Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-09-19 03:55 UTC

TimoLassmann / kalign

A fast multiple sequence alignment program.

C · PythonApache-2.0★ 162 stars⑂ 36 forkssince Apr 2019View on GitHub ↗
KindLibraryCommand-line toolhow this is determined
#sequence-alignment#bioinformatics#sequence-analysis

TimoLassmann/kalign holds a health index of 71 out of 100, placing it in the Good band. It scores highest on Engineering Quality (90/100) and lowest on Vitality (51/100). It was last updated 58 days ago. A single contributor accounts for most of its recent work.

71
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.

71
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 63 is calibrated to 71 on the published index scale (record calibration 2026-08-02).

Ownership

TimoLassmannPersonal account
38 followers21 public repossince Jul 2014

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
PyPIkalign-python3.6.09,6175125 days agobioinformaticssequence-alignmentmultiple-sequence-alignmentmsacomputational-biologygenomicsproteomicsphylogenetic-analysisevolutionary-biologybiopythonscikit-biodna-alignmentprotein-alignmentrna-alignmentfast-alignmentparallel-alignmentsimd-optimization

Metrics by category

Vitality

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

51Moderate · 21% of overall

Development activity

43Weak
How it's scored
18/36Push recency — last push 58 days ago
8.3/36Commit cadence — 12/52 weeks with commits
17/18Commit volume — 77 commits in the last year
0/10OpenSSF Scorecard: Maintained — 1 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
Inputs used
commits_last_year77
human_commit_share1
days_since_last_push58
active_weeks_last_year12

Release discipline

62Moderate
How it's scored
27/27Ships releases — 13 releases published
16.2/36Release recency — latest release 203 days ago
12.6/27Release cadence — a release every ~243.9 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count13
latest_release_tagv3.5.1
releases_from_tagsno
days_since_latest_release203
mean_days_between_releases243.9
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?

62Moderate · 17% of overall

Popularity & adoption

52Moderate
How it's scored
35.8/60Stars — 162 stars
12.9/25Forks — 36 forks
3.3/15Watchers — 5 watchers
Inputs used
forks36
stars162
watchers5
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 (Apache-2.0)
18/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges4
has_contributingyes
has_issue_templateno
has_code_of_conductno
readme_badge_servicesgithub.com
has_pull_request_templateno

Ecosystem adoption (downloads)

66Good
How it's scored
53.1/80Monthly downloads — 9,617 downloads/month across pypi
0/20Registry dependents — not reported by this ecosystem
Inputs used
packageskalign-python
dependents—
ecosystemspypi
total_downloads—
monthly_downloads9,617
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?

55Moderate · 23% of overall

Maintainer resilience (bus factor)

21At Risk
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
3.6/22.5Commit distribution — top contributor authored 84% of commits
8.1/13.5Contributor breadth — 6 contributors
0/10OpenSSF Scorecard: Contributors — project has 0 contributing companies or organizations -- score normalized to 0
Inputs used
bus_factor1
contributors_sampled6
top_contributor_share0.842

Issue & PR responsiveness

62Moderate
How it's scored
42/42Issue resolution — 100% of issues closed
12/30PR acceptance — 6/15 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
0/15OpenSSF Scorecard: Code-Review — Found 0/4 approved changesets -- score normalized to 0
Inputs used
merged_prs6
open_issues0
closed_issues47
prs_merged_7d0
prs_decided_7d0
prs_merged_30d0
prs_decided_30d0
issue_closed_ratio1
closed_unmerged_prs9
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

54Moderate
How it's scored
10/30Ownership backing — personal (user) account
0/20Verified domain — not applicable to user accounts
11.4/25Owner reach — 38 followers of TimoLassmann
21.8/25Track record — 21 public repos, account ~12 yr old
Inputs used
followers38
owner_typeUser
is_verified—
owner_loginTimoLassmann
public_repos21
account_age_days4,454
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 125 days ago
20/20Version history — 5 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packageskalign-python
ecosystemspypi
any_deprecatedno
min_days_since_publish125

Engineering Quality

Are baseline engineering and documentation practices in place?

