Improve error handling and clarity. Updated parameter handling to use… #100
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: workflow_with_cmdstanr | |
| jobs: | |
| workflow_with_cmdstanr: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macos-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release', rtools: '44'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| rtools-version: '44' | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: Install R dependencies | |
| shell: Rscript {0} | |
| run: | | |
| install.packages("SeuratObject") | |
| if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") | |
| BiocManager::install() | |
| if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") | |
| devtools::install_deps(dependencies = TRUE) | |
| - name: Install CmdStan | |
| shell: Rscript {0} | |
| run: | | |
| # TEMPORARY: Install cmdstanr from GitHub v0.9.0 for this branch | |
| if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") | |
| remotes::install_github("stan-dev/cmdstanr", ref = "v0.9.0") | |
| # ORIGINAL CRAN INSTALLATION (commented out for temporary GitHub install): | |
| # install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) | |
| cmdstanr::check_cmdstan_toolchain(fix = TRUE) | |
| cmdstanr::install_cmdstan(cores = 2) | |
| cmdstanr::cmdstan_version() | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: '"hard"' # do not install packages in Suggests | |
| cache: false | |
| extra-packages: | | |
| any::rcmdcheck | |
| any::knitr | |
| any::rmarkdown | |
| any::ggplot2 | |
| any::tibble | |
| any::dplyr | |
| any::prettydoc | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| # Build job | |
| build: | |
| runs-on: ubuntu-latest | |
| needs: workflow_with_cmdstanr | |
| if: github.event_name == 'push' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master') | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| use-public-rspm: true | |
| - name: Install R dependencies | |
| shell: Rscript {0} | |
| run: | | |
| install.packages("SeuratObject") | |
| if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") | |
| BiocManager::install() | |
| if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") | |
| devtools::install_deps(dependencies = TRUE) | |
| - name: Install CmdStan | |
| shell: Rscript {0} | |
| run: | | |
| install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) | |
| cmdstanr::check_cmdstan_toolchain(fix = TRUE) | |
| cmdstanr::install_cmdstan(cores = 2) | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: '"hard"' | |
| extra-packages: | | |
| any::pkgdown | |
| any::knitr | |
| any::rmarkdown | |
| any::ggplot2 | |
| any::tibble | |
| any::dplyr | |
| any::prettydoc | |
| - name: Build pkgdown site | |
| shell: Rscript {0} | |
| run: | | |
| pkgdown::build_site() | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: ./docs | |
| # Deploy job | |
| deploy: | |
| needs: build | |
| permissions: | |
| pages: write | |
| id-token: write | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 |