mkdocs.yml

# Required python packages to generate the documentation
# * mkdocs
# * mkdocs-material
# * pygments
# * pymdown-extensions
# * mknotebooks

# Project information
site_name: 'pycoMeth'
site_description: 'Python package for nanopore DNA methylation analysis downstream to Nanopolish'
site_author: 'Adrien Leger'
site_url: 'https://a-slide.github.io/pycoMeth/'

# Repository
repo_name: 'a-slide/pycoMeth'
repo_url: 'https://github.com/a-slide/pycoMeth'

# Copyright
copyright: 'Copyright © 2019 Adrien Leger'

# Navigation menu
nav:
    - Home: index.md
    - Installation instructions: installation.md
    - CpG_Aggregate Usage:
        - Using CpG_Aggregate: CpG_Aggregate/usage.md
        - jupyter API usage: CpG_Aggregate/API_usage.ipynb
        - Command line usage: CpG_Aggregate/CLI_usage.ipynb
    - Interval_Aggregate Usage:
        - Using Interval_Aggregate: Interval_Aggregate/usage.md
        - jupyter API usage: Interval_Aggregate/API_usage.ipynb
        - Command line usage: Interval_Aggregate/CLI_usage.ipynb
    - Meth_Comp Usage:
        - Using Meth_Comp: Meth_Comp/usage.md
        - jupyter API usage: Meth_Comp/API_usage.ipynb
        - Command line usage: Meth_Comp/CLI_usage.ipynb
    - Comp_Report Usage:        
        - Using Comp_Report: Comp_Report/usage.md
        - jupyter API usage: Comp_Report/API_usage.ipynb
        - Command line usage: Comp_Report/CLI_usage.ipynb
    - CGI_Finder Usage:
        - Using CGI_Finder: CGI_Finder/usage.md
        - jupyter API usage: CGI_Finder/API_usage.ipynb
        - Command line usage: CGI_Finder/CLI_usage.ipynb
    - Contributing: contributing.md
    - Code of conduct: code_of_conduct.md
    - Licence: licence.md
    - Changelog: changelog.md

# Theme customization
theme:
    name: 'material'
    highlightjs: true
    font: false

markdown_extensions:
  - admonition
  - codehilite
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.emoji:
      emoji_generator: !!python/name:pymdownx.emoji.to_svg
  - pymdownx.inlinehilite
  - pymdownx.magiclink:
      repo_url_shorthand: true
      user: a-slide
      repo: pycoMeth
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.superfences
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

plugins:
  - mknotebooks