Public record
Software health reportschema 0.23.0 · metrics 1.13.0 · 2026-07-21 20:45 UTC

Clinical-Genomics / scout

VCF visualization interface

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

Clinical-Genomics/scout holds a health index of 82 out of 100, placing it in the Good 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.

82
overall / 100
Good

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.

82
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

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-browser4.113.3-1946 days agoacmgbeaconcancerclingen-cgc-viccclinvarcnvcoveragednafusiongenome-visualisationlrsmatchmaker-exchangeogmoutlierspanelpanelappphenopacketrnasmasnvstrsvvariant-rankingvariant-triagevariantsvcfweswgswts

Metrics by category

Vitality

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

98Excellent · 22% of overall

Development activity

96Excellent
How it's scored
36/36Push recency — last push 1 days ago
32.5/36Commit cadence — 47/52 weeks with commits
18/18Commit volume — 376 commits in the last year
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 27 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year376
human_commit_share1
days_since_last_push1
active_weeks_last_year47

Release discipline

100Excellent
How it's scored
27/27Ships releases — 100 releases published
36/36Release recency — latest release 6 days ago
27/27Release cadence — a release every ~9.1 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count100
latest_release_tagv4.113.3
releases_from_tagsno
days_since_latest_release6
mean_days_between_releases9.1
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?

66Moderate · 18% of overall

Popularity & adoption

57Moderate
How it's scored
36.5/60Stars — 179 stars
14.2/25Forks — 51 forks
6/15Watchers — 13 watchers
Inputs used
forks51
stars179
watchers13
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
has_contributingyes
has_issue_templateno
has_code_of_conductno
has_pull_request_templateyes

Sustainability & Governance

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

79Good · 24% 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

92Excellent
How it's scored
43.3/46.8Issue resolution — 93% of issues closed
35.1/38.3PR acceptance — 2,732/2,973 decided PRs merged
13.5/15OpenSSF Scorecard: Code-Review — Found 29/30 approved changesets -- score normalized to 9
Inputs used
merged_prs2,732
open_issues245
closed_issues3,097
issue_closed_ratio0.927
closed_unmerged_prs241

Ownership & stewardship

69Moderate
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_verified—
owner_loginClinical-Genomics
public_repos123
account_age_days4,570

Package maintenance

100Excellent
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
35/35Publish recency — latest publish 6 days ago
20/20Version history — 194 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagesscout-browser
ecosystemspypi
any_deprecatedno
min_days_since_publish6

Engineering Quality

Are baseline engineering and documentation practices in place?

96Excellent · 20% of overall

Engineering practices

100Excellent
How it's scored
24/24CI workflows — 9 workflow(s)
24/24Tests present
16/16Linter config
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
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

66Moderate · 16% of overall

Security posture

65Moderate
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
6.8/7.5Code-Review — Found 29/30 approved changesets -- score normalized to 9
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 27 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_aggregate6.4
Excluded from scoring (no data or not applicable): branch_protection, signed_releases. Remaining weights renormalized.

Dependency advisories

69Moderate
How it's scored
11.5/35Direct dependencies free of known advisories — 1 affected: pdfkit 1.0.0 (high 8.4)
0/25Indirect dependencies free of known advisories — transitive set not separable from development and test dependencies in this scope
40/40No advisories left outstanding — no advisory has been public longer than 90 days
Inputs used
sourceosv
advisories2
affected_packages1
assessed_packages118
unassessed_packages0
affected_by_severityhigh 1
direct_affected_packages1
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? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score.

53Moderate · 0% of overall

Agent context & guidance

40At risk
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
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
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 — 3/566 source files over 60KB
Inputs used
primary_languageHTML
largest_source_bytes79,453
source_files_sampled566
oversized_source_files3

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.

040801201602001795162015-012020-102026-07
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

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
9Code-ReviewFound 29/30 approved changesets -- score normalized to 9
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 27 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 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.

