| #!/bin/bash |
| set -euo pipefail |
|
|
| ENCODER="${ENCODER:?must be set}" |
| SWEEP_NAME="${1:?usage: $0 <sweep-name>}" |
| REPO_URL="${REPO_URL:-https://github.com/vedatonuryilmaz/dev_genopix.git}" |
| REPO_BRANCH="${REPO_BRANCH:-ml-intern}" |
| DATA_DATASET="${DATA_DATASET:-vedatonuryilmaz/te-quant-benchmark-v1}" |
| TOOLS="${TOOLS:-snk_em,snk_ot,vis_em,rsem,salmon}" |
| SAMPLES_PER_SETTING="${SAMPLES_PER_SETTING:-4}" |
| DEVICE="${DEVICE:-cpu}" |
|
|
| git clone --branch "$REPO_BRANCH" --depth 1 "$REPO_URL" deepgenopix |
| cd deepgenopix |
| uv sync --extra hf --extra quant |
|
|
| OUTPUT_DIR="data/output/quant_benchmark/$SWEEP_NAME" |
| mkdir -p "$OUTPUT_DIR" |
|
|
| uv run python -c " |
| import json |
| from pathlib import Path |
| |
| from deepgenopix.quant import SyntheticConfig, load_quant_encoder |
| from deepgenopix.quant.synthetic import run_calibration_benchmark |
| |
| encoder = load_quant_encoder('$ENCODER', device='$DEVICE') |
| tools = tuple(item.strip() for item in '$TOOLS'.split(',') if item.strip()) |
| df = run_calibration_benchmark( |
| encoder, |
| SyntheticConfig(), |
| tools=tools, |
| samples_per_setting=int('$SAMPLES_PER_SETTING'), |
| ) |
| out = Path('$OUTPUT_DIR') |
| df.to_parquet(out / 'results.parquet', index=False) |
| df.to_csv(out / 'results.csv', index=False) |
| (out / 'summary.json').write_text(json.dumps({ |
| 'encoder': '$ENCODER', |
| 'tools': tools, |
| 'rows': int(len(df)), |
| 'sweep_name': '$SWEEP_NAME', |
| }, indent=2)) |
| print(json.dumps({'rows': int(len(df)), 'output': str(out)})) |
| " |
|
|
| uv run python scripts/hf_artifacts.py push-dataset-folder \ |
| --repo "$DATA_DATASET" \ |
| --source "$OUTPUT_DIR" \ |
| --path-in-repo "$SWEEP_NAME" \ |
| --message "quant benchmark $SWEEP_NAME" |
|
|
