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databio / pypiper

Python toolkit for building restartable pipelines
http://pypiper.databio.org
BSD 2-Clause "Simplified" License
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During testing, logging errors are generated: "ValueError: I/O operation on closed file" #186

Open donaldcampbelljr opened 1 year ago

donaldcampbelljr commented 1 year ago

This appears to be happening in all branches for me. Currently running PyTests and the terminal outputs many of these logging errors making it difficult to read testing results.

--- Logging error ---
Traceback (most recent call last):
  File "/home/drc/anaconda3/envs/condalooper_p38/lib/python3.8/logging/__init__.py", line 1088, in emit
    stream.write(msg + self.terminator)
ValueError: I/O operation on closed file.
Call stack:
  File "/home/drc/GITHUB/pypiper/pypiper/pypiper/manager.py", line 1799, in _exit_handler
    self.fail_pipeline(Exception("Pipeline failure. See details above."))
  File "/home/drc/GITHUB/pypiper/pypiper/pypiper/manager.py", line 1651, in fail_pipeline
    self.timestamp("### Pipeline failed at: ")
  File "/home/drc/GITHUB/pypiper/pypiper/pypiper/manager.py", line 1215, in timestamp
    self.info(msg)
  File "/home/drc/GITHUB/pypiper/pypiper/pypiper/manager.py", line 1134, in info
    self._logger.info(msg, *args, **kwargs)
Message: '\n### Pipeline failed at:  (06-13 16:17:19) elapsed: 0.0 _TIME_\n'
Arguments: ()