Public record
Software health reportschema 0.11.0 · metrics 1.13.0 · 2026-07-15 13:16 UTC

the-omics-os / lobster

The self-evolving agentic framework for bioinformatics

PythonCustom license★ 42 stars⑂ 9 forkssince Aug 2025View on GitHub ↗
#agents#bioinformatics#langgraph#transcriptomics#lobster#omics#proteomics

the-omics-os/lobster holds a health index of 60 out of 100, placing it in the Moderate band. It scores highest on Engineering Quality (81/100) and lowest on Security (34/100). It was last updated 5 days ago. A single contributor accounts for most of its recent work.

60
overall / 100
Moderate

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.

60
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

omics-osOrganization
14 followers9 public repossince Aug 2025

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publishTags
PyPIlobster-ai1.1.419-5812 days agobioinformaticsrna-seqsingle-cellaimachine-learningdata-analysisgenomics

Metrics by category

Vitality

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

80Good · 22% of overall

Development activity

73Good
How it's scored
36/36Push recency — last push 5 days ago
9/36Commit cadence — 13/52 weeks with commits
18/18Commit volume — 814 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_year814
human_commit_share—
days_since_last_push5
active_weeks_last_year13

Release discipline

90Excellent
How it's scored
27/27Ships releases — 56 releases published
36/36Release recency — latest release 12 days ago
27/27Release cadence — a release every ~7.6 days
0/10OpenSSF Scorecard: Signed-Releases — Project has not signed or included provenance with any releases.
Inputs used
releases_count56
latest_release_tagv1.1.419
releases_from_tagsno
days_since_latest_release12
mean_days_between_releases7.6

Community & Adoption

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

48At risk · 18% of overall

Popularity & adoption

34At risk
How it's scored
26.2/60Stars — 42 stars
7.5/25Forks — 9 forks
0/15Watchers — 0 watchers
Inputs used
forks9
stars42
watchers0
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

Community health

64Moderate
How it's scored
22.5/22.5README
16.9/22.5License — license file present, not a recognized license
18/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
has_contributingyes
has_issue_templateno
has_code_of_conductno
has_pull_request_templateno

Sustainability & Governance

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

52Moderate · 24% of overall

Maintainer resilience (bus factor)

15Critical
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
0/22.5Commit distribution — top contributor authored 100% of commits
2.7/13.5Contributor breadth — 2 contributors
3/10OpenSSF Scorecard: Contributors — project has 1 contributing companies or organizations -- score normalized to 3
Inputs used
bus_factor1
contributors_sampled2
top_contributor_share0.998

Issue & PR responsiveness

63Moderate
How it's scored
40.1/46.8Issue resolution — 86% of issues closed
22.9/38.3PR acceptance — 6/10 decided PRs merged
0/15OpenSSF Scorecard: Code-Review — Found 0/30 approved changesets -- score normalized to 0
Inputs used
merged_prs6
open_issues1
closed_issues6
issue_closed_ratio0.857
closed_unmerged_prs4

Ownership & stewardship

48At risk
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain
8.5/25Owner reach — 14 followers of the-omics-os
9.1/25Track record — 9 public repos, account ~0 yr old
Inputs used
followers14
owner_typeOrganization
is_verified—
owner_loginthe-omics-os
public_repos9
account_age_days336

Package maintenance

100Excellent
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
35/35Publish recency — latest publish 12 days ago
20/20Version history — 58 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packageslobster-ai
ecosystemspypi
any_deprecatedno
min_days_since_publish12

Engineering Quality

Are baseline engineering and documentation practices in place?

81Good · 20% of overall

Engineering practices

68Moderate
How it's scored
24/24CI workflows — 6 workflow(s)
24/24Tests present
0/16Linter config
0/9.6Pre-commit hooks
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 2 out of 2 merged PRs checked by a CI test -- score normalized to 10
Inputs used
has_ciyes
has_testsyes
has_editorconfigno
has_linter_configno
has_precommit_configno

Documentation

100Excellent
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — https://www.lobsterbio.com/
10/10Repository description
10/10Topics — 7 topics
10/10Wiki
Inputs used
topicsagents, bioinformatics, langgraph, transcriptomics, lobster, omics, proteomics
has_wikiyes
homepagehttps://www.lobsterbio.com/
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

34At risk · 16% of overall

Security posture

34At risk
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — branch protection not enabled on development/release branches
2.5/2.5CI-Tests — 2 out of 2 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
0/7.5Code-Review — Found 0/30 approved changesets -- score normalized to 0
0.8/2.5Contributors — project has 1 contributing companies or organizations -- score normalized to 3
10/10Dangerous-Workflow — no dangerous workflow patterns detected
0/7.5Dependency-Update-Tool — no 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
0/5Pinned-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
0/7.5Vulnerabilities — 149 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated18
scorecard_versionv5.5.0
checks_inconclusive0
scorecard_aggregate3.4

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.

49At 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)

74Good
How it's scored
18/18One-command bootstrap — Makefile
22/22Automated tests
0/11Lint / format config
11/11Static type checking — packages/lobster-genomics/lobster/agents/genomics/py.typed, packages/lobster-metabolomics/lobster/agents/metabolomics/py.typed, packages/lobster-metadata/lobster/agents/metadata_assistant/py.typed, packages/lobster-ml/lobster/agents/machine_learning/py.typed, packages/lobster-proteomics/lobster/agents/proteomics/py.typed, packages/lobster-research/lobster/agents/data_expert/py.typed, packages/lobster-research/lobster/agents/research/py.typed, packages/lobster-structural-viz/lobster/agents/py.typed, packages/lobster-transcriptomics/lobster/agents/transcriptomics/py.typed, packages/lobster-visualization/lobster/agents/py.typed
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
lockfilesgo.sum, uv.lock
has_dockerfileno
typed_languageno
bootstrap_filesMakefile
has_devcontainerno
has_linter_configno
typecheck_configspackages/lobster-genomics/lobster/agents/genomics/py.typed, packages/lobster-metabolomics/lobster/agents/metabolomics/py.typed, packages/lobster-metadata/lobster/agents/metadata_assistant/py.typed, packages/lobster-ml/lobster/agents/machine_learning/py.typed, packages/lobster-proteomics/lobster/agents/proteomics/py.typed, packages/lobster-research/lobster/agents/data_expert/py.typed, packages/lobster-research/lobster/agents/research/py.typed, packages/lobster-structural-viz/lobster/agents/py.typed, packages/lobster-transcriptomics/lobster/agents/transcriptomics/py.typed, packages/lobster-visualization/lobster/agents/py.typed
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

80Good
How it's scored
27/45Type-checkable code — Python with type-check config (packages/lobster-genomics/lobster/agents/genomics/py.typed, packages/lobster-metabolomics/lobster/agents/metabolomics/py.typed, packages/lobster-metadata/lobster/agents/metadata_assistant/py.typed, packages/lobster-ml/lobster/agents/machine_learning/py.typed, packages/lobster-proteomics/lobster/agents/proteomics/py.typed, packages/lobster-research/lobster/agents/data_expert/py.typed, packages/lobster-research/lobster/agents/research/py.typed, packages/lobster-structural-viz/lobster/agents/py.typed, packages/lobster-transcriptomics/lobster/agents/transcriptomics/py.typed, packages/lobster-visualization/lobster/agents/py.typed)
52.8/55Manageable file sizes — 43/1,061 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes171,948
source_files_sampled1,061
oversized_source_files43

Key facts

42GitHub stars
2contributors
814commits, last 12 months
5days since last push
56releases
1bus factor
1open issues
Go, PyPIpackage ecosystems

Data collection warnings

  • Could not fetch go package 'github.com/the-omics-os/lobster-tui' from its registry

