Track Pyomo follow-up issue dependencies and work plan

[bernalde]

Purpose

Track the remaining Pyomo-stack follow-up work in one place and make the dependency structure explicit. The main question is which items can be worked independently and which should be sequenced to avoid branch and file conflicts.

Current Issue Set

• Archive or update the Pyomo stack implementation plan after merge #13 - Archive or update the Pyomo stack implementation plan after merge
• Add smoke coverage for Pyomo user examples #14 - Add smoke coverage for Pyomo user examples
• Add post-solve ramp-rate validation to benchmark records #15 - Add post-solve ramp-rate validation to benchmark records
• Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16 - Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks
• Rebuild a single-case Pyomo benchmark debug runner #17 - Rebuild a single-case Pyomo benchmark debug runner
• Port benchmark artifact cleanup from superseded PR #3 #18 - Port benchmark artifact cleanup from superseded PR Pyomo: slim PR — remove benchmark artifacts #3

Dependency Summary

• Archive or update the Pyomo stack implementation plan after merge #13 is already effectively handled on pr/docs-examples: docs/PR_IMPLEMENTATION_PLAN.md has been moved under docs/archive/ with historical status text. It can be closed once the stacked docs PR lands, or linked to the commit that made the move.
• Add smoke coverage for Pyomo user examples #14 is already in progress via PR Add Pyomo example smoke coverage #19 (fix/issue-14-pyomo-example-smoke into pr/docs-examples). It is functionally independent, but stack-order dependent on PR PR 7/7: Pyomo documentation, examples, and CHANGELOG #12.
• Port benchmark artifact cleanup from superseded PR #3 #18 is independent of the validation/timeout/debug-runner work and should be done early on pr/benchmarks to reduce generated artifact noise.
• Add post-solve ramp-rate validation to benchmark records #15 and Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16 overlap strongly in benchmarks/validate.py, benchmarks/grid_cli.py, benchmarks/adapters.py, benchmark record metadata, and tests. These should be implemented as one coordinated pass or sequenced carefully.
• Rebuild a single-case Pyomo benchmark debug runner #17 should follow Add post-solve ramp-rate validation to benchmark records #15/Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16 so the single-case runner uses the final validation and timeout interfaces rather than introducing temporary flags or output formats.

Recommended Work Plan

1. Close or annotate Archive or update the Pyomo stack implementation plan after merge #13 after PR PR 7/7: Pyomo documentation, examples, and CHANGELOG #12 lands.
2. Let PR Add Pyomo example smoke coverage #19 close Add smoke coverage for Pyomo user examples #14 after the docs/examples stack is ready.
3. Implement Port benchmark artifact cleanup from superseded PR #3 #18 on top of pr/benchmarks.
4. Implement Add post-solve ramp-rate validation to benchmark records #15 and Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16 as a coordinated benchmark-infrastructure pass.
5. Implement Rebuild a single-case Pyomo benchmark debug runner #17 after Add post-solve ramp-rate validation to benchmark records #15/Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16 are settled.

Parallelization Guidance

Safe to work simultaneously:

• Archive or update the Pyomo stack implementation plan after merge #13 bookkeeping and Add smoke coverage for Pyomo user examples #14 PR review/rebase.
• Port benchmark artifact cleanup from superseded PR #3 #18 artifact cleanup while someone else works on Add post-solve ramp-rate validation to benchmark records #15/Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16, as long as ownership of benchmarks/results/.gitignore and benchmarks/results/README.md is clear.

Avoid simultaneous uncoordinated work:

• Add post-solve ramp-rate validation to benchmark records #15 and Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16, because they share CLI arguments, adapter signatures, benchmark record fields, and tests.
• Rebuild a single-case Pyomo benchmark debug runner #17 with Add post-solve ramp-rate validation to benchmark records #15/Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16, unless Rebuild a single-case Pyomo benchmark debug runner #17 is limited to parser scaffolding and waits to wire validation/timeout behavior until those APIs settle.

Proposed Branches

• fix/issue-18-benchmark-artifacts from pr/benchmarks
• feature/benchmark-validation-timeouts from the updated pr/benchmarks or Port benchmark artifact cleanup from superseded PR #3 #18 branch
• feature/single-case-benchmark-runner from the branch containing Add post-solve ramp-rate validation to benchmark records #15/Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16

Acceptance Criteria For This Tracker

• Each issue has a clear owner or status.
• Branch bases are explicit before implementation starts.
• Add post-solve ramp-rate validation to benchmark records #15/Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16 API decisions are made before Rebuild a single-case Pyomo benchmark debug runner #17 wires command-line behavior.
• This tracker is closed when Archive or update the Pyomo stack implementation plan after merge #13-Port benchmark artifact cleanup from superseded PR #3 #18 are closed or intentionally superseded.

[bernalde]

Status update after recent follow-up merges:

• Archive or update the Pyomo stack implementation plan after merge #13 is handled on pr/docs-examples; keep open until PR PR 7/7: Pyomo documentation, examples, and CHANGELOG #12 lands, then close or link to the archived-plan commit.
• Add smoke coverage for Pyomo user examples #14 is handled via PR Add Pyomo example smoke coverage #19 and included in pr/docs-examples; keep open until PR PR 7/7: Pyomo documentation, examples, and CHANGELOG #12 lands.
• Add post-solve ramp-rate validation to benchmark records #15 and Add IPOPT CPU-time and wall-time guard support for Pyomo benchmarks #16 were implemented by PR Add benchmark validation and timeout guards #22 and are present on pr/benchmarks; keep open until the benchmark stack lands.
• Rebuild a single-case Pyomo benchmark debug runner #17 has been merged/closed.
• Port benchmark artifact cleanup from superseded PR #3 #18 has been merged/closed.
• Audit legacy edge-case warning semantics #23 was handled separately by PR Audit edge-case warning semantics #25 and is closed; it is outside the original Archive or update the Pyomo stack implementation plan after merge #13-Port benchmark artifact cleanup from superseded PR #3 #18 tracker set.

No new coding work is currently queued by this tracker while PRs #7-#12 wait for reviewer feedback. The remaining action is stack integration and issue closure once the reviewed stack lands.

[bernalde]

Paper OCP validation issue set

Added a focused issue set for the direct-transcription lyophilization OCP benchmark work:

• Improve Paper Problem 1 n_z=20 direct-transcription convergence #26 - Improve Paper Problem 1 n_z=20 direct-transcription convergence
• Add reproducible upstream reference generation for Paper Problem 1 #27 - Add reproducible upstream reference generation for Paper Problem 1
• Prepare first Paper Problem 1 Pyomo OCP validation PR #28 - Prepare first Paper Problem 1 Pyomo OCP validation PR
• Add Paper Problem 2 flux-constrained OCP benchmark #29 - Add Paper Problem 2 flux-constrained OCP benchmark
• Compare paper-reference OCP results against LyoPRONTO baselines #30 - Compare paper-reference OCP results against LyoPRONTO baselines
• Add experimental LyoPRONTO policy OCP adapter #31 - Add experimental LyoPRONTO policy OCP adapter

Current local implementation status:

• Paper Problem 1 coarse benchmark (n_z=5) solves with IPOPT.
• Policy initializer matches the upstream MATLAB Policy 1 event at ~2.3633 h.
• Warm-started IPOPT result gives drying time ~6.186 h and Policy 1 -> Policy 2 switch near 2.395 h.
• Upstream full MATLAB workflow is not batch-runnable yet because the Python/GEKKO handoff fails locally; Add reproducible upstream reference generation for Paper Problem 1 #27 tracks making that reproducible.
• Upstream-size n_z=20 direct transcription still needs convergence work; Improve Paper Problem 1 n_z=20 direct-transcription convergence #26 tracks that blocker.

Suggested sequence before opening the first PR:

1. Decide whether Prepare first Paper Problem 1 Pyomo OCP validation PR #28 can proceed with the validated coarse mesh, or whether Improve Paper Problem 1 n_z=20 direct-transcription convergence #26 is required first.
2. If we require upstream-level resolution, work Improve Paper Problem 1 n_z=20 direct-transcription convergence #26 before PR.
3. If coarse validation is acceptable for PR 1, open Prepare first Paper Problem 1 Pyomo OCP validation PR #28 with Improve Paper Problem 1 n_z=20 direct-transcription convergence #26 and Add reproducible upstream reference generation for Paper Problem 1 #27 documented as known follow-ups.