├── .git-blame-ignore-revs ├── .github └── workflows │ ├── install-and-test.yml │ ├── publish-to-pypi.yml │ ├── test-defaults.yml │ └── test-gp-accuracy-plots.yml ├── .gitignore ├── .mailmap ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE.txt ├── README.md ├── doc ├── CONTRIBUTING.md ├── Makefile ├── README.md ├── active_learning.rst ├── cluster.rst ├── code_structure.rst ├── components.rst ├── conf.py ├── config.rst ├── dev_run_system.rst ├── example-fit.ipynb ├── example-run.ipynb ├── extensions.rst ├── index.rst ├── mcmc.rst ├── pics │ ├── al_workflow.png │ ├── axis_options_color.png │ ├── color_dd.png │ ├── error_1D.png │ ├── ex_1D_fit.png │ ├── ex_2D_fit.png │ ├── ex_2Dc.png │ ├── ex_3D_fit.png │ ├── ex_axis_opt_2D.png │ ├── example_directory.png │ ├── filter_table.png │ ├── filter_table_n.png │ ├── graphtype1D.png │ ├── graphtype2D.png │ ├── layout.png │ ├── mcmc_results.png │ ├── profit_structure.png │ ├── profit_workflow.png │ ├── rangeslider.png │ ├── run_components.png │ ├── run_req.png │ ├── sur_structure.png │ └── tools.png ├── run_system.rst ├── start.rst ├── surrogates.rst ├── ui.rst └── variables.rst ├── draft ├── Active_BBQ.py ├── Active_MGP.py ├── CONCEPT.md ├── GP_Regression │ ├── GPy │ │ └── GP_GPy.py │ └── profit │ │ └── GP_profit.py ├── Pendulum │ ├── config.yaml │ ├── cosine.nb │ ├── cosine_gpy.py │ ├── func.py │ ├── init.py │ ├── init_func.py │ ├── kernels.py │ ├── param.py │ ├── run_GP.py │ └── sqexpsin.nb ├── Random_GP.py ├── algae │ ├── Parameters and Uncertainties.docx │ ├── autoencoder_algae.ipynb │ ├── autoencoder_algae_torch.ipynb │ ├── params.txt │ ├── params_1998.txt │ ├── redmod_conf.py │ ├── test_algae.py │ └── test_algae_post.py ├── ann.ipynb ├── autoencoder.ipynb ├── autoencoder.lyx ├── autoencoder_pytorch.py ├── bench_gpfunc │ ├── Makefile │ ├── bench_inline.f90 │ ├── gpfunc_bench.f90 │ └── test.f90 ├── benchmark.py ├── component.ipynb ├── config.ipynb ├── derivative_observations_gpy.py ├── design.rst ├── distributions.ipynb ├── draft_embedding.lyx ├── draft_kernels.py ├── draft_pca_surrogate.ipynb ├── embedding.lyx ├── embedding.py ├── embeddings.ipynb ├── fortran_vs_numpy │ ├── bench_fortran_numpy.py │ └── bench_kernels.jl ├── generate_kern_vec │ ├── Makefile │ ├── bench_inline.f90 │ ├── gpfunc_bench.f90 │ ├── indexed_sum.py │ ├── test_gen_kern.ipynb │ └── test_kern_vec.py ├── gpfast.f90 ├── gpflow_fit.ipynb ├── gpflow_fit.py ├── gpytorch.py ├── highdim_output.py ├── highdim_output_algae.py ├── highdim_output_pendulum.py ├── import.jl ├── input.csv ├── kernels.lyx ├── kernels_pyccel.py ├── mockup_scripts │ ├── mockup_sur.ipynb │ └── mockup_sur_gpytorch.ipynb ├── optim │ └── draft_optim.py ├── pca_surrogate │ ├── parameters.in │ ├── post.py │ ├── profit.yaml │ ├── simulation.py │ └── template │ │ └── parameters.in ├── pce.ipynb ├── pendulum │ ├── cosine │ │ ├── cosine_gpy.py │ │ ├── cosine_test.py │ │ ├── func_cosine.py │ │ ├── init_func_cosine.py │ │ ├── kernels.f90 │ │ └── kernels.py │ ├── cosine_prod │ │ ├── cosine_prod.py │ │ ├── func_cosine_prod.py │ │ ├── init_func_cosine_prod.py │ │ ├── kernels.f90 │ │ ├── kernels.py │ │ └── test_cosine_prod.py │ ├── expsin │ │ ├── expsin.py │ │ ├── func_expsin.py │ │ ├── init_func_expsin.py │ │ ├── kernels.f90 │ │ ├── kernels.py │ │ └── test_expsin.py │ ├── pendulum_old │ │ ├── func.py │ │ ├── init.py │ │ ├── init_func.py │ │ ├── kernels.py │ │ └── param.py │ ├── pendulum_updated │ │ ├── expsin_gpy.py │ │ ├── func.py │ │ ├── init.py │ │ ├── init_func.py │ │ ├── kernels.f90 │ │ ├── kernels.py │ │ ├── param.py │ │ ├── prod_extended.py │ │ └── run_GP.py │ ├── prod_extended │ │ ├── cosine_prod.py │ │ ├── expsin_gpy.py │ │ ├── func.py │ │ ├── prod_extended.py │ │ └── test_ProdExtended.py │ ├── sinus │ │ ├── func_sinus.py │ │ ├── init_func_sinus.py │ │ ├── kernels.f90 │ │ ├── kernels.py │ │ ├── sinus_gpy.py │ │ └── sinus_test.py │ └── sinus_prod │ │ ├── func_sinus_prod.py │ │ ├── init_func_sinus_prod.py │ │ ├── kernels.f90 │ │ ├── kernels.py │ │ ├── sinus_prod.py │ │ └── test_sinus_prod.py ├── profit_int.yaml ├── quadrature.ipynb ├── redmod_conf.py ├── suruq.wl ├── test2.jl ├── test_array_temporaries.f90 ├── test_autoencoder.py ├── test_autoencoder_sklearn.py ├── test_config.py ├── test_dash.jl ├── test_derivatives_gpy.py ├── test_embedding_gp.py ├── test_gp.jl ├── test_gpytorch.py ├── test_julia.jl ├── test_kernels.ipynb ├── test_linalg.py ├── test_multioutput.ipynb ├── test_multitask.py ├── test_pyjulia.py ├── test_sparsegrid.py ├── test_sur.py ├── test_sympy.py ├── test_uqp.py ├── test_uqp_api.py ├── todo_derivatives_gpy.py ├── unqu.in └── variational_autoencoder.py ├── examples ├── api │ ├── example_fit.py │ ├── run.ipynb │ └── surrogate.ipynb └── mockup │ ├── README.md │ ├── mockup.in │ ├── mockup.py │ └── study │ ├── profit.yaml │ ├── slurm.yaml │ └── template │ ├── mockup.in │ └── mockup.py ├── logo.png ├── profit ├── __init__.py ├── al │ ├── __init__.py │ ├── active_learning.py │ ├── aquisition_functions.py │ ├── mcmc_al.py │ └── simple_al.py ├── config.py ├── defaults.py ├── main.py ├── run │ ├── __init__.py │ ├── command.py │ ├── interface.py │ ├── local.py │ ├── runner.py │ ├── slurm.py │ ├── worker.py │ └── zeromq.py ├── sur │ ├── __init__.py │ ├── ann │ │ ├── __init__.py │ │ └── artificial_neural_network.py │ ├── encoders.py │ ├── gp │ │ ├── __init__.py │ │ ├── backend │ │ │ ├── Makefile │ │ │ ├── __init__.py │ │ │ ├── gp_functions.py │ │ │ ├── gpfunc.f90 │ │ │ ├── init_kernels.py │ │ │ ├── kernels.f90 │ │ │ ├── kernels_base.f90 │ │ │ └── python_kernels.py │ │ ├── custom_surrogate.py │ │ ├── gaussian_process.py │ │ ├── gpytorch_surrogate.py │ │ └── sklearn_surrogate.py │ ├── linreg │ │ ├── __init__.py │ │ ├── linear_regression.py │ │ └── sklearn_linreg.py │ └── sur.py ├── ui │ ├── __init__.py │ ├── app.py │ ├── assets │ │ └── tabs.css │ ├── condhist.py │ └── hist_utils.py └── util │ ├── __init__.py │ ├── base_class.py │ ├── component.py │ ├── file_handler.py │ ├── halton.py │ ├── util.py │ └── variable.py ├── pyproject.toml ├── setup.cfg ├── setup.py └── tests ├── conftest.py ├── generate_comparison_plots.py ├── integration_tests ├── active_learning │ ├── study_1D │ │ └── profit_1D.yaml │ ├── study_2D │ │ └── profit_2D.yaml │ ├── study_log │ │ └── profit_log.yaml │ ├── study_mcmc │ │ ├── profit_mcmc.yaml │ │ └── y_experimental.txt │ ├── template │ │ ├── mockup_1D.in │ │ ├── mockup_1D.py │ │ ├── mockup_2D.in │ │ ├── mockup_2D.py │ │ ├── mockup_log.py │ │ ├── mockup_mcmc.in │ │ └── mockup_mcmc.py │ └── test_active_learning.py ├── mockup │ ├── simulation_files │ │ ├── custom_components.py │ │ ├── mockup_1D.py │ │ ├── mockup_2D.py │ │ ├── mockup_custom_worker1.py │ │ ├── mockup_independent.py │ │ ├── mockup_multi_output.py │ │ └── mockup_worker.py │ ├── study_1D │ │ └── profit_1D.yaml │ ├── study_2D │ │ └── profit_2D.yaml │ ├── study_custom_post1 │ │ └── profit_custom_post1.yaml │ ├── study_custom_post2 │ │ └── profit_custom_post2.yaml │ ├── study_custom_worker1 │ │ └── profit_custom_worker1.yaml │ ├── study_custom_worker2 │ │ └── profit_custom_worker2.yaml │ ├── study_custom_worker4 │ │ └── profit_custom_worker4.yaml │ ├── study_gpy │ │ └── profit_gpy.yaml │ ├── study_independent │ │ └── profit_independent.yaml │ ├── study_karhunenloeve │ │ └── profit_karhunenloeve.yaml │ ├── study_linreg │ │ └── profit_linreg.yaml │ ├── study_multi_output │ │ └── profit_multi_output.yaml │ ├── template_1D │ │ ├── mockup_1D.in │ │ └── mockup_1D.py │ ├── template_2D │ │ ├── mockup_2D.in │ │ └── mockup_2D.py │ ├── template_independent │ │ ├── mockup_independent.json │ │ └── mockup_independent.py │ ├── template_multi_output │ │ ├── mockup_multi_output.in │ │ └── mockup_multi_output.py │ └── test_mockup.py └── test_default_workflow.py └── unit_tests ├── config ├── mockup.py ├── study │ ├── profit.yaml │ ├── profit_config.py │ ├── profit_default.yaml │ ├── profit_default_2.yaml │ ├── profit_hdf5.yaml │ 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