_quarto.yml

project:
  type: website
  output-dir: _site
  render:
    - "index.qmd"
    - "install.qmd"
    - "getting_started.qmd"
    - "docs/tutorials/**/*.qmd"
    - "docs/tutorials/**/*.qmd"
    - "docs/userguides/*.qmd"
    - "docs/reference/*.qmd"
    - "!docs/*.md"
    - "!docs/_build/"
    - "!docs/javascripts/"
  resources:
    - "docs/**/*.png"
    - "docs/**/*.jpg"
    - "docs/**/*.svg"
    - "docs/**/*.gif"
    - "docs/**/*.css"
    - "docs/**/*.js"
    - "!docs/CONTRIBUTING.md"
    - "!docs/javascripts/"

quartodoc:
  package: bofire
  title: API Reference
  dir: docs/reference
  parser: google
  sections:
    - title: Data Models - Domain
      desc: Domain configuration data models
      contents:
        - data_models.domain.domain.Domain
        - data_models.domain.features.Inputs
        - data_models.domain.features.Outputs
        - data_models.domain.constraints.Constraints
    - title: Data Models - Features
      desc: Feature data models
      contents:
        - name: data_models.features.api
          members:
            - CategoricalInput
            - CategoricalOutput
            - ContinuousInput
            - ContinuousOutput
            - DiscreteInput
            - ContinuousDescriptorInput
            - CategoricalDescriptorInput
            - ContinuousMolecularInput
            - CategoricalMolecularInput
            - TaskInput
    - title: Data Models - Strategies
      desc: Strategy configuration data models
      contents:
        - name: data_models.strategies.api
          members:
            - DoEStrategy
            - FactorialStrategy
            - FractionalFactorialStrategy
            - ActiveLearningStrategy
            - BotorchStrategy
            - EntingStrategy
            - MoboStrategy
            - MultiFidelityStrategy
            - MultiobjectiveStrategy
            - AdditiveSoboStrategy
            - CustomSoboStrategy
    - title: Data Models - Kernels
      desc: Kernel configuration data models
      contents:
        - name: data_models.kernels.api
          members:
            - Kernel
            - AdditiveKernel
            - MultiplicativeKernel
            - ScaleKernel
            - MaternKernel
            - RBFKernel
            - LinearKernel
            - PolynomialKernel
            - HammingDistanceKernel
            - TanimotoKernel
            - WassersteinKernel
    - title: Data Models - Surrogates
      desc: Surrogate model configuration data models
      contents:
        - name: data_models.surrogates.api
          members:
            - Surrogate
            - SingleTaskGPSurrogate
            - MixedSingleTaskGPSurrogate
            - MultiTaskGPSurrogate
            - RobustSingleTaskGPSurrogate
            - TanimotoGPSurrogate
            - LinearSurrogate
            - PolynomialSurrogate
            - RandomForestSurrogate
            - MLPEnsemble
            - BotorchSurrogates
    - title: Strategies
      desc: Strategy implementations
      contents:
        - name: strategies.api
          members:
            - Strategy
            - RandomStrategy
            - DoEStrategy
            - FractionalFactorialStrategy
            - SoboStrategy
            - AdditiveSoboStrategy
            - MultiplicativeSoboStrategy
            - CustomSoboStrategy
            - QparegoStrategy
            - MoboStrategy
            - BotorchStrategy
            - EntingStrategy
            - MultiFidelityStrategy
            - ActiveLearningStrategy
            - ShortestPathStrategy
            - StepwiseStrategy
    - title: Surrogates
      desc: Surrogate model implementations
      contents:
        - name: surrogates.api
          members:
            - Surrogate
            - TrainableSurrogate
            - SingleTaskGPSurrogate
            - MultiTaskGPSurrogate
            - BotorchSurrogates
            - LinearDeterministicSurrogate
            - EmpiricalSurrogate
            - RandomForestSurrogate
            - MLPEnsemble
            - PiecewiseLinearGPSurrogate

website:
  title: "BoFire"
  site-url: "https://experimental-design.github.io/bofire"
  repo-url: "https://github.com/experimental-design/bofire"
  repo-actions: [edit, issue]
  page-navigation: true

  navbar:
    background: primary
    search: true
    left:
      - text: "Home"
        href: index.qmd
      - text: "Getting Started"
        href: getting_started.qmd
      - text: "User Guides"
        menu:
          - text: "Domain Configuration"
            href: docs/userguides/domain.qmd
          - text: "Strategies"
            href: docs/userguides/strategies.qmd
          - text: "Surrogate Models"
            href: docs/userguides/surrogates.qmd
          - text: "Data Models vs Functionals"
            href: docs/userguides/data_models_functionals.qmd
      - text: "Examples"
        menu:
          - text: "Basic Examples"
            href: docs/tutorials/basic_examples/index.qmd
          - text: "Advanced Examples"
            href: docs/tutorials/advanced_examples/index.qmd
          - text: "Benchmarks"
            href: docs/tutorials/benchmarks/index.qmd
          - text: "Design of Experiments"
            href: docs/tutorials/doe/index.qmd
          - text: "Serialization"
            href: docs/tutorials/serialization/index.qmd
      - text: "API Reference"
        href: docs/reference/index.qmd
    right:
      - icon: github
        href: "https://github.com/experimental-design/bofire"

  sidebar:
    - title: "Getting Started"
      style: "docked"
      contents:
        - index.qmd
        - install.qmd
        - getting_started.qmd

