Merge branch 'main' into mis

.github/workflows/typos.toml

@@ -43,4 +43,28 @@ Sur = "Sur"
 # contrib package named mis and the acronym whence the name comes
 mis = "mis"
 MIS = "MIS"
+# Ignore the shorthand ans for answer
+ans = "ans"
+# Ignore the keyword arange
+arange = "arange"
+# Ignore IIS
+IIS = "IIS"
+iis = "iis"
+# Ignore PN
+PN = "PN"
+# Ignore hd
+hd = "hd"
+# Ignore opf
+opf = "opf"
+# Ignore FRE
+FRE = "FRE"
+# Ignore MCH
+MCH = "MCH"
+# Ignore RO
+ro = "ro"
+RO = "RO"
+# Ignore EOF - end of file
+EOF = "EOF"
+# Ignore lst as shorthand for list
+lst = "lst"
 # AS NEEDED: Add More Words Below

README.md

@@ -71,6 +71,7 @@ version, we will remove testing for that Python version.
 
 ### Tutorials and Examples
 
+* [Pyomo — Optimization Modeling in Python](https://link.springer.com/book/10.1007/978-3-030-68928-5)
 * [Pyomo Workshop Slides](https://github.com/Pyomo/pyomo-tutorials/blob/main/Pyomo-Workshop-December-2023.pdf)
 * [Prof. Jeffrey Kantor's Pyomo Cookbook](https://jckantor.github.io/ND-Pyomo-Cookbook/)
 * The [companion notebooks](https://mobook.github.io/MO-book/intro.html)

doc/OnlineDocs/bibliography.rst

@@ -39,6 +39,8 @@ Bibliography
                   John D. Siirola, Jean-Paul Watson, and David L. Woodruff.
                   Pyomo - Optimization Modeling in Python, 3rd Edition.
                   Vol. 67. Springer, 2021.
+                  doi: `10.1007/978-3-030-68928-5
+                  <https://doi.org/10.1007/978-3-030-68928-5>`_
 
 .. [PyomoJournal] William E. Hart, Jean-Paul Watson, David L. Woodruff.
                   "Pyomo: modeling and solving mathematical programs in

doc/OnlineDocs/tutorial_examples.rst

@@ -3,15 +3,18 @@ Pyomo Tutorial Examples
 
 Additional Pyomo tutorials and examples can be found at the following links:
 
-`Pyomo Workshop Slides and Exercises
-<https://github.com/Pyomo/pyomo-tutorials>`_
+* `Pyomo — Optimization Modeling in Python
+  <https://link.springer.com/book/10.1007/978-3-030-68928-5>`_ ([PyomoBookIII]_)
 
-`Prof. Jeffrey Kantor's Pyomo Cookbook
-<https://jckantor.github.io/ND-Pyomo-Cookbook/>`_
+* `Pyomo Workshop Slides and Exercises
+  <https://github.com/Pyomo/pyomo-tutorials>`_
 
-The `companion notebooks <https://mobook.github.io/MO-book/intro.html>`_
-for *Hands-On Mathematical Optimization with Python*
+* `Prof. Jeffrey Kantor's Pyomo Cookbook
+  <https://jckantor.github.io/ND-Pyomo-Cookbook/>`_
 
-`Pyomo Gallery <https://github.com/Pyomo/PyomoGallery>`_
+* The `companion notebooks <https://mobook.github.io/MO-book/intro.html>`_
+  for *Hands-On Mathematical Optimization with Python*
+
+* `Pyomo Gallery <https://github.com/Pyomo/PyomoGallery>`_
 
 

pyomo/contrib/gdpopt/tests/test_LBB.py

@@ -59,6 +59,7 @@ def test_infeasible_GDP(self):
         self.assertIsNone(m.d.disjuncts[0].indicator_var.value)
         self.assertIsNone(m.d.disjuncts[1].indicator_var.value)
 
+    @unittest.skipUnless(z3_available, "Z3 SAT solver is not available")
     def test_infeasible_GDP_check_sat(self):
         """Test for infeasible GDP with check_sat option True."""
         m = ConcreteModel()

pyomo/contrib/gdpopt/tests/test_gdpopt.py

@@ -22,7 +22,6 @@
 from pyomo.common.collections import Bunch
 from pyomo.common.config import ConfigDict, ConfigValue
 from pyomo.common.fileutils import import_file, PYOMO_ROOT_DIR
-from pyomo.contrib.appsi.solvers.gurobi import Gurobi
 from pyomo.contrib.gdpopt.create_oa_subproblems import (
     add_util_block,
     add_disjunct_list,
@@ -767,6 +766,9 @@ def test_time_limit(self):
             results.solver.termination_condition, TerminationCondition.maxTimeLimit
         )
 
