mkdocs.yml

site_name: "femto"
site_description: "A comprehensive toolkit for predicting free energies."
site_url: "https://github.com/psivant/femto"
repo_url: "https://github.com/psivant/femto"
repo_name: "psivant/femto"
site_dir: "site"
watch: [mkdocs.yml, README.md, femto/, docs]
copyright: Copyright © 2023 Psivant Therapeutics, Simon Boothroyd
edit_uri: edit/main/docs/

validation:
  omitted_files: warn
  absolute_links: warn
  unrecognized_links: warn

extra:
  version:
    provider: mike

nav:
- Home:
  - Overview: index.md
- Guide:
  - MD:
    - Overview: guide-md.md
  - FE:
    - Overview: guide-fe.md
    - ATM: guide-atm.md
    - SepTop: guide-septop.md
- API reference: reference/
- Development: development.md

theme:
  name: material
  features:
  - announce.dismiss
  - content.action.edit
  - content.action.view
  - content.code.annotate
  - content.code.copy
  - content.tooltips
  - navigation.footer
  - navigation.indexes
  - navigation.sections
  - navigation.tabs
  - navigation.tabs.sticky
  - navigation.top
  - search.highlight
  - search.suggest
  - toc.follow
  palette:
  - media: "(prefers-color-scheme: light)"
    scheme: default
    primary: teal
    accent: purple
    toggle:
      icon: material/weather-sunny
      name: Switch to dark mode
  - media: "(prefers-color-scheme: dark)"
    scheme: slate
    primary: black
    accent: lime
    toggle:
      icon: material/weather-night
      name: Switch to light mode

markdown_extensions:
- attr_list
- def_list
- admonition
- footnotes
- pymdownx.highlight:
    anchor_linenums: true
    line_spans: __span
    pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.superfences
- pymdownx.magiclink
- pymdownx.snippets:
    check_paths: true
- pymdownx.details
- pymdownx.arithmatex:
    generic: true
- pymdownx.tabbed:
    alternate_style: true
- toc:
    permalink: "#"

plugins:
- autorefs
- search
- gen-files:
    scripts:
    - docs/scripts/gen_ref_pages.py
- literate-nav:
    nav_file: SUMMARY.md
- mkdocstrings:
    handlers:
      python:
        paths: [femto/]
        import:
          - https://parmed.github.io/ParmEd/html/objects.inv
          - http://docs.openmm.org/latest/api-python/objects.inv
          - https://www.mdtraj.org/1.9.6/objects.inv
        options:
          extensions: [ griffe_pydantic ]
          docstring_options:
            ignore_init_summary: true
            returns_multiple_items: false
            returns_named_value: false
          docstring_section_style: list
          heading_level: 1
          inherited_members: true
          merge_init_into_class: true
          separate_signature: true
          show_root_heading: true
          show_root_full_path: false
          show_signature_annotations: true
          show_symbol_type_heading: true
          show_symbol_type_toc: true
          signature_crossrefs: true
          summary: true
          members_order: source

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