build_check_deploy #389
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 | |
| pull_request: | |
| branches: | |
| - devel | |
| schedule: | |
| - cron: '0 8 * * 5' | |
| name: build_check_deploy | |
| jobs: | |
| build_check_deploy: | |
| runs-on: ubuntu-latest | |
| container: iseedevelopers/iseeu:latest | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v1 | |
| - name: Install dependencies | |
| run: | | |
| dependencies <- remotes::local_package_deps(dependencies = TRUE) | |
| leftovers <- setdiff(dependencies, installed.packages()) | |
| BiocManager::install(leftovers, ask=FALSE, Ncpu=2L) | |
| remotes::install_cran("rcmdcheck") | |
| BiocManager::install("iSEE/iSEE") | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: BiocCheck | |
| run: | | |
| BiocManager::install("BiocCheck") | |
| BiocCheck::BiocCheck(".") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: check-results | |
| path: check | |
| - name: Test coverage | |
| run: | | |
| install.packages("covr") | |
| covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
| shell: Rscript {0} | |
| - name: Build pkgdown | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/devel' | |
| run: | | |
| PATH=$PATH:$HOME/bin/ Rscript -e 'BiocManager::install("pkgdown"); pkgdown::build_site(".")' | |
| # deploy needs rsync? Seems so. | |
| - name: Install deploy dependencies | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/devel' | |
| run: | | |
| apt-get update && apt-get -y install rsync | |
| - name: Deploy 🚀 | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/devel' | |
| uses: JamesIves/github-pages-deploy-action@releases/v3 | |
| with: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| BRANCH: gh-pages # The branch the action should deploy to. | |
| FOLDER: docs # The folder the action should deploy. | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} |