mkdocs.yml

site_name: gen_surv
site_description: Simulate survival data in Python — Cox, AFT, competing risks, cure, piecewise and multi-state models
# The Pages workflow passes SITE_URL from actions/configure-pages, so the
# canonical links follow the deployment rather than a hardcoded address.
site_url: !ENV [SITE_URL, "https://diogoribeiro7.github.io/genSurvPy/"]
site_author: Diogo Ribeiro
copyright: Copyright © Diogo Ribeiro — MIT licensed

repo_url: https://github.com/DiogoRibeiro7/genSurvPy
repo_name: DiogoRibeiro7/genSurvPy
edit_uri: edit/develop/docs/

theme:
  name: material
  language: en
  icon:
    repo: fontawesome/brands/github
  palette:
    - media: "(prefers-color-scheme)"
      toggle:
        icon: material/brightness-auto
        name: Follow system theme
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.sections
    - navigation.indexes
    - navigation.top
    - navigation.footer
    - toc.follow
    - search.suggest
    - search.highlight
    - content.code.copy
    - content.tabs.link

plugins:
  - search
  - mkdocstrings:
      default_handler: python
      handlers:
        python:
          paths: [.]
          options:
            docstring_style: numpy
            docstring_section_style: table
            show_root_heading: true
            show_root_full_path: false
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            separate_signature: true
            show_signature_annotations: true
            signature_crossrefs: true
            merge_init_into_class: true
            members_order: source
            filters: ["!^_"]
            heading_level: 3
            show_source: true

markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: true
      toc_depth: 3
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets:
      base_path: ["."]
      check_paths: true
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true

extra_css:
  - stylesheets/extra.css

extra_javascript:
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

validation:
  omitted_files: warn
  absolute_links: warn
  unrecognized_links: warn
  anchors: warn

nav:
  - Home: index.md
  - Getting started:
      - getting-started/index.md
      - Installation: getting-started/installation.md
      - Quickstart: getting-started/quickstart.md
      - Output schemas: getting-started/schemas.md
      - Reproducibility: getting-started/reproducibility.md
  - Models:
      - models/index.md
      - Cox proportional hazards: models/cphm.md
      - Accelerated failure time: models/aft.md
      - Piecewise exponential: models/piecewise-exponential.md
      - Competing risks: models/competing-risks.md
      - Mixture cure: models/mixture-cure.md
      - Illness-death, intervals (CMM): models/cmm.md
      - Illness-death, panel (THMM): models/thmm.md
      - Time-dependent covariates: models/tdcm.md
      - Recurrent events: models/recurrent-events.md
      - The multistate engine: models/multistate.md
  - Guides:
      - guides/index.md
      - Configuration and ground truth: guides/simulation-results.md
      - Baseline hazards: guides/baselines.md
      - Censoring: guides/censoring.md
      - Covariates: guides/covariates.md
      - Summarising a dataset: guides/summaries.md
      - Plotting: guides/plotting.md
      - Exporting data: guides/export.md
      - Fitting models to the data: guides/interoperability.md
      - Command line: guides/cli.md
  - Theory:
      - theory/index.md
      - Bibliography: theory/bibliography.md
  - API:
      - api/index.md
      - generate: api/generate.md
      - Simulation results: api/results.md
      - Generators: api/generators.md
      - Baseline hazards: api/baselines.md
      - Censoring: api/censoring.md
      - Analysis: api/analysis.md
      - Interoperability: api/interoperability.md
      - Validation: api/validation.md
      - Command line: api/cli.md
  - Project:
      - project/index.md
      - Roadmap: project/roadmap.md
      - Changelog: project/changelog.md
      - Contributing: project/contributing.md
      - Troubleshooting: project/troubleshooting.md