Public recordModerate
Software health reportschema 0.27.0 · metrics 1.13.0 · 2026-07-27 22:26 UTC
CompOmics / ms2pip
MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
CompOmics/ms2pip holds a health index of 67 out of 100, placing it in the Moderate band. It scores highest on Engineering Quality (77/100) and lowest on AI Readiness (37/100). It was last updated 14 days ago. A single contributor accounts for most of its recent work.
67
overall / 100Software health index
Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At risk ceiling of 49. AI Readiness sits outside the overall score.
67
Excellent85-100Exemplary; meets essentially all checked criteria
Good70-84Healthy; minor gaps
Moderate50-69Acceptable with notable gaps; review recommended
At risk30-49Significant weaknesses; adoption warrants caution
Critical1-29Severe problems (abandoned, single-maintainer, no hygiene)
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.
Ownership
Computational Omics and Systems Biology GroupOrganization
129 followers114 public repossince Mar 2015
This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.
Package ecosystems
| Registry | Package | Version | Downloads / mo | Versions | Last publish | Tags |
|---|---|---|---|---|---|---|
| PyPI | ms2pip | 4.2.0 | 2,719 | 38 | 14 days ago | ms2pipproteomicspeptide-fragmentationpeak-intensity-predictionspectrum-predictionmachine-learningspectral-libraryfasta2speclib |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
72
Development activity
64Moderate
How it's scored
| 28.8/36 | Push recency — last push 14 days ago |
| 8.3/36 | Commit cadence — 12/52 weeks with commits |
| 17/18 | Commit volume — 78 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 19 commit(s) and 4 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 78 |
| human_commit_share | 1 |
| days_since_last_push | 14 |
| active_weeks_last_year | 12 |
Release discipline
84Good
How it's scored
| 27/27 | Ships releases — 26 releases published |
| 36/36 | Release recency — latest release 14 days ago |
| 12.6/27 | Release cadence — a release every ~139.8 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — no data |
Inputs used
| releases_count | 26 |
| latest_release_tag | v4.2.0 |
| releases_from_tags | no |
| days_since_latest_release | 14 |
| mean_days_between_releases | 139.8 |
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?
49
Popularity & adoption
44At risk
How it's scored
| 27.3/60 | Stars — 49 stars |
| 10.5/25 | Forks — 19 forks |
| 6.7/15 | Watchers — 17 watchers |
Inputs used
| forks | 19 |
| stars | 49 |
| watchers | 17 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community health
50Moderate
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (Apache-2.0) |
| 0/18 | CONTRIBUTING guide |
| 0/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 0/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| has_contributing | no |
| has_issue_template | no |
| has_code_of_conduct | no |
| has_pull_request_template | no |
Ecosystem adoption (downloads)
57Moderate
How it's scored
| 45.8/80 | Monthly downloads — 2,719 downloads/month across pypi |
| 0/20 | Registry dependents — not reported by this ecosystem |
Inputs used
| packages | ms2pip |
| dependents | — |
| ecosystems | pypi |
| total_downloads | — |
| monthly_downloads | 2,719 |
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?
68
Maintainer resilience (bus factor)
40At risk
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 7.2/22.5 | Commit distribution — top contributor authored 68% of commits |
| 13.5/13.5 | Contributor breadth — 11 contributors |
| 10/10 | OpenSSF Scorecard: Contributors — project has 5 contributing companies or organizations |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 11 |
| top_contributor_share | 0.682 |
How it's scored
| 44/46.8 | Issue resolution — 94% of issues closed |
| 30.1/38.3 | PR acceptance — 144/183 decided PRs merged |
| 1.5/15 | OpenSSF Scorecard: Code-Review — Found 1/10 approved changesets -- score normalized to 1 |
Inputs used
| merged_prs | 144 |
| open_issues | 5 |
| closed_issues | 81 |
| issue_closed_ratio | 0.942 |
| closed_unmerged_prs | 39 |
Ownership & stewardship
70Good
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain |
| 15.2/25 | Owner reach — 129 followers of CompOmics |
| 25/25 | Track record — 114 public repos, account ~11 yr old |
Inputs used
| followers | 129 |
| owner_type | Organization |
| is_verified | — |
| owner_login | CompOmics |
| public_repos | 114 |
| account_age_days | 4,143 |
Package maintenance
100Excellent
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 14 days ago |
| 20/20 | Version history — 38 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | ms2pip |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 14 |
Engineering Quality
Are baseline engineering and documentation practices in place?
77
Engineering practices
68Moderate
How it's scored
| 24/24 | CI workflows — 2 workflow(s) |
| 24/24 | Tests present |
| 0/16 | Linter config |
| 0/9.6 | Pre-commit hooks |
| 0/6.4 | .editorconfig |
| 20/20 | OpenSSF Scorecard: CI-Tests — 9 out of 9 merged PRs checked by a CI test -- score normalized to 10 |
Inputs used
| has_ci | yes |
| has_tests | yes |
| has_editorconfig | no |
| has_linter_config | no |
| has_precommit_config | no |
Documentation
90Excellent
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://ms2pip.readthedocs.io |
| 10/10 | Repository description |
| 10/10 | Topics — 6 topics |
| 0/10 | Wiki |
Inputs used
| topics | machine-learning, mass-spectrometry, peptide-identification, proteomics, spectrum-prediction, peptide-spectrum |
| has_wiki | no |
| homepage | https://ms2pip.readthedocs.io |
| has_readme | yes |
| has_docs_dir | yes |
| has_description | yes |
Security
Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?
69
Security posture
61Moderate
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 6/7.5 | Branch-Protection — branch protection is not maximal on development and all release branches |
| 2.5/2.5 | CI-Tests — 9 out of 9 merged PRs checked by a CI test -- score normalized to 10 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0.8/7.5 | Code-Review — Found 1/10 approved changesets -- score normalized to 1 |
| 2.5/2.5 | Contributors — project has 5 contributing companies or organizations |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 7.5/7.5 | Dependency-Update-Tool — update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | License — license file detected |
| 7.5/7.5 | Maintained — 19 commit(s) and 4 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 0/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — no data |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 17 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 1 |
| scorecard_aggregate | 6.1 |
Excluded from scoring (no data or not applicable): signed_releases. Remaining weights renormalized.
Dependency advisories
100Excellent
How it's scored
| 35/35 | Direct dependencies free of known advisories — no direct dependency carries a known advisory |
| 25/25 | Indirect dependencies free of known advisories — no indirect dependency carries a known advisory |
| 0/40 | No advisories left outstanding — no advisory carries a publication date |
Inputs used
| source | osv |
| advisories | 0 |
| affected_packages | 0 |
| assessed_packages | 29 |
| unassessed_packages | 0 |
| affected_by_severity | none |
| direct_affected_packages | 0 |
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? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score.
37
Agent context & guidance
32At risk
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 31.5/40 | Legible commit history — 59 of 100 human commits state their intent (structured subject or explanatory body) |
Inputs used
| has_llms_txt | no |
| legible_history_share | 0.59 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
How it's scored
| 0/18 | One-command bootstrap |
| 22/22 | Automated tests |
| 0/11 | Lint / format config |
| 0/11 | Static type checking |
| 10/10 | Reproducible environment — lockfile |
| 0/10 | Demonstrated agent practice — no agent-authored commits among the last 100 |
| 0/8 | Automated maintenance — no automated dependency updates observed |
| 0/10 | OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
Inputs used
| has_nix | no |
| has_tests | yes |
| lockfiles | uv.lock |
| has_dockerfile | no |
| typed_language | no |
| bootstrap_files | — |
| has_devcontainer | no |
| has_linter_config | no |
| typecheck_configs | — |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Code legibility for models
55Moderate
How it's scored
| 0/45 | Type-checkable code — HTML without a type-check config |
| 55/55 | Manageable file sizes — 0/25 source files over 60KB |
Inputs used
| primary_language | HTML |
| largest_source_bytes | 28,997 |
| source_files_sampled | 25 |
| oversized_source_files | 0 |
Machine-readable interfaces
40At risk
How it's scored
| 0/40 | API schema (OpenAPI/GraphQL/proto) |
| 0/20 | MCP server |
| 40/40 | Runnable examples — notebooks |
Inputs used
| example_dirs | notebooks |
| has_mcp_signal | no |
| api_schema_files | — |
Key facts
49GitHub stars
11contributors
78commits, last 12 months
14days since last push
26releases
1bus factor
5open 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.
Major 1Minor 10Patch 7
Each point covers 8 days.
OpenSSF Scorecard 6.1 / 10
6.1aggregate
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).
| 10 | Binary-Artifacts | no binaries found in the repo |
| 8 | Branch-Protection | branch protection is not maximal on development and all release branches |
| 10 | CI-Tests | 9 out of 9 merged PRs checked by a CI test -- score normalized to 10 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 1 | Code-Review | Found 1/10 approved changesets -- score normalized to 1 |
| 10 | Contributors | project has 5 contributing companies or organizations |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 10 | Dependency-Update-Tool | update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 19 commit(s) and 4 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 0 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 0 |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 0 | Security-Policy | security policy file not detected |
| n/a | Signed-Releases | no releases found |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
Direct dependencies 12
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | numpy | >=1.25,<3 | pyproject.toml |
| PyPI | pandas | >=1,<3 | pyproject.toml |
| PyPI | pyteomics | >=3.5,<5 | pyproject.toml |
| PyPI | sqlalchemy | >=1.4,<3 | pyproject.toml |
| PyPI | click | >=7,<9 | pyproject.toml |
| PyPI | xgboost | >=1.3,<3 | pyproject.toml |
| PyPI | lxml | >=4,<7 | pyproject.toml |
| PyPI | rich | >=13,<16 | pyproject.toml |
| PyPI | pydantic | >=2,<3 | pyproject.toml |
| PyPI | werkzeug | >=2,<4 | pyproject.toml |
| PyPI | psm_utils | >=1.5,<4 | pyproject.toml |
| PyPI | ms2rescore-rs | >=0.5.0,<2 | pyproject.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.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | click | 8.4.2 | direct |
| PyPI | lxml | 6.1.1 | direct |
| PyPI | ms2rescore-rs | 0.5.0 | direct |
| PyPI | numpy | 1.15.4 | direct |
| PyPI | numpy | 2.4.6 | direct |
| PyPI | pandas | 0.23.4 | direct |
| PyPI | pandas | 2.3.3 | direct |
| PyPI | psm-utils | 1.5.5 | direct |
| PyPI | pydantic | 2.13.4 | direct |
| PyPI | pyteomics | 3.5.1 | direct |
| PyPI | pyteomics | 4.7.5 | direct |
| PyPI | rich | 14.3.4 | direct |
| PyPI | sqlalchemy | 2.0.51 | direct |
| PyPI | werkzeug | 3.1.8 | direct |
| PyPI | xgboost | 2.1.4 | direct |
| PyPI | aiohappyeyeballs | 2.7.1 | indirect |
| PyPI | aiohttp | 3.14.1 | indirect |
| PyPI | aiosignal | 1.4.0 | indirect |
| PyPI | alabaster | 1.0.0 | indirect |
| PyPI | annotated-types | 0.7.0 | indirect |
| PyPI | anyio | 4.14.1 | indirect |
| PyPI | appnope | 0.1.4 | indirect |
| PyPI | asttokens | 3.0.1 | indirect |
| PyPI | attrs | 26.1.0 | indirect |
| PyPI | babel | 2.18.0 | indirect |
| PyPI | biopython | 1.72 | indirect |
| PyPI | certifi | 2026.6.17 | indirect |
| PyPI | cffi | 2.1.0 | indirect |
| PyPI | charset-normalizer | 3.4.9 | indirect |
| PyPI | colorama | 0.4.6 | indirect |
| PyPI | comm | 0.2.3 | indirect |
| PyPI | commonmark | 0.9.2 | indirect |
| PyPI | contourpy | 1.3.3 | indirect |
| PyPI | cuda-bindings | 13.3.1 | indirect |
| PyPI | cuda-pathfinder | 1.5.6 | indirect |
| PyPI | cuda-toolkit | 13.0.3.0 | indirect |
| PyPI | cycler | 0.12.1 | indirect |
| PyPI | cython | 0.29.2 | indirect |
| PyPI | debugpy | 1.8.21 | indirect |
| PyPI | decorator | 5.3.1 | indirect |
| PyPI | deeplc | 4.0.0b1 | indirect |
| PyPI | docutils | 0.22.4 | indirect |
| PyPI | executing | 2.2.1 | indirect |
| PyPI | fastobo | 0.14.1 | indirect |
| PyPI | filelock | 3.29.7 | indirect |
| PyPI | fonttools | 4.63.0 | indirect |
| PyPI | frozenlist | 1.8.0 | indirect |
| PyPI | fsspec | 2026.6.0 | indirect |
| PyPI | greenlet | 3.5.3 | indirect |
| PyPI | h11 | 0.16.0 | indirect |
| PyPI | idna | 3.18 | indirect |
| PyPI | im2deep | 2.0.0 | indirect |
| PyPI | imagesize | 2.0.0 | indirect |
| PyPI | iniconfig | 2.3.0 | indirect |
| PyPI | ipykernel | 7.3.0 | indirect |
| PyPI | ipython | 9.15.0 | indirect |
| PyPI | ipython-pygments-lexers | 1.1.1 | indirect |
| PyPI | ipywidgets | 8.1.8 | indirect |
| PyPI | jedi | 0.20.0 | indirect |
| PyPI | jinja2 | 3.1.6 | indirect |
| PyPI | joblib | 1.5.3 | indirect |
| PyPI | jupyter-client | 8.9.1 | indirect |
| PyPI | jupyter-core | 5.9.1 | indirect |
| PyPI | jupyterlab-widgets | 3.0.16 | indirect |
| PyPI | kiwisolver | 1.5.0 | indirect |
| PyPI | lark | 1.3.1 | indirect |
| PyPI | lightning | 2.6.5 | indirect |
| PyPI | lightning-utilities | 0.15.3 | indirect |
| PyPI | llvmlite | 0.48.0 | indirect |
| PyPI | markdown-it-py | 4.2.0 | indirect |
| PyPI | markupsafe | 3.0.3 | indirect |
| PyPI | matplotlib | 3.0.2 | indirect |
| PyPI | matplotlib | 3.11.0 | indirect |
| PyPI | matplotlib-inline | 0.2.2 | indirect |
| PyPI | mdurl | 0.1.2 | indirect |
| PyPI | ml-dtypes | 0.5.4 | indirect |
| PyPI | mpmath | 1.3.0 | indirect |
| PyPI | multidict | 6.7.1 | indirect |
| PyPI | narwhals | 2.23.0 | indirect |
| PyPI | nest-asyncio2 | 1.7.2 | indirect |
| PyPI | networkx | 3.6.1 | indirect |
| PyPI | numba | 0.66.0 | indirect |
| PyPI | numpydoc | 1.10.0 | indirect |
| PyPI | nvidia-cublas | 13.1.1.3 | indirect |
| PyPI | nvidia-cuda-cupti | 13.0.85 | indirect |
| PyPI | nvidia-cuda-nvrtc | 13.0.88 | indirect |
| PyPI | nvidia-cuda-runtime | 13.0.96 | indirect |
| PyPI | nvidia-cudnn-cu13 | 9.20.0.48 | indirect |
| PyPI | nvidia-cufft | 12.0.0.61 | indirect |
| PyPI | nvidia-cufile | 1.15.1.6 | indirect |
