mkdocs.yml

site_name: PhenEx
nav:
  - Home: index.md
  - Installation: installation.md
  - Tutorials:
      - CodelistPhenotype: tutorials/CodelistPhenotype_Tutorial.ipynb
      - MeasurementPhenotype: tutorials/MeasurementPhenotype_Tutorial.ipynb
      - ArithmeticPhenotype: tutorials/ArithmeticPhenotype_Tutorial.ipynb
      - LogicPhenotype: tutorials/LogicPhenotype_Tutorial.ipynb
  - API:
      - Phenotypes:
          - Phenotype: api/phenotypes/phenotype.md
          - CodelistPhenotype: api/phenotypes/codelist_phenotype.md
          - MultipleOccurrencePhenotype: api/phenotypes/multiple_occurrences_phenotype.md
          - MeasurementPhenotype: api/phenotypes/measurement_phenotype.md
          - AgePhenotype: api/phenotypes/age_phenotype.md
          - SexPhenotype: api/phenotypes/sex_phenotype.md
          - DeathPhenotype: api/phenotypes/death_phenotype.md
          - ContinuousCoveragePhenotype: api/phenotypes/continuous_coverage_phenotype.md
          - ArithmeticPhenotype: api/phenotypes/arithmetic_phenotype.md
          - LogicPhenotype: api/phenotypes/logic_phenotype.md
          - ScorePhenotype: api/phenotypes/score_phenotype.md
          - Cohort: api/phenotypes/cohort.md
      - Codelists:
          - Codelist: api/codelists/codelists.md
          - LocalCSVCodelistFactory: api/codelists/local_csv_codelist_factory.md
      - Connectors: api/ibis_connect.md
      - Reporting:
          - Report: api/reporting/reporter.md
          - Table1: api/reporting/table1.md
  - License: LICENSE.md

plugins:
  - mkdocstrings:
      handlers:
        python:
          paths: [../phenex] # search packages in the src folder
          options:
            docstring_style: "google" # or "numpy", "restructuredtext", etc.
  - mkdocs-jupyter
theme:
  name: material
  palette:
    primary: red
  features:
    - content.code.copy
markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: false # Try setting this to false
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
extra_css:
  - assets/style.css