pep8 violations

[mwaskom]

Nipype is not the most pep8-abiding package out there. Maybe this is unavoidable, but I do think in general code that follows these guidelines is something to strive for. Below is a current (7/1/2013) list of the .py files and the number of pep complaints, obtained with

for f in `find . -name "*.py"`; do count=`pep8 $f | wc -l`; echo -n "    $count    "; echo $f; done | sort -r

Reducing these counts will yield a cleaner, better codebase, so if you find yourself with 20 minutes to kill, maybe take a crack at one of the bigger numbers?

     515    ./nipype/interfaces/fsl/tests/test_model.py
     497    ./nipype/interfaces/freesurfer/tests/test_model.py
     459    ./nipype/workflows/dmri/connectivity/group_connectivity.py
     440    ./nipype/interfaces/freesurfer/tests/test_preprocess.py
     414    ./nipype/workflows/dmri/mrtrix/connectivity_mapping.py
     391    ./examples/dmri_connectivity_advanced.py
     355    ./nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py
     354    ./nipype/interfaces/cmtk/cmtk.py
     336    ./nipype/interfaces/camino/dti.py
     335    ./nipype/workflows/dmri/camino/connectivity_mapping.py
     326    ./examples/dmri_connectivity.py
     304    ./nipype/workflows/fmri/fsl/preprocess.py
     301    ./nipype/interfaces/fsl/tests/test_dti.py
     278    ./nipype/interfaces/fsl/tests/test_preprocess.py
     276    ./nipype/interfaces/camino/convert.py
     259    ./nipype/interfaces/spm/tests/test_preprocess.py
     237    ./examples/fmri_spm_face.py
     231    ./nipype/algorithms/modelgen.py
     228    ./nipype/interfaces/fsl/preprocess.py
     222    ./nipype/workflows/smri/ants/ANTSBuildTemplate.py
     222    ./nipype/interfaces/fsl/dti.py
     215    ./nipype/interfaces/freesurfer/model.py
     209    ./nipype/interfaces/freesurfer/preprocess.py
     202    ./nipype/interfaces/mrtrix/preprocess.py
     192    ./examples/fmri_fsl_feeds.py
     181    ./examples/fmri_fsl.py
     180    ./examples/fmri_spm_dartel.py
     179    ./nipype/pipeline/tests/test_engine.py
     179    ./nipype/interfaces/spm/preprocess.py
     176    ./nipype/interfaces/meshfix.py
     174    ./examples/fmri_spm.py
     167    ./nipype/interfaces/spm/tests/test_model.py
     167    ./examples/dmri_mrtrix_dti.py
     166    ./nipype/interfaces/freesurfer/utils.py
     163    ./nipype/interfaces/fsl/tests/test_maths.py
     154    ./examples/fmri_spm_nested.py
     152    ./examples/fmri_freesurfer_smooth.py
     151    ./nipype/interfaces/slicer/legacy/registration.py
     146    ./nipype/interfaces/base.py
     143    ./nipype/interfaces/cmtk/nx.py
     142    ./nipype/workflows/dmri/fsl/tbss.py
     135    ./nipype/interfaces/spm/model.py
     135    ./nipype/interfaces/slicer/registration/specialized.py
     132    ./nipype/interfaces/slicer/diffusion/diffusion.py
     130    ./nipype/workflows/dmri/fsl/dti.py
     127    ./nipype/interfaces/mrtrix/convert.py
     123    ./nipype/interfaces/fsl/utils.py
     121    ./nipype/interfaces/traits_extension.py
     120    ./nipype/algorithms/tests/test_moments.py
     116    ./examples/fmri_spm_auditory.py
     115    ./nipype/workflows/smri/freesurfer/utils.py
     109    ./nipype/workflows/dmri/camino/diffusion.py
     109    ./nipype/interfaces/mrtrix/tensors.py
     107    ./nipype/workflows/dmri/mrtrix/diffusion.py
     105    ./nipype/interfaces/ants/registration.py
     105    ./examples/dmri_camino_dti.py
     102    ./examples/smri_antsregistration_build_template.py
     101    ./nipype/interfaces/diffusion_toolkit/dti.py
     100    ./nipype/interfaces/tests/test_base.py
     100    ./examples/dmri_fsl_dti.py
      99    ./nipype/interfaces/spm/utils.py
      97    ./nipype/interfaces/mrtrix/tracking.py
      91    ./nipype/interfaces/diffusion_toolkit/odf.py
      91    ./nipype/interfaces/dcmstack.py
      90    ./examples/rsfmri_fsl.py
      89    ./nipype/interfaces/spm/tests/test_utils.py
      89    ./nipype/interfaces/slicer/registration/brainsfit.py
      87    ./nipype/interfaces/dipy/tracks.py
      80    ./examples/fmri_nipy_glm.py
      78    ./nipype/workflows/dmri/connectivity/nx.py
      78    ./nipype/interfaces/fsl/model.py
      77    ./nipype/interfaces/nipy/model.py
      76    ./nipype/interfaces/slicer/segmentation/specialized.py
      69    ./nipype/workflows/fmri/spm/preprocess.py
      66    ./nipype/utils/filemanip.py
      66    ./nipype/interfaces/slicer/surface.py
      61    ./examples/smri_ants_build_template.py
      61    ./examples/fmri_fsl_reuse.py
      59    ./nipype/workflows/dmri/mrtrix/group_connectivity.py
      55    ./nipype/interfaces/cmtk/convert.py
      55    ./examples/dmri_dtk_odf.py
      54    ./nipype/algorithms/rapidart.py
      53    ./nipype/pipeline/tests/test_utils.py
      52    ./doc/sphinxext/numpy_ext/docscrape.py
      51    ./nipype/interfaces/freesurfer/tests/test_utils.py
      51    ./examples/dmri_dtk_dti.py
      50    ./nipype/interfaces/afni/preprocess.py
      49    ./nipype/interfaces/cmtk/parcellation.py
      48    ./examples/frontiers_paper/smoothing_comparison.py
      46    ./nipype/workflows/dmri/camino/group_connectivity.py
      46    ./nipype/algorithms/misc.py
      45    ./nipype/workflows/dmri/fsl/tests/test_tbss.py
      44    ./nipype/interfaces/slicer/filtering/arithmetic.py
      42    ./examples/smri_ants_registration.py
      41    ./nipype/interfaces/dynamic_slicer.py
      39    ./nipype/interfaces/fsl/maths.py
      39    ./nipype/interfaces/ants/segmentation.py
      39    ./nipype/interfaces/afni/tests/test_preprocess.py
      38    ./nipype/interfaces/ants/legacy.py
      38    ./examples/workshop_dartmouth_2010.py
      37    ./nipype/interfaces/slicer/filtering/denoising.py
      36    ./nipype/interfaces/slicer/generate_classes.py
      36    ./nipype/interfaces/camino2trackvis/convert.py
      36    ./nipype/interfaces/ants/resampling.py
      36    ./examples/frontiers_paper/workflow_from_scratch.py
      36    ./examples/dmri_group_connectivity_mrtrix.py
      35    ./tools/interface_inputspec_testwriter.py
      34    ./nipype/interfaces/io.py
      33    ./nipype/utils/misc.py
      33    ./nipype/interfaces/matlab.py
      32    ./nipype/interfaces/slicer/filtering/resamplescalarvectordwivolume.py
      32    ./nipype/external/cloghandler.py
      31    ./nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py
      31    ./nipype/fixes/numpy/testing/noseclasses.py
      30    ./nipype/utils/docparse.py
      30    ./nipype/interfaces/utility.py
      30    ./nipype/interfaces/fsl/tests/test_base.py
      30    ./examples/dmri_group_connectivity_camino.py
      29    ./nipype/interfaces/nitime/tests/test_nitime.py
      28    ./nipype/utils/tests/test_filemanip.py
      28    ./examples/tessellation_tutorial.py
      27    ./nipype/workflows/rsfmri/fsl/resting.py
      27    ./doc/sphinxext/inheritance_diagram.py
      24    ./nipype/interfaces/nitime/analysis.py
      24    ./nipype/interfaces/camino/connectivity.py
      23    ./nipype/interfaces/slicer/registration/brainsresample.py
      23    ./nipype/interfaces/slicer/quantification/changequantification.py
      23    ./nipype/interfaces/slicer/filtering/n4itkbiasfieldcorrection.py
      23    ./nipype/interfaces/slicer/filtering/morphology.py
      23    ./nipype/interfaces/cmtk/nbs.py
      23    ./nipype/info.py
      22    ./nipype/interfaces/slicer/legacy/filtering.py
      22    ./nipype/interfaces/slicer/converters.py
      22    ./nipype/algorithms/tests/test_modelgen.py
      22    ./examples/fmri_openfmri.py
      21    ./doc/sphinxext/autosummary_generate.py
      21    ./build_docs.py
      20    ./tools/run_interface.py
      20    ./nipype/pipeline/utils.py
      18    ./tools/interfacedocgen.py
      18    ./nipype/interfaces/mne/base.py
      18    ./nipype/interfaces/fsl/tests/test_utils.py
      18    ./nipype/interfaces/dcm2nii.py
      18    ./examples/fmri_slicer_coregistration.py
      17    ./nipype/workflows/dmri/fsl/tests/test_dti.py
      17    ./nipype/interfaces/slicer/quantification/petstandarduptakevaluecomputation.py
      17    ./nipype/interfaces/slicer/legacy/diffusion/denoising.py
      17    ./nipype/fixes/numpy/testing/nosetester.py
      17    ./doc/sphinxext/numpy_ext/docscrape_sphinx.py
      17    ./doc/conf.py
      16    ./nipype/interfaces/slicer/segmentation/simpleregiongrowingsegmentation.py
      16    ./nipype/interfaces/slicer/filtering/histogrammatching.py
      15    ./nipype/interfaces/slicer/filtering/extractskeleton.py
      15    ./doc/sphinxext/numpy_ext/numpydoc.py
      14    ./nipype/workflows/fmri/fsl/estimate.py
      14    ./nipype/pipeline/plugins/dagman.py
      14    ./nipype/pipeline/plugins/base.py
      14    ./nipype/interfaces/slicer/utilities.py
      14    ./nipype/caching/memory.py
      13    ./setup.py
      13    ./nipype/workflows/misc/utils.py
      13    ./nipype/utils/onetime.py
      13    ./nipype/interfaces/slicer/legacy/segmentation.py
      13    ./nipype/interfaces/slicer/filtering/votingbinaryholefillingimagefilter.py
      13    ./nipype/interfaces/ants/utils.py
      13    ./nipype/interfaces/ants/base.py
      13    ./examples/rsfmri_fsl_compcorr.py
      12    ./nipype/interfaces/slicer/filtering/thresholdscalarvolume.py
      12    ./nipype/interfaces/nipy/utils.py
      12    ./nipype/algorithms/icc.py
      11    ./tools/run_examples.py
      11    ./nipype/pipeline/plugins/tests/test_somaflow.py
      11    ./nipype/pipeline/plugins/tests/test_pbs.py
      11    ./nipype/pipeline/plugins/tests/test_multiproc.py
      11    ./nipype/pipeline/plugins/tests/test_linear.py
      11    ./nipype/pipeline/plugins/ipythonx.py
      11    ./nipype/interfaces/slicer/filtering/checkerboardfilter.py
      11    ./nipype/interfaces/diffusion_toolkit/postproc.py
      11    ./nipype/interfaces/c3.py
      11    ./nipype/external/portalocker.py
      10    ./nipype/testing/decorators.py
      10    ./nipype/pipeline/plugins/tests/test_debug.py
      10    ./nipype/interfaces/slicer/filtering/imagelabelcombine.py
       9    ./nipype/utils/logger.py
       9    ./nipype/pipeline/plugins/ipython.py
       8    ./nipype/workflows/smri/freesurfer/bem.py
       8    ./nipype/utils/tests/test_docparse.py
       8    ./nipype/pipeline/plugins/multiproc.py
       8    ./nipype/pipeline/plugins/linear.py
       8    ./nipype/interfaces/afni/base.py
       7    ./setup_egg.py
       7    ./nipype/utils/tests/test_misc.py
       7    ./nipype/interfaces/slicer/legacy/converters.py
       7    ./doc/sphinxext/ipython_console_highlighting.py
       6    ./tools/nipype_nightly.py
       6    ./nipype/interfaces/spm/tests/test_base.py
       6    ./nipype/interfaces/nipy/preprocess.py
       6    ./nipype/algorithms/tests/test_rapidart.py
       5    ./tools/github.py
       4    ./tools/report_coverage.py
       4    ./tools/make_examples.py
       4    ./nipype/utils/matlabtools.py
       4    ./nipype/utils/config.py
       4    ./nipype/pipeline/plugins/tests/test_base.py
       4    ./nipype/pipeline/plugins/sge.py
       4    ./nipype/pipeline/plugins/pbs.py
       4    ./nipype/pipeline/plugins/lsf.py
       4    ./nipype/pipeline/plugins/debug.py
       4    ./nipype/interfaces/slicer/filtering/__init__.py
       4    ./examples/howto_caching_example.py
       3    ./tools/toollib.py
       3    ./tools/build_interface_docs.py
       3    ./nipype/pkg_info.py
       3    ./nipype/interfaces/tests/test_utility.py
       3    ./nipype/interfaces/tests/test_io.py
       3    ./nipype/interfaces/spm/__init__.py
       3    ./nipype/algorithms/tests/test_icc.py
       2    ./tools/setup.py
       2    ./tools/gitwash_dumper.py
       2    ./tools/apigen.py
       2    ./nipype/workflows/warp/setup.py
       2    ./nipype/workflows/smri/setup.py
       2    ./nipype/workflows/smri/ants/__init__.py
       2    ./nipype/workflows/setup.py
       2    ./nipype/workflows/rsfmri/setup.py
       2    ./nipype/workflows/rsfmri/fsl/setup.py
       2    ./nipype/workflows/misc/setup.py
       2    ./nipype/workflows/graph/setup.py
       2    ./nipype/workflows/fmri/spm/setup.py
       2    ./nipype/workflows/fmri/setup.py
       2    ./nipype/workflows/fmri/fsl/setup.py
       2    ./nipype/workflows/dmri/setup.py
       2    ./nipype/workflows/dmri/mrtrix/setup.py
       2    ./nipype/workflows/dmri/fsl/setup.py
       2    ./nipype/workflows/dmri/camino/setup.py
       2    ./nipype/utils/spm_docs.py
       2    ./nipype/utils/setup.py
       2    ./nipype/testing/setup.py
       2    ./nipype/testing/__init__.py
       2    ./nipype/setup.py
       2    ./nipype/pipeline/setup.py
       2    ./nipype/pipeline/plugins/sgegraph.py
       2    ./nipype/pipeline/plugins/setup.py
       2    ./nipype/pipeline/plugins/condor.py
       2    ./nipype/interfaces/spm/setup.py
       2    ./nipype/interfaces/spm/base.py
       2    ./nipype/interfaces/slicer/setup.py
       2    ./nipype/interfaces/slicer/legacy/setup.py
       2    ./nipype/interfaces/mrtrix/setup.py
       2    ./nipype/interfaces/mne/setup.py
       2    ./nipype/interfaces/fsl/setup.py
       2    ./nipype/interfaces/freesurfer/setup.py
       2    ./nipype/interfaces/dipy/setup.py
       2    ./nipype/interfaces/cmtk/setup.py
       2    ./nipype/interfaces/camino2trackvis/setup.py
       2    ./nipype/interfaces/camino/setup.py
       2    ./nipype/interfaces/ants/__init__.py
       2    ./nipype/interfaces/afni/setup.py
       2    ./nipype/fixes/setup.py
       2    ./nipype/external/setup.py
       2    ./nipype/algorithms/setup.py
       2    ./nipype/__init__.py
       2    ./examples/dmri_tbss_nki.py
       1    ./tools/build_modref_templates.py
       1    ./nipype/workflows/warp/__init__.py
       1    ./nipype/workflows/smri/freesurfer/__init__.py
       1    ./nipype/workflows/smri/__init__.py
       1    ./nipype/workflows/misc/__init__.py
       1    ./nipype/workflows/graph/__init__.py
       1    ./nipype/workflows/fmri/spm/__init__.py
       1    ./nipype/workflows/dmri/fsl/__init__.py
       1    ./nipype/workflows/dmri/camino/__init__.py
       1    ./nipype/workflows/dmri/__init__.py
       1    ./nipype/utils/tmpdirs.py
       1    ./nipype/utils/tests/__init__.py
       1    ./nipype/utils/__init__.py
       1    ./nipype/pipeline/plugins/somaflow.py
       1    ./nipype/interfaces/slicer/segmentation/__init__.py
       1    ./nipype/interfaces/slicer/registration/__init__.py
       1    ./nipype/interfaces/slicer/legacy/__init__.py
       1    ./nipype/interfaces/slicer/diffusion/__init__.py
       1    ./nipype/interfaces/slicer/base.py
       1    ./nipype/interfaces/slicer/__init__.py
       1    ./nipype/interfaces/mrtrix/__init__.py
       1    ./nipype/interfaces/fsl/__init__.py
       1    ./nipype/interfaces/freesurfer/base.py
       1    ./nipype/interfaces/freesurfer/__init__.py
       1    ./nipype/interfaces/diffusion_toolkit/base.py
       1    ./nipype/interfaces/__init__.py
       1    ./nipype/fixes/__init__.py
       1    ./nipype/caching/tests/test_memory.py
       1    ./nipype/caching/__init__.py
       1    ./nipype/algorithms/__init__.py
       0    ./nipype/workflows/smri/freesurfer/setup.py
       0    ./nipype/workflows/rsfmri/fsl/__init__.py
       0    ./nipype/workflows/rsfmri/__init__.py
       0    ./nipype/workflows/fmri/spm/tests/__init__.py
       0    ./nipype/workflows/fmri/spm/estimate.py
       0    ./nipype/workflows/fmri/fsl/__init__.py
       0    ./nipype/workflows/fmri/__init__.py
       0    ./nipype/workflows/dmri/mrtrix/__init__.py
       0    ./nipype/workflows/dmri/fsl/tests/__init__.py
       0    ./nipype/workflows/dmri/connectivity/__init__.py
       0    ./nipype/workflows/__init__.py
       0    ./nipype/testing/utils.py
       0    ./nipype/pipeline/tests/__init__.py
       0    ./nipype/pipeline/plugins/tests/test_callback.py
       0    ./nipype/pipeline/plugins/tests/__init__.py
       0    ./nipype/pipeline/plugins/pbsgraph.py
       0    ./nipype/pipeline/plugins/__init__.py
       0    ./nipype/pipeline/engine.py
       0    ./nipype/pipeline/__init__.py
       0    ./nipype/interfaces/tests/test_matlab.py
       0    ./nipype/interfaces/slicer/quantification/__init__.py
       0    ./nipype/interfaces/slicer/legacy/diffusion/__init__.py
       0    ./nipype/interfaces/setup.py
       0    ./nipype/interfaces/nitime/__init__.py
       0    ./nipype/interfaces/nipy/__init__.py
       0    ./nipype/interfaces/mne/__init__.py
       0    ./nipype/interfaces/fsl/base.py
       0    ./nipype/interfaces/dipy/tensors.py
       0    ./nipype/interfaces/dipy/__init__.py
       0    ./nipype/interfaces/diffusion_toolkit/__init__.py
       0    ./nipype/interfaces/cmtk/__init__.py
       0    ./nipype/interfaces/camino2trackvis/__init__.py
       0    ./nipype/interfaces/camino/__init__.py
       0    ./nipype/interfaces/ants/setup.py
       0    ./nipype/interfaces/afni/__init__.py
       0    ./nipype/fixes/numpy/testing/utils.py
       0    ./nipype/fixes/numpy/testing/__init__.py
       0    ./nipype/fixes/numpy/__init__.py
       0    ./nipype/external/__init__.py
       0    ./examples/smri_freesurfer.py
       0    ./doc/sphinxext/numpy_ext/__init__.py

