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Merge pull request #1133 from effigies/pin/niworkflows
RF: Resume external nipype dependency
2 parents 5dd7819 + 366904f commit 5747a6d

40 files changed

+131
-135
lines changed

‎.circleci/config.yml‎

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

‎docs/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -28,4 +28,4 @@ dependencies:
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- svgutils
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- nitime
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- nilearn
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- niworkflows>=0.3.13
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- niworkflows>=0.4.0

‎fmriprep/cli/fmriprep_bold_mask.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""Run the BOLD reference+mask workflow"""
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import os
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from niworkflows.nipype.utils.filemanip import hash_infile
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from nipype.utils.filemanip import hash_infile
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def get_parser():

‎fmriprep/cli/run.py‎

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

‎fmriprep/info.py‎

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

‎fmriprep/interfaces/bids.py‎

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@@ -14,8 +14,8 @@
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Disable warnings:
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>>> import niworkflows.nipype as nn
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>>> nn.logging.getLogger('interface').setLevel('ERROR')
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>>> from nipype import logging
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>>> logging.getLogger('interface').setLevel('ERROR')
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2020
"""
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@@ -26,13 +26,13 @@
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import gzip
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from shutil import copytree, rmtree, copyfileobj
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from niworkflows.nipype import logging
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from niworkflows.nipype.interfaces.base import (
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from nipype import logging
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from nipype.interfaces.base import (
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traits, isdefined, TraitedSpec, BaseInterfaceInputSpec,
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File, Directory, InputMultiPath, OutputMultiPath, Str,
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SimpleInterface
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)
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from niworkflows.nipype.utils.filemanip import copyfile
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from nipype.utils.filemanip import copyfile
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LOGGER = logging.getLogger('interface')
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BIDS_NAME = re.compile(

‎fmriprep/interfaces/cifti.py‎

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Original file line numberDiff line numberDiff line change
@@ -17,12 +17,12 @@
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import numpy as np
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from nilearn.image import resample_to_img
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20-
from niworkflows.nipype.interfaces.base import (
20+
from nipype.interfaces.base import (
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BaseInterfaceInputSpec, TraitedSpec, File, traits,
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SimpleInterface, Directory
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)
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from niworkflows.data import getters
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from niworkflows.nipype.utils.filemanip import split_filename
25+
from nipype.utils.filemanip import split_filename
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# CITFI structures with corresponding FS labels
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CIFTI_STRUCT_WITH_LABELS = {

‎fmriprep/interfaces/confounds.py‎

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

‎fmriprep/interfaces/fmap.py‎

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@@ -17,9 +17,9 @@
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import numpy as np
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import nibabel as nb
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from niworkflows.nipype import logging
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from niworkflows.nipype.utils.filemanip import fname_presuffix
22-
from niworkflows.nipype.interfaces.base import (
20+
from nipype import logging
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from nipype.utils.filemanip import fname_presuffix
22+
from nipype.interfaces.base import (
2323
BaseInterfaceInputSpec, TraitedSpec, File, isdefined, traits,
2424
SimpleInterface)
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@@ -241,7 +241,7 @@ def _despike2d(data, thres, neigh=None):
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242242
def _unwrap(fmap_data, mag_file, mask=None):
243243
from math import pi
244-
from niworkflows.nipype.interfaces.fsl import PRELUDE
244+
from nipype.interfaces.fsl import PRELUDE
245245
magnii = nb.load(mag_file)
246246

247247
if mask is None:
@@ -433,7 +433,7 @@ def _torads(in_file, fmap_range=None, newpath=None):
433433
"""
434434
from math import pi
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import nibabel as nb
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from niworkflows.nipype.utils.filemanip import fname_presuffix
436+
from nipype.utils.filemanip import fname_presuffix
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438438
out_file = fname_presuffix(in_file, suffix='_rad', newpath=newpath)
439439
fmapnii = nb.load(in_file)
@@ -452,7 +452,7 @@ def _tohz(in_file, range_hz, newpath=None):
452452
"""Convert a field map to Hz units"""
453453
from math import pi
454454
import nibabel as nb
455-
from niworkflows.nipype.utils.filemanip import fname_presuffix
455+
from nipype.utils.filemanip import fname_presuffix
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457457
out_file = fname_presuffix(in_file, suffix='_hz', newpath=newpath)
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fmapnii = nb.load(in_file)
@@ -485,7 +485,7 @@ def phdiff2fmap(in_file, delta_te, newpath=None):
485485
import math
486486
import numpy as np
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import nibabel as nb
488-
from niworkflows.nipype.utils.filemanip import fname_presuffix
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from nipype.utils.filemanip import fname_presuffix
489489
# GYROMAG_RATIO_H_PROTON_MHZ = 42.576
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out_file = fname_presuffix(in_file, suffix='_fmap', newpath=newpath)

‎fmriprep/interfaces/freesurfer.py‎

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Disable warnings:
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>>> import niworkflows.nipype as nn
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>>> nn.logging.getLogger('interface').setLevel('ERROR')
18+
>>> from nipype import logging
19+
>>> logging.getLogger('interface').setLevel('ERROR')
2020
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"""
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from scipy.ndimage.morphology import binary_fill_holes
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from nilearn.image import resample_to_img, new_img_like
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31-
from niworkflows.nipype.utils.filemanip import copyfile, filename_to_list, fname_presuffix
32-
from niworkflows.nipype.interfaces.base import (
31+
from nipype.utils.filemanip import copyfile, filename_to_list, fname_presuffix
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from nipype.interfaces.base import (
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isdefined, InputMultiPath, BaseInterfaceInputSpec, TraitedSpec, File, traits, Directory
3434
)
35-
from niworkflows.nipype.interfaces import freesurfer as fs
36-
from niworkflows.nipype.interfaces.base import SimpleInterface
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from niworkflows.nipype.interfaces.freesurfer.preprocess import ConcatenateLTA
35+
from nipype.interfaces import freesurfer as fs
36+
from nipype.interfaces.base import SimpleInterface
37+
from nipype.interfaces.freesurfer.preprocess import ConcatenateLTA
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class StructuralReference(fs.RobustTemplate):

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