Changes needed for rOpenSci submission

.Rbuildignore

@@ -15,3 +15,4 @@
 
 
 
+^codemeta\.json$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,71 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: Update Homebrew
+        if: matrix.config.os == 'macos-latest'
+        run: brew update
+
+      - name: Install Dependencies
+        if: matrix.config.os == 'macos-latest'
+        run: |
+          brew install gcc
+          brew install qpdf
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - name: Check R package (macOS and Linux)
+        if: matrix.config.os != 'windows-latest'
+        run: |
+          R CMD check --no-manual --as-cran > check.log 2>&1 || true
+          cat check.log
+          grep -q -E "WARNING" check.log && exit 1 || true
+
+      - name: Check R package (Windows)
+        if: matrix.config.os == 'windows-latest'
+        shell: cmd
+        run: |
+          R CMD check --no-manual --as-cran > check.log 2>&1 || true
+          type check.log
+          findstr /i "WARNING" check.log && exit 1 || true

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

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

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# The action runs when:
+# - A new release is published
+# - The DESCRIPTION or inst/CITATION are modified
+# - Can be run manually
+# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+  release:
+    types: [published]
+  push:
+    branches: [master, main]
+    paths:
+      - DESCRIPTION
+      - inst/CITATION
+  workflow_dispatch:
+
+name: Update CITATION.cff
+
+jobs:
+  update-citation-cff:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::cffr
+            any::V8
+
+      - name: Update CITATION.cff
+        run: |
+
+          library(cffr)
+
+          # Customize with your own code
+          # See https://docs.ropensci.org/cffr/articles/cffr.html
+
+          # Write your own keys
+          mykeys <- list()
+
+          # Create your CITATION.cff file
+          cff_write(keys = mykeys)
+
+        shell: Rscript {0}
+
+      - name: Commit results
+        run: |
+          git config --local user.name "github-actions[bot]"
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add CITATION.cff
+          git commit -m 'Update CITATION.cff' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"
+
+
+

DESCRIPTION

@@ -2,16 +2,26 @@ Type: Package
 Package: browseMetadata
 Title: Browse and categorise health metadata
 Version: 1.2.2
-Authors@R: 
-    person("Rachael", "Stickland", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-3398-4272"))
+Authors@R: c(
+    person("Rachael", "Stickland", , "[email protected]", 
+    role = c("aut", "cre"),
+    comment = c(ORCID = "0000-0003-3398-4272")),
+    person("Batool", "Almarzouq", , , role = "ctb",
+    comment = c(ORCID = "0000-0002-3905-2751")),
+    person("Mahwish", "Mohammad", , , role = "ctb",
+    comment = c(ORCID = "0009-0004-5295-0726")),
+    person("Daniel", "Delbarre", , , role = "ctb",
+    comment = c(ORCID = "0000-0003-4633-4252")),
+    person("Nida", "Ziauddeen", , , role = "ctb",
+    comment = c(ORCID = "0000-0002-8964-5029"))
+    )
 Maintainer: Rachael Stickland <[email protected]>
-Description: This R package helps a researcher browse datasets in SAIL databank. 
- It has scope to be applied to other health datasets. 
- It is useful in the earlier stages of a project; prior to data access, 
- researchers can use the metadata to browse and categorise variables.
+Description: Visualise and categorise publicly available metadata from health 
+  datasets. By interacting with metadata prior to gaining full access to health 
+  datasets, researchers can use this tool to browse datasets and categorise 
+  variables.
 License: GPL (>= 3)
-URL: https://aim-rsf.github.io/browseMetadata
+URL: https://aim-rsf.github.io/browseMetadata/
 Depends: 
     R (>= 2.10)
 Imports: 
@@ -21,7 +31,7 @@ Imports:
     gridExtra,
     htmlwidgets,
     plotly,
-    rjson,
+    jsonlite,
     tidyr
 Suggests: 
     knitr,

NAMESPACE

@@ -1,9 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
-export(browseMetadata)
-export(mapMetadata)
-export(mapMetadata_compare_outputs)
-export(mapMetadata_convert_outputs)
+export(browse_metadata)
+export(map_metadata)
+export(map_metadata_compare)
+export(map_metadata_convert)
 import(ggplot2)
 importFrom(cli,cli_alert_danger)
 importFrom(cli,cli_alert_info)
@@ -27,9 +27,9 @@ importFrom(graphics,plot.new)
 importFrom(gridExtra,grid.arrange)
 importFrom(gridExtra,tableGrob)
 importFrom(htmlwidgets,saveWidget)
+importFrom(jsonlite,fromJSON)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)
-importFrom(rjson,fromJSON)
 importFrom(stats,reorder)
 importFrom(tidyr,complete)
 importFrom(tidyr,pivot_longer)

R/browseMetadata-package.R

@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL