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Merge branch 'main' into feat-system-wide-singularity-update
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‎.github/ISSUE_TEMPLATE/article_request.yml‎

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id: description
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attributes:
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label: What would you like to see added?
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description: Please tell us about what article or section you think is missing. Please include images and links as appropriate, and tell us where you think the new content would best fit.
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description:
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Please tell us about what article or section you think is missing.
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Please include images and links as appropriate, and tell us where you
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think the new content would best fit.
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placeholder: Tell us what you would like to see!
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validations:
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required: true

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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id: what-happened
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attributes:
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label: What happened?
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description: Please describe what happened. Screenshots and URLs of affected parts are welcome.
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description:
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Please describe what happened. Screenshots and URLs of affected parts
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are welcome.
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placeholder: Tell us what you see!
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validations:
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required: true

‎.github/pull_request_template.md‎

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# Pull Request
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<!-- PLEASE READ THE COMMENTS BELOW -->
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## Overview
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<!-- Briefly summarize the proposed changes -->
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## Intent
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<!-- Describe the intent of the changes. -->
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## Proposed Changes
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<!-- Provide specific details of what is changing. -->
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<!-- Provide specific details of what is changing -->
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### Changes to Section Headers
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<!-- Write down which headers have changed.
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old-header -> new-header
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-->
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## Related Issues
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### Changes to Page URLs
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<!-- Write down which pages have changed.
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old/page.md -> new/page.md
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-->
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<!--
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Examples:
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## Related or Fixed Issues
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<!-- Examples:
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Fixes #123
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Related to #101
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-->
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## Accessibility Checklist
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I have ensured all of the following for new or changed content:
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- [ ] all images have appropriate alt text. [Guidelines](https://www.wcag.com/blog/good-alt-text-bad-alt-text-making-your-content-perceivable/)
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- [ ] all images with text have sufficient contrast ratio. [Checker](https://webaim.org/resources/contrastchecker/)
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- [ ] all image text is transcribed or described in body text.
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- [ ] all technical terms, jargon, and abbreviations are introduced before they are used.
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## Style Checklist
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I have done all of the following:
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- [ ] searched for other relevant pages and crosslinked from my content to them.
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- [ ] searched for other relevant pages and crosslinked from them to my content.
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- [ ] added redirects in `mkdocs.yml` for any moved headers or pages.
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- [ ] defined new technical terms, jargon, and abbreviations in the glossary.
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- [ ] searched for existing technical terms, jargon, and abbreviations in the glossary and added crosslinks to them.
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- [ ] properly formatted and introduced key branding terms. [List here](https://docs.rc.uab.edu/contributing/contributor_guide#terminology).

‎.github/shared/build_docs_pages/action.yml‎

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# builds mkdocs, reusable by other checks
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name: Build Docs Pages
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description: Build Docs Pages for mkdocs workflows.
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runs:
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using: composite
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steps:
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- uses: conda-incubator/setup-miniconda@835234971496cad1653abb28a638a281cf32541f # 3.2.0
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with:
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environment-file: build_env.yml
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activate-environment: mkdocs
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miniforge-version: latest
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- name: Build Pages # this is both a build and check step
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run: mkdocs build --strict
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shell: bash -l {0} # must have -l because conda requires login shell to function in subsequent steps

‎.github/workflows/check_docs.yml‎

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# checks for mkdocs specific issues
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name: docs
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on: # yamllint disable-line rule:truthy
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pull_request:
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branches:
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- main
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paths:
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- "build_env.yml"
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- "mkdocs.yml"
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- "build_scripts/**"
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- "docs/**"
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workflow_dispatch:
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jobs:
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check_markdown:
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uses: "./.github/workflows/reusable_check_markdown.yml"
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with:
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globs: "docs/**/*.md"
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check_docs:
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needs: check_markdown
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runs-on: ubuntu-latest
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permissions:
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contents: read
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steps:
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
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with:
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fetch-depth: 0 # mkdocs-git-revision-date-localized-plugin
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- uses: "./.github/shared/build_docs_pages/"

