Public record
Software health reportschema 0.11.0 · metrics 1.13.0 · 2026-07-17 11:56 UTC

stjude / proteinpaint

Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.

JavaScript · TypeScriptCustom license★ 48 stars⑂ 14 forkssince Mar 2023View on GitHub ↗

stjude/proteinpaint holds a health index of 74 out of 100, placing it in the Good band. It scores highest on Vitality (96/100) and lowest on AI Readiness (46/100). It was last updated today. 3 contributors account for most of its recent work.

74
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.

74
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

St. Jude Children's Research HospitalOrganization
228 followers54 public repossince Jun 2013

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publish
npm@sjcrh/proteinpaint-r2.197.0508202 days ago
npm@sjcrh/augen2.190.03842855 days ago
npm@sjcrh/proteinpaint-client2.197.02,7734912 days ago
npm@sjcrh/proteinpaint-front2.197.04,1834902 days ago
npm@sjcrh/proteinpaint-python2.196.0969408 days ago
npm@sjcrh/proteinpaint-rust2.197.02,0081262 days ago
npm@sjcrh/proteinpaint-server2.197.03,6394602 days ago

Metrics by category

Vitality

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

96Excellent · 22% of overall

Development activity

100Excellent
How it's scored
36/36Push recency — last push 0 days ago
36/36Commit cadence — 52/52 weeks with commits
18/18Commit volume — 5,529 commits in the last year
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year5,529
human_commit_share—
days_since_last_push0
active_weeks_last_year52

Release discipline

90Excellent
How it's scored
27/27Ships releases — 100 releases published
36/36Release recency — latest release 2 days ago
27/27Release cadence — a release every ~2.3 days
0/10OpenSSF Scorecard: Signed-Releases — Project has not signed or included provenance with any releases.
Inputs used
releases_count100
latest_release_tagv2.197.0
releases_from_tagsno
days_since_latest_release2
mean_days_between_releases2.3

Community & Adoption

Does the project have users, downloads, attention, and a welcoming setup for contributors?

50Moderate · 18% of overall

Popularity & adoption

38At risk
How it's scored
27.1/60Stars — 48 stars
9.3/25Forks — 14 forks
1.7/15Watchers — 3 watchers
Inputs used
forks14
stars48
watchers3
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

Community health

51Moderate
How it's scored
22.5/22.5README
16.9/22.5License — license file present, not a recognized license
0/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
6.3/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
has_contributingno
has_issue_templateno
has_code_of_conductno
has_pull_request_templateyes

Ecosystem adoption (downloads)

69Moderate
How it's scored
55.5/80Monthly downloads — 14,464 downloads/month across npm
0/20Registry dependents — not reported by this ecosystem
Inputs used
packages@sjcrh/proteinpaint-r, @sjcrh/augen, @sjcrh/proteinpaint-client, @sjcrh/proteinpaint-front, @sjcrh/proteinpaint-python, @sjcrh/proteinpaint-rust, @sjcrh/proteinpaint-server
dependents—
ecosystemsnpm
total_downloads—
monthly_downloads14,464
Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.

Sustainability & Governance

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

82Good · 24% of overall

Maintainer resilience (bus factor)

78Good
How it's scored
36/54Bus factor — 3 contributor(s) cover half of all commits
18.1/22.5Commit distribution — top contributor authored 20% of commits
13.5/13.5Contributor breadth — 24 contributors
10/10OpenSSF Scorecard: Contributors — project has 4 contributing companies or organizations
Inputs used
bus_factor3
contributors_sampled24
top_contributor_share0.197

Issue & PR responsiveness

82Good
How it's scored
42/46.8Issue resolution — 90% of issues closed
35.5/38.3PR acceptance — 3,530/3,803 decided PRs merged
4.5/15OpenSSF Scorecard: Code-Review — Found 5/15 approved changesets -- score normalized to 3
Inputs used
merged_prs3,530
open_issues93
closed_issues832
issue_closed_ratio0.899
closed_unmerged_prs273

Ownership & stewardship

72Good
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain
17/25Owner reach — 228 followers of stjude
24.7/25Track record — 54 public repos, account ~13 yr old
Inputs used
followers228
owner_typeOrganization
is_verified—
owner_loginstjude
public_repos54
account_age_days4,776

Package maintenance

100Excellent
How it's scored
25/25Published & resolvable — 7 package(s) on npm
35/35Publish recency — latest publish 2 days ago
20/20Version history — 491 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packages@sjcrh/proteinpaint-r, @sjcrh/augen, @sjcrh/proteinpaint-client, @sjcrh/proteinpaint-front, @sjcrh/proteinpaint-python, @sjcrh/proteinpaint-rust, @sjcrh/proteinpaint-server
ecosystemsnpm
any_deprecatedno
min_days_since_publish2

Engineering Quality

Are baseline engineering and documentation practices in place?

