Public record
Software health reportschema 0.27.0 · metrics 1.14.0 · 2026-07-27 21:43 UTC

scverse / muon

muon is a multimodal omics Python framework

PythonBSD-3-Clause★ 277 stars⑂ 37 forkssince Feb 2020View on GitHub ↗

scverse/muon holds a health index of 69 out of 100, placing it in the Moderate band. It scores highest on Engineering Quality (92/100) and lowest on AI Readiness (41/100). It was last updated 3 days ago. A single contributor accounts for most of its recent work.

69
overall / 100
Moderate

Software health index

Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At risk ceiling of 49. AI Readiness sits outside the overall score.

69
Excellent85-100Exemplary; meets essentially all checked criteria
Good70-84Healthy; minor gaps
Moderate50-69Acceptable with notable gaps; review recommended
At risk30-49Significant weaknesses; adoption warrants caution
Critical1-29Severe 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.

Ownership

scverseOrganization
1,520 followers87 public repossince Nov 2021

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

Metrics by category

Vitality

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

60Moderate · 22% of overall
How it's scored
36/36Push recency — last push 3 days ago
9/36Commit cadence — 13/52 weeks with commits
13/18Commit volume — 27 commits in the last year
8/10OpenSSF Scorecard: Maintained — 9 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 8
Inputs used
commits_last_year27
human_commit_share1
days_since_last_push3
active_weeks_last_year13
How it's scored
27/27Ships releases — 8 releases published
7.2/36Release recency — latest release 635 days ago
12.6/27Release cadence — a release every ~177.2 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count8
latest_release_tagv0.1.7
releases_from_tagsno
days_since_latest_release635
mean_days_between_releases177.2
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?

71Good · 18% of overall
How it's scored
39.6/60Stars — 277 stars
13/25Forks — 37 forks
5.3/15Watchers — 10 watchers
Inputs used
forks37
stars277
watchers10
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

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
has_contributingyes
has_issue_templateno
has_code_of_conductyes
has_pull_request_templateno

Sustainability & Governance

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

62Moderate · 24% of overall
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
6.5/22.5Commit distribution — top contributor authored 71% of commits
13.5/13.5Contributor breadth — 23 contributors
10/10OpenSSF Scorecard: Contributors — project has 17 contributing companies or organizations
Inputs used
bus_factor1
contributors_sampled23
top_contributor_share0.709
How it's scored
35.9/46.8Issue resolution — 77% of issues closed
36.4/38.3PR acceptance — 40/42 decided PRs merged
4.5/15OpenSSF Scorecard: Code-Review — Found 9/24 approved changesets -- score normalized to 3
Inputs used
merged_prs40
open_issues35
closed_issues116
issue_closed_ratio0.768
closed_unmerged_prs2
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain
22.9/25Owner reach — 1,520 followers of scverse
22.3/25Track record — 87 public repos, account ~4 yr old
Inputs used
followers1,520
owner_typeOrganization
is_verified
owner_loginscverse
public_repos87
account_age_days1,700

Engineering Quality

Are baseline engineering and documentation practices in place?

92Excellent · 20% of overall
How it's scored
24/24CI workflows — 3 workflow(s)
24/24Tests present
16/16Linter config
9.6/9.6Pre-commit hooks
6.4/6.4.editorconfig
14/20OpenSSF Scorecard: CI-Tests — 7 out of 10 merged PRs checked by a CI test -- score normalized to 7
Inputs used
has_ciyes
has_testsyes
has_editorconfigyes
has_linter_configyes
has_precommit_configyes

Documentation

90Excellent
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — https://muon.scverse.org/
10/10Repository description
10/10Topics — 11 topics
0/10Wiki
Inputs used
topicsmultimodal-data, multimodal-omics-analysis, multi-omics, anndata, scanpy, mudata, muon, scrna-seq, scatac-seq, cite-seq, scverse
has_wikino
homepagehttps://muon.scverse.org/
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

60Moderate · 16% of overall
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
2.2/7.5Branch-Protection — branch protection is not maximal on development and all release branches
1.8/2.5CI-Tests — 7 out of 10 merged PRs checked by a CI test -- score normalized to 7
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
2.2/7.5Code-Review — Found 9/24 approved changesets -- score normalized to 3
2.5/2.5Contributors — project has 17 contributing companies or organizations
10/10Dangerous-Workflow — no dangerous workflow patterns detected
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5License — license file detected
6/7.5Maintained — 9 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 8
5/5Packaging — packaging workflow detected
1.5/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 3
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
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated17
scorecard_versionv5.5.0
checks_inconclusive1
scorecard_aggregate5
Excluded from scoring (no data or not applicable): signed_releases. Remaining weights renormalized.
How it's scored
35/35Direct dependencies free of known advisories — no direct dependency carries a known advisory
0/25Indirect dependencies free of known advisories — transitive set not separable from development and test dependencies in this scope
0/40No advisories left outstanding — no advisory carries a publication date
Inputs used
sourceosv
advisories0
affected_packages0
assessed_packages9
unassessed_packages1
affected_by_severitynone
direct_affected_packages0
Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories, No advisories left outstanding. Remaining weights renormalized. Matched 9 resolved dependencies against OSV. 1 could not be assessed — no resolved version, an unsupported ecosystem, or beyond the reported package list. This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.

