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

…alerror
Robbybp · Sep 15, 2023 · 7c2a4b1 · 7c2a4b1
2 parents ddc60d7 + 376a2f7
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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>6.6.1</stableVersionNumber>
-			<releaseNumber>6.6.1</releaseNumber>
+			<stableVersionNumber>6.6.2</stableVersionNumber>
+			<releaseNumber>6.6.2</releaseNumber>
 
 		</developmentStatus>
 

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,3 +1,12 @@
+<!-- ##################################################################### -->
+<!-- PLEASE READ BEFORE OPENING THIS PULL REQUEST -->
+
+<!-- All changes must adhere to PEP8 standards as enforced by Black. -->
+<!-- If your changes do NOT adhere, the test suite will fail. -->
+<!-- Please read our Contributing guide for instructions on how to apply these standards. -->
+<!-- Contributing Guide: https://pyomo.readthedocs.io/en/stable/contribution_guide.html -->
+<!-- ##################################################################### -->
+
 ## Fixes # .
 
 ## Summary/Motivation:

diff --git a/.github/workflows/test_branches.yml b/.github/workflows/test_branches.yml
@@ -133,18 +133,6 @@ jobs:
         echo "PYTHON_PACKAGES=$PYTHON_PACKAGES" \
             | tr '\n' ' ' | sed 's/ \+/ /g' >> $GITHUB_ENV
 
-    # Ideally we would cache the conda downloads; however, each cache is
-    # over 850MB, and with 5 python versions, that would consume 4.2 of
-    # the 5 GB GitHub allows.
-    #
-    #- name: Conda package cache
-    #  uses: actions/cache@v3
-    #  if: matrix.PYENV == 'conda'
-    #  id: conda-cache
-    #  with:
-    #    path: cache/conda
-    #    key: conda-${{env.CACHE_VER}}.0-${{runner.os}}-${{matrix.python}}
-
     #- name: Pip package cache
     #  uses: actions/cache@v3
     #  if: matrix.PYENV == 'pip'
@@ -222,10 +210,8 @@ jobs:
       if: matrix.PYENV == 'conda'
       uses: conda-incubator/setup-miniconda@v2
       with:
-        auto-update-conda: true
+        auto-update-conda: false
         python-version: ${{ matrix.python }}
-        channels: conda-forge,gurobi,ibmdecisionoptimization,fico-xpress
-        channel-priority: strict
 
     # GitHub actions is very fragile when it comes to setting up various
     # Python interpreters, expecially the setup-miniconda interface.
@@ -283,16 +269,22 @@ jobs:
       if: matrix.PYENV == 'conda'
       run: |
         # Set up environment
-        mkdir -p $GITHUB_WORKSPACE/cache/conda
         conda config --set always_yes yes
         conda config --set auto_update_conda false
-        conda config --prepend pkgs_dirs $GITHUB_WORKSPACE/cache/conda
+        conda config --remove channels defaults
+        conda config --append channels nodefaults
+        conda config --append channels conda-forge
         # Try to install mamba
-        conda install -q -y -n base conda-libmamba-solver || MAMBA_FAILED=1
+        conda install --update-deps -q -y -n base conda-libmamba-solver \
+            || MAMBA_FAILED=1
         if test -z "$MAMBA_FAILED"; then
             echo "*** Activating the mamba environment solver ***"
             conda config --set solver libmamba
         fi
+        # Add the rest of the channels
+        conda config --append channels gurobi
+        conda config --append channels ibmdecisionoptimization
+        conda config --append channels fico-xpress
         # Print environment info
         echo "*** CONDA environment: ***"
         conda info
@@ -326,7 +318,7 @@ jobs:
             fi
         done
         echo "*** Install Pyomo dependencies ***"
-        conda install -q -y $CONDA_DEPENDENCIES
+        conda install --update-deps -q -y $CONDA_DEPENDENCIES
         if test -z "${{matrix.slim}}"; then
             echo "*** Install CPLEX ***"
             conda install -q -y 'cplex>=12.10' docplex \

diff --git a/.github/workflows/test_pr_and_main.yml b/.github/workflows/test_pr_and_main.yml
@@ -159,18 +159,6 @@ jobs:
         echo "PYTHON_PACKAGES=$PYTHON_PACKAGES" \
             | tr '\n' ' ' | sed 's/ \+/ /g' >> $GITHUB_ENV
 
-    # Ideally we would cache the conda downloads; however, each cache is
-    # over 850MB, and with 5 python versions, that would consume 4.2 of
-    # the 5 GB GitHub allows.
-    #
-    #- name: Conda package cache
-    #  uses: actions/cache@v3
-    #  if: matrix.PYENV == 'conda'
-    #  id: conda-cache
-    #  with:
-    #    path: cache/conda
-    #    key: conda-${{env.CACHE_VER}}.0-${{runner.os}}-${{matrix.python}}
-
     #- name: Pip package cache
     #  uses: actions/cache@v3
     #  if: matrix.PYENV == 'pip'
@@ -248,10 +236,8 @@ jobs:
       if: matrix.PYENV == 'conda'
       uses: conda-incubator/setup-miniconda@v2
       with:
-        auto-update-conda: true
+        auto-update-conda: false
         python-version: ${{ matrix.python }}
-        channels: conda-forge,gurobi,ibmdecisionoptimization,fico-xpress
-        channel-priority: strict
 
