Merge pull request #1490 from shoshber/raise_from

WIP/REF/FIX: Don't throw away exception stack traces

Author: Shoshana Berleant

.travis.yml

@@ -45,6 +45,7 @@ install:
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then conda install --yes vtk; fi
 - pip install python-coveralls
 - pip install nose-cov
+- pip install mock
 # Add tvtk (PIL is required by blockcanvas)
 # Install mayavi (see https://github.com/enthought/mayavi/issues/271)
 - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then

circle.yml

@@ -21,7 +21,7 @@ dependencies:
     # Set up python environment
     - pip install --upgrade pip
     - pip install -e .
-    - pip install matplotlib sphinx ipython boto coverage dipy
+    - pip install matplotlib sphinx ipython boto coverage dipy mock
     # Add tvtk
     - pip install http://effbot.org/downloads/Imaging-1.1.7.tar.gz
     - pip install -e git+https://github.com/enthought/etsdevtools.git#egg=etsdevtools

nipype/algorithms/misc.py

@@ -15,6 +15,7 @@
 from __future__ import division
 from builtins import zip
 from builtins import range
+from future.utils import raise_from
 
 import os
 import os.path as op
@@ -857,9 +858,9 @@ def __init__(self, infields=None, force_run=True, **kwargs):
     def _run_interface(self, runtime):
         try:
             import pandas as pd
-        except ImportError:
-            raise ImportError(('This interface requires pandas '
-                               '(http://pandas.pydata.org/) to run.'))
+        except ImportError as e:
+            raise_from(ImportError('This interface requires pandas '
+                                    '(http://pandas.pydata.org/) to run.'), e)
 
         try:
             import lockfile as pl

nipype/external/six.py

@@ -29,12 +29,13 @@
 import types
 
 __author__ = "Benjamin Peterson <benjamin@python.org>"
-__version__ = "1.9.0"
+__version__ = "1.10.0"
 
 
 # Useful for very coarse version differentiation.
 PY2 = sys.version_info[0] == 2
 PY3 = sys.version_info[0] == 3
+PY34 = sys.version_info[0:2] >= (3, 4)
 
 if PY3:
     string_types = str,
@@ -57,6 +58,7 @@
     else:
         # It's possible to have sizeof(long) != sizeof(Py_ssize_t).
         class X(object):
+
             def __len__(self):
                 return 1 << 31
         try:
@@ -160,6 +162,7 @@ def _resolve(self):
 
 
 class _SixMetaPathImporter(object):
+
     """
     A meta path importer to import six.moves and its submodules.
 
@@ -224,6 +227,7 @@ def get_code(self, fullname):
 
 
 class _MovedItems(_LazyModule):
+
     """Lazy loading of moved objects"""
     __path__ = []  # mark as package
 
@@ -235,8 +239,10 @@ class _MovedItems(_LazyModule):
     MovedAttribute("input", "__builtin__", "builtins", "raw_input", "input"),
     MovedAttribute("intern", "__builtin__", "sys"),
     MovedAttribute("map", "itertools", "builtins", "imap", "map"),
+    MovedAttribute("getcwd", "os", "os", "getcwdu", "getcwd"),
+    MovedAttribute("getcwdb", "os", "os", "getcwd", "getcwdb"),
     MovedAttribute("range", "__builtin__", "builtins", "xrange", "range"),
-    MovedAttribute("reload_module", "__builtin__", "imp", "reload"),
+    MovedAttribute("reload_module", "__builtin__", "importlib" if PY34 else "imp", "reload"),
     MovedAttribute("reduce", "__builtin__", "functools"),
     MovedAttribute("shlex_quote", "pipes", "shlex", "quote"),
     MovedAttribute("StringIO", "StringIO", "io"),
@@ -246,7 +252,6 @@ class _MovedItems(_LazyModule):
     MovedAttribute("xrange", "__builtin__", "builtins", "xrange", "range"),
     MovedAttribute("zip", "itertools", "builtins", "izip", "zip"),
     MovedAttribute("zip_longest", "itertools", "itertools", "izip_longest", "zip_longest"),
-
     MovedModule("builtins", "__builtin__"),
     MovedModule("configparser", "ConfigParser"),
     MovedModule("copyreg", "copy_reg"),
@@ -293,8 +298,13 @@ class _MovedItems(_LazyModule):
     MovedModule("urllib_robotparser", "robotparser", "urllib.robotparser"),
     MovedModule("xmlrpc_client", "xmlrpclib", "xmlrpc.client"),
     MovedModule("xmlrpc_server", "SimpleXMLRPCServer", "xmlrpc.server"),
-    MovedModule("winreg", "_winreg"),
 ]
+# Add windows specific modules.
+if sys.platform == "win32":
+    _moved_attributes += [
+        MovedModule("winreg", "_winreg"),
+    ]
+
 for attr in _moved_attributes:
     setattr(_MovedItems, attr.name, attr)
     if isinstance(attr, MovedModule):
@@ -308,6 +318,7 @@ class _MovedItems(_LazyModule):
 
 
 class Module_six_moves_urllib_parse(_LazyModule):
+
     """Lazy loading of moved objects in six.moves.urllib_parse"""
 