RegistryPackageVersionRelation
PyPIanytree2.13.0direct
PyPIauthlib1.7.2direct
PyPIchanjo-report4.12.2direct
PyPIclick8.4.2direct
PyPIcoloredlogs15.0.1direct
PyPIconfigobj5.0.9direct
PyPIcryptography49.0.0direct
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
PyPImarkdown3.10.2direct
PyPIpath-py12.5.0direct
PyPIpathlib1.0.1direct
PyPIpdfkit1.0.0direct
PyPIped-parser1.6.6direct
PyPIphenopackets2.0.2.post5direct
PyPIpydantic2.13.4direct
PyPIpymongo4.17.0direct
PyPIpython-dateutil2.9.0.post0direct
PyPIpyyaml6.0.3direct
PyPIquery-phenomizer1.2.1direct
PyPItabulate0.10.0direct
PyPItornado6.5.7direct
PyPIwerkzeug3.1.8direct
PyPIwtforms3.2.2direct
PyPIxlsxwriter3.2.9direct
PyPIannotated-types0.7.0indirect
PyPIbabel2.18.0indirect
PyPIbackrefs7.0indirect
PyPIblack26.5.1indirect
PyPIblinker1.9.0indirect
PyPIcertifi2026.6.17indirect
PyPIcffi2.1.0indirect
PyPIchanjo4.9.1indirect
PyPIcharset-normalizer3.4.9indirect
PyPIcolorama0.4.6indirect
PyPIcoverage7.15.1indirect
PyPIdnspython2.8.0indirect
PyPIdominate2.9.1indirect
PyPIexceptiongroup1.3.1indirect
PyPIflask-debugtoolbar0.16.0indirect
PyPIflask-sqlalchemy3.1.1indirect
PyPIghp-import2.1.0indirect
PyPIgreenlet3.5.3indirect
PyPIhumanfriendly10.0indirect
PyPIidna3.18indirect
PyPIimportlib-metadata9.0.0indirect
PyPIiniconfig2.3.0indirect
PyPIinvoke3.0.3indirect
PyPIisort8.0.1indirect
PyPIitsdangerous2.2.0indirect
PyPIjinja23.1.6indirect
PyPIjoserfc1.7.3indirect
PyPIldap32.9.1indirect
PyPIlxml6.1.1indirect
PyPImarkdown-include0.8.1indirect
PyPImarkupsafe3.0.3indirect
PyPImergedeep1.3.4indirect
PyPImkdocs1.6.1indirect
PyPImkdocs-get-deps0.2.2indirect
PyPImkdocs-material9.7.6indirect
PyPImkdocs-material-extensions1.3.1indirect
PyPImongomock4.3.0indirect
PyPImypy-extensions1.1.0indirect
PyPInumpy2.2.6indirect
PyPInumpy2.4.6indirect
PyPInumpy2.5.1indirect
PyPIpackaging26.2indirect
PyPIpaginate0.5.7indirect
PyPIpath17.1.1indirect
PyPIpathspec1.1.1indirect
PyPIplatformdirs4.10.0indirect
PyPIpluggy1.6.0indirect
PyPIprotobuf6.33.6indirect
PyPIpyasn10.6.4indirect
PyPIpycparser3.0indirect
PyPIpydantic-core2.46.4indirect
PyPIpygments2.20.0indirect
PyPIpymdown-extensions11.0.1indirect
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
PyPIpytz2026.2indirect
PyPIpyyaml-env-tag1.1indirect
PyPIrequests2.34.2indirect
PyPIresponses0.26.2indirect
PyPIruff0.15.21indirect
PyPIscout-browser4.113.3indirect
PyPIsentinels1.1.1indirect
PyPIsix1.17.0indirect
PyPIsortedcontainers2.4.0indirect
PyPIsqlalchemy2.0.51indirect
PyPIsqlservice3.1.0indirect
PyPItoml0.10.2indirect
PyPItomli2.4.1indirect
PyPItoolz1.1.0indirect
PyPItyping-extensions4.16.0indirect
PyPItyping-inspection0.4.2indirect
PyPIurllib32.7.0indirect
PyPIvisitor0.1.3indirect
PyPIwatchdog6.0.0indirect
PyPIzipp4.1.0indirect
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.

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
{
  "data": {
    "repo": {
      "topics": [],
      "is_fork": false,
      "size_kb": 105933,
      "has_wiki": true,
      "homepage": "https://clinical-genomics.github.io/scout",
      "languages": {
        "CSS": 15752,
        "HTML": 4483618,
        "Python": 3027062,
        "Makefile": 1067,
        "Dockerfile": 1574,
        "JavaScript": 61768
      },
      "pushed_at": "2026-07-20T12:06:05Z",
      "created_at": "2014-10-10T08:44:01Z",
      "owner_type": "Organization",
      "updated_at": "2026-07-15T11:53:27Z",
      "description": "VCF visualization interface",
      "is_archived": false,
      "is_disabled": false,
      "license_spdx": "BSD-3-Clause",
      "default_branch": "main",
      "license_spdx_raw": "BSD-3-Clause",
      "primary_language": "HTML",
      "significant_languages": [
        "HTML",
        "Python"
      ]
    },
    "owner": {
      "blog": "https://clinical.scilifelab.se/",
      "name": "Clinical Genomics",
      "type": "Organization",
      "login": "Clinical-Genomics",
      "company": null,
      "location": "Stockholm, Sweden",
      "followers": 96,
      "avatar_url": "https://avatars.githubusercontent.com/u/6412433?v=4",
      "created_at": "2014-01-15T18:31:13Z",
      "is_verified": null,
      "public_repos": 123,
      "account_age_days": 4570
    },
    "license": {
      "state": "standard",
      "spdx_id": "BSD-3-Clause",
      "raw_spdx": "BSD-3-Clause",
      "file_present": true,
      "scorecard_found": true,
      "profile_has_license": true
    },
    "activity": {
      "releases": [
        {
          "tag": "v4.113.3",
          "kind": "patch",
          "published_at": "2026-07-15T11:55:19Z"
        },
        {
          "tag": "v4.113.2",
          "kind": "patch",
          "published_at": "2026-06-30T15:31:44Z"
        },
        {
          "tag": "v4.113.1",
          "kind": "patch",
          "published_at": "2026-06-29T13:47:04Z"
        },
        {
          "tag": "v4.113",
          "kind": "other",
          "published_at": "2026-06-29T07:52:17Z"
        },
        {
          "tag": "v4.112",
          "kind": "other",
          "published_at": "2026-05-27T06:58:51Z"
        },
        {
          "tag": "v4.111.3",
          "kind": "patch",
          "published_at": "2026-05-12T17:13:27Z"
        },
        {
          "tag": "v4.111.2",
          "kind": "patch",
          "published_at": "2026-05-12T15:15:33Z"
        },
        {
          "tag": "v4.111.1",
          "kind": "patch",
          "published_at": "2026-05-12T12:09:53Z"
        },
        {
          "tag": "v4.111",
          "kind": "other",
          "published_at": "2026-05-11T14:38:16Z"
        },
        {
          "tag": "v4.110",
          "kind": "other",
          "published_at": "2026-04-24T06:24:26Z"
        },
        {
          "tag": "v4.109.3",
          "kind": "patch",
          "published_at": "2026-04-09T10:01:30Z"
        },
        {
          "tag": "v4.109.2",
          "kind": "patch",
          "published_at": "2026-04-08T14:10:00Z"
        },
        {
          "tag": "v4.109.1",
          "kind": "patch",
          "published_at": "2026-04-08T12:43:52Z"
        },
        {
          "tag": "v4.109.0",
          "kind": "minor",
          "published_at": "2026-04-07T13:55:35Z"
        },
        {
          "tag": "v4.108.2",
          "kind": "patch",
          "published_at": "2026-02-26T08:40:39Z"
        },
        {
          "tag": "v4.108.1",
          "kind": "patch",
          "published_at": "2026-02-25T15:20:43Z"
        },
        {
          "tag": "v4.108",
          "kind": "other",
          "published_at": "2026-02-25T13:36:52Z"
        },
        {
          "tag": "v4.107.2",
          "kind": "patch",
          "published_at": "2026-01-14T08:08:24Z"
        },
        {
          "tag": "v4.107.1",
          "kind": "patch",
          "published_at": "2026-01-13T13:10:19Z"
        },
        {
          "tag": "v4.107",
          "kind": "other",
          "published_at": "2026-01-13T09:58:02Z"
        },
        {
          "tag": "v4.106",
          "kind": "other",
          "published_at": "2025-11-13T08:30:32Z"
        },
        {
          "tag": "v4.105.2",
          "kind": "patch",
          "published_at": "2025-10-16T10:08:59Z"
        },
        {
          "tag": "v4.105.1",
          "kind": "patch",
          "published_at": "2025-10-15T10:17:02Z"
        },
        {
          "tag": "v4.104",
          "kind": "other",
          "published_at": "2025-09-03T10:37:00Z"
        },
        {
          "tag": "v4.103.3",
          "kind": "patch",
          "published_at": "2025-07-11T12:15:29Z"
        },
        {
          "tag": "v4.103.2",
          "kind": "patch",
          "published_at": "2025-07-10T08:15:22Z"
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          "headline": "Keep ACMG classification open after submit (#6405)",
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          "headline": "Normalise email/id field to lowercase when using LDAP login (#6407)",
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          "body": "* Normalize new users' emails when created by GUI\n\n* Fix test\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
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          "headline": "Normalize new users' emails when created by GUI (#6406)",
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          "body": "* Fix #6363 - comments accept markdown syntax\n\n* Update changelog PR nr\n\n* Update changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
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          "body": "* Fix links in causatives exported to managed variants format\n\n* Remove debug messages\n\n* Even better fix\n\n* Rename one more\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
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          "headline": "Fix links in causatives exported to managed variants format (#6398)",
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          "body": "…reas (#6390)\n\n* Fix PDF export to support multi-page output\n\n* Remove empty lines\n\n* PR ref in changelog\n\n* Reintroduce textarea text wrapping\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
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          "headline": "Fix editing ACMG comments on reclassify (#6388)",
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          "body": "* Fix #6263 - search for specific simple id/variant id\n\n* Changelog\n\n* maybe actually keep the case query\n\n* better tooltip\n\n* fix according to test\n\n* Fix according to review\n\n* false positive...\n\n* Update scout/adapter/mongo/query.py\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n* \n[…]\nrints/institutes/views.py\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\n\n* Rephrase warning slightly\n\n* and the tooltip similarly\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
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          "body": "* Tooltip with LoqusDB instances description\n\n* PR ref in changelog\n\n* Simplify code\n\n* Safer code, as per review\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
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          "headline": "Tooltip with LoqusDB instances description (#6384)",
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          "body": "* Fix #6374 - add live search option\n\n* right, dash instead of underscore when given directly\n\n* changelog\n\n* another space\n\n* and a handful more\n\n* and another space for those\n\n* wrong type\n\n* minor formatting\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
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          "body": "* Fix colspan for gene variants table - no variants found\n\n* Fix #5005 - extend filters on gene variants page\n\n* attempt to reuse secondary query builder\n\n* Fix #3946 - search SNVs and SVs CADD, gnomAD, SpliceAI, REVEL\n\n* Changelog\n\n* compact filter form: move the conceptually different OMIM genetic\n[…]\ncomment the shared / individual fields in the class for now\n\n* tooltip\n\n* see, copy-paste is hard\n\n* dash style var names in direct html\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
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          "headline": "Gene vars inheritance (#6357)",
          "author_name": "Daniel Nilsson",
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          "body": "* Add 'Has methylation' filter on cases page\n\n* Typo\n\n* Add a test\n\n* Persist has_methylation if case is updated\n\n* Thanks SonarQube\n\n* Updated changelog\n\n* Remove spacing at the beginning\n\n* Rename style and be done with it\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
