_quarto.yml

project:
  type: website
  pre-render: version_config.py
  output-dir: _site
  render:
    - docs/index.qmd
    - docs/**/*.qmd
    - docs/**/*.md
execute:
  enabled: true
  freeze: auto
filters:
  - docs/interlinks.lua
interlinks:
  sources:
    python:
      url: https://docs.python.org/3/
    pandas:
      url: https://pandas.pydata.org/docs/
    numpy:
      url: https://numpy.org/doc/stable/
website:
  title: spotoptim
  description: Sequential Parameter Optimization Toolbox in Python
  site-url: https://sequential-parameter-optimization.github.io/spotoptim/
  repo-url: https://github.com/sequential-parameter-optimization/spotoptim
  repo-actions:
    - edit
    - issue
  favicon: docs/images/favicon.png
  navbar:
    background: primary
    search: true
    logo: docs/images/spotlogo.png
    right:
      - icon: github
        href: https://github.com/sequential-parameter-optimization/spotoptim
        aria-label: GitHub repository
  sidebar:
    style: docked
    search: false
    collapse-level: 1
    contents:
      - text: Home
        file: docs/index.qmd
      - text: Getting Started
        file: docs/sequential-parameter-optimization-cookbook.qmd
      - text: Examples
        file: docs/examples.qmd
      - section: User Guide
        contents:
          - text: Overview
            file: docs/user_guide.qmd
          - text: The SpotOptim Class
            file: docs/user_guide/spotoptim.qmd
          - text: Surrogate Models
            file: docs/user_guide/surrogate.qmd
          - text: Acquisition & Infill
            file: docs/user_guide/optimizer.qmd
          - text: Test Functions
            file: docs/user_guide/function.qmd
          - text: Sampling & Designs
            file: docs/user_guide/sampling.qmd
          - text: Visualization
            file: docs/user_guide/plot.qmd
          - text: Reporting & Analysis
            file: docs/user_guide/reporting.qmd
          - text: Utilities
            file: docs/user_guide/utils.qmd
          - text: Neural Networks
            file: docs/user_guide/nn.qmd
          - text: Multi-Objective
            file: docs/user_guide/mo.qmd
          - text: Core Infrastructure
            file: docs/user_guide/core.qmd
          - text: Hyperparameters
            file: docs/user_guide/hyperparameters.qmd
          - text: Datasets
            file: docs/user_guide/data.qmd
          - text: Model Inspection
            file: docs/user_guide/inspection.qmd
          - text: Factor Analysis
            file: docs/user_guide/factor_analyzer.qmd
          - text: Exploratory Data Analysis
            file: docs/user_guide/eda.qmd
          - text: Triangulation Candidates
            file: docs/user_guide/tricands.qmd
      - text: Initialization
        file: docs/spotoptim_init.qmd
      - text: Sequential Optimization
        file: docs/optimize_seq.qmd
      - text: Parallel Optimization
        file: docs/optimize_parallel.qmd
      - text: Early Stopping
        file: docs/early-stopping.qmd
      - text: Running on Slurm (GWDG NHR)
        file: docs/slurm.qmd
      - section: API Reference
        contents:
          - text: Overview
            file: docs/reference/index.qmd
          - section: SpotOptim
            contents:
              - text: SpotOptim.SpotOptim
                file: docs/reference/SpotOptim.SpotOptim.qmd
              - text: SpotOptim.SpotOptimConfig
                file: docs/reference/SpotOptim.SpotOptimConfig.qmd
              - text: SpotOptim.SpotOptimState
                file: docs/reference/SpotOptim.SpotOptimState.qmd
          - section: Core
            contents:
              - text: core
                file: docs/reference/core.qmd
              - text: core.data
                file: docs/reference/core.data.qmd
              - text: SpotDataFromArray
                file: docs/reference/core.data.SpotDataFromArray.qmd
              - text: SpotDataFromTorchDataset
                file: docs/reference/core.data.SpotDataFromTorchDataset.qmd
              - text: SpotDataSet
                file: docs/reference/core.data.SpotDataSet.qmd
              - text: core.experiment
                file: docs/reference/core.experiment.qmd
              - text: ExperimentControl
                file: docs/reference/core.experiment.ExperimentControl.qmd
          - section: Surrogate Models
            contents:
              - text: surrogate
                file: docs/reference/surrogate.qmd
              - text: surrogate.kriging
                file: docs/reference/surrogate.kriging.qmd
              - text: Kriging
                file: docs/reference/surrogate.kriging.Kriging.qmd
              - text: surrogate.simple_kriging
                file: docs/reference/surrogate.simple_kriging.qmd
              - text: SimpleKriging
                file: docs/reference/surrogate.simple_kriging.SimpleKriging.qmd
              - text: surrogate.mlp_surrogate
                file: docs/reference/surrogate.mlp_surrogate.qmd
              - text: MLPSurrogate
                file: docs/reference/surrogate.mlp_surrogate.MLPSurrogate.qmd
              - text: surrogate.nystroem
                file: docs/reference/surrogate.nystroem.qmd
              - text: Nystroem
                file: docs/reference/surrogate.nystroem.Nystroem.qmd
              - text: surrogate.kernels
                file: docs/reference/surrogate.kernels.qmd
              - text: ConstantKernel
                file: docs/reference/surrogate.kernels.ConstantKernel.qmd
              - text: Kernel
                file: docs/reference/surrogate.kernels.Kernel.qmd
              - text: Product
                file: docs/reference/surrogate.kernels.Product.qmd
              - text: RBF
                file: docs/reference/surrogate.kernels.RBF.qmd
              - text: SpotOptimKernel
                file: docs/reference/surrogate.kernels.SpotOptimKernel.qmd
              - text: Sum
                file: docs/reference/surrogate.kernels.Sum.qmd
              - text: WhiteKernel
                file: docs/reference/surrogate.kernels.WhiteKernel.qmd
              - text: surrogate.pipeline
                file: docs/reference/surrogate.pipeline.qmd
              - text: Pipeline
                file: docs/reference/surrogate.pipeline.Pipeline.qmd
          - section: Sampling
            contents:
              - text: sampling
                file: docs/reference/sampling.qmd
              - text: sampling.design
                file: docs/reference/sampling.design.qmd
              - text: fullfactorial
                file: docs/reference/sampling.design.fullfactorial.qmd
              - text: generate_clustered_design
                file: 
                  docs/reference/sampling.design.generate_clustered_design.qmd
              - text: generate_collinear_design
                file: 
                  docs/reference/sampling.design.generate_collinear_design.qmd
              - text: generate_grid_design
                file: docs/reference/sampling.design.generate_grid_design.qmd
              - text: generate_qmc_lhs_design
                file: docs/reference/sampling.design.generate_qmc_lhs_design.qmd
              - text: generate_sobol_design
                file: docs/reference/sampling.design.generate_sobol_design.qmd
              - text: generate_uniform_design
                file: docs/reference/sampling.design.generate_uniform_design.qmd
              - text: sampling.effects
                file: docs/reference/sampling.effects.qmd
              - text: plot_all_partial_dependence
                file: 
                  docs/reference/sampling.effects.plot_all_partial_dependence.qmd
              - text: randorient
                file: docs/reference/sampling.effects.randorient.qmd
              - text: screening_plot
                file: docs/reference/sampling.effects.screening_plot.qmd
              - text: screening_print
                file: docs/reference/sampling.effects.screening_print.qmd
              - text: screeningplan
                file: docs/reference/sampling.effects.screeningplan.qmd
              - text: sampling.lhs
                file: docs/reference/sampling.lhs.qmd
              - text: rlh
                file: docs/reference/sampling.lhs.rlh.qmd
              - text: sampling.mm
                file: docs/reference/sampling.mm.qmd
              - text: bestlh
                file: docs/reference/sampling.mm.bestlh.qmd
              - text: jd
                file: docs/reference/sampling.mm.jd.qmd
              - text: mm
                file: docs/reference/sampling.mm.mm.qmd
              - text: mm_improvement
                file: docs/reference/sampling.mm.mm_improvement.qmd
              - text: mm_corrected_improvement
                file: docs/reference/sampling.mm.mm_corrected_improvement.qmd
              - text: mm_improvement_contour
                file: docs/reference/sampling.mm.mm_improvement_contour.qmd
              - text: mmlhs
                file: docs/reference/sampling.mm.mmlhs.qmd
              - text: mmphi
                file: docs/reference/sampling.mm.mmphi.qmd
              - text: mmphi_intensive
                file: docs/reference/sampling.mm.mmphi_intensive.qmd
              - text: mmphi_intensive_update
                file: docs/reference/sampling.mm.mmphi_intensive_update.qmd
              - text: mmphi_corrected
                file: docs/reference/sampling.mm.mmphi_corrected.qmd
              - text: mmphi_corrected_update
                file: docs/reference/sampling.mm.mmphi_corrected_update.qmd
              - text: mmsort
                file: docs/reference/sampling.mm.mmsort.qmd
              - text: perturb
                file: docs/reference/sampling.mm.perturb.qmd
              - text: phisort
                file: docs/reference/sampling.mm.phisort.qmd
