Added MERFISHVI and SpatialVI

[Starlitnightly]

from spateo.external.MERFISHVI import MERFISHVI  



MERFISHVI.setup_anndata(adata_concat, batch_key="batch")
MERFISHVI.setup_nonspatial_anndata(adata=adata_sc)

model = MERFISHVI(
    adata_spatial=adata_concat,
    adata_nonspatial=adata_sc,  # 可选的非空间模态
    n_hidden=128,
    n_latent=30,
    n_spatial=10
)

model.train(max_epochs=100)

gene_means = model.get_normalized_expression(
    n_samples=1,
    transform_batch="2000panel",
)
adata_concat.layers['Impute_2000'] = gene_means

gene_means = model.get_normalized_expression(
    n_samples=1,
    transform_batch="250panel",
)
adata_concat.layers['Impute_250'] = gene_means

adata_concat.obsm["X_MERFISHVI"] = model.get_latent_representation()

[Copilot]

Pull Request Overview

This PR introduces the MERFISHVI and SpatialVI functionality for processing AnnData objects while updating the logging module usage to force the standard library logging rather than a package-specific one. The key changes include:

• Refactored logging in spateo/external/lack.py to use stdlib logging via _logging.
• Added conditional import logic and fallback for MERFISHVI in spateo/external/init.py.
• Introduced a new module spateo/external/MERFISHVI exposing MERFISHVI and SpatialSCVI.

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated no comments.

File	Description
spateo/external/lack.py	Updated logger to use _logging and fixed a redundant self parameter in a method.
spateo/external/init.py	Added conditional import for MERFISHVI with a placeholder for missing deps.
spateo/external/MERFISHVI/init.py	Newly created module exposing MERFISHVI and SpatialSCVI.

Comments suppressed due to low confidence (1)

spateo/external/lack.py:202

• Removed the redundant self parameter in the call to info_insert_adata; please ensure the method signature now aligns correctly.

return self.info_insert_adata(key, adata_attr="var", indent_level=1, *args, **kwargs)