Public recordExcellent
Software health reportschema 0.16.0 · metrics 1.13.0 · 2026-07-21 02:48 UTC
scverse / scanpy
Single-cell analysis in Python. Scales to >100M cells.
scverse/scanpy holds a health index of 87 out of 100, placing it in the Excellent band. It scores highest on Vitality (96/100) and lowest on AI Readiness (39/100). It was last updated today. 2 contributors account for most of its recent work.
87
overall / 100Software 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.
87
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)
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
1,516 followers86 public repossince Nov 2021
This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.
Package ecosystems
| Registry | Package | Version | Downloads / mo | Versions | Last publish |
|---|---|---|---|---|---|
| PyPI | scanpy | 1.12.2 | 1,032,498 | 93 | 21 days ago |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
96
Development activity
99Excellent
How it's scored
| 36/36 | Push recency — last push 0 days ago |
| 34.6/36 | Commit cadence — 50/52 weeks with commits |
| 18/18 | Commit volume — 220 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 6 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 220 |
| human_commit_share | — |
| days_since_last_push | 0 |
| active_weeks_last_year | 50 |
Release discipline
92Excellent
How it's scored
| 27/27 | Ships releases — 98 releases published |
| 36/36 | Release recency — latest release 21 days ago |
| 19.8/27 | Release cadence — a release every ~55.6 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — no data |
Inputs used
| releases_count | 98 |
| latest_release_tag | 1.12.2 |
| releases_from_tags | no |
| days_since_latest_release | 21 |
| mean_days_between_releases | 55.6 |
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?
93
Popularity & adoption
89Excellent
How it's scored
| 55.2/60 | Stars — 2,522 stars |
| 24/25 | Forks — 757 forks |
| 9.4/15 | Watchers — 51 watchers |
Inputs used
| forks | 757 |
| stars | 2,522 |
| watchers | 51 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community health
92Excellent
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (BSD-3-Clause) |
| 18/18 | CONTRIBUTING guide |
| 13.5/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 6.3/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| has_contributing | yes |
| has_issue_template | no |
| has_code_of_conduct | yes |
| has_pull_request_template | yes |
Ecosystem adoption (downloads)
100Excellent
How it's scored
| 80/80 | Monthly downloads — 1,032,498 downloads/month across pypi |
| 0/20 | Registry dependents — not reported by this ecosystem |
Inputs used
| packages | scanpy |
| dependents | — |
| ecosystems | pypi |
| total_downloads | — |
| monthly_downloads | 1,032,498 |
Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.
Sustainability & Governance
Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?
78
Maintainer resilience (bus factor)
63Moderate
How it's scored
| 25.2/54 | Bus factor — 2 contributor(s) cover half of all commits |
| 14.6/22.5 | Commit distribution — top contributor authored 35% of commits |
| 13.5/13.5 | Contributor breadth — 100 contributors |
| 10/10 | OpenSSF Scorecard: Contributors — project has 49 contributing companies or organizations |
Inputs used
| bus_factor | 2 |
| contributors_sampled | 100 |
| top_contributor_share | 0.35 |
How it's scored
| 35.7/46.8 | Issue resolution — 76% of issues closed |
| 34/38.3 | PR acceptance — 1,837/2,068 decided PRs merged |
| 10.5/15 | OpenSSF Scorecard: Code-Review — Found 18/23 approved changesets -- score normalized to 7 |
Inputs used
| merged_prs | 1,837 |
| open_issues | 478 |
| closed_issues | 1,540 |
| issue_closed_ratio | 0.763 |
| closed_unmerged_prs | 231 |
Ownership & stewardship
75Good
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain |
| 22.9/25 | Owner reach — 1,516 followers of scverse |
| 22.3/25 | Track record — 86 public repos, account ~4 yr old |
Inputs used
| followers | 1,516 |
| owner_type | Organization |
| is_verified | — |
| owner_login | scverse |
| public_repos | 86 |
| account_age_days | 1,693 |
Package maintenance
100Excellent
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 21 days ago |
| 20/20 | Version history — 93 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | scanpy |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 21 |
Engineering Quality
Are baseline engineering and documentation practices in place?