              - text: plot_mmphi_vs_n_lhs
                file: docs/reference/sampling.mm.plot_mmphi_vs_n_lhs.qmd
              - text: plot_mmphi_corrected_vs_n_lhs
                file: docs/reference/sampling.mm.plot_mmphi_corrected_vs_n_lhs.qmd
              - text: plot_mmphi_vs_points
                file: docs/reference/sampling.mm.plot_mmphi_vs_points.qmd
              - text: plot_mmphi_corrected_vs_points
                file: docs/reference/sampling.mm.plot_mmphi_corrected_vs_points.qmd
              - text: propose_mmphi_intensive_minimizing_point
                file:
                  docs/reference/sampling.mm.propose_mmphi_intensive_minimizing_point.qmd
              - text: propose_mmphi_corrected_minimizing_point
                file:
                  docs/reference/sampling.mm.propose_mmphi_corrected_minimizing_point.qmd
              - text: subset
                file: docs/reference/sampling.mm.subset.qmd
          - section: Optimization
            contents:
              - text: optimizer
                file: docs/reference/optimizer.qmd
              - text: optimizer.schedule_free
                file: docs/reference/optimizer.schedule_free.qmd
              - text: AdamWScheduleFree
                file: 
                  docs/reference/optimizer.schedule_free.AdamWScheduleFree.qmd
          - section: Hyperparameters
            contents:
              - text: hyperparameters
                file: docs/reference/hyperparameters.qmd
              - text: hyperparameters.parameters
                file: docs/reference/hyperparameters.parameters.qmd
              - text: ParameterSet
                file: docs/reference/hyperparameters.parameters.ParameterSet.qmd
              - text: hyperparameters.repr_helpers
                file: docs/reference/hyperparameters.repr_helpers.qmd
              - text: Bounds
                file: docs/reference/hyperparameters.repr_helpers.Bounds.qmd
              - text: Parameter
                file: docs/reference/hyperparameters.repr_helpers.Parameter.qmd
          - section: Neural Networks
            contents:
              - text: nn
                file: docs/reference/nn.qmd
              - text: nn.linear_regressor
                file: docs/reference/nn.linear_regressor.qmd
              - text: LinearRegressor
                file: docs/reference/nn.linear_regressor.LinearRegressor.qmd
              - text: nn.mlp
                file: docs/reference/nn.mlp.qmd
              - text: MLP
                file: docs/reference/nn.mlp.MLP.qmd
          - section: Plotting & Visualization
            contents:
              - text: plot
                file: docs/reference/plot.qmd
              - text: plot.contour
                file: docs/reference/plot.contour.qmd
              - text: contourf_plot
                file: docs/reference/plot.contour.contourf_plot.qmd
              - text: mo_generate_plot_grid
                file: docs/reference/plot.contour.mo_generate_plot_grid.qmd
              - text: plotModel
                file: docs/reference/plot.contour.plotModel.qmd
              - text: simple_contour
                file: docs/reference/plot.contour.simple_contour.qmd
              - text: plot.mo
                file: docs/reference/plot.mo.qmd
              - text: plot_mo
                file: docs/reference/plot.mo.plot_mo.qmd
              - text: plot.visualization
                file: docs/reference/plot.visualization.qmd
              - text: plot_important_hyperparameter_contour
                file: 
                  docs/reference/plot.visualization.plot_important_hyperparameter_contour.qmd
              - text: plot_progress
                file: docs/reference/plot.visualization.plot_progress.qmd
              - text: plot_surrogate
                file: docs/reference/plot.visualization.plot_surrogate.qmd
              - text: plot_design_points
                file: docs/reference/plot.visualization.plot_design_points.qmd
          - section: Utilities
            contents:
              - text: utils
                file: docs/reference/utils.qmd
              - text: utils.boundaries
                file: docs/reference/utils.boundaries.qmd
              - text: get_boundaries
                file: docs/reference/utils.boundaries.get_boundaries.qmd
              - text: map_to_original_scale
                file: docs/reference/utils.boundaries.map_to_original_scale.qmd
              - text: utils.eval
                file: docs/reference/utils.eval.qmd
              - text: mo_cv_models
                file: docs/reference/utils.eval.mo_cv_models.qmd
              - text: mo_eval_models
                file: docs/reference/utils.eval.mo_eval_models.qmd
              - text: utils.file
                file: docs/reference/utils.file.qmd
              - text: get_experiment_filename
                file: docs/reference/utils.file.get_experiment_filename.qmd
