polyply_1.0/mkdocs.yml at master · marrink-lab/polyply_1.0 · GitHub

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site_name: Polyply
site_description: >-
  A Python suite for facilitating simulations of (bio-)macromolecules and
  nanomaterials — generation of GROMACS input files and starting coordinates.
site_author: The Polyply development team

# The published URL. Update this once the deployment target is decided.
# For GitHub Pages served from a project repo it is:
#   https://<org-or-user>.github.io/<repo>/
site_url: https://marrink-lab.github.io/polyply_1.0/

# Source repository (used for the "edit" and repo links in the header).
repo_url: https://github.com/marrink-lab/polyply_1.0
repo_name: marrink-lab/polyply_1.0
edit_uri: edit/master/docs/

copyright: Copyright &copy; 2020 University of Groningen — Apache 2.0 License

theme:
  name: material
  logo: assets/polyply_logo.png
  favicon: assets/polyply_logo.png
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.sections
    - navigation.top
    - navigation.footer
    - search.suggest
    - search.highlight
    - content.code.copy
    - toc.follow
  palette:
    # Light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  icon:
    repo: fontawesome/brands/github

plugins:
  - search
  # Keeps old wiki URLs working after the migration.
  - redirects:
      redirect_maps:
        "tutorials/martini-polymer-melts.md": "tutorials/martini-polymers.md"

markdown_extensions:
  - admonition
  - attr_list
  - md_in_html
  - tables
  - toc:
      permalink: true
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.superfences
  - pymdownx.inlinehilite
  # Render the $...$ / $$...$$ math used in some tutorials.
  - pymdownx.arithmatex:
      generic: true

# Injects the repo-root LIBRARY.md into the Polymer Library page at build time
# (single source of truth) and rewrites its links to absolute GitHub URLs.
hooks:
  - docs_hooks/include_library.py

extra_javascript:
  - javascripts/mathjax.js
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

nav:
  - Home: index.md
  - Installation: installation.md
  - Quick Start: quick-start.md
  - Polymer Library: reference/polymer-library.md
  - Tutorials:
      - Martini Polymers: tutorials/martini-polymers.md
      - GROMOS Polymer Melts: tutorials/gromos-polymer-melts.md
      - PEGylated Lipid Bilayers: tutorials/pegylated-lipid-bilayers.md
      - Single-Stranded DNA: tutorials/single-stranded-dna.md
      - Martini 3 IDPs / Proteins: tutorials/martini3-idps-proteins.md
      - PEGylated Proteins: tutorials/pegylated-proteins.md
  - Syntax Reference:
      - Build File: reference/build-file-syntax.md
      - gen_seq: reference/gen-seq-syntax.md
      - Writing .ff Input Files: reference/writing-ff-input-files.md
  - Contributing:
      - Submit Polymer Parameters: contributing/submit-polymer-parameters.md
  - FAQs: faqs.md