feat(agent): add cell-explorer-agent library and CLI#54
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Summary
cell-explorer-agentuv workspace package: dataset-scoped LLM chat agent over a provider-pluggableLLMClientprotocol (Anthropic adapter ships v1; direct / Bedrock / Vertex transports).get_dataset_schema,describe_obs_column,cluster_stats,search_genes,gene_expression_summary,top_expressed_genes,compare_groups) + 7 UI-action tools that emit partialAppConfigpayloads consumed by the frontend viewer.cell-explorer-chatsingle-shot entry point;FakeLLMClient+FakeZarrAccessdrive 84 unit/integration tests with no network dependency.cap_json_bytes; agent loop enforcesmax_tool_calls_per_turn, converts tool exceptions into structured tool-results with correlation IDs, and propagates cancellation.Scope
This is plan 1 of 3 for the chat feature. The FastAPI
/api/chatroute and the frontendchatpackage ship in follow-up PRs.Test plan
uv run pytest packages/cell-explorer-agent/tests/ -v— 84 passed, 1 skipped (TS drift check only runs in non-worktree checkout)uv run cell-explorer-chat --helprenders expected usageuv run pytest— 181 pre-existing tests remain passing alongside the new 84ANTHROPIC_API_KEYset