Merge pull request #2387 from djarecka/interfaces_base_2320

changes in Interfaces base (closes #2320)

Author: effigies

nipype/interfaces/base/core.py

@@ -412,8 +412,12 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
                         raise Exception(
                             'Trait %s (%s) (version %s < required %s)' %
                             (name, self.__class__.__name__, version, min_ver))
-            check = dict(max_ver=lambda t: t is not None)
-            names = trait_object.trait_names(**check)
+
+        # check maximum version
+        check = dict(max_ver=lambda t: t is not None)
+        names = trait_object.trait_names(**check)
+        if names and self.version:
+            version = LooseVersion(str(self.version))
             for name in names:
                 max_ver = LooseVersion(
                     str(trait_object.traits()[name].max_ver))

nipype/interfaces/base/specs.py

@@ -119,20 +119,6 @@ def _xor_warn(self, obj, name, old, new):
                            'which is already set') % (name, trait_name)
                     raise IOError(msg)
 
-    def _requires_warn(self, obj, name, old, new):
-        """Part of the xor behavior
-        """
-        if isdefined(new):
-            trait_spec = self.traits()[name]
-            msg = None
-            for trait_name in trait_spec.requires:
-                if not isdefined(getattr(self, trait_name)):
-                    if not msg:
-                        msg = 'Input %s requires inputs: %s' \
-                            % (name, ', '.join(trait_spec.requires))
-            if msg:  # only one requires warning at a time.
-                warn(msg)
-
     def _deprecated_warn(self, obj, name, old, new):
         """Checks if a user assigns a value to a deprecated trait
         """
@@ -165,29 +151,6 @@ def _deprecated_warn(self, obj, name, old, new):
                             '%s' % trait_spec.new_name: new
                         })
 
-    def _hash_infile(self, adict, key):
-        """ Inject file hashes into adict[key]"""
-        stuff = adict[key]
-        if not is_container(stuff):
-            stuff = [stuff]
-        file_list = []
-        for afile in stuff:
-            if is_container(afile):
-                hashlist = self._hash_infile({'infiles': afile}, 'infiles')
-                hash = [val[1] for val in hashlist]
-            else:
-                if config.get('execution',
-                              'hash_method').lower() == 'timestamp':
-                    hash = hash_timestamp(afile)
-                elif config.get('execution',
-                                'hash_method').lower() == 'content':
-                    hash = hash_infile(afile)
-                else:
-                    raise Exception("Unknown hash method: %s" % config.get(
-                        'execution', 'hash_method'))
-            file_list.append((afile, hash))
-        return file_list
-
     def get(self, **kwargs):
         """ Returns traited class as a dict
 

nipype/interfaces/base/support.py

@@ -168,10 +168,8 @@ def _get_bunch_hash(self):
         sorted_dict = to_str(sorted(dict_nofilename.items()))
         return dict_withhash, md5(sorted_dict.encode()).hexdigest()
 
-    def __pretty__(self, p, cycle):
-        """Support for the pretty module
-
-        pretty is included in ipython.externals for ipython > 0.10"""
+    def _repr_pretty_(self, p, cycle):
+        """Support for the pretty module from ipython.externals"""
         if cycle:
             p.text('Bunch(...)')
         else:

nipype/interfaces/base/tests/test_core.py

@@ -177,74 +177,76 @@ def __init__(self, **inputs):
     assert 'ec5755e07287e04a4b409e03b77a517c' == hashvalue
 
 
-def test_input_version():
-    class InputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int', min_ver='0.9')
+class MinVerInputSpec(nib.TraitedSpec):
+    foo = nib.traits.Int(desc='a random int', min_ver='0.9')
+
+class MaxVerInputSpec(nib.TraitedSpec):
+    foo = nib.traits.Int(desc='a random int', max_ver='0.7')
 