More detail

OpenSSF Scorecard 3.4 / 10
3.4aggregate

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 · 2026-07-15 13:15 UTC

10Binary-Artifactsno binaries found in the repo
0Branch-Protectionbranch protection not enabled on development/release branches
10CI-Tests2 out of 2 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0Code-ReviewFound 0/30 approved changesets -- score normalized to 0
3Contributorsproject has 1 contributing companies or organizations -- score normalized to 3
10Dangerous-Workflowno dangerous workflow patterns detected
0Dependency-Update-Toolno update 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
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
0Vulnerabilities149 existing vulnerabilities detected
Direct dependencies 42
RegistryPackageVersion constraintManifest
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Gogithub.com/alecthomas/chroma/v2v2.14.0lobster-tui/go.mod
Gogithub.com/charmbracelet/glamourv0.10.0lobster-tui/go.mod
Gogolang.org/x/termv0.40.0lobster-tui/go.mod
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PyPItomli_w>=1.0pyproject.toml
PyPIpsutil>=7.0.0pyproject.toml
PyPIlobster-ai-tui~=1.1.0pyproject.toml
All dependencies 530

Full resolved dependency set from the GitHub dependency graph: 53 direct and 477 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

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PyPIimportlib-resources6.5.2indirect
PyPIiniconfig2.3.0indirect
PyPIinterface-meta1.3.0indirect
PyPIinterpret—indirect
PyPIisodate0.7.2indirect
PyPIisort7.0.0indirect
PyPIjaraco-classes3.4.0indirect
PyPIjaraco-context6.0.1indirect
PyPIjaraco-functools4.3.0indirect
PyPIjeepney0.9.0indirect
PyPIjiter0.12.0indirect
PyPIjmespath1.0.1indirect
PyPIjoblib1.5.2indirect
PyPIjsonlines4.0.0indirect
PyPIjsonpatch1.33indirect
PyPIjsonpointer3.0.0indirect
PyPIjsonref1.1.0indirect
PyPIjsonschema4.25.1indirect
PyPIjsonschema-specifications2025.9.1indirect
PyPIjupyter-client8.8.0indirect
PyPIjupyter-core5.9.1indirect
PyPIkeyring25.7.0indirect
PyPIkiwisolver1.4.9indirect
PyPIkubernetes35.0.0indirect
PyPIlangchain1.2.10indirect
PyPIlangchain-anthropic1.3.3indirect
PyPIlangchain-aws1.2.5indirect
PyPIlangchain-azure-ai1.0.3indirect
PyPIlangchain-google-genai4.2.0indirect
PyPIlangchain-ollama0.3.10indirect
PyPIlangchain-openai1.1.9indirect
PyPIlangfuse3.10.0indirect
PyPIlanggraph-checkpoint2.1.2indirect
PyPIlanggraph-prebuilt1.0.7indirect
PyPIlanggraph-sdk0.3.6indirect
PyPIlangsmith0.3.45indirect
PyPIlangsmith0.4.43indirect
PyPIlatex2mathml3.78.1indirect
PyPIlazy-loader0.4indirect
PyPIlegacy-api-wrap1.5indirect
PyPIleidenalg—indirect
PyPIleidenalg0.11.0indirect
PyPIlifelines—indirect
PyPIlifelines0.30.1indirect
PyPIlinkify-it-py2.0.3indirect
PyPIllvmlite0.44.0indirect
PyPIlobster-ai—indirect
PyPIlobster-drug-discovery—indirect
PyPIlobster-drug-discovery1.1.420indirect
PyPIlobster-genomics1.1.420indirect
PyPIlobster-metabolomics1.1.420indirect
PyPIlobster-ml—indirect
PyPIlobster-proteomics1.1.420indirect
PyPIlobster-research1.1.420indirect
PyPIlobster-transcriptomics1.1.420indirect
PyPIlobster-vector—indirect
PyPIlobster-vector1.1.420indirect
PyPIlobster-visualization1.1.420indirect
PyPIlocket1.0.0indirect
PyPIlogistro2.0.1indirect
PyPImarkdown3.10indirect
PyPImarkdown-it-py4.0.0indirect
PyPImarko2.2.1indirect
PyPImarkupsafe3.0.3indirect
PyPImccabe0.7.0indirect
PyPImdit-py-plugins0.5.0indirect
PyPImdurl0.1.2indirect
PyPImeeko—indirect
PyPImeeko0.7.1indirect
PyPImemory-profiler0.61.0indirect
PyPImergedeep1.3.4indirect
PyPImkdocs1.6.1indirect
PyPImkdocs-get-deps0.2.0indirect
PyPImkdocs-material9.7.0indirect
PyPImkdocs-material-extensions1.3.1indirect
PyPImmh35.2.0indirect
PyPImofapy2—indirect
PyPImore-itertools10.8.0indirect
PyPImoto5.1.17indirect
PyPImpire2.10.2indirect
PyPImpmath1.3.0indirect
PyPImsal1.34.0indirect
PyPImsal-extensions1.3.1indirect
PyPImsgpack1.1.2indirect
PyPImultidict6.7.0indirect
PyPImultipledispatch1.0.0indirect
PyPImultiprocess0.70.18indirect
PyPImypy1.18.2indirect
PyPImypy-extensions1.1.0indirect
PyPInarwhals2.12.0indirect
PyPInatsort8.4.0indirect
PyPInbclient0.10.2indirect
PyPIndindex1.10.0indirect
PyPInetworkx—indirect
PyPInetworkx3.5indirect
PyPInh30.3.2indirect
PyPInodeenv1.9.1indirect
PyPInumba0.61.2indirect
PyPInumcodecs0.16.3indirect
PyPInumexpr2.14.1indirect
PyPInvidia-cublas-cu1212.8.4.1indirect
PyPInvidia-cuda-cupti-cu1212.8.90indirect
PyPInvidia-cuda-nvrtc-cu1212.8.93indirect
PyPInvidia-cuda-runtime-cu1212.8.90indirect
PyPInvidia-cudnn-cu129.10.2.21indirect
PyPInvidia-cufft-cu1211.3.3.83indirect
PyPInvidia-cufile-cu121.13.1.3indirect
PyPInvidia-curand-cu1210.3.9.90indirect
PyPInvidia-cusolver-cu1211.7.3.90indirect
PyPInvidia-cusparse-cu1212.5.8.93indirect
PyPInvidia-cusparselt-cu120.7.1indirect
PyPInvidia-nccl-cu122.27.5indirect
PyPInvidia-nvjitlink-cu1212.8.93indirect
PyPInvidia-nvshmem-cu123.3.20indirect
PyPInvidia-nvtx-cu1212.8.90indirect
PyPIoauthlib3.3.1indirect
PyPIobonet—indirect
PyPIobonet1.1.1indirect
PyPIocrmac1.0.0indirect
PyPIollama0.6.1indirect
PyPIomegaconf2.3.0indirect
PyPIonnxruntime1.24.2indirect
PyPIopenai—indirect
PyPIopenai2.8.1indirect
PyPIopencv-python4.11.0.86indirect
PyPIopentelemetry-api1.38.0indirect
PyPIopentelemetry-exporter-otlp-proto-common1.38.0indirect
PyPIopentelemetry-exporter-otlp-proto-grpc1.38.0indirect
PyPIopentelemetry-exporter-otlp-proto-http1.38.0indirect
PyPIopentelemetry-proto1.38.0indirect
PyPIopentelemetry-sdk1.38.0indirect
PyPIopentelemetry-semantic-conventions0.59b0indirect
PyPIorjson3.11.4indirect
PyPIormsgpack1.12.0indirect
PyPIoverrides7.7.0indirect
PyPIpaginate0.5.7indirect
PyPIpartd1.4.2indirect
PyPIpathspec0.12.1indirect
PyPIpatsy1.0.2indirect
PyPIpeptides—indirect
PyPIpeptides0.5.0indirect
PyPIpillow11.3.0indirect
PyPIpip26.0.1indirect
PyPIpipdeptree2.30.0indirect
PyPIplatformdirs4.5.0indirect
PyPIpluggy1.6.0indirect
PyPIpolars1.35.2indirect
PyPIpolars-runtime-321.35.2indirect
PyPIpolyfactory3.0.0indirect
PyPIposthog5.4.0indirect
PyPIpre-commit4.4.0indirect
PyPIpropcache0.4.1indirect
PyPIprotobuf6.33.1indirect
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PyPIpyarrow22.0.0indirect
PyPIpyasn10.6.2indirect
PyPIpyasn1-modules0.4.2indirect
PyPIpybase641.4.3indirect
PyPIpyclipper1.3.0.post6indirect
PyPIpycodestyle2.14.0indirect
PyPIpycparser2.23indirect
PyPIpydantic—indirect
PyPIpydantic2.12.4indirect
PyPIpydantic-core2.41.5indirect
PyPIpydantic-settings2.12.0indirect
PyPIpydeseq2—indirect
PyPIpydeseq20.5.2indirect
PyPIpyflakes3.4.0indirect
PyPIpygments2.19.2indirect
PyPIpyjwt2.11.0indirect
PyPIpylatexenc2.10indirect
PyPIpylint4.0.3indirect
PyPIpymdown-extensions10.17.1indirect
PyPIpymmh30.0.5indirect
PyPIpynndescent0.5.13indirect
PyPIpyobjc-core12.1indirect
PyPIpyobjc-framework-cocoa12.1indirect
PyPIpyobjc-framework-coreml12.1indirect
PyPIpyobjc-framework-quartz12.1indirect
PyPIpyobjc-framework-vision12.1indirect
PyPIpyparsing3.2.5indirect
PyPIpypdfium24.30.0indirect
PyPIpypika0.51.1indirect
PyPIpyproject-hooks1.2.0indirect
PyPIpyreadline33.5.4indirect
PyPIpytest—indirect
PyPIpytest9.0.1indirect
PyPIpytest-asyncio1.3.0indirect
PyPIpytest-benchmark5.2.3indirect
PyPIpytest-cov—indirect
PyPIpytest-cov7.0.0indirect
PyPIpytest-html4.1.1indirect
PyPIpytest-json-report1.5.0indirect
PyPIpytest-metadata3.1.1indirect
PyPIpytest-mock—indirect
PyPIpytest-mock3.15.1indirect
PyPIpytest-timeout2.4.0indirect
PyPIpytest-xdist3.8.0indirect
PyPIpython-dateutil2.9.0.post0indirect
PyPIpython-docx1.2.0indirect
PyPIpython-multipart0.0.20indirect
PyPIpython-pptx1.0.2indirect
PyPIpytokens0.3.0indirect
PyPIpytz2025.2indirect
PyPIpywin32311indirect
PyPIpywin32-ctypes0.2.3indirect
PyPIpyyaml6.0.3indirect
PyPIpyyaml-env-tag1.1indirect
PyPIpyzmq27.1.0indirect
PyPIrapidfuzz—indirect
PyPIrapidocr3.4.2indirect
PyPIrdkit—indirect
PyPIrdkit2025.9.6indirect
PyPIreadme-renderer44.0indirect
PyPIredis7.0.1indirect
PyPIreferencing0.37.0indirect
PyPIregex2025.11.3indirect
PyPIrequests-oauthlib2.0.0indirect
PyPIrequests-toolbelt1.0.0indirect
PyPIresponses0.25.8indirect
PyPIrfc39862.0.0indirect
PyPIrispy0.10.0indirect
PyPIrpds-py0.29.0indirect
PyPIrsa4.9.1indirect
PyPIrtree1.4.1indirect
PyPIruff0.14.5indirect
PyPIs3transfer0.16.0indirect
PyPIsafetensors0.6.2indirect
PyPIscanpy—indirect
PyPIscanpy1.11.5indirect
PyPIscikit-image0.25.2indirect
PyPIscikit-misc—indirect
PyPIscikit-misc0.5.2indirect
PyPIscikit-survival—indirect
PyPIscrublet—indirect
PyPIscrublet0.2.3indirect
PyPIscvi-tools—indirect
PyPIseaborn0.13.2indirect
PyPIsecretstorage3.4.1indirect
PyPIsemchunk2.2.2indirect
PyPIsentence-transformers—indirect
PyPIsentence-transformers5.4.1indirect
PyPIsession-info1.0.1indirect
PyPIsession-info20.2.3indirect
PyPIsetuptools—indirect
PyPIsetuptools80.9.0indirect
PyPIsgkit—indirect
PyPIsgkit0.8.0indirect
PyPIshap—indirect
PyPIshapely2.1.2indirect
PyPIshellingham1.5.4indirect
PyPIsimplejson3.20.2indirect
PyPIsix1.17.0indirect
PyPIsniffio1.3.1indirect
PyPIsortedcontainers2.4.0indirect
PyPIsoupsieve2.8indirect
PyPIsparse0.17.0indirect
PyPIstarlette0.49.3indirect
PyPIstdlib-list0.12.0indirect
PyPIstevedore5.5.0indirect
PyPIsympy1.14.0indirect
PyPItables3.10.2indirect
PyPItblib3.2.2indirect
PyPItenacity9.1.2indirect
PyPItexttable1.7.0indirect
PyPItextual6.7.1indirect
PyPIthreadpoolctl3.6.0indirect
PyPItifffile2025.10.16indirect
PyPItiktoken0.12.0indirect
PyPItinynetrc1.3.1indirect
PyPItokenizers0.22.1indirect
PyPItomlkit0.13.3indirect
PyPItoolz1.1.0indirect
PyPItorch—indirect
PyPItorch2.9.1indirect
PyPItorchvision0.24.1indirect
PyPItornado6.5.2indirect
PyPItqdm4.67.1indirect
PyPItraitlets5.14.3indirect
PyPItransformers—indirect
PyPItransformers4.57.1indirect
PyPItree-sitter0.25.2indirect
PyPItree-sitter-c0.24.1indirect
PyPItree-sitter-java0.23.5indirect
PyPItree-sitter-javascript0.25.0indirect
PyPItree-sitter-python0.25.0indirect
PyPItree-sitter-typescript0.23.2indirect
PyPItriton3.5.1indirect
PyPItwine6.2.0indirect
PyPItypes-requests2.33.0.20260408indirect
PyPItyping-extensions4.15.0indirect
PyPItyping-inspection0.4.2indirect
PyPItzdata2025.2indirect
PyPIuc-micro-py1.0.3indirect
PyPIumap-learn0.5.9.post2indirect
PyPIurllib32.5.0indirect
PyPIuuid-utils0.14.0indirect
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PyPIuvloop0.22.1indirect
PyPIvina—indirect
PyPIvina1.2.7indirect
PyPIvirtualenv20.35.4indirect
PyPIwatchdog6.0.0indirect
PyPIwatchfiles1.1.1indirect
PyPIwcwidth0.2.14indirect
