Updates Required for Modernization of RPB pull request

[djlaky]

Summary

The purpose of this issue is to follow up on the merging of large PR #3, providing details on what needs to be updated, removed or added to adhere to newer versions of Pyomo. Generally, the data files for the results will stay as of now and may or may not be removed with later version (or updated with the newer versions of Pyomo.DoE and measurement optimization.)

Changes

• README should be updated to a new installation that works for the code. Currently, the installation instructions (with a Windows machine) cannot reproduce the results as shown in the checkpointed .ipynb files

.ipynb files, general comments:

• Update text (e.g., titles, sections, descriptions) within all .ipynb files
• Remove some unnecessary code that are not vital to performance from .ipynb files (e.g., testing pyomo variable functionalities)
• Be explicit as to what is imported and what these functions are designed and used for
• Improve descriptions and variable naming
• Modernize code to work with the new and improved versions of parmest and Pyomo.DoE
• Move some functionalities written in .ipynb files to .py files (e.g., Counterflow_Jacobian_process, Counterflow_MO_data_process)
• Ensure codes are working (create test functions)

.py files comments:

• greybox_generalize.py will be rewritten to be compatible with newer versions of Pyomo.DoE while remaining compatible with measurement_optimization (see reference links in summary)
• measure_optimize.py will be revisited if required with updates to the greybox format
• model files (RPB_model_cocurrent.py, RPB_model_countercurrent.py, RPB_model_countercurrent_kaug.py) should be fine from other sources. Will review in detail once other general changes are realized (see previous list)
• run_countercurrent_model.py does not converge with current installation and cold run on Windows

[ksbeattie]

@djlaky we just merged #3 but would like to know what we should do with #2. Should it be closed now?