Required checks passing
57%
532 of 926 scored cells
Core data structures
78%
3 repos · 11 failing required checks
Core framework
69%
9 repos · 49 failing required checks
Core infrastructure
57%
7 repos · 30 failing required checks
Other repositories
52%
41 repos · 296 failing required checks
| Repository | ||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| R Uses cookiecutter-scverse | R Template up to date | r src layout + hatchling | r pre-commit.ci enabled | r codecov configured | r Default branch is main | i Listed in packages.json | Template | R .readthedocs.yaml present | R RTD project points here | R ≥2 core devs on RTD | R Docs on *.scverse.org | r Stable RTD build passed | Documentation | R PyPI project owned by scverse | R Trusted publishing | R Release workflow hardened | R SPEC 0 minimum Python | R Immutable releases enabled | r Recent releases immutable | r `pypi` environment protected | r Tag matches PyPI version | Packaging | R Integration tests passing | R Actions pinned to SHA | r pre-commit revs pinned | R zizmor audit is clean | R Dependabot configured | r No open Dependabot alerts | r Secret scanning + push protection | r Private vulnerability reporting | R Minimal workflow permissions | r checkout without credentials | r No unsafe pull_request_target | r SECURITY.md | Supply chain | R Default branch protected | R Requires a pull request | R Requires ≥1 approving review | r Requires status checks | Branch protection | R OSI license | R GPL-free dependencies | r Description, homepage, topic | i Actively maintained | Governance | |
| Core data structures · 3 repositories | ||||||||||||||||||||||||||||||||||||||||||||||
| anndata 16/20 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| mudata 17/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ! | ✓ | ! | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | – | ✗ | – | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| spatialdata 14/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ! | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | – | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Core framework · 9 repositories | ||||||||||||||||||||||||||||||||||||||||||||||
| decoupler 15/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ! | ✓ | ! | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| muon 16/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ! | ✓ | ! | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | – | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| pertpy 19/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ! | ✓ | ! | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| rapids-singlecell 16/20 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ! | ✓ | ! | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| scanpy 14/20 | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ! | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| scirpy 14/20 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ |
| scvi-tools 13/20 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | – | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| SnapATAC2 3/16 | ✗ | – | ✗ | – | ✗ | ✓ | ✓ | ✗ | ✗ | – | – | – | – | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | – | ✗ | – | ✗ | – | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ |
| squidpy 12/20 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Core infrastructure · 7 repositories | ||||||||||||||||||||||||||||||||||||||||||||||
| cookiecutter-scverse 8/9 | – | – | – | ✓ | – | ✓ | ✓ | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | ✗ | – | – | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | – | ✗ | ✓ | ✗ |
| ecosystem-packages 5/9 | – | – | – | ✓ | – | ✓ | ✓ | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | – | ✗ | ✓ | ✗ |
| governance 4/6 | – | – | – | ✓ | – | ✓ | ✓ | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | – | ✗ | – | ✗ | ✓ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | – | ✓ | ✓ | ✓ |
| integration-testing 4/9 | – | – | – | – | – | ✓ | ✓ | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | ✗ | – | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | – | ✗ | ✓ | ✗ |
| scverse-tutorials 11/18 | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | – | ✗ | – | – | ✗ | ✓ | ✓ | – | ✗ | – | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ |
| scverse.github.io 4/9 | – | – | – | ✗ | – | ✓ | ! | ✗ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | – | ✗ | ✓ | ✗ |
| stats 3/9 | – | – | – | – | – | ✓ | ✓ | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | ✗ | – | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✓ | – | ✗ | ✓ | ✗ |
| Other repositories · 41 repositories | ||||||||||||||||||||||||||||||||||||||||||||||
