Merge branch 'main' into RPB_MBDOE

jialuw96 · May 28, 2024 · 655c0e6 · 655c0e6
2 parents ac10aad + 0e749d0
commit 655c0e6
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diff --git a/.coin-or/projDesc.xml b/.coin-or/projDesc.xml
@@ -227,8 +227,8 @@ Carl D. Laird, Chair, Pyomo Management Committee, claird at andrew dot cmu dot e
 			     Use explicit overrides to disable use of automated
 			     version reporting.
 			-->
-			<stableVersionNumber>6.7.1</stableVersionNumber>
-			<releaseNumber>6.7.1</releaseNumber>
+			<stableVersionNumber>6.7.2</stableVersionNumber>
+			<releaseNumber>6.7.2</releaseNumber>
 
 		</developmentStatus>
 

diff --git a/.github/workflows/test_branches.yml b/.github/workflows/test_branches.yml
@@ -47,6 +47,20 @@ jobs:
       uses: crate-ci/typos@master
       with: 
         config: ./.github/workflows/typos.toml
+    - name: URL Checker
+      uses: urlstechie/[email protected]
+      with:
+        # A comma-separated list of file types to cover in the URL checks
+        file_types: .md,.rst,.py
+        # Choose whether to include file with no URLs in the prints.
+        print_all: false
+        # More verbose summary at the end of a run
+        verbose: true
+        # How many times to retry a failed request (defaults to 1)
+        retry_count: 3
+        # Exclude Jenkins because it's behind a firewall; ignore RTD because
+        # a magically-generated string is triggering a failure
+        exclude_urls: https://pyomo-jenkins.sandia.gov/,https://pyomo.readthedocs.io/en/%s/errors.html
 
 
   build:
@@ -181,7 +195,7 @@ jobs:
         # Notes:
         #  - install glpk
         #  - pyodbc needs: gcc pkg-config unixodbc freetds
-        for pkg in bash pkg-config unixodbc freetds glpk; do
+        for pkg in bash pkg-config unixodbc freetds glpk ginac; do
             brew list $pkg || brew install $pkg
         done
 
@@ -193,7 +207,8 @@ jobs:
         #  - install glpk
         #  - ipopt needs: libopenblas-dev gfortran liblapack-dev
         sudo apt-get -o Dir::Cache=${GITHUB_WORKSPACE}/cache/os \
-            install libopenblas-dev gfortran liblapack-dev glpk-utils
+            install libopenblas-dev gfortran liblapack-dev glpk-utils \
+            libginac-dev
         sudo chmod -R 777 ${GITHUB_WORKSPACE}/cache/os
 
     - name: Update Windows
@@ -264,7 +279,7 @@ 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 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"
@@ -339,7 +354,7 @@ jobs:
         echo "*** Install Pyomo dependencies ***"
         # Note: this will fail the build if any installation fails (or
         # possibly if it outputs messages to stderr)
-        conda install --update-deps -y $CONDA_DEPENDENCIES
+        conda install --update-deps -q -y $CONDA_DEPENDENCIES
         if test -z "${{matrix.slim}}"; then
             PYVER=$(echo "py${{matrix.python}}" | sed 's/\.//g')
             echo "Installing for $PYVER"

diff --git a/.github/workflows/test_pr_and_main.yml b/.github/workflows/test_pr_and_main.yml
@@ -57,6 +57,20 @@ jobs:
       uses: crate-ci/typos@master
       with: 
         config: ./.github/workflows/typos.toml
+    - name: URL Checker
+      uses: urlstechie/[email protected]
+      with:
+        # A comma-separated list of file types to cover in the URL checks
+        file_types: .md,.rst,.py
+        # Choose whether to include file with no URLs in the prints.
+        print_all: false
+        # More verbose summary at the end of a run
+        verbose: true
+        # How many times to retry a failed request (defaults to 1)
+        retry_count: 3
+        # Exclude Jenkins because it's behind a firewall; ignore RTD because
+        # a magically-generated string is triggering a failure
+        exclude_urls: https://pyomo-jenkins.sandia.gov/,https://pyomo.readthedocs.io/en/%s/errors.html
 
