log1p warns adata.X is logged when it may not be (when other layers are logged)

When I use sc.pp.log1p(adata) and then sc.pp.log1p(adata, layer='other') it warns me that the data has already been logged even though I am logging a layer as opposed to adata.X.

Would be nice to flag logging for each layer instead of when anything is logged.

import scanpy as sc

adata = sc.datasets.pbmc3k_processed()
adata.layers['other'] = adata.X
sc.pp.log1p(adata, layer='other')
sc.pp.log1p(adata)

WARNING: adata.X seems to be already log-transformed.

Versions:

scanpy==1.5.2.dev5+ge5d246aa anndata==0.7.3 umap==0.3.10 numpy==1.18.5 scipy==1.5.0 pandas==1.0.5 scikit-learn==0.23.1 statsmodels==0.11.1 python-igraph==0.7.1 louvain==0.6.1 leidenalg==0.7.0

[gokceneraslan]

Guys we should just keep the layer info here in log1p:

data.uns[‘log1p’] = {‘base’: base}

like

data.uns[‘log1p’][layer] = {‘base’: base}

[Benfeitas]

I must also mention that upon reading in the data:

• running adata.uns['log1p'] returns {};
• setting adata.uns['log1p']["base"] = None after reading doesn’t help.
• running del adata.uns['log1p'] solves the problem. Visual inspection of expression values in adata.X seem to not be log-transformed.