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update the tools episode
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- Version controlled alongside code
- Can be used to auto-generate documentation for functions/classes
- Disadvantage
- Probably not enough for users
- Probably not enough for users of the code

We will have a closer look at this in the {ref}`in-code-documentation` episode.

---

## README files

- Advantage
- Advantages
- Versioned (goes with the code development)
- It is often good enough to have a `README.md` or `README.rst` along with your code/script
- If you use README files, use either
Expand All @@ -43,8 +43,6 @@ We will have a closer look at this in the {ref}`writing-readme-files` episode.

- Two of the most popular lightweight markup languages.
- reStructuredText (RST) has more features than Markdown but the choice is a matter of taste.
- Markdown convenient for smaller documents,
but for larger and more complicated documents RST may be a better option.
- There are (unfortunately) [many flavors of Markdown](https://github.com/jgm/CommonMark/wiki/Markdown-Flavors).

```markdown
Expand Down Expand Up @@ -74,15 +72,9 @@ tables, links, ... tables, links, ...

- We will use [MyST](https://myst-parser.readthedocs.io/en/latest/)
flavored Markdown in the {ref}`sphinx` episode and the
{ref}`gh-pages` example

Experiment with Markdown:
- [Learn Markdown in 60 seconds](http://commonmark.org/help/)
- [https://dillinger.io](http://dillinger.io)
- [https://stackedit.io](https://stackedit.io)

To convert between MD and RST (and many other formats):
- [Pandoc](https://pandoc.org/)
{ref}`gh-pages` example.
- Nice resource to learn Markdown: [Learn Markdown in 60 seconds](http://commonmark.org/help/)
- [Pandoc](https://pandoc.org/) can convert between MD and RST (and many other formats).

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Expand All @@ -92,11 +84,11 @@ There are many tools that can turn RST or Markdown into beautiful HTML pages:

- [Sphinx](http://sphinx-doc.org) **← we will exercise this, this is how this lesson material is built**
- Generate HTML/PDF/LaTeX from RST and Markdown.
- Basically all Python projects use Sphinx but **Sphinx is not limited to Python**
- Basically all Python projects use Sphinx but **Sphinx is not limited to Python**.
- [Read the docs](http://readthedocs.org)
hosts public Sphinx documentation for free!
- Also hostable anywhere else, like Github pages.
- API documentation possible
- API documentation possible.

- [Jekyll](https://jekyllrb.com)
- Generates HTML from Markdown.
Expand All @@ -110,8 +102,7 @@ There are many tools that can turn RST or Markdown into beautiful HTML pages:
- [Hugo](https://gohugo.io)
- [Hexo](https://hexo.io)
- [Zola](https://www.getzola.org/) **<- this is what we use for our project website and workshop websites**

There are many more ...
- There are many more ...

GitHub, GitLab, and Bitbucket make it possible to serve HTML pages:
- [GitHub Pages](https://pages.github.com)
Expand Down Expand Up @@ -140,7 +131,7 @@ GitHub, GitLab, and Bitbucket make it possible to serve HTML pages:
- Advantage
- Popular and familiar in the physics and mathematics community
- Disadvantages
- PDF format is not ideal for copy-paste ability of examples
- PDF format is not ideal for copy-pasting of examples
- Possible, but not trivial to automate rebuilding documentation after every Git push

---
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