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Use Github Actions to deploy pkgdown
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‎.github/.gitignore‎

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*.html

‎.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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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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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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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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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: windows-latest, r: '3.6'}
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- {os: ubuntu-18.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.1.0 (ubuntu-18.04) R (4.1.0 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: '3.5', 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-18.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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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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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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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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- 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: Cache R packages
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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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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- 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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with:
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name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
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path: check

‎.github/workflows/pkgdown.yaml‎

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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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name: pkgdown
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jobs:
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pkgdown:
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runs-on: macOS-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$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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uses: actions/cache@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 dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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install.packages("pkgdown", type = "binary")
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shell: Rscript {0}
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- name: Install package
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run: R CMD INSTALL .
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- name: Deploy package
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run: |
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git config --local user.email "actions@github.com"
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git config --local user.name "GitHub Actions"
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Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

‎.github/workflows/pr-commands.yaml‎

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on:
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issue_comment:
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types: [created]
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name: Commands
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jobs:
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document:
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if: startsWith(github.event.comment.body, '/document')
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name: document
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runs-on: macOS-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: r-lib/actions/pr-fetch@v1
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/setup-r@v1
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- name: Install dependencies
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run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)'
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- name: Document
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run: Rscript -e 'roxygen2::roxygenise()'
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- name: commit
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run: |
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git config --local user.email "actions@github.com"
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git config --local user.name "GitHub Actions"
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git add man/\* NAMESPACE
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git commit -m 'Document'
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- uses: r-lib/actions/pr-push@v1
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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style:
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if: startsWith(github.event.comment.body, '/style')
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name: style
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runs-on: macOS-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: r-lib/actions/pr-fetch@v1
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/setup-r@v1
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- name: Install dependencies
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run: Rscript -e 'install.packages("styler")'
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- name: Style
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run: Rscript -e 'styler::style_pkg()'
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- name: commit
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run: |
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git config --local user.email "actions@github.com"
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git config --local user.name "GitHub Actions"
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git add \*.R
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git commit -m 'Style'
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- uses: r-lib/actions/pr-push@v1
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/test-coverage.yaml‎

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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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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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jobs:
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test-coverage:
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runs-on: ubuntu-18.04
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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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- 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: Cache R packages
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ubuntu-18.04-${{ 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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run: |
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pak::local_system_requirements(execute = TRUE)
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pak::pkg_system_requirements("covr", execute = TRUE)
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shell: Rscript {0}
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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("covr")
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shell: Rscript {0}
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- name: Test coverage
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run: covr::codecov()
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shell: Rscript {0}

‎.gitignore‎

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.Rproj.user
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.Rhistory
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.RData
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docs

‎_pkgdown.yml‎

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url: https://rohelab.github.io/sparseLRMatrix

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