Merge remote-tracking branch 'origin/master' into bf-2847

* origin/master: (63 commits)
  Update nipype/interfaces/dipy/tracks.py
  Update nipype/interfaces/dipy/reconstruction.py
  MNT: Install numpy!=1.16.0 from conda in Docker
  Add FSL auto test
  remake specs
  Update nipype/interfaces/io.py
  Remove return type named tuple
  Update nipype/info.py
  STY: Whitespace, line length
  Remove out_ prefix from EddyQuad outputs
  Apply minor edits from code review
  Use os.path.basename for the fallback output_dir in EddyQuad._list_outputs()
  Add output_dir check to EddyQuad._list_outputs()
  Remove redundant out_avg_b_png lines
  Add glob stuff back in
  Edit in response to @effigies comments on PR nipy#2825
  Fix tests for EddyQuad in interfaces/fsl/epi.py
  Add name to .zenodo.json
  Add doctest for EddyQuad
  fix: made the outputdir be mandatory and use the default val
  ...

Author: yarikoptic

.mailmap

@@ -93,7 +93,7 @@ Josh Warner <[email protected]> JDWarner <[email protected]
 Josh Warner <[email protected]> Josh Warner (Mac) <[email protected]>
 Kai Schlamp <[email protected]> medihack <[email protected]>Jessica Forbes <[email protected]> jessicaforbes <[email protected]>
 Katie Bottenhorn <[email protected]> 62442katieb <[email protected]>
-Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]> 
+Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]>
 Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]>
 Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]>
 Kesshi Jordan <[email protected]> Kesshi Jordan <[email protected]>

.travis.yml

@@ -60,6 +60,9 @@ matrix:
           NIPYPE_EXTRAS="doc,tests,nipy,profiler"
           EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
           CI_SKIP_TEST=1
+  allow_failures:
+    - python: 2.7
+      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:
@@ -86,14 +89,15 @@ before_install:
   fi;
 
 - travis_retry pip install -r requirements.txt
-- travis_retry pip install grabbit==0.1.2
-- travis_retry git clone -b 0.6.5 https://github.com/INCF/pybids.git ${HOME}/pybids && pip install -e ${HOME}/pybids
+- travis_retry pip install grabbit==0.2.6
+- travis_retry pip install -e git+https://github.com/bids-standard/pybids.git@0.7.0#egg=pybids
 
 install:
 - travis_retry pip install $EXTRA_PIP_FLAGS -e .[$NIPYPE_EXTRAS]
+- travis_retry pip install pytest-xdist
 
 script:
-- py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype
+- py.test -v --cov nipype --cov-config .coveragerc --cov-report xml:cov.xml -c nipype/pytest.ini --doctest-modules nipype -n auto
 
 after_script:
 - codecov --file cov.xml --flags unittests -e TRAVIS_JOB_NUMBER

.zenodo.json

@@ -589,6 +589,11 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "University of Washington",
+      "name": "Richie-Halford, Adam",
+      "orcid": "0000-0001-9276-9084"
     }
   ],
   "keywords": [

README.rst

@@ -91,7 +91,7 @@ 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 
+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.)
 
 

doc/devel/interface_specs.rst

@@ -12,8 +12,8 @@ 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 
+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.)
 

doc/index.rst

@@ -16,7 +16,7 @@
         these packages within a single workflow. Nipype provides an environment
         that encourages interactive exploration of algorithms from different
         packages (e.g., ANTS_, SPM_, FSL_, FreeSurfer_, Camino_, MRtrix_, MNE_, AFNI_,
-        Slicer_), eases the design of workflows within and between packages, and
+        Slicer_, DIPY_), eases the design of workflows within and between packages, and
         reduces the learning curve necessary to use different packages. Nipype is
         creating a collaborative platform for neuroimaging software development
         in a high-level language and addressing limitations of existing pipeline

doc/links_names.txt

@@ -97,6 +97,7 @@
 .. _MRtrix3: http://www.mrtrix.org/
 .. _MNE: https://martinos.org/mne/index.html
 .. _ANTS: http://stnava.github.io/ANTs/
+.. _DIPY: http://dipy.org
 
 .. General software
 .. _gcc: http://gcc.gnu.org

docker/files/run_pytests.sh

@@ -29,6 +29,7 @@ export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}
 py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}.xml \
     --cov nipype --cov-config /src/nipype/.coveragerc \
     --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}.xml \
+    -n auto \
     -c ${TESTPATH}/pytest.ini ${TESTPATH}
 exit_code=$?
 

