RF: Resume external nipype dependency

.circleci/config.yml

@@ -296,10 +296,10 @@ jobs:
           at: /tmp
       - restore_cache:
           keys:
-            - ds005-anat-v6-{{ .Branch }}-{{ epoch }}
-            - ds005-anat-v6-{{ .Branch }}
-            - ds005-anat-v6-master
-            - ds005-anat-v6-
+            - ds005-anat-v7-{{ .Branch }}-{{ epoch }}
+            - ds005-anat-v7-{{ .Branch }}
+            - ds005-anat-v7-master
+            - ds005-anat-v7-
       - run:
           name: Setting up test
           command: |
@@ -333,7 +333,7 @@ jobs:
                 --debug --write-graph --mem_mb 4096 \
                 --nthreads 2 --anat-only -vv
       - save_cache:
-         key: ds005-anat-v6-{{ .Branch }}-{{ epoch }}
+         key: ds005-anat-v7-{{ .Branch }}-{{ epoch }}
          paths:
             - /tmp/ds005/work
             - /tmp/ds005/derivatives/fmriprep
@@ -425,10 +425,10 @@ jobs:
           at: /tmp
       - restore_cache:
           keys:
-            - ds054-anat-v4-{{ .Branch }}-{{ epoch }}
-            - ds054-anat-v4-{{ .Branch }}
-            - ds054-anat-v4-master
-            - ds054-anat-v4-
+            - ds054-anat-v5-{{ .Branch }}-{{ epoch }}
+            - ds054-anat-v5-{{ .Branch }}
+            - ds054-anat-v5-master
+            - ds054-anat-v5-
       - run:
           name: Setting up test
           command: |
@@ -462,7 +462,7 @@ jobs:
                 --fs-no-reconall --debug --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
       - save_cache:
-         key: ds054-anat-v4-{{ .Branch }}-{{ epoch }}
+         key: ds054-anat-v5-{{ .Branch }}-{{ epoch }}
          paths:
             - /tmp/ds054/work
             - /tmp/ds054/derivatives
@@ -543,8 +543,8 @@ jobs:
           at: /tmp
       - restore_cache:
           keys:
-            - ds210-anat-v1-{{ epoch }}
-            - ds210-anat-v1-
+            - ds210-anat-v2-{{ epoch }}
+            - ds210-anat-v2-
       - run:
           name: Setting up test
           command: |
@@ -578,7 +578,7 @@ jobs:
                 --fs-no-reconall --debug --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
       - save_cache:
-         key: ds210-anat-v1-{{ epoch }}
+         key: ds210-anat-v2-{{ epoch }}
          paths:
             - /tmp/ds210/work
             - /tmp/ds210/derivatives

docs/environment.yml

@@ -28,4 +28,4 @@ dependencies:
     - svgutils
     - nitime
     - nilearn
-    - niworkflows>=0.3.13
+    - niworkflows>=0.4.0

fmriprep/cli/fmriprep_bold_mask.py

@@ -3,7 +3,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Run the BOLD reference+mask workflow"""
 import os
-from niworkflows.nipype.utils.filemanip import hash_infile
+from nipype.utils.filemanip import hash_infile
 
 
 def get_parser():

fmriprep/cli/run.py

@@ -228,7 +228,7 @@ def get_parser():
 
 def main():
     """Entry point"""
-    from niworkflows.nipype import logging as nlogging
+    from nipype import logging as nlogging
     from multiprocessing import set_start_method, Process, Manager
     from ..viz.reports import generate_reports
     from ..info import __version__
@@ -335,7 +335,7 @@ def build_workflow(opts, retval):
     a hard-limited memory-scope.
 
