ELIXIR-Estonia Website

This project is the source code for the website of https://elixir.ut.ee/. Changes to the main branch will be automatically deployed (after some delay, mostly during local working hours) to the hosting server.

Getting Started

This website is generated with MkDocs, with the theme Material. So you need to have Python 3 installed on your operating system to build and generate the website.

Once Python 3 is installed, here is how you can install dependencies:

# In the root folder of the project.

# 1. Create a virtual environment for Python:
python3 -m venv venv

# 2. Activate the virtual environment:
source venv/bin/activate

# 3. Install dependencies for the environment:
pip install -r requirements.txt

Once the ./venv/ directory exists, you can always activate the Python environment again using the source venv/bin/activate command (without reinstalling dependencies).

The website content is mostly located under /content/ divided into folders by menu item name. The menu items are defined in mkdocs.yml (under nav).

Typically, for content editing, you'll want to run mkdocs in the background so it would automatically compile and update web pages when you save content.

mkdocs serve

View the content in the browser at http://localhost:8000/.

Static content is generated using command mkdocs build, and stored under /site/.

More How-To's

Q: How to define links

A: Following Markdown syntax, links are typically written as [link text](https://link.address/). If you don't want to provide custom link text then providing just the full URL (https://link.address) would also render as a link (where the address also becomes the visible text).

If you want to link another page within the website in your Markdown content, use the path of the targeted file relative to the /content/ directory (e.g. [introduction](data_management/introduction.md)). MkDocs will take care of rendering the correct link for the targeted resource.

Q: How to add trainings

A: We recommend using template training-template.md when adding a new training: this also renders JSON-LD metadata in the HTML (so that TeSS could use it). The steps are following:

1. Copy training-template.md to content/news/posts/<year>/ with a custom training-specific filename (it affects the slug of the post-path).
2. Update the YAML section with training-specific values.
3. Specify training description in the Markdown section (after the front-matter).
4. Test how the news article is rendered (mkdocs serve and open the browser).
5. View the page source to find <script type="application/ld+json"> after the <article> section.

Q: How to update the page about people

A: Metadata about people and their order is stored in content/assets/members.yaml. That file also defines the location of person's image file, which should be stored under content/assets/images/people/.

Q: How to update the page about publications

A: There is a separate Python script for generating the publications page content/publications/index.md from publications/source.yaml. More information about how to update publications is described in the publications/README.md.