From d608e44d14ffcfdaa63ec15e8bff72e5b4e61076 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Wed, 6 Jun 2018 14:53:50 -0400 Subject: [PATCH 1/3] maint: do not alter external logging configuration --- nipype/utils/logger.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/nipype/utils/logger.py b/nipype/utils/logger.py index b4b5153f41..611cb00880 100644 --- a/nipype/utils/logger.py +++ b/nipype/utils/logger.py @@ -30,9 +30,15 @@ class Logging(object): def __init__(self, config): self._config = config - logging.basicConfig( - format=self.fmt, datefmt=self.datefmt, stream=sys.stdout) - # logging.basicConfig(stream=sys.stdout) + # scope our logger to not interfere with user + _nipype_logger = logging.getLogger('nipype') + _nipype_hdlr = logging.StreamHandler(stream=sys.stdout) + _nipype_hdlr.setFormatter(logging.Formatter(fmt=self.fmt, + datefmt=self.datefmt)) + # if StreamHandler was added, do not stack + if not len(_nipype_logger.handlers): + _nipype_logger.addHandler(_nipype_hdlr) + self._logger = logging.getLogger('workflow') self._utlogger = logging.getLogger('utils') self._fmlogger = logging.getLogger('filemanip') From cf3ca2f0fc393e6afd8bf4677184d1829783bcaf Mon Sep 17 00:00:00 2001 From: mathiasg Date: Wed, 6 Jun 2018 15:31:14 -0400 Subject: [PATCH 2/3] maint: make nipype loggers children --- nipype/algorithms/confounds.py | 2 +- nipype/algorithms/mesh.py | 2 +- nipype/algorithms/metrics.py | 2 +- nipype/algorithms/misc.py | 2 +- nipype/algorithms/modelgen.py | 2 +- nipype/algorithms/rapidart.py | 2 +- nipype/interfaces/afni/base.py | 2 +- nipype/interfaces/ants/base.py | 2 +- nipype/interfaces/base/core.py | 2 +- nipype/interfaces/base/support.py | 2 +- nipype/interfaces/cmtk/cmtk.py | 2 +- nipype/interfaces/cmtk/nbs.py | 2 +- nipype/interfaces/cmtk/nx.py | 2 +- nipype/interfaces/cmtk/parcellation.py | 2 +- nipype/interfaces/dipy/anisotropic_power.py | 2 +- nipype/interfaces/dipy/preprocess.py | 2 +- nipype/interfaces/dipy/reconstruction.py | 2 +- nipype/interfaces/dipy/simulate.py | 2 +- nipype/interfaces/dipy/tensors.py | 2 +- nipype/interfaces/dipy/tracks.py | 2 +- nipype/interfaces/dtitk/base.py | 2 +- nipype/interfaces/elastix/base.py | 2 +- nipype/interfaces/elastix/registration.py | 2 +- nipype/interfaces/elastix/utils.py | 2 +- nipype/interfaces/freesurfer/longitudinal.py | 2 +- nipype/interfaces/freesurfer/preprocess.py | 2 +- nipype/interfaces/freesurfer/registration.py | 2 +- nipype/interfaces/freesurfer/utils.py | 2 +- nipype/interfaces/fsl/base.py | 2 +- nipype/interfaces/io.py | 8 ++++---- nipype/interfaces/mixins/reporting.py | 2 +- nipype/interfaces/mne/base.py | 2 +- nipype/interfaces/mrtrix/convert.py | 2 +- nipype/interfaces/mrtrix/tensors.py | 2 +- nipype/interfaces/mrtrix3/base.py | 2 +- nipype/interfaces/niftyreg/base.py | 2 +- nipype/interfaces/spm/base.py | 2 +- nipype/interfaces/spm/model.py | 2 +- nipype/interfaces/utility/wrappers.py | 2 +- nipype/interfaces/vtkbase.py | 2 +- nipype/interfaces/workbench/base.py | 2 +- nipype/interfaces/workbench/metric.py | 2 +- nipype/pipeline/engine/nodes.py | 2 +- nipype/pipeline/engine/utils.py | 2 +- nipype/pipeline/engine/workflows.py | 2 +- nipype/pipeline/plugins/base.py | 2 +- nipype/pipeline/plugins/condor.py | 2 +- nipype/pipeline/plugins/lsf.py | 2 +- nipype/pipeline/plugins/multiproc.py | 2 +- nipype/pipeline/plugins/oar.py | 2 +- nipype/pipeline/plugins/pbs.py | 2 +- nipype/pipeline/plugins/sge.py | 2 +- nipype/pipeline/plugins/slurm.py | 2 +- nipype/pipeline/plugins/tools.py | 2 +- nipype/utils/config.py | 2 +- nipype/utils/filemanip.py | 2 +- nipype/utils/logger.py | 16 ++++++++-------- nipype/utils/profiler.py | 4 ++-- nipype/utils/provenance.py | 2 +- nipype/utils/tests/test_config.py | 18 +++++++++--------- nipype/workflows/fmri/spm/preprocess.py | 2 +- nipype/workflows/smri/freesurfer/recon.py | 2 +- 62 files changed, 81 insertions(+), 81 deletions(-) diff --git a/nipype/algorithms/confounds.py b/nipype/algorithms/confounds.py index a660a0fbae..d0f9a5733a 100644 --- a/nipype/algorithms/confounds.py +++ b/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): diff --git a/nipype/algorithms/mesh.py b/nipype/algorithms/mesh.py index ba1be626b7..eeb2ddbb80 100644 --- a/nipype/algorithms/mesh.py +++ b/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): diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py index 7f78088b86..d9074c48d3 100644 --- a/nipype/algorithms/metrics.py +++ b/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): diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py index ffbd6bda3f..97906c1d69 100644 --- a/nipype/algorithms/misc.py +++ b/nipype/algorithms/misc.py @@ -31,7 +31,7 @@ from . import confounds -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') class PickAtlasInputSpec(BaseInterfaceInputSpec): diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py index 6df436d4d3..7741139201 100644 --- a/nipype/algorithms/modelgen.py +++ b/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): diff --git a/nipype/algorithms/rapidart.py b/nipype/algorithms/rapidart.py index ef4d0fa75c..a4d5b592c9 100644 --- a/nipype/algorithms/rapidart.py +++ 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): diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py index f1a3a18429..d4b8e474ff 100644 --- a/nipype/interfaces/afni/base.py +++ b/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): diff --git a/nipype/interfaces/ants/base.py b/nipype/interfaces/ants/base.py index 7316c2a733..34b64a0ec1 100644 --- a/nipype/interfaces/ants/base.py +++ b/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. diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py index e5c7fb2ca6..f0ae09bd40 100644 --- a/nipype/interfaces/base/core.py +++ b/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 diff --git a/nipype/interfaces/base/support.py b/nipype/interfaces/base/support.py index 2aa1d7162a..87252fd6d3 100644 --- a/nipype/interfaces/base/support.py +++ b/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): diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py index 0510c728ef..c26220c6b0 100644 --- a/nipype/interfaces/cmtk/cmtk.py +++ b/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): diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py index 11ed59b1ad..f21f2b33ea 100644 --- a/nipype/interfaces/cmtk/nbs.py +++ b/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): diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py index dce35ad627..1b58494f2c 100644 --- a/nipype/interfaces/cmtk/nx.py +++ b/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): diff --git a/nipype/interfaces/cmtk/parcellation.py b/nipype/interfaces/cmtk/parcellation.py index 6947cb852f..0e25e8eb10 100644 --- a/nipype/interfaces/cmtk/parcellation.py +++ b/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): diff --git a/nipype/interfaces/dipy/anisotropic_power.py b/nipype/interfaces/dipy/anisotropic_power.py index 5142b828ba..e28ae2bd19 100644 --- a/nipype/interfaces/dipy/anisotropic_power.py +++ b/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): diff --git a/nipype/interfaces/dipy/preprocess.py b/nipype/interfaces/dipy/preprocess.py index 2a08c1eae0..cc589f6579 100644 --- a/nipype/interfaces/dipy/preprocess.py +++ b/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): diff --git a/nipype/interfaces/dipy/reconstruction.py b/nipype/interfaces/dipy/reconstruction.py index 33c0c6a3e0..26a7014f79 100644 --- a/nipype/interfaces/dipy/reconstruction.py +++ b/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): diff --git a/nipype/interfaces/dipy/simulate.py b/nipype/interfaces/dipy/simulate.py index d6174908d9..4a995c8fa9 100644 --- a/nipype/interfaces/dipy/simulate.py +++ b/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): diff --git a/nipype/interfaces/dipy/tensors.py b/nipype/interfaces/dipy/tensors.py index 142c3b17de..c79e063683 100644 --- a/nipype/interfaces/dipy/tensors.py +++ b/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): diff --git a/nipype/interfaces/dipy/tracks.py b/nipype/interfaces/dipy/tracks.py index 3a500317db..b7d965ece1 100644 --- a/nipype/interfaces/dipy/tracks.py +++ b/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): diff --git a/nipype/interfaces/dtitk/base.py b/nipype/interfaces/dtitk/base.py index 069016e7f3..5cfb81d9dd 100644 --- a/nipype/interfaces/dtitk/base.py +++ b/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): diff --git a/nipype/interfaces/elastix/base.py b/nipype/interfaces/elastix/base.py index 39fd4a449e..b47e1fec17 100644 --- a/nipype/interfaces/elastix/base.py +++ b/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): diff --git a/nipype/interfaces/elastix/registration.py b/nipype/interfaces/elastix/registration.py index cb0395904a..7f2565d58c 100644 --- a/nipype/interfaces/elastix/registration.py +++ b/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): diff --git a/nipype/interfaces/elastix/utils.py b/nipype/interfaces/elastix/utils.py index 56f7b253d8..505115b05a 100644 --- a/nipype/interfaces/elastix/utils.py +++ b/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): diff --git a/nipype/interfaces/freesurfer/longitudinal.py b/nipype/interfaces/freesurfer/longitudinal.py index 82208322c6..1d982a7a44 100644 --- a/nipype/interfaces/freesurfer/longitudinal.py +++ b/nipype/interfaces/freesurfer/longitudinal.py @@ -15,7 +15,7 @@ FSTraitedSpecOpenMP) __docformat__ = 'restructuredtext' -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') class RobustTemplateInputSpec(FSTraitedSpecOpenMP): diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py index 1bd1fa6252..f99696e02a 100644 --- a/nipype/interfaces/freesurfer/preprocess.py +++ b/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 diff --git a/nipype/interfaces/freesurfer/registration.py b/nipype/interfaces/freesurfer/registration.py index 64d2a3ea0e..99ee7d0179 100644 --- a/nipype/interfaces/freesurfer/registration.py +++ b/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): diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index 58df63a946..b258d41720 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/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): diff --git a/nipype/interfaces/fsl/base.py b/nipype/interfaces/fsl/base.py index 59dc759d2e..db74e900b8 100644 --- a/nipype/interfaces/fsl/base.py +++ b/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): diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 5135656d37..3ee9d073ba 100644 --- a/nipype/interfaces/io.py +++ b/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 +513,7 @@ def _fetch_bucket(self, bucket_name): # Init variables creds_path = self.inputs.creds_path - iflogger = logging.getLogger('interface') + iflogger = logging.getLogger('nipype.interface') # Get AWS credentials try: @@ -587,7 +587,7 @@ def _upload_to_s3(self, bucket, src, dst): from botocore.exceptions import ClientError # Init variables - iflogger = logging.getLogger('interface') + iflogger = logging.getLogger('nipype.interface') s3_str = 's3://' s3_prefix = s3_str + bucket.name @@ -655,7 +655,7 @@ def _list_outputs(self): """ # Init variables - iflogger = logging.getLogger('interface') + iflogger = logging.getLogger('nipype.interface') outputs = self.output_spec().get() out_files = [] # Use hardlink diff --git a/nipype/interfaces/mixins/reporting.py b/nipype/interfaces/mixins/reporting.py index 027928e128..3f4d1b1317 100644 --- a/nipype/interfaces/mixins/reporting.py +++ b/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): diff --git a/nipype/interfaces/mne/base.py b/nipype/interfaces/mne/base.py index a6a39a9918..7f53071372 100644 --- a/nipype/interfaces/mne/base.py +++ b/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): diff --git a/nipype/interfaces/mrtrix/convert.py b/nipype/interfaces/mrtrix/convert.py index 98c8d62a39..a3a280c895 100644 --- a/nipype/interfaces/mrtrix/convert.py +++ b/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): diff --git a/nipype/interfaces/mrtrix/tensors.py b/nipype/interfaces/mrtrix/tensors.py index 2ebe120aad..04c901f1f9 100644 --- a/nipype/interfaces/mrtrix/tensors.py +++ b/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): diff --git a/nipype/interfaces/mrtrix3/base.py b/nipype/interfaces/mrtrix3/base.py index 0f80bda9c1..55ca385153 100644 --- a/nipype/interfaces/mrtrix3/base.py +++ b/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): diff --git a/nipype/interfaces/niftyreg/base.py b/nipype/interfaces/niftyreg/base.py index 65d95b0c59..bd8a280aa5 100644 --- a/nipype/interfaces/niftyreg/base.py +++ b/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'): diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index ee6387a08d..214a6e7a2f 100644 --- a/nipype/interfaces/spm/base.py +++ b/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): diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py index 8a847742cf..3e26ab6e2a 100644 --- a/nipype/interfaces/spm/model.py +++ b/nipype/interfaces/spm/model.py @@ -26,7 +26,7 @@ ImageFileSPM) __docformat__ = 'restructuredtext' -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') class Level1DesignInputSpec(SPMCommandInputSpec): diff --git a/nipype/interfaces/utility/wrappers.py b/nipype/interfaces/utility/wrappers.py index f48acbc461..80a6f89738 100644 --- a/nipype/interfaces/utility/wrappers.py +++ b/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): diff --git a/nipype/interfaces/vtkbase.py b/nipype/interfaces/vtkbase.py index c6f6a64305..1ec66ea614 100644 --- a/nipype/interfaces/vtkbase.py +++ b/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 diff --git a/nipype/interfaces/workbench/base.py b/nipype/interfaces/workbench/base.py index 5b7a8633cb..4adc9dc69b 100644 --- a/nipype/interfaces/workbench/base.py +++ b/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): diff --git a/nipype/interfaces/workbench/metric.py b/nipype/interfaces/workbench/metric.py index cb449d8a79..e5bbb60739 100644 --- a/nipype/interfaces/workbench/metric.py +++ b/nipype/interfaces/workbench/metric.py @@ -10,7 +10,7 @@ from .base import WBCommand from ... import logging -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') class MetricResampleInputSpec(CommandLineInputSpec): diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py index 90d75d3047..86818f6e2c 100644 --- a/nipype/pipeline/engine/nodes.py +++ b/nipype/pipeline/engine/nodes.py @@ -41,7 +41,7 @@ standard_library.install_aliases() -logger = logging.getLogger('workflow') +logger = logging.getLogger('nipype.workflow') class