96
Engineering practices
100Excellent
How it's scored
| 24/24 | CI workflows — 4 workflow(s) |
| 24/24 | Tests present |
| 16/16 | Linter config |
| 9.6/9.6 | Pre-commit hooks |
| 6.4/6.4 | .editorconfig |
| 20/20 | OpenSSF Scorecard: CI-Tests — 29 out of 29 merged PRs checked by a CI test -- score normalized to 10 |
Inputs used
| has_ci | yes |
| has_tests | yes |
| has_editorconfig | yes |
| has_linter_config | yes |
| has_precommit_config | yes |
Documentation
90Excellent
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://scanpy.scverse.org |
| 10/10 | Repository description |
| 10/10 | Topics — 9 topics |
| 0/10 | Wiki |
Inputs used
| topics | machine-learning, data-science, visualize-data, transcriptomics, bioinformatics, scanpy, anndata, python, scverse |
| has_wiki | no |
| homepage | https://scanpy.scverse.org |
| has_readme | yes |
| has_docs_dir | yes |
| has_description | yes |
Security
Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?
69
Security posture
61Moderate
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 2.2/7.5 | Branch-Protection — branch protection is not maximal on development and all release branches |
| 2.5/2.5 | CI-Tests — 29 out of 29 merged PRs checked by a CI test -- score normalized to 10 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 5.2/7.5 | Code-Review — Found 18/23 approved changesets -- score normalized to 7 |
| 2.5/2.5 | Contributors — project has 49 contributing companies or organizations |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 7.5/7.5 | Dependency-Update-Tool — update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | License — license file detected |
| 7.5/7.5 | Maintained — 30 commit(s) and 6 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 0/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — no data |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 17 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 1 |
| scorecard_aggregate | 6.2 |
Excluded from scoring (no data or not applicable): signed_releases. Remaining weights renormalized.
Dependency advisories
100Excellent
How it's scored
| 35/35 | Direct dependencies free of known advisories — no direct dependency carries a known advisory |
| 25/25 | Indirect dependencies free of known advisories — no indirect dependency carries a known advisory |
| 0/40 | No advisories left outstanding — no advisory carries a publication date |
Inputs used
| source | osv |
| advisories | 0 |
| affected_packages | 0 |
| assessed_packages | 47 |
| unassessed_packages | 0 |
| affected_by_severity | none |
| direct_affected_packages | 0 |
Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:scanpy@1.12.2 runtime dependency closure — what installing the published package pulls in — 47 packages. 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.
39
Agent context & guidance
1Critical
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 0/40 | Legible commit history — no data |
Inputs used
| has_llms_txt | no |
| legible_history_share | — |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.
Verify loop (build / test / typecheck)
62Moderate
How it's scored
| 18/18 | One-command bootstrap — docs/Makefile |
| 22/22 | Automated tests |
| 11/11 | Lint / format config |
| 0/11 | Static type checking |
| 0/10 | Reproducible environment |
| 0/10 | Demonstrated agent practice — no data |
| 5/8 | Automated maintenance — dependency automation configured, none observed in the sampled commits |
| 0/10 | OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
Inputs used
| has_nix | no |
| has_tests | yes |
| lockfiles | — |
| has_dockerfile | no |
| typed_language | no |
| bootstrap_files | docs/Makefile |
| has_devcontainer | no |
| has_linter_config | yes |
| typecheck_configs | — |
| agent_commit_share | — |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Excluded from scoring (no data or not applicable): Demonstrated agent practice. Remaining weights renormalized.
Code legibility for models
54Moderate
How it's scored
| 0/45 | Type-checkable code — Python without a type-check config |
| 54.5/55 | Manageable file sizes — 2/205 source files over 60KB |
Inputs used
| primary_language | Python |
| largest_source_bytes | 92,167 |
| source_files_sampled | 205 |
| oversized_source_files | 2 |
Machine-readable interfaces
40At risk
How it's scored
| 0/40 | API schema (OpenAPI/GraphQL/proto) |
| 0/20 | MCP server |
| 40/40 | Runnable examples — notebooks |
Inputs used
| example_dirs | notebooks |
| has_mcp_signal | no |
| api_schema_files | — |
Key facts
2,522GitHub stars
100contributors
220commits, last 12 months
0days since last push
98releases
2bus factor
478open issues
PyPIpackage ecosystems
More detail
OpenSSF Scorecard 6.2 / 10
6.2aggregate
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).
| 10 | Binary-Artifacts | no binaries found in the repo |
| 3 | Branch-Protection | branch protection is not maximal on development and all release branches |
| 10 | CI-Tests | 29 out of 29 merged PRs checked by a CI test -- score normalized to 10 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 7 | Code-Review | Found 18/23 approved changesets -- score normalized to 7 |
| 10 | Contributors | project has 49 contributing companies or organizations |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 10 | Dependency-Update-Tool | update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 6 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 0 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 0 |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 0 | Security-Policy | security policy file not detected |
| n/a | Signed-Releases | no releases found |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
Direct dependencies 23
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | anndata | >=0.11.2 | pyproject.toml |
| PyPI | certifi | — | pyproject.toml |
| PyPI | fast-array-utils | >=1.4 | pyproject.toml |
| PyPI | h5py | >=3.11 | pyproject.toml |
| PyPI | joblib | — | pyproject.toml |
| PyPI | matplotlib | >=3.10,!=3.11.0rc1,!=3.11.0rc2,!=3.11 | pyproject.toml |
| PyPI | natsort | — | pyproject.toml |
| PyPI | networkx | >=3.4 | pyproject.toml |
| PyPI | numba | >=0.61 | pyproject.toml |
| PyPI | numpy | >=2.1 | pyproject.toml |
| PyPI | packaging | >=25 | pyproject.toml |
| PyPI | pandas | >=2.3 | pyproject.toml |
| PyPI | patsy | — | pyproject.toml |
| PyPI | pynndescent | >=0.5.13 | pyproject.toml |
| PyPI | scikit-learn | >=1.6 | pyproject.toml |
| PyPI | scipy | >=1.15 | pyproject.toml |
| PyPI | scverse-misc | >=0.1.1 | pyproject.toml |
| PyPI | seaborn | >=0.13.2 | pyproject.toml |
| PyPI | session-info2 | — | pyproject.toml |
| PyPI | statsmodels | >=0.14.5 | pyproject.toml |
| PyPI | tqdm | — | pyproject.toml |
| PyPI | typing-extensions | — | pyproject.toml |
| PyPI | umap-learn | >=0.5.12 | pyproject.toml |
All dependencies 35
Full resolved dependency set from the GitHub dependency graph: 16 direct and 19 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | anndata | — | direct |
| PyPI | fast-array-utils | — | direct |
| PyPI | h5py | — | direct |
| PyPI | matplotlib | — | direct |
| PyPI | networkx | — | direct |
| PyPI | numba | — | direct |
| PyPI | numpy | — | direct |
| PyPI | packaging | — | direct |
| PyPI | pandas | — | direct |
| PyPI | pynndescent | — | direct |
| PyPI | scikit-learn | — | direct |
| PyPI | scipy | — | direct |
| PyPI | scverse-misc | — | direct |
| PyPI | seaborn | — | direct |
| PyPI | statsmodels | — | direct |
| PyPI | umap-learn | — | direct |
| PyPI | dask | — | indirect |
| PyPI | igraph | — | indirect |
| PyPI | illico | — | indirect |
| PyPI | ipython | — | indirect |
| PyPI | leidenalg | — | indirect |
| PyPI | louvain | — | indirect |
| PyPI | magic-impute | — | indirect |
| PyPI | myst-nb | — | indirect |
| PyPI | myst-parser | — | indirect |
| PyPI | nbsphinx | — | indirect |
| PyPI | scanpydoc | — | indirect |
| PyPI | scikit-image | — | indirect |
| PyPI | scikit-misc | — | indirect |
| PyPI | sphinx | — | indirect |
| PyPI | sphinx-autodoc-typehints | — | indirect |
| PyPI | sphinx-book-theme | — | indirect |
| PyPI | sphinx-exec-jupyter | — | indirect |
| PyPI | sphinx-issues | — | indirect |
| PyPI | zarr | — | indirect |
Dependency advisories 0
Installing pypi:scanpy@1.12.2 pulls in 47 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
{
"data": {
"repo": {
"topics": [
"machine-learning",
"data-science",
"visualize-data",
"transcriptomics",
"bioinformatics",
"scanpy",
"anndata",
"python",
"scverse"
],
"is_fork": false,
"size_kb": 45191,
"has_wiki": false,
"homepage": "https://scanpy.scverse.org",
"languages": {
"R": 2937,
"Python": 1743850
},
"pushed_at": "2026-07-20T17:54:39Z",
"created_at": "2017-01-29T11:31:11Z",
"owner_type": "Organization",
"updated_at": "2026-07-19T08:24:56Z",
"description": "Single-cell analysis in Python. Scales to >100M cells.",
"is_archived": false,
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"primary_language": "Python",
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"Python"
]
},
"owner": {
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"name": "scverse",
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"followers": 1516,
"avatar_url": "https://avatars.githubusercontent.com/u/95305807?v=4",
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"public_repos": 86,
"account_age_days": 1693
},
"license": {
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"file_present": true,
"scorecard_found": true,
"profile_has_license": true
},
