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Merge pull request #320 from rstudio/zh-launcher-submit-job-resource-profile
Add support for setting resource profile in `rstudioapi::launcherSubmitJob`
2 parents 68b315e + 2db61ea commit fba4729

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‎.github/workflows/R-CMD-check.yaml‎

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# NOTE: This workflow is overkill for most R packages
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# check-standard.yaml is likely a better choice
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# usethis::use_github_action("check-standard") will install it.
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#
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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
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# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches:
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- main
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- master
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branches: [main, master]
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pull_request:
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branches:
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- main
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- master
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name: R-CMD-check
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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fail-fast: false
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matrix:
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config:
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- {os: macOS-latest, r: 'release'}
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: windows-latest, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/latest"}
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- {os: ubuntu-18.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
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- {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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id: install-r
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Install pak and query dependencies
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run: |
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install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
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saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
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shell: Rscript {0}
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- name: Restore R package cache
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uses: actions/cache@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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path: |
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${{ env.R_LIBS_USER }}/*
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!${{ env.R_LIBS_USER }}/pak
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key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
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restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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pak::local_system_requirements(execute = TRUE)
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pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
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shell: Rscript {0}
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extra-packages: any::rcmdcheck
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needs: check
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- name: Install dependencies
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run: |
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pak::local_install_dev_deps(upgrade = TRUE)
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pak::pkg_install("rcmdcheck")
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shell: Rscript {0}
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- name: Session info
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run: |
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options(width = 100)
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pkgs <- installed.packages()[, "Package"]
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sessioninfo::session_info(pkgs, include_base = TRUE)
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shell: Rscript {0}
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- name: Check
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env:
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_R_CHECK_CRAN_INCOMING_: false
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- name: Show testthat output
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if: always()
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run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@main
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- uses: r-lib/actions/check-r-package@v2
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with:
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name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
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path: check
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- name: Don't use tar from old Rtools to store the cache
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if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
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shell: bash
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run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH
50+
upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/test-coverage.yaml‎

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@@ -1,56 +1,62 @@
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches:
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- main
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- master
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branches: [main, master]
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pull_request:
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branches:
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- main
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- master
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name: test-coverage
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: ubuntu-18.04
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runs-on: ubuntu-latest
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env:
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RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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id: install-r
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- uses: actions/checkout@v4
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- name: Install pak and query dependencies
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run: |
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install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
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saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
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shell: Rscript {0}
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Restore R package cache
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uses: actions/cache@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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path: |
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${{ env.R_LIBS_USER }}/*
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!${{ env.R_LIBS_USER }}/pak
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key: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
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restore-keys: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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extra-packages: any::covr, any::xml2
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needs: coverage
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30+
- name: Test coverage
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run: |
44-
pak::local_system_requirements(execute = TRUE)
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pak::pkg_system_requirements("covr", execute = TRUE)
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
36+
)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- name: Install dependencies
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- uses: codecov/codecov-action@v5
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
4952
run: |
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pak::local_install_dev_deps(upgrade = TRUE)
51-
pak::pkg_install("covr")
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shell: Rscript {0}
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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54-
- name: Test coverage
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run: covr::codecov()
56-
shell: Rscript {0}
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎DESCRIPTION‎

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@@ -16,7 +16,7 @@ URL: https://rstudio.github.io/rstudioapi/,
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https://github.com/rstudio/rstudioapi
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BugReports: https://github.com/rstudio/rstudioapi/issues
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2
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RoxygenNote: 7.3.3
2020
Suggests:
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testthat,
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knitr,

‎R/code.R‎

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@@ -126,9 +126,11 @@ callFun <- function(fname, ...) {
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# drop arguments that aren't accepted by RStudio
127127
# (ensure backwards-compatibility with older versions of RStudio)
128128
args <- list(...)
129-
if (!"..." %in% names(formals(f)))
129+
if (!"..." %in% names(formals(f))) {
130+
args <- checkApiArguments(fname, f, args)
130131
if (length(args) > length(formals(f)))
131132
length(args) <- length(formals(f))
133+
}
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133135
# invoke the function
134136
do.call(f, args)
@@ -183,7 +185,7 @@ usingTools <- function() {
183185
}
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185187
toolsName <- function(name) {
186-
paste(".rs.api.", name, sep="")
188+
paste(".rs.api.", name, sep = "")
187189
}
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189191
toolsEnv <- function() {

