Merge pull request #759 from rku/enh/spmmcr_env_config

ENH: Add support for spm MCR configuration via environment

Author: satra

doc/users/spmmcr.rst

@@ -17,7 +17,19 @@ you can test by calling:
 
 .. testcode::
 
-   spm.SPMCommand().version
+    spm.SPMCommand().version
+
+If you want to enforce the standalone MCR version of spm for nipype globally,
+you can do so by setting the following environment variables:
+
+*SPMMCRCMD*
+    Specifies the command to use to run the spm standalone MCR version. You
+    may still override the command as described above.
+
+*FORCE_SPMMCR*
+    Set this to any value in order to enforce the use of spm standalone MCR
+    version in nipype globally. Technically, this sets the `use_mcr` flag of
+    the spm interface to True.
 
 Information about the MCR version of SPM8 can be found at:
 

nipype/interfaces/spm/base.py

@@ -129,22 +129,35 @@ def version(matlab_cmd=None, paths=None, use_mcr=None):
 
         Parameters
         ----------
-        matlab_cmd : String specifying default matlab command
-
-            default None, will look for environment variable MATLABCMD
-            and use if found, otherwise falls back on MatlabCommand
-            default of 'matlab -nodesktop -nosplash'
+        matlab_cmd: str
+            Sets the default matlab command. If None, the value of the
+            environment variable SPMMCRCMD will be used if set and use_mcr
+            is True or the environment variable FORCE_SPMMCR is set.
+            If one of FORCE_SPMMCR or SPMMCRCMD is not set, the existence
+            of the environment variable MATLABCMD is checked and its value
+            is used as the matlab command if possible.
+            If none of the above was successful, the fallback value of
+            'matlab -nodesktop -nosplash' will be used.
+        paths : str
+        use_mcr : bool
 
         Returns
         -------
         spm_path : string representing path to SPM directory
 
             returns None of path not found
         """
+        if use_mcr or 'FORCE_SPMMCR' in os.environ:
+            use_mcr = True
+            if matlab_cmd is None:
+                try:
+                    matlab_cmd = os.environ['SPMMCRCMD']
+                except KeyError:
+                    pass
         if matlab_cmd is None:
             try:
                 matlab_cmd = os.environ['MATLABCMD']
-            except:
+            except KeyError:
                 matlab_cmd = 'matlab -nodesktop -nosplash'
         mlab = MatlabCommand(matlab_cmd=matlab_cmd)
         mlab.inputs.mfile = False