Refactor code structure and update CI workflows - #96

Merged

js2264 merged 17 commits into

js2264/refactor-codebase

May 8, 2026

Commits on May 6, 2026

chores: refactor code structure to src/hicstuff and pyproject.toml and other bells and whistles

js2264
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Copilot
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f39aafb
fix: remove branch restriction for push events in CI workflow
js2264
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07195de
fix: remove 'minimap2' from aligner parameters in test_pipeline.py
js2264
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1c79c58
chores: lint
js2264
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3e675aa
chores: more linting
js2264
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f9d08af
chores: more linting

js2264
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Copilot
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d7f8f41
fix: pytest errors
js2264
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5c4bf97
refactor: all hicstuff CLI, + others

js2264
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Copilot
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6bf39d2

Commits on May 7, 2026

chores: ruff
js2264
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6bd0d8e
ci: update publish workflow for GHCR and enhance Dockerfile dependencies

js2264
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Copilot
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24a1a7a
chores: minor fixes from PR review

js2264
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Copilot
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675bf4c
feat: can nw skip fastq count in pipeline; refactored for faster fastq count nonetheless

js2264
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Copilot
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31d81b3
fix: koszullab/hicstuff#84
js2264
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9f771a1
chores: retire misc functions that are not called anywhere from hicstuff module to _misc module
js2264
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9dacba9
fix: chromosome names that are just numbers are now supported by distancelaw; fixes koszullab/hicstuff#89
js2264
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1f484fa

Commits on May 8, 2026

fix: hide cooler balance INFO logging
js2264
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da4c976
chores: lint
js2264
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ab6902d