From a1b903c6009d07a6c8e922f86745f2f536e52df5 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Fri, 1 Sep 2017 11:15:49 -0700
Subject: [PATCH 01/19] Added BIDSDataGrabber, test data and tests

---
 nipype/interfaces/bids.py | 147 ++++++++++++++++++++++++++++++++++++++
 requirements.txt          |   1 +
 2 files changed, 148 insertions(+)
 create mode 100644 nipype/interfaces/bids.py

diff --git a/nipype/interfaces/bids.py b/nipype/interfaces/bids.py
new file mode 100644
index 0000000000..343542aa09
--- /dev/null
+++ b/nipype/interfaces/bids.py
@@ -0,0 +1,147 @@
+# -*- 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:
+""" Set of interfaces that allow interaction with BIDS data. Currently
+    available interfaces are:
+
+    BIDSDataGrabber: Query data from BIDS dataset using pybids grabbids.
+
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
+    >>> os.chdir(datadir)
+
+"""
+
+from .base import (traits,
+                   DynamicTraitedSpec,
+                   BaseInterface,
+                   isdefined,
+                   Str,
+                   Undefined)
+
+from bids.grabbids import BIDSLayout
+
+
+class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
+    base_dir = traits.Directory(exists=True,
+                                desc='Path to BIDS Directory.',
+                                mandatory=True)
+    output_query = traits.Dict(key_trait=Str,
+                               value_trait=traits.Dict,
+                               desc='Queries for outfield outputs')
+    return_type = traits.Enum('filename', 'namedtuple', usedefault=True)
+
+
+class BIDSDataGrabber(BaseInterface):
+
+    """ BIDS datagrabber module that wraps around pybids to allow arbitrary
+        querying of BIDS datasets.
+
+        Examples
+        --------
+
+        >>> from nipype.interfaces.bids import BIDSDataGrabber
+        >>> from os.path import basename
+        >>> import pprint
+
+        Select all files from a BIDS project
+
+        >>> bg = BIDSDataGrabber()
+        >>> bg.inputs.base_dir = 'ds005/'
+        >>> results = bg.run()
+        >>> pprint.pprint(len(results.outputs.outfield)) # doctest: +ALLOW_UNICODE
+        116
+
+        Using dynamically created, user-defined input fields,
+        filter files based on BIDS entities.
+
+        >>> bg = BIDSDataGrabber(infields = ['subject', 'run'])
+        >>> bg.inputs.base_dir = 'ds005/'
+        >>> bg.inputs.subject = '01'
+        >>> bg.inputs.run = '01'
+        >>> results = bg.run()
+        >>> basename(results.outputs.outfield[0]) # doctest: +ALLOW_UNICODE
+        'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+
+        Using user-defined output fields, return different types of outputs,
+        filtered on common entities
+        filter files based on BIDS entities.
+
+        >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['func', 'anat'])
+        >>> bg.inputs.base_dir = 'ds005/'
+        >>> bg.inputs.subject = '01'
+        >>> bg.inputs.output_query['func'] = dict(modality='func')
+        >>> bg.inputs.output_query['anat'] = dict(modality='anat')
+        >>> results = bg.run()
+        >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
+        'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+
+        >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
+        'sub-01_T1w.nii.gz'
+    """
+    input_spec = BIDSDataGrabberInputSpec
+    output_spec = DynamicTraitedSpec
+    _always_run = True
+
+    def __init__(self, infields=None, outfields=None, **kwargs):
+        """
+        Parameters
+        ----------
+        infields : list of str
+            Indicates the input fields to be dynamically created
+
+        outfields: list of str
+            Indicates output fields to be dynamically created
+
+        """
+        if not outfields:
+            outfields = []
+        if not infields:
+            infields = []
+
+        super(BIDSDataGrabber, self).__init__(**kwargs)
+        undefined_traits = {}
+        # used for mandatory inputs check
+        self._infields = infields
+        self._outfields = outfields
+        for key in infields:
+            self.inputs.add_trait(key, traits.Any)
+            undefined_traits[key] = Undefined
+
+        if not isdefined(self.inputs.output_query):
+            self.inputs.output_query = {}
+
+        self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
+
+    def _run_interface(self, runtime):
+        return runtime
+
+    def _list_outputs(self):
+        if not self._outfields:
+            self._outfields = ['outfield']
+            self.inputs.output_query = {'outfield' : {}}
+        else:
+            for key in self._outfields:
+                if key not in self.inputs.output_query:
+                    raise ValueError("Define query for all outputs")
+
+        for key in self._infields:
+            value = getattr(self.inputs, key)
+            if not isdefined(value):
+                msg = "%s requires a value for input '%s' because" \
+                      " it was listed in 'infields'" % \
+                    (self.__class__.__name__, key)
+                raise ValueError(msg)
+
+        layout = BIDSLayout(self.inputs.base_dir)
+
+        filters = {i: getattr(self.inputs, i) for i in self._infields}
+
+        outputs = {}
+        for key, query in self.inputs.output_query.items():
+            outputs[key] = layout.get(
+                **dict(query.items() | filters.items()),
+                return_type='file')
+        return outputs
diff --git a/requirements.txt b/requirements.txt
index bcd3ab2fef..3e9009a21a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -13,4 +13,5 @@ configparser
 pytest>=3.0
 mock
 pydotplus
+pybids==0.3
 packaging

From da44acf74365dfe49668abb39406860a1d4805b1 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Fri, 1 Sep 2017 11:50:38 -0700
Subject: [PATCH 02/19] Edited contributors