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          "headline": "Add 'Has methylation' filter on cases page (#6375)",
          "author_name": "Chiara Rasi",
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          "body": "* Methylation badge on cases page\n\n* Update CHANGELOG.md\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
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          "headline": "Methylation badge on cases page (#6373)",
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          "oid": "b29cfe72fde45020ffce5868bd57e8281419244c",
          "body": "* Fix #6295 - filter dark regions/sma page for gene panels\n\n* Add a Clinical HPO Dark link button to the case page\n\n* Move filter, title style\n\n* adjust title\n\n* Format dark panels filter like variants filter collapse\n\n* reorder cards\n\n* formatting\n\n* light mode reset visibility\n\n* reuse part of fun\n[…]\nof tests\n\n* revert import\n\n* Test comments\n\n* Apply suggestion from @northwestwitch\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
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          "headline": "Fix #6295 - filter dark regions/sma page for gene panels (#6353)",
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          "body": "* Only admins can edit collaborators to share cases with\n\n* Fix field reset by non-admin user\n\n* typo\n\n* common function for string values\n\n* Rename the other function\n\n* Nope, like this\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
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          "headline": "Only admins can edit collaborators to share cases with (#6370)",
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          "body": "…to db (#6369)\n\n* send on ccv modifiers to post to db function\n\n* Update changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
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          "headline": "Fixes bug where CCV classification ignores modifiers when submitting …",
          "author_name": "molucorner",
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          "body": "* Enable link to previous ACMG classifications for SV variants\n\n* Simplify\n\n* Add PR ref to changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
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          "headline": "Fix SV ACMG links for previous classifications (#6365)",
          "author_name": "Chiara Rasi",
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          "body": "* Filter variants by gene OMIM disease inheritance\n\n* Forgot changelog\n\n* Add tests\n\n* Better label\n\n* Fix second col style\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
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          "headline": "Filter variants by gene OMIM disease inheritance (#6355)",
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          "body": "* litvar2 links to dbsnp id\n\n* fix changelog\n\n* Display simple deep links for litvar2 on all snp ids\n\n* One is enough\n\n* js script to check for litvar availability\n\n* move variant scripts to components\n\n* no, that hits cors. make a view, and do keep the link on failure to look up\n\n* a bit more docst\n[…]\nad risky for the reward\n\n* break out subfunctions to lower complexity, change a couple of linter style suggestions\n\n* use for-of instead\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
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          "headline": "Litvar links (#6351)",
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          "body": "* Cache per-case genomic info when loading variants\n\n* PR ref in changelog\n\n* No need to cache genes\n\n* Clear case case and persist build-dependent info across cases, as per review\n\n* Actually clear the case cache\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
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          "headline": "Cache per-case genomic info when loading variants (#6350)",
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          "body": "* Work in progress\n\n* New service + tests\n\n* Fix alignment controller and relative tests\n\n* Fixed also align views\n\n* Updated changelog\n\n* Fix import\n\n* some fixed\n\n* Replace with empty string\n\n* Fix other test\n\n* Thanks SonarQube\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Replace Ensembl liftover with Broad API liftover (#6293)",
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          "body": "* Minor release 4.112\n\n* small fix in changelog\n\n* Fixed changelog\n\n* Fixed changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
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          "headline": "Minor release 4.112 (#6323)",
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          "body": "* Fix #6321 - foldable matching variants on variant page\n\n* CHANGELOG\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
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          "headline": "Fix #6321 - foldable matching variants on variant page (#6346)",
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          "body": "* Fix other warnings when loading regions and genes 38\n\n* Fix some more\n\n* final touch\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
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          "headline": "Fix other warnings when loading regions and genes 38 (#6348)",
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          "body": "* Fix time limit in export causatives CLI\n\n* Fix PR ref in changelog\n\n* Trigger tests\n\n* Trigger tests\n\n* Retrigger tests\n\n* reretrigger tests\n\n* tests again\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
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          "headline": "Fix time limit in export causatives CLI (#6338)",
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          "body": "* Fix searching variants by gene with build 38 genes\n\n* Simplify\n\n* Safer code\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
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          "headline": "Fix search variants by gene with 38-only genes (#6340)",
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          "headline": "Fix #6342 - load region check chromosome prefix (#6343)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-26T09:46:45Z",
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          "body": "* Remember search options on panel filters\n\n* Work in progress\n\n* Some more improvements\n\n* Remembers filters on panel update\n\n* Updated changelog\n\n* Use constant and update changelog\n\n* Simplify panels function\n\n* Attempt at simplifying the function\n\n* Import types\n\n* Tiny fixes\n\n* Simplify some mo\n[…]\n institute select\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\nCo-authored-by: Lint Action <lint-action@samuelmeuli.com>",
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          "headline": "Remember panels filters when editing panels (#6305)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
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        {
          "oid": "19d77ca4dc8dcdce7937a4603bf2caa8861ef18c",
          "body": "…(#6312)\n\n* Improve causatives page performance by removing duplicate case queries\n\n* PR ref in changelog\n\n* Consider limit genes\n\n* Add case tags to projection for good measure\n\n* Display case status tag on causatives and verified pages\n\n* Fix merge conflict, hopefully\n\n* Nope, but not it should wo\n[…]\n\n\n* order alphabetically list and add build\n\n* Function returns an iterable\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Improve causatives page performance by removing duplicate case query …",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-25T06:23:08Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "51b3f8205cfc4b0a251ee2400db47217676615db",
          "body": "* Remove unused imports on commands export variants module\n\n* fix changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Remove unused imports on commands/export/variants module (#6334)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-25T05:27:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e36652c0f93e24a08d97c745ada9d19586e8dd18",
          "body": null,
          "is_bot": false,
          "headline": "Fix #6332 - add mitosalt SV tag (#6333)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-22T16:04:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "dc3f8944badc16f84dad93da9f3afa3759847318",
