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Pyomo doe refactor #3317
Pyomo doe refactor #3317
Commits on Jun 20, 2024
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Adding new DoE object and skeleton functions
First commit for DoE refactor. Skeleton functions added for development.
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Refactoring scenario generation
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.
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Further progress on generating FD scenarios
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.
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Scenario generator appears to work
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.
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Commits on Jun 25, 2024
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Added a check_model_labels function
Add functionality to test if the labeled model has the expected labels for the DoE model to be created.
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Added FiniteDifferenceStep initialization to the constructor. Removed and cleaned some defunct commenting/documentation.
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Significant development in create_doe_model. Modernized to new methodology. Tests to follow.
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Commits on Jun 26, 2024
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Added checks for input FIM, jacobian, labels
Added size checks to make sure everything is consistent before being automatically generated by the create_model function.
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Update Jacobian representation
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).
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Added functionality for incoming block-models
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).
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Commits on Jun 27, 2024
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Commits on Jul 1, 2024
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Create objective functionadded
Also updated the test build, result.json, and experiment class example to be well-posed DoE models.
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Moved most attributes to constructor
Also added documentation for the inputs.
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Updated run_doe to perform experimental design
Seems to work based on comparison to old code. Will look into this more later.
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Commits on Jul 2, 2024
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Adding kaug functionality to new interface
Also updated the test files and results file to match and generate the same optimal point.
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Commits on Jul 3, 2024
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Simplified kaug method and added obj cons block
Objective cons block are deactivated for the square solve as they can sometimes cause convergence issues.
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Made compute_FIM more flexible
Potentially will use this for the grid search functionality.
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Added full factorial design space exploration
This function is similar to the "grid search" function from before. Plotting capabilities still need to be added.
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Commits on Jul 4, 2024
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Commits on Jul 5, 2024
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Added small check for FIM rescaling function
Will probably move the FIM rescaling function to a `utils` or similar file name since the rescaling is agnostic to the DoE object.
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Added sequential compute_FIM method.
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.
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Made each experimental design to have its own dict key. This way the dictionary can be directly translated to a pandas dataframe.
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Also added the retrieval functions for populating the results object.
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Commits on Jul 6, 2024
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Refactored factorial design plotting function
Also added a utils module to hold agnostic tasks (e.g. rescaling the FIM)
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Commits on Jul 10, 2024
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Commits on Jul 11, 2024
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Updated variable names to be more readable
For example, changed ``mod`` to ``model`` and ``Obj`` to ``objective`` and ``L_ele`` to ``L``, etc.
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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.
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Removing deprecated tests and deprecated DoE files (result, measurements, scenario).
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Covering all different forms of DoE model (i.e., trace, det; central, forward, backward; full factorial FIM; compute FIM).
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Commits on Jul 12, 2024
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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).
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Delete pyomo/contrib/doe/tests/test_reactor_example.py
Removing old test files.
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Delete pyomo/contrib/doe/tests/test_example.py
Removing old test files.
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Delete pyomo/contrib/doe/tests/test_fim_doe.py
Removing old test files.
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Caught a bug while adding tests for checking model in the generate scenarios function.
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Updated model to have good imports
And updated the file call to be robust.
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Delete pyomo/contrib/doe/redesign directory
Removing temporary space for testing as build was ongoing.
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Delete pyomo/contrib/doe/examples/PyomoDoE-plots.ipynb
Removed old file
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Delete pyomo/contrib/doe/examples/debugging_compute_FIM.ipynb
Removing old file
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Delete pyomo/contrib/doe/examples/reactor_optimize_doe_DJL.py
Removing old file
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Merge branch 'pyomo-doe-refactor' of https://github.com/djlaky/pyomo …
…into pyomo-doe-refactor
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Commits on Jul 15, 2024
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Ran Black with correct command with flags
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Removing commented lines from example files
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Added ipopt check for build, which initializes the model using ipopt
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Commits on Jul 18, 2024
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Added test for rescale FIM function
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Fixed bug and added test for compute FIM seq with back/forw
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Adding test for model that is poorly posed
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Added tests for get values functions without blocks
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Adding tests for multi experiment not implemented and scenario buildi…
…ng withoutmodel
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Adding tests for bad FD values
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Added tests for bad objective builds
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Changed one run to use objective type
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Added not implemented error for unknown parameter value updating
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Delete pyomo/contrib/doe/examples directory
Old files removed to make room for new examples directory
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Add test for bad option in compute FIM method
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Removed bad files, have to rewrite OnlineDocs soon
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Fixed determinant obj without cholesky, added tests.
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Added examples and figure saving capabilities
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Fixed documentation, cleaned example files
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Fixing literalinclude statements
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Fixing literalinclude statements again
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Commented out new Param to Var code
Will discuss at meeting later today (8/2/2024).
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Daniel Laky committed
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Simplify component identification in doe
Per advice, using the ``context`` keyword to find parameters without using their string trees as before.
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``args`` are additional arguments that go to the get_labeled_model function. So the name was changed to ``get_labeled_model_args```
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Updating example with feedback
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Made imports explicit in other tests
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Added shortcut function for test arguments
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Cleaned up reactor experiment example
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Added else to rescale function, commented params function
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Edited language in documentation
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Fixed fragile line numbers for reactor exp in documentation
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Clarified text in documentation
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Remove more line number fragility in documentation
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Combined example files and updated documentation with change
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Add context manager, remove np.isclose in tests
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Reused reactor experiment in tests, fixed bug in experiment
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Edited small phrase in documentation
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Remove tests result.json dependency
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Delete pyomo/contrib/doe/tests/experiment_class_example.py
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Update pyomo/contrib/doe/tests/test_doe_build.py
Co-authored-by: Bethany Nicholson <blnicho@users.noreply.github.com>
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Revert "Update pyomo/contrib/doe/tests/test_doe_build.py"
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Revert "Delete pyomo/contrib/doe/tests/experiment_class_example.py"
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Revert "Delete pyomo/contrib/doe/tests/result.json"
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Revert "Delete pyomo/contrib/doe/experiment.py"
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Removed string-based location of components
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Updated shoddy tests to check real values
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Added depracation error message
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Delete pyomo/contrib/doe/tests/test_example.py
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Delete pyomo/contrib/doe/tests/experiment_class_example.py
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Delete pyomo/contrib/doe/tests/result.json
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Delete pyomo/contrib/doe/experiment.py
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Updated language in comments and URL
Have to change this URL at some point in time.
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Removed safe naming for later discussion
Also removed a potential bug for adding this in the future.
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Fixed check model labels function
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Remove other user-defined model unique naming
Added to TODO list in Pyomo#3345
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