| PyPI | nvidia-curand | 10.4.0.35 | indirect |
| PyPI | nvidia-cusolver | 12.0.4.66 | indirect |
| PyPI | nvidia-cusparse | 12.6.3.3 | indirect |
| PyPI | nvidia-cusparselt-cu13 | 0.8.1 | indirect |
| PyPI | nvidia-nccl-cu12 | 2.30.7 | indirect |
| PyPI | nvidia-nccl-cu13 | 2.29.7 | indirect |
| PyPI | nvidia-nvjitlink | 13.3.33 | indirect |
| PyPI | nvidia-nvshmem-cu13 | 3.4.5 | indirect |
| PyPI | nvidia-nvtx | 13.0.85 | indirect |
| PyPI | onnx | 1.22.0 | indirect |
| PyPI | onnx2torch | 1.5.15 | indirect |
| PyPI | packaging | 26.2 | indirect |
| PyPI | parso | 0.8.7 | indirect |
| PyPI | pexpect | 4.9.0 | indirect |
| PyPI | pillow | 12.3.0 | indirect |
| PyPI | pip | 26.1.2 | indirect |
| PyPI | platformdirs | 4.10.0 | indirect |
| PyPI | pluggy | 1.6.0 | indirect |
| PyPI | prompt-toolkit | 3.0.52 | indirect |
| PyPI | propcache | 0.5.2 | indirect |
| PyPI | protobuf | 7.35.1 | indirect |
| PyPI | psims | 1.3.6 | indirect |
| PyPI | psutil | 7.2.2 | indirect |
| PyPI | ptyprocess | 0.7.0 | indirect |
| PyPI | pure-eval | 0.2.3 | indirect |
| PyPI | pyarrow | 25.0.0 | indirect |
| PyPI | pycparser | 3.0 | indirect |
| PyPI | pydantic-core | 2.46.4 | indirect |
| PyPI | pygments | 2.20.0 | indirect |
| PyPI | pyparsing | 3.3.2 | indirect |
| PyPI | pytest | 9.1.1 | indirect |
| PyPI | python-dateutil | 2.9.0.post0 | indirect |
| PyPI | pytorch-lightning | 2.6.5 | indirect |
| PyPI | pytz | 2026.2 | indirect |
| PyPI | pyyaml | 6.0.3 | indirect |
| PyPI | pyzmq | 27.1.0 | indirect |
| PyPI | recommonmark | 0.7.1 | indirect |
| PyPI | requests | 2.34.2 | indirect |
| PyPI | roman-numerals | 4.1.0 | indirect |
| PyPI | ruff | 0.15.21 | indirect |
| PyPI | scikit-learn | 1.9.0 | indirect |
| PyPI | scipy | 1.1.0 | indirect |
| PyPI | scipy | 1.17.1 | indirect |
| PyPI | scipy | 1.18.0 | indirect |
| PyPI | semver | 3.0.4 | indirect |
| PyPI | setuptools | 83.0.0 | indirect |
| PyPI | six | 1.17.0 | indirect |
| PyPI | snowballstemmer | 3.1.1 | indirect |
| PyPI | spectrum-utils | 0.5.0 | indirect |
| PyPI | sphinx | 9.0.4 | indirect |
| PyPI | sphinx | 9.1.0 | indirect |
| PyPI | sphinx-autobuild | 2025.8.25 | indirect |
| PyPI | sphinx-automodapi | 0.22.0 | indirect |
| PyPI | sphinx-click | 6.2.0 | indirect |
| PyPI | sphinx-rtd-theme | 3.1.0 | indirect |
| PyPI | sphinxcontrib-applehelp | 2.0.0 | indirect |
| PyPI | sphinxcontrib-devhelp | 2.0.0 | indirect |
| PyPI | sphinxcontrib-htmlhelp | 2.1.0 | indirect |
| PyPI | sphinxcontrib-jquery | 4.1 | indirect |
| PyPI | sphinxcontrib-jsmath | 1.0.1 | indirect |
| PyPI | sphinxcontrib-qthelp | 2.0.0 | indirect |
| PyPI | sphinxcontrib-serializinghtml | 2.0.0 | indirect |
| PyPI | stack-data | 0.6.3 | indirect |
| PyPI | starlette | 1.3.1 | indirect |
| PyPI | sympy | 1.14.0 | indirect |
| PyPI | tables | 3.4.4 | indirect |
| PyPI | threadpoolctl | 3.6.0 | indirect |
| PyPI | toml | 0.10.2 | indirect |
| PyPI | torch | 2.13.0 | indirect |
| PyPI | torchmetrics | 1.9.0 | indirect |
| PyPI | torchvision | 0.28.0 | indirect |
| PyPI | tornado | 6.5.7 | indirect |
| PyPI | tqdm | 4.68.4 | indirect |
| PyPI | traitlets | 5.15.1 | indirect |
| PyPI | triton | 3.7.1 | indirect |
| PyPI | ty | 0.0.58 | indirect |
| PyPI | typing-extensions | 4.16.0 | indirect |
| PyPI | typing-inspection | 0.4.2 | indirect |
| PyPI | tzdata | 2026.3 | indirect |
| PyPI | urllib3 | 2.7.0 | indirect |
| PyPI | uvicorn | 0.51.0 | indirect |
| PyPI | watchfiles | 1.2.0 | indirect |
| PyPI | wcwidth | 0.8.2 | indirect |
| PyPI | websockets | 16.1 | indirect |
| PyPI | widgetsnbextension | 4.0.15 | indirect |
| PyPI | yarl | 1.24.2 | indirect |
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
{
"data": {
"repo": {
"topics": [
"machine-learning",
"mass-spectrometry",
"peptide-identification",
"proteomics",
"spectrum-prediction",
"peptide-spectrum"
],
"is_fork": false,
"size_kb": 110157,
"has_wiki": false,
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],
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{
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"details": [],
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]
},
{
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"notes": [
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},
{
"code": "weights_renormalized",
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],
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"components": [
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"details": [
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"code": "releases_published",
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"count": 26
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}
],
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{
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"details": [
{
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"days": 14
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{
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"gap": 139.8
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{
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]
},
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"notes": [],
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"inputs": {
"cap": null,
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"signals": [],
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"multiplier_pct": 100,
