Merge tag '1.1.8' into debian

1.1.8 (January 28, 2019)

  * FIX: ANTS LaplacianThickness cmdline opts fixed up (nipy#2846)
  * FIX: Resolve LinAlgError during SVD (nipy#2838)
  * ENH: Add interfaces wrapping DIPY worflows (nipy#2830)
  * ENH: Update BIDSDataGrabber for pybids 0.7 (nipy#2737)
  * ENH: Add FSL `eddy_quad` interface (nipy#2825)
  * ENH: Support tckgen -select in MRtrix3 v3+ (nipy#2823)
  * ENH: Support for BIDS event files (nipy#2845)
  * ENH: CompositeTransformUtil, new ANTs interface (nipy#2785)
  * RF: Move pytest and pytest-xdist from general requirement into tests_required (nipy#2850)
  * DOC: Add S3DataGrabber example (nipy#2849)
  * DOC: Skip conftest module in API generation (nipy#2852)
  * DOC: Hyperlink DOIs to preferred resolver (nipy#2833)
  * MAINT: Install numpy!=1.16.0 from conda in Docker (nipy#2862)
  * MAINT: Drop pytest-xdist requirement, minimum pytest version  (nipy#2856)
  * MAINT: Disable numpy 1.16.0 for Py2.7 (nipy#2855)

* tag '1.1.8': (79 commits)
  MNT: Add @feilong to .zenodo, update ordering
  MNT: Update .mailmap
  MNT: Update .zenodo ordering
  Accept invitation as Zenodo release co-author (see nipy#2864)
  MAINT: Update .mailmap
  BF: allowing bids_event_file as alternate input
  MNT: Update .zenodo ordering
  MNT: Version 1.1.8
  DOC: 1.1.8 changelog
  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
  ...

Author: yarikoptic

.mailmap

@@ -3,6 +3,7 @@ Aimi Watanabe <watanabe.aimi@gmail.com> stymy <watanabe.aimi@gmail.com>
 Alejandro Tabas <alextabas@gmail.com> qTabs <qtabas@gmail.com>
 Alejandro Tabas <alextabas@gmail.com> qtabs <alextabas@gmail.com>
 Alejandro de la Vega <aleph4@gmail.com> adelavega <delavega@utexas.edu>
+Alejandro de la Vega <aleph4@gmail.com> delavega4 <aleph4@gmail.com>
 Alexander Schaefer <alexschaefer83@gmail.com> Alexander Schaefer <aschaefer@melisse.cbs.mpg.de>
 Alexander Schaefer <alexschaefer83@gmail.com> alexschaefer83 <alexschaefer83@gmail.com>
 Alexander Schaefer <alexschaefer83@gmail.com> aschaefer <aschaefer@aschaefer-U36SD.(none)>
@@ -40,6 +41,7 @@ Christopher J. Markiewicz <effigies@gmail.com> Chris Markiewicz <effigies@gmail.
 Christopher J. Markiewicz <effigies@gmail.com> Christopher J. Johnson <effigies@gmail.com>
 Christopher J. Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@bu.edu>
 Christopher J. Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <markiewicz@stanford.edu>
+Christopher J. Markiewicz <effigies@gmail.com> Chris Markiewicz <markiewicz@stanford.edu>
 Cindee Madison <cindee@berkeley.edu> cindeem
 Cindee Madison <cindee@berkeley.edu> cindeem <>
 Colin Buchanan <colinrbuchanan@gmail.com> Colin Buchanan <cbuchanan@cray4.(none)>
@@ -62,6 +64,7 @@ Erik Ziegler <erik.sweed@gmail.com> Erik Ziegler <erik.ziegler@ulg.ac.be>
 Erik Ziegler <erik.sweed@gmail.com> erik <erik@erik-ubuntu.(none)>
 Erik Ziegler <erik.sweed@gmail.com> erikz <erik.ziegler@ulg.ac.be>
 Erik Ziegler <erik.sweed@gmail.com> swederik <erik.sweed@gmail.com>
+Feilong Ma <mafeilong@gmail.com> Ma Feilong <mafeilong@gmail.com>
 Fernando Pérez-García <fepegar@gmail.com> Fernando <fepegar@gmail.com>
 Franz Liem <franz.liem@gmail.com> fliem <franz.liem>
 Franz Liem <franz.liem@gmail.com> fliem <franz.liem@gmail.com>
@@ -93,7 +96,7 @@ Josh Warner <silvertrumpet999+github@gmail.com> JDWarner <warner.joshua@mayo.edu
 Josh Warner <silvertrumpet999+github@gmail.com> Josh Warner (Mac) <warner.joshua@mayo.edu>
 Kai Schlamp <schlamp@gmx.de> medihack <schlamp@gmx.de>Jessica Forbes <jessica-forbes@uiowa.edu> jessicaforbes <jessica-forbes@uiowa.edu>
 Katie Bottenhorn <kbott006@fiu.edu> 62442katieb <kbott006@fiu.edu>
-Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <Kesshi.Jordan@ucsf.edu> 
+Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <Kesshi.Jordan@ucsf.edu>
 Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <kesshi.jordan@gmail.com>
 Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <kesshijordan@D-108-179-130-38.dhcp4.washington.edu>
 Kesshi Jordan <Kesshi.Jordan@ucsf.edu> Kesshi Jordan <kesshijordan@D-69-91-152-99.dhcp4.washington.edu>

