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License: Other
BioEn - Bayesian Inference Of ENsembles
License: Other
On my laptop I had problems with DEER example Jupyter notebook as it did not find the BioEn executable. I installed the BioEn package with the --user flag.
bioen
-bash: bioen: command not found
The executable lives in /Users/lukas/.local/bin/bioen, which is was not on my path. A simple fix was simple to add this folder to the path. The question is whether there is a more general fix.
BioEn/bioen/analyze/observables/observables.py
Lines 265 to 268 in 1927780
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
BioEn/bioen/analyze/observables/deer/deer.py
Lines 42 to 43 in 1927780
This line contains a leak. The call to open
returns a file descriptor that is never closed again. This is OK when using only the bioen
CLI tool. It will be a problem when using the library from python and analyzing a lot of deer data examples with pkl_out
set because each process only is allowed a limited number of open file descriptors. The correct solution would be to use a context manager.
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