Contributor Guide¶

We welcome contributions from our community. To ensure a high-quality documentation experience, we have some guidelines for contributors who wish to create.

Prerequisites¶

We are using Visual Studio Code (VSCode) for development with the following extensions installed. While VSCode is not required, it can help with automating formatting, linting and Anaconda environment management. VSCode may be obtained from Visual Studio Code and documentation is available at VSCode: Docs.

It is assumed you have Anaconda installed on your local machine. See https://docs.anaconda.com/anaconda/install/ for more information on installing Anaconda.

Required VSCode Extensions¶

Python: ms-python.python (for Anaconda environment management)
Markdown All in One: yzhang.markdown-all-in-one
markdownlint: DavidAnson.vscode-markdownlint
Prettier - Code formatter: esbenp.prettier-vscode

Search for and install extensions using the extension menu (keyboard shortcut: Ctrl+Shift+X). More information on managing extensions is available at VSCode: Extension Marketplace.

Handy VSCode Hotkeys¶

Open command palette: Ctrl+Shift+P
Open extensions: Ctrl+Shift+X
Open new terminal: Ctrl+Shift+`
Find in all files: Ctrl+Shift+F
Commenting and uncommenting code using Ctrl+/
- For a single line, click anywhere on that line to place the caret, then press Ctrl+/
- For commenting a block of text, select the block, then press Ctrl+/

Note

For Mac Users VSCode hotkeys are Cmd+Shift rather than Ctrl+Shift

VSCode `settings.json` Additions¶

To make the best use of formatting extensions for this project, please add the following block to your settings.json file. These changes can be made:

Within the VSCode project file in the .vscode folder, affecting only this project. To make these changes find or create the file .vscode/settings.json --OR--
To the global VSCode settings file, affecting all projects. To change the global file, press Ctrl+Shift+P to open the Command Palette, then search for Preferences: Open Settings (JSON) and append the following content.

  "[html]": {
    "editor.defaultFormatter": "vscode.html-language-features"
  },
  "[markdown]": {
    "editor.defaultFormatter": "yzhang.markdown-all-in-one",
    "editor.formatOnSave": true,
    "editor.codeActionsOnSave": {
        "source.fixAll.markdownlint": "explicit"
    },
    "editor.tabSize": 4,
    "editor.wordWrap": "on"
  },
  "[yaml]": {
    "editor.defaultFormatter": "esbenp.prettier-vscode"
  },
  "markdown.extension.list.indentationSize": "inherit",
  "markdownlint.config": {
    "MD046": { "style": "fenced" }
  }

Obtaining a Working Copy of the Code¶

Before you can get started working on contributions, you'll need a copy of the repository. The first step, done only once, is to fork the repository in GitHub to your personal account. The repository is located at https://github.com/uabrc/uabrc.github.io. More in-depth documentation on forking can be found at GitHub: Fork a Repo.

Once the fork has been created, you can clone your fork using the Command Palette (Ctrl+Shift+P) and Git: Clone... in VSCode, or at the command line. More information on cloning can be found at GitHub: Cloning a Repository. More information on using git can be found at our git page.

Local Machine Setup (Laptop/Desktop)¶

The Python extension will activate when you open any Python file. The file test.py has been added for convenience, simply open that file to activate the extension. The extension will show the currently activated environment near the bottom-left corner of the VSCode window. There is no other known way to activate the Python extension at this time.

Please create an Anaconda environment using build_env.yml using the following in the VSCode terminal.

conda env create -f build_env.yml

Activate the environment in VSCode by clicking the currently activated environment in the bottom-left of the VSCode window. A menu will appear allowing you to select from discovered environments. You may need to reload VSCode to get the environment to appear if it was just created.

To build the documentation locally, use mkdocs build in the VSCode terminal. Be sure to fix all warnings before submitting a pull request.

Workflow for Contributing¶

The workflow below assumes you are using VSCode and all of the prerequisites listed above. Some familiarity with git and GitHub are assumed.

Create a working branch¶

You'll need to create a new branch on your local machine (the working branch). The purpose of a branch is to encapsulate a coherent set of changes to add or deprecate a feature, or fix a bug. Typically each bug is associated with one issue, or a set of very closely-related issues. See our Issue Tracker for available issues.

A branch should be created to resolve an issue, and lives only until the issue is resolved.
Give the branch a short but meaningful name for your intended changes.
For bug fixes use names like fix-broken-link or fix-page-formatting.
For new features or pages, use names like feat-lts-page or feat-accessibility-improvement.
Command to create new branch in terminal: git checkout -b <name>.

Implement your changes¶

You'll need to add, remove or otherwise modify files as appropriate to implement the changes you intend.

Stage and commit changes in small units as you go.
Be sure you are on the correct branch, i.e. your working branch!
VSCode facilitates staging and committing files.

Verify your changes¶

Activate your conda environment.
1. Open the file test.py in the repository to start the Python extension.
2. Select the interpreter using https://code.visualstudio.com/docs/python/environments#_select-and-activate-an-environment
Open a VSCode terminal using Ctrl+Shift+`.
Execute the command mkdocs serve
If a new browser tab does not open automatically, use your browser to navigate to http://localhost:8000.
Ensure your changes look and function as expected.

Make a pull request¶

Push your local working branch to your GitHub remote repository.
Navigate to the upstream repository at https://github.com/uabrc/uabrc.github.io.
Click the "Pull requests" tab and click the "New pull request" button.
Click the link "compare across forks".
There are four drop-down menus.
1. The left two drop-down menus are for the base repository and should say uabrc/uabrc.github.io and main by default. Be sure that they do.
2. In the third drop-down menu, select your fork.
3. In the fourth drop-down menu, select your working branch.
Click the "Create pull request" button to open the pull request creation form.
1. Give your pull request a concise and informative name. The name should describe what the pull request changes at a high level.
2. In the description box, give details about what was changed at a conceptual level. The actual details of the changes can be viewed in the "Commits" and "Files changed" tabs.
3. If you want reviewers to be able to make changes to your pull request (recommended) then leave the "Allow edits" checkbox checked.

Wait for review¶

From here your pull request will go through a review process. The following criteria are checked.

No linting errors
Correct formatting
Image alternate text (alt text)
Images must use the gallery functionality, formatted as ![!alttext](path/to/file). Note the leading ! in the alttext.
Valid internal and external links.
Quality, organization and accuracy of contribution.

We will do our best to check information for accuracy, as well as proofread the text. Bear in mind Research Computing staff time is limited and we are not infallible, so please double-check your pull requests! Your audience is your research colleagues at UAB and beyond, and possibly even you at a future date!

Reviewing Pull Requests¶

Note

Currently only RC Data Science staff have permissions to review pull requests.

Reviewing a pull request means obtaining a copy of the pull request branch and Verifying the Changes on your local machine or on your fork. GitHub provides a facility for obtaining pull request branches directly from the upstream repository.

Add upstream remote¶

Add the Upstream Remote using git remote add upstream https://github.com/uabrc/uabrc.github.io.git.

Pull the pull request¶

Fetch the pull request with git fetch upstream pull/<id>/head:<branch-name>.
1. Replace <id> with the pull request id number.
2. Replace <branch-name> with the branch name from the pull request source.
Checkout the branch using git checkout <branch-name>.
Follow the instructions for Verifying Changes
(Optional) make modifications to the pull request.
1. Before starting, make sure that the pull request author has allowed edits to their branch.
2. Add the Author's Fork as a Remote.
3. Push changes to the Author's Fork. Be sure to push to the correct remote!

File Organization¶

Main headings are based on UAB Research Computing services
Favor placing new pages and information into an existing section over creating
Approach documentation from a problem solving angle rather than a technology. Examples:
- Section title "Installing Software Yourself with Anaconda" vs "Anaconda"
- Section title "Running Analysis Jobs" vs "Slurm"
Put redirects for any page moves in case someone has bookmarked a page (see Redirect section below)

Markdown Formatting¶

Links must be one of the following formats including all punctuation and brackets:
- Bare:
  - <https://google.com>
  - <support@listserv.uab.edu>
- Named with a schema:
  - [website](https://google.com)
  - [email](mailto:support@listserv.uab.edu) note the mailto: schema!
- Relative internal
  - [relative internal](help/faq.md)
All internal links must be relative. For example, use ./file.md not /docs/file.md.

Redirects¶

If a page name must change, or the location of a page must change, it is necessary to create a redirect for that page so we don't break bookmarks and incoming links targeting our documentation.