              - text: utils.mapping
                file: docs/reference/utils.mapping.qmd
              - text: map_lr
                file: docs/reference/utils.mapping.map_lr.qmd
              - text: utils.pca
                file: docs/reference/utils.pca.qmd
              - text: get_loading_scores
                file: docs/reference/utils.pca.get_loading_scores.qmd
              - text: get_pca
                file: docs/reference/utils.pca.get_pca.qmd
              - text: get_pca_topk
                file: docs/reference/utils.pca.get_pca_topk.qmd
              - text: plot_loading_scores
                file: docs/reference/utils.pca.plot_loading_scores.qmd
              - text: plot_pca1vs2
                file: docs/reference/utils.pca.plot_pca1vs2.qmd
              - text: plot_pca_scree
                file: docs/reference/utils.pca.plot_pca_scree.qmd
              - text: utils.scaler
                file: docs/reference/utils.scaler.qmd
              - text: TorchStandardScaler
                file: docs/reference/utils.scaler.TorchStandardScaler.qmd
              - text: utils.stats
                file: docs/reference/utils.stats.qmd
              - text: calculate_outliers
                file: docs/reference/utils.stats.calculate_outliers.qmd
              - text: compute_coefficients_table
                file: docs/reference/utils.stats.compute_coefficients_table.qmd
              - text: compute_standardized_betas
                file: docs/reference/utils.stats.compute_standardized_betas.qmd
              - text: condition_index
                file: docs/reference/utils.stats.condition_index.qmd
              - text: cov_to_cor
                file: docs/reference/utils.stats.cov_to_cor.qmd
              - text: fit_all_lm
                file: docs/reference/utils.stats.fit_all_lm.qmd
              - text: get_all_vars_from_formula
                file: docs/reference/utils.stats.get_all_vars_from_formula.qmd
              - text: get_combinations
                file: docs/reference/utils.stats.get_combinations.qmd
              - text: get_sample_size
                file: docs/reference/utils.stats.get_sample_size.qmd
              - text: normalize_X
                file: docs/reference/utils.stats.normalize_X.qmd
              - text: pairwise_semi_partial_correlation
                file: 
                  docs/reference/utils.stats.pairwise_semi_partial_correlation.qmd
              - text: partial_correlation
                file: docs/reference/utils.stats.partial_correlation.qmd
              - text: partial_correlation_test
                file: docs/reference/utils.stats.partial_correlation_test.qmd
              - text: plot_coeff_vs_pvals
                file: docs/reference/utils.stats.plot_coeff_vs_pvals.qmd
              - text: plot_coeff_vs_pvals_by_included
                file: 
                  docs/reference/utils.stats.plot_coeff_vs_pvals_by_included.qmd
              - text: preprocess_df_for_ols
                file: docs/reference/utils.stats.preprocess_df_for_ols.qmd
              - text: semi_partial_correlation
                file: docs/reference/utils.stats.semi_partial_correlation.qmd
              - text: vif
                file: docs/reference/utils.stats.vif.qmd
          - section: Data
            contents:
              - text: data
                file: docs/reference/data.qmd
              - text: data.base
                file: docs/reference/data.base.qmd
              - text: Config
                file: docs/reference/data.base.Config.qmd
              - text: FileConfig
                file: docs/reference/data.base.FileConfig.qmd
              - text: data.diabetes
                file: docs/reference/data.diabetes.qmd
              - text: DiabetesDataset
                file: docs/reference/data.diabetes.DiabetesDataset.qmd
              - text: get_diabetes_dataloaders
                file: docs/reference/data.diabetes.get_diabetes_dataloaders.qmd
          - section: Exploratory Data Analysis
            contents:
              - text: eda
                file: docs/reference/eda.qmd
              - text: eda.plots
                file: docs/reference/eda.plots.qmd
              - text: plot_ip_boxplots
                file: docs/reference/eda.plots.plot_ip_boxplots.qmd
              - text: plot_ip_histograms
                file: docs/reference/eda.plots.plot_ip_histograms.qmd
          - section: Multi-Objective
            contents:
              - text: mo
                file: docs/reference/mo.qmd
              - text: mo.mo_mm
                file: docs/reference/mo.mo_mm.qmd
              - text: mo_mm_desirability_function
                file: docs/reference/mo.mo_mm.mo_mm_desirability_function.qmd
              - text: mo_mm_desirability_optimizer
                file: docs/reference/mo.mo_mm.mo_mm_desirability_optimizer.qmd
