Merge branch 'main' into benchmark

.github/workflows/test_branches.yml

@@ -75,15 +75,15 @@ jobs:
           python: 3.9
           TARGET: win
           PYENV: conda
-          PACKAGES: glpk
+          PACKAGES: glpk pytest-qt
 
         - os: ubuntu-latest
           python: '3.11'
           other: /conda
           skip_doctest: 1
           TARGET: linux
           PYENV: conda
-          PACKAGES:
+          PACKAGES: pytest-qt
 
         - os: ubuntu-latest
           python: 3.9
@@ -213,6 +213,15 @@ jobs:
         auto-update-conda: false
         python-version: ${{ matrix.python }}
 
+    # This is necessary for qt (UI) tests; the package utilized here does not
+    # have support for OSX.
+    - name: Set up UI testing infrastructure
+      if: ${{ matrix.TARGET != 'osx' }}
+      uses: pyvista/setup-headless-display-action@v2
+      with:
+        qt: true
+        pyvista: false
+
     # GitHub actions is very fragile when it comes to setting up various
     # Python interpreters, expecially the setup-miniconda interface.
     # Per the setup-miniconda documentation, it is important to always
@@ -309,7 +318,7 @@ jobs:
         fi
         # HACK: Remove problem packages on conda+Linux
         if test "${{matrix.TARGET}}" == linux; then
-            EXCLUDE="casadi numdifftools pint $EXCLUDE"
+            EXCLUDE="casadi numdifftools $EXCLUDE"
         fi
         EXCLUDE=`echo "$EXCLUDE" | xargs`
         if test -n "$EXCLUDE"; then
@@ -346,10 +355,11 @@ jobs:
                     | sed -r 's/\s+/ /g' | cut -d\  -f3) || echo ""
                 if test -n "$_BUILDS"; then
                     _ISPY=$(echo "$_BUILDS" | grep "^py") \
-                        || echo "No python build detected"
-                    _PYOK=$(echo "$_BUILDS" | grep "^$PYVER") \
-                        || echo "No python build matching $PYVER detected"
+                        || echo "INFO: No python build detected."
+                    _PYOK=$(echo "$_BUILDS" | grep -E "^($PYVER|pyh)") \
+                        || echo "INFO: No python build matching $PYVER detected."
                     if test -z "$_ISPY" -o -n "$_PYOK"; then
+                        echo ""
                         echo "... INSTALLING $PKG"
                         conda install -y "$PKG" || _BUILDS=""
                     fi
@@ -358,18 +368,6 @@ jobs:
                     echo "WARNING: $PKG is not available"
                 fi
             done
-            # TODO: This is a hack to stop test_qt.py from running until we
-            # can better troubleshoot why it fails on GHA
-            for QTPACKAGE in qt pyqt; do
-                # Because conda is insane, removing packages can cause
-                # unrelated packages to be updated (breaking version
-                # specifications specified previously, e.g., in
-                # setup.py).  There doesn't appear to be a good
-                # workaround, so we will just force-remove (recognizing
-                # that it may break other conda cruft).
-                conda remove --force-remove $QTPACKAGE \
-                    || echo "$QTPACKAGE not in this environment"
-            done
         fi
         # Re-try Pyomo (optional) dependencies with pip
         if test -n "$PYPI_DEPENDENCIES"; then

.github/workflows/test_pr_and_main.yml

@@ -76,15 +76,15 @@ jobs:
         - os: windows-latest
           TARGET: win
           PYENV: conda
-          PACKAGES: glpk
+          PACKAGES: glpk pytest-qt
 
         - os: ubuntu-latest
           python: '3.11'
           other: /conda
           skip_doctest: 1
           TARGET: linux
           PYENV: conda
-          PACKAGES:
+          PACKAGES: pytest-qt
 
         - os: ubuntu-latest
           python: 3.9
@@ -243,6 +243,15 @@ jobs:
         auto-update-conda: false
         python-version: ${{ matrix.python }}
 
+    # This is necessary for qt (UI) tests; the package utilized here does not
+    # have support for OSX.
+    - name: Set up UI testing infrastructure
+      if: ${{ matrix.TARGET != 'osx' }}
+      uses: pyvista/setup-headless-display-action@v2
+      with:
+        qt: true
+        pyvista: false
+
     # GitHub actions is very fragile when it comes to setting up various
     # Python interpreters, expecially the setup-miniconda interface.
     # Per the setup-miniconda documentation, it is important to always
@@ -339,7 +348,7 @@ jobs:
         fi
         # HACK: Remove problem packages on conda+Linux
         if test "${{matrix.TARGET}}" == linux; then
-            EXCLUDE="casadi numdifftools pint $EXCLUDE"
+            EXCLUDE="casadi numdifftools $EXCLUDE"
         fi
         EXCLUDE=`echo "$EXCLUDE" | xargs`
         if test -n "$EXCLUDE"; then
@@ -376,10 +385,11 @@ jobs:
                     | sed -r 's/\s+/ /g' | cut -d\  -f3) || echo ""
                 if test -n "$_BUILDS"; then
                     _ISPY=$(echo "$_BUILDS" | grep "^py") \
-                        || echo "No python build detected"
-                    _PYOK=$(echo "$_BUILDS" | grep "^$PYVER") \
-                        || echo "No python build matching $PYVER detected"
+                        || echo "INFO: No python build detected."
+                    _PYOK=$(echo "$_BUILDS" | grep -E "^($PYVER|pyh)") \
+                        || echo "INFO: No python build matching $PYVER detected."
                     if test -z "$_ISPY" -o -n "$_PYOK"; then
+                        echo ""
                         echo "... INSTALLING $PKG"
                         conda install -y "$PKG" || _BUILDS=""
                     fi
@@ -388,18 +398,6 @@ jobs:
                     echo "WARNING: $PKG is not available"
                 fi
             done
-            # TODO: This is a hack to stop test_qt.py from running until we
-            # can better troubleshoot why it fails on GHA
-            for QTPACKAGE in qt pyqt; do
-                # Because conda is insane, removing packages can cause
-                # unrelated packages to be updated (breaking version
-                # specifications specified previously, e.g., in
-                # setup.py).  There doesn't appear to be a good
-                # workaround, so we will just force-remove (recognizing
-                # that it may break other conda cruft).
-                conda remove --force-remove $QTPACKAGE \
-                    || echo "$QTPACKAGE not in this environment"
-            done
         fi
         # Re-try Pyomo (optional) dependencies with pip
         if test -n "$PYPI_DEPENDENCIES"; then

doc/OnlineDocs/advanced_topics/linearexpression.rst

@@ -2,7 +2,7 @@ LinearExpression
 ================
 
 Significant speed
-improvements can be obtained using the ``LinearExpression`` object
+improvements can sometimes be obtained using the ``LinearExpression`` object
 when there are long, dense, linear expressions. The arguments are
 
 :: 
@@ -11,7 +11,9 @@ when there are long, dense, linear expressions. The arguments are
 
 where the second and third arguments are lists that must be of the
 same length. Here is a simple example that illustrates the
-syntax. This example creates two constraints that are the same:
+syntax. This example creates two constraints that are the same; in this
+particular case the LinearExpression component would offer very little improvement
+because Pyomo would be able to detect that `campe2` is a linear expression:
 
 .. doctest::
 
@@ -38,5 +40,5 @@ syntax. This example creates two constraints that are the same:
 
 .. warning::
 
-   The lists that are passed to ``LinearModel`` are not copied, so caution must
+   The lists that are passed to ``LinearExpression`` are not copied, so caution must
    be exercised if they are modified after the component is constructed.

doc/OnlineDocs/contributed_packages/pyros.rst

@@ -723,11 +723,11 @@ For this example, we obtain the following price of robustness results:
     +==========================================+==============================+=============================+
     |   0.00                                   | 35,837,659.18                | 0.00 %                      |
     +------------------------------------------+------------------------------+-----------------------------+
-    |   0.10                                   | 36,135,191.59                | 0.82 %                      |
+    |   0.10                                   | 36,135,182.66                | 0.83 %                      |
     +------------------------------------------+------------------------------+-----------------------------+
-    |   0.20                                   | 36,437,979.81                | 1.64 %                      |
+    |   0.20                                   | 36,437,979.81                | 1.68 %                      |
     +------------------------------------------+------------------------------+-----------------------------+
-    |   0.30                                   | 43,478,190.92                | 17.57 %                     |
+    |   0.30                                   | 43,478,190.91                | 21.32 %                     |
     +------------------------------------------+------------------------------+-----------------------------+
     |   0.40                                   | ``robust_infeasible``        | :math:`\text{-----}`        |
     +------------------------------------------+------------------------------+-----------------------------+
@@ -854,10 +854,10 @@ Observe that the log contains the following information:
    :linenos:
 
    ==============================================================================
-   PyROS: The Pyomo Robust Optimization Solver, v1.2.8.
+   PyROS: The Pyomo Robust Optimization Solver, v1.2.9.
           Pyomo version: 6.7.0
           Commit hash: unknown
-          Invoked at UTC 2023-11-03T04:27:42.954101
+          Invoked at UTC 2023-12-16T00:00:00.000000
 
