Merge remote-tracking branch 'upstream/master' into dev/2.0

Manually curated by CJM

Author: effigies

.github/release-drafter.yml

@@ -0,0 +1,4 @@
+template: |
+  ## What's Changed
+
+  $CHANGES

.travis.yml

@@ -1,34 +1,65 @@
-dist: trusty
-sudo: required
+dist: xenial
+sudo: true
 
 language: python
 # our build matrix
 python:
-- 3.4
 - 3.5
 - 3.6
-- 3.7-dev
+- 3.7
 
+# NOTE: Any changes to the matrix section should be duplicated below for
+#       Python 3.4
 env:
   global:
     - EXTRA_WHEELS="https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
     - PRE_WHEELS="https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com"
     - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
   matrix:
     - INSTALL_DEB_DEPENDECIES=true
-      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      NIPYPE_EXTRAS="doc,tests,nipy,profiler"
       CI_SKIP_TEST=1
     - INSTALL_DEB_DEPENDECIES=false
-      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      NIPYPE_EXTRAS="doc,tests,profiler"
       CI_SKIP_TEST=1
     - INSTALL_DEB_DEPENDECIES=true
-      NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,ssh"
+      NIPYPE_EXTRAS="doc,tests,nipy,profiler,duecredit,ssh"
       CI_SKIP_TEST=1
     - INSTALL_DEB_DEPENDECIES=true
-      NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+      NIPYPE_EXTRAS="doc,tests,nipy,profiler"
       EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
       CI_SKIP_TEST=1
 
+# Python 3.4 is only available on Trusty, so we need to duplicate the
+# env matrix specifically for it.
+matrix:
+  include:
+    - python: 3.4
+      dist: trusty
+      env:
+        - INSTALL_DEB_DEPENDECIES=true
+          NIPYPE_EXTRAS="doc,tests,nipy,profiler"
+          CI_SKIP_TEST=1
+    - python: 3.4
+      dist: trusty
+      env:
+        - INSTALL_DEB_DEPENDECIES=false
+          NIPYPE_EXTRAS="doc,tests,profiler"
+          CI_SKIP_TEST=1
+    - python: 3.4
+      dist: trusty
+      env:
+        - INSTALL_DEB_DEPENDECIES=true
+          NIPYPE_EXTRAS="doc,tests,nipy,profiler,duecredit,ssh"
+          CI_SKIP_TEST=1
+    - python: 3.4
+      dist: trusty
+      env:
+        - INSTALL_DEB_DEPENDECIES=true
+          NIPYPE_EXTRAS="doc,tests,nipy,profiler"
+          EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
+          CI_SKIP_TEST=1
+
 addons:
   apt:
     packages:

README.rst

@@ -90,6 +90,10 @@ To participate in the Nipype development related discussions please use the foll
 
 Please add *[nipype]* to the subject line when posting on the mailing list.
 
+You can even hangout with the Nipype developers in their 
+`Gitter <https://gitter.im/nipy/nipype>`_ channel or in the BrainHack `Slack <https://brainhack.slack.com/messages/C1FR76RAL>`_ channel. (Click `here <https://brainhack-slack-invite.herokuapp.com>`_ to join the Slack workspace.)
+
+
 Contributing to the project
 ---------------------------
 

doc/_templates/indexsidebar.html

@@ -4,10 +4,11 @@ <h3>{{ _('Links') }}</h3>
 <ul>
     <li>Docs: <a href="http://nipy.org/nipype">Stable</a> · <a href="http://nipype.readthedocs.org/en/latest/">Dev</a></li>
     <li>Code: <a href="http://github.com/nipy/nipype">Github</a> · <a href="http://github.com/nipy/nipype/issues">Bugs-Requests</a></li>
-    <li>Forum: <a href="http://neurostars.org/t/nipype">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
+    <li>Forum: <a href="https://neurostars.org/search?q=nipype">User</a> · <a href="https://mail.python.org/mailman/listinfo/neuroimaging">Developer</a></li>
+    <li>Chat: <a href="https://gitter.im/nipy/nipype">Gitter</a> · <a href="https://brainhack.slack.com/messages/C1FR76RAL">Slack</a></li>
     <li><a href="about.html#funding">Funding</a> · <a href="http://nipy.org/software/license/index.html"><img src="https://img.shields.io/pypi/l/nipype.svg" alt="License"></a></li>
     <li><a href="https://travis-ci.org/nipy/nipype"><img src="https://travis-ci.org/nipy/nipype.png?branch=master" alt="travis"></a> · <a href='https://codecov.io/gh/nipy/nipype'><img src='https://codecov.io/gh/nipy/nipype/branch/master/graph/badge.svg' alt='Coverage Status' /></a></li>
     <a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
 </ul>
 
