mkdocs.yml

site_name: flowpaths
repo_url: https://github.com/algbio/flowpaths

nav:
  - Home: 
    - About: index.md
    - References: references.md
  - Decomposition models:
    - Models:
      - Minimum Flow Decomposition: minimum-flow-decomposition.md
      - $k$-Flow Decomposition: k-flow-decomposition.md
      - $k$-Least Absolute Errors: k-least-absolute-errors.md
      - $k$-Minimum Path Error: k-min-path-error.md
      - Optimizing $k$: numpathsoptimization.md
    - Additional features:
      - Flows/weights on nodes: node-expanded-digraph.md
      - Subpath constraints: subpath-constraints.md
      - Ignoring edges: ignoring-edges.md
      - Additional start/end nodes: additional-start-end-nodes.md
      - Correcting weights: minimum-error-flow.md
    - Further options:
      - Solver options and optimizations: solver-options-optimizations.md
      - Various utils: utils.md
    
  - Developing new models:
    - Abstract Path Model: abstract-path-model.md
    - Solver Wrapper: solver-wrapper.md
    - stDiGraph: stdigraph.md  
    - Minimum Generating Set: minimum-generating-set.md
    - Minimum Set Cover: minimum-set-cover.md

use_directory_urls: false

theme:
  name: material
  theme:
  palette:
    # Palette toggle for automatic mode
    - media: "(prefers-color-scheme)"
      primary: black
      toggle:
        icon: material/lightbulb-auto
        name: Switch to light mode

    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      primary: black
      scheme: default 
      toggle:
        icon: material/lightbulb
        name: Switch to dark mode

    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      primary: black
      scheme: slate
      toggle:
        icon: material/lightbulb-outline
        name: Switch to system preference

  features:
    - content.code.copy
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.expand
    - navigation.path
  logo: flowpaths-logo.svg  
  favicon: flowpaths-logo.svg
  icon:
    repo: fontawesome/brands/github

extra_javascript:
  - javascripts/katex.js
  - https://unpkg.com/katex@0/dist/katex.min.js
  - https://unpkg.com/katex@0/dist/contrib/auto-render.min.js

extra_css:
  - https://unpkg.com/katex@0/dist/katex.min.css

markdown_extensions:
  - pymdownx.highlight:
      use_pygments: true
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - attr_list
  - md_in_html
  - smarty
  - admonition
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.details


plugins:
  - search 
  - macros:
      module_name: docs/getversion
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          inventories:
          - url: https://docs.python-requests.org/en/master/objects.inv
            domains: [std, py]
          options:
            show_root_toc_entry: false
            # docstring_options:
            merge_init_into_class: true
            # docstring_section_style: spacy
            separate_signature: true 
            show_signature_annotations: true
            modernize_annotations: true
            signature_crossrefs: false
            line_length: 30
          load_external_modules: true