 
   build:
@@ -218,7 +232,7 @@ jobs:
         # Notes:
         #  - install glpk
         #  - pyodbc needs: gcc pkg-config unixodbc freetds
-        for pkg in bash pkg-config unixodbc freetds glpk; do
+        for pkg in bash pkg-config unixodbc freetds glpk ginac; do
             brew list $pkg || brew install $pkg
         done
 
@@ -230,7 +244,8 @@ jobs:
         #  - install glpk
         #  - ipopt needs: libopenblas-dev gfortran liblapack-dev
         sudo apt-get -o Dir::Cache=${GITHUB_WORKSPACE}/cache/os \
-            install libopenblas-dev gfortran liblapack-dev glpk-utils
+            install libopenblas-dev gfortran liblapack-dev glpk-utils \
+            libginac-dev
         sudo chmod -R 777 ${GITHUB_WORKSPACE}/cache/os
 
     - name: Update Windows
@@ -372,6 +387,7 @@ jobs:
                 CONDA_DEPENDENCIES="$CONDA_DEPENDENCIES $PKG"
             fi
         done
+        echo ""
         echo "*** Install Pyomo dependencies ***"
         # Note: this will fail the build if any installation fails (or
         # possibly if it outputs messages to stderr)

diff --git a/.jenkins.sh b/.jenkins.sh
@@ -43,9 +43,6 @@ fi
 if test -z "$SLIM"; then
     export VENV_SYSTEM_PACKAGES='--system-site-packages'
 fi
-if test ! -z "$CATEGORY"; then
-    export PY_CAT="-m $CATEGORY"
-fi
 
 if test "$WORKSPACE" != "`pwd`"; then
     echo "ERROR: pwd is not WORKSPACE"
@@ -122,10 +119,23 @@ if test -z "$MODE" -o "$MODE" == setup; then
     echo "PYOMO_CONFIG_DIR=$PYOMO_CONFIG_DIR"
     echo ""
 
+    # Call Pyomo build scripts to build TPLs that would normally be
+    # skipped by the pyomo download-extensions / build-extensions
+    # actions below
+    if [[ " $CATEGORY " == *" builders "* ]]; then
+        echo ""
+        echo "Running local build scripts..."
+        echo ""
+        set -x
+        python pyomo/contrib/simplification/build.py --build-deps || exit 1
+        set +x
+    fi
+
     # Use Pyomo to download & compile binary extensions
     i=0
     while /bin/true; do
         i=$[$i+1]
+        echo ""
         echo "Downloading pyomo extensions (attempt $i)"
         pyomo download-extensions $PYOMO_DOWNLOAD_ARGS
         if test $? == 0; then
@@ -178,7 +188,7 @@ if test -z "$MODE" -o "$MODE" == test; then
     python -m pytest -v \
         -W ignore::Warning \
         --junitxml="TEST-pyomo.xml" \
-        $PY_CAT $TEST_SUITES $PYTEST_EXTRA_ARGS
+        -m "$CATEGORY" $TEST_SUITES $PYTEST_EXTRA_ARGS
 
     # Combine the coverage results and upload
     if test -z "$DISABLE_COVERAGE"; then

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,81 @@ Pyomo CHANGELOG
 ===============
 
