Website for the eScience Lab at University of Manchester
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_activities
_includes
_layouts
_posts
_products
_projects
_sass
css
images
publications
.gitignore
.ruby-gemset
.ruby-version
CNAME
Gemfile
LICENSE
NOTICE
README.md
Rakefile
_config.yml
about.md
cookies.md
feed.xml
googlef6cf4c6086ba4a4c.html
index.md
people.md
posts.md
products.md
projects.md

README.md

eScienceLab.github.io

website for eScience Lab, University of Manchester

Published at http://www.esciencelab.org.uk/

License

© 2015-- University of Manchester.

Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.

Some resources are covered by other licenses or have different attributions, see NOTICE for details.

Documentation

Website is generated by Jekyll and GitHub Pages

See the Jekyll documentation

  • Pages are edited in MarkDown
  • See also various Jekyll's documentation on writing posts and writing pages
  • You can edit directly in GitHub web interface, or use git and your favourite editor
  • Edited pages are published automatically by GitHub after a few minutes.
    • For extensive changes or debugging, you might want to git clone this repository and run Jekyll locally to test your changes and see debug outputs.
    • Test locally with Docker image jekyll/jekyll:pages:
      • docker run -it --rm --name jekyll --volume=$(pwd):/srv/jekyll -p 4000:4000 jekyll/jekyll:pages jekyll serve
      • Inspect at http://0.0.0.0:4000/ - edited files are updated live
      • Stop it with Ctrl-C or docker stop jekyll.
      • You may also run Jekyll outside Docker using rvm - left as an exercise to the reader

Types of pages

The corresponding source file for a particular URL depends on what type it is.

Regular pages

Regular pages like about.md correspond directly to pages on http://www.esciencelab.org.uk/, but with / as ending instead of .md, e.g. http://www.esciencelab.org.uk/about/. These can be nested in folders, e.g. publications/index.md corresponds to http://www.esciencelab.org.uk/publications/,

Regular pages should have a header like this:

---
layout: page
title: About
permalink: /about/
---

The title is used to generate the <title> and <h1> text, and permalink can be added to modify the final relative URI. If a page should NOT be included in the menu, then also add exclude_from_nav: true.

Note that the MarkDown preview in GitHub might differ slightly from the final Jekyll's rendering on http://esciencelab.org.uk.

Pages using Jekyll templates

The layout files and some of the top-level pages use Jekyll Liquid Templates to include content from their child pages. For instance, projects.md include:

## Current funded projects

{% for project in site.projects %}
{% unless project.expired %}
* [{{ project.title }}]({{ project.url }}) - {{ project.description }}
{% endunless %}
{% endfor %}

You can recognize templates as using the {{ or {% syntax. You should be more careful when editing these, e.g. by testing with your own Jekyll locally and check the logs.

In the example above, the properties are picked up from the headers of the files in the corresponding _project folder.

Collection pages

The pages in _ folders are called collection pages, because they are listed in their parent pages. For instance the folder _products is used to generate http://www.esciencelab.org.uk/products/, where sub-pages like http://www.esciencelab.org.uk/products/researchobject/ correspond to _products/researchobject.md.

It is important to maintain the special collection page headers; each collection folder has a different layout and (somewhat) differerent properties. The easiest is to copy from a neighbouring collection page that looks complete, for instance _projects/bioexcel.md has Markdown headers like:

---
layout: project
name: bioexcel
title: BioExcel
path: bioexcel.html
collection: projects
description: Centre of Excellence for Biomolecular Research
logo: bioexcel.svg
website: http://bioexcel.eu
start_date: 2015-11-01
duration: 36 months
project_reference: http://cordis.europa.eu/project/rcn/198303
---

These properties are picked up the the corresponding layout file in _layouts, e.g. _layouts/product.html include:

        <h1 class="post-title">{{ page.title }}</h1>
        <!-- .. -->
            <img src="{{ page.logo }}" alt="{{ page.title }}" height="75" max-height="100">
        

Some of the properties might also be picked up by the collection index page at the root, e.g. products.md or even the index page.

Resources

Images should be uploaded to /images, but could also be nested in a regular folder, e.g. gamble-mim-10.1109_eScience.2012.6404489.pdf in /publications/preprints/2012 is shown in http://www.esciencelab.org.uk/publications/preprints/2012/gamble-mim-10.1109_eScience.2012.6404489.pdf.

Note that unlike an Apache httpd server, no directory listing is generated, so unless an index.md file is provided or a page specifies the folder as its permalink property, then the corresponding parent, e.g. http://www.esciencelab.org.uk/publications/preprints/2012/ will say 404 Not Found. (Tip: the folder-listing is still public in GitHub, so the URLs aren't secret)

Contributing

We appreciate any contributions to keep our website up to date. Feel free to raise a pull request or raise an issue. Every page should have an Improve this page link at the bottom, which you are free to use to suggest a change.