Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-09-18 21:31 UTC

zqfang / GSEApy

Gene Set Enrichment Analysis in Python

Python · RustBSD-3-Clause★ 710 stars⑂ 143 forkssince Jan 2016View on GitHub ↗
KindLibraryCommand-line toolhow this is determined
#gsea#enrichment-analysis#python3#rust

zqfang/GSEApy holds a health index of 84 out of 100, placing it in the Excellent band. It scores highest on Engineering Quality (88/100) and lowest on Security (55/100). It was last updated 16 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

Zhuoqing FangPersonal account
165 followers52 public repossince Nov 2013Stanford

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 publishTags
PyPIgseapy1.3.1186,4694954 days agogene-ontologygobiologyenrichmentbioinformaticscomputational-biology

Metrics by category

Vitality

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

78Good · 21% of overall

Development activity

69Good
How it's scored
28.8/36Push recency — last push 16 days ago
12.5/36Commit cadence — 18/52 weeks with commits
18/18Commit volume — 159 commits in the last year
10/10OpenSSF Scorecard: Maintained — 22 commit(s) and 1 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year159
human_commit_share0.74
days_since_last_push16
active_weeks_last_year18

Release discipline

92Excellent
How it's scored
27/27Ships releases — 47 releases published
36/36Release recency — latest release 54 days ago
19.8/27Release cadence — a release every ~55.5 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count47
latest_release_tagv1.3.1
releases_from_tagsno
days_since_latest_release54
mean_days_between_releases55.5
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?

68Good · 17% of overall

Popularity & adoption

70Good
How it's scored
46.2/60Stars — 710 stars
17.9/25Forks — 143 forks
5.8/15Watchers — 12 watchers
Inputs used
forks143
stars710
watchers12
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

Community health

50Moderate
How it's scored
22.5/22.5README
22.5/22.5License — recognized license (BSD-3-Clause)
0/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges6
has_contributingno
has_issue_templateno
has_code_of_conductno
readme_badge_servicesbadge.fury.io, github.com, readthedocs.org, shields.io
has_pull_request_templateno

Ecosystem adoption (downloads)

88Excellent
How it's scored
70.3/80Monthly downloads — 186,469 downloads/month across pypi
0/20Registry dependents — not reported by this ecosystem
Inputs used
packagesgseapy
dependents—
ecosystemspypi
total_downloads—
monthly_downloads186,469
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)

35Weak
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
2.4/22.5Commit distribution — top contributor authored 90% of commits
13.5/13.5Contributor breadth — 24 contributors
10/10OpenSSF Scorecard: Contributors — project has 30 contributing companies or organizations
Inputs used
bus_factor1
contributors_sampled24
top_contributor_share0.895

Issue & PR responsiveness

78Good
How it's scored
40.9/42Issue resolution — 98% of issues closed
23/30PR acceptance — 62/81 decided PRs merged
13/13Newcomer PR acceptance — 1/1 first-time contributors' PRs merged in 30d
1.5/15OpenSSF Scorecard: Code-Review — Found 2/18 approved changesets -- score normalized to 1
Inputs used
merged_prs62
open_issues6
closed_issues236
prs_merged_7d0
prs_decided_7d0
prs_merged_30d1
prs_decided_30d1
issue_closed_ratio0.975
closed_unmerged_prs19
first_time_authors_30d1
first_time_prs_merged_30d1
first_time_prs_decided_30d1

Ownership & stewardship

63Moderate
How it's scored
10/30Ownership backing — personal (user) account
0/20Verified domain — not applicable to user accounts
16/25Owner reach — 165 followers of zqfang
24.6/25Track record — 52 public repos, account ~12 yr old
Inputs used
followers165
owner_typeUser
is_verified—
owner_loginzqfang
public_repos52
account_age_days4,697
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 54 days ago
20/20Version history — 49 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagesgseapy
ecosystemspypi
any_deprecatedno
min_days_since_publish54

Engineering Quality

Are baseline engineering and documentation practices in place?

88Excellent · 19% of overall

Engineering practices

80Excellent
How it's scored
24/24CI workflows — 2 workflow(s)
24/24Tests present
16/16Linter config — pyproject.toml ([tool.ruff]), tox.ini
0/9.6Pre-commit hooks
0/6.4.editorconfig
16/20OpenSSF Scorecard: CI-Tests — 5 out of 6 merged PRs checked by a CI test -- score normalized to 8
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 — http://gseapy.rtfd.io/
10/10Repository description
10/10Topics — 4 topics
10/10Wiki
Inputs used
topicsgsea, enrichment-analysis, python3, rust
has_wikiyes
homepagehttp://gseapy.rtfd.io/
docs_sitehttp://gseapy.rtfd.io/
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

55Moderate · 16% of overall

Security posture

44Weak
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
2/2.5CI-Tests — 5 out of 6 merged PRs checked by a CI test -- score normalized to 8
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0.8/7.5Code-Review — Found 2/18 approved changesets -- score normalized to 1
2.5/2.5Contributors — project has 30 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 — 22 commit(s) and 1 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 — 32 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate4.4
Excluded from scoring (no data or not applicable): Packaging, 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_packages18
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:gseapy@1.3.1 runtime dependency closure — what installing the published package pulls in — 18 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.

56Moderate · 4% of overall

Agent context & guidance

14Critical
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
13.7/40Legible commit history — 19 of 74 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtno
llms_txt_url—
legible_history_share0.257
agent_instruction_files—
agent_instruction_max_bytes—

Verify loop (build / test / typecheck)

73Good
How it's scored
18/18One-command bootstrap — docs/Makefile
22/22Automated tests
11/11Lint / format config — pyproject.toml ([tool.ruff]), tox.ini
0/11Static type checking
10/10Reproducible environment — lockfile
4/10Demonstrated agent practice — 2 of the last 100 commits agent-authored or agent-credited
8/8Automated maintenance — 1 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
lockfilesCargo.lock, uv.lock
has_dockerfileno
typed_languageno
bootstrap_filesdocs/Makefile
has_devcontainerno
has_linter_configyes
typecheck_configs—
agent_commit_share0.02
toolchain_manifestsCargo.toml
dependency_bot_commit_share0.01

Code legibility for models

52Moderate
How it's scored
0/45Type-checkable code — Python without a type-check config
51.7/55Manageable file sizes — 2/33 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes74,290
source_files_sampled33
oversized_source_files2

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 — notebooks
Inputs used
example_dirsnotebooks
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

710GitHub stars
24contributors
159commits, last 12 months
16days since last push
47releases
1bus factor
6open issues
crates.io, PyPIpackage ecosystems

Data collection warnings

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
  • Could not fetch crates package 'gseapy' from its registry

More detail

Star and fork history 0 ★ / 143 ⇿
0Stars
143Forks
47Releases

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.

025507510012515013632016-072021-082026-08
Major 1Minor 6Patch 40

Each point covers 10 days.

OpenSSF Scorecard 4.4 / 10
4.4aggregate

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 · 2026-09-18 21:29 UTC

10Binary-Artifactsno binaries found in the repo
0Branch-Protectionbranch protection not enabled on development/release branches
8CI-Tests5 out of 6 merged PRs checked by a CI test -- score normalized to 8
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
1Code-ReviewFound 2/18 approved changesets -- score normalized to 1
10Contributorsproject has 30 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained22 commit(s) and 1 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
0Vulnerabilities32 existing vulnerabilities detected
Direct dependencies 14
RegistryPackageVersion constraintManifest
crates.iopyo30.29.0Cargo.toml
crates.iorand0.9Cargo.toml
crates.iorayon1.10Cargo.toml
crates.iocsv1.3Cargo.toml
crates.ioitertools0.13Cargo.toml
crates.iostatrs0.17Cargo.toml
crates.ioserde1.0Cargo.toml
crates.iorand_mt6.0.3Cargo.toml
crates.iospecial0.13.1Cargo.toml
PyPInumpy>=1.13.0pyproject.toml
PyPIscipy—pyproject.toml
PyPIpandas—pyproject.toml
PyPImatplotlib>=2.2pyproject.toml
PyPIrequests—pyproject.toml
All dependencies 198

