From 7cb203825af13de69d2f15444e8b74ae1dffaaf0 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sat, 24 Nov 2018 20:44:28 -0800
Subject: [PATCH 01/20] [MAINT] Outsource checks of inputs from interface

Another PR removing stuff from the interface class definition.
---
 nipype/interfaces/base/core.py             | 59 +++--------------
 nipype/interfaces/base/specs.py            | 65 ++++++++++++++++++-
 nipype/interfaces/base/tests/test_core.py  |  5 --
 nipype/interfaces/base/tests/test_specs.py | 74 ++++++++++++++++++++--
 nipype/interfaces/freesurfer/preprocess.py |  8 ++-
 nipype/utils/errors.py                     | 60 ++++++++++++++++++
 6 files changed, 208 insertions(+), 63 deletions(-)
 create mode 100644 nipype/utils/errors.py

diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
index 40efa1f33a..06ef43c7cf 100644
--- a/nipype/interfaces/base/core.py
+++ b/nipype/interfaces/base/core.py
@@ -40,7 +40,8 @@
 
 from .traits_extension import traits, isdefined, TraitError
 from .specs import (BaseInterfaceInputSpec, CommandLineInputSpec,
-                    StdOutCommandLineInputSpec, MpiCommandLineInputSpec)
+                    StdOutCommandLineInputSpec, MpiCommandLineInputSpec,
+                    check_mandatory_inputs)
 from .support import (Bunch, InterfaceResult, NipypeInterfaceError)
 
 from future import standard_library
@@ -343,53 +344,6 @@ def _get_filecopy_info(cls):
             info.append(dict(key=name, copy=spec.copyfile))
         return info
 
-    def _check_requires(self, spec, name, value):
-        """ check if required inputs are satisfied
-        """
-        if spec.requires:
-            values = [
-                not isdefined(getattr(self.inputs, field))
-                for field in spec.requires
-            ]
-            if any(values) and isdefined(value):
-                msg = ("%s requires a value for input '%s' because one of %s "
-                       "is set. For a list of required inputs, see %s.help()" %
-                       (self.__class__.__name__, name,
-                        ', '.join(spec.requires), self.__class__.__name__))
-                raise ValueError(msg)
-
-    def _check_xor(self, spec, name, value):
-        """ check if mutually exclusive inputs are satisfied
-        """
-        if spec.xor:
-            values = [
-                isdefined(getattr(self.inputs, field)) for field in spec.xor
-            ]
-            if not any(values) and not isdefined(value):
-                msg = ("%s requires a value for one of the inputs '%s'. "
-                       "For a list of required inputs, see %s.help()" %
-                       (self.__class__.__name__, ', '.join(spec.xor),
-                        self.__class__.__name__))
-                raise ValueError(msg)
-
-    def _check_mandatory_inputs(self):
-        """ Raises an exception if a mandatory input is Undefined
-        """
-        for name, spec in list(self.inputs.traits(mandatory=True).items()):
-            value = getattr(self.inputs, name)
-            self._check_xor(spec, name, value)
-            if not isdefined(value) and spec.xor is None:
-                msg = ("%s requires a value for input '%s'. "
-                       "For a list of required inputs, see %s.help()" %
-                       (self.__class__.__name__, name,
-                        self.__class__.__name__))
-                raise ValueError(msg)
-            if isdefined(value):
-                self._check_requires(spec, name, value)
-        for name, spec in list(
-                self.inputs.traits(mandatory=None, transient=None).items()):
-            self._check_requires(spec, name, getattr(self.inputs, name))
-
     def _check_version_requirements(self, trait_object, raise_exception=True):
         """ Raises an exception on version mismatch
         """
@@ -474,7 +428,7 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
 
         enable_rm = config.resource_monitor and self.resource_monitor
         self.inputs.trait_set(**inputs)
-        self._check_mandatory_inputs()
+        check_mandatory_inputs(self.inputs)
         self._check_version_requirements(self.inputs)
         interface = self.__class__
         self._duecredit_cite()
@@ -818,7 +772,12 @@ def cmd(self):
     def cmdline(self):
         """ `command` plus any arguments (args)
         validates arguments and generates command line"""
-        self._check_mandatory_inputs()
+        if not check_mandatory_inputs(self.inputs, raise_exc=False):
+            iflogger.warning(
+                'Some inputs are not valid. Please make sure all mandatory '
+                'inputs, required inputs and mutually-exclusive inputs are '
+                'set or in a sane state.')
+
         allargs = [self._cmd_prefix + self.cmd] + self._parse_inputs()
         return ' '.join(allargs)
 
diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index f02d5bd709..23beca98c0 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -19,6 +19,8 @@
 from packaging.version import Version
 
 from ...utils.filemanip import md5, hash_infile, hash_timestamp, to_str
+from ...utils.errors import (
+    MandatoryInputError, MutuallyExclusiveInputError, RequiredInputError)
 from .traits_extension import (
     traits,
     Undefined,
@@ -114,9 +116,8 @@ def _xor_warn(self, obj, name, old, new):
                         trait_change_notify=False, **{
                             '%s' % name: Undefined
                         })
-                    msg = ('Input "%s" is mutually exclusive with input "%s", '
-                           'which is already set') % (name, trait_name)
-                    raise IOError(msg)
+                    raise MutuallyExclusiveInputError(
+                        self, name, name_other=trait_name)
 
     def _deprecated_warn(self, obj, name, old, new):
         """Checks if a user assigns a value to a deprecated trait
@@ -375,3 +376,61 @@ 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 check_requires(inputs, spec, value):
+    """check if required inputs are satisfied
+    """
+    if not spec.requires:
+        return True
+
+    # Check value and all required inputs' values defined
+    values = [isdefined(value)] + [
+        isdefined(getattr(inputs, field))
+        for field in spec.requires]
+    return all(values)
+
+def check_xor(inputs, spec, value):
+    """ check if mutually exclusive inputs are satisfied
+    """
+    if not spec.xor:
+        return True
+
+    print(inputs)
+    values = [isdefined(value)] + [
+        isdefined(getattr(inputs, field)) for field in spec.xor]
+    return sum(values)
+
+def check_mandatory_inputs(inputs, raise_exc=True):
+    """ Raises an exception if a mandatory input is Undefined
+    """
+    # Check mandatory, not xor-ed inputs.
+    for name, spec in list(inputs.traits(mandatory=True).items()):
+        value = getattr(inputs, name)
+        # Mandatory field is defined, check xor'ed inputs
+        cxor = check_xor(inputs, spec, value)
+        if cxor != 1:
+            if raise_exc:
+                raise MutuallyExclusiveInputError(inputs, name, cxor)
+            return False
+
+        # Simplest case: no xor metadata and not defined
+        if cxor is True and not isdefined(value):
+            if raise_exc:
+                raise MandatoryInputError(inputs, name)
+            return False
+
+        # Check whether mandatory inputs require others
+        if not check_requires(inputs, spec, value):
+            if raise_exc:
+                raise RequiredInputError(inputs, name)
+            return False
+
+    # Check requirements of non-mandatory inputs
+    for name, spec in list(
+            inputs.traits(mandatory=None, transient=None).items()):
+        if not check_requires(inputs, spec, getattr(inputs, name)):
+            if raise_exc:
+                raise RequiredInputError(inputs, name)
+
+    return True
diff --git a/nipype/interfaces/base/tests/test_core.py b/nipype/interfaces/base/tests/test_core.py
index 392d38706f..19c82f34a0 100644
--- a/nipype/interfaces/base/tests/test_core.py
+++ b/nipype/interfaces/base/tests/test_core.py
@@ -95,11 +95,6 @@ class DerivedInterface(nib.BaseInterface):
     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()
-    assert DerivedInterface(goo=1)._check_mandatory_inputs() is None
-    with pytest.raises(ValueError):
-        DerivedInterface().run()
     with pytest.raises(NotImplementedError):
         DerivedInterface(goo=1).run()
 
diff --git a/nipype/interfaces/base/tests/test_specs.py b/nipype/interfaces/base/tests/test_specs.py
index f08fa68adf..4bf2dbd534 100644
--- a/nipype/interfaces/base/tests/test_specs.py
+++ b/nipype/interfaces/base/tests/test_specs.py
@@ -2,15 +2,18 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from __future__ import print_function, unicode_literals
-from future import standard_library
 import os
 import warnings
-
 import pytest
+from future import standard_library
 
