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Output

When you run taxonopy resolve, TaxonoPy writes two outputs for each input file:

  • Resolved: <input_name>.resolved.<csv|parquet>
  • Unsolved: <input_name>.unsolved.<csv|parquet>

The output directory mirrors the input directory structure. Output format is controlled by the --output-format flag (csv or parquet).

TaxonoPy also writes a manifest file to the output directory before creating any other files. This manifest lists every file the run intends to produce and is used by --full-rerun to clean up precisely. Each command writes its own manifest (taxonopy_resolve_manifest.json and taxonopy_common_names_manifest.json respectively) so they coexist safely if both commands share an output directory. See Reruns for details.

What’s Inside

Each output row corresponds to one input record. Resolved entries contain the standardized taxonomy where available, while unsolved entries preserve the original input ranks. Both outputs include resolution metadata such as status and strategy information.

Running through the sample resolution results in the following core files:

  • taxonopy resolve:
    • examples/resolved/sample.resolved.parquet
    • examples/resolved/sample.unsolved.parquet
    • examples/resolved/resolution_stats.json
    • examples/resolved/taxonopy_resolve_manifest.json
  • taxonopy common-names:
    • examples/resolved/common/sample.resolved.parquet
    • examples/resolved/common/taxonopy_common_names_manifest.json