Full resolved dependency set from the GitHub dependency graph: 27 direct and 171 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
crates.iocsv1.3.1direct
crates.ioitertools0.13.0direct
crates.iopyo30.29.0direct
crates.iorand0.8.5direct
crates.iorand0.9.2direct
crates.iorand_mt6.0.3direct
crates.iorayon1.10.0direct
crates.ioserde1.0.215direct
crates.iospecial0.13.1direct
crates.iostatrs0.17.1direct
PyPImatplotlib—direct
PyPImatplotlib3.10.9direct
PyPImatplotlib3.9.4direct
PyPInumpy—direct
PyPInumpy2.0.2direct
PyPInumpy2.2.6direct
PyPInumpy2.4.4direct
PyPIpandas—direct
PyPIpandas2.3.3direct
PyPIpandas3.0.2direct
PyPIrequests—direct
PyPIrequests2.32.5direct
PyPIrequests2.33.1direct
PyPIscipy—direct
PyPIscipy1.13.1direct
PyPIscipy1.15.3direct
PyPIscipy1.17.1direct
crates.ioapprox0.5.1indirect
crates.ioautocfg1.4.0indirect
crates.iobytemuck1.19.0indirect
crates.iobyteorder1.5.0indirect
crates.iocfg-if1.0.0indirect
crates.iocrossbeam-deque0.8.5indirect
crates.iocrossbeam-epoch0.9.18indirect
crates.iocrossbeam-utils0.8.20indirect
crates.iocsv-core0.1.11indirect
crates.ioeither1.13.0indirect
crates.ioellip1.1.0indirect
crates.iogetrandom0.2.15indirect
crates.iogetrandom0.3.4indirect
crates.ioheck0.5.0indirect
crates.ioitoa1.0.11indirect
crates.iolambert_w2.0.3indirect
crates.iolibc0.2.162indirect
crates.iolibm0.2.11indirect
crates.iomatrixmultiply0.3.9indirect
crates.iomemchr2.7.4indirect
crates.ionalgebra0.32.6indirect
crates.ionalgebra-macros0.2.2indirect
crates.ionum-complex0.4.6indirect
crates.ionum-integer0.1.46indirect
crates.ionum-lazy0.4.1indirect
crates.ionum-rational0.4.2indirect
crates.ionum-traits0.2.19indirect
crates.ionumeric_literals0.2.0indirect
crates.ioonce_cell1.21.4indirect
crates.iopaste1.0.15indirect
crates.ioportable-atomic1.10.0indirect
crates.ioppv-lite860.2.20indirect
crates.ioproc-macro21.0.89indirect
crates.iopyo3-build-config0.29.0indirect
crates.iopyo3-ffi0.29.0indirect
crates.iopyo3-macros0.29.0indirect
crates.iopyo3-macros-backend0.29.0indirect
crates.ioquote1.0.37indirect
crates.ior-efi5.3.0indirect
crates.iorand_chacha0.3.1indirect
crates.iorand_chacha0.9.0indirect
crates.iorand_core0.6.4indirect
crates.iorand_core0.9.5indirect
crates.iorand_distr0.4.3indirect
crates.iorawpointer0.2.1indirect
crates.iorayon-core1.12.1indirect
crates.ioryu1.0.18indirect
crates.iosafe_arch0.7.2indirect
crates.ioserde_derive1.0.215indirect
crates.iosimba0.8.1indirect
crates.iosyn1.0.109indirect
crates.iosyn2.0.87indirect
crates.iotarget-lexicon0.13.5indirect
crates.iotypenum1.17.0indirect
crates.iounicode-ident1.0.13indirect
crates.iowasi0.11.0+wasi-snapshot-preview1indirect
crates.iowasip21.0.2+wasi-0.2.9indirect
crates.iowide0.7.28indirect
crates.iowit-bindgen0.51.0indirect
crates.iozerocopy0.7.35indirect
crates.iozerocopy-derive0.7.35indirect
PyPIalabaster0.7.16indirect
PyPIalabaster1.0.0indirect
PyPIbabel2.18.0indirect
PyPIbackports-tarfile1.2.0indirect
PyPIbioservices—indirect
PyPIcertifi2026.4.22indirect
PyPIcffi2.0.0indirect
PyPIcharset-normalizer3.4.7indirect
