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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start-up loads the default - deprecated ids get a message naming the command-line tool - preview_registry removed (withdrawn models); V4-V5 labels, primers and measured length windows - run summary: thresholds used and their source, species calls withheld by the gate, group labels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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New web app: composition plots, count tables, downloads; taxonova 26.10.1
Verified signatureRedesigned interface with an example dataset, composition, hierarchy and confidence plots, optional ASV count table for per-sample composition, and TSV, QIIME 2 and phyloseq downloads. Installs taxonova==26.10.1 and uses the short model ids.b018397
16 days ago
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Serve taxonova 26.10.0 and the v26.10.0 models
Verified signatureInstalls taxonova==26.10.0 from PyPI instead of a bundled copy; the Docker build downloads the v26.10.0 Greengenes2 checkpoints (RRN from v1.0.0). Releases before 26.10.0 applied no confidence thresholds to the Greengenes2 models.89bbd94
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Fix the four webserver defects raised in peer review
Reviewer 2, major comment 3, on the hosted service: 1. Duplicate FASTA headers. Results were keyed on the sequence identifier, which parse_sequence_id takes as the first word of the header. Headers are not required to be unique, so sequences sharing a name collapsed to one entry and every duplicate was handed the same call and confidence. Sequences now carry unique internal ids and are reported back under the user's own names, by position. 2. Default confidence was 50% in the UI against the manuscript's recommended 70% genus and 80% species. The slider and the hidden field now default to 0.8 and the label names the rank it gates. 3. Labels appearing below the requested threshold. Parent ranks were pinned at 0.5 regardless of what the user asked for, so a request for 0.8 still accepted genus labels at 0.5; and because abstention propagates downward, a parent failing that fixed gate discarded an already-computed species call. The whole per-rank profile…e477625