anndata.concat() merging of uns doesn't work for None values

[alam-shahul]

I'm trying to use anndata.concat() to merge two AnnData objects with the following structure:

object_1 = {
...
uns: {
    "property": {
        "0": None
    }
}
...
}

object_2 = {
...
uns: {
    "property": {
        "1": None
    }
}
...
}

When I merge them using uns_merge="unique", the "property" key is missing from the merged AnnData object. However, when I replace the None value with a value like -1, it works fine. Is this the expected behavior, and if so why?

[ivirshup]

Thanks for the bug report, and sorry about the time it took to respond.

I'm not able to reproduce with either 0.7.8 or 0.8.0. Are you still seeing this?

import anndata as ad
import numpy as np

a = ad.AnnData(np.ones((3, 3)), uns={"property": {"0": None}})
b = ad.AnnData(np.ones((3, 3)), uns={"property": {"1": None}})
ad.concat([a, b], uns_merge="unique").uns["property"]
# {'0': None, '1': None}

ad.__version__
# '0.7.8'

[alam-shahul]

Okay, I guess I reported the bug slightly incorrectly. The result is correct after concatenating, but after I write to an HDF5 file with merged_datast.write(filepath) and then reload with reloaded_dataset = ad.read_h5ad(filepath), it does not contain the right keys. Is this expected?

import anndata as ad
import numpy as np
a = ad.AnnData(np.ones((3, 3)), uns={"property": {"0": None}})
b = ad.AnnData(np.ones((3, 3)), uns={"property": {"1": None}})


merged_dataset = ad.concat([a, b], uns_merge="unique")
merged_dataset.uns["property"]
# {'0': None, '1': None}

merged_dataset.write("issue.h5")

reloaded_dataset = ad.read_h5ad("issue.h5")
reloaded_dataset.uns["property"]
# {}

ad.__version__
# '0.8.0'

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[flying-sheep]

duplicate of #673. Will be fixed in #999