[We are currently building this documentation, and some pages are still work in progress]
This repo contains the sources of the SIRIUS online documentation at https://v6.docs.sirius-ms.io/. We try to keep this documentation as up-to-date as possible. Contributions from the community are very welcome. The content of this documentation is written Markdown, so no programming skills needed to create content.
If your are looking for the sources of the SIRIUS Software see boecker-lab/sirius. To download the SIRIUS software see https://bio.informatik.uni-jena.de/software/sirius/. For bug reports and feature requests regarding the SIRIUS software please use boecker-lab/sirius.
Help us improving the SIRIUS Documentation!
- For bug reports and feature requests regarding this documentation, please open an "Issue" on this GitHub repository.
- To contribute to the SIRIUS documentation, simply edit a page (located in the "_pages" directory) and click promote changes to perform an ad hoc pull request.
- For more advanced editing, fork the sirius-ms/sirius-docs.github.io repository, and make a Pull Request with your edits from your fork to the primary repository. For further information on how to build and run this documentation locally see Setup for Local Development
New pages can be created by creating a new Markdown file (.md
) under docs/_pages/
.
The link where the new site will appear and its title can specified by adding the following header to the new markdown file:
---
permalink: /changelog/
title: "Changelog"
---
Me entries are defined in thedocs/_data/navigation.yml
. Let's say we want to create an entry for the /io
page with two children referencing the headlines # Input
and # Output
:
- title: "Input, Output and Formats"
url: /io
children:
- title: "Input"
url: /io/#input
- title: "Output"
url: /io/#output
It is highly recommended to use links relative to the sites root for referencing site internal resources.
This can easily be achieved using the Liquid templating system {{ "/io/" | relative_url }}
.
Let's say we want to link "go to IO" to the page /io
of our site:
[go to IO]({{ "/io" | relative_url }})
Anchors are automatically created for each headline. The tag used for referencing the anchor is created from the headlines text with the following rules.
- It downcases the string
- remove anything that is not a letter, number, space or hyphen (see the source for how Unicode is handled)
- changes any space to a hyphen.
- If that is not unique, add "-1", "-2", "-3",... to make it unique
Example: ### My great Heading!
will get the tag #my-great-heading
.
Custom tags can be defined with: ### My great Heading! {#custom-anchor-tag}
Let's say we want to link "go to Input" to the heading ## Input
of the page /io
:
[go to Input]({{ "/io/#input" | relative_url }})
The image directory is <SIRIUS_DOC>/docs/assets/images/
. If there is no god reason to do it differently
we save all images at this location.
In principle standard markdown syntax can be used to show images. Path resolution can be done
with the Liquid templating system, e.g. {{ "/assets/images/project-space.svg" | relative_url }}
![Schema of the SIRIUS project-space]({{ "/assets/images/project-space.svg" | relative_url }})
<img src="{{ "/assets/images/project-space.svg" | relative_url }}" alt="Schema of the SIRIUS project-space1" height="24" width="48">
This is the preferred method to include images but also a bit lengthy.
{% capture fig_img %}
![Foo]({{ "/assets/images/project-space.svg" | relative_url }})
{% endcapture %}
<figure>
{{ fig_img | markdownify | remove: "<p>" | remove: "</p>" }}
<figcaption>Schema of the SIRIUS project-space.</figcaption>
</figure>
You can insert mathematical fomulas using latex math syntax within the Markdown files. The rendering is done by MathJax.
Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor
invidunt ut labore et dolore magna aliquyam erat $(200 \cdot \frac{ppm_{max}}{10^6})$.
Note the empty line before and after the Maths block!
Lorem ipsum dolor sit amet, consetetur sadipscing elitr,
sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat.
$$(200 \cdot \frac{ppm_{max}}{10^6})$$
At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren,
no sea takimata sanctus est Lorem ipsum dolor sit amet.
This page is based on Jekyll and uses the Minimal Mistakes.
The Markdown is parsed by Kramdown.
We assume the repository has been cloned into <SIRIUS_DOC>
.
- Install Ruby, RubyGems and Jekyll, see https://jekyllrb.com/docs/installation/.
- Navigate into the Jekyll project
<SIRIUS_DOC>/docs
. - Install required gems
bundle install
- (Optional) Update required gems. Might be necessary if incompatible versions of gems used by this project are already on you system.
bundle update
- Serve locally
bundle exec jekyll serve
Per default the local server is running at http://127.0.0.1:4000/docs.sirius.github.io/.
The output should look like this:
Configuration file: ~/docs.sirius.github.io/docs/_config.yml
Source: ~/docs.sirius.github.io/docs
Destination: ~/docs.sirius.github.io/docs/_site
Incremental build: disabled. Enable with --incremental
Generating...
Remote Theme: Using theme mmistakes/minimal-mistakes
Jekyll Feed: Generating feed for posts
GitHub Metadata: No GitHub API authentication could be found. Some fields may be missing or have incorrect data.
done in 11.675 seconds.
~/gems/gems/pathutil-0.16.2/lib/pathutil.rb:502: warning: Using the last argument as keyword parameters is deprecated
Auto-regeneration: enabled for '/home/fleisch/workspace/docs.sirius.github.io/docs'
Server address: http://127.0.0.1:4000/docs.sirius.github.io/
Server running... press ctrl-c to stop.
- Deploy to github pages by pushing your changes into the
master
branch of this repository. It may take a few minutes until the page is build by GitHub.