Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-09-12 17:53 UTC

Clinical-Genomics / scout

VCF visualization interface

HTML · PythonBSD-3-Clause★ 181 stars⑂ 51 forkssince Oct 2014View on GitHub ↗
KindCommand-line toolNetwork serviceLibraryhow this is determined

Clinical-Genomics/scout holds a health index of 94 out of 100, placing it in the Exceptional band. It scores highest on Vitality (98/100) and lowest on AI Readiness (53/100). It was last updated 1 day ago. 2 contributors account for most of its recent work.

94
overall / 100
Exceptional

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.

94
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 81 is calibrated to 94 on the published index scale (record calibration 2026-08-02).

Ownership

Clinical GenomicsOrganization
96 followers123 public repossince Jan 2014

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publishTags
PyPIscout-browser4.114.02,38019510 days agoacmgbeaconcancerclingen-cgc-viccclinvarcnvcoveragednafusiongenome-visualisationlrsmatchmaker-exchangeogmoutlierspanelpanelappphenopacketrnasmasnvstrsvvariant-rankingvariant-triagevariantsvcfweswgswts

Metrics by category

Vitality

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

98Exceptional · 21% of overall

Development activity

96Exceptional
How it's scored
36/36Push recency — last push 1 days ago
31.8/36Commit cadence — 46/52 weeks with commits
18/18Commit volume — 365 commits in the last year
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 23 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year365
human_commit_share1
days_since_last_push1
active_weeks_last_year46

Release discipline

100Exceptional
How it's scored
27/27Ships releases — 100 releases published
36/36Release recency — latest release 10 days ago
27/27Release cadence — a release every ~12.7 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count100
latest_release_tagv4.114.0
releases_from_tagsno
days_since_latest_release10
mean_days_between_releases12.7
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?

64Moderate · 17% of overall

Popularity & adoption

57Moderate
How it's scored
36.6/60Stars — 181 stars
14.2/25Forks — 51 forks
5.8/15Watchers — 12 watchers
Inputs used
forks51
stars181
watchers12
growth_stateorganic
growth_factor_pct100

Community health

77Good
How it's scored
22.5/22.5README
22.5/22.5License — recognized license (BSD-3-Clause)
18/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
6.3/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges3
has_contributingyes
has_issue_templateno
has_code_of_conductno
readme_badge_servicesshields.io
has_pull_request_templateyes

Ecosystem adoption (downloads)

56Moderate
How it's scored
45/80Monthly downloads — 2,380 downloads/month across pypi
0/20Registry dependents — not reported by this ecosystem
Inputs used
packagesscout-browser
dependents—
ecosystemspypi
total_downloads—
monthly_downloads2,380
unverified_packages_excluded—
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?

80Excellent · 23% of overall

Maintainer resilience (bus factor)

63Moderate
How it's scored
25.2/54Bus factor — 2 contributor(s) cover half of all commits
14/22.5Commit distribution — top contributor authored 38% of commits
13.5/13.5Contributor breadth — 33 contributors
10/10OpenSSF Scorecard: Contributors — project has 15 contributing companies or organizations
Inputs used
bus_factor2
contributors_sampled33
top_contributor_share0.377

Issue & PR responsiveness

94Exceptional
How it's scored
38.9/42Issue resolution — 93% of issues closed
27.6/30PR acceptance — 2,766/3,010 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
15/15OpenSSF Scorecard: Code-Review — all changesets reviewed
Inputs used
merged_prs2,766
open_issues247
closed_issues3,134
prs_merged_7d7
prs_decided_7d7
prs_merged_30d19
prs_decided_30d19
issue_closed_ratio0.927
closed_unmerged_prs244
first_time_authors_30d0
first_time_prs_merged_30d0
first_time_prs_decided_30d0
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

69Good
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain
14.3/25Owner reach — 96 followers of Clinical-Genomics
25/25Track record — 123 public repos, account ~12 yr old
Inputs used
followers96
owner_typeOrganization
is_verifiedno
owner_loginClinical-Genomics
public_repos123
account_age_days4,622

Package maintenance

100Exceptional
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
35/35Publish recency — latest publish 10 days ago
20/20Version history — 195 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagesscout-browser
ecosystemspypi
any_deprecatedno
min_days_since_publish10

Engineering Quality

Are baseline engineering and documentation practices in place?