---
 .zenodo.json | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.zenodo.json b/.zenodo.json
index b76c0e6313..ad164e2795 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -523,7 +523,12 @@
       "affiliation": "University of Amsterdam",
       "name": "Lukas Snoek",
       "orcid": "0000-0001-8972-204X"
-    }
+    },
+    {
+      "affiliation": "University of Texas at Austin",
+      "name": "De La Vega, Alejandro",
+      "orcid": "0000-0001-9062-3778"
+    },
   ],
   "keywords": [
     "neuroimaging",

From 8ed1c44ea23884b6d2a597d30b87c31a10452402 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Mon, 4 Sep 2017 15:42:06 -0700
Subject: [PATCH 03/19] Removed data, using test data from pybids package

---
 nipype/interfaces/bids.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/nipype/interfaces/bids.py b/nipype/interfaces/bids.py
index 343542aa09..317c871468 100644
--- a/nipype/interfaces/bids.py
+++ b/nipype/interfaces/bids.py
@@ -8,8 +8,9 @@
 
     Change directory to provide relative paths for doctests
     >>> import os
-    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
+    >>> import bids
+    >>> filepath = os.path.realpath(os.path.dirname(bids.__file__))
+    >>> datadir = os.path.realpath(os.path.join(filepath, 'grabbids/tests/data/'))
     >>> os.chdir(datadir)
 
 """
@@ -51,7 +52,7 @@ class BIDSDataGrabber(BaseInterface):
         >>> bg = BIDSDataGrabber()
         >>> bg.inputs.base_dir = 'ds005/'
         >>> results = bg.run()
-        >>> pprint.pprint(len(results.outputs.outfield)) # doctest: +ALLOW_UNICODE
+        >>> len(results.outputs.outfield) # doctest: +ALLOW_UNICODE
         116
 
         Using dynamically created, user-defined input fields,

From 52cf9e4977d3b4371d26222562b2ae0c03233caf Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Mon, 4 Sep 2017 16:14:03 -0700
Subject: [PATCH 04/19] Check if pybids is installed when importing

---
 nipype/interfaces/bids.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/bids.py b/nipype/interfaces/bids.py
index 317c871468..5e772569b2 100644
--- a/nipype/interfaces/bids.py
+++ b/nipype/interfaces/bids.py
@@ -22,7 +22,12 @@
                    Str,
                    Undefined)
 
-from bids.grabbids import BIDSLayout
+try:
+    from bids.grabbids import BIDSLayout
+except ImportError:
+    have_pybids = False
+else:
+    have_pybids = True
 
 
 class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
@@ -117,6 +122,9 @@ def __init__(self, infields=None, outfields=None, **kwargs):
         self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
 
     def _run_interface(self, runtime):
+        if not have_pybids:
+            raise ImportError("The BIDSEventsGrabber interface requires pybids."
+                              " Please make sure it is installed.")
         return runtime
 
     def _list_outputs(self):

From 6a4ce640570c2fdecfd87dce14998d4744fb0fba Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Mon, 4 Sep 2017 18:56:03 -0700
Subject: [PATCH 05/19] Tried to fix reqs and travis

---
 .travis.yml      | 6 +++---
 nipype/info.py   | 1 +
 requirements.txt | 1 -
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index f97f48dddb..4cd6d7bb7f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,9 +8,9 @@ python:
 - 3.5
 - 3.6
 env:
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler"
-- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit"
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,pybids"
+- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler,pybids"
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,pybids"
 before_install:
 - function apt_inst {
   if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
diff --git a/nipype/info.py b/nipype/info.py
index 9db9a02abd..d1a6501252 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -160,6 +160,7 @@ def get_nipype_gitversion():
     'profiler': ['psutil'],
     'duecredit': ['duecredit'],
     'xvfbwrapper': ['xvfbwrapper'],
+    'pybids' : ['pybids']
     # 'mesh': ['mayavi']  # Enable when it works
 }
 
diff --git a/requirements.txt b/requirements.txt
index 3e9009a21a..bcd3ab2fef 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -13,5 +13,4 @@ configparser
 pytest>=3.0
 mock
 pydotplus
-pybids==0.3
 packaging

From 72bd8e267e838cc91693c6eb39eb9ab01208c54f Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Fri, 8 Sep 2017 11:56:26 -0700
Subject: [PATCH 06/19] Added mandatory option for outfieds

---
 nipype/interfaces/bids.py | 27 +++++++++++++++++++++------
 1 file changed, 21 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/bids.py b/nipype/interfaces/bids.py
index 5e772569b2..db2e7c6f44 100644
--- a/nipype/interfaces/bids.py
+++ b/nipype/interfaces/bids.py
@@ -29,6 +29,7 @@
 else:
     have_pybids = True
 
+from warnings import warn
 
 class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
     base_dir = traits.Directory(exists=True,
@@ -37,6 +38,9 @@ class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
     output_query = traits.Dict(key_trait=Str,
                                value_trait=traits.Dict,
                                desc='Queries for outfield outputs')
+    raise_on_empty = traits.Bool(True, usedefault=True,
+                                 desc='Generate exception if list is empty '
+                                 'for a given field')
     return_type = traits.Enum('filename', 'namedtuple', usedefault=True)
 
 
@@ -58,7 +62,7 @@ class BIDSDataGrabber(BaseInterface):
         >>> bg.inputs.base_dir = 'ds005/'
         >>> results = bg.run()
         >>> len(results.outputs.outfield) # doctest: +ALLOW_UNICODE
-        116
+        135
 
