Merge pull request #495 from satra/fix/execconfig

fix: config updated before checking for deprecated options

Author: satra

nipype/pipeline/engine.py

@@ -498,12 +498,12 @@ def run(self, plugin=None, plugin_args=None, updatehash=False):
                 plugin_mod = getattr(sys.modules[name], '%sPlugin' % plugin)
                 runner = plugin_mod(plugin_args=plugin_args)
         flatgraph = self._create_flat_graph()
+        self.config = merge_dict(deepcopy(config._sections), self.config)
         if 'crashdump_dir' in self.config:
             warn(("Deprecated: workflow.config['crashdump_dir']\n"
                   "Please use config['execution']['crashdump_dir']"))
             self.config['execution']['crashdump_dir'] = self.config['crashdump_dir']
             del self.config['crashdump_dir']
-        self.config = merge_dict(deepcopy(config._sections), self.config)
         logger.info(str(sorted(self.config)))
         self._set_needed_outputs(flatgraph)
         execgraph = generate_expanded_graph(deepcopy(flatgraph))

nipype/pipeline/tests/test_engine.py

@@ -405,3 +405,37 @@ def _submit_job(self, node, updatehash=False):
     os.chdir(cwd)
     rmtree(wd)
 
+def test_old_config():
+    cwd = os.getcwd()
+    wd = mkdtemp()
+    os.chdir(wd)
+    from nipype.interfaces.utility import Function
+    def func1():
+        return 1
+    def func2(a):
+        return a+1
+    n1 = pe.Node(Function(input_names=[],
+                          output_names=['a'],
+                          function=func1),
+                 name='n1')
+    n2 = pe.Node(Function(input_names=['a'],
+                          output_names=['b'],
+                          function=func2),
+                 name='n2')
+    w1 = pe.Workflow(name='test')
+    modify = lambda x: x+1
+    n1.inputs.a = 1
+    w1.connect(n1, ('a', modify), n2,'a')
+    w1.base_dir = wd
+
+    w1.config = {'crashdump_dir': wd}
+    # generate outputs
+    error_raised = False
+    try:
+        w1.run(plugin='Linear')
+    except Exception, e:
+        pe.logger.info('Exception: %s' % str(e))
+        error_raised = True
+    yield assert_false, error_raised
+    os.chdir(cwd)
+    rmtree(wd)