Merge pull request #780 from rku/enh/spmmcr_env_config

Check for MCR related env vars when instantiating SPMCommand. coverage is good: https://coveralls.io/files/126696593#L250

Author: satra

nipype/interfaces/spm/base.py

@@ -237,6 +237,7 @@ def __init__(self, **inputs):
                                                               'mfile',
                                                               'paths',
                                                               'use_mcr'])
+        self._find_mlab_cmd_defaults()
         self._check_mlab_inputs()
         self._matlab_cmd_update()
 
@@ -246,6 +247,17 @@ def set_mlab_paths(cls, matlab_cmd=None, paths=None, use_mcr=None):
         cls._paths = paths
         cls._use_mcr = use_mcr
 
+    def _find_mlab_cmd_defaults(self):
+        # check if the user has set environment variables to enforce
+        # the standalone (MCR) version of SPM
+        if self._use_mcr or 'FORCE_SPMMCR' in os.environ:
+            self._use_mcr = True
+            if self._matlab_cmd is None:
+                try:
+                    self._matlab_cmd = os.environ['SPMMCRCMD']
+                except KeyError:
+                    pass
+
     def _matlab_cmd_update(self):
         # MatlabCommand has to be created here,
         # because matlab_cmb is not a proper input

nipype/interfaces/spm/tests/test_base.py

@@ -68,6 +68,34 @@ class TestClass(spm.SPMCommand):
     yield assert_true, dc.inputs.mfile
 
 
+def test_find_mlab_cmd_defaults():
+    saved_env = dict(os.environ)
+    class TestClass(spm.SPMCommand):
+        pass
+    # test without FORCE_SPMMCR, SPMMCRCMD set
+    for varname in ['FORCE_SPMMCR', 'SPMMCRCMD']:
+        try:
+            del os.environ[varname]
+        except KeyError:
+            pass
+    dc = TestClass()
+    yield assert_equal, dc._use_mcr, None
+    yield assert_equal, dc._matlab_cmd, None
+    # test with only FORCE_SPMMCR set
+    os.environ['FORCE_SPMMCR'] = '1'
+    dc = TestClass()
+    yield assert_equal, dc._use_mcr, True
+    yield assert_equal, dc._matlab_cmd, None
+    # test with both, FORCE_SPMMCR and SPMMCRCMD set
+    os.environ['SPMMCRCMD'] = 'spmcmd'
+    dc = TestClass()
+    yield assert_equal, dc._use_mcr, True
+    yield assert_equal, dc._matlab_cmd, 'spmcmd'
+    # restore environment
+    os.environ.clear();
+    os.environ.update(saved_env)
+
+
 @skipif(no_spm, "SPM not found")
 def test_cmd_update():
     class TestClass(spm.SPMCommand):