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methods-mcp

methods-mcp

PyPI Python License: MIT

Легковесный MCP-сервер по требованию для структурированного извлечения методов + эвристик воспроизводимости для академических статей. Создан для челленджа Worldwide AI Science Fellowship.

⚠️ Статус: alpha (0.1.x). Поверхность инструментов и формы вывода могут меняться между минорными версиями. Зафиксируйте точную версию в продакшене. Баг-репорты приветствуются через GitHub Issues.

Быстрая демонстрация

$ uvx --from methods-mcp methods-mcp --version
methods-mcp 0.1.6

# In a Claude Code session:
> /mcp add methods-mcp methods-mcp
> Run methods_repro_review on https://arxiv.org/abs/2509.06917

  → tool: methods_repro_review({"input_str":"https://arxiv.org/abs/2509.06917"})

# Returns a MethodsReproReview object. Read `narrative` first — it explains
# everything else in plain English, so no tool-learning is required:

{
  "status": "ok",
  "narrative":
    "Resolved the paper: 'Paper2Agent' by Miao et al. (arxiv 2509.06917, "
    "2025-09-08). Extracted 11 methods steps at moderate self-reported "
    "confidence (0.72) — the procedure is clearly described but hyperparameters "
    "and software versions are absent. Detected the associated code repository "
    "https://github.com/jmiao24/Paper2Agent from an inline link in the paper "
    "text (detection confidence 0.94). The repo scored 0.90/1.00 on the "
    "reproducibility heuristic — verdict: likely reproducible. Present signals: "
    "substantive README, dependencies file, notebooks, figure-plotting script, "
    "recent activity, permissive license. Missing: data/fixtures directory. "
    "Suggested entrypoint: `python make_figures.py`.",
  "metadata":          { ... },   # PaperMetadata
  "methods":           { ... },   # MethodsStructured (null if extraction failed)
  "code_repo":         { ... },   # CodeRepo           (null only if input unresolvable)
  "repro_assessment":  { ... },   # ReproAssessment   (null if no repo detected)
  "errors":            []         # [{step, error_type, message, hint}] on partial
}

methods-mcp — это небольшой, узконаправленный сервер Model Context Protocol. Он предоставляет любому ИИ-агенту (Claude Code, Claude Desktop, вашему скрипту Agent SDK и т.д.) восемь инструментов, которые превращают URL академической статьи в:

  • канонические метаданные,

  • полный текст с разбивкой по секциям (best-effort),

  • структурированный объект методов, проверенный Pydantic (шаги / реагенты / оборудование / анализы),

  • репозиторий кода статьи (обнаружение best-effort),

  • вердикт о воспроизводимости без выполнения для этого репозитория,

  • сводку в нескольких режимах.

Ключевая идея: тяжёлые пайплайны, такие как Paper2Agent (Stanford), тратят от 30 минут до часов на переработку статьи в готовые к использованию инструменты. methods-mcp — это вызываемый агентом, по требованию комплемент — каждый инструмент возвращает результат за секунды, без клонирования и выполнения.


Related MCP server: paperstack

Установка

uv add methods-mcp
# or, install globally:
uv tool install methods-mcp
# or, classic pip:
pip install methods-mcp

Ключи API

Для лучшей производительности установите оба:

Переменная

Обязательна?

Что вы получаете без неё

ANTHROPIC_API_KEY

Обязательна для extract_methods, summarize_paper, methods_repro_review

Эти инструменты вызывают RuntimeError: ANTHROPIC_API_KEY not set. Не-LLM инструменты (fetch_paper_text, find_code_repo, assess_repo_reproducibility) продолжают работать нормально.

