adjusting the script with new paths
This commit is contained in:
@@ -1,384 +0,0 @@
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#!/usr/bin/env bash
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set -euo pipefail
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# ============================================================
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# Organize Barcelona EDSS project safely
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# - Creates a timestamped backup first
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# - Creates a cleaner folder structure
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# - Moves files conservatively
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# - Does NOT delete anything
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# ============================================================
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PROJECT_ROOT="$(pwd)"
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TIMESTAMP="$(date +%Y%m%d_%H%M%S)"
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BACKUP_PARENT="${PROJECT_ROOT}/../Barcelona_backups"
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BACKUP_DIR="${BACKUP_PARENT}/Barcelona_backup_${TIMESTAMP}"
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echo "Project root: ${PROJECT_ROOT}"
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echo "Backup dir: ${BACKUP_DIR}"
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echo
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# ------------------------------------------------------------
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# Safety checks
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# ------------------------------------------------------------
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if [ ! -f "${PROJECT_ROOT}/README.md" ]; then
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echo "WARNING: README.md not found. Are you sure you are in the project root?"
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echo "Current directory: ${PROJECT_ROOT}"
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read -r -p "Continue anyway? [y/N] " answer
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case "$answer" in
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y|Y|yes|YES) ;;
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*) echo "Aborted."; exit 1 ;;
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esac
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fi
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if [ -d "${PROJECT_ROOT}/.git" ]; then
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if ! git diff --quiet || ! git diff --cached --quiet; then
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echo "ERROR: Git working tree is not clean."
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echo "Please commit or stash changes before organizing."
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exit 1
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fi
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fi
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echo "This script will:"
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echo "1. Create a full backup."
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echo "2. Create organized folders."
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echo "3. Move files into data/, prompts/, scripts/, results/, archive/."
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echo "4. Keep your original files in the backup."
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echo
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read -r -p "Proceed? [y/N] " answer
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case "$answer" in
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y|Y|yes|YES) ;;
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*) echo "Aborted."; exit 1 ;;
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esac
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# ------------------------------------------------------------
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# Backup
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# ------------------------------------------------------------
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mkdir -p "${BACKUP_PARENT}"
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echo
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echo "Creating backup..."
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rsync -a \
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--exclude "enarcelona/" \
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--exclude "env/" \
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--exclude ".venv/" \
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--exclude "__pycache__/" \
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"${PROJECT_ROOT}/" "${BACKUP_DIR}/"
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echo "Backup created at:"
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echo "${BACKUP_DIR}"
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# ------------------------------------------------------------
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# Create target structure
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# ------------------------------------------------------------
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echo
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echo "Creating new directory structure..."
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mkdir -p \
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data/raw \
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data/processed \
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data/ground_truth \
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data/external \
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prompts \
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scripts \
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results/benchmark_runs \
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results/final_results/model_outputs \
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results/figures \
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results/tables \
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results/logs \
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manuscript/figures \
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manuscript/tables \
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archive/old_scripts \
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archive/old_results \
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archive/tmp \
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archive/old_data \
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archive/old_project_files
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# ------------------------------------------------------------
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# Helper move functions
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# ------------------------------------------------------------
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move_if_exists() {
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src="$1"
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dest="$2"
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if [ -e "$src" ]; then
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mkdir -p "$(dirname "$dest")"
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if [ -e "$dest" ]; then
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echo "SKIP: destination exists: $dest"
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else
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echo "MOVE: $src -> $dest"
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mv "$src" "$dest"
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fi
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fi
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}
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move_glob_if_exists() {
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pattern="$1"
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dest_dir="$2"
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mkdir -p "$dest_dir"
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shopt -s nullglob
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files=( $pattern )
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shopt -u nullglob
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for f in "${files[@]}"; do
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base="$(basename "$f")"
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dest="${dest_dir}/${base}"
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if [ -e "$dest" ]; then
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echo "SKIP: destination exists: $dest"
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else
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echo "MOVE: $f -> $dest"
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mv "$f" "$dest"
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fi
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done
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}
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# ------------------------------------------------------------
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# Move prompts / attached instruction files
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# ------------------------------------------------------------
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echo
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echo "Moving prompt and instruction files..."
