Merge remote-tracking branch 'emma_pyomo/add-accidental-formulation' …

…into bashar_pwl
bammari · Sep 29, 2024 · 8e45d4b · 8e45d4b
2 parents 55941c1 + 5d023cd
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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>6.7.3</stableVersionNumber>
-			<releaseNumber>6.7.3</releaseNumber>
+			<stableVersionNumber>6.8.0</stableVersionNumber>
+			<releaseNumber>6.8.0</releaseNumber>
 
 		</developmentStatus>
 

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -4,6 +4,8 @@ about: Report a bug in Pyomo (command not working as expected, etc.)
 labels: "bug"
 ---
 
+<!-- DO NOT DELETE OR IGNORE THIS TEMPLATE.  Failing to adhere to this template and provide the necessary information may lead to your Issue being closed without consideration. -->
+
 ## Summary
 
 <!-- Explain, in a clear and concise way, the command you ran and the result you were trying to achieve.

diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -5,6 +5,8 @@ labels: enhancement
 
 ---
 
+<!-- DO NOT DELETE OR IGNORE THIS TEMPLATE.  Failing to adhere to this template and provide the necessary information may lead to your Issue being closed without consideration. -->
+
 <!-- BEFORE SUBMITTING AN ENHANCEMENT REQUEST - please browse the open issues and the [Archived Design Discussions wiki page](https://github.com/Pyomo/pyomo/wiki/Archived-Design-Discussions).-->
 
 ## Summary

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -7,6 +7,8 @@
 <!-- Contributing Guide: https://pyomo.readthedocs.io/en/stable/contribution_guide.html -->
 <!-- ##################################################################### -->
 
+<!-- DO NOT DELETE OR IGNORE THIS TEMPLATE. Failing to adhere to this template and provide the necessary information may lead to your Pull Request being closed without consideration. -->
+
 ## Fixes # .
 
 ## Summary/Motivation:

diff --git a/.github/workflows/release_wheel_creation.yml b/.github/workflows/release_wheel_creation.yml
@@ -14,10 +14,8 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-env:
-  PYOMO_SETUP_ARGS: "--with-cython --with-distributable-extensions"
-
 jobs:
+
   native_wheels:
     name: Build wheels (${{ matrix.wheel-version }}) on ${{ matrix.os }} for native and cross-compiled architecture
     runs-on: ${{ matrix.os }}
@@ -31,14 +29,26 @@ jobs:
         include:
         - wheel-version: 'cp38*'
           TARGET: 'py38'
+          GLOBAL_OPTIONS: "--with-cython --with-distributable-extensions"
         - wheel-version: 'cp39*'
           TARGET: 'py39'
+          GLOBAL_OPTIONS: "--with-cython --with-distributable-extensions"
         - wheel-version: 'cp310*'
           TARGET: 'py310'
+          GLOBAL_OPTIONS: "--with-cython --with-distributable-extensions"
         - wheel-version: 'cp311*'
           TARGET: 'py311'
+          GLOBAL_OPTIONS: "--without-cython --with-distributable-extensions"
         - wheel-version: 'cp312*'
           TARGET: 'py312'
+          GLOBAL_OPTIONS: "--without-cython --with-distributable-extensions"
+
+        exclude:
+        - wheel-version: 'cp311*'
+          os: windows-latest
+        - wheel-version: 'cp312*'
+          os: windows-latest
+
     steps:
       - uses: actions/checkout@v4
       - name: Build wheels
@@ -47,13 +57,13 @@ jobs:
           output-dir: dist
         env:
             CIBW_ARCHS_LINUX: "native"
-            CIBW_ARCHS_MACOS: "native arm64"
-            CIBW_ARCHS_WINDOWS: "native ARM64"
-            CIBW_SKIP: "*-musllinux*"
+            CIBW_ARCHS_MACOS: "x86_64 arm64"
+            CIBW_ARCHS_WINDOWS: "AMD64 ARM64"
             CIBW_BUILD: ${{ matrix.wheel-version }}
+            CIBW_SKIP: "*-musllinux*"
             CIBW_BUILD_VERBOSITY: 1
             CIBW_BEFORE_BUILD: pip install cython pybind11
-            CIBW_CONFIG_SETTINGS: '--global-option="--with-cython --with-distributable-extensions"'
+            CIBW_ENVIRONMENT: PYOMO_SETUP_ARGS="${{ matrix.GLOBAL_OPTIONS }}"
       - uses: actions/upload-artifact@v4
         with:
           name: native_wheels-${{ matrix.os }}-${{ matrix.TARGET }}
@@ -72,14 +82,19 @@ jobs:
         include:
         - wheel-version: 'cp38*'
           TARGET: 'py38'
+          GLOBAL_OPTIONS: "--with-cython --with-distributable-extensions"
         - wheel-version: 'cp39*'
           TARGET: 'py39'
+          GLOBAL_OPTIONS: "--with-cython --with-distributable-extensions"
         - wheel-version: 'cp310*'
           TARGET: 'py310'
+          GLOBAL_OPTIONS: "--with-cython --with-distributable-extensions"
         - wheel-version: 'cp311*'
           TARGET: 'py311'
+          GLOBAL_OPTIONS: "--without-cython --with-distributable-extensions"
         - wheel-version: 'cp312*'
           TARGET: 'py312'
+          GLOBAL_OPTIONS: "--without-cython --with-distributable-extensions"
     steps:
       - uses: actions/checkout@v4
       - name: Set up QEMU
@@ -93,17 +108,43 @@ jobs:
           output-dir: dist
         env:
             CIBW_ARCHS_LINUX: "aarch64"
-            CIBW_SKIP: "*-musllinux*"
             CIBW_BUILD: ${{ matrix.wheel-version }}
+            CIBW_SKIP: "*-musllinux*"
             CIBW_BUILD_VERBOSITY: 1
             CIBW_BEFORE_BUILD: pip install cython pybind11
-            CIBW_CONFIG_SETTINGS: '--global-option="--with-cython --with-distributable-extensions"'
+            CIBW_ENVIRONMENT: PYOMO_SETUP_ARGS="${{ matrix.GLOBAL_OPTIONS }}"
       - uses: actions/upload-artifact@v4
         with:
           name: alt_wheels-${{ matrix.os }}-${{ matrix.TARGET }}
           path: dist/*.whl
           overwrite: true
 
