Document dependency setup paths with and without renv
#345
Workflow file for this run
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| on: | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| push: | |
| branches: | |
| - dev | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '30 0 * * 0' # runs At 00:00 on Sunday | |
| name: Render | |
| jobs: | |
| build-deploy: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v7 | |
| - name: Set up R (needed for Rmd) | |
| id: setup-r | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Cache R package directories | |
| uses: actions/cache@v6 | |
| with: | |
| path: | | |
| ~/.cache/R | |
| ~/R | |
| key: ${{ runner.os }}-r-pak-${{ hashFiles('.github/workflows/render.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-r-pak- | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| libcurl4-openssl-dev \ | |
| libssl-dev \ | |
| libxml2-dev \ | |
| libv8-dev \ | |
| libfontconfig1-dev \ | |
| libfreetype6-dev \ | |
| libharfbuzz-dev \ | |
| libfribidi-dev \ | |
| libpng-dev \ | |
| libtiff5-dev \ | |
| libjpeg-dev \ | |
| libcairo2-dev \ | |
| libgit2-dev \ | |
| libnode-dev \ | |
| libx11-dev \ | |
| pandoc | |
| - name: Set up R package dependencies (cached, via pak) | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| pak-version: stable | |
| cache: true | |
| packages: | | |
| cran::rmarkdown | |
| cran::knitr | |
| cran::jsonlite | |
| cran::dplyr | |
| cran::ggplot2 | |
| cran::tidyr | |
| cran::TMB | |
| cran::remotes | |
| cran::reshape2 | |
| cran::Rcpp | |
| cran::glue | |
| cran::purrr | |
| cran::ggridges | |
| extra-packages: | | |
| github::nmfs-ost/stockplotr | |
| github::stan-dev/cmdstanr | |
| github::mjskay/tidybayes | |
| github::stan-dev/shinystan | |
| github::noaa-afsc/SparseNUTS | |
| github::NOAA-FIMS/FIMS | |
| github::r4ss/r4ss@convert-data-to-fims | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # add software dependencies here | |
| - name: Render Quarto Project | |
| uses: quarto-dev/quarto-actions/render@v2 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # this secret is always available for github actions | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v5 |