Redirecting pages is possible using the plugin at https://github.com/datarobot/mkdocs-redirects. To redirect a page, add a line in mkdocs.yml under the following keys. The line takes the form original page location: new page location, and each side of : must be a full path under docs/. An example is below.

plugins:
  - redirects:
      redirect_maps:
        account_management/uab_researcher.md: account_management/cheaha_account.md

Section Index Pages¶

To create a section index page:

Create a file called index.md in a reasonable directory location for that section.

Add something like the following to that section entry under nav: in mkdocs.yml.

nav:
  ...
  - Cheaha Guide:
    - cheaha/index.md  # add the index.md here.
    - Hardware: ...
    - ...
  ...

When a site visitor clicks Cheaha Guide in the nav pane, the page cheaha/index.md will be loaded.

Linting Known Issues¶

There are known issues with the markdown linter and some of our non-standard plugins, especially admonitions (specifically a conflict involving fenced vs indented code blocks). To fix these cases please use one of the following methods. The <lint warning code> can be found by hovering over the yellow squiggles in VSCode to bring up the warning lens.

Please do not use these to silence all linter warnings, only for fixing known issues. Please read the warning lenses given by VSCode to identify the cause of the warning.

Silence Linter Warning for a Block¶

<!-- markdownlint-disable <lint warning code> -->
`linter error here`

`maybe multiple lines`
<!-- markdownlint-enable <lint warning code> -->

Silence Linter Warning for a Single Line¶

We encourage denoting the warning being silenced here by filling out the <lint warning code>, though it isn't required for the single line case.

<!-- markdownlint-disable-next-line <lint warning code> -->
`linter error here just for this line`

False Positive Lint Warnings from Admonitions¶

We allow and encourage the use of admonitions in our documentation, where appropriate. Because these are created using a plugin and are "non-standard" markdown, the VSCode markdownlint extension does not recognize admonitions and may produce a false positive warning about inconsistent code block styles.

Two styles of code block are allowed in markdown: fenced and indented. To work around the false positive warning about admonitions, we require all code blocks to be fenced. This is enforced by adding an entry to the VSCode settings.json file. Now all admonitions will be consistently assigned the warning MD046, which can be disabled by placing all admonitions in between the following comment block fences. The comment lines must be indented to the same level as the start of the admonition.

<!-- markdownlint-disable MD046 -->

<!-- markdownlint-enable MD046 -->

The process can be simplified in VSCode using snippets. Bring up the command palette and type snippets and open Preferences: Configure User Snippets. Then type markdown and open it. A json file will be opened. Add the following content between the outermost braces and then save the file.

  "Disable Markdown Lint MD046 for a Block": {
    "prefix": "md046 disable",
    "body": [
      "<!-- markdownlint-disable MD046 -->",
      "$TM_SELECTED_TEXT",
      "<!-- markdownlint-enable MD046 -->"
    ],
    "description": "Disables warning Markdown Lint MD046 for the selected block."
  }

The snippet will surround selected text with the appropriate linter disable fencing for MD046. To use the snippet, opne the IntelliSense lens using ctrl + space (or cmd + space), then type md046 until the prefix shows up as the first entry in the list. Then press tab.

The workaround is needed because markdownlint has no plans to add support for admonitions. There is no markdownlint plugin for that support either, and we don't have the ability to develop such a plugin.

Slurm Hardware, Partitions, QoS Tables¶

Building hardware tables is a semi-automated script based on a manually curated table. The repository is located here: https://gitlab.rc.uab.edu/rc-data-science/data-science-internal/cluster-fabric-docs. Be warned that the scripts may move to a github.com repo in the future.

Building Partition and QoS tables is automated based on scontrol output. The repository is located here: https://github.com/wwarriner/slurm_status_tools. Be warned the link may change in the future when we fork to the UABRC group that houses the docs repo.

Accessibility¶

Color vision deficiency checker: https://www.toptal.com/designers/colorfilter/ Contrast checker: https://webaim.org/resources/contrastchecker/

Branding Guidance¶

Brand main page: https://www.uab.edu/toolkit/branding
Brand colors: https://www.uab.edu/toolkit/brand-basics/colors
Copyright guidance: https://www.uab.edu/toolkit/trademarks-licensing/uab-trademarks

Terminology¶

Research Computing (RC) for the IT group supporting campus HPC resources.
UAB Campus Network for the hard-wired network physically located on UAB campus, and the UAB Secure wifi.
UAB Campus VPN for the VPN to tunnel remote connections through the UAB Campus Network.