"activity": {
"releases_count": 98,
"commits_last_year": 220,
"latest_release_at": "2026-06-29T12:25:36Z",
"latest_release_tag": "1.12.2",
"releases_from_tags": false,
"days_since_last_push": 0,
"active_weeks_last_year": 50,
"days_since_latest_release": 21,
"mean_days_between_releases": 55.6
},
"community": {
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"has_description": true,
"has_contributing": true,
"health_percentage": 87,
"has_issue_template": false,
"has_code_of_conduct": true,
"has_pull_request_template": true
},
"ecosystem": {
"packages": [
{
"name": "scanpy",
"exists": true,
"license": "BSD-3-Clause",
"keywords": [
"Development Status :: 5 - Production/Stable",
"Environment :: Console",
"Framework :: Jupyter",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Natural Language :: English",
"Operating System :: MacOS :: MacOS X",
"Operating System :: Microsoft :: Windows",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Programming Language :: Python :: 3.14",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Visualization"
],
"ecosystem": "pypi",
"matches_repo": true,
"registry_url": "https://pypi.org/project/scanpy/",
"is_deprecated": false,
"latest_version": "1.12.2",
"repository_url": "https://github.com/scverse/scanpy",
"versions_count": 93,
"total_downloads": null,
"dependents_count": null,
"deprecation_note": null,
"maintainers_count": null,
"monthly_downloads": 1032498,
"first_published_at": "2017-07-24T09:29:35.364295Z",
"latest_published_at": "2026-06-29T12:26:21.760389Z",
"latest_version_yanked": null,
"days_since_latest_publish": 21
}
]
},
"popularity": {
"forks": 757,
"stars": 2522,
"watchers": 51,
"open_issues_and_prs": 567
},
"ai_readiness": {
"has_nix": false,
"example_dirs": [
"notebooks"
],
"has_llms_txt": false,
"has_dockerfile": false,
"has_mcp_signal": false,
"bootstrap_files": [
"docs/Makefile"
],
"api_schema_files": [],
"has_devcontainer": false,
"typecheck_configs": [],
"largest_source_bytes": 92167,
"source_files_sampled": 205,
"oversized_source_files": 2,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"dependencies": {
"manifests": [
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],
"advisories": {
"error": null,
"scope": "published_package",
"source": "osv",
"findings": [],
"collected": true,
"truncated": false,
"by_severity": {},
"advisory_count": 0,
"affected_count": 0,
"assessed_count": 47,
"assessed_package": "pypi:scanpy@1.12.2",
"unassessed_count": 0,
"direct_affected_count": 0
},
"ecosystems": [
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],
"dependencies": [
{
"name": "anndata",
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"ecosystem": "pypi",
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},
{
"name": "certifi",
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"ecosystem": "pypi",
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},
{
"name": "fast-array-utils",
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"ecosystem": "pypi",
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{
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"version_constraint": null
},
{
"name": "matplotlib",
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"ecosystem": "pypi",
"version_constraint": ">=3.10,!=3.11.0rc1,!=3.11.0rc2,!=3.11"
},
{
"name": "natsort",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
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},
{
"name": "networkx",
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"ecosystem": "pypi",
"version_constraint": ">=3.4"
},
{
"name": "numba",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=0.61"
},
{
"name": "numpy",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=2.1"
},
{
"name": "packaging",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=25"
},
{
"name": "pandas",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=2.3"
},
{
"name": "patsy",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "pynndescent",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=0.5.13"
},
{
"name": "scikit-learn",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=1.6"
},
{
"name": "scipy",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=1.15"
},
{
"name": "scverse-misc",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=0.1.1"
},
{
"name": "seaborn",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=0.13.2"
},
{
"name": "session-info2",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "statsmodels",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=0.14.5"
},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
"key": "watchers",
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]
},
{
"key": "community_health",
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"notes": [],
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"key": "readme",
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"status": "met",
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{
"key": "license",
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"status": "met",
"details": [
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"code": "license_standard",
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{
"code": "license_spdx",
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{
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"details": [],
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{
"key": "code_of_conduct",
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{
"key": "issue_template",
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"status": "missed",
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{
"key": "pr_template",
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"max_points": 6.3
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]
},
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"key": "ecosystem_adoption",
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"notes": [
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"code": "excluded_no_data",
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{
"code": "weights_renormalized",
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"value": 100,
"inputs": {
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"components": [
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"key": "monthly_downloads",
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"status": "met",
"details": [
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}
],
"max_points": 80
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{
"key": "registry_dependents",
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"points": 0,
"status": "excluded",
"details": [
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"code": "not_reported_by_this_ecosystem",
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],
"max_points": 20
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]
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],
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{
"key": "governance",
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"weight": 0.24,
"metrics": [
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"key": "maintainer_resilience",
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"components": [
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"key": "bus_factor",
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{
"key": "commit_distribution",
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"details": [
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"code": "top_contributor_share",
"params": {
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}
}
],
"max_points": 22.5
},
{
"key": "contributor_breadth",
"name": "Contributor breadth",
"detail": "100 contributors",
"points": 13.5,
"status": "met",
"details": [
{
"code": "contributors_sampled",
"params": {
"count": 100
}
}
],
"max_points": 13.5
},
{
"key": "openssf_scorecard_contributors",
"name": "OpenSSF Scorecard: Contributors",
"detail": "project has 49 contributing companies or organizations",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
}
]
},
{
"key": "responsiveness",
"band": "good",
"name": "Issue & PR responsiveness",
"note": null,
"notes": [],
"value": 80,
"inputs": {
"merged_prs": 1837,
"open_issues": 478,
"closed_issues": 1540,
"issue_closed_ratio": 0.763,
"closed_unmerged_prs": 231
},
"components": [
{
"key": "issue_resolution",
"name": "Issue resolution",
"detail": "76% of issues closed",
"points": 35.7,
"status": "partial",
"details": [
{
"code": "issues_closed_share",
"params": {
"share": 76
}
}
],
"max_points": 46.75
},
{
"key": "pr_acceptance",
"name": "PR acceptance",
"detail": "1837/2068 decided PRs merged",
"points": 34,
"status": "partial",
"details": [
{
"code": "decided_prs_merged",
"params": {
"merged": 1837,
"decided": 2068
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}
],
"max_points": 38.25
},
{
"key": "openssf_scorecard_code_review",
"name": "OpenSSF Scorecard: Code-Review",
"detail": "Found 18/23 approved changesets -- score normalized to 7",
"points": 10.5,
"status": "partial",
"details": [],
"max_points": 15
}
]
},
{
"key": "stewardship",
"band": "good",
"name": "Ownership & stewardship",
"note": null,
"notes": [],
"value": 75,
"inputs": {
"followers": 1516,
"owner_type": "Organization",
"is_verified": null,
"owner_login": "scverse",
"public_repos": 86,
"account_age_days": 1693
},
"components": [
{
"key": "ownership_backing",
"name": "Ownership backing",
"detail": "organization-owned",
"points": 30,
"status": "met",
"details": [
{
"code": "owner_organization",
"params": {}
}
],
"max_points": 30
},
{
"key": "verified_domain",
"name": "Verified domain",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 20
},
{
"key": "owner_reach",
"name": "Owner reach",
"detail": "1,516 followers of scverse",
"points": 22.9,
"status": "partial",
"details": [
{
"code": "owner_followers",
"params": {
"count": 1516,
"login": "scverse"
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}
],
"max_points": 25
},
{
"key": "track_record",
"name": "Track record",
"detail": "86 public repos, account ~4 yr old",
"points": 22.3,
"status": "partial",
"details": [
{
"code": "public_repos",
"params": {
"count": 86
}
},
{
"code": "account_age_years",
"params": {
"years": 4
}
}
],
"max_points": 25
}
]
},
{
"key": "package_maintenance",
"band": "excellent",
"name": "Package maintenance",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"packages": [
"scanpy"
],
"ecosystems": "pypi",
"any_deprecated": false,
"min_days_since_publish": 21
},
"components": [
{
"key": "published_resolvable",
"name": "Published & resolvable",
"detail": "1 package(s) on pypi",
"points": 25,
"status": "met",
"details": [
{
"code": "packages_published",
"params": {
"count": 1,
"ecosystems": "pypi"
}
}
],
"max_points": 25
},
{
"key": "publish_recency",
"name": "Publish recency",
"detail": "latest publish 21 days ago",
"points": 35,
"status": "met",
"details": [
{
"code": "publish_recency",
"params": {
"days": 21
}
}
],
"max_points": 35
},
{
"key": "version_history",
"name": "Version history",
"detail": "93 published versions",
"points": 20,
"status": "met",
"details": [
{
"code": "published_versions",
"params": {
"count": 93
}
}
],
"max_points": 20
},
{
"key": "not_deprecated",
"name": "Not deprecated",
"detail": "active, not deprecated or yanked",
"points": 20,
"status": "met",
"details": [
{
"code": "package_not_deprecated",
"params": {}
}
],
"max_points": 20
}
]
}
],
"description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
},
{
"key": "engineering",
"band": "excellent",
"name": "Engineering Quality",
"value": 96,
"weight": 0.2,
"metrics": [
{
"key": "engineering_practices",
"band": "excellent",
"name": "Engineering practices",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"has_ci": true,
"has_tests": true,
"has_editorconfig": true,
"has_linter_config": true,
"has_precommit_config": true
},
"components": [
{
"key": "ci_workflows",
"name": "CI workflows",
"detail": "4 workflow(s)",
"points": 24,
"status": "met",
"details": [
{
"code": "ci_workflows",
"params": {
"count": 4
}
}
],
"max_points": 24
},
{
"key": "tests_present",
"name": "Tests present",
"detail": null,
"points": 24,
"status": "met",
"details": [],
"max_points": 24
},
{
"key": "linter_config",
"name": "Linter config",
"detail": null,
"points": 16,
"status": "met",
"details": [],
"max_points": 16
},
{
"key": "pre_commit_hooks",
"name": "Pre-commit hooks",
"detail": null,
"points": 9.6,
"status": "met",
"details": [],
"max_points": 9.6
},
{
"key": "editorconfig",
"name": ".editorconfig",
"detail": null,
"points": 6.4,
"status": "met",
"details": [],
"max_points": 6.4
},
{
"key": "openssf_scorecard_ci_tests",
"name": "OpenSSF Scorecard: CI-Tests",
"detail": "29 out of 29 merged PRs checked by a CI test -- score normalized to 10",
"points": 20,
"status": "met",
"details": [],
"max_points": 20
}
]
},
{
"key": "documentation",
"band": "excellent",
"name": "Documentation",
"note": null,
"notes": [],
"value": 90,
"inputs": {
"topics": [
"machine-learning",
"data-science",
"visualize-data",
"transcriptomics",
"bioinformatics",
"scanpy",
"anndata",
"python",
"scverse"
],
"has_wiki": false,
"homepage": "https://scanpy.scverse.org",
"has_readme": true,
"has_docs_dir": true,
"has_description": true
},
"components": [
{
"key": "readme",
"name": "README",
"detail": null,
"points": 30,
"status": "met",
"details": [],
"max_points": 30
},
{
"key": "documentation_directory",
"name": "Documentation directory",
"detail": null,
"points": 25,
"status": "met",
"details": [],
"max_points": 25
},
{
"key": "documentation_homepage_site",
"name": "Documentation / homepage site",
"detail": "https://scanpy.scverse.org",
"points": 15,
"status": "met",
"details": [],
"max_points": 15
},
{
"key": "repository_description",
"name": "Repository description",
"detail": null,
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "topics",
"name": "Topics",
"detail": "9 topics",
"points": 10,
"status": "met",
"details": [
{
"code": "topics_count",
"params": {
"count": 9
}
}
],
"max_points": 10
},
{
"key": "wiki",
"name": "Wiki",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
}
],
"description": "Are baseline engineering and documentation practices in place?"
