Add tqdm progress bar for hmmsearch aggregation #279

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wwood wants to merge 2 commits into main from codex/add-tqdm-progress-bar-to-supplement.py

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wwood commented Jan 8, 2026

Motivation

Provide visible progress feedback while aggregating per-genome HMM search results to help monitor long-running jobs.
The aggregation loop processes results from a multiprocessing Pool, which can take substantial time across many genomes.

Description

Wrapped the result-aggregation loop in a tqdm progress bar to report progress per genome.
The loop now uses tqdm(map_result, total=len(new_genome_transcripts_and_proteins), desc="Running hmmsearch", unit="genome") in singlem/supplement.py.
No other functional changes were made to the aggregation logic or multiprocessing usage.

Testing

Ran the full test suite with pixi run -e dev pytest test as required by repository guidelines.
Automated tests completed with 224 passed, 20 skipped, 1 warning in 866.04s (about 14m26s).


          Add progress bar for hmmsearch results

f4b5a46

wwood added the codex label

— with

ChatGPT Codex Connector


          Update hmmsearch progress tracking

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