Merge branch 'main' of https://github.com/pyomo/pyomo into incidence-…

…amplrepn

.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
@@ -623,7 +621,7 @@ jobs:
         $PYTHON_EXE -m pytest -v \
             -W ignore::Warning ${{matrix.category}} \
             pyomo `pwd`/pyomo-model-libraries \
-            `pwd`/examples/pyomobook --junitxml="TEST-pyomo.xml"
+            `pwd`/examples `pwd`/doc --junitxml="TEST-pyomo.xml"
 
     - name: Run Pyomo MPI tests
       if: matrix.mpi != 0

.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
@@ -653,7 +651,7 @@ jobs:
         $PYTHON_EXE -m pytest -v \
             -W ignore::Warning ${{matrix.category}} \
             pyomo `pwd`/pyomo-model-libraries \
-            `pwd`/examples/pyomobook --junitxml="TEST-pyomo.xml"
+            `pwd`/examples `pwd`/doc --junitxml="TEST-pyomo.xml"
 
     - name: Run Pyomo MPI tests
       if: matrix.mpi != 0

.jenkins.sh

@@ -38,7 +38,7 @@ if test -z "$WORKSPACE"; then
     export WORKSPACE=`pwd`
 fi
 if test -z "$TEST_SUITES"; then
-    export TEST_SUITES="${WORKSPACE}/pyomo/pyomo ${WORKSPACE}/pyomo-model-libraries ${WORKSPACE}/pyomo/examples/pyomobook"
+    export TEST_SUITES="${WORKSPACE}/pyomo/pyomo ${WORKSPACE}/pyomo-model-libraries ${WORKSPACE}/pyomo/examples ${WORKSPACE}/pyomo/doc"
 fi
 if test -z "$SLIM"; then
     export VENV_SYSTEM_PACKAGES='--system-site-packages'

README.md

@@ -71,7 +71,7 @@ version, we will remove testing for that Python version.
 
 ### Tutorials and Examples
 
-* [Pyomo Workshop Slides](https://software.sandia.gov/downloads/pub/pyomo/Pyomo-Workshop-Summer-2018.pdf)
+* [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/)
 * [Pyomo Gallery](https://github.com/Pyomo/PyomoGallery)
 

doc/OnlineDocs/Makefile

@@ -23,4 +23,4 @@ clean clean_tests:
 	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 	@echo "Removing *.spy, *.out"
 	@find . -name \*.spy -delete
-	@find tests -name \*.out -delete
+	@find src -name \*.out -delete

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/conf.py

@@ -26,12 +26,12 @@
 sys.path.insert(0, os.path.abspath('../..'))
 
 # -- Rebuild SPY files ----------------------------------------------------
-sys.path.insert(0, os.path.abspath('tests'))
+sys.path.insert(0, os.path.abspath('src'))
 try:
     print("Regenerating SPY files...")
     from strip_examples import generate_spy_files
 
-    generate_spy_files(os.path.abspath('tests'))
+    generate_spy_files(os.path.abspath('src'))
     generate_spy_files(
         os.path.abspath(os.path.join('library_reference', 'kernel', 'examples'))
     )

doc/OnlineDocs/contributed_packages/doe/doe.rst

@@ -266,7 +266,7 @@ It allows users to define any number of design decisions. Heatmaps can be drawn
 The function ``run_grid_search`` enumerates over the design space, each MBDoE problem accomplished by ``compute_FIM`` method.
 Therefore, ``run_grid_search`` supports only two modes: ``sequential_finite`` and ``direct_kaug``.
 
-.. literalinclude:: ../../../../pyomo/contrib/doe/examples/reactor_compute_FIM.py 
+.. literalinclude:: ../../../../pyomo/contrib/doe/examples/reactor_grid_search.py 
     :language: python 
     :pyobject: main
 
@@ -284,7 +284,7 @@ Pyomo.DoE accomplishes gradient-based optimization with the ``stochastic_program
 
 This function solves twice: It solves the square version of the MBDoE problem first, and then unfixes the design variables as degree of freedoms and solves again. In this way the optimization problem can be well initialized.
 
-.. literalinclude:: ../../../../pyomo/contrib/doe/examples/reactor_compute_FIM.py 
+.. literalinclude:: ../../../../pyomo/contrib/doe/examples/reactor_optimize_doe.py 
     :language: python 
     :pyobject: main 
 

doc/OnlineDocs/contributed_packages/gdpopt.rst

@@ -175,7 +175,10 @@ To use the GDPopt-LBB solver, define your Pyomo GDP model as usual:
   >>> m.djn = Disjunction(expr=[m.y1, m.y2])
 
   Invoke the GDPopt-LBB solver
+
   >>> results = SolverFactory('gdpopt.lbb').solve(m)
+  WARNING: 09/06/22: The GDPopt LBB algorithm currently has known issues. Please
+      use the results with caution and report any bugs!
 
   >>> print(results)  # doctest: +SKIP
   >>> print(results.solver.status)

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/developer_reference/expressions/design.rst

@@ -73,7 +73,7 @@ Expression trees can be categorized in four different ways:
 
 These three categories are illustrated with the following example:
 
-.. literalinclude:: ../../tests/expr/design_categories.spy
+.. literalinclude:: ../../src/expr/design_categories.spy
 
 The following table describes four different simple expressions
 that consist of a single model component, and it shows how they
@@ -107,7 +107,7 @@ Named expressions allow for changes to an expression after it has
 been constructed.  For example, consider the expression ``f`` defined
 with the :class:`Expression <pyomo.core.base.Expression>` component:
 
-.. literalinclude:: ../../tests/expr/design_named_expression.spy
+.. literalinclude:: ../../src/expr/design_named_expression.spy
 
 Although ``f`` is an immutable expression, whose definition is
 fixed, a sub-expressions is the named expression ``M.e``.  Named
@@ -227,7 +227,7 @@ The :data:`linear_expression <pyomo.core.expr.linear_expression>`
 object is a context manager that can be used to declare a linear sum.  For
 example, consider the following two loops:
 
-.. literalinclude:: ../../tests/expr/design_cm1.spy
+.. literalinclude:: ../../src/expr/design_cm1.spy
 
 The first apparent difference in these loops is that the value of
 ``s`` is explicitly initialized while ``e`` is initialized when the
@@ -250,7 +250,7 @@ construct different expressions with different context declarations.
 Finally, note that these context managers can be passed into the :attr:`start`
 method for the :func:`quicksum <pyomo.core.util.quicksum>` function.  For example:
 
-.. literalinclude:: ../../tests/expr/design_cm2.spy
+.. literalinclude:: ../../src/expr/design_cm2.spy
 
 This sum contains terms for ``M.x[i]`` and ``M.y[i]``.  The syntax
 in this example is not intuitive because the sum is being stored

doc/OnlineDocs/developer_reference/expressions/index.rst

@@ -21,7 +21,7 @@ nodes contain operators.  Pyomo relies on so-called magic methods
 to automate the construction of symbolic expressions.  For example,
 consider an expression ``e`` declared as follows:
 
-.. literalinclude:: ../../tests/expr/index_simple.spy
+.. literalinclude:: ../../src/expr/index_simple.spy
 
 Python determines that the magic method ``__mul__`` is called on
 the ``M.v`` object, with the argument ``2``.  This method returns