[WIP] Lightweight implementation of InterfaceResult

examples/fmri_freesurfer_smooth.py

@@ -420,7 +420,7 @@
 
 
 def subjectinfo(subject_id):
-    from nipype.interfaces.base import Bunch
+    from nipype.utils.bunch import Bunch
     from copy import deepcopy
     print("Subject ID: %s\n" % str(subject_id))
     output = []

examples/fmri_fsl.py

@@ -551,7 +551,7 @@ def num_copes(files):
 
 
 def subjectinfo(subject_id):
-    from nipype.interfaces.base import Bunch
+    from nipype.utils.bunch import Bunch
     from copy import deepcopy
     print("Subject ID: %s\n" % str(subject_id))
     output = []

examples/fmri_fsl_feeds.py

@@ -24,7 +24,7 @@
 from nipype.algorithms import modelgen as model  # model generation
 from nipype.workflows.fmri.fsl import (
     create_featreg_preproc, create_modelfit_workflow, create_reg_workflow)
-from nipype.interfaces.base import Bunch
+from nipype.utils.bunch import Bunch
 """
 Preliminaries
 -------------

examples/fmri_fsl_reuse.py

@@ -190,7 +190,7 @@ def num_copes(files):
 
 
 def subjectinfo(subject_id):
-    from nipype.interfaces.base import Bunch
+    from nipype.utils.bunch import Bunch
     from copy import deepcopy
     print("Subject ID: %s\n" % str(subject_id))
     output = []

examples/fmri_nipy_glm.py

@@ -147,7 +147,7 @@
 
 
 def subjectinfo(subject_id):
-    from nipype.interfaces.base import Bunch
+    from nipype.utils.bunch import Bunch
     from copy import deepcopy
     print("Subject ID: %s\n" % str(subject_id))
     output = []

examples/fmri_spm.py

@@ -171,7 +171,7 @@
 
 
 def subjectinfo(subject_id):
-    from nipype.interfaces.base import Bunch
+    from nipype.utils.bunch import Bunch
     from copy import deepcopy
     print("Subject ID: %s\n" % str(subject_id))
     output = []

examples/fmri_spm_auditory.py

@@ -267,7 +267,7 @@ def makelist(item):
 necessary to generate an SPM design matrix.
 """
 
-from nipype.interfaces.base import Bunch
+from nipype.utils.bunch import Bunch
 subjectinfo = [
     Bunch(
         conditions=['Task'], onsets=[list(range(6, 84, 12))], durations=[[6]])

examples/fmri_spm_dartel.py

@@ -314,7 +314,7 @@ def pickFieldFlow(dartel_flow_fields, subject_id):
 
 
 def subjectinfo(subject_id):
-    from nipype.interfaces.base import Bunch
+    from nipype.utils.bunch import Bunch
     from copy import deepcopy
     print("Subject ID: %s\n" % str(subject_id))
     output = []

examples/fmri_spm_face.py

@@ -259,7 +259,7 @@ def makelist(item):
 necessary to generate an SPM design matrix.
 """
 
-from nipype.interfaces.base import Bunch
+from nipype.utils.bunch import Bunch
 """We're importing the onset times from a mat file (found on
 http://www.fil.ion.ucl.ac.uk/spm/data/face_rep/)
 """

examples/fmri_spm_nested.py

@@ -285,7 +285,7 @@ def _template_path(in_data):
 
 
 def subjectinfo(subject_id):
-    from nipype.interfaces.base import Bunch
+    from nipype.utils.bunch import Bunch
     from copy import deepcopy
     print("Subject ID: %s\n" % str(subject_id))
     output = []

examples/frontiers_paper/smoothing_comparison.py

@@ -17,7 +17,7 @@
 import nipype.pipeline.engine as pe  # pypeline engine
 import nipype.algorithms.modelgen as model  # model specification
 import nipype.workflows.fmri.fsl as fsl_wf
-from nipype.interfaces.base import Bunch
+from nipype.utils.bunch import Bunch
 import os  # system functions
 
 preprocessing = pe.Workflow(name="preprocessing")

examples/frontiers_paper/workflow_from_scratch.py

@@ -14,7 +14,7 @@
 import nipype.interfaces.spm as spm  # spm
 import nipype.pipeline.engine as pe  # pypeline engine
 import nipype.algorithms.modelgen as model  # model specification
-from nipype.interfaces.base import Bunch
+from nipype.utils.bunch import Bunch
 import os  # system functions
 """In the following section, to showcase NiPyPe, we will describe how to create
 and extend a typical fMRI processing pipeline. We will begin with a basic

nipype/algorithms/modelgen.py

@@ -23,11 +23,11 @@
 from scipy.special import gammaln
 
 from ..utils import NUMPY_MMAP
-from ..interfaces.base import (BaseInterface, TraitedSpec, InputMultiPath,
-                               traits, File, Bunch, BaseInterfaceInputSpec,
-                               isdefined)
-from ..utils.filemanip import ensure_list
+from ..utils.bunch import Bunch
 from ..utils.misc import normalize_mc_params
+from ..utils.filemanip import ensure_list
+from ..interfaces.base import (BaseInterface, TraitedSpec, InputMultiPath,
+                               traits, File, BaseInterfaceInputSpec, isdefined)
 from .. import config, logging
 iflogger = logging.getLogger('nipype.interface')
 
@@ -280,7 +280,7 @@ class SpecifyModel(BaseInterface):
     --------
 
     >>> from nipype.algorithms import modelgen
-    >>> from nipype.interfaces.base import Bunch
+    >>> from nipype.utils.bunch import Bunch
     >>> s = modelgen.SpecifyModel()
     >>> s.inputs.input_units = 'secs'
     >>> s.inputs.functional_runs = ['functional2.nii', 'functional3.nii']
@@ -481,7 +481,7 @@ class SpecifySPMModel(SpecifyModel):
     --------
 
     >>> from nipype.algorithms import modelgen
-    >>> from nipype.interfaces.base import Bunch
+    >>> from nipype.utils.bunch import Bunch
     >>> s = modelgen.SpecifySPMModel()
     >>> s.inputs.input_units = 'secs'
     >>> s.inputs.output_units = 'scans'
@@ -667,7 +667,7 @@ class SpecifySparseModel(SpecifyModel):
     --------
 
     >>> from nipype.algorithms import modelgen
-    >>> from nipype.interfaces.base import Bunch
+    >>> from nipype.utils.bunch import Bunch
     >>> s = modelgen.SpecifySparseModel()
     >>> s.inputs.input_units = 'secs'
     >>> s.inputs.functional_runs = ['functional2.nii', 'functional3.nii']

nipype/algorithms/tests/test_modelgen.py

@@ -11,7 +11,8 @@
 
 import pytest
 import numpy.testing as npt
-from nipype.interfaces.base import Bunch, TraitError
+from nipype.utils.bunch import Bunch
+from nipype.interfaces.base import TraitError
 from nipype.algorithms.modelgen import (SpecifyModel, SpecifySparseModel,
                                         SpecifySPMModel)
 

nipype/algorithms/tests/test_rapidart.py

@@ -7,7 +7,7 @@
 
 import numpy.testing as npt
 from .. import rapidart as ra
-from ...interfaces.base import Bunch
+from ...utils.bunch import Bunch
 
 
 def test_ad_init():

nipype/interfaces/base/__init__.py

@@ -8,6 +8,7 @@
 This module defines the API of all nipype interfaces.
 
 """
+from ...utils.bunch import Bunch
 from .core import (Interface, BaseInterface, SimpleInterface, CommandLine,
                    StdOutCommandLine, MpiCommandLine, SEMLikeCommandLine,
                    LibraryBaseInterface, PackageInfo)
@@ -22,5 +23,42 @@
     OutputMultiObject, InputMultiObject,
     OutputMultiPath, InputMultiPath)
 
-from .support import (Bunch, InterfaceResult, load_template,
-                      NipypeInterfaceError)
+from .support import (InterfaceRuntime, InterfaceResult, NipypeInterfaceError)
+
+__all__ = [
+    'Bunch',
+    'Interface',
+    'BaseInterface',
+    'SimpleInterface',
+    'CommandLine',
+    'StdOutCommandLine',
+    'MpiCommandLine',
+    'SEMLikeCommandLine',
+    'LibraryBaseInterface',
+    'PackageInfo',
+    'BaseTraitedSpec',
+    'TraitedSpec',
+    'DynamicTraitedSpec',
+    'BaseInterfaceInputSpec',
+    'CommandLineInputSpec',
+    'StdOutCommandLineInputSpec',
+    'traits',
+    'Undefined',
+    'TraitDictObject',
+    'TraitListObject',
+    'TraitError',
+    'isdefined',
+    'File',
+    'Directory',
+    'Str',
+    'DictStrStr',
+    'has_metadata',
+    'ImageFile',
+    'OutputMultiObject',
+    'InputMultiObject',
+    'OutputMultiPath',
+    'InputMultiPath',
+    'InterfaceRuntime',
+    'InterfaceResult',
+    'NipypeInterfaceError',
+]

nipype/interfaces/base/core.py

@@ -42,7 +42,7 @@
 from .specs import (BaseInterfaceInputSpec, CommandLineInputSpec,
                     StdOutCommandLineInputSpec, MpiCommandLineInputSpec,
                     get_filecopy_info)
-from .support import (Bunch, InterfaceResult, NipypeInterfaceError)
+from .support import (InterfaceRuntime, InterfaceResult, NipypeInterfaceError)
 
 from future import standard_library
 standard_library.install_aliases()
@@ -478,7 +478,7 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
         if self._redirect_x:
             env['DISPLAY'] = config.get_display()
 
-        runtime = Bunch(
+        runtime = InterfaceRuntime(
             cwd=cwd,
             prevcwd=syscwd,
             returncode=None,
@@ -872,9 +872,7 @@ def _run_interface(self, runtime, correct_return_codes=(0, )):
         """
 
         out_environ = self._get_environ()
-        # Initialize runtime Bunch
-        runtime.stdout = None
-        runtime.stderr = None
+        # Initialize runtime InterfaceRuntime
         runtime.cmdline = self.cmdline
         runtime.environ.update(out_environ)