Creating `Observables` in a python session might crash the interpreter.

[Max Linke]

BioEn/bioen/analyze/observables/observables.py

Lines 265 to 268 in 1927780

 print('ERROR: The experimental data type {} is not implemented in BioEn yet. ' \ 
       'Please try \"generic\" (useful for distances, NOEs, CS, J-couplings, ' \ 
       'PREs etc.)'.format(experiment)) 
 sys.exit() 

This is a hard exit of the python interpreter. When using BioEn as a library (e.g. in a notebook) it can crash the process instead of failing gracefully. To fail gracefully an exception should be raised.

To maintain well-formatted error messages in the CLI tool one can use try-except in the main function

try:
   obs = function_that_can_raise()
except Exception as e:
   print("Exception occurred")
   print("Error Message: ")
   print(e)
   if verbose:
       raise(e)  # to show stacktrace
   sys.exit(1)  # show tool exited with an error with return-code 1

[Max Linke]

Here are more cases that can unexpectedly kill the python process.

BioEn/bioen/optimize/forces.py

Line 422 in 1927780

 sys.exit(0) 

BioEn/bioen/optimize/forces.py

Line 481 in 1927780

 sys.exit(0) 

BioEn/bioen/optimize/forces.py

Line 485 in 1927780

 sys.exit(0) 

BioEn/bioen/optimize/forces.py

Line 183 in 1927780

 sys.exit(0) 

[Max Linke]

Here are all occurrences.

analyze/utils.py
32:            sys.exit()
36:        sys.exit()

optimize/log_weights.py
187:        sys.exit(0)
423:            sys.exit(0)
490:            sys.exit(0)
494:        sys.exit(0)

optimize/forces.py
183:        sys.exit(0)
422:            sys.exit(0)
481:            sys.exit(0)
485:        sys.exit(0)

analyze/observables/observables.py
268:                sys.exit()

analyze/observables/deer/deer.py
119:		sys.exit()

analyze/observables/scattering/scattering.py
119:            sys.exit()

analyze/observables/generic/generic.py
93:            sys.exit()
98:            sys.exit()

[Klaus Reuter]

This issue was fixed with v0.1.1:

• all sys.exit() calls were replaced by exceptions.
• the CLI tool run_bioen.main() catches these exceptions and prints their error message