Add CompiledReaction.from_pinned; fix ruff-format drift on main - #192
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from_pinned records the from-side pinned coordinate for every axis a transition pins on its from-side selector (full_axes minus from_axes). This was missing from #191: that PR added full_axes and widened `pinned` to cover from-pinned axes too, but `pinned` only ever carries the TO-side coordinate for those axes. For a point-to-point transition (pinned on both sides, e.g. a vaccination-dose-progression transition pinned at vax=unvaccinated on from and vax=partial on to), the from-side and to-side coordinates differ, so a consumer building a depletion-target index into from_base cannot derive it from `pinned` alone -- confirmed by diphtheria_outbreakvacc's run_hybrid_ctmc consumer, which needs exactly this to deplete the correct source cell rather than the (wrong) to-side one. Also fixes ruff-format drift left on main by #191's merge (my own _reactions.py/compile.py edits weren't format-clean) and a pre-existing, unrelated formatting issue in README.md -- both were failing the "quality" CI check on main.
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Follow-up to #191, which merged with an incomplete fix and left
main's "quality" CI check red.Missing piece from #191: that PR added
full_axesand widenedpinnedto cover from-side-pinned axes, butpinnedonly ever carries the to-side coordinate for those axes. For a point-to-point transition (pinned on both sides — e.g. a vaccination-dose-progression transition pinned atvax=unvaccinatedonfromandvax=partialonto), the from-side and to-side coordinates differ, so a consumer building a depletion-target index intofrom_basecan't derive it frompinnedalone. Caught this while wiringdiphtheria_outbreakvacc'srun_hybrid_ctmcconsumer: it was depleting the wrong (to-side) coordinate for from-pinned transitions. AddsReactionArtifactIR.from_pinned/CompiledReaction.from_pinned, threaded the same way aspinned.CI cleanup:
mainhas been failing thequality(ruff format) check since #191 merged — my own edits there weren't format-clean, plus one pre-existing, unrelated formatting drift inREADME.md. Both fixed here;ruff format --check .is clean.Testing: full suite (472/472) + mypy clean. Verified against
diphtheria_outbreakvacc's hybrid-CTMC engine tests (7/7 pass) using this branch as the sibling editable install —run_hybrid_ctmcnow depletes the correct from-pinned source cell forvax_dose1/vax_dose2/wane_full/wane_partial.