add-feature

name	add-feature
description	Procedure for adding a feature to gbcms following its Git Flow and Rust/Python architecture (branch from develop, plan the layer, implement, sync type stubs, add tests with the 4 counting invariants, update docs/CHANGELOG, QA, PR to develop). Use when starting new feature work.

add-feature

1. Create feature branch:

   git checkout develop && git pull origin develop
   git checkout -b feature/<scope>-<description>
   

2. Plan the feature:

   • Identify the layer: Rust counting, Python orchestration, CLI, or docs
   • Check .agents/rules/architecture.md for the Rust/Python boundary
   • Check existing code for reusable patterns (don't re-implement)

3. Implement:

   • Rust: rust/src/ → rebuild with maturin develop --release
   • Python: src/gbcms/
   • CLI option: add to cli.py, validate in models/core.py
   • Type stubs: update src/gbcms/_rs.pyi (the single stub for gbcms._rs)
   • If it changes a CLI default/filter: update nextflow/nextflow.config too

4. Add tests: assert all 4 counting invariants; cover edge cases.

5. Update docs: docs/cli/*, docs/nextflow/parameters.md (if NF param), docs/reference/output-formats.md (if schema changed), CHANGELOG ## [Unreleased].

6. Run QA (see the qa-check skill).

7. PR to develop:

   git push origin feature/<scope>-<description>
   gh pr create --base develop --title "feat(<scope>): <description>"