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DCA is currently incompatible with recent versions of tensorflow. This PR increases compatibility to tf>=2.0,<=2.10, which makes it compatible with openproblems. I've also added some simple Github Actions tests to ensure that these versions are truly supported.

@zozo123
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zozo123 commented Apr 7, 2023

@gokceneraslan, this PR works for me as well via scanpy. I strongly suggest merging it into the master branch.

@juliawang22
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I agree with this as well. This also relates to this issue #50, as kopt is not compatible with tensorflow 2.2 because of this change.

@asmariyaz23
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Hello,

Thank you for providing this patch. I am trying to install this version using the patch-1 branch. However I get the following error:

Python 3.8.10 (default, Jun 16 2021, 14:20:20) 
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import dca
>>> import scanpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/scratch/asmab/deepscence/DCA/lib/python3.8/site-packages/scanpy/__init__.py", line 16, in <module>
    from ._utils import check_versions
  File "/scratch/asmab/deepscence/DCA/lib/python3.8/site-packages/scanpy/_utils/__init__.py", line 28, in <module>
    from .compute.is_constant import is_constant
  File "/scratch/asmab/deepscence/DCA/lib/python3.8/site-packages/scanpy/_utils/compute/is_constant.py", line 5, in <module>
    from numba import njit
  File "/scratch/asmab/deepscence/DCA/lib/python3.8/site-packages/numba/__init__.py", line 43, in <module>
    from numba.np.ufunc import (vectorize, guvectorize, threading_layer,
  File "/scratch/asmab/deepscence/DCA/lib/python3.8/site-packages/numba/np/ufunc/__init__.py", line 3, in <module>
    from numba.np.ufunc.decorators import Vectorize, GUVectorize, vectorize, guvectorize
  File "/scratch/asmab/deepscence/DCA/lib/python3.8/site-packages/numba/np/ufunc/decorators.py", line 3, in <module>
    from numba.np.ufunc import _internal
SystemError: initialization of _internal failed without raising an exception

Could you kindly share what Python version and numpy you used?

Thank you,
Asma

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4 participants