Main CI workflow #3
Workflow file for this run
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| on: | |
| schedule: | |
| - cron: "0 0 * * *" | |
| 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-22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-22.04, 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 dependencies | |
| working-directory: pharmr_repo | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| install.packages('reticulate') | |
| shell: Rscript {0} | |
| - name: Install pharmr | |
| working-directory: pharmr_repo | |
| run: | | |
| 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 | |
| run: | | |
| python3.11 -m venv pharmpy_venv | |
| source pharmpy_venv/bin/activate | |
| pip install . | |
| shell: bash | |
| - 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: Install deploy dependencies | |
| run: | | |
| install.packages("devtools") | |
| shell: Rscript {0} | |
| - name: Update DESCRIPTION and documentation | |
| working-directory: pharmr_repo/deploy | |
| run: | | |
| reticulate::use_python('../../pharmpy_repo/pharmpy_venv/bin') | |
| 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: | | |
| reticulate::py_discover_config() | |
| reticulate::use_python('../pharmpy_repo/pharmpy_venv/bin') | |
| pharmr::print_pharmpy_version() | |
| 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 | |