mkdocs.yml

site_name: Crystalyse Documentation
site_description: Autonomous AI agents for accelerated inorganic materials design through natural language interfaces
site_url: https://crystalyse-ai.readthedocs.io/
repo_url: https://github.com/ryannduma/CrystaLyse.AI
repo_name: ryannduma/CrystaLyse.AI
edit_uri: edit/main/docs/

# Copyright
copyright: Copyright © 2025 Crystalyse Development Team
# Theme configuration
theme:
  name: material
  language: en
  palette:
    # Light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: blue
      accent: cyan
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: blue
      accent: cyan
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  
  font:
    text: Roboto
    code: Roboto Mono
  
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.expand
    - navigation.path
    - navigation.top
    - navigation.footer
    - search.highlight
    - search.share
    - search.suggest
    - content.code.copy
    - content.code.select
    - content.code.annotate
    - content.tabs.link
    - content.tooltips
    - content.action.edit
    - content.action.view
  
  icon:
    repo: fontawesome/brands/github
    edit: material/pencil 
    view: material/eye

# Documentation structure
nav:
  - Home: index.md
  - Getting Started:
    - Quickstart: quickstart.md
    - Installation: guides/installation.md
    - CLI Usage: guides/cli_usage.md
    - Session Usage: guides/session_based_usage.md
  - Core Concepts:
    - Agents: concepts/agents.md
    - Agent Modes: concepts/agent_modes.md
    - Analysis Modes: concepts/analysis_modes.md
    - Mode Switching: concepts/autonomous_mode_switching.md
    - CLI Architecture: concepts/cli_architecture.md
    - Render Gate System: concepts/render_gate_system.md
    - Memory Systems: concepts/memory.md
    - Sessions: concepts/sessions.md
    - Tools: concepts/tools.md
    - User Interface: concepts/ui.md
    - Provenance: concepts/provenance_system.md
    - Clarification: concepts/clarification_system.md
  - Features:
    - Memory System: features/memory-system.md
    - Session Management: features/session-management.md
  - Tools:
    - Overview: tools/index.md
    - Chemeleon: tools/chemeleon.md
    - MACE: tools/mace.md
    - SMACT: tools/smact.md
    - Visualisation: tools/visualisation.md
  - Reference:
    - API Overview: reference/index.md
    - CLI Reference: reference/cli/index.md
    - Configuration: reference/config/index.md
    - Errors: reference/errors/index.md
    - Architecture: architecture/overview.md

# Extensions
markdown_extensions:
  # Python Markdown
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - toc:
      permalink: true
      title: Table of contents
  
  # Python Markdown Extensions
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

# Plugins
plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
  - minify:
      minify_html: true
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          options:
            docstring_style: google
            docstring_options:
              ignore_init_summary: true
            merge_init_into_class: true
            show_signature_annotations: true
            show_source: false
            members_order: source
            group_by_category: true
            show_category_heading: true
            show_if_no_docstring: false

# Extra CSS and JavaScript
extra_css:
  - assets/stylesheets/extra.css

extra_javascript:
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

# Additional configuration
extra:
  analytics:
    provider: google
    property: G-XXXXXXXXXX  # Replace with actual GA4 property
  
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/ryannduma/CrystaLyse.AI
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/crystalyse/
    - icon: fontawesome/solid/globe
      link: https://crystalyse.ai
  
  version:
    provider: mike
    default: stable

# Validation
strict: true
validation:
  omitted_files: warn
  absolute_links: warn
  unrecognized_links: warn