Pyomo

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- General
- Apply `black` to enforce PEP8 standards in certain modules (2737, 2738,
2733, 2732, 2731, 2728, 2730, 2729, 2720, 2721, 2719, 2718)
- Add Developers' call information to README (2665)
- Deprecate `pyomo.checker` module (2734)
- Warn when infeasibility tools will not log output (2666)
- Separate identification from logging in `pyomo.util.infeasible.log_*` (2669)
- Convert subprocess timeout parameters to module attributes (2672)
- Resolve consistency issues in the Bunch class (2685)
- Remove GSL downloader from `download-extensions` (2725)
- Update enhancement GitHub issue template to link to wiki (2739)
- Add deprecation warning to `pyomo` command (2740)
- Require `version=` for all deprecation utilities (2744)
- Fix `pyomo --version` version string (2743)
- Core
- Fix minor typo in set.py (2679)
- Fix bugs in scaling transformation (2678)
- Rework handling of 'dimensionless' units in Pyomo (2691)
- Solver Interfaces
- Switch default NL writer to nlv2 and bug fixes (2676, 2710, 2726)
- Enable MOSEK10 warm-start flag and relocate var initialization (2647)
- Fix handling of POW in Baron writer (2693)
- Update GAMS license check to avoid exception when not available (2697)
- Documentation
- Fix incorrect documentation for sending options to solvers (2688)
- Fix Sphinx warnings (2712)
- Document Python Version Support policy (2735)
- Document deprecation and removal of functionality (2741)
- Document docstring formatting requirements (2742)
- Testing
- Skip failing Baron tests (2694)
- Remove residual `nose` references (2736)
- Update GHA setup-python version (2705)
- Improve GHA conda setup performance (2701)
- Add unit test for QCQO problems with MOSEK (2682)
- DAE
- Fix typo in `__init__.py` (2683)
- Add `active` filter to flattener (2643)
- GDP
- Add GDP-to-MIP transformation base class (2687)
- Contributed Packages
- DoE: New module for model-based design of experiments (2294, 2711, 2527)
- FBBT: Add tolerances to tests (2675)
- GDPopt: Switch a LBB test to use Gurobi as MINLP solver (2686)
- incidence_analysis: Add `plot` method to `IncidenceGraphInterface` (2716)
- incidence_analysis: Refactor to cache a graph instead of a matrix (2715)
- incidence_analysis: Add documentation and update API (2727, 2745)
- incidence_analysis: Add logging solve_strongly_connected_components (2723)
- MindtPy: Refactor to improve extensibility and maintainability (2654)
- Parmest: Suppress mpi-sppy output in import (2692)
- PyNumero: Add tee argument to Pyomo-SciPy square solvers (2668)
- PyNumero: Support implicit function solvers in ExternalPyomoModel (2652)
- PyROS: Fix user_time and wallclock_time bug (2670)
- PyROS: More judicious enforcement of PyROS Solver time limit (2660, 2706)
- PyROS: Update documentation (2698, 2707)
- PyROS: Adjust routine for loading DR polishing model solutions (2700)
- Viewer: Update to support PySide6 and display units and domain (2689)

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- General
- Convert `txt` to `md` files (`CHANGELOG`, `LICENSE`, `RELEASE`) (2635)
- Parallelize build of manylinux wheels (2636)
- Update source for Jenkins status badge (2639, 2640)
- Update relocated_module_attribute to work with cythonized modules (2644)
- Add utility methods to HierarchicalTimer (2651)
- Core
- Fix preservation of stale flags through clone/pickle (2633)
- Add support for local suffixes in scaling transformation (2619)
- Solver Interfaces
- Fix handling of nonconvex MIQCP problems in Xpress (2625)
- Testing
- Update GitHub actions to cancel jobs when new changes are pushed (2634)
- Remove requirement for a `pyutilib` directory in Jenkins driver (2637)
- Enable GitHub actions build on Windows Python 3.11 (2638)
- Add build services infrastructure status badge (2646)
- Add version upper bound on MOSEK warmstart test skip (2649)
- Improve compare.py handling of nosetests/pytest output (2661)
- GDP
- Add option to use multiple-bigm only on bound constraints (2624)
- Add logical_to_disjunctive and replace uses of logical_to_linear (2627)
- Contributed Packages
- FBBT: Fix bug with ExternalFunction expressions (2657)
- PyROS: Fix uncertain param bounds evaluation for FactorModelSet (2620)
- PyROS: Add origin attribute to BudgetSet (2645)
- PyROS: Fix UncertaintySet.bounding_problem method (2659)

