save h5ad error [TypeError: Can't implicitly convert non-string objects to strings]

[Jingle0814]

• I am sure this issue is not simply a general python programming problem
  (if so, please google the answers).
• I have searched github issues and confirm this issue has not reported previously.
• I have confirmed this bug is not related to dynamo version and it exists on the latest version of dynamo.

--- Hi,

If this is a question and not a bug report or enhancement request, please post to our Github Discussions channel at https://github.com/aristoteleo/dynamo-release/discussions

Describe the bug
A clear and concise description of what the bug is.
Thank you to your team for developing dynamo, I encountered an error while running dynamo.
I want to save the processed result of dynamo but could not.
first, I encountered "TypeError: Can't implicitly convert non-string objects to strings

Above error raised while writing key 'beta' of <class 'h5py._hl.group.Group'> to /"
And then I change the .var['beta'] to string type: adata_hsc_raw.var['beta'] = adata_hsc_raw.var['beta'].astype(str) .
But it reports the same error with 'gamma'.
How do I solve this problem? Thanks a lot!

To Reproduce
The code that produced the bug:

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Traceback
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Expected behavior
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Screenshots
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session_info.show():
Install session-info via pip install session-info and post the output after running session_info.show()

import dynamo
import session_info
session_info.show()

Additional context
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[Sichao25]

Hi, thanks for reporting this issue. Could you tell me which version of Dynamo you are using? I feel like this may be related to a recent pull request. It is not available in the released version yet.

[Jingle0814]

@Sichao25 Hi, the version I used is 1.1.0.

[Sichao25]

I think you can get rid of the issue by downloading from github pip install git+https://github.com/aristoteleo/dynamo-release.

[Jingle0814]

@Sichao25 hi, the 1.3.2 version also error,how do I solve this problem? Thanks a lot!

[Sichao25]

Sorry for not making this clear. You may need to a later version like pip install git+https://github.com/aristoteleo/dynamo-release@master. Besides, we add a new saving function called dyn.export_h5ad(). (The write_h5ad may also work, depending on what analysis you have performed).

We will have a new version coming soon. That will make everything easier.

[Jingle0814]

@Sichao25 hi thanks to your reply. I try the code:
python -m pip install git+https://github.com/aristoteleo/dynamo-release@master
and it success,

but when I try to load dynamo,it turns :

[Sichao25]

This is a compatibility issue with Ipython. It forces the command line to enter the Ipython mode after importing the Dynamo. You can use it like a notebook. To solve this problem, you may uninstall Ipython, or avoid using the command line.

[Jingle0814]

@Sichao25 Thank you very much for your prompt reply! By installing the latest version of dynamo and using notebook to analysis, I can save the h5ad files normally with dyn.export_h5ad() function.
Thanks again!

[Sichao25]

No problem. I will keep this issue open until we have the new version released.

[github-actions]

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 14 days

[github-actions]

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 14 days