+
+def test_input_version_1():
     class DerivedInterface1(nib.BaseInterface):
-        input_spec = InputSpec
+        input_spec = MinVerInputSpec
 
     obj = DerivedInterface1()
     obj._check_version_requirements(obj.inputs)
 
     config.set('execution', 'stop_on_unknown_version', True)
 
-    with pytest.raises(Exception):
+    with pytest.raises(ValueError) as excinfo:
         obj._check_version_requirements(obj.inputs)
+    assert "no version information" in str(excinfo.value)
 
     config.set_default_config()
 
-    class InputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int', min_ver='0.9')
 
+def test_input_version_2():
     class DerivedInterface1(nib.BaseInterface):
-        input_spec = InputSpec
+        input_spec = MinVerInputSpec
         _version = '0.8'
 
     obj = DerivedInterface1()
     obj.inputs.foo = 1
-    with pytest.raises(Exception):
-        obj._check_version_requirements()
+    with pytest.raises(Exception) as excinfo:
+        obj._check_version_requirements(obj.inputs)
+    assert "version 0.8 < required 0.9" in str(excinfo.value)
 
-    class InputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int', min_ver='0.9')
 
+def test_input_version_3():
     class DerivedInterface1(nib.BaseInterface):
-        input_spec = InputSpec
+        input_spec = MinVerInputSpec
         _version = '0.10'
 
     obj = DerivedInterface1()
     obj._check_version_requirements(obj.inputs)
 
-    class InputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int', min_ver='0.9')
 
+def test_input_version_4():
     class DerivedInterface1(nib.BaseInterface):
-        input_spec = InputSpec
+        input_spec = MinVerInputSpec
         _version = '0.9'
 
     obj = DerivedInterface1()
     obj.inputs.foo = 1
     obj._check_version_requirements(obj.inputs)
 
-    class InputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int', max_ver='0.7')
 
+def test_input_version_5():
     class DerivedInterface2(nib.BaseInterface):
-        input_spec = InputSpec
+        input_spec = MaxVerInputSpec
         _version = '0.8'
 
     obj = DerivedInterface2()
     obj.inputs.foo = 1
-    with pytest.raises(Exception):
-        obj._check_version_requirements()
+    with pytest.raises(Exception) as excinfo:
+        obj._check_version_requirements(obj.inputs)
+    assert "version 0.8 > required 0.7" in str(excinfo.value)
 
-    class InputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int', max_ver='0.9')
 
+def test_input_version_6():
     class DerivedInterface1(nib.BaseInterface):
-        input_spec = InputSpec
-        _version = '0.9'
+        input_spec = MaxVerInputSpec
+        _version = '0.7'
 
     obj = DerivedInterface1()
     obj.inputs.foo = 1

nipype/interfaces/base/traits_extension.py

@@ -54,7 +54,7 @@ class Str(Unicode):
 traits.DictStrStr = DictStrStr
 
 
-class BaseFile(BaseUnicode):
+class File(BaseUnicode):
     """ Defines a trait whose value must be the name of a file.
     """
 
@@ -96,14 +96,11 @@ def __init__(self,
         if exists:
             self.info_text = 'an existing file name'
 
-        super(BaseFile, self).__init__(value, **metadata)
+        super(File, self).__init__(value, **metadata)
 
     def validate(self, object, name, value):
-        """ Validates that a specified value is valid for this trait.
-
-            Note: The 'fast validator' version performs this check in C.
-        """
-        validated_value = super(BaseFile, self).validate(object, name, value)
+        """ Validates that a specified value is valid for this trait."""
+        validated_value = super(File, self).validate(object, name, value)
         if not self.exists:
             return validated_value
         elif os.path.isfile(value):
@@ -117,53 +114,12 @@ def validate(self, object, name, value):
         self.error(object, name, value)
 
