MAINT: fix interaction with external logging

[mgxd]

Fixes #2569 .

Changes proposed in this pull request

• remove call to logging.basicConfig
• scope sub-loggers (interface, workflow, etc) within nipype ancestor

[codecov-io]

Codecov Report

Merging #2611 into master will increase coverage by 0.03%.
The diff coverage is 94.52%.

@@            Coverage Diff             @@
##           master    #2611      +/-   ##
==========================================
+ Coverage   67.59%   67.63%   +0.03%     
==========================================
  Files         339      339              
  Lines       42814    42855      +41     
  Branches     5288     5296       +8     
==========================================
+ Hits        28941    28984      +43     
+ Misses      13191    13187       -4     
- Partials      682      684       +2

Flag	Coverage Δ
#smoketests	50.77% <92%> (ø)	⬆️
#unittests	65.12% <93.15%> (+0.03%)	⬆️

Impacted Files	Coverage Δ
nipype/utils/config.py	66.84% <0%> (ø)	⬆️
nipype/algorithms/mesh.py	30.39% <100%> (ø)	⬆️
nipype/interfaces/dipy/anisotropic_power.py	41.66% <100%> (ø)	⬆️
nipype/pipeline/engine/workflows.py	79.08% <100%> (ø)	⬆️
nipype/interfaces/cmtk/cmtk.py	18.65% <100%> (ø)	⬆️
nipype/algorithms/metrics.py	58.35% <100%> (ø)	⬆️
nipype/interfaces/elastix/registration.py	52.25% <100%> (ø)	⬆️
nipype/interfaces/afni/base.py	62.9% <100%> (ø)	⬆️
nipype/pipeline/plugins/oar.py	54.54% <100%> (ø)	⬆️
nipype/pipeline/plugins/slurm.py	16.88% <100%> (ø)	⬆️
... and 54 more

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[effigies]

I would actually remove this line, as well as the others (L590, L658), as they're overriding a file-level variable, but not changing it.

[mgxd]

nice catch, fixed.

[effigies]

Is there some way to test this automatically? Or at least post a demonstration that @jondeaton's replicating code now works as expected?

[mgxd]

@effigies any recommended way to check logging output? I mocked up an example with unittest.Testcase.assertLogs but was passing for both pre/post fix.

@jondeaton I tested this with your minimal example

import logging
from nipype.interfaces.ants import N4BiasFieldCorrection
logger = logging.getLogger('root')
logger.addHandler(logging.StreamHandler())
logger.warning("This should really only be appearing once...")

but perhaps you would like to check out this branch and verify this fix.

[effigies]

@effigies any recommended way to check logging output? I mocked up an example with unittest.Testcase.assertLogs but was passing for both pre/post fix.

No, sorry, I don't have any experience here. It would just be nice to have some confirmation.