PIN: nipype 1.1.0

docs/environment.yml

@@ -21,11 +21,12 @@ dependencies:
 - python-dateutil
 - pydot>=1.2.3
 - cython
+- nipype>=1.1.0
 
 - pip:
  - sphinx-argparse
  - doctest-ignore-unicode
  - svgutils
  - nitime
  - nilearn
- - niworkflows>=0.4.1
+ - niworkflows>=0.4.2

fmriprep/cli/run.py

@@ -255,9 +255,9 @@ def main():
  log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
  # Set logging
  logger.setLevel(log_level)
- nlogging.getLogger('workflow').setLevel(log_level)
- nlogging.getLogger('interface').setLevel(log_level)
- nlogging.getLogger('utils').setLevel(log_level)
+ nlogging.getLogger('nipype.workflow').setLevel(log_level)
+ nlogging.getLogger('nipype.interface').setLevel(log_level)
+ nlogging.getLogger('nipype.utils').setLevel(log_level)
 
  errno = 0
 
@@ -341,7 +341,7 @@ def build_workflow(opts, retval):
  from ..utils.bids import collect_participants
  from ..viz.reports import generate_reports
 
- logger = logging.getLogger('workflow')
+ logger = logging.getLogger('nipype.workflow')
 
  INIT_MSG = """
  Running fMRIPREP version {version}:

fmriprep/info.py

@@ -70,10 +70,9 @@
  'grabbit',
  'pybids>=0.5.1',
  'nitime',
- 'nipype>=1.0.4',
- 'niworkflows>=0.4.1',
+ 'nipype>=1.1.0',
+ 'niworkflows>=0.4.2',
  'statsmodels',
- 'nipype',
  'seaborn',
  'indexed_gzip>=0.8.2',
  'scikit-image',

fmriprep/interfaces/bids.py

@@ -15,7 +15,7 @@
 Disable warnings:
 
  >>> from nipype import logging
- >>> logging.getLogger('interface').setLevel('ERROR')
+ >>> logging.getLogger('nipype.interface').setLevel('ERROR')
 
 """
 
@@ -34,7 +34,7 @@
 )
 from nipype.utils.filemanip import copyfile
 
-LOGGER = logging.getLogger('interface')
+LOGGER = logging.getLogger('nipype.interface')
 BIDS_NAME = re.compile(
  '^(.*\/)?(?P<subject_id>sub-[a-zA-Z0-9]+)(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
  '(_(?P<task_id>task-[a-zA-Z0-9]+))?(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'

fmriprep/interfaces/confounds.py

@@ -21,7 +21,7 @@
 )
 from niworkflows.viz.plots import fMRIPlot
 
-LOGGER = logging.getLogger('interface')
+LOGGER = logging.getLogger('nipype.interface')
 
 
 class GatherConfoundsInputSpec(BaseInterfaceInputSpec):

fmriprep/interfaces/fmap.py

@@ -23,7 +23,7 @@
  BaseInterfaceInputSpec, TraitedSpec, File, isdefined, traits,
  SimpleInterface)
 
-LOGGER = logging.getLogger('interface')
+LOGGER = logging.getLogger('nipype.interface')
 
 
 class FieldEnhanceInputSpec(BaseInterfaceInputSpec):

fmriprep/interfaces/freesurfer.py

@@ -16,7 +16,7 @@
 Disable warnings:
 
  >>> from nipype import logging
- >>> logging.getLogger('interface').setLevel('ERROR')
+ >>> logging.getLogger('nipype.interface').setLevel('ERROR')
 
 """
 

fmriprep/interfaces/images.py

@@ -22,7 +22,7 @@
  File, InputMultiPath, OutputMultiPath)
 from nipype.interfaces import fsl
 
