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dask 2024.8.0 breaks with scipy.sparse.{csr,csc} #1579

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ilan-gold opened this issue Aug 8, 2024 · 4 comments · Fixed by #1745
Closed
3 tasks done

dask 2024.8.0 breaks with scipy.sparse.{csr,csc} #1579

ilan-gold opened this issue Aug 8, 2024 · 4 comments · Fixed by #1745
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@ilan-gold
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ilan-gold commented Aug 8, 2024

Please make sure these conditions are met

  • I have checked that this issue has not already been reported.
  • I have confirmed this bug exists on the latest version of anndata.
  • (optional) I have confirmed this bug exists on the master branch of anndata.

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See: https://dev.azure.com/scverse/anndata/_build/results?buildId=7565&view=results

Traceback:

../../../micromamba/envs/scipy-dev/lib/python3.11/functools.py:909: in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
src/anndata/tests/helpers.py:688: in assert_adata_equal
    assert_equal(
../../../micromamba/envs/scipy-dev/lib/python3.11/functools.py:909: in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
src/anndata/tests/helpers.py:551: in assert_equal_dask_array
    assert_equal(b, a.compute(), exact, elem_name)
venv/lib/python3.11/site-packages/dask/base.py:376: in compute
    (result,) = compute(self, traverse=False, **kwargs)
venv/lib/python3.11/site-packages/dask/base.py:662: in compute
    results = schedule(dsk, keys, **kwargs)
def concatenate_arrays(arrs, sorter, axis):
       return np.take(np.concatenate(arrs, axis=axis), np.argsort(sorter), axis=axis)
       ValueError: zero-dimensional arrays cannot be concatenated

Versions

-----
anndata             0.11.0.dev158+ge17c5bbb
session_info        1.0.0
-----
asciitree           NA
awkward             2.6.7
awkward_cpp         NA
cloudpickle         3.0.0
cython_runtime      NA
dask                2024.8.0
dateutil            2.9.0.post0
fsspec              2024.6.1
h5py                3.11.0
importlib_metadata  NA
jinja2              3.1.4
markupsafe          2.1.5
msgpack             1.0.8
natsort             8.4.0
numcodecs           0.13.0
numpy               2.0.1
packaging           24.1
pandas              2.2.2
psutil              6.0.0
pyarrow             17.0.0
pytz                2024.1
scipy               1.13.1
six                 1.16.0
tblib               3.0.0
tlz                 0.12.1
toolz               0.12.1
yaml                6.0.2
zarr                2.18.2
zipp                NA
-----
Python 3.11.8 | packaged by conda-forge | (main, Feb 16 2024, 20:49:36) [Clang 16.0.6 ]
macOS-13.6.1-arm64-arm-64bit
-----
Session information updated at 2024-08-08 15:54
@ilan-gold
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See dask/dask#11290

@ilan-gold ilan-gold removed this from the 0.10.9 milestone Aug 9, 2024
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github-actions bot commented Oct 9, 2024

This issue has been automatically marked as stale because it has not had recent activity.
Please add a comment if you want to keep the issue open. Thank you for your contributions!

@github-actions github-actions bot added the stale label Oct 9, 2024
@ivirshup
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ivirshup commented Nov 7, 2024

This is closable now, right?

@github-actions github-actions bot removed the stale label Nov 8, 2024
@ilan-gold
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Yes and we can unbound

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