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21b75e3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 | #!/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"
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