Report and crash files no longer contain terminal output

[effigies]

Summary

Bug reports on nipype workflows are becoming essentially useless, as the exceptions now wrap around the original exceptions and we get very little traceback information. Further, the crashfiles that are emitted merely show the same exception and no terminal output that would help diagnose.

A good example of this is nipreps/smriprep#286, where we had to provide users with explicit debugging steps. Below I paste a successful _report/report.rst, which also shows nothing. This is a significant regression.

Node: fsl
=========


 Hierarchy : _applyxfm_roi18
 Exec ID : _applyxfm_roi18


Original Inputs
---------------


* angle_rep : <undefined>
* apply_isoxfm : <undefined>
* apply_xfm : True
* args : <undefined>
* bbrslope : <undefined>
* bbrtype : <undefined>
* bgvalue : <undefined>
* bins : <undefined>
* coarse_search : <undefined>
* cost : <undefined>
* cost_func : <undefined>
* datatype : <undefined>
* display_init : <undefined>
* dof : <undefined>
* echospacing : <undefined>
* environ : {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
* fieldmap : <undefined>
* fieldmapmask : <undefined>
* fine_search : <undefined>
* force_scaling : <undefined>
* in_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/bold_std_trans_wf/_std_target_MNIInfantcohort-1.cohort1/merge/vol0000_xform-00000_merged.nii.gz
* in_matrix_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/roi2atlas/mapflow/_roi2atlas18/vol0018_flirt.mat
* in_weight : <undefined>
* interp : spline
* min_sampling : <undefined>
* no_clamp : <undefined>
* no_resample : <undefined>
* no_resample_blur : <undefined>
* no_search : <undefined>
* out_file : <undefined>
* out_log : <undefined>
* out_matrix_file : <undefined>
* output_type : NIFTI_GZ
* padding_size : <undefined>
* pedir : <undefined>
* ref_weight : <undefined>
* reference : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/split_atlas_rois/vol0018.nii.gz
* rigid2D : <undefined>
* save_log : <undefined>
* schedule : <undefined>
* searchr_x : <undefined>
* searchr_y : <undefined>
* searchr_z : <undefined>
* sinc_width : <undefined>
* sinc_window : <undefined>
* uses_qform : <undefined>
* verbose : <undefined>
* wm_seg : <undefined>
* wmcoords : <undefined>
* wmnorms : <undefined>


Execution Inputs
----------------


* angle_rep : <undefined>
* apply_isoxfm : <undefined>
* apply_xfm : True
* args : <undefined>
* bbrslope : <undefined>
* bbrtype : <undefined>
* bgvalue : <undefined>
* bins : <undefined>
* coarse_search : <undefined>
* cost : <undefined>
* cost_func : <undefined>
* datatype : <undefined>
* display_init : <undefined>
* dof : <undefined>
* echospacing : <undefined>
* environ : {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
* fieldmap : <undefined>
* fieldmapmask : <undefined>
* fine_search : <undefined>
* force_scaling : <undefined>
* in_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/bold_std_trans_wf/_std_target_MNIInfantcohort-1.cohort1/merge/vol0000_xform-00000_merged.nii.gz
* in_matrix_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/roi2atlas/mapflow/_roi2atlas18/vol0018_flirt.mat
* in_weight : <undefined>
* interp : spline
* min_sampling : <undefined>
* no_clamp : <undefined>
* no_resample : <undefined>
* no_resample_blur : <undefined>
* no_search : <undefined>
* out_file : <undefined>
* out_log : <undefined>
* out_matrix_file : <undefined>
* output_type : NIFTI_GZ
* padding_size : <undefined>
* pedir : <undefined>
* ref_weight : <undefined>
* reference : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/split_atlas_rois/vol0018.nii.gz
* rigid2D : <undefined>
* save_log : <undefined>
* schedule : <undefined>
* searchr_x : <undefined>
* searchr_y : <undefined>
* searchr_z : <undefined>
* sinc_width : <undefined>
* sinc_window : <undefined>
* uses_qform : <undefined>
* verbose : <undefined>
* wm_seg : <undefined>
* wmcoords : <undefined>
* wmnorms : <undefined>


Execution Outputs
-----------------


* out_file : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/applyxfm_roi/mapflow/_applyxfm_roi18/vol0000_xform-00000_merged_flirt.nii.gz
* out_log : <undefined>
* out_matrix_file : <undefined>


Runtime info
------------


* cmdline : flirt -in /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/bold_std_trans_wf/_std_target_MNIInfantcohort-1.cohort1/merge/vol0000_xform-00000_merged.nii.gz -ref /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/split_atlas_rois/vol0018.nii.gz -out vol0000_xform-00000_merged_flirt.nii.gz -omat vol0000_xform-00000_merged_flirt.mat -applyxfm -init /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/roi2atlas/mapflow/_roi2atlas18/vol0018_flirt.mat -interp spline
* duration : 745.396369
* hostname : f16b9a0dcf1f
* prev_wd : /tmp
* working_dir : /scratch/nibabies_21_1_wf/single_subject_470437_1mo_wf/func_preproc_ses_1mo_task_rest_acq_AP_run_02_wf/subcortical_mni_alignment_wf/applyxfm_roi/mapflow/_applyxfm_roi18


Terminal output
~~~~~~~~~~~~~~~


 


Terminal - standard output
~~~~~~~~~~~~~~~~~~~~~~~~~~


 


Terminal - standard error
~~~~~~~~~~~~~~~~~~~~~~~~~


 


Environment
~~~~~~~~~~~


* AFNI_DIR : /opt/afni
* AFNI_IMSAVE_WARNINGS : NO
* AFNI_PLUGINPATH : /opt/afni-latest
* ANTSPATH : /usr/lib/ants
* ANTS_RANDOM_SEED : 64899
* AROMA_VERSION : 0.4.5
* C3DPATH : /opt/convert3d-1.0.0
* CONDA_PYTHON : /opt/conda/bin/python
* CPATH : /opt/conda/include:
* DEBIAN_FRONTEND : noninteractive
* DOCKER_VERSION_8395080871 : 20.10.17
* FREESURFER_HOME : /opt/freesurfer
* FSLDIR : /opt/fsl
* FSLGECUDAQ : cuda.q
* FSLLOCKDIR : 
* FSLMACHINELIST : 
* FSLMULTIFILEQUIT : TRUE
* FSLOUTPUTTYPE : NIFTI_GZ
* FSLREMOTECALL : 
* FSL_DIR : /opt/fsl
* FS_LICENSE : /opt/freesurfer/license.txt
* FUNCTIONALS_DIR : /opt/freesurfer/sessions
* HOME : /home/nibabies
* HOSTNAME : f16b9a0dcf1f
* IS_DOCKER_8395080871 : 1
* KMP_DUPLICATE_LIB_OK : True
* KMP_INIT_AT_FORK : FALSE
* LANG : en_US.UTF-8
* LC_ALL : en_US.UTF-8
* LD_LIBRARY_PATH : /opt/fsl/lib:
* LOCAL_DIR : /opt/freesurfer/local
* MINC_BIN_DIR : /opt/freesurfer/mni/bin
* MINC_LIB_DIR : /opt/freesurfer/mni/lib
* MKL_NUM_THREADS : 1
* MNI_DATAPATH : /opt/freesurfer/mni/data
* MNI_DIR : /opt/freesurfer/mni
* MNI_PERL5LIB : /opt/freesurfer/mni/lib/perl5/5.8.5
* NIPYPE_NO_ET : 1
* NO_ET : 1
* OMP_NUM_THREADS : 1
* PATH : /opt/conda/bin:/opt/ICA-AROMA:/opt/freesurfer/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/fsl/bin:/opt/convert3d-1.0.0/bin:/opt/afni-latest:/usr/lib/ants:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
* PERL5LIB : /opt/freesurfer/mni/lib/perl5/5.8.5
* PYTHONNOUSERSITE : 1
* PYTHONWARNINGS : ignore
* SUBJECTS_DIR : /opt/freesurfer/subjects
* TERM : xterm

This is recent nipype (>=1.7, I think).