docker/generate_dockerfiles.sh

@@ -90,9 +90,9 @@ function generate_main_dockerfile() {
     --user neuro \
     --miniconda create_env=neuro \
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
-                               icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko
+                               icu=58.1 libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko
                                pandas psutil scikit-learn scipy traits=4.6.0' \
-                pip_install="grabbit==0.1.2 https://github.com/INCF/pybids/tarball/0.6.5" \
+                pip_install="pytest-xdist" \
                 activate=true \
     --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \
            docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \
@@ -107,7 +107,7 @@ function generate_main_dockerfile() {
     --user neuro \
     --miniconda use_env=neuro \
                 pip_opts="-e" \
-                pip_install="/src/nipype[all]" \
+                pip_install="/src/nipype[all] https://github.com/bids-standard/pybids/tarball/0.7.0" \
     --workdir /work \
     --label org.label-schema.build-date='$BUILD_DATE' \
             org.label-schema.name="NIPYPE" \

nipype/__init__.py

@@ -25,17 +25,22 @@
 
 
 class NipypeTester(object):
-    def __call__(self, doctests=True, parallel=True):
+    def __call__(self, doctests=True, parallel=False):
         try:
             import pytest
-        except:
+        except ImportError:
             raise RuntimeError(
                 'py.test not installed, run: pip install pytest')
         args = []
         if not doctests:
             args.extend(['-p', 'no:doctest'])
-        if not parallel:
-            args.append('-n0')
+        if parallel:
+            try:
+                import xdist
+            except ImportError:
+                raise RuntimeError(
+                    "pytest-xdist required for parallel run")
+            args.append('-n auto')
         args.append(os.path.dirname(__file__))
         pytest.main(args=args)
 

nipype/algorithms/modelgen.py

@@ -144,6 +144,61 @@ def scale_timings(timelist, input_units, output_units, time_repetition):
     timelist = [np.max([0., _scalefactor * t]) for t in timelist]
     return timelist
 
+def bids_gen_info(bids_event_files,
+                  condition_column='trial_type',
+                  amplitude_column=None,
+                  time_repetition=False,
+                  ):
+    """Generate subject_info structure from a list of BIDS .tsv event files.
+
+    Parameters
+    ----------
+
+    bids_event_files : list of str
+        Filenames of BIDS .tsv event files containing columns including:
+        'onset', 'duration', and 'trial_type' or the `condition_column` value.
+    condition_column : str
+        Column of files in `bids_event_files` based on the values of which
+        events will be sorted into different regressors
+    amplitude_column : str
+        Column of files in `bids_event_files` based on the values of which
+        to apply amplitudes to events. If unspecified, all events will be
+        represented with an amplitude of 1.
+
+    Returns
+    -------
+
+    list of Bunch
+    """
+    info = []
+    for bids_event_file in bids_event_files:
+        with open(bids_event_file) as f:
+            f_events = csv.DictReader(f, skipinitialspace=True, delimiter='\t')
+            events = [{k: v for k, v in row.items()} for row in f_events]
+        conditions = list(set([i[condition_column] for i in events]))
+        runinfo = Bunch(conditions=[], onsets=[], durations=[], amplitudes=[])
+        for condition in conditions:
+            selected_events = [i for i in events if i[condition_column]==condition]
+            onsets = [float(i['onset']) for i in selected_events]
+            durations = [float(i['duration']) for i in selected_events]
+            if time_repetition:
+                decimals = math.ceil(-math.log10(time_repetition))
+                onsets = [np.round(i, decimals) for i in onsets]
+                durations = [np.round(i ,decimals) for i in durations]
+            if condition:
+                runinfo.conditions.append(condition)
+            else:
+                runinfo.conditions.append('e0')
+            runinfo.onsets.append(onsets)
+            runinfo.durations.append(durations)
+            try:
+                amplitudes = [float(i[amplitude_column]) for i in selected_events]
+                runinfo.amplitudes.append(amplitudes)
+            except KeyError:
+                runinfo.amplitudes.append([1] * len(onsets))
+        info.append(runinfo)
+    return info
+
 
 def gen_info(run_event_files):
     """Generate subject_info structure from a list of event files
@@ -190,6 +245,23 @@ class SpecifyModelInputSpec(BaseInterfaceInputSpec):
         desc='List of event description files 1, 2 or 3 '
         'column format corresponding to onsets, '
         'durations and amplitudes')
+    bids_event_file = InputMultiPath(
+        File(exists=True),
+        mandatory=True,
+        xor=['subject_info', 'event_files', 'bids_event_file'],
+        desc='TSV event file containing common BIDS fields: `onset`,'
+        '`duration`, and categorization and amplitude columns')
+    bids_condition_column = traits.Str(exists=True,
+        mandatory=False,
+        default_value='trial_type',
+        usedefault=True,
+        desc='Column of the file passed to `bids_event_file` to the '
+        'unique values of which events will be assigned'
+        'to regressors')
+    bids_amplitude_column = traits.Str(exists=True,
+        mandatory=False,
+        desc='Column of the file passed to `bids_event_file` '
+        'according to which to assign amplitudes to events')
     realignment_parameters = InputMultiPath(
         File(exists=True),
         desc='Realignment parameters returned '
@@ -432,8 +504,15 @@ def _generate_design(self, infolist=None):
         if infolist is None:
             if isdefined(self.inputs.subject_info):
                 infolist = self.inputs.subject_info
-            else:
+            elif isdefined(self.inputs.event_files):
                 infolist = gen_info(self.inputs.event_files)
+            elif isdefined(self.inputs.bids_event_file):
+                infolist = bids_gen_info(
+                    self.inputs.bids_event_file,
+                    self.inputs.bids_condition_column,
+                    self.inputs.bids_amplitude_column,
+                    self.inputs.time_repetition,
+                    )
         self._sessinfo = self._generate_standard_design(
             infolist,
             functional_runs=self.inputs.functional_runs,

