def main():
if __debug__:
from mvpa.base import debug
# Lets add some targets which provide additional testing
debug.active += ['CHECK_.*']
# NOTE: it had to be done here instead of test_clf.py for
# instance, since for CHECK_RETRAIN it has to be set before object
# gets created, ie while importing clfs.warehouse
suites = collectTestSuites()
# and make global test suite
ts = unittest.TestSuite(suites.values())
# no MVPA warnings during whole testsuite
warning.handlers = []
# No python warnings (like ctypes version for slmr)
import warnings
warnings.simplefilter('ignore')
class TextTestRunnerPyMVPA(unittest.TextTestRunner):
"""Extend TextTestRunner to print out random seed which was
used in the case of failure"""
def run(self, test):
result = super(TextTestRunnerPyMVPA, self).run(test)
if not result.wasSuccessful():
print "MVPA_SEED=%s" % _random_seed
sys.exit(1)
return result
# finally run it
TextTestRunnerPyMVPA(
verbosity=int(cfg.get('tests', 'verbosity', default=1))
).run(ts)
def run(limit=None, verbosity=None):
"""Runs the full or a subset of the PyMVPA unittest suite.
Parameters
----------
limit : None or list
If None, the full test suite is run. Alternatively, a list with test IDs
can be provides. IDs are the base filenames of the test implementation,
e.g. the ID for the suite in 'mvpa/tests/test_niftidataset.py' is
'niftidataset'.
verbosity : None or int
Verbosity of unittests execution. If None, controlled by PyMVPA
configuration tests/verbosity
"""
if __debug__:
from mvpa.base import debug
# Lets add some targets which provide additional testing
debug.active += ['CHECK_.*']
# collect all tests
suites = collect_test_suites()
if limit is None:
# make global test suite (use them all)
ts = unittest.TestSuite(suites.values())
else:
ts = unittest.TestSuite([suites[s] for s in limit])
# no MVPA warnings during whole testsuite (but restore handlers later on)
handler_backup = warning.handlers
warning.handlers = []
# No python warnings (like ctypes version for slmr)
import warnings
warnings.simplefilter('ignore')
class TextTestRunnerPyMVPA(unittest.TextTestRunner):
"""Extend TextTestRunner to print out random seed which was
used in the case of failure"""
def run(self, test):
"""Run the bloody test and puke the seed value if failed"""
result = super(TextTestRunnerPyMVPA, self).run(test)
if not result.wasSuccessful():
print "MVPA_SEED=%s" % _random_seed
if verbosity is None:
verbosity = int(cfg.get('tests', 'verbosity', default=1))
# finally run it
TextTestRunnerPyMVPA(verbosity=verbosity).run(ts)
# and nose tests
run_nose_tests()
# restore warning handlers
warning.handlers = handler_backup
def __check_matplotlib():
"""Check for presence of matplotlib and set backend if requested."""
import matplotlib
backend = cfg.get('matplotlib', 'backend')
if backend:
matplotlib.use(backend)
import warnings
# And disable useless warning from matplotlib in the future
warnings.filterwarnings(
'ignore', 'This call to matplotlib.use() has no effect.*',
UserWarning)
def __check_rpy2():
"""Check either rpy2 is available and also set it for the sane execution
"""
import rpy2
versions['rpy2'] = rpy2.__version__
import rpy2.robjects
r = rpy2.robjects.r
r.options(warn=cfg.get('rpy', 'warn', default=-1))
# To shut R up while it is importing libraries to do not ruin out
# doctests
r.library = lambda libname: \
r("suppressPackageStartupMessages(library(%r))" % libname)
def _set_matplotlib_backend():
"""Check if we have custom backend to set and it is different
from current one
"""
backend = cfg.get('matplotlib', 'backend')
if backend:
import matplotlib as mpl
mpl_backend = mpl.get_backend().lower()
if mpl_backend != backend.lower():
if __debug__:
debug('EXT_', "Trying to set matplotlib backend to %s" % backend)
mpl.use(backend)
import warnings
# And disable useless warning from matplotlib in the future
warnings.filterwarnings(
'ignore', 'This call to matplotlib.use() has no effect.*',
UserWarning)
elif __debug__:
debug('EXT_',
"Not trying to set matplotlib backend to %s since it was "
"already set" % backend)
def _set_matplotlib_backend():
"""Check if we have custom backend to set and it is different
from current one
"""
backend = cfg.get('matplotlib', 'backend')
if backend:
import matplotlib as mpl
mpl_backend = mpl.get_backend().lower()
if mpl_backend != backend.lower():
if __debug__:
debug('EXT_',
"Trying to set matplotlib backend to %s" % backend)
mpl.use(backend)
import warnings
# And disable useless warning from matplotlib in the future
warnings.filterwarnings(
'ignore', 'This call to matplotlib.use() has no effect.*',
UserWarning)
elif __debug__:
debug(
'EXT_',
"Not trying to set matplotlib backend to %s since it was "
"already set" % backend)
def __check_matplotlib():
"""Check for presence of matplotlib and set backend if requested."""
import matplotlib
backend = cfg.get('matplotlib', 'backend')
if backend:
matplotlib.use(backend)
def run(limit=None, verbosity=None, exit_=False):
"""Runs the full or a subset of the PyMVPA unittest suite.
Parameters
----------
limit : None or list
If None, the full test suite is run. Alternatively, a list with test IDs
can be provides. IDs are the base filenames of the test implementation,
e.g. the ID for the suite in 'mvpa/tests/test_niftidataset.py' is
'niftidataset'.
verbosity : None or int
Verbosity of unittests execution. If None, controlled by PyMVPA
configuration tests/verbosity. Values >=3 enable all Python,
and PyMVPA warnings, >=4 adds NumPy warnings, >=5 -- nose debug info.
exit_ : bool, optional
Either to exit with an error code upon the completion.
"""
if __debug__:
from mvpa.base import debug
# Lets add some targets which provide additional testing
debug.active += ['CHECK_.*']
if verbosity is None:
verbosity = int(cfg.get('tests', 'verbosity', default=1))
# provide people with a hint about the warnings that might show up in a
# second
if verbosity:
print("T: MVPA_SEED=%s" % _random_seed)
if verbosity > 1:
print('T: Testing for availability of external software packages.')
# So we could see all warnings about missing dependencies
maxcount = warning.maxcount
warning.maxcount = 1000
# fully test of externals
externals.test_all_dependencies(verbosity=max(0, verbosity-1))
if verbosity < 3:
# no MVPA warnings during whole testsuite (but restore handlers later on)
handler_backup = warning.handlers
warning.handlers = []
# No python warnings (like ctypes version for slmr)
import warnings
warnings.simplefilter('ignore')
if verbosity < 4:
# No NumPy
np_errsettings = np.geterr()
np.seterr(**dict([(x, 'ignore') for x in np_errsettings]))
try:
if externals.exists('nose'):
# Lets just use nose
run_tests_using_nose(limit=limit,
verbosity=verbosity,
exit_=exit_)
else:
print("T: Warning -- major bulk of tests is skipped since nose "
"is unavailable")
# collect all tests
suites = collect_test_suites(verbosity=verbosity)
if limit is None:
# make global test suite (use them all)
ts = unittest.TestSuite(suites.values())
else:
ts = unittest.TestSuite([suites[s] for s in limit])
class TextTestRunnerPyMVPA(unittest.TextTestRunner):
"""Extend TextTestRunner to print out random seed which was
used in the case of failure"""
def run(self, test):
"""Run the bloody test and puke the seed value if failed"""
result = super(TextTestRunnerPyMVPA, self).run(test)
if not result.wasSuccessful():
print "MVPA_SEED=%s" % _random_seed
# finally run it
TextTestRunnerPyMVPA(verbosity=verbosity).run(ts)
finally:
# restore warning handlers
warning.maxcount = maxcount
if verbosity < 3:
# restore warning handlers
warning.handlers = handler_backup
if verbosity < 4:
# restore numpy settings
np.seterr(**np_errsettings)
def run(limit=None, verbosity=None, exit_=False):
"""Runs the full or a subset of the PyMVPA unittest suite.
Parameters
----------
limit : None or list
If None, the full test suite is run. Alternatively, a list with test IDs
can be provides. IDs are the base filenames of the test implementation,
e.g. the ID for the suite in 'mvpa/tests/test_niftidataset.py' is
'niftidataset'.
verbosity : None or int
Verbosity of unittests execution. If None, controlled by PyMVPA
configuration tests/verbosity
exit_ : bool, optional
Either to exit with an error code upon the completion.
"""
if __debug__:
from mvpa.base import debug
# Lets add some targets which provide additional testing
debug.active += ['CHECK_.*']
if verbosity is None:
verbosity = int(cfg.get('tests', 'verbosity', default=1))
# provide people with a hint about the warnings that might show up in a
# second
if verbosity:
print("T: MVPA_SEED=%s" % _random_seed)
if verbosity > 1:
print('T: Testing for availability of external software packages.')
# So we could see all warnings about missing dependencies
warning.maxcount = 1000
# fully test of externals
externals.test_all_dependencies(verbosity=max(0, verbosity - 1))
# no MVPA warnings during whole testsuite (but restore handlers later on)
handler_backup = warning.handlers
warning.handlers = []
# No python warnings (like ctypes version for slmr)
import warnings
warnings.simplefilter('ignore')
try:
if externals.exists('nose'):
# Lets just use nose
run_tests_using_nose(limit=limit, verbosity=verbosity, exit_=exit_)
else:
print(
"T: Warning -- major bulk of tests is skipped since nose "
"is unavailable")
# collect all tests
suites = collect_test_suites(verbosity=verbosity)
if limit is None:
# make global test suite (use them all)
ts = unittest.TestSuite(suites.values())
else:
ts = unittest.TestSuite([suites[s] for s in limit])
class TextTestRunnerPyMVPA(unittest.TextTestRunner):
"""Extend TextTestRunner to print out random seed which was
used in the case of failure"""
def run(self, test):
"""Run the bloody test and puke the seed value if failed"""
result = super(TextTestRunnerPyMVPA, self).run(test)
if not result.wasSuccessful():
print "MVPA_SEED=%s" % _random_seed
if verbosity is None:
verbosity = int(cfg.get('tests', 'verbosity', default=1))
# finally run it
TextTestRunnerPyMVPA(verbosity=verbosity).run(ts)
finally:
# restore warning handlers
warning.handlers = handler_backup