 
+-------------------------------------------------------------------------------
+Pyomo 6.7.2   (9 May 2024)
+-------------------------------------------------------------------------------
+
+- General
+  - Support config domains with either method or attribute domain_name (#3159)
+  - Automate TPL callback registrations (#3167)
+  - Fix type registrations for ExternalFunction arguments (#3168)
+  - Only modify module path and spec for deferred import modules (#3176)
+  - Add "mixed" standard form representation (#3201)
+  - Support "default" dispatchers in `ExitNodeDispatcher` (#3194)
+  - Redefine objective sense as a proper `IntEnum` (#3224)
+  - Fix division-by-0 bug in linear walker (#3246)
+- Core
+  - Allow `Var` objects in `LinearExpression.args` (#3189)
+  - Add type hints to components (#3173)
+  - Simplify expressions generated by `TemplateSumExpression` (#3196)
+  - Make component data public classes (#3221, #3253)
+  - Exploit repeated named expressions in `identify_variables` (#3190)
+- Documentation
+  - NFC: Add link to the HOMOWP companion notebooks (#3195)
+  - Update installation documentation to include Cython instructions (#3208)
+  - Add links to the Pyomo Book Springer page (#3211)
+- Solver Interfaces
+  - Fix division by zero error in linear presolve (#3161)
+  - Subprocess timeout update (#3183)
+  - Solver Refactor - Bug fixes for various components (#3181, #3214, #3228)
+  - NLv2: handle presolved independent linear subsystems (#3193)
+  - Update `LegacySolverWrapper` compatibility with the `pyomo` script (#3202)
+  - Fix mosek_direct to use putqconk instead of putqcon (#3199)
+  - Check _skip_trivial_constraints before the constraint body (#3226)
+  - Fix AMPL solver duplicate funcadd (#3206)
+  - Disable the use of universal newlines in the ipopt_v2 NL file (#3231)
+  - NLv2: fix reporting numbers of nonlinear discrete variables (#3238)
+  - Fix: Get SCIP solving time considering float number with some text (#3234)
+  - Solver Refactor - Add `gurobi_direct` implementation (#3225)
+- Testing
+  - Update TPL package list due to `contrib.solver` (#3164)
+  - Set maxDiff=None on the base TestCase class (#3171)
+  - Testing infrastructure updates (#3175)
+  - Typos update for March 2024 (#3219)
+  - Add openmpi to testing environment to resolve issue in mpi4py (#3236, #3239)
+  - Skip black 24.4.1 due to a bug in the parser (#3247)
+  - Skip tests on draft and WIP pull requests (#3223)
+  - Update GHA to grab gurobipy from PyPI (#3254)
+- GDP
+  - Use private_data for all original / transformed component mappings (#3166)
+  - Fix a bug in gdp.bigm transformation for nested GDPs (#3213)
+- Contributed Packages
+  - APPSI: cmodel: handle non-mutable params in var / constraint bounds (#3182)
+  - APPSI: Allow APPSI FBBT to handle nested named Expressions (#3185)
+  - APPSI: Add MAiNGO solver interface (#3165)
+  - CP: Add SequenceVar and other logical expressions for scheduling (#3227)
+  - DoE: Bug fixes (#3245)
+  - iis: Add minimal intractable system infeasibility diagnostics (#3172)
+  - incidence_analysis: Improve `solve_strongly_connected_components` 
+    performance for models with named expressions (#3186)
+  - incidence_analysis: Add function to plot incidence graph in
+    Dulmage-Mendelsohn order (#3207)
+  - incidence_analysis: Require variables and constraints to be specified
+    separately in `IncidenceGraphInterface.remove_nodes` (#3212)
+  - latex_printer: bugfix for set operations / multidimensional sets (#3177)
+  - MindtPy: Add HiGHS support (#2971)
+  - MindtPy: Add call_before_subproblem_solve callback (#3251)
+  - Parmest: New UI using experiment lists (#3160)
+  - piecewise: Add piecewise linear transformations (#3036)
+  - preprocessing: bugfix: intersect domains in variable aggregator (#3241)
+  - PyNumero: Allow CyIpopt to solve problems without objectives (#3163)
+  - PyNumero: Work around bug in CyIpopt 1.4.0 (#3222)
+  - PyNumero: Include "inventory" in readme (#3248)
+  - PyROS: Simplify custom domain validators (#3169)
+  - PyROS: Fix iteration logging for edge case involving discrete sets  (#3170)
+  - PyROS: Update solver timing system (#3198)
+  - simplification: expression simplification using GiNaC or SymPy (#3088)
+
 -------------------------------------------------------------------------------
 Pyomo 6.7.1   (21 Feb 2024)
 -------------------------------------------------------------------------------

