Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-09-12 18:24 UTC

scverse / liana

LIANA+: an all-in-one framework for cell-cell communication

PythonBSD-3-Clause★ 315 stars⑂ 37 forkssince Sep 2022View on GitHub ↗
KindCommand-line toolhow this is determined

scverse/liana holds a health index of 92 out of 100, placing it in the Excellent band. It scores highest on Engineering Quality (100/100) and lowest on AI Readiness (60/100). It was last updated 1 day ago. A single contributor accounts for most of its recent work.

92
overall / 100
Excellent

Software health index

Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean, calibrated against the distribution of the public record so bands carry percentile meaning; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At Risk ceiling of 34.

92
Exceptional93-100The record's top tier (≈ top 5%); essentially all checked criteria met
Excellent80-92Strong across the board; minor gaps
Good65-79Healthy; gaps are limited and manageable
Moderate50-64Acceptable with notable gaps; review recommended
Weak35-49Material weaknesses across several areas
At Risk20-34Significant weaknesses; adoption warrants caution
Critical1-19Severe problems (abandoned, single-maintainer, no hygiene)
VitalityCommunity &AdoptionSustainability &GovernanceEngineeringQualitySecurityAI Readiness

Score profile

Each axis is a category. The shape matters more than the average — a healthy subject fills the whole shape, while a spike-and-crater profile means strength in one dimension is masking risk in another.

The weighted overall 78 is calibrated to 92 on the published index scale (record calibration 2026-08-02).

Ownership

scverseOrganization
1,557 followers97 public repossince Nov 2021

This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publish
PyPIlianapoints to another repo — not scored1.10.013,2993116 days ago

Metrics by category

Vitality

Is the project alive — is code being written and are releases shipping?

87Excellent · 21% of overall
How it's scored
36/36Push recency — last push 1 days ago
19.4/36Commit cadence — 28/52 weeks with commits
18/18Commit volume — 240 commits in the last year
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 15 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year240
human_commit_share0.98
days_since_last_push1
active_weeks_last_year28
How it's scored
27/27Ships releases — 26 releases published
36/36Release recency — latest release 16 days ago
19.8/27Release cadence — a release every ~45.4 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count26
latest_release_tagv1.10.0
releases_from_tagsno
days_since_latest_release16
mean_days_between_releases45.4
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.

Community & Adoption

Does the project have users, downloads, attention, and a welcoming setup for contributors?

68Good · 17% of overall
How it's scored
40.5/60Stars — 315 stars
13/25Forks — 37 forks
0/15Watchers — 1 watchers
Inputs used
forks37
stars315
watchers1
growth_stateorganic
growth_factor_pct100

Community health

85Excellent
How it's scored
22.5/22.5README
22.5/22.5License — recognized license (BSD-3-Clause)
18/18CONTRIBUTING guide
13.5/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges4
has_contributingyes
has_issue_templateno
has_code_of_conductyes
readme_badge_servicescodecov.io, github.com, readthedocs.org, shields.io
has_pull_request_templateno

Sustainability & Governance

Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?

63Moderate · 23% of overall
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
9.1/22.5Commit distribution — top contributor authored 60% of commits
13.5/13.5Contributor breadth — 18 contributors
10/10OpenSSF Scorecard: Contributors — project has 26 contributing companies or organizations
Inputs used
bus_factor1
contributors_sampled18
top_contributor_share0.595
How it's scored
39.9/42Issue resolution — 95% of issues closed
23.1/30PR acceptance — 64/83 decided PRs merged
13/13Newcomer PR acceptance — 11/11 first-time contributors' PRs merged in 30d
0/15OpenSSF Scorecard: Code-Review — Found 1/14 approved changesets -- score normalized to 0
Inputs used
merged_prs64
open_issues9
closed_issues176
prs_merged_7d9
prs_decided_7d9
prs_merged_30d16
prs_decided_30d17
issue_closed_ratio0.951
closed_unmerged_prs19
first_time_authors_30d2
first_time_prs_merged_30d11
first_time_prs_decided_30d11
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain
23/25Owner reach — 1,557 followers of scverse
22.6/25Track record — 97 public repos, account ~4 yr old
Inputs used
followers1,557
owner_typeOrganization
is_verifiedno
owner_loginscverse
public_repos97
account_age_days1,747

Engineering Quality

Are baseline engineering and documentation practices in place?

