Changelog

v0.1.0 (2025–2026)

Initial release of fastcxt.

Architecture

  • Bidirectional Mamba encoder-decoder architecture

  • Single-pass inference with built-in uncertainty (Gaussian NLL)

  • FiLM conditioning on mutation rate

  • Variable sample size support via InputProjection

  • Optional tree topology integration for O(n log n) scaling

Simulation & preprocessing

  • stdpopsim-first simulation pipeline with scenario registry

  • 12 stdpopsim species + 3 custom msprime scenarios

  • Accessibility mask support for missing data

  • Clean PreprocessJob-based preprocessing pipeline

Applications

  • Dedicated Anopheles gambiae analysis protocol (fastcxt.mosquito)

  • TimeAtlas data structure for genome-wide TMRCA storage and queries

  • End-to-end Ag1000G strategy document (docs/ag1000g_strategy.md)

Visualization

  • Geographic collection site maps (Cartopy projections)

  • Population connectivity arcs colored by between-population TMRCA

  • Genome-wide TMRCA landscape across all chromosome arms

  • Population-level TMRCA heatmap with geographic inset

  • Multi-panel selective sweep analysis (Rdl locus on chr2L)

  • Dense pairwise TMRCA raster heatmaps

  • Composite dashboard combining all panels

  • Dark-theme, publication-quality styling throughout

Infrastructure

  • Centralized cluster path configuration (fastcxt.paths)

  • uv / hatchling build system

  • Comprehensive Sphinx documentation with Furo theme

  • 110+ unit and integration tests