GITHUB_TOKEN

Необязательна, но рекомендуется для assess_repo_reproducibility / methods_repro_review

Вы ограничены неаутентифицированным лимитом GitHub (60 запросов/час на IP). Каждая оценка репозитория — это ~3 вызова, так что вы упрётесь в потолок после ~15–20 репозиториев/час. С токеном: 5,000 запросов/час (практически безлимитно).

export ANTHROPIC_API_KEY=sk-ant-...
export GITHUB_TOKEN=ghp_...          # optional but recommended

Ни один ключ не логируется и не сохраняется — они отправляются только на api.anthropic.com и api.github.com соответственно. См. SECURITY.md.

Использование из Claude Code

/mcp add methods-mcp methods-mcp

Возьмите https://arxiv.org/abs/2509.06917 и выполните methods_repro_review. Опишите, что делает статья, шаги методов и насколько воспроизводимым выглядит репозиторий.

Использование из Claude Agent SDK

from claude_agent_sdk import ClaudeAgentOptions, ClaudeSDKClient

options = ClaudeAgentOptions(
    mcp_servers={
        "methods-mcp": {
            "type": "stdio",
            "command": "methods-mcp",
            "args": [],
        }
    },
    allowed_tools=["mcp__methods-mcp__methods_repro_review"],
)

async with ClaudeSDKClient(options=options) as client:
    await client.query(
        "Run methods_repro_review on https://arxiv.org/abs/2509.06917 "
        "and tell me whether the repo looks reproducible."
    )
    async for msg in client.receive_response():
        print(msg)

Инструменты

Инструмент

Что делает

health

Проверка живости сервера и конфигурации.

get_paper_metadata(input_str)

Разрешение URL / arXiv ID / DOI в канонические метаданные. Для arXiv-входов используется экспортный API arXiv для получения названия, авторов и аннотации.

fetch_paper_text(input_str, prefer="auto"|"html"|"pdf")

Полный текст + разбивка по секциям. По умолчанию для arXiv-статей используется ar5iv HTML (дёшево, структурировано), иначе PDF-фолбэк.

extract_methods(input_str, model=None)

Управляемое LLM, проверенное Pydantic структурированное извлечение методов. Возвращает {steps, reagents, equipment, analyses, confidence}.

find_code_repo(input_str)

Обнаружение репозитория кода статьи через текст статьи → аннотацию → Papers With Code.

assess_repo_reproducibility(repo_url, paper_id=None)

Эвристическая оценка воспроизводимости без клонирования через GitHub REST API. Взвешенные сигналы (README, зависимости, фикстуры, ноутбуки, скрипты для графиков, недавняя поддержка, лицензия) → {verdict, score, recommended_entrypoint}.

summarize_paper(input_str, mode="tldr"|"abstract"|"exec")

Сводка LLM на трёх уровнях глубины.

methods_repro_review(input_str)

Композитный — метаданные + методы + репозиторий + воспроизводимость одним вызовом.

Все инструменты возвращают модели Pydantic v2 (проверенные, сериализуемые в JSON). Полный список типов см. в src/methods_mcp/schemas.py.

Заметки по дизайну

  • extract_methods использует tool-use от Anthropic, чтобы заставить модель выдать экземпляр Pydantic-схемы MethodsStructured. При ошибке валидации мы отправляем одно сообщение с ошибкой валидации и пробуем снова перед тем, как поднять исключение.

  • assess_repo_reproducibility не клонирует и не выполняет ничего. Он оценивает репозиторий по публично читаемым метаданным GitHub + рекурсивному дереву файлов. Это осознанный компромисс против пакетных инструментов, которые пытаются реально перезапустить статью.

  • fetch_paper_text предпочитает ar5iv HTML парсингу PDF для arXiv-статей. Для не-arXiv входов используется фолбэк на pypdf.

  • Модель по умолчанию — claude-sonnet-4-6. Переопределяется через переменную окружения METHODS_MCP_MODEL или аргумент model= при вызове.

