Merge remote-tracking branch 'upstream/master' into enh/antsCT

* upstream/master:
  fix import of specs
  [MAINT] Outsource ``get_filecopy_info()`` from interfaces
  [MAINT] One less DeprecationWarning (configparser)
  [MAINT] Import only Sequence to avoid DeprecationWarning
  fixed
  [MAINT] DeprecationWarning: use ``HasTraits.trait_set`` instead
  [HOTFIX] Latest nilearn-0.5.0 breaks tests
  [MAINT] Stop using deprecated ``logger.warn()``
  [FIX] MapNodes failed when ``MultiProcPlugin`` passed by instance

Author: satra

nipype/algorithms/confounds.py

@@ -327,7 +327,7 @@ def _run_interface(self, runtime):
                 tr = self.inputs.series_tr
 
             if self.inputs.normalize and tr is None:
-                IFLOGGER.warn('FD plot cannot be normalized if TR is not set')
+                IFLOGGER.warning('FD plot cannot be normalized if TR is not set')
 
             self._results['out_figure'] = op.abspath(self.inputs.out_figure)
             fig = plot_confound(
@@ -1267,7 +1267,7 @@ def _full_rank(X, cmax=1e15):
     c = smax / smin
     if c < cmax:
         return X, c
-    IFLOGGER.warn('Matrix is singular at working precision, regularizing...')
+    IFLOGGER.warning('Matrix is singular at working precision, regularizing...')
     lda = (smax - cmax * smin) / (cmax - 1)
     s = s + lda
     X = np.dot(U, np.dot(np.diag(s), V))

nipype/algorithms/mesh.py

@@ -422,5 +422,5 @@ class P2PDistance(ComputeMeshWarp):
 
     def __init__(self, **inputs):
         super(P2PDistance, self).__init__(**inputs)
-        IFLOGGER.warn('This interface has been deprecated since 1.0, please '
-                      'use ComputeMeshWarp')
+        IFLOGGER.warning('This interface has been deprecated since 1.0, please '
+                         'use ComputeMeshWarp')

nipype/algorithms/misc.py

@@ -589,7 +589,7 @@ def _run_interface(self, runtime):
             extraheadingBool = True
 
         if len(self.inputs.in_files) == 1:
-            iflogger.warn('Only one file input!')
+            iflogger.warning('Only one file input!')
 
         if isdefined(self.inputs.row_headings):
             iflogger.info('Row headings have been provided. Adding "labels"'

nipype/algorithms/modelgen.py

@@ -602,7 +602,7 @@ def _generate_design(self, infolist=None):
                 try:
                     out = np.loadtxt(filename)
                 except IOError:
-                    iflogger.warn('Error reading outliers file %s', filename)
+                    iflogger.warning('Error reading outliers file %s', filename)
                     out = np.array([])
 
                 if out.size > 0:

nipype/info.py

@@ -163,7 +163,7 @@ def get_nipype_gitversion():
     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
     'tests': TESTS_REQUIRES,
     'specs': ['yapf'],
-    'nipy': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
+    'nipy': ['nitime', 'nilearn<0.5.0', 'dipy', 'nipy', 'matplotlib'],
     'profiler': ['psutil>=5.0'],
     'duecredit': ['duecredit'],
     'xvfbwrapper': ['xvfbwrapper'],

nipype/interfaces/base/core.py

@@ -42,6 +42,7 @@
 from .specs import (BaseInterfaceInputSpec, CommandLineInputSpec,
                     StdOutCommandLineInputSpec, MpiCommandLineInputSpec)
 from .support import (Bunch, InterfaceResult, NipypeInterfaceError)
+from .specs import get_filecopy_info
 
 from future import standard_library
 standard_library.install_aliases()
@@ -122,11 +123,15 @@ def _list_outputs(self):
         """ List expected outputs"""
         raise NotImplementedError
 
