scripts/00_setup/env.sh

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

# Source this file before running any experiment script:
#   source scripts/00_setup/env.sh

export PROJECT_ROOT="${PROJECT_ROOT:-/Users/ouzhang/Desktop/genRL/project}"
export RUN_ROOT="${RUN_ROOT:-${PROJECT_ROOT}/paper_runs}"
export DATA_ROOT="${DATA_ROOT:-${RUN_ROOT}/data}"
export MODEL_ROOT="${MODEL_ROOT:-${RUN_ROOT}/models}"
export RESULT_ROOT="${RESULT_ROOT:-${RUN_ROOT}/results}"
export FIGURE_ROOT="${FIGURE_ROOT:-${RUN_ROOT}/figures}"

export GENERATOR_DIR="${GENERATOR_DIR:-${PROJECT_ROOT}/GENERator}"
export GENERANNO_DIR="${GENERANNO_DIR:-${PROJECT_ROOT}/GENERanno}"

export DEEPSTARR_DATASET_ID="${DEEPSTARR_DATASET_ID:-GenerTeam/DeepSTARR-enhancer-activity}"
export DEEPSTARR_DIR="${DEEPSTARR_DIR:-${DATA_ROOT}/DeepSTARR-enhancer-activity}"
export CONDITIONED_DEEPSTARR_DIR="${CONDITIONED_DEEPSTARR_DIR:-${DATA_ROOT}/DeepSTARR-enhancer-activity-conditioned}"

export GENERATOR_MODEL_ID="${GENERATOR_MODEL_ID:-GenerTeam/GENERator-eukaryote-1.2b-base}"
export GENERANNO_MODEL_ID="${GENERANNO_MODEL_ID:-GenerTeam/GENERanno-eukaryote-0.5b-base}"
export GENERATOR_BASE_MODEL="${GENERATOR_BASE_MODEL:-${PROJECT_ROOT}/GENERATOR-eukaryote-1.2b-base}"
export GENERANNO_BASE_MODEL="${GENERANNO_BASE_MODEL:-${PROJECT_ROOT}/models/GENERanno-eukaryote-0.5b-base}"

export PREDICTOR_DIR="${PREDICTOR_DIR:-${RESULT_ROOT}/deepstarr_regression}"
export PREDICTOR_MODEL="${PREDICTOR_MODEL:-${PREDICTOR_DIR}/best_model}"

export AR_UNCOND_MODEL="${AR_UNCOND_MODEL:-${MODEL_ROOT}/deepstarr_sft}"
export AR_COND_MODEL="${AR_COND_MODEL:-${MODEL_ROOT}/deepstarr_sft_conditioned}"
export DIFFUSION_MODEL="${DIFFUSION_MODEL:-${MODEL_ROOT}/deepstarr_discrete_diffusion}"

export WANDB_MODE="${WANDB_MODE:-offline}"
export TOKENIZERS_PARALLELISM="${TOKENIZERS_PARALLELISM:-false}"

mkdir -p "${RUN_ROOT}" "${DATA_ROOT}" "${MODEL_ROOT}" "${RESULT_ROOT}" "${FIGURE_ROOT}"