Merge pull request #3 from Pyomo/main

Update doe-develop1 with pyomo/main

.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>6.1.1</stableVersionNumber>
-			<releaseNumber>6.1.1</releaseNumber>
+			<stableVersionNumber>6.1.2</stableVersionNumber>
+			<releaseNumber>6.1.2</releaseNumber>
 
 		</developmentStatus>
 

.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

CHANGELOG.txt

@@ -2,6 +2,21 @@
 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
 -------------------------------------------------------------------------------

RELEASE.txt

@@ -1,4 +1,4 @@
-We are pleased to announce the release of Pyomo 6.1.1.
+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

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),

doc/OnlineDocs/library_reference/common/deprecation.rst

@@ -0,0 +1,6 @@
+pyomo.common.deprecation
+========================
+
+.. automodule:: pyomo.common.deprecation
+   :members:
+   :member-order: bysource

doc/OnlineDocs/library_reference/common/fileutils.rst

@@ -0,0 +1,6 @@
+pyomo.common.fileutils
+======================
+
+.. automodule:: pyomo.common.fileutils
+   :members:
+   :member-order: bysource

doc/OnlineDocs/library_reference/common/formatting.rst

@@ -0,0 +1,6 @@
+pyomo.common.formatting
+=======================
+
+.. automodule:: pyomo.common.formatting
+   :members:
+   :member-order: bysource

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

doc/OnlineDocs/library_reference/common/tempfiles.rst

@@ -0,0 +1,7 @@
+
+pyomo.common.tempfiles
+======================
+
+.. automodule:: pyomo.common.tempfiles
+   :members:
+   :member-order: bysource

doc/OnlineDocs/library_reference/solvers/index.rst

@@ -7,3 +7,4 @@ Solver Interfaces
    gams.rst
    cplex_persistent.rst
    gurobi_persistent.rst
+   xpress_persistent.rst

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:

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           |
 +--------------------------+---------------------------------------------------------+---------------------------------------------+

pyomo/common/config.py

@@ -43,6 +43,47 @@
 ADVANCED_OPTION = 1
 DEVELOPER_OPTION = 2
 
+def Bool(val):
+    """Domain validator for bool-like objects.
+
+    This is a more strict domain than ``bool``, as it will error on
+    values that do not "look" like a Boolean value (i.e., it accepts
+    ``True``, ``False``, 0, 1, and the case insensitive strings
+    ``'true'``, ``'false'``, ``'yes'``, ``'no'``, ``'t'``, ``'f'``,
+    ``'y'``, and ``'n'``)
+
+    """
+    if type(val) is bool:
+        return val
+    if isinstance(val, str):
+        v = val.upper()
+        if v in {'TRUE', 'YES', 'T', 'Y', '1'}:
+            return True
+        if v in {'FALSE', 'NO', 'F', 'N', '0'}:
+            return False
+    elif int(val) == float(val):
+        v = int(val)
+        if v in {0, 1}:
+            return bool(v)
+    raise ValueError(
+        "Expected Boolean, but received %s" % (val,))
+
+def Integer(val):
+    """Domain validation function admitting integers
+
+    This domain will admit integers, as well as any values that are
+    "reasonably exactly" convertible to integers.  This is more strict
+    than ``int``, as it will generate errors for floating point values
+    that are not integer.
+
+    """
+    ans = int(val)
+    # We want to give an error for floating point numbers...
+    if ans != float(val):
+        raise ValueError(
+            "Expected integer, but received %s" % (val,))
+    return ans
+
 def PositiveInt(val):
     """Domain validation function admitting strictly positive integers
 
@@ -237,7 +278,38 @@ def __call__(self, value):
             value, self._domain.__name__))
 
 
-class Module:
+class ListOf(object):
+    """Domain validator for lists of a specified type
+
+    Parameters
+    ----------
+    itemtype: type
+        The type for each element in the list
+
+    domain: Callable
+        A domain validator (callable that takes the incoming value,
+        validates it, and returns the appropriate domain type) for each
+        element in the list.  If not specified, defaults to the
+        `itemtype`.
+
+    """
+    def __init__(self, itemtype, domain=None):
+        self.itemtype = itemtype
+        if domain is None:
+            self.domain = self.itemtype
+        else:
+            self.domain = domain
+        self.__name__ = 'ListOf(%s)' % (
+            getattr(self.domain, '__name__', self.domain),)
+
+    def __call__(self, value):
+        if hasattr(value, '__iter__') and not isinstance(value, self.itemtype):
+            return [self.domain(v) for v in value]
+        else:
+            return [self.domain(value)]
+
+
+class Module(object):
     """ Domain validator for modules.
 
     Modules can be specified as module objects, by module name,
@@ -585,6 +657,8 @@ def from_enum_or_string(cls, arg):
 
 .. autosummary::
 
+   Bool
+   Integer
    PositiveInt
    NegativeInt
    NonNegativeInt
@@ -595,6 +669,8 @@ def from_enum_or_string(cls, arg):
    NonNegativeFloat
    In
    InEnum
+   ListOf
+   Module
    Path
    PathList
 

pyomo/common/dependencies.py

@@ -14,7 +14,9 @@
 import logging
 import sys
 
-from .deprecation import deprecated, deprecation_warning
+from .deprecation import (
+    deprecated, deprecation_warning, in_testing_environment,
+)
 from . import numeric_types
 
 class DeferredImportError(ImportError):
@@ -581,7 +583,7 @@ def _finalize_matplotlib(module, available):
     # we are in the middle of testing, we need to switch the backend to
     # 'Agg', otherwise attempts to generate plots on CI services without
     # terminal windows will fail.
-    if any(m in sys.modules for m in ('nose', 'nose2', 'sphinx', 'pytest')):
+    if in_testing_environment():
         module.use('Agg')
     import matplotlib.pyplot
 

pyomo/common/deprecation.py

@@ -123,6 +123,7 @@ def wrapper(*args, **kwargs):
     wrapper.__doc__ += _deprecation_docstring(func, msg, version, remove_in)
     return wrapper
 
+
 def _find_calling_frame(module_offset):
     g = [globals()]
     calling_frame = inspect.currentframe().f_back
@@ -135,6 +136,19 @@ def _find_calling_frame(module_offset):
             break
     return calling_frame
 
+
+def in_testing_environment():
+    """Return True if we are currently running in a "testing" environment
+
+    This currently includes if nose, nose2, pytest, or Sphinx are
+    running (imported).
+
+    """
+
+    return any(mod in sys.modules for mod in (
+        'nose', 'nose2', 'pytest', 'sphinx'))
+
+
 def deprecation_warning(msg, logger=None, version=None,
                         remove_in=None, calling_frame=None):
     """Standardized formatter for deprecation warnings
@@ -168,7 +182,7 @@ def deprecation_warning(msg, logger=None, version=None,
             # function/method that called deprecation_warning
             cf = _find_calling_frame(1)
         if cf is not None:
-            logger = cf.f_globals['__package__']
+            logger = cf.f_globals.get('__package__', None)
             if logger is not None and not logger.startswith('pyomo'):
                 logger = None
         if logger is None:
@@ -189,9 +203,18 @@ def deprecation_warning(msg, logger=None, version=None,
     if calling_frame is not None:
         info = inspect.getframeinfo(calling_frame)
         msg += "\n(called from %s:%s)" % (info.filename.strip(), info.lineno)
+        if deprecation_warning.emitted_warnings is not None:
+            if msg in deprecation_warning.emitted_warnings:
+                return
+            deprecation_warning.emitted_warnings.add(msg)
 
     logging.getLogger(logger).warning(msg)
 
+if in_testing_environment():
+    deprecation_warning.emitted_warnings = None
+else:
+    deprecation_warning.emitted_warnings = set()
+
 
 def deprecated(msg=None, logger=None, version=None, remove_in=None):
     """Decorator to indicate that a function, method or class is deprecated.
@@ -376,14 +399,14 @@ class RenamedClass(type):
         >>> class DerivedOldClass(OldClass):
         ...     pass
         WARNING: DEPRECATED: Declaring class 'DerivedOldClass' derived from
-            'OldClass'. The class 'OldClass' has been renamed to 'NewClass'
+            'OldClass'. The class 'OldClass' has been renamed to 'NewClass'.
             (deprecated in 6.0) ...
 
         As does instantiating the old class:
 
         >>> old = OldClass()
         WARNING: DEPRECATED: Instantiating class 'OldClass'.  The class
-            'OldClass' has been renamed to 'NewClass'  (deprecated in 6.0) ...
+            'OldClass' has been renamed to 'NewClass'.  (deprecated in 6.0) ...
 
         Finally, isinstance and issubclass still work, for example:
 
@@ -394,7 +417,7 @@ class RenamedClass(type):
         >>> new = NewSubclass()
         >>> isinstance(new, OldClass)
         WARNING: DEPRECATED: Checking type relative to 'OldClass'.  The class
-            'OldClass' has been renamed to 'NewClass'  (deprecated in 6.0) ...
+            'OldClass' has been renamed to 'NewClass'.  (deprecated in 6.0) ...
         True
 
     """