 from ....utils.filemanip import split_filename
 from ... import base as nib
 from ...base import traits, Undefined
+from ..specs import (
+    check_mandatory_inputs, MandatoryInputError,
+    MutuallyExclusiveInputError, RequiredInputError
+)
 from ....interfaces import fsl
 from ...utility.wrappers import Function
 from ....pipeline import Node
@@ -55,8 +58,8 @@ 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 +436,66 @@ def test_ImageFile():
     with pytest.raises(nib.TraitError):
         x.nocompress = 'test.nii.gz'
     x.nocompress = 'test.mgh'
+
+
+def test_inputs_checks():
+
+    class InputSpec(nib.TraitedSpec):
+        goo = nib.traits.Int(desc='a random int', mandatory=True)
+
+    class DerivedInterface(nib.BaseInterface):
+        input_spec = InputSpec
+        resource_monitor = False
+
+    assert check_mandatory_inputs(
+        DerivedInterface(goo=1).inputs)
+    with pytest.raises(MandatoryInputError):
+        check_mandatory_inputs(
+            DerivedInterface().inputs)
+    with pytest.raises(MandatoryInputError):
+        DerivedInterface().run()
+
+    class InputSpec(nib.TraitedSpec):
+        goo = nib.traits.Int(desc='a random int', mandatory=True,
+                             requires=['woo'])
+        woo = nib.traits.Int(desc='required by goo')
+
+    class DerivedInterface(nib.BaseInterface):
+        input_spec = InputSpec
+        resource_monitor = False
+
+    assert check_mandatory_inputs(
+        DerivedInterface(goo=1, woo=1).inputs)
+    with pytest.raises(RequiredInputError):
+        check_mandatory_inputs(
+            DerivedInterface(goo=1).inputs)
+    with pytest.raises(RequiredInputError):
+        DerivedInterface(goo=1).run()
+
+    class InputSpec(nib.TraitedSpec):
+        goo = nib.traits.Int(desc='a random int', mandatory=True,
+                             xor=['woo'])
+        woo = nib.traits.Int(desc='a random int', mandatory=True,
+                             xor=['goo'])
+
+    class DerivedInterface(nib.BaseInterface):
+        input_spec = InputSpec
+        resource_monitor = False
+
+    # If either goo or woo are set, then okay!
+    assert check_mandatory_inputs(
+        DerivedInterface(goo=1).inputs)
+    assert check_mandatory_inputs(
+        DerivedInterface(woo=1).inputs)
+
+    # None are set, raise MandatoryInputError
+    with pytest.raises(MutuallyExclusiveInputError):
+        check_mandatory_inputs(
+            DerivedInterface().inputs)
+
+    # Both are set, raise MutuallyExclusiveInputError
+    with pytest.raises(MutuallyExclusiveInputError):
+        check_mandatory_inputs(
+            DerivedInterface(goo=1, woo=1).inputs)
+    with pytest.raises(MutuallyExclusiveInputError):
+        DerivedInterface(goo=1, woo=1).run()
diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py
index 2941968f85..b25c7fc6f6 100644
--- a/nipype/interfaces/freesurfer/preprocess.py
+++ b/nipype/interfaces/freesurfer/preprocess.py
@@ -21,6 +21,7 @@
 from ..base import (TraitedSpec, File, traits, Directory, InputMultiPath,
                     OutputMultiPath, CommandLine, CommandLineInputSpec,
                     isdefined)
+from ..base.specs import check_mandatory_inputs
 from .base import (FSCommand, FSTraitedSpec, FSTraitedSpecOpenMP,
                    FSCommandOpenMP, Info)
 from .utils import copy2subjdir
@@ -634,7 +635,12 @@ def _get_filelist(self, outdir):
     def cmdline(self):
         """ `command` plus any arguments (args)
         validates arguments and generates command line"""
-        self._check_mandatory_inputs()
+        if not check_mandatory_inputs(self.inputs, raise_exc=False):
+            iflogger.warning(
+                'Some inputs are not valid. Please make sure all mandatory '
+                'inputs, required inputs and mutually-exclusive inputs are '
+                'set or in a sane state.')
+
         outdir = self._get_outdir()
         cmd = []
         if not os.path.exists(outdir):
diff --git a/nipype/utils/errors.py b/nipype/utils/errors.py
new file mode 100644
index 0000000000..74cf1340c6
--- /dev/null
+++ b/nipype/utils/errors.py
@@ -0,0 +1,60 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Errors and exceptions
+"""
+from __future__ import (print_function, division, unicode_literals,
+                        absolute_import)
+
+
+class MandatoryInputError(ValueError):
+    """Raised when one input with the ``mandatory`` metadata set to ``True`` is
+    not defined."""
+    def __init__(self, inputspec, name):
+        classname = inputspec.__class__.__name__
+        if classname.endswith('InputSpec'):
+            classname = classname[:len('InputSpec')]
+        msg = (
+            'Interface "{classname}" requires a value for input {name}. '
+            'For a list of required inputs, see {classname}.help().').format(
+                classname=classname, name=name)
+        super(MandatoryInputError, self).__init__(msg)
+
+class MutuallyExclusiveInputError(ValueError):
+    """Raised when none or more than one mutually-exclusive inputs are set."""
+    def __init__(self, inputspec, name, values_defined=None, name_other=None):
+        classname = inputspec.__class__.__name__
+        if classname.endswith('InputSpec') and classname != 'InputSpec':
+            classname = classname[:-len('InputSpec')]
+
+        if values_defined:
+            xor = [name]+ inputspec.traits()[name].xor
+            msg = ('Interface "{classname}" has mutually-exclusive inputs. '
+                   'Exactly one of ({xor}) should be set, but {n:d} were set. '
+                   'For a list of mutually-exclusive inputs, see '
+                   '{classname}.help().').format(classname=classname,
+                                                 xor='|'.join(xor),
+                                                 n=values_defined)
+
+        else:
+            msg = ('Interface "{classname}" has mutually-exclusive inputs. '
+                   'Input "{name}" is mutually exclusive with input '
+                   '"{name_other}", which is already set').format(
+                       classname=classname, name=name, name_other=name_other)
+        super(MutuallyExclusiveInputError, self).__init__(msg)
+
+class RequiredInputError(ValueError):
+    """Raised when one input requires some other and those or some of
+    those are ``Undefined``."""
+    def __init__(self, inputspec, name):
+        classname = inputspec.__class__.__name__
+        if classname.endswith('InputSpec'):
+            classname = classname[:-len('InputSpec')]
+        requires = inputspec.traits()[name].requires
+
+        msg = ('Interface "{classname}" requires a value for input {name} '
+               'because one of ({requires}) is set. For a list of required '
+               'inputs, see {classname}.help().').format(
+                    classname=classname, name=name,
+                    requires=', '.join(requires))
+        super(RequiredInputError, self).__init__(msg)

From a15c6fb5e9786f5911f39eccbf56ad7049e0e0f7 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sat, 24 Nov 2018 21:05:50 -0800
Subject: [PATCH 02/20] remove forgotten print

---
 nipype/interfaces/base/specs.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 23beca98c0..107a90672c 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -396,7 +396,6 @@ def check_xor(inputs, spec, value):
     if not spec.xor:
         return True
 
-    print(inputs)
     values = [isdefined(value)] + [
         isdefined(getattr(inputs, field)) for field in spec.xor]
     return sum(values)

From a3600d910ba3487e138dc3a1f0532f4f21e2d005 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sat, 24 Nov 2018 22:49:04 -0800
Subject: [PATCH 03/20] fix mutually-exclusive check

---
 nipype/interfaces/base/specs.py | 23 ++++++++++++-----------
 nipype/utils/errors.py          |  4 ++--
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 107a90672c..1e5bca3494 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -378,26 +378,25 @@ class MpiCommandLineInputSpec(CommandLineInputSpec):
                          "SGE)")
 
 
-def check_requires(inputs, spec, value):
+def check_requires(inputs, requires, value):
     """check if required inputs are satisfied
     """
-    if not spec.requires:
+    if not requires:
         return True
 
     # Check value and all required inputs' values defined
     values = [isdefined(value)] + [
         isdefined(getattr(inputs, field))
-        for field in spec.requires]
+        for field in requires]
     return all(values)
 
-def check_xor(inputs, spec, value):
+def check_xor(inputs, xor):
     """ check if mutually exclusive inputs are satisfied
     """
-    if not spec.xor:
+    if len(xor) == 1:
         return True
 
-    values = [isdefined(value)] + [
-        isdefined(getattr(inputs, field)) for field in spec.xor]
+    values = [isdefined(getattr(inputs, field)) for field in xor]
     return sum(values)
 
 def check_mandatory_inputs(inputs, raise_exc=True):
@@ -407,10 +406,12 @@ def check_mandatory_inputs(inputs, raise_exc=True):
     for name, spec in list(inputs.traits(mandatory=True).items()):
         value = getattr(inputs, name)
         # Mandatory field is defined, check xor'ed inputs
-        cxor = check_xor(inputs, spec, value)
+        xor = list(set([name] + spec.xor))
+        cxor = check_xor(inputs, xor)
         if cxor != 1:
             if raise_exc:
-                raise MutuallyExclusiveInputError(inputs, name, cxor)
+                raise MutuallyExclusiveInputError(
+                    inputs, name, values_defined=cxor)
             return False
 
         # Simplest case: no xor metadata and not defined
@@ -420,7 +421,7 @@ def check_mandatory_inputs(inputs, raise_exc=True):
             return False
 
         # Check whether mandatory inputs require others
-        if not check_requires(inputs, spec, value):
+        if not check_requires(inputs, spec.requires, value):
             if raise_exc:
                 raise RequiredInputError(inputs, name)
             return False
@@ -428,7 +429,7 @@ def check_mandatory_inputs(inputs, raise_exc=True):
     # Check requirements of non-mandatory inputs
     for name, spec in list(
             inputs.traits(mandatory=None, transient=None).items()):
-        if not check_requires(inputs, spec, getattr(inputs, name)):
+        if not check_requires(inputs, spec.requires, getattr(inputs, name)):
             if raise_exc:
                 raise RequiredInputError(inputs, name)
 
diff --git a/nipype/utils/errors.py b/nipype/utils/errors.py
index 74cf1340c6..a55f3179f2 100644
--- a/nipype/utils/errors.py
+++ b/nipype/utils/errors.py
@@ -27,8 +27,8 @@ def __init__(self, inputspec, name, values_defined=None, name_other=None):
         if classname.endswith('InputSpec') and classname != 'InputSpec':
             classname = classname[:-len('InputSpec')]
 
-        if values_defined:
-            xor = [name]+ inputspec.traits()[name].xor
+        if values_defined is not None:
+            xor = list(set([name]+ inputspec.traits()[name].xor))
             msg = ('Interface "{classname}" has mutually-exclusive inputs. '
                    'Exactly one of ({xor}) should be set, but {n:d} were set. '
                    'For a list of mutually-exclusive inputs, see '

From c095d65e867415341883fbcf77cc3243a20232fa Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sat, 24 Nov 2018 23:19:49 -0800
Subject: [PATCH 04/20] fix bug trying to append a spec.xor that is None

