Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
oslerinhealth
committed
May 19, 2021
1 parent
5af9dea
commit 6bac749
Showing
5 changed files
with
353 additions
and
24 deletions.
There are no files selected for viewing
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
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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,240 @@ | ||
| on: | ||
| push: | ||
| tags: | ||
| - '*.[sc]' | ||
| workflow_dispatch: | ||
|
|
||
| name: Check | ||
| jobs: | ||
| create_release: | ||
| name: Create release | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| upload_url: ${{ steps.create_release.outputs.upload_url }} | ||
| steps: | ||
| - name: Get tag name | ||
| id: get_tag_name | ||
| run: echo ::set-output name=VERSION::${GITHUB_REF/refs\/tags\//} | ||
| - name: Attempt to Delete Release | ||
| uses: adigherman/actions/delete-release-by-tag@master | ||
| id: delete-release | ||
| with: | ||
| github_token: ${{ secrets.GITHUB_TOKEN }} | ||
| repository: ${{ github.repository }} | ||
| tag: ${{ steps.get_tag_name.outputs.VERSION }} | ||
| - name: Create release | ||
| id: create_release | ||
| uses: actions/create-release@v1 | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
| tag_name: ${{ steps.get_tag_name.outputs.VERSION }} | ||
| release_name: Neuroc Release ${{ steps.get_tag_name.outputs.VERSION }} | ||
| draft: false | ||
| prerelease: false | ||
|
|
||
| neuroconductor_check: | ||
| needs: create_release | ||
| runs-on: ${{ matrix.config.os }} | ||
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: macOS-latest, r: '3.5', r_ver: '3.5', latex: "true", vdiffr: false} | ||
| - {os: macOS-latest, r: 'oldrel', r_ver: '3.6', latex: "true", vdiffr: false} | ||
| - {os: macOS-latest, r: 'release', r_ver: '4.0', latex: "true", vdiffr: false} | ||
| - {os: macOS-latest, r: 'devel', r_ver: '4.1', latex: "true", vdiffr: false} | ||
| - {os: windows-latest, r: '3.5', r_ver: '3.5'} | ||
| - {os: windows-latest, r: 'oldrel', r_ver: '3.6'} | ||
| - {os: windows-latest, r: 'release', r_ver: '4.0'} | ||
| - {os: windows-latest, r: 'devel', r_ver: '4.1'} | ||
| - {os: ubuntu-20.04, r: '3.5', r_ver: '3.5', latex: "true", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
| - {os: ubuntu-20.04, r: 'oldrel', r_ver: '3.6', latex: "true", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
| - {os: ubuntu-20.04, r: 'release', r_ver: '4.0', latex: "true", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", coveralls: "true"} | ||
| - {os: ubuntu-20.04, r: 'devel', r_ver: '4.1', latex: "true", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
|
|
||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| TIC_DEPLOY_KEY: ${{ secrets.TIC_DEPLOY_KEY }} | ||
| RSPM: ${{ matrix.config.rspm }} | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| COVERALLS_TOKEN: ${{ secrets.COVERALLS_TOKEN }} | ||
| continue-on-error: ${{ startsWith(matrix.config.r, 'devel') }} | ||
| VDIFFR_RUN_TESTS: ${{ matrix.config.vdiffr }} | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
| - uses: r-lib/actions/setup-r@master | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
|
|
||
| - uses: r-lib/actions/setup-tinytex@master | ||
| if: matrix.config.latex == 'true' | ||
|
|
||
| - name: Install additional latex modules | ||
| if: matrix.config.latex == 'true' | ||
| run: | | ||
| tlmgr update --self | ||
| tlmgr install filecontents upquote courier courier-scaled biber biblatex collection-luatex ae thumbpdf grfext | ||
| tlmgr update --all | ||
| - uses: r-lib/actions/setup-pandoc@master | ||
|
|
||
| - name: Setup git identity | ||
| run: | | ||
| git config user.name adigherman | ||
| git config user.email adig@jhu.edu | ||
| - name: Install system dependencies (unix) | ||
| if: runner.os == 'Linux' | ||
| uses: adigherman/actions/install-sysdeps-linux@master | ||
|
|
||
| - name: Install system dependencies (macos) | ||
| if: runner.os == 'macOS' | ||
| uses: adigherman/actions/install-sysdeps-macos@master | ||
|
|
||
| - name: Setup msys2 (windows) | ||
| if: runner.os == 'Windows' | ||
| uses: msys2/setup-msys2@v2 | ||
| with: | ||
| msystem: MINGW64 | ||
| update: true | ||
| install: git mingw-w64-x86_64-toolchain | ||
|
|
||
| - name: Install system dependencies (windows) | ||
| if: runner.os == 'Windows' | ||
| uses: adigherman/actions/install-sysdeps-windows@master | ||
|
|
||
| - name: Get repo name | ||
| uses: adigherman/actions/get-repo-name@master | ||
| id: get-name | ||
| with: | ||
| github_slug: ${{ github.repository }} | ||
|
|
||
| - name: Get package version | ||
