scripts/pod_bootstrap_ablation_v2.sh

#!/usr/bin/env bash
# Generic A-ablation bootstrap. All extra args go to train.py.
# Args: <run_name> <subset_frac> <extra_args...>
set -euo pipefail
RUN_NAME="${1:?run_name}"
SUBSET="${2:?subset_frac}"
shift 2
EXTRA=("$@")

echo "[bootstrap] A ablation: run=$RUN_NAME subset=$SUBSET extra=${EXTRA[*]}"
cd /workspace
REPO_DIR=""
for d in PhysioJEPA physiojepa; do
  if [ -d "$d" ]; then REPO_DIR="$d"; break; fi
done
[ -n "$REPO_DIR" ] || { echo "no repo dir"; exit 1; }
cd "$REPO_DIR"

PY=/usr/bin/python3
$PY -m pip install --quiet --upgrade pip
$PY -m pip install --quiet \
    'datasets>=4.8.4' 'einops>=0.8.2' 'matplotlib>=3.10.0' \
    'neurokit2>=0.2.13' 'python-dotenv>=1.0' 'pyyaml>=6.0' \
    'scikit-learn>=1.5' 'scipy>=1.13' 'tqdm>=4.66' \
    'wandb>=0.18' 'wfdb>=4.3.1' 'huggingface_hub>=0.25' 'requests'

if [ -f /workspace/.env ]; then cp /workspace/.env .env; fi

if [ ! -f /workspace/cache/mimic_index.json ]; then
  echo "[bootstrap] downloading MIMIC + building index"
  PYTHONPATH=src $PY scripts/prepare_data.py \
    --root /workspace/cache/mimic --index /workspace/cache/mimic_index.json
fi

PYTHONPATH=src $PY -c "
import json, pathlib
roots = sorted([str(p) for p in pathlib.Path('/workspace/cache/mimic').glob('shard_*')
                if (p / 'dataset_info.json').exists()])
pathlib.Path('/workspace/cache/shard_roots.json').write_text(json.dumps(roots))
print('shards:', len(roots))
"

mkdir -p /workspace/runs
echo "[bootstrap] launching"
PYTHONPATH=src PYTHONUNBUFFERED=1 $PY -u scripts/train.py \
  --config configs/base.yaml \
  --model A \
  --run_name "$RUN_NAME" \
  --epochs 25 \
  --shard_roots_json /workspace/cache/shard_roots.json \
  --index_path /workspace/cache/mimic_index.json \
  --output_dir /workspace/runs \
  --num_workers 8 \
  --subset_frac "$SUBSET" \
  --log_every 25 \
  --seed 42 \
  "${EXTRA[@]}" \
  2>&1 | tee "/workspace/runs/${RUN_NAME}.log"

echo "[bootstrap] done"