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Use upstream sklearn PCA if possible #3267
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #3267 +/- ##
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+ Coverage 76.95% 77.03% +0.08%
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Files 109 110 +1
Lines 12465 12492 +27
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+ Hits 9592 9623 +31
+ Misses 2873 2869 -4
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flying-sheep
commented
Sep 27, 2024
Merged
3 tasks
ilan-gold
reviewed
Oct 15, 2024
Contributor
|
Some comments and questions, some changes needed. Overall, much cleaner :) |
ilan-gold
approved these changes
Oct 18, 2024
kaushalprasadhial
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to sanchit-misra/scanpy
that referenced
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Feb 4, 2025
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this PR fixes #2744 and
moves
_pca_with_sparsebehind a check for scipy <1.4, which has @ivirshup’s port of that code ENH Allow fitting PCA on sparse X with arpack solvers scikit-learn/scikit-learn#18689simplifies our logic around which parameters lead to which dispatch
this makes it useful to get this in before Implement sparse
covariance_eighPCA using Dask #3263throws a warning when people use the
lobpcgsolver, since the closure of PCA on sparse, noncentered data scikit-learn/scikit-learn#12794 (comment) makes it unlikely that we can count on that getting in any time soonI filed Add svd_solver="lobpcg" option to PCA scikit-learn/scikit-learn#30075. Depending on how that PR is received, we can update the warning here: either they like it, then we can remove the warning (we remove our legacy code once we depend on a scipy version that has lobpcg upstream), or they don’t, then we leave the warning for now and remove lobpcg support in the future.