              - text: mo_xy_desirability_plot
                file: docs/reference/mo.mo_mm.mo_xy_desirability_plot.qmd
              - text: mo.pareto
                file: docs/reference/mo.pareto.qmd
              - text: is_pareto_efficient
                file: docs/reference/mo.pareto.is_pareto_efficient.qmd
              - text: mo_pareto_optx_plot
                file: docs/reference/mo.pareto.mo_pareto_optx_plot.qmd
              - text: mo_xy_contour
                file: docs/reference/mo.pareto.mo_xy_contour.qmd
              - text: mo_xy_surface
                file: docs/reference/mo.pareto.mo_xy_surface.qmd
          - section: Inspection
            contents:
              - text: inspection
                file: docs/reference/inspection.qmd
              - text: inspection.importance
                file: docs/reference/inspection.importance.qmd
              - text: generate_imp
                file: docs/reference/inspection.importance.generate_imp.qmd
              - text: generate_mdi
                file: docs/reference/inspection.importance.generate_mdi.qmd
              - text: plot_feature_importances
                file: 
                  docs/reference/inspection.importance.plot_feature_importances.qmd
              - text: plot_feature_scatter_matrix
                file: 
                  docs/reference/inspection.importance.plot_feature_scatter_matrix.qmd
              - text: plot_importances
                file: docs/reference/inspection.importance.plot_importances.qmd
              - text: inspection.predictions
                file: docs/reference/inspection.predictions.qmd
              - text: plot_actual_vs_predicted
                file: 
                  docs/reference/inspection.predictions.plot_actual_vs_predicted.qmd
          - section: Factor Analyzer
            contents:
              - text: factor_analyzer
                file: docs/reference/factor_analyzer.qmd
              - text: factor_analyzer.confirmatory_factor_analyzer
                file: 
                  docs/reference/factor_analyzer.confirmatory_factor_analyzer.qmd
              - text: ConfirmatoryFactorAnalyzer
                file: 
                  docs/reference/factor_analyzer.confirmatory_factor_analyzer.ConfirmatoryFactorAnalyzer.qmd
              - text: ModelSpecification
                file: 
                  docs/reference/factor_analyzer.confirmatory_factor_analyzer.ModelSpecification.qmd
              - text: ModelSpecificationParser
                file: 
                  docs/reference/factor_analyzer.confirmatory_factor_analyzer.ModelSpecificationParser.qmd
              - text: factor_analyzer.factor_analyzer
                file: docs/reference/factor_analyzer.factor_analyzer.qmd
              - text: FactorAnalyzer
                file: 
                  docs/reference/factor_analyzer.factor_analyzer.FactorAnalyzer.qmd
              - text: calculate_bartlett_sphericity
                file: 
                  docs/reference/factor_analyzer.factor_analyzer.calculate_bartlett_sphericity.qmd
              - text: calculate_kmo
                file: 
                  docs/reference/factor_analyzer.factor_analyzer.calculate_kmo.qmd
              - text: factor_analyzer.factor_analyzer_rotator
                file: docs/reference/factor_analyzer.factor_analyzer_rotator.qmd
              - text: Rotator
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_rotator.Rotator.qmd
              - text: factor_analyzer.factor_analyzer_utils
                file: docs/reference/factor_analyzer.factor_analyzer_utils.qmd
              - text: apply_impute_nan
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.apply_impute_nan.qmd
              - text: commutation_matrix
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.commutation_matrix.qmd
              - text: corr
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.corr.qmd
              - text: cov
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.cov.qmd
              - text: covariance_to_correlation
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.covariance_to_correlation.qmd
              - text: duplication_matrix
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.duplication_matrix.qmd
              - text: duplication_matrix_pre_post
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.duplication_matrix_pre_post.qmd
              - text: fill_lower_diag
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.fill_lower_diag.qmd
              - text: get_first_idxs_from_values
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.get_first_idxs_from_values.qmd
              - text: get_free_parameter_idxs
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.get_free_parameter_idxs.qmd
              - text: get_symmetric_lower_idxs
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.get_symmetric_lower_idxs.qmd
              - text: get_symmetric_upper_idxs
