Merge pull request #174 from effigies/enh/nipype_submodule

ENH: Import nipype as submodule

Author: chrisgorgo

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "niworkflows/nipype"]
+	path = nipype
+	url = https://github.com/nipy/nipype.git

circle.yml

@@ -15,6 +15,8 @@ dependencies:
     - mkdir -p ~/data/ ~/docker ${CIRCLE_TEST_REPORTS}/py2 ${CIRCLE_TEST_REPORTS}/py3
     - mkdir -p $SCRATCH && sudo setfacl -d -m group:ubuntu:rwx $SCRATCH && sudo setfacl -m group:ubuntu:rwx $SCRATCH
     - mkdir -p $SCRATCH/py2 $SCRATCH/py3
+    - git submodule init && (git submodule update || true)
+    - git submodule sync && git -C nipype fetch origin && git submodule update
   override:
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi :
         timeout: 6000
@@ -38,4 +40,4 @@ deployment:
     commands:
       - sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" niworkflows/info.py
       - printf "[distutils]\nindex-servers =\n    pypi\n\n[pypi]\nusername:$PYPI_USER\npassword:$PYPI_PASS\n" > ~/.pypirc
-      - python setup.py sdist upload -r pypi
+      - python setup.py sdist upload -r pypi

nipype

@@ -10,21 +10,21 @@
 from multiprocessing import cpu_count
 from packaging.version import Version
 
-from nipype.interfaces.ants.registration import Registration, RegistrationOutputSpec
-from nipype.interfaces.ants.resampling import ApplyTransforms
-from nipype.interfaces.ants import AffineInitializer
-from nipype.interfaces.base import (traits, isdefined, BaseInterface, BaseInterfaceInputSpec,
-                                    File, InputMultiPath)
+from niworkflows.nipype.interfaces.ants.registration import Registration, RegistrationOutputSpec
+from niworkflows.nipype.interfaces.ants.resampling import ApplyTransforms
+from niworkflows.nipype.interfaces.ants import AffineInitializer
+from niworkflows.nipype.interfaces.base import (
+    traits, isdefined, BaseInterface, BaseInterfaceInputSpec, File)
 
 from niworkflows.data import getters
-from niworkflows import __packagename__, NIWORKFLOWS_LOG, __version__
-
-niworkflows_version = Version(__version__)
-
+from niworkflows import NIWORKFLOWS_LOG, __version__
 
 import nibabel as nb
 import numpy as np
 
+niworkflows_version = Version(__version__)
+
+
 class RobustMNINormalizationInputSpec(BaseInterfaceInputSpec):
     # Enable deprecation
     package_version = niworkflows_version

niworkflows/anat/mni.py

@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 from __future__ import absolute_import, division, print_function, unicode_literals
-from nipype.interfaces import ants
-from nipype.interfaces import afni
-from nipype.interfaces import fsl
-from nipype.interfaces import utility as niu
-from nipype.pipeline import engine as pe
+from niworkflows.nipype.interfaces import ants
+from niworkflows.nipype.interfaces import afni
+from niworkflows.nipype.interfaces import fsl
+from niworkflows.nipype.interfaces import utility as niu
+from niworkflows.nipype.pipeline import engine as pe
 
 
 def afni_wf(name='AFNISkullStripWorkflow', unifize=False, n4_nthreads=1):

niworkflows/anat/skullstrip.py

@@ -5,9 +5,10 @@
 # @Last Modified time: 2016-11-30 16:25:44
 from __future__ import absolute_import, division, print_function, unicode_literals
 
-from nipype.pipeline import engine as pe
-from nipype.interfaces import utility as niu
-from nipype.interfaces import afni
+from niworkflows.nipype.pipeline import engine as pe
+from niworkflows.nipype.interfaces import utility as niu
+from niworkflows.nipype.interfaces import afni
+
 
 def reorient_wf(name='ReorientWorkflow'):
     """A workflow to reorient images to 'RPI' orientation"""

niworkflows/common/orient.py

@@ -8,7 +8,8 @@
 from abc import abstractmethod
 from io import open
 
-from nipype.interfaces.base import File, traits, BaseInterface, BaseInterfaceInputSpec, TraitedSpec
+from niworkflows.nipype.interfaces.base import (
+    File, traits, BaseInterface, BaseInterfaceInputSpec, TraitedSpec)
 from niworkflows import NIWORKFLOWS_LOG
 from nilearn.masking import apply_mask, unmask
 from nilearn.image import threshold_img, load_img

niworkflows/common/report.py

@@ -10,6 +10,11 @@
 """
 from __future__ import absolute_import, division, print_function
 import datetime
+from os import path as op
+import runpy
+
+nipype_info = runpy.run_path(op.join(op.abspath(op.dirname(__file__)),
+                                     'nipype', 'info.py'))
 
 __version__ = '0.0.8-dev'
 __packagename__ = 'niworkflows'
@@ -39,8 +44,9 @@
     'Programming Language :: Python :: 3.5',
 ]
 
-REQUIRES = ['nipype', 'future', 'nilearn>=0.2.6', 'sklearn', 'pandas', 'matplotlib',
-            'jinja2', 'svgutils', 'tinycss', 'packaging']
+REQUIRES = nipype_info['REQUIRES'] + [
+    'nilearn>=0.2.6', 'sklearn', 'pandas', 'matplotlib', 'jinja2', 'svgutils',
+    'tinycss']
 SETUP_REQUIRES = []
 REQUIRES += SETUP_REQUIRES
 

niworkflows/info.py

@@ -2,7 +2,9 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-from nipype.interfaces.base import BaseInterface
+from __future__ import absolute_import, unicode_literals
+
+from niworkflows.nipype.interfaces.base import BaseInterface
 
 
 class SimpleInterface(BaseInterface):

niworkflows/interfaces/base.py

@@ -7,10 +7,10 @@
 
 import os
 
-from nilearn.image import mean_img
-from nipype.interfaces import fsl, ants
-from nipype.interfaces.base import File, BaseInterfaceInputSpec, traits, isdefined
-from nipype.algorithms import confounds
+from niworkflows.nipype.interfaces import fsl, ants
+from niworkflows.nipype.interfaces.base import (
+    File, BaseInterfaceInputSpec, traits, isdefined)
+from niworkflows.nipype.algorithms import confounds
 from niworkflows.common import report as nrc
 from niworkflows import NIWORKFLOWS_LOG
 from nilearn.masking import compute_epi_mask