Fix for new matlab setup

.ci/runtests.sh

@@ -9,7 +9,7 @@ elif [ "$ARCH" == "Windows" ]; then
     cd "D:\jenkins\workspace\COBRAToolbox-windows\MATLAB_VER\R2016b\label\windows-biocore"
     whoami
     echo " -- Launching MATLAB --"
-    nohup "C:\Program Files\Matlab\R2016b\bin\matlab.exe" -logfile output.log -wait -r "restoredefaultpath;matlabrc; cd test; testAll;" &
+    nohup "C:\Program Files\Matlab\R2016b\bin\matlab.exe" -useStartupFolderPref -logfile output.log -wait -r "cd test; testAll;" & # #fprintf('%s\n', getenv('USERPROFILE')); pwd; initCobraToolbox; exit;
     tail -n0 -F --pid=$! output.log 2>/dev/null
 fi
 

initCobraToolbox.m

@@ -167,33 +167,33 @@ function initCobraToolbox()
 
         % temporary disable ssl verification
         [status_setSSLVerify, result_setSSLVerify] = system('git config http.sslVerify false');
-
+        
         if status_setSSLVerify ~= 0
-            fprintf(result_setSSLVerify);
+            fprintf(strrep(result_setSSLVerify, '\', '\\'));
             warning('Your global git configuration could not be changed.');
         end
 
         % Update/initialize submodules
         [status_gitSubmodule, result_gitSubmodule] = system('git submodule update --init');
-
+        
         if status_gitSubmodule ~= 0
-            fprintf(result_gitSubmodule);
+            fprintf(strrep(result_gitSubmodule, '\', '\\'));
             error('The submodules could not be initialized.');
         end
 
         % reset each submodule
         [status_gitReset, result_gitReset] = system('git submodule foreach --recursive git reset --hard');
 
         if status_gitReset ~= 0
-            fprintf(result_gitReset);
+            fprintf(strrep(result_gitReset, '\', '\\'));
             warning('The submodules could not be reset.');
         end
 
         % restore global configuration by unsetting http.sslVerify
         [status_setSSLVerify, result_setSSLVerify] = system('git config --unset http.sslVerify');
 
         if status_setSSLVerify ~= 0
-            fprintf(result_setSSLVerify);
+            fprintf(strrep(result_setSSLVerify, '\', '\\'));
             warning('Your global git configuration could not be restored.');
         end