Pubmed Search MCP Harness

PubMed Search MCP: Cline Harness Skill

Use this skill when working in the PubMed Search MCP repository with Cline and you need a dependable loop for literature-search tools, pipeline behavior, and release checks.

What To Use First

• Rules: .clinerules/
• Workflows: .clinerules/workflows/
  • Run /pubmed-full-check.md for local gates.
  • Run /pubmed-skills-audit.md after changing skills or rules.
  • Run /pubmed-release-publish.md for release prep.
• User-facing research skills: .claude/skills/pubmed-* and .claude/skills/pipeline-persistence.
  • If a .claude/skills instruction conflicts with current implementation, prefer .clinerules/.

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: python3 scripts/check_cline_skills.py

Research Guardrails

• Prefer unified_search as the primary multi-source entrypoint.
• Preserve session/pipeline state instead of relying on agent memory.
• Use build_research_chronicle and read_research_chronicle for durable research-history artifacts; the former timeline tools are no longer public.
• Respect NCBI email/API-key policy and institutional access configuration.
• Keep exported citations reproducible: PMIDs, DOI, source, date filters, and query strategy matter.