    Developed by: Natalie M. Isenberg (1), Jason A. F. Sherman (1),
                  John D. Siirola (2), Chrysanthos E. Gounaris (1)
@@ -914,37 +914,34 @@ Observe that the log contains the following information:
    ------------------------------------------------------------------------------
    Itn  Objective    1-Stg Shift  2-Stg Shift  #CViol  Max Viol     Wall Time (s)
    ------------------------------------------------------------------------------
-   0     3.5838e+07  -            -            5       1.8832e+04   1.555        
-   1     3.5838e+07  2.2045e-12   2.7854e-12   7       3.7766e+04   2.991        
-   2     3.6116e+07  1.2324e-01   3.9256e-01   8       1.3466e+06   4.881        
-   3     3.6285e+07  5.1968e-01   4.5604e-01   6       4.8734e+03   6.908        
-   4     3.6285e+07  2.6524e-13   1.3909e-13   1       3.5036e+01   9.176        
-   5     3.6285e+07  2.0167e-13   5.4357e-02   6       2.9103e+00   11.457       
-   6     3.6285e+07  2.2335e-12   1.2150e-01   5       4.1726e-01   13.868       
-   7     3.6285e+07  2.2340e-12   1.1422e-01   0       9.3279e-10g  20.917       
+   0     3.5838e+07  -            -            5       1.8832e+04   1.741        
+   1     3.5838e+07  3.5184e-15   3.9404e-15   10      4.2516e+06   3.766        
+   2     3.5993e+07  1.8105e-01   7.1406e-01   13      5.2004e+06   6.288
+   3     3.6285e+07  5.1968e-01   7.7753e-01   4       1.7892e+04   8.247
+   4     3.6285e+07  9.1166e-13   1.9702e-15   0       7.1157e-10g  11.456
    ------------------------------------------------------------------------------
    Robust optimal solution identified.
    ------------------------------------------------------------------------------
    Timing breakdown:
 
    Identifier                ncalls   cumtime   percall      %
    -----------------------------------------------------------
-   main                           1    20.918    20.918  100.0
+   main                           1    11.457    11.457  100.0
         ------------------------------------------------------
-        dr_polishing              7     1.472     0.210    7.0
-        global_separation        47     1.239     0.026    5.9
-        local_separation        376     9.244     0.025   44.2
-        master                    8     5.259     0.657   25.1
-        master_feasibility        7     0.486     0.069    2.3
-        preprocessing             1     0.403     0.403    1.9
-        other                   n/a     2.815       n/a   13.5
+        dr_polishing              4     0.682     0.171    6.0
+        global_separation        47     1.109     0.024    9.7
+        local_separation        235     5.810     0.025   50.7
+        master                    5     1.353     0.271   11.8
+        master_feasibility        4     0.247     0.062    2.2
+        preprocessing             1     0.429     0.429    3.7
+        other                   n/a     1.828       n/a   16.0
         ======================================================
    ===========================================================
 
    ------------------------------------------------------------------------------
    Termination stats:
-    Iterations            : 8
-    Solve time (wall s)   : 20.918
+    Iterations            : 5
+    Solve time (wall s)   : 11.457
     Final objective value : 3.6285e+07
     Termination condition : pyrosTerminationCondition.robust_optimal
    ------------------------------------------------------------------------------

doc/OnlineDocs/src/test_examples.py

@@ -35,7 +35,11 @@ class TestOnlineDocExamples(unittest.BaselineTestDriver, unittest.TestCase):
         list(filter(os.path.isdir, glob.glob(os.path.join(currdir, '*'))))
     )
 
-    solver_dependencies = {}
+    solver_dependencies = {
+        'test_data_pyomo_diet1': ['glpk'],
+        'test_data_pyomo_diet2': ['glpk'],
+        'test_kernel_examples': ['glpk'],
+    }
     # Note on package dependencies: two tests actually need
     # pyutilib.excel.spreadsheet; however, the pyutilib importer is
     # broken on Python>=3.12, so instead of checking for spreadsheet, we

pyomo/common/numeric_types.py

@@ -212,8 +212,8 @@ def check_if_numeric_type(obj):
         # trigger the resolution of numpy_available and check if this
         # type was automatically registered
         bool(numpy_available)
-        if obj_class in native_numeric_types:
-            return True
+        if obj_class in native_types:
+            return obj_class in native_numeric_types
 
     try:
         obj_plus_0 = obj + 0

pyomo/common/unittest.py

@@ -555,6 +555,20 @@ def assertRaisesRegex(self, expected_exception, expected_regex, *args, **kwargs)
         context = contextClass(expected_exception, self, expected_regex)
         return context.handle('assertRaisesRegex', args, kwargs)
 
+    def assertExpressionsEqual(self, a, b, include_named_exprs=True, places=None):
+        from pyomo.core.expr.compare import assertExpressionsEqual
+
+        return assertExpressionsEqual(self, a, b, include_named_exprs, places)
+
+    def assertExpressionsStructurallyEqual(
+        self, a, b, include_named_exprs=True, places=None
+    ):
+        from pyomo.core.expr.compare import assertExpressionsStructurallyEqual
+
+        return assertExpressionsStructurallyEqual(
+            self, a, b, include_named_exprs, places
+        )
+
 
 class BaselineTestDriver(object):
     """Generic driver for performing baseline tests in bulk

pyomo/contrib/parmest/examples/reactor_design/bootstrap_example.py

@@ -9,7 +9,7 @@
 #  This software is distributed under the 3-clause BSD License.
 #  ___________________________________________________________________________
 
-import pandas as pd
+from pyomo.common.dependencies import pandas as pd
 from os.path import join, abspath, dirname
 import pyomo.contrib.parmest.parmest as parmest
 from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (

pyomo/contrib/parmest/examples/reactor_design/datarec_example.py

@@ -9,8 +9,7 @@
 #  This software is distributed under the 3-clause BSD License.
 #  ___________________________________________________________________________
 
-import numpy as np
-import pandas as pd
+from pyomo.common.dependencies import numpy as np, pandas as pd
 import pyomo.contrib.parmest.parmest as parmest
 from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (
     reactor_design_model,

pyomo/contrib/parmest/examples/reactor_design/leaveNout_example.py

@@ -9,8 +9,7 @@
 #  This software is distributed under the 3-clause BSD License.
 #  ___________________________________________________________________________
 
-import numpy as np
-import pandas as pd
+from pyomo.common.dependencies import numpy as np, pandas as pd
 from os.path import join, abspath, dirname
 import pyomo.contrib.parmest.parmest as parmest
 from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (

pyomo/contrib/parmest/examples/reactor_design/likelihood_ratio_example.py

@@ -9,8 +9,7 @@
 #  This software is distributed under the 3-clause BSD License.
 #  ___________________________________________________________________________
 
-import numpy as np
-import pandas as pd
+from pyomo.common.dependencies import numpy as np, pandas as pd
 from itertools import product
 from os.path import join, abspath, dirname
 import pyomo.contrib.parmest.parmest as parmest

pyomo/contrib/parmest/examples/reactor_design/multisensor_data_example.py

@@ -9,7 +9,7 @@
 #  This software is distributed under the 3-clause BSD License.
 #  ___________________________________________________________________________
 
-import pandas as pd
+from pyomo.common.dependencies import pandas as pd
 from os.path import join, abspath, dirname
 import pyomo.contrib.parmest.parmest as parmest
 from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (

pyomo/contrib/parmest/examples/reactor_design/parameter_estimation_example.py

@@ -9,7 +9,7 @@
 #  This software is distributed under the 3-clause BSD License.
 #  ___________________________________________________________________________
 
-import pandas as pd
+from pyomo.common.dependencies import pandas as pd
 from os.path import join, abspath, dirname
 import pyomo.contrib.parmest.parmest as parmest
 from pyomo.contrib.parmest.examples.reactor_design.reactor_design import (

pyomo/contrib/parmest/examples/reactor_design/reactor_design.py

@@ -12,7 +12,7 @@
 Continuously stirred tank reactor model, based on
 pyomo/examples/doc/pyomobook/nonlinear-ch/react_design/ReactorDesign.py
 """
-import pandas as pd
+from pyomo.common.dependencies import pandas as pd
 from pyomo.environ import (
     ConcreteModel,
     Param,

pyomo/contrib/parmest/examples/reactor_design/timeseries_data_example.py

@@ -9,7 +9,7 @@
 #  This software is distributed under the 3-clause BSD License.
 #  ___________________________________________________________________________
 
-import pandas as pd
+from pyomo.common.dependencies import pandas as pd
 from os.path import join, abspath, dirname
 
 import pyomo.contrib.parmest.parmest as parmest

pyomo/contrib/parmest/examples/rooney_biegler/bootstrap_example.py

@@ -9,7 +9,7 @@
 #  This software is distributed under the 3-clause BSD License.
 #  ___________________________________________________________________________
 
-import pandas as pd
+from pyomo.common.dependencies import pandas as pd
 import pyomo.contrib.parmest.parmest as parmest
 from pyomo.contrib.parmest.examples.rooney_biegler.rooney_biegler import (
     rooney_biegler_model,