Code Documentation Base Template

[Pawel024]

This pull request sets up the base code documentation infrastructure:

• Added Doxygen configuration for extracting API docs from source code
• Added Sphinx + Breathe configuration to process and build the Doxygen output into a clean documentation with the ReadTheDocs theme
• Populated 2 example module index pages (fem.rst, geometry.rst) and formatted comments/docstrings for FunctionSpace and FemField so that they are rendered in the docs
• Added a README describing what we use for documentation

[Copilot]

Pull request overview

This PR introduces a documentation build pipeline for MiTo by combining Doxygen (C++ API extraction) with Sphinx+Breathe (HTML site generation), and adds tutorial pages that embed example source code and captured outputs.

Changes:

• Added Doxygen + Sphinx (ReadTheDocs theme) configuration and build artifacts for generating API docs.
• Added Sphinx pages for geometry/fem modules and a tutorials section with 5 tutorial pages.
• Added CI workflow + script to build/run tutorials, generate _tutorial_outputs, and build/deploy docs to GitHub Pages.

Reviewed changes

Copilot reviewed 18 out of 20 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
lib/mito/geometry/GeometricSimplex.h	Small change in parametrization assembly (origin handling) while prepping docs-friendly comments.
lib/mito/fem/FunctionSpace.h	Converted class header comment to Doxygen-style (@brief, @tparam).
lib/mito/fem/FemField.h	Converted class header comment to Doxygen-style (@brief, @tparam).
docs/source/index.rst	Added documentation site landing page and toctree structure.
docs/source/geometry.rst	Added module index page rendering key geometry classes via Breathe.
docs/source/fem.rst	Added module index page rendering key FEM classes via Breathe.
docs/source/tutorials.rst	Added tutorials index and local build instructions.
docs/source/tutorial_1_functions.rst	Added tutorial page embedding tutorial source and captured output.
docs/source/tutorial_2_tensors.rst	Added tutorial page embedding tutorial source and captured output.
docs/source/tutorial_3_fields.rst	Added tutorial page embedding tutorial source and captured output.
docs/source/tutorial_4_divergence_theorem_2d.rst	Added tutorial page embedding tutorial source and captured output (plus artifacts section).
docs/source/tutorial_5_divergence_theorem_2d_in_3d.rst	Added tutorial page embedding tutorial source and captured output.
docs/source/conf.py	Added Sphinx configuration (extensions, Breathe, theme, highlighting).
docs/requirements.txt	Added Python dependencies for building Sphinx docs.
docs/README.md	Added documentation build README for developers.
docs/Makefile	Added Sphinx make targets for local docs builds.
docs/Doxyfile	Added Doxygen configuration to generate XML consumed by Breathe.
.github/workflows/docs.yaml	Added CI workflow to build/run tutorials, build docs, and deploy to GitHub Pages.
.github/scripts/build_and_run_tutorials.sh	Added script to build/run each tutorial and collect outputs/artifacts for Sphinx inclusion.
.gitignore	Ignored generated Doxygen/Sphinx outputs and tutorial output artifacts produced in CI.

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[Copilot]

Pull request overview

Copilot reviewed 18 out of 20 changed files in this pull request and generated 2 comments.

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