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- General
- Update PauseGC to work in nested contexts (2507)
- Simplify deepcopy/pickle logic to speed up model clone (2510)
- Fix generate_standard_repn to handle unexpected NPV expressions (2511)
- Add thread safe proxies for PauseGC, TempFileManager singletons (2514)
- Fix ConstructionTimer bug for components indexed by nonfinite sets (2518)
- Add calculate_variable_from_constraint differentiation mode option (2549)
- Update URL for downloading GSL and GJH (2556, 2588)
- Update logic for retrying failed downloads (2569)
- Add support and testing for Python 3.11 (2596, 2618)
- Update deprecation utilities to improve user messages (2606)
- Core
- Refactor expression hierarchy, add RelationalExpression base class (2499)
- Support cloning individual blocks (2504)
- Block performance improvements (2508)
- Add support for creating a slice to a single ComponentData object (2509)
- Fix missing import of value in pyomo.core.base.external (2525)
- Improve handling of restricted words on Blocks (2535)
- Improve Reference() performance (2537)
- Fix mapping gradient/hessian for external functions with string args (2539)
- Fix bug for sum_product(Var, Param, Param) (2551)
- Add deprecation path for expression objects moved to relational_expr (2554)
- Exception when setting value of Expression to non-numeric expression (2567)
- Improve deepcopy performance (2628)
- Documentation
- Fix examples in working_models.rst (2502)
- Solver Interfaces
- Improve SCIP results object (2462)
- Improve warning message when LP writer raises KeyError (2497)
- Fix Gurobi work limit bug (2530)
- Updates and fixes for the NLv2 writer (2540, 2622, 2568)
- Fix Xpress when stopped due to MAXTIME or MAXNODES (2553)
- Add support for MOSEK 10 affine conic constraints (2557)
- Fix missing explicit space in GAMS put command (2578)
- Fix GAMS logfile storage location (2580)
- LP writer performance improvements (2583, 2585)
- Update handling of MOSEK Env and Python module (2591)
- Release MOSEK license when optimize raises a mosek.Error (2593)
- Update list of allowable characters in CPLEX filenames (2597)
- Testing
- Update performance driver to be usable outside of Pyomo (2505)
- Update the performance test driver (2538)
- Reduce amount of environment code cached in GitHub actions (2565)
- Update GitHub actions versions from v2 to v3 (2566)
- Allow nan to compare equal in assertStructuredAlmostEqual() (2582)
- Add test utilities for comparing expressions (2590)
- Skip a test in MOSEK 10 due to a bug in warm starting MIQPs (2614)
- Update skipped CBC test that works with CBC 2.10.6 (2615)
- Add SCIP to GitHub actions environment (2602)
- GDP
- Use OrderedSet instead of list in GDPTree to improve performance (2516)
- Reduce calls to logical_to_linear in GDP transformations (2519)
- Add utility for gathering BigM values after transformation (2520)
- Add tighter logical constraints in transformations of nested GDPs (2550)
- Fix pickling of transformed GDP models (2576)
- Add multiple-bigM transformation (2592)
- Improve performance of BigM transformation (2605)
- Remove weakref mapping Disjunctions to their algebraic_constraint (2617)
- Contributed Packages
- APPSI: Fix exception raised by appsi_gurobi during Python shutdown (2498)
- APPSI: Improve handling of Gurobi results (2517)
- APPSI: Add interface to HiGHS solver (2561)
- APPSI: Only release Gurobi license after deleting all instances (2599)
- APPSI: Patch IntEnum to preserve pre-3.11 formatting (2607)
- CP: New package for constraint programming (2570, 2612)
- GDPopt: Add warning when reporting results from LBB (2534)
- GDPopt: Delete dummy objective when we're done using it (2552)
- GDPopt: Add enumerate solution approach (2559, 2575)
- IIS: Add package for computing the IIS of an infeasible Pyomo model (2512)
- MindtPy: Fix bug in termination condition (2587)
- MindtPy: Fix bug in checking absolute and relative gap (2608)
- MPC: Data structures/utils for rolling horizon dynamic optimization (2477)
- Parmest: Solve square problem to initialize regression problem (2438)
- Parmest: Return ContinuousSet values from theta_est() (2464)
- PyNumero: Fix NumPy deprecation warnings (2521)
- PyNumero: Add interfaces to SciPy square solvers (2523)
- PyNumero: Check AmplInterface availability in SciPy solver tests (2594)
- PyNumero: Add ProjectedExtendedNLP class (2601)
- PyNumero: Add interface to SciPy scalar Newton solver (2603)
- PyROS: Rewrite UncertaintySet docstrings/improve validation (2488)
- PyROS: Updates to subproblem initialization and solver call routines (2515)
- PyROS: Fix collection of sub-solver solve times (2543)

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- General
- Resolve dill incompatibility with attempt_import (2419)
- Speed up book tests and improve import/logging infrastructure (2449)
- Make typing overloads available at runtime (2471)
- Update list of known TPLs to reflect Python 3.10 (2478)
- Add NL writer version 2 but don't activate by default (2473)
- Add deprecation.relocated_module utility (2492)
- Core
- Support cython functions through Initializer (2421)
- Ensure UnindexedComponent_set is correctly pickled/restored (2416)
- Update as_numeric() to raise an exception on non-is_numeric_type() Pyomo
objects (2444)
- replace_expressions: support replacing variables with constants (2410)
- Update component_data_objects and component_data_iterindex to not
return duplicate data (2456)
- Fix exception handling logic bug in quicksum (2458)
- Reduce recursion in model clone/deepcopy (2487)
- Resolve exception cloning empty LinearExpression objects (2489)
- Resolve errors from inplace operators on Expression objects (2493)
- Documentation
- Fix typos and incorrect link (2420, 2482)
- Fix Sphinx warnings in documentation builds (2434)
- Solver Interfaces
- Add support for SCIP 8.0 (2409)
- Add explicit space to GAMS put statements to support GAMS 39+ (2450)
- Catch exceptions in BARON interface when parsing objective bounds (2467)
- Testing
- Skip SCIP 8.0 tests on PyPy (2424)
- Force conda to use conda-forge channel in GHA (2430)
- Fix GHA win/3.10 Python version inconsistency (2433)
- Enable Pyomo.DAE Simulator tests on PyPy (2443)
- Abort the Jenkins build if virtualenv creation fails (2451)
- Remove scipy from GHA PyPy builds (2474)
- Move performance testing driver scripts to scripts/performance (2476)
- Improve common.timing test robustness (2490)
- Contributed Packages
- APPSI: Improve error message in nl writer when all variables fixed (2407)
- APPSI: Fix bug in Gurobi interface when modifying the objective (2454)
- APPSI: Solve blocks that use variables that are not on the block (2453)
- APPSI: Method to release Gurobi license from persistent interface (2480)
- community_detection: Trap exceptions from networkx (2415)
- FBBT: Add tolerances to tests (2445)
- GDPopt: Refactor to improve extensibility and maintainability (2406)
- incidence_analysis: Add method for weakly connected components (2418)
- MindtPy: Fix bug in copying variable values between models (2432)
- MindtPy: Add support for appsi_cplex and appsi_gurobi (2373)
- Parmest: Add utils submodule and support to convert Params to Vars (2352)
- Parmest: Fix use of relocated_module_attribute (2472)
- PyROS: Fixes to ellipsoidal sets (2425)
- PyROS: Account for variable domains (2426)
- PyROS: Fix objective validation (2371)
- PyROS: Avoid master feasibility problem unit consistency checks (2459)
- PyROS: Fix discrete uncertainty set separation (2469)
- PyROS: Update exception handling parsing BARON lower/upper bounds (2486)

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- General
- Extend linux distribution map logic (2361)
- Improve string processing in ConfigList, ConfigDict, and ListOf (2360)
- Update copyright assertion (2368, 2378)
- Deprecate name_buffer argument to getname (2370)
- Defer construction of the main Pyomo parser (2385)
- Improve error checking parsing ConfigDict string value (2399)
- Core
- Add indices to ComponentData objects (2351)
- Ignore SetOf, BuildAction, and BuildCheck when checking units (2366)
- Improve support for absolute value in differentiation and FBBT (2347)
- Allow relative tolerance when comparing unit dimensionality (2395)
- Solver Interfaces
- Fix bug in GLPK solver plugin (2348)
- Update BARON solution parser (2367)
- Testing
- Turn on failure for codecov-action (2343)
- Fixes to GHA due to updates to Ubuntu runner and Conda (2356, 2384, 2396)
- Update setup-python and pypy in GHA (2364)
- Pin version of openmpi used for testing (2369)
- DAE Updates
- Fix typo preventing a DAE test from running (2349)
- Contributed Packages
- APPSI: Minor improvements and generalizations (2383, 2386, 2389,
2391, 2388, 2392)
- incidence_analysis: Add option to ignore inequality constraints in
IncidenceGraphInterface (2350)
- MC++: Update interface tests (2400)
- MindtPy: Add quadratic_strategy option to pass quadratic constraints
or objectives to MIP solvers (2338)
- Parmest: Skip tests when seaborn and matplotlib are missing (2394)
- PyROS: Improve feasibility problem formulation, objective validation
(2353, 2371)

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- General
- Distribute the ampl_function_demo C source / cmake files (2319)
- Add GitHub URL to setup.py for PyPI (2325)
- Use constant indentation for long lines in the HierarchicalTimer (2336)
- Core
- Remove incomplete pyomo/core/base/alias.py module (2284)
- Remove Python 3.6 support (2312)
- Solver Interfaces
- Remove PICO solver interface (2341)
- Testing
- Add Windows pip single test (2334)
- Fix test docstrings in piecewise to silence warnings (2342)
- Contributed Packages
- APPSI: Update Gurobi solver unavailable message (2320)
- APPSI: Remove distributables for Windows (2326)
- APPSI: Fix bugs when working with the Gurobi solution pool (2335)
- APPSI: Fix bug in persistent update for FBBT (2340)
- Preprocessing: Stop using polynomial_degree to check for linear and
constant expressions (2324)
- PyNumero: Improve coverage of mpi block matrix tests (2318)
- PyNumero: Skip bound/domain validation in ExternalPyomoModel (2323)
- PyNumero: Remove deprecated usage of numpy.bool (2339)
- PyROS: Fix variable default initialization (2331)

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