100Exceptional · 19% of overall

Engineering practices

100Exceptional
How it's scored
24/24CI workflows — 4 workflow(s)
24/24Tests present
16/16Linter config — pyproject.toml ([tool.ruff])
9.6/9.6Pre-commit hooks
6.4/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 15 out of 15 merged PRs checked by a CI test -- score normalized to 10
Inputs used
has_ciyes
has_testsyes
has_editorconfigyes
has_linter_configyes
has_precommit_configyes

Documentation

100Exceptional
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — http://liana.readthedocs.io/
10/10Repository description
10/10Topics — 7 topics
10/10Wiki
Inputs used
topicscell-cell-communication, ligand-receptor, python, single-cell, single-cell-rna-seq, spatial, spatialomics
has_wikiyes
homepagehttp://liana.readthedocs.io/
docs_sitehttp://liana.readthedocs.io/
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?

78Good · 16% of overall
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — no data
2.5/2.5CI-Tests — 15 out of 15 merged PRs checked by a CI test -- score normalized to 10
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0/7.5Code-Review — Found 1/14 approved changesets -- score normalized to 0
2.5/2.5Contributors — project has 26 contributing companies or organizations
10/10Dangerous-Workflow — no dangerous workflow patterns detected
7.5/7.5Dependency-Update-Tool — update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5License — license file detected
7.5/7.5Maintained — 30 commit(s) and 15 issue activity found in the last 90 days -- score normalized to 10
5/5Packaging — packaging workflow detected
5/5Pinned-Dependencies — all dependencies are pinned
0/5SAST — SAST tool is not run on all commits -- score normalized to 0
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — no data
7.5/7.5Token-Permissions — GitHub workflow tokens follow principle of least privilege
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate7.2
Excluded from scoring (no data or not applicable): Branch-Protection, Signed-Releases. Remaining weights renormalized.

Dependency advisories

100Exceptional
How it's scored
35/35Direct dependencies free of known advisories — no direct dependency carries a known advisory
25/25Indirect dependencies free of known advisories — no indirect dependency carries a known advisory
0/40No advisories left outstanding — no advisory carries a publication date
Inputs used
sourceosv
advisories0
affected_packages0
assessed_packages58
unassessed_packages0
affected_by_severitynone
direct_affected_packages0
Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:liana@1.10.0 runtime dependency closure — what installing the published package pulls in — 58 packages. Reachability is not analyzed.

AI Readiness

How well is the repo equipped to be developed and maintained with AI coding agents? Carries a deliberately small weight (4%): agent tooling is a real maintenance signal, but a repository with none can still reach 100/100.

60Moderate · 4% of overall
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
15/15Machine-readable docs (llms.txt) — llms.txt served by the project website (https://docs.claude.com/llms.txt)
18.5/40Legible commit history — 34 of 98 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtyes
llms_txt_urlhttps://docs.claude.com/llms.txt
legible_history_share0.347
agent_instruction_files—
agent_instruction_max_bytes—
How it's scored
0/18One-command bootstrap
22/22Automated tests
11/11Lint / format config — pyproject.toml ([tool.ruff])
11/11Static type checking — src/liana/py.typed
0/10Reproducible environment
10/10Demonstrated agent practice — 22 of the last 100 commits agent-authored or agent-credited
8/8Automated maintenance — 2 of the last 100 commits are automated dependency updates
10/10OpenSSF Scorecard: Pinned-Dependencies — all dependencies are pinned
Inputs used
has_nixno
has_testsyes
lockfiles—
has_dockerfileno
typed_languageno
bootstrap_files—
has_devcontainerno
has_linter_configyes
typecheck_configssrc/liana/py.typed
agent_commit_share0.22
toolchain_manifests—
dependency_bot_commit_share0.02
How it's scored
27/45Type-checkable code — Python with type-check config (src/liana/py.typed)
55/55Manageable file sizes — 0/130 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes43,349
source_files_sampled130
oversized_source_files0

Key facts

315GitHub stars
18contributors
240commits, last 12 months
1days since last push
26releases
1bus factor
9open issues
PyPIpackage ecosystems

Data collection warnings

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
  • Star history carried forward from 2026-07-10: GitHub restricted the stargazers API to repository admins, so it can no longer be collected. The repository has 315 stars today.
  • pypi package 'liana' points at a different repository (https://github.com/saezlab/liana-py); excluded from ecosystem scoring

More detail

Star and fork history 305 ★ / 37 ⇿
305Stars
37Forks
26Releases

When each star and fork was added, collected from GitHub and bucketed by day. Cumulative growth sits directly above the daily additions it is made of, so the two read against each other: steady organic accretion looks nothing like an abrupt, short-lived burst. Where that difference is measurable, it is reported as growth authenticity.

