Instructions

You are interfacing with the src/ directory of the literature meta-analysis project. This directory contains 45+ public APIs spread across 6 submodules.

Agentic Interface (MCP Strategy)

When operating within this workspace, adhere to the following interaction protocols:

1. No-Mock Constraint: If you write tests for these modules, you MUST use pytest-httpserver or local data objects. Do not use mocker.patch or MagicMock.
2. Execution Context: Execute modules using the thin orchestrators located in scripts/, or by running uv run pytest in the tests/ directory. Do not write temporary execution blocks inside src/.
3. Data Immutability: The code here processes JSONL and TriG outputs. Ensure you have parsed manuscript/config.yaml using your file reading tools to understand runtime constraints.

Architecture Guidelines for AI Agents

• Modularity: Business logic never resides in scripts/. It belongs here.
• Reproducibility: When adding new NLP or analytical functions, ensure RNG seeds are hardcoded (typically seed=42) to guarantee deterministic analysis.
• Documentation Parity: If you modify any file here, you must run python3 -m infrastructure.validation.cli markdown to verify nothing was broken.

Refer to the specific SKILL.md in each subdirectory for granular file-level guidance.