stan-ode-forcing-function/.github/workflows/render.yml at main · ImmuSystems-Lab/stan-ode-forcing-function · GitHub

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---
name: Render and Deploy to GitHub Pages

on:
  push:
    branches: [main]

jobs:
  render:
    runs-on: ubuntu-latest
    container:
      image: rocker/verse:latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Install LaTeX packages to render PDF outputs
        run: >-
          Rscript -e
          'tinytex::tlmgr_install(c(
          "adjustbox",
          "amsfonts",
          "booktabs",
          "caption",
          "enumitem",
          "eurosym",
          "float",
          "fontspec",
          "grffile",
          "jknapltx",
          "pdfcol",
          "rsfs",
          "soul",
          "tcolorbox",
          "titling",
          "ulem",
          "unicode-math",
          "upquote"
          ))'

      - name: Install RStan and dependencies
        run: >-
          Rscript -e
          'pak::local_install_deps("stanodeffr", dependencies = TRUE)'

      - name: Install cmdstanpy and dependencies
        run: |-
          cd stanodeffpy/
          wget -qO- https://astral.sh/uv/install.sh | sh
          . $HOME/.local/bin/env
          uv sync

      - name: Render RMarkdown into all output formats
        run: >-
          Rscript -e '
          rmarkdown::render(
          "stanodeffr/01-stan-ode-forcing-function.Rmd",
          output_format = "all",
          output_dir = "public/r"
          )
          '

      - name: Render Jupyter notebook into all output formats
        run: |-
          cd stanodeffpy/
          . $HOME/.local/bin/env
          uv run jupyter execute --inplace 01-stan-ode-forcing-function.ipynb
          for format in markdown html python pdf; do
            uv run \
            jupyter nbconvert \
            --output-dir ../public/python \
            --to $format \
            01-stan-ode-forcing-function.ipynb
          done

      - name: Create index.html pages to see all vignette files
        run: |
          cd public/
          apt update
          apt -y install tree
          tree -H '.' \
            -T 'Vignettes for Stan ODE forcing function' \
            -I index.html \
            -I 01-stan-ode-forcing-function_files \
            --noreport \
            --houtro "" \
            -o index.html

      - name: Deploy to GitHub Pages
        uses: peaceiris/actions-gh-pages@v4.1.0
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}