Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-10-12 18:50 UTC

scalableminds / webknossos-libs

Python API and CLI tools for working with WEBKNOSSOS datasets, annotations and server interactions. Includes converter to OME-Zarr.

PythonNo license detected★ 29 stars⑂ 14 forkssince Dec 2016View on GitHub ↗
KindCommand-line toolLibraryNetwork servicehow this is determined

scalableminds/webknossos-libs holds a health index of 91 out of 100, placing it in the Excellent band. It scores highest on Vitality (96/100) and lowest on Security (47/100). It was last updated today. 3 contributors account for most of its recent work.

91
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.

91
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 77 is calibrated to 91 on the published index scale (record calibration 2026-08-02).

Ownership

scalable mindsOrganization · verified domain
25 followers128 public repossince Apr 2012

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publish
PyPIwebknossos4.2.313,0622120 days ago
PyPIcluster_tools4.2.313,0991960 days ago

Metrics by category

Vitality

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

96Exceptional · 21% of overall
How it's scored
36/36Push recency — last push 0 days ago
30.5/36Commit cadence — 44/52 weeks with commits
18/18Commit volume — 223 commits in the last year
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year223
human_commit_share1
days_since_last_push0
active_weeks_last_year44

Release discipline

100Exceptional
How it's scored
27/27Ships releases — 100 releases published
36/36Release recency — latest release 0 days ago
27/27Release cadence — a release every ~9.4 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count100
latest_release_tagv4.2.3
releases_from_tagsno
days_since_latest_release0
mean_days_between_releases9.4
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?

57Moderate · 17% of overall
How it's scored
23.5/60Stars — 29 stars
9.3/25Forks — 14 forks
3.9/15Watchers — 6 watchers
Inputs used
forks14
stars29
watchers6
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history
How it's scored
22.5/22.5README
0/22.5License — no license file detected
18/18CONTRIBUTING guide
13.5/13.5Code of conduct
0/7.2Issue template
6.3/6.3PR template
Inputs used
has_readmeyes
has_licenseno
readme_badges6
has_contributingyes
has_issue_templateno
has_code_of_conductyes
readme_badge_servicesshields.io
has_pull_request_templateyes
How it's scored
58.9/80Monthly downloads — 26,161 downloads/month across pypi
0/20Registry dependents — not reported by this ecosystem
Inputs used
packageswebknossos, cluster_tools
dependents—
ecosystemspypi
total_downloads—
monthly_downloads26,161
unverified_packages_excluded—
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?

84Excellent · 23% of overall
How it's scored
36/54Bus factor — 3 contributor(s) cover half of all commits
15.1/22.5Commit distribution — top contributor authored 33% of commits
13.5/13.5Contributor breadth — 32 contributors
10/10OpenSSF Scorecard: Contributors — project has 9 contributing companies or organizations
Inputs used
bus_factor3
contributors_sampled32
top_contributor_share0.329
How it's scored
36/42Issue resolution — 86% of issues closed
24.3/30PR acceptance — 892/1,101 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_prs892
open_issues66
closed_issues394
prs_merged_7d9
prs_decided_7d9
prs_merged_30d21
prs_decided_30d23
issue_closed_ratio0.857
closed_unmerged_prs209
first_time_authors_30d0
first_time_prs_merged_30d0
first_time_prs_decided_30d0
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.
How it's scored
30/30Ownership backing — organization-owned
20/20Verified domain
10.2/25Owner reach — 25 followers of scalableminds
25/25Track record — 128 public repos, account ~14 yr old
Inputs used
followers25
owner_typeOrganization
is_verifiedyes
owner_loginscalableminds
public_repos128
account_age_days5,292

Package maintenance

100Exceptional
How it's scored
25/25Published & resolvable — 2 package(s) on pypi
35/35Publish recency — latest publish 0 days ago
20/20Version history — 212 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packageswebknossos, cluster_tools
ecosystemspypi
any_deprecatedno
min_days_since_publish0

Engineering Quality

Are baseline engineering and documentation practices in place?

