scripts/common/rerun_all_discovery.sh

#!/usr/bin/env bash
PANDA_ROOT="${PANDA_ROOT:-$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)}"
# Phase C: rerun all mechanistic discovery on new checkpoints.
# Runs analysis scripts 70-85 for each system with both variants where applicable.
set -euo pipefail
cd "$PANDA_ROOT"

LDLIBS=$(python -c "import site,os; print(os.path.join(site.getsitepackages()[0],'nvidia','cusparselt','lib'))" 2>/dev/null || echo "")

echo "=== Phase C: mechanistic discovery reruns ==="

# All rely on the panda import + checkpoints/ + data/corpus/*/harmonized/
run() {
  local name="$1"; shift
  LD_LIBRARY_PATH="$LDLIBS" nohup python -u "$@" > "logs/${name}.log" 2>&1 &
  disown
  echo "launched $name"
}

# 70 — prototype geometry (fast, no GPU)
run rerun_70_proto python scripts/analysis/70_prototype_geometry.py

# 80 — prototype-gene attribution (both systems, both variants)
CUDA_VISIBLE_DEVICES=2 run rerun_80_attr_marker python scripts/analysis/80_prototype_gene_attribution.py

# 82 — co-attribution modules
run rerun_82_coatt python scripts/analysis/82_gene_coattribution_modules.py

# 83 — training trajectory
run rerun_83_traj python scripts/analysis/83_prototype_training_trajectory.py

echo "kick off complete — check logs/rerun_*.log"