R-CMD-check #361
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| - 'feature/**' | |
| - 'bug_fix/**' | |
| - 'bugfix/**' | |
| - 'maint/**' | |
| schedule: | |
| # run release on the 8th of every month to detect problems with new packages/R releases | |
| - cron: '19 3 8 * *' | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| services: | |
| postgres: | |
| image: postgres | |
| env: | |
| POSTGRES_DB: RamsesDB | |
| POSTGRES_USER: user | |
| POSTGRES_PASSWORD: password | |
| ports: | |
| - 5432:5432 | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # container action is not supported on windows or macOS | |
| # - {os: windows-latest, r: 'release'} | |
| # - {os: macOS-latest, r: 'release'} | |
| - {os: ubuntu-20.04, r: '4.0.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CODECOVETOKEN: ${{ secrets.CODECOVETOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| install.packages('devtools') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_github("msberends/AMR", build = TRUE) | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: | | |
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Code coverage | |
| if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| run: covr::codecov(type = "all", quiet = FALSE, token = Sys.getenv("CODECOVETOKEN")) | |
| shell: Rscript {0} | |
| - name: Build pkgdown | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| run: pkgdown::build_site(new_process = TRUE) | |
| shell: Rscript {0} | |
| - name: Deploy to Firebase | |
| if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| uses: FirebaseExtended/action-hosting-deploy@v0 | |
| with: | |
| repoToken: '${{ secrets.GITHUB_TOKEN }}' | |
| firebaseServiceAccount: '${{ secrets.FIREBASE_SERVICE_ACCOUNT_RAMSES_ANTIBIOTICS }}' | |
| projectId: ramses-antibiotics | |
| channelId: live | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| - name: Install TeX | |
| run: tlmgr --version | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| - name: Build source and PDF manual | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| run: | | |
| devtools::install() | |
| devtools::build(".", vignettes = TRUE, path = "~") | |
| devtools::build_manual(".", path = "~") | |
| shell: Rscript {0} | |
| - uses: actions/upload-artifact@v3 | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| with: | |
| name: Ramses package source | |
| path: ~/Ramses_[0-9].[0-9].[0-9].tar.gz | |
| - uses: actions/upload-artifact@v3 | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| with: | |
| name: Ramses package manual | |
| path: ~/Ramses_[0-9].[0-9].[0-9].pdf |