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aristoteleo / spateo-release

Spatiotemporal modeling of spatial transcriptomics
https://spateo-release.readthedocs.io/
BSD 2-Clause "Simplified" License
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AttributeError: module 'spateo.tl' has no attribute 'weighted_spatial_graph' #225

Open xhli2 opened 4 months ago

xhli2 commented 4 months ago

hello,when i run the demo of Cell-cell_interaction, weights_graph, distance_graph, adata = st.tl.weighted_spatial_graph( adata, n_neighbors=10, ) with error AttributeError: module 'spateo.tl' has no attribute 'weighted_spatial_graph'

dzhu8 commented 4 months ago

Hi, thank you for using our package, and sorry for the inconvenience! As the package is still in development, some things change quickly. The cell-cell interaction tutorial is out of date and includes references to some deprecated functions, including this one. The tutorials will be updated soon, and remind me periodically if this is not the case.

MickYang2333 commented 1 month ago

Hi, thank you for using our package, and sorry for the inconvenience! As the package is still in development, some things change quickly. The cell-cell interaction tutorial is out of date and includes references to some deprecated functions, including this one. The tutorials will be updated soon, and remind me periodically if this is not the case.

Hi, could I know is it still possible for me to conduct cell-cell interaction analysis using this package before the new tutorial release, when weights_graph, distance_graph, adata = st.tl.weighted_spatial_graph( adata, n_neighbors=10, ) no longer be able to use?

xhli2 commented 4 weeks ago

Hi, thank you for using our package, and sorry for the inconvenience! As the package is still in development, some things change quickly. The cell-cell interaction tutorial is out of date and includes references to some deprecated functions, including this one. The tutorials will be updated soon, and remind me periodically if this is not the case.

Hi, could I know is it still possible for me to conduct cell-cell interaction analysis using this package before the new tutorial release, when weights_graph, distance_graph, adata = st.tl.weighted_spatial_graph( adata, n_neighbors=10, ) no longer be able to use?

And I find another author and his branch ,finally I find this function st.tl.weighted_spatial_graph( adata, n_neighbors=10, )

MickYang2333 commented 3 weeks ago

Hi, thank you for using our package, and sorry for the inconvenience! As the package is still in development, some things change quickly. The cell-cell interaction tutorial is out of date and includes references to some deprecated functions, including this one. The tutorials will be updated soon, and remind me periodically if this is not the case.

Hi, could I know is it still possible for me to conduct cell-cell interaction analysis using this package before the new tutorial release, when weights_graph, distance_graph, adata = st.tl.weighted_spatial_graph( adata, n_neighbors=10, ) no longer be able to use?

And I find another author and his branch ,finally I find this function st.tl.weighted_spatial_graph( adata, n_neighbors=10, )

That's great! Which branch did you use? It will be helpful, thank you so much

xhli2 commented 3 weeks ago

Hi, thank you for using our package, and sorry for the inconvenience! As the package is still in development, some things change quickly. The cell-cell interaction tutorial is out of date and includes references to some deprecated functions, including this one. The tutorials will be updated soon, and remind me periodically if this is not the case.

Hi, could I know is it still possible for me to conduct cell-cell interaction analysis using this package before the new tutorial release, when weights_graph, distance_graph, adata = st.tl.weighted_spatial_graph( adata, n_neighbors=10, ) no longer be able to use?

And I find another author and his branch ,finally I find this function st.tl.weighted_spatial_graph( adata, n_neighbors=10, )

That's great! Which branch did you use? It will be helpful, thank you so much

Maybe this repo https://github.com/jiangfuqing/Spateo.git

MickYang2333 commented 3 weeks ago

Hi, thank you for using our package, and sorry for the inconvenience! As the package is still in development, some things change quickly. The cell-cell interaction tutorial is out of date and includes references to some deprecated functions, including this one. The tutorials will be updated soon, and remind me periodically if this is not the case.

Hi, could I know is it still possible for me to conduct cell-cell interaction analysis using this package before the new tutorial release, when weights_graph, distance_graph, adata = st.tl.weighted_spatial_graph( adata, n_neighbors=10, ) no longer be able to use?

And I find another author and his branch ,finally I find this function st.tl.weighted_spatial_graph( adata, n_neighbors=10, )

That's great! Which branch did you use? It will be helpful, thank you so much

Maybe this repo https://github.com/jiangfuqing/Spateo.git

It finally works! Thank you so much.

Xiaojieqiu commented 3 weeks ago

@dzhu8 can you please fix the notebooks please? it is important to get the latest working notebooks soon

dzhu8 commented 3 weeks ago

hello,when i run the demo of Cell-cell_interaction, weights_graph, distance_graph, adata = st.tl.weighted_spatial_graph( adata, n_neighbors=10, ) with error AttributeError: module 'spateo.tl' has no attribute 'weighted_spatial_graph'

Deepest apologies for the delay! A few updated tutorials have now been uploaded to the tutorials repository: https://github.com/aristoteleo/spateo-tutorials, and should be available on-site soon. Send a message if there are other issues or questions.

Xiaojieqiu commented 3 weeks ago

@dzhu8 did the notebook github page updated? https://spateo-release.readthedocs.io/en/latest/tutorials/index.html