I get a write error:

[zznx]

I get a write error: Above error raised while writing key 0 of <class 'h5py._hl.group.Group'> from /. if a name of the index to the var table is an int. Setting the name to a string fixes this.

Originally posted by @jeffhsu3 in https://github.com/theislab/anndata/issues/52#issuecomment-585151866

[ivirshup]

Is adata.var.index.name an integer? If so, changing it to a string as suggested by the error message should solve your problem.

[zznx]

Thank you anyway, but my problem is still unsolved. How to solve it @ivirshup

OSError: Unable to create link (name already exists)

Above error raised while writing key 'full_name' of <class 'h5py._hl.group.Group'> from /.

Above error raised while writing key 'raw/var' of <class 'h5py._hl.files.File'> from /.

[wangjiawen2013]

I met the same error

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[ivirshup]

if a name of the index to the var table is an int. Setting the name to a string fixes this.

Reading this again, makes me think issue has been resolved. We don't support integer column names.

[KaWingLee9]

Maybe check the data strcture will help. For example, I had an error while writing adata.obsm['spatial'], I changed the dtype of the array. Another error occurs while writing adata.obs['array_row'], then I changed the data into int. So I guess data structure and data type are very important while wirting h5ad.

[flying-sheep]

Of course we support int dtypes. But we would need a minimum reproducible example: https://matthewrocklin.com/minimal-bug-reports

[axol0tl]

I also keep having issues with saving anndata objects after modifying them with scanpy (filtering genes) and adding some cols to .obs

[ivirshup]

@axol0tl, please open a full bug report with an example and traceback:

https://github.com/scverse/anndata/issues/new?assignees=&labels=Bug+🐛&projects=&template=bug-report.yml

[axol0tl]

ah, I realized that if there are any str values in anndata.obs -> it will not save h5ad. sorry, my bad. saved the info into a csv and dropped those cols, deleted anndata.raw, and was able to save anndata