mkdocs.yml

site_name: ZEPHYRUS
site_url: https://proteus-framework.org/ZEPHYRUS/
repo_url: https://github.com/FormingWorlds/ZEPHYRUS
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: How-to/installation.md
      - Run tests: How-to/run_tests.md
      - Build documentation: How-to/documentation.md

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

  - Explanations:
      - Model overview: Explanations/model.md
      - Coupling to PROTEUS: Explanations/proteus.md
      - Limitations: Explanations/limitations.md
      - Testing suite: Explanations/testing.md

  - Reference:
      - Model parameters: Reference/parameters.md
      - API reference:
        - Overview: Reference/api/index.md
        - Escape: Reference/api/escape.md
        - Collision: Reference/api/collision.md
        - Constants: Reference/api/constants.md
        - Planet parameters: Reference/api/planet_parameters.md
      - Validation:
        - Escape: Validation/escape.md
        - Collision: Validation/collision.md
    
  - Community:
      - Contact: Community/contact.md
      - Contributing: Community/CONTRIBUTING.md
      - Code of Conduct: Community/CODE_OF_CONDUCT.md
      - Developers: https://proteus-framework.org/people

  - Source code: https://github.com/FormingWorlds/ZEPHYRUS

  - Other PROTEUS modules:
      - PROTEUS framework: proteus_framework.md
      - 🔗 PROTEUS:  https://proteus-framework.org/PROTEUS/
      - 🔗 JANUS: https://proteus-framework.org/JANUS/
      - 🔗 MORS: https://proteus-framework.org/MORS/
      - 🔗 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/
      - 🔗 SPIDER:  https://proteus-framework.org/SPIDER/
      - 🔗 Atmodeller: https://atmodeller.readthedocs.io/en/latest/
      - 🔗 FastChem: https://github.com/FormingWorlds/FastChem
      - 🔗 SOCRATES: https://github.com/FormingWorlds/SOCRATES/

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

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.tabbed:
      alternate_style: true
  - footnotes
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format


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

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

use_directory_urls: false

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