diff --git a/CHANGES b/CHANGES index 7ad890a151..7cccdd2cc1 100644 --- a/CHANGES +++ b/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. diff --git a/doc/users/spmmcr.rst b/doc/users/spmmcr.rst index 18dbe195df..376741a2c9 100644 --- a/doc/users/spmmcr.rst +++ b/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) diff --git a/examples/fmri_spm.py b/examples/fmri_spm.py index df02330853..0d124c56da 100755 --- a/examples/fmri_spm.py +++ b/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 ' diff --git a/nipype/__init__.py b/nipype/__init__.py index 1f1c4db0c0..a5183e022c 100644 --- a/nipype/__init__.py +++ b/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) diff --git a/nipype/interfaces/__init__.py b/nipype/interfaces/__init__.py index b81deb9d70..861ebcd739 100644 --- a/nipype/interfaces/__init__.py +++ b/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 diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py index 92d20db995..2b2d5d426c 100644 --- a/nipype/interfaces/fsl/utils.py +++ b/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') diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index 8b75c6dcad..0120721fe6 100644 --- a/nipype/interfaces/spm/base.py +++ b/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) diff --git a/nipype/pipeline/engine.py b/nipype/pipeline/engine.py index b3cb48825b..e3a7ad2757 100644 --- a/nipype/pipeline/engine.py +++ b/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',