refactor(tests,docs): polish docstrings, type annotations, and linting rules#23

Merged

ilypopv merged 25 commits into

mainfrom

Jun 4, 2026

Commits on Jun 4, 2026

docs(cli): add type annotations, docstrings, and comments to krakenparser entrypoint
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refactor(pipeline): harden pipeline orchestration with static type hints and docstrings
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refactor(utils): add explicit type annotations and docstrings to utils.py
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refactor(init): add explicit type annotation to __all__ export sequence
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refactor(counts): modernize matrix transposition utility with Path typing and docstrings
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refactor(counts): add type annotations and docstrings to processing_script.py
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refactor(counts): add type annotations and docstrings to split_mpa.py
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refactor(kpplot): expand sub-package initialization namespace and enforce explicit export typing
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refactor(kpplot): implement static type hinting and docstrings in plotting base
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refactor(kpplot): add strict literal constraints, type annotations, and docstrings to clustermap.py
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refactor(kpplot): add strict literal constraints, type annotations, and docstrings to stackedbar.py
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refactor(kpplot): add strict literal constraints, type annotations, and docstrings to streamgraph.py
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refactor(mpa): implement explicit type hints, and docstrings in mpa_table.py
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refactor(mpa): add strict type annotations, context managers, and docstrings to transform2mpa.py
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refactor(stats): implement strict type hints, logging, and docstrings in diversity.py
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refactor(stats): implement vectorization, explicit type hints, and docstrings in relabund.py
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refactor(tests): document fixture architecture and add mock configurations to conftest.py
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refactor(tests): parameterize CLI error paths and clean up entrypoint testing in test_cli.py
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refactor(tests): clarify end-to-end execution scope and clean up pipeline tests in test_full_pipeline.py
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refactor(tests): structure integration endpoints and contract checks in test_integration.py
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refactor(tests): structure visualization layers, contract assertions, and full-param pipelines in test_kpplot.py
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refactor(tests): group logic flows and add descriptive assertions to test_units.py
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docs(paper): add disclosures section to paper.md
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chore(release): bump version to 1.1.2
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docs(paper): fix layout spacing in paper.md
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