     # GitHub actions is very fragile when it comes to setting up various
     # Python interpreters, expecially the setup-miniconda interface.
@@ -309,16 +295,22 @@ jobs:
       if: matrix.PYENV == 'conda'
       run: |
         # Set up environment
-        mkdir -p $GITHUB_WORKSPACE/cache/conda
         conda config --set always_yes yes
         conda config --set auto_update_conda false
-        conda config --prepend pkgs_dirs $GITHUB_WORKSPACE/cache/conda
+        conda config --remove channels defaults
+        conda config --append channels nodefaults
+        conda config --append channels conda-forge
         # Try to install mamba
-        conda install -q -y -n base conda-libmamba-solver || MAMBA_FAILED=1
+        conda install --update-deps -q -y -n base conda-libmamba-solver \
+            || MAMBA_FAILED=1
         if test -z "$MAMBA_FAILED"; then
             echo "*** Activating the mamba environment solver ***"
             conda config --set solver libmamba
         fi
+        # Add the rest of the channels
+        conda config --append channels gurobi
+        conda config --append channels ibmdecisionoptimization
+        conda config --append channels fico-xpress
         # Print environment info
         echo "*** CONDA environment: ***"
         conda info
@@ -352,7 +344,7 @@ jobs:
             fi
         done
         echo "*** Install Pyomo dependencies ***"
-        conda install -q -y $CONDA_DEPENDENCIES
+        conda install --update-deps -q -y $CONDA_DEPENDENCIES
         if test -z "${{matrix.slim}}"; then
             echo "*** Install CPLEX ***"
             conda install -q -y 'cplex>=12.10' docplex \

diff --git a/.github/workflows/typos.toml b/.github/workflows/typos.toml
@@ -38,4 +38,6 @@ caf = "caf"
 WRONLY = "WRONLY"
 # Ignore the name Hax
 Hax = "Hax"
+# Big Sur
+Sur = "Sur"
 # AS NEEDED: Add More Words Below
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,78 @@ Pyomo CHANGELOG
 ===============
 
 
+-------------------------------------------------------------------------------
+Pyomo 6.6.2   (23 Aug 2023)
+-------------------------------------------------------------------------------
+
+ADVANCE CHANGE NOTICE
+  - This will be the last release to support Python 3.7.
+
+- General
+  - Fall back on `multiprocessing.dummy` when `multiprocessing.Pool` is not
+    available (#2890)
+  - Clean up implicit function imports (#2892)
+  - Ensure all pyomo modules import without warnings (#2897)
+  - Resolve `FileDownloader.get_os_version` exception for missing
+    `lsb_release` (#2911)
+  - Improve `calculate_variable_from_constraint` error messages (#2914)
+  - Add function for collecting expressions with unit inconsistencies (#2904)
+  - Fix loading Scalar Param from `.dat` file (#2923)
+- Core
+  - Resolve kernel pickle/clone errors (#2916)
+  - Reorganize numeric expression modules (#2909)
+  - Resolve error categorizing some Var discrete domains as "integer" (#2954)
+  - Named expressions: `expr` should always return `NumericValue` (#2948)
+  - Support kwargs in partial objects passed to Initializer() (#2960)
+  - Remove `expr.current` (#2910)
+- Documentation
+  - Fixing a 'that' vs. 'which' mistake in error about bounds crossing (#2950)
+  - Add Explicit Linting Instructions to PR Template (#2947)
+  - Update `pyomo.common` documentation (#2912)
+  - Remove HTML4 Forcing in Online Docs (#2949)
+  - Improved documentation for SOS (#2875)
+  - Silence deprecation warnings (#2854)
+- Solvers Interfaces
+  - Resolve handling of `{}**0` in Linear/QuadraticRepn (#2857)
+  - Fix Linear/QuadraticRepnVisitor handling of `{}**{float}` (#2863, #2865)
+  - GAMS: fix pickling models, update tests (#2913)
+  - Xpress: fix NLP results processing for Xpress 9.2.0 (#2921)
+  - Improve NaN handling in LP, NL writers (#2930)
+  - Ensure constants written correctly to LP/NL files (#2953)
+- Testing
+  - Remove the 'singletest' job from "branches" builds (#2917)
+  - Reactivate NEOS-MOSEK Tests (#2870)
+  - New version of `crate-ci/typos` GitHub Actions (#2869, #2931)
+- DAE
+  - Improve error message when attempting to discretize models with circular
+    references (#2943)
+- GDP
+  - Fixing a typo in gdp.hull transformation (#2915)
+  - Add some more instances to the GDP constrained layout example (#2838)
+  - Adding (reversible) `gdp.transform_current_disjunctive_logic`
+    transformation (#2809)
+- Contributed Packages
+  - APPSI: change default behavior to not care where variables live (#2903)
+  - APPSI: Correctly Process Objective Bounds from Gurobi for Nonconvex QCPs
+    (#2898)
+  - community_detection: fix networkx dependency in doctests (#2885)
+  - cp: Fix bug with `land` in `contrib.logical_to_disjunctive` transformation
+    (#2879)
+  - DoE: Update tutorial notebook (#2889)
+  - incidence_analysis: Filter variables with non-constant, fixed expressions
+    that resolve to zero in `get_incident_variables` (#2882)
+  - incidence_analysis: Correct behavior of `linear_only` argument in
+    `get_incident_variables` (#2883)
+  - MindtPy: Refactor to improve extensibility and maintainability (#2887)
+  - PyNumero: Add `PyNumeroEvaluationError` (#2901)
+  - PyNumero: Make min and max work with MPIBlockVector when some blocks have
+    size 0 (#2896)
+  - PyNumero: Remove old, unused PyNumero code (#2895)
+  - PyNumero: Fix typo in docstring (#2873)
+  - sensitivity_toolbox: Send lists to `numpy.vstack` rather than iterators
+    (#2881)
+  - viewer: Fix model viewer (#2924)
+
 -------------------------------------------------------------------------------
 Pyomo 6.6.1    (30 May 2023)
 -------------------------------------------------------------------------------

