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CHG: Initial merge from development fork
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‎.github/workflows/pages.yml‎

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# separate terms of service, privacy policy, and support
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# documentation.
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# Sample workflow for building and deploying a Jekyll site to GitHub Pages
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name: Deploy Jekyll site to Pages
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# NOTE:
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# - Search https://ctan.org/ for package names of missing TeX Live packages as
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# needed
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#
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# TODO:
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# - Pull userguide.pdf from its workflow or otherwise incorporate it into this
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# workflow so that is available via direct download link (rather than blob in
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# source code repo)
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# - Then update link in docs/index.md
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# - Add test job to check for expected output given certain input on change to
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# latex2md.py?
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#
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name: Convert LaTeX Documentation to Markdown and Deploy to GitHub Pages
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on:
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push:
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branches: ["main"]
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paths:
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- ".github/workflows/pages.yml"
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- "docs/assets/**"
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- "docs/getting-started/**"
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- "docs/installation/**"
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- "docs/publications/bibtex/references.bib"
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- "docs/publications/index.md"
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- "docs/supplements/**"
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- "docs/troubleshooting/**"
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- "docs/using-issm/**"
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- "docs/Gemfile"
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- "docs/Gemfile.lock"
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- "docs/index.md"
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# Run if 'Publications' page has been updated
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workflow_run:
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workflows: ["Update Publications Page"]
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types:
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- completed
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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env:
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BIBINPUTS: "./publications/bibtex/"
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# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
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permissions:
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contents: read
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# Build job
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build:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: docs
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Install TeX Live
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uses: teatimeguest/setup-texlive-action@v3
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with:
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packages: |
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scheme-basic
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- name: Install dependencies for opendetex
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uses: awalsh128/cache-apt-pkgs-action@latest
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with:
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packages: libfl-dev
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version: 1.0
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- name: Checkout opendetex source from repo
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uses: actions/checkout@v4
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with:
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repository: pkubowicz/opendetex
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path: '${{ github.workspace }}/ext/opendetex'
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- name: Compile and install opendetex
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run: |
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cd ${{ github.workspace }}/ext/opendetex
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make
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sudo make install
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- name: Convert LaTeX to Markdown
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run: |
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export BIBINPUTS=${{ env.BIBINPUTS }}
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../bin/latex2jtd.sh ./
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- name: Setup Ruby
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: '3.3' # Not needed with a .ruby-version file
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bundler-cache: true # runs 'bundle install' and caches installed gems automatically
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cache-version: 0 # Increment this number if you need to re-download cached gems
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working-directory: '${{ github.workspace }}/docs'
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- name: Setup Pages
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id: pages
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uses: actions/configure-pages@v5
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- name: Upload artifact
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# Automatically uploads an artifact from the './_site' directory by default
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uses: actions/upload-pages-artifact@v3
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with:
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path: "docs/_site/"
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# Deployment job
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deploy:

‎.github/workflows/pdf.yml‎

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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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# NOTE:
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# - Search https://ctan.org/ for package names of missing TeX Live packages as
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# needed
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#
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name: Generate User Guide
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on:
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push:
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branches: ["main"]
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paths:
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- ".github/workflows/pdf.yml"
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- "docs/**"
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- "userguide/**"
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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env:
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BIBINPUTS: "../publications/bibtex/"
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TARGET: "userguide"
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jobs:
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complete:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: userguide
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Install TeX Live
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uses: teatimeguest/setup-texlive-action@v3
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with:
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packages: |
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scheme-basic
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aguplus
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amsfonts
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amsmath
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bibtex
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collection-fontsrecommended
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enumitem
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fancyhdr
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fancyvrb
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float
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fontawesome
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geometry
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graphics
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hyperref
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jknapltx
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listings
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multirow
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natbib
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pdfcol
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tcolorbox
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tools
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upquote
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xcolor
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- name: Generate User Guide
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run: |
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export BIBINPUTS=${{ env.BIBINPUTS }}
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export TARGET=${{ env.TARGET }}
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./userguide.sh
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- name: Deploy to ISSM Repository
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uses: lubu12/copy-files-to-repository@v1
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env:
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API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
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with:
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source-files: ${{ env.TARGET }}/${{ env.TARGET }}.pdf
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destination-username: 'TidbitSoftware'
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destination-repository: 'ISSM'
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destination-directory: ''
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destination-branch: 'main'
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commit-email: '[email protected]'
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commit-message: 'CHG: Updated user guide'

‎.github/workflows/publications.yml‎

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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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# TODO:
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# - Add build step to remove duplicate DOI's
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#
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name: Update Publications Page
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on:
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push:
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branches: ["main"]
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paths:
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- ".github/workflows/publications.yml"
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- "docs/publications/bin/**"
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- "docs/publications/doi/**"
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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# Sets permissions of the GITHUB_TOKEN to write back to repo
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permissions:
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contents: write
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env:
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TARGET: "./index.md"
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jobs:
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complete:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: docs/publications
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Generate Publications Page
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run: |
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./bin/generate_publications_page.sh > ${{ env.TARGET }}
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- name: Commit and Push Updated Publications Page
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run: |
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git config --global user.name "${{ github.actor }}"
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git config --global user.email "${{ github.actor }}@users.noreply.github.com"
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git add ${{ env.TARGET }}
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git commit -m 'CHG: Updated Publications page'
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git push

‎.gitignore‎

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# Not sure what a .gitignore is?
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# See: https://git-scm.com/docs/gitignore
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# These are directly copied from Jekyll's first-party docs on `.gitignore` files:
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# https://jekyllrb.com/tutorials/using-jekyll-with-bundler/#commit-to-source-control
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# Ignore the default location of the built site, and caches and metadata generated by Jekyll
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_site/
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.sass-cache/
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.jekyll-cache/
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.jekyll-metadata
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# Ignore folders generated by Bundler
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.bundle/
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vendor/
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docs/.ruby-version
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docs/Gemfile.lock
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docs/getting-started/*.md
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docs/getting-started/plotting/*.md
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docs/installation/*.md
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docs/installation/hpc/*.md
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docs/supplements/*.md
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docs/troubleshooting/*.md
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docs/using-issm/*.md
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docs/using-issm/advanced/*.md
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docs/using-issm/capabilities/*.md
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docs/using-issm/capabilities/hydrology/*.md
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docs/using-issm/parameterization/*.md
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docs/using-issm/tutorials/*.md
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userguide/_minted-userguide
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userguide/userguide.atfi
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userguide/userguide.aux
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userguide/userguide.bbl
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userguide/userguide.blg
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userguide/userguide.log
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userguide/userguide.out
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userguide/userguide.pdf
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userguide/userguide.pyg
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userguide/userguide.toc
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userguide/.log

‎Gemfile.lock‎

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