'UMAP' object has no attribute '_knn_search_index'. Did you mean: 'knn_search_index'?

[pakiessling]

visualizer.save("Xenium-text-visualizer.vis")

/hpcwork/p0020567/enviroments/overlpy2/lib/python3.12/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index.
  warnings.warn("Transforming to str index.", ImplicitModificationWarning)
Traceback (most recent call last):
  File "/rwthfs/rz/cluster/work/rwth1209/projects/Overlpy_Manuscript/test.py", line 26, in <module>
    visualizer.save("Xenium-text-visualizer.vis")
  File "/hpcwork/p0020567/enviroments/overlpy2/lib/python3.12/site-packages/ovrlpy/_ovrlp.py", line 1206, in save
    pickle.dumps(self.embedder_2d._knn_search_index)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'UMAP' object has no attribute '_knn_search_index'. Did you mean: 'knn_search_index'?

Hi, bekomme den Fehler für umap-learn 0.5.7

Ist das viellecht die falsche Version?

[sebastiantiesmeyer]

Thanks for the report! Our analysis uses umap-learn 0.5.6 I will fix it in the upcoming days, maybe you could try and downgrade for now?

…

On Tue, 26 Nov 2024 at 15:54, pakiessling ***@***.***> wrote: visualizer.save("Xenium-text-visualizer.vis") /hpcwork/p0020567/enviroments/overlpy2/lib/python3.12/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to str index. warnings.warn("Transforming to str index.", ImplicitModificationWarning) Traceback (most recent call last): File "/rwthfs/rz/cluster/work/rwth1209/projects/Overlpy_Manuscript/test.py", line 26, in <module> visualizer.save("Xenium-text-visualizer.vis") File "/hpcwork/p0020567/enviroments/overlpy2/lib/python3.12/site-packages/ovrlpy/_ovrlp.py", line 1206, in save pickle.dumps(self.embedder_2d._knn_search_index) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'UMAP' object has no attribute '_knn_search_index'. Did you mean: 'knn_search_index'? Hi, bekomme den Fehler für umap-learn 0.5.7 Ist das viellecht die falsche Version? — Reply to this email directly, view it on GitHub <#37>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGCTE7DYYCNEPUIAGLFZIR32CSDRJAVCNFSM6AAAAABSQUNN5KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGY4TIOJXHA4DAMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[niklasmueboe]

Maybe it is better to pickle the whole UMAP (and also PCA) object? That way we are not dependent on future API changes in other packages.

[niklasmueboe]

The load and save functionality has been remoed with the newest release. To save/load your object you can still use the pickle module of the standard library.