properdocs.yml

site_name: MyoGen
site_description: Modular neuromuscular simulation framework for motor-unit activity, force, and EMG.
site_url: https://nsquaredlab.github.io/MyoGen/
repo_url: https://github.com/NsquaredLab/MyoGen
repo_name: MyoGen
edit_uri: edit/main/docs/
copyright: Copyright © 2025-2026 n-squared lab, FAU Erlangen-Nürnberg

# superpowers specs/plans live under docs/ but are not site pages
exclude_docs: |
  superpowers/

# Never ship Jupyter notebooks: strip the gallery's "Download Jupyter notebook"
# button and delete every generated .ipynb from the built site.
hooks:
  - docs/hooks/no_notebooks.py

extra_css:
  - stylesheets/gallery.css

extra_javascript:
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

theme:
  name: material
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.sections
    - navigation.indexes
    - navigation.top
    - search.suggest
    - search.highlight
    - content.code.copy
    - content.code.annotate
    - toc.follow
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: white
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: black
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  font:
    text: Inter
    code: JetBrains Mono
  icon:
    repo: fontawesome/brands/github

plugins:
  - search
  - section-index
  - gallery:
      conf_script: docs/gallery_conf.py
      # Source-only by default: examples render as markdown (prose + code) with
      # "download full example code" links, but are NOT executed — many MyoGen
      # examples use multiprocessing/joblib (which breaks under gallery exec) or
      # form slow inter-dependent chains. Opt in to execution locally with
      # MKDOCS_GALLERY_PLOT=true.
      plot_gallery: !ENV [MKDOCS_GALLERY_PLOT, false]
  - mkdocstrings:
      handlers:
        python:
          paths: [.]
          inventories:
            - https://docs.python.org/3/objects.inv
            - https://numpy.org/doc/stable/objects.inv
            - https://docs.scipy.org/doc/scipy/objects.inv
          options:
            docstring_style: numpy
            show_source: true
            show_root_heading: true
            show_root_full_path: false
            members_order: source
            separate_signature: true
            show_signature_annotations: true
            signature_crossrefs: true
            merge_init_into_class: true
            heading_level: 2
            filters:
              - "!^_"

markdown_extensions:
  - admonition
  - attr_list
  - pymdownx.arithmatex:
      generic: true
  - def_list
  - md_in_html
  - tables
  - toc:
      permalink: true
  - pymdownx.details
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.highlight:
      anchor_linenums: true
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.magiclink
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

nav:
  - Home: index.md
  - Getting Started: getting-started.md
  - Neo blocks: neo-blocks.md
  - Examples:
      - Basics: auto_examples/01_basic/index.md
      - Fine-tuning: auto_examples/02_finetune/index.md
      - Watanabe (paper): auto_examples/03_papers/watanabe/index.md
      - Clinical: auto_examples/04_clinical/index.md
  - API reference:
      - api/index.md
      - Top-level: api/myogen.md
      - Simulator: api/simulator.md
      - Currents: api/currents.md
      - Injection & I/O: api/io-and-neuron.md
      - Plotting: api/plotting.md
      - Utilities: api/utils.md
      - Types: api/types.md