• Try clicking those boxes!

- [x] Open the door
- [ ] Get on the floor
- [ ] Walk the dinosaur

• Open the door
• Get on the floor
• Walk the dinosaur

Lines

Line breaks

• There’s a few ways to perform a .md line break.

Two spaces 
break lines  
one space 
does not.

Two spaces break lines
one space does not.

Line breaks

• Invisible line breaks are very annoying and \ is often preferred.

Back slash\
breaks lines
just like  
two spaces.

Back slash
breaks lines. just like
two spaces.

Line breaks

• These work inside lists.

- Some items\
  are long.
- Some aren't.

• Some items
  are long.
• Some aren’t.

HTML

• The HTML <br/> will often works as well.

Even in the middle<br/>of lines.

Even in the middle
of lines.

Links

URL links

• As a rule, you can link anywhere on the internet.
• Place the link text in [] and the URL in ()

[Read more](https://en.wikipedia.org/wiki/Markdown)

Read more

Images

• Use ![] before a link to an image file, like a .png, .jpg, or .svg.

![](https://raw.githubusercontent.com/cd-public/scicom/refs/heads/main/qmd/src/julia.png)

Relative Links

• Within a GitHub markdown document, you can also link to images within the repository.
• This .md document is in /main/qmd/src/ so I can just use:

![](julia.png)

Footnotes

• Generally, by the time you are using footnotes you should switch to a different platform (LaTeX).
• But they exist!

Use numbered[^1] or named[^footnote] notes.

[^1]: I'm number one!
    [^footnote]: I'm a footnote!

Use numbered¹ or named² notes.

1. I’m number one!

2. I’m a footnote!

Sections

Headings

• In my markdown, headings correspond to slides or sections.
• They are # prefixed and get their own line.

# Heading

Heading

Subheadings

• In my markdown, headings correspond to slides or sections.
• They are # prefixed and get their own line.

## Subheadings

### Get

#### Progressively

##### Smaller

Subheadings

Get

Progressively

Smaller

Links

• We can link to sections using all lowercase (and replace spaces with -)

The previous heading was [Links](#links) part of the notes.

The previous heading was Links part of the notes.

Callouts

Optional Features

• Some editors support callout blocks.

> [!NOTE]
> GitHub note.

::: {.callout-note}
Quarto note.
:::

> 📝 **Note:** Blockquote/emoji hack.

[!NOTE] GitHub note (doesn’t work here).

Note

Quarto note.

📝 Note: Blockquote/emoji hack.

Tables

Markdown DataFrames

• The way pandas worked under the hood on these slides was actually outputing markdown tables.

|NumPy|**pandas**|
|-----|----------|
|array|DataFrame |
|typed|Any values|

NumPy	pandas
array	DataFrame
typed	Any values

Markdown Arrays

• You can leave out headers to get something closer to an unlabeled table or a 2D array.

|     |          |
|-----|----------|
|9275 | 10       |
|37500| 15       |

9275	10
37500	15

Align text

|Left, | center, | right! |          
|:-----|:-------:|-------:|
|Text  | x       | 13     |
|Names |         |   113  |

Left,	center,	right!
Text	x	13
Names		113

Exercise

GitHub Skills

- Complete the GitHub Skills lesson "[Communicate using Markdown](https://github.com/skills/communicate-using-markdown)"
- Add a README.md to your repository from the [Git exercise](0B_git.qmd#exercise)

• Complete the GitHub Skills lesson “Communicate using Markdown”
• Add a README.md to your repository from the Git exercise