docs: add comprehensive project documentation#96
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- Replace setup.py + requirements.txt with pyproject.toml (uv) - Add .pre-commit-config.yaml (ruff-format, ruff lint, ty advisory) - Update CI workflow to use uv + ruff + ty - Update Dockerfile for uv - Add uv.lock, linumpy/py.typed - Delete setup.py, requirements.txt, requirements-pytest.txt - Run ruff format on all Python files - Run ruff check --fix (341 auto-fixes applied)
Add 12 documentation files covering: - Pipeline overview and performance analysis - Library modules and scripts reference - GPU acceleration guide - Nextflow workflows - File format specs (mosaic grid, shifts) - Slice config and interpolation features - Reconstruction diagnostics - AI documentation index
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PR J — Documentation
Adds 12 comprehensive documentation files covering all aspects of the project.
Files added
docs/PIPELINE_OVERVIEW.md— End-to-end pipeline descriptiondocs/PIPELINE_PERFORMANCE_ANALYSIS.md— Performance benchmarks and tipsdocs/LIBRARY_MODULES.md— Library module referencedocs/SCRIPTS_REFERENCE.md— CLI scripts referencedocs/GPU_ACCELERATION.md— GPU acceleration guidedocs/NEXTFLOW_WORKFLOWS.md— Nextflow workflow docsdocs/MOSAIC_GRID_FORMAT.md— Mosaic grid file format specdocs/SHIFTS_FILE_FORMAT.md— Shifts file format specdocs/SLICE_CONFIG_FEATURE.md— Slice configuration featuredocs/SLICE_INTERPOLATION_FEATURE.md— Slice interpolation featuredocs/RECONSTRUCTION_DIAGNOSTICS.md— Reconstruction diagnostic toolsdocs/AI_DOCUMENTATION_INDEX.md— Documentation indexDependencies