Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-10-21 05:37 UTC

BiocPy / biocframe

Bioconductor-like data frames

PythonMIT★ 6 stars⑂ 3 forkssince Jul 2022View on GitHub ↗
KindLibraryhow this is determined
#dataframe

BiocPy/biocframe holds a health index of 80 out of 100, placing it in the Excellent band. It scores highest on Engineering Quality (93/100) and lowest on Community & Adoption (47/100). It was last updated 1 day ago. A single contributor accounts for most of its recent work.

80
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.

80
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 68 is calibrated to 80 on the published index scale (record calibration 2026-08-02).

Ownership

BiocPyOrganization
164 followers41 public repossince Jun 2022

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publishTags
PyPIbiocframe0.8.110,8676350 days agobioconductorbiocpybioinformaticsdataframe

Metrics by category

Vitality

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

63Moderate · 21% of overall

Development activity

65Good
How it's scored
36/36Push recency — last push 1 days ago
6.2/36Commit cadence — 9/52 weeks with commits
12.7/18Commit volume — 25 commits in the last year
10/10OpenSSF Scorecard: Maintained — 16 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year25
human_commit_share0.66
days_since_last_push1
active_weeks_last_year9

Release discipline

60Moderate
How it's scored
27/27Ships releases — 3 releases published
0/36Release recency — latest release 1,411 days ago
27/27Release cadence — a release every ~4.4 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count3
latest_release_tag0.2.2
releases_from_tagsno
days_since_latest_release1,411
mean_days_between_releases4.4
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?

47Weak · 17% of overall

Popularity & adoption

14Critical
How it's scored
11.3/60Stars — 6 stars
2.5/25Forks — 3 forks
0/15Watchers — 1 watchers
Inputs used
forks3
stars6
watchers1
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 (MIT)
18/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges7
has_contributingyes
has_issue_templateno
has_code_of_conductno
readme_badge_servicesgithub.com, readthedocs.org, shields.io
has_pull_request_templateno

Ecosystem adoption (downloads)

67Good
How it's scored
53.8/80Monthly downloads — 10,867 downloads/month across pypi
0/20Registry dependents — not reported by this ecosystem
Inputs used
packagesbiocframe
dependents—
ecosystemspypi
total_downloads—
monthly_downloads10,867
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?

66Good · 23% of overall

Maintainer resilience (bus factor)

30At Risk
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
5.2/22.5Commit distribution — top contributor authored 77% of commits
5.4/13.5Contributor breadth — 4 contributors
10/10OpenSSF Scorecard: Contributors — project has 17 contributing companies or organizations
Inputs used
bus_factor1
contributors_sampled4
top_contributor_share0.767

Issue & PR responsiveness

84Excellent
How it's scored
42/42Issue resolution — 100% of issues closed
29.2/30PR acceptance — 112/115 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
1.5/15OpenSSF Scorecard: Code-Review — Found 2/17 approved changesets -- score normalized to 1
Inputs used
merged_prs112
open_issues0
closed_issues35
prs_merged_7d0
prs_decided_7d0
prs_merged_30d0
prs_decided_30d0
issue_closed_ratio1
closed_unmerged_prs3
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.

Ownership & stewardship

66Good
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain
15.9/25Owner reach — 164 followers of BiocPy
20.5/25Track record — 41 public repos, account ~4 yr old
Inputs used
followers164
owner_typeOrganization
is_verifiedno
owner_loginBiocPy
public_repos41
account_age_days1,593

Package maintenance

100Exceptional
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
35/35Publish recency — latest publish 50 days ago
20/20Version history — 63 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagesbiocframe
ecosystemspypi
any_deprecatedno
min_days_since_publish50

Engineering Quality

Are baseline engineering and documentation practices in place?