‎R/launcher-functions.R‎

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Original file line numberDiff line numberDiff line change
@@ -296,6 +296,9 @@ launcherNfsMount <- function(host,
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#' @param resourceLimits A list of resource limits. See
297297
#' \code{\link[=launcherResourceLimit]{launcherResourceLimit()}} for more
298298
#' information.
299+
#'
300+
#' @param resourceProfile A resource profile name to be used for the job. The
301+
#' resource profile must be defined in the cluster configuration.
299302
#'
300303
#' @param queues A list of available submission queues for the cluster. Only
301304
#' applicable to batch systems like LSF.
@@ -329,6 +332,7 @@ launcherSubmitJob <- function(name,
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mounts = NULL,
330333
placementConstraints = NULL,
331334
resourceLimits = NULL,
335+
resourceProfile = NULL,
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queues = NULL,
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334338
config = NULL,
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placementConstraints = placementConstraints,
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queues = queues,
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resourceLimits = resourceLimits,
358+
resourceProfile = resourceProfile,
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stderrFile = stderrFile,
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stdin = stdin,
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stdoutFile = stdoutFile,

‎R/utils.R‎

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rendered
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1919
}
20+
21+
checkApiArguments <- function(fname, f, args) {
22+
23+
# allow opt-out just in case
24+
enabled <- getOption("rstudioapi.checkApiArguments", default = TRUE)
25+
if (identical(enabled, FALSE))
26+
return(args)
27+
28+
# check for arguments supplied by the user that aren't available
29+
# in the current version of RStudio
30+
unsupportedArgNames <- setdiff(names(args), names(formals(f)))
31+
if (length(unsupportedArgNames) == 0L)
32+
return(args)
33+
34+
# check which of these arguments is NULL; if all arguments are NULL,
35+
# then we accept the call
36+
isNullArg <- vapply(args[unsupportedArgNames], is.null, FUN.VALUE = logical(1))
37+
badArgNames <- names(isNullArg)[!isNullArg]
38+
if (length(badArgNames) == 0L) {
39+
args[unsupportedArgNames] <- NULL
40+
return(args)
41+
}
42+
43+
# if we get here, the user tried to supply a value for a parameter that isn't
44+
# supported in this version of RStudio; emit an error
45+
fmt <- ifelse(
46+
length(badArgNames) == 1L,
47+
"Parameter %s is not supported by %s in this version of RStudio.",
48+
"Parameters %s are not supported by %s in this version of RStudio."
49+
)
50+
51+
msg <- sprintf(fmt, paste(shQuote(badArgNames), collapse = ", "), shQuote(fname))
52+
stop(msg, call. = FALSE)
53+
54+
}

‎README.Rmd‎

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<!-- badges: start -->
2020
[![CRAN status](https://www.r-pkg.org/badges/version/rstudioapi)](https://CRAN.R-project.org/package=rstudioapi)
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[![Codecov test coverage](https://codecov.io/gh/rstudio/rstudioapi/branch/main/graph/badge.svg)](https://app.codecov.io/gh/rstudio/rstudioapi?branch=main)
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[![R-CMD-check](https://github.com/rstudio/rstudioapi/workflows/R-CMD-check/badge.svg)](https://github.com/rstudio/rstudioapi/actions)
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[![R-CMD-check](https://github.com/rstudio/rstudioapi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rstudio/rstudioapi/actions/workflows/R-CMD-check.yaml)
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[![Codecov test coverage](https://codecov.io/gh/rstudio/rstudioapi/graph/badge.svg)](https://app.codecov.io/gh/rstudio/rstudioapi)
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<!-- badges: end -->
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The `rstudioapi` package is designed to make it easy to conditionally access the

‎README.md‎

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status](https://www.r-pkg.org/badges/version/rstudioapi)](https://CRAN.R-project.org/package=rstudioapi)
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[![Codecov test
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coverage](https://codecov.io/gh/rstudio/rstudioapi/branch/main/graph/badge.svg)](https://app.codecov.io/gh/rstudio/rstudioapi?branch=main)
12-
[![R-CMD-check](https://github.com/rstudio/rstudioapi/workflows/R-CMD-check/badge.svg)](https://github.com/rstudio/rstudioapi/actions)
12+
[![R-CMD-check](https://github.com/rstudio/rstudioapi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rstudio/rstudioapi/actions/workflows/R-CMD-check.yaml)
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<!-- badges: end -->
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The `rstudioapi` package is designed to make it easy to conditionally

‎man/launcherSubmitJob.Rd‎

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‎vignettes/r-session.Rmd‎

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---
2-
title: "Interacting with the R Session"
2+
title: "Interact with the R Session"
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output: rmarkdown::html_vignette
44
vignette: >
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%\VignetteIndexEntry{Interact with the R Session}

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