Jacques Dainat (Juke34) Gathered Knowledge

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Table of Contents

• Foreword
• Project layout
• For collaborators teachers and developers
  • Modify content
  • MkDocs
    • Welcome to MkDocs
    • Installation
      • Manual
      • Conda
    • Testing and building the website

Foreword

You can find here some of the knwoledge I have gathered duting my bioinformatician life. The site itself lives https://juke34.github.io/knowledge/, where you can find all the relevant information.

Project layout

    README.md               # General readme 
    mkdocs.yml              # The configuration file for the site rendering.
    conda_env.yml           # Conda env to build and test the site locally
    docs/                   # material that will be publish with the static web site
        index.md            # The documentation homepage (Website Home page).
        pages/              # Folder dedicated to a topic 
            images/         # Folder containing images related to the topic
            xxx/            # Folder containing the .md files related to the topic topic
            ...    
    Images                  # Images used in the README

For collaborators teachers and developers

This part is for collaborators-teachers and developers.

Modify content

When you are in the repository, add and/or modify your markdown tutorials in the docs directory. The arborescence of the website menu is to setup in the mkdocs.yml file

Mkdocs

Welcome to MkDocs

For full documentation visit mkdocs.org.
For full documentation about the material mkdocs theme.

Installation

Manual

As prerequisite you need python >=3.8 and pip.

Install Mkdocs:

pip install mkdocs

For the theme:
pip install mkdocs-material

For the extensions:
pip install pymdown-extensions

For the plugins:
pip install mkdocs-minify-plugin
pip install mkdocs-macros-plugin pip install mkdocs-include-markdown-plugin

Conda

Clone the repository and move in it.
Then install all dependencies using conda and the conda_env.yml shipped with this repo:

conda env create -f conda_env.yml

Activate the environment and you are good:

conda activate education

Testing and building the website

• mkdocs serve - Start the live-reloading docs server, to test the site locally (http://127.0.0.1:8000/).

• mkdocs gh-deploy - Deploys the site on github pages.

• mkdocs build - Build the documentation site.

• mkdocs new [dir-name] - Create a new project.

• mkdocs -h - Print help message and exit.