  • methods_repro_review возвращает самодокументируемый ответ. Каждый вызов устанавливает верхнеуровневый status ("ok" / "partial" / "empty") и строку narrative, которая резюмирует всё полученное на простом английском — включая каждую числовую оценку в контексте. Читатель, который читает только narrative + status, получает полную картину без необходимости изучать формы под-объектов. Под-объекты могут быть null, когда недоступны (например, repro_assessment: null для статьи без обнаруженного репозитория — status остаётся "ok", потому что "нет репозитория" — не ошибка). Неудачные под-шаги добавляют структурированную запись в errors с {step, error_type, message, hint}, где hint — это практическая подсказка на простом английском для распознанных паттернов (отсутствующие ключи API, лимиты скорости, 404, таймауты и т.д.), и null в противном случае.

Объяснение оценок и вердиктов

Выводы инструментов содержат три числовых поля, которые выглядят похоже, но означают очень разные вещи. Это сигналы для триажа, помогающие агенту решить, стоит ли копать глубже в статью, а не калиброванные утверждения о корректности.

Поле

Диапазон

Как вычисляется

Как читать

methods.confidence

0–1

Самоотчёт LLM. Модель-экстрактор устанавливает его по инструкциям в системном промпте: ≥0.8 только если в статье даны явные реагенты/объёмы/оборудование, ~0.3 если раздел методов скудный. Некалиброванный.

Мягкий сигнал для "это влажная лабораторная статья с конкретной процедурой или разреженная системная статья?" Полезен как флаг; не воспринимайте как процент доверия.

code_repo.confidence

0–1

Зависит от detection_method. papers-with-code: фиксированный 0.95 (авторитетный API статья→репозиторий). paper-text: вычисляется как 0.6 + 0.2·(strong-phrase-present) + 0.015·score_margin, с потолком 0.95. abstract-link: фиксированный 0.85. none: 0.0.

Показывает, как был найден репозиторий и насколько решительно. Высокий балл + paper-text означает, что сильная фраза вроде "код доступен по адресу …" находилась рядом с URL.

repro_assessment.overall_score

0–1

Взвешенная сумма 8 бинарных сигналов, все вычисляются из GitHub REST API (без клонирования и выполнения): has_readme (0.10), readme_substantial (0.15), has_dependencies_file (0.20), has_data_or_fixtures (0.10), has_notebook (0.10), has_figure_script (0.20), actively_maintained (0.10), permissive_license (0.05). Каждый присутствующий сигнал добавляет свой вес.

Единственная полностью детерминированная оценка из трёх. Всё равно эвристика, а не доказательство — высокий балл означает, что репозиторий выглядит хорошо структурированным для воспроизведения. Для реальной валидации см. Paper2Agent.

Вердиктные корзины (repro_assessment.verdict) — это пороги на overall_score:

Verdict

Score

Meaning

likely-reproducible

≥ 0.70

Присутствует большинство сигналов, благоприятных для воспроизведения. Стоит попробовать запустить.

partial

≥ 0.45

Есть некоторая инфраструктура, вероятны пробелы. Будьте готовы восполнить недостающие части.

unlikely

≥ 0.20

Минимальный сигнал. Возможно, просто выгрузка кода без каркаса для повторного запуска.

insufficient-info

< 0.20 или репозиторий недоступен

Недостаточно данных для выводов. Не делайте выводов ни в ту, ни в другую сторону.

Значения перечислений, которые вы увидите в выводах:

  • code_repo.detection_method: paper-text | abstract-link | papers-with-code | metadata | none

  • metadata.source: arxiv | biorxiv | doi | url | unknown

Безопасность и ограничения

Что этот сервер фактически делает при установке и запуске:

  • Сетевые вызовы только к: export.arxiv.org, ar5iv.labs.arxiv.org, arxiv.org (PDF), api.github.com, paperswithcode.com, api.anthropic.com. Никакой телеметрии, никакой аналитики, никаких обращений домой.

  • Читает ANTHROPIC_API_KEY (обязателен для LLM-инструментов) и опционально GITHUB_TOKEN из переменных окружения. Они отправляются только в Anthropic / GitHub соответственно. Никогда не логируются и не сохраняются на диск.