90Excellent · 19% of overall

Engineering practices

84Excellent
How it's scored
24/24CI workflows — 4 workflow(s)
24/24Tests present
16/16Linter config — pyproject.toml ([tool.black])
0/9.6Pre-commit hooks
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 1 out of 1 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://github.com/TimoLassmann/kalign/blob/main/README.md
10/10Repository description
10/10Topics — 3 topics
10/10Wiki
Inputs used
topicssequence-alignment, bioinformatics, sequence-analysis
has_wikiyes
homepage—
docs_sitehttps://github.com/TimoLassmann/kalign/blob/main/README.md
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

54Moderate · 16% of overall

Security posture

43Weak
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
2.2/7.5Branch-Protection — branch protection is not maximal on development and all release branches
2.5/2.5CI-Tests — 1 out of 1 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 0/4 approved changesets -- score normalized to 0
0/2.5Contributors — project has 0 contributing companies or organizations -- score normalized to 0
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
0/7.5Maintained — 1 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
5/5Packaging — packaging workflow detected
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
5/5SAST — SAST tool is run on all commits
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
6.8/7.5Vulnerabilities — 1 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated17
scorecard_versionv5.5.0
checks_inconclusive1
scorecard_aggregate4.3
Excluded from scoring (no data or not applicable): 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_packages1
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:kalign-python@3.6.0 runtime dependency closure — what installing the published package pulls in — 1 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.

72Good · 4% of overall

Agent context & guidance

69Good
How it's scored
45/45Agent instructions — CLAUDE.md
0/15Machine-readable docs (llms.txt)
24/40Legible commit history — 45 of 100 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtno
llms_txt_url—
legible_history_share0.45
agent_instruction_filesCLAUDE.md
agent_instruction_max_bytes5,171

Verify loop (build / test / typecheck)

64Moderate
How it's scored
0/18One-command bootstrap
22/22Automated tests
11/11Lint / format config — pyproject.toml ([tool.black])
11/11Static type checking — python-kalign/py.typed
10/10Reproducible environment — lockfile
10/10Demonstrated agent practice — 26 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_dockerfileno
typed_languageyes
bootstrap_files—
has_devcontainerno
has_linter_configyes
typecheck_configspython-kalign/py.typed
agent_commit_share0.26
toolchain_manifests—
dependency_bot_commit_share0

Code legibility for models

100Exceptional
How it's scored
45/45Type-checkable code — C (statically typed)
55/55Manageable file sizes — 0/148 source files over 60KB
Inputs used
primary_languageC
largest_source_bytes43,401
source_files_sampled148
oversized_source_files0

Key facts

162GitHub stars
6contributors
77commits, last 12 months
58days since last push
13releases
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 ★ / 36 ⇿
0Stars
36Forks
13Releases

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.

01325383632019-102023-022026-06
Major 0Minor 2Patch 8

Each point covers 7 days.

OpenSSF Scorecard 4.3 / 10
4.3aggregate

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 · 2026-09-19 03:55 UTC

10Binary-Artifactsno binaries found in the repo
3Branch-Protectionbranch protection is not maximal on development and all release branches
10CI-Tests1 out of 1 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 0/4 approved changesets -- score normalized to 0
0Contributorsproject has 0 contributing companies or organizations -- score normalized to 0
10Dangerous-Workflowno dangerous workflow patterns detected
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
0Maintained1 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
10Packagingpackaging workflow detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
10SASTSAST tool is run on all commits
0Security-Policysecurity policy file not detected
n/aSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
9Vulnerabilities1 existing vulnerabilities detected
Direct dependencies 1
RegistryPackageVersion constraintManifest
PyPInumpy>=1.19.0pyproject.toml
All dependencies 137

Full resolved dependency set from the GitHub dependency graph: 2 direct and 135 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
PyPInumpy2.4.6direct
PyPInumpy2.5.1direct
PyPIabout-time4.2.1indirect
PyPIalabaster1.0.0indirect
PyPIalembic1.18.5indirect
PyPIalive-progress3.3.0indirect
PyPIannotated-types0.7.0indirect
PyPIarray-api-compat1.15.0indirect
PyPIast-serialize0.6.0indirect
PyPIautograd1.9.1indirect
PyPIbabel2.18.0indirect
PyPIbackports-tarfile1.2.0indirect
PyPIbiom-format2.1.17indirect
PyPIbiopython1.87indirect
PyPIblack26.5.1indirect
PyPIblinker1.9.0indirect
PyPIbuild1.5.0indirect
PyPIcertifi2026.7.22indirect
PyPIcffi2.1.0indirect
PyPIcharset-normalizer3.4.9indirect
PyPIclick8.4.2indirect
PyPIcma4.4.4indirect
PyPIcolorama0.4.6indirect
PyPIcolorlog6.11.0indirect
PyPIcomm0.2.3indirect
PyPIcontourpy1.3.3indirect
PyPIcoverage7.15.2indirect
PyPIcryptography49.0.0indirect
PyPIcycler0.12.1indirect
PyPIdash4.4.1indirect
PyPIdecorator5.3.1indirect
PyPIdeprecated1.3.1indirect
PyPIdocutils0.22.4indirect
PyPIexecnet2.1.2indirect
PyPIflake87.3.0indirect
PyPIflask3.1.3indirect
PyPIfonttools4.63.0indirect
PyPIgraphemeu0.7.2indirect
PyPIgreenlet3.5.4indirect
PyPIh5py3.16.0indirect
PyPIid1.6.1indirect
PyPIidna3.18indirect
PyPIimagesize2.0.0indirect
PyPIimportlib-metadata9.0.0indirect
PyPIiniconfig2.3.0indirect
PyPIitsdangerous2.2.0indirect
PyPIjanus2.0.0indirect
PyPIjaraco-classes3.4.0indirect
PyPIjaraco-context6.1.2indirect
PyPIjaraco-functools4.6.0indirect
PyPIjeepney0.9.0indirect
PyPIjinja23.1.6indirect
PyPIkalign-python3.6.0indirect
PyPIkeyring25.7.0indirect
PyPIkiwisolver1.5.0indirect
PyPIkneed0.8.6indirect
PyPIlibrt0.13.0indirect
PyPImako1.3.12indirect
PyPImarkdown-it-py4.2.0indirect
PyPImarkupsafe3.0.3indirect
PyPImatplotlib3.11.1indirect
PyPImccabe0.7.0indirect
PyPImdit-py-plugins0.6.1indirect
PyPImdurl0.1.2indirect
PyPImoocore0.3.2indirect
PyPImore-itertools11.1.0indirect
PyPImypy2.3.0indirect
PyPImypy-extensions1.1.0indirect
PyPImyst-parser5.1.0indirect
PyPInarwhals2.24.0indirect
PyPInatsort8.4.0indirect
PyPInest-asyncio1.6.0indirect
PyPInh30.3.6indirect
PyPIoptuna4.9.0indirect
PyPIpackaging26.2indirect
PyPIpandas3.0.3indirect
PyPIpathspec1.1.1indirect
PyPIpatsy1.0.2indirect
PyPIpillow12.3.0indirect
PyPIplatformdirs4.11.0indirect
PyPIplotly6.9.0indirect
PyPIpluggy1.6.0indirect
PyPIpy-cpuinfo9.0.0indirect
PyPIpycodestyle2.14.0indirect
PyPIpycparser3.0indirect
PyPIpydantic2.13.4indirect
PyPIpydantic-core2.46.4indirect
PyPIpyflakes3.4.0indirect
PyPIpygments2.20.0indirect
PyPIpymoo0.6.2indirect
PyPIpyparsing3.3.2indirect
PyPIpyproject-hooks1.2.0indirect
PyPIpytest9.1.1indirect
PyPIpytest-benchmark5.2.3indirect
PyPIpytest-cov7.1.0indirect
PyPIpytest-xdist3.8.0indirect
PyPIpython-dateutil2.9.0.post0indirect
PyPIpytokens0.4.1indirect
PyPIpywin32-ctypes0.2.3indirect
PyPIpyyaml6.0.3indirect
PyPIreadme-renderer45.0indirect
PyPIrequests2.34.2indirect
PyPIrequests-toolbelt1.0.0indirect
PyPIretrying1.4.2indirect
PyPIrfc39862.0.0indirect
PyPIrich15.0.0indirect
PyPIroman-numerals4.1.0indirect
PyPIscikit-bio0.7.3indirect
PyPIscipy1.17.1indirect
PyPIscipy1.18.0indirect
PyPIseaborn0.13.2indirect
PyPIsecretstorage3.5.0indirect
PyPIsetuptools83.0.0indirect
PyPIsix1.17.0indirect
PyPIsnowballstemmer3.1.1indirect
PyPIsphinx9.0.4indirect
PyPIsphinx9.1.0indirect
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
PyPIsqlalchemy2.0.51indirect
PyPIstatsmodels0.14.6indirect
PyPItomli2.4.1indirect
PyPItqdm4.69.0indirect
PyPItwine6.2.0indirect
PyPItyping-extensions4.16.0indirect
PyPItyping-inspection0.4.2indirect
PyPItzdata2026.3indirect
PyPIurllib32.7.0indirect
PyPIwerkzeug3.1.8indirect
PyPIwrapt2.2.2indirect
PyPIzipp4.1.0indirect
Dependency advisories 0

Installing pypi:kalign-python@3.6.0 pulls in 1 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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Spotted something off in this report, or have thoughts to share? Wrong measurements, missed tooling, ideas, questions — anything is welcome. Every message is read and gets a response.

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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.