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Contributing to BioMCP

BioMCP does not accept outside pull requests.

We do welcome:

  • GitHub Issues for bugs, regressions, and reproducible problems
  • GitHub Discussions for feature ideas, usage questions, and documentation requests

This policy keeps release provenance, supply-chain control, and copyright review for AI-assisted code with the core maintainers. We still want problem reports and product feedback, and the team will fix confirmed issues in the main repo.

When you open an issue or discussion, include:

  • the BioMCP version
  • the command you ran
  • the relevant output or error text
  • any source or API context needed to reproduce the problem

Repo-Local Test Setup

Install cargo-nextest before running repo-local Rust verification:

cargo install cargo-nextest --locked

make test uses cargo nextest run. make spec-contracts is the deterministic routine executable-contract lane used by March spec-only and make release-gate; it runs validation-lane docs/static surface contracts without live smoke. make release-live-smoke is the explicit opt-in live public-upstream confidence lane. make spec and make spec-pr remain available for the active canary tree under spec/entity/ and spec/surface/ with pytest-xdist (-n auto --dist loadfile). The executable docs themselves call tools/biomcp-ci, which owns release-binary resolution, the repo-owned .cache/biomcp-specs/ cache/XDG roots, optional-key stripping, and warm-hit BIOMCP_CACHE_MODE=infinite replay when CI sets BIOMCP_SPEC_CACHE_HIT=1. make check now runs lint, test, test-contracts, and check-quality-ratchet, so the canonical local gate already includes the Python/docs contract lane. make release-gate is the single routine release-readiness command; it runs make check and then make spec-contracts. Use make test-contracts to rerun just the release-critical Python/docs lane.

Local Pre-Commit Hook

Developers who opt in to the repo-local pre-commit hook should install it at $(git rev-parse --git-path hooks/pre-commit). The hook is local Git state; the repo does not install it automatically.

Use this shape so scripts/pre-commit-reject-march-artifacts.sh runs before cargo fmt --check and cargo clippy --lib --tests -- -D warnings:

hook_path="$(git rev-parse --git-path hooks/pre-commit)"
mkdir -p "$(dirname "$hook_path")"
cat >"$hook_path" <<'HOOK'
#!/usr/bin/env bash
set -euo pipefail

ROOT="$(git rev-parse --show-toplevel)"
cd "$ROOT"

scripts/pre-commit-reject-march-artifacts.sh
cargo fmt --check
cargo clippy --lib --tests -- -D warnings
HOOK
chmod +x "$hook_path"

The helper allows only .march/code-review-log.md and .march/validation-profiles.toml under .march/, and it permits staged deletions so cleanup commits can remove old March artifacts from tracking.

Timing Method

Measured on beelink on 2026-04-23 with /usr/bin/time -p using warm-cache steady-state runs. Each command was run once untimed to warm build artifacts and the repo-owned spec cache under .cache/biomcp-specs/, then once with timing enabled. The make spec-pr row was refreshed on 2026-04-24 after the spec-v2 canary cutover. make release-gate is a thin wrapper over make check and make spec-contracts, so its warm timing tracks the current sum of those warmed routine component lanes.

Command Observed warm-cache Notes
make check 344.11s now includes make test-contracts
make spec-contracts 386.98s deterministic routine lane, including release rebuild and 48 spec assertions (2026-05-23)
make spec-pr 56.16s full canary lane (refreshed 2026-04-24)
make release-live-smoke operator-run opt-in live public-upstream smoke; not part of routine gates
make release-gate 763.21s observed make check plus make spec-contracts routine gate (2026-05-23)