| 202611_workshop_SBI2 1/5 | – | – | – | – | – | ✓ | – | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | – | – | – | – | ✗ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | – | ✗ | ✓ | ✗ |
| acumen 7/20 | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | – | ✗ | ✓ | ✗ | ✗ | ✗ | – | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| annbatch 15/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| anndata-plot 8/17 | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | – | ✗ | ✓ | ✗ | ✗ | ? | ✗ | ✗ | – | – | ✓ | ✗ | ✓ | – | ✗ | – | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| anndataR 3/9 | – | – | – | – | – | ✗ | ! | ✗ | – | – | – | – | – | – | – | – | – | – | ✓ | ✓ | – | – | ✓ | – | ✗ | – | ✗ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ! | – | ✗ | ✓ | ✗ |
| cellrank 8/19 | ✗ | – | ✓ | ✗ | ✗ | ✓ | – | ✗ | ✓ | ✗ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| cupy-stubs 12/17 | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | – | ✗ | ✗ | – | – | – | – | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ! | ✓ | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| deres 10/20 | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | – | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ! | ✗ |
| fast-array-utils 11/19 | ✗ | – | ✓ | ✓ | ✗ | ✓ | – | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ! | ✓ | ✗ | – | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ! | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| formulaic-contrasts 12/20 | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | – | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| gatac 4/13 | ✗ | – | ✗ | – | ✗ | ✓ | – | ✗ | ✓ | ✗ | ✗ | ✗ | – | ✗ | – | – | ✗ | ✗ | ✓ | – | ✗ | – | ✗ | – | – | – | – | – | ✓ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| gatac-reproducibility 1/5 | – | – | – | – | – | ✓ | – | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | – | – | – | – | ✓ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | – | ✗ | ✓ | ✗ |
| gatac-tutorials 2/10 | ✗ | – | ✗ | – | ✗ | ✓ | – | ✗ | ✗ | – | – | – | – | ✗ | – | – | ✗ | ✗ | ✓ | – | ✗ | – | ✗ | – | – | – | – | – | ✓ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | ✓ | ✗ |
| genomic-features 8/20 | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | – | ✗ | ✓ | ✓ | ✗ | ✗ | – | ✗ | ✓ | ✗ | ✓ | ✗ | ✓ | – | ✗ | – | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| gget 6/16 | ✗ | – | ✗ | ✗ | ✗ | ✓ | – | ✗ | ✗ | – | – | – | – | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| gpu-ci-config 6/9 | – | – | – | ✓ | – | ✓ | – | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | – | ✗ | ✓ | ✗ |
| liana 16/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | – | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| mantispy 12/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | – | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✓ | ! | – | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| napari-spatialdata 9/17 | ✗ | – | ✗ | ✗ | ✗ | ✓ | – | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | – | – | ✗ | ✗ | ✓ | ✗ | ✗ | – | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| pandas-uuid 9/19 | ✗ | – | ✓ | ✓ | ✓ | ✓ | – | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ! | ✓ | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ! | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| prelude-runner 5/14 | ✗ | – | ✓ | ✓ | ✗ | ✓ | – | ✗ | ✗ | – | – | – | – | ✗ | – | – | ✗ | ✗ | ✓ | – | ✗ | – | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| PyDESeq2 13/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| pytometry 13/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | – | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| repo-health 7/11 | – | – | ✓ | ✗ | ✗ | ✓ | – | ✗ | – | – | – | – | – | – | – | – | – | ✓ | ✓ | – | ✗ | – | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| sbi2_2026 1/9 | – | – | – | ✗ | – | ✓ | – | ✗ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | – | ✗ | ✓ | ✗ |
| scverse-backends 10/19 | ✗ | – | ✓ | ✓ | ✓ | ✓ | – | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| scverse-doc 14/20 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | – | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✓ | ! | ✓ | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| scverse-io 2/5 | – | – | – | – | – | ✓ | – | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | – | – | – | – | ✓ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | – | ✗ | ✓ | ✗ |
| scverse-misc 15/20 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | – | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | – | ✓ | – | ✗ | – | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ |
| scvi-colab 7/16 | ✗ | – | ✗ | ✓ | ✓ | ✓ | – | ✗ | ✗ | – | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | – | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ |
| session-info2 12/19 | ✗ | – | ✓ | ✓ | ✗ | ✓ | – | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ! | ✓ | ✗ | – | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| shadows 3/16 | ✗ | – | ✓ | – | ✗ | ✓ | – | ✗ | ✗ | – | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ | – | ✗ | – | ✗ | – | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ! | ✗ |
| sp-ops 5/13 | ✗ | – | ✗ | – | ✗ | ✓ | – | ✗ | ✓ | ✓ | ✗ | ✗ | – | ✗ | – | – | ✗ | ✗ | ✓ | – | ✗ | – | ✗ | – | – | – | – | – | ✗ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| spatial-sample-aggregation 6/17 | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | – | ✗ | ✓ | ✗ | ✗ | ? | ✗ | ✗ | – | – | ✓ | ✗ | ✓ | – | ✗ | – | ✗ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ! | ✗ |
| spatialdata-integration-testing 3/10 | ✗ | – | ✗ | – | ✗ | ✓ | – | ✗ | ✗ | – | – | – | – | ✗ | – | – | ✗ | ✗ | ✓ | – | ✗ | – | ✗ | – | – | – | – | – | ✓ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| spatialdata-io 15/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | – | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | ✓ | ✗ | ✓ | ✗ | ✗ | ✓ | ✗ | – | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| spatialdata-plot 16/20 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | – | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ | ! | ✓ | ✗ | – | ✓ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✗ |
| zarr-convention-dataframe 2/5 | – | – | – | – | – | ✓ | – | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | – | – | – | – | ✓ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | – | ✗ | ✓ | ✗ |
| zarr-convention-enum 2/5 | – | – | – | – | – | ✓ | – | ✓ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | – | – | – | – | ✓ | ✓ | ✓ | – | – | – | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | – | ✗ | ✓ | ✗ |
| zarr-kvikio 11/18 | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | – | ✗ | ✓ | ✓ | ✗ | ✗ | – | ✗ | – | – | ✓ | ✗ | ✓ | – | ✗ | – | ✗ | – | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✓ | ✗ |
| zulip-bots 2/9 | – | – | – | ✗ | – | ✓ | – | ✗ | – | – | – | – | – | – | – | – | – | – | ✓ | – | – | – | ✓ | – | ✗ | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | – | ✗ | ✓ | ✗ |
No repository matches those filters.
59 repositories excluded from the dashboard
- .github — Org-level community health files, not a project
- 202504_workshop_GSCN — archived
- 202510_workshop_GSCN — Workshop material
- 2025_03_hackathon_owkin — Hackathon repository
- 202609_workshop_GSCN — Workshop material
- 2026_03_hackathon_proteomics — Hackathon repository
- 2026_04_hackathon_padua — Hackathon repository
- 2026_08_hackathon_cellpainting — Hackathon repository
- 2026_09_workshop_physalia — Workshop material
- anndata-rs — Rust crate
- anndata-tutorials — archived
- antibody-based-spatial-proteomics-guide — Community guide, prose only
- aws — private
- benchmark — Ad-hoc benchmarking scripts, not a released package
- cell-painting-io — archived
- cellpainting2026 — Event repository
- cellrank_notebooks — Tutorial notebooks
- conference-2024 — Conference material
- conference-2025 — Conference material
- cookiecutter-scverse-instance — Example output of the template, regenerated automatically
- cookiecutter-scverse-presentation — Slides introducing the template
- cookiecutter-scverse-reproducibility — private
- decoupler-harness — private
- decoupler-tutorials — Tutorial notebooks
- ecobomb — private
- event-template — Template for event repositories
- gscn2026 — Website for the GSCN 2026 workshop
- internal-governance — private
- irlba — private
- liana-tutorials — Tutorial notebooks
- multi-condition-comparisions — archived
- muon-site — Website
- muon-tutorials — Tutorial notebooks
- Muon.jl — Julia package
- org — private
- pertpy-datasets — Dataset hosting
- pertpy-tutorials — Tutorial notebooks
- plotting_api — archived
- postdata — private
- rapids-singlecell-tutorials — Tutorial notebooks
- rustar-aligner — Rust crate
- sc-proteomics2026 — Event repository
- scanpy-tutorials — archived
- scverse-conference-websites — private
- scverse-stats — private
- scverse-zulip-agent — private
- scvi-tools-site — Website
- scvi-tools-skeleton — archived
- scvi-tutorials — Tutorial notebooks
- simple-scvi — Teaching example, not a released package
- single-cell-analysis-blueprint — fork
- single-cell-spatial-proteomics — Community collaboration repository, prose only
- spatialdata-basel-workshop-2024 — Workshop material
- spatialdata-plot-tutorials — Tutorial notebooks
- spatialdata-spec — private
- spatialdata-tutorials — Tutorial notebooks
- squidpy-tutorials — Tutorial notebooks
- test-gpu-ci — fork
- xarray-interview — private
Exclusions live in config/repos.yaml. repo-health audit-exclusions
fails when an active repository is in neither that file nor packages.json.
