matchms
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
Independent static run, no language model, over the same files as the Cisco scan above. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks. Use pyopenms instead for LC-MS feature detection or proteomics pipelines.
- Package
- 8 files, 101 KB
- SKILL.md
- 1404 words, 12+ sections
- Code
- Python (1)
- Allowed tools
ReadWriteEditBash- License
- Apache-2.0
- Compatibility
- Requires Python >=3.10,<3.15, uv, and matchms 0.33.1. Local file workflows need no credentials; metabolomics-USI loading requires network access.
SKILL.md covers: Matchms · Purpose and Scope · Install the Verified Release · Operating Workflow · Current API Guardrails · Quick Start: Clean and Search a Library · Pair Scoring · Choose a Similarity Method · Large Comparisons · Bundled Library-Search CLI · Spectrum Objects and Visualization · References
Findings
No findings. SAFE
What is in the package
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 13 KB |
references/filtering.md | doc | 12 KB |
references/importing_exporting.md | doc | 11 KB |
references/migration.md | doc | 8.4 KB |
references/similarity.md | doc | 14 KB |
references/sources.md | doc | 9.6 KB |
references/workflows.md | doc | 14 KB |
scripts/library_search.py | script | 21 KB |
External hosts referenced
github.com matchms.readthedocs.io matchms.github.io metabolomics-usi.gnps2.org arxiv.org pmc.ncbi.nlm.nih.gov ccms-ucsd.github.io docs.pubchempy.org doi.org export.arxiv.org joss.theoj.org pubmed.ncbi.nlm.nih.gov pypi.org www.pnas.org
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-matchms-scan.json
- Badge for your README:
- Request a re-scan