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move_if_exists "attach/Komplett.txt" "prompts/Komplett.txt"
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move_if_exists "attach/just_edss_schema.gbnf" "prompts/just_edss_schema.gbnf"
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move_if_exists "attach/just_edss_text.txt" "prompts/just_edss_text.txt"
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# Move leftover attach folder if empty or archive it
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if [ -d "attach" ]; then
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if [ -z "$(ls -A attach)" ]; then
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rmdir attach
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else
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move_if_exists "attach" "archive/old_project_files/attach"
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fi
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fi
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# ------------------------------------------------------------
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# Move important data files
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# ------------------------------------------------------------
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echo
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echo "Moving data files..."
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move_if_exists "Data/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned.csv" \
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"data/processed/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned.csv"
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move_if_exists "Data/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_unique.csv" \
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"data/processed/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_unique.csv"
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move_if_exists "Data/Join_edssandsub.tsv" \
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"data/ground_truth/Join_edssandsub.tsv"
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move_if_exists "Data/GT_Numbers.csv" \
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"data/ground_truth/GT_Numbers.csv"
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move_if_exists "Data/Annika1.csv" \
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"data/ground_truth/Annika1.csv"
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move_if_exists "Data/comparison.tsv" \
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"data/ground_truth/comparison.tsv"
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move_if_exists "Data/edss_distribution_summary.csv" \
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"data/processed/edss_distribution_summary.csv"
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move_if_exists "Data/empirical_confidence_table.csv" \
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"data/processed/empirical_confidence_table.csv"
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move_if_exists "Data/functional_system_colors.json" \
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"data/processed/functional_system_colors.json"
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move_if_exists "Data/Test.csv" \
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"archive/tmp/Test.csv"
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move_if_exists "Data/Hernan" \
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"data/external/Hernan"
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move_if_exists "Data/iteration" \
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"archive/old_data/iteration"
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# Old generated JSON/results from Data folder
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move_glob_if_exists "Data/*results*.json" "archive/old_results"
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move_glob_if_exists "Data/join_*.tsv" "archive/old_results"
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# Move remaining Data folder if anything left
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if [ -d "Data" ]; then
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if [ -z "$(ls -A Data)" ]; then
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rmdir Data
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else
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move_if_exists "Data" "archive/old_data/Data_remaining"
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fi
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fi
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# ------------------------------------------------------------
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# Move benchmark results
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# ------------------------------------------------------------
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echo
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echo "Moving benchmark results..."
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if [ -d "results_edss_benchmark" ]; then
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move_glob_if_exists "results_edss_benchmark/run_*" "results/benchmark_runs"
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move_if_exists "results_edss_benchmark/endresults" \
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"results/final_results/model_outputs"
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move_if_exists "results_edss_benchmark/confusion_matrices" \
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"results/figures/confusion_matrices"
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if [ -z "$(ls -A results_edss_benchmark 2>/dev/null || true)" ]; then
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rmdir results_edss_benchmark
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else
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move_if_exists "results_edss_benchmark" \
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"archive/old_results/results_edss_benchmark_remaining"
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fi
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fi
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# ------------------------------------------------------------
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# Move old/general results
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# ------------------------------------------------------------
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echo
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echo "Moving existing results files..."
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if [ -d "results" ]; then
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# Figures
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move_glob_if_exists "results/*.png" "results/figures"
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move_glob_if_exists "results/*.PNG" "results/figures"
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move_glob_if_exists "results/*.jpg" "results/figures"
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move_glob_if_exists "results/*.jpeg" "results/figures"
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move_glob_if_exists "results/*.svg" "results/figures"
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# Tables
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move_glob_if_exists "results/*.csv" "results/tables"
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move_glob_if_exists "results/*.tsv" "results/tables"
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move_glob_if_exists "results/*.xlsx" "results/tables"
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# Subfolders that look like old results
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move_if_exists "results/Jan_visual" "archive/old_results/Jan_visual"
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move_if_exists "results/Lab_meeting" "archive/old_results/Lab_meeting"
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move_if_exists "results/just_edss" "archive/old_results/just_edss"
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fi
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# Root-level result tables
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move_if_exists "edss_distribution_summary.csv" \
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"results/tables/edss_distribution_summary.csv"
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# Logs
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move_if_exists "edss_benchmark_terminal.log" \
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"results/logs/edss_benchmark_terminal.log"
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# ------------------------------------------------------------
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# Move scripts
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# ------------------------------------------------------------
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echo
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echo "Moving scripts..."
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move_if_exists "audit.py" "scripts/audit_outputs.py"
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move_if_exists "certainty.py" "scripts/analyze_certainty.py"
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move_if_exists "certainty_show.py" "scripts/certainty_show.py"
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move_if_exists "figure1.py" "scripts/figure1.py"
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move_if_exists "show_plots.py" "scripts/show_plots.py"
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move_if_exists "show_plots.py.orig" "archive/old_scripts/show_plots.py.orig"
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# Apps / old entry points
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move_if_exists "app.py" "archive/old_scripts/app.py"
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move_if_exists "total_app.py" "archive/old_scripts/total_app.py"
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# Existing project visuals folder
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move_if_exists "project/visuals" "results/figures/project_visuals"
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||||
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if [ -d "project" ]; then
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if [ -z "$(ls -A project)" ]; then
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rmdir project
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||||
else
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move_if_exists "project" "archive/old_project_files/project"
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fi
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fi
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# ------------------------------------------------------------
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# Environment folder
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||||
# ------------------------------------------------------------
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echo
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echo "Handling virtual environment..."
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||||
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if [ -d "enarcelona" ]; then
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echo "Leaving virtual environment in place: enarcelona/"
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echo "It should remain ignored by .gitignore."
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fi
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||||
# ------------------------------------------------------------
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||||
# Create README notes
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||||
# ------------------------------------------------------------
|
||||
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||||
echo
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||||
echo "Writing organization notes..."
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||||
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||||
cat > "PROJECT_STRUCTURE.md" <<'EOF'
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# Project Structure
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||||
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||||
This project was reorganized into:
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||||
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- `data/`
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- `raw/`: original raw data, if retained locally
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||||
- `processed/`: cleaned or derived input data
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||||
- `ground_truth/`: manually annotated reference data
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||||
- `external/`: externally provided data
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||||
|
||||
- `prompts/`
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||||
- EDSS instructions and prompt/schema assets
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||||
|
||||
- `scripts/`
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||||
- runnable analysis and plotting scripts
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||||
|
||||
- `results/`
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||||
- `benchmark_runs/`: full model benchmark runs
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||||
- `final_results/`: final selected model outputs
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||||
- `figures/`: generated figures
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||||
- `tables/`: generated tables
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||||
- `logs/`: terminal logs
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||||
|
||||
- `manuscript/`
|
||||
- final figures and tables for paper/thesis writing
|
||||
|
||||
- `archive/`
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||||
- old scripts, old results, temporary files, and unclear legacy files
|
||||
|
||||
Important:
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||||
The reorganization was performed after creating a full timestamped backup.
|
||||
EOF
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||||
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||||
# ------------------------------------------------------------
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||||
# Final checks
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||||
# ------------------------------------------------------------
|
||||
|
||||
echo
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||||
echo "Organization complete."
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||||
echo
|
||||
echo "Backup is here:"
|
||||
echo "${BACKUP_DIR}"
|
||||
echo
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||||
echo "New top-level structure:"
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||||
find . -maxdepth 2 -type d | sort
|
||||
echo
|
||||
|
||||
if [ -d ".git" ]; then
|
||||
echo "Git status:"
|
||||
git status --short
|
||||
fi
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||||
|
||||
echo
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||||
echo "Next recommended commands:"
|
||||
echo " git status"
|
||||
echo " git add ."
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||||
echo " git commit -m \"Reorganize project structure\""
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||||
@@ -1258,7 +1258,7 @@
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||||
|
||||
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||||
# %% API call - Multi-model, multi-iteration EDSS + timing/resource benchmark
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||||
#
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||||
|
||||
#import time
|
||||
#import json
|
||||
#import os
|
||||
@@ -1279,9 +1279,9 @@
|
||||
# print("Install with: pip install psutil")
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## CONFIGURATION
|
||||
## =========================
|
||||
# =========================
|
||||
# CONFIGURATION
|
||||
# =========================
|
||||
#
|
||||
#load_dotenv()
|
||||
#
|
||||
@@ -1289,21 +1289,21 @@
|
||||
#OPENAI_BASE_URL = os.getenv("OPENAI_BASE_URL")