          "body": "* Expand export causatives cli to export as managed infile\n\n* Doesn't work yet\n\n* I'm stuck\n\n* Looks like it's working\n\n* Removed unused line\n\n* Fix code style issues with Black\n\n* trigger tests\n\n* Updated changelog\n\n* Fixed, almost\n\n* wip\n\n* Fix code here and there and test\n\n* Fix restrict query by\n[…]\nent as per review\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Lint Action <lint-action@samuelmeuli.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "CLI export causatives as managed (#6290)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-22T09:25:14Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "35065f67b3c1a72abfa312474ed97615fc2e6de8",
          "body": "* Do not default to build 37 when loading variants from a case\n\n* Fix changelog\n\n* typo\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Do not default to build 37 when loading variants from a case (#6331)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-22T08:56:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "688b22e4c5b34a0ef0a4bcc25654246bfa1e14c6",
          "body": "* Clearer logs with case ID when variants loading fails\n\n* PR ref\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Clearer logs with case ID when variants loading fails (#6329)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-22T08:34:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5a4727247ec6acb606d2fae107f0b9f95c2dc5a7",
          "body": null,
          "is_bot": false,
          "headline": "Fix #6326 - display pending panel change comments (#6327)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-22T08:16:17Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4f8a199c618c5947e957aa0469e6301e10b43d3a",
          "body": "…315)\n\n* Display matching causatives' case status and tags on variant page\n\n* Add some spacing\n\n* PR ref on changelog\n\n* Better spacing\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Display matching causatives' case status and tags on variant page (#6…",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-22T05:57:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "591d14eef28c529d44498564e205c87f608ec298",
          "body": "… ACMG (#6325)\n\n* fix bug where likely beign overwrites benign as classification for ACMG\n\n* update changelog",
          "is_bot": false,
          "headline": "Fixes bug where likely benign overwrites benign as classification for…",
          "author_name": "molucorner",
          "author_login": "molucorner",
          "committed_at": "2026-05-22T05:39:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ec9aae80ec3ff266ab7dcdf151e93c05a47e8bef",
          "body": "* Fix #6307 - add export category tags\n\n* type hints\n\n* header\n\n* unused import\n\n* CAUSATIVE is better, right\n\n* changelog...",
          "is_bot": false,
          "headline": "Fix #6307 - add export category tags (#6324)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-21T14:12:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d8ff563272f6f91ec161a514d0cfa677ddb2eae3",
          "body": "* Fix trying to load research in build 37 for cases with build 38\n\n* tiny fix\n\n* Add PR reference\n\n* Fix test accordingly\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix trying to load research in build 37 for cases with build 38 (#6322)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-21T12:58:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ba9b6eecfd311a51ff7911c81a29e273d73dbae6",
          "body": "* Add contigs on exported VCF files - managed and causatives\n\n* forgot changelog\n\n* Update scout/constants/variants_export.py\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n* Use different chrom size according to build\n\n* Remove comment\n\n* Added 2 new lines in VCF (source) and cli, according tp review\n\n* Add missing import\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Add contigs on exported VCF files - managed and causatives (#6310)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-21T08:51:19Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4bb63239033db832b945d54ffe268e668f2edea7",
          "body": "* Do not capitalize Paraphase region names\n\n* Also do the sorting right\n\n* Leave status as it was, as it's mostly gene names\n\n* Apply suggestion from @dnil\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n* Update scout/server/blueprints/cases/templates/cases/case_sma_dark.html\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Do not capitalize Paraphase region names (#6301)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-19T08:43:34Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "04756caa11732725830eddc80f3986ef6bf71a41",
          "body": "* Fix adding one managed variant in build 38\n\n* Remove typo\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix adding one managed variant in build 38 (#6300)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-19T05:47:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7ca2c4d278dec254d65b6ac31b6d7025aa216c1a",
          "body": "Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Display build in managed variants page (#6297)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-19T05:25:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "421dedc8df186613a7a2c8ced2b844abc7f94328",
          "body": "* Fix #6291 - compress demo case fusion vcf\n\n* and add the files\n\n* change filename in tests\n\n* Update changelog\n\n* Update changelog",
          "is_bot": false,
          "headline": "Fix #6291 - compress demo case fusion vcf (#6292)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-15T10:37:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e76928c195b7a84eb4ee39513eba3c05332b1e3a",
          "body": "* Version 4.111.3 - reintroduce alias for panel\n\n* and 38 fallback",
          "is_bot": false,
          "headline": "Version 4.111.3 - reintroduce alias for panel (#6289)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-12T17:10:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "67ff628bf08be63f93addc1439d1e687abce81be",
          "body": "…… (#6288)\n\n* Fix #6287 - partly revert aliasing, use GRCh38 to mean add chr prefix also for export variants\n\n* add help text\n\n* Prefix for export transcripts as well\n\n* Changelog\n\n* use f string\n\n* add to docs as well\n\n* citations\n\n* Ahem",
          "is_bot": false,
          "headline": "Fix #6287 - partly revert aliasing, use GRCh38 to mean add chr prefix…",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-12T15:13:42Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1c2acc5b661e0b4b09b4881409e46b23af371933",
          "body": null,
          "is_bot": false,
          "headline": "Version 4.111.1 (#6285)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-12T12:08:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "159651021368fdad14795996abe3cb749d4f6a86",
          "body": "* Fix #6282 - build aliases for export commands\n\n* Build for MT/M shift as well\n\n* fix test accordingly\n\n* unused imports",
          "is_bot": false,
          "headline": "Fix #6282 - build aliases for export commands (#6283)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-12T11:35:15Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "303a47ce37c367d56516939b0c5ba4da1e43b79f",
          "body": "* Version 4.111.0 release candidate\n\n* Changelog\n\n* Fixed changelog\n\n* Upgrade uv.lock to include latest chanjo and chanjo-report\n\n* update chanjo-report to 4.12.2\n\n* fresh uv.lock\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Version 4.111.0 release candidate (#6264)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-11T14:31:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "55e6691b6643692779b029bb23b762952119cd37",
          "body": "* Fix #6276 - CLI mito report to use both M and MT\n\n* Might as well push the chanjo-report version to latest\n\n* right\n\n* Fix #6278 - describe MT var loading in admin docs\n\n* docs\n\n* ahem, that is passed to build_query",
          "is_bot": false,
          "headline": "Fix #6276 - CLI mito report to use both M and MT (#6277)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-11T14:05:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a3be8242dfcb504766266e76a86d79a795fe6d66",
          "body": "* Fix #6274 - institute settings loqusdb cleared for non-admin\n\n* add tests and more getters\n\n* en passant types and html fixes\n\n* update docstring\n\n* Show all cases, show all vars are apparently user land\n\n* Update CHANGELOG.md\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\n\n* update comments\n\n* test comments\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Fix #6274 - institute settings loqusdb cleared for non-admin (#6275)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-11T06:18:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "90e564fc5f6fac56eee21870570d1706b54ff534",
