Aesthetic fix and switch to GitHub's upload-pages-artifact action (#375)

* Solves #374
* Fixes badges on the website and in the website sidebar.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: samcunliffe

.github/workflows/doxygen-gh-pages.yml

@@ -14,6 +14,15 @@ on:
   merge_group:
   workflow_dispatch:
 
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
 jobs:
   doxygen:
     runs-on: macos-latest
@@ -47,31 +56,19 @@ jobs:
         run: cp doc/js/cookie.js html/cookie.js
         shell: bash
 
-      - name: Upload the website
-        uses: actions/upload-artifact@v4
+      - name: Upload static files as artifact
+        uses: actions/upload-pages-artifact@v3
         with:
-          name: tdms_website
-          path: html/*
-          retention-days: 1
+          path: html
 
   publish:
+    if: github.ref == 'refs/heads/main' # only deploy from main
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     needs: doxygen
-    if: github.event_name == 'push' && github.ref_name == 'main'
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v5
-
-      - name: Download the content for deployment
-        uses: actions/download-artifact@v5
-        with:
-          name: tdms_website
-          path: html
-          # Recreate and download to the html directory just for tidiness sake.
-
-      - name: Commit to GitHub Pages
-        uses: JamesIves/github-pages-deploy-action@v4
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          branch: gh-pages
-          folder: html
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

README.md

@@ -1,12 +1,8 @@
-<!-- \cond
- -->
-<!-- 👆 this comment and the endcond below, tells doxygen to ignore the badges
-and title at the top of README.md when building the project page (the title
-would be duplicated) everything else in README.md is also the project homepage. -->
+<!--! \cond -->
 
-# TDMS · [![latest release](https://badgen.net/github/release/UCL/TDMS)](https://github.com/UCL/TDMS/releases) [![license](https://badgen.net/badge/license/GPL-3.0/blue)](https://github.com/UCL/TDMS/blob/main/LICENSE) [![Build and test](https://github.com/UCL/TDMS/actions/workflows/ci.yml/badge.svg)](https://github.com/UCL/TDMS/actions/workflows/ci.yml) [![MATLAB tests](https://github.com/UCL/TDMS/actions/workflows/matlab_tests.yml/badge.svg)](https://github.com/UCL/TDMS/actions/workflows/matlab_tests.yml) [![codecov](https://codecov.io/gh/UCL/TDMS/branch/main/graph/badge.svg?token=3kqP14kslL)](https://codecov.io/gh/UCL/TDMS) [![DOI:10.5281/zenodo.7950603](doc/assets/doi-badge.svg)](https://zenodo.org/badge/latestdoi/448864310)
+# TDMS · [![latest release](https://badgen.net/github/release/UCL/TDMS)](https://github.com/UCL/TDMS/releases) [![license](https://badgen.net/badge/license/GPL-3.0/blue)](https://github.com/UCL/TDMS/blob/main/LICENSE) [![Build and test](https://github.com/UCL/TDMS/actions/workflows/ci.yml/badge.svg)](https://github.com/UCL/TDMS/actions/workflows/ci.yml) [![MATLAB tests](https://github.com/UCL/TDMS/actions/workflows/matlab_tests.yml/badge.svg)](https://github.com/UCL/TDMS/actions/workflows/matlab_tests.yml) [![codecov](https://codecov.io/gh/UCL/TDMS/branch/main/graph/badge.svg?token=3kqP14kslL)](https://codecov.io/gh/UCL/TDMS) [![DOI](https://zenodo.org/badge/448864310.svg)](https://zenodo.org/badge/latestdoi/448864310)
 
-<!-- \endcond -->
+<!--! \endcond -->
 
 # Time-Domain Maxwell Solver
 

doc/Doxyfile

@@ -25,7 +25,7 @@ GENERATE_LATEX         = NO
 EXTRACT_PRIVATE        = YES
 STRIP_CODE_COMMENTS    = NO
 
-# make behavior useful a CI test: warn undocumented
+# make behavior useful as a CI test: warn undocumented
 WARNINGS               = YES
 WARN_IF_UNDOCUMENTED   = YES
 WARN_IF_DOC_ERROR      = YES