Public record
Software health reportschema 0.11.0 · metrics 2.10.0 · 2026-07-15 14:46 UTC

bradyajohnston / molecularnodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

PythonGPL-3.0★ 1,317 stars⑂ 124 forkssince Apr 2022View on GitHub ↗
KindLibraryhow this is determined
#blender#biochemistry#protein#protein-structure#protein-visualization#sciart#visualisation#structural-biology#blender-addon#protein-data-bank#molecule#proteins#pdb#molecular-modeling#molecular#molecular-graphics#molecular-dynamics#molecular-structures#mmcif#3d-visualization

bradyajohnston/molecularnodes holds a health index of 84 out of 100, placing it in the Excellent band. It scores highest on Engineering Quality (87/100) and lowest on AI Readiness (44/100). It was last updated 6 days ago. A single contributor accounts for most of its recent work.

84
overall / 100
Excellent

Software health index

Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean, calibrated against the distribution of the public record so bands carry percentile meaning; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At Risk ceiling of 34.

84
Exceptional93-100The record's top tier (≈ top 5%); essentially all checked criteria met
Excellent80-92Strong across the board; minor gaps
Good65-79Healthy; gaps are limited and manageable
Moderate50-64Acceptable with notable gaps; review recommended
Weak35-49Material weaknesses across several areas
At Risk20-34Significant weaknesses; adoption warrants caution
Critical1-19Severe problems (abandoned, single-maintainer, no hygiene)
VitalityCommunity &AdoptionSustainability &GovernanceEngineeringQualitySecurityAI Readiness

Score profile

Each axis is a category. The shape matters more than the average — a healthy subject fills the whole shape, while a spike-and-crater profile means strength in one dimension is masking risk in another.

The weighted overall 71 is calibrated to 84 on the published index scale (record calibration 2026-08-02).

Ownership

Brady JohnstonPersonal account
462 followers124 public repossince Feb 2018Freelance scientific animator & developer.

This repository is owned by a personal account. A single-owner project carries more continuity risk than an organization-backed one.

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publish
PyPImolecularnodes4.5.12-27119 days ago

Metrics by category

Vitality

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

82Excellent · 21% of overall

Development activity

82Excellent
How it's scored
36/36Push recency — last push 6 days ago
21.5/36Commit cadence — 31/52 weeks with commits
18/18Commit volume — 134 commits in the last year
7/10OpenSSF Scorecard: Maintained — 0 commit(s) and 9 issue activity found in the last 90 days -- score normalized to 7
Inputs used
commits_last_year134
human_commit_share—
days_since_last_push6
active_weeks_last_year31

Release discipline

81Excellent
How it's scored
27/27Ships releases — 92 releases published
27/36Release recency — latest release 119 days ago
27/27Release cadence — a release every ~20.5 days
0/10OpenSSF Scorecard: Signed-Releases — Project has not signed or included provenance with any releases.
Inputs used
releases_count92
latest_release_tagv4.5.12
releases_from_tagsno
days_since_latest_release119
mean_days_between_releases20.5

Community & Adoption

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

73Good · 17% of overall

Popularity & adoption

75Good
How it's scored
50.6/60Stars — 1,317 stars
17.4/25Forks — 124 forks
7.1/15Watchers — 20 watchers
Inputs used
forks124
stars1,317
watchers20
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

Community health

70Good
How it's scored
22.5/22.5README
22.5/22.5License — recognized license (GPL-3.0)
18/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges—
has_contributingyes
has_issue_templateno
has_code_of_conductno
readme_badge_services—
has_pull_request_templateno

Sustainability & Governance

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

68Good · 23% of overall

Maintainer resilience (bus factor)

36Weak
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
3.4/22.5Commit distribution — top contributor authored 85% of commits
13.5/13.5Contributor breadth — 33 contributors
10/10OpenSSF Scorecard: Contributors — project has 15 contributing companies or organizations
Inputs used
bus_factor1
contributors_sampled33
top_contributor_share0.847

Issue & PR responsiveness

82Excellent
How it's scored
35/42Issue resolution — 83% of issues closed
27.6/30PR acceptance — 503/546 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
9/15OpenSSF Scorecard: Code-Review — Found 20/30 approved changesets -- score normalized to 6
Inputs used
merged_prs503
open_issues85
closed_issues426
prs_merged_7d—
prs_decided_7d—
prs_merged_30d—
prs_decided_30d—
issue_closed_ratio0.834
closed_unmerged_prs43
first_time_authors_30d—
first_time_prs_merged_30d—
first_time_prs_decided_30d—
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

68Good
How it's scored
10/30Ownership backing — personal (user) account
0/20Verified domain — not applicable to user accounts
19.2/25Owner reach — 462 followers of BradyAJohnston
25/25Track record — 124 public repos, account ~8 yr old
Inputs used
followers462
owner_typeUser
is_verified—
owner_loginBradyAJohnston
public_repos124
account_age_days3,086
Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.

