SPIMquant/mkdocs.yml at main · khanlab/SPIMquant · 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
site_name: SPIMquant Documentation
site_url: https://www.khanlab.ca/SPIMquant/
site_description: Quantitative analysis of SPIM (lightsheet) brain data
site_author: Ali Khan

repo_name: khanlab/SPIMquant
repo_url: https://github.com/khanlab/SPIMquant

nav:
  - Home: index.md
  - How It Works: workflow_overview.md
  - Getting Started:
      - Installation: getting_started/installation.md
      - Quick Start: getting_started/quickstart.md
      - Hardware Requirements: getting_started/hardware.md
  - Usage:
      - Command Line Interface: usage/cli.md
      - Configuration: usage/configuration.md
      - Running Workflows: usage/workflows.md
      - Group Analysis: usage/group_analysis.md
      - Cloud Processing: usage/cloud.md
  - How-To Guides:
      - Segmentation Methods: howto/segmentation.md
      - MRI Registration: howto/mri_registration.md
  - Reference:
      - CLI Reference: reference/cli_reference.md
      - Output Files: reference/outputs.md
      - Workflow Visualization: workflow_visualization.md
  - Examples:
      - Sample Datasets: examples/datasets.md
  - FAQ: faq.md
  - Contributing: contributing.md

theme:
  name: material
  palette:
    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.expand
    - navigation.top
    - search.suggest
    - search.highlight
    - content.code.copy
    - content.tabs.link

markdown_extensions:
  - toc:
      toc_depth: 3
      permalink: true
  - admonition
  - pymdownx.details
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.tabbed:
      alternate_style: true
  - attr_list
  - md_in_html
  - tables

plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          options:
            show_source: true
            merge_init_into_class: true
            docstring_style: numpy

hooks:
  - docs/hooks.py