Help

Command reference for the TaxonoPy CLI.

taxonopy --help

usage: taxonopy [-h] [--cache-dir CACHE_DIR] [--cache-input CACHE_INPUT]
                [--show-cache-path] [--cache-stats] [--clear-cache]
                [--show-config] [--version]
                {resolve,trace,common-names} ...

TaxonoPy: Resolve taxonomic names using GNVerifier and trace data provenance.

positional arguments:
  {resolve,trace,common-names}
    resolve             Run the taxonomic resolution workflow
    trace               Trace data provenance of TaxonoPy objects
    common-names        Merge vernacular names (post-process) into resolved
                        outputs

options:
  -h, --help            show this help message and exit
  --cache-dir CACHE_DIR
                        Directory for TaxonoPy cache (can also be set with
                        TAXONOPY_CACHE_DIR environment variable) (default:
                        None)
  --cache-input CACHE_INPUT
                        Input dataset path to compute cache stats for when no
                        command is provided (default: None)
  --show-cache-path     Display the current cache directory path and exit
                        (default: False)
  --cache-stats         Display statistics about the cache and exit (default:
                        False)
  --clear-cache         Clear the TaxonoPy object cache. May be used in
                        isolation. (default: False)
  --show-config         Show current configuration and exit (default: False)
  --version             Show version number and exit

taxonopy resolve --help

usage: taxonopy resolve [-h] -i INPUT -o OUTPUT_DIR
                        [--output-format {csv,parquet}]
                        [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                        [--log-file LOG_FILE] [--force-input] [--full-rerun]
                        [--batch-size BATCH_SIZE] [--all-matches]
                        [--capitalize] [--fuzzy-uninomial] [--fuzzy-relaxed]
                        [--species-group] [--refresh-cache] [--cache-stats]

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Path to input Parquet or CSV file/directory
  -o OUTPUT_DIR, --output-dir OUTPUT_DIR
                        Directory to save resolved and unsolved output files
  --output-format {csv,parquet}
                        Output file format
  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        Set logging level
  --log-file LOG_FILE   Optional file to write logs to
  --force-input         Force use of input metadata without resolution
  --full-rerun          Replace existing cache/output if detected for this
                        input

GNVerifier Settings:
  --batch-size BATCH_SIZE
                        Max number of name queries per GNVerifier
                        API/subprocess call
  --all-matches         Return all matches instead of just the best one
  --capitalize          Capitalize the first letter of each name
  --fuzzy-uninomial     Enable fuzzy matching for uninomial names
  --fuzzy-relaxed       Relax fuzzy matching criteria
  --species-group       Enable group species matching

Cache Management:
  --refresh-cache       Force refresh of cached objects (input parsing,
                        grouping) before running.
  --cache-stats         Display cache statistics for this input and exit.

taxonopy trace --help

usage: taxonopy trace [-h] [--cache-stats] {entry} ...

positional arguments:
  {entry}
    entry        Trace an individual taxonomic entry by UUID

options:
  -h, --help     show this help message and exit
  --cache-stats  Display cache statistics for the provided input and exit.

taxonopy trace entry --help

usage: taxonopy trace entry [-h] --uuid UUID --from-input FROM_INPUT
                            [--format {json,text}] [--verbose]

options:
  -h, --help            show this help message and exit
  --uuid UUID           UUID of the taxonomic entry
  --from-input FROM_INPUT
                        Path to the original input dataset
  --format {json,text}  Output format
  --verbose             Show full details including all UUIDs in groups

taxonopy common-names --help

usage: taxonopy common-names [-h] --resolved-dir ANNOTATION_DIR --output-dir
                             OUTPUT_DIR

options:
  -h, --help            show this help message and exit
  --resolved-dir ANNOTATION_DIR
                        Directory containing your *.resolved.parquet files
  --output-dir OUTPUT_DIR
                        Directory to write annotated .parquet files