Main CI workflow #27
Workflow file for this run
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: | |
| workflow_dispatch: | |
| workflow_call: | |
| name: Main CI workflow | |
| jobs: | |
| deploy: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-2022, r: 'release'} | |
| - {os: macOS-12, r: 'release'} | |
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout pharmr | |
| uses: actions/checkout@v3 | |
| with: | |
| path: pharmr_repo | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| working-directory: pharmr_repo | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.11" | |
| - name: Restore R package cache | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@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- | |
| - name: Install system dependencies | |
| working-directory: pharmr_repo | |
| 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 png (temporary) | |
| working-directory: pharmr_repo | |
| if: runner.os == 'Windows' | |
| run: | | |
| install.packages('png', repos='https://mran.microsoft.com/snapshot/2022-11-27') | |
| shell: Rscript {0} | |
| - name: Install R packages | |
| working-directory: pharmr_repo | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| install.packages('reticulate') | |
| install.packages('devtools') | |
| install.packages('promises') | |
| remotes::install_local(force=TRUE) | |
| shell: Rscript {0} | |
| - name: Checkout Pharmpy | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: pharmpy/pharmpy | |
| path: pharmpy_repo | |
| fetch-depth: 0 | |
| - name: Install Pharmpy in venv | |
| working-directory: pharmpy_repo | |
| if: runner.os != 'Windows' | |
| run: | | |
| python3 -m venv pharmpy_venv | |
| source pharmpy_venv/bin/activate | |
| pip install . | |
| - name: Install Pharmpy in venv | |
| working-directory: pharmpy_repo | |
| if: runner.os == 'Windows' | |
| run: | | |
| python -m venv pharmpy_venv | |
| pharmpy_venv\Scripts\activate | |
| pip install . | |
| - name: Test Pharmpy | |
| working-directory: pharmr_repo | |
| run: | | |
| reticulate::py_discover_config() | |
| reticulate::use_python('../pharmpy_repo/pharmpy_venv/bin') | |
| pharmr::print_pharmpy_version() | |
| shell: Rscript {0} | |
| - name: Update DESCRIPTION and documentation | |
| working-directory: pharmr_repo/deploy | |
| run: | | |
| reticulate::py_run_file('build_functions.py') | |
| devtools::document() | |
| shell: Rscript {0} | |
| - name: Check | |
| working-directory: pharmr_repo | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | |
| rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: results-cran | |
| path: check | |