[REF] Fix use of logging module in utils, algorithms and interfaces. #2276
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Fix logging formatting in ants, cmtk, elastic, freesurfer, fsl, mrtrix, mrtrix3, nilearn, and spm interfaces. Okay, it was mostly in cmtk, io, and mrtrix. - In nipype/interfaces/io.py logging is imported multiple times, and iflogger is redefined a couple of times. Not sure if that’s the right way to go. - Is this okay: - `iflogger.debug('saving inputs {}', inputs)` (nipype/interfaces/base.py#L1210) - Also caught a couple of things in nipype/interfaces/cmtk/nx.py. Namely a couple of unused variables and at one point redefining `file`. 
Codecov Report
@@ Coverage Diff @@ ## master #2276 +/- ## ======================================= Coverage 72.52% 72.52% ======================================= Files 1188 1188 Lines 59134 59134 Branches 8506 8506 ======================================= Hits 42889 42889 Misses 14859 14859 Partials 1386 1386
Continue to review full report at Codecov.
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| @tsalo - there is one conflict due to a merge? could you please resolve and update this PR? |
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Partially addresses #1242.
Changes proposed in this pull request
I went through
nipype.utils,nipype.algorithms, andnipype.interfaces, fixing the logging calls where I found them.