~ 35.63% faster filtering#3330

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kaushalprasadhial wants to merge 118 commits intoscverse:mainfrom

sanchit-misra:scanpy_filter

Commits on Oct 25, 2024

updated for filter_cell
kaushalprasadhial
authored

Commits on Nov 15, 2024

print statment removal
kaushalprasadhial
authored

Commits on Feb 4, 2025

[pre-commit.ci] pre-commit autoupdate (#3119)

pre-commit-ci[bot]
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Ubuntu
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(chore): add preparation-of-release documentation (#3122)

authored and
Ubuntu
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[pre-commit.ci] pre-commit autoupdate (#3131)

authored and
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Unpin numpy 2 (#3115)

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Bugfix: Gene score edge case where gene_list gene is chosen as control gene (#2875)

authored and
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Use version guards instead of “except ImportError” (#3145)

flying-sheep
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[pre-commit.ci] pre-commit autoupdate (#3148)

pre-commit-ci[bot]
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Ubuntu
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fix layer use_raw (#3150)

Intron7
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Revert "fix layer use_raw (#3150)" (#3154)

Intron7
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[pre-commit.ci] pre-commit autoupdate (#3156)

authored and
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Allow all valid legend_loc options (#3163)

flying-sheep
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Fix tests for dask PCA (#3162)

flying-sheep
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Run benchmarks for off axis (#3147)

flying-sheep
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Fix `layers` parameter in `score_genes` with `.raw` (#3155)

Intron7
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Ubuntu
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Refactor score_genes (#3170)

flying-sheep
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Ubuntu
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Switch from using rubric in release notes (#3172)

flying-sheep
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[pre-commit.ci] pre-commit autoupdate (#3174)

pre-commit-ci[bot]
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Ubuntu
committed
Fix NaN dispersion (#3176)

flying-sheep
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committed
Cache data for subsequent test runs (#3177)

flying-sheep
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Ubuntu
committed
Some refactoring ahead of key_added (#3182)

flying-sheep
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Ubuntu
committed
Auto-metric and fix logs (#3186)

flying-sheep
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Ubuntu
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Add Ruff FBT (#3189)

flying-sheep
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Ubuntu
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Add Ruff pytest-style (#3191)

flying-sheep
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Add key_added to umap, tsne, and pca (#3184)

flying-sheep
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Ubuntu
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Fix [source] links (#3194)

flying-sheep
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[pre-commit.ci] pre-commit autoupdate (#3197)

pre-commit-ci[bot]
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Ubuntu
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(fix): resolve data ordering to match axis for stacked violin plots (#3196)

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[pre-commit.ci] pre-commit autoupdate (#3207)

pre-commit-ci[bot]
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[pre-commit.ci] pre-commit autoupdate (#3210)

pre-commit-ci[bot]
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(fix): Upper bound `dask` (#3217)

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Update notebooks (#3216)

flying-sheep
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[pre-commit.ci] pre-commit autoupdate (#3213)

pre-commit-ci[bot]
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[pre-commit.ci] pre-commit autoupdate (#3225)

pre-commit-ci[bot]
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fa2 library changed to fa2_modified (#3220)

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[pre-commit.ci] pre-commit autoupdate (#3232)

pre-commit-ci[bot]
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Switch to towncrier (#3231)

authored and
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Fix towncrier git CLI call (#3236)

flying-sheep
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Backport PR #3235 on branch main ((chore): generate 1.10.3 release notes) (#3238)

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Fix release note building and check (#3239)

flying-sheep
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impl median function for aggregation (#3180)

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Upload scrublet scores on test failure (#3069)

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Fix stacked_violin’s `standard_scale` parameter (#3243)

flying-sheep
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Finish `scale`→`density_norm` deprecation (#3244)

flying-sheep
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Rely on Ruff for TYPE_CHECKING block mgmt (#3248)

flying-sheep
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Clean up dendrogram typing (#3249)

flying-sheep
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Deprecate defunct `order` parameter in `stacked_violin` (#3252)

flying-sheep
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Fix *Plot.style() methods (#3206)

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[pre-commit.ci] pre-commit autoupdate (#3256)

pre-commit-ci[bot]
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committed
Add `SIM` checks (#3258)

flying-sheep
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Fix compat typing and old_positionals usage (#3264)

flying-sheep
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Split up PCA tests (#3268)

flying-sheep
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[pre-commit.ci] pre-commit autoupdate (#3270)

pre-commit-ci[bot]
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Remove 3.9 support (#3283)

flying-sheep
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Fix #3206’s release note (#3287)

flying-sheep
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(fix): conditional imports to avoid `anndata.io` warning (#3289)

ilan-gold
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Fix benchmark job: Use upstream asv (#3292)

flying-sheep
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Use upstream sklearn PCA if possible (#3267)

flying-sheep
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Ubuntu
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Test all PCA param combinations (#3294)

flying-sheep
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Add explicit support to PCA for `'covariance_eigh'` svd_solver (#3296)

flying-sheep
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Implement sparse `covariance_eigh` PCA using Dask (#3263)

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Fix HVG with 1-obs batches (#3286)

flying-sheep
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Allow specifying a collection of colors to scatterplots (#3299)

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(fix): correct anndata release for `io` usage (#3298)

ilan-gold
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[pre-commit.ci] pre-commit autoupdate (#3274)

pre-commit-ci[bot]
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(fix): clarify sparse pca usage (#3306)

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Fix sc.pl.highest_expr_genes with a categorical column (#3302)

flying-sheep
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Fix some `Returns` docstrs re: `inplace` semantics (#3311)

ryan-williams
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Catch PerfectSeparationWarning during regress_out (#3275)

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Refactor regress_out (#3316)

flying-sheep
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Enforce `np.bool_` usage via Ruff (#3321)

flying-sheep
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Update `test_rank_genes_groups.py` reference (#3285)

emmanuel-ferdman
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Support `layer` in `sc.pl.highest_expr_genes` (#3324)

flying-sheep
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Align `get.obs_df`’s docs with its code (#3328)

flying-sheep
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[pre-commit.ci] pre-commit autoupdate (#3329)

pre-commit-ci[bot]
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(fix): sort pca test args (#3333)

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Add PYI lints (#3339)

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(feat): `calculate_qc_metrics` with `dask` (#3307)

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Fix docs (#3343)

flying-sheep
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move all `njit` calls into a decorator (#3335)

flying-sheep
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Update notebooks (#3349)

flying-sheep
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Speedup (~20x) of scanpy.pp.regress_out function using Linear Least Square method. (#3284)

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Fix zappy compatibility for clip_array (#3317)

flying-sheep
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[pre-commit.ci] pre-commit autoupdate (#3354)

pre-commit-ci[bot]
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Backport PR #3357 on branch main ((chore): generate 1.10.4 release notes) (#3359)

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Actually working min-deps job (#3337)

flying-sheep
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Fix CI (#3364)

flying-sheep
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[pre-commit.ci] pre-commit autoupdate (#3373)

pre-commit-ci[bot]
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Deprecate RandomState (using names only) (#3372)

flying-sheep
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Updated Harmony Integrate Docs to better match interface to Harmonypy package (#3362)

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Use deprecation decorator (#3380)

flying-sheep
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(fix): bound sklearn because of dask-ml on the release candidate (#3393)

ilan-gold
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[pre-commit.ci] pre-commit autoupdate (#3388)

pre-commit-ci[bot]
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Remove calls to `.format` (#3325)

flying-sheep
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Constrain all extras for min-deps job (#3367)

flying-sheep
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Add a “improved documentation” category to enhancement template (#3403)

flying-sheep
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Modify error message if certifi is not installed (#3402)

flying-sheep
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Add replace option to subsample and rename function to sample (#943)

gokceneraslan
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Switch to session-info2 (#3384)

flying-sheep
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Scipy 1.15 compat, some test refactors (#3409)

flying-sheep
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Deprecate visium (#3407)

flying-sheep
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Add sample probabilities (#3410)

flying-sheep
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(chore): generate 1.11.0 release notes (#3412)

flying-sheep
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Note that it’s an rc

flying-sheep
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[pre-commit.ci] pre-commit autoupdate (#3404)

pre-commit-ci[bot]
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Fix Markdown syntax for preprocessing docs page (#3418)

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Doc fixes for 1.11 (#3415)

flying-sheep
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Mention towncrier in contribution docs (#3427)

flying-sheep
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Fix wilcoxon for >10M cells (#3426)

flying-sheep
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Update author/maintainer metadata (#3413)

flying-sheep
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Formatting (#3414)

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(chore) upper bound zarr version in tests to <3 (#3432)

flying-sheep
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Fix flaky doublet test (#3436)

flying-sheep
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(chore): Update to Ruff 0.9 and add EM lints (#3437)

flying-sheep
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Grammar fixes in `sc.tl` docstrings (#3438)

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updated for filter_cell
kaushalprasadhial
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print statment removal
kaushalprasadhial
committed