feat: migrate BRENDA data from max_*.txt to kcat/mw/sa.tsv - #455
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Replaces the 2018-vintage max_KCAT.txt/max_MW.txt/max_SA.txt (EC-prefixed, //-suffixed organism, no header) with kcat.tsv/mw.tsv/sa.tsv: BRENDA 2026.1 snapshots produced by the geckopy brenda-refresh CLI and already shipped in geckopy's own src/geckopy/data/brenda/. Adopting the exact filenames and format geckopy already uses (rather than inventing a separate max_*.tsv convention) means a user can point both toolboxes' BRENDA folder at the same directory without renaming anything. loadBRENDAdata.m updated to match: skip the `#`-prefixed release-version line and the column-header line (both new), read bare EC codes and plain organism strings (both no longer need stripping), and read the max column of kcat.tsv/sa.tsv's two aggregates (max, median) -- unchanged single-aggregate behaviour, just fed from wider files. Not ported: the opt-in median aggregation geckopy's load_brenda_data exposes via adapter.params.kcat_aggregate_brenda -- a separate, smaller feature that wasn't part of what this migration was asked to cover. Test fixtures affected: the ecTestGEM small BRENDA files, and two existing fuzzyKcatMatching tests (tc0021, tc0022) that build their own scratch BRENDA fixtures inline -- all reformatted to the new shape with identical values, so no test assertions changed. Added testLoadBRENDAdataParsesNewTsvFormat_tc0041 to cover the new format's own distinguishing features (header/comment skip, bare EC codes, max-not-median column selection) directly. Verified against the real production files (84,904 rows total): parses cleanly in well under a second, no malformed rows, no NaNs.
Unit test results41 tests 41 ✅ 10s ⏱️ Results for commit d3bf92b. |
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Summary
Replaces the 2018-vintage
max_KCAT.txt/max_MW.txt/max_SA.txt(EC-prefixed,//-suffixed organism, no header) withkcat.tsv/mw.tsv/sa.tsv: BRENDA 2026.1 snapshots produced by thegeckopy brenda-refreshCLI and already shipped in geckopy's ownsrc/geckopy/data/brenda/. This adopts the exact filenames and format geckopy already uses (rather than inventing a separatemax_*.tsvconvention, as an earlier, abandoned attempt at this migration did) — pointing both toolboxes' BRENDA folder at the same directory now just works, with no renaming.loadBRENDAdata.mupdated to match:#-prefixed release-version line and the column-header line (both new)extractAfter/regexprepstripping)Not ported: the opt-in median aggregation geckopy's
load_brenda_dataexposes viaadapter.params.kcat_aggregate_brenda— a separate, smaller feature not part of what this migration covers.Test plan
fuzzyKcatMatchingtests (tc0021,tc0022) that build their own scratch BRENDA fixtures inline — all reformatted to the new shape with identical values, so no test assertions changed.testLoadBRENDAdataParsesNewTsvFormat_tc0041covering the new format's own distinguishing features (header/comment skip, bare EC codes, max-not-median column selection) directly.