205 bug with guess is lognorm when anndatas are views

[noamteyssier]

No description provided.

[gemini-code-assist]

Summary of Changes

Hello @noamteyssier, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses a critical bug in the guess_is_lognorm function that prevented it from properly processing AnnData views, which are common in single-cell data analysis workflows. The fix ensures that the function can robustly determine if data is log-normalized, regardless of whether it's a full AnnData object or a view. This enhances the reliability of data preprocessing steps and includes a new test to prevent regressions.

Highlights

• Bug Fix: The guess_is_lognorm utility function now correctly handles AnnData objects that are views (subsets) of larger AnnData objects. Previously, it would fail when encountering such views.
• Improved Data Handling: A new condition has been added to guess_is_lognorm to explicitly convert the data matrix (adata.X) of an AnnData view to a dense array using toarray() before processing, ensuring compatibility with np.modf.
• New Test Case: A dedicated test, test_is_lognorm_vew, has been introduced to validate the correct behavior of guess_is_lognorm when provided with an AnnData view.
• Version Update: The project version has been incremented from 0.6.3 to 0.6.4 in pyproject.toml, reflecting this bug fix and improvement.

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[gemini-code-assist]

Code Review

This pull request addresses a bug in guess_is_lognorm when handling AnnData views. The fix correctly adds a condition to handle view objects by converting adata.X to a dense array. A new test case is also included to validate this fix. The changes are logical and well-tested. I have a couple of minor suggestions for improving code style and fixing a typo.

[gemini-code-assist]

For conciseness, the two isinstance checks can be combined into a single call by passing a tuple of the types to check against.

Suggested change

	if isinstance(adata.X, csr_matrix) or isinstance(adata.X, csc_matrix):
	if isinstance(adata.X, (csr_matrix, csc_matrix)):

[gemini-code-assist]

There's a typo in the test function name. It appears vew should be view. Correcting this will improve readability and maintainability.

Suggested change

	def test_is_lognorm_vew():
	def test_is_lognorm_view():