mkdocs.yml

site_name: Aragog
site_url: https://proteus-framework.org/aragog
repo_url: https://github.com/FormingWorlds/aragog
repo_name: GitHub

copyright: '&copy; 2023-2026 <a href="https://formingworlds.space">Forming Worlds Lab</a>'

nav:
  - Home:
      - About: index.md
      - Getting started: getting_started.md

  - How-to guides:
      - Setup:
          - Installation: How-to/installation.md
      - Running Aragog:
          - Standalone usage: How-to/usage-paths.md
          - Coupling Aragog to PROTEUS: How-to/proteus_coupling.md
          - Configuration: How-to/configuration.md
          - Usage: How-to/usage.md
      - Solver tuning:
          - Solver method tuning: How-to/solver-method-tuning.md
          - Melt-fraction step cap: How-to/phi-step-cap.md
          - Mesh refinement: How-to/mesh-refinement.md
          - UTBL parameterisation: How-to/utbl-parameterisation.md
      - Outputs & testing:
          - Inspecting NetCDF output: How-to/netcdf.md
          - Build tests: How-to/build_tests.md
      - Maintenance:
          - Releasing: How-to/releasing.md
          - Developer workflow: How-to/developer_workflow.md

  - Tutorials:
      - First run: Tutorials/firstrun.md
      - Building a test: Tutorials/build_test.md
      - Fixed surface temperature: Tutorials/surface_temperature.md
      - Properties at the solidus: Tutorials/phase_blend.md
      - Refining the mesh: Tutorials/mesh_refinement.md
      - Solid-state convection: Tutorials/solid_state_convection.md
      - A crust on the magma ocean: Tutorials/surface_lid.md
      - The melting point of a core alloy: Tutorials/core_alloy_liquidus.md

  - Explanations:
      - Overview:
          - Model overview: Explanations/model.md
          - Code architecture: Explanations/code_architecture.md
          - Coupling to PROTEUS: Explanations/proteus_coupling.md
          - Aragog vs SPIDER: Explanations/spider_comparison.md
          - Testing suite: Explanations/testing.md
      - Physics:
          - Energy equation: Explanations/energy_equation.md
          - Heat transport: Explanations/heat_transport.md
          - Mixing-length theory: Explanations/mixing_length.md
          - Solid-state convection: Explanations/solid_state_convection.md
          - Two-phase flow: Explanations/two_phase_flow.md
          - Phase transitions: Explanations/phase_transitions.md
          - Pressure EOS: Explanations/pressure_eos.md
          - Core BC modes: Explanations/core_bc.md
          - Core alloy liquidus: Explanations/core_alloy_liquidus.md
          - Surface boundary conditions: Explanations/surface_bc.md
          - Surface lid: Explanations/surface_lid.md
      - Numerics:
          - CVODE and JAX: Explanations/cvode_jax.md
          - JAX Jacobian factory: Explanations/jax_jacobian_factory.md
          - Melt-fraction step cap: Explanations/phi_step_cap_rationale.md
          - Mesh refinement: Explanations/mesh_refinement.md
      - Diagnostics:
          - EOS sanity checks: Explanations/eos_sanity_checks.md
          - Energy diagnostics: Explanations/energy_diagnostics.md

  - Validation:
      - Overview: Validation/index.md
      - Core: Validation/core.md
      - Core alloy liquidus: Validation/core_alloy_liquidus.md
      - Surface boundary: Validation/surface.md
      - Surface lid: Validation/surface_lid.md
      - Phase transitions: Validation/phase_transitions.md
      - Numerics: Validation/numerics.md
      - Mesh refinement: Validation/mesh_refinement.md
      - Solid-state convection: Validation/solid_state_convection.md

  - Reference:
      - API reference:
          - Overview: Reference/api/index.md
          - Config: Reference/api/aragog.config.md
          - Solver: Reference/api/aragog.solver.md
          - EOS package: Reference/api/aragog.eos.md
          - Mesh: Reference/api/aragog.mesh.md
          - Output: Reference/api/aragog.output.md
          - JAX backend: Reference/api/aragog.jax.md
          - Core evolution: Reference/api/aragog.core.md
          - Rheology: Reference/api/aragog.rheology.md
          - Stagnant-lid rheology: Reference/api/aragog.rheology_lid.md
          - Surface lid: Reference/api/aragog.surface_lid.md
      - CLI: Reference/cli.md
      - Data: Reference/data.md
      - Publications: Reference/publications.md

  - Community:
      - Code of Conduct: Community/CODE_OF_CONDUCT.md
      - Contributing: Community/CONTRIBUTING.md
      - Contact: Community/contact.md
      - Developers: https://proteus-framework.org/people

  - Source code:
      - GitHub repository: https://github.com/FormingWorlds/aragog

  - Issues:
      - GitHub issues: https://github.com/FormingWorlds/aragog/issues

  - Other PROTEUS modules:
      - PROTEUS framework: proteus-framework.md
      - "\U0001F517 PROTEUS": https://proteus-framework.org/PROTEUS/
      - "\U0001F517 MORS": https://proteus-framework.org/MORS/
      - "\U0001F517 JANUS": https://proteus-framework.org/JANUS/
      - "\U0001F517 ZEPHYRUS": https://proteus-framework.org/ZEPHYRUS/
      - "\U0001F517 CALLIOPE": https://proteus-framework.org/CALLIOPE/
      - "\U0001F517 AGNI": https://www.h-nicholls.space/AGNI/
      - "\U0001F517 Obliqua": https://proteus-framework.org/Obliqua/
      - "\U0001F517 VULCAN": https://proteus-framework.org/VULCAN/
      - "\U0001F517 Zalmoxis": https://proteus-framework.org/Zalmoxis/
      - "\U0001F517 SPIDER": https://proteus-framework.org/SPIDER/
      - "\U0001F517 Atmodeller": https://github.com/FormingWorlds/Atmodeller/
      - "\U0001F517 FastChem": https://github.com/FormingWorlds/FastChem/
      - "\U0001F517 SOCRATES": https://proteus-framework.org/SOCRATES/

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  # Default assets (the header stays dark in both schemes, so one glyph serves both)
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  logo: assets/glyph_phase_dark.png

  # The toggle icon shows the current mode, matching the project website
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extra_css:
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markdown_extensions:
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# footer:
extra:
  generator: false
  social:
    - icon: material/web
      link: https://proteus-framework.org/
      name: PROTEUS website
    - icon: material/email
      link: mailto:dev@proteus-framework.org
      name: Mail PROTEUS developers
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/fwl-aragog/
      name: Aragog on PyPI
    - icon: fontawesome/brands/github
      link: https://github.com/FormingWorlds/aragog
      name: Aragog on GitHub

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plugins:
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use_directory_urls: false

watch:
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  - README.md