Render and publish the tutorials #98
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| name: Render and publish the tutorials | |
| on: | |
| workflow_dispatch: | |
| # pull_request: | |
| # push: | |
| # branches: ['release'] | |
| jobs: | |
| render-tutorials: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| name: ${{ matrix.config.r }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { r: '4.3.3' } | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # ensure that more than the last commit is checked out so that we can get time stamps | |
| # Restore the timestamps - I am going to try to use these to work out what is new and what is not | |
| - name: Restore Timestamps | |
| uses: chetan/git-restore-mtime-action@v1 | |
| # Install system dependencies | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev make | |
| # install graphviz | |
| - name: Install Graphviz | |
| run: sudo apt-get install graphviz | |
| # install R | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.R }} | |
| - name: Repos | |
| run: | | |
| cat("\noptions(repos=c(stan='https://mc-stan.org/r-packages/',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE) | |
| shell: Rscript {0} | |
| ## Install R packages | |
| - name: install R packages | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 2 | |
| packages: | | |
| any::rmarkdown | |
| any::magick | |
| any::pdftools | |
| any::quarto | |
| any::tidyverse | |
| any::mvabund | |
| any::pander | |
| any::GGally | |
| any::plotrix | |
| any::PBSmapping | |
| any::gmodels | |
| any::mvtnorm | |
| any::coda | |
| any::gganimate | |
| any::gridExtra | |
| any::ggfortify | |
| any::DHARMa | |
| any::glmmTMB | |
| any::performance | |
| any::see | |
| stan-dev/cmdstanr | |
| any::brms | |
| any::knitr | |
| any::simstudy | |
| any::sf | |
| any::stars | |
| any::gstat | |
| any::patchwork | |
| any::remotes | |
| any::inlabru | |
| any::Hmisc | |
| any::igraph | |
| any::ggraph | |
| any::easystats | |
| any::gridGraphics | |
| any::HDInterval | |
| any::bayestestR | |
| any::emmeans | |
| github::jmgirard/standist | |
| - name: Install other R packages | |
| run: | | |
| Rscript -e "install.packages('INLA',repos=c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'), dep=TRUE)" | |
| Rscript -e "install.packages('RandomFields', repos = c('https://spatstat.r-universe.dev', 'https://cloud.r-project.org'))" | |
| Rscript -e "install.packages('RandomFieldsUtils', repos = c('https://spatstat.r-universe.dev', 'https://cloud.r-project.org'))" | |
| Rscript -e "install.packages('tidybayes')" | |
| Rscript -e "remotes::install_github('jmgirard/standist')" | |
| - name: Install CmdStan | |
| shell: Rscript {0} | |
| run: | | |
| cmdstanr::check_cmdstan_toolchain(fix = TRUE) | |
| cmdstanr::install_cmdstan(cores = parallel::detectCores()) | |
| #install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) | |
| #cmdstanr::check_cmdstan_toolchain(fix = TRUE) | |
| #cmdstanr::install_cmdstan(cores = 2) | |
| #version <- "2.35.0" | |
| #url <- sprintf("https://github.com/stan-dev/cmdstan/releases/download/v%s/cmdstan-%s.tar.gz", version, version) | |
| #cmdstanr::install_cmdstan(cores = 2, release_url = url) | |
| #cmdstanr::check_cmdstan_toolchain(fix = TRUE) | |
| #cmdstanr::install_cmdstan(cores = 2) | |
| #cmdstan <- file.path(Sys.getenv("RUNNER_TEMP"), "cmdstan") | |
| #file.rename(cmdstanr::cmdstan_path(), cmdstan) | |
| #lines <- paste0("\nCMDSTAN=", cmdstan, "\n") | |
| #cat(lines, file = "~/.Renviron", append = TRUE) | |
| cmdstanr:::get_cmdstan_flags("STANCFLAGS") | |
| cmdstanr::cmdstanr_example() | |
| - name: install tinytex | |
| uses: r-lib/actions/setup-tinytex@v2 | |
| - run: | | |
| tlmgr --version | |
| tlmgr update --self | |
| - name: Install additional LaTeX packages | |
| run: | | |
| tlmgr install titlesec | |
| tlmgr list --only-installed | |
| - name: Install Google Fonts | |
| run: | | |
| ## The following wget can no longer be performed as google returns a html rather than a zip | |
| #wget -O Architects_Daughter.zip https://fonts.google.com/download?family=Architects%20Daughter | |
| # unzip -d architects_daughter/ Architects_Daughter.zip | |
| # mv architects_daughter /usr/share/fonts/ | |
| unzip -d architects_daughter/ resources/Architects_Daughter.zip | |
| mv architects_daughter /usr/share/fonts/ | |
| #wget -O inconsolata.zip https://fonts.google.com/download?family=Inconsolata | |
| unzip -d inconsolata/ resources/Inconsolata.zip | |
| mv inconsolata /usr/share/fonts/ | |
| #wget -O noto_sans.zip https://fonts.google.com/download?family=Noto%20Sans | |
| unzip -d noto_sans/ resources/Noto_Sans.zip | |
| mv noto_sans /usr/share/fonts/ | |
| fc-cache -fv | |
| fc-list | |
| ##fc-list -v | grep -i archi | |
| ##fc-list -v | grep -i inconsolata | |
| ##fc-list -v | grep -i noto | |
| # install quarto | |
| - name: Install quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| - name: Change ImageMagick policy to allow pdf->png conversion. | |
| run: | | |
| sudo sed -i 's/^.*policy.*coder.*none.*PDF.*//' /etc/ImageMagick-6/policy.xml | |
| # configure git | |
| - name: Configure git | |
| run: | | |
| git config --global user.name "pcinereus" | |
| git config --global user.email "[email protected]" | |
| git config --global init.defaultBranch main | |
| # Checkout the gh-pages branch into the tut folder | |
| # - name: Retrieve previous compiled pages | |
| # uses: actions/checkout@v4 | |
| # with: | |
| # path: tut # Specify the target folder for checkout | |
| # ref: gh-pages | |
| - name: Touch those files that have changed since the last commit | |
| run: | | |
| git diff --name-only HEAD HEAD~1 | xargs touch | |
| # - name: Check that the docs folder is there and populated | |
| # run: | | |
| # ls -la | |
| # ls -la docs | |
| # ls -la tut | |
| # Download artifacts | |
| #- name: download artifacts | |
| # uses: actions/download-artifact@v4 | |
| # with: | |
| # name: artifact | |
| # github-token: ${{ secrets.GH_PAT }} # token with actions:read permissions on target repo | |
| # path: data | |
| # run-id: 8493870822 | |
| #- name: Display structure of downloaded files | |
| # run: ls -R data | |
| # render tutorials | |
| - name: Make tutorials | |
| run: | | |
| echo "library(quarto); quarto_render(\"tut/index.qmd\")" | R --no-save --no-restore; | |
| #make -i tut | |
| make -i pres | |
| #run: | | |
| # echo "library(quarto); quarto_render(\"tut/index.qmd\")" | R --no-save --no-restore; | |
| # echo "library(quarto); quarto_render(\"tut/10_git.qmd\")" | R --no-save --no-restore; | |
| # upload artifacts | |
| #- name: upload artifacts | |
| # uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: artifact | |
| # path: data/reef_data_synthetic_*.csv | |
| # if-no-files-found: ignore | |
| # overwrite: true | |
| # Deploy site to gh-pages branch | |
| - name: Deploy | |
| uses: JamesIves/[email protected] | |
| with: | |
| branch: gh-pages | |
| folder: docs |