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"code": "abandonment_maintained",
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}
],
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},
{
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"value": 49,
"weight": 0.18,
"metrics": [
{
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"note": null,
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"inputs": {
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"points": 27.3,
"status": "partial",
"details": [
{
"code": "stars",
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"count": 49
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}
],
"max_points": 60
},
{
"key": "forks",
"name": "Forks",
"detail": "19 forks",
"points": 10.5,
"status": "partial",
"details": [
{
"code": "forks",
"params": {
"count": 19
}
}
],
"max_points": 25
},
{
"key": "watchers",
"name": "Watchers",
"detail": "17 watchers",
"points": 6.7,
"status": "partial",
"details": [
{
"code": "watchers",
"params": {
"count": 17
}
}
],
"max_points": 15
}
]
},
{
"key": "community_health",
"band": "moderate",
"name": "Community health",
"note": null,
"notes": [],
"value": 50,
"inputs": {
"has_readme": true,
"has_license": true,
"has_contributing": false,
"has_issue_template": false,
"has_code_of_conduct": false,
"has_pull_request_template": false
},
"components": [
{
"key": "readme",
"name": "README",
"detail": null,
"points": 22.5,
"status": "met",
"details": [],
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},
{
"key": "license",
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"detail": "recognized license (Apache-2.0)",
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"status": "met",
"details": [
{
"code": "license_standard",
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},
{
"code": "license_spdx",
"params": {
"spdx": "Apache-2.0"
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],
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},
{
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"name": "CONTRIBUTING guide",
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"points": 0,
"status": "missed",
"details": [],
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},
{
"key": "code_of_conduct",
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{
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{
"key": "pr_template",
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"max_points": 6.3
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},
{
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"name": "Ecosystem adoption (downloads)",
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"notes": [
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"code": "excluded_no_data",
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},
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],
"value": 57,
"inputs": {
"packages": [
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"monthly_downloads": 2719
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"components": [
{
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"points": 45.8,
"status": "partial",
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{
"code": "downloads_monthly",
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"count": 2719,
"ecosystems": "pypi"
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}
],
"max_points": 80
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{
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"detail": "not reported by this ecosystem",
"points": 0,
"status": "excluded",
"details": [
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"code": "not_reported_by_this_ecosystem",
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}
],
"max_points": 20
}
]
}
],
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},
{
"key": "governance",
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"name": "Sustainability & Governance",
"value": 68,
"weight": 0.24,
"metrics": [
{
"key": "maintainer_resilience",
"band": "at_risk",
"name": "Maintainer resilience (bus factor)",
"note": null,
"notes": [],
"value": 40,
"inputs": {
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"components": [
{
"key": "bus_factor",
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"code": "bus_factor",
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}
],
"max_points": 54
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{
"key": "commit_distribution",
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"status": "partial",
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{
"code": "top_contributor_share",
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}
],
"max_points": 22.5
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{
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"details": [
{
"code": "contributors_sampled",
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}
],
"max_points": 13.5
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{
"key": "openssf_scorecard_contributors",
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"status": "met",
"details": [],
"max_points": 10
}
]
},
{
"key": "responsiveness",
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"note": null,
"notes": [],
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"inputs": {
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"open_issues": 5,
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"issue_closed_ratio": 0.942,
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"components": [
{
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"details": [
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}
],
"max_points": 46.75
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{
"key": "pr_acceptance",
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"points": 30.1,
"status": "partial",
"details": [
{
"code": "decided_prs_merged",
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}
],
"max_points": 38.25
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{
"key": "openssf_scorecard_code_review",
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"points": 1.5,
"status": "partial",
"details": [],
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]
},
{
"key": "stewardship",
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"note": null,
"notes": [],
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"inputs": {
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"is_verified": null,
"owner_login": "CompOmics",
"public_repos": 114,
"account_age_days": 4143
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"components": [
{
"key": "ownership_backing",
"name": "Ownership backing",
"detail": "organization-owned",
"points": 30,
"status": "met",
"details": [
{
"code": "owner_organization",
"params": {}
}
],
"max_points": 30
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{
"key": "verified_domain",
"name": "Verified domain",
"detail": null,
"points": 0,
"status": "missed",
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},
{
"key": "owner_reach",
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"points": 15.2,
"status": "partial",
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"code": "owner_followers",
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"login": "CompOmics"
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}
],
"max_points": 25
},
{
"key": "track_record",
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"points": 25,
"status": "met",
"details": [
{
"code": "public_repos",
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},
{
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}
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]
},
{
"key": "package_maintenance",
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"name": "Package maintenance",
"note": null,
"notes": [],
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"inputs": {
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"ecosystems": "pypi",
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"min_days_since_publish": 14
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"components": [
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"key": "published_resolvable",
"name": "Published & resolvable",
"detail": "1 package(s) on pypi",
"points": 25,
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"ecosystems": "pypi"
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}
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{
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}
],
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{
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"points": 20,
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"details": [
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}
],
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{
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]
}
],
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},
{
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"weight": 0.2,
"metrics": [
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"key": "engineering_practices",
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"note": null,
"notes": [],
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"inputs": {
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"details": [
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"code": "ci_workflows",
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{
"key": "tests_present",
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"details": [],
"max_points": 24
},
{
"key": "linter_config",
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"points": 0,
"status": "missed",
"details": [],
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{
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"details": [],
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},
{
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"details": [],
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{
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]
},
{
"key": "documentation",
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"note": null,
"notes": [],
"value": 90,
"inputs": {
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{
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{
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{
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}
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{
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]
}
],
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{
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"weight": 0.16,
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},
{
