scripts/pod_bootstrap_definitive.sh

#!/usr/bin/env bash
# Definitive full-scale run. Args: <model A|B|F> <run_name> [extra train.py args...]
set -euo pipefail
MODEL="${1:?model letter}"; RUN_NAME="${2:?run_name}"; shift 2; EXTRA=("$@")

echo "[bootstrap] definitive run: model=$MODEL run=$RUN_NAME extra=${EXTRA[*]}"
cd /workspace
REPO_DIR=""; for d in PhysioJEPA physiojepa; do [ -d "$d" ] && REPO_DIR="$d" && break; done
[ -n "$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'

[ -f /workspace/.env ] && cp /workspace/.env .env

# Step 1: download MIMIC shards + build index (idempotent)
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

# Step 2: precompute mmap windows (idempotent — checks inside)
if [ ! -f /workspace/cache/windows_meta.json ]; then
  echo "[bootstrap] precomputing windows → mmap"
  PYTHONPATH=src $PY -u scripts/precompute_windows.py \
    --index /workspace/cache/mimic_index.json \
    --out_dir /workspace/cache
fi

# Step 3: train
mkdir -p /workspace/runs
echo "[bootstrap] launching training: model=$MODEL"
PYTHONPATH=src PYTHONUNBUFFERED=1 $PY -u scripts/train.py \
  --config configs/base.yaml \
  --model "$MODEL" \
  --run_name "$RUN_NAME" \
  --epochs 100 \
  --batch_size 64 \
  --fast_cache_dir /workspace/cache \
  --output_dir /workspace/runs \
  --num_workers 12 \
  --log_every 100 \
  --mask_ratio 0.75 \
  --seed 42 \
  "${EXTRA[@]}" \
  2>&1 | tee "/workspace/runs/${RUN_NAME}.log"

echo "[bootstrap] done"