Merge pull request #2611 from mgxd/fix/log

MAINT: fix interaction with external logging

Author: effigies

nipype/algorithms/confounds.py

@@ -24,7 +24,7 @@
 from ..utils import NUMPY_MMAP
 from ..utils.misc import normalize_mc_params
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class ComputeDVARSInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/mesh.py

@@ -17,7 +17,7 @@
                                BaseInterfaceInputSpec)
 from ..interfaces.vtkbase import tvtk
 from ..interfaces import vtkbase as VTKInfo
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class TVTKBaseInterface(BaseInterface):

nipype/algorithms/metrics.py

@@ -26,7 +26,7 @@
     isdefined)
 from ..interfaces.nipy.base import NipyBaseInterface
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class DistanceInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/misc.py

@@ -31,7 +31,7 @@
 
 from . import confounds
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class PickAtlasInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/modelgen.py

@@ -29,7 +29,7 @@
 from ..utils.filemanip import ensure_list
 from ..utils.misc import normalize_mc_params
 from .. import config, logging
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def gcd(a, b):

nipype/algorithms/rapidart.py

@@ -31,7 +31,7 @@
 from ..utils.filemanip import ensure_list, save_json, split_filename
 from ..utils.misc import find_indices, normalize_mc_params
 from .. import logging, config
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def _get_affine_matrix(params, source):

nipype/interfaces/afni/base.py

@@ -19,7 +19,7 @@
 from ...external.due import BibTeX
 
 # Use nipype's logging system
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class Info(PackageInfo):

nipype/interfaces/ants/base.py

@@ -12,7 +12,7 @@
 from ... import logging, LooseVersion
 from ..base import (CommandLine, CommandLineInputSpec, traits, isdefined,
                     PackageInfo)
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 # -Using -1 gives primary responsibilty to ITKv4 to do the correct
 #  thread limitings.

nipype/interfaces/base/core.py

@@ -49,7 +49,7 @@
 from future import standard_library
 standard_library.install_aliases()
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 PY35 = sys.version_info >= (3, 5)
 PY3 = sys.version_info[0] > 2

nipype/interfaces/base/support.py

@@ -20,7 +20,7 @@
 from ... import logging
 from ...utils.misc import is_container
 from ...utils.filemanip import md5, to_str, hash_infile
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class NipypeInterfaceError(Exception):

nipype/interfaces/cmtk/cmtk.py

@@ -19,7 +19,7 @@
 
 from ..base import (BaseInterface, BaseInterfaceInputSpec, traits, File,
                     TraitedSpec, Directory, OutputMultiPath, isdefined)
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def length(xyz, along=False):

nipype/interfaces/cmtk/nbs.py

@@ -13,7 +13,7 @@
 from ..base import (LibraryBaseInterface, BaseInterfaceInputSpec, traits, File,
                     TraitedSpec, InputMultiPath, OutputMultiPath, isdefined)
 from .base import have_cv
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def ntwks_to_matrices(in_files, edge_key):

nipype/interfaces/cmtk/nx.py

@@ -18,7 +18,7 @@
                     TraitedSpec, InputMultiPath, OutputMultiPath, isdefined)
 from .base import have_cmp
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def read_unknown_ntwk(ntwk):

nipype/interfaces/cmtk/parcellation.py

@@ -18,7 +18,7 @@
                     BaseInterfaceInputSpec, traits, File,
                     TraitedSpec, Directory, isdefined)
 from .base import have_cmp
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def create_annot_label(subject_id, subjects_dir, fs_dir, parcellation_name):

nipype/interfaces/dipy/anisotropic_power.py

@@ -8,7 +8,7 @@
 from ..base import TraitedSpec, File, isdefined
 from .base import DipyDiffusionInterface, DipyBaseInterfaceInputSpec
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class APMQballInputSpec(DipyBaseInterfaceInputSpec):

nipype/interfaces/dipy/preprocess.py

@@ -12,7 +12,7 @@
 from ..base import (traits, TraitedSpec, File, isdefined)
 from .base import DipyBaseInterface
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class ResampleInputSpec(TraitedSpec):

nipype/interfaces/dipy/reconstruction.py

@@ -18,7 +18,7 @@
 from ..base import TraitedSpec, File, traits, isdefined
 from .base import DipyDiffusionInterface, DipyBaseInterfaceInputSpec
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class RESTOREInputSpec(DipyBaseInterfaceInputSpec):

nipype/interfaces/dipy/simulate.py

@@ -13,7 +13,7 @@
 from ..base import (traits, TraitedSpec, BaseInterfaceInputSpec, File,
                     InputMultiPath, isdefined)
 from .base import DipyBaseInterface
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class SimulateMultiTensorInputSpec(BaseInterfaceInputSpec):

nipype/interfaces/dipy/tensors.py

@@ -8,7 +8,7 @@
 from ..base import TraitedSpec, File, isdefined
 from .base import DipyDiffusionInterface, DipyBaseInterfaceInputSpec
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class DTIInputSpec(DipyBaseInterfaceInputSpec):

nipype/interfaces/dipy/tracks.py

@@ -11,7 +11,7 @@
 from ..base import (TraitedSpec, BaseInterfaceInputSpec, File, isdefined,
                     traits)
 from .base import DipyBaseInterface
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class TrackDensityMapInputSpec(BaseInterfaceInputSpec):

nipype/interfaces/dtitk/base.py

@@ -36,7 +36,7 @@
 from nipype.interfaces.fsl.base import Info
 import warnings
 
-LOGGER = logging.getLogger('interface')
+LOGGER = logging.getLogger('nipype.interface')
 
 
 class DTITKRenameMixin(object):

nipype/interfaces/elastix/base.py

@@ -14,7 +14,7 @@
 
 from ... import logging
 from ..base import CommandLineInputSpec, Directory, traits
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class ElastixBaseInputSpec(CommandLineInputSpec):

nipype/interfaces/elastix/registration.py

@@ -18,7 +18,7 @@
 from .base import ElastixBaseInputSpec
 from ..base import CommandLine, TraitedSpec, File, traits, InputMultiPath
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class RegistrationInputSpec(ElastixBaseInputSpec):

nipype/interfaces/elastix/utils.py

@@ -16,7 +16,7 @@
 from ... import logging
 from ..base import (BaseInterface, BaseInterfaceInputSpec, isdefined,
                     TraitedSpec, File, traits)
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class EditTransformInputSpec(BaseInterfaceInputSpec):

nipype/interfaces/freesurfer/longitudinal.py

@@ -15,7 +15,7 @@
                    FSTraitedSpecOpenMP)
 
 __docformat__ = 'restructuredtext'
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class RobustTemplateInputSpec(FSTraitedSpecOpenMP):

nipype/interfaces/freesurfer/preprocess.py

@@ -26,7 +26,7 @@
 from .utils import copy2subjdir
 
 __docformat__ = 'restructuredtext'
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 # Keeping this to avoid breaking external programs that depend on it, but
 # this should not be used internally

nipype/interfaces/freesurfer/registration.py

@@ -17,7 +17,7 @@
 from ..base import (isdefined, TraitedSpec, File, traits, Directory)
 
 __docformat__ = 'restructuredtext'
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class MPRtoMNI305InputSpec(FSTraitedSpec):

nipype/interfaces/freesurfer/utils.py

@@ -43,7 +43,7 @@
 ]
 implicit_filetypes = ['gii']
 
-logger = logging.getLogger('interface')
+logger = logging.getLogger('nipype.interface')
 
 
 def copy2subjdir(cls, in_file, folder=None, basename=None, subject_id=None):

nipype/interfaces/fsl/base.py

@@ -37,7 +37,7 @@
                     PackageInfo)
 from ...external.due import BibTeX
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class Info(PackageInfo):

nipype/interfaces/io.py

@@ -62,7 +62,7 @@
 except:
     pass
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def copytree(src, dst, use_hardlink=False):
@@ -513,7 +513,6 @@ def _fetch_bucket(self, bucket_name):
 