.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

@@ -110,16 +110,16 @@
       "affiliation": "National Institutes of Health",
       "name": "Clark, Michael G. "
     },
-    {
-      "affiliation": "Dartmouth College",
-      "name": "Visconti di Oleggio Castello, Matteo",
-      "orcid": "0000-0001-7931-5272"
-    },
     {
       "affiliation": "Mayo Clinic, Neurology, Rochester, MN, USA",
       "name": "Dayan, Michael",
       "orcid": "0000-0002-2666-0969"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Visconti di Oleggio Castello, Matteo",
+      "orcid": "0000-0001-7931-5272"
+    },
     {
       "affiliation": "UC Berkeley",
       "name": "Clark, Dav",
@@ -142,15 +142,20 @@
       "name": "Berleant, Shoshana"
     },
     {
-      "affiliation": "UC San Diego",
-      "name": "Cipollini, Ben",
-      "orcid": "0000-0002-7782-0790"
+      "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
+      "name": "Horea, Christian",
+      "orcid": "0000-0001-7037-2449"
     },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Halchenko, Yaroslav O.",
       "orcid": "0000-0003-3456-2493"
     },
+    {
+      "affiliation": "UC San Diego",
+      "name": "Cipollini, Ben",
+      "orcid": "0000-0002-7782-0790"
+    },
     {
       "affiliation": "Montreal Neurological Institute and Hospital",
       "name": "Markello, Ross",
@@ -179,11 +184,6 @@
       "name": "Varoquaux, Gael",
       "orcid": "0000-0003-1076-5122"
     },
-    {
-      "affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
-      "name": "Horea, Christian",
-      "orcid": "0000-0001-7037-2449"
-    },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
       "name": "Wassermann , Demian",
@@ -235,6 +235,11 @@
       "name": "Iqbal, Shariq",
       "orcid": "0000-0003-2766-8425"
     },
+    {
+      "affiliation": "University of Washington",
+      "name": "Richie-Halford, Adam",
+      "orcid": "0000-0001-9276-9084"
+    },
     {
       "name": "Schwartz, Yannick"
     },
@@ -257,6 +262,11 @@
     {
       "name": "Kent, James"
     },
+    {
+      "affiliation": "University of Texas at Austin",
+      "name": "De La Vega, Alejandro",
+      "orcid": "0000-0001-9062-3778"
+    },
     {
       "name": "Watanabe, Aimi"
     },
@@ -380,6 +390,16 @@
     {
       "name": "Hallquist, Michael"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Ma, Feilong",
+      "orcid": "0000-0002-6838-3971"
+    },
+    {
+      "affiliation": "TIB \u2013 Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany",
+      "name": "Leinweber, Katrin",
+      "orcid": "0000-0001-5135-5758"
+    },
     {
       "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
       "name": "Chetverikov, Andrey",
@@ -461,11 +481,6 @@
       "name": "Geisler, Daniel",
       "orcid": "0000-0003-2076-5329"
     },
-    {
-      "affiliation": "University of Texas at Austin",
-      "name": "De La Vega, Alejandro",
-      "orcid": "0000-0001-9062-3778"
-    },
     {
       "affiliation": "University of illinois urbana champaign",
       "name": "Sharp, Paul"

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/about.rst

@@ -215,7 +215,7 @@ this way you can use the initial paper published in 2011 (see below).
 	month            = "08",
 	doi              = "10.3389/fninf.2011.00013",
 	pubmed           = "21897815",
-	url              = "http://dx.doi.org/10.3389/fninf.2011.00013",
+	url              = "https://doi.org/10.3389/fninf.2011.00013",
 	issn             = "1662-5196"}
 