---
 nipype/interfaces/base/specs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 1e5bca3494..dc476965c5 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -406,7 +406,7 @@ def check_mandatory_inputs(inputs, raise_exc=True):
     for name, spec in list(inputs.traits(mandatory=True).items()):
         value = getattr(inputs, name)
         # Mandatory field is defined, check xor'ed inputs
-        xor = list(set([name] + spec.xor))
+        xor = list(set([name] + spec.xor or []))
         cxor = check_xor(inputs, xor)
         if cxor != 1:
             if raise_exc:

From 61d553c42c24bc27b0977cabccabccec84b2b92c Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sat, 24 Nov 2018 23:45:40 -0800
Subject: [PATCH 05/20] fix precedence

---
 nipype/interfaces/base/specs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index dc476965c5..a62cdec437 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -406,7 +406,7 @@ def check_mandatory_inputs(inputs, raise_exc=True):
     for name, spec in list(inputs.traits(mandatory=True).items()):
         value = getattr(inputs, name)
         # Mandatory field is defined, check xor'ed inputs
-        xor = list(set([name] + spec.xor or []))
+        xor = list(set([name] + (spec.xor or [])))
         cxor = check_xor(inputs, xor)
         if cxor != 1:
             if raise_exc:

From 1ade70c18b0b033a2fc9216a018cea38549846ea Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 00:42:48 -0800
Subject: [PATCH 06/20] outsource ``_check_version_requirements``

---
 nipype/interfaces/base/core.py             |  50 +-------
 nipype/interfaces/base/specs.py            |  51 ++++++++-
 nipype/interfaces/base/tests/test_core.py  | 127 +--------------------
 nipype/interfaces/base/tests/test_specs.py |  90 ++++++++++++++-
 nipype/utils/errors.py                     |  28 ++++-
 5 files changed, 171 insertions(+), 175 deletions(-)

diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
index 06ef43c7cf..dcc4580191 100644
--- a/nipype/interfaces/base/core.py
+++ b/nipype/interfaces/base/core.py
@@ -29,7 +29,7 @@
 import simplejson as json
 from dateutil.parser import parse as parseutc
 
-from ... import config, logging, LooseVersion
+from ... import config, logging
 from ...utils.provenance import write_provenance
 from ...utils.misc import trim, str2bool, rgetcwd
 from ...utils.filemanip import (FileNotFoundError, split_filename,
@@ -41,7 +41,7 @@
 from .traits_extension import traits, isdefined, TraitError
 from .specs import (BaseInterfaceInputSpec, CommandLineInputSpec,
                     StdOutCommandLineInputSpec, MpiCommandLineInputSpec,
-                    check_mandatory_inputs)
+                    check_mandatory_inputs, check_version)
 from .support import (Bunch, InterfaceResult, NipypeInterfaceError)
 
 from future import standard_library
@@ -344,46 +344,6 @@ def _get_filecopy_info(cls):
             info.append(dict(key=name, copy=spec.copyfile))
         return info
 
-    def _check_version_requirements(self, trait_object, raise_exception=True):
-        """ Raises an exception on version mismatch
-        """
-        unavailable_traits = []
-        # check minimum version
-        check = dict(min_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:
-                min_ver = LooseVersion(
-                    str(trait_object.traits()[name].min_ver))
-                if min_ver > version:
-                    unavailable_traits.append(name)
-                    if not isdefined(getattr(trait_object, name)):
-                        continue
-                    if raise_exception:
-                        raise Exception(
-                            'Trait %s (%s) (version %s < required %s)' %
-                            (name, self.__class__.__name__, version, min_ver))
-
-        # 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))
-                if max_ver < version:
-                    unavailable_traits.append(name)
-                    if not isdefined(getattr(trait_object, name)):
-                        continue
-                    if raise_exception:
-                        raise Exception(
-                            'Trait %s (%s) (version %s > required %s)' %
-                            (name, self.__class__.__name__, version, max_ver))
-        return unavailable_traits
-
     def _run_interface(self, runtime):
         """ Core function that executes interface
         """
@@ -429,7 +389,7 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
         enable_rm = config.resource_monitor and self.resource_monitor
         self.inputs.trait_set(**inputs)
         check_mandatory_inputs(self.inputs)
-        self._check_version_requirements(self.inputs)
+        check_version(self.inputs, version=self.version)
         interface = self.__class__
         self._duecredit_cite()
 
@@ -555,8 +515,8 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
         if predicted_outputs:
             _unavailable_outputs = []
             if outputs:
-                _unavailable_outputs = \
-                    self._check_version_requirements(self._outputs())
+                _unavailable_outputs = check_version(
+                    self._outputs(), self.version)
             for key, val in list(predicted_outputs.items()):
                 if needed_outputs and key not in needed_outputs:
                     continue
diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index a62cdec437..c6e860ff51 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -20,7 +20,8 @@
 
 from ...utils.filemanip import md5, hash_infile, hash_timestamp, to_str
 from ...utils.errors import (
-    MandatoryInputError, MutuallyExclusiveInputError, RequiredInputError)
+    MandatoryInputError, MutuallyExclusiveInputError, RequiredInputError,
+    VersionIOError)
 from .traits_extension import (
     traits,
     Undefined,
@@ -434,3 +435,51 @@ def check_mandatory_inputs(inputs, raise_exc=True):
                 raise RequiredInputError(inputs, name)
 
     return True
+
+def check_version(traited_spec, version=None, raise_exc=True):
+    """ Raises an exception on version mismatch
+    """
+
+    # no version passed on to check against
+    if not version:
+        return []
+
+    # check minimum version
+    names = traited_spec.trait_names(
+        min_ver=lambda t: t is not None) + \
+        traited_spec.trait_names(
+        max_ver=lambda t: t is not None)
+
+    # no traits defined any versions
+    if not names:
+        return []
+
+    version = Version(str(version))
+    unavailable_traits = []
+    for name in names:
+        value_set = isdefined(getattr(traited_spec, name))
+        min_ver = traited_spec.traits()[name].min_ver
+        if min_ver:
+            min_ver = Version(str(min_ver))
+
+        max_ver = traited_spec.traits()[name].max_ver
+        if max_ver:
+            max_ver = Version(str(max_ver))
+
+        if min_ver and max_ver:
+            if max_ver < min_ver:
+                raise AssertionError(
+                    'Trait "%s" (%s) has incongruent version metadata '
+                    '(``max_ver`` is lower than ``min_ver``).' % (
+                        traited_spec.__class__.__name__, name))
+
+        if min_ver and (min_ver > version):
+            unavailable_traits.append(name)
+            if value_set and raise_exc:
+                raise VersionIOError(traited_spec, name, version)
+        if max_ver and (max_ver < version):
+            unavailable_traits.append(name)
+            if value_set and raise_exc:
+                raise VersionIOError(traited_spec, name, version)
+
+    return list(set(unavailable_traits))
diff --git a/nipype/interfaces/base/tests/test_core.py b/nipype/interfaces/base/tests/test_core.py
index 19c82f34a0..cba88be0a5 100644
--- a/nipype/interfaces/base/tests/test_core.py
+++ b/nipype/interfaces/base/tests/test_core.py
@@ -172,136 +172,15 @@ def __init__(self, **inputs):
     assert '8562a5623562a871115eb14822ee8d02' == hashvalue
 
 
-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 = MinVerInputSpec
-
-    obj = DerivedInterface1()
-    obj._check_version_requirements(obj.inputs)
-
+def test_stop_on_unknown_version():
     config.set('execution', 'stop_on_unknown_version', True)
 
+    ci = nib.CommandLine(command='which')
     with pytest.raises(ValueError) as excinfo:
-        obj._check_version_requirements(obj.inputs)
+        _ = ci.version
     assert "no version information" in str(excinfo.value)
-
     config.set_default_config()
 
-
-def test_input_version_2():
-    class DerivedInterface1(nib.BaseInterface):
-        input_spec = MinVerInputSpec
-        _version = '0.8'
-
-    obj = DerivedInterface1()
-    obj.inputs.foo = 1
-    with pytest.raises(Exception) as excinfo:
-        obj._check_version_requirements(obj.inputs)
-    assert "version 0.8 < required 0.9" in str(excinfo.value)
-
-
-def test_input_version_3():
-    class DerivedInterface1(nib.BaseInterface):
-        input_spec = MinVerInputSpec
-        _version = '0.10'
-
-    obj = DerivedInterface1()
-    obj._check_version_requirements(obj.inputs)
-
-
-def test_input_version_4():
-    class DerivedInterface1(nib.BaseInterface):
-        input_spec = MinVerInputSpec
-        _version = '0.9'
-
-    obj = DerivedInterface1()
-    obj.inputs.foo = 1
-    obj._check_version_requirements(obj.inputs)
-
-
-def test_input_version_5():
-    class DerivedInterface2(nib.BaseInterface):
-        input_spec = MaxVerInputSpec
-        _version = '0.8'
-
-    obj = DerivedInterface2()
-    obj.inputs.foo = 1
-    with pytest.raises(Exception) as excinfo:
-        obj._check_version_requirements(obj.inputs)
-    assert "version 0.8 > required 0.7" in str(excinfo.value)
-
-
-def test_input_version_6():
-    class DerivedInterface1(nib.BaseInterface):
-        input_spec = MaxVerInputSpec
-        _version = '0.7'
-
-    obj = DerivedInterface1()
-    obj.inputs.foo = 1
-    obj._check_version_requirements(obj.inputs)
-
-
-def test_output_version():
-    class InputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int')
-
-    class OutputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int', min_ver='0.9')
-
-    class DerivedInterface1(nib.BaseInterface):
-        input_spec = InputSpec
-        output_spec = OutputSpec
-        _version = '0.10'
-        resource_monitor = False
-
-    obj = DerivedInterface1()
-    assert obj._check_version_requirements(obj._outputs()) == []
-
-    class InputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int')
-
-    class OutputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int', min_ver='0.11')
-
-    class DerivedInterface1(nib.BaseInterface):
-        input_spec = InputSpec
-        output_spec = OutputSpec
-        _version = '0.10'
-        resource_monitor = False
-
-    obj = DerivedInterface1()
-    assert obj._check_version_requirements(obj._outputs()) == ['foo']
-
-    class InputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int')
-
-    class OutputSpec(nib.TraitedSpec):
-        foo = nib.traits.Int(desc='a random int', min_ver='0.11')
-
-    class DerivedInterface1(nib.BaseInterface):
-        input_spec = InputSpec
-        output_spec = OutputSpec
-        _version = '0.10'
-        resource_monitor = False
-
-        def _run_interface(self, runtime):
-            return runtime
-
-        def _list_outputs(self):
-            return {'foo': 1}
-
-    obj = DerivedInterface1()
-    with pytest.raises(KeyError):
-        obj.run()
-
-
 def test_Commandline():
     with pytest.raises(Exception):
         nib.CommandLine()
diff --git a/nipype/interfaces/base/tests/test_specs.py b/nipype/interfaces/base/tests/test_specs.py
index 4bf2dbd534..9e3fba03de 100644
--- a/nipype/interfaces/base/tests/test_specs.py
+++ b/nipype/interfaces/base/tests/test_specs.py
@@ -11,8 +11,9 @@
 from ... import base as nib
 from ...base import traits, Undefined
 from ..specs import (
-    check_mandatory_inputs, MandatoryInputError,
-    MutuallyExclusiveInputError, RequiredInputError
+    check_mandatory_inputs, check_version,
+    MandatoryInputError, MutuallyExclusiveInputError,
+    RequiredInputError, VersionIOError
 )
 from ....interfaces import fsl
 from ...utility.wrappers import Function
@@ -137,7 +138,7 @@ class MyInterface(nib.BaseInterface):
     myif.inputs.foo = 1
     assert myif.inputs.foo == 1
     set_bar = lambda: setattr(myif.inputs, 'bar', 1)
-    with pytest.raises(IOError):
+    with pytest.raises(MutuallyExclusiveInputError):
         set_bar()
     assert myif.inputs.foo == 1
     myif.inputs.kung = 2
@@ -499,3 +500,86 @@ class DerivedInterface(nib.BaseInterface):
             DerivedInterface(goo=1, woo=1).inputs)
     with pytest.raises(MutuallyExclusiveInputError):
         DerivedInterface(goo=1, woo=1).run()
+
+
+
+def test_input_version():
+    class MinVerInputSpec(nib.TraitedSpec):
+        foo = nib.traits.Int(desc='a random int', min_ver='0.5')
+
+
+    assert check_version(MinVerInputSpec(), '0.6') == []
+    assert check_version(MinVerInputSpec(), '0.4') == ['foo']
+    with pytest.raises(VersionIOError):
+        check_version(MinVerInputSpec(foo=1), '0.4')
+
+
+    class MaxVerInputSpec(nib.TraitedSpec):
+        foo = nib.traits.Int(desc='a random int', max_ver='0.7')
+
+
+    assert check_version(MaxVerInputSpec(), '0.6') == []
+    assert check_version(MaxVerInputSpec(), '0.8') == ['foo']
+    with pytest.raises(VersionIOError):
+        check_version(MaxVerInputSpec(foo=1), '0.8')
+
+
+    class MinMaxVerInputSpec(nib.TraitedSpec):
+        foo = nib.traits.Int(desc='a random int', max_ver='0.7',
+                             min_ver='0.5')
+
+
+    assert check_version(MinMaxVerInputSpec(), '0.6') == []
+    assert check_version(MinMaxVerInputSpec(), '0.4') == ['foo']
+    assert check_version(MinMaxVerInputSpec(), '0.8') == ['foo']
+    with pytest.raises(VersionIOError):
+        check_version(MinMaxVerInputSpec(foo=1), '0.8')
+    with pytest.raises(VersionIOError):
+        check_version(MinMaxVerInputSpec(foo=1), '0.4')
+
+
+    class FixedVerInputSpec(nib.TraitedSpec):
+        foo = nib.traits.Int(desc='a random int', max_ver='0.6.2',
+                             min_ver='0.6.2')
+
+
+    assert check_version(FixedVerInputSpec(), '0.6.2') == []
+    assert check_version(FixedVerInputSpec(), '0.6.1') == ['foo']
+    assert check_version(FixedVerInputSpec(), '0.6.3') == ['foo']
+    with pytest.raises(VersionIOError):
+        check_version(FixedVerInputSpec(foo=1), '0.6.1')
+    with pytest.raises(VersionIOError):
+        check_version(FixedVerInputSpec(foo=1), '0.6.3')
+
+
+    class IncongruentVerInputSpec(nib.TraitedSpec):
+        foo = nib.traits.Int(desc='a random int', max_ver='0.5',
+                             min_ver='0.7')
+
+    with pytest.raises(AssertionError):
+        check_version(IncongruentVerInputSpec(), '0.6')
+    with pytest.raises(AssertionError):
+        check_version(IncongruentVerInputSpec(foo=1), '0.6')
+
+
+    class InputSpec(nib.TraitedSpec):
+        foo = nib.traits.Int(desc='a random int')
+
+    class OutputSpec(nib.TraitedSpec):
+        foo = nib.traits.Int(desc='a random int', min_ver='0.11')
+
+    class DerivedInterface1(nib.BaseInterface):
+        input_spec = InputSpec
+        output_spec = OutputSpec
+        _version = '0.10'
+        resource_monitor = False
+
+        def _run_interface(self, runtime):
+            return runtime
+
+        def _list_outputs(self):
+            return {'foo': 1}
+
+    obj = DerivedInterface1()
+    with pytest.raises(KeyError):
+        obj.run()
diff --git a/nipype/utils/errors.py b/nipype/utils/errors.py
index a55f3179f2..c1ceb38b5c 100644
--- a/nipype/utils/errors.py
+++ b/nipype/utils/errors.py
@@ -12,7 +12,7 @@ class MandatoryInputError(ValueError):
     not defined."""
     def __init__(self, inputspec, name):
         classname = inputspec.__class__.__name__
-        if classname.endswith('InputSpec'):
+        if classname.endswith('InputSpec') and classname != 'InputSpec':
             classname = classname[:len('InputSpec')]
         msg = (
             'Interface "{classname}" requires a value for input {name}. '
@@ -48,7 +48,7 @@ class RequiredInputError(ValueError):
     those are ``Undefined``."""
     def __init__(self, inputspec, name):
         classname = inputspec.__class__.__name__
-        if classname.endswith('InputSpec'):
+        if classname.endswith('InputSpec') and classname != 'InputSpec':
             classname = classname[:-len('InputSpec')]
         requires = inputspec.traits()[name].requires
 
@@ -58,3 +58,27 @@ def __init__(self, inputspec, name):
                     classname=classname, name=name,
                     requires=', '.join(requires))
         super(RequiredInputError, self).__init__(msg)
+
+class VersionIOError(ValueError):
+    """Raised when one input with the ``mandatory`` metadata set to ``True`` is
+    not defined."""
+    def __init__(self, spec, name, version):
+        classname = spec.__class__.__name__
+        if classname.endswith('InputSpec') and classname != 'InputSpec':
+            classname = classname[:len('InputSpec')]
+        if classname.endswith('OutputSpec') and classname != 'OutputSpec':
+            classname = classname[:len('OutputSpec')]
+
+        max_ver = spec.traits()[name].max_ver
+        min_ver = spec.traits()[name].min_ver
+
+        msg = ('Interface "{classname}" has version requirements for '
+               '{name}, but version {version} was found. ').format(
+               classname=classname, name=name, version=version)
+
+        if min_ver:
+            msg += 'Minimum version is %s. ' % min_ver
+        if max_ver:
+            msg += 'Maximum version is %s. ' % max_ver
+
+        super(VersionIOError, self).__init__(msg)

From 94c08234de3dec4309bc1614d653e9e79602a4b5 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 01:38:04 -0800
Subject: [PATCH 07/20] fix multiple xor check

---
 nipype/interfaces/base/specs.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index c6e860ff51..4da090c8c5 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -397,7 +397,9 @@ def check_xor(inputs, xor):
     if len(xor) == 1:
         return True
 
-    values = [isdefined(getattr(inputs, field)) for field in xor]
+    values = [isdefined(getattr(inputs, xor[0]))]
+    values += [any([isdefined(getattr(inputs, field))
+               for field in xor[1:]])]
     return sum(values)
 
 def check_mandatory_inputs(inputs, raise_exc=True):

From fddec6968caddb227627ee686b4ab992a8d71e28 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 01:55:42 -0800
Subject: [PATCH 08/20] fix check_requires for non-mandatory requires

---
 nipype/interfaces/base/specs.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 4da090c8c5..2b130463f0 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -386,9 +386,8 @@ def check_requires(inputs, requires, value):
         return True
 
     # Check value and all required inputs' values defined
-    values = [isdefined(value)] + [
-        isdefined(getattr(inputs, field))
-        for field in requires]
+    values = [isdefined(getattr(inputs, field))
+              for field in requires]
     return all(values)
 
 def check_xor(inputs, xor):
@@ -432,7 +431,8 @@ def check_mandatory_inputs(inputs, raise_exc=True):
     # Check requirements of non-mandatory inputs
     for name, spec in list(
             inputs.traits(mandatory=None, transient=None).items()):
-        if not check_requires(inputs, spec.requires, getattr(inputs, name)):
+        value = getattr(inputs, name)  # value must be set to follow requires
+        if isdefined(value) and not check_requires(inputs, spec.requires, value):
             if raise_exc:
                 raise RequiredInputError(inputs, name)
 

