Update documentation with Zensical

[stuitje]

This PR updates Aragog with Zensical, to partially address issues FormingWorlds/PROTEUS#635 and FormingWorlds/PROTEUS#650.

It also updates several pages:

• Homepage has been updated to have the same style as other modules;
• Getting started page added;
• Proteus framework module landing page added, to link to other modules;
• API reference has been split up across several pages ;
• Larger model overview in line with Laurent Soucasse's notes, for each chapter a page;
• README has been updated to refer to the Forming Worlds fork, and the new installation guide of last merge is now included.

[Copilot]

Pull request overview

This PR migrates Aragog’s documentation site to the PROTEUS/Zensical-based layout and expands/restructures the MkDocs content to match the PROTEUS framework documentation style.

Changes:

• Updated MkDocs navigation/theme configuration and introduced PROTEUS styling assets.
• Added new documentation pages (Getting started, PROTEUS framework landing page, split model overview chapters, split API reference pages, Community pages).
• Updated repository metadata/docs tooling (README links/badges, docs build workflow, docs dependency set including Zensical).

Reviewed changes

Copilot reviewed 25 out of 28 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
README.md	Updates badges/links and installation guidance for the FormingWorlds fork.
pyproject.toml	Adds Zensical to docs dependencies/extras.
mkdocs.yml	Reworks site nav/theme, enables mkdocstrings, adds PROTEUS styling and site metadata.
docs/Tutorials/firstrun.md	Adjusts tutorial section heading formatting.
docs/stylesheets/proteus_theme.css	Adds PROTEUS-wide MkDocs Material theme customizations.
docs/stylesheets/docstrings.css	Improves mkdocstrings rendering (wrapping/line breaks).
docs/Reference/api/utilities.md	New mkdocstrings API page for aragog.utilities.
docs/Reference/api/solver.md	New mkdocstrings API page for aragog.solver.
docs/Reference/api/phase.md	New mkdocstrings API page for aragog.phase.
docs/Reference/api/parser.md	New mkdocstrings API page for aragog.parser.
docs/Reference/api/package.md	New mkdocstrings API page for the package root.
docs/Reference/api/output.md	New mkdocstrings API page for aragog.output.
docs/Reference/api/mesh.md	New mkdocstrings API page for aragog.mesh.
docs/Reference/api/interfaces.md	New mkdocstrings API page for aragog.interfaces.
docs/Reference/api/data.md	New mkdocstrings API page for aragog.data.
docs/Reference/api/core.md	New mkdocstrings API page for aragog.core.
docs/Reference/api/api_overview.md	Refactors API overview after splitting the reference pages.
docs/proteus_framework.md	Adds a PROTEUS framework landing page linking module docs.
docs/index.md	Updates homepage content to the new PROTEUS-aligned landing style.
docs/getting_started.md	Adds a new “Getting started” entry point and quick links.
docs/Explanations/transport.md	Adds a dedicated model overview chapter on transport properties.
docs/Explanations/thermodynamics.md	Adds a dedicated model overview chapter on thermodynamics.
docs/Explanations/numerical_methods.md	Adds a dedicated model overview chapter on numerical methods.
docs/Explanations/enthalpy_balance.md	Adds a dedicated model overview chapter on the enthalpy balance.
docs/Community/contact.md	Adds community contact channels page.
docs/Community/CODE_OF_CONDUCT.md	Adds a documentation-scoped Code of Conduct page.
.github/workflows/docs.yaml	Switches docs publishing to GitHub Pages artifact/deploy flow and Zensical build.

Comments suppressed due to low confidence (2)

docs/Reference/api/api_overview.md:4

• The relative link to the model overview is incorrect from docs/Reference/api/api_overview.md (it currently points to docs/Reference/Explanations/...). It should go up two levels (e.g. ../../Explanations/enthalpy_balance.md).
  mkdocs.yml:181
• watch includes CODE_OF_CONDUCT.md, but there is no root-level CODE_OF_CONDUCT.md in this repo (the file is under docs/Community/). Either update the watch path or remove it to avoid confusing mkdocs serve behavior.

watch:
  - aragog/
  - docs/
  - README.md
  - CODE_OF_CONDUCT.md

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[nichollsh]

Generally looks good - the zensical pages are really clean, and a big improvement of the older mkdocs ones.

In addition to my comments below and those from copilot, I noticed that clicking the top-left PROTEUS logo does not direct you to the main proteus-framework website.

[stuitje]

Generally looks good - the zensical pages are really clean, and a big improvement of the older mkdocs ones.

In addition to my comments below and those from copilot, I noticed that clicking the top-left PROTEUS logo does not direct you to the main proteus-framework website.

Thanks Harrison, everything should be covered now!

[timlichtenberg]

please just go from my side; i cannto review today and are working on aragog anyway, so will update your chanegs sometime with new info on the used equations anyway

[nichollsh]

Looking great :) Thanks, @stuitje

Shall we merge this first and then incorporate @timlichtenberg's ongoing changes through another PR afterwards?

[timlichtenberg]

Yes, my follow-up PR is still some time away.