mkdocs.yml

theme:
    name: material
    icon:
        logo: material/snowflake
    features:
        - navigation.sections  # Sections are included in the navigation on the left.
        - toc.integrate  # Table of contents is integrated on the left; does not appear separately on the right.

site_name: cryoJAX
site_description: The documentation for cryoJAX.
site_author: Michael O'Brien
site_url: https://mjo22.github.io/cryojax/

repo_url: https://github.com/mjo22/cryojax
repo_name: mjo22/cryojax
edit_uri: ""

strict: false

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_css:
    - _static/custom_css.css

markdown_extensions:
    - pymdownx.arithmatex:
        generic: true
    - pymdownx.superfences  # Seems to enable syntax highlighting when used with the Material theme.
    - pymdownx.details  # Allowing hidden expandable regions denoted by ???
    - admonition
    - toc:
        permalink: "¤"  # Adds a clickable permalink to each section heading
        toc_depth: 4

plugins:
    - autorefs  # Cross-links to headings
    - mknotebooks
    - mkdocstrings:
        handlers:
          python:
            paths: [src]  # search packages in the src folder
            options:
              annotations_path: full
              group_by_category: false
              inherited_members: true
              show_root_heading: true
              show_root_members_full_path: true
              show_root_full_path: true
              show_if_no_docstring: true
              show_signature_annotations: true
              signature_crossrefs: true
              show_source: false
              show_bases: false
              members_order: source
              heading_level: 4

nav:
    - 'index.md'
    - Examples:
        - Introductory:
            - Compute a scattering potential: 'examples/compute-potential.ipynb'
            - Simulate an image: 'examples/simulate-image.ipynb'
            - Read a particle stack: 'examples/read-dataset.ipynb'
        - Intermediate:
            - Simulate a superposition of images: 'examples/simulate-micrograph.ipynb'
            - Write a STAR file of simulated data: 'examples/simulate-relion-dataset.ipynb'
            - Run a cross-correlation search: 'examples/cross-correlation-search.ipynb'
    - Simulator API:
        - 'api/simulator/scattering_potential.md'
        - 'api/simulator/instrument_config.md'
        - 'api/simulator/potential_integrators.md'