Reruns

The Guard

TaxonoPy checks for existing output before processing. If a prior run is detected for the current input, it exits with a warning rather than silently overwriting:

Existing cache (...) and/or output (...) detected for this input.
Rerun with --full-rerun to replace them.

Detection uses two signals:

• the presence of a taxonopy_resolve_manifest.json in the output directory (written by any run using TaxonoPy v0.3.0 or later), or
• .resolved.* files in the output directory root (legacy fallback for output produced by earlier versions).

--full-rerun

--full-rerun is the explicit escape hatch through the guard. It clears the input-scoped cache namespace and removes all TaxonoPy-specific files from the output directory before proceeding.

taxonopy resolve \
    --input examples/input \
    --output-dir examples/resolved \
    --full-rerun

What it touches

• Cache: the namespace scoped to the current command, TaxonoPy version, and input fingerprint. Other namespaces (different inputs, different versions) are not affected.
• Output files: only the files listed in taxonopy_resolve_manifest.json. Any other files in the output directory are left untouched.

What it does not touch

• Files not listed in the manifest — including any non-TaxonoPy files you have placed in the output directory.
• Cache namespaces from other runs.

No manifest found

If --full-rerun is used but no manifest is present (e.g. output from a pre-v0.3.0 run, or a manually populated directory), TaxonoPy logs a warning and proceeds without removing any files:

--full-rerun: no manifest found in <output-dir>; no output files were removed.

The run then writes fresh output and a new manifest.

The Manifest

Every TaxonoPy run writes a manifest file to the output directory before creating any output. This means interrupted runs leave a complete record of what should be cleaned up — --full-rerun deletes exactly those files and nothing else.

Manifest files are command-scoped so they coexist safely if multiple commands share an output directory:

Command	Manifest file
resolve	taxonopy_resolve_manifest.json
common-names	taxonopy_common_names_manifest.json

Schema

{
    "taxonopy_version": "0.3.0",
    "command": "resolve",
    "created_at": "2025-07-19T10:38:04.123456",
    "input": "examples/input",
    "cache_namespace": "~/.cache/taxonopy/resolve_v0.3.0_a3f9b2c1d4e5f678",
    "files": [
        "sample.resolved.parquet",
        "sample.unsolved.parquet",
        "resolution_stats.json",
        "taxonopy_resolve_manifest.json"
    ]
}

All paths in files are relative to the output directory. cache_namespace is null for common-names, which does not use an input-scoped cache.