def runTests(self):
from fipy.tools import numerix
printoptions = numerix.get_printoptions()
if "legacy" in printoptions:
numerix.set_printoptions(legacy="1.13")
super(_TestProgram, self).runTests()
def GetMesh(self):
"""Create and get the FiPy mesh.
"""
np.set_printoptions(threshold=np.nan)
# print self.vertices
# print self.faces
# print self.cells
return fipy.meshes.mesh2D.Mesh2D(self.vertices, self.faces, self.cells)
def testmod(m=None,
name=None,
globs=None,
verbose=None,
report=True,
optionflags=0,
extraglobs=None,
raise_on_error=False,
exclude_empty=False):
"""Test examples in the given module. Return (#failures, #tests).
Largely duplicated from :func:`doctest.testmod`, but using
:class:`_SelectiveDocTestParser`.
Test examples in docstrings in functions and classes reachable
from module m (or the current module if m is not supplied), starting
with m.__doc__.
Also test examples reachable from dict m.__test__ if it exists and is
not None. m.__test__ maps names to functions, classes and strings;
function and class docstrings are tested even if the name is private;
strings are tested directly, as if they were docstrings.
Return (#failures, #tests).
See help(doctest) for an overview.
Optional keyword arg "name" gives the name of the module; by default
use m.__name__.
Optional keyword arg "globs" gives a dict to be used as the globals
when executing examples; by default, use m.__dict__. A copy of this
dict is actually used for each docstring, so that each docstring's
examples start with a clean slate.
Optional keyword arg "extraglobs" gives a dictionary that should be
merged into the globals that are used to execute examples. By
default, no extra globals are used. This is new in 2.4.
Optional keyword arg "verbose" prints lots of stuff if true, prints
only failures if false; by default, it's true iff "-v" is in sys.argv.
Optional keyword arg "report" prints a summary at the end when true,
else prints nothing at the end. In verbose mode, the summary is
detailed, else very brief (in fact, empty if all tests passed).
Optional keyword arg "optionflags" or's together module constants,
and defaults to 0. This is new in 2.3. Possible values (see the
docs for details):
DONT_ACCEPT_TRUE_FOR_1
DONT_ACCEPT_BLANKLINE
NORMALIZE_WHITESPACE
ELLIPSIS
SKIP
IGNORE_EXCEPTION_DETAIL
REPORT_UDIFF
REPORT_CDIFF
REPORT_NDIFF
REPORT_ONLY_FIRST_FAILURE
as well as FiPy's flags
GMSH
SCIPY
TVTK
SERIAL
PARALLEL
PROCESSOR_0
PROCESSOR_0_OF_2
PROCESSOR_1_OF_2
PROCESSOR_0_OF_3
PROCESSOR_1_OF_3
PROCESSOR_2_OF_3
Optional keyword arg "raise_on_error" raises an exception on the
first unexpected exception or failure. This allows failures to be
postmortem debugged.
"""
# If no module was given, then use __main__.
if m is None:
# DWA - m will still be None if this wasn't invoked from the command
# line, in which case the following TypeError is about as good an error
# as we should expect
m = sys.modules.get('__main__')
# Check that we were actually given a module.
if not inspect.ismodule(m):
raise TypeError("testmod: module required; %r" % (m, ))
# If no name was given, then use the module's name.
if name is None:
name = m.__name__
# Find, parse, and run all tests in the given module.
finder = doctest.DocTestFinder(exclude_empty=exclude_empty,
parser=_SelectiveDocTestParser())
if raise_on_error:
runner = doctest.DebugRunner(verbose=verbose, optionflags=optionflags)
else:
runner = doctest.DocTestRunner(verbose=verbose,
optionflags=optionflags)
from fipy.tools import numerix
printoptions = numerix.get_printoptions()
if "legacy" in printoptions:
numerix.set_printoptions(legacy="1.13")
for test in finder.find(m, name, globs=globs, extraglobs=extraglobs):
runner.run(test)
if report:
runner.summarize()
report_skips()
results = doctest.TestResults(runner.failures, runner.tries)
if "legacy" in printoptions:
numerix.set_printoptions(legacy=printoptions["legacy"])
return results
def run_tests(self):
import sys
if self.Trilinos or self.trilinos or self.no_pysparse:
try:
## The import scipy statement is added to allow
## the --Trilinos tests to run without throwing a
## segmentation fault. This is caused by weird
## behavior in scipy and PyTrilinos depending on
## the order in which modules are imported
try:
import scipy
except:
pass
import PyTrilinos
except ImportError as a:
print("!!! Trilinos library is not installed", file=sys.stderr)
return
if self.pyamgx:
try:
## Unregister the function pyamgx.finalize
## from atexit. This prevents
## pyamgx from printing an error message
## about memory leaks and a dump of leaked memory.
## The memory leaks happen because
## the tests do not use the pyamgx solvers
## "cleanly", i.e., they do not use the
## `with` statement.
import pyamgx
import atexit
if hasattr(atexit, 'unregister'):
atexit.unregister(pyamgx.finalize)
else:
atexit._exithandlers.remove((pyamgx.finalize, (), {}))
except ImportError as e:
print("!!! pyamgx package is not installed", file=sys.stederr)
return
if self.inline:
try:
import weave
except ImportError as a:
print("!!! weave library is not installed", file=sys.stderr)
return
if self.pythoncompiled is not None:
import os
os.environ['PYTHONCOMPILED'] = self.pythoncompiled
self.printPackageInfo()
from pkg_resources import EntryPoint
import unittest
loader_ep = EntryPoint.parse("x=" + self.test_loader)
loader_class = loader_ep.load(require=False)
from fipy.tools import numerix
printoptions = numerix.get_printoptions()
if "legacy" in printoptions:
numerix.set_printoptions(legacy="1.13")
try:
unittest.main(None,
None, [unittest.__file__] + self.test_args,
testLoader=loader_class())
except SystemExit as exitErr:
# unittest.main(..., exit=...) not available until Python 2.7
from fipy.tests.doctestPlus import report_skips
report_skips()
if self.timetests is not None:
pass
else:
raise
if "legacy" in printoptions:
numerix.set_printoptions(legacy=printoptions["legacy"])
if self.timetests is not None:
from fipy.tests.doctestPlus import _DocTestTimes
import numpy
_DocTestTimes = numpy.rec.fromrecords(_DocTestTimes,
formats='f8,S255',
names='time,test')
_DocTestTimes.sort(order=('time', 'test'))
numpy.savetxt(self.timetests, _DocTestTimes[::-1], fmt="%8.4f\t%s")
raise exitErr
from datetime import datetime, timedelta
home_dir = os.getcwd()
dir_name = "/results"
dir_name2 = home_dir + dir_name
test = os.listdir(dir_name2)
for item in test:
if item.endswith("9a.txt"):
os.remove(os.path.join(dir_name2, item))
if item.endswith("9a.vtk"):
os.remove(os.path.join(dir_name2, item))
if item.endswith("9a.vtp"):
os.remove(os.path.join(dir_name2, item))
np.set_printoptions(threshold=sys.maxsize)
class NullIO(StringIO):
def write(self, txt):
pass
######################
#
# plant
#
#######################
pl = pb.MappedPlant() #pb.MappedRootSystem() #pb.MappedPlant()
path = "../../../modelparameter/plant/" #"../../../modelparameter/rootsystem/"
name = "oneroot_mgiraud" #"smallPlant_mgiraud"#"manyleaves"#"smallPlant"# "oneroot" #"Anagallis_femina_Leitner_2010" # Zea_mays_1_Leitner_2010
pl.readParameters(path + name + ".xml")
if self.pythoncompiled is not None:
import os
os.environ['PYTHONCOMPILED'] = self.pythoncompiled
self.printPackageInfo()
from pkg_resources import EntryPoint
import unittest
loader_ep = EntryPoint.parse("x=" + self.test_loader)
loader_class = loader_ep.load(require=False)
from fipy.tools import numerix
printoptions = numerix.get_printoptions()
if "legacy" in printoptions:
numerix.set_printoptions(legacy="1.13")
try:
unittest.main(None,
None, [unittest.__file__] + self.test_args,
testLoader=loader_class())
except SystemExit, exitErr:
# unittest.main(..., exit=...) not available until Python 2.7
from fipy.tests.doctestPlus import report_skips
report_skips()
if self.timetests is not None:
pass
else:
raise
if "legacy" in printoptions:
def run_tests(self):
import sys
if self.Trilinos or self.trilinos or self.no_pysparse:
try:
## The import scipy statement is added to allow
## the --Trilinos tests to run without throwing a
## segmentation fault. This is caused by weird
## behavior in scipy and PyTrilinos depending on
## the order in which modules are imported
try:
import scipy
except:
pass
import PyTrilinos
except ImportError as a:
print("!!! Trilinos library is not installed", file=sys.stderr)
return
if self.pyamgx:
try:
## Unregister the function pyamgx.finalize
## from atexit. This prevents
## pyamgx from printing an error message
## about memory leaks and a dump of leaked memory.
## The memory leaks happen because
## the tests do not use the pyamgx solvers
## "cleanly", i.e., they do not use the
## `with` statement.
import pyamgx
import atexit
if hasattr(atexit, 'unregister'):
atexit.unregister(pyamgx.finalize)
else:
atexit._exithandlers.remove(
(pyamgx.finalize, (), {}))
except ImportError as e:
print("!!! pyamgx package is not installed", file=sys.stederr)
return
if self.inline:
try:
import weave
except ImportError as a:
print("!!! weave library is not installed", file=sys.stderr)
return
if self.pythoncompiled is not None:
import os
os.environ['PYTHONCOMPILED'] = self.pythoncompiled
self.printPackageInfo()
from pkg_resources import EntryPoint
import unittest
loader_ep = EntryPoint.parse("x="+self.test_loader)
loader_class = loader_ep.load(require=False)
from fipy.tools import numerix
printoptions = numerix.get_printoptions()
if "legacy" in printoptions:
numerix.set_printoptions(legacy="1.13")
try:
unittest.main(
None, None, [unittest.__file__]+self.test_args,
testLoader = loader_class()
)
except SystemExit as exitErr:
# unittest.main(..., exit=...) not available until Python 2.7
from fipy.tests.doctestPlus import report_skips
report_skips()
if self.timetests is not None:
pass
else:
raise
if "legacy" in printoptions:
numerix.set_printoptions(legacy=printoptions["legacy"])
if self.timetests is not None:
from fipy.tests.doctestPlus import _DocTestTimes
import numpy
_DocTestTimes = numpy.rec.fromrecords(_DocTestTimes, formats='f8,S255', names='time,test')
_DocTestTimes.sort(order=('time', 'test'))
numpy.savetxt(self.timetests, _DocTestTimes[::-1], fmt="%8.4f\t%s")
raise exitErr
def testmod(m=None, name=None, globs=None, verbose=None,
report=True, optionflags=0, extraglobs=None,
raise_on_error=False, exclude_empty=False):
"""Test examples in the given module. Return (#failures, #tests).
Largely duplicated from :func:`doctest.testmod`, but using
:class:`_SelectiveDocTestParser`.
Test examples in docstrings in functions and classes reachable
from module m (or the current module if m is not supplied), starting
with m.__doc__.
Also test examples reachable from dict m.__test__ if it exists and is
not None. m.__test__ maps names to functions, classes and strings;
function and class docstrings are tested even if the name is private;
strings are tested directly, as if they were docstrings.
Return (#failures, #tests).
See help(doctest) for an overview.
Optional keyword arg "name" gives the name of the module; by default
use m.__name__.
Optional keyword arg "globs" gives a dict to be used as the globals
when executing examples; by default, use m.__dict__. A copy of this
dict is actually used for each docstring, so that each docstring's
examples start with a clean slate.
Optional keyword arg "extraglobs" gives a dictionary that should be
merged into the globals that are used to execute examples. By
default, no extra globals are used. This is new in 2.4.
Optional keyword arg "verbose" prints lots of stuff if true, prints
only failures if false; by default, it's true iff "-v" is in sys.argv.
Optional keyword arg "report" prints a summary at the end when true,
else prints nothing at the end. In verbose mode, the summary is
detailed, else very brief (in fact, empty if all tests passed).
Optional keyword arg "optionflags" or's together module constants,
and defaults to 0. This is new in 2.3. Possible values (see the
docs for details):
DONT_ACCEPT_TRUE_FOR_1
DONT_ACCEPT_BLANKLINE
NORMALIZE_WHITESPACE
ELLIPSIS
SKIP
IGNORE_EXCEPTION_DETAIL
REPORT_UDIFF
REPORT_CDIFF
REPORT_NDIFF
REPORT_ONLY_FIRST_FAILURE
as well as FiPy's flags
GMSH
SCIPY
TVTK
SERIAL
PARALLEL
PROCESSOR_0
PROCESSOR_0_OF_2
PROCESSOR_1_OF_2
PROCESSOR_0_OF_3
PROCESSOR_1_OF_3
PROCESSOR_2_OF_3
Optional keyword arg "raise_on_error" raises an exception on the
first unexpected exception or failure. This allows failures to be
postmortem debugged.
"""
# If no module was given, then use __main__.
if m is None:
# DWA - m will still be None if this wasn't invoked from the command
# line, in which case the following TypeError is about as good an error
# as we should expect
m = sys.modules.get('__main__')
# Check that we were actually given a module.
if not inspect.ismodule(m):
raise TypeError("testmod: module required; %r" % (m,))
# If no name was given, then use the module's name.
if name is None:
name = m.__name__
# Find, parse, and run all tests in the given module.
finder = doctest.DocTestFinder(exclude_empty=exclude_empty,
parser=_SelectiveDocTestParser())
if raise_on_error:
runner = doctest.DebugRunner(verbose=verbose, optionflags=optionflags)
else:
runner = doctest.DocTestRunner(verbose=verbose, optionflags=optionflags)
from fipy.tools import numerix
printoptions = numerix.get_printoptions()
if "legacy" in printoptions:
numerix.set_printoptions(legacy="1.13")
for test in finder.find(m, name, globs=globs, extraglobs=extraglobs):
runner.run(test)
if report:
runner.summarize()
report_skips()
results = doctest.TestResults(runner.failures, runner.tries)
if "legacy" in printoptions:
numerix.set_printoptions(legacy=printoptions["legacy"])
return results