93Exceptional · 19% of overall

Engineering practices

88Excellent
How it's scored
24/24CI workflows — 3 workflow(s)
24/24Tests present
16/16Linter config — pyproject.toml ([tool.ruff]), tox.ini
9.6/9.6Pre-commit hooks
0/6.4.editorconfig
14/20OpenSSF Scorecard: CI-Tests — 19 out of 24 merged PRs checked by a CI test -- score normalized to 7
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://biocpy.github.io/biocframe/
10/10Repository description
10/10Topics — 1 topics
10/10Wiki
Inputs used
topicsdataframe
has_wikiyes
homepagehttps://biocpy.github.io/biocframe/
docs_sitehttps://biocpy.github.io/biocframe/
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

70Good · 16% of overall

Security posture

62Moderate
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — no data
1.8/2.5CI-Tests — 19 out of 24 merged PRs checked by a CI test -- score normalized to 7
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0.8/7.5Code-Review — Found 2/17 approved changesets -- score normalized to 1
2.5/2.5Contributors — project has 17 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
2.5/2.5License — license file detected
7.5/7.5Maintained — 16 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
3.5/5SAST — SAST tool is not run on all commits -- score normalized to 7
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
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate6.2
Excluded from scoring (no data or not applicable): Branch-Protection, Signed-Releases. Remaining weights renormalized.

Dependency advisories

100Exceptional
How it's scored
35/35Direct dependencies free of known advisories — no direct dependency carries a known advisory
25/25Indirect dependencies free of known advisories — no indirect dependency carries a known advisory
0/40No advisories left outstanding — no advisory carries a publication date
Inputs used
sourceosv
advisories0
affected_packages0
assessed_packages2
unassessed_packages0
affected_by_severitynone
direct_affected_packages0
Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:biocframe@0.8.1 runtime dependency closure — what installing the published package pulls in — 2 packages. 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.

61Moderate · 4% of overall

Agent context & guidance

39Weak
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
38.8/40Legible commit history — 48 of 66 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtno
llms_txt_url—
legible_history_share0.727
agent_instruction_files—
agent_instruction_max_bytes—

Verify loop (build / test / typecheck)

70Good
How it's scored
18/18One-command bootstrap — docs/Makefile
22/22Automated tests
11/11Lint / format config — pyproject.toml ([tool.ruff]), tox.ini
11/11Static type checking — src/biocframe/py.typed
0/10Reproducible environment
0/10Demonstrated agent practice — no agent-authored commits among the last 100
8/8Automated maintenance — 8 of the last 100 commits are automated dependency updates
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfiles—
has_dockerfileno
typed_languageno
bootstrap_filesdocs/Makefile
has_devcontainerno
has_linter_configyes
typecheck_configssrc/biocframe/py.typed
agent_commit_share0
toolchain_manifests—
dependency_bot_commit_share0.08

Code legibility for models

79Good
How it's scored
27/45Type-checkable code — Python with type-check config (src/biocframe/py.typed)
51.8/55Manageable file sizes — 1/17 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes72,949
source_files_sampled17
oversized_source_files1

Key facts

6GitHub stars
4contributors
25commits, last 12 months
1days since last push
3releases
1bus factor
0open issues
PyPIpackage ecosystems

Data collection warnings

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token

More detail

Star and fork history 0 ★ / 3 ⇿
0Stars
3Forks
3Releases

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.

12233312022-112023-052023-10
Major 0Minor 0Patch 2
OpenSSF Scorecard 6.2 / 10
6.2aggregate

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 · 2026-10-21 05:37 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
7CI-Tests19 out of 24 merged PRs checked by a CI test -- score normalized to 7
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
1Code-ReviewFound 2/17 approved changesets -- score normalized to 1
10Contributorsproject has 17 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained16 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
7SASTSAST tool is not run on all commits -- score normalized to 7
0Security-Policysecurity policy file not detected
n/aSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
10Vulnerabilities0 existing vulnerabilities detected
Direct dependencies 2
RegistryPackageVersion constraintManifest
PyPIbiocutils>=0.3.3pyproject.toml
PyPInumpy>=1.26.0pyproject.toml
All dependencies 170

