Developer Workflow

This page summarizes common local quality and profiling workflows.

Environment

python -m venv venv
source venv/bin/activate
make dev.setup

Core Quality Checks

make lint
make typecheck
make guard.private-api
make test.fast
make quality

Integration Suite

make test.integration
venv/bin/pytest -q tests/integration/test_output_format_matrix.py
venv/bin/pytest -q tests/integration/test_cli_output_contracts.py

Benchmarking Hotspots

Run benchmark summary in terminal:

make bench.profile

Tune iterations/warmups:

N=10 WARMUPS=2 make bench.profile

Save benchmark output for comparison:

make bench.profile.save

Saved output path:

output/bench_profile.tsv

Notes

Benchmark values can vary by machine load; compare medians across repeated runs.
The benchmark command currently tracks: - genome_assembly_metrics - character_frequency - relative_synonymous_codon_usage - translate_sequence