diff --git a/RELEASE.md b/RELEASE.md
@@ -1,4 +1,4 @@
-We are pleased to announce the release of Pyomo 6.7.1.
+We are pleased to announce the release of Pyomo 6.7.2.
 
 Pyomo is a collection of Python software packages that supports a
 diverse set of optimization capabilities for formulating and analyzing
@@ -10,9 +10,14 @@ The following are highlights of the 6.7 release series:
  - Removed support for Python 3.7
  - New writer for converting linear models to matrix form
  - Improved handling of nested GDPs
+ - Redesigned user API for parameter estimation
  - New packages:
-    - latex_printer (print Pyomo models to a LaTeX compatible format)
+    - iis: new capability for identifying minimal intractable systems
+    - latex_printer: print Pyomo models to a LaTeX compatible format
     - contrib.solver: preview of redesigned solver interfaces
+    - simplification: simplify Pyomo expressions
+ - New solver interfaces
+    - MAiNGO: Mixed-integer nonlinear global optimization
  - ...and of course numerous minor bug fixes and performance enhancements
 
 A full list of updates and changes is available in the

diff --git a/conftest.py b/conftest.py
@@ -11,6 +11,22 @@
 
 import pytest
 
+_implicit_markers = {'default'}
+_extended_implicit_markers = _implicit_markers.union({'solver'})
+
+
+def pytest_collection_modifyitems(items):
+    """
+    This method will mark any unmarked tests with the implicit marker ('default')
+
+    """
+    for item in items:
+        try:
+            next(item.iter_markers())
+        except StopIteration:
+            for marker in _implicit_markers:
+                item.add_marker(getattr(pytest.mark, marker))
+
 
 def pytest_runtest_setup(item):
     """
@@ -32,23 +48,20 @@ def pytest_runtest_setup(item):
     the default mode; but if solver tests are also marked with an explicit
     category (e.g., "expensive"), we will skip them.
     """
-    marker = item.iter_markers()
     solvernames = [mark.args[0] for mark in item.iter_markers(name="solver")]
     solveroption = item.config.getoption("--solver")
     markeroption = item.config.getoption("-m")
-    implicit_markers = ['default']
-    extended_implicit_markers = implicit_markers + ['solver']
-    item_markers = set(mark.name for mark in marker)
+    item_markers = set(mark.name for mark in item.iter_markers())
     if solveroption:
         if solveroption not in solvernames:
             pytest.skip("SKIPPED: Test not marked {!r}".format(solveroption))
             return
     elif markeroption:
         return
     elif item_markers:
-        if not set(implicit_markers).issubset(
-            item_markers
-        ) and not item_markers.issubset(set(extended_implicit_markers)):
+        if not _implicit_markers.issubset(item_markers) and not item_markers.issubset(
+            _extended_implicit_markers
+        ):
             pytest.skip('SKIPPED: Only running default, solver, and unmarked tests.')
 