PyPIwebsocket-client1.9.0indirect
PyPIwebsockets15.0.1indirect
PyPIwerkzeug3.1.3indirect
PyPIwheel—indirect
PyPIwheel0.46.3indirect
PyPIwrapt1.17.3indirect
PyPIxarray—indirect
PyPIxarray2025.11.0indirect
PyPIxgboost—indirect
PyPIxlsxwriter3.2.9indirect
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PyPIyarl1.22.0indirect
PyPIzarr3.1.3indirect
PyPIzict3.0.0indirect
PyPIzipp3.23.0indirect
PyPIzstandard0.23.0indirect
PyPIzstandard0.25.0indirect
Raw JSON report machine-readable
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            ]
          }
        ],
        "description": "Is the project alive — is code being written and are releases shipping?"
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      {
        "key": "community",
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        "metrics": [
          {
            "key": "popularity",
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            "components": [
              {
                "key": "stars",
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                "max_points": 60
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              {
                "key": "forks",
                "name": "Forks",
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              {
                "key": "watchers",
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          {
            "key": "community_health",
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            "notes": [],
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              {
                "key": "license",
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                "key": "code_of_conduct",
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        "description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
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      {
        "key": "governance",
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        "name": "Sustainability & Governance",
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              "top_contributor_share": 0.998
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            "components": [
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                "key": "bus_factor",
                "name": "Bus factor",
                "detail": "1 contributor(s) cover half of all commits",
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                  {
                    "code": "bus_factor",
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                      "count": 1
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                "max_points": 54
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              {
                "key": "commit_distribution",
                "name": "Commit distribution",
                "detail": "top contributor authored 100% of commits",
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                  {
                    "code": "top_contributor_share",
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                      "share": 100
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                ],
                "max_points": 22.5
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              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "2 contributors",
                "points": 2.7,
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                "details": [
                  {
                    "code": "contributors_sampled",
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                ],
                "max_points": 13.5
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              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 1 contributing companies or organizations -- score normalized to 3",
                "points": 3,
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                "details": [],
                "max_points": 10
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            ]
          },
          {
            "key": "responsiveness",
            "band": "moderate",
            "name": "Issue & PR responsiveness",
            "note": null,
            "notes": [],
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            "inputs": {
              "merged_prs": 6,
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              "closed_issues": 6,
              "issue_closed_ratio": 0.857,
              "closed_unmerged_prs": 4
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                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "86% of issues closed",
                "points": 40.1,
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                    "code": "issues_closed_share",
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                      "share": 86
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                ],
                "max_points": 46.75
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              {
                "key": "pr_acceptance",
                "name": "PR acceptance",
                "detail": "6/10 decided PRs merged",
                "points": 22.9,
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                "details": [
                  {
                    "code": "decided_prs_merged",
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                      "merged": 6,
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                "max_points": 38.25
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              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
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                "points": 0,
                "status": "missed",
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            ]
          },
          {
            "key": "stewardship",
            "band": "at_risk",
            "name": "Ownership & stewardship",
            "note": null,
            "notes": [],
            "value": 48,
            "inputs": {
              "followers": 14,
              "owner_type": "Organization",
              "is_verified": null,
              "owner_login": "the-omics-os",
              "public_repos": 9,
              "account_age_days": 336
            },
            "components": [
              {
                "key": "ownership_backing",
                "name": "Ownership backing",
                "detail": "organization-owned",
                "points": 30,
                "status": "met",
                "details": [
                  {
                    "code": "owner_organization",
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                ],
                "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": "14 followers of the-omics-os",
                "points": 8.5,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
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                      "count": 14,
                      "login": "the-omics-os"
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                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "9 public repos, account ~0 yr old",
                "points": 9.1,
                "status": "partial",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 9
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                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 0
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                  }
                ],
                "max_points": 25
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            ]
          },
          {
            "key": "package_maintenance",
            "band": "excellent",
            "name": "Package maintenance",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "packages": [
                "lobster-ai"
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              "ecosystems": "pypi",
              "any_deprecated": false,
              "min_days_since_publish": 12
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            "components": [
              {
                "key": "published_resolvable",
                "name": "Published & resolvable",
                "detail": "1 package(s) on pypi",
                "points": 25,
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                "details": [
                  {
                    "code": "packages_published",
                    "params": {
                      "count": 1,
                      "ecosystems": "pypi"
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                  }
                ],
                "max_points": 25
              },
              {
                "key": "publish_recency",
                "name": "Publish recency",
                "detail": "latest publish 12 days ago",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "publish_recency",
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                ],
                "max_points": 35
              },
              {
                "key": "version_history",
                "name": "Version history",
                "detail": "58 published versions",
                "points": 20,
                "status": "met",
                "details": [
                  {
                    "code": "published_versions",
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                      "count": 58
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                  }
                ],
                "max_points": 20
              },
              {
                "key": "not_deprecated",
                "name": "Not deprecated",
                "detail": "active, not deprecated or yanked",
                "points": 20,
                "status": "met",
                "details": [
                  {
                    "code": "package_not_deprecated",
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                ],
                "max_points": 20
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            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
      },
      {
        "key": "engineering",
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        "name": "Engineering Quality",
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        "weight": 0.2,
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          {
            "key": "engineering_practices",
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            "name": "Engineering practices",
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            "notes": [],
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            "components": [
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                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": "6 workflow(s)",
                "points": 24,
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                "details": [
                  {
                    "code": "ci_workflows",
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                      "count": 6
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                ],
                "max_points": 24
              },
              {
                "key": "tests_present",
                "name": "Tests present",
                "detail": null,
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              {
                "key": "linter_config",
                "name": "Linter config",
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                "key": "pre_commit_hooks",
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              {
                "key": "editorconfig",
                "name": ".editorconfig",
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              {
                "key": "openssf_scorecard_ci_tests",
                "name": "OpenSSF Scorecard: CI-Tests",
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          },
          {
            "key": "documentation",
            "band": "excellent",
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            "notes": [],
            "value": 100,
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            "components": [
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                "key": "readme",
                "name": "README",
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              {
                "key": "documentation_directory",
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              {
                "key": "documentation_homepage_site",
                "name": "Documentation / homepage site",
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              {
                "key": "repository_description",
                "name": "Repository description",
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                "points": 10,
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              },
              {
                "key": "topics",
                "name": "Topics",
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                "details": [
                  {
                    "code": "topics_count",
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                "max_points": 10
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              {
                "key": "wiki",
                "name": "Wiki",
                "detail": null,
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                "max_points": 10
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            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
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      {
        "key": "security",
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        "name": "Security",
        "value": 34,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
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              "source": "openssf_scorecard",
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            "components": [
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                "key": "binary_artifacts",
                "name": "Binary-Artifacts",
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                "points": 7.5,
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              {
                "key": "branch_protection",
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                "detail": "branch protection not enabled on development/release branches",
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                "key": "ci_tests",
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                "key": "cii_best_practices",
                "name": "CII-Best-Practices",
                "detail": "no effort to earn an OpenSSF best practices badge detected",
                "points": 0,
                "status": "missed",
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                "key": "code_review",
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              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 1 contributing companies or organizations -- score normalized to 3",
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                "details": [],
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              },