82Good · 20% of overall

Engineering practices

94Excellent
How it's scored
24/24CI workflows — 14 workflow(s)
24/24Tests present
16/16Linter config — .eslintrc.cjs
9.6/9.6Pre-commit hooks
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 11 out of 11 merged PRs checked by a CI test -- score normalized to 10
Inputs used
has_ciyes
has_testsyes
has_editorconfigno
has_linter_configyes
has_precommit_configyes

Documentation

65Moderate
How it's scored
30/30README
0/25Documentation directory
15/15Documentation / homepage site — https://proteinpaint.stjude.org/
10/10Repository description
0/10Topics
10/10Wiki
Inputs used
topics—
has_wikiyes
homepagehttps://proteinpaint.stjude.org/
has_readmeyes
has_docs_dirno
has_descriptionyes

Security

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

49At risk · 16% of overall

Security posture

49At risk
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
4.5/7.5Branch-Protection — branch protection is not maximal on development and all release branches
2.5/2.5CI-Tests — 11 out of 11 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
2.2/7.5Code-Review — Found 5/15 approved changesets -- score normalized to 3
2.5/2.5Contributors — project has 4 contributing companies or organizations
10/10Dangerous-Workflow — no dangerous workflow patterns detected
7.5/7.5Dependency-Update-Tool — update tool detected
0/5Fuzzing — project is not fuzzed
2.2/2.5License — license file detected
7.5/7.5Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
5/5Packaging — packaging workflow detected
0.5/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 1
0/5SAST — SAST tool is not run on all commits -- score normalized to 0
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — Project has not signed or included provenance with any releases.
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
0/7.5Vulnerabilities — 35 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated18
scorecard_versionv5.5.0
checks_inconclusive0
scorecard_aggregate5

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.

46At risk · 0% of overall

Agent context & guidance

1Critical
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
0/40Legible commit history — no data
Inputs used
has_llms_txtno
legible_history_share—
agent_instruction_files—
agent_instruction_max_bytes—
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.

Verify loop (build / test / typecheck)

67Moderate
How it's scored
0/18One-command bootstrap
22/22Automated tests
11/11Lint / format config — .eslintrc.cjs
11/11Static type checking — augen/tsconfig.json, client/tsconfig.json, client/types/tsconfig.json, server/tsconfig.json, shared/types/tsconfig.json, shared/utils/tsconfig.json, tsconfig.json
10/10Reproducible environment — devcontainer, Dockerfile, lockfile
0/10Demonstrated agent practice — no data
0/8Automated maintenance — no data
1/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 1
Inputs used
has_nixno
has_testsyes
lockfilesCargo.lock, package-lock.json
has_dockerfileyes
typed_languageno
bootstrap_files—
has_devcontaineryes
has_linter_configyes
typecheck_configsaugen/tsconfig.json, client/tsconfig.json, client/types/tsconfig.json, server/tsconfig.json, shared/types/tsconfig.json, shared/utils/tsconfig.json, tsconfig.json
agent_commit_share—
toolchain_manifests—
dependency_bot_commit_share—
Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance. Remaining weights renormalized.

Code legibility for models

81Good
How it's scored
27/45Type-checkable code — JavaScript with type-check config (augen/tsconfig.json, client/tsconfig.json, client/types/tsconfig.json, server/tsconfig.json, shared/types/tsconfig.json, shared/utils/tsconfig.json, tsconfig.json)
54.1/55Manageable file sizes — 26/1,549 source files over 60KB
Inputs used
primary_languageJavaScript
largest_source_bytes1,090,033
source_files_sampled1,549
oversized_source_files26

Key facts

48GitHub stars
24contributors
5,529commits, last 12 months
0days since last push
100releases
3bus factor
93open issues
crates.io, npm, PyPIpackage ecosystems