PyPIcolorama0.4.6indirect
PyPIcontourpy1.3.0indirect
PyPIcontourpy1.3.2indirect
PyPIcontourpy1.3.3indirect
PyPIcoverage7.10.7indirect
PyPIcoverage7.13.5indirect
PyPIcryptography47.0.0indirect
PyPIcycler0.12.1indirect
PyPIcython—indirect
PyPIdocutils—indirect
PyPIdocutils0.21.2indirect
PyPIdocutils0.22.4indirect
PyPIexceptiongroup1.3.1indirect
PyPIfonttools4.60.2indirect
PyPIfonttools4.62.1indirect
PyPIgseapy—indirect
PyPIgseapy1.3.0indirect
PyPIid1.6.1indirect
PyPIidna3.13indirect
PyPIimagesize1.5.0indirect
PyPIimagesize2.0.0indirect
PyPIimportlib-metadata8.7.1indirect
PyPIimportlib-metadata9.0.0indirect
PyPIimportlib-resources6.5.2indirect
PyPIiniconfig2.1.0indirect
PyPIiniconfig2.3.0indirect
PyPIipykernel—indirect
PyPIipython—indirect
PyPIjaraco-classes3.4.0indirect
PyPIjaraco-context6.1.1indirect
PyPIjaraco-context6.1.2indirect
PyPIjaraco-functools4.4.0indirect
PyPIjeepney0.9.0indirect
PyPIjinja23.1.6indirect
PyPIjoblib—indirect
PyPIkeyring25.7.0indirect
PyPIkiwisolver1.4.7indirect
PyPIkiwisolver1.5.0indirect
PyPIlxml6.1.0indirect
PyPImarkdown-it-py3.0.0indirect
PyPImarkdown-it-py4.0.0indirect
PyPImarkupsafe3.0.3indirect
PyPImdurl0.1.2indirect
PyPImore-itertools10.8.0indirect
PyPImore-itertools11.0.2indirect
PyPInbsphinx—indirect
PyPInh30.3.5indirect
PyPInose—indirect
PyPInumpydoc—indirect
PyPInumpydoc1.10.0indirect
PyPInumpydoc1.9.0indirect
PyPIpackaging26.2indirect
PyPIpillow11.3.0indirect
PyPIpillow12.2.0indirect
PyPIpip—indirect
PyPIpluggy1.6.0indirect
PyPIpycparser2.23indirect
PyPIpycparser3.0indirect
PyPIpygments2.20.0indirect
PyPIpyparsing3.3.2indirect
PyPIpytest—indirect
PyPIpytest8.4.2indirect
PyPIpytest9.0.3indirect
PyPIpytest-cov7.1.0indirect
PyPIpython-dateutil2.9.0.post0indirect
PyPIpytz2026.1.post1indirect
PyPIpywin32-ctypes0.2.3indirect
PyPIpyyaml—indirect
PyPIpyyaml6.0.3indirect
PyPIreadme-renderer44.0indirect
PyPIrequests-toolbelt1.0.0indirect
PyPIrfc39862.0.0indirect
PyPIrich15.0.0indirect
PyPIroman-numerals4.1.0indirect
PyPIruff0.15.12indirect
PyPIsecretstorage3.3.3indirect
PyPIsecretstorage3.5.0indirect
PyPIsetuptools—indirect
PyPIsetuptools-rust—indirect
PyPIsix1.17.0indirect
PyPIsnowballstemmer3.0.1indirect
PyPIsphinx—indirect
PyPIsphinx7.4.7indirect
PyPIsphinx8.1.3indirect
PyPIsphinx9.0.4indirect
PyPIsphinx9.1.0indirect
PyPIsphinx-rtd-theme—indirect
PyPIsphinx-rtd-theme3.1.0indirect
PyPIsphinxcontrib-applehelp2.0.0indirect
PyPIsphinxcontrib-devhelp2.0.0indirect
PyPIsphinxcontrib-htmlhelp2.1.0indirect
PyPIsphinxcontrib-jquery4.1indirect
PyPIsphinxcontrib-jsmath1.0.1indirect
PyPIsphinxcontrib-qthelp2.0.0indirect
PyPIsphinxcontrib-serializinghtml2.0.0indirect
PyPItomli2.4.1indirect
PyPItwine—indirect
PyPItwine6.2.0indirect
PyPItyping-extensions4.15.0indirect
PyPItzdata2026.2indirect
PyPIurllib32.6.3indirect
PyPIzipp3.23.1indirect
Dependency advisories 0

Installing pypi:gseapy@1.3.1 pulls in 18 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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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.