Fix/deprecation notices

[noamteyssier]

No description provided.

[gemini-code-assist]

Summary of Changes

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This pull request addresses deprecation notices by updating a core dependency and correcting an attribute usage. It ensures compatibility with newer versions of anndata, preventing potential issues and maintaining code stability.

Highlights

• Dependency Update: The anndata package dependency has been added to pyproject.toml with a minimum version of 0.12.10.
• Deprecation Fix: The deprecated adata.isview attribute in src/cell_eval/utils.py was updated to adata.is_view to align with the current anndata API.

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Changelog

• pyproject.toml
  • Added anndata>=0.12.10 to the project dependencies.
• src/cell_eval/utils.py
  • Replaced the deprecated adata.isview attribute with adata.is_view within the guess_is_lognorm function.

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[gemini-code-assist]

Code Review

This pull request addresses deprecation notices by updating adata.isview to adata.is_view and adding anndata as an explicit dependency. While the change for the deprecation is correct, I found a pre-existing bug in the surrounding logic that could cause a crash when processing views of dense AnnData objects. I've added a comment explaining the issue and suggesting a fix.

[gemini-code-assist]

The logic in this elif block has a potential bug. On the next line, .toarray() is called. If adata is a view on a dense numpy.ndarray, adata.X will also be a numpy.ndarray and will not have a .toarray() method, causing an AttributeError.

You should handle dense and sparse views differently. For example:

    elif adata.is_view:
        if sp.issparse(adata.X):
            frac, _ = np.modf(adata.X.tocsr().data)
        else:
            frac, _ = np.modf(adata.X)

This also avoids the memory-intensive .toarray() call for sparse views and is more robust.