mkdocs.yml

site_name: DNALLM Documentation
site_description: A comprehensive toolkit for fine-tuning and inference with DNA Language Models
site_author: Zhangtaolab
# site_url: https://zhangtaolab.org/DNALLM/
repo_url: https://github.com/zhangtaolab/DNALLM
repo_name: zhangtaolab/DNALLM
edit_uri: edit/main/docs/

# Include example directory for notebooks
watch:
  - example/notebooks
  - example/marimo
  - example/mcp_example

theme:
  name: material
  
  # Logo and favicon
  logo: pic/DNALLM_logo_white.svg
  favicon: pic/DNALLM_logo_web.svg
  
  # Features
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.expand
    - navigation.top
    - search.highlight
    - search.share
    - content.code.copy
    - content.code.annotate
    - content.tabs.link
    - content.tooltips
    - header.autohide

  palette:
    # Palette toggle for automatic mode
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode
    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default 
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to system preference

nav:
  - Introduction: index.md
  - Getting Started: 
    - Quick Start: getting_started/quick_start.md
    - Installation: getting_started/installation.md
  - User Guide:
    - Getting Started: user_guide/getting_started.md
    - Common Workflows: user_guide/common_workflows.md
    - Best Practices: user_guide/best_practices.md
    - Performance Guide: user_guide/performance_guide.md
    - Troubleshooting: user_guide/troubleshooting.md
    - Tutorial:
      - End-to-End Workflow: user_guide/tutorial/end_to_end_workflow.md
    - Data Processing:
      - Data Preparation: user_guide/data_processing/data_preparation.md
      - Quality Control: user_guide/data_processing/quality_control.md
      - Format Conversion: user_guide/data_processing/format_conversion.md
      - Data Augmentation: user_guide/data_processing/data_augmentation.md
    - Fine Tuning:
      - Overview: user_guide/fine_tuning/index.md
      - Getting Started: user_guide/fine_tuning/getting_started.md
      - Configuration: user_guide/fine_tuning/configuration.md
      - Advanced Techniques: user_guide/fine_tuning/advanced_techniques.md
      - Task Guides: user_guide/fine_tuning/task_guides.md
    - Inference:
      - Getting Started: user_guide/inference/getting_started.md
      - Basic Inference: user_guide/inference/basic_inference.md
      - Advanced Inference: user_guide/inference/advanced_inference.md
      - Mutagenesis Analysis: user_guide/inference/mutagenesis_analysis.md
      - Visualization: user_guide/inference/visualization.md
      - Performance Optimization: user_guide/inference/performance_optimization.md
    - Benchmark:
      - Overview: user_guide/benchmark/index.md
      - Getting Started: user_guide/benchmark/getting_started.md
      - Configuration: user_guide/benchmark/configuration.md
      - Advanced Techniques: user_guide/benchmark/advanced_techniques.md
      - Examples: user_guide/benchmark/examples.md
    - MCP:
      - Configuration: user_guide/mcp/configuration.md
      - Server Setup: user_guide/mcp/startserver.md
      - Usage Guide: user_guide/mcp/usage.md
    - CLI Tools:
      - Overview: user_guide/cli/index.md
      - Usage Guide: user_guide/cli/usage.md
      - Configuration Generator: user_guide/cli/config_generator.md
      - MCP Server: user_guide/cli/mcp_server.md
    - Performance Optimization:
      - GPU Optimization: user_guide/performance/gpu_optimization.md
      - Memory Optimization: user_guide/performance/memory_optimization.md
      - Inference Speed: user_guide/performance/inference_speed.md
      - Model Quantization: user_guide/performance/model_quantization.md
    - Models: user_guide/models.md
    - Case Studies:
      - Promoter Prediction: user_guide/case_studies/promoter_prediction.md
      - Motif Detection: user_guide/case_studies/motif_detection.md
      - Sequence Generation: user_guide/case_studies/sequence_generation.md
      - Multi-Task Learning: user_guide/case_studies/multi_task_learning.md
  - API:
    - Overview: api/index.md
    - Configuration:
      - Configs: api/configuration/configs.md
    - Models:
      - Model: api/models/model.md
      - Auto Loading: api/models/modeling_auto.md
      - Tokenizer: api/models/tokenizer.md
      - Classification Heads: api/models/head.md
      - Special Models:
        - Basenji2: api/models/special/basenji2.md
        - Borzoi: api/models/special/borzoi.md
        - DNABERT2: api/models/special/dnabert2.md
        - EVO: api/models/special/evo.md
        - Enformer: api/models/special/enformer.md
        - GPN: api/models/special/gpn.md
        - LucaOne: api/models/special/lucaone.md
        - megaDNA: api/models/special/megadna.md
        - MutBERT: api/models/special/mutbert.md
        - Omni-DNA: api/models/special/omnidna.md
        - SPACE: api/models/special/space.md
    - Datahandling:
      - Data: api/datahandling/data.md
      - Auto Builders: api/datahandling/dataset_auto.md
    - Inference:
      - Inference: api/inference/inference.md
      - Benchmark: api/inference/benchmark.md
      - Mutagenesis: api/inference/mutagenesis.md
      - Interpretation: api/inference/interpret.md
      - Plot: api/inference/plot.md
    - Finetune:
      - Trainer: api/finetune/trainer.md
    - MCP:
      - Server: api/mcp/server.md
      - Config Manager: api/mcp/config_manager.md
      - Config Validators: api/mcp/config_validators.md
