Introduced environment variable DAMASK_ROOT.

It is set in the DAMASK root folder by running damask_env.sh
Much needed in the testing routines so far (try ./testing/run_tests.py)
damask_env.sh could also trigger other scripts to get to a working setup after fresh checkout. For example it could run 
./processing/setup/setup_processing.py
./code/setup/setup_code.py
if it finds that we have a fresh checkout.

code/setup/setup_code.py

@@ -29,7 +29,8 @@ for arch in architectures:
 			childFile.write(line.replace(me['versions'][0],version))
 		childFile.close()
 
-os.system('make --directory %s'%wd)
+if raw_input("Do you want to compile the spectral code now? (y/n)") is 'y':
+  os.system('make --directory %s'%wd)
 
 if '--clean' in [s.lower() for s in sys.argv]:
   os.system('make --directory %s clean'%wd)

damask_env.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+# Sets environment variable DAMASK_ROOT to allow python to locate various scripts.
+# run with --bashrc to set DAMASK_ROOT permanently.
+# should maybe got to /etc/profile.d/ for permanent "installation"
+#http://stackoverflow.com/questions/630372/determine-the-path-of-the-executing-bash-script
+MY_PATH="`dirname \"$0\"`"              # relative
+MY_PATH="`( cd \"$MY_PATH\" && pwd )`"  # absolutized and normalized
+if [ -z "$MY_PATH" ] ; then
+  # error; for some reason, the path is not accessible
+  # to the script (e.g. permissions re-evaled after suid)
+  echo "set_damask_root.sh failed"
+  exit 1  # fail
+fi
+#echo "$MY_PATH"
+DAMASK_ROOT=$MY_PATH
+export DAMASK_ROOT
+echo "DAMASK_ROOT: $DAMASK_ROOT"
+
+PYTHONPATH=$DAMASK_ROOT:$PYTHONPATH
+export PYTHONPATH
+#echo "PYTHONPATH: $PYTHONPATH"
+
+if [ "$1" = "--bashrc" ] ; then
+  echo -e "\nDAMASK_ROOT=$DAMASK_ROOT; export DAMASK_ROOT" >> $HOME/.bashrc
+  echo -e "\nPYTHONPATH=$DAMASK_ROOT:$PYTHONPATH; export PYTHONPATH" >> $HOME/.bashrc
+  else
+  echo "Run with option --bashrc to set DAMASK_ROOT and adjust PYTHONPATH permanently through .bashrc"
+fi
+echo "Now starting a new child bash that inherits the appropriate DAMASK_ROOT and PYTHONPATH variables. Have even more fun ..."
+echo "To run the automated tests call ./testing/run_tests.py"
+bash

processing/msc_tools.py

@@ -1,10 +1,9 @@
 class MSC_TOOLS():
-    import string
-    
+    import os,string
     
     def submit_job(self,
                  run_marc_path='/msc/marc2010/tools/',
-                 subroutine_dir='../../../code/',
+                 subroutine_dir=None,
                  subroutine_name='DAMASK_marc2010',
                  compile='yes',
                  compiled_dir='../../../code/',
@@ -13,8 +12,12 @@ class MSC_TOOLS():
                  #IOdir='',
                  host=[]
                  ):
+      import os
       import subprocess, shlex   
       import shutil   
+           
+      if subroutine_dir is None: 
+        subroutine_dir=os.getenv('DAMASK_ROOT')+'/code/'
       # Define all options [see Marc Installation and Operation Guide, pp 23]
       run_marc=run_marc_path+'run_marc'
       jid=' -jid '+modelname+'_'+jobname

set_python_env.py

@@ -1,21 +1,21 @@
 #!/usr/bin/env python
-import os,site,sys
-
-# More elegant was to determine DAMASK install dir?
-#p=os.path.abspath(__file__)
-#l=p.split('/')
-#p=p[:-len(l[-1])]
-#print p
-#site.addsitedir(p) # adds the paths in the *.pth file to the python search path
-
-basepath=os.path.expanduser('~')+'/DAMASK/'
-
-
-sys.path.insert(0,basepath+'processing')
-sys.path.insert(0,basepath+'processing/post')
-sys.path.insert(0,basepath+'processing/pre')
-sys.path.insert(0,basepath+'processing/setup')
-#print sys.path
+import os,sys
+#import site
+# maybe there is an alternative by using site.addsitedir() and *.pth file(s)?
+damask_root=os.getenv('DAMASK_ROOT')
+if damask_root is None:
+  print('Environment variable DAMASK_ROOT not set.\nPlease run DAMASK/damask_env.sh first.')
+  sys.exit()
+print('Setting PYTHONPATH for DAMASK')  
+path_list=['processing'
+           ,'processing/setup'
+           ,'processing/pre'
+           ,'processing/post'
+           ]
+for p in path_list:
+  if p not in sys.path:
+    sys.path.insert(0, damask_root+'/'+p)
+print sys.path