-LOGGER = logging.getLogger('interface')
+LOGGER = logging.getLogger('nipype.interface')
 
 
 class IntraModalMergeInputSpec(BaseInterfaceInputSpec):

fmriprep/interfaces/itk.py

@@ -21,7 +21,7 @@
  SimpleInterface)
 from nipype.interfaces.ants.resampling import ApplyTransformsInputSpec
 
-LOGGER = logging.getLogger('interface')
+LOGGER = logging.getLogger('nipype.interface')
 
 
 class MCFLIRT2ITKInputSpec(BaseInterfaceInputSpec):

fmriprep/interfaces/multiecho.py

@@ -27,7 +27,7 @@
  traits, TraitedSpec, File, InputMultiPath, SimpleInterface,
  BaseInterfaceInputSpec)
 
-LOGGER = logging.getLogger('interface')
+LOGGER = logging.getLogger('nipype.interface')
 
 
 class FirstEchoInputSpec(BaseInterfaceInputSpec):

fmriprep/interfaces/nilearn.py

@@ -23,7 +23,7 @@
  File, InputMultiPath, SimpleInterface
 )
 
-LOGGER = logging.getLogger('interface')
+LOGGER = logging.getLogger('nipype.interface')
 
 
 class MaskEPIInputSpec(BaseInterfaceInputSpec):

fmriprep/interfaces/utils.py

@@ -21,7 +21,7 @@
 )
 from nipype.interfaces.io import add_traits
 
-IFLOGGER = logging.getLogger('interfaces')
+IFLOGGER = logging.getLogger('nipype.interfaces')
 
 
 class TPM2ROIInputSpec(BaseInterfaceInputSpec):

fmriprep/utils/bspline.py

@@ -10,7 +10,7 @@
 from datetime import datetime as dt
 
 from nipype import logging
-LOGGER = logging.getLogger('interfaces')
+LOGGER = logging.getLogger('nipype.interfaces')
 
 
 class BSplineFieldmap(object):

fmriprep/workflows/bold/base.py

@@ -43,7 +43,7 @@
 from .util import init_bold_reference_wf
 
 DEFAULT_MEMORY_MIN_GB = 0.01
-LOGGER = logging.getLogger('workflow')
+LOGGER = logging.getLogger('nipype.workflow')
 
 
 def init_func_preproc_wf(bold_file, ignore, freesurfer,

fmriprep/workflows/bold/stc.py

@@ -14,7 +14,7 @@
 from niworkflows.interfaces.utils import CopyXForm
 
 DEFAULT_MEMORY_MIN_GB = 0.01
-LOGGER = logging.getLogger('workflow')
+LOGGER = logging.getLogger('nipype.workflow')
 
 
 # pylint: disable=R0914

fmriprep/workflows/bold/t2s.py

@@ -18,7 +18,7 @@
 from .util import init_skullstrip_bold_wf
 
 DEFAULT_MEMORY_MIN_GB = 0.01
-LOGGER = logging.getLogger('workflow')
+LOGGER = logging.getLogger('nipype.workflow')
 
 
 # pylint: disable=R0914

fmriprep/workflows/fieldmap/base.py

@@ -45,7 +45,7 @@
 from .syn import init_syn_sdc_wf
 from .unwarp import init_sdc_unwarp_wf
 
-LOGGER = logging.getLogger('workflow')
+LOGGER = logging.getLogger('nipype.workflow')
 FMAP_PRIORITY = {
  'epi': 0,
  'fieldmap': 1,

fmriprep/workflows/fieldmap/syn.py

@@ -34,7 +34,7 @@
 from ..bold.util import init_skullstrip_bold_wf
 
 DEFAULT_MEMORY_MIN_GB = 0.01
-LOGGER = logging.getLogger('workflow')
+LOGGER = logging.getLogger('nipype.workflow')
 
 
 def init_syn_sdc_wf(omp_nthreads, bold_pe=None,

requirements.txt

@@ -1,2 +1,2 @@
-niworkflows>=0.4.1
+niworkflows>=0.4.2
 versioneer