First commit for DoE refactor. Skeleton functions added for development.

Mid-way through updating the scenario generation for the finite difference of the sensitivity matrix. Added an example file from the refactor hack-a-thon in November 2023.

Worked around Block construction. Pass-by-reference issues with with Experiment object requires some sort of cloning of the model for each block.

Still working through global connecting constraints for design variables.

Finished some more edits. Will check back in tomorrow to clean and make sure the scenario generator is working properly. Need to work on whether the full model should be present or not for the central case. Could use the "global model" to be "case 0" and reassign the  values to be one of the cases.

Add functionality to test if the labeled model has the expected labels for the DoE model to be created.

Added FiniteDifferenceStep initialization to the constructor. Removed and cleaned some defunct commenting/documentation.

Significant development in create_doe_model. Modernized to new methodology. Tests to follow.

Added size checks to make sure everything is consistent before being automatically generated by the create_model function.

Made the Jacobian representation consistent with the paper as well as sources on what the sensitivity matrix should be (i.e., (n_experiment_outputs x n_parameters) such that Q^T @ Q is (n_parameters x n_parameters).

Changed how the tree is traversed so the parameter location starts after the "base_model" or "scenario_blocks[0]" keyword. This way, an arbitrary block structure should be support. This will help for making multiple instances of the DoE model (i.e., multiple simultaneous estimations or stochastic-based experiment implementation).

Also updated the test build, result.json, and experiment class example to be well-posed DoE models.

Also added documentation for the inputs.

Seems to work based on comparison to old code. Will look into this more later.

Also updated the test files and results file to match and generate the same optimal point.

Matches the old interface

Objective cons block are deactivated for the square solve as they can sometimes cause convergence issues.

Potentially will use this for the grid search functionality.

This function is similar to the "grid search" function from before. Plotting capabilities still need to be added.

Will probably move the FIM rescaling function to a `utils` or similar file name since the rescaling is agnostic to the DoE object.

The FIM output of both methods is quite different but the determinant value is similar. We are looking into this to see if the method is computed incorrectly.

Made each experimental design to have its own dict key. This way the dictionary can be directly translated to a pandas dataframe.

Also added the retrieval functions for populating the results object.

Also added a utils module to hold agnostic tasks (e.g. rescaling the FIM)

For example, changed ``mod`` to ``model`` and ``Obj`` to ``objective`` and ``L_ele`` to ``L``, etc.

Wanted to be able to re-run the analysis with all the required inputs for the model barring the optional input ``args`` from the user.

As an aside, the L_init, jac_init, and fim_init values may be moot at this point.

Removing deprecated tests and deprecated DoE files (result, measurements, scenario).

Covering all different forms of DoE model (i.e., trace, det; central, forward, backward; full factorial FIM; compute FIM).

Added functions to make sure the finite differencing scheme is working properly and that design variable fixing is working properly for all currently available finite difference types (i.e., central, backward, forward).

Removing old test files.

Removing old test files.

Removing old test files.

Caught a bug while adding tests for checking model in the generate scenarios function.

And updated the file call to be robust.

Removing temporary space for testing as build was ongoing.

Removed old file

Removing old file

Removing old file

…into pyomo-doe-refactor

…ng withoutmodel

Old files removed to make room for new examples directory