Argument parsing bugfix, plus writeout suppression options. #9
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The loadOptions function parses either options fed to it or options obtained from STDIN. It used to choose where to take options based on whether or not any args were given to it at all. This had the problem that if no options were given to it, it would pull options from the calling script whether or not these were intended for it at all. This can result in silent failure of propka.run.single(). Now, loadOptions takes a keyword argument 'commandline' that, when False, takes its arguments from its own input. When True, it takes them from STDIN. The run.single() function also reflect this change.
This is useful for external codes that don't need the file output, but would like performance gains from not waiting for a file to be written to disk each time. For Molecular_container.__init__(), writeout=False will suppress writeout of propka inputs. For run.single(), writeout=False will suppress writeout of both inputs and results.
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@dotsdl I just looked at the proposed changes in this pull request along with your initial discussion about suppresion of output in issue #10 and I have a few comments and questions I'd like to discuss with the maintainers (I suppose @charnley is the one right now). The suppression of output, I feel, is a great addition that could be interesting to do in circomstances like yours - especially if you are truly limited by the output of propka. But since it would be a major undertaking (and you are the first to request this suppresion), have you tried using redirects, i.e. which will remove the output you do not need. Alternatively, if you feel like discarding it entirely you can always redirect to Returning to the the proposed set of changes you have given in this pull request I think that the output suppresion should, for now, be discarded or at least put in issue #10. Your bug-fix regarding the input parameter processing is of course a welcome addition. Perhaps @charnley can comment on what he thinks and how to proceed. |
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I think there may be a bit of confusion on the motivation for these changes. I am not running propka from the shell, but instead feeding The output displayed to stdout is a separate issue, and one that I haven't addressed at all in these commits. I realize that adding options for suppressing printed output isn't a particularly exciting feature, but it makes it much easier to envision propka being used on whole trajectories inside of larger codebases if this were the case. |
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Ahh, I understand now and can see why your particular setup would require this suppression. The propka code is littered with |
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@dotsdl I think you can close this PR. The |
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