Intenenal ions squared#1022

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trishorts wants to merge 45 commits into

smith-chem-wisc:masterfrom

trishorts:intenenalIonsSquared

Commits on Feb 17, 2026

Commits on Feb 19, 2026

working quite well
trishorts
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Commits on Feb 20, 2026

Commits on Feb 24, 2026

Commits on Jun 3, 2026

Merge remote-tracking branch 'upstream/master' into intenenalIonsSquared
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refactor(predictions): port internal-ion models to rewritten Koina API

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refactor(internal-ions): drop unused HasPhosphorylation/HasMetalOnTerminalAcidic

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fix(internal-ions): exclude terminal spans and tolerate duplicate spectra

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test(internal-ions): fix relocated msp path and guard local-data eval fixture

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fix(internal-ions): harden observed-fragment analysis pipeline

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refactor(internal-ions): idempotent generation, shared charge set, drop dead using

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refactor(spectral-library): revert cosmetic churn from internal-ion change

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test(internal-ions): flag Step11 analysis harness for removal

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test(internal-ions): cover observed-fragment analysis pipeline

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