| uses: adigherman/actions/get-repo-version@master | ||
| id: get-version-number | ||
|
|
||
| - name: Get release asset info | ||
| uses: adigherman/actions/get-release-asset@master | ||
| id: get-release-asset | ||
| with: | ||
| repo_name: ${{ steps.get-name.outputs.repo_name }} | ||
| repo_version: ${{ steps.get-version-number.outputs.package_version }} | ||
| runner_os: ${{ runner.os }} | ||
| R_version: ${{ matrix.config.r_ver }} | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Cache R packages | ||
| if: runner.os != 'Windows' | ||
| uses: actions/cache@v1 | ||
| 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' | ||
| env: | ||
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | ||
| run: | | ||
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | ||
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | ||
| sudo -s eval "$sysreqs" | ||
| - name: Install helper packages | ||
| run: | | ||
| remotes::install_github("ropensci/tic") | ||
| remotes::install_github("muschellij2/ghtravis") | ||
| remotes::install_github("muschellij2/aghast") | ||
| remotes::install_cran("covr") | ||
| shell: Rscript {0} | ||
|
|
||
| # - name: Install Binaries | ||
| # run: Rscript -e "tic::before_install()" | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_cran("rcmdcheck") | ||
| remotes::install_cran("markdown") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Session info | ||
| run: | | ||
| options(width = 100) | ||
| pkgs <- installed.packages()[, "Package"] | ||
| sessioninfo::session_info(pkgs, include_base = TRUE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: "Check" | ||
| run: | | ||
| Rscript -e 'tic::script()' | ||
| ls -l check | ||
| shell: bash | ||
|
|
||
| - 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: ${{ runner.os }}-r${{ matrix.config.r }}-results | ||
| path: check | ||
|
|
||
| - name: Before Deploy | ||
| run: Rscript -e "tic::before_deploy()" | ||
|
|
||
| - name: Upload Release Asset | ||
| uses: actions/upload-release-asset@v1.0.1 | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
| upload_url: ${{ needs.create_release.outputs.upload_url }} | ||
| asset_path: ${{ steps.get-release-asset.outputs.asset_path }} | ||
| asset_name: ${{ steps.get-release-asset.outputs.asset_name }} | ||
| asset_content_type: application/octet-stream | ||
|
|
||
| - name: Deploy | ||
| run: Rscript -e "tic::deploy()" | ||
|
|
||
| - name: After Deploy | ||
| run: Rscript -e "tic::after_deploy()" | ||
|
|
||
| - name: Enable Repo on Coveralls | ||
| if: matrix.config.coveralls == 'true' | ||
| id: enable_coveralls | ||
| run: | | ||
| curl -s -H "Accept: application/json" \ | ||
| -H "Content-Type: application/json" \ | ||
| -H "Authorization: token $COVERALLS_TOKEN" \ | ||
| -d '{"repo": {"service": "github","name": "'$GITHUB_REPOSITORY'"}}' \ | ||
| -X POST https://coveralls.io/api/repos | ||
| - name: Get Coveralls Repo Token | ||
| if: matrix.config.coveralls == 'true' | ||
| id: get_coverall_repo_token | ||
| run: | | ||
| echo "COVERALLS_REPO_TOKEN=$(\ | ||
| curl -s -H "Accept: application/json" \ | ||
| -H "Content-Type: application/json" \ | ||
| -H "Authorization: token $COVERALLS_TOKEN" \ | ||
| https://coveralls.io/api/repos/github/$GITHUB_REPOSITORY \ | ||
| | jq '.token')" >> $GITHUB_ENV | ||
| - name: Generate and Upload R Package Coverage | ||
| if: matrix.config.coveralls == 'true' | ||
| continue-on-error: true | ||
| run: covr::coveralls(service_name='drone', repo_token=${{ env.COVERALLS_REPO_TOKEN }}) | ||
| shell: Rscript {0} |
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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| on: | ||
| push: | ||
| tags: | ||
| - '*.[sc]' | ||
| workflow_dispatch: | ||
|
|
||
| name: Pkgdown | ||
|
|
||
| jobs: | ||
| pkgdown: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: r-lib/actions/setup-r@master | ||
| - uses: r-lib/actions/setup-pandoc@master | ||
| - name: Setup git identity | ||
| run: | | ||
| git config user.name adigherman | ||
| git config user.email adig@jhu.edu | ||
| - name: Install system dependencies | ||
| run: | | ||
| sudo apt-get install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev | ||
| - name: Install R dependencies | ||
| run: | | ||
| install.packages("remotes") | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_dev("pkgdown") | ||
| shell: Rscript {0} | ||
| - name: Install package | ||
| run: R CMD INSTALL . | ||
| - name: Deploy package | ||
| run: pkgdown::deploy_to_branch(new_process = FALSE) | ||
| shell: Rscript {0} |
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
Oops, something went wrong.