         Using dynamically created, user-defined input fields,
         filter files based on BIDS entities.
@@ -99,8 +103,8 @@ def __init__(self, infields=None, outfields=None, **kwargs):
             Indicates the input fields to be dynamically created
 
         outfields: list of str
-            Indicates output fields to be dynamically created
-
+            Indicates output fields to be dynamically created.
+            If no matching items, returns Undefined.
         """
         if not outfields:
             outfields = []
@@ -150,7 +154,18 @@ def _list_outputs(self):
 
         outputs = {}
         for key, query in self.inputs.output_query.items():
-            outputs[key] = layout.get(
-                **dict(query.items() | filters.items()),
-                return_type='file')
+            args = query.copy()
+            args.update(filters)
+            filelist = layout.get(return_type='file',
+                                      **args)
+            if len(filelist) == 0:
+                msg = 'Output key: %s returned no files' % (
+                    key)
+                if self.inputs.raise_on_empty:
+                    raise IOError(msg)
+                else:
+                    warn(msg)
+                    filelist = Undefined
+            else:
+                outputs[key] = filelist
         return outputs

From dc64c7284cb972dd288883515cd11999cb22e4fe Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Wed, 13 Sep 2017 19:24:58 -0500
Subject: [PATCH 07/19] Install pybids from github in travis

---
 .travis.yml | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 4cd6d7bb7f..73d42a15f9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,9 +8,9 @@ python:
 - 3.5
 - 3.6
 env:
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,pybids"
-- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler,pybids"
-- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit,pybids"
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+- INSTALL_DEB_DEPENDECIES=false NIPYPE_EXTRAS="doc,tests,fmri,profiler"
+- INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,fmri,profiler,duecredit"
 before_install:
 - function apt_inst {
   if $INSTALL_DEB_DEPENDECIES; then sudo rm -rf /dev/shm; fi &&
@@ -36,7 +36,12 @@ before_install:
   conda install python=${TRAVIS_PYTHON_VERSION} &&
   conda config --add channels conda-forge &&
   conda install -y nipype icu &&
-  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*; }
+  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*;
+  pushd $HOME;
+  git clone https://github.com/INCF/pybids.git;
+  cd pybids;
+  pip install -e .;
+  popd; }
 #  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
 - travis_retry apt_inst
 - travis_retry conda_inst

From 406c72914e67e147ea484b6684d9be5fce463eb9 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Wed, 13 Sep 2017 19:26:05 -0500
Subject: [PATCH 08/19] Fix docstring, and Directory import

---
 nipype/interfaces/bids.py | 109 +++++++++++++++++++-------------------
 1 file changed, 55 insertions(+), 54 deletions(-)

diff --git a/nipype/interfaces/bids.py b/nipype/interfaces/bids.py
index db2e7c6f44..cf2e63d545 100644
--- a/nipype/interfaces/bids.py
+++ b/nipype/interfaces/bids.py
@@ -2,21 +2,22 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """ Set of interfaces that allow interaction with BIDS data. Currently
-    available interfaces are:
+available interfaces are:
 
-    BIDSDataGrabber: Query data from BIDS dataset using pybids grabbids.
+BIDSDataGrabber: Query data from BIDS dataset using pybids grabbids.
 
-    Change directory to provide relative paths for doctests
-    >>> import os
-    >>> import bids
-    >>> filepath = os.path.realpath(os.path.dirname(bids.__file__))
-    >>> datadir = os.path.realpath(os.path.join(filepath, 'grabbids/tests/data/'))
-    >>> os.chdir(datadir)
+Change directory to provide relative paths for doctests
+>>> import os
+>>> import bids
+>>> filepath = os.path.realpath(os.path.dirname(bids.__file__))
+>>> datadir = os.path.realpath(os.path.join(filepath, 'grabbids/tests/data/'))
+>>> os.chdir(datadir)
 
 """
 
 from .base import (traits,
                    DynamicTraitedSpec,
+                   Directory,
                    BaseInterface,
                    isdefined,
                    Str,
@@ -32,9 +33,9 @@
 from warnings import warn
 
 class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
-    base_dir = traits.Directory(exists=True,
-                                desc='Path to BIDS Directory.',
-                                mandatory=True)
+    base_dir = Directory(exists=True,
+                         desc='Path to BIDS Directory.',
+                         mandatory=True)
     output_query = traits.Dict(key_trait=Str,
                                value_trait=traits.Dict,
                                desc='Queries for outfield outputs')
@@ -47,49 +48,49 @@ class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
 class BIDSDataGrabber(BaseInterface):
 
