snpick/mkdocs.yml at main · PathoGenOmics-Lab/snpick · 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
site_name: SNPick
site_description: Fast, memory-efficient extraction of variable sites from FASTA alignments
site_url: https://pathogenomics-lab.github.io/snpick/
site_author: Paula Ruiz-Rodriguez
repo_url: https://github.com/PathoGenOmics-Lab/snpick
repo_name: PathoGenOmics-Lab/snpick
edit_uri: edit/main/docs/
copyright: Copyright &copy; Paula Ruiz-Rodriguez &amp; Mireia Coscolla — I²SysBio (UV-CSIC)

theme:
  name: material
  custom_dir: overrides
  logo: assets/logo.svg
  favicon: assets/logo.png
  language: en
  palette:
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: deep purple
      accent: pink
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: deep purple
      accent: pink
      toggle:
        icon: material/brightness-4
        name: Switch to system preference
  font:
    text: Inter
    code: JetBrains Mono
  features:
    - announce.dismiss
    - navigation.instant
    - navigation.instant.prefetch
    - navigation.instant.progress
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.sections
    - navigation.indexes
    - navigation.top
    - navigation.footer
    - navigation.tracking
    - navigation.path
    - toc.follow
    - search.suggest
    - search.highlight
    - search.share
    - content.code.copy
    - content.code.annotate
    - content.code.select
    - content.tabs.link
    - content.tooltips
    - content.action.edit
    - content.action.view
  icon:
    repo: fontawesome/brands/github
    edit: material/pencil
    view: material/eye

nav:
  - Home: index.md
  - Installation: installation.md
  - Usage: usage.md
  - Tutorial: tutorials/tutorial.ipynb
  - Output formats: output.md
  - Benchmarks: benchmarks.md
  - Architecture: architecture.md
  - Contributing: contributing.md
  - Changelog: changelog.md
  - Tags: tags.md

markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: true
      title: On this page
  - pymdownx.betterem
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      base_path: [".", "docs"]
      auto_append: ["includes/abbreviations.md"]
      check_paths: true
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
      slugify: !!python/object/apply:pymdownx.slugs.slugify
        kwds:
          case: lower
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

plugins:
  - search
  - tags
  - mkdocs-jupyter:
      execute: false
      include_source: true
      ignore_h1_titles: true
  - glightbox:
      touchNavigation: true
      loop: false
      effect: zoom
      draggable: true
  - git-revision-date-localized:
      type: timeago
      enable_creation_date: true
      enable_git_follow: false
      fallback_to_build_date: true
  - social:
      # Social cards need Cairo/Pango; generate them only in CI (where the libs
      # are installed), so local builds don't require the native dependencies.
      enabled: !ENV [CI, false]
      cards_layout_options:
        background_color: "#5e35b1"
  - minify:
      minify_html: true

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/PathoGenOmics-Lab
      name: PathoGenOmics-Lab on GitHub
    - icon: fontawesome/brands/python
      link: https://anaconda.org/bioconda/snpick
      name: SNPick on Bioconda

extra_css:
  - stylesheets/extra.css

# The abbreviations glossary is auto-appended via snippets, not a standalone page.
exclude_docs: |
  includes/