Software health reportschema 0.23.0 · metrics 2.10.0 · 2026-07-21 20:45 UTC

Clinical-Genomics / scout

VCF visualization interface

HTML · PythonBSD-3-Clause★ 179 stars⑂ 51 forkssince Oct 2014View on GitHub ↗

KindNetwork serviceLibraryCommand-line toolhow this is determined

Clinical-Genomics/scout holds a health index of 95 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.

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.

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)

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 82 is calibrated to 95 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

Registry	Package	Version	Downloads / mo	Versions	Last publish	Tags
PyPI	scout-browser	4.113.3	-	194	6 days ago	acmg beacon cancer clingen-cgc-vicc clinvar cnv coverage dna fusion genome-visualisation lrs matchmaker-exchange ogm outliers panel panelapp phenopacket rna sma snv str sv variant-ranking variant-triage variants vcf wes wgs wts

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

36/36	Push recency — last push 1 days ago
32.5/36	Commit cadence — 47/52 weeks with commits
18/18	Commit volume — 376 commits in the last year
10/10	OpenSSF Scorecard: Maintained — 30 commit(s) and 27 issue activity found in the last 90 days -- score normalized to 10

Inputs used

commits_last_year	376
human_commit_share	1
days_since_last_push	1
active_weeks_last_year	47

Release discipline

100Exceptional

How it's scored

27/27	Ships releases — 100 releases published
36/36	Release recency — latest release 6 days ago
27/27	Release cadence — a release every ~9.1 days
0/10	OpenSSF Scorecard: Signed-Releases — no data

Inputs used

releases_count	100
latest_release_tag	v4.113.3
releases_from_tags	no
days_since_latest_release	6
mean_days_between_releases	9.1

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?

66Good · 17% of overall

Popularity & adoption

57Moderate

How it's scored

36.5/60	Stars — 179 stars
14.2/25	Forks — 51 forks
6/15	Watchers — 13 watchers

Inputs used

forks	51
stars	179
watchers	13
growth_state	organic
growth_factor_pct	100

Community health

77Good

How it's scored

22.5/22.5	README
22.5/22.5	License — recognized license (BSD-3-Clause)
18/18	CONTRIBUTING guide
0/13.5	Code of conduct
0/7.2	Issue template
6.3/6.3	PR template

Inputs used

has_readme	yes
has_license	yes
readme_badges	—
has_contributing	yes
has_issue_template	no
has_code_of_conduct	no
readme_badge_services	—
has_pull_request_template	yes

Sustainability & Governance

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

84Excellent · 23% of overall

Maintainer resilience (bus factor)

63Moderate

How it's scored

25.2/54	Bus factor — 2 contributor(s) cover half of all commits
14/22.5	Commit distribution — top contributor authored 38% of commits
13.5/13.5	Contributor breadth — 33 contributors
10/10	OpenSSF Scorecard: Contributors — project has 15 contributing companies or organizations

Inputs used

bus_factor	2
contributors_sampled	33
top_contributor_share	0.377

Issue & PR responsiveness

92Excellent

How it's scored

38.9/42	Issue resolution — 93% of issues closed
27.6/30	PR acceptance — 2,732/2,973 decided PRs merged
0/13	Newcomer PR acceptance — no first-time contributor's PR decided in 30d
13.5/15	OpenSSF Scorecard: Code-Review — Found 29/30 approved changesets -- score normalized to 9

Inputs used

merged_prs	2,732
open_issues	245
closed_issues	3,097
prs_merged_7d	—
prs_decided_7d	—
prs_merged_30d	—
prs_decided_30d	—
issue_closed_ratio	0.927
closed_unmerged_prs	241
first_time_authors_30d	—
first_time_prs_merged_30d	—
first_time_prs_decided_30d	—

Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

87Excellent

How it's scored

30/30	Ownership backing — organization-owned
0/20	Verified domain — verified-domain status not read for this organization
14.3/25	Owner reach — 96 followers of Clinical-Genomics
25/25	Track record — 123 public repos, account ~12 yr old

Inputs used

followers	96
owner_type	Organization
is_verified	—
owner_login	Clinical-Genomics
public_repos	123
account_age_days	4,570

Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.

Package maintenance

100Exceptional

How it's scored

25/25	Published & resolvable — 1 package(s) on pypi
35/35	Publish recency — latest publish 6 days ago
20/20	Version history — 194 published versions
20/20	Not deprecated — active, not deprecated or yanked

Inputs used

packages	scout-browser
ecosystems	pypi
any_deprecated	no
min_days_since_publish	6

Engineering Quality

Are baseline engineering and documentation practices in place?