     """
-    from niworkflows.nipype import logging, config as ncfg
+    from nipype import logging, config as ncfg
     from ..info import __version__
     from ..workflows.base import init_fmriprep_wf
     from ..utils.bids import collect_participants

fmriprep/info.py

@@ -70,7 +70,8 @@
     'grabbit',
     'pybids>=0.5.1',
     'nitime',
-    'niworkflows>=0.3.13',
+    'nipype>=1.0.4',
+    'niworkflows>=0.4.0',
     'statsmodels',
     'nipype',
     'seaborn',

fmriprep/interfaces/bids.py

@@ -14,8 +14,8 @@
 
 Disable warnings:
 
-    >>> import niworkflows.nipype as nn
-    >>> nn.logging.getLogger('interface').setLevel('ERROR')
+    >>> from nipype import logging
+    >>> logging.getLogger('interface').setLevel('ERROR')
 
 """
 
@@ -26,13 +26,13 @@
 import gzip
 from shutil import copytree, rmtree, copyfileobj
 
-from niworkflows.nipype import logging
-from niworkflows.nipype.interfaces.base import (
+from nipype import logging
+from nipype.interfaces.base import (
     traits, isdefined, TraitedSpec, BaseInterfaceInputSpec,
     File, Directory, InputMultiPath, OutputMultiPath, Str,
     SimpleInterface
 )
-from niworkflows.nipype.utils.filemanip import copyfile
+from nipype.utils.filemanip import copyfile
 
 LOGGER = logging.getLogger('interface')
 BIDS_NAME = re.compile(

fmriprep/interfaces/cifti.py

@@ -17,12 +17,12 @@
 import numpy as np
 from nilearn.image import resample_to_img
 
-from niworkflows.nipype.interfaces.base import (
+from nipype.interfaces.base import (
     BaseInterfaceInputSpec, TraitedSpec, File, traits,
     SimpleInterface, Directory
 )
 from niworkflows.data import getters
-from niworkflows.nipype.utils.filemanip import split_filename
+from nipype.utils.filemanip import split_filename
 
 # CITFI structures with corresponding FS labels
 CIFTI_STRUCT_WITH_LABELS = {

fmriprep/interfaces/confounds.py

@@ -13,9 +13,9 @@
 import shutil
 import numpy as np
 import pandas as pd
-from niworkflows.nipype import logging
-from niworkflows.nipype.utils.filemanip import fname_presuffix
-from niworkflows.nipype.interfaces.base import (
+from nipype import logging
+from nipype.utils.filemanip import fname_presuffix
+from nipype.interfaces.base import (
     traits, TraitedSpec, BaseInterfaceInputSpec, File, Directory, isdefined,
     SimpleInterface
 )

fmriprep/interfaces/fmap.py

@@ -17,9 +17,9 @@
 
 import numpy as np
 import nibabel as nb
-from niworkflows.nipype import logging
-from niworkflows.nipype.utils.filemanip import fname_presuffix
-from niworkflows.nipype.interfaces.base import (
+from nipype import logging
+from nipype.utils.filemanip import fname_presuffix
+from nipype.interfaces.base import (
     BaseInterfaceInputSpec, TraitedSpec, File, isdefined, traits,
     SimpleInterface)
 
@@ -241,7 +241,7 @@ def _despike2d(data, thres, neigh=None):
 
 def _unwrap(fmap_data, mag_file, mask=None):
     from math import pi
-    from niworkflows.nipype.interfaces.fsl import PRELUDE
+    from nipype.interfaces.fsl import PRELUDE
     magnii = nb.load(mag_file)
 
     if mask is None:
@@ -433,7 +433,7 @@ def _torads(in_file, fmap_range=None, newpath=None):
     """
     from math import pi
     import nibabel as nb
-    from niworkflows.nipype.utils.filemanip import fname_presuffix
+    from nipype.utils.filemanip import fname_presuffix
 
     out_file = fname_presuffix(in_file, suffix='_rad', newpath=newpath)
     fmapnii = nb.load(in_file)
@@ -452,7 +452,7 @@ def _tohz(in_file, range_hz, newpath=None):
     """Convert a field map to Hz units"""
     from math import pi
     import nibabel as nb
-    from niworkflows.nipype.utils.filemanip import fname_presuffix
+    from nipype.utils.filemanip import fname_presuffix
 
     out_file = fname_presuffix(in_file, suffix='_hz', newpath=newpath)
     fmapnii = nb.load(in_file)
@@ -485,7 +485,7 @@ def phdiff2fmap(in_file, delta_te, newpath=None):
     import math
     import numpy as np
     import nibabel as nb
-    from niworkflows.nipype.utils.filemanip import fname_presuffix
+    from nipype.utils.filemanip import fname_presuffix
     #  GYROMAG_RATIO_H_PROTON_MHZ = 42.576
 
     out_file = fname_presuffix(in_file, suffix='_fmap', newpath=newpath)

fmriprep/interfaces/freesurfer.py

@@ -15,8 +15,8 @@
 
 Disable warnings:
 
