Merge pull request #2748 from blnicho/finalize-release-6.5.0

Finalize Pyomo 6.5.0 release

Author: blnicho

.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>6.4.4</stableVersionNumber>
-			<releaseNumber>6.4.4</releaseNumber>
+			<stableVersionNumber>6.5.0</stableVersionNumber>
+			<releaseNumber>6.5.0</releaseNumber>
 
 		</developmentStatus>
 

CHANGELOG.md

@@ -1,6 +1,68 @@
 Pyomo CHANGELOG
 ===============
 
+-------------------------------------------------------------------------------
+Pyomo 6.5.0    (16 Feb 2023)
+-------------------------------------------------------------------------------
+
+- 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: taht -> that 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)
+
 -------------------------------------------------------------------------------
 Pyomo 6.4.4    (9 Dec 2022)
 -------------------------------------------------------------------------------

RELEASE.md

@@ -1,4 +1,4 @@
-We are pleased to announce the release of Pyomo 6.4.4.
+We are pleased to announce the release of Pyomo 6.5.0.
 
 Pyomo is a collection of Python software packages that supports a
 diverse set of optimization capabilities for formulating and analyzing
@@ -9,11 +9,13 @@ The following are highlights of the 6.0 release series:
  - Improved stability and robustness of core Pyomo code and solver interfaces
  - Integration of Boolean variables into GDP
  - Integration of NumPy support into the Pyomo expression system
+ - Implemented a more performant NL file writer (NLv2)
  - Added support for Python 3.10, 3.11
  - Removed support for Python 3.6
  - New packages:
     - APPSI (Auto-Persistent Pyomo Solver Interfaces)
     - CP (Constraint programming models and solver interfaces)
+    - DoE (Model based design of experiments)
     - External grey box models
     - IIS (Standard interface to solver IIS capabilities)
     - MPC (Data structures/utils for rolling horizon dynamic optimization)

pyomo/checker/checker.py

@@ -14,7 +14,7 @@
 
 
 @deprecated(
-    'The pyomo.checker module has been deprecated.', version='TBD', remove_in='6.6'
+    'The pyomo.checker module has been deprecated.', version='6.5.0', remove_in='6.6.0'
 )
 class IModelChecker(Interface):
     def check(self, runner, script, info):

pyomo/checker/runner.py

@@ -61,7 +61,7 @@ def generic_visit(self, node):
 
 
 @deprecated(
-    'The pyomo.checker module has been deprecated.', version='TBD', remove_in='6.6'
+    'The pyomo.checker module has been deprecated.', version='6.5.0', remove_in='6.6.0'
 )
 class ModelCheckRunner(object):
 

pyomo/checker/script.py

@@ -13,7 +13,7 @@
 
 
 @deprecated(
-    'The pyomo.checker module has been deprecated.', version='TBD', remove_in='6.6'
+    'The pyomo.checker module has been deprecated.', version='6.5.0', remove_in='6.6.0'
 )
 class ModelScript(object):
     def __init__(self, filename=None, text=None):

pyomo/common/getGSL.py

@@ -11,4 +11,4 @@
 
 from pyomo.common.deprecation import (relocated_module)
 
-relocated_module('pyomo.common.gsl', version='TBD')
+relocated_module('pyomo.common.gsl', version='6.5.0')

pyomo/common/gsl.py

@@ -19,7 +19,7 @@
 @deprecated(
     "Use of get_gsl is deprecated and NO LONGER FUNCTIONS as of February 9, "
     "2023. ",
-    version='TBD')
+    version='6.5.0')
 def get_gsl(downloader):
     logger.info("As of February 9, 2023, AMPL GSL can no longer be downloaded\
                 through download-extensions. Visit https://portal.ampl.com/\

pyomo/common/plugin.py

@@ -11,5 +11,5 @@
 
 from pyomo.common.deprecation import (relocated_module)
 