|
||||
#
|
||||
#MODEL_CONFIGS = [
|
||||
## {
|
||||
## "model_name": "qwen3.6-35b-a3b",
|
||||
## "use_response_format": False,
|
||||
## "temperature": 0.0,
|
||||
## "max_tokens": 4096,
|
||||
##
|
||||
## # If your backend is vLLM / Qwen chat-template compatible,
|
||||
## # this may reduce long hidden reasoning and JSON truncation.
|
||||
## # If your server errors because of extra_body, set this to None.
|
||||
## "extra_body": {
|
||||
## "chat_template_kwargs": {
|
||||
## "enable_thinking": False
|
||||
## }
|
||||
## },
|
||||
## },
|
||||
# {
|
||||
# "model_name": "qwen3.6-35b-a3b",
|
||||
# "use_response_format": False,
|
||||
# "temperature": 0.0,
|
||||
# "max_tokens": 4096,
|
||||
#
|
||||
# # If your backend is vLLM / Qwen chat-template compatible,
|
||||
# # this may reduce long hidden reasoning and JSON truncation.
|
||||
# # If your server errors because of extra_body, set this to None.
|
||||
# "extra_body": {
|
||||
# "chat_template_kwargs": {
|
||||
# "enable_thinking": False
|
||||
# }
|
||||
# },
|
||||
# },
|
||||
# {
|
||||
# "model_name": "gemma-4-31B-it",
|
||||
# "use_response_format": False,
|
||||
@@ -1328,10 +1328,10 @@
|
||||
#NUM_ITERATIONS = 10
|
||||
#STOP_ON_FIRST_ERROR = False
|
||||
#
|
||||
## For testing, set to e.g. 2.
|
||||
## For full run, set to None.
|
||||
# For testing, set to e.g. 2.
|
||||
# For full run, set to None.
|
||||
#MAX_ROWS = 2
|
||||
## MAX_ROWS = 2
|
||||
# MAX_ROWS = 2
|
||||
#
|
||||
#MAX_TOKENS = 4096
|
||||
#TEMPERATURE = 0.0
|
||||
@@ -1340,14 +1340,14 @@
|
||||
#
|
||||
#SAVE_EVERY_N_ROWS = 1
|
||||
#
|
||||
## Retries for invalid JSON / truncated JSON
|
||||
# Retries for invalid JSON / truncated JSON
|
||||
#MAX_JSON_RETRIES = 2
|
||||
#RETRY_SLEEP_SEC = 2
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## CLIENT
|
||||
## =========================
|
||||
# =========================
|
||||
# CLIENT
|
||||
# =========================
|
||||
#
|
||||
#client = OpenAI(
|
||||
# api_key=OPENAI_API_KEY,
|
||||
@@ -1355,9 +1355,9 @@
|
||||
#)
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## HELPERS
|
||||
## =========================
|
||||
# =========================
|
||||
# HELPERS
|
||||
# =========================
|
||||
#
|
||||
#def safe_dir_name(name: str) -> str:
|
||||
# name = str(name).strip()
|
||||
@@ -1433,9 +1433,9 @@
|
||||
# return max(self.samples_mb)
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## JSON EXTRACTION
|
||||
## =========================
|
||||
# =========================
|
||||
# JSON EXTRACTION
|
||||
# =========================
|
||||
#
|
||||
#def extract_json_from_text(text):
|
||||
# if text is None:
|
||||
@@ -1587,17 +1587,17 @@
|
||||
# return None
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## READ INSTRUCTIONS
|
||||
## =========================
|
||||
# =========================
|
||||
# READ INSTRUCTIONS
|
||||
# =========================
|
||||
#
|
||||
#with open(EDSS_INSTRUCTIONS_PATH, "r", encoding="utf-8") as f:
|
||||
# EDSS_INSTRUCTIONS = f.read().strip()
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## PROMPT
|
||||
## =========================
|
||||
# =========================
|
||||
# PROMPT
|
||||
# =========================
|
||||
#
|
||||
#def build_prompt(patient_text):
