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Commit History
9 days ago
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Region list in region order: V4, V4-V5, V3-V4, V5-V7, full-length 16S, then the rRNA operon
7f63629 -
Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture
Taxonova 26.11.1 offers Greengenes2 2024.09 (V4, V4-V5, V3-V4, V5-V7, whole 16S) and the GROND operon model. The reference selector is replaced by one Region list; the line under it names the reference of the chosen model. The V4-V5 parity fixture keeps its 66 Greengenes2 reads and their 3 mutated copies. A test checks that the 26.11.0 SILVA and RDP ids and file names are unknown to the web app. The Dockerfile asserts that the models directory holds exactly the files the registry lists.2a0d367
10 days ago
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Backend for 26.11: classify through the package, operating point by default, lazy models, registry-only catalogue
- classifier.py runs taxonova classify through package_adapter instead of a copy of the 26.10 handler body, so the species gate and the V4-V5 species-group rule apply as on the command line - no confidence sent: the model's operating point; /classify keeps 0.8 - models load on first use into a bounded cache; start-up loads the default - deprecated ids get a message naming the command-line tool - preview_registry removed (withdrawn models); V4-V5 labels, primers and measured length windows - run summary: thresholds used and their source, species calls withheld by the gate, group labels reported at the genus, low-information reads9e4e9f9
15 days ago
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Reference list: no '(default)' label
Verified signatureaf77d7b -
Region names without repetition
Verified signature69b285b -
Full names always: exact labels, no names switch
Verified signaturef1da1dc -
Reference database selector and per-reference name display
Verified signaturea69199c