Review pass: citation files with the Zenodo DOI, site from gh-pages, CI on dev, version 1.0.2

.Rbuildignore

@@ -10,3 +10,6 @@
 ^\.github$
 ^doc$
 ^Meta$
+^CITATION\.cff$
+^vignettes/articles$
+^Python$

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

@@ -1,13 +1,15 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# R CMD check on every push and pull request, written by washr::setup_ci().
+# Derived from https://github.com/r-lib/actions/tree/v2/examples (check-standard),
+# with the dev branch in the triggers as the openwashdata review standard requires.
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
+    branches: [main, master, dev]
+  workflow_dispatch:
 
-name: R-CMD-check.yaml
-
-permissions: read-all
+name: R-CMD-check
 
 jobs:
   R-CMD-check:
@@ -48,4 +50,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          build_args: 'c("--no-manual")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,47 @@
+# 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:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -6,3 +6,4 @@
 inst/doc
 /doc/
 /Meta/
+docs

CITATION.cff

@@ -1,15 +1,15 @@
-# --------------------------------------------
-# CITATION file created with {cffr} R package
+# ------------------------------------------------
+# CITATION.cff file created with {cffr} R package
 # See also: https://docs.ropensci.org/cffr/
-# --------------------------------------------
+# ------------------------------------------------
 
 cff-version: 1.2.0
 message: 'To cite package "glossarywho" in publications use:'
-type: software
+type: dataset
 license: CC-BY-4.0
 title: 'glossarywho: WHO Glossary'
-version: 0.1.0
-doi: 10.5281/zenodo.14754017
+version: 1.0.2
+doi: 10.5281/zenodo.14754016
 abstract: This package provides access to a tidy version of the WHO Glossary (https://www.who.int/publications/i/item/9789240105485)
   and thematic areas for each term.
 authors:
@@ -18,11 +18,20 @@ authors:
   email: ydubey@ethz.ch
   orcid: https://orcid.org/0009-0001-2849-970X
 repository-code: https://github.com/openwashdata/glossarywho
-url: https://github.com/openwashdata/glossarywho
+url: https://openwashdata.github.io/glossarywho/
 date-released: '2025-01-28'
 contact:
 - family-names: Dubey
   given-names: Yash
   email: ydubey@ethz.ch
   orcid: https://orcid.org/0009-0001-2849-970X
+keywords:
+- open data
+- washdata
+- glossary
+- health data
+- health statistics
+- public health indicators
+- data governance
+- WHO
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: glossarywho
 Type: Package
 Title: WHO Glossary
-Version: 0.1.0
+Version: 1.0.2
 Authors@R: c(
     person("Yash", "Dubey", , "ydubey@ethz.ch", role = c("cre", "aut"),
            comment = c(ORCID = "0009-0001-2849-970X"))
@@ -14,11 +14,14 @@ Depends:
     R (>= 3.5)
 RoxygenNote: 7.3.2
 Language: en-GB
-Config/Needs/website: rmarkdown
+Config/Needs/website: rmarkdown, dplyr, readr, stringr, gt, kableExtra, ggplot2, tidyverse, wordcloud, tm
 Date: 2025-01-28
 URL: https://openwashdata.github.io/glossarywho/, https://github.com/openwashdata/glossarywho
 BugReports: https://github.com/openwashdata/glossarywho/issues
 Suggests: 
     knitr,
     rmarkdown
 VignetteBuilder: knitr
+X-schema.org-keywords: open data, washdata, glossary, health data, health statistics, public health indicators, data governance, WHO
+X-schema.org-spatialCoverage: Global
+X-schema.org-temporalCoverage: 2025-01-01/2025-12-31

NEWS.md

@@ -0,0 +1,11 @@
+# glossarywho 1.0.2
+
+* Metadata-only patch after the v1.0.1 Zenodo record, which was cut while DESCRIPTION still said 0.1.0. CITATION.cff and inst/CITATION carry the Zenodo concept DOI and declare the work as a dataset; DESCRIPTION gains keywords and the spatial and temporal coverage; the pkgdown site is deployed from gh-pages; R CMD check runs in CI on dev and main. The data are unchanged.
+
+# glossarywho 1.0.1
+
+* Release archived on Zenodo.
+
+# glossarywho 1.0.0
+
+* First release on GitHub.

README.Rmd

@@ -29,6 +29,8 @@ knitr::opts_chunk$set(
 [![License: CC BY
 4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14754016.svg)](https://zenodo.org/doi/10.5281/zenodo.14754016)
+[![R-CMD-check](https://github.com/openwashdata/glossarywho/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/openwashdata/glossarywho/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 The goal of glossarywho is to provide data from the [WHO Glossary](https://www.who.int/publications/i/item/9789240105485) in a tidy format. Access definitions by themes [here](https://openwashdata.github.io/glossarywho/articles/Themes.html) or use the search bar at the top of the page.
@@ -177,7 +179,7 @@ wordcloud(words = names(sort(colSums(as.matrix(dtm)), decreasing = TRUE)),
 ## License
 
 Data are available as
-[CC-BY](https://github.com/openwashdata/%7B%7B%7Bpackagename%7D%7D%7D/blob/main/LICENSE.md).
+[CC-BY](https://github.com/openwashdata/glossarywho/blob/main/LICENSE.md).
 