 

diff --git a/doc/OnlineDocs/contributed_packages/pynumero/pynumero.sparse.block_vector.rst b/doc/OnlineDocs/contributed_packages/pynumero/pynumero.sparse.block_vector.rst
@@ -77,7 +77,7 @@ NumPy compatible functions:
   * `numpy.arccos() <https://numpy.org/doc/stable/reference/generated/numpy.arccos.html>`_
   * `numpy.sinh() <https://numpy.org/doc/stable/reference/generated/numpy.sinh.html>`_
   * `numpy.cosh() <https://numpy.org/doc/stable/reference/generated/numpy.cosh.html>`_
-  * `numpy.abs() <https://numpy.org/doc/stable/reference/generated/numpy.abs.html>`_
+  * `numpy.abs() <https://numpy.org/doc/stable/reference/generated/numpy.absolute.html>`_
   * `numpy.tanh() <https://numpy.org/doc/stable/reference/generated/numpy.tanh.html>`_
   * `numpy.arccosh() <https://numpy.org/doc/stable/reference/generated/numpy.arccosh.html>`_
   * `numpy.arcsinh() <https://numpy.org/doc/stable/reference/generated/numpy.arcsinh.html>`_

diff --git a/doc/OnlineDocs/contribution_guide.rst b/doc/OnlineDocs/contribution_guide.rst
@@ -404,50 +404,10 @@ Contrib packages will be tested along with Pyomo.  If test failures
 arise, then these packages will be disabled and an issue will be
 created to resolve these test failures.
 
-The following two examples illustrate the two ways
-that ``pyomo.contrib`` can be used to integrate third-party
-contributions.
-
-Including External Packages
-+++++++++++++++++++++++++++
-
-The `pyomocontrib_simplemodel
-<http://pyomocontrib-simplemodel.readthedocs.io/en/latest/>`_ package
-is derived from Pyomo, and it defines the class SimpleModel that
-illustrates how Pyomo can be used in a simple, less object-oriented
-manner. Specifically, this class mimics the modeling style supported
-by `PuLP <https://github.com/coin-or/pulp>`_.
-
-While ``pyomocontrib_simplemodel`` can be installed and used separate
-from Pyomo, this package is included in ``pyomo/contrib/simplemodel``.
-This allows this package to be referenced as if were defined as a
-subpackage of ``pyomo.contrib``.  For example::
-
-    from pyomo.contrib.simplemodel import *
-    from math import pi
-
-    m = SimpleModel()
-
-    r = m.var('r', bounds=(0,None))
-    h = m.var('h', bounds=(0,None))
-
-    m += 2*pi*r*(r + h)
-    m += pi*h*r**2 == 355
-
-    status = m.solve("ipopt")
-
-This example illustrates that a package can be distributed separate
-from Pyomo while appearing to be included in the ``pyomo.contrib``
-subpackage.  Pyomo requires a separate directory be defined under
-``pyomo/contrib`` for each such package, and the Pyomo developer
-team will approve the inclusion of third-party packages in this
-manner.
-
-
 Contrib Packages within Pyomo
 +++++++++++++++++++++++++++++
 
-Third-party contributions can also be included directly within the
+Third-party contributions can be included directly within the
 ``pyomo.contrib`` package.  The ``pyomo/contrib/example`` package
 provides an example of how this can be done, including a directory
 for plugins and package tests.  For example, this package can be
@@ -465,7 +425,7 @@ import this package, but if an import failure occurs, Pyomo will
 silently ignore it.  Otherwise, this pyomo package will be treated
 like any other.  Specifically:
 
-* Plugin classes defined in this package are loaded when `pyomo.environ` is loaded.
+* Plugin classes defined in this package are loaded when ``pyomo.environ`` is loaded.
 
 * Tests in this package are run with other Pyomo tests.
 
diff --git a/doc/OnlineDocs/modeling_extensions/dae.rst b/doc/OnlineDocs/modeling_extensions/dae.rst
@@ -738,7 +738,7 @@ supported by CasADi. A list of available integrators for each package is
 given below. Please refer to the `SciPy
 <https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html>`_
 and `CasADi
-<http://casadi.sourceforge.net/api/html/db/d3d/classcasadi_1_1Integrator.html>`_ documentation directly for the most up-to-date information about
+<https://web.casadi.org/python-api/#integrator>`_ documentation directly for the most up-to-date information about
 these packages and for more information about the various integrators and
 options.