From 34cb9c9e79e15f73da9399dba6cf3a9e94430232 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 02:39:44 -0800
Subject: [PATCH 09/20] fix massaging xored inputs

---
 nipype/interfaces/base/specs.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 2b130463f0..f65ffd4008 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -408,7 +408,10 @@ def check_mandatory_inputs(inputs, raise_exc=True):
     for name, spec in list(inputs.traits(mandatory=True).items()):
         value = getattr(inputs, name)
         # Mandatory field is defined, check xor'ed inputs
-        xor = list(set([name] + (spec.xor or [])))
+        xor = spec.xor or []
+        xor = list(xor) if isinstance(xor, (list, tuple)) \
+            else [xor]
+        xor = list(set([name] + xor))
         cxor = check_xor(inputs, xor)
         if cxor != 1:
             if raise_exc:

From 41a48bdd946adea929eaeb60897c3bfc3257c7c7 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 08:10:10 -0800
Subject: [PATCH 10/20] fix test_extra_Registration

---
 .../ants/tests/test_extra_Registration.py     |  7 ++--
 nipype/utils/errors.py                        | 33 ++++++++++---------
 2 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/nipype/interfaces/ants/tests/test_extra_Registration.py b/nipype/interfaces/ants/tests/test_extra_Registration.py
index 745b825c65..c65bb445be 100644
--- a/nipype/interfaces/ants/tests/test_extra_Registration.py
+++ b/nipype/interfaces/ants/tests/test_extra_Registration.py
@@ -1,9 +1,10 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from __future__ import unicode_literals
-from nipype.interfaces.ants import registration
 import os
 import pytest
+from nipype.interfaces.ants import registration
+from nipype.utils.errors import MandatoryInputError
 
 
 def test_ants_mand(tmpdir):
@@ -17,6 +18,6 @@ def test_ants_mand(tmpdir):
     ants.inputs.fixed_image = [os.path.join(datadir, 'T1.nii')]
     ants.inputs.metric = ['MI']
 
-    with pytest.raises(ValueError) as er:
+    with pytest.raises(MandatoryInputError) as er:
         ants.run()
-    assert "ANTS requires a value for input 'radius'" in str(er.value)
+    assert 'Interface "ANTS" requires a value for input radius.' in str(er.value)
diff --git a/nipype/utils/errors.py b/nipype/utils/errors.py
index c1ceb38b5c..18c4a25116 100644
--- a/nipype/utils/errors.py
+++ b/nipype/utils/errors.py
@@ -11,9 +11,7 @@ class MandatoryInputError(ValueError):
     """Raised when one input with the ``mandatory`` metadata set to ``True`` is
     not defined."""
     def __init__(self, inputspec, name):
-        classname = inputspec.__class__.__name__
-        if classname.endswith('InputSpec') and classname != 'InputSpec':
-            classname = classname[:len('InputSpec')]
+        classname = _classname_from_spec(inputspec)
         msg = (
             'Interface "{classname}" requires a value for input {name}. '
             'For a list of required inputs, see {classname}.help().').format(
@@ -23,9 +21,7 @@ def __init__(self, inputspec, name):
 class MutuallyExclusiveInputError(ValueError):
     """Raised when none or more than one mutually-exclusive inputs are set."""
     def __init__(self, inputspec, name, values_defined=None, name_other=None):
-        classname = inputspec.__class__.__name__
-        if classname.endswith('InputSpec') and classname != 'InputSpec':
-            classname = classname[:-len('InputSpec')]
+        classname = _classname_from_spec(inputspec)
 
         if values_defined is not None:
             xor = list(set([name]+ inputspec.traits()[name].xor))
@@ -47,9 +43,7 @@ class RequiredInputError(ValueError):
     """Raised when one input requires some other and those or some of
     those are ``Undefined``."""
     def __init__(self, inputspec, name):
-        classname = inputspec.__class__.__name__
-        if classname.endswith('InputSpec') and classname != 'InputSpec':
-            classname = classname[:-len('InputSpec')]
+        classname = _classname_from_spec(inputspec)
         requires = inputspec.traits()[name].requires
 
         msg = ('Interface "{classname}" requires a value for input {name} '
@@ -63,12 +57,7 @@ class VersionIOError(ValueError):
     """Raised when one input with the ``mandatory`` metadata set to ``True`` is
     not defined."""
     def __init__(self, spec, name, version):
-        classname = spec.__class__.__name__
-        if classname.endswith('InputSpec') and classname != 'InputSpec':
-            classname = classname[:len('InputSpec')]
-        if classname.endswith('OutputSpec') and classname != 'OutputSpec':
-            classname = classname[:len('OutputSpec')]
-
+        classname = _classname_from_spec(spec)
         max_ver = spec.traits()[name].max_ver
         min_ver = spec.traits()[name].min_ver
 
@@ -82,3 +71,17 @@ def __init__(self, spec, name, version):
             msg += 'Maximum version is %s. ' % max_ver
 
         super(VersionIOError, self).__init__(msg)
+
+def _classname_from_spec(spec):
+    classname = spec.__class__.__name__
+
+    kind = 'Output' if 'Output' in classname else 'Input'
+    # General pattern is that spec ends in KindSpec
+    if classname.endswith(kind + 'Spec') and classname != (kind + 'Spec'):
+        classname = classname[:-len(kind + 'Spec')]
+
+    # Catch some special cases such as ANTS
+    if classname.endswith(kind) and classname != kind:
+        classname = classname[:-len(kind)]
+
+    return classname

From 8f8ceb178e4115401630983c285342a7c11129e5 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 08:21:47 -0800
Subject: [PATCH 11/20] fixed fsl.utils doctests

---
 nipype/interfaces/fsl/utils.py | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py
index f4ef73c0e9..45d09b53e6 100644
--- a/nipype/interfaces/fsl/utils.py
+++ b/nipype/interfaces/fsl/utils.py
@@ -238,16 +238,31 @@ class Smooth(FSLCommand):
     >>> sm.cmdline # doctest: +ELLIPSIS
     'fslmaths functional2.nii -kernel gauss 3.397 -fmean functional2_smooth.nii.gz'
 
-    One of sigma or fwhm must be set:
+    One of sigma or fwhm must be set. Printing the ``cmdline`` will issue
+    a warning:
 
     >>> from nipype.interfaces.fsl import Smooth
     >>> sm = Smooth()
     >>> sm.inputs.output_type = 'NIFTI_GZ'
     >>> sm.inputs.in_file = 'functional2.nii'
-    >>> sm.cmdline #doctest: +ELLIPSIS
+    >>> sm.cmdline  # doctest: +ELLIPSIS
+    'fslmaths functional2.nii functional2_smooth.nii.gz'
+
+    The warning is: ::
+        181125-08:12:09,489 nipype.interface WARNING:
+            Some inputs are not valid. Please make sure all mandatory
+            inputs, required inputs and mutually-exclusive inputs are
+            set or in a sane state.
+
+    Attempting to run the interface without the necessary inputs will
+    lead to an error (in this case, a ``MutuallyExclusiveInputError``):
+
+    >>> sm.run()  # doctest: +ELLIPSIS
     Traceback (most recent call last):
      ...
-    ValueError: Smooth requires a value for one of the inputs ...
+    nipype.utils.errors.MutuallyExclusiveInputError: \
+    Interface "Smooth" has mutually-exclusive inputs. \
+    Exactly one of (fwhm|sigma) should be set...
 
     """
 

From d0c6ab852d1fd566e45ad52080abe84f8df7da78 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 08:52:22 -0800
Subject: [PATCH 12/20] cmdline returns ``None`` instead of raising if error on
 inputs

---
 nipype/interfaces/base/core.py                |  8 ++-
 .../freesurfer/tests/test_preprocess.py       | 70 ++++++++++++-------
 nipype/interfaces/fsl/utils.py                |  8 +--
 3 files changed, 52 insertions(+), 34 deletions(-)

diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
index 335c6fecae..77f1991df6 100644
--- a/nipype/interfaces/base/core.py
+++ b/nipype/interfaces/base/core.py
@@ -726,9 +726,11 @@ def cmdline(self):
         validates arguments and generates command line"""
         if not check_mandatory_inputs(self.inputs, raise_exc=False):
             iflogger.warning(
-                'Some inputs are not valid. Please make sure all mandatory '
-                'inputs, required inputs and mutually-exclusive inputs are '
-                'set or in a sane state.')
+                'Command line could not be generated because some inputs '
+                'are not valid. Please make sure all mandatory inputs, '
+                'required inputs and mutually-exclusive inputs are set '
+                'or in a sane state.')
+            return None
 
         allargs = [self._cmd_prefix + self.cmd] + self._parse_inputs()
         return ' '.join(allargs)
diff --git a/nipype/interfaces/freesurfer/tests/test_preprocess.py b/nipype/interfaces/freesurfer/tests/test_preprocess.py
index f9fc09515a..6853bb7015 100644
--- a/nipype/interfaces/freesurfer/tests/test_preprocess.py
+++ b/nipype/interfaces/freesurfer/tests/test_preprocess.py
@@ -7,24 +7,26 @@
 import pytest
 from nipype.testing.fixtures import create_files_in_directory
 
-from nipype.interfaces import freesurfer
+from nipype.interfaces import freesurfer as fs
 from nipype.interfaces.freesurfer import Info
 from nipype import LooseVersion
+from nipype.utils import errors as nue
 
 
 @pytest.mark.skipif(
-    freesurfer.no_freesurfer(), reason="freesurfer is not installed")
+    fs.no_freesurfer(), reason="freesurfer is not installed")
 def test_robustregister(create_files_in_directory):
     filelist, outdir = create_files_in_directory
 
-    reg = freesurfer.RobustRegister()
+    reg = fs.RobustRegister()
     cwd = os.getcwd()
 
     # make sure command gets called
     assert reg.cmd == 'mri_robust_register'
 
+    assert reg.cmdline is None
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError):
+    with pytest.raises(nue.MandatoryInputError):
         reg.run()
 
     # .inputs based parameters setting
@@ -36,7 +38,7 @@ def test_robustregister(create_files_in_directory):
                            (cwd, filelist[0][:-4], filelist[0], filelist[1]))
 
     # constructor based parameter setting
-    reg2 = freesurfer.RobustRegister(
+    reg2 = fs.RobustRegister(
         source_file=filelist[0],
         target_file=filelist[1],
         outlier_sens=3.0,
@@ -49,17 +51,18 @@ def test_robustregister(create_files_in_directory):
 
 
 @pytest.mark.skipif(
-    freesurfer.no_freesurfer(), reason="freesurfer is not installed")
+    fs.no_freesurfer(), reason="freesurfer is not installed")
 def test_fitmsparams(create_files_in_directory):
     filelist, outdir = create_files_in_directory
 
-    fit = freesurfer.FitMSParams()
+    fit = fs.FitMSParams()
 
     # make sure command gets called
     assert fit.cmd == 'mri_ms_fitparms'
 
+    assert fit.cmdline is None
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError):
+    with pytest.raises(nue.MandatoryInputError):
         fit.run()
 
     # .inputs based parameters setting
@@ -69,7 +72,7 @@ def test_fitmsparams(create_files_in_directory):
                                                          filelist[1], outdir)
 
     # constructor based parameter setting
-    fit2 = freesurfer.FitMSParams(
+    fit2 = fs.FitMSParams(
         in_files=filelist,
         te_list=[1.5, 3.5],
         flip_list=[20, 30],
@@ -80,17 +83,18 @@ def test_fitmsparams(create_files_in_directory):
 
 
 @pytest.mark.skipif(
-    freesurfer.no_freesurfer(), reason="freesurfer is not installed")
+    fs.no_freesurfer(), reason="freesurfer is not installed")
 def test_synthesizeflash(create_files_in_directory):
     filelist, outdir = create_files_in_directory
 
-    syn = freesurfer.SynthesizeFLASH()
+    syn = fs.SynthesizeFLASH()
 
     # make sure command gets called
     assert syn.cmd == 'mri_synthesize'
 
+    assert syn.cmdline is None
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError):
+    with pytest.raises(nue.MandatoryInputError):
         syn.run()
 
     # .inputs based parameters setting
@@ -105,7 +109,7 @@ def test_synthesizeflash(create_files_in_directory):
                             os.path.join(outdir, 'synth-flash_30.mgz')))
 
     # constructor based parameters setting
-    syn2 = freesurfer.SynthesizeFLASH(
+    syn2 = fs.SynthesizeFLASH(
         t1_image=filelist[0], pd_image=filelist[1], flip_angle=20, te=5, tr=25)
     assert syn2.cmdline == ('mri_synthesize 25.00 20.00 5.000 %s %s %s' %
                             (filelist[0], filelist[1],
@@ -113,16 +117,17 @@ def test_synthesizeflash(create_files_in_directory):
 
 
 @pytest.mark.skipif(
-    freesurfer.no_freesurfer(), reason="freesurfer is not installed")
+    fs.no_freesurfer(), reason="freesurfer is not installed")
 def test_mandatory_outvol(create_files_in_directory):
     filelist, outdir = create_files_in_directory
-    mni = freesurfer.MNIBiasCorrection()
+    mni = fs.MNIBiasCorrection()
 
     # make sure command gets called
     assert mni.cmd == "mri_nu_correct.mni"
 
+    assert mni.cmdline is None
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError):
+    with pytest.raises(nue.MandatoryInputError):
         mni.cmdline
 
     # test with minimal args
@@ -141,7 +146,7 @@ def test_mandatory_outvol(create_files_in_directory):
         'mri_nu_correct.mni --i %s --n 4 --o new_corrected_file.mgz' % (filelist[0]))
 
     # constructor based tests
-    mni2 = freesurfer.MNIBiasCorrection(
+    mni2 = fs.MNIBiasCorrection(
         in_file=filelist[0], out_file='bias_corrected_output', iterations=2)
     assert mni2.cmdline == (
         'mri_nu_correct.mni --i %s --n 2 --o bias_corrected_output' %
@@ -149,17 +154,24 @@ def test_mandatory_outvol(create_files_in_directory):
 
 
 @pytest.mark.skipif(
-    freesurfer.no_freesurfer(), reason="freesurfer is not installed")
-def test_bbregister(create_files_in_directory):
+    fs.no_freesurfer(), reason="freesurfer is not installed")
+def test_bbregister(capsys, create_files_in_directory):
     filelist, outdir = create_files_in_directory
-    bbr = freesurfer.BBRegister()
+    bbr = fs.BBRegister()
 
     # make sure command gets called
     assert bbr.cmd == "bbregister"
 
+    # cmdline issues a warning in this stats
+    assert bbr.cmdline is None
+    captured = capsys.readouterr()
+
+    assert 'WARNING' in captured.out
+    assert 'Some inputs are not valid.' in captured.out
+
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError):
-        bbr.cmdline
+    with pytest.raises(nue.MandatoryInputError):
+        bbr.run()
 
     bbr.inputs.subject_id = 'fsaverage'
     bbr.inputs.source_file = filelist[0]
@@ -167,10 +179,14 @@ def test_bbregister(create_files_in_directory):
 
     # Check that 'init' is mandatory in FS < 6, but not in 6+
     if Info.looseversion() < LooseVersion("6.0.0"):
-        with pytest.raises(ValueError):
-            bbr.cmdline
+        assert bbr.cmdline is None
+        captured = capsys.readouterr()
+        assert 'Some inputs are not valid.' in captured.out
+
+        with pytest.raises(nue.VersionIOError):
+            bbr.run()
     else:
-        bbr.cmdline
+        assert bbr.cmdline is not None
 
     bbr.inputs.init = 'fsl'
 
@@ -187,5 +203,5 @@ def test_bbregister(create_files_in_directory):
 def test_FSVersion():
     """Check that FSVersion is a string that can be compared with LooseVersion
     """
-    assert isinstance(freesurfer.preprocess.FSVersion, str)
-    assert LooseVersion(freesurfer.preprocess.FSVersion) >= LooseVersion("0")
+    assert isinstance(fs.preprocess.FSVersion, str)
+    assert LooseVersion(fs.preprocess.FSVersion) >= LooseVersion("0")
diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py
index 45d09b53e6..fac48dcec5 100644
--- a/nipype/interfaces/fsl/utils.py
+++ b/nipype/interfaces/fsl/utils.py
@@ -238,15 +238,15 @@ class Smooth(FSLCommand):
     >>> sm.cmdline # doctest: +ELLIPSIS
     'fslmaths functional2.nii -kernel gauss 3.397 -fmean functional2_smooth.nii.gz'
 
-    One of sigma or fwhm must be set. Printing the ``cmdline`` will issue
-    a warning:
+    One of sigma or fwhm must be set. Accessing the ``cmdline`` property
+    will return ``None`` and issue a warning:
 
     >>> from nipype.interfaces.fsl import Smooth
     >>> sm = Smooth()
     >>> sm.inputs.output_type = 'NIFTI_GZ'
     >>> sm.inputs.in_file = 'functional2.nii'
-    >>> sm.cmdline  # doctest: +ELLIPSIS
-    'fslmaths functional2.nii functional2_smooth.nii.gz'
+    >>> sm.cmdline is None  # doctest: +ELLIPSIS
+    True
 
     The warning is: ::
         181125-08:12:09,489 nipype.interface WARNING:

From 1b948cfedf02202b0e2d2b8ffff2c1bd1fd48883 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 11:35:43 -0800
Subject: [PATCH 13/20] fix one more use-case

---
 nipype/interfaces/base/specs.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 96289f47a0..434cf0e6fa 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -427,6 +427,15 @@ def check_mandatory_inputs(inputs, raise_exc=True):
         value = getattr(inputs, name)
         # Mandatory field is defined, check xor'ed inputs
         xor = spec.xor or []
+        has_xor = bool(xor)
+        has_value = isdefined(value)
+
+        # Simplest case: no xor metadata and not defined
+        if not has_xor and not has_value:
+            if raise_exc:
+                raise MandatoryInputError(inputs, name)
+            return False
+
         xor = list(xor) if isinstance(xor, (list, tuple)) \
             else [xor]
         xor = list(set([name] + xor))
@@ -437,14 +446,8 @@ def check_mandatory_inputs(inputs, raise_exc=True):
                     inputs, name, values_defined=cxor)
             return False
 
-        # Simplest case: no xor metadata and not defined
-        if cxor is True and not isdefined(value):
-            if raise_exc:
-                raise MandatoryInputError(inputs, name)
-            return False
-
         # Check whether mandatory inputs require others
-        if not check_requires(inputs, spec.requires):
+        if has_value and not check_requires(inputs, spec.requires):
             if raise_exc:
                 raise RequiredInputError(inputs, name)
             return False

From 1a558a4d0250191afec8f13927810cb863c1f51e Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 11:48:35 -0800
Subject: [PATCH 14/20] fixed tests

---
 .../freesurfer/tests/test_preprocess.py       | 21 +++++++++++--------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/nipype/interfaces/freesurfer/tests/test_preprocess.py b/nipype/interfaces/freesurfer/tests/test_preprocess.py
index 6853bb7015..3d908914b8 100644
--- a/nipype/interfaces/freesurfer/tests/test_preprocess.py
+++ b/nipype/interfaces/freesurfer/tests/test_preprocess.py
@@ -11,6 +11,7 @@
 from nipype.interfaces.freesurfer import Info
 from nipype import LooseVersion
 from nipype.utils import errors as nue
+from nipype.utils.tests.test_cmd import capture_sys_output
 