90Excellent · 19% of overall
How it's scored
24/24CI workflows — 6 workflow(s)
24/24Tests present
16/16Linter config — cluster_tools/pyproject.toml ([tool.ruff]), webknossos/pyproject.toml ([tool.ruff])
0/9.6Pre-commit hooks
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 25 out of 25 merged PRs checked by a CI test -- score normalized to 10
Inputs used
has_ciyes
has_testsyes
has_editorconfigno
has_linter_configyes
has_precommit_configno

Documentation

100Exceptional
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — https://docs.webknossos.org/webknossos-py/index.html
10/10Repository description
10/10Topics — 4 topics
10/10Wiki
Inputs used
topicswebknossos, volume-em, hacktoberfest, ome-zarr-converter
has_wikiyes
homepagehttps://docs.webknossos.org/webknossos-py/index.html
docs_sitehttps://docs.webknossos.org/webknossos-py/index.html
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

47Weak · 16% of overall
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
3/7.5Branch-Protection — branch protection is not maximal on development and all release branches
2.5/2.5CI-Tests — 25 out of 25 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
4.5/7.5Code-Review — Found 20/30 approved changesets -- score normalized to 6
2.5/2.5Contributors — project has 9 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
0/2.5License — license file not detected
7.5/7.5Maintained — 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10
0/5Packaging — no data
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 — no data
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
0/7.5Vulnerabilities — 113 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate4.9
Excluded from scoring (no data or not applicable): Packaging, Signed-Releases. Remaining weights renormalized.
How it's scored
6.3/35Direct dependencies free of known advisories — 4 affected: aiohttp 3.10.9 (critical 9.1), protobuf 6.32.0 (high 7.5), python-dotenv 1.0.1 (moderate 6.6), +1 more
0/25Indirect dependencies free of known advisories — transitive set not separable from development and test dependencies in this scope
23.1/40No advisories left outstanding — 4 advisory-carrying package(s) unaddressed past 90 days; oldest published 825 days ago
Inputs used
sourceosv
advisories254
affected_packages33
assessed_packages317
unassessed_packages0
affected_by_severitycritical 4, high 16, moderate 11, low 2
direct_affected_packages4
Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories. Remaining weights renormalized. Matched 317 resolved dependencies against OSV. This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.

AI Readiness

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

86Excellent · 4% of overall
How it's scored
45/45Agent instructions — webknossos/AGENTS.md, webknossos/CLAUDE.md
15/15Machine-readable docs (llms.txt) — llms.txt served by the project website (https://docs.webknossos.org/llms.txt)
38.4/40Legible commit history — 72 of 100 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtyes
llms_txt_urlhttps://docs.webknossos.org/llms.txt
legible_history_share0.72
agent_instruction_fileswebknossos/AGENTS.md, webknossos/CLAUDE.md
agent_instruction_max_bytes1,542
How it's scored
18/18One-command bootstrap — Makefile
22/22Automated tests
11/11Lint / format config — cluster_tools/pyproject.toml ([tool.ruff]), webknossos/pyproject.toml ([tool.ruff])
11/11Static type checking — webknossos/webknossos/py.typed
10/10Reproducible environment — Dockerfile, lockfile
10/10Demonstrated agent practice — 43 of the last 100 commits agent-authored or agent-credited
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_configswebknossos/webknossos/py.typed
agent_commit_share0.43
toolchain_manifests—
dependency_bot_commit_share0
How it's scored
27/45Type-checkable code — Python with type-check config (webknossos/webknossos/py.typed)
53.8/55Manageable file sizes — 6/281 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes2,503,110
source_files_sampled281
oversized_source_files6
How it's scored
40/40API schema (OpenAPI/GraphQL/proto) — webknossos/webknossos/proofreading/agglomerate_graph.proto
0/20MCP server
40/40Runnable examples — examples
Inputs used
example_dirsexamples
has_mcp_signalno
api_schema_fileswebknossos/webknossos/proofreading/agglomerate_graph.proto
interfaces_expected_ofnetwork-service

Key facts

29GitHub stars
32contributors
223commits, last 12 months
0days since last push
100releases
3bus factor
66open issues
PyPIpackage ecosystems

Data collection warnings

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
  • deps.dev does not index pypi:webknossos@4.2.3; advisories assessed against the repository dependency graph instead

More detail

Star and fork history 0 ★ / 14 ⇿
0Stars
14Forks
62Releases

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.

03581013151412018-022021-122025-09
Major 1Minor 5Patch 56

Each point covers 7 days.

