fix: completelly move nilearn on to niworkflows

Author: oesteban

fmriprep/workflows/base.py

@@ -19,7 +19,7 @@
 from nipype import __version__ as nipype_ver
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
-from nilearn import __version__ as nilearn_ver
+from niworkflows.interfaces.nilearn import NILEARN_VERSION
 
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.bids import (
@@ -507,7 +507,7 @@ def init_single_subject_wf(
 
 ### References
 
-""".format(nilearn_ver=nilearn_ver)
+""".format(nilearn_ver=NILEARN_VERSION)
 
     # Filter out standard spaces to a separate dict
     std_spaces = OrderedDict([

fmriprep/workflows/bold/registration.py

@@ -33,10 +33,10 @@
 from niworkflows.interfaces.itk import MultiApplyTransforms
 from niworkflows.interfaces.registration import FLIRTRPT
 from niworkflows.interfaces.utils import GenerateSamplingReference
+from niworkflows.interfaces.nilearn import Merge
 
 from ...config import DEFAULT_MEMORY_MIN_GB
 from ...interfaces import DerivativesDataSink
-from ...interfaces.nilearn import Merge
 
 
 LOGGER = logging.getLogger('nipype.workflow')

fmriprep/workflows/bold/resampling.py

@@ -26,10 +26,10 @@
 from niworkflows.interfaces.utils import GenerateSamplingReference
 from niworkflows.interfaces.utility import KeySelect
 from niworkflows.interfaces.surf import GiftiSetAnatomicalStructure
+from niworkflows.interfaces.nilearn import Merge
 
 from ...config import DEFAULT_MEMORY_MIN_GB
 from ...interfaces import DerivativesDataSink
-from ...interfaces.nilearn import Merge
 
 from .util import init_bold_reference_wf
 

setup.cfg

@@ -22,9 +22,8 @@ python_requires = >=3.5
 install_requires =
     indexed_gzip >=0.8.8
     nibabel >=2.2.1
-    nilearn !=0.5.0, !=0.5.1
     nipype >=1.3.0rc1
-    niworkflows ~=0.10.4
+    niworkflows @ git+https://github.com/oesteban/niworkflows.git@7f7986a643d18a312285b9a6ea5934d0d45b5451
     numpy
     pandas
     psutil >=5.4