mkdocs.yml

site_name: ComProScanner Documentation
site_description: A comprehensive Python package for extracting composition-property data from scientific articles for building databases
site_author: Aritra Roy
site_url: https://slimeslab.github.io/ComProScanner/

repo_name: slimeslab/ComProScanner
repo_url: https://github.com/slimeslab/ComProScanner
edit_uri: edit/main/docs/

copyright: Copyright &copy; 2025 SLIMES Lab - Licensed under <a href="about/license/" style="color:#009485" onMouseOver="this.style.color='#ff9100'" onMouseOut="this.style.color='#009485'">MIT</a>

theme:
  name: material
  custom_dir: docs/overrides
  logo: assets/comproscanner_logo_small.png
  favicon: assets/comproscanner_logo_small.ico
  palette:
    # Palette toggle for light mode
    - scheme: default
      primary: teal
      accent: orange
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Palette toggle for dark mode
    - scheme: slate
      primary: teal
      accent: orange
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  font:
    text: Roboto
    code: Roboto Mono
  features:
    - navigation.instant
    - navigation.instant.progress
    - navigation.tracking
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.sections
    - navigation.expand
    - navigation.path
    - navigation.top
    - navigation.footer
    - navigation.indexes
    - toc.follow
    - toc.integrate
    - search.suggest
    - search.highlight
    - search.share
    - header.autohide
    - content.code.copy
    - content.code.annotate
    - content.tabs.link
    - content.tooltips

plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"/]+|(?!\b)(?=[A-Z][a-z])|\.(?!\d)|&[lg]t;'
  - minify:
      minify_html: true
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths: [src] # Points to the source code
          options:
            show_symbol_type_toc: true
            allow_inspection: true
            docstring_style: google
            heading_level: 2
            show_root_heading: true
            show_root_full_path: false
            show_signature_annotations: true
            separate_signature: true
            members_order: source

markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - toc:
      permalink: true
      title: On this page
  - 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

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/slimeslab
      name: GitHub Profile
    - icon: fontawesome/solid/globe
      link: https://slimeslab.github.io
      name: Personal Website
  version:
    provider: mike
  analytics:
    provider: google
    property:
    feedback:
      title: Was this page helpful?
      ratings:
        - icon: material/emoticon-happy-outline
          name: This page was helpful
          data: 1
          note: >-
            Thanks for your feedback!
        - icon: material/emoticon-sad-outline
          name: This page could be improved
          data: 0
          note: >-
            Thanks for your feedback! Help us improve by
            <a href="https://github.com/slimeslab/ComProScanner/issues/new" target="_blank" rel="noopener">opening an issue</a>.

extra_css:
  - stylesheets/extra.css

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

nav:
  - Home: index.md
  - Getting Started:
      - Installation: getting-started/installation.md
      - Quick Start: getting-started/quick-start.md
  - User Guide:
      - Metadata Collection: usage/metadata-collection.md
      - Article Processing: usage/article-processing.md
      - Data Extraction: usage/data-extraction.md
      - Data Cleaning: usage/data-cleaning.md
      - Evaluation:
          - Overview: usage/evaluation/overview.md
          - Semantic Evaluation: usage/evaluation/semantic.md
          - Agentic Evaluation: usage/evaluation/agentic.md
      - Visualization:
          - Overview: usage/visualization/overview.md
          - Data Visualization: usage/visualization/data-viz.md
          - Evaluation Visualization: usage/visualization/eval-viz.md
  - RAG Configuration: rag-config.md
  - API Overview: api.md
  - About:
      - Project Structure: about/project-structure.md
      - License: about/license.md
      - Changelog: about/changelog.md
      - Contribution: about/contribution.md
      - Citation: about/citation.md
      - Contact: about/contact.md