mkdocs.yml

site_name: DiffBio
site_description: End-to-end differentiable bioinformatics pipelines built on JAX/Flax NNX, Datarax, Artifex, Opifex, and Calibrax
site_author: Mahdi Shafiei
site_url: https://diffbio.readthedocs.io/en/latest/
repo_url: https://github.com/avitai/DiffBio
repo_name: avitai/DiffBio
edit_uri: edit/main/docs/

# Configuration for clean, scientific appearance
theme:
  name: material
  language: en

  palette:
    # Light mode with automatic detection
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: amber
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Dark mode with automatic detection
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: amber
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

  features:
    # Navigation features with collapsible sections
    - navigation.path
    - navigation.top
    # Instant loading for better UX
    - navigation.instant
    - navigation.instant.prefetch
    - navigation.instant.progress
    # Enable navigation tracking
    - navigation.tracking
    # Table of contents
    - toc.follow
    # Search features
    - search.highlight
    - search.share
    - search.suggest
    # Content features
    - content.code.copy
    - content.code.annotate
    - content.tabs.link
    - content.tooltips

  icon:
    repo: fontawesome/brands/github
    logo: "material/dna"  # Bioinformatics/DNA icon

  font:
    text: Roboto
    code: Roboto Mono

  favicon: "_static/favicon.png"

# Extra configuration
extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/avitai/DiffBio
    - icon: fontawesome/brands/python
      link: https://pypi.org/project/diffbio/

# Navigation structure for DiffBio
nav:
  - Home: index.md

  - Getting Started:
      - Installation: getting-started/installation.md
      - Quick Start: getting-started/quickstart.md
      - Core Concepts: getting-started/core-concepts.md

  - User Guide:
      - Concepts:
          - Differentiable Bioinformatics: user-guide/concepts/differentiable-bioinformatics.md
          - Soft Operations: user-guide/concepts/soft-operations.md
          - Genomics:
              - Sequence Alignment: user-guide/concepts/sequence-alignment.md
              - Pileup Generation: user-guide/concepts/pileup-generation.md
              - Variant Calling: user-guide/concepts/variant-calling.md
              - Genomic Processing: user-guide/concepts/genomic-processing.md
          - Single-Cell & Spatial:
              - Single-Cell Analysis: user-guide/concepts/single-cell-analysis.md
              - Omics Integration: user-guide/concepts/omics-integration.md
          - Molecular & Structural:
              - Drug Discovery: user-guide/concepts/drug-discovery.md
              - Structural Biology: user-guide/concepts/structural-biology.md
          - Methods:
              - Representation Learning: user-guide/concepts/representation-learning.md
      - Operators:
          - Overview: user-guide/operators/overview.md
          - Core:
              - Smith-Waterman: user-guide/operators/smith-waterman.md
              - Pileup Operator: user-guide/operators/pileup.md
              - Quality Filter: user-guide/operators/quality-filter.md
          - Alignment: user-guide/operators/alignment.md
          - Epigenomics: user-guide/operators/epigenomics.md
          - RNA-seq: user-guide/operators/rnaseq.md
          - Single-Cell: user-guide/operators/singlecell.md
          - Preprocessing: user-guide/operators/preprocessing.md
          - Normalization: user-guide/operators/normalization.md
          - Statistical: user-guide/operators/statistical.md
          - Assembly & Mapping: user-guide/operators/assembly-mapping.md
          - Multi-omics: user-guide/operators/multiomics.md
          - Metabolomics: user-guide/operators/metabolomics.md
          - Variant: user-guide/operators/variant.md
          - Population Genetics: user-guide/operators/population.md
          - CRISPR: user-guide/operators/crispr.md
          - Protein Structure: user-guide/operators/protein.md
          - Foundation Models: user-guide/operators/foundation-models.md
          - RNA Structure: user-guide/operators/rna-structure.md
          - Molecular Dynamics: user-guide/operators/molecular-dynamics.md
          - Drug Discovery: user-guide/operators/drug-discovery.md
      - Pipelines:
          - Pipeline Overview: user-guide/pipelines/overview.md
          - Variant Calling: user-guide/pipelines/variant-calling.md
          - Enhanced Variant Calling: user-guide/pipelines/enhanced-variant-calling.md
          - Single-Cell Analysis: user-guide/pipelines/single-cell.md
          - Preprocessing: user-guide/pipelines/preprocessing.md
          - Differential Expression: user-guide/pipelines/differential-expression.md
      - Losses:
          - Overview: user-guide/losses/overview.md
          - Single-Cell Losses: user-guide/losses/singlecell.md
          - Statistical Losses: user-guide/losses/statistical.md
          - Metric Losses: user-guide/losses/metric.md
      - Training:
          - Training Overview: user-guide/training/overview.md
          - Training Utilities: user-guide/training/utilities.md
      - Data:
          - Data Sources: user-guide/sources.md
          - Dataset Splitters: user-guide/splitters.md

