Public record
Software health reportschema 0.34.0 · metrics 2.10.0 · 2026-09-14 05:59 UTC

CompOmics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.

HTML · Jupyter NotebookApache-2.0★ 50 stars⑂ 19 forkssince Mar 2017View on GitHub ↗
KindCommand-line toolLibraryhow this is determined

CompOmics/ms2pip holds a health index of 78 out of 100, placing it in the Good band. It scores highest on Engineering Quality (86/100) and lowest on AI Readiness (50/100). It was last updated 62 days ago. A single contributor accounts 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

132 followers117 public repossince Mar 2015

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publishTags
PyPIms2pip4.2.023,7033862 days agoms2pipproteomicspeptide-fragmentationpeak-intensity-predictionspectrum-predictionmachine-learningspectral-libraryfasta2speclib

Metrics by category

Vitality

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

65Good · 21% of overall
How it's scored
18/36Push recencylast push 62 days ago
8.3/36Commit cadence12/52 weeks with commits
17/18Commit volume78 commits in the last year
10/10OpenSSF Scorecard: Maintained19 commit(s) and 4 issue activity found in the last 90 days -- score normalized to 10
Inputs used
commits_last_year78
human_commit_share1
days_since_last_push62
active_weeks_last_year12
How it's scored
27/27Ships releases26 releases published
36/36Release recencylatest release 62 days ago
12.6/27Release cadencea release every ~139.8 days
0/10OpenSSF Scorecard: Signed-Releasesno data
Inputs used
releases_count26
latest_release_tagv4.2.0
releases_from_tagsno
days_since_latest_release62
mean_days_between_releases139.8
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?

54Moderate · 17% of overall
How it's scored
27.4/60Stars50 stars
10.5/25Forks19 forks
6.7/15Watchers17 watchers
Inputs used
forks19
stars50
watchers17
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history
How it's scored
22.5/22.5README
22.5/22.5Licenserecognized 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_badges8
has_contributingno
has_issue_templateno
has_code_of_conductno
readme_badge_servicesshields.io
has_pull_request_templateno
How it's scored
58.3/80Monthly downloads23,703 downloads/month across pypi
0/20Registry dependentsnot reported by this ecosystem
Inputs used
packagesms2pip
dependents
ecosystemspypi
total_downloads
monthly_downloads23,703
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?

68Good · 23% of overall
How it's scored
9/54Bus factor1 contributor(s) cover half of all commits
7.2/22.5Commit distributiontop contributor authored 68% of commits
13.5/13.5Contributor breadth11 contributors
10/10OpenSSF Scorecard: Contributorsproject has 5 contributing companies or organizations
Inputs used
bus_factor1
contributors_sampled11
top_contributor_share0.682
How it's scored
40/42Issue resolution95% of issues closed
23.6/30PR acceptance144/183 decided PRs merged
0/13Newcomer PR acceptanceno first-time contributor's PR decided in 30d
1.5/15OpenSSF Scorecard: Code-ReviewFound 1/10 approved changesets -- score normalized to 1
Inputs used
merged_prs144
open_issues4
closed_issues82
prs_merged_7d0
prs_decided_7d0
prs_merged_30d0
prs_decided_30d0
issue_closed_ratio0.953
closed_unmerged_prs39
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 backingorganization-owned
0/20Verified domain
15.3/25Owner reach132 followers of CompOmics
25/25Track record117 public repos, account ~11 yr old
Inputs used
followers132
owner_typeOrganization
is_verifiedno
owner_loginCompOmics
public_repos117
account_age_days4,191

Package maintenance

100Exceptional
How it's scored
25/25Published & resolvable1 package(s) on pypi
35/35Publish recencylatest publish 62 days ago
20/20Version history38 published versions
20/20Not deprecatedactive, not deprecated or yanked
Inputs used
packagesms2pip
ecosystemspypi
any_deprecatedno
min_days_since_publish62

Engineering Quality

Are baseline engineering and documentation practices in place?

86Excellent · 19% of overall
How it's scored
24/24CI workflows2 workflow(s)
24/24Tests present
16/16Linter configpyproject.toml ([tool.ruff], [tool.black])
0/9.6Pre-commit hooks
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests9 out of 9 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

90Excellent
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage sitehttps://ms2pip.readthedocs.io
10/10Repository description
10/10Topics6 topics
0/10Wiki
Inputs used
topicsmachine-learning, mass-spectrometry, peptide-identification, proteomics, spectrum-prediction, peptide-spectrum
has_wikino
homepagehttps://ms2pip.readthedocs.io
docs_sitehttps://ms2pip.readthedocs.io
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

