Public record
Software health reportschema 0.12.0 · metrics 2.10.0 · 2026-07-17 21:56 UTC

EBi-Metagenomics / mgnify-pipelines-toolkit

This Python package contains a collection of scripts and tools for including in MGnify pipelines

PythonApache-2.0★ 1 star⑂ 2 forkssince Nov 2023View on GitHub ↗
KindLibraryCommand-line toolhow this is determined

EBi-Metagenomics/mgnify-pipelines-toolkit holds a health index of 78 out of 100, placing it in the Good band. It scores highest on Vitality (94/100) and lowest on Community & Adoption (24/100). It was last updated 4 days ago. 2 contributors account for most of its recent work.

78
overall / 100
Good

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.

78
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 67 is calibrated to 78 on the published index scale (record calibration 2026-08-02).

Ownership

MGnifyOrganization
171 followers225 public repossince Oct 2017

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publishTags
PyPImgnify_pipelines_toolkit1.5.41,147724 days agobioinformaticspipelinesmetagenomics

Metrics by category

Vitality

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

94Exceptional · 21% of overall

Development activity

90Excellent
How it's scored
36/36Push recency — last push 4 days ago
26.3/36Commit cadence — 38/52 weeks with commits
18/18Commit volume — 330 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_year330
human_commit_share—
days_since_last_push4
active_weeks_last_year38

Release discipline

100Exceptional
How it's scored
27/27Ships releases — 72 releases published
36/36Release recency — latest release 4 days ago
27/27Release cadence — a release every ~13 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count72
latest_release_tagv1.5.4
releases_from_tagsno
days_since_latest_release4
mean_days_between_releases13
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?

24At Risk · 17% of overall

Popularity & adoption

2Critical
How it's scored
0/60Stars — 1 stars
0/25Forks — 2 forks
1.7/15Watchers — 3 watchers
Inputs used
forks2
stars1
watchers3
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 (Apache-2.0)
0/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges—
has_contributingno
has_issue_templateno
has_code_of_conductno
readme_badge_services—
has_pull_request_templateno

Sustainability & Governance

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

86Excellent · 23% of overall

Maintainer resilience (bus factor)

62Moderate
How it's scored
25.2/54Bus factor — 2 contributor(s) cover half of all commits
13.8/22.5Commit distribution — top contributor authored 38% of commits
13.5/13.5Contributor breadth — 11 contributors
10/10OpenSSF Scorecard: Contributors — project has 4 contributing companies or organizations
Inputs used
bus_factor2
contributors_sampled11
top_contributor_share0.385

Issue & PR responsiveness

99Exceptional
How it's scored
0/42Issue resolution — no issues or no data
29.4/30PR acceptance — 157/160 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
15/15OpenSSF Scorecard: Code-Review — all changesets reviewed
Inputs used
merged_prs157
open_issues0
closed_issues0
prs_merged_7d—
prs_decided_7d—
prs_merged_30d—
prs_decided_30d—
issue_closed_ratio—
closed_unmerged_prs3
first_time_authors_30d—
first_time_prs_merged_30d—
first_time_prs_decided_30d—
Excluded from scoring (no data or not applicable): Issue resolution, Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

89Excellent
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain — verified-domain status not read for this organization
16.1/25Owner reach — 171 followers of EBI-Metagenomics
25/25Track record — 225 public repos, account ~8 yr old
Inputs used
followers171
owner_typeOrganization
is_verified—
owner_loginEBI-Metagenomics
public_repos225
account_age_days3,194
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 4 days ago
20/20Version history — 72 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagesmgnify_pipelines_toolkit
ecosystemspypi
any_deprecatedno
min_days_since_publish4

Engineering Quality

Are baseline engineering and documentation practices in place?

76Good · 19% of overall

Engineering practices

90Excellent
How it's scored
24/24CI workflows — 4 workflow(s)
24/24Tests present
16/16Linter config
9.6/9.6Pre-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_configyes

Documentation

55Moderate
How it's scored
30/30README
0/25Documentation directory
15/15Documentation / homepage site — https://www.ebi.ac.uk/metagenomics
10/10Repository description
0/10Topics
0/10Wiki
Inputs used
topics—
has_wikino
homepagehttps://www.ebi.ac.uk/metagenomics
docs_sitehttps://www.ebi.ac.uk/metagenomics
has_readmeyes
has_docs_dirno
has_descriptionyes

Security

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

46Weak · 16% of overall

Security posture

46Weak
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0.8/7.5Branch-Protection — branch protection is not maximal on development and all 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
7.5/7.5Code-Review — all changesets reviewed
2.5/2.5Contributors — project has 4 contributing companies or organizations
10/10Dangerous-Workflow — no dangerous workflow patterns detected
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5License — license file detected
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 — no data
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
0/7.5Vulnerabilities — 10 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated17
scorecard_versionv5.5.0
checks_inconclusive1
scorecard_aggregate4.6
Excluded from scoring (no data or not applicable): Signed-Releases. Remaining weights renormalized.

AI Readiness

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

45Weak · 4% of overall

Agent context & guidance

1Critical
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
0/40Legible commit history — no data
Inputs used
has_llms_txtno
llms_txt_url—
legible_history_share—
agent_instruction_files—
agent_instruction_max_bytes—
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.

