R, MATLAB, and Julia in HPC

This repository contains the source code for the UPPMAX/HPC2N R, MATLAB, and Julia in HPC course

Getting PDFs of the material

You can clone the repository:

git clone https://github.com/UPPMAX/R-matlab-julia-HPC.git

After doing that, you can convert the .rst files to .pdf files with this online tool: https://cloudconvert.com/rst-to-pdf

The documentation files you see on the rendered pages (https://uppmax.github.io/R-matlab-julia-HPC/) are found under R-matlab-julia-HPC/docs/<language>.

Build locally

Clone the repository and navigate to the root of it:

git clone https://github.com/UPPMAX/R-matlab-julia-HPC.git
cd R-matlab-julia-HPC

Create a Python venv and activate it:

mkdir env
python -m venv env
source env/bin/activate

Tip

Add env/ to your ~/.gitignore, environments are meant to be reproduced from specifications and not meant to be checked in to version control.

In your new venv (your console prompt should assure you it has been properly activated), update pip and install the requirements:

pip install --upgrade pip
pip install -r mkdocs-requirements.txt

You may have to deactivate and reactivate the venv at this point to make Bash find mkdocs, even if which does find mkdocs.

Build and deploy the website, from this project's root folder:

mkdocs serve

Building Sphinx version

1. Create and activate separate Python venv, with Python 3.12 or earlier (see issue237 if you have 3.13 or later):

```console
mkdir oldsphinxenv
python -m venv oldsphinxenv
source oldsphinxenv/bin/activate
```

1. Install the correct requirements for Sphinx:

   pip install --upgrade pip
   pip install -r requirements.txt

2. Build and deploy, automatically choosing an open port:

   sphinx-autobuild --port 0 docs-sphinx/ build/

Where is it indicated which files are not checked for broken URLs?

In the file .github/workflows/check_links.yaml line 34.

Where is it indicated which files are not checked for spelling?

In the file .github/workflows/check_spelling.yaml line 39.

Where is it indicated which files are not checked for Markdown style?

In the file .markdownlintignore.

Which admonitions work?

Theme	Admonitions test page
ReadTheDocs	Admonitions test page
materials	Admonitions test page

Credits

• The old and online version is built with Sphinx using a theme provided by Read the Docs
• The newer version is built with MkDocs using the ReadTheDocs theme

Files used by continuous integration scripts

Filename	Descriptions
mlc_config.json	Configuration of the link checker, use markdown-link-check --config mlc_config.json --quiet docs/**/*.md to do link checking locally
.spellcheck.yml	Configuration of the spell checker, use ./scripts/check_spelling.sh to do spell check locally
.wordlist.txt	Whitelisted words for the spell checker, use ./scripts/check_spelling.sh to do spell check locally
.markdownlint.jsonc	Configuration of the Markdown linter, use ./scripts/fix_markdown_style_errors.sh to do markdown linting locally. The name of this file is a default name.
.markdownlintignore	Files ignored by the Markdown linter, use ./scripts/fix_markdown_style_errors.sh to do markdown linting locally. The name of this file is a default name.
.lycheeignore	?URLs ignored by the link checker