Generalize make_txt_embedding{,_json}.py#56
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`make_txt_embedding.py:` - Add PRESETS dict (bioclip-2, bioclip-2.5-vith14) and --preset CLI flag - Add --model / --tokenizer / --embed-dim CLI flags for arbitrary models (e.g. BioCAP, future BioCLIP releases) - Replace hardcoded model_str/tokenizer_str/768 with parameterized values - Add Usage / Examples block to the module docstring `make_txt_embedding_json.py`: - Add drop_corrupted_rows() that removes rows whose any taxonomic rank matches an ISO-8601 timestamp or the literal string 'true' / 'false' - Filter is on by default; --no-corruption-filter reproduces the pre-existing upstream behavior used for BioCLIP 2 taxon JSON generation Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
egrace479
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May 29, 2026
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A couple consistency notes.
I think we may want the default behavior to be no-corruption-filter since that wouldn't change existing outputs; it's probably better not to 'quietly' do extra filtering. We should watch for these items in future catalog iterations.
The newest catalog is the only one with the ISO and boolean issues, so this change will not impact any existing text embeddings. As such, the default to remove such entries is fine, especially since it print a statement about their removal.
Co-Authored-By: Elizabeth Campolongo <egrace479@users.noreply.github.com>
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@egrace479 reverted to ab54735 |
egrace479
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May 29, 2026
Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com>
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make_txt_embedding.py:make_txt_embedding_json.py: