try to fix setup script to allow specifying existing repo

.github/workflows/main.yml

@@ -26,10 +26,8 @@ jobs:
       - name: Checkout the Squid repo
         uses: actions/checkout@v4
       - name: Run the setup script for Ubuntu 22.04
-        run: ./setup_22.04.sh
+        run: ./setup_22.04.sh -r=.
         working-directory: ./software
-        env:
-          SRC_ROOT: "${{ runner.temp }}"
       - name: Run the cuda setup script
         run: ./setup_cuda_22.04.sh
         working-directory: ./software

software/setup_22.04.sh

@@ -6,17 +6,28 @@ if [[ -n "$TRACE" ]]; then
   set -x
 fi
 
-if [[ -z "$SRC_ROOT" ]]; then
-  readonly SRC_ROOT="$HOME/Desktop"
-fi
-echo "Using SRC_ROOT=$SRC_ROOT"
-echo "Disk space summary (before setup):"
-df -h
+SQUID_REPO_PATH="$HOME/Desktop/Squid"
+
+for i in "$@"; do
+  case $i in
+    -r=*|--repo_path=*)
+      SQUID_REPO_PATH="${i#*=}"
+      shift
+      ;;
+    -*|--*)
+      echo "Unknown option $i"
+      exit 1
+      ;;
+    *)
+      ;;
+  esac
+done
+
+echo "Using SQUID_REPO_PATH='${SQUID_REPO_PATH}'"
 
-mkdir -p "$SRC_ROOT"
 readonly SQUID_REPO_HTTP="https://github.com/Cephla-Lab/Squid.git"
-readonly SQUID_REPO_NAME="Squid"
-readonly SQUID_SOFTWARE_ROOT="$SRC_ROOT/$SQUID_REPO_NAME/software"
+readonly SQUID_SOFTWARE_ROOT="${SQUID_REPO_PATH}/software"
+readonly SQUID_REPO_PATH_PARENT="$(dirname "${SQUID_REPO_PATH}")"
 readonly DAHENG_CAMERA_DRIVER_ROOT="$SQUID_SOFTWARE_ROOT/drivers and libraries/daheng camera/Galaxy_Linux-x86_Gige-U3_32bits-64bits_1.2.1911.9122"
 readonly DAHENG_CAMERA_DRIVER_API_ROOT="$SQUID_SOFTWARE_ROOT/drivers and libraries/daheng camera/Galaxy_Linux_Python_1.0.1905.9081/api"
 readonly TOUPCAM_UDEV_RULE_PATH="$SQUID_SOFTWARE_ROOT/drivers and libraries/toupcam/linux/udev/99-toupcam.rules"
@@ -28,10 +39,17 @@ sudo apt install python3-pip -y
 sudo apt install python3-pyqtgraph python3-pyqt5 -y
 sudo apt install python3-pyqt5.qtsvg
 
-# clone the repo
 sudo apt-get install git -y
-cd "$SRC_ROOT"
-git clone "$SQUID_REPO_HTTP" "$SQUID_REPO_NAME"
+## clone the repo if we don't already have it.
+# No matter, make sure the repo's parent dir is there
+mkdir -p "${SQUID_REPO_PATH_PARENT}"
+if [[ ! -d "${SQUID_REPO_PATH}" ]]; then
+  git clone "$SQUID_REPO_HTTP" "${SQUID_REPO_PATH}"
+else
+  echo "Using existing repo at '${SQUID_REPO_PATH}' at HEAD=$(cd "${SQUID_REPO_PATH}" && git rev-parse HEAD)"
+fi
+
+
 cd "$SQUID_SOFTWARE_ROOT"
 mkdir -p "$SQUID_SOFTWARE_ROOT/cache"