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Merge pull request #140 from aim-rsf/rOpenSci
Changes needed for rOpenSci submission
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‎.Rbuildignore

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^codemeta\.json$

‎.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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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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- {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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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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- name: Update Homebrew
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if: matrix.config.os == 'macos-latest'
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run: brew update
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- name: Install Dependencies
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if: matrix.config.os == 'macos-latest'
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run: |
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brew install gcc
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brew install qpdf
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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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- name: Check R package (macOS and Linux)
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if: matrix.config.os != 'windows-latest'
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run: |
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R CMD check --no-manual --as-cran > check.log 2>&1 || true
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cat check.log
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grep -q -E "WARNING" check.log && exit 1 || true
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- name: Check R package (Windows)
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if: matrix.config.os == 'windows-latest'
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shell: cmd
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run: |
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R CMD check --no-manual --as-cran > check.log 2>&1 || true
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type check.log
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findstr /i "WARNING" check.log && exit 1 || true

‎.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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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v4
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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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file: ./cobertura.xml
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plugin: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ 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

‎.github/workflows/update-citation-cff.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
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# The action runs when:
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# - A new release is published
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# - The DESCRIPTION or inst/CITATION are modified
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# - Can be run manually
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# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
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on:
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release:
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types: [published]
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push:
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branches: [master, main]
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paths:
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- DESCRIPTION
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- inst/CITATION
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workflow_dispatch:
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name: Update CITATION.cff
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jobs:
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update-citation-cff:
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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@v3
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- uses: r-lib/actions/setup-r@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::cffr
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any::V8
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- name: Update CITATION.cff
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run: |
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library(cffr)
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# Customize with your own code
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# See https://docs.ropensci.org/cffr/articles/cffr.html
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# Write your own keys
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mykeys <- list()
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# Create your CITATION.cff file
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cff_write(keys = mykeys)
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shell: Rscript {0}
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- name: Commit results
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run: |
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git config --local user.name "github-actions[bot]"
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git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
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git add CITATION.cff
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git commit -m 'Update CITATION.cff' || echo "No changes to commit"
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git push origin || echo "No changes to commit"
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‎DESCRIPTION

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Package: browseMetadata
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Title: Browse and categorise health metadata
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Version: 1.2.2
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Authors@R:
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person("Rachael", "Stickland", , "rstickland@turing.ac.uk", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0003-3398-4272"))
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Authors@R: c(
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person("Rachael", "Stickland", , "rstickland@turing.ac.uk",
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role = c("aut", "cre"),
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comment = c(ORCID = "0000-0003-3398-4272")),
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person("Batool", "Almarzouq", , , role = "ctb",
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comment = c(ORCID = "0000-0002-3905-2751")),
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person("Mahwish", "Mohammad", , , role = "ctb",
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comment = c(ORCID = "0009-0004-5295-0726")),
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person("Daniel", "Delbarre", , , role = "ctb",
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comment = c(ORCID = "0000-0003-4633-4252")),
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person("Nida", "Ziauddeen", , , role = "ctb",
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comment = c(ORCID = "0000-0002-8964-5029"))
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)
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Maintainer: Rachael Stickland <rstickland@turing.ac.uk>
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Description: This R package helps a researcher browse datasets in SAIL databank.
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It has scope to be applied to other health datasets.
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It is useful in the earlier stages of a project; prior to data access,
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researchers can use the metadata to browse and categorise variables.
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Description: Visualise and categorise publicly available metadata from health
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datasets. By interacting with metadata prior to gaining full access to health
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datasets, researchers can use this tool to browse datasets and categorise
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variables.
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License: GPL (>= 3)
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URL: https://aim-rsf.github.io/browseMetadata
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URL: https://aim-rsf.github.io/browseMetadata/
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Depends:
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R (>= 2.10)
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Imports:
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gridExtra,
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htmlwidgets,
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plotly,
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rjson,
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jsonlite,
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tidyr
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Suggests:
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knitr,

‎NAMESPACE

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# Generated by roxygen2: do not edit by hand
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export(browseMetadata)
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export(mapMetadata)
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export(mapMetadata_compare_outputs)
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export(mapMetadata_convert_outputs)
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export(browse_metadata)
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export(map_metadata)
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export(map_metadata_compare)
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export(map_metadata_convert)
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import(ggplot2)
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importFrom(cli,cli_alert_danger)
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importFrom(cli,cli_alert_info)
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importFrom(gridExtra,grid.arrange)
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importFrom(gridExtra,tableGrob)
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importFrom(htmlwidgets,saveWidget)
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importFrom(jsonlite,fromJSON)
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importFrom(plotly,layout)
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importFrom(plotly,plot_ly)
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importFrom(rjson,fromJSON)
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importFrom(stats,reorder)
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importFrom(tidyr,complete)
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importFrom(tidyr,pivot_longer)

‎R/browseMetadata-package.R

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#' @keywords internal
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"_PACKAGE"
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## usethis namespace: start
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## usethis namespace: end
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NULL

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