map_cells_to_space "could not determine the shape of object type 'Series'" error

[pakiessling]

Hi I am on scanpy=1.9.3 squidpy=1.2.3 tangram=1.0.4 torch=1.13.1+cu117

I am trying to integrate single cell and merfish data.

A marker list of 104 genes was correctly prepared and I have verified that both adata were correctly populated with training and overlap data.

tg.map_cells_to_space in cluster mode fails with could not determine the shape of object type 'Series'

Did I mess something up?

[pakiessling]

Might be related to this https://github.com/pytorch/pytorch/issues/51112

[pakiessling]

Issue is fixed by changing enviroment to:

name: tangram-env dependencies:

• python==3.8.5
• pip==20.2.2
• pytorch==1.4.0
• scipy==1.5.2
• matplotlib-base==3.3.1
• seaborn==0.11.1
• jupyterlab==2.2.6
• nb_conda==2.2.1
• pip:
  • numpy==1.22
  • pandas==1.2.0
  • scanpy==1.6.0
  • scikit-learn
  • tqdm

It seems like an upgrade to a package broke the setup of the torch tensor.

Maybe consider changing the enviroment.yml for a quick fix? @lewlin @gaddamshreya

[gaddamshreya]

@pakiessling Thank for your interest in Tangram! Also, thank you for finding the solution to this issue! I will review and make the change.

Best, Shreya