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.get_symmetric_upper_idxs.qmd
              - text: impute_values
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.impute_values.qmd
              - text: inv_chol
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.inv_chol.qmd
              - text: merge_variance_covariance
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.merge_variance_covariance.qmd
              - text: partial_correlations
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.partial_correlations.qmd
              - text: smc
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.smc.qmd
              - text: unique_elements
                file: 
                  docs/reference/factor_analyzer.factor_analyzer_utils.unique_elements.qmd
          - section: Functions
            contents:
              - text: function
                file: docs/reference/function.qmd
              - text: function.forr08a
                file: docs/reference/function.forr08a.qmd
              - text: aerofoilcd
                file: docs/reference/function.forr08a.aerofoilcd.qmd
              - text: branin
                file: docs/reference/function.forr08a.branin.qmd
              - text: onevar
                file: docs/reference/function.forr08a.onevar.qmd
              - text: function.mo
                file: docs/reference/function.mo.qmd
              - text: activity_pred
                file: docs/reference/function.mo.activity_pred.qmd
              - text: conversion_pred
                file: docs/reference/function.mo.conversion_pred.qmd
              - text: dtlz1
                file: docs/reference/function.mo.dtlz1.qmd
              - text: dtlz2
                file: docs/reference/function.mo.dtlz2.qmd
              - text: fonseca_fleming
                file: docs/reference/function.mo.fonseca_fleming.qmd
              - text: fun_myer16a
                file: docs/reference/function.mo.fun_myer16a.qmd
              - text: kursawe
                file: docs/reference/function.mo.kursawe.qmd
              - text: mo_conv2_max
                file: docs/reference/function.mo.mo_conv2_max.qmd
              - text: mo_conv2_min
                file: docs/reference/function.mo.mo_conv2_min.qmd
              - text: schaffer_n1
                file: docs/reference/function.mo.schaffer_n1.qmd
              - text: zdt1
                file: docs/reference/function.mo.zdt1.qmd
              - text: zdt2
                file: docs/reference/function.mo.zdt2.qmd
              - text: zdt3
                file: docs/reference/function.mo.zdt3.qmd
              - text: zdt4
                file: docs/reference/function.mo.zdt4.qmd
              - text: zdt6
                file: docs/reference/function.mo.zdt6.qmd
              - text: function.remote
                file: docs/reference/function.remote.qmd
              - text: objective_remote
                file: docs/reference/function.remote.objective_remote.qmd
              - text: function.so
                file: docs/reference/function.so.qmd
              - text: ackley
                file: docs/reference/function.so.ackley.qmd
              - text: lennard_jones
                file: docs/reference/function.so.lennard_jones.qmd
              - text: michalewicz
                file: docs/reference/function.so.michalewicz.qmd
              - text: noisy_sphere
                file: docs/reference/function.so.noisy_sphere.qmd                
              - text: robot_arm_hard
                file: docs/reference/function.so.robot_arm_hard.qmd
              - text: robot_arm_obstacle
                file: docs/reference/function.so.robot_arm_obstacle.qmd
              - text: rosenbrock
                file: docs/reference/function.so.rosenbrock.qmd
              - text: sphere
                file: docs/reference/function.so.sphere.qmd
              - text: wingwt
                file: docs/reference/function.so.wingwt.qmd
              - text: function.torch_objective
                file: docs/reference/function.torch_objective.qmd
              - text: TorchObjective
                file: docs/reference/function.torch_objective.TorchObjective.qmd
          - section: Tricands
            contents:
              - text: tricands
                file: docs/reference/tricands.qmd
              - text: tricands.tricands
                file: docs/reference/tricands.tricands.qmd
              - text: tricands
                file: docs/reference/tricands.tricands.tricands.qmd
              - text: tricands_fringe
                file: docs/reference/tricands.tricands.tricands_fringe.qmd
              - text: tricands_interior
                file: docs/reference/tricands.tricands.tricands_interior.qmd
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quartodoc:
  package: spotoptim
  source_dir: src
  dir: docs/reference
  parser: google
  render_interlinks: true