    - title: "User Guides"
      contents:
        - docs/userguides/domain.qmd
        - docs/userguides/strategies.qmd
        - docs/userguides/surrogates.qmd
        - docs/userguides/data_models_functionals.qmd

    - title: "Examples"
      contents:
        - section: "Basic Examples"
          contents:
            - docs/tutorials/basic_examples/index.qmd
            - docs/tutorials/basic_examples/basic_terminology.qmd
            - docs/tutorials/basic_examples/Reaction_Optimization_Example.qmd
            - docs/tutorials/basic_examples/Model_Fitting_and_analysis.qmd
            - docs/tutorials/basic_examples/Outlier_Detection_and_Robust_GP.qmd
            - docs/tutorials/basic_examples/Unknown_Constraint_Classification.qmd
            - docs/tutorials/basic_examples/index_kernel.qmd
        - section: "Advanced Examples"
          contents:
            - docs/tutorials/advanced_examples/index.qmd
            - docs/tutorials/advanced_examples/custom_sobo.qmd
            - docs/tutorials/advanced_examples/desirability_objectives.qmd
            - docs/tutorials/advanced_examples/genetic_algorithm.qmd
            - docs/tutorials/advanced_examples/enting_strategy_suzuki_miyaura_reaction.qmd
            - docs/tutorials/advanced_examples/merging_objectives.qmd
            - docs/tutorials/advanced_examples/multifidelity_bo.qmd
            - docs/tutorials/advanced_examples/objectives_on_inputs.qmd
            - docs/tutorials/advanced_examples/random_forest_in_bofire.qmd
            - docs/tutorials/advanced_examples/transfer_learning_bo.qmd
            - docs/tutorials/advanced_examples/octane_number.qmd
        - section: "Benchmarks"
          contents:
            - docs/tutorials/benchmarks/index.qmd
            - docs/tutorials/benchmarks/001-Himmelblau.qmd
            - docs/tutorials/benchmarks/002-DTLZ2.qmd
            - docs/tutorials/benchmarks/003-Hartmann_with_nchoosek.qmd
            - docs/tutorials/benchmarks/004-30dimBranin.qmd
            - docs/tutorials/benchmarks/005-Himmelblau_with_outliers.qmd
            - docs/tutorials/benchmarks/006-Bayesian_optimization_over_molecules.qmd
            - docs/tutorials/benchmarks/007-LSRBO.qmd
            - docs/tutorials/benchmarks/008-ZDT1.qmd
            - docs/tutorials/benchmarks/009-BNH.qmd
            - docs/tutorials/benchmarks/010-TNK.qmd
            - docs/tutorials/benchmarks/011-ActiveLearning.qmd
            - docs/tutorials/benchmarks/012-engineered_features.qmd
            - docs/tutorials/benchmarks/013-spherical_kernel.qmd
        - section: "Design of Experiments"
          contents:
            - docs/tutorials/doe/index.qmd
            - docs/tutorials/doe/basic_examples.qmd
            - docs/tutorials/doe/design_with_explicit_formula.qmd
            - docs/tutorials/doe/fractional_factorial.qmd
            - docs/tutorials/doe/nchoosek_constraint.qmd
            - docs/tutorials/doe/optimality_criteria.qmd
        - section: "Serialization"
          contents:
            - docs/tutorials/serialization/index.qmd
            - docs/tutorials/serialization/models_serial.qmd
            - docs/tutorials/serialization/strategies_serial.qmd

    - title: "API Reference"
      contents:
        - docs/reference/domain.qmd
        - docs/reference/constraints.qmd
        - docs/reference/objectives.qmd
        - docs/reference/features.qmd
        - docs/reference/utils.qmd

format:
  html:
    theme:
      light: [cosmo, theme-light.scss]
      dark: [cosmo, theme-dark.scss]
    css: styles.css
    toc: true
    toc-depth: 3
    code-copy: true
    code-fold: false
    code-tools: true
    number-sections: false
    link-external-newwindow: true

filters:
  - quarto

execute:
  enabled: true
  freeze: auto
  cache: true

jupyter: python3