#!/usr/bin/env bash
set -euo pipefail

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
source "${SCRIPT_DIR}/../00_setup/env.sh"

bash "${SCRIPT_DIR}/../01_data/download_deepstarr.sh"
bash "${SCRIPT_DIR}/../01_data/summarize_deepstarr.sh"
bash "${SCRIPT_DIR}/../01_data/prepare_conditioned_deepstarr.sh"
bash "${SCRIPT_DIR}/../01_data/make_random_gc_baseline.sh"

bash "${SCRIPT_DIR}/../02_predictor/train_predictor.sh"
bash "${SCRIPT_DIR}/../02_predictor/plot_predictor_validation.sh"

bash "${SCRIPT_DIR}/../03_ar_generation/train_ar_unconditional.sh"
bash "${SCRIPT_DIR}/../03_ar_generation/train_ar_conditioned.sh"
bash "${SCRIPT_DIR}/../03_ar_generation/evaluate_ar_unconditional.sh"
bash "${SCRIPT_DIR}/../03_ar_generation/evaluate_ar_conditioned.sh"

bash "${SCRIPT_DIR}/../05_scoring/score_ar_unconditional.sh"
bash "${SCRIPT_DIR}/../05_scoring/score_ar_conditioned.sh"

bash "${SCRIPT_DIR}/../04_diffusion/train_diffusion_conditioned.sh"
bash "${SCRIPT_DIR}/../04_diffusion/evaluate_diffusion_pll_only.sh"
bash "${SCRIPT_DIR}/../04_diffusion/evaluate_diffusion_with_predictor.sh"

bash "${SCRIPT_DIR}/../06_sequence_metrics/compute_sequence_metrics.sh"
bash "${SCRIPT_DIR}/../08_visualization/make_paper_figures.sh"

echo "Core paper experiments completed under ${RUN_ROOT}"