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:

Minimal data may be provided to reproduce the bug Traceback Post the error message from the Tracebook output:

Expected behavior A clear and concise description of what you expected to happen.

Screenshots If applicable, add screenshots to help explain your problem.

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 Add any other context about the problem here.

[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[bot]]

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[bot]]

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