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feat: add modularity to scanpy.metrics

Status: Merged (completed).

scverse/scanpynumber 3613

#3613 In scverse/scanpy;

· by amalia-k510 was closed on Jan 22, 2026

docs: Sphinx 9 support and MyST-parser fixes

Status: Merged (completed).

scverse/scanpynumber 3948

#3948 In scverse/scanpy;

· by flying-sheep was closed on Jan 19, 2026

chore: add speed note to leiden warning

Status: Merged (completed).

scverse/scanpynumber 3949

#3949 In scverse/scanpy;

· by ilan-gold was closed on Jan 23, 2026

Get modularity score after community detection in leiden/louvain

Status: Closed (completed).

Enhancement

#2908 In scverse/scanpy;

· by AlSzmigiel was closed on Jan 22, 2026

feat: add dotplot variant

Status: Merged (completed).

scverse/scanpynumber 3890

#3890 In scverse/scanpy;

· by VladimirShitov was closed on Nov 12, 2025

fix: allow read_10x_mtx to read numeric gene IDs

Status: Merged (completed).

scverse/scanpynumber 3932

#3932 In scverse/scanpy;

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

ci: use Python 3.14 more

Status: Merged (completed).

scverse/scanpynumber 3936

#3936 In scverse/scanpy;

· by flying-sheep was closed on Jan 7, 2026

Include scipy-stubs in the optional dev dependencies

Development Process 🚀

Status: Merged (completed).

scverse/scanpynumber 3690

#3690 In scverse/scanpy;

· by jorenham was closed on Jul 14, 2025

docs: Add cruft config and update authors

Area - Documentation 📒

Development Process 🚀

Status: Merged (completed).

scverse/scanpynumber 3896

#3896 In scverse/scanpy;

· by Zethson was closed on Nov 18, 2025

docs: remove falsely advertised parameters from sc.pl.scatter

Status: Merged (completed).

scverse/scanpynumber 3894

#3894 In scverse/scanpy;

· by flying-sheep was closed on Nov 14, 2025

ci: bump actions/checkout 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 3900

#3900 In scverse/scanpy;

· by dependabot was closed on Nov 25, 2025

docs: document array type support

Status: Merged (completed).

scverse/scanpynumber 3895

#3895 In scverse/scanpy;

· by flying-sheep was closed on Dec 22, 2025

ci: pre-commit autoupdate

Status: Merged (completed).

scverse/scanpynumber 3931

#3931 In scverse/scanpy;

· by pre-commit-ci was closed on Dec 22, 2025

fix: add compat with pandas 3

Status: Merged (completed).

scverse/scanpynumber 3929

#3929 In scverse/scanpy;

· by flying-sheep was closed on Dec 30, 2025

ci: fix min-vers install time, skip yanked release

Status: Merged (completed).

scverse/scanpynumber 3923

#3923 In scverse/scanpy;

· by flying-sheep was closed on Dec 18, 2025

ci: slightly increase tolerance for test_wilcoxon_tie_correction

Status: Merged (completed).

scverse/scanpynumber 3922

#3922 In scverse/scanpy;

· by flying-sheep was closed on Dec 18, 2025

feat: allow use_graph and neighbors_key for metrics

Status: Merged (completed).

scverse/scanpynumber 3898

#3898 In scverse/scanpy;

· by flying-sheep was closed on Dec 19, 2025

Deprecate louvain

Status: Merged (completed).

scverse/scanpynumber 3658

#3658 In scverse/scanpy;

· by flying-sheep was closed on Jun 6, 2025

Catch all warnings

Status: Merged (completed).

scverse/scanpynumber 3724

#3724 In scverse/scanpy;

· by flying-sheep was closed on Jul 23, 2025

(feat): sc.get.aggregate via dask

Status: Merged (completed).

scverse/scanpynumber 3700

#3700 In scverse/scanpy;

· by ilan-gold was closed on Jul 24, 2025

(fix): import Version from correct location

Development Process 🚀

Status: Merged (completed).

scverse/scanpynumber 3733

#3733 In scverse/scanpy;

· by flying-sheep was closed on Jul 24, 2025

(chore): slightly modernize settings module

Development Process 🚀

Status: Merged (completed).

scverse/scanpynumber 3650

#3650 In scverse/scanpy;

· by flying-sheep was closed on May 27, 2025

chore: remove zappy and test zarr v3

Status: Merged (completed).

scverse/scanpynumber 3884

#3884 In scverse/scanpy;

· by flying-sheep was closed on Nov 10, 2025

feat: support csc in dask arrays in get.aggregate

Status: Merged (completed).

scverse/scanpynumber 3872

#3872 In scverse/scanpy;

· by ilan-gold was closed on Nov 10, 2025

feat: add jaccard as an additional method in sc.pp.neighbors

Status: Merged (completed).

scverse/scanpynumber 3831

#3831 In scverse/scanpy;

· by jpintar was closed on Nov 10, 2025