STYLE TIPS - DELETE THIS PAGE BEFORE PUBLISHING¶
Tip
Check the code (.rst) source to see how these examples are written in restructured text.
Many of the examples Writing your documentation using sample data¶
Where possible, you want write documentation instructions to be general enough for users can follow along with their own data. To help do this, you can use the sample data admonition to intersperse sample data-specific instructions into your generic instructions.
To do this, start your documentation with a description and where possible, a citation of the data:
Sample data
How to use provided sample data
In this guide, we will use an RNA-Seq dataset (“Zika infected hNPCs”). This experiment compared human neuroprogenetor cells (hNPCs) infected with the Zika virus to non-infected hNPCs. You can read more about the experimental conditions and methods here. Where appropriate, a note (in this orange colored background) in the instructions will indicate which options to select to make use of this provided dataset.
Sample data citation: Yi L, Pimentel H, Pachter L (2017) Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLOS ONE 12(4): e0175744. 10.1371/journal.pone.0175744
Then, as you have instructions, intersperse the sample data .. admonition
First, enter the cutoff value for your dataset
Sample data
“Zika infected hNPCs” dataset:
Enter 30
Continue with next step…
Other admonitions¶
There are several admonitions you can use, but tip and warning are the most common for our documentation.
Tip
If you don’t see a desired species/genome contact us to have it added
Warning
When naming your samples and conditions, avoid spaces and special characters (e.g. !#$%^&/, etc.). Also be sure to be consistent with spelling.
Buttons and keyboard combinations¶
Where it adds clarity you can use this text to add buttons:
- Click Cancel to continue
- Press Control + P to print your result
- Fix the
link in custom_url.txt to use this button to launch a quicklaunch link in the DE (the embed HTML the DE generates may not render properly in RTD)
Detail expand questions¶
You can have questions by using .. admonition:: Question and .. admonition:: Answer. Just make sure you pay attention to spacing as below.
Question
- Test your reader’s knowledge with a question
Answer
Give them an answer
- Test your reader’s knowledge with a question
Answer
Give them an answer
URLs/Links¶
Have hyperlinks open in a new tab to avoid pushing the reader off the documentation page. Always use substitutions. Best practice is to define your substitutions in the cyverse_rst_defined_substitutions.txt file in this repo for easy future updating.
Bad link …
Good link …
Even better link (because it is defined in a separate file)
Images¶
Images should only be used when necessary.
Choose an image size that works for your page:
Better size:
Images should have a 1px black border:
