_quarto.yml

# Cloned from https://github.com/TileDB-Inc/tiledb-quarto-template
project:
  type: website
  output-dir: docs
  render:
    # The first item will be the landing page
    - "documentation/index.md"
    - "documentation"
    - "documentation/reference"
    - "examples/README.md"
    - "examples"

format:
  html:
    # https://quarto.org/docs/output-formats/page-layout.html#grid-customization
    grid:
      sidebar-width: 350px
      body-width: 1000px
      margin-width: 350px
      gutter-width: 1rem
    toc: true
    theme: 
      light: [flatly, "quarto-materials/tiledb.scss"]
    mainfont: Helvetica
    fontsize: 1rem
    linkcolor: "#4d9fff"
    code-copy: true
    code-overflow: wrap
    css: "quarto-materials/tiledb.css"

quartodoc:
  title: "Python"
  package: tiledbvcf
  dir: "documentation/reference"
  sections:
    - title: "tiledbvcf"
      desc: ""
      contents:
        - Dataset
        - ReadConfig
        - config_logging

website:
  favicon: "documentation/assets/tiledb.ico"
  site-url: https://tiledb-inc.github.io/TileDB-VCF/
  repo-url: https://github.com/TileDB-Inc/TileDB-VCF
  # You may want one or both of these, or neither:
  repo-actions: [edit, issue]
  page-navigation: true
  navbar:
    background: light
    logo: "quarto-materials/tiledb-logo.png"
    collapse-below: lg
    left:
      - text: "Home page"
        href: "https://tiledb.com"
      - text: "Login"
        href: "https://cloud.tiledb.com/auth/login"
      - text: "Contact us"
        href: "https://tiledb.com/contact"
      - text: "Repo"
        href: "https://github.com/TileDB-Inc/TileDB-VCF"

  sidebar:
    - style: "floating"
      collapse-level: 2
      align: left
      contents:
        - href: "documentation/index.md"

        - section: "Examples"
          contents:
            # - href: "examples/overview.md"
            - href: "examples/tutorial_tiledbvcf_basics.ipynb"
            - href: "examples/tutorial_tiledbvcf_allele_frequencies.ipynb"
            - href: "examples/tutorial_tiledbvcf_gwas.ipynb"

        - section: "Ingestion"
          contents:
            # - href: "documentation/ingestion/overview.md"
            - href: "documentation/ingestion/cli.md"
            - href: "documentation/ingestion/python.md"
            - href: "documentation/ingestion/distributed-ingestion.md"

        - section: "API Reference"
          contents:
            - href: "documentation/api-reference/cli.md"
            - href: "documentation/reference/index.qmd"

        - section: "How To"
          contents:
            # - href: "documentation/how-to/overview.md"
            - href: "documentation/how-to/create-a-dataset.md"
            - href: "documentation/how-to/export-to-vcf.md"
            - href: "documentation/how-to/handle-large-queries.md"
            - href: "documentation/how-to/ingest-samples.md"
            - href: "documentation/how-to/perform-distributed-queries-with-tiledb-cloud.md"
            - href: "documentation/how-to/perform-distributed-queries-with-dask.md"
            - href: "documentation/how-to/perform-distributed-queries-with-spark.md"
            - href: "documentation/how-to/read-from-the-dataset.md"
            - href: "documentation/how-to/work-with-cloud-object-stores.md"

        - section: "Background"
          contents:
            - href: "documentation/the-solution.md"
            - href: "documentation/data-model.md"