+    @unittest.skipUnless(
+        license_available, "No BARON license--8PP logical problem exceeds demo size"
+    )
     def test_LOA_8PP_logical_default_init(self):
         """Test logic-based outer approximation with 8PP."""
         exfile = import_file(join(exdir, 'eight_process', 'eight_proc_logical.py'))
@@ -870,6 +872,9 @@ def test_LOA_8PP_maxBinary(self):
         )
         ct.check_8PP_solution(self, eight_process, results)
 
+    @unittest.skipUnless(
+        license_available, "No BARON license--8PP logical problem exceeds demo size"
+    )
     def test_LOA_8PP_logical_maxBinary(self):
         """Test logic-based OA with max_binary initialization."""
         exfile = import_file(join(exdir, 'eight_process', 'eight_proc_logical.py'))
@@ -1050,7 +1055,11 @@ def assert_correct_disjuncts_active(
 
         self.assertTrue(fabs(value(eight_process.profit.expr) - 68) <= 1e-2)
 
-    @unittest.skipUnless(Gurobi().available(), "APPSI Gurobi solver is not available")
+    @unittest.skipUnless(
+        SolverFactory('appsi_gurobi').available(exception_flag=False)
+        and SolverFactory('appsi_gurobi').license_is_valid(),
+        "Legacy APPSI Gurobi solver is not available",
+    )
     def test_auto_persistent_solver(self):
         exfile = import_file(join(exdir, 'eight_process', 'eight_proc_model.py'))
         m = exfile.build_eight_process_flowsheet()
@@ -1126,6 +1135,9 @@ def test_RIC_8PP_default_init(self):
         )
         ct.check_8PP_solution(self, eight_process, results)
 
+    @unittest.skipUnless(
+        license_available, "No BARON license--8PP logical problem exceeds demo size"
+    )
     def test_RIC_8PP_logical_default_init(self):
         """Test logic-based outer approximation with 8PP."""
         exfile = import_file(join(exdir, 'eight_process', 'eight_proc_logical.py'))

pyomo/contrib/gdpopt/util.py

@@ -553,6 +553,13 @@ def _add_bigm_constraint_to_transformed_model(m, constraint, block):
     # making a Reference to the ComponentData so that it will look like an
     # indexed component for now. If I redesign bigm at some point, then this
     # could be prettier.
-    bigm._transform_constraint(Reference(constraint), parent_disjunct, None, [], [])
+    bigm._transform_constraint(
+        Reference(constraint),
+        parent_disjunct,
+        None,
+        [],
+        [],
+        1 - parent_disjunct.binary_indicator_var,
+    )
     # Now get rid of it because this is a class attribute!
     del bigm._config

pyomo/contrib/incidence_analysis/config.py

@@ -36,6 +36,13 @@ class IncidenceMethod(enum.Enum):
     """Use ``pyomo.repn.plugins.nl_writer.AMPLRepnVisitor``"""
 
 
+class IncidenceOrder(enum.Enum):
+
+    dulmage_mendelsohn_upper = 0
+
+    dulmage_mendelsohn_lower = 1
+
+
 _include_fixed = ConfigValue(
     default=False,
     domain=bool,

pyomo/contrib/incidence_analysis/tests/test_visualize.py

@@ -0,0 +1,47 @@
+#  ___________________________________________________________________________
+#
+#  Pyomo: Python Optimization Modeling Objects
+#  Copyright (c) 2008-2024
+#  National Technology and Engineering Solutions of Sandia, LLC
+#  Under the terms of Contract DE-NA0003525 with National Technology and
+#  Engineering Solutions of Sandia, LLC, the U.S. Government retains certain
+#  rights in this software.
+#  This software is distributed under the 3-clause BSD License.
+#  ___________________________________________________________________________
+
+import pyomo.common.unittest as unittest
+from pyomo.common.dependencies import (
+    matplotlib,
+    matplotlib_available,
+    scipy_available,
+    networkx_available,
+)
+from pyomo.contrib.incidence_analysis.visualize import spy_dulmage_mendelsohn
+from pyomo.contrib.incidence_analysis.tests.models_for_testing import (
+    make_gas_expansion_model,
+    make_dynamic_model,
+    make_degenerate_solid_phase_model,
+)
+
+
+@unittest.skipUnless(matplotlib_available, "Matplotlib is not available")
+@unittest.skipUnless(scipy_available, "SciPy is not available")
+@unittest.skipUnless(networkx_available, "NetworkX is not available")
+class TestSpy(unittest.TestCase):
+    def test_spy_dulmage_mendelsohn(self):
+        models = [
+            make_gas_expansion_model(),
+            make_dynamic_model(),
+            make_degenerate_solid_phase_model(),
+        ]
+        for m in models:
+            fig, ax = spy_dulmage_mendelsohn(m)
+            # Note that this is a weak test. We just test that we can call the
+            # plot method, it doesn't raise an error, and gives us back the
+            # types we expect. We don't attempt to validate the resulting plot.
+            self.assertTrue(isinstance(fig, matplotlib.pyplot.Figure))
+            self.assertTrue(isinstance(ax, matplotlib.pyplot.Axes))
+
+
+if __name__ == "__main__":
+    unittest.main()