site_name: MultiMolecule
site_url: https://multimolecule.danling.org
site_author: MultiMolecule
site_description: Neural Networks for RNA, DNA, and Protein
copyright: All rights reserved &copy; 2024-Present, MultiMolecule Contributors

repo_name: MultiMolecule
repo_url: https://github.com/DLS5-Omics/multimolecule

nav:
  - index.md
  - data:
    - data.md
    - Dataset: data/dataset.md
    - PandasDataset: data/pandas.md
  - datasets:
    - datasets/index.md
    - DNA:
      - GENCODE: datasets/gencode.md
    - RNA:
      - RNAcentral: datasets/rnacentral.md
      - Rfam: datasets/rfam.md
      - bpRNA-1m: datasets/bprna.md
  - module:
    - module/index.md
    - heads: module/heads.md
    - embeddings: module/embeddings.md
  - models:
    - models/index.md
    - DNA:
      - CaLM: models/calm.md
    - RNA:
      - ERNIE-RNA: models/ernierna.md
      - RiNALMo: models/rinalmo.md
      - RNABERT: models/rnabert.md
      - RNAErnie: models/rnaernie.md
      - RNA-FM: models/rnafm.md
      - RNA-MSM: models/rnamsm.md
      - SpliceBERT: models/splicebert.md
      - 3UTRBERT: models/utrbert.md
      - UTR-LM: models/utrlm.md
    - utils:
        - configuration_utils: models/configuration_utils.md
        - modeling_outputs: models/modeling_outputs.md
  - tokenisers:
    - tokenisers/index.md
    - DNA:
      - DnaTokenizer: tokenisers/dna.md
      - DNA Alphabet: tokenisers/dna/alphabet.md
    - RNA:
      - RnaTokenizer: tokenisers/rna.md
      - RNA Alphabet: tokenisers/rna/alphabet.md
    - Protein:
      - ProteinTokenizer: tokenisers/protein.md
      - Protein Alphabet: tokenisers/protein/alphabet.md
  - about:
    - about/index.md
    - License: about/license.md
    - License FAQ: about/license-faq.md
    - Privacy Notice: about/privacy.md

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  custom_dir: overrides
  language: "zh"
  palette:
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      scheme: slate
      primary: blue grey
      accent: teal
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: blue grey
      accent: teal
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
  logo: "assets/images/logo.png"
  favicon: "assets/images/logo.ico"
  features:
    - announce.dismiss
    # - content.action.edit
    # - content.action.view
    - content.code.annotate
    - content.code.copy
    - content.code.select
    - content.tabs.link
    - content.tooltips
    - header.autohide
    - navigation.expand
    - navigation.footer
    - navigation.indexes
    - navigation.instant
    - navigation.instant.prefetch
    - navigation.instant.progress
    - navigation.prune
    - navigation.sections
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
    # - toc.integrate
  font: false

extra:
  analytics:
    provider: google
    property: "G-YFVBYNKMD6"
  consent:
    title: Cookie Consent
    description: >-
      We use cookies to recognize your repeated visits and preferences, as well
      as to measure the effectiveness of our documentation and whether users
      find what they're searching for. With your consent, you're helping us to
      make our documentation better. Please check out our
      <a href="https://multimolecule.danling.org/about/privacy">Privacy Notice</a> for more information.
  generator: false
  manifest: "manifest.webmanifest"

extra_css:
  - assets/css/fonts.css
  - assets/css/extra.css

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
  - javascripts/shortcuts.js

markdown_extensions:
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  - admonition
  - attr_list
  - callouts
  - def_list
  - footnotes
  - markdown_gfm_admonition
  - md_in_html
  - mdx_math
  - meta
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:materialy.gemoji
      emoji_generator: !!python/name:materialy.to_png
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
      auto_title: true
      linenums: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.magiclink
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets
  - pymdownx.superfences:
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          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
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  - pymdownx.tasklist:
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  - pymdownx.tilde
  - smarty
  - tables
  - toc:
      permalink: true

plugins:
  - git-committers
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      handlers:
        python:
          options:
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            parameter_headings: true
            show_root_heading: true
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            separate_signature: true
            show_signature_annotations: true
            signature_crossrefs: true
          import:
            - https://docs.python.org/3/objects.inv
            - https://pytorch.org/docs/stable/objects.inv
            - https://huggingface.co/docs/transformers/master/en/objects.inv
            - https://huggingface.co/docs/datasets/master/en/objects.inv
            - https://pandas.pydata.org/docs/objects.inv
            - https://danling.org/objects.inv
            - https://chanfig.danling.org/objects.inv
  - section-index
  - i18n:
      docs_structure: suffix
      fallback_to_default: true
      languages:
        - locale: en
          build: true
          default: true
          name: English
        - locale: zh
          build: true
          default: false
          name: 汉语
      reconfigure_material: true
      reconfigure_search: true
  - git-revision-date-localized:
      type: iso_datetime
  - rss:
      match_path: .*
      date_from_meta:
        as_creation: date
      categories:
        - categories
        - tags
  - search:
      separator: '[\s\u200b\-]'
  - tags
  # - typeset

watch:
  - ../multimolecule/