+  pure_python:
+    name: pure_python_wheel
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install twine wheel setuptools pybind11
+      - name: Build pure python wheel
+        run: |
+          python setup.py --without-cython sdist --format=gztar bdist_wheel
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: purepythonwheel
+          path: dist/*.whl
+          overwrite: true
+
   generictarball:
     name: ${{ matrix.TARGET }}
     runs-on: ${{ matrix.os }}

diff --git a/.github/workflows/test_branches.yml b/.github/workflows/test_branches.yml
@@ -21,8 +21,8 @@ defaults:
 env:
   PYTHONWARNINGS: ignore::UserWarning
   PYTHON_CORE_PKGS: wheel
-  PYPI_ONLY: z3-solver
-  PYPY_EXCLUDE: scipy numdifftools seaborn statsmodels
+  PYPI_ONLY: z3-solver linear-tree
+  PYPY_EXCLUDE: scipy numdifftools seaborn statsmodels linear-tree
   CACHE_VER: v221013.1
   NEOS_EMAIL: [email protected]
   SRC_REF: ${{ github.head_ref || github.ref }}

diff --git a/.github/workflows/test_pr_and_main.yml b/.github/workflows/test_pr_and_main.yml
@@ -30,7 +30,7 @@ env:
   PYTHONWARNINGS: ignore::UserWarning
   PYTHON_CORE_PKGS: wheel
   PYPI_ONLY: z3-solver linear-tree
-  PYPY_EXCLUDE: scipy numdifftools seaborn statsmodels
+  PYPY_EXCLUDE: scipy numdifftools seaborn statsmodels linear-tree
   CACHE_VER: v221013.1
   NEOS_EMAIL: [email protected]
   SRC_REF: ${{ github.head_ref || github.ref }}
@@ -57,21 +57,6 @@ 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
-        #  - RTD because a magically-generated string triggers failures
-        exclude_urls: https://pyomo-jenkins.sandia.gov/,https://pyomo.readthedocs.io/en/%s/errors.html
 
 
   build:

diff --git a/.github/workflows/url_check.yml b/.github/workflows/url_check.yml
@@ -0,0 +1,32 @@
+name: URL Validation
+
+on:
+  schedule:
+    - cron: '0 3 * * 0'
+  workflow_dispatch:
+    inputs:
+      git-ref:
+        description: Git Hash (Optional)
+        required: false
+
+jobs:
+  url_check:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout Pyomo source
+      uses: actions/checkout@v4
+    - 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
+        #  - RTD because a magically-generated string triggers failures
+        exclude_urls: https://pyomo-jenkins.sandia.gov/,https://pyomo.readthedocs.io/en/%s/errors.html
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,69 @@ Pyomo CHANGELOG
 ===============
 
