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"invalid shape in fixed-type tuple" when saving adata after ranking genes #832
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@gokceneraslan - thanks for the fast response. This broke our (cellxgene) travis pipeline as well. Do you have any info on eta for a fix/workaround other than pinning the module version? TY! |
Just a heads up, there is a remaining issue on anndata master where reading older files with h5py 2.10.0 results in bytestring indexes.
… On Sep 12, 2019, at 05:28, Bruce Martin ***@***.***> wrote:
@gokceneraslan - thanks for the fast response. This broke our (cellxgene) travis pipeline as well. Do you have any info on eta for a fix/workaround other than pinning the module version? TY!
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I'm having the same error with Back in the 1.4.3 dev version scanpy it no longer writes the object after loading, and gives me the following error:
Everything however seems to work fine when I throw out the rank_genes_groups results from Edit: actually cellxgene still isn't working, but I could at least save again. |
I can replicate that with: import scanpy as sc
pbmc = sc.datasets.pbmc68k_reduced()
pbmc.write("tmp.h5ad")
fromdisk = sc.read("tmp.h5ad") # Do we read okay
fromdisk.write(pbmc) # Can we round trip Some context around this, and my current thinking on a solution:
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Sorry for the lack of minimal reproducible example... and thanks for creating one :). |
Where might bytestrings be useful? If you say text, I have a very strong opposing opinion as I’m a survivor of Python 2 and don’t want to see an UnicodeDecodeError in my life again 😉 |
I think fixed length bytestrings would be useful when the data isn’t actually text. I think the assumption of a fixed length with text data, especially if it might have Unicode characters, is just asking for trouble.
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It is, too bad numpy has no good variable-length string array type. When would bytes make sense? Bytes just mean “data, but I don’t know its structure or am about to write it to disk” |
I'm using Scanpy with the following software versions:
python==3.7
scanpy==1.4.4
numpy==1.17.2
anndata==0.6.22.post1
on Ubuntu 18.04. I am able to save my AnnData object just fine with
and to load it again with
however if I save it after I run the command
the AnnData object will save but when I try to reload it, I get an error message:
Any idea what is going on or what I can do to make it past this error? It only started happening after I updated my operating system to Ubuntu 18 and my Python to 3.7 and reinstalled scanpy from conda.
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