Add core symbolic gradient support to Pyomo.DoE - #3898

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snarasi2 wants to merge 442 commits into

snarasi2:codex/merge-pyomo-doe-symbolic

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Commits on Feb 15, 2026

Fixed issues with merging changes
sscini
committed
7a0f623
Merge branch 'Pyomo:main' into parmest_obj_regularization
sscini
authored
31a61e9

Commits on Feb 17, 2026

L2 regularization working
sscini
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d44f13d
Merge branch 'Pyomo:main' into parmest_obj_regularization
sscini
authored
906f280
Made the theta_ref a series.
sscini
committed
fec94fd
Updated doc strings.
sscini
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6ecb2a3
Update parmest.py
sscini
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865e51e
added helper comments.
sscini
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5ffa566

Commits on Feb 19, 2026

Updated implementation to add vectorized L2 calc, and reviewer questions
sscini
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53ca679
Adjusted logging, ran black
sscini
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ab583bb
Changed value to avoid zero for L2 term
sscini
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ac96277
Commented out or removed print statements
sscini
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08bce8f
Merge branch 'Pyomo:main' into parmest_obj_regularization
sscini
authored
26bc6b6
Merge branch 'Pyomo:main' into Q_opt-redesign
sscini
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854366b
Added in files from main now, removed example
sscini
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c55143d
Merge branch 'Pyomo:main' into multistart-in-parmest
sscini
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8f3a902
Added old files in temporarily for reference
sscini
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3c87d7a
Ran black
sscini
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4e09d33
Merge branch 'Q_opt-redesign' into multistart-in-parmest
sscini
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4f94329
Made quick working example, and small modification for multistart
sscini
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12d0af1

Commits on Feb 23, 2026

Merge branch 'Pyomo:main' into Q_opt-redesign
sscini
authored
72204d9
Merge branch 'main' into parmest_obj_regularization
sscini
authored
7aa3b17
Add `lhs` iniatialization method and test
smondal13
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0833295
Add tests for optimize_experiments(). All tests passed
smondal13
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ca0a4dd
Remove cherry-picked example artifacts from DOE test changes
smondal13
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02aa81a
Add more tests for warnings, combinations
smondal13
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d1493a5
Refactor result dict in `optimize_experiments()`
smondal13
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802438b
Add test of opt values with hardcoded values
smondal13
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5ae8280

Commits on Feb 24, 2026

Merge branch 'main' into multistart-in-parmest
sscini
authored
0a1167d

Commits on Feb 27, 2026

Commits on Mar 2, 2026

Commits on Mar 3, 2026

Commits on Mar 6, 2026

Merge branch 'Pyomo:main' into Q_opt-redesign
sscini
authored
ed2cf54
Merge branch 'Pyomo:main' into multistart-in-parmest
sscini
authored
2b41ba5
Merge branch 'Pyomo:main' into parmest_obj_regularization
sscini
authored
ec100ae
Updated interface, added block scenario tests.
sscini
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cc0513a
Merge branch 'Q_opt-redesign' into multistart-in-parmest
sscini
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2e5ac42
Added validation for prior_FIM and fixed inconsistencies
sscini
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e20e457
Adjusted implementation, added new tests in separate file
sscini
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813a981
Initial implementation
sscini
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96a4792
Merge branch 'main' into add-multiexperiment
smondal13
authored
592d54c
Merge branch 'Pyomo:main' into parmest_obj_regularization
sscini
authored
850819c
Merge branch 'Pyomo:main' into multistart-in-parmest
sscini
authored
44a0b83
Merge branch 'Pyomo:main' into profile-likelihood
sscini
authored
8b9db82
Merge branch 'Pyomo:main' into Q_opt-redesign
sscini
authored
9c0d0a3

Commits on Mar 8, 2026

Commits on Mar 9, 2026

Commits on Mar 10, 2026

Refactor `_enum_label` method placement and add review documentation for `_DoEResultsJSONEncoder` and `optimize_experiments()` API
smondal13
committed
8ee7b2b

Commits on Mar 13, 2026

fix(doe): clarify lhs parallel fallback logs
smondal13
committed
3c034b7

Commits on Mar 17, 2026

Remove the review file
smondal13
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c4103d9
Add comments to explain the test
smondal13
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1518abe
Merge branch 'Pyomo:main' into profile-likelihood
sscini
authored
6444c54
Merge branch 'main' into Q_opt-redesign
sscini
authored
4df5b48
Merge branch 'main' into parmest_obj_regularization
sscini
authored
a0decd0
Refactor DesignOfExperiments to accept a single experiment or a list
smondal13
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e4fbf66
- update init_method type hint in DesignOfExperiments constructor
smondal13
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ee6e63f
fix(doc): clarify design variables and FIM in multi-experiment documentation
smondal13
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ebc7aa3
Rename documentation
smondal13
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8f4732d
Merge branch 'main' into add-multiexperiment
smondal13
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735762c
Rename
smondal13
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584091c
Merge branch 'add-multiexperiment' of github.com:smondal13/pyomo into add-multiexperiment
smondal13
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3a52f2d

Commits on Mar 18, 2026

fix(doc): Test failure
smondal13
committed
3678ecb

Commits on Mar 24, 2026

Commits on Mar 25, 2026

Update test_parmest.py
sscini
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9fe600f
Merge branch 'main' into Q_opt-redesign
sscini
authored
48ba6a6

Commits on Mar 27, 2026

Merge branch 'Pyomo:main' into Q_opt-redesign
sscini
authored
ba4091c
Removed covariance functionality from theta_est, in progress
sscini
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eba10b3
Update simple_reaction_parmest_example.py
sscini
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c997944
Update simple_reaction_parmest_example.py
sscini
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d2b5d74
Update parameter_estimation_example.py
sscini
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ae9808f
Adjusted tests, ran black
sscini
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9fa6528
Update test_parmest.py
sscini
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cb1ecea
Delete scenarios.csv
sscini
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261a78f
feat(doe): add multiexp greybox support
smondal13
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990b812
Merge branch 'Q_opt-redesign' into multistart-in-parmest
sscini
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664d687
Merge branch 'multistart-in-parmest' into profile-likelihood
sscini
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ea876b1
Merge branch 'Pyomo:main' into parmest_obj_regularization
sscini
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9786fc5
feat(tests): add tests for multi-experiment grey box optimization
smondal13
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0266ca3
Merge branch 'Pyomo:main' into add-multiexperiment
smondal13
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c1ca9c6
Merge branch 'Pyomo:main' into multiexp-greybox
smondal13
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1e1c048
feat(doe): enhance multi-experiment support and add synchronization for parameter scenarios
smondal13
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bc08c2a
enforce consistency in unknown parameter values and order for multi-experiment optimization
smondal13
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35ee2f9
update error message for objective_option and improve test assertions
smondal13
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3e66a71

Commits on Mar 29, 2026

Added tests to correct files, ran black.
sscini
committed
6d46119

Commits on Mar 30, 2026

Commits on Mar 31, 2026

Merge branch 'profile-likelihood' into regularization-profilelikelihood-combo
sscini
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74119bd

Commits on Apr 1, 2026

Add symbolic gradient support to Pyomo.DoE
Shilpa Narasimhan
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50cbc4a
Add symbolic DoE regression tests
Shilpa Narasimhan
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85116d5
Allow writeable in typos config
Shilpa Narasimhan
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12e5e95
Port polynomial and reactor symbolic tests
Shilpa Narasimhan
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b35253a
Document symbolic gradient methods in DoE
Shilpa Narasimhan
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431b28e
Refactor ExperimentGradients setup
Shilpa Narasimhan
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f55a294
Add polynomial DoE regression coverage
Shilpa Narasimhan
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ca66ac6

Commits on Apr 2, 2026

Add broader gradient consistency tests
Shilpa Narasimhan
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8d8b8bd
Add factorial results dataframe tests
Shilpa Narasimhan
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5c373fb
Add reactor regression and CI fixes
Shilpa Narasimhan
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103a121
Add plotting guard coverage tests
Shilpa Narasimhan
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76f53c4
Update model in regularization core, reordered, ran black
sscini
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1c1c253
Updated model structure, reordered, ran black
sscini
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14bc329
Merge branch 'main' into Q_opt-redesign
blnicho
authored
3dca7d7
Refactor the result dict
smondal13
committed
0f653a8
Merge branch 'main' into add-multiexperiment
smondal13
authored
c85e4fb
Clarify cyipopt HSL skip reason
Shilpa Narasimhan
committed
f28d86d

Commits on Apr 3, 2026

Updated covariance.rst file
slilonfe5
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aeafe4d

Commits on Apr 7, 2026

Merge branch 'Pyomo:main' into parmest_obj_regularization
sscini
authored
f84786c
Merge branch 'Pyomo:main' into Q_opt-redesign
sscini
authored
959d58e
Merge branch 'Pyomo:main' into multistart-in-parmest
sscini
authored
5530e9d
Merge branch 'Pyomo:main' into regularization-profilelikelihood-combo
sscini
authored
aa6d670
Added new files
slilonfe5
committed
74369fd
Merge branch 'main' into parmest-doe-doc-reorg
slilonfe5
authored
c3e5466
Added and updated documentation files
slilonfe5
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1eb8c7f
Added abstraction.rst and updated doe.rst
slilonfe5
committed
dbe9f2c

Commits on Apr 8, 2026

Merge branch 'Pyomo:main' into Q_opt-redesign
sscini
authored
b21c34d

Commits on Apr 9, 2026

Reuse polynomial example in DoE tests
Shilpa Narasimhan
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80552f2
Drop unused data arg from polynomial example
Shilpa Narasimhan
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d708d55
Clarify symbolic sensitivity math comments
Shilpa Narasimhan
committed
f53fe17
Remove no-op polynomial finalization
Shilpa Narasimhan
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11d475e
Simplify polynomial test imports
Shilpa Narasimhan
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e704f68
Merge branch 'main' into Q_opt-redesign
sscini
authored
1b6c63a

Commits on Apr 10, 2026

Remove redundant polynomial FIM smoke test
Shilpa Narasimhan
committed
0d0a14f
Strengthen polynomial DoE regression test
Shilpa Narasimhan
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401c03a
Use symbolic path for dataframe tests
Shilpa Narasimhan
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0dd08eb
Align symbolic DoE test coverage
Shilpa Narasimhan
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65571da
Guard DoE utils tests on ipopt
Shilpa Narasimhan
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9eb4959
Strengthen symbolic Jacobian tests
Shilpa Narasimhan
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702dc89
Remove out-of-scope FIM metric test
Shilpa Narasimhan
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d652cea
Tighten Jacobian regression assertions
Shilpa Narasimhan
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b5ea7f1
Drop workflow changes from symbolic PR
Shilpa Narasimhan
committed
9a78180

Commits on Apr 11, 2026

Checkpoint reactor test conversions to RB/polynomial
Shilpa Narasimhan
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c593f0b
Checkpoint remaining reactor test cleanup
Shilpa Narasimhan
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36d5694
Replace remaining reactor DoE tests
Shilpa Narasimhan
committed
dae72f4
Clarify GreyBox MA57 skip reason
Shilpa Narasimhan
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0545dcf
Add symbolic DoE PR notes
Shilpa Narasimhan
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270bf8c
Refactor Jacobian rule setup
Shilpa Narasimhan
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33d0b98
Tighten FD scenario validation
Shilpa Narasimhan
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4209df5
Format DoE module with black
Shilpa Narasimhan
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653e3be

Commits on Apr 13, 2026

Merge branch 'main' into Q_opt-redesign
sscini
authored
f768ea3

Commits on Apr 14, 2026

Merge branch 'main' into add-multiexperiment
smondal13
authored
5c856e2
Merge branch 'main' into add-multiexperiment
smondal13
authored
8a95a60

Commits on Apr 15, 2026

Merge branch 'main' into Q_opt-redesign
sscini
authored
867e642

Commits on Apr 17, 2026

Merge branch 'main' into add-multiexperiment
smondal13
authored
c83ea69

Commits on Apr 21, 2026

Merge branch 'main' into Q_opt-redesign
sscini
authored
6d7eb7a
Merge branch 'main' into parmest_obj_regularization
sscini
authored
a123706

Commits on Apr 22, 2026

Merge branch 'main' into add-multiexperiment
smondal13
authored
0089ff1
Merge branch 'main' into Q_opt-redesign
sscini
authored
a39d367

Commits on Apr 24, 2026

Merge branch 'Pyomo:main' into regularization-profilelikelihood-combo
sscini
authored
98392ba
Merge branch 'Pyomo:main' into Q_opt-redesign
sscini
authored
deb3c5a
Merge branch 'main' into add-multiexperiment
smondal13
authored
211f16c
Merge branch 'Q_opt-redesign' into regularization-profilelikelihood-combo
sscini
committed
24e086a
Merge branch 'multistart-in-parmest' into regularization-profilelikelihood-combo
sscini
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d45e04c
Merge pull request #2 from smondal13/add-multiexperiment
adowling2
authored
50de094
Merge branch 'parmest_obj_regularization' into regularization-profilelikelihood-combo
sscini
committed
b419cc0
Merge pull request #3 from slilonfe5/parmest-doe-doc-reorg
adowling2
authored
61c4c26
Merge pull request #1 from sscini/regularization-profilelikelihood-combo
adowling2
authored
cae4afb
Resolve DoE merge conflicts and restore fd_scenario_blocks architecture
Shilpa Narasimhan
committed
e9e4f4e
Apply Black formatting to DoE files
Shilpa Narasimhan
committed
0977386