 
 @pytest.mark.skipif(
@@ -128,7 +129,7 @@ def test_mandatory_outvol(create_files_in_directory):
     assert mni.cmdline is None
     # test raising error with mandatory args absent
     with pytest.raises(nue.MandatoryInputError):
-        mni.cmdline
+        mni.run()
 
     # test with minimal args
     mni.inputs.in_file = filelist[0]
@@ -155,7 +156,7 @@ def test_mandatory_outvol(create_files_in_directory):
 
 @pytest.mark.skipif(
     fs.no_freesurfer(), reason="freesurfer is not installed")
-def test_bbregister(capsys, create_files_in_directory):
+def test_bbregister(create_files_in_directory):
     filelist, outdir = create_files_in_directory
     bbr = fs.BBRegister()
 
@@ -163,11 +164,12 @@ def test_bbregister(capsys, create_files_in_directory):
     assert bbr.cmd == "bbregister"
 
     # cmdline issues a warning in this stats
-    assert bbr.cmdline is None
-    captured = capsys.readouterr()
+    with capture_sys_output() as (stdout, stderr):
+        assert bbr.cmdline is None
 
-    assert 'WARNING' in captured.out
-    assert 'Some inputs are not valid.' in captured.out
+    captured = stdout.getvalue()
+    assert 'WARNING' in captured
+    assert 'Command line could not be generated' in captured
 
     # test raising error with mandatory args absent
     with pytest.raises(nue.MandatoryInputError):
@@ -179,9 +181,10 @@ def test_bbregister(capsys, create_files_in_directory):
 
     # Check that 'init' is mandatory in FS < 6, but not in 6+
     if Info.looseversion() < LooseVersion("6.0.0"):
-        assert bbr.cmdline is None
-        captured = capsys.readouterr()
-        assert 'Some inputs are not valid.' in captured.out
+        with capture_sys_output() as (stdout, stderr):
+            assert bbr.cmdline is None
+        captured = stdout.getvalue()
+        assert 'Command line could not be generated' in captured
 
         with pytest.raises(nue.VersionIOError):
             bbr.run()

From b08b5ad4acd40d8486c1bbdf62257e959e1e1d93 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 15:42:18 -0800
Subject: [PATCH 15/20] fix errors checking xor

---
 nipype/interfaces/base/specs.py | 17 +++++++++--------
 nipype/interfaces/fsl/utils.py  |  4 +---
 nipype/utils/errors.py          |  7 +++++--
 3 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 434cf0e6fa..d4c828699d 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -408,15 +408,15 @@ def check_requires(inputs, requires):
               for field in requires]
     return all(values)
 
-def check_xor(inputs, xor):
+def check_xor(inputs, name, xor):
     """ check if mutually exclusive inputs are satisfied
     """
-    if len(xor) == 1:
+    if len(xor) == 0:
         return True
 
-    values = [isdefined(getattr(inputs, xor[0]))]
+    values = [isdefined(getattr(inputs, name))]
     values += [any([isdefined(getattr(inputs, field))
-               for field in xor[1:]])]
+               for field in xor])]
     return sum(values)
 
 def check_mandatory_inputs(inputs, raise_exc=True):
@@ -436,10 +436,11 @@ def check_mandatory_inputs(inputs, raise_exc=True):
                 raise MandatoryInputError(inputs, name)
             return False
 
-        xor = list(xor) if isinstance(xor, (list, tuple)) \
-            else [xor]
-        xor = list(set([name] + xor))
-        cxor = check_xor(inputs, xor)
+        xor = set(list(xor) if isinstance(xor, (list, tuple))
+                  else [xor])
+        xor.discard(name)
+        xor = list(xor)
+        cxor = check_xor(inputs, name, xor)
         if cxor != 1:
             if raise_exc:
                 raise MutuallyExclusiveInputError(
diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py
index fac48dcec5..dcf545525f 100644
--- a/nipype/interfaces/fsl/utils.py
+++ b/nipype/interfaces/fsl/utils.py
@@ -260,9 +260,7 @@ class Smooth(FSLCommand):
     >>> sm.run()  # doctest: +ELLIPSIS
     Traceback (most recent call last):
      ...
-    nipype.utils.errors.MutuallyExclusiveInputError: \
-    Interface "Smooth" has mutually-exclusive inputs. \
-    Exactly one of (fwhm|sigma) should be set...
+    MutuallyExclusiveInputError: Interface ...
 
     """
 
diff --git a/nipype/utils/errors.py b/nipype/utils/errors.py
index 18c4a25116..7051eda366 100644
--- a/nipype/utils/errors.py
+++ b/nipype/utils/errors.py
@@ -25,12 +25,15 @@ def __init__(self, inputspec, name, values_defined=None, name_other=None):
 
         if values_defined is not None:
             xor = list(set([name]+ inputspec.traits()[name].xor))
-            msg = ('Interface "{classname}" has mutually-exclusive inputs. '
+            msg = ('Interface "{classname}" has mutually-exclusive inputs '
+                   '(processing "{name}", with value={value}). '
                    'Exactly one of ({xor}) should be set, but {n:d} were set. '
                    'For a list of mutually-exclusive inputs, see '
                    '{classname}.help().').format(classname=classname,
                                                  xor='|'.join(xor),
-                                                 n=values_defined)
+                                                 n=values_defined,
+                                                 name=name,
+                                                 value=getattr(inputspec, name))
 
         else:
             msg = ('Interface "{classname}" has mutually-exclusive inputs. '

From 44a724d0c1053948ce1fd4efeefa51ecfe504d6c Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 15:48:57 -0800
Subject: [PATCH 16/20] fix fs.preprocess test

---
 .../interfaces/freesurfer/tests/test_preprocess.py | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/nipype/interfaces/freesurfer/tests/test_preprocess.py b/nipype/interfaces/freesurfer/tests/test_preprocess.py
index 3d908914b8..01b99eaa2f 100644
--- a/nipype/interfaces/freesurfer/tests/test_preprocess.py
+++ b/nipype/interfaces/freesurfer/tests/test_preprocess.py
@@ -11,7 +11,6 @@
 from nipype.interfaces.freesurfer import Info
 from nipype import LooseVersion
 from nipype.utils import errors as nue
-from nipype.utils.tests.test_cmd import capture_sys_output
 
 
 @pytest.mark.skipif(
@@ -156,7 +155,7 @@ def test_mandatory_outvol(create_files_in_directory):
 
 @pytest.mark.skipif(
     fs.no_freesurfer(), reason="freesurfer is not installed")
-def test_bbregister(create_files_in_directory):
+def test_bbregister(caplog, create_files_in_directory):
     filelist, outdir = create_files_in_directory
     bbr = fs.BBRegister()
 
@@ -164,11 +163,9 @@ def test_bbregister(create_files_in_directory):
     assert bbr.cmd == "bbregister"
 
     # cmdline issues a warning in this stats
-    with capture_sys_output() as (stdout, stderr):
-        assert bbr.cmdline is None
+    assert bbr.cmdline is None
 
-    captured = stdout.getvalue()
-    assert 'WARNING' in captured
+    captured = caplog.text
     assert 'Command line could not be generated' in captured
 
     # test raising error with mandatory args absent
@@ -181,9 +178,8 @@ def test_bbregister(create_files_in_directory):
 
     # Check that 'init' is mandatory in FS < 6, but not in 6+
     if Info.looseversion() < LooseVersion("6.0.0"):
-        with capture_sys_output() as (stdout, stderr):
-            assert bbr.cmdline is None
-        captured = stdout.getvalue()
+        assert bbr.cmdline is None
+        captured = caplog.text
         assert 'Command line could not be generated' in captured
 
         with pytest.raises(nue.VersionIOError):

From f7b5650b817da5fdb6493658c84f41cd6a9de800 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 16:01:45 -0800
Subject: [PATCH 17/20] fix fsl.tests.test_preprocess

---
 .../freesurfer/tests/test_preprocess.py       |  2 +-
 .../interfaces/fsl/tests/test_preprocess.py   | 33 +++++++++++++------
 2 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/nipype/interfaces/freesurfer/tests/test_preprocess.py b/nipype/interfaces/freesurfer/tests/test_preprocess.py
index 01b99eaa2f..64dd3b8379 100644
--- a/nipype/interfaces/freesurfer/tests/test_preprocess.py
+++ b/nipype/interfaces/freesurfer/tests/test_preprocess.py
@@ -162,7 +162,7 @@ def test_bbregister(caplog, create_files_in_directory):
     # make sure command gets called
     assert bbr.cmd == "bbregister"
 
-    # cmdline issues a warning in this stats
+    # cmdline issues a warning: mandatory inputs missing
     assert bbr.cmdline is None
 
     captured = caplog.text
diff --git a/nipype/interfaces/fsl/tests/test_preprocess.py b/nipype/interfaces/fsl/tests/test_preprocess.py
index 4b387201cf..578fb745a2 100644
--- a/nipype/interfaces/fsl/tests/test_preprocess.py
+++ b/nipype/interfaces/fsl/tests/test_preprocess.py
@@ -15,6 +15,7 @@
 from nipype.interfaces.fsl import Info
 from nipype.interfaces.base import File, TraitError, Undefined, isdefined
 from nipype.interfaces.fsl import no_fsl
+from nipype.utils import errors as nue
 
 
 def fsl_name(obj, fname):
@@ -39,7 +40,7 @@ def test_bet(setup_infile):
     assert better.cmd == 'bet'
 
     # Test raising error with mandatory args absent
-    with pytest.raises(ValueError):
+    with pytest.raises(nue.MandatoryInputError):
         better.run()
 
     # Test generated outfile name
@@ -195,7 +196,7 @@ def setup_flirt(tmpdir):
 
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
-def test_flirt(setup_flirt):
+def test_flirt(caplog, setup_flirt):
     # setup
     tmpdir, infile, reffile = setup_flirt
 
@@ -230,12 +231,24 @@ def test_flirt(setup_flirt):
 
     flirter = fsl.FLIRT()
     # infile not specified
-    with pytest.raises(ValueError):
-        flirter.cmdline
+    assert flirter.cmdline is None
+    captured = caplog.text
+    assert 'Command line could not be generated' in captured
+
+    # interface should raise error with mandatory inputs unset
+    with pytest.raises(nue.MandatoryInputError):
+        flirter.run()
+
     flirter.inputs.in_file = infile
     # reference not specified
-    with pytest.raises(ValueError):
-        flirter.cmdline
+    assert flirter.cmdline is None
+    captured = caplog.text
+    assert 'Command line could not be generated' in captured
+
+    # interface should raise error with reference still unset
+    with pytest.raises(nue.MandatoryInputError):
+        flirter.run()
+
     flirter.inputs.reference = reffile
 
     # Generate outfile and outmatrix
@@ -380,10 +393,10 @@ def test_mcflirt_opt(setup_flirt):
 def test_mcflirt_noinput():
     # Test error is raised when missing required args
     fnt = fsl.MCFLIRT()
-    with pytest.raises(ValueError) as excinfo:
+    with pytest.raises(nue.MandatoryInputError) as excinfo:
         fnt.run()
     assert str(excinfo.value).startswith(
-        "MCFLIRT requires a value for input 'in_file'")
+        'Interface "MCFLIRT" requires a value for input in_file.')
 