Verify loop (build / test / typecheck)

74Good
How it's scored
18/18One-command bootstrap — Taskfile.yml
22/22Automated tests
11/11Lint / format config
0/11Static type checking
10/10Reproducible environment — Dockerfile, lockfile
0/10Demonstrated agent practice — no data
0/8Automated maintenance — no data
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfilesuv.lock
has_dockerfileyes
typed_languageno
bootstrap_filesTaskfile.yml
has_devcontainerno
has_linter_configyes
typecheck_configs—
agent_commit_share—
toolchain_manifests—
dependency_bot_commit_share—
Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance. Remaining weights renormalized.

Code legibility for models

55Moderate
How it's scored
0/45Type-checkable code — Python without a type-check config
55/55Manageable file sizes — 0/86 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes48,176
source_files_sampled86
oversized_source_files0

Key facts

1GitHub stars
11contributors
330commits, last 12 months
4days since last push
72releases
2bus factor
0open issues
PyPIpackage ecosystems

More detail

OpenSSF Scorecard 4.6 / 10
4.6aggregate

Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).Scorecard v5.5.0 · 2026-07-17 21:56 UTC

10Binary-Artifactsno binaries found in the repo
1Branch-Protectionbranch protection is not maximal on development and all 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
10Code-Reviewall changesets reviewed
10Contributorsproject has 4 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense 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
n/aSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
0Vulnerabilities10 existing vulnerabilities detected
Direct dependencies 10
RegistryPackageVersion constraintManifest
PyPIbiopython==1.85pyproject.toml
PyPIpandas==2.2.3pyproject.toml
PyPIpandera==0.27.1pyproject.toml
PyPIpydantic<2.12.0pyproject.toml
PyPIpyfastx==2.2.0pyproject.toml
PyPIintervaltree==3.1.0pyproject.toml
PyPIclick~=8.1.8pyproject.toml
PyPIrequests~=2.32pyproject.toml
PyPIbcbio-gff==0.7.1pyproject.toml
PyPIdatamodel-code-generator==0.54.1pyproject.toml
All dependencies 65

Full resolved dependency set from the GitHub dependency graph: 10 direct and 55 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
PyPIbcbio-gff0.7.1direct
PyPIbiopython1.85direct
PyPIclick8.1.8direct
PyPIdatamodel-code-generator0.54.1direct
PyPIintervaltree3.1.0direct
PyPIpandas2.2.3direct
PyPIpandera0.27.1direct
PyPIpydantic2.11.10direct
PyPIpyfastx2.2.0direct
PyPIrequests2.32.5direct
PyPIannotated-types0.7.0indirect
PyPIargcomplete3.6.3indirect
PyPIattrs25.4.0indirect
PyPIblack26.5.1indirect
PyPIcertifi2025.11.12indirect
PyPIcfgv3.5.0indirect
PyPIcharset-normalizer3.4.4indirect
PyPIcolorama0.4.6indirect
PyPIdistlib0.4.0indirect
PyPIfilelock3.20.1indirect
PyPIgenson1.3.0indirect
PyPIidentify2.6.15indirect
PyPIidna3.11indirect
PyPIinflect7.5.0indirect
PyPIiniconfig2.3.0indirect
PyPIisal1.8.0indirect
PyPIisort8.0.1indirect
PyPIjinja23.1.6indirect
PyPIjsonschema4.25.1indirect
PyPIjsonschema-specifications2025.9.1indirect
PyPImarkupsafe3.0.3indirect
PyPImgnify-pipelines-toolkit1.5.2indirect
PyPImore-itertools10.8.0indirect
PyPImypy-extensions1.1.0indirect
PyPInodeenv1.10.0indirect
PyPInumpy2.4.0indirect
PyPIpackaging25.0indirect
PyPIpathspec1.1.1indirect
PyPIplatformdirs4.5.1indirect
PyPIpluggy1.6.0indirect
PyPIpre-commit4.2.0indirect
PyPIpydantic-core2.33.2indirect
PyPIpytest8.3.5indirect
PyPIpytest-md0.2.0indirect
PyPIpytest-workflow2.1.0indirect
PyPIpython-dateutil2.9.0.post0indirect
PyPIpytokens0.4.1indirect
PyPIpytz2025.2indirect
PyPIpyyaml6.0.3indirect
PyPIreferencing0.37.0indirect
PyPIrpds-py0.30.0indirect
PyPIruff0.8.4indirect
PyPIsix1.17.0indirect
PyPIsortedcontainers2.4.0indirect
PyPItomli2.4.0indirect
PyPItypeguard4.4.4indirect
PyPItyping-extensions4.15.0indirect
PyPItyping-inspect0.9.0indirect
PyPItyping-inspection0.4.2indirect
PyPItzdata2025.3indirect
PyPIurllib32.6.2indirect
PyPIvirtualenv20.35.4indirect
PyPIxopen2.0.2indirect
PyPIzlib-ng1.0.0indirect
PyPIzstandard0.25.0indirect
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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 v0.12.0 — full methodology · metrics wiki.

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