Node(EngineBase): diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py index 0a59aac26a..4ec36afe68 100644 --- a/nipype/pipeline/engine/utils.py +++ b/nipype/pipeline/engine/utils.py @@ -52,7 +52,7 @@ from funcsigs import signature standard_library.install_aliases() -logger = logging.getLogger('workflow') +logger = logging.getLogger('nipype.workflow') PY3 = sys.version_info[0] > 2 try: diff --git a/nipype/pipeline/engine/workflows.py b/nipype/pipeline/engine/workflows.py index a10dabef30..d2f040786e 100644 --- a/nipype/pipeline/engine/workflows.py +++ b/nipype/pipeline/engine/workflows.py @@ -39,7 +39,7 @@ from future import standard_library standard_library.install_aliases() -logger = logging.getLogger('workflow') +logger = logging.getLogger('nipype.workflow') class Workflow(EngineBase): diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index c41a4a07ce..122d7e57cd 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -25,7 +25,7 @@ from ..engine import MapNode from .tools import report_crash, report_nodes_not_run, create_pyscript -logger = logging.getLogger('workflow') +logger = logging.getLogger('nipype.workflow') class PluginBase(object): diff --git a/nipype/pipeline/plugins/condor.py b/nipype/pipeline/plugins/condor.py index ae2e46cccb..9f5ca632e5 100644 --- a/nipype/pipeline/plugins/condor.py +++ b/nipype/pipeline/plugins/condor.py @@ -10,7 +10,7 @@ from ...interfaces.base import CommandLine from ... import logging from .base import SGELikeBatchManagerBase, logger -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') class CondorPlugin(SGELikeBatchManagerBase): diff --git a/nipype/pipeline/plugins/lsf.py b/nipype/pipeline/plugins/lsf.py index dffc1acd82..bdaabc31e6 100644 --- a/nipype/pipeline/plugins/lsf.py +++ b/nipype/pipeline/plugins/lsf.py @@ -11,7 +11,7 @@ from ... import logging from ...interfaces.base import CommandLine from .base import SGELikeBatchManagerBase, logger -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') class LSFPlugin(SGELikeBatchManagerBase): diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index c54d268ff7..616d0b191d 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -37,7 +37,7 @@ def indent(text, prefix): # Init logger -logger = logging.getLogger('workflow') +logger = logging.getLogger('nipype.workflow') # Run node diff --git a/nipype/pipeline/plugins/oar.py b/nipype/pipeline/plugins/oar.py index 8880ee5093..c68b42379f 100644 --- a/nipype/pipeline/plugins/oar.py +++ b/nipype/pipeline/plugins/oar.py @@ -14,7 +14,7 @@ from ... import logging from ...interfaces.base import CommandLine from .base import SGELikeBatchManagerBase, logger -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') class OARPlugin(SGELikeBatchManagerBase): diff --git a/nipype/pipeline/plugins/pbs.py b/nipype/pipeline/plugins/pbs.py index 7808e52156..0738638765 100644 --- a/nipype/pipeline/plugins/pbs.py +++ b/nipype/pipeline/plugins/pbs.py @@ -12,7 +12,7 @@ from ...interfaces.base import CommandLine from .base import SGELikeBatchManagerBase, logger -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') class PBSPlugin(SGELikeBatchManagerBase): diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py index fc487e66cf..a4ce28297c 100644 --- a/nipype/pipeline/plugins/sge.py +++ b/nipype/pipeline/plugins/sge.py @@ -19,7 +19,7 @@ from ... import logging from ...interfaces.base import CommandLine from .base import SGELikeBatchManagerBase, logger -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') DEBUGGING_PREFIX = str(int(random.uniform(100, 999))) diff --git a/nipype/pipeline/plugins/slurm.py b/nipype/pipeline/plugins/slurm.py index b608cbf1ee..285d2d6584 100644 --- a/nipype/pipeline/plugins/slurm.py +++ b/nipype/pipeline/plugins/slurm.py @@ -17,7 +17,7 @@ from ...interfaces.base import CommandLine from .base import SGELikeBatchManagerBase, logger -iflogger = logging.getLogger('interface') +iflogger = logging.getLogger('nipype.interface') class SLURMPlugin(SGELikeBatchManagerBase): diff --git a/nipype/pipeline/plugins/tools.py b/nipype/pipeline/plugins/tools.py index 79922bf998..cb5b3dc78f 100644 --- a/nipype/pipeline/plugins/tools.py +++ b/nipype/pipeline/plugins/tools.py @@ -18,7 +18,7 @@ from ... import logging from ...utils.filemanip import savepkl, crash2txt, makedirs -logger = logging.getLogger('workflow') +logger = logging.getLogger('nipype.workflow') def report_crash(node, traceback=None, hostname=None): diff --git a/nipype/utils/config.py b/nipype/utils/config.py index 843748dfe6..e4e518960c 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -353,7 +353,7 @@ def stop_display(self): if self._display is not None: from .. import logging self._display.stop() - logging.getLogger('interface').debug( + logging.getLogger('nipype.interface').debug( 'Closing display (if virtual)') diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py index 1e4db4c6b1..2265178651 100644 --- a/nipype/utils/filemanip.py +++ b/nipype/utils/filemanip.py @@ -30,7 +30,7 @@ from future import standard_library standard_library.install_aliases() -fmlogger = logging.getLogger('utils') +fmlogger = logging.getLogger('nipype.utils') related_filetype_sets = [ ('.hdr', '.img', '.mat'), diff --git a/nipype/utils/logger.py b/nipype/utils/logger.py index 611cb00880..2c8fe4607a 100644 --- a/nipype/utils/logger.py +++ b/nipype/utils/logger.py @@ -39,16 +39,16 @@ def __init__(self, config): if not len(_nipype_logger.handlers): _nipype_logger.addHandler(_nipype_hdlr) - self._logger = logging.getLogger('workflow') - self._utlogger = logging.getLogger('utils') - self._fmlogger = logging.getLogger('filemanip') - self._iflogger = logging.getLogger('interface') + self._logger = logging.getLogger('nipype.workflow') + self._utlogger = logging.getLogger('nipype.utils') + self._fmlogger = logging.getLogger('nipype.filemanip') + self._iflogger = logging.getLogger('nipype.interface') self.loggers = { - 'workflow': self._logger, - 'utils': self._utlogger, - 'filemanip': self._fmlogger, - 'interface': self._iflogger + 'nipype.workflow': self._logger, + 'nipype.utils': self._utlogger, + 'nipype.filemanip': self._fmlogger, + 'nipype.interface': self._iflogger } self._hdlr = None self.update_logging(self._config) diff --git a/nipype/utils/profiler.py b/nipype/utils/profiler.py index 8d6891fbf8..d8ec32ffe3 100644 --- a/nipype/utils/profiler.py +++ b/nipype/utils/profiler.py @@ -17,7 +17,7 @@ from builtins import open, range from .. import config, logging -proflogger = logging.getLogger('utils') +proflogger = logging.getLogger('nipype.utils') resource_monitor = config.resource_monitor # Init variables @@ -351,7 +351,7 @@ def _use_resources(n_procs, mem_gb): from nipype import logging from nipype.utils.profiler import _use_cpu - iflogger = logging.getLogger('interface') + iflogger = logging.getLogger('nipype.interface') # Getsize of one character string BSIZE = sys.getsizeof(' ') - sys.getsizeof(' ') diff --git a/nipype/utils/provenance.py b/nipype/utils/provenance.py index adf01fbe64..fb2306ee4b 100644 --- a/nipype/utils/provenance.py +++ b/nipype/utils/provenance.py @@ -22,7 +22,7 @@ from .. import get_info, logging, __version__ from .filemanip import (md5, hashlib, hash_infile) -logger = logging.getLogger('utils') +logger = logging.getLogger('nipype.utils') foaf = pm.Namespace("foaf", "http://xmlns.com/foaf/0.1/") dcterms = pm.Namespace("dcterms", "http://purl.org/dc/terms/") nipype_ns = pm.Namespace("nipype", "http://nipy.org/nipype/terms/") diff --git a/nipype/utils/tests/test_config.py b/nipype/utils/tests/test_config.py index 38a55b6a07..a3c0480b29 100644 --- a/nipype/utils/tests/test_config.py +++ b/nipype/utils/tests/test_config.py @@ -253,9 +253,9 @@ def test_debug_mode(): if_config = config.get('logging', 'interface_level') ut_config = config.get('logging', 'utils_level') - wf_level = logging.getLogger('workflow').level - if_level = logging.getLogger('interface').level - ut_level = logging.getLogger('utils').level + wf_level = logging.getLogger('nipype.workflow').level + if_level = logging.getLogger('nipype.interface').level + ut_level = logging.getLogger('nipype.utils').level config.enable_debug_mode() @@ -267,9 +267,9 @@ def test_debug_mode(): assert config.get('logging', 'interface_level') == 'DEBUG' assert config.get('logging', 'utils_level') == 'DEBUG' - assert logging.getLogger('workflow').level == 10 - assert logging.getLogger('interface').level == 10 - assert logging.getLogger('utils').level == 10 + assert logging.getLogger('nipype.workflow').level == 10 + assert logging.getLogger('nipype.interface').level == 10 + assert logging.getLogger('nipype.utils').level == 10 # Restore config and levels config.set('execution', 'stop_on_first_crash', sofc_config) @@ -287,6 +287,6 @@ def test_debug_mode(): assert config.get('logging', 'interface_level') == if_config assert config.get('logging', 'utils_level') == ut_config - assert logging.getLogger('workflow').level == wf_level - assert logging.getLogger('interface').level == if_level - assert logging.getLogger('utils').level == ut_level + assert logging.getLogger('nipype.workflow').level == wf_level + assert logging.getLogger('nipype.interface').level == if_level + assert logging.getLogger('nipype.utils').level == ut_level diff --git a/nipype/workflows/fmri/spm/preprocess.py b/nipype/workflows/fmri/spm/preprocess.py index 3583659019..f2957e4b03 100644 --- a/nipype/workflows/fmri/spm/preprocess.py +++ b/nipype/workflows/fmri/spm/preprocess.py @@ -11,7 +11,7 @@ from ...smri.freesurfer.utils import create_getmask_flow from .... import logging -logger = logging.getLogger('workflow') +logger = logging.getLogger('nipype.workflow') def create_spm_preproc(name='preproc'): diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py index 05018fd931..f0ad4ad6fd 100644 --- a/nipype/workflows/smri/freesurfer/recon.py +++ b/nipype/workflows/smri/freesurfer/recon.py @@ -12,7 +12,7 @@ from .utils import getdefaultconfig from .... import logging -logger = logging.getLogger('workflow') +logger = logging.getLogger('nipype.workflow') def create_skullstripped_recon_flow(name="skullstripped_recon_all"): From 765521cfc33be08754b2499a1c7463a6ddc03508 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Thu, 7 Jun 2018 17:46:03 -0400 Subject: [PATCH 3/3] ref: remove redundant initializations --- nipype/interfaces/io.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 3ee9d073ba..8597ac4c65 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -513,7 +513,6 @@ def _fetch_bucket(self, bucket_name): # Init variables creds_path = self.inputs.creds_path - iflogger = logging.getLogger('nipype.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('nipype.interface') s3_str = 's3://' s3_prefix = s3_str + bucket.name @@ -655,7 +653,6 @@ def _list_outputs(self): """ # Init variables - iflogger = logging.getLogger('nipype.interface') outputs = self.output_spec().get() out_files = [] # Use hardlink