Merge pull request #843 from mwaskom/revert_interface_import

Partial revert of imoports in nipype namespace

Author: satra

CHANGES

@@ -1,6 +1,7 @@
 Next Release
 ============
 
+* API: Interfaces to external packages are no longer available in the top-level ``nipype`` namespace, and must be imported directly (e.g. ``from nipype.interfaces import fsl``).
 * ENH: New ANTs interface: ApplyTransformsToPoints
 * FIX: MRTrix tracking algorithms were ignoring mask parameters.
 

doc/users/spmmcr.rst

@@ -9,7 +9,7 @@ the following commands are executed at the beginning of your script:
 
 .. testcode::
 
-    from nipype import spm
+    from nipype.interfaces import spm
     matlab_cmd = '/path/to/run_spm8.sh /path/to/Compiler_Runtime/v713/ script'
     spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
 

examples/fmri_spm.py

@@ -18,7 +18,7 @@
 from nipype import config
 config.enable_provenance()
 
-from nipype import spm, fsl
+from nipype.interfaces import spm, fsl
 
 # In order to use this example with SPM's matlab common runtime
 # matlab_cmd = ('/Users/satra/Downloads/spm8/run_spm8.sh '

nipype/__init__.py

@@ -75,6 +75,5 @@ def _test_local_install():
 
 
 from pipeline import Node, MapNode, JoinNode, Workflow
-from interfaces import (fsl, spm, freesurfer, afni, ants, slicer, dipy, nipy,
-                        mrtrix, camino, DataGrabber, DataSink, SelectFiles,
+from interfaces import (DataGrabber, DataSink, SelectFiles,
                         IdentityInterface, Rename, Function, Select, Merge)

nipype/interfaces/__init__.py

@@ -9,4 +9,3 @@
 
 from io import DataGrabber, DataSink, SelectFiles
 from utility import IdentityInterface, Rename, Function, Select, Merge
-import fsl, spm, freesurfer, afni, ants, slicer, dipy, nipy, mrtrix, camino

nipype/interfaces/fsl/utils.py

@@ -343,7 +343,7 @@ class ImageMaths(FSLCommand):
     Examples
     --------
 
-    >>> from nipype import fsl
+    >>> from nipype.interfaces import fsl
     >>> from nipype.testing import anatfile
     >>> maths = fsl.ImageMaths(in_file=anatfile, op_string= '-add 5',
     ...                        out_file='foo_maths.nii')

nipype/interfaces/spm/base.py

@@ -5,7 +5,7 @@
 In order to use the standalone MCR version of spm, you need to ensure that
 the following commands are executed at the beginning of your script::
 
-   from nipype import spm
+   from nipype.interfaces import spm
    matlab_cmd = '/path/to/run_spm8.sh /path/to/Compiler_Runtime/v713/ script'
    spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
 

nipype/pipeline/engine.py

@@ -1099,7 +1099,8 @@ class Node(WorkflowBase):
     Examples
     --------
 
-    >>> from nipype import Node, spm
+    >>> from nipype import Node
+    >>> from nipype.interfaces import spm
     >>> realign = Node(spm.Realign(), 'realign')
     >>> realign.inputs.in_files = 'functional.nii'
     >>> realign.inputs.register_to_mean = True
@@ -1984,7 +1985,8 @@ class MapNode(Node):
     Examples
     --------
 
-    >>> from nipype import MapNode, fsl
+    >>> from nipype import MapNode
+    >>> from nipype.interfaces import fsl
     >>> realign = MapNode(fsl.MCFLIRT(), 'in_file', 'realign')
     >>> realign.inputs.in_file = ['functional.nii',
     ...                           'functional2.nii',