Merge pull request #241 from effigies/dep/nipype

effigies · web-flow · commit a82096a18d3c · 2018-05-31T12:04:12.000-04:00
Resume external nipype dependency
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -23,15 +23,6 @@ jobs:
             - /tmp/cache/docker.tar.gz
             - /tmp/cache/ubuntu.tar.gz
       - checkout
-      - run:
-          name: Checkout Nipype
-          command: |
-            git submodule init
-            git submodule update || true
-            git submodule sync
-            git -C nipype fetch origin
-            git submodule update
-
       - run:
           name: Update Niworkflows version
           command: |
@@ -130,14 +121,6 @@ jobs:
     working_directory: /tmp/src/niworkflows
     steps:
       - checkout
-      - run:
-          name: Checkout Nipype
-          command: |
-            git submodule init
-            git submodule update || true
-            git submodule sync
-            git -C nipype fetch origin
-            git submodule update
 
       - run:
           name: Update Niworkflows version
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +0,0 @@
-[submodule "niworkflows/nipype"]
-	path = nipype
-	url = https://github.com/nipy/nipype.git
diff --git a/nipype b/nipype
diff --git a/niworkflows/__about__.py b/niworkflows/__about__.py
@@ -9,11 +9,6 @@
 """
 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__ = '0.3.14-dev'
 __packagename__ = 'niworkflows'
@@ -53,7 +48,8 @@
     'Programming Language :: Python :: 3.6',
 ]
 
-REQUIRES = nipype_info['REQUIRES'] + [
+REQUIRES = [
+    'nipype>=1.0.4',
     'nilearn>=0.2.6',
     'sklearn',
     'pandas',
diff --git a/niworkflows/anat/skullstrip.py b/niworkflows/anat/skullstrip.py
@@ -2,8 +2,8 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from __future__ import absolute_import, division, print_function, unicode_literals
-from ..nipype.interfaces import ants, afni, fsl, utility as niu
-from ..nipype.pipeline import engine as pe
+from nipype.interfaces import ants, afni, fsl, utility as niu
+from nipype.pipeline import engine as pe
 
 
 def afni_wf(name='AFNISkullStripWorkflow', unifize=False, n4_nthreads=1):
diff --git a/niworkflows/common/orient.py b/niworkflows/common/orient.py
@@ -3,8 +3,8 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from __future__ import absolute_import, division, print_function, unicode_literals
 
-from ..nipype.pipeline import engine as pe
-from ..nipype.interfaces import afni, utility as niu
+from nipype.pipeline import engine as pe
+from nipype.interfaces import afni, utility as niu
 
 
 def reorient_wf(name='ReorientWorkflow'):
diff --git a/niworkflows/interfaces/fixes.py b/niworkflows/interfaces/fixes.py
@@ -7,8 +7,8 @@
 from .. import __version__
 from .utils import _copyxform
 
-from ..nipype.interfaces.ants.resampling import ApplyTransforms
-from ..nipype.interfaces.ants.registration import Registration
+from nipype.interfaces.ants.resampling import ApplyTransforms
+from nipype.interfaces.ants.registration import Registration
 
 
 class FixHeaderApplyTransforms(ApplyTransforms):
diff --git a/niworkflows/interfaces/masks.py b/niworkflows/interfaces/masks.py
@@ -14,11 +14,11 @@
 import scipy.ndimage as nd
 
 from .. import NIWORKFLOWS_LOG
-from ..nipype.interfaces import fsl, ants
-from ..nipype.interfaces.base import (
+from nipype.interfaces import fsl, ants
+from nipype.interfaces.base import (
     File, BaseInterfaceInputSpec, traits, isdefined, InputMultiPath, Str)
-from ..nipype.interfaces.mixins import reporting
-from ..nipype.algorithms import confounds
+from nipype.interfaces.mixins import reporting
+from nipype.algorithms import confounds
 from . import report_base as nrc
 
 
diff --git a/niworkflows/interfaces/mni.py b/niworkflows/interfaces/mni.py
@@ -12,9 +12,9 @@
 import nibabel as nb
 import numpy as np
 
-from ..nipype.interfaces.ants.registration import RegistrationOutputSpec
-from ..nipype.interfaces.ants import AffineInitializer
-from ..nipype.interfaces.base import (
+from nipype.interfaces.ants.registration import RegistrationOutputSpec
+from nipype.interfaces.ants import AffineInitializer
+from nipype.interfaces.base import (
     traits, isdefined, BaseInterface, BaseInterfaceInputSpec, File)
 
 from ..data import getters
diff --git a/niworkflows/interfaces/plotting.py b/niworkflows/interfaces/plotting.py
@@ -8,8 +8,8 @@
 import numpy as np
 import pandas as pd
 
