Support sparse matrices in vectorize_counts_and_tree#1
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r0hansaxena wants to merge 10 commits intomainfrom
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Support sparse matrices in vectorize_counts_and_tree#1r0hansaxena wants to merge 10 commits intomainfrom
r0hansaxena wants to merge 10 commits intomainfrom
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* Update action versions in gh action workflows * Specify cibuildwheel version
) * ENH: add graphembed_rs wrapping for network embedding (scikit-bio#2212) * Fix lint errors in _graphembed.py * ENH: Parse string taxonomies into tree * Add changelog entry for string parsing (scikit-bio#2406) * ENH: Generalize taxonomy parsing in TreeNode.from_taxonomy * Restrict rank regex to standard prefixes and add extract_rank option * Update tests to Greengenes2 nomenclature and test extract_rank * fix Greengenes * docs: generalize taxonomy parsing description * Improve taxonomy rank extraction and null handling in from_taxonomy * cleaning up graphembed commits
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Description
Adds support for sparse matrix inputs to vectorize_counts_and_tree, improving memory efficiency when working with large biological datasets. Internally routes to a new sparse-aware helper that uses scipy sparse operations instead of dense matrix expansion