Repository navigation
assign_standard_kcat: median-vs-mean eligibility count and NaN handling - #49
Merged
Merged
Conversation
Matches the eligibility-count and NaN-handling fix landing on the MATLAB side (SysBioChalmers/GECKO#475): a subsystem's threshold count and its own median should only ever consider reactions with a real kcat. - `_compute_subsystem_kcats`: only skipped rows with a literal zero kcat, so a NaN-kcat row both counted toward a subsystem's threshold eligibility and got folded into `np.median`, silently turning the whole subsystem's computed kcat into NaN. - `_fill_zero_kcats`: only replaced literal zero kcats, leaving a NaN kcat unset and unmarked after `assign_standard_kcat` returns, contrary to the docstring and to MATLAB `isnan` check in `fillZeroKcat`.
edkerk
added a commit
to CompMetEng/raven-gecko-parity
that referenced
this pull request
Sep 7, 2026
`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).
edkerk
added a commit
that referenced
this pull request
Sep 8, 2026
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.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Found while resolving CompMetEng/raven-gecko-parity#80 (parity ledger note on getStandardKcat/assign_standard_kcat).
_compute_subsystem_kcats: a NaN-kcat reaction counted toward a subsystem's threshold eligibility and was folded intonp.median, silently turning that subsystem's computed kcat into NaN._fill_zero_kcats: a NaN kcat was left unset and unmarked afterassign_standard_kcatreturns, contrary to the docstring.Companion MATLAB fix: SysBioChalmers/GECKO#475.