mkdocs.yml

site_name: GEMDAT
site_url: https://gemdat.readthedocs.io
repo_url: https://github.com/GEMDAT-repos/GEMDAT
repo_name: GitHub

nav:
  - Home: index.md
  - Getting started: getting_started.md
  - Visualization: plotting.md
  - Dashboard: dashboard.md
  - Examples:
    # - Index: notebooks/README.md
    - Introduction: notebooks/introduction.ipynb
    - Loading a CIF File: notebooks/cif_sites.ipynb
    - Generate sites from trajectory: notebooks/volume_sites.ipynb
    - Shape analysis: notebooks/shape_analysis.ipynb
    - Jumps: notebooks/jumps.ipynb
    - Pathways: notebooks/paths.ipynb
    - Percolation: notebooks/percolation.ipynb
    - Multiple paths: notebooks/multiple_paths.ipynb
    - Orientation tracking: notebooks/orientations.ipynb
  - Python API:
    - gemdat: api/gemdat.md
    - gemdat.collective: api/gemdat_collective.md
    - gemdat.io: api/gemdat_io.md
    - gemdat.plots: api/gemdat_plots.md
    - gemdat.rdf: api/gemdat_rdf.md
    - gemdat.metrics: api/gemdat_metrics.md
    - gemdat.trajectory: api/gemdat_trajectory.md
    - gemdat.transitions: api/gemdat_transitions.md
    - gemdat.jumps: api/gemdat_jumps.md
    - gemdat.utils: api/gemdat_utils.md
    - gemdat.volume: api/gemdat_volume.md
  - Contributing: CONTRIBUTING.md
  - Code of Conduct: CODE_OF_CONDUCT.md
  - 🔗 Source code: https://github.com/GEMDAT-repos/GEMDAT
  - 🔗 Issues: https://github.com/GEMDAT-repos/GEMDAT/issues

theme:
  name: material
  primary: blue
  accent: red
  palette:
    accent: indigo

extra_css:
  - stylesheets/extra.css

markdown_extensions:
  - admonition
  - attr_list
  - markdown_include.include:
      base_path: docs
  - pymdownx.extra
  - pymdownx.arithmatex:
      generic: true

extra_javascript:
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

plugins:
- search
- mkdocstrings:
    # https://mkdocstrings.github.io/usage/
    handlers:
      python:
        paths: [src]
        import:
        - https://docs.python.org/3/objects.inv
        - https://numpy.org/doc/stable/objects.inv
        - https://docs.scipy.org/doc/scipy/objects.inv
        - https://pandas.pydata.org/docs/objects.inv
        - https://matplotlib.org/stable/objects.inv
        - https://pymatgen.org/objects.inv
        - https://scikit-image.org/docs/stable/objects.inv
        options:
          docstring_style: numpy
          docstring_options:
            ignore_init_summary: yes
          show_submodules: no
          show_source: true
          show_root_heading: false
          show_root_full_path: false
          docstring_section_style: list
          members_order: alphabetical
          merge_init_into_class: yes
          filters: ["!^_"]
- mkdocs-jupyter:
    include_source: True
    include_requirejs: true  # Fix plotly rendering: https://github.com/danielfrg/mkdocs-jupyter/issues/107
    ignore:
      - gendocs.py
      - genvariables.py
      - .ipynb_checkpoints/*


watch:
  - src/
  - docs/
  - README.md
  - CONTRIBUTING.md
  - CODE_OF_CONDUCT.md