Template CyVerse Manual Repo

You should import this repo to build CyVerse Platform/Service Guides

See what this template looks like rendered on ReadTheDocs

How CyVerse Learning Center documentation is built

Each CyVerse Tutorial, Guide, or Quickstart has its own ReadtheDocs page which in turn is built from its own repo (See the template repos at https://github.com/CyVerse-learning-materials). Starting from a ResStructured text file (index.rst) The documentation is built using Sphinx, and hosted on a repo configured with GitHub Webhooks/Services. Finally, the site is added to ReadtheDocs. Directions for completing this workflow are below (See Building a Tutorial from Scratch).

Documentation types

• Tutorials: Tutorials teach. Users should be able to follow an example dataset through the steps of a tutorial and gain understanding about what is happening along those steps. These are in-depth guides that usually address a scientific question by covering the major steps of a scientific workflow. A tutorial is ‘successful’ when a user is able to follow the tutorial a second time with their own data and obtain reasonable results.
• Platform Guide: A Platform Guide is a slightly modified form of tutorial that covers an entire platform or service.
• Quick Starts: These materials are short tutorials that cover the minimal amount of information needed to complete an operational task (e.g. uploading data, reformatting a file, etc. ); there is no significant explanation of the science or interpretation of results. QSs highlight available resources, answer common questions (derived from user forum), and refer users to the most appropriate materials.
• Manuals: A Manual is a more comprehensive documentation piece on a CyVerse platform or software product.

Examples:

• Uploading a file: Quick Start
• Cleaning FastQ reads: Quick Start
• Uploading files to SRA: Could be both
• Assembling a transcriptome: Tutorial
• An intro to the Discovery Environment: Guide

What this repo contains

Item	Description	Notes
index.rst	Edit this template to create your documentation	documents written in markdown will need to be covered to restructured text
step1.rst	If documentation has more than one page, use this for the second through second-to-last page; copy as needed	copy as needed for additional pages 1..(n-1)
step2.rst	If documentation has more than one page, this should always be the last page
/img (folder)	Place images for your tutorials here	CyVerse logos and other useful images are already here
example_directives_delete.rst	Example page with code for common restructured text objects
cyverse_rst_defined_substitutions.txt	restructured text substitutions for common URLs and images
conf.py	Place to add tutorial and author name;versioning
README.md	These instructions	Delete these before publishing your documentation
/slides (folder)	Place slides associated with your tutorial here	version controlled files preferred, PPT acceptable
/misc (folder)	miscellaneous needed for building documentation
License.md	License	this license file applies to all materials created by CyVerse for this documentation
Contributors_maintainers.md	Contact information and recognition

Simple contribution instructions

Reporting an error or issue via GitHub

• Click the 'issues' tab at the top of this GitHub page to let us know about a simple mistake such as a typo or missing file.

OR

• Send an email to [email protected]

More complex contributions

Fixing and/or improving documentation via GitHub

1. Fork this repo to your GitHub account
2. Make edits directly to the index.rst file. Edits may be made to the fork the web interface to your GitHub account or clone the repo to work on your local computer. For very significant changes (we suggest making a new branch).
3. Commit change; if working from a local copy, push those changes to your fork in Github.
4. Submit a pull request back to the master repository; you may need to act on feedback before your request is merged.

Building Documentation from Scratch

If you want to go beyond just creating a markdown file, you will need to install some software.

You will need the following software

1. Python (2.7.9 or later) - This is required for the Sphinx package that will build our documentation:

   • https://www.python.org/downloads/

2. If needed, install pip:

   • https://packaging.python.org/installing/#install-pip-setuptools-and-wheel

3. Sphinx - This will build our tutorials into HTML and other formats (this uses the Python package installer 'pip' so Python must be installed first); we will also install the theme we need for our documentation

    $ pip install sphinx sphinx-autobuild sphinx_rtd_theme
   

4. RestView - Optional, but makes it easy to preview ReStructured text files http://rst.ninjs.org/ or install:

    $ pip install restview
   

5. git - We use git to version control our documentation and manage with GitHub

   • https://git-scm.com/book/en/v2/Getting-Started-Installing-Git

You will need the following accounts

1. GitHub account - makes it possible to collaborate on the documentation:
   • https://github.com/

Procedure

1. Import (not clone) the CyVerse base tutorial repo following GitHub's directions here: https://help.github.com/articles/importing-a-repository-with-github-importer/

   • The CyVerse manual template repo URL is https://github.com/CyVerse-learning-materials/cyverse_manual_template.git
   • Name your repo for the name of your quickstart or tutorial, e.g. 'name_tutorial'

2. Edit the index.rst. Save images or other files in the appropriate directories. See our recommended style guide for writing documentation below.

3. Since tutorials will likely span multiple pages, you can copy internal pages page as many times as needed. Update the table of contents at the top of the 'index.rst' accordingly. We will have only one tutorial or quick start per repo.

4. Save your work:

   • individual pages (e.g. 'index.rst, step2.rst')
   • images (as '.png' files in the the 'img' folder)
   • changes or additions to 'cyverse_rst_defined_substitutions.txt'

5. Edit the 'conf.py' file to set the project and author information

6. Build the tutorial:

    $ make html
   

7. Your HTML site will be in the _build directory that has been created (you can preview this in your web browser at this time).

8. Commit your changes and push the tutorial back to GitHub.

9. Notify [email protected] that your tutorial is ready for inclusion in the main CyVerse documentation repo. We will review and verify the contribution, and add you as a maintainer repo in the CyVerse collection. You should make future edits following the instructions above for 'Fixing and/or improving documentation via GitHub.' Alternatively, you can host your tutorial independently on ReadTheDocs following their instructions for importing documentation. We will also follow up about ensuring test data associated with the documentation are available and open.

Documentation Style Guide

General Principles

• Write instructions in short numbered steps
• Where possible limit step to one action; small final actions such as 'press submit' should be separated by a semicolon
• Limit the use of screenshots; where they are needed, use ReStructured text directives for substitution of images
• Use the 'raw ::html' directive to enter hyperlinks so that they will open in a new tab. See each repo for an example of the code
• Example data associated with documentation should be anonymously available on CyVerse Data Commons ([email protected] can help you with this)
• Discovery Environment applications should be directly linked to documentation (clicking the 'info' button on any application will give you the 'App URL')
• Atmosphere images should be directly linked to documentation (e.g. "atmo.cyverse.org/application/images/####"

Specific examples

Instruction	Example
Steps generally begin with a verb or preposition	Click on the button Under the "Result" menu
Locations of files are given in absolute paths	/dir1/dir2/file.extension
Top-level menus in Discovery Environment Apps in double quotes	Under "Input" select...
Subheadings/steps in Discovery Environment Apps in single quotes	For 'sensitivity' enter...
Buttons and keywords in bold	Click on Apps Select Arabidopsis Set 'sensitivity' to Medium