snakePipes 3.0.0 logging

[katsikora]

I get no logs, and the numbered run logs are empty.

[WardDeb]

Hi Katarzyna,

Can you add a reproducible example ?
I can then have a look.

[katsikora]

Hi Ward,

I finally got the logs but only after the run has exit... Is this expected?

Best,

Katarzyna

[WardDeb]

Yea, I got rid of it when simplifying runAndCleanup. I figured real time stdout/stderr in console is enough information, and we don't need to flush the buffer on every line. In case you want this back one could just add f.flush() again after writing a line:

snakepipes/snakePipes/common_functions.py

Line 738 in 0d30e2f

f.write(stdout.decode('utf-8'))

[katsikora]

Hmmm, interesting, so the buffer must be quite large.
Perhaps indeed flushing after each line would be useful. I'd prefer to have the log available as soon as possible if I'm working on fixing something.

[thomasmanke]

is the same information not visible under .snakemake/log/ ?