Merge pull request #1832 from oesteban/fix/remove-sklearn-dependency

MAINT: Cleaning up dependencies

Author: oesteban

fmriprep/cli/run.py

@@ -43,7 +43,7 @@ def get_parser():
     from templateflow.api import templates
     from packaging.version import Version
     from ..__about__ import __version__
-    from ..workflows.bold.resampling import NONSTANDARD_REFERENCES
+    from ..config import NONSTANDARD_REFERENCES
     from .version import check_latest, is_flagged
 
     verstr = 'fmriprep v{}'.format(__version__)

fmriprep/config.py

@@ -0,0 +1,6 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""fMRIPrep settings."""
+
+DEFAULT_MEMORY_MIN_GB = 0.01
+NONSTANDARD_REFERENCES = ['anat', 'T1w', 'run', 'func', 'sbref', 'fsnative']

fmriprep/interfaces/nilearn.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 (
@@ -457,7 +457,7 @@ def init_single_subject_wf(
             FreeSurfer SUBJECTS_DIR
 
     """
-    from .bold.resampling import NONSTANDARD_REFERENCES
+    from ..config import NONSTANDARD_REFERENCES
     if name in ('single_subject_wf', 'single_subject_fmripreptest_wf'):
         # for documentation purposes
         subject_data = {
@@ -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/base.py

@@ -23,6 +23,7 @@
 from niworkflows.interfaces.cifti import GenerateCifti
 from niworkflows.interfaces.utils import DictMerge
 
+from ...config import DEFAULT_MEMORY_MIN_GB
 from ...utils.meepi import combine_meepi_source
 
 from ...interfaces import DerivativesDataSink
@@ -42,7 +43,7 @@
 from .outputs import init_func_derivatives_wf
 from .util import init_bold_reference_wf
 
-DEFAULT_MEMORY_MIN_GB = 0.01
+
 LOGGER = logging.getLogger('nipype.workflow')
 FSAVERAGE_DENSITY = {
     '642': 'fsaverage3',
@@ -266,7 +267,7 @@ def init_func_preproc_wf(
         * :py:func:`~fmriprep.workflows.fieldmap.init_nonlinear_sdc_wf`
 
     """
-    from .resampling import NONSTANDARD_REFERENCES
+    from ...config import NONSTANDARD_REFERENCES
     from ..fieldmap.base import init_sdc_wf  # Avoid circular dependency (#1066)
 
     # Filter out standard spaces to a separate dict

fmriprep/workflows/bold/base.py

@@ -33,13 +33,12 @@
     TPM2ROI, AddTPMs, AddTSVHeader, TSV2JSON, DictMerge
 )
 
+from ...config import DEFAULT_MEMORY_MIN_GB
 from ...interfaces import (
     GatherConfounds, ICAConfounds,
     FMRISummary, DerivativesDataSink
 )
 
-DEFAULT_MEMORY_MIN_GB = 0.01
-
 
 def init_bold_confs_wf(
     mem_gb,

fmriprep/workflows/bold/confounds.py

@@ -14,8 +14,7 @@
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces import NormalizeMotionParams
 from niworkflows.interfaces.itk import MCFLIRT2ITK
-
-DEFAULT_MEMORY_MIN_GB = 0.01
+from ...config import DEFAULT_MEMORY_MIN_GB
 
 
 # pylint: disable=R0914

fmriprep/workflows/bold/hmc.py

@@ -6,12 +6,10 @@
 from niworkflows.interfaces.cifti import CiftiNameSource
 from niworkflows.interfaces.surf import GiftiNameSource
 
+from ...config import DEFAULT_MEMORY_MIN_GB
 from ...interfaces import DerivativesDataSink
 
 
-DEFAULT_MEMORY_MIN_GB = 0.01
-
-
 def init_func_derivatives_wf(
     bids_root,
     cifti_output,

fmriprep/workflows/bold/outputs.py

@@ -33,13 +33,12 @@
 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
 
 
-DEFAULT_MEMORY_MIN_GB = 0.01
-
 LOGGER = logging.getLogger('nipype.workflow')
 
 

fmriprep/workflows/bold/registration.py

@@ -26,15 +26,13 @@
 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
 
-DEFAULT_MEMORY_MIN_GB = 0.01
-NONSTANDARD_REFERENCES = ['anat', 'T1w', 'run', 'func', 'sbref', 'fsnative']
-
 
 def init_bold_surf_wf(mem_gb, output_spaces, medial_surface_nan, name='bold_surf_wf'):
     """