 ## Citation
 

README.md

@@ -8,6 +8,8 @@
 [![License: CC BY
 4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14754016.svg)](https://zenodo.org/doi/10.5281/zenodo.14754016)
+[![R-CMD-check](https://github.com/openwashdata/glossarywho/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/openwashdata/glossarywho/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 The goal of glossarywho is to provide data from the [WHO
@@ -71,7 +73,7 @@ definitions |>
   gt::as_raw_html()
 ```
 
-<div id="gthuikjmpm" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
+<div id="cpbitriozf" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
   &#10;  <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false" style="-webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3;" bgcolor="#FFFFFF">
   <thead style="border-style: none;">
     <tr class="gt_col_headings" style="border-style: none; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3;">
@@ -87,8 +89,7 @@ definitions |>
     <tr style="border-style: none;"><td headers="Term" class="gt_row gt_left" style="border-style: none; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; text-align: left;" valign="middle" align="left">Delineated geographical areas within</td>
 <td headers="Description" class="gt_row gt_left" style="border-style: none; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; text-align: left;" valign="middle" align="left">a particular territory created for the  purpose of  administration. For  example:  county, district, province, state, region,  subnational or national (3).</td></tr>
   </tbody>
-  &#10;  
-</table>
+  &#10;</table>
 </div>
 
 ### themes
@@ -103,11 +104,11 @@ themes |>
   gt::as_raw_html()
 ```
 
-<div id="tvtevdguga" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
+<div id="yldaukcfji" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
   &#10;  <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false" style="-webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3;" bgcolor="#FFFFFF">
   <thead style="border-style: none;">
     <tr class="gt_col_headings" style="border-style: none; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3;">
-      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Thematic Area" style="border-style: none; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; text-align: left;" bgcolor="#FFFFFF" valign="bottom" align="left">Thematic Area</th>
+      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Thematic-Area" style="border-style: none; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; text-align: left;" bgcolor="#FFFFFF" valign="bottom" align="left">Thematic Area</th>
       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Term" style="border-style: none; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; text-align: left;" bgcolor="#FFFFFF" valign="bottom" align="left">Term</th>
     </tr>
   </thead>
@@ -119,8 +120,7 @@ themes |>
     <tr style="border-style: none;"><td headers="Thematic Area" class="gt_row gt_left" style="border-style: none; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; text-align: left;" valign="middle" align="left">Data source,collection, and collation</td>
 <td headers="Term" class="gt_row gt_left" style="border-style: none; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; text-align: left;" valign="middle" align="left">Primary data</td></tr>
   </tbody>
-  &#10;  
-</table>
+  &#10;</table>
 </div>
 
 For an overview of the variable names, see the following table.
@@ -219,7 +219,7 @@ themes |>
          panel.grid.minor.y = element_blank())
 ```
 
-<img src="man/figures/README-unnamed-chunk-8-1.png" width="100%" style="display: block; margin: auto;" />
+<img src="man/figures/README-unnamed-chunk-8-1.png" alt="" width="100%" style="display: block; margin: auto;" />
 
 ``` r
 # Wordcloud of most common words from definitions
@@ -248,12 +248,12 @@ wordcloud(words = names(sort(colSums(as.matrix(dtm)), decreasing = TRUE)),
           colors = brewer.pal(8, "Dark2"))
 ```
 
-<img src="man/figures/README-unnamed-chunk-9-1.png" width="100%" style="display: block; margin: auto;" />
+<img src="man/figures/README-unnamed-chunk-9-1.png" alt="" width="100%" style="display: block; margin: auto;" />
 
 ## License
 
 Data are available as
-[CC-BY](https://github.com/openwashdata/%7B%7B%7Bpackagename%7D%7D%7D/blob/main/LICENSE.md).
+[CC-BY](https://github.com/openwashdata/glossarywho/blob/main/LICENSE.md).
 
 ## Citation
 
@@ -264,19 +264,20 @@ citation("glossarywho")
 #> To cite package 'glossarywho' in publications use:
 #> 
 #>   Dubey Y (2025). "glossarywho: WHO Glossary."
-#>   doi:10.5281/zenodo.14754017
-#>   <https://doi.org/10.5281/zenodo.14754017>,
-#>   <https://github.com/openwashdata/glossarywho>.
+#>   doi:10.5281/zenodo.14754016
+#>   <https://doi.org/10.5281/zenodo.14754016>.
+#>   <https://openwashdata.github.io/glossarywho/>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Misc{dubey:2025,
 #>     title = {glossarywho: WHO Glossary},
 #>     author = {Yash Dubey},
 #>     year = {2025},
-#>     doi = {10.5281/zenodo.14754017},
-#>     url = {https://github.com/openwashdata/glossarywho},
+#>     doi = {10.5281/zenodo.14754016},
+#>     url = {https://openwashdata.github.io/glossarywho/},
 #>     abstract = {This package provides access to a tidy version of the WHO Glossary (https://www.who.int/publications/i/item/9789240105485) and thematic areas for each term.},
-#>     version = {0.1.0},
+#>     keywords = {open data,washdata,glossary,health data,health statistics,public health indicators,data governance,WHO},
+#>     version = {1.0.2},
 #>   }
 ```