-relocated_module('pyomo.common.plugin_base', version='TBD')
+relocated_module('pyomo.common.plugin_base', version='6.5.0')
 

pyomo/contrib/incidence_analysis/interface.py

@@ -380,31 +380,31 @@ def n_edges(self):
     @property
     @deprecated(
         msg="``var_index_map`` is deprecated. Please use ``get_matrix_coord`` instead.",
-        version="6.4.5",
+        version="6.5.0",
     )
     def var_index_map(self):
         return self._var_index_map
 
     @property
     @deprecated(
         msg="``con_index_map`` is deprecated. Please use ``get_matrix_coord`` instead.",
-        version="6.4.5",
+        version="6.5.0",
     )
     def con_index_map(self):
         return self._con_index_map
 
     @property
     @deprecated(
         msg="The ``row_block_map`` attribute is deprecated and will be removed.",
-        version="6.4.5",
+        version="6.5.0",
     )
     def row_block_map(self):
         return None
 
     @property
     @deprecated(
         msg="The ``col_block_map`` attribute is deprecated and will be removed.",
-        version="6.4.5",
+        version="6.5.0",
     )
     def col_block_map(self):
         return None
@@ -694,9 +694,9 @@ def block_triangularize(self, variables=None, constraints=None):
 
         .. note::
 
-           **Breaking change in Pyomo 6.4.5**
+           **Breaking change in Pyomo 6.5.0**
 
-           The pre-6.4.5 ``block_triangularize`` method returned maps from
+           The pre-6.5.0 ``block_triangularize`` method returned maps from
            each variable or constraint to the index of its block in a block
            lower triangularization as the original intent of this function
            was to identify when variables do or don't share a diagonal block
@@ -708,7 +708,7 @@ def block_triangularize(self, variables=None, constraints=None):
            This functionality was previously available via the
            ``get_diagonal_blocks`` method, which was confusing as it did not
            capture that the partition was the diagonal of a block
-           *triangularization* (as opposed to diagonalization). The pre-6.4.5
+           *triangularization* (as opposed to diagonalization). The pre-6.5.0
            functionality of ``block_triangularize`` is still available via the
            ``map_nodes_to_block_triangular_indices`` method.
 
@@ -729,7 +729,7 @@ def block_triangularize(self, variables=None, constraints=None):
             " Please use ``IncidenceGraphInterface.block_triangularize``"
             " instead."
         ),
-        version="6.4.5",
+        version="6.5.0",
     )
     def get_diagonal_blocks(self, variables=None, constraints=None):
         variables, constraints = self._validate_input(variables, constraints)

pyomo/contrib/incidence_analysis/triangularize.py

@@ -147,9 +147,9 @@ def block_triangularize(matrix, matching=None):
 
     .. note::
 
-       **Breaking change in Pyomo 6.4.5**
+       **Breaking change in Pyomo 6.5.0**
 
-       The pre-6.4.5 ``block_triangularize`` function returned maps from
+       The pre-6.5.0 ``block_triangularize`` function returned maps from
        each row or column to the index of its block in a block
        lower triangularization as the original intent of this function
        was to identify when coordinates do or don't share a diagonal block
@@ -161,7 +161,7 @@ def block_triangularize(matrix, matching=None):
        This functionality was previously available via the
        ``get_diagonal_blocks`` method, which was confusing as it did not
        capture that the partition was the diagonal of a block
-       *triangularization* (as opposed to diagonalization). The pre-6.4.5
+       *triangularization* (as opposed to diagonalization). The pre-6.5.0
        functionality of ``block_triangularize`` is still available via the
        ``map_coords_to_block_triangular_indices`` function.
 
@@ -200,7 +200,7 @@ def map_coords_to_block_triangular_indices(matrix, matching=None):
         "``get_blocks_from_maps`` is deprecated. This functionality has been"
         " incorporated into ``block_triangularize``."
     ),
-    version="6.4.5",
+    version="6.5.0",
 )
 def get_blocks_from_maps(row_block_map, col_block_map):
     blocks = set(row_block_map.values())
@@ -220,7 +220,7 @@ def get_blocks_from_maps(row_block_map, col_block_map):
         "``get_diagonal_blocks`` has been deprecated. Please use"
         " ``block_triangularize`` instead."
     ),
-    version="6.4.5",
+    version="6.5.0",
 )
 def get_diagonal_blocks(matrix, matching=None):
     return block_triangularize(matrix, matching=matching)

pyomo/contrib/incidence_analysis/util.py

@@ -10,10 +10,13 @@
 #  ___________________________________________________________________________
 
 from pyomo.common.deprecation import relocated_module
+
 msg = (
     "The 'pyomo.contrib.incidence_analysis.util' module has been moved to"
     " 'pyomo.contrib.incidence_analysis.scc_solver'. However, we recommend"
     " importing this functionality (e.g. solve_strongly_connected_components)"
     " directly from 'pyomo.contrib.incidence_analysis'."
 )
-relocated_module("pyomo.contrib.incidence_analysis.scc_solver", version='TBD', msg=msg)
+relocated_module(
+    "pyomo.contrib.incidence_analysis.scc_solver", version='6.5.0', msg=msg
+)

pyomo/repn/plugins/nl_writer.py

@@ -536,7 +536,7 @@ def __init__(self, ostream, rowstream, colstream, config):
             deprecation_warning(
                 f'{str(old)} ({int(old)}) is deprecated.  '
                 f'Please use {str(new)} ({int(new)})',
-                version='TBD',
+                version='6.5.0',
             )
 
     def __enter__(self):

pyomo/scripting/plugins/check.py

@@ -130,8 +130,8 @@ def main_exec(options):
     + _default_deprecation_msg(
         None,
         'The pyomo.checker module has been deprecated',
-        version='TBD',
-        remove_in='6.6',
+        version='6.5.0',
+        remove_in='6.6.0',
     )
     + """.
 

pyomo/scripting/pyomo_main.py

@@ -64,12 +64,12 @@ def main(args=None):
         if args[0] not in ['-h', '--help', '--version']:
             deprecation_warning("Running the 'pyomo' script with no subcommand is deprecated. "
                                 "Defaulting to 'pyomo solve'",
-                                version='TBD')
+                                version='6.5.0')
             args = ['solve'] + args[0:]
     elif args[0] not in pyomo_parser.subparsers:
         deprecation_warning("Running the 'pyomo' script with no subcommand is deprecated. "
                             "Defaulting to 'pyomo solve'",
-                            version='TBD')
+                            version='6.5.0')
         args = ['solve'] + args[0:]
     #
     # Process arguments

pyomo/version/info.py

@@ -13,22 +13,22 @@
 
 # NOTE: releaselevel should be left at 'invalid' for trunk development
 #     and set to 'final' for releases.  During development, the
-#     major.minor.micro should point ot the NEXT release (generally, the
+#     major.minor.micro should point to the NEXT release (generally, the
 #     next micro release after the current release).
 #
 # Note: When cutting a release, also update the major/minor/micro in
 #
-#     pyomo/RELEASE.txt
+#     pyomo/RELEASE.md
 #
 # The VOTD zipbuilder will automatically change releaselevel to "VOTD
 # {hash}" and set the serial number to YYMMDDhhmm.  The serial number
 # should generally be left at 0, unless a downstream package is tracking
 # main and needs a hard reference to "suitably new" development.
 major = 6
-minor = 4
-micro = 5
-releaselevel = 'invalid'
-# releaselevel='final'
+minor = 5
+micro = 0
+# releaselevel = 'invalid'
+releaselevel='final'
 serial = 0
 
 if releaselevel == 'final':
@@ -51,7 +51,7 @@
         #
         # __file__ fails if script is called in different ways on Windows
         # __file__ fails if someone does os.chdir() before
-        # sys.argv[0] also fails because it doesn't always contains the path
+        # sys.argv[0] also fails because it doesn't always contain the path
         from inspect import getfile as _getfile, currentframe as _frame
         from os.path import abspath as _abspath