         # Init variables
         creds_path = self.inputs.creds_path
-        iflogger = logging.getLogger('interface')
 
         # Get AWS credentials
         try:
@@ -587,7 +586,6 @@ def _upload_to_s3(self, bucket, src, dst):
         from botocore.exceptions import ClientError
 
         # Init variables
-        iflogger = logging.getLogger('interface')
         s3_str = 's3://'
         s3_prefix = s3_str + bucket.name
 
@@ -655,7 +653,6 @@ def _list_outputs(self):
         """
 
         # Init variables
-        iflogger = logging.getLogger('interface')
         outputs = self.output_spec().get()
         out_files = []
         # Use hardlink

nipype/interfaces/mixins/reporting.py

@@ -12,7 +12,7 @@
 from ..base import (
     File, BaseInterface, BaseInterfaceInputSpec, TraitedSpec)
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class ReportCapableInputSpec(BaseInterfaceInputSpec):

nipype/interfaces/mne/base.py

@@ -11,7 +11,7 @@
 from ..base import (traits, File, Directory, TraitedSpec, OutputMultiPath)
 from ..freesurfer.base import FSCommand, FSTraitedSpec
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class WatershedBEMInputSpec(FSTraitedSpec):

nipype/interfaces/mrtrix/convert.py

@@ -19,7 +19,7 @@
 from ..base import TraitedSpec, File, isdefined
 from ..dipy.base import DipyBaseInterface, HAVE_DIPY as have_dipy
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def transform_to_affine(streams, header, affine):

nipype/interfaces/mrtrix/tensors.py

@@ -11,7 +11,7 @@
 from ...utils.filemanip import split_filename
 from ..base import (CommandLineInputSpec, CommandLine, BaseInterface, traits,
                     File, TraitedSpec, isdefined)
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class DWI2SphericalHarmonicsImageInputSpec(CommandLineInputSpec):

nipype/interfaces/mrtrix3/base.py

@@ -6,7 +6,7 @@
 
 from ... import logging
 from ..base import (CommandLineInputSpec, CommandLine, traits, File, isdefined)
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class MRTrix3BaseInputSpec(CommandLineInputSpec):

nipype/interfaces/niftyreg/base.py

@@ -26,7 +26,7 @@
 from ..base import CommandLine, CommandLineInputSpec, traits, Undefined
 from ...utils.filemanip import split_filename
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 def get_custom_path(command, env_dir='NIFTYREGDIR'):

nipype/interfaces/spm/base.py

@@ -37,7 +37,7 @@
 from ...external.due import due, Doi, BibTeX
 
 __docformat__ = 'restructuredtext'
-logger = logging.getLogger('interface')
+logger = logging.getLogger('nipype.interface')
 
 
 def func_is_3d(in_file):

nipype/interfaces/spm/model.py

@@ -26,7 +26,7 @@
                    ImageFileSPM)
 
 __docformat__ = 'restructuredtext'
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class Level1DesignInputSpec(SPMCommandInputSpec):

nipype/interfaces/utility/wrappers.py

@@ -22,7 +22,7 @@
 from ...utils.filemanip import ensure_list
 from ...utils.functions import getsource, create_function_from_source
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class FunctionInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):

nipype/interfaces/vtkbase.py

@@ -12,7 +12,7 @@
 import os
 from .. import logging
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 # Check that VTK can be imported and get version
 _vtk_version = None

nipype/interfaces/workbench/base.py

@@ -19,7 +19,7 @@
 from ...utils.filemanip import split_filename
 from ..base import CommandLine, PackageInfo
 
-iflogger = logging.getLogger('interface')
+iflogger = logging.getLogger('nipype.interface')
 
 
 class Info(PackageInfo):