          "body": "…t and typos (#6270)\n\n* Old expected_coverage option removed from docs, blog post, some layout and typos\n\n* Fix #6266 - Update docs on case config custom images (#6267)\n\n* changelog\n\n* like this perhaps\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Old expected_coverage option removed from docs, blog post, some layou…",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-07T12:20:46Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1cdef7999703ee83ad8241a45d73815e3e5f70d7",
          "body": "Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Dowload Ensembl data last when downloading everything (#6269)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-07T11:13:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "96dff2ea1f96059627db830ff47073118fe6aaeb",
          "body": null,
          "is_bot": false,
          "headline": "Fix #6266 - Update docs on case config custom images (#6267)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-07T07:46:41Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6b2920dd17bc9466a524adc555186067cdcf8393",
          "body": "* Fix #6154 - add CLI command to delete rank model from db\n\n* test text\n\n* Update tests/commands/delete/test_delete_rank_model.py\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\n\n* Update scout/adapter/mongo/rank_model.py\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>\n\n* DeleteResult type\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmail.com>",
          "is_bot": false,
          "headline": "Fix #6154 - add CLI command to delete rank model from db (#6262)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-05-05T13:24:18Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e0f97a233646911b69345b8b943f623fa2005ab3",
          "body": "* Simplest solution: hide empty categories\n\n* Update scout/server/blueprints/institutes/templates/overview/cases.html\n\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>\n\n* Trigger test\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Hide empty categories of cases on caseS page (#6260)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-05T12:22:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a8291e2b74e0b9b09defb22ace1017d27ec10a4d",
          "body": "* Improve merging managed variants description when upserting\n\n* Remove redundant code\n\n* This is broken\n\n* Changelog\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Small fix on managed variant upsert (#6259)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-05T06:50:17Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "2d494e0c485c7f38230825faf403a1b0f1b5b714",
          "body": "Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>",
          "is_bot": false,
          "headline": "Fix merging managed variants on None institute (#6258)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-04T13:28:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "98fb08b54fa432012ccfe533f6b07b98aaedadb0",
          "body": "* Update description and institutes on managed variants collision\n\n* Better Handle duplicates on managed variants uploads from file\n\n* Fix code style issues with Black\n\n* Update changelog\n\n* Remove the if and update docs, as per review\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Lint Action <lint-action@samuelmeuli.com>",
          "is_bot": false,
          "headline": "Fix duplicated managed variants from same causatives (#6256)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-05-04T07:26:03Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ef4d0a58037c0f3b013ef4484f666c25b0f2b742",
          "body": "* Fix #6253 - managed variants follow build on case page\n\n* and pass from controller\n\n* add an explicit 37 default - redundant, but more obvious\n\n* Update CHANGELOG.md",
          "is_bot": false,
          "headline": "Build sens match managed (#6254)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-04-30T21:08:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "518465b4c7e7f7794c39165da220a5db99618aaf",
          "body": "* Fix managed variants counter\n\n* PR ref in changelog\n\n* Fixed changelog\n\n* Some more fizes\n\n---------\n\nCo-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>\nCo-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>",
          "is_bot": false,
          "headline": "Fix managed variants counter (#6252)",
          "author_name": "Chiara Rasi",
          "author_login": "northwestwitch",
          "committed_at": "2026-04-30T10:08:00Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e3c32d08fe0d2c3ba5d042b7a6040c977cc9807c",
          "body": "* Fix #6243 - hg38 variants default gnomAD link to non-UK-biobank\n\n* and not only the gene link\n\n* and the gene links - note that we are using 4.1 for constraints, so build 38",
          "is_bot": false,
          "headline": "Fix #6243 - hg38 variants default gnomAD link to non-UK-biobank (#6250)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-04-30T09:53:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "68ae4b24fe75e351f8df6a17f480baffee8dfd81",
          "body": "* Fix missing commits on Saltshaker report\n\n* test removing analysis_types constant import\n\n* Update changelog",
          "is_bot": false,
          "headline": "Fix missing commits on Saltshaker report (#6246)",
          "author_name": "Daniel Nilsson",
          "author_login": "dnil",
          "committed_at": "2026-04-30T07:19:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
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              "days_since_last_human_commit_is_floor": false
            },
            "components": [
              {
                "key": "project_is_still_maintained",
                "name": "Project is still maintained",
                "detail": "last human commit 6 days ago",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "abandonment_maintained",
                    "params": {
                      "days": 6
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                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Is the project alive — is code being written and are releases shipping?"
      },
      {
        "key": "community",
        "band": "moderate",
        "name": "Community & Adoption",
        "value": 66,
        "weight": 0.18,
        "metrics": [
          {
            "key": "popularity",
            "band": "moderate",
            "name": "Popularity & adoption",
            "note": null,
            "notes": [],
            "value": 57,
            "inputs": {
              "forks": 51,
              "stars": 179,
              "watchers": 13,
              "growth_state": "organic",
              "growth_factor_pct": 100
            },
            "components": [
              {
                "key": "stars",
                "name": "Stars",
                "detail": "179 stars",
                "points": 36.5,
                "status": "partial",
                "details": [
                  {
                    "code": "stars",
                    "params": {
                      "count": 179
                    }
                  }
                ],
                "max_points": 60
              },
              {
                "key": "forks",
                "name": "Forks",
                "detail": "51 forks",
                "points": 14.2,
                "status": "partial",
                "details": [
                  {
                    "code": "forks",
                    "params": {
                      "count": 51
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "watchers",
                "name": "Watchers",
                "detail": "13 watchers",
                "points": 6,
                "status": "partial",
                "details": [
                  {
                    "code": "watchers",
                    "params": {
                      "count": 13
                    }
                  }
                ],
                "max_points": 15
              }
            ]
          },
          {
            "key": "community_health",
            "band": "good",
            "name": "Community health",
            "note": null,
            "notes": [],
            "value": 77,
            "inputs": {
              "has_readme": true,
              "has_license": true,
              "has_contributing": true,
              "has_issue_template": false,