  options:
    children: embedded
  sections:
    - title: SpotOptim
      contents:
        - SpotOptim.SpotOptim
        - SpotOptim.SpotOptimConfig
        - SpotOptim.SpotOptimState
    - title: Core
      contents:
        - core
        - core.data
        - core.data.SpotDataFromArray
        - core.data.SpotDataFromTorchDataset
        - core.data.SpotDataSet
        - core.experiment
        - core.experiment.ExperimentControl        
    - title: Surrogate Models
      contents:
        - surrogate
        - surrogate.kriging
        - surrogate.kriging.Kriging
        - surrogate.simple_kriging
        - surrogate.simple_kriging.SimpleKriging
        - surrogate.mlp_surrogate
        - surrogate.mlp_surrogate.MLPSurrogate
        - surrogate.nystroem
        - surrogate.nystroem.Nystroem
        - surrogate.kernels
        - surrogate.kernels.ConstantKernel
        - surrogate.kernels.Kernel
        - surrogate.kernels.Product
        - surrogate.kernels.RBF
        - surrogate.kernels.SpotOptimKernel
        - surrogate.kernels.Sum
        - surrogate.kernels.WhiteKernel
        - surrogate.pipeline
        - surrogate.pipeline.Pipeline
    - title: Sampling
      contents:
        - sampling
        - sampling.design
        - sampling.design.fullfactorial
        - sampling.design.generate_clustered_design
        - sampling.design.generate_collinear_design
        - sampling.design.generate_grid_design
        - sampling.design.generate_qmc_lhs_design
        - sampling.design.generate_sobol_design
        - sampling.design.generate_uniform_design
        - sampling.effects
        - sampling.effects.plot_all_partial_dependence
        - sampling.effects.randorient
        - sampling.effects.screening_plot
        - sampling.effects.screening_print
        - sampling.effects.screeningplan
        - sampling.lhs
        - sampling.lhs.rlh
        - sampling.mm
        - sampling.mm.bestlh
        - sampling.mm.jd
        - sampling.mm.mm
        - sampling.mm.mm_improvement
        - sampling.mm.mm_corrected_improvement
        - sampling.mm.mm_improvement_contour
        - sampling.mm.mmlhs
        - sampling.mm.mmphi
        - sampling.mm.mmphi_intensive
        - sampling.mm.mmphi_intensive_update
        - sampling.mm.mmphi_corrected
        - sampling.mm.mmphi_corrected_update
        - sampling.mm.mmsort
        - sampling.mm.perturb
        - sampling.mm.phisort
        - sampling.mm.plot_mmphi_vs_n_lhs
        - sampling.mm.plot_mmphi_corrected_vs_n_lhs
        - sampling.mm.plot_mmphi_vs_points
        - sampling.mm.plot_mmphi_corrected_vs_points
        - sampling.mm.propose_mmphi_intensive_minimizing_point
        - sampling.mm.propose_mmphi_corrected_minimizing_point
        - sampling.mm.subset
    - title: Optimization
      contents:
        - optimizer
        - optimizer.schedule_free
        - optimizer.schedule_free.AdamWScheduleFree
    - title: Hyperparameters
      contents:
        - hyperparameters
        - hyperparameters.parameters
        - hyperparameters.parameters.ParameterSet
        - hyperparameters.repr_helpers
        - hyperparameters.repr_helpers.Bounds
        - hyperparameters.repr_helpers.Parameter
    - title: Neural Networks
      contents:
        - nn
        - nn.linear_regressor
        - nn.linear_regressor.LinearRegressor
        - nn.mlp
        - nn.mlp.MLP
    - title: Plotting & Visualization
      contents:
        - plot
        - plot.contour
        - plot.contour.contourf_plot
        - plot.contour.mo_generate_plot_grid
        - plot.contour.plotModel
        - plot.contour.simple_contour
        - plot.mo
        - plot.mo.plot_mo
        - plot.visualization
        - plot.visualization.plot_important_hyperparameter_contour
        - plot.visualization.plot_progress
        - plot.visualization.plot_surrogate
        - plot.visualization.plot_design_points
    - title: Utilities
      contents:
        - utils
        - utils.boundaries
        - utils.boundaries.get_boundaries
        - utils.boundaries.map_to_original_scale
        - utils.eval
        - utils.eval.mo_cv_models
        - utils.eval.mo_eval_models
        - utils.file
        - utils.file.get_experiment_filename
        - utils.mapping
        - utils.mapping.map_lr
        - utils.pca
        - utils.pca.get_loading_scores
        - utils.pca.get_pca
        - utils.pca.get_pca_topk
        - utils.pca.plot_loading_scores
        - utils.pca.plot_pca1vs2
        - utils.pca.plot_pca_scree
        - utils.scaler
        - utils.scaler.TorchStandardScaler
        - utils.stats
        - utils.stats.calculate_outliers
        - utils.stats.compute_coefficients_table
        - utils.stats.compute_standardized_betas
        - utils.stats.condition_index
        - utils.stats.cov_to_cor
        - utils.stats.fit_all_lm
        - utils.stats.get_all_vars_from_formula
        - utils.stats.get_combinations
