feat: JOSS submission, test suite overhaul, and strategic refactoring#13

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jameslehoux merged 10 commits into

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claude/3dxrd-tracking-week2-Bt9ed

May 17, 2026

Commits on May 17, 2026

chore: add ruff linting/formatting, CHANGELOG, py.typed, __version__
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docs: add JOSS paper draft, bibliography, and CITATION.cff
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test: add 45 new unit tests for undertested modules
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fix(notebook): clear stale outputs and fix misleading markdown
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test: comprehensive suite improvements — error paths, invariants, integration
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refactor: address strategic review — Otsu, ndarray, shared utils, SpotRecord
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fix: resolve all ruff lint errors (UP037, F821, F401, SIM117, I001, E741)
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Add image to README for visual enhancement
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style: apply ruff format to 6 files
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fix(ci): use --output-dir instead of --output /dev/null for nbconvert
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