96Exceptional · 19% of overall

Engineering practices

100Exceptional

How it's scored

24/24	CI workflows — 9 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 — 30 out of 30 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://clinical-genomics.github.io/scout
10/10	Repository description
0/10	Topics
10/10	Wiki

Inputs used

topics	—
has_wiki	yes
homepage	https://clinical-genomics.github.io/scout
docs_site	https://clinical-genomics.github.io/scout
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?

66Good · 16% of overall

Security posture

65Good

How it's scored

7.5/7.5	Binary-Artifacts — no binaries found in the repo
0/7.5	Branch-Protection — no data
2.5/2.5	CI-Tests — 30 out of 30 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
6.8/7.5	Code-Review — Found 29/30 approved changesets -- score normalized to 9
2.5/2.5	Contributors — project has 15 contributing companies or organizations
10/10	Dangerous-Workflow — no dangerous workflow patterns detected
0/7.5	Dependency-Update-Tool — no 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 27 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
5/5	SAST — SAST tool is run on all commits
2/5	Security-Policy — security policy file detected
0/7.5	Signed-Releases — no data
0/7.5	Token-Permissions — detected GitHub workflow tokens with excessive permissions
6.8/7.5	Vulnerabilities — 1 existing vulnerabilities detected

Inputs used

source	openssf_scorecard
checks_evaluated	16
scorecard_version	v5.5.0
checks_inconclusive	2
scorecard_aggregate	6.4

Excluded from scoring (no data or not applicable): Branch-Protection, Signed-Releases. Remaining weights renormalized.

Dependency advisories

69Good

How it's scored

11.5/35	Direct dependencies free of known advisories — 1 affected: pdfkit 1.0.0 (high 8.4)
0/25	Indirect dependencies free of known advisories — transitive set not separable from development and test dependencies in this scope
40/40	No advisories left outstanding — no advisory has been public longer than 90 days

Inputs used

source	osv
advisories	2
affected_packages	1
assessed_packages	118
unassessed_packages	0
affected_by_severity	high 1
direct_affected_packages	1

Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories. Remaining weights renormalized. Matched 118 resolved dependencies against OSV. 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? 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

0/45	Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15	Machine-readable docs (llms.txt)
40/40	Legible commit history — 100 of 100 human commits state their intent (structured subject or explanatory body)

Inputs used

has_llms_txt	no
llms_txt_url	—
legible_history_share	1
agent_instruction_files	—
agent_instruction_max_bytes	—

Verify loop (build / test / typecheck)

61Moderate

How it's scored

18/18	One-command bootstrap — Makefile
22/22	Automated tests
11/11	Lint / format config
0/11	Static type checking
10/10	Reproducible environment — Dockerfile, lockfile
0/10	Demonstrated agent practice — no agent-authored commits among the last 100
0/8	Automated maintenance — no automated dependency updates observed
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	uv.lock
has_dockerfile	yes
typed_language	no
bootstrap_files	Makefile
has_devcontainer	no
has_linter_config	yes
typecheck_configs	—
agent_commit_share	0
toolchain_manifests	—
dependency_bot_commit_share	0

Code legibility for models

55Moderate

How it's scored

0/45	Type-checkable code — HTML without a type-check config
54.7/55	Manageable file sizes — 3/566 source files over 60KB

Inputs used

primary_language	HTML
largest_source_bytes	79,453
source_files_sampled	566
oversized_source_files	3

Key facts

179GitHub stars

33contributors

376commits, last 12 months

1days since last push

100releases

2bus factor

245open issues

PyPIpackage ecosystems

Data collection warnings

deps.dev does not index pypi:scout-browser@4.113.3; advisories assessed against the repository dependency graph instead

More detail

Star and fork history 179 ★ / 51 ⇿

179Stars

51Forks

99Releases

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.

Major 0Minor 1Patch 42

Each point covers 11 days.

OpenSSF Scorecard 6.4 / 10

6.4aggregate

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 · 2026-07-21 20:44 UTC

10	Binary-Artifacts	no binaries found in the repo
n/a	Branch-Protection	internal 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
10	CI-Tests	30 out of 30 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
9	Code-Review	Found 29/30 approved changesets -- score normalized to 9
10	Contributors	project has 15 contributing companies or organizations
10	Dangerous-Workflow	no dangerous workflow patterns detected
0	Dependency-Update-Tool	no update tool detected
0	Fuzzing	project is not fuzzed
10	License	license file detected
10	Maintained	30 commit(s) and 27 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
10	SAST	SAST tool is run on all commits
4	Security-Policy	security policy file detected
n/a	Signed-Releases	no releases found
0	Token-Permissions	detected GitHub workflow tokens with excessive permissions
9	Vulnerabilities	1 existing vulnerabilities detected

Direct dependencies 36

Registry	Package	Version constraint	Manifest
PyPI	werkzeug	`—`	pyproject.toml
PyPI	Flask	`>=2.0`	pyproject.toml
PyPI	Flask-Bootstrap	`—`	pyproject.toml
PyPI	Flask-CORS	`—`	pyproject.toml
PyPI	path.py	`—`	pyproject.toml
PyPI	markdown	`—`	pyproject.toml
PyPI	WTForms	`—`	pyproject.toml
PyPI	Flask-WTF	`—`	pyproject.toml
PyPI	Flask-Mail	`—`	pyproject.toml
PyPI	coloredlogs	`—`	pyproject.toml
PyPI	query_phenomizer	`—`	pyproject.toml
PyPI	Flask-Babel	`>=3`	pyproject.toml
PyPI	livereload	`>=2.7`	pyproject.toml
PyPI	tornado	`>=6.4.1`	pyproject.toml
PyPI	python-dateutil	`—`	pyproject.toml
PyPI	pymongo	`—`	pyproject.toml
PyPI	pathlib	`—`	pyproject.toml
PyPI	pdfkit	`—`	pyproject.toml
PyPI	phenopackets	`—`	pyproject.toml
PyPI	xlsxwriter	`—`	pyproject.toml
PyPI	click	`—`	pyproject.toml
PyPI	cryptography	`—`	pyproject.toml
PyPI	defusedxml	`—`	pyproject.toml
PyPI	importlib_resources	`—`	pyproject.toml
PyPI	authlib	`—`	pyproject.toml
PyPI	flask-login	`—`	pyproject.toml
PyPI	cyvcf2	`—`	pyproject.toml
PyPI	configobj	`—`	pyproject.toml
PyPI	ped_parser	`—`	pyproject.toml
PyPI	pydantic	`>=2`	pyproject.toml
PyPI	PyYaml	`>=5.1`	pyproject.toml
PyPI	intervaltree	`==3.0.2`	pyproject.toml
PyPI	anytree	`—`	pyproject.toml
PyPI	tabulate	`—`	pyproject.toml
PyPI	flask-ldap3-login	`>=1.0.2`	pyproject.toml
PyPI	chanjo-report	`>=4.12.2`	pyproject.toml

All dependencies 118

Full resolved dependency set from the GitHub dependency graph: 36 direct and 82 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

Registry	Package	Version	Relation
PyPI	anytree	`2.13.0`	direct
PyPI	authlib	`1.7.2`	direct
PyPI	chanjo-report	`4.12.2`	direct
PyPI	click	`8.4.2`	direct
PyPI	coloredlogs	`15.0.1`	direct
PyPI	configobj	`5.0.9`	direct
PyPI	cryptography	`49.0.0`	direct
PyPI	cyvcf2	`0.34.0`	direct
PyPI	defusedxml	`0.7.1`	direct
PyPI	flask	`3.1.3`	direct
PyPI	flask-babel	`4.0.0`	direct
PyPI	flask-bootstrap	`3.3.7.1`	direct
PyPI	flask-cors	`6.0.5`	direct
PyPI	flask-ldap3-login	`1.0.2`	direct
PyPI	flask-login	`0.7.0.dev0`	direct
PyPI	flask-mail	`0.10.0`	direct
PyPI	flask-wtf	`1.3.0`	direct
PyPI	importlib-resources	`7.1.0`	direct
PyPI	intervaltree	`3.0.2`	direct
PyPI	livereload	`2.7.1`	direct
PyPI	markdown	`3.10.2`	direct
PyPI	path-py	`12.5.0`	direct
PyPI	pathlib	`1.0.1`	direct
PyPI	pdfkit	`1.0.0`	direct
PyPI	ped-parser	`1.6.6`	direct
PyPI	phenopackets	`2.0.2.post5`	direct
PyPI	pydantic	`2.13.4`	direct
PyPI	pymongo	`4.17.0`	direct
PyPI	python-dateutil	`2.9.0.post0`	direct
PyPI	pyyaml	`6.0.3`	direct
PyPI	query-phenomizer	`1.2.1`	direct
PyPI	tabulate	`0.10.0`	direct
PyPI	tornado	`6.5.7`	direct
PyPI	werkzeug	`3.1.8`	direct
PyPI	wtforms	`3.2.2`	direct
PyPI	xlsxwriter	`3.2.9`	direct
PyPI	annotated-types	`0.7.0`	indirect
PyPI	babel	`2.18.0`	indirect
PyPI	backrefs	`7.0`	indirect
PyPI	black	`26.5.1`	indirect
PyPI	blinker	`1.9.0`	indirect
PyPI	certifi	`2026.6.17`	indirect
PyPI	cffi	`2.1.0`	indirect
PyPI	chanjo	`4.9.1`	indirect
PyPI	charset-normalizer	`3.4.9`	indirect
PyPI	colorama	`0.4.6`	indirect
PyPI	coverage	`7.15.1`	indirect
PyPI	dnspython	`2.8.0`	indirect
PyPI	dominate	`2.9.1`	indirect
PyPI	exceptiongroup	`1.3.1`	indirect
PyPI	flask-debugtoolbar	`0.16.0`	indirect
PyPI	flask-sqlalchemy	`3.1.1`	indirect
PyPI	ghp-import	`2.1.0`	indirect
PyPI	greenlet	`3.5.3`	indirect
PyPI	humanfriendly	`10.0`	indirect
PyPI	idna	`3.18`	indirect
PyPI	importlib-metadata	`9.0.0`	indirect
PyPI	iniconfig	`2.3.0`	indirect
PyPI	invoke	`3.0.3`	indirect
PyPI	isort	`8.0.1`	indirect
PyPI	itsdangerous	`2.2.0`	indirect
PyPI	jinja2	`3.1.6`	indirect
PyPI	joserfc	`1.7.3`	indirect
PyPI	ldap3	`2.9.1`	indirect
PyPI	lxml	`6.1.1`	indirect
PyPI	markdown-include	`0.8.1`	indirect
PyPI	markupsafe	`3.0.3`	indirect
PyPI	mergedeep	`1.3.4`	indirect
PyPI	mkdocs	`1.6.1`	indirect
PyPI	mkdocs-get-deps	`0.2.2`	indirect
PyPI	mkdocs-material	`9.7.6`	indirect
PyPI	mkdocs-material-extensions	`1.3.1`	indirect
PyPI	mongomock	`4.3.0`	indirect
PyPI	mypy-extensions	`1.1.0`	indirect
PyPI	numpy	`2.2.6`	indirect
PyPI	numpy	`2.4.6`	indirect
PyPI	numpy	`2.5.1`	indirect
PyPI	packaging	`26.2`	indirect
PyPI	paginate	`0.5.7`	indirect
PyPI	path	`17.1.1`	indirect
PyPI	pathspec	`1.1.1`	indirect
PyPI	platformdirs	`4.10.0`	indirect
PyPI	pluggy	`1.6.0`	indirect
PyPI	protobuf	`6.33.6`	indirect
PyPI	pyasn1	`0.6.4`	indirect
PyPI	pycparser	`3.0`	indirect
PyPI	pydantic-core	`2.46.4`	indirect
PyPI	pygments	`2.20.0`	indirect
PyPI	pymdown-extensions	`11.0.1`	indirect
PyPI	pymysql	`1.2.0`	indirect
PyPI	pyreadline3	`3.5.6`	indirect
PyPI	pyscss	`1.4.0`	indirect
PyPI	pytest	`9.1.1`	indirect
PyPI	pytest-cov	`7.1.0`	indirect
PyPI	pytest-flask	`1.3.0`	indirect
PyPI	pytest-mock	`3.15.1`	indirect
PyPI	pytest-test-groups	`1.2.1`	indirect
PyPI	pytokens	`0.4.1`	indirect
PyPI	pytz	`2026.2`	indirect
PyPI	pyyaml-env-tag	`1.1`	indirect
PyPI	requests	`2.34.2`	indirect
PyPI	responses	`0.26.2`	indirect
PyPI	ruff	`0.15.21`	indirect
PyPI	scout-browser	`4.113.3`	indirect
PyPI	sentinels	`1.1.1`	indirect
PyPI	six	`1.17.0`	indirect
PyPI	sortedcontainers	`2.4.0`	indirect
PyPI	sqlalchemy	`2.0.51`	indirect
PyPI	sqlservice	`3.1.0`	indirect
PyPI	toml	`0.10.2`	indirect
PyPI	tomli	`2.4.1`	indirect
PyPI	toolz	`1.1.0`	indirect
PyPI	typing-extensions	`4.16.0`	indirect
PyPI	typing-inspection	`0.4.2`	indirect
PyPI	urllib3	`2.7.0`	indirect
PyPI	visitor	`0.1.3`	indirect
PyPI	watchdog	`6.0.0`	indirect
PyPI	zipp	`4.1.0`	indirect

Dependency advisories 1

This repository publishes no package the index resolves, so its own dependency graph was assessed — 118 packages, which also include development and test pins that never ship: 1 carry known advisories, of which 1 are direct.

Package	Version	Relation	Severity	Advisories	Fixed in
pdfkit	`1.0.0`	direct	high	2	—

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.

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 v0.23.0 — full methodology · metrics wiki.

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

Software health index

Score profile

Ownership

Package ecosystems

Metrics by category

Key facts

Data collection warnings

More detail

Feedback

Related records