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mkdocs.yml
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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.visualization: api/graphium.visualization.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.png
logo: images/logo.svg
extra_css:
- _assets/css/custom.css
- _assets/css/custom-graphium.css
extra_javascript:
- https://polyfill.io/v3/polyfill.min.js?features=es6
- 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