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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,74 +1,55 @@ | ||
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: main | ||
| branches: [main, master] | ||
| pull_request: | ||
| branches: [main, master] | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
| schedule: | ||
| - cron: '30 5 * * 2' | ||
|
|
||
| name: pkgdown | ||
|
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||
| jobs: | ||
| pkgdown: | ||
| runs-on: ubuntu-20.04 | ||
| runs-on: ubuntu-latest | ||
| # Only restrict concurrency for non-PR jobs | ||
| concurrency: | ||
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | ||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v1 | ||
| - uses: r-lib/actions/setup-pandoc@v2 | ||
|
|
||
| - uses: r-lib/actions/setup-pandoc@v1 | ||
|
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| - uses: r-lib/actions/setup-tinytex@v1 | ||
|
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||
| - name: Install remotes | ||
| run: | | ||
| install.packages('remotes') | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
| - name: Install udunits on Ubuntu | ||
| if: runner.os == 'Linux' | ||
| run: sudo apt-get install libudunits2-dev | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Cache R packages | ||
| uses: actions/cache@v1 | ||
| - uses: r-lib/actions/setup-r@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- | ||
| use-public-rspm: true | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| install.packages("remotes") | ||
| # To get links for homepage | ||
| remotes::install_cran("devtools") | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_dev("pkgdown") | ||
| remotes::install_github('nlmixr2/lotri') | ||
| remotes::install_github('nlmixr2/rxode2ll') | ||
| remotes::install_github("nlmixr2/rxode2parse") | ||
| remotes::install_github("nlmixr2/rxode2random") | ||
| remotes::install_github("nlmixr2/rxode2et") | ||
| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: | | ||
| any::pkgdown | ||
| nlmixr2/lotri | ||
| nlmixr2/rxode2ll | ||
| nlmixr2/rxode2parse | ||
| nlmixr2/rxode2random | ||
| nlmixr2/rxode2et | ||
| local::. | ||
| needs: website | ||
|
|
||
| - name: Build site | ||
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install package | ||
| run: R CMD INSTALL . | ||
|
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||
| - name: Deploy package | ||
| run: | | ||
| git config --local user.email "actions@github.com" | ||
| git config --local user.name "GitHub Actions" | ||
| Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' | ||
| - name: Deploy to GitHub pages 🚀 | ||
| if: github.event_name != 'pull_request' | ||
| uses: JamesIves/github-pages-deploy-action@v4.4.1 | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs |
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.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [main, master] | ||
| pull_request: | ||
| branches: [main, master] | ||
|
|
||
| name: test-coverage | ||
|
|
||
| jobs: | ||
| test-coverage: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
|
|
||
| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: | | ||
| any::covr | ||
| nlmixr2/lotri | ||
| nlmixr2/rxode2ll | ||
| nlmixr2/rxode2parse | ||
| nlmixr2/rxode2random | ||
| nlmixr2/rxode2et | ||
| nlmixr2/rxode2 | ||
| needs: coverage | ||
|
|
||
| - name: Test coverage | ||
| run: | | ||
| covr::codecov( | ||
| quiet = FALSE, | ||
| clean = FALSE, | ||
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | ||
| ) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Show testthat output | ||
| if: always() | ||
| run: | | ||
| ## -------------------------------------------------------------------- | ||
| find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
| shell: bash | ||
|
|
||
| - name: Upload test results | ||
| if: failure() | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: coverage-test-failures | ||
| path: ${{ runner.temp }}/package |