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3 Commits
98df7c70f1
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Certainty
| Author | SHA1 | Date | |
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 shahin
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c9cf9ae9a0 | ||
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shahin
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1b7c6a3852 | ||
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shahin
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bb9fcf20ae |
@@ -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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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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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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cat > "PROJECT_STRUCTURE.md" <<'EOF'
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# Project Structure
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This project was reorganized into:
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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/`
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- final figures and tables for paper/thesis writing
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- `archive/`
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- old scripts, old results, temporary files, and unclear legacy files
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Important:
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The reorganization was performed after creating a full timestamped backup.
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EOF
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# ------------------------------------------------------------
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# Final checks
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# ------------------------------------------------------------
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echo
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echo "Organization complete."
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echo
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echo "Backup is here:"
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echo "${BACKUP_DIR}"
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echo
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echo "New top-level structure:"
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find . -maxdepth 2 -type d | sort
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echo
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if [ -d ".git" ]; then
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echo "Git status:"
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git status --short
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fi
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echo
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echo "Next recommended commands:"
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echo " git status"
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echo " git add ."
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echo " git commit -m \"Reorganize project structure\""
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+1967
-1027
File diff suppressed because it is too large
Load Diff
+9747
-186
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user