Full resolved dependency set from the GitHub dependency graph: 7 direct and 163 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
PyPIbiocutils—direct
PyPIbiocutils0.4.1direct
PyPInumpy—direct
PyPInumpy2.0.2direct
PyPInumpy2.2.6direct
PyPInumpy2.4.6direct
PyPInumpy2.5.2direct
PyPIaccessible-pygments0.0.5indirect
PyPIalabaster0.7.16indirect
PyPIalabaster1.0.0indirect
PyPIappnope1.0.0indirect
PyPIast-serialize0.8.0indirect
PyPIasttokens3.0.2indirect
PyPIattrs26.1.0indirect
PyPIbabel2.18.0indirect
PyPIbeautifulsoup44.15.0indirect
PyPIcertifi2026.7.22indirect
PyPIcffi2.0.0indirect
PyPIcffi2.1.1indirect
PyPIcharset-normalizer3.5.1indirect
PyPIclick8.1.8indirect
PyPIclick8.4.2indirect
PyPIcolorama0.4.6indirect
PyPIcomm0.2.3indirect
PyPIcoverage7.10.7indirect
PyPIcoverage7.15.4indirect
PyPIdebugpy1.8.21indirect
PyPIdecorator5.3.1indirect
PyPIdocutils0.21.2indirect
PyPIdocutils0.22.4indirect
PyPIexceptiongroup1.3.1indirect
PyPIexecuting2.2.1indirect
PyPIfastjsonschema2.21.2indirect
PyPIfastjsonschema2.22.2indirect
PyPIfuro—indirect
PyPIfuro2025.12.19indirect
PyPIgreenlet3.2.5indirect
PyPIgreenlet3.5.5indirect
PyPIidna3.19indirect
PyPIimagesize1.5.0indirect
PyPIimagesize2.0.1indirect
PyPIimportlib-metadata8.7.1indirect
PyPIimportlib-metadata9.0.0indirect
PyPIiniconfig2.1.0indirect
PyPIiniconfig2.3.0indirect
PyPIipykernel6.31.0indirect
PyPIipykernel7.3.0indirect
PyPIipython8.18.1indirect
PyPIipython8.39.0indirect
PyPIipython9.16.1indirect
PyPIipython-pygments-lexers1.1.1indirect
PyPIjedi0.19.2indirect
PyPIjedi0.20.0indirect
PyPIjinja23.1.6indirect
PyPIjsonschema4.25.1indirect
PyPIjsonschema4.26.0indirect
PyPIjsonschema-specifications2025.9.1indirect
PyPIjupyter-cache1.0.1indirect
PyPIjupyter-client8.6.3indirect
PyPIjupyter-client8.9.1indirect
PyPIjupyter-core5.8.1indirect
PyPIjupyter-core5.9.1indirect
PyPIlibrt0.15.0indirect
PyPIlinkify-it-py2.0.3indirect
PyPIlinkify-it-py2.1.1indirect
PyPImarkdown-it-py3.0.0indirect
PyPImarkdown-it-py4.2.0indirect
PyPImarkupsafe3.0.3indirect
PyPImatplotlib-inline0.2.2indirect
PyPImdit-py-plugins0.4.2indirect
PyPImdit-py-plugins0.6.1indirect
PyPImdurl0.1.2indirect
PyPImypy1.19.1indirect
PyPImypy2.3.1indirect
PyPImypy-extensions1.1.0indirect
PyPImyst-nb—indirect
PyPImyst-nb1.3.0indirect
PyPImyst-nb1.4.0indirect
PyPImyst-parser—indirect
PyPImyst-parser3.0.1indirect
PyPImyst-parser4.0.1indirect
PyPImyst-parser5.1.0indirect
PyPInbclient0.10.2indirect
PyPInbclient0.11.0indirect
PyPInbformat5.10.4indirect
PyPInbformat5.11.1indirect
PyPInest-asyncio1.6.0indirect
PyPInest-asyncio21.7.2indirect
PyPIpackaging26.3indirect
