scverse / anndata

Annotated data.
http://anndata.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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`dask` `2024.8.0` breaks with `scipy.sparse.{csr,csc}` #1579

Open ilan-gold opened 1 month ago

ilan-gold commented 1 month ago

Please make sure these conditions are met

Report

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 commented 1 month ago

See https://github.com/dask/dask/issues/11290