methods-mcp
PYPI · METHODS-MCP · SCANNED SEP 20
MCP server for structured methods extraction + reproducibility heuristics on academic papers.
Available components
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security99
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- Runs hatchling.build at install time, a recognised native-build step with no shell scripting around it. View diagnostics → Pass
- 6 of 38 dependencies flagged as unhealthy. View diagnostics → Partial
Provenance & Transparency35
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Provenance check failed: no build-provenance attestation is published. See how to fix → View diagnostics → Fail
- License check failed: the license (MIT License) isn't a recognized OSI-approved license. See how to fix → Fail
- Actively maintained (last published 157 days ago).Pass
- Publishes a security disclosure policy (SECURITY.md).Pass
Schema Quality & AI Usability71
- AI-judged instruction clarity (good).Pass
- Tool/resource definitions use about 861 tokens (~107/item across 8 items; 8 tools + 0 resources), lean.Pass
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management87
- Stability observed for 26 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage71
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 0% of tool parameters carry a description.Fail
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 8 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 9 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
How do I install the methods-mcp server?
methods-mcp runs locally as a PyPI package, launched with uvx methods-mcp. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
pypi · methods-mcp
claude mcp add flynnlachendro-methods-mcp -- uvx methods-mcp
{
"mcpServers": {
"flynnlachendro-methods-mcp": {
"command": "uvx",
"args": [
"methods-mcp"
]
}
}
} {
"servers": {
"flynnlachendro-methods-mcp": {
"command": "uvx",
"args": [
"methods-mcp"
]
}
}
} codex mcp add flynnlachendro-methods-mcp -- uvx methods-mcp
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"flynnlachendro-methods-mcp": {
"type": "local",
"command": [
"uvx",
"methods-mcp"
],
"enabled": true
}
}
} openclaw mcp add flynnlachendro-methods-mcp --command uvx --arg methods-mcp
mcp_servers:
flynnlachendro-methods-mcp:
command: "uvx"
args: ["methods-mcp"] {
"McpServers": {
"flynnlachendro-methods-mcp": {
"Transport": "stdio",
"Command": "uvx",
"Arguments": [
"methods-mcp"
]
}
}
} assistant mcp add flynnlachendro-methods-mcp -t stdio -c uvx -a methods-mcp
{
"mcpServers": {
"flynnlachendro-methods-mcp": {
"command": "uvx",
"args": [
"methods-mcp"
]
}
}
} Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 19 Sept 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 80 to 83. That category is still filling its 30-day observation window: 24 days of observed history at the previous scan, 25 at this one. The score rises as the window fills, whether or not the server changes.
- 18 Sept 26 −3
- Stability: pass → 0.80 functional
- 17 Sept 26 0
- Stability: 0.97 → pass security
- 16 Sept 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 93 to 97. That category is still filling its 30-day observation window: 28 days of observed history at the previous scan, 29 at this one. The score rises as the window fills, whether or not the server changes.
- 15 Sept 26 +15
- Malware scan: unverified → pass ▲ security
- 14 Sept 26 −14
- Malware scan: pass → unverified ▼ security
- 12 Sept 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 80 to 83. That category is still filling its 30-day observation window: 24 days of observed history at the previous scan, 25 at this one. The score rises as the window fills, whether or not the server changes.
- 11 Sept 26 −3
- Stability: pass → 0.80 functional
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 20 Sept 2026 · Analysed pypi/methods-mcp@0.1.7
Provenance No attestation
The registry publishes no build provenance for this version, so there is nothing to verify.
| Result | No attestation |
|---|---|
| Ecosystem | pypi |
Background: How many MCP packages publish verified provenance →
Install scripts 1 script
| Hook | Tier | Command |
|---|---|---|
| build_backend | allowlisted | hatchling.build |
Background: Why install scripts are a supply-chain risk →
Dependencies 38 packages
| Packages resolved | 38 |
|---|---|
| Stale | 5 |
| No linked repository | 1 |
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
assess_repo_reproducibility Assess Repo Reproducibility ~103
Heuristic, no-clone reproducibility assessment of a GitHub repo. Returns a verdict (likely-reproducible / partial / unlikely / insufficient-info) plus weighted signals: README quality, dependency files, fixture data, notebooks, figure-generating scripts, recent maintenance, license. No code is downloaded or executed. Set GITHUB_TOKEN to raise the API rate limit.
| Name | Type | Req | Description |
|---|---|---|---|
| paper_id | – | – | – |
| repo_url | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| notes | string | yes | – |
| overall_score | number | yes | – |
| paper_id | – | – | – |
| recommended_entrypoint | – | – | E.g. 'python make_figures.py' if a likely figure-generating script was found. |
| repo_url | string | yes | – |
| signals | array | – | – |
| verdict | string | yes | – |
No examples provided.
extract_methods Extract Methods ~104
Extract a structured methods object from a paper. Pulls full text, isolates the methods-relevant section(s), then asks Claude (default: claude-sonnet-4-6) to fill out a Pydantic schema with steps, reagents, equipment, and analyses. Validation-enforced — invalid responses trigger one repair attempt before raising. Requires ANTHROPIC_API_KEY in the server's environment.
| Name | Type | Req | Description |
|---|---|---|---|
| input_str | string | yes | – |
| model | – | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| analyses | array | – | – |
| confidence | number | yes | LLM self-reported confidence in the structured extraction. |
| equipment | array | – | – |
| extraction_model | string | yes | Model identifier used for extraction. |
| notes | – | – | Free-form caveats from the extractor (e.g. 'methods section is sparse'). |
| paper_id | string | yes | – |
| reagents | array | – | – |
| steps | array | – | – |
| summary | string | yes | 2-3 sentence overview of the methods. |
No examples provided.