[satra]

i agree - my general principle has been to fix these violations whenever i'm changing code - perhaps in a final commit right before merge - otherwise it's difficult to read.

however, we could simply go through and do a pep8/flake8 fix - i suspect a lot of these come from the desc=... metadata in the input and output specs. but there is almost no excuse for some of the base classes.

[mwaskom]

Updated the list...we've made some progress.

[souravsingh]

@mwaskom I would like to work on this.Which files are updated?

[miykael]

Hi @souravsingh,

I've run the for f in find . -name "*.py"; do count=pep8 $f | wc -l; echo -n " $count "; echo $f; done | sort -r command on the current master branch and received the following list:

444    ./nipype/interfaces/camino/dti.py
432    ./nipype/workflows/dmri/fsl/epi.py
430    ./nipype/workflows/dmri/mrtrix/connectivity_mapping.py
386    ./examples/dmri_connectivity_advanced.py
360    ./nipype/interfaces/mipav/developer.py
357    ./nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py
348    ./nipype/workflows/dmri/camino/connectivity_mapping.py
339    ./nipype/workflows/fmri/fsl/preprocess.py
324    ./examples/dmri_connectivity.py
278    ./nipype/interfaces/fsl/dti.py
274    ./nipype/interfaces/semtools/diffusion/gtract.py
265    ./nipype/interfaces/cmtk/cmtk.py
263    ./nipype/utils/nipype2boutiques.py
255    ./nipype/pipeline/tests/test_engine.py
239    ./examples/fmri_spm_face.py
232    ./nipype/external/provcopy.py
231    ./nipype/interfaces/camino/convert.py
229    ./nipype/workflows/smri/ants/ANTSBuildTemplate.py
229    ./nipype/interfaces/freesurfer/preprocess.py
210    ./nipype/interfaces/freesurfer/model.py
199    ./nipype/interfaces/fsl/utils.py
186    ./nipype/interfaces/freesurfer/utils.py
182    ./nipype/interfaces/semtools/utilities/brains.py
182    ./nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py
180    ./examples/fmri_spm_dartel.py
178    ./nipype/interfaces/mrtrix/preprocess.py
173    ./nipype/interfaces/spm/preprocess.py
172    ./examples/fmri_spm.py
170    ./examples/fmri_fsl.py
166    ./nipype/interfaces/semtools/segmentation/specialized.py
166    ./nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py
165    ./examples/dmri_mrtrix_dti.py
162    ./nipype/interfaces/mrtrix/tensors.py
161    ./nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py
156    ./nipype/interfaces/mrtrix/tracking.py
153    ./examples/fmri_spm_nested.py
151    ./examples/fmri_freesurfer_smooth.py
150    ./nipype/interfaces/slicer/legacy/registration.py
147    ./nipype/interfaces/fsl/preprocess.py
145    ./nipype/interfaces/fsl/tests/test_maths.py
144    ./nipype/interfaces/ants/visualization.py
143    ./nipype/interfaces/fsl/tests/test_FILMGLS.py
142    ./examples/fmri_ants_openfmri.py
141    ./nipype/interfaces/spm/model.py
139    ./nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py
138    ./nipype/interfaces/fsl/tests/test_auto_FLIRT.py
138    ./nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py
138    ./nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py
138    ./nipype/interfaces/afni/preprocess.py
135    ./nipype/algorithms/metrics.py
130    ./nipype/interfaces/slicer/diffusion/diffusion.py
130    ./nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py
129    ./nipype/workflows/dmri/fsl/tbss.py
129    ./nipype/interfaces/fsl/model.py
127    ./nipype/interfaces/traits_extension.py
126    ./nipype/interfaces/slicer/registration/specialized.py
125    ./nipype/interfaces/camino/odf.py
124    ./nipype/interfaces/spm/utils.py
124    ./nipype/interfaces/spm/tests/test_auto_VBMSegment.py
124    ./nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py
121    ./nipype/workflows/dmri/camino/diffusion.py
121    ./nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py
120    ./nipype/algorithms/tests/test_moments.py
120    ./examples/smri_antsregistration_build_template.py
119    ./nipype/interfaces/fsl/tests/test_auto_FNIRT.py
118    ./nipype/interfaces/tests/test_base.py
115    ./nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py
115    ./nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py
114    ./nipype/interfaces/ants/tests/test_auto_Registration.py
114    ./examples/fmri_spm_auditory.py
113    ./nipype/interfaces/semtools/diffusion/diffusion.py
113    ./nipype/interfaces/io.py
112    ./nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py
112    ./nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py
111    ./nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py
109    ./nipype/interfaces/semtools/registration/specialized.py
107    ./nipype/workflows/dmri/mrtrix/diffusion.py
106    ./nipype/interfaces/fsl/tests/test_auto_MELODIC.py
106    ./nipype/interfaces/cmtk/nx.py
106    ./nipype/interfaces/afni/tests/test_auto_TCorrMap.py
105    ./examples/dmri_camino_dti.py
103    ./nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py
103    ./nipype/interfaces/afni/tests/test_auto_Allineate.py
102    ./nipype/interfaces/ants/registration.py
100    ./nipype/workflows/dmri/connectivity/group_connectivity.py
100    ./nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py
 98    ./nipype/pipeline/engine.py
 98    ./nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py
 97    ./nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py
 96    ./examples/dmri_fsl_dti.py
 95    ./nipype/interfaces/diffusion_toolkit/dti.py
 94    ./nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py
 93    ./nipype/interfaces/meshfix.py
 92    ./nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py
 91    ./nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py
 91    ./nipype/interfaces/fsl/tests/test_auto_Complex.py
 91    ./nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py
 89    ./nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py
 88    ./nipype/interfaces/slicer/registration/brainsfit.py
 88    ./examples/fmri_nipy_glm.py
 87    ./nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py
 87    ./nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py
 86    ./nipype/interfaces/tests/test_auto_FreeSurferSource.py
 85    ./nipype/interfaces/ants/segmentation.py
 85    ./examples/rsfmri_vol_surface_preprocessing_nipy.py
 84    ./nipype/interfaces/semtools/filtering/featuredetection.py
 84    ./nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py
 83    ./nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py
 83    ./nipype/interfaces/mrtrix/convert.py
 83    ./nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py
 82    ./nipype/pipeline/utils.py
 82    ./nipype/interfaces/semtools/registration/brainsfit.py
 82    ./nipype/interfaces/fsl/tests/test_auto_FUGUE.py
 81    ./nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py
 81    ./nipype/interfaces/freesurfer/tests/test_auto_SegStats.py
 80    ./nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py
 80    ./nipype/interfaces/fsl/tests/test_auto_BEDPOSTX4.py
 79    ./nipype/interfaces/slicer/generate_classes.py
 79    ./nipype/interfaces/fsl/tests/test_auto_TOPUP.py
 78    ./nipype/workflows/dmri/connectivity/nx.py
 78    ./nipype/interfaces/fsl/tests/test_auto_Randomise.py
 78    ./nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py
 78    ./nipype/algorithms/tests/test_errormap.py
 77    ./nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py
 77    ./nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py
 76    ./nipype/workflows/fmri/spm/preprocess.py
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 75    ./nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py
 75    ./nipype/interfaces/fsl/tests/test_auto_BET.py
 75    ./nipype/interfaces/diffusion_toolkit/odf.py
 75    ./nipype/interfaces/ants/tests/test_auto_ANTS.py
 74    ./nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py
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 74    ./nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py
 73    ./nipype/interfaces/fsl/tests/test_auto_Slicer.py
 73    ./nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py
 72    ./nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py
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 70    ./nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py
 70    ./nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py
 69    ./nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py
 69    ./nipype/interfaces/freesurfer/tests/test_auto_Binarize.py
 69    ./nipype/interfaces/camino/tests/test_auto_TrackPICo.py
 68    ./nipype/interfaces/tests/test_auto_Dcm2nii.py
 68    ./nipype/interfaces/fsl/tests/test_auto_FAST.py
 68    ./nipype/interfaces/base.py
 68    ./examples/smri_ants_build_template.py
 67    ./nipype/interfaces/fsl/tests/test_auto_FLAMEO.py
 66    ./nipype/interfaces/slicer/segmentation/specialized.py
 66    ./nipype/interfaces/cmtk/parcellation.py
 65    ./nipype/interfaces/slicer/surface.py
 65    ./nipype/interfaces/fsl/tests/test_auto_XFibres4.py
 65    ./nipype/interfaces/fsl/tests/test_auto_DTIFit.py
 64    ./nipype/interfaces/spm/tests/test_utils.py
 64    ./nipype/interfaces/spm/tests/test_auto_Normalize.py
 64    ./nipype/interfaces/nipy/model.py
 64    ./nipype/interfaces/freesurfer/tests/test_preprocess.py
 64    ./nipype/interfaces/camino/tests/test_auto_Track.py
 64    ./nipype/interfaces/camino/tests/test_auto_TrackDT.py
 64    ./nipype/interfaces/camino/tests/test_auto_TrackBallStick.py
 63    ./nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py
 63    ./nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py
 63    ./nipype/interfaces/fsl/tests/test_auto_Overlay.py
 63    ./nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py
 63    ./nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py
 63    ./nipype/interfaces/ants/tests/test_auto_JointFusion.py
 62    ./nipype/algorithms/modelgen.py
 62    ./examples/rsfmri_vol_surface_preprocessing.py
 61    ./nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py
 60    ./nipype/workflows/smri/freesurfer/utils.py
 60    ./nipype/interfaces/spm/tests/test_auto_Segment.py
 60    ./nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py
 60    ./nipype/interfaces/ants/tests/test_auto_Atropos.py
 60    ./nipype/interfaces/afni/svm.py
 60    ./examples/fmri_fsl_reuse.py
 59    ./nipype/interfaces/fsl/tests/test_auto_EpiReg.py
 58    ./nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py
 58    ./nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py
 58    ./nipype/interfaces/afni/tests/test_auto_Bandpass.py
 57    ./nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py
 57    ./nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py
 57    ./nipype/interfaces/cmtk/convert.py
 56    ./nipype/workflows/dmri/mrtrix/group_connectivity.py
 56    ./nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py
 56    ./nipype/interfaces/camino/calib.py
 55    ./nipype/pipeline/tests/test_utils.py
 55    ./nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py
 55    ./nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py
 55    ./nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py
 55    ./nipype/interfaces/fsl/tests/test_auto_Eddy.py
 55    ./nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py
 55    ./nipype/interfaces/afni/tests/test_auto_SVMTrain.py
 55    ./nipype/algorithms/rapidart.py
 54    ./nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py
 54    ./nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py
 54    ./nipype/interfaces/fsl/tests/test_auto_PRELUDE.py
 54    ./nipype/interfaces/freesurfer/tests/test_utils.py
 54    ./nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py
 54    ./nipype/interfaces/camino/tests/test_auto_SFPeaks.py
 54    ./nipype/interfaces/ants/resampling.py
 53    ./nipype/workflows/dmri/fsl/tests/test_tbss.py
 53    ./nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py
 53    ./nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py
 53    ./nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py
 53    ./nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py
 53    ./nipype/interfaces/afni/tests/test_auto_Volreg.py
 52    ./nipype/interfaces/slicer/tests/test_auto_ModelMaker.py
 52    ./nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py
 51    ./nipype/pipeline/tests/test_join.py
 51    ./nipype/interfaces/spm/tests/test_auto_Realign.py
 51    ./nipype/interfaces/fsl/tests/test_auto_FIRST.py
 51    ./nipype/interfaces/fsl/tests/test_auto_ExtractROI.py
 51    ./nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py
 51    ./nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py
 50    ./nipype/interfaces/spm/tests/test_auto_Normalize12.py
 50    ./nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py
 50    ./nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py
 50    ./nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py
 50    ./nipype/interfaces/camino/tests/test_auto_ModelFit.py
 50    ./nipype/interfaces/camino/tests/test_auto_DTLUTGen.py
 50    ./nipype/interfaces/ants/tests/test_auto_GenWarpFields.py
 50    ./nipype/interfaces/ants/tests/test_auto_antsIntroduction.py
 49    ./nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py
 49    ./nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py
 49    ./nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py
 49    ./nipype/algorithms/tests/test_modelgen.py
 49    ./examples/frontiers_paper/smoothing_comparison.py
 49    ./examples/dmri_dtk_odf.py
 49    ./doc/sphinxext/numpy_ext/docscrape.py
 48    ./nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py
 48    ./nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py
 48    ./nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py
 48    ./nipype/interfaces/fsl/tests/test_dti.py
 48    ./nipype/interfaces/ants/legacy.py
 47    ./nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py
 47    ./nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py
 47    ./nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py
 47    ./nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py
 47    ./nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py
 46    ./nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py
 46    ./nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py
 46    ./nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py
 46    ./nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py
 46    ./nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py
 46    ./nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py
 45    ./setup.py
 45    ./nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py
 45    ./nipype/interfaces/spm/tests/test_auto_Coregister.py
 45    ./nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py
 45    ./nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py
 45    ./nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py
 45    ./nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py
 45    ./nipype/interfaces/fsl/tests/test_auto_ErodeImage.py
 45    ./nipype/interfaces/fsl/tests/test_auto_DilateImage.py
 45    ./nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py
 45    ./nipype/interfaces/dynamic_slicer.py
 45    ./nipype/fixes/numpy/testing/noseclasses.py
 45    ./nipype/algorithms/tests/test_auto_ArtifactDetect.py
 45    ./examples/dmri_dtk_dti.py
