squeeze/mkdocs.yml at main · GeorgePearse/squeeze · GitHub

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docs_dir: docs
site_dir: site

site_name: UMAP
site_description: Uniform Manifold Approximation and Projection
site_author: Leland McInnes
site_url: https://lmcinnes.github.io/umap/
repo_url: https://github.com/lmcinnes/umap
repo_name: lmcinnes/umap
edit_uri: edit/master/doc/
copyright: Copyright &copy; 2017-2024 Leland McInnes

theme:
  name: material
  logo: doc/logo_large.png
  favicon: doc/logo_large.png
  features:
    - navigation.instant
    - navigation.expand
    - navigation.top
    - content.code.copy
    - content.tooltips
    - search.suggest
    - search.highlight
  palette:
    - scheme: default
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
      primary: indigo
      accent: indigo
    - scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
      primary: indigo
      accent: indigo

plugins:
  - search:
      lang: en

extra_javascript:
  - https://cdn.plot.ly/plotly-2.27.0.min.js
  - https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.min.js
  - javascripts/mermaid.js

markdown_extensions:
  - admonition
  - pymdownx.arithmatex
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.emoji
  - pymdownx.highlight:
      use_pygments: true
      auto_title: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.magiclink
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde
  - tables
  - toc:
      permalink: true
  - md_in_html
  - attr_list

nav:
  - Home: index.md
  - Getting Started:
      - Installation: basic_usage.md
      - How UMAP Works: how_umap_works.md
      - Reproducibility: reproducibility.md
  - Algorithms:
      - Overview: algorithms/index.md
      - UMAP: algorithms/umap.md
      - t-SNE: algorithms/tsne.md
      - PCA: algorithms/pca.md
      - Isomap: algorithms/isomap.md
      - LLE: algorithms/lle.md
      - MDS: algorithms/mds.md
      - PHATE: algorithms/phate.md
      - TriMap: algorithms/trimap.md
      - PaCMAP: algorithms/pacmap.md
      - Numerical Stability: algorithms/numerical_stability.md
  - User Guide:
      - Basic Usage: basic_usage.md
      - Parameters: parameters.md
      - Supervised Dimensionality Reduction: supervised.md
      - Clustering: clustering.md
      - Inverse Transform: inverse_transform.md
      - Sparse Data: sparse.md
  - Advanced Topics:
      - Composing Models: composing_models.md
      - Aligned UMAP: aligned_umap_basic_usage.md
      - Aligned UMAP - Politics Demo: aligned_umap_politics_demo.md
      - Embedding Space: embedding_space.md
      - Exploratory Analysis: exploratory_analysis.md
  - Variants and Extensions:
      - densMAP: densmap_demo.md
      - Parametric UMAP: parametric_umap.md
      - Mutual Nearest Neighbors UMAP: mutual_nn_umap.md
      - Transform & Inference: transform.md
      - Landmarked Parametric UMAP: transform_landmarked_pumap.md
  - Visualization and Interactive:
      - Plotting: plotting.md
      - Interactive Visualization: interactive_viz.md
      - Outlier Detection: outliers.md
      - Document Embedding: document_embedding.md
      - Nomic Atlas - Text Embeddings: nomic_atlas_umap_of_text_embeddings.md
      - Nomic Atlas - MNIST Training: nomic_atlas_visualizing_mnist_training_dynamics.md
  - Performance & Optimization:
      - Performance: performance.md
      - Benchmarking: benchmarking.md
      - Interactive Metrics Comparison: interactive_metrics.md
      - Precomputed k-NN: precomputed_k-nn.md
      - Evaluation Metrics: evaluation_metrics.md
  - Reference & Support:
      - API Reference: api.md
      - FAQ: faq.md
      - Scientific Papers: scientific_papers.md
      - Release Notes: release_notes.md
      - Development Roadmap: development_roadmap.md