2.0 Release css/js/config files

In this repo are some configuration files needed to bring existing repos to the Learning Center 2.0 spec.

2.0 Upgraded Files

file	Notes	Location to place in the target repo (relative to top level directory)
triage-for-2-0-release.md	This is a github template for issues. When the repo is ready to be evaluted for 2.0, an issue should be created using this emplate.	./github/ISSUE_TEMPLATE/triage-for-2-0-release.md
cyverse.css	Repo css	misc/static/cyverse.css
cyverse.js	Repo js	misc/static/cyverse.js
detail-expand.css	Repo css	misc/static/detail-expand.css
intercom-script-for-learning.js	Intercom js	misc/static/intercom-script-for-learning.js
question-answer.js	Q&A js	misc/static/question-answer.js
jquery.tablesorter.min.js	Repo css	misc/static/jquery.tablesorter.min.js
cyverse_spinx_conf.py*	sphinx config file	misc/cyverse_spinx_conf.py
conf.py*	sphinx config	conf.py
cyverse_rst_defined_substitutions.txt*	list of URLS	cyverse_rst_defined_substitutions.txt
custom_urls.txt*	repo-specific of URLS	custom_urls.txt
README.md*	Project Readme	README.md

* - These files may have some project-specific features so you should not automatically copy over existing files.

Organizing repos

The script organize_repos.sh is designed to take a list of repo git urls (e.g. https://github.com/CyVerse-learning-materials/trimmomatic_quickstart.git), clone those repositories, create a branch for the new release, and commit that branch back to GitHub

FOR THE 2.0 RELEASE ALL WORK SHOULD BE DONE ON THE BRANCH learning_center_2_0_release_candidate Once the repo passes triage (from the 2.0 release template issue) the work can be merged to master. Then a 2.0 release can be created.

Upgrading a Repo to 2.0

In many cases you can automatically upgrade an existing repo to the 2.0 spec. Here are the steps.

1. Clone this repo to a location on your computer

   $ git clone https://github.com/CyVerse-learning-materials/learning-center-2.0-release.git
   

2. Make a directory to contain the repo(s) you wish to upgrade

   $ mkdir repos_to_upgrade
   

3. In the directory you have created, clone the repo(s) you wish to upgrade

   $ cd repos_to_upgrade
   $ git clone repo_1_url.git
   $ git clone repo_2_url.git
   $ git clone repo_3_url.git
   

4. You should now have a directory which contains your git repository (you may or may not have tree command but as long as you have this setup you are fine).

   $ tree -L 1 repos_to_upgrade/
   
     repos_to_upgrade/
     ├── repo_1
     ├── repo_2
     └── repo_3
   

5. Change back into this learning-center-2.0-release directory

   $ cd ../learning-center-2.0-release
   

6. Run the upgrade script using the -d option to specify the directory with your repo(s)

    $ bash upgrade.sh -d ../repos_to_upgrade
   

7. This script will copy new files/versions into the repo and attempt to replace some of the logos and texts in existing files. This may break the repo to be upgraded. An HTML file with a preview build will be created (e.g. my_repo/_build). Please preview every page in the repo and ensure things look good.

8. Once you have made changes, push the needed repo back to github. Then create an issue (there should now be a template issue Triage for Release). Create the issue (Please make sure the repo name is in the issue title). Do your best to complete the checklist and then notify [email protected] your repo is ready for the 2.0 release.

FOR THE 2.0 RELEASE ALL WORK SHOULD BE DONE ON THE BRANCH learning_center_2_0_release_candidate Once the repo passes triage (from the 2.0 release template issue) the work can be merged to master. Then a 2.0 release can be created on GitHub.

How to maintain links in CyVerse learning materials

CyVerse uses RestructuredText (RST) to build documentation. To add links within your documentation, RST allows you a few ways, but the preferred way is to use a substitution . Combined with the include directive we can have a single page with all the URLs for links in the documentation. If a link changes, this means you can update a single page and fix the link everywhere it appears.

There are two places we recommend you place links

• cyverse_rst_defined_substitutions.txt - This is a list of common CyVerse-related links (like our homepage or commonly cites URLS like learning center articles).
• custom_urls - You can place all of the URLS particular to your repo in in this one file, making them easier to manage.

Not all repos will meet this standard and that's OK, although the upgrade is a change to move towards better compliance.

Link formatting

1. CyVerse documentation templates contain the directive (if you don't have this line add it)

   .. include:: cyverse_rst_defined_substitutions.txt
   

2. Your documentation template should also contain the file cyverse_rst_defined_substitutions.txt

3. As you create your documentation, add your URLs to the cyverse_rst_defined_substitutions.txt file in this format

     .. |LINK TITLE| raw:: html
   
      <a href="https://link.url/" target="_blank">LINK TITLE</a>
   
   

4. When you are writing your documentation, enter links by using the link title you have specified surrounded with the | character, i.e.

   |LINK TITLE|
   

Tips and adding to this master file

1. Unfortunately all repos cannot automatically copy from this master file. If the cyverse_rst_defined_substitutions.txt file in this repo is newer than the one in your template, you will need to manually copy it. We will update the templates on a regular basis.

2. When adding to the cyverse_rst_defined_substitutions.txt file in this repo try to keep this alphabetical.

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 [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. 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

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.