 
+-------------------------------------------------------------------------------
+Pyomo 6.8.0   (20 Aug 2024)
+-------------------------------------------------------------------------------
+
+SIGNIFICANT CHANGE NOTICE
+
+- Internal data storage for Constraint objects (see #3293)
+- No longer release cythonized wheel for Python 3.11+ (see #3355)
+
+CHANGELOG
+
+- General
+  - Add ParameterizedQuadraticRepn and corresponding walker (#3324)
+  - Update Pyomo for NumPy 2.0 compatibility (#3292, #3353)
+  - Add ParameterizedLinearRepn and corresponding walker (#3268)
+  - Update Release Process Workflow for changes in `pip` (#3355)
+- Core
+  - Handle uninitialized variable in `propagate_solution` of scaling
+    transformation (#3275)
+  - Add `context` option to `SuffixFinder` (#3348)
+  - Remove the `_suppress_ctypes` attribute from Block (#3347)
+  - Improve `Set` initialization performance (#3302)
+  - Update Constraint to only store the original expression (not
+    lower/body/upper) (#3293)
+  - Kernel: fix bug in conic geomean (#3310)
+  - Fix bug with IndexedSet objects and the within argument (#3288)
+  - Support validate/filter for IndexedSet components using index (#3338)
+- Solver Interfaces
+  - Resolve NLv2 incompatibility with multithreading (#3332)
+  - Resolve writer performance degradation  (#3343)
+  - Fix bug with inconsistent use of `result` and `results` (#3337)
+  - LegacySolverWrapper: restore 'options' attribute (#3334)
+  - Fix bug in XpressDirect._load_slacks (#3318)
+  - NLv2: support expressions with nested external functions (#3319)
+  - Ignore errors on ASL solver version check (#3298)
+  - Add SAS solver interface (#2886, #3309)
+- Testing
+  - Omnibus testing / platform portability fixes (#3335)
+  - Change BARON download URL (#3328)
+  - Disable interface/testing for NEOS/octeract (#3322)
+  - Fix typo in Jenkins driver (#3312)
+  - Jenkins: update logic for recording variables (#3311)
+  - Unpin Codecov / Update coverage (#3303)
+- GDP
+  - Don't transform known-to-be infeasible Disjuncts in multiple BigM (#3314)
+- Contributed Packages
+  - alternative_solutions: Add a new contrib package for generating
+    alternative solutions (#3270)
+  - APPSI: Allow maingo_solvermodel to be imported without maingopy (#3330)
+  - APPSI: Sort indices while removing constraints to fix bug in HiGHs
+    interface (#3281)
+  - CP: Add beforeChild handling for bools in logical expressions  (#3315)
+  - DoE: Refactor to improve API and maintainability (#3317)
+  - incidence_analysis: Raise error in `generate_strongly_connected_components`
+    instead of asserting (#3305)
+  - parmest: Add missing main call for example file (#3349)
+  - piecewise: Add incremental PW linear to MIP transformation (#3287)
+  - piecewise: Add nonlinear-to-piecewise-linear transformation (#3333)
+  - PyNumero: Support user-provided CyIpopt callbacks with 13 arguments (#3289)
+  - PyNumero: Support PyomoNLP scaling factors on sub-blocks (#3295)
+  - PyROS: Temporarily Adjust NL Writer Feasibility Tolerance (#3280)
+  - viewer: Add option to specify the model by variable name (#3271)
+
 -------------------------------------------------------------------------------
 Pyomo 6.7.3   (29 May 2024)
 -------------------------------------------------------------------------------

diff --git a/RELEASE.md b/RELEASE.md
@@ -1,24 +1,19 @@
-We are pleased to announce the release of Pyomo 6.7.3.
+We are pleased to announce the release of Pyomo 6.8.0.
 
 Pyomo is a collection of Python software packages that supports a
 diverse set of optimization capabilities for formulating and analyzing
 optimization models.
 
-The following are highlights of the 6.7 release series:
-
- - Added support for Python 3.12
- - 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:
-    - 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
+The following are highlights of the 6.8 release series:
+
+- Support for Numpy2
+- Refactor of Design of Experiments (`contrib.doe`)
+- New packages:
+  - alternative_solutions: alternative (near) optimal solutions
+- New solver interfaces:
+  - SAS: Statistical Analysis System
+  - v2: Ongoing solver interface refactor
+- ...and of course numerous minor bug fixes and performance enhancements
 
 A full list of updates and changes is available in the
 [`CHANGELOG.md`](https://github.com/Pyomo/pyomo/blob/main/CHANGELOG.md).
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,6 +5,8 @@ labels: enhancement @@
     ---
+    <!-- DO NOT DELETE OR IGNORE THIS TEMPLATE.  Failing to adhere to this template and provide the necessary information may lead to your Issue being closed without consideration. -->
     <!-- BEFORE SUBMITTING AN ENHANCEMENT REQUEST - please browse the open issues and the [Archived Design Discussions wiki page](https://github.com/Pyomo/pyomo/wiki/Archived-Design-Discussions).-->
     ## Summary
@@ Expand Down @@