Merge branch 'installation'

Author: Shoshana Berleant

doc/users/install.rst

@@ -83,6 +83,10 @@ or::
 
     nosetests --with-doctest nipype
 
+or::
+
+    nosetests --with-doctest nipype
+
 A successful test run should complete in a few minutes and end with
 something like::
 

doc/users/pipeline_tutorial.rst

@@ -49,7 +49,7 @@ Requirements
   - FSL_, FreeSurfer_, Camino_, ConnectomeViewer and MATLAB_ are available and
     callable from the command line
 
-  - SPM_ 5/8 is installed and callable in matlab
+  - SPM_ 5/8/12 is installed and callable in matlab
 
   - Space: 3-10 GB
 

nipype/algorithms/misc.py

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

nipype/external/six.py

@@ -21,7 +21,6 @@
 # SOFTWARE.
 
 from __future__ import absolute_import
-from future.utils import raise_from
 
 import functools
 import itertools
@@ -187,8 +186,8 @@ def find_module(self, fullname, path=None):
     def __get_module(self, fullname):
         try:
             return self.known_modules[fullname]
-        except KeyError as e:
-            raise_from(ImportError("This loader does not know module " + fullname), e)
+        except KeyError:
+            raise ImportError("This loader does not know module " + fullname)
 
     def load_module(self, fullname):
         try:

nipype/interfaces/afni/base.py

@@ -5,7 +5,6 @@
 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
@@ -83,9 +82,9 @@ def outputtype_to_ext(cls, outputtype):
 
         try:
             return cls.ftypes[outputtype]
-        except KeyError as e:
+        except KeyError:
             msg = 'Invalid AFNIOUTPUTTYPE: ', outputtype
-            raise_from(KeyError(msg), e)
+            raise KeyError(msg)
 
     @classmethod
     def outputtype(cls):

nipype/pipeline/plugins/ipython.py

@@ -5,7 +5,6 @@
 
 from future import standard_library
 standard_library.install_aliases()
-from future.utils import raise_from
 
 from pickle import dumps
 
@@ -64,20 +63,19 @@ def run(self, graph, config, updatehash=False):
             name = 'ipyparallel'
             __import__(name)
             self.iparallel = sys.modules[name]
-        except ImportError as e:
-            raise_from(ImportError("Ipython kernel not found. Parallel execution "
-                                   "will be unavailable"), e)
+        except ImportError:
+            raise ImportError("Ipython kernel not found. Parallel execution "
+                              "will be unavailable")
         try:
             self.taskclient = self.iparallel.Client()
         except Exception as e:
             if isinstance(e, TimeoutError):
-                raise_from(Exception("No IPython clients found."), e)
+                raise Exception("No IPython clients found.")
             if isinstance(e, IOError):
-                raise_from(Exception("ipcluster/ipcontroller has not been started"), e)
+                raise Exception("ipcluster/ipcontroller has not been started")
             if isinstance(e, ValueError):
-                raise_from(Exception("Ipython kernel not installed"), e)
-            else:
-                raise e
+                raise Exception("Ipython kernel not installed")
+            raise e
         return super(IPythonPlugin, self).run(graph, config, updatehash=updatehash)
 
     def _get_result(self, taskid):

nipype/pipeline/plugins/ipythonx.py

@@ -4,7 +4,6 @@
 """
 
 import sys
-from future.utils import raise_from
 
 IPython_not_loaded = False
 try:
@@ -37,16 +36,16 @@ def run(self, graph, config, updatehash=False):
             name = 'IPython.kernel.client'
             __import__(name)
             self.ipyclient = sys.modules[name]
-        except ImportError as e:
-            raise_from(ImportError("Ipython kernel not found. Parallel execution "
-                                   "will be unavailable"), e)
+        except ImportError:
+            raise ImportError("Ipython kernel not found. Parallel execution "
+                              "will be unavailable")
         try:
             self.taskclient = self.ipyclient.TaskClient()
         except Exception as e:
             if isinstance(e, ConnectionRefusedError):
-                raise_from(Exception("No IPython clients found."), e)
+                raise Exception("No IPython clients found.")
             if isinstance(e, ValueError):
-                raise_from(Exception("Ipython kernel not installed"), e)
+                raise Exception("Ipython kernel not installed")
         return super(IPythonXPlugin, self).run(graph, config, updatehash=updatehash)
 
     def _get_result(self, taskid):