AI Readiness

How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score.

41At risk · 0% of overall
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
15.5/40Legible commit history — 29 of 100 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtno
legible_history_share0.29
agent_instruction_files
agent_instruction_max_bytes
How it's scored
18/18One-command bootstrap — docs/Makefile
22/22Automated tests
11/11Lint / format config
0/11Static type checking
0/10Reproducible environment
2/10Demonstrated agent practice — 1 of the last 100 commits agent-authored or agent-credited
0/8Automated maintenance — no automated dependency updates observed
3/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 3
Inputs used
has_nixno
has_testsyes
lockfiles
has_dockerfileno
typed_languageno
bootstrap_filesdocs/Makefile
has_devcontainerno
has_linter_configyes
typecheck_configs
agent_commit_share0.01
toolchain_manifests
dependency_bot_commit_share0
How it's scored
0/45Type-checkable code — Python without a type-check config
55/55Manageable file sizes — 0/31 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes52,400
source_files_sampled31
oversized_source_files0
How it's scored
0/40API schema (OpenAPI/GraphQL/proto)
0/20MCP server
40/40Runnable examples — notebooks
Inputs used
example_dirsnotebooks
has_mcp_signalno
api_schema_files

Key facts

277GitHub stars
23contributors
27commits, last 12 months
3days since last push
8releases
1bus factor
35open issues
PyPIpackage ecosystems

Data collection warnings

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token

More detail

Star and fork history 0 ★ / 37 ⇿
0Stars
37Forks
8Releases

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.

01325383712021-052023-122026-06
Major 0Minor 1Patch 7

Each point covers 5 days.

OpenSSF Scorecard 5.0 / 10
5.0aggregate

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 · 2026-07-27 21:42 UTC

10Binary-Artifactsno binaries found in the repo
3Branch-Protectionbranch protection is not maximal on development and all release branches
7CI-Tests7 out of 10 merged PRs checked by a CI test -- score normalized to 7
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
3Code-ReviewFound 9/24 approved changesets -- score normalized to 3
10Contributorsproject has 17 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
8Maintained9 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 8
10Packagingpackaging workflow detected
3Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 3
0SASTSAST tool is not run on all commits -- score normalized to 0
0Security-Policysecurity policy file not detected
n/aSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
10Vulnerabilities0 existing vulnerabilities detected
All dependencies 10

Full resolved dependency set from the GitHub dependency graph: 0 direct and 10 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
PyPIcommonmark0.9.1indirect
PyPImuonindirect
PyPInbsphinx0.9.3indirect
PyPIpydata-sphinx-theme0.15.2indirect
PyPIreadthedocs-sphinx-search0.3.2indirect
PyPIrecommonmark0.7.1indirect
PyPIsphinx7.2.6indirect
PyPIsphinx-automodapi0.17.0indirect
PyPIsphinx-book-theme1.1.2indirect
PyPIsphinx-rtd-theme2.0.0indirect
Dependency advisories 0

This repository publishes no package the index resolves, so its own dependency graph was assessed — 9 packages, which also include development and test pins that never ship: 0 carry known advisories, of which 0 are direct. 1 could not be assessed — no resolved version, an unsupported ecosystem, or beyond the reported package list.