-    def _get_filecopy_info(self):
-        """ Provides information about file inputs to copy or link to cwd.
-            Necessary for pipeline operation
+    @classmethod
+    def _get_filecopy_info(cls):
+        """Provides information about file inputs to copy or link to cwd.
+        Necessary for pipeline operation
         """
-        raise NotImplementedError
+        iflogger.warning(
+            '_get_filecopy_info member of Interface was deprecated '
+            'in nipype-1.1.6 and will be removed in 1.2.0')
+        return get_filecopy_info(cls)
 
 
 class BaseInterface(Interface):
@@ -330,19 +335,6 @@ def _outputs(self):
 
         return outputs
 
-    @classmethod
-    def _get_filecopy_info(cls):
-        """ Provides information about file inputs to copy or link to cwd.
-            Necessary for pipeline operation
-        """
-        info = []
-        if cls.input_spec is None:
-            return info
-        metadata = dict(copyfile=lambda t: t is not None)
-        for name, spec in sorted(cls.input_spec().traits(**metadata).items()):
-            info.append(dict(key=name, copy=spec.copyfile))
-        return info
-
     def _check_requires(self, spec, name, value):
         """ check if required inputs are satisfied
         """
@@ -1180,8 +1172,8 @@ def __init__(self, check_import=True, *args, **kwargs):
                 except ImportError:
                     failed_imports.append(pkg)
             if failed_imports:
-                iflogger.warn('Unable to import %s; %s interface may fail to '
-                              'run', failed_imports, self.__class__.__name__)
+                iflogger.warning('Unable to import %s; %s interface may fail to '
+                                 'run', failed_imports, self.__class__.__name__)
 
     @property
     def version(self):

nipype/interfaces/base/specs.py

@@ -13,6 +13,7 @@
                         absolute_import)
 
 import os
+from inspect import isclass
 from copy import deepcopy
 from warnings import warn
 from builtins import str, bytes
@@ -375,3 +376,21 @@ class MpiCommandLineInputSpec(CommandLineInputSpec):
     n_procs = traits.Int(desc="Num processors to specify to mpiexec. Do not "
                          "specify if this is managed externally (e.g. through "
                          "SGE)")
+
+
+def get_filecopy_info(cls):
+    """Provides information about file inputs to copy or link to cwd.
+    Necessary for pipeline operation
+    """
+    if cls.input_spec is None:
+        return None
+
+    # normalize_filenames is not a classmethod, hence check first
+    if not isclass(cls) and hasattr(cls, 'normalize_filenames'):
+        cls.normalize_filenames()
+    info = []
+    inputs = cls.input_spec() if isclass(cls) else cls.inputs
+    metadata = dict(copyfile=lambda t: t is not None)
+    for name, spec in sorted(inputs.traits(**metadata).items()):
+        info.append(dict(key=name, copy=spec.copyfile))
+    return info

nipype/interfaces/base/tests/test_core.py

@@ -62,15 +62,12 @@ def __init__(self):
         nif.aggregate_outputs()
     with pytest.raises(NotImplementedError):
         nif._list_outputs()
-    with pytest.raises(NotImplementedError):
-        nif._get_filecopy_info()
 
 
 def test_BaseInterface():
     config.set('monitoring', 'enable', '0')
 
     assert nib.BaseInterface.help() is None
-    assert nib.BaseInterface._get_filecopy_info() == []
 
     class InputSpec(nib.TraitedSpec):
         foo = nib.traits.Int(desc='a random int')
@@ -90,10 +87,6 @@ class DerivedInterface(nib.BaseInterface):
     assert DerivedInterface.help() is None
     assert 'moo' in ''.join(DerivedInterface._inputs_help())
     assert DerivedInterface()._outputs() is None
-    assert DerivedInterface._get_filecopy_info()[0]['key'] == 'woo'
-    assert DerivedInterface._get_filecopy_info()[0]['copy']
-    assert DerivedInterface._get_filecopy_info()[1]['key'] == 'zoo'
-    assert not DerivedInterface._get_filecopy_info()[1]['copy']
     assert DerivedInterface().inputs.foo == nib.Undefined
     with pytest.raises(ValueError):
         DerivedInterface()._check_mandatory_inputs()

nipype/interfaces/base/tests/test_specs.py

@@ -14,7 +14,7 @@
 from ....interfaces import fsl
 from ...utility.wrappers import Function
 from ....pipeline import Node
-
+from ..specs import get_filecopy_info
 
 standard_library.install_aliases()
 
@@ -55,8 +55,8 @@ def test_TraitedSpec_tab_completion():
     bet_nd = Node(fsl.BET(), name='bet')
     bet_interface = fsl.BET()
     bet_inputs = bet_nd.inputs.class_editable_traits()
-    bet_outputs = bet_nd.outputs.class_editable_traits() 
-    
+    bet_outputs = bet_nd.outputs.class_editable_traits()
+
     # Check __all__ for bet node and interface inputs
     assert set(bet_nd.inputs.__all__) == set(bet_inputs)
     assert set(bet_interface.inputs.__all__) == set(bet_inputs)
@@ -433,3 +433,45 @@ def test_ImageFile():
     with pytest.raises(nib.TraitError):
         x.nocompress = 'test.nii.gz'
     x.nocompress = 'test.mgh'
+
+
+def test_filecopy_info():
+    class InputSpec(nib.TraitedSpec):
+        foo = nib.traits.Int(desc='a random int')
+        goo = nib.traits.Int(desc='a random int', mandatory=True)
+        moo = nib.traits.Int(desc='a random int', mandatory=False)
+        hoo = nib.traits.Int(desc='a random int', usedefault=True)
+        zoo = nib.File(desc='a file', copyfile=False)
+        woo = nib.File(desc='a file', copyfile=True)
+
+    class DerivedInterface(nib.BaseInterface):
+        input_spec = InputSpec
+        resource_monitor = False
+
+        def normalize_filenames(self):
+            """A mock normalize_filenames for freesurfer interfaces that have one"""
+            self.inputs.zoo = 'normalized_filename.ext'
+
+    assert get_filecopy_info(nib.BaseInterface) == []
+
+    # Test on interface class, not instantiated
+    info = get_filecopy_info(DerivedInterface)
+    assert info[0]['key'] == 'woo'
+    assert info[0]['copy']
+    assert info[1]['key'] == 'zoo'
+    assert not info[1]['copy']
+    info = None
+
+    # Test with instantiated interface
+    derived = DerivedInterface()
+    # First check that zoo is not defined
+    assert derived.inputs.zoo == Undefined
+    # After the first call to get_filecopy_info zoo is defined
+    info = get_filecopy_info(derived)
+    # Ensure that normalize_filenames was called
+    assert derived.inputs.zoo == 'normalized_filename.ext'
+    # Check the results are consistent
+    assert info[0]['key'] == 'woo'
+    assert info[0]['copy']
+    assert info[1]['key'] == 'zoo'
+    assert not info[1]['copy']

nipype/interfaces/base/traits_extension.py

@@ -25,7 +25,7 @@
 
 from builtins import str, bytes
 import os
-import collections
+from collections import Sequence
 
 # perform all external trait imports here
 from traits import __version__ as traits_version
@@ -323,7 +323,7 @@ def validate(self, object, name, value):
 
         # want to treat range and other sequences (except str) as list
         if not isinstance(value, (str, bytes)) and isinstance(
-                value, collections.Sequence):
+                value, Sequence):
             value = list(value)
 
         if not isdefined(value) or \

nipype/interfaces/dipy/reconstruction.py

@@ -124,9 +124,9 @@ def _run_interface(self, runtime):
         sigma = mean_std * (1 + bias)
 
         if sigma == 0:
-            IFLOGGER.warn('Noise std is 0.0, looks like data was masked and '
-                          'noise cannot be estimated correctly. Using default '
-                          'tensor model instead of RESTORE.')
+            IFLOGGER.warning('Noise std is 0.0, looks like data was masked and '
+                             'noise cannot be estimated correctly. Using default '
+                             'tensor model instead of RESTORE.')
             dti = TensorModel(gtab)
         else:
             IFLOGGER.info('Performing RESTORE with noise std=%.4f.', sigma)
@@ -258,11 +258,11 @@ def _run_interface(self, runtime):
             ratio = abs(response[1] / response[0])
 
         if ratio > 0.25:
-            IFLOGGER.warn('Estimated response is not prolate enough. '
-                          'Ratio=%0.3f.', ratio)
+            IFLOGGER.warning('Estimated response is not prolate enough. '
+                             'Ratio=%0.3f.', ratio)
         elif ratio < 1.e-5 or np.any(np.isnan(response)):
             response = np.array([1.8e-3, 3.6e-4, 3.6e-4, S0])
-            IFLOGGER.warn(
+            IFLOGGER.warning(
                 'Estimated response is not valid, using a default one')
         else:
             IFLOGGER.info('Estimated response: %s', str(response[:3]))
@@ -344,8 +344,8 @@ def _run_interface(self, runtime):
         ratio = response[0][1] / response[0][0]
 
