refactor, added tests

Author: chrisgorgo

bin/nipype_cmd

@@ -1,69 +1,8 @@
 #!/usr/bin/env python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Script to auto-generate our API docs.
-"""
-# stdlib imports
-import os
-import argparse
 import sys
-import inspect
-from nipype.interfaces.base import Interface
+from nipype.utils.nipype_cmd import main
 
-
-def listClasses(module=None):
-    if module:
-        __import__(module)
-        pkg = sys.modules[module]
-        print "Available Interfaces:"
-        for k,v in pkg.__dict__.items():
-            if inspect.isclass(v) and issubclass(v, Interface):
-                print "\t%s"%k
-
-def add_options(parser=None, module=None, function=None):
-    interface = None
-    if parser and module and function:
-        __import__(module)
-        interface = getattr(sys.modules[module],function)()
-
-        for k,v in interface.inputs.items():
-            if hasattr(v, "mandatory") and v.mandatory:
-                parser.add_argument(k, help=v.desc)
-            else:
-                parser.add_argument("--%s"%k, dest=k,
-                                help=v.desc)
-    return parser, interface
-
-def run_instance(interface, options):
-    if interface:
-        print "setting function inputs"
-        for k,_ in interface.inputs.items():
-            if getattr(options, k) != None:
-                setattr(interface.inputs, k,
-                        getattr(options, k))
-        print interface.inputs
-        res = interface.run()
-        print res.outputs    
-
-
-def parse_args():
-    
-    if len(sys.argv) == 2 and not sys.argv[1].startswith("-"):
-        listClasses(sys.argv[1])
-        return
-    
-    parser = argparse.ArgumentParser(description='Nipype interface runner')
-    parser.add_argument("module", type=str, help="Module name")
-    parser.add_argument("interface", type=str, help="Interface name")
-    parsed = parser.parse_args(args=sys.argv[1:3])
-    
-    _, prog = os.path.split(sys.argv[0])
-    interface_parser = argparse.ArgumentParser(description="Run %s"%parsed.interface, prog=" ".join([prog] + sys.argv[1:3]))
-    interface_parser, interface  = add_options(interface_parser, parsed.module, parsed.interface)
-    args = interface_parser.parse_args(args=sys.argv[3:])
-    run_instance(interface, args)
-
-
-#*****************************************************************************
 if __name__ == '__main__':
-    parse_args()
+    main(sys.argv)

nipype/utils/nipype_cmd.py

@@ -0,0 +1,60 @@
+import os
+import argparse
+import inspect
+import sys
+from nipype.interfaces.base import Interface
+
+
+def listClasses(module=None):
+    if module:
+        __import__(module)
+        pkg = sys.modules[module]
+        print "Available Interfaces:"
+        for k,v in pkg.__dict__.items():
+            if inspect.isclass(v) and issubclass(v, Interface):
+                print "\t%s"%k
+
+def add_options(parser=None, module=None, function=None):
+    interface = None
+    if parser and module and function:
+        __import__(module)
+        interface = getattr(sys.modules[module],function)()
+
+        for k,v in interface.inputs.items():
+            if hasattr(v, "mandatory") and v.mandatory:
+                parser.add_argument(k, help=v.desc)
+            else:
+                parser.add_argument("--%s"%k, dest=k,
+                                help=v.desc)
+    return parser, interface
+
+def run_instance(interface, options):
+    if interface:
+        print "setting function inputs"
+        for input_name, _ in interface.inputs.items():
+            if getattr(options, input_name) != None:
+                str_value = getattr(options, input_name)
+                casted_value = getattr(interface.inputs, input_name)(str_value)
+                setattr(interface.inputs, input_name,
+                        casted_value)
+        print interface.inputs
+        res = interface.run()
+        print res.outputs    
+
+
+def main(argv):
+    
+    if len(argv) == 2 and not argv[1].startswith("-"):
+        listClasses(argv[1])
+        sys.exit(0)
+    
+    parser = argparse.ArgumentParser(description='Nipype interface runner')
+    parser.add_argument("module", type=str, help="Module name")
+    parser.add_argument("interface", type=str, help="Interface name")
+    parsed = parser.parse_args(args=argv[1:3])
+    
+    _, prog = os.path.split(argv[0])
+    interface_parser = argparse.ArgumentParser(description="Run %s"%parsed.interface, prog=" ".join([prog] + argv[1:3]))
+    interface_parser, interface  = add_options(interface_parser, parsed.module, parsed.interface)
+    args = interface_parser.parse_args(args=argv[3:])
+    run_instance(interface, args)

nipype/utils/tests/test_cmd.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+
+from StringIO import StringIO
+import unittest, sys
+from nipype.utils import nipype_cmd
+from contextlib import contextmanager
+
+@contextmanager
+def capture_sys_output():
+    caputure_out, capture_err = StringIO(), StringIO()
+    current_out, current_err = sys.stdout, sys.stderr
+    try:
+        sys.stdout, sys.stderr = caputure_out, capture_err
+        yield caputure_out, capture_err
+    finally:
+        sys.stdout, sys.stderr = current_out, current_err
+
+
+class TestNipypeCMD(unittest.TestCase):
+
+    def test_main_returns_2_on_empty(self):
+        with self.assertRaises(SystemExit) as cm:
+            with capture_sys_output() as (stdout, stderr):
+                nipype_cmd.main(['nipype_cmd'])
+        
+        exit_exception = cm.exception
+        self.assertEqual(exit_exception.code, 2)
+        
+        self.assertEqual(stderr.getvalue(), 
+"""usage: runfiles.py [-h] module interface
+runfiles.py: error: too few arguments
+""")
+        self.assertEqual(stdout.getvalue(), '')
+        
+    def test_main_returns_0_on_help(self):
+        with self.assertRaises(SystemExit) as cm:
+            with capture_sys_output() as (stdout, stderr):
+                nipype_cmd.main(['nipype_cmd', '-h'])
+        
+        exit_exception = cm.exception
+        self.assertEqual(exit_exception.code, 0)
+        
+        self.assertEqual(stderr.getvalue(), '')
+        self.assertEqual(stdout.getvalue(),
+"""usage: runfiles.py [-h] module interface\n\nNipype interface runner
+
+positional arguments:
+  module      Module name
+  interface   Interface name
+
+optional arguments:
+  -h, --help  show this help message and exit
+""")
+
+if __name__ == '__main__':
+    unittest.main()