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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            "notes": [],
            "value": 75,
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              "followers": 1520,
              "owner_type": "Organization",
              "is_verified": null,
              "owner_login": "scverse",
              "public_repos": 87,
              "account_age_days": 1700
            },
            "components": [
              {
                "key": "ownership_backing",
                "name": "Ownership backing",
                "detail": "organization-owned",
                "points": 30,
                "status": "met",
                "details": [
                  {
                    "code": "owner_organization",
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                "max_points": 30
              },
              {
                "key": "verified_domain",
                "name": "Verified domain",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 20
              },
              {
                "key": "owner_reach",
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                "detail": "1,520 followers of scverse",
                "points": 22.9,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
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                      "count": 1520,
                      "login": "scverse"
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                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "87 public repos, account ~4 yr old",
                "points": 22.3,
                "status": "partial",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 87
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                  },
                  {
                    "code": "account_age_years",
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                      "years": 4
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                ],
                "max_points": 25
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            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
      },
      {
        "key": "engineering",
        "band": "excellent",
        "name": "Engineering Quality",
        "value": 92,
        "weight": 0.2,
        "metrics": [
          {
            "key": "engineering_practices",
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            "note": null,
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              "has_editorconfig": true,
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            "components": [
              {
                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": "3 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
                  {
                    "code": "ci_workflows",
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              {
                "key": "tests_present",
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                "detail": null,
                "points": 24,
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              {
                "key": "linter_config",
                "name": "Linter config",
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                "points": 16,
                "status": "met",
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              },
              {
                "key": "pre_commit_hooks",
                "name": "Pre-commit hooks",
                "detail": null,
                "points": 9.6,
                "status": "met",
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              },
              {
                "key": "editorconfig",
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                "details": [],
                "max_points": 6.4
              },
              {
                "key": "openssf_scorecard_ci_tests",
                "name": "OpenSSF Scorecard: CI-Tests",
                "detail": "7 out of 10 merged PRs checked by a CI test -- score normalized to 7",
                "points": 14,
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            ]
          },
          {
            "key": "documentation",
            "band": "excellent",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 90,
            "inputs": {
              "topics": [
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                "anndata",
                "scanpy",
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                "scatac-seq",
                "cite-seq",
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              "has_wiki": false,
              "homepage": "https://muon.scverse.org/",
              "has_readme": true,
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            "components": [
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                "key": "readme",
                "name": "README",
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                "points": 30,
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              {
                "key": "documentation_directory",
                "name": "Documentation directory",
                "detail": null,
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              },
              {
                "key": "documentation_homepage_site",
                "name": "Documentation / homepage site",
                "detail": "https://muon.scverse.org/",
                "points": 15,
                "status": "met",
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              },
              {
                "key": "repository_description",
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                "detail": null,
                "points": 10,
                "status": "met",
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              },
              {
                "key": "topics",
                "name": "Topics",
                "detail": "11 topics",
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                "details": [
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              {
                "key": "wiki",
                "name": "Wiki",
                "detail": null,
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                "status": "missed",
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              }
            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
      },
      {
        "key": "security",
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        "name": "Security",
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        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
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            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
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                }
              },
              {
                "code": "weights_renormalized",
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            ],
            "value": 50,
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              "source": "openssf_scorecard",
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              "scorecard_version": "v5.5.0",
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            "components": [
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                "key": "binary_artifacts",
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                "key": "branch_protection",
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              },
              {
                "key": "ci_tests",
                "name": "CI-Tests",
                "detail": "7 out of 10 merged PRs checked by a CI test -- score normalized to 7",
                "points": 1.8,
                "status": "partial",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "cii_best_practices",
                "name": "CII-Best-Practices",
                "detail": "no effort to earn an OpenSSF best practices badge detected",
                "points": 0,
                "status": "missed",
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              },
              {
                "key": "code_review",
                "name": "Code-Review",
                "detail": "Found 9/24 approved changesets -- score normalized to 3",
                "points": 2.2,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 17 contributing companies or organizations",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "dangerous_workflow",
                "name": "Dangerous-Workflow",
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                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "dependency_update_tool",
                "name": "Dependency-Update-Tool",
                "detail": "no update tool detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "fuzzing",
                "name": "Fuzzing",
                "detail": "project is not fuzzed",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "license file detected",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "maintained",
                "name": "Maintained",
                "detail": "9 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 8",
                "points": 6,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "packaging",
                "name": "Packaging",
                "detail": "packaging workflow detected",
                "points": 5,
                "status": "met",
                "details": [],
                "max_points": 5
              },
              {
                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 3",
                "points": 1.5,
                "status": "partial",
                "details": [],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "SAST tool is not run on all commits -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file not detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "detected GitHub workflow tokens with excessive permissions",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "0 existing vulnerabilities detected",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
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            ]
          },
          {
            "key": "dependency_advisories",
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            "note": "Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories, No advisories left outstanding. Remaining weights renormalized. Matched 9 resolved dependencies against OSV; 1 could not be assessed (no resolved version, an unsupported ecosystem, or beyond the reported package list). This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.",
            "notes": [
              {
                "code": "excluded_no_data",
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              },
              {
                "code": "weights_renormalized",
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              {
                "code": "advisories_scope_repository",
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              },
              {
                "code": "advisories_unassessed",
                "params": {
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              },
              {
                "code": "advisories_repo_graph_caveat",
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              },
              {
                "code": "advisories_reachability",
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              }
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            "value": 100,
            "inputs": {
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              "affected_packages": 0,
              "assessed_packages": 9,
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              "affected_by_severity": "none",
              "direct_affected_packages": 0
            },
            "components": [
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                "key": "direct_dependencies_free_of_known_advisories",
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                "detail": "no direct dependency carries a known advisory",
                "points": 35,
                "status": "met",
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                "max_points": 35
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              {
                "key": "indirect_dependencies_free_of_known_advisories",
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                "points": 0,
                "status": "excluded",
                "details": [
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                    "code": "advisories_scope_not_separable",
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                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
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                "detail": "no advisory carries a publication date",
                "points": 0,
                "status": "excluded",
                "details": [
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                    "code": "advisories_no_publication_date",
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                ],
                "max_points": 40
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            ]
          },
          {
            "key": "malicious_dependencies",
            "band": "excellent",
            "name": "Malicious dependencies",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "source": "osv",
              "meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
              "packages": [],
              "red_flag": false,
              "assessed_packages": 9,
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              "direct_malicious_packages": 0,
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            },
            "components": [
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                "key": "no_dependency_reported_as_a_malicious_package",
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                "status": "met",
                "details": [
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                    "code": "no_malicious_dependencies",
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                "max_points": 100
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            ]
          },
          {
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            "notes": [
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                "code": "jurisdiction_evidence_limits",
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            "value": 100,
            "inputs": {
              "meaning": "self-published location evidence; not nationality or citizenship",
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              "policy_countries": [
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              "commit_weight_rule": {
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              "review_only_matches": 0,
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            "components": [
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                "key": "policy_exposure_multiplier",
                "name": "Policy exposure multiplier",
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                "status": "met",
                "details": [
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                    "code": "jurisdiction_no_match",
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                ],
                "max_points": 100
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          }
        ],
        "description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
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      {
        "key": "ai_readiness",
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                "key": "agent_instructions",
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                "key": "machine_readable_docs_llms_txt",
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          },
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            "key": "ai_verify_loop",
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            "note": null,
            "notes": [],
            "value": 56,
            "inputs": {
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                "status": "met",
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                "key": "automated_tests",
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              {
                "key": "lint_format_config",
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                "key": "static_type_checking",
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                "points": 0,
                "status": "missed",
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                "max_points": 11
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              {
                "key": "reproducible_environment",
                "name": "Reproducible environment",
                "detail": null,
                "points": 0,
                "status": "missed",
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              {
                "key": "demonstrated_agent_practice",
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                ],
                "max_points": 10
              },
              {
                "key": "automated_maintenance",
                "name": "Automated maintenance",
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                "points": 0,
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                "details": [
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                ],
                "max_points": 8
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              {
                "key": "openssf_scorecard_pinned_dependencies",
                "name": "OpenSSF Scorecard: Pinned-Dependencies",
                "detail": "dependency not pinned by hash detected -- score normalized to 3",
                "points": 3,
                "status": "partial",
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                "max_points": 10
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          },
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            "key": "ai_code_legibility",
            "band": "moderate",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 55,
            "inputs": {
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              "largest_source_bytes": 52400,
              "source_files_sampled": 31,
              "oversized_source_files": 0
            },
            "components": [
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                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "Python without a type-check config",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_typecheck_config_language",
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                ],
                "max_points": 45
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              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
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                "points": 55,
                "status": "met",
                "details": [
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                    "code": "oversized_source_files",
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                ],
                "max_points": 55
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            ]
          },
          {
            "key": "ai_interfaces",
            "band": "at_risk",
            "name": "Machine-readable interfaces",
            "note": null,
            "notes": [],
            "value": 40,
            "inputs": {
              "example_dirs": [
                "notebooks"
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              "has_mcp_signal": false,
              "api_schema_files": []
            },
            "components": [
              {
                "key": "api_schema_openapi_graphql_proto",
                "name": "API schema (OpenAPI/GraphQL/proto)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 40
              },
              {
                "key": "mcp_server",
                "name": "MCP server",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 20
              },
              {
                "key": "runnable_examples",
                "name": "Runnable examples",
                "detail": "notebooks",
                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
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                "max_points": 40
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            ]
          }
        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
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    "metrics_version": "1.14.0"
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  "warnings": [
    "Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-27T21:43:24.802373Z",
  "schema_version": "0.27.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/s/scverse/muon.svg",
  "full_name": "scverse/muon",
  "license_state": "standard",
  "license_spdx": "BSD-3-Clause"
}

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 v1.14.0, schema v0.27.0 — full methodology · metrics wiki.

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