Data Analysis
matchms
Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows.
85100Total Score
Core Capability
83 / 100
Functional Suitability
10 / 12
Reliability
10 / 12
Performance & Context
8 / 8
Agent Usability
13 / 16
Human Usability
7 / 8
Security
9 / 12
Maintainability
10 / 12
Agent-Specific
16 / 20
Medical Task
20 / 20 Passed
91Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows
4/4
87Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows
4/4
85Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms
4/4
85Packaged executable path(s): scripts/similarity_pipeline.py
4/4
85End-to-end case for Scope-focused workflow aligned to: Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows
4/4
Veto GatesRequired pass for any deployment consideration
Skill Veto✓ All 4 gates passed
✓
Operational Stability
System remains stable across varied inputs and edge cases
PASS✓
Structural Consistency
Output structure conforms to expected skill contract format
PASS✓
Result Determinism
Equivalent inputs produce semantically equivalent outputs
PASS✓
System Security
No prompt injection, data leakage, or unsafe tool use detected
PASSResearch Veto✅ PASS — Applicable
| Dimension | Result | Detail |
|---|---|---|
| Scientific Integrity | PASS | The archived review kept this workflow anchored to supplied data fields and observable execution behavior, not fabricated results. |
| Practice Boundaries | PASS | Practice boundaries held because the package remained focused on Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms rather than overclaiming what the records supported. |
| Methodological Ground | PASS | The archived evaluation treated the workflow as method-linked rather than ad hoc. |
| Code Usability | PASS | The legacy audit did not record a code-usability failure in the packaged analysis path. |
Core Capability83 / 100 — 8 Categories
Functional Suitability
The archived deduction in functional suitability traces back to: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
10 / 12
83%
Reliability
Reliability was softened by the legacy issue 'Improve stress-case output rigor'. Stress and boundary scenarios show weaker consistency
10 / 12
83%
Performance & Context
The legacy audit gave full marks to performance context for this package.
8 / 8
100%
Agent Usability
The archived review left some headroom in how quickly an agent can lock onto the intended analysis path.
13 / 16
81%
Human Usability
Human usability remained solid, with minor room to simplify the way analysis outcomes are presented.
7 / 8
88%
Security
A modest security gap remained in the archived evaluation despite otherwise controlled workflow behavior.
9 / 12
75%
Maintainability
The analysis package is maintainable overall, though the archived score suggests modest cleanup headroom.
10 / 12
83%
Agent-Specific
Agent specific was softened by the legacy issue 'Improve stress-case output rigor'. Stress and boundary scenarios show weaker consistency
16 / 20
80%
Core Capability Total83 / 100
Medical TaskExecution Average: 86.6 / 100 — Assertions: 20/20 Passed
91
Canonical
Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows
4/4 ✓
87
Variant A
Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows
4/4 ✓
85
Edge
Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms
4/4 ✓
85
Variant B
Packaged executable path(s): scripts/similarity_pipeline.py
4/4 ✓
85
Stress
End-to-end case for Scope-focused workflow aligned to: Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows
4/4 ✓
91
Canonical✅ Pass
Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows
This canonical case stayed within the packaged analysis boundary and kept a reviewable task contract.
Basic 36/40|Specialized 55/60|Total 91/100
✅A1The matchms output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
87
Variant A✅ Pass
Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows
This variant a case stayed within the packaged analysis boundary and kept a reviewable task contract.
Basic 34/40|Specialized 53/60|Total 87/100
✅A1The matchms output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Edge✅ Pass
Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms
The archived run treated Process, clean, and compare mass spectrometry (MS/MS) spectra with... as a bounded analysis workflow rather than a purely narrative instruction path.
Basic 33/40|Specialized 52/60|Total 85/100
✅A1The matchms output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Variant B✅ Pass
Packaged executable path(s): scripts/similarity_pipeline.py
The archived run treated Packaged executable path(s): scripts/similarity_pipeline.py as a bounded analysis workflow rather than a purely narrative instruction path.
Basic 32/40|Specialized 53/60|Total 85/100
✅A1The matchms output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Stress✅ Pass
End-to-end case for Scope-focused workflow aligned to: Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows
Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.
Basic 29/40|Specialized 56/60|Total 85/100
✅A1The matchms output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
Medical Task Total86.6 / 100
Key Strengths
- Primary routing is Data Analysis with execution mode B
- Static quality score is 83/100 and dynamic average is 78.6/100
- Assertions and command execution outcomes are recorded per input for human review
- Execution verification summary: Script verification 0/1; adjustment=0. similarity_pipeline.py: rc=1