osipy/mkdocs.yml at main · Devguru-codes/osipy · 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
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
site_name: osipy
site_description: OSIPI-compliant MRI perfusion analysis library
site_url: https://osipy.readthedocs.io
repo_url: https://github.com/OSIPI/osipy
repo_name: OSIPI/osipy

theme:
  name: material
  palette:
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/link
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/toggle-switch
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: black
      accent: indigo
      toggle:
        icon: material/toggle-switch-off
        name: Switch to system preference
  features:
    - content.action.edit
    - content.action.view
    - content.code.annotate
    - content.code.copy
    - content.tabs.link
    - content.tooltips
    - navigation.footer
    - navigation.indexes
    - navigation.instant
    - navigation.instant.prefetch
    - navigation.path
    - navigation.sections
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
  font:
    text: Roboto
    code: Roboto Mono
  icon:
    logo: material/brain
    repo: fontawesome/brands/github

extra_css:
  - stylesheets/extra.css

plugins:
  - search
  - gen-files:
      scripts:
        - docs/gen_ref_pages.py
        - docs/gen_config_docs.py
  - literate-nav:
      nav_file: SUMMARY.md
  - mkdocstrings:
      handlers:
        python:
          paths: [.]
          options:
            docstring_style: numpy
            docstring_section_style: spacy
            show_source: false
            show_root_heading: true
            show_root_full_path: false
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            members_order: source
            merge_init_into_class: true
            separate_signature: true
            signature_crossrefs: true

markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.mark
  - pymdownx.critic
  - pymdownx.keys
  - pymdownx.snippets
  - admonition
  - pymdownx.details
  - attr_list
  - md_in_html
  - abbr
  - footnotes
  - def_list
  - tables
  - toc:
      permalink: true
      toc_depth: 3

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

nav:
  - Home: index.md
  - Tutorials:
    - tutorials/index.md
    - Getting Started: tutorials/getting-started.md
    - DCE-MRI Analysis: tutorials/dce-analysis.md
    - ASL CBF Quantification: tutorials/asl-analysis.md
    - IVIM Analysis: tutorials/ivim-analysis.md
    - DSC-MRI Analysis: tutorials/dsc-analysis.md
  - How-To Guides:
    - how-to/index.md
    - Data Loading:
      - Load Perfusion Data: how-to/load-perfusion-data.md
    - AIF Selection:
      - Use Custom AIF: how-to/use-custom-aif.md
      - Choose Population AIF: how-to/choose-population-aif.md
    - GPU Acceleration:
      - Configure GPU/CPU Backend: how-to/enable-gpu-acceleration.md
    - Export & Visualization:
      - Export BIDS: how-to/export-bids.md
      - Visualize Maps: how-to/visualize-parameter-maps.md
    - Model Fitting:
      - Compare Models: how-to/fit-multiple-models.md
      - Handle Failures: how-to/handle-fitting-failures.md
    - Pipelines:
      - Run Pipeline from YAML (CLI): how-to/run-pipeline-cli.md
      - Run Complete Pipeline (Python API): how-to/run-complete-pipeline.md
    - Extension:
      - Add Pharmacokinetic Model: how-to/add-pharmacokinetic-model.md
      - Add ASL Model: how-to/add-asl-quantification-model.md
      - Add Deconvolution Method: how-to/add-deconvolution-method.md
      - Add BBB ASL Model: how-to/add-bbb-asl-model.md
  - Reference: reference/
  - Explanation:
    - explanation/index.md
    - Software Architecture:
      - Architecture Overview: explanation/architecture.md
      - xp Abstraction Pattern: explanation/xp-abstraction.md
      - OSIPI Standards: explanation/osipi-standards.md
    - MRI Physics:
      - Pharmacokinetic Models: explanation/pharmacokinetic-models.md
      - ASL Physics: explanation/asl-physics.md
      - IVIM Theory: explanation/ivim-theory.md
      - DSC Deconvolution: explanation/dsc-deconvolution.md
  - Contributing:
    - contributing.md
  - Product Requirements: prd.md