 
 # test fnirt
@@ -441,9 +454,9 @@ def test_fnirt(setup_flirt):
                                                 iout)
         assert fnirt.cmdline == cmd
 
-    # Test ValueError is raised when missing mandatory args
+    # Test nue.MandatoryInputError is raised when missing mandatory args
     fnirt = fsl.FNIRT()
-    with pytest.raises(ValueError):
+    with pytest.raises(nue.MandatoryInputError):
         fnirt.run()
     fnirt.inputs.in_file = infile
     fnirt.inputs.ref_file = reffile

From 294850bc9c56668ec00c6696419a530a12195373 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 16:01:45 -0800
Subject: [PATCH 18/20] fix fsl.tests.test_preprocess

---
 .../freesurfer/tests/test_preprocess.py       |  2 +-
 .../interfaces/fsl/tests/test_preprocess.py   | 33 +++++++++++++------
 nipype/interfaces/fsl/utils.py                |  2 +-
 nipype/pytest.ini                             |  2 +-
 nipype/utils/errors.py                        |  5 ++-
 5 files changed, 30 insertions(+), 14 deletions(-)

diff --git a/nipype/interfaces/freesurfer/tests/test_preprocess.py b/nipype/interfaces/freesurfer/tests/test_preprocess.py
index 01b99eaa2f..64dd3b8379 100644
--- a/nipype/interfaces/freesurfer/tests/test_preprocess.py
+++ b/nipype/interfaces/freesurfer/tests/test_preprocess.py
@@ -162,7 +162,7 @@ def test_bbregister(caplog, create_files_in_directory):
     # make sure command gets called
     assert bbr.cmd == "bbregister"
 
-    # cmdline issues a warning in this stats
+    # cmdline issues a warning: mandatory inputs missing
     assert bbr.cmdline is None
 
     captured = caplog.text
diff --git a/nipype/interfaces/fsl/tests/test_preprocess.py b/nipype/interfaces/fsl/tests/test_preprocess.py
index 4b387201cf..578fb745a2 100644
--- a/nipype/interfaces/fsl/tests/test_preprocess.py
+++ b/nipype/interfaces/fsl/tests/test_preprocess.py
@@ -15,6 +15,7 @@
 from nipype.interfaces.fsl import Info
 from nipype.interfaces.base import File, TraitError, Undefined, isdefined
 from nipype.interfaces.fsl import no_fsl
+from nipype.utils import errors as nue
 
 
 def fsl_name(obj, fname):
@@ -39,7 +40,7 @@ def test_bet(setup_infile):
     assert better.cmd == 'bet'
 
     # Test raising error with mandatory args absent
-    with pytest.raises(ValueError):
+    with pytest.raises(nue.MandatoryInputError):
         better.run()
 
     # Test generated outfile name
@@ -195,7 +196,7 @@ def setup_flirt(tmpdir):
 
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
-def test_flirt(setup_flirt):
+def test_flirt(caplog, setup_flirt):
     # setup
     tmpdir, infile, reffile = setup_flirt
 
@@ -230,12 +231,24 @@ def test_flirt(setup_flirt):
 
     flirter = fsl.FLIRT()
     # infile not specified
-    with pytest.raises(ValueError):
-        flirter.cmdline
+    assert flirter.cmdline is None
+    captured = caplog.text
+    assert 'Command line could not be generated' in captured
+
+    # interface should raise error with mandatory inputs unset
+    with pytest.raises(nue.MandatoryInputError):
+        flirter.run()
+
     flirter.inputs.in_file = infile
     # reference not specified
-    with pytest.raises(ValueError):
-        flirter.cmdline
+    assert flirter.cmdline is None
+    captured = caplog.text
+    assert 'Command line could not be generated' in captured
+
+    # interface should raise error with reference still unset
+    with pytest.raises(nue.MandatoryInputError):
+        flirter.run()
+
     flirter.inputs.reference = reffile
 
     # Generate outfile and outmatrix
@@ -380,10 +393,10 @@ def test_mcflirt_opt(setup_flirt):
 def test_mcflirt_noinput():
     # Test error is raised when missing required args
     fnt = fsl.MCFLIRT()
-    with pytest.raises(ValueError) as excinfo:
+    with pytest.raises(nue.MandatoryInputError) as excinfo:
         fnt.run()
     assert str(excinfo.value).startswith(
-        "MCFLIRT requires a value for input 'in_file'")
+        'Interface "MCFLIRT" requires a value for input in_file.')
 
 
 # test fnirt
@@ -441,9 +454,9 @@ def test_fnirt(setup_flirt):
                                                 iout)
         assert fnirt.cmdline == cmd
 
-    # Test ValueError is raised when missing mandatory args
+    # Test nue.MandatoryInputError is raised when missing mandatory args
     fnirt = fsl.FNIRT()
-    with pytest.raises(ValueError):
+    with pytest.raises(nue.MandatoryInputError):
         fnirt.run()
     fnirt.inputs.in_file = infile
     fnirt.inputs.ref_file = reffile
diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py
index dcf545525f..b85101f867 100644
--- a/nipype/interfaces/fsl/utils.py
+++ b/nipype/interfaces/fsl/utils.py
@@ -259,7 +259,7 @@ class Smooth(FSLCommand):
 
     >>> sm.run()  # doctest: +ELLIPSIS
     Traceback (most recent call last):
-     ...
+        ...
     MutuallyExclusiveInputError: Interface ...
 
     """
diff --git a/nipype/pytest.ini b/nipype/pytest.ini
index 70f12b64aa..5f22555598 100644
--- a/nipype/pytest.ini
+++ b/nipype/pytest.ini
@@ -1,6 +1,6 @@
 [pytest]
 norecursedirs = .git build dist doc nipype/external tools examples src
 addopts = --doctest-modules -n auto
-doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE
+doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL
 env =
     PYTHONHASHSEED=0
diff --git a/nipype/utils/errors.py b/nipype/utils/errors.py
index 7051eda366..1fff7404c6 100644
--- a/nipype/utils/errors.py
+++ b/nipype/utils/errors.py
@@ -24,7 +24,10 @@ def __init__(self, inputspec, name, values_defined=None, name_other=None):
         classname = _classname_from_spec(inputspec)
 
         if values_defined is not None:
-            xor = list(set([name]+ inputspec.traits()[name].xor))
+            xor = inputspec.traits()[name].xor or []
+            xor = set(list(xor) if isinstance(xor, (list, tuple))
+                      else [xor])
+            xor.add(name)
             msg = ('Interface "{classname}" has mutually-exclusive inputs '
                    '(processing "{name}", with value={value}). '
                    'Exactly one of ({xor}) should be set, but {n:d} were set. '

From 89da56a19a2d3d32f4771568fda979e8a9866296 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 19:10:52 -0800
Subject: [PATCH 19/20] install caplog fixture

---
 nipype/info.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/nipype/info.py b/nipype/info.py
index 9e162524dd..c21dfbd8bf 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -157,7 +157,13 @@ def get_nipype_gitversion():
 if sys.version_info <= (3, 4):
     REQUIRES.append('configparser')
 
-TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-env', 'coverage<5']
+TESTS_REQUIRES = [
+    'pytest-capturelog',
+    'pytest-cov',
+    'pytest-env',
+    'codecov',
+    'coverage<5',
+]
 
 EXTRA_REQUIRES = {
     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],

From fff59eb64a43ef33a96aba257e9bbdbe7bd6ce98 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sun, 25 Nov 2018 20:31:25 -0800
Subject: [PATCH 20/20] pin pytest>=3.4 for reliable caplog fixture

---
 nipype/info.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nipype/info.py b/nipype/info.py
index c21dfbd8bf..8d41b3c88a 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -107,7 +107,7 @@ def get_nipype_gitversion():
 SCIPY_MIN_VERSION = '0.14'
 TRAITS_MIN_VERSION = '4.6'
 DATEUTIL_MIN_VERSION = '2.2'
-PYTEST_MIN_VERSION = '3.0'
+PYTEST_MIN_VERSION = '3.4'
 FUTURE_MIN_VERSION = '0.16.0'
 SIMPLEJSON_MIN_VERSION = '3.8.0'
 PROV_VERSION = '1.5.2'
@@ -158,7 +158,6 @@ def get_nipype_gitversion():
     REQUIRES.append('configparser')
 
 TESTS_REQUIRES = [
-    'pytest-capturelog',
     'pytest-cov',
     'pytest-env',
     'codecov',