Development log - progenax — differentiable initial conditions for N-body simulations

This section is progenax’s internal development history — dated design specifications, full-package code-review audits, and validation recovery/scaling notes, kept for the record. The pages are point-in-time snapshots: each one describes the state of the package on its date, and several reference APIs that were later renamed or retired. Where that happens the page carries an admonition pointing at the current entry point, but the body text is otherwise preserved unedited as historical evidence.

For the current state of the package, start from the release notes, the architecture overview, and the validation backbone. For the live test counts and coverage see the test dashboard.

Code-review audits¶

Full-package technical reviews (scientific correctness, numerics, JAX/differentiability, testing, provenance), newest first:

Code reviews — the landing record for the 2026-06 post-hardening (A−, 90/100) and expert-audit (B+, 87/100) reviews, each with its resolution table showing every Critical/Major finding fixed.
Progenax: Comprehensive Code, Architecture & Science Review — the original 2025-12-07 comprehensive code/architecture/science review (A, 95/100).

Design specs¶

IC redesign spec (2026-02-12) — the original specification for the protocol-based, composable, differentiable IC architecture (single-population build_spatial_ic + matching SpatialProfile/VelocityDF protocols).

Milestones, fixes, and recovery notes¶

progenax Phase 1 - COMPLETE — the 2025-12-06 Phase 1 completion snapshot (legacy gravax.ic ported to a standalone JAX-native package).
IMF Stack Fix Implementation Plan — the IMF-stack correction plan (Chabrier log₁₀ basis, parameter-gradient and domain-behavior fixes).
IMF HMC Recovery — Proposal Figure — the IMF-only NUTS slope-recovery proposal figure (α₃ across 1.7–2.8 via NumPyro).
Binary-Aware IMF Recovery via NUTS — the binary-aware IMF recovery spec: the Moe+17-aware mixture likelihood that removes the binary bias.
Binary-Aware IMF Recovery — Implementation Plan — the matching implementation plan (task-by-task build of the validation script).
Precision Scaling Panel (d) Implementation Plan — the σ(α)-vs-N precision-scaling panel added to the binary-aware recovery figure.
PP20 ζ(p) transcription fix — the PP20 magnification-factor ζ(p) transcription-bug fix (now superseded by the experimental gravoturb rewrite; see the page’s update banner).