Merge branch 'main' into add_highs_support

.github/workflows/test_branches.yml

@@ -40,7 +40,8 @@ jobs:
         python-version: '3.10'
     - name: Black Formatting Check
       run: |
-        pip install black
+        # Note v24.4.1 fails due to a bug in the parser
+        pip install 'black!=24.4.1'
         black . -S -C --check --diff --exclude examples/pyomobook/python-ch/BadIndent.py
     - name: Spell Check
       uses: crate-ci/typos@master
@@ -92,7 +93,7 @@ jobs:
           skip_doctest: 1
           TARGET: linux
           PYENV: conda
-          PACKAGES: mpi4py==3.1.5
+          PACKAGES: openmpi mpi4py
 
         - os: ubuntu-latest
           python: '3.10'
@@ -263,8 +264,7 @@ jobs:
         if test -z "${{matrix.slim}}"; then
             python -m pip install --cache-dir cache/pip cplex docplex \
                 || echo "WARNING: CPLEX Community Edition is not available"
-            python -m pip install --cache-dir cache/pip \
-                -i https://pypi.gurobi.com gurobipy==10.0.3 \
+            python -m pip install --cache-dir cache/pip gurobipy==10.0.3\
                 || echo "WARNING: Gurobi is not available"
             python -m pip install --cache-dir cache/pip xpress \
                 || echo "WARNING: Xpress Community Edition is not available"

.github/workflows/test_pr_and_main.yml

@@ -7,6 +7,11 @@ on:
   pull_request:
     branches:
       - main
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
   workflow_dispatch:
     inputs:
       git-ref:
@@ -34,6 +39,8 @@ jobs:
   lint:
     name: lint/style-and-typos
     runs-on: ubuntu-latest
+    if: |
+      contains(github.event.pull_request.title, '[WIP]') != true && !github.event.pull_request.draft
     steps:
     - name: Checkout Pyomo source
       uses: actions/checkout@v4
@@ -43,7 +50,8 @@ jobs:
         python-version: '3.10'
     - name: Black Formatting Check
       run: |
-        pip install black
+        # Note v24.4.1 fails due to a bug in the parser
+        pip install 'black!=24.4.1'
         black . -S -C --check --diff --exclude examples/pyomobook/python-ch/BadIndent.py
     - name: Spell Check
       uses: crate-ci/typos@master
@@ -93,7 +101,7 @@ jobs:
           skip_doctest: 1
           TARGET: linux
           PYENV: conda
-          PACKAGES: mpi4py==3.1.5
+          PACKAGES: openmpi mpi4py
 
         - os: ubuntu-latest
           python: '3.11'
@@ -293,8 +301,7 @@ jobs:
         if test -z "${{matrix.slim}}"; then
             python -m pip install --cache-dir cache/pip cplex docplex \
                 || echo "WARNING: CPLEX Community Edition is not available"
-            python -m pip install --cache-dir cache/pip \
-                -i https://pypi.gurobi.com gurobipy==10.0.3 \
+            python -m pip install --cache-dir cache/pip gurobipy==10.0.3 \
                 || echo "WARNING: Gurobi is not available"
             python -m pip install --cache-dir cache/pip xpress \
                 || echo "WARNING: Xpress Community Edition is not available"
@@ -734,7 +741,7 @@ jobs:
   cover:
     name: process-coverage-${{ matrix.TARGET }}
     needs: build
-    if: always() # run even if a build job fails
+    if: success() || failure() # run even if a build job fails, but not if cancelled
     runs-on: ${{ matrix.os }}
     timeout-minutes: 10
     strategy:

.github/workflows/typos.toml

@@ -40,6 +40,9 @@ WRONLY = "WRONLY"
 Hax = "Hax"
 # Big Sur
 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

doc/OnlineDocs/conf.py

@@ -84,6 +84,7 @@
     'sphinx.ext.todo',
     'sphinx_copybutton',
     'enum_tools.autoenum',
+    'sphinx.ext.autosectionlabel',
     #'sphinx.ext.githubpages',
 ]
 

doc/OnlineDocs/contributed_packages/iis.rst

@@ -1,6 +1,135 @@
+Infeasibility Diagnostics
+!!!!!!!!!!!!!!!!!!!!!!!!!
+
+There are two closely related tools for infeasibility diagnosis:
+
+  - :ref:`Infeasible Irreducible System (IIS) Tool`
+  - :ref:`Minimal Intractable System finder (MIS) Tool`
+
+The first simply provides a conduit for solvers that compute an
+infeasible irreducible system (e.g., Cplex, Gurobi, or Xpress).  The
+second provides similar functionality, but uses the ``mis`` package
+contributed to Pyomo.
+
+
 Infeasible Irreducible System (IIS) Tool
 ========================================
 
 .. automodule:: pyomo.contrib.iis.iis
 
 .. autofunction:: pyomo.contrib.iis.write_iis
+
+Minimal Intractable System finder (MIS) Tool
+============================================
+
+The file ``mis.py`` finds sets of actions that each, independently,
+would result in feasibility.  The zero-tolerance is whatever the
+solver uses, so users may want to post-process output if it is going
+to be used for analysis. It also computes a minimal intractable system
+(which is not guaranteed to be unique).  It was written by Ben Knueven
+as part of the watertap project (https://github.com/watertap-org/watertap)
+and is therefore governed by a license shown
+at the top of ``mis.py``.
+
+The algorithms come from John Chinneck's slides, see: https://www.sce.carleton.ca/faculty/chinneck/docs/CPAIOR07InfeasibilityTutorial.pdf
+
+Solver
+------
+
+At the time of this writing, you need to use IPopt even for LPs.
+
+Quick Start
+-----------
+
+The file ``trivial_mis.py`` is a tiny example listed at the bottom of
+this help file, which references a Pyomo model with the Python variable
+`m` and has these lines:
+
+.. code-block:: python
+
+   from pyomo.contrib.mis import compute_infeasibility_explanation
+   ipopt = pyo.SolverFactory("ipopt")
+   compute_infeasibility_explanation(m, solver=ipopt)
+
+.. Note::
+   This is done instead of solving the problem.
+
+.. Note::
+   IDAES users can pass ``get_solver()`` imported from ``ideas.core.solvers``
+   as the solver.
+
+Interpreting the Output
+-----------------------
+
+Assuming the dependencies are installed, running ``trivial_mis.py``
+(shown below) will
+produce a lot of warnings from IPopt and then meaningful output (using a logger).
+
+Repair Options
+^^^^^^^^^^^^^^
+
+This output for the trivial example shows three independent ways that the model could be rendered feasible:
+
+
+.. code-block:: text
+   
+   Model Trivial Quad may be infeasible. A feasible solution was found with only the following variable bounds relaxed:
+	ub of var x[1] by 4.464126126706818e-05
+	lb of var x[2] by 0.9999553410114216
+   Another feasible solution was found with only the following variable bounds relaxed:
+	lb of var x[1] by 0.7071067726864677
+	ub of var x[2] by 0.41421355687130673
+	ub of var y by 0.7071067651855212
+   Another feasible solution was found with only the following inequality constraints, equality constraints, and/or variable bounds relaxed:
+	constraint: c by 0.9999999861866736
+
+
+Minimal Intractable System (MIS)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This output shows a minimal intractable system:
+
+
+.. code-block:: text
+
+   Computed Minimal Intractable System (MIS)!
+   Constraints / bounds in MIS:
+	lb of var x[2]
+	lb of var x[1]
+	constraint: c
+   
+Constraints / bounds in guards for stability
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This part of the report is for nonlinear programs (NLPs).
+
+When we’re trying to reduce the constraint set, for an NLP there may be constraints that when missing cause the solver 
+to fail in some catastrophic fashion. In this implementation this is interpreted as failing to get a `results` 
+object back from the call to `solve`. In these cases we keep the constraint in the problem but it’s in the 
+set of “guard” constraints – we can’t really be sure they’re a source of infeasibility or not, 
+just that “bad things” happen when they’re not included.
+
+Perhaps ideally we would put a constraint in the “guard” set if IPopt failed to converge, and only put it in the 
+MIS if IPopt converged to a point of local infeasibility. However, right now the code generally makes the 
+assumption that if IPopt fails to converge the subproblem is infeasible, though obviously that is far from the truth. 
+Hence for difficult NLPs even the “Phase 1” may “fail” – in that when finished the subproblem containing just the 
+constraints in the elastic filter may be feasible -- because IPopt failed to converge and we assumed that meant the 
+subproblem was not feasible.
+
+Dealing with NLPs is far from clean, but that doesn’t mean the tool can’t return useful results even when its assumptions are not satisfied.
+
+trivial_mis.py
+--------------
+
+.. code-block:: python
+
+   import pyomo.environ as pyo
+   m = pyo.ConcreteModel("Trivial Quad")
+   m.x = pyo.Var([1,2], bounds=(0,1))
+   m.y = pyo.Var(bounds=(0, 1))
+   m.c = pyo.Constraint(expr=m.x[1] * m.x[2] == -1)
+   m.d = pyo.Constraint(expr=m.x[1] + m.y >= 1)
+
+   from pyomo.contrib.mis import compute_infeasibility_explanation
+   ipopt = pyo.SolverFactory("ipopt")
+   compute_infeasibility_explanation(m, solver=ipopt)

doc/OnlineDocs/contributed_packages/pynumero/backward_compatibility.rst

@@ -0,0 +1,14 @@
+Backward Compatibility
+======================
+
+While PyNumero is a third-party contribution to Pyomo, we intend to maintain
+the stability of its core functionality. The core functionality of PyNumero
+consists of:
+
+1. The ``NLP`` API and ``PyomoNLP`` implementation of this API
+2. HSL and MUMPS linear solver interfaces
+3. ``BlockVector`` and ``BlockMatrix`` classes
+4. CyIpopt and SciPy solver interfaces
+
+Other parts of PyNumero, such as ``ExternalGreyBoxBlock`` and
+``ImplicitFunctionSolver``, are experimental and subject to change without notice.

doc/OnlineDocs/contributed_packages/pynumero/index.rst

@@ -13,6 +13,7 @@ PyNumero. For more details, see the API documentation (:ref:`pynumero_api`).
    installation.rst
    tutorial.rst
    api.rst
+   backward_compatibility.rst
 
 
 Developers

doc/OnlineDocs/contributed_packages/pyros.rst

@@ -903,10 +903,10 @@ Observe that the log contains the following information:
    :linenos:
 
    ==============================================================================
-   PyROS: The Pyomo Robust Optimization Solver, v1.2.9.
-          Pyomo version: 6.7.0
+   PyROS: The Pyomo Robust Optimization Solver, v1.2.11.
+          Pyomo version: 6.7.2
           Commit hash: unknown
-          Invoked at UTC 2023-12-16T00:00:00.000000
+          Invoked at UTC 2024-03-28T00:00:00.000000
 
    Developed by: Natalie M. Isenberg (1), Jason A. F. Sherman (1),
                  John D. Siirola (2), Chrysanthos E. Gounaris (1)
@@ -926,6 +926,7 @@ Observe that the log contains the following information:
     keepfiles=False
     tee=False
     load_solution=True
+    symbolic_solver_labels=False
     objective_focus=<ObjectiveType.worst_case: 1>
     nominal_uncertain_param_vals=[0.13248000000000001, 4.97, 4.97, 1800]
     decision_rule_order=1

doc/OnlineDocs/contribution_guide.rst

@@ -71,6 +71,10 @@ at least 70% coverage of the lines modified in the PR and prefer coverage
 closer to 90%. We also require that all tests pass before a PR will be 
 merged.
 
+.. note::
+   If you are having issues getting tests to pass on your Pull Request,
+   please tag any of the core developers to ask for help.
+
 The Pyomo main branch provides a Github Actions workflow (configured
 in the ``.github/`` directory) that will test any changes pushed to
 a branch with a subset of the complete test harness that includes
@@ -82,13 +86,16 @@ This will enable the tests to run automatically with each push to your fork.
 
 At any point in the development cycle, a "work in progress" pull request
 may be opened by including '[WIP]' at the beginning of the PR
-title. This allows your code changes to be tested by the full suite of
-Pyomo's automatic
-testing infrastructure. Any pull requests marked '[WIP]' will not be
+title. Any pull requests marked '[WIP]' or draft will not be
 reviewed or merged by the core development team. However, any
 '[WIP]' pull request left open for an extended period of time without
 active development may be marked 'stale' and closed.
 
+.. note::
+   Draft and WIP Pull Requests will **NOT** trigger tests. This is an effort to
+   reduce our CI backlog. Please make use of the provided
+   branch test suite for evaluating / testing draft functionality.
+
 Python Version Support
 ++++++++++++++++++++++
 

doc/OnlineDocs/library_reference/common/enums.rst

@@ -0,0 +1,7 @@
+
+pyomo.common.enums
+==================
+
+.. automodule:: pyomo.common.enums
+   :members:
+   :member-order: bysource

doc/OnlineDocs/library_reference/common/index.rst

@@ -11,6 +11,7 @@ or rely on any other parts of Pyomo.
    config.rst
    dependencies.rst
    deprecation.rst
+   enums.rst
    errors.rst
    fileutils.rst
    formatting.rst

examples/pyomobook/pyomo-components-ch/obj_declaration.txt

@@ -55,7 +55,7 @@ Model unknown
     None
 value
 x[Q] + 2*x[R]
-1
+minimize
 6.5
 Model unknown
 

pyomo/common/deprecation.py

@@ -542,7 +542,7 @@ def __renamed__warning__(msg):
 
         if new_class is None and '__renamed__new_class__' not in classdict:
             if not any(
-                hasattr(base, '__renamed__new_class__')
+                hasattr(mro, '__renamed__new_class__')
                 for mro in itertools.chain.from_iterable(
                     base.__mro__ for base in renamed_bases
                 )