Template CyVerse Tutorial Repo

README Version 2.0, May 2020

You should import this repo to build CyVerse Tutorials

See what this template looks like rendered on ReadTheDocs

How CyVerse Learning Center documentation is built

Each piece of CyVerse Learning Center has its own ReadtheDocs page which in turn is built from its own GitHub 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 the CyVerse ReadtheDocs account. Directions for completing this workflow are below (see Building a Tutorial from Scratch).

Documentation types

• Manuals - A Manual is a more comprehensive documentation piece on a CyVerse platform or software product.
  • Written by: CyVerse Staff, with community contributions welcome
• Platform Guide - A Platform Guide is a slightly modified form of tutorial that covers an entire platform or service.
  • Written by: CyVerse Staff, with community contributions welcome
• 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. Quick Starts highlight available resources, answer common questions, and refer users to the most appropriate materials.
  • Written by: CyVerse Staff or community members
• 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.
  • Written by: CyVerse Staff or community members

Examples of when to use what type of template:

• Uploading a file: Quick Start
• Cleaning FastQ reads: Quick Start
• Basic introduction to an app: Quick Start
• Assembling a transcriptome using multiple apps and explaining the science: Tutorial
• An intro to the Discovery Environment: Platform Guide
• Comprehensive listing of all the basic functionalities of Discovery Environment: Manual

What this repo contains

Item	Description	Notes
index.rst	This is the homepage of your documentation. It list the title and goal of the documentation, lists a maintainer, and usually indicates what prerequisite platforms, files, and services are needed to complete the tutorial
step1.rst	If documentation has more than one page, use this for the second and subsequent pages	Copy as needed for additional pages
/img	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	Delete this page before publishing your materials
cyverse_rst_defined_substitutions.txt	Restructured text substitutions for common URLs and images
custom_urls.txt	Place URLs particular to your repository here in a single page, suing restructured text substitutions to create hyperlinks	Be sure any documentation page referring to this one has the directive .. include:: custom_urls.txt
conf.py and /misc/cyverse_sphinx_conf.py	Edit the tutorial and author name; versioning
README.md	These instructions	Delete before publishing your documentation
/slides	Place slides associated with your tutorial here	Version controlled files preferred, PPT acceptable
/misc	Miscellaneous needed for building documentation
License.md	License	This license file applies to all materials created by CyVerse for this documentation

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 the maintainer listed in the documentation or Tutorials@CyVerse.org

More complex contributions

Fixing and/or improving documentation via GitHub

1. Fork this repo to your GitHub account
2. Make desired edits. 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

You will need the following accounts

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

Obtaining the template

1. Choose one of the template repositories at https://github.com/CyVerse-learning-materials/ (these are pinned at the top of this page). Click the Use this template button. Name your repo for the name of your documentation e.g. 'name_tutorial'. You may choose public or private. There is no need to include all branches (leave unchecked).

2. Once you have a new repo made from the template, clone this new repo to your local machine for editing.

    $git clone MY-TUTORIAL
   

Authoring tools (local install)

In order to build our documentation you can install the authoring tools or skip this section and use the Docker container we have built.

You will need the following software

1. Python (3.7 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

   Note You can use the minimal_requirements.txt in /readthedocstools to install these requirements. If you run into problems try this with the whole requirements.txt - both of which are in the learning-center-2.0-release repo (see /readthedocstools in that repo).

    $ pip3 install -r /readthedocstools/minimal_requirements.txt
   

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

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

Editing the template

1. Edit the index.rst and other files as needed. Save images or other files in the appropriate directories. See the recommended style guide in the template.

2. 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 documentation piece per repo.

3. Save your work such as:

   • 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 and custom_urls.txt

4. Edit the conf.py and /misc/cyverse_sphinx_conf.py files to set the project and author information

5. Build the tutorial:

      $ make html
   

   Alternatively you can make an automatically building previewing using this command

      $ sphinx-autobuild -b html --host 0.0.0.0 --port 8000 --poll . _build_html
   

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

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

Authoring tools (Docker)

For your convenience, all of the documentation software has been packed in a Docker container.

1. If needed, install Docker (See Get Docker) then pull the Docker image:

      $ docker pull jasonjwilliamsny/cyverse-learning-materials-tools:1.0
   

2. Run the container interactively (-it). Map port 8000 inside the container to port 8000 outside (-p 8000:8000) and use the volume command (-v) to mount the container to a directory of your choice. This directory should be the place where you cloned your repo in step 1 of this section. You will need to be able to open files using a web browser and use a text editor to edit files.

      $ docker run -it -p 8000:8000 -v LOCALDIRECTORY:/DOCKERDOCUMENTATION jasonjwilliamsny/cyverse-learning-materials-tools:1.0
   

3. From inside the Docker container bash terminal, navigate to the mounted directory (e.g. DOCKERDOCUMENTATION). You should see your cloned repository there. You can now follow the steps in the Obtaining the template section with the following modifications:

   • To preview your documentation, from inside the docker container use the following command to view build and preview your documentation. NOTE this command will only work if you are in the same directory as your documentation repository and you are inside the docker container shell.

         $ sphinx-autobuild -b html --host 0.0.0.0 --port 8000 --poll . _build_html
     

     You documentation should be served at http://0.0.0.0:8000. Open a web browser on your computer to see the preview. As you make changes to the documentation, the browser should automatically update within a few seconds of making the change.

4. Follow the directions in the "Editing the template" section above.

Wrapping up and hosting documentation in the Learning Center

Once you have built your documentation, notify Tutorials@CyVerse.org 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. 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 (Tutorials@cyverse.org 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

Sample and test data for Learning Center materials

ALL materials with sample or test data on the Learning Center should be
available with anonymous/public read access at /iplant/home/shared/cyverse_training

/iplant/home/shared/cyverse_training:
  C- /iplant/home/shared/cyverse_training/classrooms
  C- /iplant/home/shared/cyverse_training/cyverse_austria_training
  C- /iplant/home/shared/cyverse_training/datasets
  C- /iplant/home/shared/cyverse_training/example
  C- /iplant/home/shared/cyverse_training/manuals
  C- /iplant/home/shared/cyverse_training/platform_guides
  C- /iplant/home/shared/cyverse_training/quickstarts
  C- /iplant/home/shared/cyverse_training/tutorials
  C- /iplant/home/shared/cyverse_training/workshop_materials

In general, data should be in the appropriate manuals,platform_guides, quickstarts, tutorials, or workshop_materials folders.