 45    ./doc/conf.py
 44    ./nipype/workflows/dmri/camino/group_connectivity.py
 44    ./nipype/interfaces/spm/tests/test_auto_Level1Design.py
 44    ./nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py
 44    ./nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py
 44    ./nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py
 44    ./nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py
 44    ./nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py
 43    ./nipype/utils/misc.py
 43    ./nipype/interfaces/utility.py
 43    ./nipype/interfaces/slicer/filtering/arithmetic.py
 43    ./nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py
 43    ./nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py
 43    ./nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py
 43    ./nipype/interfaces/nitime/analysis.py
 43    ./nipype/interfaces/mipav/tests/test_auto_RandomVol.py
 43    ./nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py
 43    ./nipype/interfaces/fsl/tests/test_auto_SUSAN.py
 43    ./nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py
 43    ./nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py
 43    ./nipype/interfaces/afni/tests/test_auto_Retroicor.py
 42    ./nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py
 42    ./nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py
 42    ./nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py
 42    ./nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py
 42    ./nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py
 42    ./nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py
 42    ./nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py
 42    ./nipype/interfaces/camino/tests/test_auto_MESD.py
 42    ./nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py
 42    ./nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py
 41    ./nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py
 41    ./nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py
 41    ./nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py
 41    ./nipype/interfaces/fsl/tests/test_auto_Threshold.py
 41    ./nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py
 41    ./nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py
 41    ./nipype/interfaces/camino/tests/test_auto_SFLUTGen.py
 41    ./nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py
 41    ./nipype/interfaces/afni/tests/test_auto_Means.py
 41    ./nipype/interfaces/afni/tests/test_auto_Eval.py
 40    ./nipype/interfaces/spm/tests/test_auto_Threshold.py
 40    ./nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py
 40    ./nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py
 40    ./nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py
 40    ./nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py
 40    ./nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py
 40    ./nipype/interfaces/mne/tests/test_auto_WatershedBEM.py
 40    ./nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py
 40    ./nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py
 40    ./nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py
 40    ./nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py
 40    ./nipype/interfaces/camino/tests/test_auto_PicoPDFs.py
 40    ./nipype/interfaces/afni/tests/test_auto_TCorr1D.py
 40    ./nipype/interfaces/afni/tests/test_auto_BlurInMask.py
 39    ./nipype/interfaces/tests/test_auto_MatlabCommand.py
 39    ./nipype/interfaces/fsl/tests/test_auto_ImageMeants.py
 39    ./nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py
 39    ./nipype/interfaces/fsl/maths.py
 39    ./nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py
 39    ./nipype/interfaces/afni/tests/test_auto_Warp.py
 39    ./nipype/interfaces/afni/tests/test_auto_TShift.py
 39    ./nipype/interfaces/afni/tests/test_auto_Calc.py
 39    ./nipype/algorithms/tests/test_auto_SpecifySparseModel.py
 38    ./nipype/interfaces/spm/tests/test_auto_NewSegment.py
 38    ./nipype/interfaces/spm/tests/test_auto_FactorialDesign.py
 38    ./nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py
 38    ./nipype/interfaces/semtools/diffusion/tractography/ukftractography.py
 38    ./nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py
 38    ./nipype/interfaces/fsl/tests/test_auto_WarpUtils.py
 38    ./nipype/interfaces/fsl/tests/test_auto_VecReg.py
 38    ./nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py
 38    ./nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py
 38    ./nipype/interfaces/fsl/tests/test_auto_InvWarp.py
 38    ./nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py
 38    ./nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py
 38    ./nipype/external/cloghandler.py
 38    ./examples/fmri_fsl_feeds.py
 37    ./nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py
 37    ./nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py
 37    ./nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py
 37    ./nipype/interfaces/mrtrix/tests/test_auto_Threshold.py
 37    ./nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py
 37    ./nipype/interfaces/fsl/tests/test_model.py
 37    ./nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py
 37    ./nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py
 37    ./nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py
 37    ./nipype/interfaces/elastix/tests/test_auto_Registration.py
 37    ./nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py
 37    ./examples/workshop_dartmouth_2010.py
 37    ./examples/dmri_group_connectivity_mrtrix.py
 36    ./nipype/interfaces/spm/tests/test_auto_SliceTiming.py
 36    ./nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py
 36    ./nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py
 36    ./nipype/interfaces/fsl/tests/test_auto_SliceTimer.py
 36    ./nipype/interfaces/fsl/tests/test_auto_MeanImage.py
 36    ./nipype/interfaces/fsl/tests/test_auto_MaxImage.py
 36    ./nipype/interfaces/fsl/tests/test_auto_ApplyMask.py
 36    ./nipype/interfaces/freesurfer/tests/test_auto_Smooth.py
 36    ./nipype/algorithms/misc.py
 36    ./examples/fmri_openfmri.py
 35    ./nipype/utils/tests/test_misc.py
 35    ./nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py
 35    ./nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py
 35    ./nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py
 35    ./nipype/interfaces/slicer/filtering/denoising.py
 35    ./nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py
 35    ./nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py
 35    ./nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py
 35    ./nipype/interfaces/fsl/tests/test_auto_WarpPoints.py
 35    ./nipype/interfaces/fsl/epi.py
 35    ./nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py
 35    ./nipype/interfaces/elastix/utils.py
 35    ./nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py
 35    ./nipype/interfaces/camino/tests/test_auto_QBallMX.py
 35    ./nipype/interfaces/camino/tests/test_auto_LinRecon.py
 35    ./nipype/interfaces/afni/tests/test_auto_SVMTest.py
 35    ./nipype/external/six.py
 35    ./examples/frontiers_paper/workflow_from_scratch.py
 34    ./nipype/pipeline/plugins/slurmgraph.py
 34    ./nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py
 34    ./nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py
 34    ./nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py
 34    ./nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py
 34    ./nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py
 34    ./nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py
 34    ./nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py
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 15    ./nipype/interfaces/nipy/tests/test_auto_Trim.py
 15    ./nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py
 15    ./nipype/interfaces/fsl/tests/test_auto_Level1Design.py
 15    ./nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py
 15    ./nipype/interfaces/camino/utils.py
 15    ./nipype/interfaces/afni/tests/test_auto_AFNICommand.py
 15    ./nipype/algorithms/tests/test_auto_StimulusCorrelation.py
 15    ./nipype/algorithms/tests/test_auto_PickAtlas.py
 15    ./nipype/algorithms/tests/test_auto_Distance.py
 15    ./nipype/algorithms/tests/test_auto_AddNoise.py
 14    ./tools/make_examples.py
 14    ./nipype/interfaces/tests/test_auto_MpiCommandLine.py
 14    ./nipype/interfaces/tests/test_auto_GroupAndStack.py
 14    ./nipype/interfaces/tests/test_auto_DcmStack.py
 14    ./nipype/interfaces/tests/test_auto_DataFinder.py
 14    ./nipype/interfaces/slicer/filtering/extractskeleton.py
 14    ./nipype/interfaces/nipy/utils.py
 14    ./nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py
 14    ./nipype/interfaces/nipy/tests/test_auto_Similarity.py
 14    ./nipype/interfaces/ants/tests/test_auto_ANTSCommand.py
 14    ./nipype/algorithms/tests/test_auto_Similarity.py
 14    ./doc/sphinxext/numpy_ext/docscrape_sphinx.py
 14    ./doc/sphinxext/autosummary_generate.py
 13    ./nipype/workflows/smri/freesurfer/recon.py
 13    ./nipype/utils/config.py
 13    ./nipype/pipeline/plugins/dagman.py
 13    ./nipype/interfaces/tests/test_auto_SlicerCommandLine.py
 13    ./nipype/interfaces/tests/test_auto_SelectFiles.py
 13    ./nipype/interfaces/tests/test_auto_DataGrabber.py
 13    ./nipype/interfaces/semtools/brains/classify.py
 13    ./nipype/interfaces/fsl/tests/test_utils.py
 13    ./nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py
 13    ./nipype/__init__.py
 13    ./nipype/algorithms/tests/test_auto_MergeCSVFiles.py
 12    ./nipype/workflows/misc/utils.py
 12    ./nipype/pipeline/plugins/ipythonx.py
 12    ./nipype/interfaces/tests/test_matlab.py
 12    ./nipype/interfaces/spm/tests/test_auto_SPMCommand.py
 12    ./nipype/interfaces/slicer/legacy/segmentation.py
 12    ./nipype/interfaces/slicer/filtering/votingbinaryholefillingimagefilter.py
 12    ./nipype/interfaces/semtools/converters.py
 12    ./nipype/interfaces/semtools/brains/utilities.py
 12    ./nipype/interfaces/nipy/tests/test_auto_ComputeMask.py
 12    ./nipype/interfaces/fsl/tests/test_auto_FSLCommand.py
 12    ./nipype/interfaces/fsl/tests/test_auto_FEATRegister.py
 12    ./nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py
 12    ./nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py
 12    ./nipype/interfaces/dipy/tests/test_auto_TensorMode.py
 12    ./nipype/interfaces/dipy/tests/test_auto_DTI.py
 12    ./nipype/interfaces/dipy/tests/test_auto_Denoise.py
 12    ./nipype/interfaces/dcm2nii.py
 12    ./nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py
 12    ./nipype/interfaces/c3.py
 12    ./nipype/algorithms/tests/test_auto_ICC.py
 11    ./tools/github.py
 11    ./nipype/workflows/dmri/dipy/denoise.py
 11    ./nipype/testing/decorators.py
 11    ./nipype/pipeline/plugins/tests/test_somaflow.py
 11    ./nipype/pipeline/plugins/tests/test_pbs.py
 11    ./nipype/pipeline/plugins/tests/test_multiproc.py
 11    ./nipype/pipeline/plugins/tests/test_linear.py
 11    ./nipype/pipeline/plugins/tests/test_debug.py
 11    ./nipype/pipeline/plugins/slurm.py
 11    ./nipype/pipeline/plugins/ipython.py
 11    ./nipype/interfaces/tests/test_auto_Split.py
 11    ./nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py
 11    ./nipype/interfaces/tests/test_auto_Rename.py
 11    ./nipype/interfaces/tests/test_auto_MergeNifti.py
 11    ./nipype/interfaces/tests/test_auto_JSONFileSink.py
 11    ./nipype/interfaces/tests/test_auto_CommandLine.py
 11    ./nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py
 11    ./nipype/interfaces/slicer/filtering/thresholdscalarvolume.py
 11    ./nipype/interfaces/semtools/legacy/registration.py
 11    ./nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py
 11    ./nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py
 11    ./nipype/external/portalocker.py
 11    ./nipype/algorithms/tests/test_auto_TSNR.py
 11    ./nipype/algorithms/tests/test_auto_CreateNifti.py
 10    ./tools/run_examples.py
 10    ./nipype/utils/logger.py
 10    ./nipype/interfaces/tests/test_auto_SplitNifti.py
 10    ./nipype/interfaces/tests/test_auto_Select.py
 10    ./nipype/interfaces/tests/test_auto_Merge.py
 10    ./nipype/interfaces/slicer/filtering/checkerboardfilter.py
 10    ./nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py
 10    ./nipype/interfaces/ants/utils.py
 10    ./nipype/algorithms/tests/test_auto_SimpleThreshold.py
 10    ./nipype/algorithms/tests/test_auto_ModifyAffine.py
 10    ./nipype/algorithms/tests/test_auto_AddCSVRow.py
 10    ./examples/dmri_preprocessing.py
  9    ./nipype/pipeline/plugins/linear.py
  9    ./nipype/interfaces/tests/test_auto_CopyMeta.py
  9    ./nipype/interfaces/spm/tests/test_base.py
  9    ./nipype/interfaces/slicer/filtering/imagelabelcombine.py
  9    ./nipype/interfaces/fsl/tests/test_auto_L2Model.py
  9    ./nipype/interfaces/dipy/tests/test_auto_Resample.py
  9    ./nipype/algorithms/tests/test_auto_AddCSVColumn.py
  9    ./doc/sphinxext/ipython_console_highlighting.py
  8    ./tools/nipype_nightly.py
  8    ./tools/gitwash_dumper.py
  8    ./nipype/workflows/dmri/fsl/tests/test_dti.py
  8    ./nipype/utils/tests/test_docparse.py
  8    ./nipype/interfaces/tests/test_auto_SQLiteSink.py
  8    ./nipype/interfaces/tests/test_auto_Function.py
  8    ./nipype/interfaces/tests/test_auto_AssertEqual.py
  8    ./nipype/interfaces/semtools/registration/brainsresize.py
  8    ./nipype/algorithms/tests/test_auto_SplitROIs.py
  8    ./nipype/algorithms/tests/test_auto_Matlab2CSV.py
  8    ./nipype/algorithms/tests/test_auto_Gunzip.py
  8    ./nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py
  8    ./examples/howto_caching_example.py
  7    ./nipype/pipeline/plugins/multiproc.py
  7    ./nipype/interfaces/tests/test_auto_JSONFileGrabber.py
  7    ./nipype/interfaces/slicer/utilities.py
  7    ./nipype/interfaces/fsl/tests/test_preprocess.py
  7    ./nipype/interfaces/dipy/tensors.py
  7    ./nipype/algorithms/icc.py
  7    ./examples/dmri_tbss_nki.py
  6    ./tools/apigen.py
  6    ./nipype/workflows/dmri/fsl/tests/test_epi.py
  6    ./nipype/workflows/dmri/fsl/__init__.py
  6    ./nipype/utils/spm_docs.py
  6    ./nipype/pipeline/plugins/pbs.py
  6    ./nipype/interfaces/tests/test_auto_LookupMeta.py
  6    ./nipype/interfaces/tests/test_auto_CSVReader.py
  6    ./nipype/interfaces/slicer/legacy/converters.py
  6    ./nipype/interfaces/semtools/testing/landmarkscompare.py
  6    ./nipype/interfaces/semtools/testing/generateaveragelmkfile.py
  6    ./nipype/interfaces/freesurfer/base.py
  6    ./nipype/interfaces/afni/base.py
  6    ./nipype/algorithms/tests/test_auto_MergeROIs.py
  6    ./examples/smri_cbs_skullstripping.py
  5    ./tools/toollib.py
  5    ./nipype/testing/__init__.py
  5    ./nipype/pkg_info.py
  5    ./nipype/pipeline/plugins/lsf.py
  5    ./nipype/interfaces/tests/test_utility.py
  5    ./nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py
  5    ./nipype/interfaces/tests/test_auto_IOBase.py
  5    ./nipype/interfaces/tests/test_auto_BaseInterface.py
  5    ./nipype/interfaces/semtools/testing/featuredetection.py
  5    ./nipype/interfaces/semtools/diffusion/maxcurvature.py
  5    ./nipype/algorithms/tests/test_rapidart.py
  5    ./nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py
  4    ./tools/build_interface_docs.py
  4    ./nipype/workflows/smri/freesurfer/bem.py
  4    ./nipype/workflows/dmri/connectivity/__init__.py
  4    ./nipype/utils/matlabtools.py
  4    ./nipype/pipeline/plugins/tests/test_base.py
  4    ./nipype/pipeline/plugins/debug.py
  4    ./nipype/interfaces/slicer/filtering/__init__.py
  4    ./nipype/interfaces/semtools/featurecreator.py
  4    ./nipype/interfaces/semtools/diffusion/tractography/commandlineonly.py
  4    ./nipype/interfaces/freesurfer/__init__.py
  4    ./nipype/algorithms/tests/test_icc_anova.py
  3    ./nipype/interfaces/tests/test_auto_IdentityInterface.py
  3    ./nipype/interfaces/diffusion_toolkit/base.py
  3    ./nipype/interfaces/ants/__init__.py
  2    ./tools/setup.py
  2    ./tools/report_coverage.py
  2    ./tools/build_modref_templates.py
  2    ./setup_egg.py
  2    ./nipype/workflows/smri/ants/__init__.py
  2    ./nipype/workflows/fmri/fsl/__init__.py
  2    ./nipype/testing/utils.py
  2    ./nipype/pipeline/plugins/somaflow.py
  2    ./nipype/pipeline/plugins/condor.py
  2    ./nipype/interfaces/__init__.py
  2    ./nipype/algorithms/tests/test_mesh_ops.py
  1    ./nipype/workflows/warp/__init__.py
  1    ./nipype/workflows/smri/__init__.py
  1    ./nipype/workflows/smri/freesurfer/__init__.py
  1    ./nipype/workflows/misc/__init__.py
  1    ./nipype/workflows/graph/__init__.py
  1    ./nipype/workflows/fmri/spm/__init__.py
  1    ./nipype/workflows/dmri/fsl/artifacts.py
  1    ./nipype/workflows/dmri/camino/__init__.py
  1    ./nipype/utils/tmpdirs.py
  1    ./nipype/utils/tests/__init__.py
  1    ./nipype/utils/__init__.py
  1    ./nipype/pipeline/__init__.py
  1    ./nipype/interfaces/vista/__init__.py
  1    ./nipype/interfaces/slicer/segmentation/__init__.py
  1    ./nipype/interfaces/slicer/registration/__init__.py
  1    ./nipype/interfaces/slicer/quantification/__init__.py
  1    ./nipype/interfaces/slicer/legacy/__init__.py
  1    ./nipype/interfaces/slicer/__init__.py
  1    ./nipype/interfaces/slicer/diffusion/__init__.py
  1    ./nipype/interfaces/slicer/base.py
  1    ./nipype/interfaces/semtools/utilities/__init__.py
  1    ./nipype/interfaces/semtools/segmentation/__init__.py
  1    ./nipype/interfaces/semtools/registration/__init__.py
  1    ./nipype/interfaces/semtools/filtering/__init__.py
  1    ./nipype/interfaces/semtools/diffusion/__init__.py
  1    ./nipype/interfaces/mrtrix/__init__.py
  1    ./nipype/interfaces/mrtrix3/utils.py
  1    ./nipype/interfaces/mrtrix3/__init__.py
  1    ./nipype/interfaces/mrtrix3/connectivity.py
  1    ./nipype/interfaces/mrtrix3/base.py
  1    ./nipype/interfaces/mipav/__init__.py
  1    ./nipype/interfaces/fsl/tests/test_XFibres.py
  1    ./nipype/interfaces/fsl/base.py
  1    ./nipype/interfaces/afni/__init__.py
  1    ./nipype/fixes/__init__.py
  1    ./nipype/caching/tests/test_memory.py
  1    ./nipype/caching/__init__.py
  1    ./nipype/algorithms/__init__.py
  0    ./nipype/workflows/rsfmri/__init__.py
  0    ./nipype/workflows/rsfmri/fsl/__init__.py
  0    ./nipype/workflows/__init__.py
  0    ./nipype/workflows/fmri/spm/tests/__init__.py
  0    ./nipype/workflows/fmri/spm/estimate.py
  0    ./nipype/workflows/fmri/__init__.py
  0    ./nipype/workflows/fmri/fsl/tests/__init__.py
  0    ./nipype/workflows/dmri/mrtrix/__init__.py
  0    ./nipype/workflows/dmri/__init__.py
  0    ./nipype/workflows/dmri/fsl/utils.py
  0    ./nipype/workflows/dmri/fsl/tests/__init__.py
  0    ./nipype/workflows/dmri/dipy/__init__.py
  0    ./nipype/workflows/data/__init__.py
  0    ./nipype/pipeline/tests/__init__.py
  0    ./nipype/pipeline/plugins/tests/test_callback.py
  0    ./nipype/pipeline/plugins/tests/__init__.py
  0    ./nipype/pipeline/plugins/pbsgraph.py
  0    ./nipype/pipeline/plugins/__init__.py
  0    ./nipype/interfaces/vista/tests/__init__.py
  0    ./nipype/interfaces/tests/__init__.py
  0    ./nipype/interfaces/spm/tests/__init__.py
  0    ./nipype/interfaces/spm/__init__.py
  0    ./nipype/interfaces/slicer/tests/__init__.py
  0    ./nipype/interfaces/slicer/segmentation/tests/__init__.py
  0    ./nipype/interfaces/slicer/registration/tests/__init__.py
  0    ./nipype/interfaces/slicer/quantification/tests/__init__.py
  0    ./nipype/interfaces/slicer/legacy/tests/__init__.py
  0    ./nipype/interfaces/slicer/legacy/diffusion/tests/__init__.py
  0    ./nipype/interfaces/slicer/legacy/diffusion/__init__.py
  0    ./nipype/interfaces/slicer/filtering/tests/__init__.py
  0    ./nipype/interfaces/slicer/diffusion/tests/__init__.py
  0    ./nipype/interfaces/setup.py
  0    ./nipype/interfaces/semtools/utilities/tests/__init__.py
  0    ./nipype/interfaces/semtools/tests/__init__.py
  0    ./nipype/interfaces/semtools/testing/__init__.py
  0    ./nipype/interfaces/semtools/segmentation/tests/__init__.py
  0    ./nipype/interfaces/semtools/registration/tests/__init__.py
  0    ./nipype/interfaces/semtools/legacy/tests/__init__.py
  0    ./nipype/interfaces/semtools/legacy/__init__.py
  0    ./nipype/interfaces/semtools/__init__.py
  0    ./nipype/interfaces/semtools/filtering/tests/__init__.py
  0    ./nipype/interfaces/semtools/diffusion/tractography/tests/__init__.py
  0    ./nipype/interfaces/semtools/diffusion/tractography/__init__.py
  0    ./nipype/interfaces/semtools/diffusion/tests/__init__.py
  0    ./nipype/interfaces/semtools/brains/tests/__init__.py
  0    ./nipype/interfaces/semtools/brains/__init__.py
  0    ./nipype/interfaces/nitime/tests/__init__.py
  0    ./nipype/interfaces/nitime/__init__.py
  0    ./nipype/interfaces/nipy/tests/__init__.py
  0    ./nipype/interfaces/nipy/__init__.py
  0    ./nipype/interfaces/mrtrix/tests/__init__.py
  0    ./nipype/interfaces/mrtrix3/tracking.py
  0    ./nipype/interfaces/mrtrix3/tests/__init__.py
  0    ./nipype/interfaces/mrtrix3/reconst.py
  0    ./nipype/interfaces/mrtrix3/preprocess.py
  0    ./nipype/interfaces/mne/tests/__init__.py
  0    ./nipype/interfaces/mne/__init__.py
  0    ./nipype/interfaces/mipav/tests/__init__.py
  0    ./nipype/interfaces/fsl/tests/test_BEDPOSTX.py
  0    ./nipype/interfaces/fsl/tests/__init__.py
  0    ./nipype/interfaces/fsl/__init__.py
  0    ./nipype/interfaces/freesurfer/tests/__init__.py
  0    ./nipype/interfaces/elastix/tests/__init__.py
  0    ./nipype/interfaces/elastix/__init__.py
  0    ./nipype/interfaces/elastix/base.py
  0    ./nipype/interfaces/dipy/tracks.py
  0    ./nipype/interfaces/dipy/tests/__init__.py
  0    ./nipype/interfaces/dipy/simulate.py
  0    ./nipype/interfaces/dipy/preprocess.py
  0    ./nipype/interfaces/dipy/__init__.py
  0    ./nipype/interfaces/diffusion_toolkit/tests/__init__.py
  0    ./nipype/interfaces/diffusion_toolkit/__init__.py
  0    ./nipype/interfaces/cmtk/tests/__init__.py
  0    ./nipype/interfaces/cmtk/__init__.py
  0    ./nipype/interfaces/camino/tests/__init__.py
  0    ./nipype/interfaces/camino/__init__.py
  0    ./nipype/interfaces/camino2trackvis/tests/__init__.py
  0    ./nipype/interfaces/camino2trackvis/__init__.py
  0    ./nipype/interfaces/ants/tests/__init__.py
  0    ./nipype/interfaces/afni/tests/__init__.py
  0    ./nipype/fixes/numpy/testing/utils.py
  0    ./nipype/fixes/numpy/testing/__init__.py
  0    ./nipype/fixes/numpy/__init__.py
  0    ./nipype/external/__init__.py
  0    ./nipype/caching/tests/__init__.py
  0    ./nipype/algorithms/tests/test_splitmerge.py
  0    ./nipype/algorithms/tests/test_overlap.py
  0    ./nipype/algorithms/tests/__init__.py
  0    ./nipype/algorithms/mesh.py
  0    ./examples/smri_freesurfer.py
  0    ./doc/sphinxext/numpy_ext/__init__.py

Hope this helps.

[miykael]

By the way, if you add the flag --select=E101 to the pep8 command, you can look for certain specific errors or warnings. For example for:

E101 indentation contains mixed spaces and tabs
E114 indentation is not a multiple of four (comment)
E115 expected an indented block (comment)
E116 unexpected indentation (comment)
E122 continuation line missing indentation or outdented
E124 closing bracket does not match visual indentation
E125 continuation line with same indent as next logical line
E127 continuation line over-indented for visual indent
E128 continuation line under-indented for visual indent
E131 continuation line unaligned for hanging indent
E201 whitespace after '(' '[' '{'
E202 whitespace before ')' ']'
E203 whitespace before ',' ':'
E221 multiple spaces before operator
E222 multiple spaces after operator
E225 missing whitespace around operator
E228 missing whitespace around modulo operator
E231 missing whitespace after ',' ':'
E251 unexpected spaces around keyword / parameter equals
E261 at least two spaces before inline comment
E262 inline comment should start with '# '
E265 block comment should start with '# '
E266 too many leading '#' for block comment
E271 multiple spaces after keyword
E301 expected 1 blank line, found 0
E302 expected 2 blank lines, found 1
E303 too many blank lines (2)
E501 line too long (100 > 79 characters)
E502 the backslash is redundant between brackets
E701 multiple statements on one line (colon)
E712 comparison to True should be 'if cond is True:' or 'if cond:'
W191 indentation contains tabs
W292 no newline at end of file
W391 blank line at end of file
W503 line break before binary operator

Now, you got me hooked, too. I'm happy to do some pep8 cleaning. I would recommend that we do it by pep8 error or warning? This allows it to cut it down into smaller task and makes the reviewing faster.

@souravsingh, which files or errors would you like to tackle?

[souravsingh]

@miykael I would like to work on the first few errors, since they look easy to me.

[miykael]

@souravsingh, I've already started with some errors, and it turns out that it can be done rather fast if you use pep8 together with autopep8. I've used the following code:

pep8ID=E265

for f in `find . -name "*.py"`
do
    if [[ "$f" != *"test_auto"* ]]
    then

        count=`pep8 --select $pep8ID $f | wc -l`

        if [ "$count" -ne "0" ]
        then
            autopep8 -i --select $pep8ID $f
            pep8 --select $pep8ID $f
        fi
    fi
done

And I'm almost done with Errors 100-200. Here's the list of all errors that I've already looked at: master...miykael:master

I'm sorry if I've done what you actually wanted to do. But this pep8 issue was bugging me already since a while and you got me motivated to take a closer look at it :-)

[satra]

hey guys, please note that the pep8 errors in any of the "test_auto..." files should be fixed in the spec generator

https://github.com/nipy/nipype/blob/master/tools/checkspecs.py

so skip those - even with autopep8.

[miykael]

Thanks, @satra. So far I'm not even looking at the files that contain the string "test_auto". I thought of tackling the ckeckspecs.py file last.

[souravsingh]

Ok @miykael,I will work on the last few Errors and Warnings

[miykael]

Perfect @souravsingh. Here's a list of the other existing pep8 errors and warnings:

  16  E401 multiple imports on one line
 391  E402 module level import not at top of file
8283  E501 line too long (80 > 79 characters)
  68  E502 the backslash is redundant between brackets
   9  E701 multiple statements on one line (colon)
   4  E703 statement ends with a semicolon
   6  E711 comparison to None should be 'if cond is not None:'
  15  E712 comparison to False should be 'if cond is False:' or 'if not cond:'
   6  E713 test for membership should be 'not in'
  12  E714 test for object identity should be 'is not'
  40  E731 do not assign a lambda expression, use a def
   1  E901 IndentationError: unindent does not match any outer indentation level
  51  W191 indentation contains tabs
   8  W291 trailing whitespace
  17  W292 no newline at end of file
   1  W293 blank line contains whitespace
  55  W391 blank line at end of file
  58  W503 line break before binary operator

[miykael]

@souravsingh, on which errors and warnings are you working on? I have some time this weekend and would be happy to do some more pep8 style correction.

[souravsingh]

I was working on making a PR when I saw this