mkdocs.yml

# MkDocs Configuration for Multi-Modal Academic Research System
site_name: Multi-Modal Academic Research System
site_description: Comprehensive documentation for the Multi-Modal Academic Research System - A Python application for collecting, processing, and querying academic content using RAG with OpenSearch and Google Gemini.
site_author: Development Team
site_url: https://yourdomain.com/docs

# Repository
repo_name: multi-modal-research
repo_url: https://github.com/yourusername/multi-modal-academic-research-system
edit_uri: edit/main/docs/

# Copyright
copyright: Copyright © 2024 Multi-Modal Research Team

# Theme Configuration
theme:
  name: material

  # Color Palette
  palette:
    # Light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode

    # Dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

  # Font
  font:
    text: Roboto
    code: Roboto Mono

  # Logo and favicon
  logo: assets/logo.png
  favicon: assets/favicon.png

  # Features
  features:
    - announce.dismiss
    - content.action.edit
    - content.action.view
    - content.code.annotate
    - content.code.copy
    - content.tabs.link
    - content.tooltips
    - navigation.expand
    - navigation.footer
    - navigation.indexes
    - navigation.instant
    - navigation.instant.prefetch
    - navigation.instant.progress
    - navigation.path
    - navigation.prune
    - navigation.sections
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
    - toc.integrate

  # Custom CSS
  extra_css:
    - stylesheets/extra.css

# Plugins
plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"/]+|(?!\b)(?=[A-Z][a-z])|\.(?!\d)|&[lg]t;'
      lang:
        - en
  # - minify:
  #     minify_html: true
  #     minify_js: true
  #     minify_css: true
  # - git-revision-date-localized:
  #     enable_creation_date: true
  #     type: timeago
  - tags:
      tags_file: tags.md

# Extensions
markdown_extensions:
  # Python Markdown
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: true
      toc_depth: 3

  # PyMdown 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.snippets
  - 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

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

# Extra
extra:
  version:
    provider: mike
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/yourusername/multi-modal-academic-research-system
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/multi-modal-research/
  analytics:
    provider: google
    property: G-XXXXXXXXXX
  consent:
    title: Cookie consent
    description: >-
      We use cookies to recognize your repeated visits and preferences, as well
      as to measure the effectiveness of our documentation and whether users
      find what they're searching for. With your consent, you're helping us to
      make our documentation better.

# Navigation Structure
nav:
  - Home: index.md
  - Getting Started:
      - Overview: README.md
      - Installation: setup/installation.md
      - Quick Start: setup/quick-start.md
      - Configuration: setup/configuration.md

  - Architecture:
      - System Overview: architecture/overview.md
      - Data Flow: architecture/data-flow.md
      - Technology Stack: architecture/technology-stack.md

  - Core Modules:
      - Data Collectors: modules/data-collectors.md
      - Data Processors: modules/data-processors.md
      - Indexing System: modules/indexing.md
      - Database: modules/database.md
      - API Server: modules/api.md
      - Orchestration: modules/orchestration.md
      - User Interface: modules/ui.md

  - Tutorials:
      - Overview: tutorials/README.md
      - Collecting Papers: tutorials/collect-papers.md
      - Custom Searches: tutorials/custom-searches.md
      - Export Citations: tutorials/export-citations.md
      - Visualization: tutorials/visualization.md
      - Extending System: tutorials/extending.md

  - Deployment:
      - Overview: deployment/README.md
      - Local Setup: deployment/local.md
      - Docker: deployment/docker.md
      - OpenSearch: deployment/opensearch.md
      - Production: deployment/production.md

  - Database:
      - Schema Overview: database/schema.md
      - Collections Table: database/collections-table.md
      - Type-Specific Tables: database/type-tables.md

  - API Reference:
      - REST API: api/rest-api.md
      - Database API: api/database-api.md

  - Troubleshooting:
      - Common Issues: troubleshooting/common-issues.md
      - OpenSearch: troubleshooting/opensearch.md
      - API Errors: troubleshooting/api-errors.md
      - FAQ: troubleshooting/faq.md

  - Advanced Topics:
      - Embedding Models: advanced/embedding-models.md
      - Hybrid Search: advanced/hybrid-search.md
      - Gemini Integration: advanced/gemini.md
      - Performance: advanced/performance.md
      - Custom Collectors: advanced/custom-collectors.md

  - Reference:
      - Documentation Index: DOCUMENTATION_INDEX.md
      - Documentation Summary: DOCUMENTATION_SUMMARY.md