Leaked file descriptor in Deer observables class

[Max Linke]

BioEn/bioen/analyze/observables/deer/deer.py

Lines 42 to 43 in 1927780

 pickle.dump([self.labels, self.moddepth, self.nrestraints, self.exp_tmp, 
              self.exp_err_tmp, self.sim_tmp], open(self.out_pkl, 'wb')) 

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.

[Klaus Reuter]

Thanks, the code was improved by introducting a context manager (though CPython should close the file handle automatically, latest when the instance of the Deer class is destructed).

[Max Linke]

though CPython should close the file handle automatically, latest when the instance of the Deer class is destructed

I thought so too. But some time ago I fixed similar code in the python-mmtf package that showed a lot of leaked file descriptors in tests of MDAnalysis.