‎.github/workflows/check_python.yml‎

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# checks python files for python linting and formatting issues
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name: python
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on: # yamllint disable-line rule:truthy
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push:
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branches:
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- main
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paths:
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- "**.py"
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pull_request:
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branches:
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- main
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paths:
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- "**.py"
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workflow_dispatch:
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jobs:
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check_python:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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strategy:
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matrix:
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args: ["check", "format --check --diff"]
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steps:
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
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- uses: astral-sh/ruff-action@eaf0ecdd668ceea36159ff9d91882c9795d89b49 # 3.4.0
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with:
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args: ${{ matrix.args }}
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version: 0.12.0

‎.github/workflows/check_yaml.yml‎

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# checks yaml for yaml-specific linting and formatting issues
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name: yaml
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on: # yamllint disable-line rule:truthy
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push:
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branches:
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- main
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paths:
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- "**.yml"
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- "**.yaml"
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pull_request:
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branches:
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- main
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paths:
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- "**.yml"
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- "**.yaml"
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workflow_dispatch:
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jobs:
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check_yaml:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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steps:
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
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- uses: karancode/yamllint-github-action@4052d365f09b8d34eb552c363d1141fd60e2aeb2 # 3.0.0
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with:
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yamllint_config_filepath: ".yamllint.yaml"
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yamllint_strict: true
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yamllint_comment: true

‎.github/workflows/ci.yml‎

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‎.github/workflows/deploy_docs.yml‎

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# deploys documentation to gh-pages
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name: docs
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on: # yamllint disable-line rule:truthy
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push:
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branches:
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- main
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paths:
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- "build_env.yml"
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- "mkdocs.yml"
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- "build_scripts/**"
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- "docs/**"
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workflow_dispatch:
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jobs:
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check_markdown:
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uses: "./.github/workflows/reusable_check_markdown.yml"
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with:
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globs: "docs/**/*.md"
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deploy_docs:
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needs: check_markdown
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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permissions:
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contents: read
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pages: write
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id-token: write
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steps:
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
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with:
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fetch-depth: 0 # mkdocs-git-revision-date-localized-plugin
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- uses: "./.github/shared/build_docs_pages/"
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- uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # 5.0.0
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- uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa # 3.0.1
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with:
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path: "./site"
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- uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # 4.0.5

‎.github/workflows/reusable_check_markdown.yml‎

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# checks markdown files for markdown specific linting and formatting issues
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# reusable by other checks
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name: markdown
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on: # yamllint disable-line rule:truthy
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push:
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branches:
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- main
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paths:
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- "**.md"
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- "!docs/**" # covered by check_docs.yml
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pull_request:
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branches:
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- main
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paths:
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- "**.md"
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- "!docs/**" # covered by check_docs.yml
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workflow_dispatch:
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workflow_call:
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inputs:
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globs:
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type: string
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jobs:
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check_markdown:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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steps:
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- uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
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- name: Configure Globs
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id: globs
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run: |
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if [ -n "${{ inputs.globs }}" ]; then
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GLOBS_STRING="${{ inputs.globs }}"
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else
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GLOBS_STRING='**/*.md !docs/**/*.md'
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fi
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IFS=' ' read -r -a GLOBS_ARRAY <<< "$GLOBS_STRING"
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NEWLINE_DELIMITED_GLOBS=""
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for glob in "${GLOBS_ARRAY[@]}"; do
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if [ -n "$NEWLINE_DELIMITED_GLOBS" ]; then
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NEWLINE_DELIMITED_GLOBS+=$'\n'
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fi
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NEWLINE_DELIMITED_GLOBS+="$glob"
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done
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echo "globs<<EOF" >> "$GITHUB_OUTPUT"
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echo "$NEWLINE_DELIMITED_GLOBS" >> "$GITHUB_OUTPUT"
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echo "EOF" >> "$GITHUB_OUTPUT"
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- uses: DavidAnson/markdownlint-cli2-action@992badcdf24e3b8eb7e87ff9287fe931bcb00c6e # 20.0.0
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with:
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config: ".markdownlint-cli2.jsonc"
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globs: "${{ steps.globs.outputs.globs }}"

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