A first-run path for new users.

bash <<'EOF'
set -e

REPO_URL="https://github.com/schurerlab/Pymacs.git"
TMP_DIR="$(mktemp -d)"
TARGET_DIR="$(pwd)"

cleanup() {
  rm -rf "$TMP_DIR"
}

trap cleanup EXIT

echo "======================================"
echo " PyMACS Quick Start Install"
echo "======================================"
echo
echo "This will copy a fresh PyMACS instance into:"
echo "  $TARGET_DIR"
echo

if ! command -v git >/dev/null 2>&1; then
  echo "ERROR: git is not installed or not available in PATH."
  echo "Please install git first, then run this command again."
  exit 1
fi

if [ "$(find "$TARGET_DIR" -mindepth 1 -maxdepth 1 | wc -l)" -gt 0 ]; then
  echo "WARNING: This directory is not empty."
  echo "Files with the same names as PyMACS files may be overwritten."
  echo
  printf "Continue copying PyMACS into this directory? [y/N]: "
  read -r answer </dev/tty
  case "$answer" in
    y|Y|yes|YES) ;;
    *)
      echo "Install cancelled."
      exit 0
      ;;
  esac
fi

echo
echo "Cloning PyMACS into a temporary folder..."
git clone "$REPO_URL" "$TMP_DIR/pymacs"

cd "$TMP_DIR/pymacs"

if command -v git-lfs >/dev/null 2>&1 || git lfs version >/dev/null 2>&1; then
  echo "Git LFS detected. Pulling large tracked files..."
  git lfs install
  git lfs pull
else
  echo "WARNING: Git LFS was not detected."
  echo "Core PyMACS files will still be copied, but large example assets may remain as LFS pointer files."
  echo "Install Git LFS later and re-run this installer if you need the full example datasets."
fi

echo
echo "Copying PyMACS files into your current directory..."

shopt -s dotglob nullglob
for item in "$TMP_DIR/pymacs"/*; do
  base="$(basename "$item")"
  if [ "$base" = ".git" ]; then
    continue
  fi

  if [ -e "$TARGET_DIR/$base" ]; then
    printf "Overwrite existing %s? [y/N]: " "$base"
    read -r overwrite </dev/tty
    case "$overwrite" in
      y|Y|yes|YES)
        rm -rf "$TARGET_DIR/$base"
        ;;
      *)
        echo "Skipping $base"
        continue
        ;;
    esac
  fi

  cp -R "$item" "$TARGET_DIR/"
done

echo "Cleaning up temporary clone..."
cleanup
trap - EXIT

cd "$TARGET_DIR"

echo
echo "Done. PyMACS has been copied into:"
echo "  $TARGET_DIR"
echo
echo "Next recommended steps:"
echo "  conda env create -f environment_cgenff.yml"
echo "  conda env create -f environment_mdanalysis.yml"
echo
echo "Then follow the Step 1 / Step 2 / Step 3 workflow on this page."
EOF