OpenSSF Scorecard 4.9 / 10
4.9aggregate

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 · 2026-10-12 18:50 UTC

10Binary-Artifactsno binaries found in the repo
4Branch-Protectionbranch protection is not maximal on development and all release branches
10CI-Tests25 out of 25 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
6Code-ReviewFound 20/30 approved changesets -- score normalized to 6
10Contributorsproject has 9 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
0Licenselicense file not detected
10Maintained30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10
n/aPackagingpackaging workflow not 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
n/aSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
0Vulnerabilities113 existing vulnerabilities detected
Direct dependencies 30
RegistryPackageVersion constraintManifest
PyPItyping-extensions~=4.15.0cluster_tools/pyproject.toml
PyPIaiohttp~=3.14.1webknossos/pyproject.toml
PyPIattrs>=22.0.0webknossos/pyproject.toml
PyPIboltons>=21.0.0webknossos/pyproject.toml
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PyPIcertifi>=2023webknossos/pyproject.toml
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PyPIcluster-tools—webknossos/pyproject.toml
PyPIhttpx~=0.27.0webknossos/pyproject.toml
PyPIimageio>=2.37.0webknossos/pyproject.toml
PyPIlz4>=4.0.0webknossos/pyproject.toml
PyPIloxun~=2.0.0webknossos/pyproject.toml
PyPInatsort~=8.4.0webknossos/pyproject.toml
PyPInetworkx~=3.2.1webknossos/pyproject.toml
PyPInumpy>=2.0.0,<3.0.0webknossos/pyproject.toml
PyPIpackaging>=21.0webknossos/pyproject.toml
PyPIprotobuf<7,>=3.12.0webknossos/pyproject.toml
PyPIgoogle-api-python-client>= 2.0.0webknossos/pyproject.toml
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PyPIpython-dateutil>=2.9.0webknossos/pyproject.toml
PyPIpython-dotenv~=1.0.1webknossos/pyproject.toml
PyPIrich~=13.8.0webknossos/pyproject.toml
PyPIscipy>=1.13webknossos/pyproject.toml
PyPItensorstore==0.1.76webknossos/pyproject.toml
PyPItensorstore~=0.1.78webknossos/pyproject.toml
PyPItyper~=0.12.5webknossos/pyproject.toml
PyPItyping-extensions~=4.0webknossos/pyproject.toml
PyPIuniversal-pathlib~=0.2webknossos/pyproject.toml
PyPIwkw==1.1.24webknossos/pyproject.toml
PyPIzipp>=3.5.0,<4.0.0webknossos/pyproject.toml
All dependencies 317

Full resolved dependency set from the GitHub dependency graph: 52 direct and 265 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

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PyPIoauthlib3.3.1indirect
PyPIopenapi-schema-validator0.4.4indirect
PyPIopenapi-spec-validator0.5.7indirect
PyPIpaginate0.5.7indirect
PyPIpandas3.0.5indirect
PyPIpartd1.4.2indirect
PyPIpathable0.4.4indirect
PyPIpathlib-abc0.5.1indirect
PyPIpathlib-abc0.5.2indirect
PyPIpathspec0.12.1indirect
PyPIpathspec1.1.1indirect
PyPIpillow10.4.0indirect
PyPIpillow12.3.0indirect
PyPIplatformdirs4.3.6indirect
PyPIpluggy1.5.0indirect
PyPIpluggy1.6.0indirect
PyPIpooch1.5.2indirect
PyPIpropcache0.2.0indirect
PyPIpropcache0.5.2indirect
PyPIproto-plus1.27.0indirect
PyPIproto-plus1.28.3indirect
PyPIpy-partiql-parser0.6.3indirect
PyPIpyasn10.6.1indirect
PyPIpyasn10.6.2indirect
PyPIpyasn10.6.4indirect
PyPIpyasn1-modules0.4.1indirect
PyPIpyasn1-modules0.4.2indirect
PyPIpycparser2.22indirect
PyPIpycparser3.0indirect
PyPIpygments2.18.0indirect
PyPIpygments2.19.1indirect
PyPIpygments2.21.0indirect
PyPIpylibczirw5.1.1indirect
PyPIpymdown-extensions10.16.1indirect
PyPIpyparsing3.3.2indirect
PyPIpyrsistent0.20.0indirect
PyPIpytest8.3.5indirect
PyPIpytest-cov7.1.0indirect
PyPIpytest-custom-exit-code0.3.0indirect
PyPIpytest-split0.10.0indirect
PyPIpytest-sugar1.0.0indirect
PyPIpytest-timeout2.3.1indirect
PyPIpytest-timeout2.4.0indirect
PyPIpytest-timestamper0.0.10indirect
PyPIpytest-xdist3.8.0indirect
PyPIpywin32312indirect
PyPIpyxdg0.28indirect
PyPIpyyaml6.0.2indirect
PyPIpyyaml6.0.3indirect
PyPIpyyaml-env-tag0.1indirect
PyPIregex2026.7.19indirect
PyPIrequests2.32.3indirect
PyPIrequests2.34.2indirect
PyPIrequests-oauthlib2.0.0indirect
PyPIresponses0.26.2indirect
PyPIrfc3339-validator0.1.4indirect
PyPIrsa4.9indirect
PyPIrsa4.9.1indirect
PyPIruff0.11.2indirect
PyPIruff0.15.22indirect
PyPIs3fs2026.7.0indirect
PyPIs3transfer0.19.2indirect
PyPIscikit-image0.25.2indirect
PyPIscikit-image0.26.0indirect
PyPIscikit-learn1.9.0indirect
PyPIscm-pims0.7.1indirect
PyPIsetuptools84.0.0indirect
PyPIshellingham1.5.4indirect
PyPIsix1.16.0indirect
PyPIsix1.17.0indirect
PyPIslicerator1.1.0indirect
PyPIsniffio1.3.1indirect
PyPIsortedcontainers2.4.0indirect
PyPIsoupsieve2.6indirect
PyPIsympy1.14.0indirect
PyPItabulate0.10.0indirect
PyPItblib3.0.0indirect
PyPItermcolor3.3.0indirect
PyPIthreadpoolctl3.6.0indirect
PyPItifffile2024.8.30indirect
PyPItifffile2025.5.10indirect
PyPItifffile2026.3.3indirect
PyPItifffile2026.8.23indirect
PyPItomli2.2.1indirect
PyPItomli2.4.1indirect
PyPItoolz1.0.0indirect
PyPItornado6.4.2indirect
PyPItypes-python-dateutil2.9.0.20260807indirect
PyPItzdata2026.3indirect
PyPIuritemplate4.2.0indirect
PyPIurllib32.2.3indirect
PyPIurllib32.3.0indirect
PyPIurllib32.7.0indirect
PyPIvalidators0.35.0indirect
PyPIwaitress3.0.2indirect
PyPIwatchdog5.0.3indirect
PyPIwcwidth0.7.0indirect
PyPIwebsocket-client1.8.0indirect
PyPIwerkzeug3.1.8indirect
PyPIwrapt2.3.0indirect
PyPIxmltodict1.0.4indirect
PyPIyarl1.14.0indirect
PyPIyarl1.24.5indirect
PyPIzarr2.18.3indirect
PyPIzarr3.1.6indirect
PyPIzarr3.3.0indirect
PyPIzict3.0.0indirect
Dependency advisories 33

This repository publishes no package the index resolves, so its own dependency graph was assessed — 317 packages, which also include development and test pins that never ship: 33 carry known advisories, of which 4 are direct.

PackageVersionRelationSeverityAdvisoriesFixed in
aiohttp3.10.9directcritical703.14.3
anyio4.6.0indirectcritical44.14.2
h110.14.0indirectcritical20.16.0
pillow10.4.0indirectcritical3412.3.0
protobuf6.32.0directhigh26.33.5
fsspec2025.3.0indirecthigh12026.6.0
fsspec2025.9.0indirecthigh12026.6.0
httplib20.31.1indirecthigh20.32.0
jinja23.1.4indirecthigh63.1.6
lxml6.0.0indirecthigh26.1.0
markdown3.7indirecthigh23.8.1
msgpack1.1.0indirecthigh21.2.1
pyasn10.6.1indirecthigh100.6.4
pyasn10.6.2indirecthigh80.6.4
pymdown-extensions10.16.1indirecthigh611.0.1
soupsieve2.6indirecthigh82.9.0
tornado6.4.2indirecthigh266.5.9
urllib32.2.3indirecthigh162.8.0
urllib32.3.0indirecthigh162.8.0
urllib32.7.0indirecthigh62.8.0
python-dotenv1.0.1directmoderate21.2.2
zipp3.5.1directmoderate23.19.1
distributed2023.9.3indirectmoderate22026.1.0
idna3.10indirectmoderate23.15
mkdocs-material9.6.20indirectmoderate29.7.7
multidict6.7.1indirectmoderate16.9.1
oauthlib3.2.2indirectmoderate44.0.0
oauthlib3.3.1indirectmoderate44.0.0
pytest8.3.5indirectmoderate29.0.3
requests2.32.3indirectmoderate42.33.0
werkzeug3.1.8indirectmoderate13.1.9
pygments2.18.0indirectlow22.20.0
pygments2.19.1indirectlow22.20.0

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

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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 v0.34.0 — full methodology · metrics wiki.

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