  • Ничего не записывает в вашу файловую систему. Никаких кэш-каталогов, скачанных PDF или временных файлов.

  • Не выполняет пользовательский код. Никаких eval, exec, subprocess, pickle.loads или вызовов оболочки. Инструмент воспроизводимости намеренно не клонирует и не запускает репозитории — он оценивает только через GitHub REST API.

Ограничения, о которых стоит знать:

  • Враждебные статьи могут давать вводящий в заблуждение структурированный вывод. Инструмент extract_methods отправляет текст статьи в Claude. Статья с контентом для prompt-инъекций может дать неверные (но валидные по схеме) структурированные методы. Относитесь к выводу как к вспомогательному средству исследования, а не к истине в последней инстанции.

  • Вердикт о воспроизводимости — это эвристика, а не доказательство. Высокий балл означает, что репозиторий выглядит хорошо структурированным для воспроизведения; это не гарантирует, что запуск кода воспроизведёт статью. Для полной валидации см. Paper2Agent.

  • Предназначен для локального использования через stdio. HTTP/SSE-транспорты предоставлены для удобства разработки, но должны быть доступны только в доверенных сетях (нет защиты от SSRF сверх того, что предоставляет httpx).

Сообщение о проблемах:

Проблемы безопасности: пожалуйста, напишите на flynnlachendro@hotmail.co.uk (также см. SECURITY.md). Функциональные ошибки: откройте issue на GitHub.

Совместное использование с paper-mcp

Для более широкого поиска статей / инструментов графа цитирования запустите paper-mcp (Bhvaik) в той же сессии Claude Code. paper-mcp выполняет поиск по заголовкам, получение полных текстов, цитаты и ссылки; methods-mcp добавляет поверх слой структурированных методов + воспроизводимости. Эти два инструмента намеренно спроектированы для совместной работы.

Локальная разработка

git clone https://github.com/FlynnLachendro/methods-mcp
cd methods-mcp
uv sync --extra dev --extra agent

uv run pytest                      # 49 tests, offline (respx-mocked httpx + unittest.mock for Anthropic)
uv run ruff format .
uv run ruff check . --fix
uv run mypy src

uv run methods-mcp --help

Лицензия

MIT — см. LICENSE.

Благодарности

Создано для первого набора Worldwide AI Science Fellowship. Спасибо Michael Raspuzzi за свободное техническое задание.

Построено на основе:

Available Tools

8 tools
assess_repo_reproducibilityA

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.

ParametersJSON Schema
NameRequiredDescriptionDefault
paper_idNo
repo_urlYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
notesYes
signalsNo
verdictYes
paper_idNo
repo_urlYes
overall_scoreYes
recommended_entrypointNoE.g. 'python make_figures.py' if a likely figure-generating script was found.

TDQS

A3.5/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations are entirely absent, so the description carries the full disclosure burden — and it meets it. It explicitly states the operation is non-destructive ('No code is downloaded or executed'), that this is a heuristic scoring exercise, that weighted signals feed the verdict, and even discloses the GitHub API rate-limit dependency plus the GITHUB_TOKEN mitigation. This is comprehensive behavior disclosure with no annotation support needed.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is tight and dense with zero filler: first sentence states purpose and mode, second summarizes the verdict taxonomy, third enumerates the signals, fourth discloses side-effect-free behavior, fifth gives the auth hint. Every sentence earns its place and the most decision-relevant facts (heuristic, no-clone) are front-loaded.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The overall assessment logic, safety profile, and auth requirement are well covered, and an output schema exists so the return structure doesn't need full restatement. However, completeness is undermined by the unexplained paper_id parameter and the lack of any guidance on when this tool applies versus methods_repro_review. For a moderately complex heuristic tool this is adequate but leaves discernible gaps.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate — and largely fails to. repo_url's purpose is inferable from context but is never actually explained. paper_id (an accepted parameter, optional with null default) is completely unexplained: an agent cannot tell whether it links the assessment to a paper in the system, serves as a label, or affects scoring. No parameter receive explicit definitional help.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The opening line is specific: 'Heuristic, no-clone reproducibility assessment of a GitHub repo' — a clear verb (assess) plus a concrete resource (GitHub repo reproducibility), with the heuristic/no-clone qualifiers delimiting its scope. It states the return verdicts and the signal dimensions, so an agent understands what this produces. It doesn't explicitly distinguish itself from the closest sibling, methods_repro_review, but the 'no-clone' and 'heuristic vs deep review' framing sufficiently separates it.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description never states when to choose this tool over alternatives. It enumerates what it does — heuristic signals, no code execution — but gives no explicit 'use when you need a quick pass' or 'for a full methods review use methods_repro_review instead.' Given rich sibling context (methods_repro_review, find_code_repo, extract_methods), the absence of routing or exclusion guidance is a real gap.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

