#!/bin/bash
PANDA_ROOT="${PANDA_ROOT:-$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)}"
# Phase E: after all 6 v3 retrains complete, run the full downstream chain.
set -e

cd "$PANDA_ROOT"
export LD_LIBRARY_PATH=$(python -c "import site,os; print(os.path.join(site.getsitepackages()[0],'nvidia','cusparselt','lib'))"):/home/bcheng/.conda/pkgs/libstdcxx-15.2.0-h39759b7_7/lib/:${LD_LIBRARY_PATH:-}

echo "=== phase E step 1: zero-shot predictions on Dingwall/Dahlin/Veres with v3 models ==="
# skin -> Dingwall
python scripts/pan_skin/30_zero_shot_aldrich.py --system_v v3  2>&1 | tail -5 || echo "[warn] aldrich script may need path fix"

echo "=== phase E step 2: post-hoc EDEN detection using Dingwall paper markers ==="
python scripts/analysis/98_eden_posthoc_detection.py 2>&1 | tail -10

echo "=== phase E step 2b: En1 spatial-repressor + local-activator dual-role analysis ==="
python scripts/analysis/99_en1_dual_role_analysis.py 2>&1 | tail -20

echo "=== phase E step 3: expanded pathway analysis (91 modules, 3 systems) ==="
for sys in pan_skin hematopoiesis pancreas; do
  echo "--- $sys ---"
  python scripts/analysis/57_pathway_analysis.py --system $sys 2>&1 | tail -5
done

echo "=== phase E step 4: regenerate UMAPs with distinct-hue palette + v3 predictions ==="
python scripts/figures/build_pca_vs_marker_umaps.py 2>&1 | tail -20

echo "=== phase E step 5: regenerate supplement PDF ==="
python scripts/figures/build_figure_supplement.py 2>&1 | tail -5

echo "=== phase E step 6: rebuild paper PDF ==="
pdflatex -interaction=nonstopmode PAPER.tex > /tmp/latex.log 2>&1
pdflatex -interaction=nonstopmode PAPER.tex > /tmp/latex.log 2>&1
rm -f PAPER.aux PAPER.log PAPER.out

echo "=== phase E DONE ==="