     """ BIDS datagrabber module that wraps around pybids to allow arbitrary
-        querying of BIDS datasets.
-
-        Examples
-        --------
-
-        >>> from nipype.interfaces.bids import BIDSDataGrabber
-        >>> from os.path import basename
-        >>> import pprint
-
-        Select all files from a BIDS project
-
-        >>> bg = BIDSDataGrabber()
-        >>> bg.inputs.base_dir = 'ds005/'
-        >>> results = bg.run()
-        >>> len(results.outputs.outfield) # doctest: +ALLOW_UNICODE
-        135
-
-        Using dynamically created, user-defined input fields,
-        filter files based on BIDS entities.
-
-        >>> bg = BIDSDataGrabber(infields = ['subject', 'run'])
-        >>> bg.inputs.base_dir = 'ds005/'
-        >>> bg.inputs.subject = '01'
-        >>> bg.inputs.run = '01'
-        >>> results = bg.run()
-        >>> basename(results.outputs.outfield[0]) # doctest: +ALLOW_UNICODE
-        'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
-
-        Using user-defined output fields, return different types of outputs,
-        filtered on common entities
-        filter files based on BIDS entities.
-
-        >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['func', 'anat'])
-        >>> bg.inputs.base_dir = 'ds005/'
-        >>> bg.inputs.subject = '01'
-        >>> bg.inputs.output_query['func'] = dict(modality='func')
-        >>> bg.inputs.output_query['anat'] = dict(modality='anat')
-        >>> results = bg.run()
-        >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
-        'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
-
-        >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
-        'sub-01_T1w.nii.gz'
+    querying of BIDS datasets.
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.bids import BIDSDataGrabber
+    >>> from os.path import basename
+    >>> import pprint
+
+    Select all files from a BIDS project
+
+    >>> bg = BIDSDataGrabber()
+    >>> bg.inputs.base_dir = 'ds005/'
+    >>> results = bg.run()
+    >>> len(results.outputs.outfield) # doctest: +ALLOW_UNICODE
+    135
+
+    Using dynamically created, user-defined input fields,
+    filter files based on BIDS entities.
+
+    >>> bg = BIDSDataGrabber(infields = ['subject', 'run'])
+    >>> bg.inputs.base_dir = 'ds005/'
+    >>> bg.inputs.subject = '01'
+    >>> bg.inputs.run = '01'
+    >>> results = bg.run()
+    >>> basename(results.outputs.outfield[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+
+    Using user-defined output fields, return different types of outputs,
+    filtered on common entities
+    filter files based on BIDS entities.
+
+    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['func', 'anat'])
+    >>> bg.inputs.base_dir = 'ds005/'
+    >>> bg.inputs.subject = '01'
+    >>> bg.inputs.output_query['func'] = dict(modality='func')
+    >>> bg.inputs.output_query['anat'] = dict(modality='anat')
+    >>> results = bg.run()
+    >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+
+    >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_T1w.nii.gz'
     """
     input_spec = BIDSDataGrabberInputSpec
     output_spec = DynamicTraitedSpec

From 0915a9d0ec055ebb0115f631baa78d8d15563918 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Wed, 13 Sep 2017 19:27:19 -0500
Subject: [PATCH 09/19] Use logger

---
 nipype/interfaces/bids.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nipype/interfaces/bids.py b/nipype/interfaces/bids.py
index cf2e63d545..190608fb2a 100644
--- a/nipype/interfaces/bids.py
+++ b/nipype/interfaces/bids.py
@@ -14,7 +14,7 @@
 >>> os.chdir(datadir)
 
 """
-
+from .. import logging
 from .base import (traits,
                    DynamicTraitedSpec,
                    Directory,
@@ -30,7 +30,7 @@
 else:
     have_pybids = True
 
-from warnings import warn
+LOGGER = logging.getLogger('workflows')
 
 class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
     base_dir = Directory(exists=True,
@@ -165,7 +165,7 @@ def _list_outputs(self):
                 if self.inputs.raise_on_empty:
                     raise IOError(msg)
                 else:
-                    warn(msg)
+                    LOGGER.warning(msg)
                     filelist = Undefined
             else:
                 outputs[key] = filelist

From 651bc85c831e32bbc5e4f1ccfb2c08275f208cae Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Wed, 13 Sep 2017 20:37:12 -0500
Subject: [PATCH 10/19] Smart defaults

---
 nipype/interfaces/bids.py | 102 +++++++++++++++++++-------------------
 1 file changed, 50 insertions(+), 52 deletions(-)

diff --git a/nipype/interfaces/bids.py b/nipype/interfaces/bids.py
index 190608fb2a..1bb15bc6bf 100644
--- a/nipype/interfaces/bids.py
+++ b/nipype/interfaces/bids.py
@@ -14,6 +14,7 @@
 >>> os.chdir(datadir)
 
 """
+from os.path import join, dirname
 from .. import logging
 from .base import (traits,
                    DynamicTraitedSpec,
@@ -24,7 +25,8 @@
                    Undefined)
 
 try:
-    from bids.grabbids import BIDSLayout
+    from bids import grabbids as gb
+    import json
 except ImportError:
     have_pybids = False
 else:
@@ -57,40 +59,34 @@ class BIDSDataGrabber(BaseInterface):
     >>> from os.path import basename
     >>> import pprint
 
-    Select all files from a BIDS project
+    By default, the BIDSDataGrabber fetches anatomical and functional images
+    from a project, and makes BIDS entities (e.g. subject) available for
+    filtering outputs.
 
     >>> bg = BIDSDataGrabber()
     >>> bg.inputs.base_dir = 'ds005/'
-    >>> results = bg.run()
-    >>> len(results.outputs.outfield) # doctest: +ALLOW_UNICODE
-    135
-
-    Using dynamically created, user-defined input fields,
-    filter files based on BIDS entities.
-
-    >>> bg = BIDSDataGrabber(infields = ['subject', 'run'])
-    >>> bg.inputs.base_dir = 'ds005/'
     >>> bg.inputs.subject = '01'
-    >>> bg.inputs.run = '01'
     >>> results = bg.run()
-    >>> basename(results.outputs.outfield[0]) # doctest: +ALLOW_UNICODE
+    >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_T1w.nii.gz'
+
+    >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
     'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
 
-    Using user-defined output fields, return different types of outputs,
-    filtered on common entities
-    filter files based on BIDS entities.
 
