This skill was deprecated on 2026-05-12 as a duplicate of python-developer. Both skills provided production-quality Python implementation; the only meaningful difference was bioinformatics framing in this skill's prose examples. The actual Python practices (type hints, docstrings, pytest, error handling, CLI scaffolding) are identical.
What to use instead
| Need | Use |
|---|---|
| Production-quality Python implementation | python-developer |
| Bioinformatics-specific data analysis | bioinformatician |
| Biological validation of bioinformatics code | biologist-commentator |
| Bioinformatics production code | bioinformatician → python-developer → biologist-commentator |
python-developer integrates with mathematician, statistician, copilot, and programming-pm for full pipeline coordination.
Rationale
The closer-reading audit (2026-05-12, planning entry 2026-05-12-tier-2-deprecate-software-developer-skill.md) found:
- Identical responsibilities (production code with tests, docs, type hints, error handling)
- Identical tooling expectations (pytest, type checking, coverage)
software-developerhad bioinformatics framing in examples;python-developerhad broader integration (mathematician/statistician handoffs)- Bioinformatics-specific work is better served by chaining
bioinformatician(analysis) →python-developer(productionize) →biologist-commentator(validate) than by maintaining a separate "production bioinformatics" skill
Migration
Orchestrators that previously dispatched software-developer (programming-pm, principal-investigator, biologist-commentator, systematic-troubleshooter, systems-architect, copilot) now reference python-developer directly. See the deprecation planning entry for the full file list updated in this change.