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 as e:
-            raise_from(IOError("mkfs.vfat failed"), e)
+        except subprocess.CalledProcessError:
+            raise IOError("mkfs.vfat failed")
 
         try:
             self.fusefat = subprocess.Popen(args=mount_args,
                                             stdout=self.dev_null,
                                             stderr=self.dev_null)
-        except OSError as e:
-            raise_from(IOError("fusefat is not installed"), e)
+        except OSError:
+            raise IOError("fusefat is not installed")
 
         time.sleep(self.delay)
 

nipype/utils/misc.py

@@ -5,7 +5,6 @@
 
 from future import standard_library
 standard_library.install_aliases()
-from future.utils import raise_from
 from builtins import next
 from pickle import dumps, loads
 import inspect
@@ -91,14 +90,14 @@ def create_function_from_source(function_source, imports=None):
             import_keys = list(ns.keys())
         exec(function_source, ns)
 
-    except Exception as e:
-        msg = '\nError executing function:\n %s\n' % function_source
+    except Exception as msg:
+        msg = str(msg) + '\nError executing function:\n %s\n' % function_source
         msg += '\n'.join(["Functions in connection strings have to be standalone.",
                           "They cannot be declared either interactively or inside",
                           "another function or inline in the connect string. Any",
                           "imports should be done inside the function"
                           ])
-        raise_from(RuntimeError(msg), e)
+        raise RuntimeError(msg)
     ns_funcs = list(set(ns) - set(import_keys + ['__builtins__']))
     assert len(ns_funcs) == 1, "Function or inputs are ill-defined"
     funcname = ns_funcs[0]
@@ -200,14 +199,14 @@ def package_check(pkg_name, version=None, app=None, checker=LooseVersion,
         msg += ' with version >= %s' % (version,)
     try:
         mod = __import__(pkg_name)
-    except ImportError as e:
-        raise_from(exc_failed_import(msg), e)
+    except ImportError:
+        raise exc_failed_import(msg)
     if not version:
         return
     try:
         have_version = mod.__version__
-    except AttributeError as e:
-        raise_from(exc_failed_check('Cannot find version for %s' % pkg_name), e)
+    except AttributeError:
+        raise exc_failed_check('Cannot find version for %s' % pkg_name)
     if checker(have_version) < checker(version):
         raise exc_failed_check(msg)
 

nipype/utils/spm_docs.py

@@ -4,7 +4,6 @@
 
 import os
 
-from future.utils import raise_from
 from nipype.interfaces import matlab
 
 
@@ -56,5 +55,5 @@ def _strip_header(doc):
         except ValueError:
             index = len(doc)
         return doc[:index]
-    except KeyError as e:
-        raise_from(IOError('This docstring was not generated by Nipype!\n'), e)
+    except KeyError:
+        raise IOError('This docstring was not generated by Nipype!\n')

nipype/workflows/dmri/connectivity/group_connectivity.py

@@ -1,8 +1,4 @@
-asdf;alksjahgldhjgioae
-
-
 from __future__ import print_function
-from future.utils import raise_from
 
 import os.path as op
 
@@ -463,9 +459,9 @@ def create_average_networks_by_group_workflow(group_list, data_dir, subjects_dir
     try:
         l4infosource.inputs.group_id1 = list(group_list.keys())[0]
         l4infosource.inputs.group_id2 = list(group_list.keys())[1]
-    except IndexError as e:
+    except IndexError:
         print('The create_average_networks_by_group_workflow requires 2 groups')
-        raise_from(Exception(), e)
+        raise Exception
 
     l4info = dict(networks=[['group_id', '']], CMatrices=[['group_id', '']], fibmean=[['group_id', 'mean_fiber_length']],
                   fibdev=[['group_id', 'fiber_length_std']])