PR 3/7: Pyomo utilities and single-step optimization#8
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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.
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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>
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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).
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- Blocking issues: equipment capability can be silently omitted when
eq_capis provided withoutnVial; infeasible/non-optimal solves are returned as usable solutions;extract_solution_to_arrayadvertises the standard output format but writes rawdmdtand 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-pr8failed 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.
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Summary
Core Pyomo building blocks.
utils.pyprovides parameter conversion from LyoPRONTO dicts to Pyomo-compatible formats, variable bound defaults, and warmstart helpers.single_step.pyimplements 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 modeltests/test_pyomo_models/test_model_single_step.py— 307 lines of teststests/test_pyomo_models/README.md— Test documentationKey Design Decisions
Pch(0.05–0.5 Torr),Tsh(-50–50°C),Tsub(-60–0°C)exp()PR Chain
Testing
~307 lines of new tests covering single-step model creation, solving, and parameter validation.