Open donaldcampbelljr opened 6 months ago
is it just that pytests require the multi flag to be set?
not sure this is a bug...
hmm, I think it's not.. But what we should do in this case? Should we skip tests or set multi=True
I think all the pypiper tests set multi=True
. it's just what you have to do to use pypiper with pytests.
look at all the existing pypiper tests. I think they're already doing that. This is just a known thing with pypiper, because pytest is capturing output.
I am able to use multi=True
to get the tests to pass when using pypiper in our Bedboss tests:
with TemporaryDirectory() as d:
pm = pypiper.PipelineManager(
name="bedclassifier",
outfolder=d,
recover=True,
pipestat_sample_name="Generic_Digest",
multi=True
)
bedclass = BedClassifier(input_file=values[0], output_dir=d, pm=pm)
pm.complete()
However, terminal gets filled with logging errors claiming that the pipeline failed:
--- Logging error ---
Traceback (most recent call last):
File "/usr/lib/python3.10/logging/__init__.py", line 1103, in emit
stream.write(msg + self.terminator)
ValueError: I/O operation on closed file.
Call stack:
File "/home/drc/GITHUB/bedboss/bedboss/.venv2/lib/python3.10/site-packages/pypiper/manager.py", line 2201, in _exit_handler
self.fail_pipeline(Exception("Pipeline failure. See details above."))
File "/home/drc/GITHUB/bedboss/bedboss/.venv2/lib/python3.10/site-packages/pypiper/manager.py", line 2036, in fail_pipeline
self.info("Failure reason: " + str(exc))
File "/home/drc/GITHUB/bedboss/bedboss/.venv2/lib/python3.10/site-packages/pypiper/manager.py", line 1468, in info
self._logger.info(msg, *args, **kwargs)
Message: 'Failure reason: Pipeline failure. See details above.'
Arguments: ()
Exception ignored in atexit callback: <bound method PipelineManager._exit_handler of <pypiper.manager.PipelineManager object at 0x7f0cf268aad0>>
Traceback (most recent call last):
File "/home/drc/GITHUB/bedboss/bedboss/.venv2/lib/python3.10/site-packages/pypiper/manager.py", line 2201, in _exit_handler
self.fail_pipeline(Exception("Pipeline failure. See details above."))
File "/home/drc/GITHUB/bedboss/bedboss/.venv2/lib/python3.10/site-packages/pypiper/manager.py", line 2045, in fail_pipeline
raise exc
Exception: Pipeline failure. See details above.
This becomes exhausting if there is a test failure and you need to read the log.
If you set the flag
multi=True
, it works fine and we no longer get the illegal seek error.Originally posted by @donaldcampbelljr in https://github.com/databio/bedboss/issues/30#issuecomment-1944492602