nipype/algorithms/tests/test_auto_SpecifyModel.py

@@ -5,6 +5,19 @@
 
 def test_SpecifyModel_inputs():
     input_map = dict(
+        bids_amplitude_column=dict(
+            exists=True,
+            mandatory=False,
+        ),
+        bids_condition_column=dict(
+            exists=True,
+            mandatory=False,
+            usedefault=True,
+        ),
+        bids_event_file=dict(
+            mandatory=True,
+            xor=['subject_info', 'event_files', 'bids_event_file'],
+        ),
         event_files=dict(
             mandatory=True,
             xor=['subject_info', 'event_files'],

nipype/algorithms/tests/test_auto_SpecifySPMModel.py

@@ -5,6 +5,19 @@
 
 def test_SpecifySPMModel_inputs():
     input_map = dict(
+        bids_amplitude_column=dict(
+            exists=True,
+            mandatory=False,
+        ),
+        bids_condition_column=dict(
+            exists=True,
+            mandatory=False,
+            usedefault=True,
+        ),
+        bids_event_file=dict(
+            mandatory=True,
+            xor=['subject_info', 'event_files', 'bids_event_file'],
+        ),
         concatenate_runs=dict(usedefault=True, ),
         event_files=dict(
             mandatory=True,

nipype/algorithms/tests/test_auto_SpecifySparseModel.py

@@ -5,6 +5,19 @@
 
 def test_SpecifySparseModel_inputs():
     input_map = dict(
+        bids_amplitude_column=dict(
+            exists=True,
+            mandatory=False,
+        ),
+        bids_condition_column=dict(
+            exists=True,
+            mandatory=False,
+            usedefault=True,
+        ),
+        bids_event_file=dict(
+            mandatory=True,
+            xor=['subject_info', 'event_files', 'bids_event_file'],
+        ),
         event_files=dict(
             mandatory=True,
             xor=['subject_info', 'event_files'],

nipype/info.py

@@ -105,10 +105,10 @@ def get_nipype_gitversion():
 # Numpy bug in python 3.7:
 # https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
 NUMPY_MIN_VERSION_37 = '1.15.3'
+NUMPY_BAD_VERSION_27 = '1.16.0'
 SCIPY_MIN_VERSION = '0.14'
 TRAITS_MIN_VERSION = '4.6'
 DATEUTIL_MIN_VERSION = '2.2'
-PYTEST_MIN_VERSION = '3.6'
 FUTURE_MIN_VERSION = '0.16.0'
 SIMPLEJSON_MIN_VERSION = '3.8.0'
 PROV_VERSION = '1.5.2'
@@ -136,7 +136,8 @@ def get_nipype_gitversion():
 REQUIRES = [
     'nibabel>=%s' % NIBABEL_MIN_VERSION,
     'networkx>=%s' % NETWORKX_MIN_VERSION,
-    'numpy>=%s ; python_version < "3.7"' % NUMPY_MIN_VERSION,
+    'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27),
+    'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION,
     'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37,
     'python-dateutil>=%s' % DATEUTIL_MIN_VERSION,
     'scipy>=%s' % SCIPY_MIN_VERSION,
@@ -147,19 +148,21 @@ def get_nipype_gitversion():
     'neurdflib',
     'click>=%s' % CLICK_MIN_VERSION,
     'funcsigs',
-    'pytest>=%s' % PYTEST_MIN_VERSION,
-    'pytest-xdist',
-    'mock',
     'pydotplus',
     'pydot>=%s' % PYDOT_MIN_VERSION,
     'packaging',
     'futures; python_version == "2.7"',
+    'configparser; python_version <= "3.4"',
 ]
 
-if sys.version_info <= (3, 4):
-    REQUIRES.append('configparser')
-
-TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-env', 'coverage<5']
+TESTS_REQUIRES = [
+    'mock',
+    'pytest',
+    'pytest-cov',
+    'codecov',
+    'pytest-env',
+    'coverage<5'
+]
 
 EXTRA_REQUIRES = {
     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
@@ -169,7 +172,7 @@ def get_nipype_gitversion():
     'profiler': ['psutil>=5.0'],
     'duecredit': ['duecredit'],
     'xvfbwrapper': ['xvfbwrapper'],
-    'pybids': ['pybids==0.6.5'],
+    'pybids': ['pybids>=0.7.0'],
     'ssh': ['paramiko'],
     # 'mesh': ['mayavi']  # Enable when it works
 }

nipype/interfaces/ants/__init__.py

@@ -5,7 +5,7 @@
 
 # Registraiton programs
 from .registration import (ANTS, Registration, RegistrationSynQuick,
-                           MeasureImageSimilarity)
+                           CompositeTransformUtil, MeasureImageSimilarity)
 
 # Resampling Programs
 from .resampling import (ApplyTransforms, ApplyTransformsToPoints,