diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..3f6b112 --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +# Sphinx Documentation files +doc/_build + diff --git a/logo/logomodelCMT-1.0.png b/doc/assets/logo/logomodelCMT-1.0.png similarity index 100% rename from logo/logomodelCMT-1.0.png rename to doc/assets/logo/logomodelCMT-1.0.png diff --git a/logo/logomodelCMT-2.0.png b/doc/assets/logo/logomodelCMT-2.0.png similarity index 100% rename from logo/logomodelCMT-2.0.png rename to doc/assets/logo/logomodelCMT-2.0.png diff --git a/logo/logomodelCMT-3.0.png b/doc/assets/logo/logomodelCMT-3.0.png similarity index 100% rename from logo/logomodelCMT-3.0.png rename to doc/assets/logo/logomodelCMT-3.0.png diff --git a/logo/logomodelCMT-4.0.png b/doc/assets/logo/logomodelCMT-4.0.png similarity index 100% rename from logo/logomodelCMT-4.0.png rename to doc/assets/logo/logomodelCMT-4.0.png diff --git a/doc/breathe.rst b/doc/breathe.rst new file mode 100644 index 0000000..8d811c2 --- /dev/null +++ b/doc/breathe.rst @@ -0,0 +1,4 @@ +Breathe stuff +------------- + +.. autodoxygenindex:: \ No newline at end of file diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 0000000..ef4e9ba --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,32 @@ +# 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" diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 0000000..8c9ca02 --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,23 @@ +.. 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 `_ +documentation for details. + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + introduction.md + breathe.md + + diff --git a/doc/introduction.md b/doc/introduction.md new file mode 100644 index 0000000..99d308a --- /dev/null +++ b/doc/introduction.md @@ -0,0 +1,2 @@ +# Introduction +Some general intro \ No newline at end of file diff --git a/doc/requirements.txt b/doc/requirements.txt new file mode 100644 index 0000000..684b20c --- /dev/null +++ b/doc/requirements.txt @@ -0,0 +1,35 @@ +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