96Exceptional · 19% of overall

Engineering practices

100Exceptional
How it's scored
24/24CI workflows — 9 workflow(s)
24/24Tests present
16/16Linter config — pyproject.toml ([tool.ruff], [tool.black], [tool.isort])
9.6/9.6Pre-commit hooks
6.4/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 30 out of 30 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

90Excellent
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — https://clinical-genomics.github.io/scout
10/10Repository description
0/10Topics
10/10Wiki
Inputs used
topics—
has_wikiyes
homepagehttps://clinical-genomics.github.io/scout
docs_sitehttps://clinical-genomics.github.io/scout
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

67Good · 16% of overall

Security posture

65Good
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 — 30 out of 30 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
7.5/7.5Code-Review — all changesets reviewed
2.5/2.5Contributors — project has 15 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
7.5/7.5Maintained — 30 commit(s) and 23 issue activity found in the last 90 days -- score normalized to 10
5/5Packaging — packaging workflow detected
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
5/5SAST — SAST tool is run on all commits
2/5Security-Policy — security policy file detected
0/7.5Signed-Releases — no data
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
6.8/7.5Vulnerabilities — 1 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate6.5
Excluded from scoring (no data or not applicable): Branch-Protection, Signed-Releases. Remaining weights renormalized.

Dependency advisories

76Good
How it's scored
11.5/35Direct dependencies free of known advisories — 1 affected: pdfkit 1.0.0 (high 8.4)
25/25Indirect dependencies free of known advisories — no indirect dependency carries a known advisory
40/40No advisories left outstanding — no advisory has been public longer than 90 days
Inputs used
sourceosv
advisories2
affected_packages1
assessed_packages80
unassessed_packages0
affected_by_severityhigh 1
direct_affected_packages1
Matched the pypi:scout-browser@4.114.0 runtime dependency closure — what installing the published package pulls in — 80 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.

53Moderate · 4% of overall

Agent context & guidance

40Weak
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
40/40Legible commit history — 100 of 100 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtno
llms_txt_url—
legible_history_share1
agent_instruction_files—
agent_instruction_max_bytes—

Verify loop (build / test / typecheck)

61Moderate
How it's scored
18/18One-command bootstrap — Makefile
22/22Automated tests
11/11Lint / format config — pyproject.toml ([tool.ruff], [tool.black], [tool.isort])
0/11Static type checking
10/10Reproducible environment — Dockerfile, lockfile
0/10Demonstrated agent practice — no agent-authored commits among the last 100
0/8Automated maintenance — no automated dependency updates observed
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfilesuv.lock
has_dockerfileyes
typed_languageno
bootstrap_filesMakefile
has_devcontainerno
has_linter_configyes
typecheck_configs—
agent_commit_share0
toolchain_manifests—
dependency_bot_commit_share0

Code legibility for models

55Moderate
How it's scored
0/45Type-checkable code — HTML without a type-check config
54.7/55Manageable file sizes — 3/580 source files over 60KB
Inputs used
primary_languageHTML
largest_source_bytes79,453
source_files_sampled580
oversized_source_files3

Key facts

181GitHub stars
33contributors
365commits, last 12 months
1days since last push
100releases
2bus factor
247open issues
PyPIpackage ecosystems

Data collection warnings

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
  • Star history carried forward from 2026-07-09: GitHub restricted the stargazers API to repository admins, so it can no longer be collected. The repository has 181 stars today.

More detail

Star and fork history 179 ★ / 51 ⇿
179Stars
51Forks
98Releases

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 2026-07-09. 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.

040801201602001795162015-012020-102026-07
Major 0Minor 1Patch 41

Each point covers 11 days.

