def run_examples(example, pipelines, plugin):
print 'running example: %s with plugin: %s'%(example, plugin)
from nipype.utils.config import NipypeConfig
config = NipypeConfig()
config.enable_debug_mode()
__import__(example)
for pipeline in pipelines:
wf = getattr(sys.modules[example], pipeline)
wf.base_dir = os.path.join(os.getcwd(), 'output', example, plugin)
if os.path.exists(wf.base_dir):
rmtree(wf.base_dir)
wf.config = {'execution' :{'hash_method': 'timestamp', 'stop_on_first_rerun': 'true'}}
wf.run(plugin=plugin, plugin_args={'n_procs': 4})
#run twice to check if nothing is rerunning
wf.run(plugin=plugin)
def run_examples(example, pipelines, plugin):
print 'running example: %s with plugin: %s' % (example, plugin)
from nipype.utils.config import NipypeConfig
config = NipypeConfig()
config.enable_debug_mode()
__import__(example)
for pipeline in pipelines:
wf = getattr(sys.modules[example], pipeline)
wf.base_dir = os.path.join(os.getcwd(), 'output', example, plugin)
if os.path.exists(wf.base_dir):
rmtree(wf.base_dir)
wf.config = {
'execution': {
'hash_method': 'timestamp',
'stop_on_first_rerun': 'true'
}
}
wf.run(plugin=plugin, plugin_args={'n_procs': 4})
#run twice to check if nothing is rerunning
wf.run(plugin=plugin)
""" Test the nipype interface caching mechanism
"""
from tempfile import mkdtemp
from shutil import rmtree
from nose.tools import assert_equal
from nipype.caching import Memory
from nipype.pipeline.tests.test_engine import TestInterface
from nipype.utils.config import NipypeConfig
config = NipypeConfig()
config.set_default_config()
nb_runs = 0
class SideEffectInterface(TestInterface):
def _run_interface(self, runtime):
global nb_runs
nb_runs += 1
runtime.returncode = 0
return runtime
def test_caching():
temp_dir = mkdtemp(prefix='test_memory_')
old_rerun = config.get('execution', 'stop_on_first_rerun')
try:
# Prevent rerun to check that evaluation is computed only once
from nipype.utils.config import NipypeConfig from nipype.utils.logger import Logging config = NipypeConfig() logging = Logging(config)
""" Test the nipype interface caching mechanism
"""
from tempfile import mkdtemp
from shutil import rmtree
from nose.tools import assert_equal
from nipype.caching import Memory
from nipype.pipeline.tests.test_engine import TestInterface
from nipype.utils.config import NipypeConfig
config = NipypeConfig()
config.set_default_config()
nb_runs = 0
class SideEffectInterface(TestInterface):
def _run_interface(self, runtime):
global nb_runs
nb_runs += 1
runtime.returncode = 0
return runtime
def test_caching():
temp_dir = mkdtemp(prefix='test_memory_')
old_rerun = config.get('execution', 'stop_on_first_rerun')
try:
# Prevent rerun to check that evaluation is computed only once
config.set('execution', 'stop_on_first_rerun', 'true')
