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Batch Mode

Batch mode runs many target/proteome combinations from a manifest.

Generate A Manifest

thyme-batch generate-manifest \
  --base-config pipelines/thyme/batch_setup/batch_example/example_base_config.yaml \
  --targets pipelines/thyme/batch_setup/batch_example/targets_tiny.csv \
  --proteomes pipelines/thyme/batch_setup/batch_example/proteomes_tiny.csv \
  --batch-root /tmp/thyme_batch

targets.csv requires target_id. proteomes.csv requires proteome_id. Additional columns are dot-path config overrides, for example:

  • target_protein.structuredb_id
  • proteome.source
  • proteome.proteome_fasta_path
  • decoder.beam_width

Run And Summarize

thyme-batch run \
  --manifest /tmp/thyme_batch/manifest.csv \
  --max-workers 4 \
  --resume

thyme-batch summarize \
  --manifest /tmp/thyme_batch/manifest.csv

Each row gets its own config, output directory, stdout/stderr logs, status JSON, and metrics artifacts.

W&B Logging

When --wandb-project is provided, batch mode creates one W&B run per manifest row. Logged fields include target/proteome/config IDs, pipeline git SHA, top scores, diversity, runtime, decode success, sequence counts, and artifacts.