Add an optional missingValue argument to deltaGCSV - #702
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deltaGCSV had no concept of a "no measurement" sentinel and stored every matched CSV value verbatim, including yeast-GEM's own 10000000.0 convention (checkrxnDirection.m gates on this exact value) -- indistinguishable, once loaded, from a real measurement. missingValue defaults to [] (disabled, unchanged behaviour): a value equal to it (within a small relative tolerance) is left as NaN instead of being stored. Opt-in on both sides now: raven_toolbox's load_delta_g_csv gained the equivalent missing_value parameter, also defaulting to literal-by-default, with DELTA_G_MISSING available to opt into yeast-GEM's convention explicitly.
Function test results300 tests 274 ✅ 1m 8s ⏱️ Results for commit 91d800b. |
edkerk
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Aug 28, 2026
…ity (#705) Follow-up to #702, resolving the remaining half of SysBioChalmers/raven-gecko-parity#16. #702 added an optional `missingValue` argument to `deltaGCSV` but defaulted it to `[]` (disabled), while raven-toolbox's `load_delta_g_csv` defaults `missing_value` to `DELTA_G_MISSING` (1e7). So with defaults, the two disagreed: loading yeast-GEM's own ΔG CSVs, RAVEN stamped the 777 sentinel rows as literal 1e7 measurements while raven-toolbox left them unset. This defaults `missingValue` to `1e7`, so both implementations drop the sentinel out of the box. No real ΔG (in kJ/mol) takes this value, so the default is safe. Passing `[]` disables it and stores every value literally, mirroring `missing_value=None`. The comparison tolerance already matched (`math.isclose` rel_tol=1e-9). Tests: adds `deltaGCsvDropsSentinelByDefault` and `deltaGCsvKeepsSentinelWhenDisabled` to tAnnotation.
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Fixes SysBioChalmers/raven-gecko-parity#16.
deltaGCSVhad no concept of a "no measurement" sentinel and stored everymatched CSV value verbatim, including yeast-GEM's own
10000000.0convention(
checkrxnDirection.mgates on this exact value) — indistinguishable, onceloaded, from a real measurement.
missingValuedefaults to[](disabled, unchanged behaviour): a value equalto it (within a small relative tolerance) is left as
NaNinstead of beingstored. Opt-in on both sides now: raven-toolbox's
load_delta_g_csvgained theequivalent
missing_valueparameter, also literal-by-default, withDELTA_G_MISSINGavailable to opt into yeast-GEM's convention explicitly.