-    >>> import niworkflows.nipype as nn
-    >>> nn.logging.getLogger('interface').setLevel('ERROR')
+    >>> from nipype import logging
+    >>> logging.getLogger('interface').setLevel('ERROR')
 
 """
 
@@ -28,13 +28,13 @@
 from scipy.ndimage.morphology import binary_fill_holes
 from nilearn.image import resample_to_img, new_img_like
 
-from niworkflows.nipype.utils.filemanip import copyfile, filename_to_list, fname_presuffix
-from niworkflows.nipype.interfaces.base import (
+from nipype.utils.filemanip import copyfile, filename_to_list, fname_presuffix
+from nipype.interfaces.base import (
     isdefined, InputMultiPath, BaseInterfaceInputSpec, TraitedSpec, File, traits, Directory
 )
-from niworkflows.nipype.interfaces import freesurfer as fs
-from niworkflows.nipype.interfaces.base import SimpleInterface
-from niworkflows.nipype.interfaces.freesurfer.preprocess import ConcatenateLTA
+from nipype.interfaces import freesurfer as fs
+from nipype.interfaces.base import SimpleInterface
+from nipype.interfaces.freesurfer.preprocess import ConcatenateLTA
 
 
 class StructuralReference(fs.RobustTemplate):

fmriprep/interfaces/images.py

@@ -15,12 +15,12 @@
 import nilearn.image as nli
 from textwrap import indent
 
-from niworkflows.nipype import logging
-from niworkflows.nipype.utils.filemanip import fname_presuffix
-from niworkflows.nipype.interfaces.base import (
+from nipype import logging
+from nipype.utils.filemanip import fname_presuffix
+from nipype.interfaces.base import (
     traits, TraitedSpec, BaseInterfaceInputSpec, SimpleInterface,
     File, InputMultiPath, OutputMultiPath)
-from niworkflows.nipype.interfaces import fsl
+from nipype.interfaces import fsl
 
 LOGGER = logging.getLogger('interface')
 
@@ -570,7 +570,7 @@ def reorient(in_file, newpath=None):
 def extract_wm(in_seg, wm_label=3, newpath=None):
     import nibabel as nb
     import numpy as np
-    from niworkflows.nipype.utils.filemanip import fname_presuffix
+    from nipype.utils.filemanip import fname_presuffix
 
     nii = nb.load(in_seg)
     data = np.zeros(nii.shape, dtype=np.uint8)
@@ -622,7 +622,7 @@ def demean(in_file, in_mask, only_mask=False, newpath=None):
     import os
     import numpy as np
     import nibabel as nb
-    from niworkflows.nipype.utils.filemanip import fname_presuffix
+    from nipype.utils.filemanip import fname_presuffix
 
     out_file = fname_presuffix(in_file, suffix='_demeaned',
                                newpath=os.getcwd())

fmriprep/interfaces/itk.py

@@ -14,12 +14,12 @@
 import numpy as np
 import nibabel as nb
 
-from niworkflows.nipype import logging
-from niworkflows.nipype.utils.filemanip import fname_presuffix
-from niworkflows.nipype.interfaces.base import (
+from nipype import logging
+from nipype.utils.filemanip import fname_presuffix
+from nipype.interfaces.base import (
     traits, TraitedSpec, BaseInterfaceInputSpec, File, InputMultiPath, OutputMultiPath,
     SimpleInterface)
-from niworkflows.nipype.interfaces.ants.resampling import ApplyTransformsInputSpec
+from nipype.interfaces.ants.resampling import ApplyTransformsInputSpec
 
