mkdocs.yml

site_name: DeepCV
site_description: DeepCV - Deep Learning Framework for Discovering Collective Variables
site_url: https://lubergroup.pages.uzh.ch/deepcv
site_dir: public
site_author: Luber Group, UZH

repo_url: https://gitlab.uzh.ch/lubergroup/deepcv
repo_name: GitLab

theme:
  name: material
  features:
    - navigation.sections

nav:
  - Introduction: 
    - DeepCV: index.md
    - DAENN: introduction/daenn.md
    - Descriptors: introduction/descriptors.md
  - Installation:
    - Overview: installation/overview.md
    - Environment setup: installation/env-setup.md
    - Installing: installation/install.md
    - Compiling: installation/compile.md
  - Usage:
    - Overview: usage/overview.md
    - Datasets: usage/prepare-dataset.md
    - Input file: usage/input-file.md
    - Models: usage/training-model.md
    - Enhanced sampling:
      - Metadynamics: usage/metad-sim.md
    - Analysis:
      - Free energy surface: usage/fes-analysis.md
      - Metastable states: usage/states-analysis.md
  - Citing: citing.md

plugins:
  - search
  - bibtex:
      bib_file: "docs/ref.bib"
      # cite_style: "pandoc"

markdown_extensions:
  - pymdownx.arithmatex
  - pymdownx.extra
  - pymdownx.magiclink
  - pymdownx.tilde
  - pymdownx.tasklist
  - pymdownx.smartsymbols
  - pymdownx.mark
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.tabbed
  - admonition
  - footnotes
  - toc

extra_javascript:
    - 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-MML-AM_CHTML'