vepyr/mkdocs.yml at master · biodatageeks/vepyr · 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
site_name: vepyr
site_url: https://biodatageeks.org/vepyr/
repo_url: https://github.com/biodatageeks/vepyr
repo_name: biodatageeks/vepyr

# Internal planning notes and design specs live under docs/superpowers/ and are
# not part of the published site.
exclude_docs: |
  superpowers/

nav:
  - Home:
      - Home: index.md
      - Quick start: quickstart.md
      - Architecture: architecture.md
      - Caches: caches.md
      - Plugins: plugins.md
      - Polars DataFrames: dataframes.md
      - Command line: cli.md
      - Nextflow: nextflow.md
      - API: api.md
      - Performance: performance.md
      - Testing vs Ensembl VEP: testing-vep.md
      - Download Ensembl VEP and plugin caches: downloads.md
      - Developers: developers.md
      - Applying a fix (runbook): runbooks/applying-a-vepyr-fix.md
      - Contact: contact.md

theme:
  name: material
  logo: assets/logo.png
  favicon: assets/logo.png
  features:
    - content.code.copy
    - content.code.select
    - content.code.annotate
    - content.tabs.link
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.footer
    - navigation.instant
    - navigation.instant.progress
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: deep purple
      accent: amber
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: deep purple
      accent: amber
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

plugins:
  - search
  - glightbox:
      # Route Material's #only-light / #only-dark variants into separate
      # galleries so the lightbox never steps onto the hidden-theme copy.
      auto_themed: true
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          options:
            docstring_style: numpy
            show_source: false
            show_root_heading: true
            members_order: source

markdown_extensions:
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - pymdownx.details
  - pymdownx.highlight:
      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
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.tasklist:
      custom_checkbox: true
  - toc:
      permalink: true

extra:
  analytics:
    provider: google
    property: G-X2YYYSXDCD