64Moderate · 16% of overall
How it's scored
7.5/7.5Binary-Artifactsno binaries found in the repo
6/7.5Branch-Protectionbranch protection is not maximal on development and all release branches
2.5/2.5CI-Tests9 out of 9 merged PRs checked by a CI test -- score normalized to 10
0/2.5CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0.8/7.5Code-ReviewFound 1/10 approved changesets -- score normalized to 1
2.5/2.5Contributorsproject has 5 contributing companies or organizations
10/10Dangerous-Workflowno dangerous workflow patterns detected
7.5/7.5Dependency-Update-Toolupdate tool detected
0/5Fuzzingproject is not fuzzed
2.5/2.5Licenselicense file detected
7.5/7.5Maintained19 commit(s) and 4 issue activity found in the last 90 days -- score normalized to 10
5/5Packagingpackaging workflow detected
0/5Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
0/5SASTSAST tool is not run on all commits -- score normalized to 0
0/5Security-Policysecurity policy file not detected
0/7.5Signed-Releasesno data
0/7.5Token-Permissionsdetected GitHub workflow tokens with excessive permissions
1.5/7.5Vulnerabilities8 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated17
scorecard_versionv5.5.0
checks_inconclusive1
scorecard_aggregate5.5
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 advisoriesno direct dependency carries a known advisory
25/25Indirect dependencies free of known advisoriesno indirect dependency carries a known advisory
0/40No advisories left outstandingno advisory carries a publication date
Inputs used
sourceosv
advisories0
affected_packages0
assessed_packages29
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:ms2pip@4.2.0 runtime dependency closure — what installing the published package pulls in — 29 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.

50Moderate · 4% of overall
How it's scored
0/45Agent instructionsno CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
31.5/40Legible commit history59 of 100 human commits state their intent (structured subject or explanatory body)
Inputs used
has_llms_txtno
llms_txt_url
legible_history_share0.59
agent_instruction_files
agent_instruction_max_bytes
How it's scored
0/18One-command bootstrap
22/22Automated tests
11/11Lint / format configpyproject.toml ([tool.ruff], [tool.black])
0/11Static type checking
10/10Reproducible environmentlockfile
0/10Demonstrated agent practiceno agent-authored commits among the last 100
0/8Automated maintenanceno automated dependency updates observed
0/10OpenSSF Scorecard: Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
Inputs used
has_nixno
has_testsyes
lockfilesuv.lock
has_dockerfileno
typed_languageno
bootstrap_files
has_devcontainerno
has_linter_configyes
typecheck_configs
agent_commit_share0
toolchain_manifests
dependency_bot_commit_share0
How it's scored
0/45Type-checkable codeHTML without a type-check config
55/55Manageable file sizes0/25 source files over 60KB
Inputs used
primary_languageHTML
largest_source_bytes28,997
source_files_sampled25
oversized_source_files0
How it's scored
0/40API schema (OpenAPI/GraphQL/proto)not applicable to this kind of software
0/20MCP servernot applicable to this kind of software
40/40Runnable examplesnotebooks
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

50GitHub stars
11contributors
78commits, last 12 months
62days since last push
26releases
1bus factor
4open 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 ★ / 19 ⇿
0Stars
19Forks
23Releases

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.

051015201942017-032021-052025-06
Major 1Minor 10Patch 7

Each point covers 8 days.

OpenSSF Scorecard 5.5 / 10
5.5aggregate

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 · 2026-09-14 05:58 UTC

10Binary-Artifactsno binaries found in the repo
8Branch-Protectionbranch protection is not maximal on development and all release branches
10CI-Tests9 out of 9 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
1Code-ReviewFound 1/10 approved changesets -- score normalized to 1
10Contributorsproject has 5 contributing companies or organizations
10Dangerous-Workflowno dangerous workflow patterns detected
10Dependency-Update-Toolupdate tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained19 commit(s) and 4 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
2Vulnerabilities8 existing vulnerabilities detected
Direct dependencies 12
RegistryPackageVersion constraintManifest
PyPInumpy>=1.25,<3pyproject.toml
PyPIpandas>=1,<3pyproject.toml
PyPIpyteomics>=3.5,<5pyproject.toml
PyPIsqlalchemy>=1.4,<3pyproject.toml
PyPIclick>=7,<9pyproject.toml
PyPIxgboost>=1.3,<3pyproject.toml
PyPIlxml>=4,<7pyproject.toml
PyPIrich>=13,<16pyproject.toml
PyPIpydantic>=2,<3pyproject.toml
PyPIwerkzeug>=2,<4pyproject.toml
PyPIpsm_utils>=1.5,<4pyproject.toml
PyPIms2rescore-rs>=0.5.0,<2pyproject.toml
All dependencies 176

Full resolved dependency set from the GitHub dependency graph: 15 direct and 161 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
PyPIclick8.4.2direct
PyPIlxml6.1.1direct
PyPIms2rescore-rs0.5.0direct
PyPInumpy1.15.4direct
PyPInumpy2.4.6direct
PyPIpandas0.23.4direct
PyPIpandas2.3.3direct
PyPIpsm-utils1.5.5direct
PyPIpydantic2.13.4direct
PyPIpyteomics3.5.1direct
PyPIpyteomics4.7.5direct
PyPIrich14.3.4direct
PyPIsqlalchemy2.0.51direct
PyPIwerkzeug3.1.8direct
PyPIxgboost2.1.4direct
PyPIaiohappyeyeballs2.7.1indirect
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PyPIaiosignal1.4.0indirect
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PyPIbiopython1.72indirect
PyPIcertifi2026.6.17indirect
PyPIcffi2.1.0indirect
PyPIcharset-normalizer3.4.9indirect
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PyPIcomm0.2.3indirect
PyPIcommonmark0.9.2indirect
PyPIcontourpy1.3.3indirect
PyPIcuda-bindings13.3.1indirect
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PyPIcuda-toolkit13.0.3.0indirect
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PyPIjinja23.1.6indirect
PyPIjoblib1.5.3indirect
PyPIjupyter-client8.9.1indirect
PyPIjupyter-core5.9.1indirect
PyPIjupyterlab-widgets3.0.16indirect
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PyPIlightning-utilities0.15.3indirect
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PyPImatplotlib3.0.2indirect
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PyPInarwhals2.23.0indirect
PyPInest-asyncio21.7.2indirect
PyPInetworkx3.6.1indirect
PyPInumba0.66.0indirect
PyPInumpydoc1.10.0indirect
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PyPInvidia-cuda-cupti13.0.85indirect
PyPInvidia-cuda-nvrtc13.0.88indirect
PyPInvidia-cuda-runtime13.0.96indirect
PyPInvidia-cudnn-cu139.20.0.48indirect
PyPInvidia-cufft12.0.0.61indirect
PyPInvidia-cufile1.15.1.6indirect
PyPInvidia-curand10.4.0.35indirect
PyPInvidia-cusolver12.0.4.66indirect
PyPInvidia-cusparse12.6.3.3indirect
PyPInvidia-cusparselt-cu130.8.1indirect
PyPInvidia-nccl-cu122.30.7indirect
PyPInvidia-nccl-cu132.29.7indirect
PyPInvidia-nvjitlink13.3.33indirect
PyPInvidia-nvshmem-cu133.4.5indirect
PyPInvidia-nvtx13.0.85indirect
PyPIonnx1.22.0indirect
PyPIonnx2torch1.5.15indirect
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PyPIplatformdirs4.10.0indirect
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PyPIprompt-toolkit3.0.52indirect
PyPIpropcache0.5.2indirect
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PyPIpycparser3.0indirect
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PyPIpygments2.20.0indirect
PyPIpyparsing3.3.2indirect
PyPIpytest9.1.1indirect
PyPIpython-dateutil2.9.0.post0indirect
PyPIpytorch-lightning2.6.5indirect
PyPIpytz2026.2indirect
PyPIpyyaml6.0.3indirect
PyPIpyzmq27.1.0indirect
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PyPIrequests2.34.2indirect
PyPIroman-numerals4.1.0indirect
PyPIruff0.15.21indirect
PyPIscikit-learn1.9.0indirect
PyPIscipy1.1.0indirect
PyPIscipy1.17.1indirect
PyPIscipy1.18.0indirect
PyPIsemver3.0.4indirect
PyPIsetuptools83.0.0indirect
PyPIsix1.17.0indirect
PyPIsnowballstemmer3.1.1indirect
PyPIspectrum-utils0.5.0indirect
PyPIsphinx9.0.4indirect
PyPIsphinx9.1.0indirect
PyPIsphinx-autobuild2025.8.25indirect
PyPIsphinx-automodapi0.22.0indirect
PyPIsphinx-click6.2.0indirect
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
PyPIstack-data0.6.3indirect
PyPIstarlette1.3.1indirect
PyPIsympy1.14.0indirect
PyPItables3.4.4indirect
PyPIthreadpoolctl3.6.0indirect
PyPItoml0.10.2indirect
PyPItorch2.13.0indirect
PyPItorchmetrics1.9.0indirect
PyPItorchvision0.28.0indirect
PyPItornado6.5.7indirect
PyPItqdm4.68.4indirect
PyPItraitlets5.15.1indirect
PyPItriton3.7.1indirect
PyPIty0.0.58indirect
PyPItyping-extensions4.16.0indirect
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PyPItzdata2026.3indirect
PyPIurllib32.7.0indirect
PyPIuvicorn0.51.0indirect
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PyPIwebsockets16.1indirect
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Dependency advisories 0

Installing pypi:ms2pip@4.2.0 pulls in 29 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

Feedback

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.

The message is kept through sign-in.

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 statisticsPyPI.