UCL-ARC · connoraird · Oct 31, 2025 · Oct 31, 2025 · Oct 31, 2025 · Oct 31, 2025
diff --git a/.github/workflows/pages.yaml b/.github/workflows/pages.yaml
@@ -31,9 +31,19 @@ jobs:
         uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955 # v4
       - uses: actions/setup-python@v6 
         with:
-          python-version: '3.13' 
+          python-version: '3.13'
+          cache: 'pip'
       - name: Generate Ford docs
-        run: pip install -r requirements.txt; sudo apt install graphviz; ford ford-home.md
+        run: |
+          pip install -r requirements.txt
+          sudo apt install graphviz
+          ford ford-home.md
+      - name: Install Doxygen
+        run: |
+          sudo apt-get update 
+          sudo apt-get install -y doxygen
+      - name: Run Doxygen to generate documentation
+        run: doxygen ./documentation/doxygen/Doxyfile
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:

diff --git a/README.md b/README.md
@@ -1,19 +1,22 @@
 ---
-title: How to use this Repo
+title: Developer Docs
 ---
 
-# Fortran Tooling
+<!-- Doxygen config
+@page developer-docs Developer Docs
+-->
+
 
 This repository aims to improve Fortran best practices within UCL and the wider Fortran community by documenting a growing list of Fortran tools recommended by [UCL ARC](https://ucl.ac.uk/arc).
 
-## src code
+# src code
 
 There are two src codes within this repository [mesh_generator](./src/mesh_generator/) and [poisson](./src/poisson/). These are designed to work together.
 
 - `mesh_generator` generates a basic square 2D triangular mesh (see [mesh_generator.f90](./src/mesh_generator/mesh_generator.f90) for more details).
 - `poisson` is a solver which finds the solution of the steady-state heat conduction equation represented by the Poisson equation over a 2D triangular mesh (see [poisson.f90](./src/poisson/poisson.f90) for more details).
 
-## Building
+# Building
 
 A bash [build.sh](./build.sh) script is provided for building all the source code and tests found in this repository. 
 Optionally, the script can also install the project dependacies.  
@@ -24,7 +27,7 @@ Note that using the CMake backend requires a local installation of pFUnit (see m
 Alternatively, instructions for building the project without the script are provided below.
 Instructions for installing pFUnit using the script are also provided.
 
-### CMake
+## CMake
 
 >Note: the CMake contains some [pFUnit tests](./testing/pFUnit/) which require a local version of pFUnit to be built on your device.
 It can be installed either via the provided build.sh script or by following the installation instruction in the [pFUnit repo](https://github.com/Goddard-Fortran-Ecosystem/pFUnit).
@@ -42,15 +45,15 @@ cmake --build build-cmake
 
 This will produce executables for the two src codes, `fortran-tooling-mesh-generator` and `fortran-tooling-poisson`.
 
-### FPM
+## FPM
 
 To build the project using FPM, from the root of the repo, run
 
 ```sh
 fpm build
 ```
 
-### pFUnit
+## Building pFUnit
 
 The [build.sh](./build.sh) scripts provides a wrapper for simplifying the installation of pFUint.  To run the installer, execute
 
@@ -59,9 +62,9 @@ The [build.sh](./build.sh) scripts provides a wrapper for simplifying the instal
 ```
 where `<PATH_TO_PFUNIT>` is the **absolute** path to the local where pFUnit will be installed. Optionally, adding the flag `--test-pfunit` will test the pFUnit installation. 
 
-## Running the src
+# Running the src
 
-### Mesh generator
+## Mesh generator
 
 If you have built using CMake, you can run the mesh generator by directly calling the executable
 
@@ -74,7 +77,7 @@ If you have built using FPM, you can also run the mesh generator via FPM
 fpm run mesh_generator -- <box_size> <edge_size>
 ```
 
-### Poisson solver
+## Poisson solver
 If you have built using CMake, you can also run the poisson solver by directly calling the executable
 ```sh
 ./build/fortran-tooling-poisson <path_to_mesh_file>
@@ -85,7 +88,7 @@ If you have built using FPM, you can also run the mesh generator via FPM
 fpm run poisson -- <path_to_mesh_file>
 ```
 
-## Running the tests
+# Running the tests
 
 If you have built using CMake, you can run the tests by running the following from within the `build-cmake` directory.
 
@@ -99,7 +102,7 @@ If you have built using FPM, you can run the tests by running the following from
 fpm test
 ```
 
-## pre-commit
+# pre-commit
 
 [pre-commit](https://pre-commit.com/) is utilised within this repo. pre-commit is a tool to help enforce formatting standards as early as possible.
 pre-commit works by running a provided set of checks every time a `git commit` is attempted.
@@ -117,9 +120,9 @@ Then, from the root of the repo, you start using pre-commit by running
 pre-commit install
 ```
 
-## Documentation
+# Generating documentation
 
-### Ford
+## Ford docs
 
 To generate the Ford documentation locally run the command 
 
@@ -132,5 +135,16 @@ This will create a folder `docs/ford-docs` within the root of the repo. Within `
 information about how Ford is set up within this repo is provided in the generated
 documentation at `Tools->Documentation->Ford`.
 
-> Note: the name of the output directory for our docs, `ford-docs`, is defined in [ford-home.md](./ford-home.md) as the value
-> for `output_dir`
+
+## Doxygen docs
+
+To generate the Doxygen documentation locally run the command
+
+```sh
+doxygen documentation/doxygen/Doxyfile
+```
+
+This will create a folder `docs/doxygen-docs` within the root of the repo. Within `docs/doxygen-docs` there will
+be an `index.html` file. Open this file in a browser to view the generated dociumentation. Further information
+about how Doxygen is set up within this repo is provided in the generated documentation at
+`Tools->documentaion->Doxygen`.
diff --git a/debugging/index.md b/debugging/index.md
@@ -2,13 +2,20 @@
 title: Debugging
 ---
 
-# Fortran debugging
+<!-- Doxygen config
+@page debugging Debugging
+-->
 
-## Candidate Tools
+
+# Candidate Tools
 
 | tool | description | Known issues |
 | ---- | ----------- | ------------ |
-| [GDB](https://www.sourceware.org/gdb/) | | <ul></ul>  |
-| [linaro DDT](https://www.linaroforge.com/linaroDdt/) | | <ul></ul>  |
+| [GDB](https://www.sourceware.org/gdb/) | | |
+| [linaro DDT](https://www.linaroforge.com/linaroDdt/) | | |
 | [mdb](https://github.com/TomMelt/mdb) | A lightweight wrapper of [gdb](https://www.sourceware.org/gdb/) and [lldb](https://lldb.llvm.org/) intended to make debugging MPI a lot simpler. | <ul><li>Not compatible with Apple ARM.</li><li> Maintained by only one person</li></ul> |
-| print statement | Great for small programs and simple problems but provides very limited information and requires recompiling to alter that information. We recommend spending the time to learn how to use a debugging tool such as the others in this list. | <ul></ul>  |
+| print statement | Great for small programs and simple problems but provides very limited information and requires recompiling to alter that information. We recommend spending the time to learn how to use a debugging tool such as the others in this list. | |
+
+<!-- Doxygen config
+**Subpages:** @subpage mdb
+-->
diff --git a/debugging/mdb.md b/debugging/mdb.md
@@ -2,7 +2,12 @@
 title: mdb
 ---
 
-# [mdb](https://github.com/TomMelt/mdb)
+<!-- Doxygen config
+@page mdb mdb
+@ingroup debugging
+-->
+
+[mdb](https://github.com/TomMelt/mdb) is a parallel debugger developed by [Thomas Meltzer](https://github.com/TomMelt)
 
 ## Prerequisite
 

diff --git a/docs/.gitignore b/docs/.gitignore
@@ -3,3 +3,5 @@ _site
 .jekyll-cache
 .jekyll-metadata
 vendor
+ford-docs
+doxygen-docs