Merge pull request #4 from Pyomo/main

Update doe-review with pyomo/main
Pyomo · Oct 4, 2021 · 4685d98 · 4685d98
2 parents cd1e4ba + f0bc6b5
commit 4685d98
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diff --git a/.coin-or/projDesc.xml b/.coin-or/projDesc.xml
@@ -68,7 +68,7 @@ optimization models.
 		<!--Fill in your text below (outside the comment block).       -->
 
 		<projectManager>
-Carl D. Laird, Chair, Pyomo Management Committee, cdlaird at sandia dot gov
+Carl D. Laird, Chair, Pyomo Management Committee, claird at andrew dot cmu dot edu
 		</projectManager>
 
 		<!-- Fill in the URLS you would like use for your main         -->
@@ -227,8 +227,8 @@ Carl D. Laird, Chair, Pyomo Management Committee, cdlaird at sandia dot gov
 			     Use explicit overrides to disable use of automated
 			     version reporting.
 			-->
-			<stableVersionNumber>6.0.1</stableVersionNumber>
-			<releaseNumber>6.0.1</releaseNumber>
+			<stableVersionNumber>6.1.2</stableVersionNumber>
+			<releaseNumber>6.1.2</releaseNumber>
 
 		</developmentStatus>
 

diff --git a/.coveragerc b/.coveragerc
@@ -7,7 +7,9 @@ omit =
 # The [run] section must be at the end, as the build harness will add a
 # "data_file" directive to the end of this file.
 [run]
-concurrency = multiprocessing,thread
+concurrency =
+    multiprocessing
+    thread
 parallel = True
 source =
     pyomo

diff --git a/.github/workflows/test_branches.yml b/.github/workflows/test_branches.yml
@@ -18,14 +18,14 @@ env:
   PYTHONWARNINGS: ignore::UserWarning
   PYTHON_CORE_PKGS: wheel
   PYPI_ONLY: z3-solver
-  CACHE_VER: v210630.0
+  CACHE_VER: v210812.0
   NEOS_EMAIL: [email protected]
 
 jobs:
   build:
     name: ${{ matrix.TARGET }}/${{ matrix.python }}${{ matrix.other }}
     runs-on: ${{ matrix.os }}
-    timeout-minutes: 90
+    timeout-minutes: 120
     strategy:
       fail-fast: false
       matrix:
@@ -361,7 +361,8 @@ jobs:
         }
         if (-not (Test-Path "$INSTALLER" -PathType Leaf)) {
             echo "...downloading GAMS"
-            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER"
+            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER" `
+                -RetryIntervalSec 30 -MaximumRetryCount 8 -TimeoutSec 150
         }
         echo "...installing GAMS"
         if ( "${{matrix.TARGET}}" -eq "win" ) {
@@ -411,7 +412,8 @@ jobs:
         }
         if (-not (Test-Path "$INSTALLER" -PathType Leaf)) {
             echo "...downloading BARON ($URL)"
-            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER"
+            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER" `
+                -RetryIntervalSec 30 -MaximumRetryCount 8 -TimeoutSec 150
         }
         echo "...installing BARON"
         if ( "${{matrix.TARGET}}" -eq "win" ) {

diff --git a/.github/workflows/test_pr_and_main.yml b/.github/workflows/test_pr_and_main.yml
@@ -21,14 +21,14 @@ env:
   PYTHONWARNINGS: ignore::UserWarning
   PYTHON_CORE_PKGS: wheel
   PYPI_ONLY: z3-solver
-  CACHE_VER: v210630.0
+  CACHE_VER: v210812.0
   NEOS_EMAIL: [email protected]
 
 jobs:
   build:
     name: ${{ matrix.TARGET }}/${{ matrix.python }}${{ matrix.other }}
     runs-on: ${{ matrix.os }}
-    timeout-minutes: 90
+    timeout-minutes: 120
     strategy:
       fail-fast: false
       matrix:
@@ -380,7 +380,8 @@ jobs:
         }
         if (-not (Test-Path "$INSTALLER" -PathType Leaf)) {
             echo "...downloading GAMS"
-            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER"
+            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER" `
+                -RetryIntervalSec 30 -MaximumRetryCount 8 -TimeoutSec 150
         }
         echo "...installing GAMS"
         if ( "${{matrix.TARGET}}" -eq "win" ) {
@@ -430,7 +431,8 @@ jobs:
         }
         if (-not (Test-Path "$INSTALLER" -PathType Leaf)) {
             echo "...downloading BARON ($URL)"
-            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER"
+            Invoke-WebRequest -Uri "$URL" -OutFile "$INSTALLER" `
+                -RetryIntervalSec 30 -MaximumRetryCount 8 -TimeoutSec 150
         }
         echo "...installing BARON"
         if ( "${{matrix.TARGET}}" -eq "win" ) {

diff --git a/CHANGELOG.txt b/CHANGELOG.txt
@@ -2,6 +2,90 @@
 Pyomo CHANGELOG
 ===============
 
+-------------------------------------------------------------------------------
+Pyomo 6.1.2  20 Aug 2021
+-------------------------------------------------------------------------------
+
+- General
+  - Add test for missing/extra __init__.py files (#2090)
+  - Update deprecation warnings to only be emitted once per context (#2095)
+- Core
+  - Replace Set.card() with Set.at() (#2096)
+- DAE
+  - Remove use of OrderedSet.__getitem__ from contset.py (#2091)
+- Contributed Packages
+  - APPSI: Build/install APPSI extension outside of source tree (#2092)
+  - MindtPy: Support gurobi_persistent in LP/NLP-based B&B algorithm (#2071)
+
+-------------------------------------------------------------------------------
+Pyomo 6.1.1  17 Aug 2021
+-------------------------------------------------------------------------------
+
+- General
+  - Adding missing __init__.py files across Pyomo (#2086)
+
+-------------------------------------------------------------------------------
+Pyomo 6.1    17 Aug 2021
+-------------------------------------------------------------------------------
+
+- General
+  - Support using TicTocTimer as a context manager (#2012)
+  - Add optional dependency target in setup.py (#2017)
+  - Added utilities for subsets of model components (#1998)
+  - Improvements in deprecation warning system (#2045, #2058, #2056)
+  - Resolve TeeStream deadlock issues (#2072)
+  - Move PYOMO_CONFIG_DIR into pyomo.common.envvar (#2065)
+  - Add a DynamicImplicitDomain domain validator (#2043)
+  - Generate standard repn misidentifies nonlinear expr (#2074)
+  - Add Module() validator to the config system (#2062)
+- Core
+  - Yield Iterator from IndexedComponent (#2007)
+  - Use yield from in pyomo.core (#1984)
+  - Improvements to sorted_robust and string formatting (#2020, #2024)
+  - Integrating numpy with the Pyomo expression system (#2027, #2034, #2070)
+  - Resolve Set bugs (#2048)
+  - Prevent attaching global Sets to Blocks (#2042)
+  - Correct scalar mutable param getitem implementation (#2066)
+  - Fix Var bounds with unitted mutable Params (#2067)
+  - Improve @disable_methods decorator (#2069)
+  - Allow native numeric types in relational expressions (#2073)
+  - Fixing symbol names in Initializer deprecation layer (#2079)
+  - Deprecate OrderedSet.__getitem__ in favor of OrderedSet.card() (#2053)
+- Documentation
+  - Create a list of related packages (#2016)
+- Solver Interfaces
+  - Clean up dependencies and solver.available() IO (#2011)
+  - Update Baron writer to recognize priority Suffix (#2035)
+  - Add OCTERACT to the list of known NEOS solvers (#2064)
+  - Resolve tee issues with Xpress 8.9+ (#2059)
+  - Increase timeout for ASL version request (#2083)
+- Testing
+  - Miscellaneous testing fixes (#2023)
+  - Improve management of tempfiles in tests (#2036)
+  - Update GHA to ubuntu-latest; resolve ampl/mp build error (#2015)
+  - Move constrained_layout tests to 'expensive' suite (#2018)
+  - Update xpress, appsi tests to manage CWD (#2031)
+  - Improve comparison of Book examples to baselines (#2044)
+  - Add retry/timeout to powershell downloads (#2077)
+- GDP Updates
+  - gdp.hull: Only create one disaggregated variable for all Disjuncts in
+    which a Var does not appear (#2005)
+- Contributed Packages
+  - FBBT: descend_into option for FBBT (#2025)
+  - FBBT: Interval arithmetic edge cases for FBBT (#2026)
+  - FBBT: Improved handling for product expressions (#2038)
+  - incidence_analysis: methods for generating and solving strongly
+    connected components of a square model (#2009)
+  - incidence_analysis: Add Dulmage-Mendelsohn partition (#2063)
+  - PETSc: Remove PETSc solver (#1986)
+  - PyROS: Pyomo Robust Optimization Solver (#2006, #2061)
+  - sensitivity_toolbox: Add kaug dsdp mode (#1613)
+  - APPSI: API Cleanup (#1944), bug-fix in update_variables (#2051)
+  - MindtPy: Increase code coverage (#2021)
+  - MindtPy: Replace is not by != (#2081)
+  - PyNumero: ExternalGreyBox subclass to embed implicit functions (#2022)
+
+
 -------------------------------------------------------------------------------
 Pyomo 6.0.1   4 Jun 2021
 -------------------------------------------------------------------------------

diff --git a/RELEASE.txt b/RELEASE.txt
@@ -1,4 +1,4 @@
-We are pleased to announce the release of Pyomo 6.0.1.
+We are pleased to announce the release of Pyomo 6.1.2.
 
 Pyomo is a collection of Python software packages that supports a
 diverse set of optimization capabilities for formulating and analyzing
@@ -9,18 +9,12 @@ 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
- - New packages: APPSI, structural model analysis, external grey box models
-
-Note: As a major release, Pyomo 6.0 has certain backwards
-incompatibilities with the 5.x series and the 2nd Edition of the Pyomo
-Book.  Most notably:
-
- - Removed support for Python 2.7 or 3.5
- - Moved PySP into a separate package at https://github.com/Pyomo/pysp
- - Renamed "Simple" components to "Scalar" components
- - Removed support for implicit ranged inequalities (a <= m.x <= b)
- - Removed support for component reconstruct method
- - Removed support for casting relational expressions to bool
+ - Integration of NumPy support into the Pyomo expression system
+ - New packages:
+    - APPSI (Auto-Persistent Pyomo Solver Interfaces)
+    - External grey box models
+    - PyROS (Pyomo Robust Optimization Solver)
+    - Structural model analysis
 
 A full list of updates and changes is available in the CHANGELOG.txt
 

diff --git a/doc/OnlineDocs/conf.py b/doc/OnlineDocs/conf.py
@@ -39,6 +39,7 @@
 # -- Options for intersphinx ---------------------------------------------
 
 intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
     'matplotlib': ('https://matplotlib.org/stable/', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
     'pandas': ('https://pandas.pydata.org/docs/', None),

diff --git a/doc/OnlineDocs/contributed_packages/pyros.rst b/doc/OnlineDocs/contributed_packages/pyros.rst
@@ -360,17 +360,17 @@ PyROS will return one of six termination conditions upon completion. These termi
 +---------------------------------------------------+----------------------------------------------------------------+
 |  **Termination Condition**                        | **Description**                                                |
 +---------------------------------------------------+----------------------------------------------------------------+
-|   ``grcsTerminationCondition.robust_optimal``     |  The final solution is robust optimal                          |
+|   ``pyrosTerminationCondition.robust_optimal``    |  The final solution is robust optimal                          |
 +---------------------------------------------------+----------------------------------------------------------------+
-|   ``grcsTerminationCondition.robust_feasible``    |  The final solution is robust feasible                         |
+|   ``pyrosTerminationCondition.robust_feasible``   |  The final solution is robust feasible                         |
 +---------------------------------------------------+----------------------------------------------------------------+
-|   ``grcsTerminationCondition.robust_infeasible``  |  The posed problem is robust infeasible                        |
+|   ``pyrosTerminationCondition.robust_infeasible`` |  The posed problem is robust infeasible                        |
 +---------------------------------------------------+----------------------------------------------------------------+
-|   ``grcsTerminationCondition.max_iter``           |  Maximum number of GRCS iteration reached                      |
+|   ``pyrosTerminationCondition.max_iter``          |  Maximum number of GRCS iteration reached                      |
 +---------------------------------------------------+----------------------------------------------------------------+
-|   ``grcsTerminationCondition.time_out``           |  Maximum number of time reached                                |
+|   ``pyrosTerminationCondition.time_out``          |  Maximum number of time reached                                |
 +---------------------------------------------------+----------------------------------------------------------------+
-|   ``grcsTerminationCondition.subsolver_error``    |  Unacceptable return status(es) from a user-supplied sub-solver|
+|   ``pyrosTerminationCondition.subsolver_error``   |  Unacceptable return status(es) from a user-supplied sub-solver|
 +---------------------------------------------------+----------------------------------------------------------------+
 
 
@@ -409,19 +409,19 @@ If we choose to designate all variables as either design or state variables, wit
   >>> # === Query results ===
   >>> time = results_1.time
   >>> iterations = results_1.iterations
-  >>> termination_condition = results_1.grcs_termination_condition
+  >>> termination_condition = results_1.pyros_termination_condition
   >>> objective = results_1.final_objective_value
   >>> # === Print some results ===
   >>> single_stage_final_objective = round(objective,-1)
   >>> print("Final objective value: %s" % single_stage_final_objective)
   Final objective value: 48367380.0
   >>> print("PyROS termination condition: %s" % termination_condition)
-  PyROS termination condition: grcsTerminationCondition.robust_optimal
+  PyROS termination condition: pyrosTerminationCondition.robust_optimal
 
 PyROS Results Object
 """""""""""""""""""""""""""
 The results object returned by PyROS allows you to query the following information from the solve call:
-total iterations of the algorithm ``iterations``, CPU time ``time``, the GRCS algorithm termination condition ``grcs_termination_condition``,
+total iterations of the algorithm ``iterations``, CPU time ``time``, the GRCS algorithm termination condition ``pyros_termination_condition``,
 and the final objective function value ``final_objective_value``. If the option ``load_solution`` = ``True`` (default), the variables in the model will be
 loaded to the solution determined by PyROS and can be obtained by querying the model variables. Note that in the results obtained above, we set ``load_solution`` = ``False``.
 This is to ensure that the next set of runs shown here can utilize the original deterministic model, as the initial point can affect the performance of sub-solvers.
@@ -505,7 +505,7 @@ We can then loop through this array and call PyROS within a loop to identify rob
   ...                                        "solve_master_globally": True,
   ...                                        "decision_rule_order": 1
   ...                                     })
-  ...   if results.grcs_termination_condition != pyros.grcsTerminationCondition.robust_optimal:
+  ...   if results.pyros_termination_condition != pyros.pyrosTerminationCondition.robust_optimal:
   ...       print("This instance didn't solve to robust optimality.")
   ...       robust_optimal_objective.append("-----")
   ...   else:

diff --git a/doc/OnlineDocs/library_reference/common/config.rst b/doc/OnlineDocs/library_reference/common/config.rst
@@ -29,6 +29,7 @@ Domain validators
    InEnum
    Path
    PathList
+   DynamicImplicitDomain
 
 .. autoclass:: ConfigBase
    :members:
@@ -49,6 +50,10 @@ Domain validators
    :members:
    :undoc-members:
 
+.. autoclass:: DynamicImplicitDomain
+   :members:
+   :undoc-members:
+
 .. autofunction:: PositiveInt
 .. autofunction:: NegativeInt
 .. autofunction:: NonNegativeInt

diff --git a/doc/OnlineDocs/library_reference/common/deprecation.rst b/doc/OnlineDocs/library_reference/common/deprecation.rst
@@ -0,0 +1,6 @@
+pyomo.common.deprecation
+========================
+
+.. automodule:: pyomo.common.deprecation
+   :members:
+   :member-order: bysource
diff --git a/doc/OnlineDocs/library_reference/common/fileutils.rst b/doc/OnlineDocs/library_reference/common/fileutils.rst
@@ -0,0 +1,6 @@
+pyomo.common.fileutils
+======================
+
+.. automodule:: pyomo.common.fileutils
+   :members:
+   :member-order: bysource
diff --git a/doc/OnlineDocs/library_reference/common/formatting.rst b/doc/OnlineDocs/library_reference/common/formatting.rst
@@ -0,0 +1,6 @@
+pyomo.common.formatting
+=======================
+
+.. automodule:: pyomo.common.formatting
+   :members:
+   :member-order: bysource
diff --git a/doc/OnlineDocs/library_reference/common/index.rst b/doc/OnlineDocs/library_reference/common/index.rst
@@ -11,4 +11,7 @@ or rely on any other parts of Pyomo.
    config.rst
    dependencies.rst
    deprecation.rst
+   fileutils.rst
+   formatting.rst
+   tempfiles.rst
    timing.rst
diff --git a/doc/OnlineDocs/library_reference/common/tempfiles.rst b/doc/OnlineDocs/library_reference/common/tempfiles.rst
@@ -0,0 +1,7 @@
+
+pyomo.common.tempfiles
+======================
+
+.. automodule:: pyomo.common.tempfiles
+   :members:
+   :member-order: bysource
diff --git a/doc/OnlineDocs/library_reference/solvers/index.rst b/doc/OnlineDocs/library_reference/solvers/index.rst
@@ -7,3 +7,4 @@ Solver Interfaces
    gams.rst
    cplex_persistent.rst
    gurobi_persistent.rst
+   xpress_persistent.rst
diff --git a/doc/OnlineDocs/library_reference/solvers/xpress_persistent.rst b/doc/OnlineDocs/library_reference/solvers/xpress_persistent.rst
@@ -0,0 +1,7 @@
+XpressPersistent
+================
+
+.. autoclass:: pyomo.solvers.plugins.solvers.xpress_persistent.XpressPersistent
+   :members:
+   :inherited-members:
+   :show-inheritance:
diff --git a/doc/OnlineDocs/related_packages.rst b/doc/OnlineDocs/related_packages.rst
@@ -44,14 +44,14 @@ Domain-Specific Applications
 +==========================+=========================================================+=============================================+
 |  Chama                   | https://github.com/sandialabs/chama                     |  Sensor placement optimization              |
 +--------------------------+---------------------------------------------------------+---------------------------------------------+
-|  Egret                   | https://github.com/grid-parity-exchange/egret           |  Formulation and solution of Unit Commitment|
+|  Egret                   | https://github.com/grid-parity-exchange/egret           |  Formulation and solution of unit commitment|
 |                          |                                                         |  and optimal power flow problems            |
 +--------------------------+---------------------------------------------------------+---------------------------------------------+
 |  IDAES                   | https://github.com/idaes/idaes-pse                      |  Institute for the Design of Advanced       |
 |                          |                                                         |  Energy Systems                             |
 +--------------------------+---------------------------------------------------------+---------------------------------------------+
-|  Prescient               | https://github.com/grid-parity-exchange/prescient       |  Parallel solution of structured            |
-|                          |                                                         |  NLPs.                                      |
+|  Prescient               | https://github.com/grid-parity-exchange/prescient       |  Production Cost Model for power systems    |
+|                          |                                                         |  simulation and analysis                    |
 +--------------------------+---------------------------------------------------------+---------------------------------------------+
 |  PyPSA                   | https://github.com/pypsa/pypsa                          |  Python for Power system Analysis           |
 +--------------------------+---------------------------------------------------------+---------------------------------------------+