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ci: write zarr 3 format with supported anndata versions

Status: Merged (completed).

scverse/scanpynumber 3959

#3959 In scverse/scanpy;

· by flying-sheep was closed on Jan 29, 2026

Backport PR #3959 on branch 1.12.x (ci: write zarr 3 format with supported anndata versions)

Status: Merged (completed).

scverse/scanpynumber 3961

#3961 In scverse/scanpy;

· by meeseeksmachine was closed on Jan 29, 2026

ci: fix and deduplicate rank_gene_groups tests

Status: Merged (completed).

scverse/scanpynumber 3966

#3966 In scverse/scanpy;

· by flying-sheep was closed on Feb 6, 2026

Backport PR #3966 on branch 1.12.x (ci: fix and deduplicate rank_gene_groups tests)

Status: Merged (completed).

scverse/scanpynumber 3967

#3967 In scverse/scanpy;

· by meeseeksmachine was closed on Feb 6, 2026

ci: fix anndata.test.helpers usage

Status: Merged (completed).

scverse/scanpynumber 3968

#3968 In scverse/scanpy;

· by flying-sheep was closed on Feb 9, 2026

Backport PR #3968 on branch 1.12.x (ci: fix anndata.test.helpers usage)

Status: Merged (completed).

scverse/scanpynumber 3969

#3969 In scverse/scanpy;

· by meeseeksmachine was closed on Feb 9, 2026

ci: pyproject-fmt

Status: Merged (completed).

scverse/scanpynumber 3964

#3964 In scverse/scanpy;

· by flying-sheep was closed on Feb 10, 2026

fix: removed unecessary warning when a file name comprises multiple dots

Status: Merged (completed).

scverse/scanpynumber 3924

#3924 In scverse/scanpy;

· by nicolasrochette was closed on Feb 10, 2026

Backport PR #3924 on branch 1.12.x (fix: removed unecessary warning when a file name comprises multiple dots)

Status: Merged (completed).

scverse/scanpynumber 3972

#3972 In scverse/scanpy;

· by meeseeksmachine was closed on Feb 10, 2026

chore: add in accessors to silence deprecation warnings

Status: Merged (completed).

scverse/scanpynumber 3974

#3974 In scverse/scanpy;

· by ilan-gold was closed on Feb 16, 2026

Backport PR #3974 on branch 1.12.x (chore: add in accessors to silence deprecation warnings)

Status: Merged (completed).

scverse/scanpynumber 3976

#3976 In scverse/scanpy;

· by meeseeksmachine was closed on Feb 16, 2026

style: unify import messages

Status: Merged (completed).

scverse/scanpynumber 3979

#3979 In scverse/scanpy;

· by flying-sheep was closed on Feb 17, 2026

Backport PR #3979 on branch 1.12.x (style: unify import messages)

Status: Merged (completed).

scverse/scanpynumber 3981

#3981 In scverse/scanpy;

· by meeseeksmachine was closed on Feb 17, 2026

fix: handle all-zero genes in seurat_v3

Status: Merged (completed).

scverse/scanpynumber 3980

#3980 In scverse/scanpy;

· by flying-sheep was closed on Feb 17, 2026

Backport PR #3980 on branch 1.12.x (fix: handle all-zero genes in seurat_v3)

Status: Merged (completed).

scverse/scanpynumber 3982

#3982 In scverse/scanpy;

· by meeseeksmachine was closed on Feb 17, 2026

docs: deduplicate louvain and leiden parameter docs

Status: Merged (completed).

scverse/scanpynumber 3986

#3986 In scverse/scanpy;

· by LarytheLord was closed on Feb 26, 2026

ci: circumvent hatch incompatibility

Status: Merged (completed).

scverse/scanpynumber 3987

#3987 In scverse/scanpy;

· by flying-sheep was closed on Feb 26, 2026

docs: specify sc.tl.score_genes array type support

Status: Merged (completed).

scverse/scanpynumber 3989

#3989 In scverse/scanpy;

· by flying-sheep was closed on Feb 26, 2026

Backport PR #3989 on branch 1.12.x (docs: specify sc.tl.score_genes array type support)

Status: Merged (completed).

scverse/scanpynumber 3990

#3990 In scverse/scanpy;

· by meeseeksmachine was closed on Feb 26, 2026

fix: raise ValueError when combat batch has fewer than 2 cells

Status: Merged (completed).

scverse/scanpynumber 3994

#3994 In scverse/scanpy;

· by LiudengZhang was closed on Mar 14, 2026

Backport PR #3994 on branch 1.12.x (fix: raise ValueError when combat batch has fewer than 2 cells)

Status: Merged (completed).

scverse/scanpynumber 4001

#4001 In scverse/scanpy;

· by meeseeksmachine was closed on Mar 14, 2026

refactor: Move datasets to scverse AWS S3 urls

Status: Merged (completed).

scverse/scanpynumber 4011

#4011 In scverse/scanpy;

· by Zethson was closed on Mar 31, 2026

fix: use fast-array-utils’ threadsafe njit

Status: Merged (completed).

scverse/scanpynumber 4015

#4015 In scverse/scanpy;

· by flying-sheep was closed on Mar 31, 2026

ci: bump codecov/codecov-action from 5 to 6

dependenciesPull requests that update a dependency filePull requests that update a dependency file

github_actionsPull requests that update GitHub Actions codePull requests that update GitHub Actions code

Status: Merged (completed).

scverse/scanpynumber 4018

#4018 In scverse/scanpy;

· by dependabot was closed on Mar 30, 2026

Backport PR #4018 on branch 1.12.x (ci: bump codecov/codecov-action from 5 to 6)

dependenciesPull requests that update a dependency filePull requests that update a dependency file

github_actionsPull requests that update GitHub Actions codePull requests that update GitHub Actions code

Status: Merged (completed).

scverse/scanpynumber 4019

#4019 In scverse/scanpy;

· by meeseeksmachine was closed on Mar 30, 2026