      - Model Manager: api/mcp/model_manager.md
    - Tasks:
      - Task: api/tasks/task.md
      - Metrics: api/tasks/metrics.md
    - Utils:
      - Sequence: api/utils/sequence.md
      - Logger: api/utils/logger.md
      - Support: api/utils/support.md
  - Concepts:
    - Biology:
      - DNA Sequences: concepts/biology/dna_sequences.md
      - Genomic Features: concepts/biology/genomic_features.md
      - Biological Tasks: concepts/biology/biological_tasks.md
      - Sequence Analysis: concepts/biology/sequence_analysis.md
    - Training: concepts/training.md
    - Inference: concepts/inference.md
    - MCP: concepts/mcp.md
    - Architecture:
      - Model Architectures: concepts/architecture/model_architectures.md
      - Tokenization: concepts/architecture/tokenization.md
      - Attention Mechanisms: concepts/architecture/attention_mechanisms.md
      - Embedding Layers: concepts/architecture/embedding_layers.md
    - Technical Guides:
      - Transfer Learning: concepts/technical/transfer_learning.md
      - Fine-tuning Strategies: concepts/technical/fine_tuning_strategies.md
      - Evaluation Metrics: concepts/technical/evaluation_metrics.md
      - Performance Optimization: concepts/technical/performance_optimization.md
  - Resources:
    - Model Zoo: resources/model_zoo.md
    - Data Handling: resources/datahandling.md
    - Model Selection: resources/model_selection.md
    - Model Troubleshooting: resources/troubleshooting_models.md
    - Model Guides:
      - BERT Models: resources/models/bert_models.md
      - Caduceus Models: resources/models/caduceus_models.md
      - ESM Models: resources/models/esm_models.md
      - Hyena Models: resources/models/hyena_models.md
      - Llama Models: resources/models/llama_models.md
      - Mamba Models: resources/models/mamba_models.md
      - EVO Models: resources/models/evo_models.md
      - Flash Attention Models: resources/models/flash_attention_models.md
      - Special Models: resources/models/special_models.md
  - Examples:
    - Notebooks:
      - Overview: example/notebooks/overview.md
      - Fine-Tuning:
        - Binary Classification: example/notebooks/finetune_binary/finetune_binary.ipynb
        - Multi-Label Classification: example/notebooks/finetune_multi_labels/finetune_multi_labels.ipynb
        - NER Fine-tuning: example/notebooks/finetune_NER_task/finetune_NER_task.ipynb
        - NER Data Generation: example/notebooks/finetune_NER_task/data_generation_and_inference.ipynb
        - Custom Head: example/notebooks/finetune_custom_head/finetune.ipynb
        - Generation: example/notebooks/finetune_generation/finetune_generation.ipynb
        - LoRA Fine-tuning: example/notebooks/lora_finetune_inference/lora_finetune.ipynb
        - LoRA Inference: example/notebooks/lora_finetune_inference/lora_inference.ipynb
      - Inference:
        - Basic Inference: example/notebooks/inference/inference.ipynb
        - EVO Models: example/notebooks/generation_evo_models/inference.ipynb
        - MegaDNA Models: example/notebooks/generation_megaDNA/inference.ipynb
        - Sequence Generation: example/notebooks/generation/inference.ipynb
        - tRNA Inference: example/notebooks/inference_for_tRNA/inference.ipynb
      - Analysis:
        - Mutagenesis: example/notebooks/in_silico_mutagenesis/in_silico_mutagenesis.ipynb
        - Interpretation: example/notebooks/interpretation/interpretation.ipynb
        - Embedding: example/notebooks/embedding_attention.ipynb
      - Benchmarking:
        - Benchmark: example/notebooks/benchmark/benchmark.ipynb
      - Data Preparation:
        - Fine-tuning Data: example/notebooks/data_prepare/finetune/finetune_data.ipynb
        - Prediction Data: example/notebooks/data_prepare/predict/predict_data.ipynb
      - MCP Examples:
        - LangChain Agents: example/mcp_example/mcp_client_ollama_langchain_agents.ipynb
        - Pydantic AI: example/mcp_example/mcp_client_ollama_pydantic_ai.ipynb
    - Marimo Demos:
      - Fine-tuning Demo: example/marimo/finetune/finetune_demo.py
      - Inference Demo: example/marimo/inference/inference_demo.py
      - Benchmark Demo: example/marimo/benchmark/benchmark_demo.py
  - FAQ: 
    - Overview: faq/index.md
    - Installation: faq/install_troubleshooting.md
    - Models: faq/models_troubleshooting.md
    - Benchmark: faq/benchmark_troubleshooting.md
    - Fine-tuning: faq/finetuning_troubleshooting.md
    - Data Processing: faq/data_processing_troubleshooting.md
    - CLI: faq/cli_troubleshooting.md
    - Inference: faq/inference_troubleshooting.md
    - MCP: faq/mcp_troubleshooting.md

plugins:
  - search
  - mkdocs-jupyter:
      include_source: True
      execute: False  # Set to True to execute notebooks during build (requires more time)
      allow_errors: False
      ignore_hashes: True
      timeout: 60  # Timeout for notebook execution in seconds
      write_markdown_columns: False
      remove_tag_config:
        remove_stderr_tags: # 移除标准错误输出（Warning通常在这里）
          - hide_warnings
  - mkdocstrings:
      handlers:
        python:
          options:
            docstring_style: google
            show_source: true
            show_root_heading: true
            show_root_toc_entry: true
            show_category_heading: true
            merge_init_into_class: true
            separate_signature: true


markdown_extensions:
  - admonition
  - codehilite
  - toc:
      permalink: true
  - pymdownx.superfences