mkdocs.yml

site_name: "graphium"
site_description: "Graphium: Scaling molecular GNNs to infinity."
site_url: "https://github.com/datamol-io/graphium"
repo_url: "https://github.com/datamol-io/graphium"
repo_name: "valence-discovery/graphium"
copyright: Copyright 2020 - 2023 datamol.io

remote_branch: "gh-pages"
use_directory_urls: false
docs_dir: "docs"

nav:
  - Overview: index.md
  - Baseline: baseline.md
  - API:
      - graphium.nn:
          - graphium.nn: api/graphium.nn/graphium.nn.md
          - graphium.nn.architectures: api/graphium.nn/architectures.md
          - graphium.nn.encoders: api/graphium.nn/encoders.md
          - graphium.nn.pyg_layers: api/graphium.nn/pyg_layers.md
      - graphium.features: api/graphium.features.md
      - graphium.trainer: api/graphium.trainer.md
      - graphium.data: api/graphium.data.md
      - graphium.utils: api/graphium.utils.md
      - graphium.config: api/graphium.config.md
      - graphium.ipu: api/graphium.ipu.md
      - graphium.finetuning: api/graphium.finetuning.md
  - Tutorials:
      - feature_processing:
          - Add new positional encoding: tutorials/feature_processing/add_new_positional_encoding.ipynb
          - Convert CSV to Parquet files: tutorials/feature_processing/csv_to_parquet.ipynb
          - Timing parallel processing: tutorials/feature_processing/timing_parallel.ipynb
      - gnn_layers:
          - Add new gnn layers: tutorials/gnn/add_new_gnn_layers.ipynb
          - Making GNN networks: tutorials/gnn/making_gnn_networks.ipynb
          - Using GNN layers: tutorials/gnn/using_gnn_layers.ipynb
      - model_training:
          - Simple Molecular Model: tutorials/model_training/simple-molecular-model.ipynb
          - Training on IPU: tutorials/model_training/running-multitask-ipu.ipynb
  - Design: design.md
  - Datasets: datasets.md
  - Pretrained Models: pretrained_models.md
  - CLI:
    - About: cli/reference.md
    - Commands:
      - graphium: cli/graphium.md
      - graphium-train: cli/graphium-train.md
  - Contribute: contribute.md
  - License: license.md

theme:
  name: material
  # NOTE(hadim): to customize the material primary and secondary
  # color check `docs/_assets/css/custom-graphium.css`.
  features:
    - navigation.tabs
    - navigation.expand
  favicon: images/logo-mini-dark.png
  logo: images/logo-mini-white.svg

extra_css:
  - _assets/css/custom.css
  - _assets/css/custom-graphium.css

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

markdown_extensions:
  - admonition
  - markdown_include.include
  - pymdownx.emoji
  - pymdownx.magiclink
  - pymdownx.superfences
  - pymdownx.tabbed
  - pymdownx.tasklist
  - pymdownx.details
  - pymdownx.arithmatex:
      generic: true
  - toc:
      permalink: true

watch:
  - graphium/

plugins:
  - search

  - mkdocstrings:
      handlers:
        python:
          setup_commands:
            - import sys
            - sys.path.append("docs")
            - sys.path.append("graphium")
          options:
            new_path_syntax: yes
            show_root_heading: yes
            heading_level: 3
            show_source: false

  - mkdocs-jupyter:
      execute: False

  - mike:
      version_selector: true

extra:
  version:
    # Multi versioning provider for mkdocs-material (used for the JS selector)
    provider: mike