Fix checking out of other plugins branches/commits (#209)

* Don't exit if successful

* add sleep, reorg a bit

* Double &

* One more

Author: bethac07

worker/run-worker.sh

@@ -47,34 +47,23 @@ python3.8 instance-monitor.py &
 # 5. UPDATE AND/OR INSTALL PLUGINS
 if [[ ${USE_PLUGINS} == 'True' ]]; then
   if [[ ${UPDATE_PLUGINS} == 'True' ]]; then
-    echo "Updating CellProfiler-plugins."
-    cd CellProfiler-plugins
-    git fetch --all
-    git pull
-    cd ..
+    (echo "Updating CellProfiler-plugins." & cd CellProfiler-plugins && git fetch --all && git pull && cd ..)
   fi
   if [[ -z "$PLUGINS_COMMIT" ]]; then
     PLUGINS_COMMIT='False'
   fi
   if [[ ${PLUGINS_COMMIT} != 'False' ]]; then
-    echo "Checking out specific CellProfiler-plugins commit."
-    cd CellProfiler-plugins
-    git checkout ${PLUGINS_COMMIT} || echo "No such commit, branch, or version; failing here." & exit 1
-    cd ..
+    (echo "Checking out specific CellProfiler-plugins commit." & cd CellProfiler-plugins && git checkout ${PLUGINS_COMMIT} && cd .. && echo "checkout successful" && sleep 3) || (echo "No such commit, branch, or version; failing here." & exit 1)
   fi 
   if [[ ${INSTALL_REQUIREMENTS} == 'True' ]]; then
     cd CellProfiler-plugins
     if [[ -z "$REQUIREMENTS" ]]; then
       REQUIREMENTS = $REQUIREMENTS_FILE
     fi
     if [[ -d "active_plugins" ]]; then
-      echo "Installing CellProfiler-plugins requirements."
-      pip install -e . ${REQUIREMENTS} || echo "Requirements install failed." & exit 1
-      cd ..
+      (echo "Installing CellProfiler-plugins requirements." & pip install -e . ${REQUIREMENTS} && cd ..) || (echo "Requirements install failed." & exit 1)
     else 
-      echo "Detected deprecated CellProfiler-plugins repo organization. Installing requirements."
-      pip install -r ${REQUIREMENTS} || echo "Requirements file not present or install failed; failing here." & exit 1
-      cd ..
+      (echo "Detected deprecated CellProfiler-plugins repo organization. Installing requirements." & pip install -r ${REQUIREMENTS} && cd ..) || (echo "Requirements file not present or install failed; failing here." & exit 1)
     fi
   fi
 fi