  - API Reference:
      - Core:
          - Base Classes: api/core/base.md
          - Soft Operations: api/core/soft-ops.md
          - Configuration: api/core/configuration.md
      - Operators:
          - Core:
              - Smith-Waterman: api/operators/smith-waterman.md
              - Pileup: api/operators/pileup.md
              - Quality Filter: api/operators/quality-filter.md
          - Alignment: api/operators/alignment.md
          - Epigenomics: api/operators/epigenomics.md
          - RNA-seq: api/operators/rnaseq.md
          - Single-Cell: api/operators/singlecell.md
          - Preprocessing: api/operators/preprocessing.md
          - Normalization: api/operators/normalization.md
          - Statistical: api/operators/statistical.md
          - Assembly: api/operators/assembly.md
          - Mapping: api/operators/mapping.md
          - Multi-omics: api/operators/multiomics.md
          - Metabolomics: api/operators/metabolomics.md
          - Variant: api/operators/variant.md
          - Population Genetics: api/operators/population.md
          - CRISPR: api/operators/crispr.md
          - Protein Structure: api/operators/protein.md
          - Foundation Models: api/operators/foundation-models.md
          - RNA Structure: api/operators/rna-structure.md
          - Molecular Dynamics: api/operators/molecular-dynamics.md
          - Drug Discovery: api/operators/drug-discovery.md
      - Pipelines:
          - Variant Calling: api/pipelines/variant-calling.md
          - Enhanced Variant Calling: api/pipelines/enhanced-variant-calling.md
          - Single-Cell: api/pipelines/single-cell.md
          - Preprocessing: api/pipelines/preprocessing.md
          - Differential Expression: api/pipelines/differential-expression.md
      - Losses:
          - Alignment Losses: api/losses/alignment.md
          - Biological Regularization: api/losses/biological-regularization.md
          - Single-Cell Losses: api/losses/singlecell.md
          - Statistical Losses: api/losses/statistical.md
          - Metric Losses: api/losses/metric.md
      - Utils:
          - Training Utilities: api/utils/training.md
      - Data:
          - Data Sources: api/sources.md
          - Dataset Splitters: api/splitters.md

  - Examples:
      - Overview: examples/overview.md
      - Basic:
          - Operator Pattern: examples/basic/operator-pattern.md
          - MolNet Data Loading: examples/basic/molnet-data-loading.md
          - Molecular Fingerprints: examples/basic/molecular-fingerprints.md
          - Molecular Similarity: examples/basic/molecular-similarity.md
          - Scaffold Splitting: examples/basic/scaffold-splitting.md
          - DNA Encoding: examples/basic/dna-encoding.md
          - Sequence Alignment: examples/basic/simple-alignment.md
          - Pileup Generation: examples/basic/pileup-generation.md
          - Single-Cell Clustering: examples/basic/single-cell-clustering.md
          - RNA Structure: examples/basic/rna-structure.md
          - Protein Structure: examples/basic/protein-structure.md
          - HMM Sequence Model: examples/basic/hmm-sequence-model.md
          - Preprocessing: examples/basic/preprocessing.md
      - Intermediate:
          - Imputation: examples/intermediate/imputation.md
          - Trajectory: examples/intermediate/trajectory.md
          - Cell Annotation: examples/intermediate/cell-annotation.md
          - Doublet Detection: examples/intermediate/doublet-detection.md
          - Batch Correction: examples/intermediate/batch-correction.md
          - Perturbation Data Loading: examples/intermediate/perturbation-data-loading.md
      - Advanced:
          - Spatial Analysis: examples/advanced/spatial-analysis.md
          - GRN Inference: examples/advanced/grn-inference.md
          - Single-Cell Pipeline: examples/advanced/singlecell-pipeline.md
          - Calibrax Metrics: examples/advanced/calibrax-metrics.md
          - scVI Benchmark: examples/advanced/scvi-benchmark.md
          - Drug Discovery Workflow: examples/advanced/drug-discovery-workflow.md
          - ADMET Prediction: examples/advanced/admet-prediction.md
          - AttentiveFP: examples/advanced/attentive-fp.md
          - Variant Calling Pipeline: examples/advanced/variant-calling.md
          - Single-Cell Batch Correction: examples/advanced/singlecell-batch-correction.md
          - Differential Expression: examples/advanced/differential-expression.md
          - RNA Velocity: examples/advanced/rna-velocity.md
          - Epigenomics Analysis: examples/advanced/epigenomics-analysis.md
          - Multi-omics Integration: examples/advanced/multiomics-integration.md

  - Development:
      - Contributing: development/contributing.md
      - Testing: development/testing.md
      - Example Documentation Design: development/example-documentation-design.md
      - Benchmarks: development/benchmarks.md

# Plugins configuration
plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
  - mkdocstrings:
      handlers:
        python:
          paths: [src]
          options:
            docstring_style: google
            docstring_options:
              ignore_init_summary: true
            merge_init_into_class: true
            show_submodules: true
            show_source: false
            show_bases: true
            show_inheritance_diagram: false
            group_by_category: true
            heading_level: 2
            members_order: source
            separate_signature: true
            show_signature_annotations: true
            signature_crossrefs: true
            show_if_no_docstring: true
            show_root_heading: true
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            filters:
              - "!^_"
              - "^__init__$"
            inherited_members: true

# Markdown extensions for scientific/bioinformatics content
markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: "¤"
      title: "On this page"
      toc_depth: 4
  # PyMdown Extensions for enhanced formatting
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      base_path: docs
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

# MathJax for scientific/bioinformatics equations
extra_javascript:
  - javascripts/mathjax.js
  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

# Custom CSS
extra_css:
  - _static/extra.css

# Build configuration
strict: false
docs_dir: docs
site_dir: site

# File watching configuration for development
watch:
  - src/diffbio/
  - docs/
  - mkdocs.yml
  - README.md