troubleshoot

A troubleshooting guide for Atomic Agents applications, covering common errors and incorrect results. Atomic Agents is a Python framework whose agents and tools exchange validated structured data.

In plain words
What is it for?
Use it to investigate import errors, schema validation failures, malformed language-model output, provider configuration problems, history or context issues, and MCP transport errors.
Why use it?
It helps identify the known cause of a failure from the exact error or wrong output, so fixes are based on the framework's behavior rather than guesswork.

Skill for Claude CodeCodex

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/eigenwise/atomic-agents/troubleshoot
Any agent
npx skills add Eigenwise/atomic-agents --skill troubleshoot
Clone the repo
git clone --depth 1 https://github.com/Eigenwise/atomic-agents

Made for: Claude Code, Codex.

Per session 103 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,429 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00103 $0.01429
Opus 5 $0.00051 $0.00714
Sonnet 5 $0.00021 $0.00286
Haiku 4.5 $0.00010 $0.00143

Measured yesterday against content hash 51951ffc4a31, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

troubleshoot scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

claude-plugin/atomic-agents/skills/troubleshoot/SKILL.md · 67 lines

How it starts

The opening of the file, as written. The whole thing — 67 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Troubleshoot an Atomic Agents App

Diagnostic workflow for the "it's broken" moment. Most atomic-agents failures are one of a dozen known causes with mechanical fixes. Match the symptom, apply the fix, verify by re-running.

Workflow

  1. Capture the failure. Get the exact traceback or wrong-output sample plus the code that produces it (agent construction, schemas, client wiring). If the user pasted only a fragment of the error, ask for the full traceback before guessing.
  2. Match against the symptom table below. The quoted strings are the framework's real messages — match on them.
  3. Apply the fix and re-run the failing snippet. Do not declare the problem solved without a passing re-run.
  4. No match? Load the reference for the failing area (table at the bottom) and reason from there. For a whole-codebase audit rather than one failure, delegate to the atomic-reviewer subagent instead.

Symptom table

Import and definition errors

Symptom Cause Fix
ImportError/ModuleNotFoundError on atomic_agents.lib.*, atomic_agents.agents.base_agent, or BaseAgent v1 import paths, removed in v2 Import from the top level: from atomic_agents import AtomicAgent, AgentConfig, BaseIOSchema, BaseTool; context pieces from atomic_agents.context
ValueError: <Name> must have a non-empty docstring to serve as its description at import time BaseIOSchema subclass without a docstring Add a docstring describing the schema — it flows into the LLM prompt, so write it for the model
ValidationError when constructing AgentConfig, complaining about client Raw provider SDK client passed; AgentConfig.client requires an Instructor-wrapped client Wrap it: instructor.from_openai(...), instructor.from_anthropic(...), instructor.from_genai(...)
TypeError about missing type parameters, or output typed as BasicChatOutputSchema when a custom schema was expected AtomicAgent instantiated without generics Write AtomicAgent[InputSchema, OutputSchema](config=...) — the type parameters carry runtime information (they drive Instructor's response_model)

Read the full file on GitHub · 67 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. yesterday First seen · 67 lines · 103 tokens per session scan A 51951ffc4a31

Subscribe to this mod's changes

troubleshoot is a skill published in the GitHub repository Eigenwise/atomic-agents (6,213 stars, last pushed 7d ago), licensed MIT. It adds 103 tokens to every session and 1,429 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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