Fix rendering issues #298
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| name: Render and deploy Quarto files | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| quarto-render-and-deploy: | |
| runs-on: ubuntu-latest | |
| container: rocker/verse:latest | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GH_PAT: ${{ secrets.GH_PAT }} | |
| GITHUB_PAT: ${{ secrets.GH_PAT }} | |
| PYENV_PATHS_ROOT: '~/.pyenv' | |
| PYENV_PATHS_VENV: '~/.virtualenvs/venv' | |
| PYENV_PATHS_RETICULATE: '~/.local/share/r-reticulate' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt update | |
| sudo apt upgrade | |
| sudo apt install -y libudunits2-dev libgdal-dev | |
| type -p curl >/dev/null || (sudo apt update && sudo apt install curl -y) | |
| curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg \ | |
| && sudo chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg \ | |
| && echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | sudo tee /etc/apt/sources.list.d/github-cli.list > /dev/null \ | |
| && sudo apt update \ | |
| && sudo apt install gh -y | |
| shell: /bin/bash {0} | |
| - name: Renv setup | |
| uses: r-lib/actions/setup-renv@v2 | |
| - name: Renv and R install status | |
| shell: Rscript {0} | |
| run: | | |
| renv::status() | |
| renv::diagnostics() | |
| # Paste string to describe cache | |
| writeLines( | |
| paste0("PY_CACHE_STR=python", | |
| paste( | |
| readLines(".python-version"), | |
| digest::digest(readLines("pyenv/requirements.txt")), | |
| sep = "-" | |
| )), | |
| Sys.getenv("GITHUB_ENV")) | |
| - name: Restore reticulate cache | |
| id: restore-reticulate-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ env.PYENV_PATHS_RETICULATE }} | |
| key: local-share-reticulate-${{ env.PY_CACHE_STR }} | |
| restore-keys: local-share-reticulate- | |
| - name: Restore venv cache | |
| id: restore-venv-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ env.PYENV_PATHS_VENV }} | |
| key: pyenv-${{ env.PY_CACHE_STR }} | |
| restore-keys: pyenv- | |
| - name: Restore pyenv cache | |
| id: restore-pyenv-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ env.PYENV_PATHS_ROOT }} | |
| key: reticulate-venv-${{ env.PY_CACHE_STR }} | |
| restore-keys: reticulate-venv- | |
| - name: Setup Python/venv with reqs file in reticulate | |
| if: ${{ steps.restore-pyenv-cache.outputs.cache-hit != 'true' && steps.restore-venv-cache.outputs.cache-hit != 'true' && steps.restore-reticulate-cache.outputs.cache-hit != 'true' }} | |
| id: setup-reticulate-venv | |
| shell: Rscript {0} | |
| run: | | |
| reticulate::install_python(version=readLines(".python-version")) | |
| reticulate::py_install(c("virtualenv")) | |
| reticulate::virtualenv_root() | |
| reticulate::virtualenv_create("venv", requirements="pyenv/requirements.txt") | |
| reticulate::use_virtualenv("venv") | |
| reticulate::py_config() | |
| # Set reticulate_python env var | |
| writeLines( | |
| paste0("RETICULATE_PYTHON=", reticulate::virtualenv_python("venv")), | |
| Sys.getenv("GITHUB_ENV")) | |
| # Paste string to describe cache | |
| writeLines( | |
| paste0("PY_CACHE_STR=python", | |
| paste( | |
| readLines(".python-version"), | |
| digest::digest(readLines("pyenv/requirements.txt")), | |
| sep = "-" | |
| )), | |
| Sys.getenv("GITHUB_ENV")) | |
| - name: Reticulate checks | |
| shell: Rscript {0} | |
| run: | | |
| devtools::session_info() | |
| reticulate::py_config() | |
| - uses: quarto-dev/quarto-actions/setup@v2 | |
| with: | |
| version: 1.5.57 | |
| tinytex: true | |
| - name: Render Quarto Project | |
| shell: /bin/bash {0} | |
| run: | | |
| quarto render --execute-debug | |
| - name: "Deploy to gh-pages" | |
| uses: peaceiris/actions-gh-pages@v4 | |
| if: github.ref == 'refs/heads/main' | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ./docs | |
| - name: Broken Link Check | |
| uses: technote-space/broken-link-checker-action@v2 | |
| with: | |
| RECURSIVE: false |