148 exception fail fast

[t-sanchez]

• Implement better control of verbosity (low by default) and optionally high with --verbose attribute.
• Make the pipeline fail fast in case of an error, and catch the exception at the subject-level. Keep running on other subjects and print a summary at the end of the pipeline run.
• Update documentation in usage.rst
• Start moving inputs to attributes (Move some inputs to attributes for the workflows #177)
• Add absolute paths to executables (Fix file not found issue #179)
  This should fix Change handling of exceptions towards a faster failure of modules #148, Change the default level of verbosity #151, Implement a check of incompatible input parameters #172, Fix file not found issue #179.

[pep8speaks]

Hello @t-sanchez! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file pymialsrtk/interfaces/postprocess.py:

Line 195:80: E501 line too long (84 > 79 characters)

Comment last updated at 2022-09-06 16:14:19 UTC

[t-sanchez]

This was tested against several use cases:

• multiparameter reconstruction:

docker run -t --rm -u $(id -u):$(id -g) -v $DATA_PATH:/bids_dir -v $OUT_PATH:/output_dir sebastientourbier/mialsuperresolutiontoolkit-bidsapp:v2.1.0-dev /bids_dir /output_dir participant --param_file /bids_dir/code/simu_run-50.json --participant_label simu005 --nipype_nb_of_cores 1  --openmp_nb_of_cores 3 --masks_derivatives_dir masks

• Reconstruction with labelmaps:

docker run -t --rm -u $(id -u):$(id -g) -v $DATA_PATH:/bids_dir -v $OUT_PATH:/output_dir -v $ATLAS_PATH:/sta sebastientourbier/mialsuperresolutiontoolkit-bidsapp:v2.1.0-dev /bids_dir /output_dir participant --param_file /bids_dir/code/simu_run-30.json --participant_label 04 --nipype_nb_of_cores 1  --openmp_nb_of_cores 3 --masks_derivatives_dir masks --labels_derivatives_dir labels

• Preprocessing only pipeline

docker run -t --rm -u $(id -u):$(id -g) -v $DATA_PATH:/bids_dir -v $OUT_PATH:/output_dir sebastientourbier/mialsuperresolutiontoolkit-bidsapp:v2.1.0-dev-verbose /bids_dir /output_dir participant --param_file /bids_dir/code/clinical_run_prepro.json --participant_label chuv012 chuv026 --run_type preprocessing --nipype_nb_of_cores 1  --openmp_nb_of_cores 3 > out_prepro.txt

• Reconstruction with reorientation

docker run -t --rm -u $(id -u):$(id -g) -v $DATA_PATH:/bids_dir -v $OUT_PATH:/output_dir -v $ATLAS_PATH:/sta sebastientourbier/mialsuperresolutiontoolkit-bidsapp:v2.1.0-dev /bids_dir /output_dir participant --param_file /bids_dir/code/simu_run-21.json --participant_label simu005 --nipype_nb_of_cores 1  --openmp_nb_of_cores 3 --masks_derivatives_dir masks --labels_derivatives_dir labels > out_reorient.txt

• A run that was known to generate some file not found errors:

docker run --rm -t -u $(id -u):$(id -g) -v $DATA_PATH:/bids_dir -v $OUT_PATH:/output_dir -v $ATLAS_PATH:/sta sebastientourbier/mialsuperresolutiontoolkit-bidsapp:v2.1.0-dev /bids_dir /output_dir participant --param_file /bids_dir/code/clinical_run-5.json --openmp_nb_of_cores 3 --nipype_nb_of_cores 1 --participant_label chuv012 chuv026 --masks_derivatives_dir masks > 210_old.out