Merge remote-tracking branch 'upstream/master' into afni_volreg_inweightvol

Author: effigies

CHANGES

@@ -6,6 +6,7 @@ Upcoming release
 
 ###### [Full changelog](https://github.com/nipy/nipype/milestone/16?closed=1)
 
+* FIX: Change to interface workdir within ``Interface.run()`` instead Node (https://github.com/nipy/nipype/pull/2384)
 * FIX: PBS plugin submissions (https://github.com/nipy/nipype/pull/2344)
 * FIX: Graph plugins submissions (https://github.com/nipy/nipype/pull/2359)
 * FIX: Logging error if % in interface command (https://github.com/nipy/nipype/pull/2364)

doc/users/saving_workflows.rst

@@ -66,34 +66,34 @@ This will create a file "outputtestsave.py" with the following content:
 	inode = Node(IdentityInterface(fields=['a'], mandatory_inputs=True), name="inode")
 	# Node: testsave.testfunc
 	testfunc = Node(Function(input_names=['a'], output_names=['output']), name="testfunc")
+	testfunc.interface.ignore_exception = False
 	def testfunc_1(in1):
 	    """dummy func
 	    """
 	    out = in1 + 'foo' + "out1"
 	    return out
 
 	testfunc.inputs.function_str = getsource(testfunc_1)
-	testfunc.inputs.ignore_exception = False
 	testfunc.inputs.in1 = '-sub'
 	testsave.connect(inode, "a", testfunc, "in1")
 	# Node: testsave.bet2
 	bet2 = MapNode(BET(), iterfield=['infile'], name="bet2")
+	bet2.interface.ignore_exception = False
 	bet2.iterables = ('frac', [0.4, 0.5])
 	bet2.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
-	bet2.inputs.ignore_exception = False
 	bet2.inputs.output_type = 'NIFTI_GZ'
 	bet2.terminal_output = 'stream'
 	# Node: testsave.bet
 	bet = Node(BET(), name="bet")
+	bet.interface.ignore_exception = False
 	bet.iterables = ('frac', [0.3, 0.4])
 	bet.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
-	bet.inputs.ignore_exception = False
 	bet.inputs.output_type = 'NIFTI_GZ'
 	bet.terminal_output = 'stream'
 	# Node: testsave.maths
 	maths = Node(ImageMaths(), name="maths")
+	maths.interface.ignore_exception = False
 	maths.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
-	maths.inputs.ignore_exception = False
 	maths.inputs.output_type = 'NIFTI_GZ'
 	maths.terminal_output = 'stream'
 	testsave.connect(bet2, ('mask_file', func), maths, "in_file2")

nipype/caching/memory.py

@@ -94,7 +94,7 @@ def __call__(self, **kwargs):
         return out
 
     def __repr__(self):
-        return '{}({}.{}}, base_dir={})'.format(
+        return '{}({}.{}), base_dir={})'.format(
             self.__class__.__name__, self.interface.__module__,
             self.interface.__name__, self.base_dir)
 

nipype/interfaces/afni/model.py

@@ -142,7 +142,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         desc='this option lets you input a rectangular array of 1 or more '
         'baseline vectors from a file. This method is a fast way to '
         'include a lot of baseline regressors in one step. ',
-        argstr='ortvec %s')
+        argstr='-ortvec %s %s')
     x1D = File(desc='specify name for saved X matrix', argstr='-x1D %s')
     x1D_stop = traits.Bool(
         desc='stop running after writing .xmat.1D file', argstr='-x1D_stop')

nipype/interfaces/afni/tests/test_auto_Deconvolve.py

@@ -73,7 +73,7 @@ def test_Deconvolve_inputs():
             nohash=True,
             usedefault=True,
         ),
-        ortvec=dict(argstr='ortvec %s', ),
+        ortvec=dict(argstr='-ortvec %s %s', ),
         out_file=dict(argstr='-bucket %s', ),
         outputtype=dict(),
         polort=dict(argstr='-polort %d', ),

nipype/interfaces/base/core.py

@@ -170,12 +170,14 @@ class BaseInterface(Interface):
     references_ = []
     resource_monitor = True  # Enabled for this interface IFF enabled in the config
 
-    def __init__(self, from_file=None, resource_monitor=None, **inputs):
+    def __init__(self, from_file=None, resource_monitor=None,
+                 ignore_exception=False, **inputs):
         if not self.input_spec:
             raise Exception(
                 'No input_spec in class: %s' % self.__class__.__name__)
 
         self.inputs = self.input_spec(**inputs)
+        self.ignore_exception = ignore_exception
 
         if resource_monitor is not None:
             self.resource_monitor = resource_monitor
@@ -470,7 +472,6 @@ def run(self, cwd=None, **inputs):
         os.chdir(cwd)  # Change to the interface wd
 
         enable_rm = config.resource_monitor and self.resource_monitor
-        force_raise = not getattr(self.inputs, 'ignore_exception', False)
         self.inputs.trait_set(**inputs)
         self._check_mandatory_inputs()
         self._check_version_requirements(self.inputs)
@@ -530,7 +531,7 @@ def run(self, cwd=None, **inputs):
             runtime.traceback_args = ('\n'.join(
                 ['%s' % arg for arg in exc_args]), )
 
-            if force_raise:
+            if not self.ignore_exception:
                 raise
         finally:
             # This needs to be done always

nipype/pipeline/plugins/slurmgraph.py

@@ -44,6 +44,7 @@ class SLURMGraphPlugin(GraphPluginBase):
     _template = "#!/bin/bash"
 
     def __init__(self, **kwargs):
+        self._sbatch_args = ''
         if 'plugin_args' in kwargs and kwargs['plugin_args']:
             if 'retry_timeout' in kwargs['plugin_args']:
                 self._retry_timeout = kwargs['plugin_args']['retry_timeout']

nipype/utils/filemanip.py

@@ -3,6 +3,13 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Miscellaneous file manipulation functions
 
+  .. testsetup::
+    # Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname(os.path.realpath( __file__ ))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
+    >>> os.chdir(datadir)
+
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
@@ -222,19 +229,38 @@ def check_forhash(filename):
         return False, None
 
 
-def hash_infile(afile, chunk_len=8192, crypto=hashlib.md5):
-    """ Computes hash of a file using 'crypto' module"""
-    hex = None
-    if op.isfile(afile):
-        crypto_obj = crypto()
-        with open(afile, 'rb') as fp:
-            while True:
-                data = fp.read(chunk_len)
-                if not data:
-                    break
-                crypto_obj.update(data)
-        hex = crypto_obj.hexdigest()
-    return hex
+def hash_infile(afile, chunk_len=8192, crypto=hashlib.md5,
+                raise_notfound=False):
+    """
+    Computes hash of a file using 'crypto' module
+
+    >>> hash_infile('smri_ants_registration_settings.json')
+    '49b956387ed8d95a4eb44576fc5103b6'
+
+    >>> hash_infile('surf01.vtk')
+    'fdf1cf359b4e346034372cdeb58f9a88'
+
+    >>> hash_infile('spminfo')
+    '0dc55e3888c98a182dab179b976dfffc'
+
+    >>> hash_infile('fsl_motion_outliers_fd.txt')
+    'defd1812c22405b1ee4431aac5bbdd73'
+
+
+    """
+    if not op.isfile(afile):
+        if raise_notfound:
+            raise RuntimeError('File "%s" not found.' % afile)
+        return None
+
+    crypto_obj = crypto()
+    with open(afile, 'rb') as fp:
+        while True:
+            data = fp.read(chunk_len)
+            if not data:
+                break
+            crypto_obj.update(data)
+    return crypto_obj.hexdigest()
 
 
 def hash_timestamp(afile):

nipype/workflows/smri/ants/ANTSBuildTemplate.py

@@ -183,7 +183,7 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''):
             output_names=['out']),
         run_without_submitting=True,
         name='MakeTransformsLists')
-    MakeTransformsLists.inputs.ignore_exception = True
+    MakeTransformsLists.interface.ignore_exception = True
     TemplateBuildSingleIterationWF.connect(
         BeginANTS, 'warp_transform', MakeTransformsLists, 'warpTransformList')
     TemplateBuildSingleIterationWF.connect(BeginANTS, 'affine_transform',
@@ -263,7 +263,7 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''):
             output_names=['TransformListWithGradientWarps']),
         run_without_submitting=True,
         name='MakeTransformListWithGradientWarps')
-    ApplyInvAverageAndFourTimesGradientStepWarpImage.inputs.ignore_exception = True
+    ApplyInvAverageAndFourTimesGradientStepWarpImage.interface.ignore_exception = True
 
     TemplateBuildSingleIterationWF.connect(
         AvgAffineTransform, 'affine_transform',

nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py

@@ -360,7 +360,7 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''):
             output_names=['TransformListWithGradientWarps']),
         run_without_submitting=True,
         name='99_MakeTransformListWithGradientWarps')
-    ApplyInvAverageAndFourTimesGradientStepWarpImage.inputs.ignore_exception = True
+    ApplyInvAverageAndFourTimesGradientStepWarpImage.interface.ignore_exception = True
 
     TemplateBuildSingleIterationWF.connect(
         AvgAffineTransform, 'affine_transform',