The value of the smallest subnormal for <class 'numpy.float64'> type is zero.

[OlgaGKononova]

After installation of hdbscan, getting bunch of warnings:

lib/python3.9/site-packages/numpy/core/getlimits.py:499: UserWarning: The value of the smallest subnormal for <class 'numpy.float64'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
lib/python3.9/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)
lib/python3.9/site-packages/numpy/core/getlimits.py:499: UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero.
  setattr(self, word, getattr(machar, word).flat[0])
lib/python3.9/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)

From what I understand, this comes from compiling C code.

Current numpy version 1.25, downgrading numpy doesn't help to solve the issue.

[tpelc2]

having the same issue

[lmcinnes]

This seems to potentially relate to some changes in Cython and or numpy; it is very hard to know or track down exactly where in the hdbscan code this is actually getting triggered.