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mrustlmrustl
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Merge pull request #15 from KWB-R/dev
Release v0.2.0
2 parents 76ee94d + c0eb00a commit a170fb4

29 files changed

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‎.Rbuildignore‎

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^index\.md$
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^README\.md$
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^R/\.setup\.R
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^\.github$

‎.github/workflows/R-CMD-check.yaml‎

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on:
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push:
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branches:
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- master
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- main
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- dev
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pull_request:
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branches:
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- master
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- main
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- dev
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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: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: windows-latest, r: 'devel'}
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- {os: windows-latest, r: 'oldrel'}
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- {os: windows-latest, r: 'release'}
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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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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@master
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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), "depends.Rds", version = 2)
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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@v1
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('depends.Rds') }}
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restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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env:
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RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
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run: |
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Rscript -e "remotes::install_github('r-hub/sysreqs')"
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sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
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sudo -s eval "$sysreqs"
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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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run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@master
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with:
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name: ${{ runner.os }}-r${{ 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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- dev
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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: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$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@master
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/setup-r@master
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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 add man/\* NAMESPACE
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git commit -m 'Document'
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- uses: r-lib/actions/pr-push@master
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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@master
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/setup-r@master
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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 add \*.R
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git commit -m 'Style'
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- uses: r-lib/actions/pr-push@master
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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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- master
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- main
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pull_request:
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branches:
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- master
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- main
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name: test-coverage
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jobs:
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test-coverage:
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runs-on: macOS-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$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@v1
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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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install.packages(c("remotes"))
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("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}

‎.travis.yml‎

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‎DESCRIPTION‎

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Package: kwb.endnote
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Title: Helper Functions for Analysing KWB Endnote Library
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(Exported as .xml)
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Version: 0.1.0
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Version: 0.2.0
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Authors@R:
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c(person(given = "Michael",
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family = "Rustler",
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role = "ctb",
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email = "hauke.sonnenberg@kompetenz-wasser.de",
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comment = c(ORCID = "0000-0001-9134-2871")),
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person(given = "FAKIN",
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role = "fnd"),
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person(given = "Kompetenzzentrum Wasser Berlin gGmbH (KWB)",
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role = "cph"))
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Description: Helper Functions For Analysing KWB Endnote Library
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tibble,
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tidyr,
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wordcloud2,
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xml2
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xml2,
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plotly
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Suggests:
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covr,
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knitr,
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github::kwb-r/kwb.utils
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 6.1.1
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RoxygenNote: 7.1.1
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VignetteBuilder: knitr

‎NEWS.md‎

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# kwb.endnote 0.0.0.9000
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* Move to GitHub Actions as CI (from Travis/Appveyor)
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* Added a `NEWS.md` file to track changes to the package.
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* see https://style.tidyverse.org/news.html for writing a good `NEWS.md`

‎R/check_for_differences.R‎

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#' ### Check differences between two different versions of "KWB_documents.xml"
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#' ############################################################################
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#'
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#' old_xml <- extdata_file("2019-01-14_KWB_documents.xml")
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#' new_xml <- extdata_file("2019-07-09_KWB_documents.xml")
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#' old_xml <- extdata_file("2020-05-25_KWB-documents.xml")
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#' new_xml <- extdata_file("2020-06-17_KWB-documents.xml")
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#' old_list <- kwb.endnote::create_endnote_list(old_xml)
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#' new_list <- kwb.endnote::create_endnote_list(new_xml)
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#' old_df <- kwb.endnote::create_references_df(old_list)

‎R/create_references_df_from_list.R‎

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# colbind: Wrapper around dplyr::bind_cols(). Makes sure that no rows get lost
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# if the data frame to add has no rows.
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colbind <- function(df, df_2) {
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if (nrow(df_2) == 0L) {
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# Return the original data frame if the data frame to add has no columns
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if (ncol(df_2) == 0L) {
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return(df)
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}
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# Give the data frame to add one empty row (full of NA)
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df_2 <- df_2[1L, ]
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}
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dplyr::bind_cols(df, df_2)
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}
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#' @noRd
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#' @keywords internal
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null_to_na <- function(x, na_fill = NA_character_) {
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collapse_val = "",
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element = 1)
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}
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replace_newline_with_semicolon <- function(text) {
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gsub("\r", ", ", text)
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}
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get_titles_style <- function(path) get_style(c("titles", path))
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get_period_style <- function(path) get_style(c("periodical", path))
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get_dates_style <- function(path) get_style(c("dates", path))
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ref_type_name = attr(get_record_entry("ref-type"), which = "name"),
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abstract = get_abstract(record_list, collapse)
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) %>%
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dplyr::bind_cols(get_keywords(record_list, collapse = collapse)) %>%
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dplyr::bind_cols(get_authors(record_list, collapse = collapse)) %>%
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dplyr::bind_cols(get_secondary_authors(record_list, collapse = collapse)) %>%
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dplyr::bind_cols(get_tertiary_authors(record_list, collapse = collapse)) %>%
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dplyr::bind_cols(
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colbind(get_keywords(record_list, collapse = collapse)) %>%
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colbind(get_authors(record_list, collapse = collapse)) %>%
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colbind(get_secondary_authors(record_list, collapse = collapse)) %>%
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colbind(get_tertiary_authors(record_list, collapse = collapse)) %>%
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colbind(
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tibble::tibble(
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database_name = get_record_entry("database")[[1]],
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database_path = attr(get_record_entry("database"), which = "path"),
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authaddress = get_style("auth-address"),
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edition = get_style("edition"),
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worktype = get_style("work-type"),
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label = get_style("label"),
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label = replace_newline_with_semicolon(get_style("label")),
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isbn = get_style("isbn"),
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language = get_style("language")
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language = replace_newline_with_semicolon(get_style("language"))
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)
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) %>%
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dplyr::bind_cols(get_pdfurls(record_list, collapse = collapse)) %>%
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dplyr::bind_cols(tibble::tibble(
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colbind(get_pdfurls(record_list, collapse = collapse)) %>%
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colbind(tibble::tibble(
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urls_related = get_style(c("urls", "related-urls", "url")),
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electronic_resource_num = get_style("electronic-resource-num"),
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custom1 = get_style("custom1"),

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