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Merge pull request #2 from villegar/main
Experimental RO-crate R package
2 parents 56bf35d + 25fb7f1 commit 810499a

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‎.Rbuildignore‎

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^.*\.Rproj$
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^\.Rproj\.user$
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^\.github$
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^codecov.yml$
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^cran-comments.md$
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^README.Rmd$
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^LICENSE.md$

‎.github/.gitignore‎

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*.html

‎.github/workflows/R-CMD-check.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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#
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# NOTE: This workflow is overkill for most R packages and
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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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on:
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push:
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branches: [main, master]
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pull_request:
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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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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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# use 4.0 or 4.1 to check with rtools40's older compiler
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- {os: windows-latest, r: 'oldrel-4'}
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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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- {os: ubuntu-latest, r: 'oldrel-2'}
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- {os: ubuntu-latest, r: 'oldrel-3'}
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- {os: ubuntu-latest, r: 'oldrel-4'}
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env:
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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@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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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-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/pkgdown.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: [main, master]
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pull_request:
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown.yaml
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permissions: read-all
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jobs:
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pkgdown:
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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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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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::pkgdown, local::.
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needs: website
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/github-pages-deploy-action@v4.5.0
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with:
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clean: false
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branch: gh-pages
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folder: docs

‎.github/workflows/pr-commands.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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issue_comment:
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types: [created]
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name: pr-commands.yaml
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permissions: read-all
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jobs:
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document:
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if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
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name: document
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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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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/pr-fetch@v2
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::roxygen2
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needs: pr-document
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- name: Document
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run: roxygen2::roxygenise()
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shell: Rscript {0}
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- name: commit
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run: |
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
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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@v2
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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style:
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if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
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name: style
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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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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/pr-fetch@v2
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/setup-r@v2
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- name: Install dependencies
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run: install.packages("styler")
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shell: Rscript {0}
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- name: Style
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run: styler::style_pkg()
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shell: Rscript {0}
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- name: commit
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run: |
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
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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@v2
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with:
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repo-token: ${{ secrets.GITHUB_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: [main, master]
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pull_request:
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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-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@v4
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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-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: Test coverage
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run: |
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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")
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)
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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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- 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: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- 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

‎.gitignore‎

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# RStudio Connect folder
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rsconnect/
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.Rproj.user

‎DESCRIPTION‎

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Package: rocrateR
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Title: RO-Crate R Package Wrapper
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Version: 0.0.1.9000
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Authors@R: c(
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person(given = "Roberto",
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family = "Villegas-Diaz",
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role = c("aut", "cre"),
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email = "r.villegas-diaz@outlook.com",
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comment = c(ORCID = "0000-0001-5036-8661")),
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person("Research Object community", role = c("cph")))
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Description: R package for creating, manipulating and reading RO-Crates. Latest
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supported version 1.2 of the specification.
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License: MIT + file LICENSE
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Suggests:
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testthat (>= 3.0.0)
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Config/testthat/edition: 3
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Encoding: UTF-8
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Language: en-GB
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2
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Imports:
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jsonlite,
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tibble

‎LICENSE‎

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MIT License
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Copyright (c) 2024 Research Object community
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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YEAR: 2025
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COPYRIGHT HOLDER: Research Object community

‎LICENSE.md‎

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# MIT License
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Copyright (c) 2025 Research Object community
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

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