Merge pull request #1561 from satra/rel/0.12.1

fix: remove psutils usage by default

Author: satra

nipype/info.py

@@ -8,9 +8,9 @@
 # full release.  '.dev' as a _version_extra string means this is a development
 # version
 _version_major = 0
-_version_minor = 13
-_version_micro = 0
-_version_extra = '-dev'  # Remove -dev for release
+_version_minor = 12
+_version_micro = 1
+_version_extra = ''  # Remove -dev for release
 
 
 def get_nipype_gitversion():

nipype/interfaces/base.py

@@ -50,10 +50,19 @@
 from .. import __version__
 from ..external.six import string_types, text_type
 
+runtime_profile = str2bool(config.get('execution', 'profile_runtime'))
+
 nipype_version = LooseVersion(__version__)
 
 iflogger = logging.getLogger('interface')
 
+if runtime_profile:
+    try:
+        import psutil
+    except ImportError as exc:
+        iflogger.info('Unable to import packages needed for runtime profiling. '\
+                    'Turning off runtime profiler. Reason: %s' % exc)
+        runtime_profile = False
 
 __docformat__ = 'restructuredtext'
 
@@ -1350,15 +1359,6 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False):
     # Init logger
     logger = logging.getLogger('workflow')
 
-    # Default to profiling the runtime
-    try:
-        import psutil
-        runtime_profile = True
-    except ImportError as exc:
-        logger.info('Unable to import packages needed for runtime profiling. '\
-                    'Turning off runtime profiler. Reason: %s' % exc)
-        runtime_profile = False
-
     # Init variables
     PIPE = subprocess.PIPE
     cmdline = runtime.cmdline

nipype/interfaces/tests/test_runtime_profiler.py

@@ -8,16 +8,21 @@
 
 # Import packages
 import unittest
-from nipype.interfaces.base import traits, CommandLine, CommandLineInputSpec
-
-try:
-    import psutil
-    run_profiler = True
-    skip_profile_msg = 'Run profiler tests'
-except ImportError as exc:
-    skip_profile_msg = 'Missing python packages for runtime profiling, skipping...\n'\
-                       'Error: %s' % exc
-    run_profiler = False
+from nipype.interfaces.base import (traits, CommandLine, CommandLineInputSpec,
+                                    runtime_profile)
+
+run_profile = runtime_profile
+
+if run_profile:
+    try:
+        import psutil
+        skip_profile_msg = 'Run profiler tests'
+    except ImportError as exc:
+        skip_profile_msg = 'Missing python packages for runtime profiling, skipping...\n'\
+                           'Error: %s' % exc
+        run_profile = False
+else:
+    skip_profile_msg = 'Not running profiler'
 
 # UseResources inputspec
 class UseResourcesInputSpec(CommandLineInputSpec):
@@ -355,7 +360,7 @@ def _run_function_workflow(self, num_gb, num_threads):
         return start_str, finish_str
 
     # Test resources were used as expected in cmdline interface
-    @unittest.skipIf(run_profiler == False, skip_profile_msg)
+    @unittest.skipIf(run_profile == False, skip_profile_msg)
     def test_cmdline_profiling(self):
         '''
         Test runtime profiler correctly records workflow RAM/CPUs consumption
@@ -397,7 +402,7 @@ def test_cmdline_profiling(self):
                         msg=threads_err)
 
     # Test resources were used as expected
-    @unittest.skipIf(run_profiler == False, skip_profile_msg)
+    @unittest.skipIf(run_profile == False, skip_profile_msg)
     def test_function_profiling(self):
         '''
         Test runtime profiler correctly records workflow RAM/CPUs consumption

nipype/interfaces/utility.py

@@ -22,14 +22,21 @@
 import nibabel as nb
 
 from .base import (traits, TraitedSpec, DynamicTraitedSpec, File,
-                   Undefined, isdefined, OutputMultiPath,
+                   Undefined, isdefined, OutputMultiPath, runtime_profile,
                    InputMultiPath, BaseInterface, BaseInterfaceInputSpec)
 from .io import IOBase, add_traits
 from ..external.six import string_types
 from ..testing import assert_equal
 from ..utils.filemanip import (filename_to_list, copyfile, split_filename)
 from ..utils.misc import getsource, create_function_from_source
 
+if runtime_profile:
+    try:
+        import psutil
+    except ImportError as exc:
+        logger.info('Unable to import packages needed for runtime profiling. '\
+                    'Turning off runtime profiler. Reason: %s' % exc)
+        runtime_profile = False
 
 class IdentityInterface(IOBase):
     """Basic interface class generates identity mappings
@@ -459,20 +466,10 @@ def _function_handle_wrapper(queue, **kwargs):
             if isdefined(value):
                 args[name] = value
 
-        # Runtime profiler on if dependecies available
-        try:
-            import psutil
-            from nipype.interfaces.base import get_max_resources_used
-            import multiprocessing
-            runtime_profile = True
-        except ImportError as exc:
-            logger.info('Unable to import packages needed for runtime profiling. '\
-                        'Turning off runtime profiler. Reason: %s' % exc)
-            runtime_profile = False
-
         # Profile resources if set
-        #runtime_profile=False
         if runtime_profile:
+            from nipype.interfaces.base import get_max_resources_used
+            import multiprocessing
             # Init communication queue and proc objs
             queue = multiprocessing.Queue()
             proc = multiprocessing.Process(target=_function_handle_wrapper,

nipype/utils/config.py

@@ -57,6 +57,7 @@
 parameterize_dirs = true
 poll_sleep_duration = 60
 xvfb_max_wait = 10
+profile_runtime = false
 
 [check]
 interval = 1209600