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,31 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - name: "Pyomo contributors"
+title: "Pyomo: a Python-based, open-source optimization modeling language with a diverse set of optimization capabilities"
+url: "https://github.com/Pyomo/pyomo"
+license-url: "https://github.com/Pyomo/pyomo/blob/main/LICENSE.md"
+preferred-citation:
+  type: book
+  authors:
+    - family-names: "Bynum"
+      given-names: "Michael L"
+    - family-names: "Hackebeil"
+      given-names: "Gabriel A"
+    - family-names: "Hart"
+      given-names: "William E"
+    - family-names: "Laird"
+      given-names: "Carl D"
+    - family-names: "Nicholson"
+      given-names: "Bethany L"
+    - family-names: "Siirola"
+      given-names: "John D"
+    - family-names: "Watson"
+      given-names: "Jean-Paul"
+    - family-names: "Woodruff"
+      given-names: "David L"
+  title: "Pyomo - optimization modeling in Python, 3rd Edition"
+  publisher: "Springer"
+  volume: 67
+  year: 2021
+  doi: "10.1007/978-3-030-68928-5"
diff --git a/RELEASE.md b/RELEASE.md
@@ -1,4 +1,4 @@
-We are pleased to announce the release of Pyomo 6.6.1.
+We are pleased to announce the release of Pyomo 6.6.2.
 
 Pyomo is a collection of Python software packages that supports a
 diverse set of optimization capabilities for formulating and analyzing

diff --git a/doc/OnlineDocs/conf.py b/doc/OnlineDocs/conf.py
@@ -146,13 +146,6 @@
 
 html_theme = 'sphinx_rtd_theme'
 
-# Force HTML4: If we don't explicitly force HTML4, then the background
-# of the Parameters/Returns/Return type headers is shaded the same as the
-# method prototype (tested 15 April 21 with Sphinx=3.5.4 and
-# sphinx-rtd-theme=0.5.2).
-html4_writer = True
-# html5_writer = True
-
 if not on_rtd:  # only import and set the theme if we're building docs locally
     import sphinx_rtd_theme
 

diff --git a/doc/OnlineDocs/contributed_packages/incidence/overview.rst b/doc/OnlineDocs/contributed_packages/incidence/overview.rst
@@ -32,15 +32,19 @@ from Bethany Nicholson and John Siirola at Sandia.
 How can I cite Incidence Analysis?
 ----------------------------------
 
-We are working on a journal article about Incidence Analysis and the underlying
-methods. In the meantime, if you use Incidence Analysis in your research, you
-may cite the following conference paper:
+If you use Incidence Analysis in your research, we would appreciate you citing
+the following paper:
 
 .. code-block:: bibtex
 
-    @inproceedings{Parker2023Dulmage,
-      title={{An application of the Dulmage-Mendelsohn partition to the analysis of a discretized dynamic chemical looping combustion reactor model}},
-      author={Robert Parker and Chinedu Okoli and Bethany Nicholson and John Siirola and Lorenz Biegler},
-      booktitle={Proceedings of FOCAPO/CPC 2023},
-      year={2023}
+    @article{parker2023dulmage,
+    title = {Applications of the {Dulmage-Mendelsohn} decomposition for debugging nonlinear optimization problems},
+    journal = {Computers \& Chemical Engineering},
+    volume = {178},
+    pages = {108383},
+    year = {2023},
+    issn = {0098-1354},
+    doi = {https://doi.org/10.1016/j.compchemeng.2023.108383},
+    url = {https://www.sciencedirect.com/science/article/pii/S0098135423002533},
+    author = {Robert B. Parker and Bethany L. Nicholson and John D. Siirola and Lorenz T. Biegler},
     }