         if abs(ratio - 0.2) > 0.1:
-            IFLOGGER.warn('Estimated response is not prolate enough. '
-                          'Ratio=%0.3f.', ratio)
+            IFLOGGER.warning('Estimated response is not prolate enough. '
+                             'Ratio=%0.3f.', ratio)
 
         csd_model = ConstrainedSphericalDeconvModel(
             gtab, response, sh_order=self.inputs.sh_order)

nipype/interfaces/dipy/tracks.py

@@ -73,8 +73,8 @@ def _run_interface(self, runtime):
             data_dims = refnii.shape[:3]
             kwargs = dict(affine=affine)
         else:
-            IFLOGGER.warn('voxel_dims and data_dims are deprecated as of dipy '
-                          '0.7.1. Please use reference input instead')
+            IFLOGGER.warning('voxel_dims and data_dims are deprecated as of dipy '
+                             '0.7.1. Please use reference input instead')
 
             if not isdefined(self.inputs.data_dims):
                 data_dims = header['dim']

nipype/interfaces/freesurfer/base.py

@@ -189,16 +189,6 @@ class FSSurfaceCommand(FSCommand):
     including the full path in the filename, we can also avoid this behavior.
     """
 
-    def _get_filecopy_info(self):
-        self._normalize_filenames()
-        return super(FSSurfaceCommand, self)._get_filecopy_info()
-
-    def _normalize_filenames(self):
-        """Filename normalization routine to perform only when run in Node
-        context
-        """
-        pass
-
     @staticmethod
     def _associated_file(in_file, out_name):
         """Based on MRIsBuildFileName in freesurfer/utils/mrisurf.c

nipype/interfaces/freesurfer/utils.py

@@ -316,8 +316,8 @@ def _format_arg(self, name, spec, value):
                             "Cannot create {} file with extension "
                             "{}".format(value, ext))
                     else:
-                        logger.warn('Creating %s file with extension %s: %s%s',
-                                    value, ext, base, ext)
+                        logger.warning('Creating %s file with extension %s: %s%s',
+                                       value, ext, base, ext)
 
             if value in implicit_filetypes:
                 return ""
@@ -554,8 +554,8 @@ def _format_arg(self, name, spec, value):
                             "Cannot create {} file with extension "
                             "{}".format(value, ext))
                     else:
-                        logger.warn('Creating %s file with extension %s: %s%s',
-                                    value, ext, base, ext)
+                        logger.warning('Creating %s file with extension %s: %s%s',
+                                       value, ext, base, ext)
             if value in implicit_filetypes:
                 return ""
         return super(SurfaceTransform, self)._format_arg(name, spec, value)
@@ -1289,9 +1289,11 @@ def _list_outputs(self):
 
         return outputs
 
-    def _normalize_filenames(self):
-        """ In a Node context, interpret out_file as a literal path to
-        reduce surprise.
+    def normalize_filenames(self):
+        """
+        Filename normalization routine to perform only when run in Node
+        context.
+        Interpret out_file as a literal path to reduce surprise.
         """
         if isdefined(self.inputs.out_file):
             self.inputs.out_file = os.path.abspath(self.inputs.out_file)
@@ -3837,8 +3839,11 @@ def _list_outputs(self):
                                                     self.inputs.out_name)
         return outputs
 
-    def _normalize_filenames(self):
-        """ Find full paths for pial, thickness and sphere files for copying
+    def normalize_filenames(self):
+        """
+        Filename normalization routine to perform only when run in Node
+        context.
+        Find full paths for pial, thickness and sphere files for copying.
         """
         in_file = self.inputs.in_file
 

nipype/interfaces/fsl/base.py

@@ -107,8 +107,8 @@ def output_type(cls):
         try:
             return os.environ['FSLOUTPUTTYPE']
         except KeyError:
-            IFLOGGER.warn('FSLOUTPUTTYPE environment variable is not set. '
-                          'Setting FSLOUTPUTTYPE=NIFTI')
+            IFLOGGER.warning('FSLOUTPUTTYPE environment variable is not set. '
+                             'Setting FSLOUTPUTTYPE=NIFTI')
             return 'NIFTI'
 
