requirement of anndata = "0.7.5" makes it impossible to load anndata saved with newer version (e.g. 0.8.0) about pyrovelocity HOT 7 CLOSED

Hi Alex,

We do plan to update all outdated dependencies to latest stable versions. However, until we are able to do that, the instructions in https://github.com/pinellolab/pyrovelocity/tree/8ec0b77d8a69b22708dc4639fa2b1332161acfe5/reproducibility/environment with manual overrides as suggested by Alvin should generally allow use of the library.

We will close this issue for now. Many thanks!

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Thanks! That seems to be working for now.

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Hi Alexander,

Thank you for the feedback! This behavior of anndata is weird. Are you using poetry or bioconda way to install the package? I'll spend some time fix this error later.

Best,
Alvin

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Hi Alvin,

thanks for getting back. I have used bioconda.

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Would be great to fix this! I haven't found a way to work around this problem, so it basically prevents me from using the package with the anndata objects I have.

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Sorry for the delay. I just came back from vacation, will explore this problem this week.

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Hi Alex,

I tested on my side on the google cloud using notebook instance, please refer to here. A simple way to upgrade the anndata without breaking the other package is to conda activate pyrovelocity && pip install -U anndata==0.8.0rc1. Please let me know if this works for you. To build another bioconda package, however there are a few conflicts during conda-build with anndata==0.8.0, I still need some time to submit another bioconda version for one-liner installation. Thanks!

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