},
{
"key": "security",
"band": "moderate",
"name": "Security",
"value": 69,
"weight": 0.16,
"metrics": [
{
"key": "security_posture",
"band": "moderate",
"name": "Security posture",
"note": "Excluded from scoring (no data or not applicable): Signed-Releases. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"signed_releases"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 61,
"inputs": {
"source": "openssf_scorecard",
"checks_evaluated": 17,
"scorecard_version": "v5.5.0",
"checks_inconclusive": 1,
"scorecard_aggregate": 6.2
},
"components": [
{
"key": "binary_artifacts",
"name": "Binary-Artifacts",
"detail": "no binaries found in the repo",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "branch_protection",
"name": "Branch-Protection",
"detail": "branch protection is not maximal on development and all release branches",
"points": 2.2,
"status": "partial",
"details": [],
"max_points": 7.5
},
{
"key": "ci_tests",
"name": "CI-Tests",
"detail": "29 out of 29 merged PRs checked by a CI test -- score normalized to 10",
"points": 2.5,
"status": "met",
"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",
"details": [],
"max_points": 2.5
},
{
"key": "code_review",
"name": "Code-Review",
"detail": "Found 18/23 approved changesets -- score normalized to 7",
"points": 5.2,
"status": "partial",
"details": [],
"max_points": 7.5
},
{
"key": "contributors",
"name": "Contributors",
"detail": "project has 49 contributing companies or organizations",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "dangerous_workflow",
"name": "Dangerous-Workflow",
"detail": "no dangerous workflow patterns detected",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "dependency_update_tool",
"name": "Dependency-Update-Tool",
"detail": "update tool detected",
"points": 7.5,
"status": "met",
"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": "30 commit(s) and 6 issue activity found in the last 90 days -- score normalized to 10",
"points": 7.5,
"status": "met",
"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 0",
"points": 0,
"status": "missed",
"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
}
]
},
{
"key": "dependency_advisories",
"band": "excellent",
"name": "Dependency advisories",
"note": "Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:scanpy@1.12.2 runtime dependency closure — what installing the published package pulls in — 47 packages. Reachability is not analyzed.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"no_advisories_left_outstanding"
]
}
},
{
"code": "weights_renormalized",
"params": {}
},
{
"code": "advisories_scope_published",
"params": {
"package": "pypi:scanpy@1.12.2",
"assessed": 47
}
},
{
"code": "advisories_reachability",
"params": {}
}
],
"value": 100,
"inputs": {
"source": "osv",
"advisories": 0,
"affected_packages": 0,
"assessed_packages": 47,
"unassessed_packages": 0,
"affected_by_severity": "none",
"direct_affected_packages": 0
},
"components": [
{
"key": "direct_dependencies_free_of_known_advisories",
"name": "Direct dependencies free of known advisories",
"detail": "no direct dependency carries a known advisory",
"points": 35,
"status": "met",
"details": [
{
"code": "no_direct_advisories",
"params": {}
}
],
"max_points": 35
},
{
"key": "indirect_dependencies_free_of_known_advisories",
"name": "Indirect dependencies free of known advisories",
"detail": "no indirect dependency carries a known advisory",
"points": 25,
"status": "met",
"details": [
{
"code": "no_indirect_advisories",
"params": {}
}
],
"max_points": 25
},
{
"key": "no_advisories_left_outstanding",
"name": "No advisories left outstanding",
"detail": "no advisory carries a publication date",
"points": 0,
"status": "excluded",
"details": [
{
"code": "advisories_no_publication_date",
"params": {}
}
],
"max_points": 40
}
]
},
{
"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": 47,
"malicious_packages": 0,
"direct_malicious_packages": 0,
"withdrawn_malicious_packages": 0,
"installable_malicious_packages": 0
},
"components": [
{
"key": "no_dependency_reported_as_a_malicious_package",
"name": "No dependency reported as a malicious package",
"detail": "no dependency is reported as a malicious package",
"points": 100,
"status": "met",
"details": [
{
"code": "no_malicious_dependencies",
"params": {}
}
],
"max_points": 100
}
]
},
{
"key": "high_risk_jurisdiction_exposure",
"band": "excellent",
"name": "High-Risk Jurisdiction Exposure",
"note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
"notes": [
{
"code": "jurisdiction_evidence_limits",
"params": {}
}
],
"value": 100,
"inputs": {
"meaning": "self-published location evidence; not nationality or citizenship",
"red_flag": false,
"exposures": [],
"policy_countries": [
"Russia",
"Iran",
"North Korea"
],
"review_only_matches": 0,
"assessed_self_published_locations": 12
},
