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

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site_name: tfbpmodeling
site_description: "Transcription Factor Binding and Perturbation modeling tools for analyzing TF binding and gene expression relationships"
site_author: "chase mateusiak <chasem@wustl.edu>, michael brent <brent@wustl.edu>"
site_url: "https://brentlab.github.io/tfbpmodeling/"
repo_url: "https://github.com/brentlab/tfbpmodeling"
repo_name: "tfbpmodeling"
edit_uri: "edit/main/docs/"
watch: ['tfbpmodeling', 'docs']

theme:
  name: readthedocs

plugins:
- search
- mkdocstrings:
    handlers:
      python:
        paths: [tfbpmodeling]
        options:
          docstring_style: sphinx
          show_source: true
          show_root_heading: true
          show_root_toc_entry: false
          merge_init_into_class: true
          separate_signature: true

markdown_extensions:
  - toc:
      permalink: true
  - admonition
  - codehilite
  - extra

nav:
- Home: index.md
- Getting Started:
  - Installation: getting-started/installation.md
  - Quick Start: getting-started/quickstart.md
  - Input Data Formats: getting-started/input-formats.md
- Output Reference:
  - Output Structure: output.md
- Tutorials:
  - Cluster Usage: tutorials/cluster-usage.md
- API Reference:
  - Core Modules:
    - interface: api/interface.md
    - modeling_input_data: api/modeling_input_data.md
    - bootstrapped_input_data: api/bootstrapped_input_data.md
    - bootstrap_model_results: api/bootstrap_model_results.md
  - Evaluation:
    - interactor_significance_results: api/interactor_significance_results.md
    - evaluate_interactor_significance_lassocv: api/evaluate_interactor_significance_lassocv.md
    - evaluate_interactor_significance_linear: api/evaluate_interactor_significance_linear.md
  - Cross-Validation:
    - stratified_cv: api/stratified_cv.md
    - stratified_cv_r2: api/stratified_cv_r2.md
- Development:
  - Contributing: development/contributing.md