Fix MathJax/Doxygen clash in visualisation.md

Author: henryleberre

.github/workflows/doc.yml

@@ -30,17 +30,18 @@ jobs:
         git ls-remote "${{ secrets.DOC_PUSH_URL }}" -q
         code=$?
         if [ "$code" -ne "0" ]; then exit 0; fi
-        git config --global user.name  "MFC Action"
-        git config --global user.email "MFC Action"
+        git config --global user.name  'MFC Action'
+        git config --global user.email '<>'
         git clone "${{ secrets.DOC_PUSH_URL }}"
         cd "$(find . -name '*.github.io')"
         mv .github ..
         rm -rf $(pwd)/*
         mv ../.github       .
         mv ../install/doc/mfc/* .
         git add -A
-        git commit -m "${GITHUB_SHA::7}: $(date +%d/%m/%Y-%H:%M:%S)" || true
+        git commit -m "Docs @ ${GITHUB_SHA::7}" || true
         git push
 
 # DOC_PUSH_URL should be of the format:
-# - "https://${{ github.repository_owner }}:${{ TOKEN }}@github.com/${{ github.repository_owner }}/${{ github.repository_owner }}.github.io"
+# --> https://<username>:<token>@github.com/<username>/<repository>
+

README.md

@@ -34,7 +34,7 @@ Please contact the developers, like [Spencer](mailto:[email protected]), if you hav
 We have an active Slack channel to help ease in new MFC users and support development.
 
 MFC has both API and high-level documentation. 
-It is available on [the website](https://mflowcode.github.io/) and in markdown format at [doc/landing/readme.md](doc/landing/readme.md).
+It is available on [the website](https://mflowcode.github.io/) and in markdown format at [doc/documentation/readme.md](doc/documentation/readme.md).
 
 If you use MFC, consider citing it:
 * <a href="https://doi.org/10.1016/j.cpc.2020.107396">

doc/Doxyfile.in

@@ -1188,7 +1188,7 @@ HTML_FOOTER            = doxygen/footer.html
 # obsolete.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_STYLESHEET        = style.css
+HTML_STYLESHEET        =
 
 # The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
 # cascading style sheets that are included after the standard style sheets

doc/documentation/visualisation.md

@@ -41,9 +41,9 @@ If there are sub-grid bubbles `bubbles` $=$ `T`, then the bubble variables are a
 These depend on the bubble dynamics model used.
 If `polytropic` $=$ `T` then the conservative variables are appended by 
 
-$$ n_b R_1, n_b \dot{R_1}, \dots, n_b R_{N_b}, n_b \dot{R}_{N_b} $$
+$$ n_b R_1, n_b {\\dot R}_1, \dots, n_b R_{N_b}, n_b {\\dot R}_{N_b} $$
 
 where $n_B$ is the bubble number density and $N_b$ are the number of bubble sizes (see matching variable in the input file, `Nb`).
 The primitive bubble variables do not include $n_B$:
 
-$$ R_1, \dot{R_1}, \dots, R_{N_b}, \dot{R_{N_b}} $$
+$$ R_1, {\\dot R}_1, \dots, R_{N_b}, {\\dot R}_{N_b} $$

doc/index.html

@@ -32,7 +32,7 @@
         <header class="w-full top-0 bg-slate-900 text-white flex flex-col items-center drop-shadow-2xl">
             <div class="px-4 md:px-0 container mx-auto py-8 flex flex-row items-center justify-between">
                 <div class="flex flex-row items-center gap-x-2">
-                    <a href="https://github.com/MFlowCode/MFC" class="flex flex-row items-center gap-x-2">
+                    <a href="https://mflowcode.github.io/" class="flex flex-row items-center gap-x-2">
                         <img class="h-8 md:h-12 rounded-full bg-white" src="res/logo.png" />
                         <h1 class="font-bold text-3xl">MFC</h1>
                     </a>