Merge branch 'devel' into extra_docs_vignette_markdownboard #377
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| 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} |