     @staticmethod

nipype/interfaces/mrtrix3/base.py

@@ -77,7 +77,7 @@ def _format_arg(self, name, trait_spec, value):
                 from multiprocessing import cpu_count
                 value = cpu_count()
             except:
-                iflogger.warn('Number of threads could not be computed')
+                iflogger.warning('Number of threads could not be computed')
                 pass
             return trait_spec.argstr % value
 

nipype/pipeline/engine/nodes.py

@@ -32,6 +32,8 @@
 from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined,
                                 DynamicTraitedSpec, Bunch, InterfaceResult,
                                 Interface, isdefined)
+from ...interfaces.base.specs import get_filecopy_info
+
 from .utils import (
     _parameterization_dir, save_hashfile as _save_hashfile, load_resultfile as
     _load_resultfile, save_resultfile as _save_resultfile, nodelist_runner as
@@ -656,7 +658,8 @@ def _run_command(self, execute, copyfiles=True):
 
     def _copyfiles_to_wd(self, execute=True, linksonly=False):
         """copy files over and change the inputs"""
-        if not hasattr(self._interface, '_get_filecopy_info'):
+        filecopy_info = get_filecopy_info(self.interface)
+        if not filecopy_info:
             # Nothing to be done
             return
 
@@ -669,7 +672,7 @@ def _copyfiles_to_wd(self, execute=True, linksonly=False):
             outdir = op.join(outdir, '_tempinput')
             makedirs(outdir, exist_ok=True)
 
-        for info in self._interface._get_filecopy_info():
+        for info in filecopy_info:
             files = self.inputs.trait_get().get(info['key'])
             if not isdefined(files) or not files:
                 continue

nipype/pipeline/engine/utils.py

@@ -304,13 +304,15 @@ def save_resultfile(result, cwd, name):
             tosave = _uncollapse(outputs.copy(), collapsed)
         except AttributeError:
             tosave = outputs = result.outputs.dictcopy()  # outputs was a bunch
-        result.outputs.set(**modify_paths(tosave, relative=True, basedir=cwd))
+        for k, v in list(modify_paths(tosave, relative=True, basedir=cwd).items()):
+            setattr(result.outputs, k, v)
 
     savepkl(resultsfile, result)
     logger.debug('saved results in %s', resultsfile)
 
     if result.outputs:
-        result.outputs.set(**outputs)
+        for k, v in list(outputs.items()):
+            setattr(result.outputs, k, v)
 
 
 def load_resultfile(path, name):
@@ -360,8 +362,9 @@ def load_resultfile(path, name):
                 except AttributeError:
                     outputs = result.outputs.dictcopy()  # outputs == Bunch
                 try:
-                    result.outputs.set(
-                        **modify_paths(outputs, relative=False, basedir=path))
+                    for k, v in list(modify_paths(outputs, relative=False,
+                                                  basedir=path).items()):
+                        setattr(result.outputs, k, v)
                 except FileNotFoundError:
                     logger.debug('conversion to full path results in '
                                  'non existent file')

nipype/pipeline/engine/workflows.py

@@ -566,6 +566,8 @@ def run(self, plugin=None, plugin_args=None, updatehash=False):
             plugin = config.get('execution', 'plugin')
         if not isinstance(plugin, (str, bytes)):
             runner = plugin
+            plugin = runner.__class__.__name__[:-len('Plugin')]
+            plugin_args = runner.plugin_args
         else:
             name = '.'.join(__name__.split('.')[:-2] + ['plugins'])
             try:

nipype/pkg_info.py

@@ -51,7 +51,10 @@ def pkg_commit_hash(pkg_path):
         raise IOError('Missing commit info file %s' % pth)
     cfg_parser = configparser.RawConfigParser()
     with open(pth, encoding='utf-8') as fp:
-        cfg_parser.readfp(fp)
+        if sys.version_info >= (3, 2):
+            cfg_parser.read_file(fp)
+        else:
+            cfg_parser.readfp(fp)
     archive_subst = cfg_parser.get('commit hash', 'archive_subst_hash')
     if not archive_subst.startswith('$Format'):  # it has been substituted
         return 'archive substitution', archive_subst

nipype/utils/filemanip.py

@@ -471,7 +471,7 @@ def copyfile(originalfile,
             fmlogger.debug('Copying File: %s->%s', newfile, originalfile)
             shutil.copyfile(originalfile, newfile)
         except shutil.Error as e:
-            fmlogger.warn(e.message)
+            fmlogger.warning(e.message)
 
     # Associated files
     if copy_related_files: