PR 3/7: Pyomo utilities and single-step optimization by bernalde · Pull Request #8 · SECQUOIA/LyoPRONTO

bernalde · 2026-03-03T00:41:56Z

Summary

Core Pyomo building blocks. utils.py provides parameter conversion from LyoPRONTO dicts to Pyomo-compatible formats, variable bound defaults, and warmstart helpers. single_step.py implements a single time-step steady-state optimization (one NLP solve per step), mirroring the scipy optimizer's step-by-step approach.

PR 3 of 7 in the Pyomo integration series.

Changes

lyopronto/pyomo_models/utils.py — Shared utilities (variable bounds, parameter loading, warmstart)
lyopronto/pyomo_models/single_step.py — Single time-step Pyomo model
tests/test_pyomo_models/test_model_single_step.py — 307 lines of tests
tests/test_pyomo_models/README.md — Test documentation

Key Design Decisions

Variable bounds: Pch (0.05–0.5 Torr), Tsh (-50–50°C), Tsub (-60–0°C)
Log-transform: Vapor pressure uses log form to avoid numerical issues with exp()
Warmstart: Scipy solution used to initialize Pyomo variables

PR Chain

#	PR	Status
0	Sync upstream (#5)	Merged
1	CI/CD for Pyomo (#6)	Open
2	Pyomo dependencies (#7)	Open
3	Utils & single-step (this PR)
4	Multi-period model	Pending
5	Optimizer functions	Pending
6	Benchmarks	Pending
7	Docs & examples	Pending

Testing

~307 lines of new tests covering single-step model creation, solving, and parameter validation.

pytest -m 'pyomo' exits with code 5 when no pyomo-marked tests exist. This is expected until PR #8 adds the first pyomo tests. Treat exit code 5 as success so the Pyomo Tests job passes gracefully.

Source fixes: - calc_knownRp.py: use constant.Torr_to_mTorr instead of literal 1000.0 in early-return path, with regression test Test fixes: - Fix percent-dried scale bug: 0.99 -> 99.0 across test_regression.py (5), test_optimizer.py (1), test_opt_Pch_Tsh_coverage.py (2+2), test_opt_Pch_coverage.py (2) - test_coverage_gaps.py: remove duplicate TestIneqConstraints class - test_functions.py: add value assertions to TestIneqConstraints - test_regression.py: skip column 0 (time) in stability test - test_calculators.py: add meaningful assertion in test_higher_pressure_dries_faster - test_web_interface.py, test_calc_unknownRp_coverage.py: use reference_data_path fixture instead of relative paths - test_calc_knownRp.py: add regression test for mTorr conversion Config fixes: - pyproject.toml: remove duplicate [tool.pytest.ini_options] (pytest.ini takes precedence) - pytest.ini: update minversion from 3.8 to 7.4 - requirements-dev.txt: add pytest-mock (matches pyproject.toml [dev]) CI fixes: - pr-tests.yml, tests.yml, slow-tests.yml: consolidate triple pip install into single pip install -e ".[dev]" - Remove hardcoded PR #8 reference from pyomo fallback messages Script fixes: - run_local_ci.sh: remove emojis, replace grep -oP with portable -oE, remove set -e/dead-code if-block, remove hardcoded -n 8, use pip install -e ".[dev]" Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

pytest -m 'pyomo' exits with code 5 when no pyomo-marked tests exist. This is expected until PR #8 adds the first pyomo tests. Treat exit code 5 as success so the Pyomo Tests job passes gracefully.

This PR adds the foundational Pyomo modules: lyopronto/pyomo_models/utils.py (254 lines): - Warmstart utilities for initializing from scipy solutions - Variable scaling functions for numerical stability - Validation helpers for checking physical constraints - Result extraction and formatting utilities lyopronto/pyomo_models/single_step.py (427 lines): - Single time-point optimization formulation - Direct Pyomo model for one drying step - Basis for multi-period trajectory optimization - Physics constraints as Pyomo constraints Tests: - tests/test_pyomo_models/test_model_single_step.py - tests/test_pyomo_models/README.md These utilities are used by the multi-period model (PR 4) and the optimizer functions (PR 5).

bernalde

Blocking issues: equipment capability can be silently omitted when eq_cap is provided without nVial; infeasible/non-optimal solves are returned as usable solutions; extract_solution_to_array advertises the standard output format but writes raw dmdt and a placeholder dried percentage.
Nonblocking issues: the Pyomo test skip guard imports the Pyomo submodule before checking availability.
Questions: none.
Tests run and outcomes:

env PYTHONPATH=/tmp/LyoPRONTO_pr8 MPLCONFIGDIR=/tmp/mplconfig pytest tests/test_pyomo_models/test_init.py tests/test_pyomo_models/test_model_single_step.py -m "not slow": 11 passed.
env PYTHONPATH=/tmp/LyoPRONTO_pr8 MPLCONFIGDIR=/tmp/mplconfig pytest tests/test_pyomo_models/test_model_single_step.py -m "slow": 3 passed.
env PYTHONPATH=/tmp/LyoPRONTO_pr8 MPLCONFIGDIR=/tmp/mplconfig pytest tests/ -m "not notebook and not pyomo" --ignore=tests/test_pyomo_models: 235 passed, 2 skipped.
Initial run from /tmp/lyopronto-pr8 failed because the dash in the worktree directory name made pytest import the repo root under an invalid package name; reran from /tmp/LyoPRONTO_pr8.

Merge recommendation: do not merge as-is.

I would not merge this until the blocking issues above are addressed.

bernalde

Checked the PR #7 follow-up comments against this stacked PR. One copyright-header issue carries forward.

bernalde

Reviewed current head c271b60. No blocking issues found. GitHub would not allow APPROVE because the authenticated account is the PR author, so I am submitting this as COMMENT. One nonblocking CI coverage issue is inline. Tests run: pytest tests/test_pyomo_models/test_init.py tests/test_pyomo_models/test_model_single_step.py -m "not slow" passed 13; pytest tests/test_pyomo_models/test_model_single_step.py -m "slow" passed 4; pytest tests/test_pyomo_models/ -v passed 17; pytest tests/ -n auto -v -m "not notebook and not pyomo" --ignore=tests/test_pyomo_models --cov=lyopronto --cov-report=term-missing passed 235, skipped 2; pytest tests/ -n auto -v -m "pyomo" --cov=lyopronto --cov-report=term-missing passed 13; python -m ruff check lyopronto/pyomo_models tests/test_pyomo_models passed; git diff --check origin/pr/pyomo-dependencies...HEAD passed.

bernalde · 2026-05-30T21:20:08Z

        if [ "${{ steps.mode.outputs.mode }}" == "fast" ]; then
          echo "Draft PR: Skipping notebook and pyomo tests for fast feedback"
-          pytest tests/ -n auto -v -m "not notebook and not pyomo"
+          pytest tests/ -n auto -v -m "not notebook and not pyomo" --ignore=tests/test_pyomo_models


Nonblocking: Ignoring the whole tests/test_pyomo_models directory here means the non-Pyomo PR job no longer runs tests/test_pyomo_models/test_init.py, and the Pyomo job uses -m "pyomo", so that unmarked initializer/export smoke test is not covered there either. This weakens CI coverage for the optional-package import path added in PR #7. Prefer ignoring only the Pyomo-dependent model/solver test files, or move/mark the initializer test so it is still exercised by one CI job; apply the same pattern to the matching --ignore=tests/test_pyomo_models changes in the other workflows.

bernalde force-pushed the pr/pyomo-utils-singlestep branch from fa26a34 to 65fc2c3 Compare March 3, 2026 00:51

bernalde force-pushed the pr/pyomo-dependencies branch 2 times, most recently from 6fa03b3 to 58d26cd Compare March 3, 2026 01:09

bernalde force-pushed the pr/pyomo-utils-singlestep branch from 65fc2c3 to b8a82c3 Compare March 3, 2026 01:09

bernalde force-pushed the pr/pyomo-dependencies branch from 58d26cd to 72e8b86 Compare March 3, 2026 01:29

bernalde force-pushed the pr/pyomo-utils-singlestep branch from b8a82c3 to 53ad6d9 Compare March 3, 2026 01:29

bernalde force-pushed the pr/pyomo-dependencies branch from 72e8b86 to 9b54119 Compare March 3, 2026 18:07

bernalde force-pushed the pr/pyomo-utils-singlestep branch from 53ad6d9 to 389c49e Compare March 3, 2026 18:07

bernalde force-pushed the pr/pyomo-dependencies branch from 9b54119 to a4d2f9a Compare April 1, 2026 20:56

bernalde force-pushed the pr/pyomo-utils-singlestep branch 3 times, most recently from c4356ba to 15eb233 Compare April 2, 2026 22:19

bernalde force-pushed the pr/pyomo-dependencies branch from a4d2f9a to c60cf5e Compare April 2, 2026 22:19

bernalde force-pushed the pr/pyomo-utils-singlestep branch from 15eb233 to 38607c8 Compare May 7, 2026 21:39

bernalde commented May 7, 2026

View reviewed changes

Comment thread lyopronto/pyomo_models/single_step.py

Comment thread lyopronto/pyomo_models/single_step.py Outdated

Comment thread lyopronto/pyomo_models/utils.py Outdated

Comment thread tests/test_pyomo_models/test_model_single_step.py Outdated

Address single-step Pyomo review comments

c100fba

bernalde commented May 7, 2026

View reviewed changes

Comment thread lyopronto/pyomo_models/utils.py Outdated

Update Pyomo single-step headers

c271b60

bernalde commented May 30, 2026

View reviewed changes

bernalde merged commit 6008792 into pr/pyomo-dependencies May 30, 2026
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PR 3/7: Pyomo utilities and single-step optimization#8

PR 3/7: Pyomo utilities and single-step optimization#8
bernalde merged 3 commits into
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pr/pyomo-utils-singlestep

bernalde commented Mar 3, 2026

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bernalde commented Mar 3, 2026

Summary

Changes

Key Design Decisions

PR Chain

Testing

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