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Merge pull request #82 from rsquaredacademy/develop
Migrations
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‎.github/workflows/R-CMD-check.yaml

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@@ -1,16 +1,14 @@
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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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- master
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- develop
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branches: [master, develop]
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pull_request:
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branches:
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- master
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- develop
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branches: [master, develop]
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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:
@@ -22,63 +20,33 @@ jobs:
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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: windows-latest, r: 'release'}
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- {os: macOS-latest, r: 'release'}
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- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/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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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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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@v1
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows'
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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: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/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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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("rcmdcheck")
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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_REMOTE_: false
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run: 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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extra-packages: any::rcmdcheck
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needs: check
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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: ${{ runner.os }}-r${{ matrix.config.r }}-results
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path: check
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upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/rhub.yaml

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# R-hub's generic GitHub Actions workflow file. It's canonical location is at
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# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
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# You can update this file to a newer version using the rhub2 package:
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#
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# rhub::rhub_setup()
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#
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# It is unlikely that you need to modify this file manually.
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name: R-hub
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run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
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on:
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workflow_dispatch:
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inputs:
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config:
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description: 'A comma separated list of R-hub platforms to use.'
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type: string
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default: 'linux,windows,macos'
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name:
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description: 'Run name. You can leave this empty now.'
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type: string
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id:
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description: 'Unique ID. You can leave this empty now.'
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type: string
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jobs:
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setup:
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runs-on: ubuntu-latest
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outputs:
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containers: ${{ steps.rhub-setup.outputs.containers }}
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platforms: ${{ steps.rhub-setup.outputs.platforms }}
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steps:
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# NO NEED TO CHECKOUT HERE
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- uses: r-hub/actions/setup@v1
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with:
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config: ${{ github.event.inputs.config }}
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id: rhub-setup
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linux-containers:
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needs: setup
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if: ${{ needs.setup.outputs.containers != '[]' }}
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runs-on: ubuntu-latest
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name: ${{ matrix.config.label }}
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strategy:
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fail-fast: false
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matrix:
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config: ${{ fromJson(needs.setup.outputs.containers) }}
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container:
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image: ${{ matrix.config.container }}
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steps:
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- uses: r-hub/actions/checkout@v1
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- uses: r-hub/actions/platform-info@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/setup-deps@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/run-check@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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other-platforms:
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needs: setup
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if: ${{ needs.setup.outputs.platforms != '[]' }}
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.label }}
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strategy:
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fail-fast: false
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matrix:
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config: ${{ fromJson(needs.setup.outputs.platforms) }}
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steps:
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- uses: r-hub/actions/checkout@v1
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- uses: r-hub/actions/setup-r@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}
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- uses: r-hub/actions/platform-info@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/setup-deps@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}
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- uses: r-hub/actions/run-check@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}

‎.github/workflows/test-coverage.yaml

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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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- master
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- develop
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branches: [master, develop]
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pull_request:
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branches:
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- master
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- develop
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branches: [master, develop]
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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: macOS-latest
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v1
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-pandoc@v1
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Query dependencies
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- name: Test coverage
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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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")
37+
)
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covr::to_cobertura(cov)
3039
shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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- uses: codecov/codecov-action@v4
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
38-
39-
- name: Install dependencies
43+
fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
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file: ./cobertura.xml
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plugin: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
4051
run: |
41-
install.packages(c("remotes"))
42-
remotes::install_deps(dependencies = TRUE)
43-
remotes::install_cran("covr")
44-
shell: Rscript {0}
52+
## --------------------------------------------------------------------
53+
find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
54+
shell: bash
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- name: Test coverage
47-
run: covr::codecov()
48-
shell: Rscript {0}
56+
- 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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@@ -12,7 +12,7 @@ Depends:
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License: MIT + file LICENSE
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URL: https://rsquaredacademy.github.io/inferr/, https://github.com/rsquaredacademy/inferr
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BugReports: https://github.com/rsquaredacademy/inferr/issues
15-
Imports:
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Imports:
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data.table,
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magrittr,
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Rcpp,
@@ -22,10 +22,11 @@ Suggests:
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covr,
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knitr,
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rmarkdown,
25-
testthat,
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testthat (>= 3.0.0),
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xplorerr
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Encoding: UTF-8
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LazyData: true
2929
VignetteBuilder: knitr
30-
RoxygenNote: 7.1.1
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RoxygenNote: 7.3.2
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LinkingTo: Rcpp
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Config/testthat/edition: 3

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