              "has_code_of_conduct": false,
              "has_pull_request_template": true
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 22.5,
                "status": "met",
                "details": [],
                "max_points": 22.5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "recognized license (BSD-3-Clause)",
                "points": 22.5,
                "status": "met",
                "details": [
                  {
                    "code": "license_standard",
                    "params": {}
                  },
                  {
                    "code": "license_spdx",
                    "params": {
                      "spdx": "BSD-3-Clause"
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributing_guide",
                "name": "CONTRIBUTING guide",
                "detail": null,
                "points": 18,
                "status": "met",
                "details": [],
                "max_points": 18
              },
              {
                "key": "code_of_conduct",
                "name": "Code of conduct",
                "detail": null,
                "points": 0,
                "status": "missed",
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              },
              {
                "key": "issue_template",
                "name": "Issue template",
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                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.2
              },
              {
                "key": "pr_template",
                "name": "PR template",
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                "points": 6.3,
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                "details": [],
                "max_points": 6.3
              }
            ]
          }
        ],
        "description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
      },
      {
        "key": "governance",
        "band": "good",
        "name": "Sustainability & Governance",
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        "weight": 0.24,
        "metrics": [
          {
            "key": "maintainer_resilience",
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            "name": "Maintainer resilience (bus factor)",
            "note": null,
            "notes": [],
            "value": 63,
            "inputs": {
              "bus_factor": 2,
              "contributors_sampled": 33,
              "top_contributor_share": 0.377
            },
            "components": [
              {
                "key": "bus_factor",
                "name": "Bus factor",
                "detail": "2 contributor(s) cover half of all commits",
                "points": 25.2,
                "status": "partial",
                "details": [
                  {
                    "code": "bus_factor",
                    "params": {
                      "count": 2
                    }
                  }
                ],
                "max_points": 54
              },
              {
                "key": "commit_distribution",
                "name": "Commit distribution",
                "detail": "top contributor authored 38% of commits",
                "points": 14,
                "status": "partial",
                "details": [
                  {
                    "code": "top_contributor_share",
                    "params": {
                      "share": 38
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "33 contributors",
                "points": 13.5,
                "status": "met",
                "details": [
                  {
                    "code": "contributors_sampled",
                    "params": {
                      "count": 33
                    }
                  }
                ],
                "max_points": 13.5
              },
              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 15 contributing companies or organizations",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "responsiveness",
            "band": "excellent",
            "name": "Issue & PR responsiveness",
            "note": null,
            "notes": [],
            "value": 92,
            "inputs": {
              "merged_prs": 2732,
              "open_issues": 245,
              "closed_issues": 3097,
              "issue_closed_ratio": 0.927,
              "closed_unmerged_prs": 241
            },
            "components": [
              {
                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "93% of issues closed",
                "points": 43.3,
                "status": "partial",
                "details": [
                  {
                    "code": "issues_closed_share",
                    "params": {
                      "share": 93
                    }
                  }
                ],
                "max_points": 46.75
              },
              {
                "key": "pr_acceptance",
                "name": "PR acceptance",
                "detail": "2732/2973 decided PRs merged",
                "points": 35.1,
                "status": "partial",
                "details": [
                  {
                    "code": "decided_prs_merged",
                    "params": {
                      "merged": 2732,
                      "decided": 2973
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                  }
                ],
                "max_points": 38.25
              },
              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
                "detail": "Found 29/30 approved changesets -- score normalized to 9",
                "points": 13.5,
                "status": "partial",
                "details": [],
                "max_points": 15
              }
            ]
          },
          {
            "key": "stewardship",
            "band": "moderate",
            "name": "Ownership & stewardship",
            "note": null,
            "notes": [],
            "value": 69,
            "inputs": {
              "followers": 96,
              "owner_type": "Organization",
              "is_verified": null,
              "owner_login": "Clinical-Genomics",
              "public_repos": 123,
              "account_age_days": 4570
            },
            "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": "96 followers of Clinical-Genomics",
                "points": 14.3,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
                    "params": {
                      "count": 96,
                      "login": "Clinical-Genomics"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "123 public repos, account ~12 yr old",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 123
                    }
                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 12
                    }
                  }
                ],
                "max_points": 25
              }
            ]
          },
          {
            "key": "package_maintenance",
            "band": "excellent",
            "name": "Package maintenance",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "packages": [
                "scout-browser"
              ],
              "ecosystems": "pypi",
              "any_deprecated": false,
              "min_days_since_publish": 6
            },
            "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 6 days ago",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "publish_recency",
                    "params": {
                      "days": 6
                    }
                  }
                ],
                "max_points": 35
              },
              {
                "key": "version_history",
                "name": "Version history",
                "detail": "194 published versions",
                "points": 20,
                "status": "met",
                "details": [
                  {
                    "code": "published_versions",
                    "params": {
                      "count": 194
                    }
                  }
                ],
                "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": "9 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
                  {
                    "code": "ci_workflows",
                    "params": {
                      "count": 9
                    }
                  }
                ],
                "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": "30 out of 30 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": [],
              "has_wiki": true,
              "homepage": "https://clinical-genomics.github.io/scout",