-    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['func', 'anat'])
+    Dynamically created, user-defined output fields can also be defined to
+    return different types of outputs from the same project. All outputs
+    are filtered on common entities, which can be explicitly defined as
+    infields.
+
+    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
     >>> bg.inputs.base_dir = 'ds005/'
     >>> bg.inputs.subject = '01'
-    >>> bg.inputs.output_query['func'] = dict(modality='func')
-    >>> bg.inputs.output_query['anat'] = dict(modality='anat')
+    >>> bg.inputs.output_query['dwi'] = dict(modality='dwi')
     >>> results = bg.run()
-    >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
-    'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+    >>> basename(results.outputs.dwi[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_dwi.nii.gz'
 
-    >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
-    'sub-01_T1w.nii.gz'
     """
     input_spec = BIDSDataGrabberInputSpec
     output_spec = DynamicTraitedSpec
@@ -107,51 +103,53 @@ def __init__(self, infields=None, outfields=None, **kwargs):
             Indicates output fields to be dynamically created.
             If no matching items, returns Undefined.
         """
-        if not outfields:
-            outfields = []
-        if not infields:
-            infields = []
-
         super(BIDSDataGrabber, self).__init__(**kwargs)
-        undefined_traits = {}
-        # used for mandatory inputs check
+        if not have_pybids:
+            raise ImportError("The BIDSEventsGrabber interface requires pybids."
+                              " Please make sure it is installed.")
+
+        # If outfields is None use anat and func as default
+        if outfields is None:
+            outfields = ['func', 'anat']
+            self.inputs.output_query = {
+                "func": {"modality": "func"},
+                "anat": {"modality": "anat"}}
+        else:
+            self.inputs.output_query = {}
+
+        # If infields is None, use all BIDS entities
+        if infields is None:
+            bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
+            bids_config = json.load(open(bids_config, 'r'))
+            infields = [i['name'] for i in bids_config['entities']]
+
         self._infields = infields
         self._outfields = outfields
+
+        # used for mandatory inputs check
+        undefined_traits = {}
         for key in infields:
             self.inputs.add_trait(key, traits.Any)
             undefined_traits[key] = Undefined
 
-        if not isdefined(self.inputs.output_query):
-            self.inputs.output_query = {}
-
         self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
 
     def _run_interface(self, runtime):
-        if not have_pybids:
-            raise ImportError("The BIDSEventsGrabber interface requires pybids."
-                              " Please make sure it is installed.")
         return runtime
 
     def _list_outputs(self):
-        if not self._outfields:
-            self._outfields = ['outfield']
-            self.inputs.output_query = {'outfield' : {}}
-        else:
-            for key in self._outfields:
-                if key not in self.inputs.output_query:
-                    raise ValueError("Define query for all outputs")
+        layout = gb.BIDSLayout(self.inputs.base_dir)
+
+        for key in self._outfields:
+            if key not in self.inputs.output_query:
+                raise ValueError("Define query for all outputs")
 
+        # If infield is not given nm input value, silently ignore
+        filters = {}
         for key in self._infields:
             value = getattr(self.inputs, key)
-            if not isdefined(value):
-                msg = "%s requires a value for input '%s' because" \
-                      " it was listed in 'infields'" % \
-                    (self.__class__.__name__, key)
-                raise ValueError(msg)
-
-        layout = BIDSLayout(self.inputs.base_dir)
-
-        filters = {i: getattr(self.inputs, i) for i in self._infields}
+            if isdefined(value):
+                filters[key] = value
 
         outputs = {}
         for key, query in self.inputs.output_query.items():

From dd03863d9df998f8e2c06c066c7ff80f5f23a51d Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Wed, 13 Sep 2017 21:04:30 -0500
Subject: [PATCH 11/19] Try fix CI

---
 docker/base.Dockerfile    |   5 +-
 nipype/interfaces/bids.py | 170 --------------------------------------
 2 files changed, 4 insertions(+), 171 deletions(-)
 delete mode 100644 nipype/interfaces/bids.py

diff --git a/docker/base.Dockerfile b/docker/base.Dockerfile
index a5b5134c2c..3de42492ce 100644
--- a/docker/base.Dockerfile
+++ b/docker/base.Dockerfile
@@ -148,5 +148,8 @@ ENV MATLABCMD="/opt/mcr/v85/toolbox/matlab" \
     SPMMCRCMD="/opt/spm12/run_spm12.sh /opt/mcr/v85/ script" \
     FORCE_SPMMCR=1
 
-WORKDIR /work
+# Install pybids
+RUN git clone https://github.com/INCF/pybids.git
+RUN pip install -e .
 
