Restore the primary assay in AnnData.X

[Copilot]

get_anndata() was clearing AnnData.X and storing the primary expression matrix only in layers["counts"], which prevents scanpy workflows from using the returned object normally.

• AnnData construction
  • Preserve the first requested assay in adata.X.
  • Retain all requested assays in adata.layers, including the primary assay.
• Regression coverage
  • Verify primary-assay mapping with multiple assays.

adata = get_anndata(metadata, assays=["counts", "cpm"])

adata.X                 # counts matrix
adata.layers["counts"]  # counts matrix
adata.layers["cpm"]     # CPM matrix

• Fixes get_anndata() returns X = None and puts counts in layers["counts"]. #7

[stemangiola]

@jdhenaos could you please review?