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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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bug of align_preprocess #270

Open caiquanyou opened 2 months ago

caiquanyou commented 2 months ago

align_preprocess in spateo/alignment/methods/deprecated_utils.py miss one parameter 'layer'

YifanLu2000 commented 1 month ago

Hi, thanks for raising the issue. Could you please provide the version you're currently running? The spateo.align.morpho_align function was restructured after the 626c16e commit, which introduced significant API changes. As a result, the deprecated_utils.py file is no longer in use. If you're interested, you might want to try the latest version of spateo.align.morpho_align, which is more efficient and flexible. A related basic tutorial can be found at here (we'll update the other tutorials as soon as possible). Let me know if that helps!

ItayBASH commented 2 weeks ago

your API of st.tdr.cell_directions as used in the tutorial "morphogenesis vector fields and trajectories" doesn't work anymore because of the same "bug", because in the end it calls to align_preprocess with the parameter 'layer'