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[wip]Fix/deprecated 2551 (closes #2551 #2508) #2552

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Merged
merged 5 commits into from
Apr 26, 2018
Merged

[wip]Fix/deprecated 2551 (closes #2551 #2508) #2552

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9ec00dc
removing ignore_exception=True from CommandLine call (ignore_exceptio…
djarecka Apr 25, 2018
708ac1c
removing terminal_output from CommandLine call (ignore_exception is d…
djarecka Apr 25, 2018
448b875
Revert "removing terminal_output from CommandLine call (ignore_except…
djarecka Apr 26, 2018
573582e
Revert "removing ignore_exception=True from CommandLine call (ignore_…
djarecka Apr 26, 2018
22e9dca
adding ignore_exception to run, removing terminal_output input trait …
djarecka Apr 26, 2018
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15 changes: 6 additions & 9 deletions nipype/interfaces/base/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -445,7 +445,7 @@ def _duecredit_cite(self):
r['path'] = self.__module__
due.cite(**r)

def run(self, cwd=None, **inputs):
def run(self, cwd=None, ignore_exception=None, **inputs):
"""Execute this interface.

This interface will not raise an exception if runtime.returncode is
Expand All @@ -464,6 +464,10 @@ def run(self, cwd=None, **inputs):
"""
from ...utils.profiler import ResourceMonitor

# if ignore_exception is not provided, taking self.ignore_exception
if ignore_exception is None:
ignore_exception = self.ignore_exception

# Tear-up: get current and prev directories
syscwd = rgetcwd(error=False) # Recover when wd does not exist
if cwd is None:
Expand Down Expand Up @@ -531,7 +535,7 @@ def run(self, cwd=None, **inputs):
runtime.traceback_args = ('\n'.join(
['%s' % arg for arg in exc_args]), )

if not self.ignore_exception:
if not ignore_exception:
raise
finally:
# This needs to be done always
Expand Down Expand Up @@ -919,10 +923,6 @@ def __init__(self, command=None, terminal_output=None, **inputs):
if terminal_output is not None:
self.terminal_output = terminal_output

# Attach terminal_output callback for backwards compatibility
self.inputs.on_trait_change(self._terminal_output_update,
'terminal_output')

@property
def cmd(self):
"""sets base command, immutable"""
Expand Down Expand Up @@ -950,9 +950,6 @@ def terminal_output(self, value):
for v in VALID_TERMINAL_OUTPUT])))
self._terminal_output = value

def _terminal_output_update(self):
self.terminal_output = self.terminal_output

def raise_exception(self, runtime):
raise RuntimeError(
('Command:\n{cmdline}\nStandard output:\n{stdout}\n'
Expand Down