"components": [
{
"key": "policy_exposure_multiplier",
"name": "Policy exposure multiplier",
"detail": "no confirmed policy-scope location match",
"points": 100,
"status": "met",
"details": [
{
"code": "jurisdiction_no_match",
"params": {}
}
],
"max_points": 100
}
]
}
],
"description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
},
{
"key": "ai_readiness",
"band": "at_risk",
"name": "AI Readiness",
"value": 39,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "critical",
"name": "Agent context & guidance",
"note": "Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
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]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 1,
"inputs": {
"has_llms_txt": false,
"legible_history_share": null,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"components": [
{
"key": "agent_instructions",
"name": "Agent instructions",
"detail": "no CLAUDE.md / AGENTS.md / editor rules",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_instructions",
"params": {}
}
],
"max_points": 45
},
{
"key": "machine_readable_docs_llms_txt",
"name": "Machine-readable docs (llms.txt)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
},
{
"key": "legible_commit_history",
"name": "Legible commit history",
"detail": "no data",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 40
}
]
},
{
"key": "ai_verify_loop",
"band": "moderate",
"name": "Verify loop (build / test / typecheck)",
"note": "Excluded from scoring (no data or not applicable): Demonstrated agent practice. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
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]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 62,
"inputs": {
"has_nix": false,
"has_tests": true,
"lockfiles": [],
"has_dockerfile": false,
"typed_language": false,
"bootstrap_files": [
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],
"has_devcontainer": false,
"has_linter_config": true,
"typecheck_configs": [],
"agent_commit_share": null,
"toolchain_manifests": [],
"dependency_bot_commit_share": 0
},
"components": [
{
"key": "one_command_bootstrap",
"name": "One-command bootstrap",
"detail": "docs/Makefile",
"points": 18,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "docs/Makefile"
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}
],
"max_points": 18
},
{
"key": "automated_tests",
"name": "Automated tests",
"detail": null,
"points": 22,
"status": "met",
"details": [],
"max_points": 22
},
{
"key": "lint_format_config",
"name": "Lint / format config",
"detail": null,
"points": 11,
"status": "met",
"details": [],
"max_points": 11
},
{
"key": "static_type_checking",
"name": "Static type checking",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "reproducible_environment",
"name": "Reproducible environment",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
},
{
"key": "demonstrated_agent_practice",
"name": "Demonstrated agent practice",
"detail": "no data",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
},
{
"key": "automated_maintenance",
"name": "Automated maintenance",
"detail": "dependency automation configured, none observed in the sampled commits",
"points": 5,
"status": "partial",
"details": [
{
"code": "dependency_bot_config_only",
"params": {}
}
],
"max_points": 8
},
{
"key": "openssf_scorecard_pinned_dependencies",
"name": "OpenSSF Scorecard: Pinned-Dependencies",
"detail": "dependency not pinned by hash detected -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
},
{
"key": "ai_code_legibility",
"band": "moderate",
"name": "Code legibility for models",
"note": null,
"notes": [],
"value": 54,
"inputs": {
"primary_language": "Python",
"largest_source_bytes": 92167,
"source_files_sampled": 205,
"oversized_source_files": 2
},
"components": [
{
"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",
"params": {
"language": "Python"
}
}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "2/205 source files over 60KB",
"points": 54.5,
"status": "partial",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 205,
"oversized": 2
}
}
],
"max_points": 55
}
]
},
{
"key": "ai_interfaces",
"band": "at_risk",
"name": "Machine-readable interfaces",
"note": null,
"notes": [],
"value": 40,
"inputs": {
"example_dirs": [
"notebooks"
],
"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",
"params": {
"files": "notebooks"
}
}
],
"max_points": 40
}
]
}
],
"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."
}
],
"metrics_version": "1.13.0"
},
"warnings": [],
"report_type": "repository",
"generated_at": "2026-07-21T02:48:53.084706Z",
"schema_version": "0.16.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/s/scverse/scanpy.svg",
"full_name": "scverse/scanpy",
"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 v1.13.0, schema v0.16.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.