pubmed-search-mcp-harness

name: pubmed-search-mcp-harness description: "Codex harness for PubMed Search MCP. Triggers: pubmed search, literature search, unified_search, pipeline, fulltext, release checklist, Codex."

PubMed Search MCP: Codex Harness Skill

Use this skill when working with Codex on PubMed Search MCP research workflows, pipeline state, fulltext access, exports, and release checks.

What To Read First

• AGENTS.md for Codex workspace instructions.
• .github/agents/research.agent.md for research-agent behavior.
• .github/hooks/ and scripts/hooks/copilot/ for pipeline enforcement assets.
• .claude/skills/pubmed-* and .claude/skills/pipeline-persistence for user-facing workflows.
• .clinerules/ for project/release rules that also apply to Codex.

Canonical Commands

• Lint: uv run ruff check .
• Format check: uv run ruff format --check .
• Types: uv run mypy src/ tests/
• Tests: uv run pytest
• Tool docs sync: uv run python scripts/count_mcp_tools.py --update-docs
• Skill audit: python scripts/check_cline_skills.py

Research Guardrails

• Prefer unified_search as the primary multi-source entrypoint.
• For external Python package/API questions, prefer the stable pubmed_search.api facade over MCP presentation modules.
• Preserve session/pipeline state instead of relying on agent memory.
• Respect NCBI email/API-key policy and institutional access configuration.
• Keep exported citations reproducible with PMIDs, DOI, source, date filters, and query strategy.