fix: miscellaneous improvements and fixes

In particular, after allowing printing the inheritance of interfaces,
links for ZZZCommandBase interfaces were broken, as originally filtered
out and not built. Now they are being built and we are back to 5
warnings.

Author: oesteban

doc/interfaces.rst

@@ -5,6 +5,11 @@
 ========================
 Interfaces and Workflows
 ========================
+:Release: |version|
+:Date: |today|
+
+Previous versions: `1.3.0 <http://nipype.readthedocs.io/en/1.3.0/>`_ `1.2.3 <http://nipype.readthedocs.io/en/1.2.3/>`_
+
 Workflows
 ---------
 .. important::

examples/fmri_spm_auditory.py

@@ -316,7 +316,7 @@ def makelist(item):
 
 Use the :class:`~nipype.pipeline.engine.workflows.Workflow` to create a
 graph-based execution pipeline for first level analysis.
-Set the :py:attr:`~nipype.pipeline.engine.workflows.Workflow.base_dir`
+Set the :py:attr:`~nipype.pipeline.engine.workflows.base.EngineBase.base_dir`
 option to instruct the pipeline engine to use ``spm_auditory_tutorial/workingdir``
 as the filesystem location to use when running the processes and keeping their
 outputs.

nipype/interfaces/afni/__init__.py

@@ -1,10 +1,11 @@
 # -*- 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:
-"""The afni module provides classes for interfacing with the `AFNI
-<http://afni.nimh.nih.gov/afni>`_ command line tools.
+"""
+AFNI_ is a software suite for the analysis and display of anatomical and functional MRI data.
+
+.. include:: ../../../doc/links_names.txt
 
-Top-level namespace for afni.
 """
 
 from .base import Info

nipype/interfaces/afni/base.py

@@ -1,7 +1,7 @@
 # -*- 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:
-"""Provide interface to AFNI commands."""
+"""Provide a base interface to AFNI commands."""
 import os
 from sys import platform
 from distutils import spawn
@@ -108,12 +108,17 @@ def standard_image(img_name):
 
 class AFNICommandBase(CommandLine):
     """
-    A base class to fix a linking problem in OSX and afni.
+    A base class to fix a linking problem in OSX and AFNI.
+
+    See Also
+    --------
+    `This thread
+    <http://afni.nimh.nih.gov/afni/community/board/read.php?1,145346,145347#msg-145347>`__
+    about the particular environment variable that fixes this problem.
 
-    See http://afni.nimh.nih.gov/afni/community/board/read.php?1,145346,145347#msg-145347
     """
 
-    def _run_interface(self, runtime):
+    def _run_interface(self, runtime, correct_return_codes=(0,)):
         if platform == "darwin":
             runtime.environ["DYLD_FALLBACK_LIBRARY_PATH"] = "/usr/local/afni/"
         return super(AFNICommandBase, self)._run_interface(runtime)
@@ -142,6 +147,7 @@ class AFNICommand(AFNICommandBase):
     """Shared options for several AFNI commands."""
 
     input_spec = AFNICommandInputSpec
+    output_spec = AFNICommandOutputSpec
     _outputtype = None
 
     references_ = [
@@ -294,13 +300,6 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True, ext=None)
         return fname
 
 
-def no_afni():
-    """Check whether AFNI is not available."""
-    if Info.version() is None:
-        return True
-    return False
-
-
 class AFNIPythonCommandInputSpec(CommandLineInputSpec):
     outputtype = traits.Enum(
         "AFNI", list(Info.ftypes.keys()), desc="AFNI output filetype"
@@ -323,3 +322,10 @@ def cmd(self):
     @property
     def _cmd_prefix(self):
         return "{} ".format(self.inputs.py27_path)
+
+
+def no_afni():
+    """Check whether AFNI is not available."""
+    if Info.version() is None:
+        return True
+    return False

nipype/pipeline/engine/base.py

@@ -1,11 +1,7 @@
-#!/usr/bin/env python
 # -*- 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:
-"""Defines functionality for pipelined execution of interfaces
-
-The `EngineBase` class implements the more general view of a task.
-"""
+"""Defines functionality for pipelined execution of interfaces."""
 from copy import deepcopy
 import re
 import numpy as np
@@ -16,10 +12,15 @@
 
 
 class EngineBase(object):
-    """Defines common attributes and functions for workflows and nodes."""
+    """
+    Defines common attributes and functions for workflows and nodes.
+
+    Implements the more general view of a task.
+    """
 
     def __init__(self, name=None, base_dir=None):
-        """ Initialize base parameters of a workflow or node
+        """
+        Initialize base parameters of a workflow or node.
 
         Parameters
         ----------
@@ -31,15 +32,19 @@ def __init__(self, name=None, base_dir=None):
             default=None, which results in the use of mkdtemp
 
         """
+        self._name = None
         self._hierarchy = None
         self.name = name
         self._id = self.name  # for compatibility with node expansion using iterables
 
         self.base_dir = base_dir
+        """Define the work directory for this instance of workflow element."""
+
         self.config = deepcopy(config._sections)
 
     @property
     def name(self):
+        """Set the unique name of this workflow element."""
         return self._name
 
     @name.setter
@@ -50,6 +55,7 @@ def name(self, name):
 
     @property
     def fullname(self):
+        """Build the full name down the hierarchy."""
         if self._hierarchy:
             return "%s.%s" % (self._hierarchy, self.name)
         return self.name
@@ -64,20 +70,22 @@ def outputs(self):
 
     @property
     def itername(self):
-        """Name for expanded iterable"""
+        """Get the name of the expanded iterable."""
         itername = self._id
         if self._hierarchy:
             itername = "%s.%s" % (self._hierarchy, self._id)
         return itername
 
     def clone(self, name):
-        """Clone an EngineBase object
+        """
+        Clone an EngineBase object.
 
         Parameters
         ----------
 
         name : string (mandatory)
             A clone of node or workflow must have a new name
+
         """
         if name == self.name:
             raise ValueError('Cloning requires a new name, "%s" is ' "in use." % name)
@@ -96,15 +104,20 @@ def _check_inputs(self, parameter):
         return hasattr(self.inputs, parameter)
 
     def __str__(self):
+        """Convert to string."""
         return self.fullname
 
     def __repr__(self):
+        """Get Python representation."""
         return self.itername
 
     def save(self, filename=None):
+        """Store this workflow element to a file."""
         if filename is None:
             filename = "temp.pklz"
         savepkl(filename, self)
 
-    def load(self, filename):
+    @staticmethod
+    def load(filename):
+        """Load this workflow element from a file."""
         return loadpkl(filename)

nipype/sphinxext/apidoc/__init__.py

@@ -41,12 +41,6 @@ class Config(NapoleonConfig):
     _config_values = {
         "nipype_skip_classes": (
             [
-                "AFNI(Python)?Command",
-                "ANTS",
-                "FSLCommand",
-                "FS(Command|Script)",
-                "Info",
-                "^SPM",
                 "Tester",
                 "InputSpec",
                 "OutputSpec",