fetch_paper_text Fetch Paper Text ~95
Return best-effort full text + section split for a paper. prefer: one of "auto" (default), "html" (force ar5iv HTML — arXiv only), or "pdf". Sections are normalised to lowercase canonical names: abstract, introduction, methods, experiments, results, discussion, conclusion, limitations, related_work.
| Name | Type | Req | Description |
|---|---|---|---|
| input_str | string | yes | – |
| prefer | string | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| char_count | integer | yes | – |
| extraction_method | string | yes | – |
| paper_id | string | yes | – |
| sections | object | – | Section name (lowercased) -> text. Empty if extraction couldn't segment. |
| source_url | string | yes | – |
| text | string | yes | – |
No examples provided.
find_code_repo Find Code Repo ~58
Discover the code repo (if any) associated with a paper. Strategy: scan the paper's full text and abstract for github.com URLs; fall back to Papers With Code lookup for arXiv papers.
| Name | Type | Req | Description |
|---|---|---|---|
| input_str | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| confidence | number | yes | – |
| detection_method | string | yes | – |
| notes | – | – | – |
| paper_id | – | – | – |
| repo_url | – | – | – |
No examples provided.
get_paper_metadata Get Paper Metadata ~78
Resolve an arXiv ID/URL, bioRxiv URL, DOI, or generic URL to canonical metadata. For arXiv inputs this hits the arXiv export API to fetch title/authors/abstract. Other sources return the resolved URL with empty bibliographic fields (cheap by design).
| Name | Type | Req | Description |
|---|---|---|---|
| input_str | string | yes | – |
| Name | Type | Req | Description |
|---|---|---|---|
| abstract | – | – | – |
| authors | array | – | – |
| html_url | – | – | ar5iv HTML URL for arXiv papers. |
| paper_id | string | yes | Canonical identifier (e.g. arXiv ID, DOI). |
| pdf_url | – | – | – |
| primary_url | string | yes | – |
| publication_date | – | – | ISO 8601 date when known. |
| raw_input | string | yes | The original URL/ID the caller supplied. |
| source | string | yes | – |
| title | string | yes | – |
| venue | – | – | – |
No examples provided.
health Health ~21
Return a small health report — confirms the server is alive and configured.
Input schema present but exposes no named parameters.
| Name | Type | Req | Description |
|---|---|---|---|
| anthropic_configured | boolean | yes | – |
| server | string | – | – |
| transports | array | yes | – |
| version | string | yes | – |
No examples provided.
methods_repro_review Methods Repro Review ~269
Resolve a paper + extract methods + find its code repo + assess reproducibility — in one call. Returns a `MethodsReproReview` object. **Read `narrative` first** — it's a plain-English summary of everything retrieved, with every numeric score echoed in context (e.g. "moderate confidence (0.72)"). Then: - `status`: `"ok"` (all sub-steps succeeded), `"partial"` (some failed — see `errors`), or `"empty"` (couldn't even resolve the input paper). - `metadata`, `methods`, `code_repo`, `repro_assessment`: the structured sub-results. Any step that failed contributes `null` for its key; `null` means **unavailable**, not zero. - `errors`: list of `{step, error_type, message, hint}` — one entry per failed sub-step, with an actionable hint where the failure pattern is recognised (e.g. missing ANTHROPIC_API_KEY, rate-limit, 404, timeout). For the meaning of numeric scores and verdict buckets, see the "Scores & verdicts explained" section of the README.
| Name | Type | Req | Description |
|---|---|---|---|
| input_str | string | yes | – |
| model | – | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| code_repo | – | – | – |
| errors | array | – | – |
| metadata | – | – | – |
| methods | – | – | – |
| narrative | string | yes | – |
| repro_assessment | – | – | – |
| status | string | yes | Top-level status of a composite-tool call. `ok` — every sub-step succeeded. `partial` — at least one sub-step failed (see `errors`) but we have usable results. `empty` — we couldn't even resolve the… |
No examples provided.
summarize_paper Summarize Paper ~81
Generate an LLM summary of a paper in one of three modes. abstract = 2-3 sentences close to the authors' framing. tldr = one-line takeaway. exec = executive summary (what / found / why-it-matters).
| Name | Type | Req | Description |
|---|---|---|---|
| input_str | string | yes | – |
| mode | string | – | – |
| model | – | – | – |
| Name | Type | Req | Description |
|---|---|---|---|
| extraction_model | string | yes | – |
| key_findings | array | – | – |
| methodology_oneliner | string | yes | – |
| mode | string | yes | – |
| paper_id | string | yes | – |
| summary | string | yes | – |
No examples provided.
What is the methods-mcp server?
methods-mcp is listed in the public MCP registry as io.github.FlynnLachendro/methods-mcp. MCP server for structured methods extraction + reproducibility heuristics on academic papers. This page covers its PyPI package (methods-mcp).
Is the methods-mcp server safe to use?
methods-mcp scores 77 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 20 September 2026. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the methods-mcp server expose?
methods-mcp exposes 8 tools: health, get_paper_metadata, fetch_paper_text, extract_methods, find_code_repo, and 3 more. Their descriptions and schemas cost roughly 809 tokens of context every time the server is loaded.
Is the methods-mcp server still maintained?
methods-mcp is still listed as active in the MCP registry. We last reached this channel on 20 September 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.