extract_methodsA

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.

ParametersJSON Schema
NameRequiredDescriptionDefault
modelNo
input_strYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
notesNoFree-form caveats from the extractor (e.g. 'methods section is sparse').
stepsNo
summaryYes2-3 sentence overview of the methods.
analysesNo
paper_idYes
reagentsNo
equipmentNo
confidenceYesLLM self-reported confidence in the structured extraction.
extraction_modelYesModel identifier used for extraction.

TDQS

A4/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Since annotations are absent, the description carries the full burden and does substantial work: it discloses that the tool fetches full text, isolates methods sections, calls an external Claude model, validates against a Pydantic schema, performs one repair attempt, and requires ANTHROPIC_API_KEY. These are behavioral traits an agent needs to anticipate dependencies and side effects.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description front-loads the core purpose, then moves through process and prerequisites in three compact paragraphs. No filler or repetition of the tool name.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The description covers the pipeline, validation/repair behavior, and auth prerequisite, and an output schema exists so return semantics needn't be restated. However, it leaves the required input parameter semantically ambiguous, which is a meaningful gap for invoking the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0% and the description only partially compensates: it mentions the default model (claude-sonnet-4-6) but never defines the required input_str (e.g., paper ID vs plain text) or the effect of passing a custom model. An agent cannot confidently populate parameters from this definition alone.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb ('Extract') and resource ('structured methods object') plus source ('a paper'), and names output components (steps, reagents, equipment, analyses). It is clearly distinguishable from sibling tools like summarize_paper and fetch_paper_text.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description makes the general use case clear (extracting structured methods), but it never explicitly says when to prefer this over siblings such as fetch_paper_text or methods_repro_review, and it gives no exclusion criteria. Usage is implied from the purpose rather than explicitly guided.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

fetch_paper_textB

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.

ParametersJSON Schema
NameRequiredDescriptionDefault
preferNoauto
input_strYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
textYes
paper_idYes
sectionsNoSection name (lowercased) -> text. Empty if extraction couldn't segment.
char_countYes
source_urlYes
extraction_methodYes

TDQS

B3.4/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full behavioral burden. It discloses 'best-effort' semantics (implying possible partial/failed text retrieval), the arXiv-only constraint for the html preference, and the section normalization behavior. However, it does not disclose what happens when html is requested for non-arXiv papers (fallback behavior) or how failures surface to the caller.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Roughly 60 words with the core purpose front-loaded in the first sentence. Each subsequent sentence explains the prefer values and the canonical section names without waste. It is appropriately tight, though slightly terse.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values are partially covered there. The description discloses section-normalization output behavior. But the undefined 'input_str' format is a critical gap: an agent cannot reliably invoke the tool without knowing what identifier to pass. The failure/fallback semantics of 'best-effort' and non-arXiv html requests are also unspecified. For a 2-param tool at 0% schema coverage, the description needed to compensate and did not.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must define both parameters. 'prefer' is explained thoroughly (auto/html/pdf values, default, and the html constraint), but 'input_str' — the single required parameter — is never explained. An agent has no idea whether it expects an arXiv ID, DOI, or URL. This is the most critical parameter for calling the tool and is left undefined.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description opens with a specific verb+resource: 'Return best-effort full text + section split for a paper.' This clearly distinguishes it from siblings like get_paper_metadata (metadata only) and summarize_paper (summary), making it easy for an agent to know this tool retrieves the raw full text with section boundaries.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The purpose implicitly signals when to use this tool (need full text + sections, not metadata or analysis), but there is no explicit when-to-use or when-not-to-use guidance, and no alternative tools are named. The agent must infer the selection logic from the name and description alone.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