OpenSSF Scorecard 6.5 / 10
6.5aggregate

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 17:53 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-Tests30 out of 30 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
10Code-Reviewall changesets reviewed
10Contributorsproject has 15 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained30 commit(s) and 23 issue activity found in the last 90 days -- score normalized to 10
10Packagingpackaging workflow detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
10SASTSAST tool is run on all commits
4Security-Policysecurity policy file detected
n/aSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
9Vulnerabilities1 existing vulnerabilities detected
Direct dependencies 36
RegistryPackageVersion constraintManifest
PyPIwerkzeug—pyproject.toml
PyPIFlask>=2.0pyproject.toml
PyPIFlask-Bootstrap—pyproject.toml
PyPIFlask-CORS—pyproject.toml
PyPIpath.py—pyproject.toml
PyPImarkdown—pyproject.toml
PyPIWTForms—pyproject.toml
PyPIFlask-WTF—pyproject.toml
PyPIFlask-Mail—pyproject.toml
PyPIcoloredlogs—pyproject.toml
PyPIquery_phenomizer—pyproject.toml
PyPIFlask-Babel>=3pyproject.toml
PyPIlivereload>=2.7pyproject.toml
PyPItornado>=6.4.1pyproject.toml
PyPIpython-dateutil—pyproject.toml
PyPIpymongo—pyproject.toml
PyPIpathlib—pyproject.toml
PyPIpdfkit—pyproject.toml
PyPIphenopackets—pyproject.toml
PyPIxlsxwriter—pyproject.toml
PyPIclick—pyproject.toml
PyPIcryptography—pyproject.toml
PyPIdefusedxml—pyproject.toml
PyPIimportlib_resources—pyproject.toml
PyPIauthlib—pyproject.toml
PyPIflask-login—pyproject.toml
PyPIcyvcf2—pyproject.toml
PyPIconfigobj—pyproject.toml
PyPIped_parser—pyproject.toml
PyPIpydantic>=2pyproject.toml
PyPIPyYaml>=5.1pyproject.toml
PyPIintervaltree==3.0.2pyproject.toml
PyPIanytree—pyproject.toml
PyPItabulate—pyproject.toml
PyPIflask-ldap3-login>=1.0.2pyproject.toml
PyPIchanjo-report>=4.12.2pyproject.toml
All dependencies 122