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],
"value": 61,
"inputs": {
"source": "openssf_scorecard",
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"components": [
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"status": "met",
"details": [],
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},
{
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"points": 6,
"status": "partial",
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},
{
"key": "ci_tests",
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},
{
"key": "cii_best_practices",
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"points": 0,
"status": "missed",
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},
{
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},
{
"key": "contributors",
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"points": 2.5,
"status": "met",
"details": [],
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},
{
"key": "dangerous_workflow",
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"detail": "no dangerous workflow patterns detected",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "dependency_update_tool",
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"detail": "update tool detected",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "fuzzing",
"name": "Fuzzing",
"detail": "project is not fuzzed",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "license",
"name": "License",
"detail": "license file detected",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "maintained",
"name": "Maintained",
"detail": "19 commit(s) and 4 issue activity found in the last 90 days -- score normalized to 10",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "packaging",
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"points": 5,
"status": "met",
"details": [],
"max_points": 5
},
{
"key": "pinned_dependencies",
"name": "Pinned-Dependencies",
"detail": "dependency not pinned by hash detected -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "sast",
"name": "SAST",
"detail": "SAST tool is not run on all commits -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "security_policy",
"name": "Security-Policy",
"detail": "security policy file not detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "signed_releases",
"name": "Signed-Releases",
"detail": "no releases found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "token_permissions",
"name": "Token-Permissions",
"detail": "detected GitHub workflow tokens with excessive permissions",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "vulnerabilities",
"name": "Vulnerabilities",
"detail": "0 existing vulnerabilities detected",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
}
]
},
{
"key": "dependency_advisories",
"band": "excellent",
"name": "Dependency advisories",
"note": "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.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
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}
},
{
"code": "weights_renormalized",
"params": {}
},
{
"code": "advisories_scope_published",
"params": {
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}
},
{
"code": "advisories_reachability",
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}
],
"value": 100,
"inputs": {
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"affected_packages": 0,
"assessed_packages": 29,
"unassessed_packages": 0,
"affected_by_severity": "none",
"direct_affected_packages": 0
},
"components": [
{
"key": "direct_dependencies_free_of_known_advisories",
"name": "Direct dependencies free of known advisories",
"detail": "no direct dependency carries a known advisory",
"points": 35,
"status": "met",
"details": [
{
"code": "no_direct_advisories",
"params": {}
}
],
"max_points": 35
},
{
"key": "indirect_dependencies_free_of_known_advisories",
"name": "Indirect dependencies free of known advisories",
"detail": "no indirect dependency carries a known advisory",
"points": 25,
"status": "met",
"details": [
{
"code": "no_indirect_advisories",
"params": {}
}
],
"max_points": 25
},
{
"key": "no_advisories_left_outstanding",
"name": "No advisories left outstanding",
"detail": "no advisory carries a publication date",
"points": 0,
"status": "excluded",
"details": [
{
"code": "advisories_no_publication_date",
"params": {}
}
],
"max_points": 40
}
]
},
{
"key": "malicious_dependencies",
"band": "excellent",
"name": "Malicious dependencies",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"source": "osv",
"meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
"packages": [],
"red_flag": false,
"assessed_packages": 29,
"malicious_packages": 0,
"direct_malicious_packages": 0,
"withdrawn_malicious_packages": 0,
"installable_malicious_packages": 0
},
"components": [
{
"key": "no_dependency_reported_as_a_malicious_package",
"name": "No dependency reported as a malicious package",
"detail": "no dependency is reported as a malicious package",
"points": 100,
"status": "met",
"details": [
{
"code": "no_malicious_dependencies",
"params": {}
}
],
"max_points": 100
}
]
},
{
"key": "high_risk_jurisdiction_exposure",
"band": "excellent",
"name": "High-Risk Jurisdiction Exposure",
"note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
"notes": [
{
"code": "jurisdiction_evidence_limits",
"params": {}
}
],
"value": 100,
"inputs": {
"meaning": "self-published location evidence; not nationality or citizenship",
