pymsm/mkdocs.yml at main · melhk/pymsm · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
theme:
    name: material
    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.
        # - header.autohide  # header disappears as you scroll
    palette:
        - scheme: default
          primary: white
          accent: amber
          toggle:
             icon: material/weather-night
             name: Switch to dark mode
        - scheme: slate
          primary: black
          accent: amber
          toggle:
             icon: material/weather-sunny
             name: Switch to light mode
    icon:
      repo: fontawesome/brands/github  # GitHub logo in top right
    logo: pymsm_icon.svg # logo in top left
    favicon: pymsm_icon.svg # logo in top left


site_name: PyMSM
site_description: The documentation for the PyMSM software library.
site_author: Hagai Rossman, Ayya Keshet

repo_url: https://github.com/hrossman/pymsm/
repo_name: hrossman/pymsm
edit_uri: ""  # No edit button, as some of our pages are in /docs and some in /examples via symlink, so it's impossible for them all to be accurate

strict: false  # Don't allow warnings during the build process

markdown_extensions:
    - tables
    - pymdownx.highlight:
        anchor_linenums: true
    - pymdownx.inlinehilite
    - pymdownx.arithmatex:  # Render LaTeX via MathJax
        generic: true
    - pymdownx.details  # Allowing hidden expandable regions denoted by ???
    - pymdownx.snippets:  # Include one Markdown file into another
        base_path: docs
    - admonition
    - toc:
        permalink: "¤"  # Adds a clickable permalink to each section heading
        toc_depth: 4  # Prevents h5, h6 from showing up in the TOC.
    - pymdownx.superfences:
        custom_fences:
          - name: mermaid
            class: mermaid
            format: !!python/name:pymdownx.superfences.fence_code_format


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


nav:
    - index.md
    - Usage:
      - usage/Preparing_a_dataset.ipynb
      - usage/fitting_a_multistate_model.ipynb
      - usage/path_sampling.ipynb
      - usage/Datasets.ipynb
      - usage/competing_risks_stackplot.ipynb
      - usage/examining_a_model.ipynb
      - usage/custom_fitters.md
      - usage/Simulator.md
    - Full examples:
      - full_examples/Rotterdam_example.ipynb
      - full_examples/COVID_hospitalization_example.ipynb
      - full_examples/AIDSI_example.ipynb
      - full_examples/EBMT_example.ipynb
    - API:
      - api/multistate_model.md
      - api/multistate_simulator.md
      - api/pathobject.md


plugins:
  - mknotebooks
  - search
  - mkdocstrings

extra:
  copyright: Copyright &copy; 2022 Hagai Rossman, Ayya Keshet, Malka Gorfine
  analytics:
    provider: google
    property: G-4PXS01G51T