mkdocs.yml

site_name: "Helical Docs"
site_url: https://helical.readthedocs.io/
repo_url: https://github.com/helicalAI/helical
repo_name: helicalAI/helical
copyright: <a href="https://www.helical-ai.com/">Helical Team</a> <br> Copyright &copy; 2024
nav:
  - Single-Cell Models:
    - Geneformer: 
      - Model Card: ./model_cards/geneformer.md
      - Config: ./configs/geneformer_config.md
      - Model: ./models/geneformer.md
      - Fine-Tuning Model: ./fine_tuning_models/geneformer_fine_tune.md
    - scGPT: 
      - Model Card: ./model_cards/scgpt.md
      - Config: ./configs/scgpt_config.md
      - Model: ./models/scgpt.md
      - Fine-Tuning Model: ./fine_tuning_models/scgpt_fine_tune.md
    - UCE: 
      - Model Card: ./model_cards/uce.md
      - Config: ./configs/uce_config.md
      - Model: ./models/uce.md
      - Fine-Tuning Model: ./fine_tuning_models/uce_fine_tune.md
  - RNA Sequence Models:
    - Helix-mRNA: 
      - Model Card: ./model_cards/helix_mrna.md
      - Config: ./configs/helix_mrna_config.md
      - Model: ./models/helix_mrna.md
      - Fine-Tuning Model: ./fine_tuning_models/helix_mrna_fine_tune.md
    - Mamba2-mRNA: 
      - Model Card: ./model_cards/mamba2_mrna.md
      - Config: ./configs/mamba2_mrna_config.md
      - Model: ./models/mamba2_mrna.md
      - Fine-Tuning Model: ./fine_tuning_models/mamba2_mrna_fine_tune.md
  - DNA Sequence Models:
    - HyenaDNA:
      - Model Card: ./model_cards/hyenadna.md
      - Config: ./configs/hyenadna_config.md
      - Model: ./models/hyenadna.md
      - Fine-Tuning Model: ./fine_tuning_models/hyenadna_fine_tune.md
    - Caduceus:
      - Model Card: ./model_cards/caduceus.md
      - Config: ./configs/caduceus_config.md
      - Model: ./models/caduceus.md
      - Fine-Tuning Model: ./fine_tuning_models/caduceus_fine_tune.md
  - Helical Base Models: ./models/base_models.md
  - Fine-Tuning Heads: ./models/fine_tuning_heads.md
  - Example Notebooks:
    - Quick-Start-Tutorial: ./notebooks/Quick-Start-Tutorial.ipynb
    - Helix-mRNA: ./notebooks/Helix-mRNA.ipynb
    - Cell-Type Annotation: ./notebooks/Cell-Type-Annotation.ipynb
    - Cell-Type-Classification-Fine-Tuning: ./notebooks/Cell-Type-Classification-Fine-Tuning.ipynb
    - Geneformer-vs-UCE: ./notebooks/Geneformer-vs-UCE.ipynb
    - Hyena-DNA-Inference: ./notebooks/Hyena-DNA-Inference.ipynb
    - HyenaDNA-Fine-Tuning: ./notebooks/HyenaDNA-Fine-Tuning.ipynb
   
theme:
  name: material
  logo: assets/logo1.png
  favicon: assets/official_logo_fav.png
  icon:
    repo: fontawesome/brands/git-alt 
  font:
    text: Montserrat
  palette:
    scheme: slate
    primary: custom
  features:
    - content.code.copy
extra_css:
  - stylesheets/extra.css
extra:
  generator: false
  version:
    provider: mike
    default: latest
markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
plugins:
  - search
  - mkdocstrings:
      # default_handler: python
      handlers:
        python: 
          options:
            docstring_style: numpy
  - mkdocs-jupyter