Package maintenance

100Exceptional
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
35/35Publish recency — latest publish 119 days ago
20/20Version history — 27 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagesmolecularnodes
ecosystemspypi
any_deprecatedno
min_days_since_publish119

Engineering Quality

Are baseline engineering and documentation practices in place?

87Excellent · 19% of overall

Engineering practices

78Good
How it's scored
24/24CI workflows — 5 workflow(s)
24/24Tests present
16/16Linter config
9.6/9.6Pre-commit hooks
0/6.4.editorconfig
4/20OpenSSF Scorecard: CI-Tests — 6 out of 29 merged PRs checked by a CI test -- score normalized to 2
Inputs used
has_ciyes
has_testsyes
has_editorconfigno
has_linter_configyes
has_precommit_configyes

Documentation

100Exceptional
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — https://bradyajohnston.github.io/MolecularNodes/
10/10Repository description
10/10Topics — 20 topics
10/10Wiki
Inputs used
topicsblender, biochemistry, protein, protein-structure, protein-visualization, sciart, visualisation, structural-biology, blender-addon, protein-data-bank, molecule, proteins, pdb, molecular-modeling, molecular, molecular-graphics, molecular-dynamics, molecular-structures, mmcif, 3d-visualization
has_wikiyes
homepagehttps://bradyajohnston.github.io/MolecularNodes/
docs_sitehttps://bradyajohnston.github.io/MolecularNodes/
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

46Weak · 16% of overall

Security posture

46Weak
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — no data
0.5/2.5CI-Tests — 6 out of 29 merged PRs checked by a CI test -- score normalized to 2
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
4.5/7.5Code-Review — Found 20/30 approved changesets -- score normalized to 6
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
5.2/7.5Maintained — 0 commit(s) and 9 issue activity found in the last 90 days -- score normalized to 7
5/5Packaging — packaging workflow detected
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
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
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated17
scorecard_versionv5.5.0
checks_inconclusive1
scorecard_aggregate4.6
Excluded from scoring (no data or not applicable): Branch-Protection. Remaining weights renormalized.

AI Readiness

How well is the repo equipped to be developed and maintained with AI coding agents? Carries a deliberately small weight (4%): agent tooling is a real maintenance signal, but a repository with none can still reach 100/100.

44Weak · 4% 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
llms_txt_url—
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)

52Moderate
How it's scored
0/18One-command bootstrap
22/22Automated tests
11/11Lint / format config
0/11Static type checking
10/10Reproducible environment — lockfile
0/10Demonstrated agent practice — no data
0/8Automated maintenance — no data
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfilesuv.lock
has_dockerfileno
typed_languageno
bootstrap_files—
has_devcontainerno
has_linter_configyes
typecheck_configs—
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

55Moderate
How it's scored
0/45Type-checkable code — Python without a type-check config
54.6/55Manageable file sizes — 1/131 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes90,872
source_files_sampled131
oversized_source_files1

Machine-readable interfaces

100Exceptional
How it's scored
0/40API schema (OpenAPI/GraphQL/proto) — not applicable to this kind of software
0/20MCP server — not applicable to this kind of software
40/40Runnable examples — examples
Inputs used
example_dirsexamples
has_mcp_signalno
api_schema_files—
interfaces_expected_of—
Excluded from scoring (no data or not applicable): API schema (OpenAPI/GraphQL/proto), MCP server. Remaining weights renormalized.

Key facts

1,317GitHub stars
33contributors
134commits, last 12 months
6days since last push
92releases
1bus factor
85open issues
PyPIpackage ecosystems

More detail

OpenSSF Scorecard 4.6 / 10
4.6aggregate

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 · 2026-07-15 14:46 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
2CI-Tests6 out of 29 merged PRs checked by a CI test -- score normalized to 2
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
6Code-ReviewFound 20/30 approved changesets -- score normalized to 6
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
7Maintained0 commit(s) and 9 issue activity found in the last 90 days -- score normalized to 7
10Packagingpackaging workflow detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
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
10Vulnerabilities0 existing vulnerabilities detected
Direct dependencies 8
RegistryPackageVersion constraintManifest
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PyPImdanalysis>=2.10pyproject.toml
PyPIbiotite>=1.5pyproject.toml
PyPImrcfile—pyproject.toml
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PyPIPyYAML—pyproject.toml
PyPIimdclient>=0.2.3pyproject.toml
PyPIpandas<3.0.0pyproject.toml
All dependencies 183

Full resolved dependency set from the GitHub dependency graph: 8 direct and 175 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

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Raw JSON report machine-readable

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Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.

Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v2.10.0, schema v0.11.0 — full methodology · metrics wiki.

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