 LOGGER = logging.getLogger('interface')
 
@@ -222,8 +222,8 @@ def _run_interface(self, runtime):
 
 
 def _mat2itk(args):
-    from niworkflows.nipype.interfaces.c3 import C3dAffineTool
-    from niworkflows.nipype.utils.filemanip import fname_presuffix
+    from nipype.interfaces.c3 import C3dAffineTool
+    from nipype.utils.filemanip import fname_presuffix
 
     in_file, in_ref, in_src, index, newpath = args
     # Generate a temporal file name
@@ -247,7 +247,7 @@ def _applytfms(args):
     multiprocessing's map
     """
     import nibabel as nb
-    from niworkflows.nipype.utils.filemanip import fname_presuffix
+    from nipype.utils.filemanip import fname_presuffix
     from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
 
     in_file, in_xform, ifargs, index, newpath = args

fmriprep/interfaces/multiecho.py

@@ -21,9 +21,9 @@
 import nibabel as nb
 from nilearn.masking import (apply_mask, unmask)
 
-from niworkflows.nipype import logging
-from niworkflows.nipype.utils.filemanip import (split_filename, fname_presuffix)
-from niworkflows.nipype.interfaces.base import (
+from nipype import logging
+from nipype.utils.filemanip import (split_filename, fname_presuffix)
+from nipype.interfaces.base import (
     traits, TraitedSpec, File, InputMultiPath, SimpleInterface,
     BaseInterfaceInputSpec)
 

fmriprep/interfaces/nilearn.py

@@ -16,9 +16,9 @@
 from nilearn.masking import compute_epi_mask
 from nilearn.image import concat_imgs
 
-from niworkflows.nipype import logging
-from niworkflows.nipype.utils.filemanip import fname_presuffix
-from niworkflows.nipype.interfaces.base import (
+from nipype import logging
+from nipype.utils.filemanip import fname_presuffix
+from nipype.interfaces.base import (
     traits, isdefined, TraitedSpec, BaseInterfaceInputSpec,
     File, InputMultiPath, SimpleInterface
 )

fmriprep/interfaces/patches.py

@@ -11,7 +11,7 @@
 from time import sleep
 
 from numpy.linalg.linalg import LinAlgError
-from niworkflows.nipype.algorithms import confounds as nac
+from nipype.algorithms import confounds as nac
 
 
 class RobustACompCor(nac.ACompCor):

fmriprep/interfaces/reports.py

@@ -14,11 +14,11 @@
 import re
 
 from collections import Counter
-from niworkflows.nipype.interfaces.base import (
+from nipype.interfaces.base import (
     traits, TraitedSpec, BaseInterfaceInputSpec,
     File, Directory, InputMultiPath, Str, isdefined,
     SimpleInterface)
-from niworkflows.nipype.interfaces import freesurfer as fs
+from nipype.interfaces import freesurfer as fs
 
 from .bids import BIDS_NAME
 

fmriprep/interfaces/surf.py

@@ -13,7 +13,7 @@
 import numpy as np
 import nibabel as nb
 
-from niworkflows.nipype.interfaces.base import (
+from nipype.interfaces.base import (
     BaseInterfaceInputSpec, TraitedSpec, File, traits, isdefined,
     SimpleInterface
 )

fmriprep/interfaces/utils.py

@@ -13,13 +13,13 @@
 import nibabel as nb
 import scipy.ndimage as nd
 
-from niworkflows.nipype import logging
-from niworkflows.nipype.utils.filemanip import fname_presuffix
-from niworkflows.nipype.interfaces.base import (
+from nipype import logging
+from nipype.utils.filemanip import fname_presuffix
+from nipype.interfaces.base import (
     traits, isdefined, File, InputMultiPath,
     TraitedSpec, DynamicTraitedSpec, BaseInterfaceInputSpec, SimpleInterface
 )
-from niworkflows.nipype.interfaces.io import add_traits
+from nipype.interfaces.io import add_traits
 
 IFLOGGER = logging.getLogger('interfaces')