 
-class File(BaseFile):
-    """
-    Defines a trait whose value must be the name of a file.
-    Disables the default C-level fast validator.
-    """
-
-    def __init__(self,
-                 value='',
-                 filter=None,
-                 auto_set=False,
-                 entries=0,
-                 exists=False,
-                 **metadata):
-        """ Creates a File trait.
-
-        Parameters
-        ----------
-        value : string
-            The default value for the trait
-        filter : string
-            A wildcard string to filter filenames in the file dialog box used by
-            the attribute trait editor.
-        auto_set : boolean
-            Indicates whether the file editor updates the trait value after
-            every key stroke.
-        exists : boolean
-            Indicates whether the trait value must be an existing file or
-            not.
-
-        Default Value
-        -------------
-        *value* or ''
-        """
-        # if not exists:
-        #     # Define the C-level fast validator to use:
-        #     fast_validate = (11, str)
-
-        super(File, self).__init__(value, filter, auto_set, entries, exists,
-                                   **metadata)
-
-
 # -------------------------------------------------------------------------------
-#  'BaseDirectory' and 'Directory' traits:
+#  'Directory' trait
 # -------------------------------------------------------------------------------
 
 
-class BaseDirectory(BaseUnicode):
+class Directory(BaseUnicode):
     """
     Defines a trait whose value must be the name of a directory.
     """
@@ -177,7 +133,7 @@ def __init__(self,
                  entries=0,
                  exists=False,
                  **metadata):
-        """ Creates a BaseDirectory trait.
+        """ Creates a Directory trait.
 
         Parameters
         ----------
@@ -201,13 +157,10 @@ def __init__(self,
         if exists:
             self.info_text = 'an existing directory name'
 
-        super(BaseDirectory, self).__init__(value, **metadata)
+        super(Directory, self).__init__(value, **metadata)
 
     def validate(self, object, name, value):
-        """ Validates that a specified value is valid for this trait.
-
-            Note: The 'fast validator' version performs this check in C.
-        """
+        """ Validates that a specified value is valid for this trait."""
         if isinstance(value, (str, bytes)):
             if not self.exists:
                 return value
@@ -222,44 +175,6 @@ def validate(self, object, name, value):
         self.error(object, name, value)
 
 
-class Directory(BaseDirectory):
-    """
-    Defines a trait whose value must be the name of a directory.
-    Disables the default C-level fast validator.
-    """
-
-    def __init__(self,
-                 value='',
-                 auto_set=False,
-                 entries=0,
-                 exists=False,
-                 **metadata):
-        """ Creates a Directory trait.
-
-        Parameters
-        ----------
-        value : string
-            The default value for the trait
-        auto_set : boolean
-            Indicates whether the directory editor updates the trait value
-            after every key stroke.
-        exists : boolean
-            Indicates whether the trait value must be an existing directory or
-            not.
-
-        Default Value
-        -------------
-        *value* or ''
-        """
-        # Define the C-level fast validator to use if the directory existence
-        # test is not required:
-        # if not exists:
-        #     self.fast_validate = (11, str)
-
-        super(Directory, self).__init__(value, auto_set, entries, exists,
-                                        **metadata)
-
-
 # lists of tuples
 # each element consists of :
 # - uncompressed (tuple[0]) extension

nipype/pipeline/engine/utils.py

@@ -1158,9 +1158,6 @@ def _standardize_iterables(node):
     iterables = node.iterables
     # The candidate iterable fields
     fields = set(node.inputs.copyable_trait_names())
-    # Flag indicating whether the iterables are in the alternate
-    # synchronize form and are not converted to a standard format.
-    # synchronize = False  # OE: commented out since it is not used
     # A synchronize iterables node without an itersource can be in
     # [fields, value tuples] format rather than
     # [(field, value list), (field, value list), ...]

nipype/utils/misc.py

@@ -285,7 +285,6 @@ def dict_diff(dold, dnew, indent=0):
     # Values in common keys would differ quite often,
     # so we need to join the messages together
     for k in new_keys.intersection(old_keys):
-        same = False
         try:
             new, old = dnew[k], dold[k]
             same = new == old