add pkgdown website and deploy workflow

.Rbuildignore

@@ -6,3 +6,6 @@
 ^\.github$
 ^CODE_OF_CONDUCT\.md$
 ^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+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@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - 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@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -13,7 +13,6 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+docs

DESCRIPTION

@@ -35,4 +35,6 @@ Language: en-GB
 LazyData: true
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
+URL: https://github.com/OxfordIHTM/codeditr, http://oxford-ihtm.io/codeditr/
 Config/testthat/edition: 3
+

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: http://oxford-ihtm.io/codeditr/
+template:
+  bootstrap: 5
+

codecov.yml

@@ -1,8 +1,5 @@
 comment: false
 
-codecov:
- token: ${{ secrets.CODECOV_TOKEN }}
-
 coverage:
   status:
     project:

inst/WORDLIST

@@ -1,5 +1,6 @@
 CMD
 CoDEdit
+CodeFactor
 Codecov
 DD
 FreeId

pkgdown/_pkgdown.yml

@@ -0,0 +1,72 @@
+title: codeditr
+
+url: https://oxford-ihtm.io/codeditr/
+
+development:
+  mode: auto
+
+template:
+  bootstrap: 5
+  bootswatch: litera
+  theme: haddock
+  ganalytics: #
+
+home:
+  links:
+  - text: Read more about the International Classification of Diseases
+    href: https://www.who.int/standards/classifications/classification-of-diseases
+  - text: Read more about the WHO CoDEdit tool
+    href: https://www.who.int/standards/classifications/classification-of-diseases/services/codedit-tool
+
+navbar:
+  bg: primary
+  type: light
+  structure:
+    left:  [home, intro, reference, articles, news]
+    right: [twitter, facebook, linkedin, github]
+
+  components:
+    # articles:
+    #   text: Articles
+    #   menu:
+    #   - text: "ICD-11 Foundation"
+    #     href: articles/icd11_foundation.html
+    twitter:
+      icon: "fab fa-twitter fa-lg"
+      href: http://twitter.com/OxIHTM
+    facebook:
+      icon: "fab fa-facebook fa-lg"
+      href: https://www.facebook.com/MSc-in-International-Health-and-Tropical-Medicine-University-of-Oxford-433056700228246/
+    linkedin:
+      icon: "fab fa-linkedin fa-lg"
+      href: https://www.linkedin.com/company/international-health-and-tropical-medicine
+
+
+reference:
+  - title: Description
+    contents:
+    - codeditr-package
+
+  - title: Recode
+    contents:
+    - cod_recode_sex
+    - cod_recode_age_type
+
+  - title: Calculate
+    contents:
+    - cod_calculate_age
+
+  - title: Check
+    contents:
+    - cod_check_age
+    - cod_check_missing
+
+  - title: Utilities
+    contents:
+    - get_age_values
+
+  - title: Supporting datasets
+    contents:
+    - icd10_example
+    - icd11_example
+