PyPIpandas—indirect
PyPIpandas2.3.3indirect
PyPIpandas3.0.5indirect
PyPIparso0.8.7indirect
PyPIpathspec1.1.1indirect
PyPIpexpect4.9.0indirect
PyPIplatformdirs4.11.4indirect
PyPIplatformdirs4.4.0indirect
PyPIpluggy1.6.0indirect
PyPIpolars—indirect
PyPIpolars1.36.1indirect
PyPIpolars1.44.0indirect
PyPIpolars-runtime-321.36.1indirect
PyPIpolars-runtime-321.44.0indirect
PyPIprompt-toolkit3.0.52indirect
PyPIprompt-toolkit3.0.53indirect
PyPIpsutil7.2.2indirect
PyPIptyprocess0.7.0indirect
PyPIpure-eval0.2.3indirect
PyPIpycparser2.23indirect
PyPIpycparser3.0indirect
PyPIpygments2.21.0indirect
PyPIpytest—indirect
PyPIpytest8.4.2indirect
PyPIpytest9.1.1indirect
PyPIpytest-cov—indirect
PyPIpytest-cov7.1.0indirect
PyPIpython-dateutil2.9.0.post0indirect
PyPIpytz2026.3.post1indirect
PyPIpywin32312indirect
PyPIpyyaml6.0.3indirect
PyPIpyzmq27.2.0indirect
PyPIreferencing0.36.2indirect
PyPIreferencing0.37.0indirect
PyPIrequests2.32.5indirect
PyPIrequests2.34.2indirect
PyPIroman-numerals4.1.0indirect
PyPIrpds-py0.27.1indirect
PyPIrpds-py0.30.0indirect
PyPIrpds-py2026.6.3indirect
PyPIsetuptools—indirect
PyPIsetuptools82.0.1indirect
PyPIsetuptools84.0.0indirect
PyPIsix1.17.0indirect
PyPIsnowballstemmer3.1.1indirect
PyPIsoupsieve2.8.4indirect
PyPIsoupsieve2.9.2indirect
PyPIsphinx—indirect
PyPIsphinx7.4.7indirect
PyPIsphinx8.1.3indirect
PyPIsphinx9.0.4indirect
PyPIsphinx9.1.0indirect
PyPIsphinx-autodoc-typehints—indirect
PyPIsphinx-autodoc-typehints2.3.0indirect
PyPIsphinx-autodoc-typehints3.0.1indirect
PyPIsphinx-autodoc-typehints3.13.4indirect
PyPIsphinx-autodoc-typehints3.6.1indirect
PyPIsphinx-basic-ng1.0.0b2indirect
PyPIsphinxcontrib-applehelp2.0.0indirect
PyPIsphinxcontrib-devhelp2.0.0indirect
PyPIsphinxcontrib-htmlhelp2.1.0indirect
PyPIsphinxcontrib-jsmath1.0.1indirect
PyPIsphinxcontrib-qthelp2.0.0indirect
PyPIsphinxcontrib-serializinghtml2.0.0indirect
PyPIsqlalchemy2.0.52indirect
PyPIstack-data0.6.3indirect
PyPItabulate0.10.0indirect
PyPItabulate0.9.0indirect
PyPItomli2.4.1indirect
PyPItornado6.5.8indirect
PyPItraitlets5.15.1indirect
PyPItraitlets5.16.1indirect
PyPItyping-extensions4.16.0indirect
PyPItzdata2026.3indirect
PyPIuc-micro-py1.0.3indirect
PyPIuc-micro-py2.0.0indirect
PyPIurllib32.6.3indirect
PyPIurllib32.7.0indirect
PyPIwcwidth0.8.2indirect
PyPIzipp3.23.1indirect
PyPIzipp4.1.0indirect
Dependency advisories 0

Installing pypi:biocframe@0.8.1 pulls in 2 packages, direct and transitive: 0 carry known advisories, of which 0 are direct dependencies.

No known advisories affect the assessed dependencies.

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.