scripts/build_portable_bundle.sh

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

ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
BUNDLE_DIR="${ROOT_DIR}/portable_rdock_pipeline"
STALE_BUNDLE_DIR="${ROOT_DIR}/portable_rdock_pipeline.stale.$$"

rm -rf "${STALE_BUNDLE_DIR}" 2>/dev/null || true
if [ -e "${BUNDLE_DIR}" ]; then
  mv "${BUNDLE_DIR}" "${STALE_BUNDLE_DIR}" 2>/dev/null || true
fi
rm -rf "${BUNDLE_DIR}" 2>/dev/null || true
mkdir -p "${BUNDLE_DIR}/scripts" "${BUNDLE_DIR}/configs" "${BUNDLE_DIR}/data/examples" "${BUNDLE_DIR}/tests_minimal" "${BUNDLE_DIR}/docs"

cp -R "${ROOT_DIR}/docking_pipeline" "${BUNDLE_DIR}/docking_pipeline"
cp -R "${ROOT_DIR}/libs" "${BUNDLE_DIR}/libs"
find "${BUNDLE_DIR}/libs/docking" -type f -name "backend_*mina.py" -delete
rm -f "${BUNDLE_DIR}/libs/benchmark/redocking_validation.py"
rm -f "${BUNDLE_DIR}/libs/docking/backend_haddock.py"
cp "${ROOT_DIR}/scripts/prepare_pdb_ligand_dataset.py" "${BUNDLE_DIR}/scripts/prepare_pdb_ligand_dataset.py"
cp "${ROOT_DIR}/scripts/download_example_smiles.py" "${BUNDLE_DIR}/scripts/download_example_smiles.py"
cp "${ROOT_DIR}/scripts/find_pdb_ligand_candidates.py" "${BUNDLE_DIR}/scripts/find_pdb_ligand_candidates.py"
cp "${ROOT_DIR}/scripts/run_strategy_benchmark_server.sh" "${BUNDLE_DIR}/scripts/run_strategy_benchmark_server.sh"
cp "${ROOT_DIR}/scripts/slurm_prepare_500k_dataset.sh" "${BUNDLE_DIR}/scripts/slurm_prepare_500k_dataset.sh"
cp "${ROOT_DIR}/scripts/slurm_smoke_500k_ablation.sh" "${BUNDLE_DIR}/scripts/slurm_smoke_500k_ablation.sh"
cp "${ROOT_DIR}/scripts/slurm_regressor_ablation_500k.sh" "${BUNDLE_DIR}/scripts/slurm_regressor_ablation_500k.sh"
cp "${ROOT_DIR}/scripts/slurm_strategy_benchmark_500k.sh" "${BUNDLE_DIR}/scripts/slurm_strategy_benchmark_500k.sh"
cp "${ROOT_DIR}/scripts/build_portable_bundle.sh" "${BUNDLE_DIR}/scripts/build_portable_bundle.sh"
cp "${ROOT_DIR}/configs/multifidelity_defaults.yaml" "${BUNDLE_DIR}/configs/multifidelity_defaults.yaml"
cp "${ROOT_DIR}/configs/reference_free_triage_bandit_defaults.yaml" "${BUNDLE_DIR}/configs/reference_free_triage_bandit_defaults.yaml"
cp "${ROOT_DIR}/configs/known_good_pdb_complexes.yaml" "${BUNDLE_DIR}/configs/known_good_pdb_complexes.yaml"
cp "${ROOT_DIR}/data/examples/example_smiles.smi" "${BUNDLE_DIR}/data/examples/example_smiles.smi"
cp "${ROOT_DIR}/data/examples/example_smiles_1000.smi" "${BUNDLE_DIR}/data/examples/example_smiles_1000.smi"
cp "${ROOT_DIR}/data/examples/example_pdb_dataset_config.yaml" "${BUNDLE_DIR}/data/examples/example_pdb_dataset_config.yaml"
if [ -d "${ROOT_DIR}/data/examples/rdock_3ptb_pubchem_50k_collect_only" ]; then
  cp -R "${ROOT_DIR}/data/examples/rdock_3ptb_pubchem_50k_collect_only" "${BUNDLE_DIR}/data/examples/"
fi
cp "${ROOT_DIR}/environment.yml" "${BUNDLE_DIR}/environment.yml"
cp "${ROOT_DIR}/setup_server.sh" "${BUNDLE_DIR}/setup_server.sh"
cp "${ROOT_DIR}/check_environment.sh" "${BUNDLE_DIR}/check_environment.sh"
cp "${ROOT_DIR}/README_SERVER.md" "${BUNDLE_DIR}/README_SERVER.md"
cp -R "${ROOT_DIR}/docs/." "${BUNDLE_DIR}/docs/"
rm -f "${BUNDLE_DIR}"/docs/pipeline_methodology_fix_report_*.txt
rm -f "${BUNDLE_DIR}"/docs/plip_analog_run_report_*.txt
rm -rf "${BUNDLE_DIR}/tests_minimal"
cp -R "${ROOT_DIR}/tests_minimal" "${BUNDLE_DIR}/tests_minimal"

find "${BUNDLE_DIR}" -name "__pycache__" -type d -prune -exec rm -rf {} +
find "${BUNDLE_DIR}" -name "*.pyc" -delete
find "${BUNDLE_DIR}" -name ".DS_Store" -delete
rm -rf "${BUNDLE_DIR}/rdock"
rm -rf "${STALE_BUNDLE_DIR}" 2>/dev/null || true

removed_backend_token="s""mina"
if grep -RIl "${removed_backend_token}" "${BUNDLE_DIR}" >/tmp/portable_removed_backend_refs.txt; then
  echo "ERROR: removed backend references remain in portable bundle:" >&2
  cat /tmp/portable_removed_backend_refs.txt >&2
  exit 1
fi

echo "Built portable bundle at ${BUNDLE_DIR}"