What each check means
| Check | Tier | Needs | Description |
|---|---|---|---|
template/cruft |
required | cont | .cruft.json exists and names the scverse template |
template/up-to-date |
required | cont, meta | .cruft.json commit matches the latest cookiecutter-scverse release |
template/src-layout |
recommended | cont | Builds with hatchling from a src/ layout |
template/pre-commit-ci |
recommended | meta | pre-commit.ci runs on pull requests |
template/codecov |
recommended | cont, meta | A codecov config or a codecov check run exists |
template/default-branch |
recommended | meta | The default branch is called main |
template/packages-json |
informational | web | Listed in scverse.org's ecosystem index, under a category the dashboard knows |
docs/readthedocs-yaml |
required | cont | A .readthedocs.yaml build config is committed |
docs/rtd-linked |
required | rtd | The Read the Docs project of the same slug builds *this* repository |
docs/rtd-core-devs |
required | rtd | At least two scverse core devs can administer the RTD project |
docs/scverse-domain |
required | rtd, meta | Documentation is served from <package>.scverse.org, not readthedocs.io |
docs/rtd-build |
recommended | rtd | The most recent build of the stable version succeeded |
packaging/pypi-org |
required | pypi | ownership.organization on PyPI is the scverse org |
packaging/trusted-publishing |
required | pypi | The latest release carries PEP 740 attestations naming this repo's workflow |
packaging/release-workflow |
required | cont | Publishes via pypa/gh-action-pypi-publish with id-token: write, no password, in an environment |
packaging/spec0-python |
required | cont, py | requires-python has dropped the Python versions SPEC 0 has dropped |
packaging/immutable-releases |
required | admin | The repository has immutable releases turned on |
packaging/releases-immutable |
recommended | meta | The last few published releases are actually marked immutable |
packaging/pypi-environment |
recommended | admin | A deployment environment named pypi exists and has protection rules |
packaging/version-sync |
recommended | meta, pypi | The newest GitHub release tag matches the newest PyPI version |
integration/upstream-tests |
required | meta | This package's test suite passes in scverse/integration-testing against upstream core packages |
security/actions-pinned |
required | cont | Every uses: names a full 40-character commit SHA |
security/precommit-pinned |
recommended | cont | Every rev: in .pre-commit-config.yaml is a commit SHA |
security/zizmor-clean |
required | cont | A zizmor audit of every workflow, action and Dependabot config reports no findings |
security/dependabot |
required | cont | .github/dependabot.yml covers both the github-actions and pre-commit ecosystems |
security/dependabot-alerts |
recommended | sec | No unresolved Dependabot security alerts |
security/secret-scanning |
recommended | admin | Secret scanning and push protection are both enabled |
security/private-vuln-reporting |
recommended | admin | Researchers can report vulnerabilities privately |
security/workflow-permissions |
required | cont, admin | Every workflow declares a top-level permissions:, and the repo default is read-only |
security/persist-credentials |
recommended | cont | actions/checkout steps set persist-credentials: false (zizmor artipacked) |
security/dangerous-triggers |
recommended | cont | pull_request_target does not check out untrusted PR code (zizmor dangerous-triggers) |
security/security-md |
recommended | meta | A security policy exists, in this repo or via the org's .github repo |
branch/protected |
required | meta, admin? | Neither force-pushes nor deletion are allowed on the default branch |
branch/requires-pr |
required | meta, admin? | Changes to the default branch must go through a pull request |
branch/requires-review |
required | meta, admin? | A pull request needs at least one approving review to merge |
branch/status-checks |
recommended | meta, admin? | At least one status check must pass before merging |
governance/license |
required | meta | The repo carries a recognised OSI-approved license |
governance/gpl-free |
required | cont, pypi | No runtime dependency, direct or transitive, is GPL-licensed, unless the repo is GPL itself |
governance/description-topics |
recommended | meta | The repo has a description, a homepage and the scverse topic |
governance/maintained |
informational | meta | Pushed to within the last year |