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This is currently blocked by pySPM being on 3.12 maximum, due to this:
topostats/io.py:19: in <module>
from AFMReader import asd, gwy, ibw, jpk, spm, stp, top, topostats # pylint: disable=no-name-in-module
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
../../.pyenv/versions/3.13.13/envs/topo13/lib/python3.13/site-packages/AFMReader/spm.py:6: in <module>
import pySPM
../../.pyenv/versions/3.13.13/envs/topo13/lib/python3.13/site-packages/pySPM/__init__.py:9: in <module>
from . import align, utils
../../.pyenv/versions/3.13.13/envs/topo13/lib/python3.13/site-packages/pySPM/align.py:16: in <module>
from scipy.ndimage.filters import gaussian_filter
../../.pyenv/versions/3.13.13/envs/topo13/lib/python3.13/site-packages/scipy/ndimage/filters.py:25: in __getattr__
return _sub_module_deprecation(sub_package='ndimage', module='filters',
../../.pyenv/versions/3.13.13/envs/topo13/lib/python3.13/site-packages/scipy/_lib/deprecation.py:68: in _sub_module_deprecation
warnings.warn(message, category=DeprecationWarning, stacklevel=3)
E DeprecationWarning: Please import `gaussian_filter` from the `scipy.ndimage` namespace; the `scipy.ndimage.filters` namespace is deprecated and will be removed in SciPy 2.0.0.
Activity
SylviaWhittle commentedon May 6, 2026
We could fork pySPM to update this until they do?