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…on-selected samples; adjust legend handling for better clarity.
…in the restricted namespace for improved functionality.
…ce plot_qoi_param with swarmplot option
…arnings for serialization/deserialization
…warnings for unavailable libraries
…ate type hints for tensor parameters
…alias; improve import structure for type checking
…ument for customizable parameter sorting
- plot vertical line on ref parameters value. - plot Pareto front - run and plot the Pareto points
…should be loaded on the command line.
this patch enables to directly on the command line specify the xml, ini, or db file that should be loaded.
…lass attributes documentation
…izable for clarity and consistency
…sistency, remove mode options from summary_function, and define internal functions
…ncy and update usage in load_output; update disable_wal_mode to _disable_wal_mode in imports and usage
…y in imports and usage
…_mcds parameter type
mcds_list_to_qoi_df_long implementation for calculate_qoi_from_sa_db
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This pull request updates the documentation and example notebooks for UQ-PhysiCell, focusing on improving clarity, navigation, and API reference completeness.
Many thanks to @elmbeech for his PRs, contributions, and valuable suggestions.
GUI Enhancements
.xml,.ini, or.dbfiles (@elmbeech).Model Analysis context
Bayesian Optimization (BO) context
torch,botorch, andgpytorchDocumentation improvements:
uq_physicell.database.ma_db,uq_physicell.database.bo_db) and utility modules (uq_physicell.model_analysis.utils,uq_physicell.utils.sumstats,uq_physicell.utils.model_wrapper) indoc/api_reference.mdto provide more comprehensive API documentation. [1] [2]doc/conf.pyto include both class and__init__docstrings for better documentation detail.doc/calibration.md) by adding Sphinx{ref}links and section anchors for Bayesian Optimization and ABC calibration methods. [1] [2]doc/examples.mdfor easier discovery of available tutorials.Example notebooks: