restructure engine module

Author: oesteban

nipype/caching/memory.py

@@ -21,7 +21,7 @@
 
 from ..interfaces.base import BaseInterface
 from ..pipeline.engine import Node
-from ..pipeline.utils import modify_paths
+from ..pipeline.engine.utils import modify_paths
 
 ################################################################################
 # PipeFunc object: callable interface to nipype.interface objects

nipype/pipeline/engine/base.py

@@ -27,11 +27,11 @@
 from copy import deepcopy
 import re
 import numpy as np
-from nipype.interfaces.traits_extension import traits, Undefined
-from nipype.interfaces.base import DynamicTraitedSpec
-from nipype.utils.filemanip import loadpkl, savepkl
+from ...interfaces.traits_extension import traits, Undefined
+from ...interfaces.base import DynamicTraitedSpec
+from ...utils.filemanip import loadpkl, savepkl
 
-from nipype import logging
+from ... import logging
 logger = logging.getLogger('workflow')
 
 

nipype/pipeline/engine/utils.py

@@ -32,16 +32,16 @@
 
 import networkx as nx
 
-from ..external.six import string_types
-from ..utils.filemanip import (fname_presuffix, FileNotFoundError,
-                               filename_to_list, get_related_files)
-from ..utils.misc import create_function_from_source, str2bool
-from ..interfaces.base import (CommandLine, isdefined, Undefined,
-                               InterfaceResult)
-from ..interfaces.utility import IdentityInterface
-from ..utils.provenance import ProvStore, pm, nipype_ns, get_id
-
-from .. import logging, config
+from ...external.six import string_types
+from ...utils.filemanip import (fname_presuffix, FileNotFoundError,
+                                filename_to_list, get_related_files)
+from ...utils.misc import create_function_from_source, str2bool
+from ...interfaces.base import (CommandLine, isdefined, Undefined,
+                                InterfaceResult)
+from ...interfaces.utility import IdentityInterface
+from ...utils.provenance import ProvStore, pm, nipype_ns, get_id
+
+from ... import logging, config
 logger = logging.getLogger('workflow')
 
 try:
@@ -361,7 +361,7 @@ def walk(children, level=0, path=None, usename=True):
 
     Examples
     --------
-    >>> from nipype.pipeline.utils import walk
+    >>> from nipype.pipeline.engine.utils import walk
     >>> iterables = [('a', lambda: [1, 2]), ('b', lambda: [3, 4])]
     >>> [val['a'] for val in walk(iterables)]
     [1, 1, 2, 2]
@@ -396,7 +396,7 @@ def synchronize_iterables(iterables):
 
     Examples
     --------
-    >>> from nipype.pipeline.utils import synchronize_iterables
+    >>> from nipype.pipeline.engine.utils import synchronize_iterables
     >>> iterables = dict(a=lambda: [1, 2], b=lambda: [3, 4])
     >>> synced = synchronize_iterables(iterables)
     >>> synced == [{'a': 1, 'b': 3}, {'a': 2, 'b': 4}]

nipype/pipeline/plugins/base.py

@@ -21,10 +21,11 @@
 import scipy.sparse as ssp
 
 
-from ..utils import (nx, dfs_preorder, topological_sort)
-from ..engine import (MapNode, str2bool)
+from ...utils.filemanip import savepkl, loadpkl
+from ...utils.misc import str2bool
+from ..engine.utils import (nx, dfs_preorder, topological_sort)
+from ..engine import MapNode
 
-from nipype.utils.filemanip import savepkl, loadpkl
 
 from ... import logging
 logger = logging.getLogger('workflow')

nipype/pipeline/plugins/debug.py

@@ -4,7 +4,7 @@
 """
 
 from .base import (PluginBase, logger)
-from ..utils import (nx)
+from ..engine.utils import (nx)
 
 
 class DebugPlugin(PluginBase):

nipype/pipeline/plugins/linear.py

@@ -6,7 +6,7 @@
 
 from .base import (PluginBase, logger, report_crash, report_nodes_not_run,
                    str2bool)
-from ..utils import (nx, dfs_preorder, topological_sort)
+from ..engine.utils import (nx, dfs_preorder, topological_sort)
 
 
 class LinearPlugin(PluginBase):

nipype/workflows/fmri/spm/preprocess.py

@@ -10,7 +10,8 @@
 from ....interfaces.matlab import no_matlab
 from ...smri.freesurfer.utils import create_getmask_flow
 
-logger = pe.logger
+from .... import logging
+logger = logging.getLogger('workflow')
 
 
 def create_spm_preproc(name='preproc'):