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ec.source: one format, one parser and a record of tuning - #32
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parseKcatSource and formatKcatSource read and write <origin>[ (<detail>)][ | tuned=<methods> (prior=<value>)]. The writers build their strings with the formatter and the readers use the parsed origin. setKcatForReactions writes manual. sensitivityTuning and cmaesKcatTuning keep the origin and detail and add the tuning method, with the kcat before the first tuning as prior, and sensitivityTuning no longer writes the old source into ec.notes. A standard row with a tuning status is kept by getStandardKcat and removeStandardKcat.
Unit test results74 tests 74 ✅ 10s ⏱️ Results for commit da57444. |
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Describes the provenance entries of `ec.source` (`<origin>[ (<detail>)][ | tuned=<method>[+<method>...] (prior=<value>)]`), the tuning status, and `parseKcatSource` and `formatKcatSource` (Python `parse_kcat_source` and `format_kcat_source`), with `manual` for `setKcatForReactions`. The pages on applying kcats, growth-rate tuning and tuning against experimental data describe `manual`, the tuning status and the origin that the trust tiers use. Applies after the release that contains [GECKO#32](CompMetEng/GECKO#32) and [geckopy#91](CompMetEng/geckopy#91).
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parseKcatSourceandformatKcatSourceread and write the provenance text ofec.source,<origin>[ (<detail>)][ | tuned=<method>[+<method>...] (prior=<value>)], for examplebrenda (wc=0, origin=2) | tuned=cmaes (prior=6.55). Every writer builds its text with the formatter, and the readers use the parsed origin, so a source with a detail or a tuning status is recognised.setKcatForReactionswrites the originmanual(it wrotesetKcatForReactions) and drops any tuning status.sensitivityTuningandcmaesKcatTuningkeep the origin and detail of every kcat they change and add the method (sensitivity,cmaes) to its tuning status, with the kcat before the first tuning asprior.sensitivityTuningno longer writes the old kcat and source intoec.notes.getStandardKcatandremoveStandardKcatkeep a standard row that has a tuning status.Part of raven-gecko-parity#151.