Fix: .A attribute removed in new SciPy versions

[MiquelSendra]

I replaced all deprecated .A attribute calls on sparse matrices with a .toarray() fallback, through a little helper _to_dense() fucntion within the Embryo class. What it does:

• Prevents AttributeError: 'csr_matrix' object has no attribute 'A' on SciPy ≥1.11.
• Makes sure the compatibility with both sparse and dense AnnData matrices.
• Introduces _to_dense() to simplify sparse-to-dense conversions.

I tested locally on AnnData objects with store_anndata=True using new and old Scanpy and SciPy versions. Gives no errors.

Summary of edits:

• Added _to_dense() static method inside Embryo class (just at the begginig)
• Updated all .X.A calls to self._to_dense(... .X).

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