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ec_fseof: anchor scan floor and restrict candidates, matching ecFSEOF.m - #50
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…o gated reactions Brings the ecModel wrapper's search space back in line with ecFSEOF.m on the two points that are wrapper-specific rather than inherited from the raven_toolbox.analysis.fseof selection-criterion divergence already tracked as an accepted difference on the RAVEN pair (CompMetEng/raven-gecko-parity#74). - `ec_fseof`: the scan floor was raven-toolbox's default fixed fraction of the theoretical maximum, not the production target's flux at biomass-optimum, so every enforced-flux level in the scan (not just the selection rule) differed from ecFSEOF.m whenever the target had no baseline flux at growth-optimum. - `ec_fseof`: candidates were not restricted to gene-associated, non-standard reactions before classification, unlike ecFSEOF.m, so every un-annotated or standard-pseudogene reaction could surface as a target even though it can not be engineered. Needs CompMetEng/raven-toolbox#147 (adds fseof's `min_target`) merged first; until then this fails to import against raven-toolbox@develop.
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`ecFSEOF`/`ec_fseof`: floor now anchored to biomass-optimal target flux and candidates restricted to gene-associated reactions (CompMetEng/geckopy#50, CompMetEng/raven-toolbox#147); the selection-criterion divergence is left as the same accepted difference already tracked on the RAVEN pair's `FSEOF` row. `getStandardKcat`/`assign_standard_kcat`: MATLAB now aggregates by median, and both sides agree on threshold eligibility and NaN handling (SysBioChalmers/GECKO#475, CompMetEng/geckopy#49).
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Flattens the Keep-a-Changelog ### Added/Fixed/Changed subsections into one bullet list (matching raven-toolbox's CHANGELOG.md format) and drops the version header's brackets to match. Also folds in #49 and #50, which had merged straight to main since 0.3.0 and were missing from develop until the merge two commits back.
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Resolves the two wrapper-specific divergences from CompMetEng/raven-gecko-parity#74 (the third, the selection criterion itself, is inherited from raven_toolbox.analysis.fseof's own accepted divergence from RAVEN and is left as-is).
ec_fseof: the scan floor was raven-toolbox's default fixed fraction of the theoretical maximum, not the production target's flux at biomass-optimum, so every enforced-flux level differed fromecFSEOF.mwhenever the target had no baseline flux at growth-optimum.ec_fseof: candidates were not restricted to gene-associated, non-standard reactions before classification, so an un-annotated or standard-pseudogene reaction could surface as a target even though it cannot be engineered.Depends on CompMetEng/raven-toolbox#147 (adds
fseof'smin_target); geckopy tracks raven-toolbox@develop, so CI here won't pass until that merges.