find_code_repoA

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.

ParametersJSON Schema
NameRequiredDescriptionDefault
input_strYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
notesNo
paper_idNo
repo_urlNo
confidenceYes
detection_methodYes

TDQS

A4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden. It discloses the algorithm: scanning for GitHub URLs and using a Papers With Code fallback. This is meaningful behavioral transparency beyond just 'finds a repo.' It also hints at a potential outcome ('if any'), implying it might not always find a repo. However, it does not mention limitations like other repo hosts or what happens when a paper is not on arXiv. Still, the strategy is a strong disclosure of internal behavior.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is two sentences with zero fluff. The first sentence states the purpose clearly and the second provides the strategy. It is front-loaded with the core action, and every word contributes value. The structure is efficient and easy to parse.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The tool is relatively simple with one parameter and an output schema, so the return format is presumably covered by the output schema. However, the input parameter is not described, which is a critical gap. The description explains the method but leaves the agent unsure what to pass as input_str. Given the lack of annotations, the description must carry more weight, and this omission makes it incomplete.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema has one required parameter, 'input_str', with no description and 0% schema description coverage. The description refers to 'a paper' but does not explain what input_str should contain (e.g., a paper ID, URL, or title). It does not clarify the expected format or how the tool will use it. The description fails to compensate for the lack of schema detail, leaving the agent uncertain about the parameter's meaning. This is a significant gap.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose: 'Discover the code repo (if any) associated with a paper.' It uses a specific verb ('discover') and resource ('code repo'), and the scope is clear. This distinguishes it from siblings like get_paper_metadata or assess_repo_reproducibility, which handle metadata or reproducibility assessment. The strategy also clarifies the exact function.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies when to use it: whenever you need to locate a paper's code repository. It provides a concrete strategy (scanning full text/abstract for GitHub URLs, falling back to Papers With Code for arXiv papers), which gives context on its operation. It does not explicitly exclude scenarios or name alternative tools, but the purpose is clear enough that an agent would know it is the right tool for finding code repos. Lacks explicit 'when not to use' guidance, so a 4 is appropriate.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

get_paper_metadataA

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).

ParametersJSON Schema
NameRequiredDescriptionDefault
input_strYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
titleYes
venueNo
sourceYes
authorsNo
pdf_urlNo
abstractNo
html_urlNoar5iv HTML URL for arXiv papers.
paper_idYesCanonical identifier (e.g. arXiv ID, DOI).
raw_inputYesThe original URL/ID the caller supplied.
primary_urlYes
publication_dateNoISO 8601 date when known.

TDQS

A4/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden of behavioral disclosure. It reveals that arXiv inputs trigger an API call to fetch metadata, while others return a resolved URL with empty bibliographic fields (termed 'cheap by design'). However, it does not mention side effects, error conditions, or rate limits, and does not explicitly declare it as read-only. It adds useful context but is not fully transparent.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is two sentences with no fluff. The core purpose is front-loaded, followed by the key behavioral distinction for arXiv versus other sources. Every sentence earns its place, and it is appropriately concise for a tool with one parameter.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's simplicity (one parameter, no annotations) and the existence of an output schema, the description covers essential behavior: resolving inputs and returning specific metadata for arXiv, while handling other sources efficiently. It could be more complete by mentioning error handling or URL format requirements, but these are minor gaps. Overall, it provides enough context for an agent to call the tool correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It does by explaining that input_str accepts arXiv IDs/URLs, bioRxiv URLs, DOIs, or generic URLs, adding meaning beyond the schema's simple 'string' type. It does not specify exact formats or validation rules, but the accepted types are clearly stated, which is sufficient for a single simple parameter.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb ('Resolve') and a clear resource ('arXiv ID/URL, bioRxiv URL, DOI, or generic URL') with a defined output ('canonical metadata'). It also differentiates behavior by input type, which helps distinguish it from sibling tools like fetch_paper_text that likely handle full text.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The intended use is implied by the purpose ('resolve... to canonical metadata'), but there is no explicit mention of when to use this tool versus alternatives or when not to use it. It does not compare with siblings or provide selection criteria, such as 'use fetch_paper_text for full text'. Guidance is only implicit.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

healthA

Return a small health report — confirms the server is alive and configured.

ParametersJSON Schema
NameRequiredDescriptionDefault

No parameters

Output Schema

ParametersJSON Schema
NameRequiredDescription
serverNo
versionYes
transportsYes
anthropic_configuredYes

TDQS

A4.3/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full burden. It discloses that the tool returns a report and indicates a read-only behavior ('confirms' and 'report'). It does not mention side effects or permissions, but for a health check, these are arguably non-issues. The description goes beyond trivial naming by explaining the report's content.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is one concise, front-loaded sentence that states the action and its purpose without any fluff. Every word contributes value. It is appropriately sized for a tool this trivial.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a zero-parameter tool with an output schema present, the description is fully sufficient. It tells the agent what the tool returns and what it confirms. No additional details (e.g., exact format) are needed because the output schema handles that. The description is complete for its purpose.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The tool has zero parameters, so the schema fully covers parameter semantics (coverage is 100%). The baseline for 0-parameter tools is 4, and the description adds no unnecessary parameter information. It correctly focuses on the output and purpose.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('Return') and resource ('health report') and specifies the purpose: 'confirms the server is alive and configured.' This clearly distinguishes it from the sibling tools, all of which are paper-related and involve data retrieval or analysis.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies the tool is for checking server status but does not explicitly state when to use it versus alternatives or provide exclusions. There is no mention of 'use this when...' or 'instead of...'. Given the simplicity and obvious distinctiveness from paper-processing siblings, the implicit context is acceptable but not explicitly stated.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

methods_repro_reviewA

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.

ParametersJSON Schema
NameRequiredDescriptionDefault
modelNo
input_strYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
errorsNo
statusYesTop-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 paper input; no sub-steps ran.
methodsNo
metadataNo
code_repoNo
narrativeYes
repro_assessmentNo

TDQS

A3.6/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden of disclosing behavior, and it does so well. It explains the possible status values (ok/partial/empty), the semantics of null keys (unavailable, not zero), and the structure of errors including hints. It also tells the agent to read 'narrative' first and mentions failure patterns like missing ANTHROPIC_API_KEY, rate-limit, and timeouts. It does not explicitly state read-only semantics or potential side effects, but the error hints imply network calls; overall it is transparent for a composite read tool.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is reasonably concise for the complexity, with the core purpose front-loaded in the first sentence and the return structure laid out in a clear bullet list. It avoids redundancy and uses formatting to separate fields. It references the README for score meanings, which is a minor downside but acceptable given the length. Overall, it is well-structured and not bloated.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Despite the complexity (composite of four steps), the description omits critical details needed to call the tool: the input format for input_str and the meaning of model. It also defers score/verdict details to the README, which is a gap because the agent receives no inline explanation. With no annotations and no parameter descriptions, the description is not self-sufficient for correct invocation, leaving the agent with unanswered questions about required inputs.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must explain both parameters. It only hints that input_str is a paper identifier ('Resolve a paper') but never specifies the format (DOI, arXiv ID, URL, or free text). The model parameter is completely unmentioned, leaving the agent clueless about its purpose or allowed values. This is a significant gap that forces the agent to guess or consult external docs.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states a specific verb and resource: it resolves a paper, extracts methods, finds a code repo, and assesses reproducibility in one call. It enumerates the sub-steps explicitly, which distinguishes it from the single-purpose sibling tools (e.g., extract_methods, find_code_repo) and makes its combined scope immediately obvious. The phrase 'in one call' reinforces its composite nature.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies the tool is a convenience for getting all four results at once, but it does not explicitly state when to use it versus calling individual siblings, nor does it mention any exclusions or prerequisites. It says 'in one call' but does not say 'use this when you need all steps' or 'if you only need X, use Y'. This leaves the agent to infer the use case without explicit routing guidance.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

summarize_paperA

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).

ParametersJSON Schema
NameRequiredDescriptionDefault
modeNotldr
modelNo
input_strYes

Output Schema

ParametersJSON Schema
NameRequiredDescription
modeYes
summaryYes
paper_idYes
key_findingsNo
extraction_modelYes
methodology_onelinerYes

TDQS

A3.7/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full burden of behavioral disclosure. It reveals that summaries are LLM-generated and specifies the output format for each mode, which is useful. However, it does not mention read-only status, side effects, required permissions, or any potential costs or delays. This is a moderate level of transparency.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is exceptionally concise and well-structured. It opens with a clear purpose sentence, then lists each mode with its output specification using a bullet-like format. Every sentence contributes value with no redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The tool appears simple (3 params, 1 required), and the description explains the output for each mode. However, the required parameter 'input_str' is not defined, and the 'model' parameter is left unexplained. No mention of error handling or typical usage scenarios. The description is adequate for a simple tool but has noticeable gaps.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It does explain the 'mode' enum values thoroughly, adding meaning beyond the schema. However, it does not clarify 'input_str' (presumably the paper text) or 'model' (which model to use). This partial compensation earns a middle score.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose with a specific verb ('Generate') and resource ('a paper'), and defines three distinct modes of output. This distinguishes it from sibling tools like extract_methods or fetch_paper_text, which have different functions. The mode definitions add precision.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explains the three mode options in detail, which helps an agent decide which mode to use. However, it does not explicitly state when to use this tool versus alternatives such as extract_methods or methods_repro_review. The usage context is implied by the name and purpose, but not explicitly guided.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

  1. 8 tool updatesv0.1.7
    • First observedassess_repo_reproducibility
    • First observedextract_methods
    • First observedfetch_paper_text
    • First observedfind_code_repo
    • First observedget_paper_metadata
    • First observedhealth
    • First observedmethods_repro_review
    • First observedsummarize_paper

TDQS

A3.8/5.0

Scored across 8 tools

Disambiguation5/5

Each tool has a clearly distinct purpose: health check, metadata resolution, text fetching, methods extraction, code repo discovery, reproducibility assessment, summarization, and a combined orchestration tool. The composite tool is explicitly described as a one-call pipeline, so no confusion with individual steps.

Naming Consistency3/5

Most tools follow a verb_noun pattern (get, fetch, extract, find, assess, summarize), but 'health' is a bare noun and 'methods_repro_review' is a noun phrase without a verb. These deviations break the otherwise consistent snake_case convention.

Tool Count5/5

8 tools is well within the ideal range, and each tool maps to a specific stage in the paper analysis pipeline. No redundancy or unnecessary duplication, and the count feels appropriately scoped for the server's reproducibility-focused purpose.

Completeness4/5

The tool surface covers the entire workflow from paper resolution to reproducibility assessment, including a composite endpoint. Minor gaps like search or fine-grained section access are absent but not essential to the stated domain, making the set largely complete.

Maintenance

ActivityInactive
ResponsivenessNo issues

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