 

doc/changelog/1.X.X-changelog

@@ -1,6 +1,30 @@
+1.1.8 (January 28, 2019)
+========================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/29?closed=1)
+
+  * FIX: ANTS LaplacianThickness cmdline opts fixed up (https://github.com/nipy/nipype/pull/2846)
+  * FIX: Resolve LinAlgError during SVD (https://github.com/nipy/nipype/pull/2838)
+  * ENH: Add interfaces wrapping DIPY worflows (https://github.com/nipy/nipype/pull/2830)
+  * ENH: Update BIDSDataGrabber for pybids 0.7 (https://github.com/nipy/nipype/pull/2737)
+  * ENH: Add FSL `eddy_quad` interface (https://github.com/nipy/nipype/pull/2825)
+  * ENH: Support tckgen -select in MRtrix3 v3+ (https://github.com/nipy/nipype/pull/2823)
+  * ENH: Support for BIDS event files (https://github.com/nipy/nipype/pull/2845)
+  * ENH: CompositeTransformUtil, new ANTs interface (https://github.com/nipy/nipype/pull/2785)
+  * RF: Move pytest and pytest-xdist from general requirement into tests_required (https://github.com/nipy/nipype/pull/2850)
+  * DOC: Add S3DataGrabber example (https://github.com/nipy/nipype/pull/2849)
+  * DOC: Skip conftest module in API generation (https://github.com/nipy/nipype/pull/2852)
+  * DOC: Hyperlink DOIs to preferred resolver (https://github.com/nipy/nipype/pull/2833)
+  * MAINT: Install numpy!=1.16.0 from conda in Docker (https://github.com/nipy/nipype/pull/2862)
+  * MAINT: Drop pytest-xdist requirement, minimum pytest version  (https://github.com/nipy/nipype/pull/2856)
+  * MAINT: Disable numpy 1.16.0 for Py2.7 (https://github.com/nipy/nipype/pull/2855)
+
+
 1.1.7 (December 17, 2018)
 =========================
 
+##### [Full changelog](https://github.com/nipy/nipype/milestone/28?closed=1)
+
   * FIX: Copy node list before generating a flat graph (https://github.com/nipy/nipype/pull/2828)
   * FIX: Update pytest req'd version to 3.6 (https://github.com/nipy/nipype/pull/2827)
   * FIX: Set ResourceMonitor.fname to an absolute path (https://github.com/nipy/nipype/pull/2824)

doc/conf.py

@@ -73,7 +73,7 @@
 
 # General information about the project.
 project = u'nipype'
-copyright = u'2009-18, Neuroimaging in Python team'
+copyright = u'2009-19, Neuroimaging in Python team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.1.7"
+release = "1.1.8"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

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/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `1.1.6 <http://nipype.readthedocs.io/en/1.1.6/>`_ `1.1.5 <http://nipype.readthedocs.io/en/1.1.5/>`_
+Previous versions: `1.1.7 <http://nipype.readthedocs.io/en/1.1.7/>`_ `1.1.6 <http://nipype.readthedocs.io/en/1.1.6/>`_
 
 
 .. container:: doc2

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/confounds.py

@@ -26,6 +26,16 @@
 IFLOGGER = logging.getLogger('nipype.interface')
 
 
+def fallback_svd(a, full_matrices=True, compute_uv=True):
+    try:
+        return np.linalg.svd(a, full_matrices=full_matrices, compute_uv=compute_uv)
+    except np.linalg.LinAlgError:
+        pass
+
+    from scipy.linalg import svd
+    return svd(a, full_matrices=full_matrices, compute_uv=compute_uv, lapack_driver='gesvd')
+
+
 class ComputeDVARSInputSpec(BaseInterfaceInputSpec):
     in_file = File(
         exists=True, mandatory=True, desc='functional data, after HMC')
@@ -271,7 +281,7 @@ class FramewiseDisplacement(BaseInterface):
     .. [Power2012] Power et al., Spurious but systematic correlations in functional
          connectivity MRI networks arise from subject motion, NeuroImage 59(3),
          2012. doi:`10.1016/j.neuroimage.2011.10.018
-         <http://dx.doi.org/10.1016/j.neuroimage.2011.10.018>`_.
+         <https://doi.org/10.1016/j.neuroimage.2011.10.018>`_.
 
 
     """
@@ -1191,7 +1201,7 @@ def compute_noise_components(imgseries, mask_images, num_components,
         # "The covariance matrix C = MMT was constructed and decomposed into its
         # principal components using a singular value decomposition."
         try:
-            u, _, _ = np.linalg.svd(M, full_matrices=False)
+            u, _, _ = fallback_svd(M, full_matrices=False)
         except np.linalg.LinAlgError:
             if self.inputs.failure_mode == 'error':
                 raise
@@ -1273,7 +1283,7 @@ def _full_rank(X, cmax=1e15):
     X: array of shape(nrows, ncols) after regularization
     cmax=1.e-15, float tolerance for condition number
     """
-    U, s, V = np.linalg.svd(X, 0)
+    U, s, V = fallback_svd(X, full_matrices=False)
     smax, smin = s.max(), s.min()
     c = smax / smin
     if c < cmax: