ENH: Reduce within-package absolute imports

Author: effigies

nipype/algorithms/icc.py

@@ -8,7 +8,7 @@
 from scipy.linalg import pinv
 from ..interfaces.base import BaseInterfaceInputSpec, TraitedSpec, \
     BaseInterface, traits, File
-from nipype.utils import NUMPY_MMAP
+from ..utils import NUMPY_MMAP
 
 
 class ICCInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/metrics.py

@@ -30,7 +30,7 @@
 from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
                                InputMultiPath,
                                BaseInterfaceInputSpec, isdefined)
-from nipype.utils import NUMPY_MMAP
+from ..utils import NUMPY_MMAP
 
 iflogger = logging.getLogger('interface')
 

nipype/algorithms/misc.py

@@ -34,7 +34,7 @@
                                BaseInterfaceInputSpec, isdefined,
                                DynamicTraitedSpec, Undefined)
 from ..utils.filemanip import fname_presuffix, split_filename
-from nipype.utils import NUMPY_MMAP
+from ..utils import NUMPY_MMAP
 
 from . import confounds
 

nipype/interfaces/fsl/ICA_AROMA.py

@@ -10,17 +10,11 @@
     ...                            '../../testing/data'))
     >>> os.chdir(datadir)
 """
-from nipype.interfaces.base import (
-    TraitedSpec,
-    CommandLineInputSpec,
-    CommandLine,
-    File,
-    Directory,
-    traits,
-    OutputMultiPath
-)
+from ..base import (TraitedSpec, CommandLineInputSpec, CommandLine,
+                    File, Directory, traits)
 import os
 
+
 class ICA_AROMAInputSpec(CommandLineInputSpec):
     feat_dir = Directory(exists=True, mandatory=True,
                          argstr='-feat %s',

nipype/interfaces/fsl/fix.py

@@ -54,7 +54,7 @@
 
 """
 
-from nipype.interfaces.base import (
+from ..base import (
     TraitedSpec,
     CommandLineInputSpec,
     CommandLine,
@@ -64,11 +64,8 @@
     BaseInterfaceInputSpec,
     traits
 )
-from nipype.interfaces.traits_extension import (
-    Directory,
-    File,
-    isdefined
-)
+from ..traits_extension import Directory, File, isdefined
+
 import os
 
 class TrainingSetCreatorInputSpec(BaseInterfaceInputSpec):

nipype/interfaces/niftyseg/base.py

@@ -16,8 +16,8 @@
 See the docstrings of the individual classes for examples.
 """
 
-from nipype.interfaces.niftyreg.base import no_nifty_package
-from nipype.interfaces.niftyfit.base import NiftyFitCommand
+from ..niftyreg.base import no_nifty_package
+from ..niftyfit.base import NiftyFitCommand
 import subprocess
 import warnings
 

nipype/interfaces/utility/wrappers.py

@@ -19,7 +19,7 @@
 
 from builtins import str, bytes
 
-from nipype import logging
+from ... import logging
 from ..base import (traits, DynamicTraitedSpec, Undefined, isdefined, runtime_profile,
                     BaseInterfaceInputSpec)
 from ..io import IOBase, add_traits

nipype/pipeline/engine/utils.py

@@ -24,7 +24,7 @@
 import pickle
 from functools import reduce
 import numpy as np
-from nipype.utils.misc import package_check
+from ...utils.misc import package_check
 
 package_check('networkx', '1.3')
 

nipype/utils/__init__.py

@@ -1,6 +1,4 @@
 # -*- coding: utf-8 -*-
-from __future__ import absolute_import
-
-from nipype.utils.config import NUMPY_MMAP
-from nipype.utils.onetime import OneTimeProperty, setattr_on_read
-from nipype.utils.tmpdirs import TemporaryDirectory, InTemporaryDirectory
+from .config import NUMPY_MMAP
+from .onetime import OneTimeProperty, setattr_on_read
+from .tmpdirs import TemporaryDirectory, InTemporaryDirectory

nipype/workflows/dmri/fsl/artifacts.py

@@ -4,8 +4,6 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from __future__ import division
 
-from nipype.utils import NUMPY_MMAP
-
 from ....interfaces.io import JSONFileGrabber
 from ....interfaces import utility as niu
 from ....interfaces import ants
@@ -903,6 +901,7 @@ def _xfm_jacobian(in_xfm):
 
 def _get_zoom(in_file, enc_dir):
     import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
 
     zooms = nb.load(in_file, mmap=NUMPY_MMAP).header.get_zooms()
 

nipype/workflows/smri/freesurfer/autorecon1.py

@@ -1,9 +1,9 @@
 # -*- coding: utf-8 -*-
 
-from nipype.utils import NUMPY_MMAP
-from nipype.interfaces.utility import Function,IdentityInterface
-import nipype.pipeline.engine as pe  # pypeline engine
-from nipype.interfaces.freesurfer import *
+from ....utils import NUMPY_MMAP
+from ....pipeline import engine as pe
+from ....interfaces.utility import Function, IdentityInterface
+from ....interfaces.freesurfer import *
 from .utils import copy_file
 
 

nipype/workflows/smri/freesurfer/autorecon2.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
-from nipype.interfaces.utility import Function, IdentityInterface, Merge
-import nipype.pipeline.engine as pe  # pypeline engine
-from nipype.interfaces.freesurfer import *
+from ....interfaces.utility import Function, IdentityInterface, Merge
+from ....pipeline import engine as pe
+from ....interfaces.freesurfer import *
 from .utils import copy_file
 
 def copy_ltas(in_file, subjects_dir, subject_id, long_template):

nipype/workflows/smri/freesurfer/autorecon3.py

@@ -1,9 +1,9 @@
 # -*- coding: utf-8 -*-
-from nipype.interfaces.utility import IdentityInterface, Merge, Function
-import nipype.pipeline.engine as pe  # pypeline engine
-from nipype.interfaces.freesurfer import *
+from ....interfaces.utility import IdentityInterface, Merge, Function
+from ....pipeline import engine as pe
+from ....interfaces.freesurfer import *
 from .ba_maps import create_ba_maps_wf
-from nipype.interfaces.io import DataGrabber
+from ....interfaces.io import DataGrabber
 
 def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                       th3=True, exvivo=True, entorhinal=True, fsvernum=5.3):

nipype/workflows/smri/freesurfer/ba_maps.py

@@ -1,11 +1,10 @@
 # -*- coding: utf-8 -*-
 import os
-import nipype
-from nipype.interfaces.utility import Function,IdentityInterface
-import nipype.pipeline.engine as pe  # pypeline engine
-from nipype.interfaces.freesurfer import *
-from nipype.interfaces.io import DataGrabber
-from nipype.interfaces.utility import Merge
+from ....interfaces.utility import Function, IdentityInterface
+from ....pipeline import engine as pe  # pypeline engine
+from ....interfaces.freesurfer import *
+from ....interfaces.io import DataGrabber
+from ....interfaces.utility import Merge
 
 def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
                       entorhinal=True):

nipype/workflows/smri/niftyreg/groupwise.py

@@ -7,9 +7,9 @@
 """
 
 from builtins import str, range
-import nipype.interfaces.utility as niu
-import nipype.interfaces.niftyreg as niftyreg
-import nipype.pipeline.engine as pe
+from ....interfaces import utility as niu
+from ....interfaces import niftyreg as niftyreg
+from ....pipeline import engine as pe
 
 
 def create_linear_gw_step(name="linear_gw_niftyreg",