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Release v1.6 β€” faster migration engine + survey solver#1

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ovitrac wants to merge 2 commits into
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release/1.6
Open

Release v1.6 β€” faster migration engine + survey solver#1
ovitrac wants to merge 2 commits into
mainfrom
release/1.6

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@ovitrac

@ovitrac ovitrac commented Jun 28, 2026

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Summary

Brings the public tree to v1.6.

Engine

  • patankar/migration: pass the constant sparse Jacobian to the BDF integrator (cold-start speed-up); C0eq guardrail and unit-C0eq resume fix.

Survey

  • New survey/chain_engine.py β€” unified real-units N-layer Γ— K-step migration solver core.
  • New survey/physical_query.py β€” physical-primary survey query (evaluates the real-units chain at the actual time-prior points; no Fo-surface interpolation).
  • New survey/utils/ β€” cf_at_user_grid safe CF extraction.
  • survey/workers.py β€” canonical equilibrium helpers _cfeq_from_sol / _eq_knee (single source of truth).
  • Refreshed shared survey modules (io, models, priors, aggregation, survey, README).

Versioning

  • Package 1.50 β†’ 1.6 (setup.py, pyproject.toml, patankar/__init__.py, README).
  • Survey module 0.1.0 β†’ 0.4.0 (+ CHANGELOG [0.4.0]).
  • New TODO.md.

Cache

  • Full PubChem / ToxTree cache sync (PubChem 3,009 β†’ 11,131; ToxTree 4,373 β†’ 12,738), isolated in its own commit 660bf58 for review.

Validation

  • pytest tests/ β€” 52 passed.
  • All new modules import cleanly.

Notes

  • Two commits: code/doc (1cae682) and cache (660bf58).
  • The new engine modules ship import-safe but are reachable only through the multilayer/two-step survey path (tracked in TODO.md).
  • HTML documentation is not regenerated here (handled by the dedicated doc pipeline).

ovitrac added 2 commits June 28, 2026 16:39
- patankar/migration: pass constant sparse Jacobian to BDF; C0eq
  guardrail and unit-C0eq resume fix
- survey: new chain_engine (N-layer x K-step real-units solver),
  physical_query (physical-primary query), utils.cf_at_user_grid
- survey/workers: canonical _cfeq_from_sol / _eq_knee helpers
- refresh shared survey modules; bump 1.50 -> 1.6, survey -> 0.4.0
- PubChem cache 3,009 -> 11,131 entries
- ToxTree cache 4,373 -> 12,738 entries
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