-from ..nipype.utils.filemanip import fname_presuffix
-from ..nipype.interfaces.base import (
+from nipype.utils.filemanip import fname_presuffix
+from nipype.interfaces.base import (
     File, BaseInterfaceInputSpec, TraitedSpec, SimpleInterface, traits
 )
 from ..viz.plots import fMRIPlot
diff --git a/niworkflows/interfaces/registration.py b/niworkflows/interfaces/registration.py
@@ -14,12 +14,12 @@
 from nilearn import image as nli
 from nilearn.image import index_img
 from .. import NIWORKFLOWS_LOG
-from ..nipype.utils.filemanip import fname_presuffix
-from ..nipype.interfaces.base import (
+from nipype.utils.filemanip import fname_presuffix
+from nipype.interfaces.base import (
     traits, isdefined, TraitedSpec, BaseInterfaceInputSpec, File, SimpleInterface)
-from ..nipype.interfaces.mixins import reporting
-from ..nipype.interfaces import freesurfer as fs
-from ..nipype.interfaces import fsl, ants, afni
+from nipype.interfaces.mixins import reporting
+from nipype.interfaces import freesurfer as fs
+from nipype.interfaces import fsl, ants, afni
 
 from . import report_base as nrc
 from .mni import (
@@ -417,7 +417,7 @@ def _run_interface(self, runtime):
 
 
 def _get_vols_to_discard(img):
-    from niworkflows.nipype.algorithms.confounds import is_outlier
+    from nipype.algorithms.confounds import is_outlier
     data_slice = img.dataobj[:, :, :, :50]
     global_signal = data_slice.mean(axis=0).mean(axis=0).mean(axis=0)
     return is_outlier(global_signal)
diff --git a/niworkflows/interfaces/report_base.py b/niworkflows/interfaces/report_base.py
@@ -7,8 +7,8 @@
 from nilearn.masking import apply_mask, unmask
 from nilearn.image import threshold_img, load_img
 
-from ..nipype.interfaces.base import File, traits
-from ..nipype.interfaces.mixins import reporting
+from nipype.interfaces.base import File, traits
+from nipype.interfaces.mixins import reporting
 from .. import NIWORKFLOWS_LOG
 from ..viz.utils import cuts_from_bbox, compose_view
 
diff --git a/niworkflows/interfaces/segmentation.py b/niworkflows/interfaces/segmentation.py
@@ -9,9 +9,9 @@
 from __future__ import absolute_import, division, print_function, unicode_literals
 import os
 
-from ..nipype.interfaces.base import File
-from ..nipype.interfaces import fsl, freesurfer
-from ..nipype.interfaces.mixins import reporting
+from nipype.interfaces.base import File
+from nipype.interfaces import fsl, freesurfer
+from nipype.interfaces.mixins import reporting
 from . import report_base as nrc
 from .. import NIWORKFLOWS_LOG
 
diff --git a/niworkflows/interfaces/utils.py b/niworkflows/interfaces/utils.py
@@ -15,10 +15,10 @@
 from textwrap import indent
 
 from .. import __version__
-from ..nipype import logging
-from ..nipype.utils.filemanip import fname_presuffix
-from ..nipype.utils.misc import normalize_mc_params
-from ..nipype.interfaces.base import (
+from nipype import logging
+from nipype.utils.filemanip import fname_presuffix
+from nipype.utils.misc import normalize_mc_params
+from nipype.interfaces.base import (
     File, BaseInterfaceInputSpec, TraitedSpec, traits, SimpleInterface
 )
 
diff --git a/niworkflows/nipype b/niworkflows/nipype
diff --git a/niworkflows/tests/test_registration.py b/niworkflows/tests/test_registration.py
@@ -6,7 +6,7 @@
 import os
 from shutil import copy
 
-from niworkflows.nipype.interfaces.base import Bunch
+from nipype.interfaces.base import Bunch
 from niworkflows.interfaces.registration import (
     FLIRTRPT, RobustMNINormalizationRPT, ANTSRegistrationRPT, BBRegisterRPT,
     MRICoregRPT, ApplyXFMRPT, SimpleBeforeAfterRPT)
diff --git a/niworkflows/tests/test_segmentation.py b/niworkflows/tests/test_segmentation.py
@@ -7,7 +7,7 @@
 from shutil import copy
 import pytest
 
-from niworkflows.nipype.interfaces.base import Bunch
+from nipype.interfaces.base import Bunch
 from niworkflows.interfaces.segmentation import FASTRPT, ReconAllRPT
 from niworkflows.interfaces.masks import (
     BETRPT, BrainExtractionRPT, SimpleShowMaskRPT, ROIsPlot
@@ -102,7 +102,7 @@ def _agg(objekt, runtime):
 @pytest.mark.parametrize("segments", [True, False])
 def test_FASTRPT(monkeypatch, segments, reference, reference_mask):
     """ test FAST with the two options for segments """
-    from niworkflows.nipype.interfaces.fsl.maths import ApplyMask
+    from nipype.interfaces.fsl.maths import ApplyMask
 
     def _agg(objekt, runtime):
         outputs = Bunch(tissue_class_map=os.path.join(
diff --git a/niworkflows/viz/utils.py b/niworkflows/viz/utils.py
@@ -23,7 +23,7 @@
 from seaborn import color_palette
 
 from .. import NIWORKFLOWS_LOG
-from ..nipype.utils import filemanip
+from nipype.utils import filemanip
 
 try:
     from shutil import which
diff --git a/setup.py b/setup.py
@@ -39,9 +39,7 @@ def main():
         tests_require=ldict['TESTS_REQUIRES'],
         extras_require=ldict['EXTRA_REQUIRES'],
         # Data
-        package_data={'niworkflows': ['data/t1-mni_registration*.json',
-                                      'nipype/pipeline/engine/report_template.html',
-                                      'nipype/external/d3.js']},
+        package_data={'niworkflows': ['data/t1-mni_registration*.json']},
         include_package_data=True,
     )
 

Original file line number	Diff line number	Diff line change
`@@ -1,3 +0,0 @@`
`1`		`-[submodule "niworkflows/nipype"]`
`2`		`- path = nipype`
`3`		`- url = https://github.com/nipy/nipype.git`