spython execute not capturing stderr in streaming logs

[tjgalvin]

It appears as though that aegean within the singularity container outputs it logs to the stderr. In the current form I am not currently capturing the stderr in the prefect logs. It seems that the actual subprocess call is managed within spython (the python module that constructs singularity commands) does not output the stderr to the logger object I am looping over in flint.sclient.run_singularity_command.

I am not sure whether we can easily hijack this output object ourselves, or whether an upstream pr should be considered.

[tjgalvin]

I have raised an initial PR in spython: singularityhub/singularity-cli#209

[tjgalvin]

This fix has been brought into spythong 0.3.1. Pinging this as a dependency, updated the call into the execute method. Closing.