Numpy compatibility issue

[Midnighter]

When I install biom-format and numpy >= 2 in an environment, I get a lot of errors of the sort:

ValueError('numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject')

That is even though, version 2.1.16 promises numpy 2.0 compatibility.

I think, the reason is that you do not restrict the numpy version in your build instructions and your wheels are compiled against numpy <2.

[build-system]
requires = ["setuptools","wheel", "numpy", "cython"]

[wasade]

Thanks, could you issue a PR to trigger CI?On Aug 4, 2024, at 17:04, Moritz E. Beber @.***> wrote: When I install biom-format and numpy >= 2 in an environment, I get a lot of errors of the sort: ValueError('numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject')

That is even though, version 2.1.16 promises numpy 2.0 compatibility. I think, the reason is that you do not restrict the numpy version in your build instructions and your wheels are compiled against numpy <2. [build-system] requires = ["setuptools","wheel", "numpy", "cython"]

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>

[Midnighter]

I can, but the nasty side-effect of that will be loss of compatibility with numpy <2. Is that what the project wants?

[wasade]

It isn’t but would like to see what happens. I’m OOO for the next few weeks so cannot look close, but would greatly appreciate any effort that could be contributed for numpy 1 and 2 supportOn Aug 4, 2024, at 17:58, Moritz E. Beber @.***> wrote: I can, but the nasty side-effect of that will be loss of compatibility with numpy <2. Is that what the project wants?

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[iBuitron]

same here but when installing with poetry:

  File "/home/reveur/python/environmental/quickBio/ed.py", line 1, in <module>
    import biom
  File "/home/reveur/python/environmental/quickBio/.venv/lib/python3.11/site-packages/biom/__init__.py", line 51, in <module>
    from .table import Table
  File "/home/reveur/python/environmental/quickBio/.venv/lib/python3.11/site-packages/biom/table.py", line 196, in <module>
    from ._filter import _filter
  File "biom/_filter.pyx", line 1, in init biom._filter
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

(this installation comming from scikit-bio using poetry)

NOTE: if i installing with pip, it works fine.

Report on Scikit-bio forum: https://github.com/scikit-bio/scikit-bio/issues/2101