fix import, export, and documentation #17
Workflow file for this run
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| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - main | |
| name: build_check_deploy | |
| jobs: | |
| build_check_deploy: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| NOT_CRAN: true | |
| TZ: UTC | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v1 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| # This lets us augment with additional dependencies | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
| echo "$sysreqs" | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), Ncpu = 2L) | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Install BiocCheck | |
| run: | | |
| BiocManager::install("BiocCheck") | |
| shell: Rscript {0} | |
| - name: BiocCheck | |
| run: | | |
| BiocCheck::BiocCheck(".") | |
| shell: Rscript {0} | |
| - name: R CMD check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: check-results | |
| path: check | |
| - name: Test coverage | |
| run: | | |
| install.packages("covr") | |
| covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
| shell: Rscript {0} | |
| - name: Build pkgdown | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/main' | |
| 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/main' | |
| run: | | |
| apt-get update && apt-get -y install rsync | |
| - name: Deploy 🚀 | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/main' | |
| uses: JamesIves/github-pages-deploy-action@releases/v3 | |
| with: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| BRANCH: gh-pages # The branch the action should deploy to. | |
| FOLDER: docs # The folder the action should deploy. | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Publish to Registry | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/main' | |
| uses: elgohr/Publish-Docker-Github-Action@master | |
| with: | |
| name: docker.pkg.github.com/${{ github.repository }}/TVTB:latest | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| registry: docker.pkg.github.com |