        - utils.stats.get_sample_size
        - utils.stats.normalize_X
        - utils.stats.pairwise_semi_partial_correlation
        - utils.stats.partial_correlation
        - utils.stats.partial_correlation_test
        - utils.stats.plot_coeff_vs_pvals
        - utils.stats.plot_coeff_vs_pvals_by_included
        - utils.stats.preprocess_df_for_ols
        - utils.stats.semi_partial_correlation
        - utils.stats.vif
    - title: Data
      contents:
        - data
        - data.base
        - data.base.Config
        - data.base.FileConfig
        - data.diabetes
        - data.diabetes.DiabetesDataset
        - data.diabetes.get_diabetes_dataloaders
    - title: Exploratory Data Analysis
      contents:
        - eda
        - eda.plots
        - eda.plots.plot_ip_boxplots
        - eda.plots.plot_ip_histograms
    - title: Multi-Objective
      contents:
        - mo
        - mo.mo_mm
        - mo.mo_mm.mo_mm_desirability_function
        - mo.mo_mm.mo_mm_desirability_optimizer
        - mo.mo_mm.mo_xy_desirability_plot
        - mo.pareto
        - mo.pareto.is_pareto_efficient
        - mo.pareto.mo_pareto_optx_plot
        - mo.pareto.mo_xy_contour
        - mo.pareto.mo_xy_surface
    - title: Inspection
      contents:
        - inspection
        - inspection.importance
        - inspection.importance.generate_imp
        - inspection.importance.generate_mdi
        - inspection.importance.plot_feature_importances
        - inspection.importance.plot_feature_scatter_matrix
        - inspection.importance.plot_importances
        - inspection.predictions
        - inspection.predictions.plot_actual_vs_predicted
    - title: Factor Analyzer
      contents:
        - factor_analyzer
        - factor_analyzer.confirmatory_factor_analyzer
        - factor_analyzer.confirmatory_factor_analyzer.ConfirmatoryFactorAnalyzer
        - factor_analyzer.confirmatory_factor_analyzer.ModelSpecification
        - factor_analyzer.confirmatory_factor_analyzer.ModelSpecificationParser
        - factor_analyzer.factor_analyzer
        - factor_analyzer.factor_analyzer.FactorAnalyzer
        - factor_analyzer.factor_analyzer.calculate_bartlett_sphericity
        - factor_analyzer.factor_analyzer.calculate_kmo
        - factor_analyzer.factor_analyzer_rotator
        - factor_analyzer.factor_analyzer_rotator.Rotator
        - factor_analyzer.factor_analyzer_utils
        - factor_analyzer.factor_analyzer_utils.apply_impute_nan
        - factor_analyzer.factor_analyzer_utils.commutation_matrix
        - factor_analyzer.factor_analyzer_utils.corr
        - factor_analyzer.factor_analyzer_utils.cov
        - factor_analyzer.factor_analyzer_utils.covariance_to_correlation
        - factor_analyzer.factor_analyzer_utils.duplication_matrix
        - factor_analyzer.factor_analyzer_utils.duplication_matrix_pre_post
        - factor_analyzer.factor_analyzer_utils.fill_lower_diag
        - factor_analyzer.factor_analyzer_utils.get_first_idxs_from_values
        - factor_analyzer.factor_analyzer_utils.get_free_parameter_idxs
        - factor_analyzer.factor_analyzer_utils.get_symmetric_lower_idxs
        - factor_analyzer.factor_analyzer_utils.get_symmetric_upper_idxs
        - factor_analyzer.factor_analyzer_utils.impute_values
        - factor_analyzer.factor_analyzer_utils.inv_chol
        - factor_analyzer.factor_analyzer_utils.merge_variance_covariance
        - factor_analyzer.factor_analyzer_utils.partial_correlations
        - factor_analyzer.factor_analyzer_utils.smc
        - factor_analyzer.factor_analyzer_utils.unique_elements
    - title: Functions
      contents:
        - function
        - function.forr08a
        - function.forr08a.aerofoilcd
        - function.forr08a.branin
        - function.forr08a.onevar
        - function.mo
        - function.mo.activity_pred
        - function.mo.conversion_pred
        - function.mo.dtlz1
        - function.mo.dtlz2
        - function.mo.fonseca_fleming
        - function.mo.fun_myer16a
        - function.mo.kursawe
        - function.mo.mo_conv2_max
        - function.mo.mo_conv2_min
        - function.mo.schaffer_n1
        - function.mo.zdt1
        - function.mo.zdt2
        - function.mo.zdt3
        - function.mo.zdt4
        - function.mo.zdt6
        - function.remote
        - function.remote.objective_remote
        - function.so
        - function.so.ackley
        - function.so.lennard_jones
        - function.so.michalewicz
        - function.so.noisy_sphere
        - function.so.robot_arm_hard
        - function.so.robot_arm_obstacle
        - function.so.rosenbrock
        - function.so.sphere
        - function.so.wingwt
        - function.torch_objective
        - function.torch_objective.TorchObjective
    - title: Tricands
      contents:
        - tricands
        - tricands.tricands
        - tricands.tricands.tricands
        - tricands.tricands.tricands_fringe
        - tricands.tricands.tricands_interior