Add Behave component tests and reorganize test structure #12

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philiptzou wants to merge 5 commits into main from codex/add-behave-dependency-and-component-tests

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philiptzou commented Aug 11, 2025

Summary

clarify testing docs and add Makefile targets for unit and component suites
remove vendored minimap2 and download binary on the fly during component tests
exercise codon-alignment end-to-end via Behave using real sequence data

Testing

pipenv run flake8 .
pipenv run mypy .
pipenv run pytest tests/unit --cov=postalign --cov-report=term-missing
pipenv run behave tests/component

https://chatgpt.com/codex/tasks/task_e_689a0cf9bab88324b7878fd9bb5a5f20


          Test infrastructure updates

dcb2061

philiptzou added the codex label

— with

ChatGPT Codex Connector

philiptzou and others added 4 commits

August 11, 2025 12:00


          Use CLI pipeline for codon alignment tests

4bfbdaf


          Support complex Typer option types

ed968bd


          Simplify gap placement score option

aec7a5f


          Fix requirements.txt

b913931

philiptzou force-pushed the codex/add-behave-dependency-and-component-tests branch from e2848ec to b913931 Compare

August 12, 2025 01:08

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