mkdocs.yml

site_name: Zalmoxis
site_url: https://proteus-framework.org/Zalmoxis
repo_url: https://github.com/FormingWorlds/Zalmoxis

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: How-to/installation.md
      - Configuration: How-to/configuration.md
      - Usage: How-to/usage.md
      - Parameter grids: How-to/grids.md
      - Coupling to PROTEUS: How-to/proteus_coupling.md
      - Build tests: How-to/build_tests.md
      - Releasing: How-to/releasing.md

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

  - Explanations:
      - Model overview: Explanations/model.md
      - Equations of state: Explanations/eos_physics.md
      - Multi-material mixing: Explanations/mixing.md
      - Binodal suppression: Explanations/binodal.md
      - Process flow: Explanations/process_flow.md
      - Coupling to PROTEUS: Explanations/proteus_coupling.md
      - Code architecture: Explanations/code_architecture.md
      - Testing suite: Explanations/testing.md
      - First-principles verification: Explanations/verification.md

  - Reference:
      - API reference:
          - Overview: Reference/api/index.md
          - Config: Reference/api/zalmoxis.config.md
          - Solver: Reference/api/zalmoxis.solver.md
          - Output: Reference/api/zalmoxis.output.md
          - Structure model: Reference/api/zalmoxis.structure_model.md
          - Energetics: Reference/api/zalmoxis.energetics.md
          - EOS package: Reference/api/zalmoxis.eos.md
          - EOS dispatch: Reference/api/zalmoxis.eos.dispatch.md
          - EOS interpolation: Reference/api/zalmoxis.eos.interpolation.md
          - EOS output: Reference/api/zalmoxis.eos.output.md
          - PALEOS tables: Reference/api/zalmoxis.eos.paleos.md
          - PALEOS API: Reference/api/zalmoxis.eos.paleos_api.md
          - PALEOS API cache: Reference/api/zalmoxis.eos.paleos_api_cache.md
          - Seager EOS: Reference/api/zalmoxis.eos.seager.md
          - T-dependent EOS: Reference/api/zalmoxis.eos.tdep.md
          - Adiabat / temperature: Reference/api/zalmoxis.eos.temperature.md
          - Analytic EOS: Reference/api/zalmoxis.eos_analytic.md
          - EOS export: Reference/api/zalmoxis.eos_export.md
          - EOS properties: Reference/api/zalmoxis.eos_properties.md
          - Vinet EOS: Reference/api/zalmoxis.eos_vinet.md
          - JAX EOS package: Reference/api/zalmoxis.jax_eos.md
          - Melting curves: Reference/api/zalmoxis.melting_curves.md
          - Mixing: Reference/api/zalmoxis.mixing.md
          - Binodal: Reference/api/zalmoxis.binodal.md
          - Constants: Reference/api/zalmoxis.constants.md
      - Data: Reference/data.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/Zalmoxis

  - Issues:
      - GitHub issues: https://github.com/FormingWorlds/Zalmoxis/issues
  
  - Other PROTEUS modules:
      - PROTEUS framework: 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/
      - 🔗 Aragog: https://proteus-framework.org/aragog/
      - 🔗 SPIDER: https://proteus-framework.org/SPIDER/
      - 🔗 Atmodeller: https://github.com/FormingWorlds/Atmodeller/
      - 🔗 FastChem: https://github.com/FormingWorlds/FastChem/
      - 🔗 SOCRATES: https://proteus-framework.org/SOCRATES/

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

  icon:
    repo: fontawesome/brands/github 

  # 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
  - footnotes
  - md_in_html
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

# 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-zalmoxis/
      name: Zalmoxis on PyPI
    - icon: fontawesome/brands/github
      link: https://github.com/FormingWorlds/Zalmoxis
      name: Zalmoxis on GitHub

extra_javascript:
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  - https://unpkg.com/katex@0/dist/contrib/auto-render.min.js
  - javascripts/katex.js
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
  - javascripts/header-links.js

plugins:
  - search
  - tags
  - 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:
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            docstring_options:
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            docstring_section_style: table
            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
            members_order: alphabetical
            merge_init_into_class: yes
            filters: ["!^_"]

use_directory_urls: false

watch:
  - src/
  - README.md
  - CONTRIBUTING.md
  - CODE_OF_CONDUCT.md