OxfordIHTM · ernestguevarra · Jan 29, 2026 · Jan 29, 2026
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -9,3 +9,4 @@
 ^docs$
 ^pkgdown$
 ^README\.html$
+^CITATION\.cff$
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -2,23 +2,23 @@
 
 ## Bugs
 
-* Submit an issue on the [issues page](https://github.com/OxfordIHTM/oxfordtheme/issues)
+* Submit an issue on the [issues page](https://github.com/OxfordIHTM/oxfordthema/issues)
 
 ## Code contributions
 
 * Fork this repository to your Github account
 
-* Clone your version on your account down to your machine from your account
+* Clone your forked version to your machine
 
-```
-git clone https://github.com/<yourgithubusername>/oxfordtheme.git
+```bash
+git clone https://github.com/<yourgithubusername>/oxfordthema.git
 ```
 
-* Make sure to track progress upstream i.e., on our version of `oxfordtheme`
-at `OxfordIHTM/oxfordtheme`, by doing
+* Make sure to track progress upstream i.e., on our version of `oxfordthema`
+at `OxfordIHTM/oxfordthema`, by doing
 
-```
-git remote add upstream https://github.com/OxfordIHTM/oxfordtheme.git
+```bash
+git remote add upstream https://github.com/OxfordIHTM/oxfordthema.git
 ```
 
 * Before making changes make sure to pull changes in from `upstream` by doing
@@ -32,4 +32,4 @@ documentation
 
 * Push up changes to your account
 
-* Submit a pull request at `OxfordIHTM/oxfordtheme`
+* Submit a pull request at `OxfordIHTM/oxfordthema`
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:

diff --git a/.github/workflows/mirror-codeberg.yaml b/.github/workflows/mirror-codeberg.yaml
@@ -0,0 +1,19 @@
+name: Mirror to other git server
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+jobs:
+  mirror:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: yesolutions/mirror-action@master
+        with:
+          REMOTE: https://codeberg.org/OxfordIHTM/oxthema
+          GIT_USERNAME: ${{ secrets.CODEBERG_USERNAME }}
+          GIT_PASSWORD: ${{ secrets.CODEBERG_TOKEN }}
diff --git a/.github/workflows/netlify.yaml b/.github/workflows/netlify.yaml
@@ -0,0 +1,53 @@
+on:
+  pull_request:
+    branches: [main, master]
+
+name: pkgdown-pr
+
+jobs:
+  netlify:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - 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: Install package
+        run: R CMD INSTALL .
+
+      - name: Create website
+        run: |
+          pkgdown::build_site()
+        shell: Rscript {0}
+
+      - name: Create index file
+        run: |
+          echo '<!DOCTYPE html><html><head><meta http-equiv="refresh" content="0;URL=/dev/index.html" />  <script language="javascript"> window.location.replace('/dev/index.html')</script></head></html>' > ./docs/index.html
+
+      - name: Deploy to Netlify
+        uses: nwtgck/actions-netlify@v3.0
+        with:
+          publish-dir: './docs'
+          production-branch: main
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message:
+            'Deploy from GHA: ${{ github.event.pull_request.title || github.event.head_commit.message }} (${{ github.sha }})'
+          # these default to 'true'
+          enable-commit-comment: false
+          enable-github-deployment: false
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -23,18 +24,29 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        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 }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |