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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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Numpy.core.getlimits.py UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero. #347

Open oschwengers opened 11 hours ago

oschwengers commented 11 hours ago

Unfortunately, somewhere on the last mile towards v1.10.0, the following numpy UserWarning started to appeared in each invocation of Bakta:

conda-envs/bakta-test/lib/python3.11/site-packages/numpy/_core/getlimits.py:555: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
conda-envs/bakta-test/lib/python3.11/site-packages/numpy/_core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  return self._float_to_str(self.smallest_subnormal)
conda-envs/bakta-test/lib/python3.11/site-packages/numpy/_core/getlimits.py:555: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
conda-envs/bakta-test/lib/python3.11/site-packages/numpy/_core/getlimits.py:89: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  return self._float_to_str(self.smallest_subnormal)

As reported in #346 and discudded here, it seems to be related to some ffast-math compilation flag set by any of Bakta's dependency - or dependency's dependency...

If someone has an idea or solution how to solve or circumvent this, please let us know.