piqtree/mkdocs.yml at main · iqtree/piqtree · GitHub

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site_name: piqtree
site_url: "https://github.com/iqtree/piqtree"
site_author: "Gavin Huttley"
repo_url: "https://github.com/iqtree/piqtree"
repo_name: 'GitHub'
exclude_docs: |
  scripts/*
theme:
    name: material
    features:
      - navigation.indexes
    highlightjs: true
    hljs_languages:
        - yaml
        - python
        - text
markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          paths: [src]
          options:
            show_root_heading: true
            docstring_style: numpy
            docstring_section_style: spacy
            docstring_options:
              ignore_init_summary: true
            merge_init_into_class: true
  - mkdocs-jupyter:
      allow_errors: false
      include_requirejs: true
      execute: true
      remove_tag_config:
          remove_input_tags:
              - hide_code

nav:
  - Introduction: index.md
  - Quickstart:
    - quickstart/index.md
    - quickstart/construct_ml_tree.md
    - quickstart/fit_tree_topology.md
    - quickstart/simulate_alignment.md
    - quickstart/using_substitution_models.md
    - quickstart/using_model_finder.md
    - quickstart/calculate_jc_distances.md
    - quickstart/construct_nj_tree.md
    - quickstart/construct_consensus_tree.md
    - quickstart/make_random_tree.md
    - quickstart/calculate_rf_distances.md
    - Available substitution models: quickstart/available_submodels.py
    - Available state frequency options: quickstart/available_frequency_options.py
    - Available rate-heterogeneity options:  quickstart/available_rate_heterogeneity_options.py
  - Apps:
    - apps/index.md
    - The available piqtree apps: apps/available_help.py
    - Selecting models for phylogenetic analysis: apps/model_finder.py
    - Estimate a phylogenetic tree: apps/phylo.py
    - Fit a model to one tree: apps/fit_tree.py
    - Pairwise JC distances: apps/pairwise_dist.py
    - NJ tree: apps/nj.py
    - Parallel processing across alignments: apps/app_pipeline.py
  - API reference:
      - api/index.md
      - Trees:
          - api/tree/build_tree.md
          - api/tree/fit_tree.md
          - api/tree/nj_tree.md
          - api/tree/consensus_tree.md
          - api/tree/random_tree.md
      - Alignments:
          - api/alignment/simulate_alignment.md
      - Substitution models:
          - api/model/model_finder.md
          - api/model/ModelFinderResult.md
          - api/model/Model.md
          - api/model/make_model.md
          - api/model/SubstitutionModel.md
          - api/model/FreqType.md
          - api/model/RateModel.md
      - Genetic distances:
          - api/genetic_distance/jc_distances.md
      - Tree distances:
          - api/tree_distance/robinson_foulds.md
  - Contributing:
    - developers/index.md
    - developers/environment_setup.md
    - developers/iqtree_submodule.md
    - developers/contributing.md
    - developers/testing.md
    - developers/troubleshooting.md
    - developers/release.md
  - Citation: citation.md