Setup sphinx documentation

.github/workflows/documentation.yml

@@ -0,0 +1,31 @@
+name: documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          sudo apt install doxygen
+          pip install -r doc/requirements.txt
+      - name: Doxygen generate xml
+        run: |
+          doxygen doc/Doxyfile
+      - name: Sphinx build
+        run: |
+          sphinx-build doc doc/build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: doc/build/
+          force_orphan: true

.gitignore

@@ -55,3 +55,9 @@ Testing/
 
 # Output data
 **/outputData*
+
+# Documentation build files
+doc/_build
+
+# Python virtual environment for docs building
+.venv

README.dev.md

@@ -0,0 +1,37 @@
+# corticalsim3D development documentation
+
+
+## Note
+
+Testing and contributing is very welcome, especially if you can contribute new algorithms and features.
+
+
+# Development
+
+## Building the documentation locally
+
+Documentation is generated with [Sphinx](https://www.sphinx-doc.org/) and [Doxygen](https://www.doxygen.nl/) (for automatically generating the technical documentation), with [Breathe](https://breathe.readthedocs.io/) providing a bridge between the Sphinx and Doxygen documentation systems. To build the documentation locally, follow these steps:
+
+### Linux
+Install doxygen:
+
+```
+sudo apt install doxygen
+```
+
+Then, install Sphinx and the other Python dependencies from the root of the repository:
+
+```
+python -m venv .venv
+source .venv/bin/activate
+pip install -r doc/requirements.txt
+```
+
+Then we generate the Doxygen technical documentation XML files and use Sphinx to generate the HTML files with the full documentation:
+
+```
+doxygen doc/Doxyfile
+sphinx-build doc doc/build
+```
+
+And we can view the generated documentation by opening `doc/build/index.html` in a browser.

README.md

@@ -2,7 +2,7 @@
 
 ![alt text](assets/logo/logomodelCMT-1.0.png)
 
-This is a program for simulating cortical microtubule dynamics (CMT) on experimentally extracted microscopic images of cell
+This is a program for simulating cortical microtubule dynamics (CMT) on experimentally extracted microscopic images of cells
 
 Application:
 
@@ -93,10 +93,3 @@ Run the `corticalsim3d` executable with the `corticalsim3D/config/parameters_ARR
 ```bash
 ./build/corticalsim3d ./corticalsim3D/config/parameters_ARRAY.txt
 ```
-
-# TODO
-
-- [ ] Reproduce the installation instructions for Windows and update them as necessary.
-- [ ] Add specific installation instructions for dependencies for different Linux distributions (Ubuntu, Debian, Arch...).
-- [ ] Add installation instructions for MacOSX.
-- [ ] Meson: Option to install the executable into a custom directory