Setup sphinx documentation

.gitignore

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+# Sphinx Documentation files
+doc/_build
+

doc/breathe.rst

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+Breathe stuff
+-------------
+
+.. autodoxygenindex::

doc/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'CorticalSim 3D'
+copyright = '2026, Eva Deinum, Bandan Chakrabortty, Jaro Camphuijsen, Alex Hadjiivanov'
+author = 'Eva Deinum, Bandan Chakrabortty, Jaro Camphuijsen, Alex Hadjiivanov'
+release = ''
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['myst_parser', 'breathe', 'sphinx_rtd_theme']
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+
+# Add breathe extension for c++ docs in sphinx with doxygen
+breathe_projects = {"corticalsim3d": "corticalsim3D"}
+breathe_default_project = "corticalsim3d"

doc/index.rst

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+.. CorticalSim 3D documentation master file, created by
+   sphinx-quickstart on Tue Mar 17 14:38:49 2026.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+CorticalSim 3D documentation
+============================
+
+.. image:: assets/logo/logomodelCMT-4.0.png
+
+Add your content using ``reStructuredText`` syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   introduction.md
+   breathe.md
+
+

doc/introduction.md

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+# Introduction
+Some general intro

doc/requirements.txt

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+alabaster==1.0.0
+annotated-types==0.7.0
+appdirs==1.4.4
+babel==2.18.0
+certifi==2026.2.25
+charset-normalizer==3.4.6
+docutils==0.22.4
+idna==3.11
+imagesize==2.0.0
+Jinja2==3.1.6
+markdown-it-py==4.0.0
+MarkupSafe==3.0.3
+mdit-py-plugins==0.5.0
+mdurl==0.1.2
+myst-parser==5.0.0
+packaging==26.0
+pydantic==2.12.5
+pydantic-extra-types==2.11.1
+pydantic_core==2.41.5
+Pygments==2.19.2
+PyYAML==6.0.3
+requests==2.32.5
+roman-numerals==4.1.0
+snowballstemmer==3.0.1
+Sphinx==9.1.0
+sphinx_immaterial==0.13.9
+sphinxcontrib-applehelp==2.0.0
+sphinxcontrib-devhelp==2.0.0
+sphinxcontrib-htmlhelp==2.1.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==2.0.0
+sphinxcontrib-serializinghtml==2.0.0
+typing-inspection==0.4.2
+typing_extensions==4.15.0
+urllib3==2.6.3