              "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://clinical-genomics.github.io/scout",
                "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": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              },
              {
                "key": "wiki",
                "name": "Wiki",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
      },
      {
        "key": "security",
        "band": "moderate",
        "name": "Security",
        "value": 66,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
            "band": "moderate",
            "name": "Security posture",
            "note": "Excluded from scoring (no data or not applicable): Branch-Protection, Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "branch_protection",
                    "signed_releases"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 65,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 16,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 2,
              "scorecard_aggregate": 6.4
            },
            "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": "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",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "ci_tests",
                "name": "CI-Tests",
                "detail": "30 out of 30 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 29/30 approved changesets -- score normalized to 9",
                "points": 6.8,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 15 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": "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": "30 commit(s) and 27 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 run on all commits",
                "points": 5,
                "status": "met",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file detected",
                "points": 2,
                "status": "partial",
                "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": "1 existing vulnerabilities detected",
                "points": 6.8,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "dependency_advisories",
            "band": "moderate",
            "name": "Dependency advisories",
            "note": "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.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "indirect_dependencies_free_of_known_advisories"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              },
              {
                "code": "advisories_scope_repository",
                "params": {
                  "assessed": 118
                }
              },
              {
                "code": "advisories_repo_graph_caveat",
                "params": {}
              },
              {
                "code": "advisories_reachability",
                "params": {}
              }
            ],
            "value": 69,
            "inputs": {
              "source": "osv",
              "advisories": 2,
              "affected_packages": 1,
              "assessed_packages": 118,
              "unassessed_packages": 0,
              "affected_by_severity": "high 1",
              "direct_affected_packages": 1
            },
            "components": [
              {
                "key": "direct_dependencies_free_of_known_advisories",
                "name": "Direct dependencies free of known advisories",
                "detail": "1 affected: pdfkit 1.0.0 (high 8.4)",
                "points": 11.5,
                "status": "partial",
                "details": [
                  {
                    "code": "advisories_affected",
                    "params": {
                      "count": 1,
                      "packages": "pdfkit 1.0.0 (high 8.4)"
                    }
                  }
                ],
                "max_points": 35
              },
              {
                "key": "indirect_dependencies_free_of_known_advisories",
                "name": "Indirect dependencies free of known advisories",
                "detail": "transitive set not separable from development and test dependencies in this scope",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_scope_not_separable",
                    "params": {}
                  }
                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
                "detail": "no advisory has been public longer than 90 days",
                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "advisories_none_stale",
                    "params": {
                      "days": 90
                    }
                  }
                ],
                "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": 118,
              "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": 11
            },
            "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": "moderate",
        "name": "AI Readiness",
        "value": 53,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "at_risk",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 40,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 1,
              "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": "100 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 40,
                "status": "met",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 100,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "moderate",
            "name": "Verify loop (build / test / typecheck)",
            "note": null,
            "notes": [],
            "value": 61,
            "inputs": {
              "has_nix": false,
              "has_tests": true,
              "lockfiles": [
                "uv.lock"
              ],
              "has_dockerfile": true,
              "typed_language": false,
              "bootstrap_files": [
                "Makefile"
              ],
              "has_devcontainer": false,
              "has_linter_config": true,
              "typecheck_configs": [],
              "agent_commit_share": 0,
              "toolchain_manifests": [],
              "dependency_bot_commit_share": 0
            },
            "components": [
              {
                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
                "detail": "Makefile",
                "points": 18,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "Makefile"
                    }
                  }
                ],
                "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": "Dockerfile, lockfile",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "Dockerfile, lockfile"
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "no agent-authored commits among the last 100",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_authored_commits",
                    "params": {
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "automated_maintenance",
                "name": "Automated maintenance",
                "detail": "no automated dependency updates observed",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_dependency_automation",
                    "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": 55,
            "inputs": {
              "primary_language": "HTML",
              "largest_source_bytes": 79453,
              "source_files_sampled": 566,
              "oversized_source_files": 3
            },
            "components": [
              {
                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "HTML without a type-check config",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_typecheck_config_language",
                    "params": {
                      "language": "HTML"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "3/566 source files over 60KB",
                "points": 54.7,
                "status": "partial",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 566,
                      "oversized": 3
                    }
                  }
                ],
                "max_points": 55
              }
            ]
          }
        ],
        "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": [
    "deps.dev does not index pypi:scout-browser@4.113.3; advisories assessed against the repository dependency graph instead"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-21T20:45:21.884918Z",
  "schema_version": "0.23.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/c/Clinical-Genomics/scout.svg",
  "full_name": "Clinical-Genomics/scout",
  "license_state": "standard",
  "license_spdx": "BSD-3-Clause"
}

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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 v1.13.0, schema v0.23.0 — full methodology · metrics wiki.

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