Pyomo.DoE Development Plan

[adowling2]

The purpose of this meta issue is to track our development plans for Pyomo.DoE.

Immediate (November/December 2022):

• Merge version 1 of Pyomo.DoE, Add Pyomo.DOE to contrib  #2294
• Merge Pyomo.DoE logo, Adding Pyomo.DOE logo files #2527

Pyomo.DoE Version 2 (start review in March 2023):

• Remove extra index (using blocks)
• Deprecate/remove sIpopt (pending discussion)
• Update to use the TicTocTimer, see Add Pyomo.DOE to contrib  #2294 (comment)
• Replace string options with Enum, see Add Pyomo.DOE to contrib  #2294 (comment)
• Documentation and tutorial enhancements
• Allow users to specify the names of the index sets (e.g., do not require time to be hard-coded as t, see Add Pyomo.DOE to contrib  #2294 (comment), Add Pyomo.DOE to contrib  #2294 (comment))

Pyomo.DoE Version 3+:

• Generalize measurement variance to consider correlations (not just diagonal)
• Add grey box objective function calculation
• Support decomposition with parapint
• Refactor interface for Pyomo.DoE and parmest to not define extra information (e.g., parameters, measurements) using strings, see Add Pyomo.DOE to contrib  #2294 (comment)

[adowling2]

Please assign this issue to @jialuw96 and @hglynch

[jialuw96]

• user define model time name Add Pyomo.DOE to contrib  #2294 (comment)
• Create simple names for variables; Add Pyomo.DOE to contrib  #2294 (comment)
• Get away from the two main indexed / unindexed branchs; Add Pyomo.DOE to contrib  #2294 (comment)

[jialuw96]

Pyomo.DoE Version 2 (Some other problems for discussion and enhancements, each one should be a small PR):

• Which is a better way to grab pyomo model variable values?
  • Get rid of eval;
  • Use getattr (Need string name)
  • Use ComponentUID as in https://github.com/IDAES/idaes-pse/blob/274e58bef55f2f969f0df97cbb1fb7d99342388e/idaes/apps/uncertainty_propagation/sens.py#L296 (Need string name)
  • find_component (Need handle to Var)
• How to flatten variables with multiple indexes, for e.g. m.C['CA', 'A1', 16, 2]?
  • I saw the use of UnindexedComponent_Set and add_component. Is this a good way?
• Is there something like a textbook for good development of a Pyomo package that I can refer to? (Or maybe a well developed contributed package that I can use as reference) I have the Pyomo cookbook but it is for users I think.

[blnicho]

• Improve test coverage (currently at ~66% but would prefer 85-100% coverage)

[jialuw96]

Note with @blnicho from IDAES meeting

• Create block objects as way 3 in the figure
• In user create_model(): return not only m, but also Var data to parameters, design variables, and measurements as in
  https://github.com/Parapint/parapint/blob/fad622d912c03d7c23b70241d5d18b96942a4d4b/parapint/examples/burgers.py#L173
• In this way we can handle multiple indexed variables in a safe way

[adowling2]

Update documentation:

• @adowling2 careful read through
• Incorporate new Pyomo.DoE logo

[adowling2]

@blnicho @jsiirola Is Monday, Feb. 6 a reasonable cut-off date for minor PRs, e.g., updates to Pyomo.DoE documentation, before the next Pyomo release?

My thought is this gives the dev call on Feb. 7 to wrangle outstanding reviews and merge.

[blnicho]

@adowling2 yes Feb. 6 is fine for a cut-off date.

[adowling2]

@blnicho @jsiirola FYI, @jialuw96 and I are working on using blocks in Pyomo.DoE in jialuw96#15 which is a PR from one branch in @jialuw96's fork into a second branch on her fork. Once this is ready for review from the Pyomo team, we'll open PR into pyomo/main.

[jialuw96]

Pyomo.DoE version 3+:

• add the integrator on an already discretized model.
• reduce_collocation_points Pyomo.DoE version 2  #2794 (comment)
• a better name for calculate_FIM, which I temporarily name as result_analysis now
• check time index Pyomo.DoE version 2  #2794 (comment)
• figure_drawing is not intuitive. Pyomo.DoE version 2  #2794 (comment)
• Example tests should have assertions Pyomo.DoE version 2  #2794 (comment)
• use repr() instead of str() Pyomo.DoE version 2  #2794 (comment)

[adowling2]

Pyomo.DoE version 3+:

• Add tests for scenario.py Pyomo.DoE version 2  #2794 (comment)
• Add README file or top comment for each example Pyomo.DoE version 2  #2794 (comment)
• Choose better function names to eliminate confusion between compare and compute Pyomo.DoE version 2  #2794 (comment)

[djlaky]

@adowling2 @blnicho Any objections to closing this in favor of the new issue I made today (#3345)?