PR 2/7: Pyomo optional dependencies and module structure

lyopronto/pyomo_models/__init__.py

@@ -0,0 +1,49 @@
+# Copyright 2019-2025, Gayathri Shivkumar, Petr S. Kazarin, Alina A. Alexeenko
+# Maintained by Isaac S. Wheeler
+#
+# This file is part of LyoPRONTO.
+# LyoPRONTO is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+"""
+Pyomo-based optimization models for lyophilization process.
+
+This module provides Pyomo-based formulations for lyophilization optimization,
+complementing the existing scipy-based optimizers. The Pyomo models offer:
+
+- Mathematical programming formulations with explicit constraints
+- Support for IPOPT and other NLP solvers
+- Multi-period trajectory optimization
+- Orthogonal collocation discretization
+
+Usage:
+    # Install optimization dependencies first:
+    # pip install .[optimization]
+
+    from lyopronto.pyomo_models import optimize_Tsh_pyomo
+
+    result = optimize_Tsh_pyomo(vial, product, ht, Pchamber, Tshelf, dt, eq_cap, nVial)
+
+The optimizers maintain API compatibility with scipy-based versions:
+- optimize_Tsh_pyomo: Optimize shelf temperature trajectory
+- optimize_Pch_pyomo: Optimize chamber pressure trajectory  
+- optimize_Pch_Tsh_pyomo: Optimize both pressure and temperature
+
+Note: Requires IPOPT solver. Install via: idaes get-extensions --extra petsc
+"""
+
+# Placeholder - actual implementations will be added in subsequent PRs
+__all__ = []
+
+# Version will be set when implementations are added
+__version__ = "0.1.0-dev"

pyproject.toml

@@ -40,6 +40,10 @@ classifiers = [
 ]
 
 [project.optional-dependencies]
+optimization = [
+    "pyomo>=6.7.0",
+    "idaes-pse>=2.9.0",
+]
 dev = [
     "pytest>=7.4.0",
     "pytest-mock>=3",
@@ -58,7 +62,9 @@ docs = [
     "mike>=2.1",
     "mkdocs-ipynb>=0.1.1",
 ]
-
+all = [
+    "lyopronto[optimization,dev,docs]",
+]
 
 [project.urls]
 Homepage = "http://lyopronto.geddes.rcac.purdue.edu"
@@ -88,4 +94,75 @@ markers = [
     "fast: Quick tests that run in under 1 second",
     "notebook: Tests that execute Jupyter notebooks for documentation",
     "main: Tests that cover functionality previously included in main.py",
+    "pyomo: Tests requiring Pyomo and IPOPT solver (deselect with '-m not pyomo')",
+    "serial: Tests that must run serially (not in parallel)",
+]
+
+[tool.mypy]
+python_version = "3.8"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+ignore_missing_imports = true
+# Exclude pyomo_models from type checking - Pyomo uses dynamic attribute
+# assignment (model.Var = pyo.Var(...)) which generates many false-positive
+# mypy errors. The code is tested via pytest instead.
+exclude = [
+    "lyopronto/pyomo_models/",
+]
+
+[tool.ruff]
+# Target Python 3.8+ (matches project.requires-python)
+target-version = "py38"
+line-length = 88  # Black-compatible
+src = ["lyopronto", "tests", "benchmarks"]
+
+[tool.ruff.lint]
+# Enable recommended rules + some extras
+select = [
+    "E",      # pycodestyle errors
+    "W",      # pycodestyle warnings
+    "F",      # Pyflakes
+    "I",      # isort (import sorting)
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "UP",     # pyupgrade
+    "SIM",    # flake8-simplify
+]
+ignore = [
+    "E501",   # Line too long (handled by formatter)
+    "B008",   # Do not perform function calls in argument defaults
+    "SIM108", # Use ternary operator (sometimes less readable)
 ]
+
+# Allow autofix for all enabled rules
+fixable = ["ALL"]
+unfixable = []
+
+[tool.ruff.lint.per-file-ignores]
+# Tests can use assert and have longer lines
+"tests/**/*.py" = ["S101", "E501"]
+# Pyomo test files have conditional imports at module level (intentional pattern)
+"tests/test_pyomo_models/*.py" = ["E402", "E722", "F401"]
+# Pyomo models use closures in loops for rule functions (Pyomo pattern)
+"lyopronto/pyomo_models/*.py" = ["B023", "B007", "E722", "SIM102", "F811"]
+# Legacy scipy optimizers use closures in loops (legacy pattern)
+"lyopronto/opt_*.py" = ["B023"]
+# Package __init__ re-exports modules for public API  
+"lyopronto/__init__.py" = ["F401"]
+# Benchmarks may have more complex imports
+"benchmarks/**/*.py" = ["E501"]
+# Legacy examples may have style issues
+"examples/legacy/**/*.py" = ["ALL"]
+# Notebooks have different import patterns
+"**/*.ipynb" = ["E402", "B007"]
+# Test design space has complex warning handling
+"tests/test_design_space.py" = ["SIM117"]
+
+[tool.ruff.format]
+# Use double quotes (Black-compatible)
+quote-style = "double"
+# Indent with spaces
+indent-style = "space"
+# Unix line endings
+line-ending = "lf"

tests/test_pyomo_models/__init__.py

@@ -0,0 +1,2 @@
+# Copyright 2019-2025, SECQUOIA
+# Tests for Pyomo-based optimization models.