              {
                "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": 2.2,
                "status": "partial",
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                "max_points": 2.5
              },
              {
                "key": "maintained",
                "name": "Maintained",
                "detail": "30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
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              {
                "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 not run on all commits -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file not detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "Project has not signed or included provenance with any releases.",
                "points": 0,
                "status": "missed",
                "details": [],
                "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": "149 existing vulnerabilities detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
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            ]
          },
          {
            "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,
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              "policy_countries": [
                "Russia",
                "Iran",
                "North Korea"
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              "review_only_matches": 0,
              "assessed_self_published_locations": 2
            },
            "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": "at_risk",
        "name": "AI Readiness",
        "value": 49,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "critical",
            "name": "Agent context & guidance",
            "note": "Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "legible_commit_history"
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                }
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            "band": "good",
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            "note": "Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
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              "typecheck_configs": [
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                "packages/lobster-metabolomics/lobster/agents/metabolomics/py.typed",
                "packages/lobster-metadata/lobster/agents/metadata_assistant/py.typed",
                "packages/lobster-ml/lobster/agents/machine_learning/py.typed",
                "packages/lobster-proteomics/lobster/agents/proteomics/py.typed",
                "packages/lobster-research/lobster/agents/data_expert/py.typed",
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            },
            "components": [
              {
                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
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                "points": 18,
                "status": "met",
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              },
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              },
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                "points": 11,
                "status": "met",
                "details": [
                  {
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                      "files": "packages/lobster-genomics/lobster/agents/genomics/py.typed, packages/lobster-metabolomics/lobster/agents/metabolomics/py.typed, packages/lobster-metadata/lobster/agents/metadata_assistant/py.typed, packages/lobster-ml/lobster/agents/machine_learning/py.typed, packages/lobster-proteomics/lobster/agents/proteomics/py.typed, packages/lobster-research/lobster/agents/data_expert/py.typed, packages/lobster-research/lobster/agents/research/py.typed, packages/lobster-structural-viz/lobster/agents/py.typed, packages/lobster-transcriptomics/lobster/agents/transcriptomics/py.typed, packages/lobster-visualization/lobster/agents/py.typed"
                    }
                  }
                ],
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              },
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                  }
                ],
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              },
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                ],
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              },
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          },
          {
            "key": "ai_code_legibility",
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        ],
        "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": [
    "Could not fetch go package 'github.com/the-omics-os/lobster-tui' from its registry"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-15T13:16:10.225765Z",
  "schema_version": "0.11.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/t/the-omics-os/lobster.svg",
  "full_name": "the-omics-os/lobster",
  "license_state": "custom",
  "license_spdx": null
}

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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 — PyPI.