mkdocs.yml

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

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

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

  - How-to guides:
      - Installation: 
        - Quick installation: How-to/installation.md
        - Quadruple precision: How-to/quadruple_installation.md
      - Testing: How-to/test.md
      - Building tests: How-to/build_tests.md
      - External mesh input: How-to/external_mesh_input.md
      - Coupling to PROTEUS: How-to/proteus_coupling.md
      - Releasing: How-to/releasing.md

  - Tutorials:
      - First run: Tutorials/first_run.md

  - Explanations:
      - Testing suite: Explanations/testing.md
      - Model overview:
        - Thermodynamics: Explanations/basic_thermodynamics.md
        - Mass conservation and energy transport: Explanations/transport.md
        - Material properties: Explanations/material_properties.md
        - Mass coordinates: Explanations/mass_coordinates.md
        - Parameterised fluxes: Explanations/parameterised_fluxes.md
        - Phase separation and thermal evolution (Abe 1993): Explanations/abe1993.md
        - Internal heating: Explanations/internal_heating.md
        - Atmosphere: Explanations/atmosphere.md
        - Boundary conditions: Explanations/boundary_conditions.md
        - Hybrid equation of state: Explanations/hybrid_eos.md
        - Toy model and numerical schemes: Explanations/toy_model.md

  - Reference:
      - Runtime options: Reference/options.md
      - Publications: Reference/publications.md

  - Validation:
      - Overview: Validation/index.md
      - atmosphere.c: Validation/atmosphere.md
      - bc.c: Validation/bc.md
      - energy.c: Validation/energy.md
      - eos.c: Validation/eos.md
      - eos_adamswilliamson.c: Validation/eos_adamswilliamson.md
      - eos_composite.c: Validation/eos_composite.md
      - eos_lookup.c: Validation/eos_lookup.md
      - ic.c: Validation/ic.md
      - interp.c: Validation/interp.md
      - matprop.c: Validation/matprop.md
      - mesh.c: Validation/mesh.md
      - reaction.c: Validation/reaction.md
      - rheologicalfront.c: Validation/rheologicalfront.md
      - rhs.c: Validation/rhs.md
      - twophase.c: Validation/twophase.md

  - Community:
      - Code of Conduct: Community/CODE_OF_CONDUCT.md
      - Contact: Community/contact.md
      - Developers: https://proteus-framework.org/people
      - Issues: https://github.com/FormingWorlds/SPIDER/issues
      
  - Source code: https://github.com/FormingWorlds/SPIDER

  - Other PROTEUS modules:
      - PROTEUS submodules: proteus_framework.md
      - 🔗 PROTEUS:  https://proteus-framework.org/PROTEUS/
      - 🔗 MORS:  https://proteus-framework.org/MORS/
      - 🔗 JANUS: https://proteus-framework.org/JANUS/
      - 🔗 ZEPHYRUS: https://proteus-framework.org/ZEPHYRUS/
      - 🔗 CALLIOPE: https://proteus-framework.org/CALLIOPE/
      - 🔗 AGNI: https://www.h-nicholls.space/AGNI/
      - 🔗 Obliqua: https://proteus-framework.org/Obliqua/
      - 🔗 VULCAN: https://proteus-framework.org/VULCAN/
      - 🔗 Zalmoxis: https://proteus-framework.org/Zalmoxis/
      - 🔗 Aragog: https://proteus-framework.org/aragog/
      - 🔗 Atmodeller: https://github.com/FormingWorlds/Atmodeller/
      - 🔗 FastChem: https://github.com/FormingWorlds/FastChem/
      - 🔗 SOCRATES: https://proteus-framework.org/SOCRATES/

theme:
  name: material
  custom_dir: docs/overrides
  features:
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.expand
    - content.code.copy
    - content.tabs.link

  # Fonts are self-hosted via stylesheets/fonts/fonts.css
  font: false

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

  # The toggle icon shows the current mode, matching the project website
  palette:
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: custom
      accent: custom
      toggle:
        icon: lucide/moon
        name: Switch to light mode

    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: custom
      accent: custom
      toggle:
        icon: lucide/sun
        name: Switch to dark mode

extra_css:
  - stylesheets/extra.css
  - stylesheets/layout.css
  - stylesheets/footnotes.css
 
markdown_extensions:
  - admonition
  - attr_list
  - markdown_include.include:
      base_path: docs
  - pymdownx.extra
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.details
  - md_in_html
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - footnotes

extra_javascript:
  - javascripts/header-links.js
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

# 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-proteus/
      name: PROTEUS on PyPI
    - icon: fontawesome/brands/github
      link: https://github.com/FormingWorlds/PROTEUS
      name: PROTEUS on GitHub
      
plugins:
- search
- tags
- bibtex:
      bib_file: "docs/refs.bib"

- mkdocstrings:
    # https://mkdocstrings.github.io/usage/
    handlers:
      python:
        paths: [src]
        inventories:
        - https://installer.readthedocs.io/en/stable/objects.inv
        - https://docs.python.org/3/objects.inv
        - https://numpy.org/doc/stable/objects.inv
        - https://docs.scipy.org/doc/scipy/objects.inv
        - https://pandas.pydata.org/docs/objects.inv
        - https://matplotlib.org/stable/objects.inv
        options:
          docstring_style: numpy
          docstring_options:
            ignore_init_summary: yes
          show_submodules: no
          show_source: true
          show_symbol_type_heading: True
          show_root_heading: true
          show_root_toc_entry: true
          show_docstring_attributes: true
          show_root_full_path: false
          docstring_section_style: list
          members_order: alphabetical
          merge_init_into_class: yes
          filters: ["!^_"]

use_directory_urls: false

watch:
  - docs/
  - README.md