-{% endblock %}
+{% endblock %} 

doc/devel/gitwash/known_projects.inc

@@ -3,7 +3,7 @@
 .. PROJECTNAME placeholders
 .. _PROJECTNAME: http://neuroimaging.scipy.org
 .. _`PROJECTNAME github`: http://github.com/nipy
-.. _`PROJECTNAME mailing list`: http://projects.scipy.org/mailman/listinfo/nipy-devel
+.. _`PROJECTNAME mailing list`: https://mail.python.org/mailman/listinfo/neuroimaging
 
 .. numpy
 .. _numpy: http://numpy.scipy.org

doc/devel/interface_specs.rst

@@ -12,6 +12,10 @@ In case of trouble, we encourage you to post on `NeuroStars <https://neurostars.
 NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.
 You can also post on the nipype developers mailing list: http://mail.python.org/mailman/listinfo/neuroimaging.
 As we are sharing a mailing list with the nipy community, please add ``[nipype]`` to the message title.
+Alternatively, you're welcome to chat with us in the Nipype 
+`Gitter <https://gitter.im/nipy/nipype>`_ channel or in the 
+BrainHack `Slack <https://brainhack.slack.com/messages/C1FR76RAL>`_ channel.
+(Click `here <https://brainhack-slack-invite.herokuapp.com>`_ to join the Slack workspace.)
 
 
 Overview

doc/links_names.txt

@@ -38,7 +38,7 @@
 .. _`nipy launchpad`: https://launchpad.net/nipy
 .. _launchpad: https://launchpad.net/
 .. _`nipy trunk`: https://code.launchpad.net/~nipy-developers/nipy/trunk
-.. _`nipy mailing list`: http://projects.scipy.org/mailman/listinfo/nipy-devel
+.. _`nipy mailing list`: https://mail.python.org/mailman/listinfo/neuroimaging
 .. _`nipy bugs`: https://bugs.launchpad.net/nipy
 
 .. Code support stuff

nipype/interfaces/utility/base.py

@@ -13,7 +13,7 @@
 
 from ..base import (traits, TraitedSpec, DynamicTraitedSpec, File, Undefined,
                     isdefined, OutputMultiPath, InputMultiPath, BaseInterface,
-                    BaseInterfaceInputSpec, Str)
+                    BaseInterfaceInputSpec, Str, SimpleInterface)
 from ..io import IOBase, add_traits
 from ...utils.filemanip import ensure_list, copyfile, split_filename
 
@@ -197,7 +197,6 @@ def _list_outputs(self):
 
 
 class RenameInputSpec(DynamicTraitedSpec):
-
     in_file = File(exists=True, mandatory=True, desc="file to rename")
     keep_ext = traits.Bool(
         desc=("Keep in_file extension, replace "
@@ -211,12 +210,11 @@ class RenameInputSpec(DynamicTraitedSpec):
 
 
 class RenameOutputSpec(TraitedSpec):
-
     out_file = traits.File(
         exists=True, desc="softlink to original file with new name")
 
 
-class Rename(IOBase):
+class Rename(SimpleInterface, IOBase):
     """Change the name of a file based on a mapped format string.
 
     To use additional inputs that will be defined at run-time, the class
@@ -296,15 +294,11 @@ def _rename(self):
 
     def _run_interface(self, runtime):
         runtime.returncode = 0
-        _ = copyfile(self.inputs.in_file,
-                     os.path.join(os.getcwd(), self._rename()))
+        out_file = os.path.join(runtime.cwd, self._rename())
+        _ = copyfile(self.inputs.in_file, out_file)
+        self._results['out_file'] = out_file
         return runtime
 
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        outputs["out_file"] = os.path.join(os.getcwd(), self._rename())
-        return outputs
-
 
 class SplitInputSpec(BaseInterfaceInputSpec):
     inlist = traits.List(