"red_flag": false,
"exposures": [],
"policy_countries": [
"Russia",
"Iran",
"North Korea"
],
"review_only_matches": 0,
"assessed_self_published_locations": 8
},
"components": [
{
"key": "policy_exposure_multiplier",
"name": "Policy exposure multiplier",
"detail": "no confirmed policy-scope location match",
"points": 100,
"status": "met",
"details": [
{
"code": "jurisdiction_no_match",
"params": {}
}
],
"max_points": 100
}
]
}
],
"description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
},
{
"key": "ai_readiness",
"band": "at_risk",
"name": "AI Readiness",
"value": 37,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "at_risk",
"name": "Agent context & guidance",
"note": null,
"notes": [],
"value": 32,
"inputs": {
"has_llms_txt": false,
"legible_history_share": 0.59,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"components": [
{
"key": "agent_instructions",
"name": "Agent instructions",
"detail": "no CLAUDE.md / AGENTS.md / editor rules",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_instructions",
"params": {}
}
],
"max_points": 45
},
{
"key": "machine_readable_docs_llms_txt",
"name": "Machine-readable docs (llms.txt)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
},
{
"key": "legible_commit_history",
"name": "Legible commit history",
"detail": "59 of 100 human commits state their intent (structured subject or explanatory body)",
"points": 31.5,
"status": "partial",
"details": [
{
"code": "legible_history",
"params": {
"legible": 59,
"sampled": 100
}
}
],
"max_points": 40
}
]
},
{
"key": "ai_verify_loop",
"band": "at_risk",
"name": "Verify loop (build / test / typecheck)",
"note": null,
"notes": [],
"value": 32,
"inputs": {
"has_nix": false,
"has_tests": true,
"lockfiles": [
"uv.lock"
],
"has_dockerfile": false,
"typed_language": false,
"bootstrap_files": [],
"has_devcontainer": false,
"has_linter_config": false,
"typecheck_configs": [],
"agent_commit_share": 0,
"toolchain_manifests": [],
"dependency_bot_commit_share": 0
},
"components": [
{
"key": "one_command_bootstrap",
"name": "One-command bootstrap",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 18
},
{
"key": "automated_tests",
"name": "Automated tests",
"detail": null,
"points": 22,
"status": "met",
"details": [],
"max_points": 22
},
{
"key": "lint_format_config",
"name": "Lint / format config",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "static_type_checking",
"name": "Static type checking",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "reproducible_environment",
"name": "Reproducible environment",
"detail": "lockfile",
"points": 10,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "lockfile"
}
}
],
"max_points": 10
},
{
"key": "demonstrated_agent_practice",
"name": "Demonstrated agent practice",
"detail": "no agent-authored commits among the last 100",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_authored_commits",
"params": {
"sampled": 100
}
}
],
"max_points": 10
},
{
"key": "automated_maintenance",
"name": "Automated maintenance",
"detail": "no automated dependency updates observed",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_dependency_automation",
"params": {}
}
],
"max_points": 8
},
{
"key": "openssf_scorecard_pinned_dependencies",
"name": "OpenSSF Scorecard: Pinned-Dependencies",
"detail": "dependency not pinned by hash detected -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
},
{
"key": "ai_code_legibility",
"band": "moderate",
"name": "Code legibility for models",
"note": null,
"notes": [],
"value": 55,
"inputs": {
"primary_language": "HTML",
"largest_source_bytes": 28997,
"source_files_sampled": 25,
"oversized_source_files": 0
},
"components": [
{
"key": "type_checkable_code",
"name": "Type-checkable code",
"detail": "HTML without a type-check config",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_typecheck_config_language",
"params": {
"language": "HTML"
}
}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "0/25 source files over 60KB",
"points": 55,
"status": "met",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 25,
"oversized": 0
}
}
],
"max_points": 55
}
]
},
{
"key": "ai_interfaces",
"band": "at_risk",
"name": "Machine-readable interfaces",
"note": null,
"notes": [],
"value": 40,
"inputs": {
"example_dirs": [
"notebooks"
],
"has_mcp_signal": false,
"api_schema_files": []
},
"components": [
{
"key": "api_schema_openapi_graphql_proto",
"name": "API schema (OpenAPI/GraphQL/proto)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 40
},
{
"key": "mcp_server",
"name": "MCP server",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 20
},
{
"key": "runnable_examples",
"name": "Runnable examples",
"detail": "notebooks",
"points": 40,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "notebooks"
}
}
],
"max_points": 40
}
]
}
],
"description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
}
],
"metrics_version": "1.13.0"
},
"warnings": [
"Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token"
],
"report_type": "repository",
"generated_at": "2026-07-27T22:26:51.449767Z",
"schema_version": "0.27.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/c/CompOmics/ms2pip.svg",
"full_name": "CompOmics/ms2pip",
"license_state": "standard",
"license_spdx": "Apache-2.0"
}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 v1.13.0, schema v0.27.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.