Star history is shown as collected on 2026-07-10. GitHub restricted the stargazers API to repository administrators in July 2026, so this series can no longer be extended; the current star total above remains live.

012525037530537102022-102024-092026-08
Major 0Minor 10Patch 13

Each point covers 4 days.

OpenSSF Scorecard 7.2 / 10
7.2aggregate

Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).Scorecard v5.5.0 · 2026-09-12 18:24 UTC

10Binary-Artifactsno binaries found in the repo
n/aBranch-Protectioninternal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md
10CI-Tests15 out of 15 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0Code-ReviewFound 1/14 approved changesets -- score normalized to 0
10Contributorsproject has 26 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained30 commit(s) and 15 issue activity found in the last 90 days -- score normalized to 10
10Packagingpackaging workflow detected
10Pinned-Dependenciesall dependencies are pinned
0SASTSAST tool is not run on all commits -- score normalized to 0
0Security-Policysecurity policy file not detected
n/aSigned-Releasesno releases found
10Token-PermissionsGitHub workflow tokens follow principle of least privilege
10Vulnerabilities0 existing vulnerabilities detected
Direct dependencies 10
RegistryPackageVersion constraintManifest
PyPIanndata>=0.13pyproject.toml
PyPIfast-array-utils—pyproject.toml
PyPImudata>=0.4pyproject.toml
PyPInumba—pyproject.toml
PyPIpandas—pyproject.toml
PyPIplotnine>=0.10.1pyproject.toml
PyPIscanpy>=1.12pyproject.toml
PyPIscverse-misc>=0.1.4pyproject.toml
PyPIsession-info2—pyproject.toml
PyPItqdm>=4pyproject.toml
All dependencies 312

Full resolved dependency set from the GitHub dependency graph: 16 direct and 296 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
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PyPIanndata0.12.7direct
PyPIfast-array-utils1.3.1direct
PyPImudata—direct
PyPImudata0.3.2direct
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PyPIpandas2.3.3direct
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PyPIscanpy1.11.5direct
PyPIscanpy1.12direct
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PyPIthreadpoolctl3.6.0indirect
PyPItifffile2026.3.3indirect
PyPItifffile2026.8.23indirect
PyPItoolz1.1.0indirect
PyPItorch2.13.0indirect
PyPItorch2.13.0+cpuindirect
PyPItornado6.5.4indirect
PyPItraitlets5.14.3indirect
PyPItwine—indirect
PyPItwine6.2.0indirect
PyPItypeguard4.4.4indirect
PyPItyping-extensions4.15.0indirect
PyPItyping-inspection0.4.4indirect
PyPItzdata2025.3indirect
PyPIumap-learn0.5.11indirect
PyPIuniversal-pathlib0.3.10indirect
PyPIurllib32.6.3indirect
PyPIvalidators0.35.0indirect
PyPIvirtualenv20.36.1indirect
PyPIwcwidth0.3.2indirect
PyPIwrapt2.0.1indirect
PyPIxarray2026.7.0indirect
PyPIxarray-dataclass3.0.0indirect
PyPIxarray-spatial0.10.17indirect
PyPIxarray-spatial0.5.3indirect
PyPIxlrd2.0.2indirect
PyPIyarl1.24.5indirect
PyPIzarr3.1.5indirect
PyPIzict3.0.0indirect
PyPIzipp3.23.0indirect
PyPIzstandard0.25.0indirect
Dependency advisories 0

Installing pypi:liana@1.10.0 pulls in 58 packages, direct and transitive: 0 carry known advisories, of which 0 are direct dependencies.

No known advisories affect the assessed dependencies.

An advisory means the version recorded in the dependency graph falls inside an advisory’s affected range. Reachability is not analysed, and the graph includes development and test pins — a finding may concern tooling rather than shipped software.

Raw JSON report machine-readable

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Spotted something off in this report, or have thoughts to share? Wrong measurements, missed tooling, ideas, questions — anything is welcome. Every message is read and gets a response.

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Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.

Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v2.10.0, schema v0.34.0 — full methodology · metrics wiki.

How one result sits in the wider record: aggregate statistics — PyPI.