tfbpapi/mkdocs.yml at main · BrentLab/tfbpapi · GitHub

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site_name: tfbpapi
site_description: "A collection of objects and functions to work with calling cards sequencing tools"
site_author: "ben mueller <email@email.com>, chase mateusiak <chasem@wustl.edu>, michael brent <brent@wustl.edu>"
site_url: "https://brentlab.github.io/tfbpapi/"
repo_url: "https://github.com/brentlab/tfbpapi"
repo_name: "tfbpapi"
edit_uri: "edit/master/docs/"
watch: ['tfbpapi', 'docs']

theme:
  name: material

plugins:
- search
- autorefs
- section-index
- mkdocs-jupyter:
      remove_tag_config:
          remove_input_tags:
              - hide
          remove_output_tags:
              - hide
- mkdocstrings:
    handlers:
          python:
            paths: [tfbpapi]  # search packages in the src folder
            merge_init_into_class: True
            options:
              docstring_style: 'sphinx'

markdown_extensions:
  - smarty
  - toc:
      permalink: True
  - sane_lists
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: "!!python/name:pymdownx.superfences.fence_code_format"

extra_javascript:
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
  - https://cdn.jsdelivr.net/npm/mermaid/dist/mermaid.min.js
  - js/init-mermaid.js

nav:
- Home: index.md
- Tutorials:
  - Database Interface: tutorials/database_interface.ipynb
  - LassoCV: tutorials/lassoCV.ipynb
  - Interactor Modeling Workflow: tutorials/interactor_modeling_workflow.ipynb
- API:
  - Models:
    - Overview: ml_models/index.md
    - SigmoidModel: ml_models/SigmoidModel.md
    - Lasso Modeling: ml_models/lasso_modeling.md
  - Database Interface:
    - Records Only Classes:
      - interface/BindingManualQCAPI.md
      - interface/DataSourceAPI.md
      - interface/DtoAPI.md
      - interface/ExpressionManualQCAPI.md
      - interface/FileFormatAPI.md
      - interface/GenomicFeatureAPI.md
      - interface/RegulatorAPI.md
    - Records and Files Classes:
      - BindingAPI: interface/BindingAPI.md
      - BindingConcatenatedAPI: interface/BindingConcatenatedAPI.md
      - CallingCardsBackgroundAPI: interface/CallingCardsBackgroundAPI.md
      - ExpressionAPI: interface/ExpressionAPI.md
      - PromoterSetAPI: interface/PromoterSetAPI.md
      - PromoterSetSigAPI: interface/PromoterSetSigAPI.md
    - Developer Classes:
      - interface/AbstractAPI.md
      - interface/AbstractRecordsAndFilesAPI.md
      - interface/AbstractRecordsOnlyAPI.md
      - interface/Cache.md
      - interface/ParamsDict.md