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[Foreword](#foreword)\n   * [Project layout](#project-layout)\n   * [For collaborators teachers and developers](#for-collaborators-teachers-and-developers)     \n     * [Modify content](#modify-content)   \n     * [MkDocs](#mkdocs)\n        * [Welcome to MkDocs](#welcome-to-mkdocs)\n        * [Installation](#installation)\n          * [Manual](#manual)\n          * [Conda](#conda)\n        * [Testing and building the website](#testing-and-building-the-website)\n   * [Acknowledgement](#acknowledgement)\n   * [License](#license)\n\n\n## Foreword\n\nThe course itself lives [https://southgreenplatform.github.io/training_reproducible_research/](https://southgreenplatform.github.io/training_reproducible_research/),\nwhere you can find all the relevant information.  \nThis work is based on the NBIS / ELIXIR *Tools for Reproducible Research* course.\n\n## Project layout\n\n```\n    README.md               # General readme \n    mkdocs.yml              # The configuration file for the site rendering.\n    conda_env.yml           # Conda env to build and test the site locally\n    docs/                   # material that will be publish with the static web site\n        index.md            # The documentation homepage (Website Home page).\n        pages/              # Folder dedicated to the course materials use by mkdocs for the website\n            images          # Images used in the course materials in general\n            xxx/            # Folder containning the course materials for one topic\n                xxx.md      # Page taking about all or a part of the topic\n                images/     # Images related to the topic\n            ...    \n        lectures/           # Folder dedicated to lectures (within docs to ease embedding within the course)\n            README.md       # readme\n            environment.yml # conda env to use for rendering the Rmarkdown lecture files\n            template.css    # CSS used by all Rmarkdown lecture files\n            Snakefile       # Automating rendering of all Rmarkdown lecture files\n            xxx             # folder related to one lecture\n                xxx.Rmd     # Lecture in Rmarkdown format\n                xxx.pdf     # PDF rendering of Rmarkdown file\n                xxx.html    # HTML rendering of Rmarkdown file\n    tutorials/              # Folder dedicated to tutorials\n        xxx                 # folder related to one tutorial\n    Images                  # Images used in the README\n```  \n\n## For collaborators teachers and developers\n\nThis part is for collaborators-teachers and developers.\n\n### Modify content\n\nWhen you are in the repository, add and/or modify your markdown tutorials in the docs directory.\nThe arborescence of the website menu is to setup in the `mkdocs.yml` file\n\n### Mkdocs\n\n#### Welcome to MkDocs\n\nFor full documentation visit [mkdocs.org](https://www.mkdocs.org).  \nFor full documentation about the [material mkdocs theme](https://squidfunk.github.io/mkdocs-material/).\n\n#### Installation\n\n##### Manual\n\nAs prerequisite you need python \u003e=3.8 and pip.  \n\nInstall Mkdocs:\n\n`pip install mkdocs`\n\nFor the theme:  \n`pip install mkdocs-material`\n\nFor the extensions:  \n`pip install pymdown-extensions`\n\nFor the plugins:  \n`pip install mkdocs-minify-plugin`  \n`pip install mkdocs-macros-plugin`\n`pip install mkdocs-embed-external-markdown`\n\n##### Conda\n\nClone the repository and move in it.  \nThen install all dependencies using conda and the `conda_env.yml` shipped with this repo:\n\n```\nconda env create -f conda_env.yml\n```\n\nActivate the environment and you are good:\n\n```\nconda activate education\n```\n\n#### Testing and building the website\n\n\n* `mkdocs serve` - Start the live-reloading docs server, to test the site locally (http://127.0.0.1:8000/).\n* `mkdocs gh-deploy` - Deploys the site on github pages.\n\n* `mkdocs build` - Build the documentation site.\n* `mkdocs new [dir-name]` - Create a new project.\n* `mkdocs -h` - Print help message and exit.\n\n\n\n##  Acknowledgement\n\n * NBIS - This work is based on the NBIS / ELIXIR course *Tools for Reproducible Research* that can be found [here](https://github.com/NBISweden/workshop-reproducible-research).\n [\u003cimg align=\"right\" src=\"images/NBIS.png\" width=\"100\" height=\"50\" /\u003e](https://nbis.se)\n * @jhayer and @HadrienG about help in use and rendering with mkdocs and other features.\n * All contributors\n\n## License\n\nThis work is licensed under a [Creative Commons Attribution 4.0 International License][cc-by].\n\n[cc-by]: http://creativecommons.org/licenses/by/4.0/\n[cc-by-shield]: https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsouthgreenplatform%2Ftraining_reproducible_research","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsouthgreenplatform%2Ftraining_reproducible_research","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsouthgreenplatform%2Ftraining_reproducible_research/lists"}