convert.py is non-functional from the CLI

[Doomsbay]

Summary

The README advertises TSV → PROTAX-GPU conversion via scripts/convert.py, but the script cannot be run from the command line. It crashes on import due to hardcoded paths, and its CLI entry point performs no conversion.

Affected files

• README.md L29 ("Compatible with TSV and PROTAX input format")
• README.md L38 (convert.py — Converts .TSV to PROTAX-GPU format)
• scripts/convert.py

Details

Crashes on import. Lines 398–404 run at module top level with hardcoded developer paths:

test = Path("/home/roy/Downloads/taxonomy.tsv")
test_ref = Path("/home/roy/Downloads/sequences.tsv")
read_jax_model(test_ref)  # crashes here → np.load("8M_tax.npz") at L302

The crash occurs inside read_jax_model at L302, which tries to load "8M_tax.npz" — a hardcoded intermediate file that doesn't exist outside the original developer's environment. The test_ref path is passed but never reached before this failure.

CLI entry point does nothing. The argparse block (L409–424) only prints "converting taxonomy..." / "converting model..."; it never calls convert_tsv(), assign_tax(), or convert_sequences().

Unfinished pieces.

• trim_subtaxa() — # TODO doesn't work yet (L106–107)
• convert_sequences() — # TODO remove hardcoded values (L260)
• read_jax_model() — # TODO: remove this leftover test code (L343)
• assign_tax() depends on a hardcoded refs.npz intermediate file (L218)

Net effect: the advertised TSV pipeline is both undocumented and non-functional — there is no working path to convert your own TSV data.

Steps to reproduce

1. git clone the repo and install per the README.
2. Run python scripts/convert.py --taxonomy <some.tsv> (or run it with no args).

Expected behavior

The script converts the given TSV taxonomy/sequence files into the .npz format the package consumes.

Actual behavior

FileNotFoundError: [Errno 2] No such file or directory: '8M_tax.npz'

(raised at import time from the top-level read_jax_model(test_ref) call at L404, which tries to load the hardcoded "8M_tax.npz" intermediate file at L302). Even if that file existed, the --taxonomy/--model flags only print a message and perform no conversion.

Environment

• Repo commit: 392614a
• Python: 3.12

Proposed fix

1. Short term: remove or gate the top-level execution code so the script does not crash on import, and note in the README that convert.py is a work in progress.
2. Long term: wire the argparse block to the conversion functions, remove the hardcoded paths, and document the expected TSV format.
3. Either way: clarify whether convert.py is the intended way to produce the taxonomy .npz, or whether it is deprecated.