+WORKDIR /work
diff --git a/nipype/interfaces/bids.py b/nipype/interfaces/bids.py
deleted file mode 100644
index 1bb15bc6bf..0000000000
--- a/nipype/interfaces/bids.py
+++ /dev/null
@@ -1,170 +0,0 @@
-# -*- 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:
-""" Set of interfaces that allow interaction with BIDS data. Currently
-available interfaces are:
-
-BIDSDataGrabber: Query data from BIDS dataset using pybids grabbids.
-
-Change directory to provide relative paths for doctests
->>> import os
->>> import bids
->>> filepath = os.path.realpath(os.path.dirname(bids.__file__))
->>> datadir = os.path.realpath(os.path.join(filepath, 'grabbids/tests/data/'))
->>> os.chdir(datadir)
-
-"""
-from os.path import join, dirname
-from .. import logging
-from .base import (traits,
-                   DynamicTraitedSpec,
-                   Directory,
-                   BaseInterface,
-                   isdefined,
-                   Str,
-                   Undefined)
-
-try:
-    from bids import grabbids as gb
-    import json
-except ImportError:
-    have_pybids = False
-else:
-    have_pybids = True
-
-LOGGER = logging.getLogger('workflows')
-
-class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
-    base_dir = Directory(exists=True,
-                         desc='Path to BIDS Directory.',
-                         mandatory=True)
-    output_query = traits.Dict(key_trait=Str,
-                               value_trait=traits.Dict,
-                               desc='Queries for outfield outputs')
-    raise_on_empty = traits.Bool(True, usedefault=True,
-                                 desc='Generate exception if list is empty '
-                                 'for a given field')
-    return_type = traits.Enum('filename', 'namedtuple', usedefault=True)
-
-
-class BIDSDataGrabber(BaseInterface):
-
-    """ BIDS datagrabber module that wraps around pybids to allow arbitrary
-    querying of BIDS datasets.
-
-    Examples
-    --------
-
-    >>> from nipype.interfaces.bids import BIDSDataGrabber
-    >>> from os.path import basename
-    >>> import pprint
-
-    By default, the BIDSDataGrabber fetches anatomical and functional images
-    from a project, and makes BIDS entities (e.g. subject) available for
-    filtering outputs.
-
-    >>> bg = BIDSDataGrabber()
-    >>> bg.inputs.base_dir = 'ds005/'
-    >>> bg.inputs.subject = '01'
-    >>> results = bg.run()
-    >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
-    'sub-01_T1w.nii.gz'
-
-    >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
-    'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
-
-
-    Dynamically created, user-defined output fields can also be defined to
-    return different types of outputs from the same project. All outputs
-    are filtered on common entities, which can be explicitly defined as
-    infields.
-
-    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
-    >>> bg.inputs.base_dir = 'ds005/'
-    >>> bg.inputs.subject = '01'
-    >>> bg.inputs.output_query['dwi'] = dict(modality='dwi')
-    >>> results = bg.run()
-    >>> basename(results.outputs.dwi[0]) # doctest: +ALLOW_UNICODE
-    'sub-01_dwi.nii.gz'
-
-    """
-    input_spec = BIDSDataGrabberInputSpec
-    output_spec = DynamicTraitedSpec
-    _always_run = True
-
-    def __init__(self, infields=None, outfields=None, **kwargs):
-        """
-        Parameters
-        ----------
-        infields : list of str
-            Indicates the input fields to be dynamically created
-
-        outfields: list of str
-            Indicates output fields to be dynamically created.
-            If no matching items, returns Undefined.
-        """
-        super(BIDSDataGrabber, self).__init__(**kwargs)
-        if not have_pybids:
-            raise ImportError("The BIDSEventsGrabber interface requires pybids."
-                              " Please make sure it is installed.")
-
-        # If outfields is None use anat and func as default
-        if outfields is None:
-            outfields = ['func', 'anat']
-            self.inputs.output_query = {
-                "func": {"modality": "func"},
-                "anat": {"modality": "anat"}}
-        else:
-            self.inputs.output_query = {}
-
-        # If infields is None, use all BIDS entities
-        if infields is None:
-            bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
-            bids_config = json.load(open(bids_config, 'r'))
-            infields = [i['name'] for i in bids_config['entities']]
-
-        self._infields = infields
-        self._outfields = outfields
-
-        # used for mandatory inputs check
-        undefined_traits = {}
-        for key in infields:
-            self.inputs.add_trait(key, traits.Any)
-            undefined_traits[key] = Undefined
-
-        self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
-
-    def _run_interface(self, runtime):
-        return runtime
-
-    def _list_outputs(self):
-        layout = gb.BIDSLayout(self.inputs.base_dir)
-
-        for key in self._outfields:
-            if key not in self.inputs.output_query:
-                raise ValueError("Define query for all outputs")
-
-        # If infield is not given nm input value, silently ignore
-        filters = {}
-        for key in self._infields:
-            value = getattr(self.inputs, key)
-            if isdefined(value):
-                filters[key] = value
-
-        outputs = {}
-        for key, query in self.inputs.output_query.items():
-            args = query.copy()
-            args.update(filters)
-            filelist = layout.get(return_type='file',
-                                      **args)
-            if len(filelist) == 0:
-                msg = 'Output key: %s returned no files' % (
-                    key)
-                if self.inputs.raise_on_empty:
-                    raise IOError(msg)
-                else:
-                    LOGGER.warning(msg)
-                    filelist = Undefined
-            else:
-                outputs[key] = filelist
-        return outputs

From f460eaa9b42f3fdaebbadcd54672f4d7a2e16910 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Wed, 13 Sep 2017 21:20:30 -0500
Subject: [PATCH 12/19] Moved to bids utils

---
 nipype/interfaces/bids_utils.py | 169 ++++++++++++++++++++++++++++++++
 1 file changed, 169 insertions(+)
 create mode 100644 nipype/interfaces/bids_utils.py

diff --git a/nipype/interfaces/bids_utils.py b/nipype/interfaces/bids_utils.py
new file mode 100644
index 0000000000..fda56f79b2
--- /dev/null
+++ b/nipype/interfaces/bids_utils.py
@@ -0,0 +1,169 @@
+# -*- 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:
+""" Set of interfaces that allow interaction with BIDS data. Currently
+available interfaces are:
+
+BIDSDataGrabber: Query data from BIDS dataset using pybids grabbids.
+
+Change directory to provide relative paths for doctests
+>>> import os
+>>> import bids
+>>> filepath = os.path.realpath(os.path.dirname(bids.__file__))
+>>> datadir = os.path.realpath(os.path.join(filepath, 'grabbids/tests/data/'))
+>>> os.chdir(datadir)
+
+"""
+from os.path import join, dirname
+from .. import logging
+from .base import (traits,
+                   DynamicTraitedSpec,
+                   Directory,
+                   BaseInterface,
+                   isdefined,
+                   Str,
+                   Undefined)
+
+try:
+    from bids import grabbids as gb
+    import json
+except ImportError:
+    have_pybids = False
+else:
+    have_pybids = True
+
+LOGGER = logging.getLogger('workflows')
+
+class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
+    base_dir = Directory(exists=True,
+                         desc='Path to BIDS Directory.',
+                         mandatory=True)
+    output_query = traits.Dict(key_trait=Str,
+                               value_trait=traits.Dict,
+                               desc='Queries for outfield outputs')
+    raise_on_empty = traits.Bool(True, usedefault=True,
+                                 desc='Generate exception if list is empty '
+                                 'for a given field')
+    return_type = traits.Enum('filename', 'namedtuple', usedefault=True)
+
+
+class BIDSDataGrabber(BaseInterface):
+
+    """ BIDS datagrabber module that wraps around pybids to allow arbitrary
+    querying of BIDS datasets.
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.bids_utils import BIDSDataGrabber
+    >>> from os.path import basename
+
+    By default, the BIDSDataGrabber fetches anatomical and functional images
+    from a project, and makes BIDS entities (e.g. subject) available for
+    filtering outputs.
+
+    >>> bg = BIDSDataGrabber()
+    >>> bg.inputs.base_dir = 'ds005/'
+    >>> bg.inputs.subject = '01'
+    >>> results = bg.run()
+    >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_T1w.nii.gz'
+
+    >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+
+
+    Dynamically created, user-defined output fields can also be defined to
+    return different types of outputs from the same project. All outputs
+    are filtered on common entities, which can be explicitly defined as
+    infields.
+
+    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
+    >>> bg.inputs.base_dir = 'ds005/'
+    >>> bg.inputs.subject = '01'
+    >>> bg.inputs.output_query['dwi'] = dict(modality='dwi')
+    >>> results = bg.run()
+    >>> basename(results.outputs.dwi[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_dwi.nii.gz'
+
+    """
+    input_spec = BIDSDataGrabberInputSpec
+    output_spec = DynamicTraitedSpec
+    _always_run = True
+
+    def __init__(self, infields=None, outfields=None, **kwargs):
+        """
+        Parameters
+        ----------
+        infields : list of str
+            Indicates the input fields to be dynamically created
+
+        outfields: list of str
+            Indicates output fields to be dynamically created.
+            If no matching items, returns Undefined.
+        """
+        super(BIDSDataGrabber, self).__init__(**kwargs)
+        if not have_pybids:
+            raise ImportError("The BIDSEventsGrabber interface requires pybids."
+                              " Please make sure it is installed.")
+
+        # If outfields is None use anat and func as default
+        if outfields is None:
+            outfields = ['func', 'anat']
+            self.inputs.output_query = {
+                "func": {"modality": "func"},
+                "anat": {"modality": "anat"}}
+        else:
+            self.inputs.output_query = {}
+
+        # If infields is None, use all BIDS entities
+        if infields is None:
+            bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
+            bids_config = json.load(open(bids_config, 'r'))
+            infields = [i['name'] for i in bids_config['entities']]
+
+        self._infields = infields
+        self._outfields = outfields
+
+        # used for mandatory inputs check
+        undefined_traits = {}
+        for key in infields:
+            self.inputs.add_trait(key, traits.Any)
+            undefined_traits[key] = Undefined
+
+        self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
+
+    def _run_interface(self, runtime):
+        return runtime
+
+    def _list_outputs(self):
+        layout = gb.BIDSLayout(self.inputs.base_dir)
+
+        for key in self._outfields:
+            if key not in self.inputs.output_query:
+                raise ValueError("Define query for all outputs")
+
+        # If infield is not given nm input value, silently ignore
+        filters = {}
+        for key in self._infields:
+            value = getattr(self.inputs, key)
+            if isdefined(value):
+                filters[key] = value
+
+        outputs = {}
+        for key, query in self.inputs.output_query.items():
+            args = query.copy()
+            args.update(filters)
+            filelist = layout.get(return_type='file',
+                                      **args)
+            if len(filelist) == 0:
+                msg = 'Output key: %s returned no files' % (
+                    key)
+                if self.inputs.raise_on_empty:
+                    raise IOError(msg)
+                else:
+                    LOGGER.warning(msg)
+                    filelist = Undefined
+            else:
+                outputs[key] = filelist
+        return outputs

From 3cc3a236384ac235df1dbe1feea7d15f1d5decba Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Wed, 13 Sep 2017 21:41:22 -0500
Subject: [PATCH 13/19] Try fix Circle

---
 circle.yml             | 2 ++
 docker/base.Dockerfile | 4 ----
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/circle.yml b/circle.yml
index 5624dbb7f8..f414972934 100644
--- a/circle.yml
+++ b/circle.yml
@@ -27,6 +27,8 @@ dependencies:
     - if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi
     - (cd $HOME/docker && gzip -d cache.tar.gz && docker load --input $HOME/docker/cache.tar) || true :
         timeout: 6000
+    - git clone https://github.com/INCF/pybids.git && cd pybids && python setup.py develop
+
   override:
     # Get data
     - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
diff --git a/docker/base.Dockerfile b/docker/base.Dockerfile
index 3de42492ce..5b39951f64 100644
--- a/docker/base.Dockerfile
+++ b/docker/base.Dockerfile
@@ -148,8 +148,4 @@ ENV MATLABCMD="/opt/mcr/v85/toolbox/matlab" \
     SPMMCRCMD="/opt/spm12/run_spm12.sh /opt/mcr/v85/ script" \
     FORCE_SPMMCR=1
 
-# Install pybids
-RUN git clone https://github.com/INCF/pybids.git
-RUN pip install -e .
-
 WORKDIR /work

From e2e78c4b9fcc4f730f40e64267b3162b7a347ad8 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Thu, 14 Sep 2017 00:19:15 -0500
Subject: [PATCH 14/19] Return type argument

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

diff --git a/nipype/interfaces/bids_utils.py b/nipype/interfaces/bids_utils.py
index fda56f79b2..11d342baf6 100644
--- a/nipype/interfaces/bids_utils.py
+++ b/nipype/interfaces/bids_utils.py
@@ -154,7 +154,7 @@ def _list_outputs(self):
         for key, query in self.inputs.output_query.items():
             args = query.copy()
             args.update(filters)
-            filelist = layout.get(return_type='file',
+            filelist = layout.get(return_type=self.inputs.return_type,
                                       **args)
             if len(filelist) == 0:
                 msg = 'Output key: %s returned no files' % (

From 60dce3ff855ef8a988c9ed36fb9bb1157921e701 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Thu, 14 Sep 2017 00:22:32 -0500
Subject: [PATCH 15/19] Undefined output if no match

---
 nipype/interfaces/bids_utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/bids_utils.py b/nipype/interfaces/bids_utils.py
index 11d342baf6..ebbf2a1149 100644
--- a/nipype/interfaces/bids_utils.py
+++ b/nipype/interfaces/bids_utils.py
@@ -164,6 +164,6 @@ def _list_outputs(self):
                 else:
                     LOGGER.warning(msg)
                     filelist = Undefined
-            else:
-                outputs[key] = filelist
+                    
+            outputs[key] = filelist
         return outputs

From 97d832ba6668d74c3711ac6f1b2a51bc8e1c8fd5 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Thu, 14 Sep 2017 01:04:50 -0500
Subject: [PATCH 16/19] Fix return type

---
 nipype/interfaces/bids_utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/bids_utils.py b/nipype/interfaces/bids_utils.py
index ebbf2a1149..e1606e7d92 100644
--- a/nipype/interfaces/bids_utils.py
+++ b/nipype/interfaces/bids_utils.py
@@ -44,7 +44,7 @@ class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
     raise_on_empty = traits.Bool(True, usedefault=True,
                                  desc='Generate exception if list is empty '
                                  'for a given field')
-    return_type = traits.Enum('filename', 'namedtuple', usedefault=True)
+    return_type = traits.Enum('file', 'namedtuple', usedefault=True)
 
 
 class BIDSDataGrabber(BaseInterface):
@@ -164,6 +164,6 @@ def _list_outputs(self):
                 else:
                     LOGGER.warning(msg)
                     filelist = Undefined
-                    
+
             outputs[key] = filelist
         return outputs

From ce148eb573c570baac04ce7e7f39795125e660e8 Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Tue, 19 Sep 2017 17:49:13 -0500
Subject: [PATCH 17/19] Install pybids for tesing in Dockerfile

---
 Dockerfile | 3 +++
 circle.yml | 1 -
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 502216cf8d..14a6dec135 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -87,6 +87,9 @@ COPY requirements.txt requirements.txt
 RUN pip install -r requirements.txt && \
     rm -rf ~/.cache/pip
 
+RUN git clone https://github.com/INCF/pybids.git && \
+    cd pybids && python setup.py develop
+
 # Installing nipype
 COPY . /src/nipype
 RUN cd /src/nipype && \
diff --git a/circle.yml b/circle.yml
index f414972934..82d67432d6 100644
--- a/circle.yml
+++ b/circle.yml
@@ -27,7 +27,6 @@ dependencies:
     - if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi
     - (cd $HOME/docker && gzip -d cache.tar.gz && docker load --input $HOME/docker/cache.tar) || true :
         timeout: 6000
-    - git clone https://github.com/INCF/pybids.git && cd pybids && python setup.py develop
 
   override:
     # Get data

From fc6dd01cf8c8b88ebcfbb79cb33b552ffab451c4 Mon Sep 17 00:00:00 2001
From: Alejandro de la Vega <aleph4@gmail.com>
Date: Wed, 20 Sep 2017 00:12:28 -0500
Subject: [PATCH 18/19] Update circle.yml

---
 circle.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/circle.yml b/circle.yml
index 82d67432d6..5624dbb7f8 100644
--- a/circle.yml
+++ b/circle.yml
@@ -27,7 +27,6 @@ dependencies:
     - if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi
     - (cd $HOME/docker && gzip -d cache.tar.gz && docker load --input $HOME/docker/cache.tar) || true :
         timeout: 6000
-
   override:
     # Get data
     - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi

From 03243d881e341e399ac55e9092ec1d0fa39005ef Mon Sep 17 00:00:00 2001
From: adelavega <delavega@utexas.edu>
Date: Fri, 22 Sep 2017 11:11:57 -0500
Subject: [PATCH 19/19] Added reference to io

---
 nipype/interfaces/io.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
index 516c92c804..f2e3fcd943 100644
--- a/nipype/interfaces/io.py
+++ b/nipype/interfaces/io.py
@@ -40,6 +40,7 @@
 from .base import (
     TraitedSpec, traits, Str, File, Directory, BaseInterface, InputMultiPath,
     isdefined, OutputMultiPath, DynamicTraitedSpec, Undefined, BaseInterfaceInputSpec)
+from .bids_utils import BIDSDataGrabber
 
 try:
     import pyxnat