 
@@ -347,6 +358,7 @@ class Module_six_moves_urllib_parse(_LazyModule):
 
 
 class Module_six_moves_urllib_error(_LazyModule):
+
     """Lazy loading of moved objects in six.moves.urllib_error"""
 
 
@@ -366,6 +378,7 @@ class Module_six_moves_urllib_error(_LazyModule):
 
 
 class Module_six_moves_urllib_request(_LazyModule):
+
     """Lazy loading of moved objects in six.moves.urllib_request"""
 
 
@@ -415,6 +428,7 @@ class Module_six_moves_urllib_request(_LazyModule):
 
 
 class Module_six_moves_urllib_response(_LazyModule):
+
     """Lazy loading of moved objects in six.moves.urllib_response"""
 
 
@@ -435,6 +449,7 @@ class Module_six_moves_urllib_response(_LazyModule):
 
 
 class Module_six_moves_urllib_robotparser(_LazyModule):
+
     """Lazy loading of moved objects in six.moves.urllib_robotparser"""
 
 
@@ -452,6 +467,7 @@ class Module_six_moves_urllib_robotparser(_LazyModule):
 
 
 class Module_six_moves_urllib(types.ModuleType):
+
     """Create a six.moves.urllib namespace that resembles the Python 3 namespace"""
     __path__ = []  # mark as package
     parse = _importer._get_module("moves.urllib_parse")
@@ -522,6 +538,9 @@ def get_unbound_function(unbound):
 
     create_bound_method = types.MethodType
 
+    def create_unbound_method(func, cls):
+        return func
+
     Iterator = object
 else:
     def get_unbound_function(unbound):
@@ -530,6 +549,9 @@ def get_unbound_function(unbound):
     def create_bound_method(func, obj):
         return types.MethodType(func, obj, obj.__class__)
 
+    def create_unbound_method(func, cls):
+        return types.MethodType(func, None, cls)
+
     class Iterator(object):
 
         def next(self):
@@ -568,16 +590,16 @@ def iterlists(d, **kw):
     viewitems = operator.methodcaller("items")
 else:
     def iterkeys(d, **kw):
-        return iter(d.iterkeys(**kw))
+        return d.iterkeys(**kw)
 
     def itervalues(d, **kw):
-        return iter(d.itervalues(**kw))
+        return d.itervalues(**kw)
 
     def iteritems(d, **kw):
-        return iter(d.iteritems(**kw))
+        return d.iteritems(**kw)
 
     def iterlists(d, **kw):
-        return iter(d.iterlists(**kw))
+        return d.iterlists(**kw)
 
     viewkeys = operator.methodcaller("viewkeys")
 
@@ -600,21 +622,22 @@ def b(s):
     def u(s):
         return s
     unichr = chr
-    if sys.version_info[1] <= 1:
-        def int2byte(i):
-            return bytes((i,))
-    else:
-        # This is about 2x faster than the implementation above on 3.2+
-        int2byte = operator.methodcaller("to_bytes", 1, "big")
+    import struct
+    int2byte = struct.Struct(">B").pack
+    del struct
     byte2int = operator.itemgetter(0)
     indexbytes = operator.getitem
     iterbytes = iter
     import io
     StringIO = io.StringIO
     BytesIO = io.BytesIO
     _assertCountEqual = "assertCountEqual"
-    _assertRaisesRegex = "assertRaisesRegex"
-    _assertRegex = "assertRegex"
+    if sys.version_info[1] <= 1:
+        _assertRaisesRegex = "assertRaisesRegexp"
+        _assertRegex = "assertRegexpMatches"
+    else:
+        _assertRaisesRegex = "assertRaisesRegex"
+        _assertRegex = "assertRegex"
 else:
     def b(s):
         return s
@@ -780,6 +803,7 @@ def with_metaclass(meta, *bases):
     # metaclass for one level of class instantiation that replaces itself with
     # the actual metaclass.
     class metaclass(meta):
+
         def __new__(cls, name, this_bases, d):
             return meta(name, bases, d)
     return type.__new__(metaclass, 'temporary_class', (), {})

nipype/interfaces/afni/base.py

@@ -5,6 +5,7 @@
 import os
 from sys import platform
 from builtins import object
+from future.utils import raise_from
 
 from ... import logging
 from ...utils.filemanip import split_filename
@@ -82,9 +83,9 @@ def outputtype_to_ext(cls, outputtype):
 
         try:
             return cls.ftypes[outputtype]
-        except KeyError:
+        except KeyError as e:
             msg = 'Invalid AFNIOUTPUTTYPE: ', outputtype
-            raise KeyError(msg)
+            raise_from(KeyError(msg), e)
 