Data collection warnings

  • Could not fetch crates package 'PP_rust_utilities' from its registry

More detail

OpenSSF Scorecard 5.0 / 10
5.0aggregate

Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).Scorecard v5.5.0 · 2026-07-17 11:56 UTC

10Binary-Artifactsno binaries found in the repo
6Branch-Protectionbranch protection is not maximal on development and all release branches
10CI-Tests11 out of 11 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
3Code-ReviewFound 5/15 approved changesets -- score normalized to 3
10Contributorsproject has 4 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
9Licenselicense file detected
10Maintained30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
10Packagingpackaging workflow detected
1Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 1
0SASTSAST tool is not run on all commits -- score normalized to 0
0Security-Policysecurity policy file not detected
0Signed-ReleasesProject has not signed or included provenance with any releases.
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
0Vulnerabilities35 existing vulnerabilities detected
Direct dependencies 68
RegistryPackageVersion constraintManifest
npmsemver^7.8.5client/package.json
npmhtml-to-image^1.11.13package.json
crates.ioanyhow1.0.99rust/Cargo.toml
crates.iokodama0.3rust/Cargo.toml
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crates.iobgzip0.3.1rust/Cargo.toml
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crates.ionalgebra0.32.2rust/Cargo.toml
crates.ioplotters0.3.4rust/Cargo.toml
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crates.iocolorgrad0.6.2rust/Cargo.toml
crates.iostatrs^0.16.0rust/Cargo.toml
crates.iolibc0.2rust/Cargo.toml
crates.iofishers_exact^1.0.1rust/Cargo.toml
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crates.iolibmath^0.2.1rust/Cargo.toml
crates.iojson^0.12.4rust/Cargo.toml
crates.ioserde^1.0.147rust/Cargo.toml
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crates.ionum^0.4.1rust/Cargo.toml
crates.ior_mathlib^0.2.0rust/Cargo.toml
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crates.ior2d2_sqlite0.29.0rust/Cargo.toml
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crates.ioasync-stream0.3.6rust/Cargo.toml
crates.iobase640.22.1rust/Cargo.toml
npmtar^7.1.0rust/package.json
npm@sjcrh/augen2.190.0server/package.json
npm@sjcrh/proteinpaint-python2.196.0server/package.json
npm@sjcrh/proteinpaint-r2.197.0server/package.json
npm@sjcrh/proteinpaint-rust2.197.0server/package.json
npm@sjcrh/proteinpaint-shared2.197.0server/package.json
npm@sjcrh/proteinpaint-types2.197.0server/package.json
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npmtiny-async-pool^1.2.0server/package.json
npmtough-cookie^4.1.4server/package.json
All dependencies 1,596

Full resolved dependency set from the GitHub dependency graph: 106 direct and 1,490 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
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crates.iourl2.5.7direct
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npm@sjcrh/proteinpaint-rust2.195.0direct
npm@sjcrh/proteinpaint-rust2.197.0direct
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crates.iofutures-core0.3.31indirect
crates.iofutures-executor0.3.31indirect
crates.iofutures-io0.3.31indirect
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        {
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          "login": "robinpaul85",
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          "type": "User",
          "login": "gavrielm",
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        {
          "type": "User",
          "login": "aacic",
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          "avatar_url": "https://avatars.githubusercontent.com/u/32873451?v=4"
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        {
          "type": "User",
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          "avatar_url": "https://avatars.githubusercontent.com/u/179725832?v=4"
        },
        {
          "login": "Copilot",
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      "ci_workflows": [
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        "CD-publish-blat-server-image.yml",
        "CD-publish-deps-image.yml",
        "CD-publish-dev-container.yml",
        "CD-publish-rust-binaries.yml",
        "CD-publish-rust-bookworm-env-image.yml",
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        "CD-rust-build.yml",
        "CI-combined-coverage.yaml",
        "CI-integration.yml",
        "CI-merge-change-log.yml",
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      "has_linter_config": true,
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            "reason": "no dangerous workflow patterns detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dangerous-workflow"
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            "name": "Dependency-Update-Tool",
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            "name": "Fuzzing",
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          {
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          {
            "key": "ecosystem_adoption",
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            "value": 69,
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                "key": "registry_dependents",
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                    "code": "account_age_years",
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                "key": "publish_recency",
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                "key": "version_history",
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  "schema_version": "0.11.0",
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  "license_state": "custom",
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}

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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 v0.11.0 — full methodology · metrics wiki.

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