Full resolved dependency set from the GitHub dependency graph: 36 direct and 86 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
PyPIanytree2.13.0direct
PyPIauthlib1.8.0direct
PyPIchanjo-report4.12.2direct
PyPIclick8.5.0direct
PyPIcoloredlogs15.0.1direct
PyPIconfigobj5.0.9direct
PyPIcryptography50.0.1direct
PyPIcyvcf20.34.0direct
PyPIdefusedxml0.7.1direct
PyPIflask3.1.3direct
PyPIflask-babel4.0.0direct
PyPIflask-bootstrap3.3.7.1direct
PyPIflask-cors6.0.5direct
PyPIflask-ldap3-login1.0.2direct
PyPIflask-login0.7.0.dev0direct
PyPIflask-mail0.10.0direct
PyPIflask-wtf1.3.0direct
PyPIimportlib-resources7.1.0direct
PyPIintervaltree3.0.2direct
PyPIlivereload2.7.1direct
PyPImarkdown3.10.3direct
PyPIpath-py12.5.0direct
PyPIpathlib1.0.1direct
PyPIpdfkit1.0.0direct
PyPIped-parser1.6.6direct
PyPIphenopackets2.0.2.post5direct
PyPIpydantic2.13.5direct
PyPIpymongo4.17.0direct
PyPIpython-dateutil2.9.0.post0direct
PyPIpyyaml6.0.3direct
PyPIquery-phenomizer1.2.1direct
PyPItabulate0.10.0direct
PyPItornado6.5.8direct
PyPIwerkzeug3.1.8direct
PyPIwtforms3.2.2direct
PyPIxlsxwriter3.2.9direct
PyPIannotated-types0.8.0indirect
PyPIbabel2.18.0indirect
PyPIbackrefs8.0indirect
PyPIblack26.5.1indirect
PyPIblinker1.9.0indirect
PyPIcertifi2026.7.22indirect
PyPIcffi2.1.1indirect
PyPIchanjo4.9.1indirect
PyPIcharset-normalizer3.5.1indirect
PyPIcolorama0.4.6indirect
PyPIcoverage7.16.0indirect
PyPIdnspython2.8.0indirect
PyPIdominate2.9.1indirect
PyPIexceptiongroup1.3.1indirect
PyPIflake87.3.0indirect
PyPIflask-debugtoolbar0.16.0indirect
PyPIflask-sqlalchemy3.1.1indirect
PyPIghp-import2.1.0indirect
PyPIgreenlet3.5.5indirect
PyPIhumanfriendly10.0indirect
PyPIidna3.19indirect
PyPIimportlib-metadata9.0.1indirect
PyPIiniconfig2.3.0indirect
PyPIinvoke3.0.3indirect
PyPIisort9.0.1indirect
PyPIitsdangerous2.2.0indirect
PyPIjinja23.1.6indirect
PyPIjoserfc1.7.5indirect
PyPIldap32.9.1indirect
PyPIlxml6.1.2indirect
PyPImarkdown-include0.8.1indirect
PyPImarkupsafe3.0.3indirect
PyPImccabe0.7.0indirect
PyPImergedeep1.3.4indirect
PyPImkdocs1.6.1indirect
PyPImkdocs-get-deps0.2.2indirect
PyPImkdocs-material9.7.7indirect
PyPImkdocs-material-extensions1.3.1indirect
PyPImongomock4.3.0indirect
PyPImypy-extensions1.1.0indirect
PyPInumpy2.2.6indirect
PyPInumpy2.4.6indirect
PyPInumpy2.5.2indirect
PyPIpackaging26.3indirect
PyPIpaginate0.5.7indirect
PyPIpath17.1.1indirect
PyPIpathspec1.1.1indirect
PyPIplatformdirs4.11.6indirect
PyPIpluggy1.6.0indirect
PyPIprotobuf6.33.6indirect
PyPIpyasn10.6.4indirect
PyPIpycodestyle2.14.0indirect
PyPIpycparser3.0indirect
PyPIpydantic-core2.46.5indirect
PyPIpyflakes3.4.0indirect
PyPIpygments2.21.0indirect
PyPIpymdown-extensions11.0.2indirect
PyPIpymysql1.2.0indirect
PyPIpyreadline33.5.6indirect
PyPIpyscss1.4.0indirect
PyPIpytest9.1.1indirect
PyPIpytest-cov7.1.0indirect
PyPIpytest-flask1.3.0indirect
PyPIpytest-mock3.15.1indirect
PyPIpytest-test-groups1.2.1indirect
PyPIpytokens0.4.1indirect
PyPIpytz2026.3.post1indirect
PyPIpyyaml-env-tag1.1indirect
PyPIrequests2.34.2indirect
PyPIresponses0.26.3indirect
PyPIruff0.16.5indirect
PyPIscout-browser4.114.0indirect
PyPIsentinels1.1.1indirect
PyPIsix1.17.0indirect
PyPIsortedcontainers2.4.0indirect
PyPIsqlalchemy2.0.52indirect
PyPIsqlservice3.1.0indirect
PyPItoml0.10.2indirect
PyPItomli2.4.1indirect
PyPItoolz1.1.0indirect
PyPItyping-extensions4.16.0indirect
PyPItyping-inspection0.4.4indirect
PyPIurllib32.7.0indirect
PyPIvisitor0.1.3indirect
PyPIwatchdog6.0.0indirect
PyPIzipp4.1.0indirect
Dependency advisories 1

Installing pypi:scout-browser@4.114.0 pulls in 80 packages, direct and transitive: 1 carry known advisories, of which 1 are direct dependencies.

PackageVersionRelationSeverityAdvisoriesFixed in
pdfkit1.0.0directhigh2—

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

Feedback

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.