     @classmethod
     def outputtype(cls):

nipype/pipeline/plugins/ipython.py

@@ -5,6 +5,8 @@
 
 from future import standard_library
 standard_library.install_aliases()
+from future.utils import raise_from
+
 from pickle import dumps
 
 import sys
@@ -62,19 +64,20 @@ def run(self, graph, config, updatehash=False):
             name = 'ipyparallel'
             __import__(name)
             self.iparallel = sys.modules[name]
-        except ImportError:
-            raise ImportError("ipyparallel not found. Parallel execution "
-                              "will be unavailable")
+        except ImportError as e:
+            raise_from(ImportError("ipyparallel not found. Parallel execution "
+                                   "will be unavailable"), e)
         try:
             self.taskclient = self.iparallel.Client()
         except Exception as e:
             if isinstance(e, TimeoutError):
-                raise Exception("No IPython clients found.")
+                raise_from(Exception("No IPython clients found."), e)
             if isinstance(e, IOError):
-                raise Exception("ipcluster/ipcontroller has not been started")
+                raise_from(Exception("ipcluster/ipcontroller has not been started"), e)
             if isinstance(e, ValueError):
-                raise Exception("Ipython kernel not installed")
-            raise e
+                raise_from(Exception("Ipython kernel not installed"), e)
+            else:
+                raise e
         return super(IPythonPlugin, self).run(graph, config, updatehash=updatehash)
 
     def _get_result(self, taskid):

nipype/pipeline/plugins/ipythonx.py

@@ -4,6 +4,7 @@
 """
 
 import sys
+from future.utils import raise_from
 
 from ...interfaces.base import LooseVersion
 IPython_not_loaded = False
@@ -44,16 +45,16 @@ def run(self, graph, config, updatehash=False):
             name = 'IPython.kernel.client'
             __import__(name)
             self.ipyclient = sys.modules[name]
-        except ImportError:
-            raise ImportError("Ipython kernel not found. Parallel execution "
-                              "will be unavailable")
+        except ImportError as e:
+            raise_from(ImportError("Ipython kernel not found. Parallel execution "
+                                   "will be unavailable"), e)
         try:
             self.taskclient = self.ipyclient.TaskClient()
         except Exception as e:
             if isinstance(e, ConnectionRefusedError):
-                raise Exception("No IPython clients found.")
+                raise_from(Exception("No IPython clients found."), e)
             if isinstance(e, ValueError):
-                raise Exception("Ipython kernel not installed")
+                raise_from(Exception("Ipython kernel not installed"), e)
         return super(IPythonXPlugin, self).run(graph, config, updatehash=updatehash)
 
     def _get_result(self, taskid):

nipype/testing/tests/test_utils.py

@@ -5,8 +5,10 @@
 
 import os
 import warnings
+import subprocess
+from mock import patch, MagicMock
 from nipype.testing.utils import TempFATFS
-from nose.tools import assert_true
+from nose.tools import assert_true, assert_raises
 
 
 def test_tempfatfs():
@@ -17,3 +19,12 @@ def test_tempfatfs():
     else:
         with fatfs as tmpdir:
             yield assert_true, os.path.exists(tmpdir)
+
+@patch('subprocess.check_call', MagicMock(
+    side_effect=subprocess.CalledProcessError('','')))
+def test_tempfatfs_calledprocesserror():
+    yield assert_raises, IOError, TempFATFS
+
+@patch('subprocess.Popen', MagicMock(side_effect=OSError()))
+def test_tempfatfs_oserror():
+    yield assert_raises, IOError, TempFATFS

nipype/testing/utils.py

@@ -12,7 +12,7 @@
 from tempfile import mkdtemp
 from ..utils.misc import package_check
 from nose import SkipTest
-
+from future.utils import raise_from
 
 def skip_if_no_package(*args, **kwargs):
     """Raise SkipTest if package_check fails
@@ -62,15 +62,15 @@ def __init__(self, size_in_mbytes=8, delay=0.5):
         try:
             subprocess.check_call(args=mkfs_args, stdout=self.dev_null,
                                   stderr=self.dev_null)
-        except subprocess.CalledProcessError:
-            raise IOError("mkfs.vfat failed")
+        except subprocess.CalledProcessError as e:
+            raise_from(IOError("mkfs.vfat failed"), e)
 
         try:
             self.fusefat = subprocess.Popen(args=mount_args,
                                             stdout=self.dev_null,
                                             stderr=self.dev_null)
-        except OSError:
-            raise IOError("fusefat is not installed")
+        except OSError as e:
+            raise_from(IOError("fusefat is not installed"), e)
 
         time.sleep(self.delay)