cardiotensor/mkdocs.yml at main · JosephBrunet/cardiotensor · GitHub

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site_name: Cardiotensor
site_url: https://josephbrunet.github.io/cardiotensor/
site_author: Joseph Brunet
site_description: >-
  Toolkit designed for quantifying and visualising 3D cardiomyocytes orientations in heart images

# Repository
repo_name: cardiotensor
repo_url: https://github.com/JosephBrunet/cardiotensor

edit_uri: edit/main/docs/

# Copyright
copyright: Copyright &copy; 2024 - 2026 - Joseph Brunet


# Page tree
nav:
  - Introduction: index.md
  - Getting Started:
    - getting-started/index.md
    - Installation: getting-started/installation.md
    - First steps: getting-started/first-steps.md
    - Example: getting-started/examples.md
  - Getting Technical:
    - getting-technical/index.md
    - Conventions: getting-technical/conventions.md
    - Structure Tensor: getting-technical/structure_tensor.md
    - Angles: getting-technical/angles.md
    - Fractional Anisotropy: getting-technical/fractional_anisotropy.md
    - Tractography: getting-technical/tractography.md
  - Advanced:
    - advanced/index.md
    - Python API: advanced/python-api.md
    - Transmural Analysis: advanced/cardio-analysis.md
    - Streamlines: advanced/streamlines.md
    - SLURM Launcher: advanced/slurm-launcher.md
  - Reference:
    - reference/index.md
    - CLI Commands: reference/cli.md
    - Configuration file: reference/configuration.md
    - API: reference/api.md
  - Contributing: contributing.md
  - Citing: citing.md


theme:
  name: material
  palette:
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/link
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: astral-dark
      toggle:
        icon: material/toggle-switch-off
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      scheme: astral-light
      toggle:
        icon: material/toggle-switch
        name: Switch to system preferences
  logo: assets/logos/heart_logo_dark.png
  favicon: assets/favicon.png
  icon:
    repo: fontawesome/brands/github
  features:
    - navigation.path
    - navigation.instant
    - navigation.instant.prefetch
    - navigation.instant.progress
    - navigation.sections
    - navigation.indexes
    - navigation.tracking
    - content.code.annotate
    - toc.follow
    - navigation.footer
    - navigation.top
    - content.code.copy
    - content.tabs.link


# Additional configuration
extra:
  status:
    new: Recently added
    deprecated: Deprecated
  analytics:
    provider: google
    property: !ENV GOOGLE_ANALYTICS_KEY
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/JosephBrunet
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/cardiotensor/
    - icon: fontawesome/brands/x-twitter
      link: https://x.com/Joseph__Brunet

extra_css:
  - https://cdn.jsdelivr.net/npm/katex@0.16.9/dist/katex.min.css
  - stylesheets/extra.css
  - stylesheets/mkdocstrings.css


extra_javascript:
  - javascripts/extra.js
  - https://cdn.jsdelivr.net/npm/katex@0.16.9/dist/katex.min.js
  - https://cdn.jsdelivr.net/npm/katex@0.16.9/dist/contrib/auto-render.min.js
  - javascripts/math-render.js

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.snippets:
  - pymdownx.magiclink:
  - attr_list:
  - toc:
      anchorlink: true
      anchorlink_class: "toclink"
      permalink: true
  - md_in_html:
  - pymdownx.inlinehilite:
  - pymdownx.superfences:
  - markdown.extensions.attr_list:
  - pymdownx.keys:
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.arithmatex:
      generic: true


plugins:
  - search
  - autorefs
  # - gen-files:
  #     scripts:
  #     - docs/gen_ref_pages.py
  # - literate-nav:
  #     nav_file: SUMMARY.md
  - section-index
  - git-revision-date-localized:
      enable_creation_date: true
      type: timeago
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths: [src]
          options:
            show_submodules: true
            allow_inspection: true
            show_bases: true
            docstring_section_style: list
            filters: ["!^_"]
            heading_level: 1
            inherited_members: true
            merge_init_into_class: true
            parameter_headings: true
            separate_signature: true
            show_root_heading: true
            show_root_full_path: false
            show_signature_annotations: true
            show_source: false
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            signature_crossrefs: true
            summary: true


validation:
  omitted_files: warn
  absolute_links: warn
  unrecognized_links: warn