Modernize packaging, pipeline, and report generation workflows#341

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alsmith151 wants to merge 160 commits into

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Commits on Apr 24, 2026

Commits on Apr 26, 2026

Commits on Apr 27, 2026

Commits on Apr 28, 2026

refactor: harden snakemake workflow
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Commits on Apr 29, 2026

Commits on Apr 30, 2026

Commits on May 28, 2026

feat: update pre-commit hooks and improve error logging in fastq processing
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test: add integration test for differential interactions with real pydeseq2
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fix: add missing return type annotations and fix pandas 2.0 deprecations in utils
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feat: expose public API via capcruncher.api with lazy loading
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refactor: use Polars to read fragment map in count_interactions
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refactor: split utils.py into focused submodules (bed, genomics, io)
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refactor: consolidate flag coercion and add BED pandera schema
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feat: populate subpackage __init__.py files and expand top-level API
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build: add pixi.toml and migrate CI tests job to pixi
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build: migrate deps to pyproject.toml and drop legacy packaging files
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ci: update action versions and migrate to uv sync in CD and docs
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chore: update pre-commit hooks and extend gitignore
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refactor: apply ruff formatting and update import paths across codebase
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fix: sort imports in api __init__ files to pass ruff I001
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fix: resolve ty errors and add pixi.lock
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fix: resolve ty imports properly instead of suppressing them
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fix: exclude .pixi from ruff and gitignore, format api/__init__.py
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refactor: update import statements and enhance error handling in various modules
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fix: change [project] to [workspace] in pixi.toml
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feat: add flash script and update pytest parallelism in pixi.toml
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fix: drop invalid BED rows and strip flash2 unsupported arg
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fix: install pre-commit hooks and fix all linting issues
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fix: remove fake test binaries and fix pipeline tool invocations
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Commits on May 31, 2026

fix: wire genes track, fix xdist scheduling, and update golden values
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Commits on Jun 1, 2026

fix: improve logging for missing viewpoints and handle empty output in pileup function
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Commits on Jun 8, 2026

Commits on Jun 9, 2026

Commits on Jun 10, 2026