v0.4.0-alpha1

VAMPIRE v0.3.0 → v0.4.0a1: What's Changed

1. Architecture: Full scan / anno Split

• vampire.scan and vampire.anno are now independent top-level modules (#5)
• Each has its own pp (preprocessing), pl (plotting), and tl (tools) subpackages
• API aligned with the Scanpy ecosystem

2. Major Visualization Additions

• vp.anno.pl.trackplot() — multi-track genomic plots (bedgraph / bed / heatmap)
• vp.anno.pl.waterfall() — mutation waterfall plots
• vp.anno.pl.logo() — sequence motif logos
• trackplot arrow rendering and heatmap colorscale fixes

3. Downstream Analysis Overhaul

• Rewritten / enhanced heatmap, align, and haplotype functions
• Core motif polishing and CIGAR statistics logic fixed in the anno module

4. Dependencies & Compatibility

• Upgraded to polars>=1.0 (polars 1.x API migration)
• Removed unused packages: Levenshtein, rich, logomaker
• Added minimum version constraints to prevent dependency drift

5. CI / Docs / Tooling

• GitHub Actions test workflows with multi-Python-version matrix
• Sphinx documentation site builds
• ruff lint configuration (since removed in v0.4.0a2)

6. Attached Data

The attached chm13_cen1_tracks.pkl is use for vp.anno.pl.trackplot() (new name is vp.anno.pl.tracksplot()) as an example data.