|
||||
# return f'''Du bist ein medizinischer Assistent für EDSS-Extraktion aus klinischen Berichten.
|
||||
@@ -1676,9 +1676,9 @@
|
||||
#'''
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## VALIDATION / NORMALIZATION
|
||||
## =========================
|
||||
# =========================
|
||||
# VALIDATION / NORMALIZATION
|
||||
# =========================
|
||||
#
|
||||
#def normalize_model_output(parsed):
|
||||
# if not isinstance(parsed, dict):
|
||||
@@ -1755,9 +1755,9 @@
|
||||
# return parsed
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## API CALL
|
||||
## =========================
|
||||
# =========================
|
||||
# API CALL
|
||||
# =========================
|
||||
#
|
||||
#def make_chat_completion(model_config, prompt):
|
||||
# model_name = model_config["model_name"]
|
||||
@@ -1794,9 +1794,9 @@
|
||||
# return client.chat.completions.create(**kwargs)
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## INFERENCE FUNCTION WITH RETRIES
|
||||
## =========================
|
||||
# =========================
|
||||
# INFERENCE FUNCTION WITH RETRIES
|
||||
# =========================
|
||||
#
|
||||
#def run_inference(patient_text, model_config):
|
||||
# model_name = model_config["model_name"]
|
||||
@@ -1912,9 +1912,9 @@
|
||||
# }
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## BUILD PATIENT TEXT
|
||||
## =========================
|
||||
# =========================
|
||||
# BUILD PATIENT TEXT
|
||||
# =========================
|
||||
#
|
||||
#def build_patient_text(row):
|
||||
# return (
|
||||
@@ -1925,9 +1925,9 @@
|
||||
# )
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## FLATTEN RESULTS FOR CSV
|
||||
## =========================
|
||||
# =========================
|
||||
# FLATTEN RESULTS FOR CSV
|
||||
# =========================
|
||||
#
|
||||
#def flatten_result(record):
|
||||
# flat = {
|
||||
@@ -2012,9 +2012,9 @@
|
||||
# return pd.DataFrame([summary])
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## INCREMENTAL SAVE HELPERS
|
||||
## =========================
|
||||
# =========================
|
||||
# INCREMENTAL SAVE HELPERS
|
||||
# =========================
|
||||
#
|
||||
#def append_jsonl(path, record):
|
||||
# with open(path, "a", encoding="utf-8") as f:
|
||||
@@ -2030,9 +2030,9 @@
|
||||
# df_one.to_csv(path, mode="a", header=not file_exists, index=False)
|
||||
#
|
||||
#
|
||||
## =========================
|
||||
## MAIN LOOP
|
||||
## =========================
|
||||
# =========================
|
||||
# MAIN LOOP
|
||||
# =========================
|
||||
#
|
||||
#if __name__ == "__main__":
|
||||
#
|
||||
@@ -2277,26 +2277,26 @@ MODEL_CONFIGS = [
|
||||
"max_tokens": 4096,
|
||||
"extra_body": None,
|
||||
},
|
||||
# {
|
||||
# "model_name": "GPT-OSS-120B",
|
||||
# "use_response_format": True,
|
||||
# "temperature": 0.0,
|
||||
# "max_tokens": 4096,
|
||||
# "extra_body": None,
|
||||
# },
|
||||
{
|
||||
"model_name": "GPT-OSS-120B",
|
||||
"use_response_format": True,
|
||||
"temperature": 0.0,
|
||||
"max_tokens": 4096,
|
||||
"extra_body": None,
|
||||
},
|
||||
]
|
||||
|
||||
INPUT_CSV = "/home/shahin/Lab/Doktorarbeit/Barcelona/Data/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_unique.csv"
|
||||
EDSS_INSTRUCTIONS_PATH = "/home/shahin/Lab/Doktorarbeit/Barcelona/attach/Komplett.txt"
|
||||
INPUT_CSV ="/home/shahin/Lab/Doktorarbeit/Barcelona/data/processed/MS_Briefe_400_with_unique_id_SHA3_explore_cleaned_unique.csv"
|
||||
EDSS_INSTRUCTIONS_PATH = "/home/shahin/Lab/Doktorarbeit/Barcelona/prompts/Komplett.txt"
|
||||
|
||||
RESULTS_ROOT = "/home/shahin/Lab/Doktorarbeit/Barcelona/results_edss_benchmark"
|
||||
RESULTS_ROOT = "/home/shahin/Lab/Doktorarbeit/Barcelona/results/benchmark_runs"
|
||||
|
||||
NUM_ITERATIONS = 10
|
||||
NUM_ITERATIONS = 2
|
||||
STOP_ON_FIRST_ERROR = False
|
||||
|
||||
# For testing, set to e.g. 2.
|
||||
# For full run, set to None.
|
||||
MAX_ROWS = None
|
||||
MAX_ROWS = 2
|
||||
# MAX_ROWS = 2
|
||||
|
||||
MAX_TOKENS = 4096
|
||||
|
||||
Reference in New Issue
Block a user