Merge branch 'master' into dev/2.0

Author: effigies

.circleci/config.yml

@@ -1,5 +1,5 @@
 _machine_kwds: &machine_kwds
-  image: circleci/classic:201710-02
+  image: circleci/classic:201808-01
 
 _store_artifacts_kwds: &store_artifacts_kwds
   path: /home/circleci/work/tests
@@ -325,6 +325,16 @@ jobs:
           command: |
             pyenv local 3.5.2
             pip install dist/nipype-*-py3-none-any.whl
+      - run:
+          name: Validate Python 3.7 installation
+          command: |
+            pyenv local 3.7.0
+            pip install --upgrade pip
+            # Pre-install a version of numpy that will not pass
+            pip install numpy==1.15.0
+            pip install dist/nipype-*-py3-none-any.whl
+            # Numpy should be upgraded to >= 1.15.3
+            test "$(pip show numpy | grep Version)" \> "Version: 1.15.2"
       - store_artifacts:
           path: /home/circleci/nipype/dist
 

.zenodo.json

@@ -89,32 +89,32 @@
       "name": "Clark, Daniel",
       "orcid": "0000-0002-8121-8954"
     },
-    {
-      "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
-      "name": "Dewey, Blake E",
-      "orcid": "0000-0003-4554-5058"
-    },
     {
       "affiliation": "National Institute of Mental Health",
       "name": "Nielson, Dylan M.",
       "orcid": "0000-0003-4613-6643"
     },
+    {
+      "affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
+      "name": "Dewey, Blake E",
+      "orcid": "0000-0003-4554-5058"
+    },
     {
       "name": "Madison, Cindee"
     },
     {
       "affiliation": "Molecular Imaging Research Center, CEA, France",
       "name": "Bougacha, Salma"
     },
+    {
+      "affiliation": "National Institutes of Health",
+      "name": "Clark, Michael G. "
+    },
     {
       "affiliation": "Dartmouth College",
       "name": "Visconti di Oleggio Castello, Matteo",
       "orcid": "0000-0001-7931-5272"
     },
-    {
-      "affiliation": "National Institutes of Health",
-      "name": "Clark, Michael G. "
-    },
     {
       "affiliation": "Mayo Clinic, Neurology, Rochester, MN, USA",
       "name": "Dayan, Michael",
@@ -199,14 +199,14 @@
       "name": "Gilles de Hollander",
       "orcid": "0000-0003-1988-5091"
     },
+    {
+      "name": "Mordom, David"
+    },
     {
       "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland",
       "name": "Gillman, Ashley",
       "orcid": "0000-0001-9130-1092"
     },
-    {
-      "name": "Mordom, David"
-    },
     {
       "name": "Buchanan, Colin"
     },
@@ -218,11 +218,6 @@
       "name": "Pauli, Wolfgang M.",
       "orcid": "0000-0002-0966-0254"
     },
-    {
-      "affiliation": "Duke University",
-      "name": "Iqbal, Shariq",
-      "orcid": "0000-0003-2766-8425"
-    },
     {
       "affiliation": "Nathan s Kline institute for psychiatric research",
       "name": "Sikka, Sharad"
@@ -235,6 +230,11 @@
     {
       "name": "Forbes, Jessica"
     },
+    {
+      "affiliation": "Duke University",
+      "name": "Iqbal, Shariq",
+      "orcid": "0000-0003-2766-8425"
+    },
     {
       "name": "Schwartz, Yannick"
     },
@@ -278,11 +278,6 @@
       "name": "Eshaghi, Arman",
       "orcid": "0000-0002-6652-3512"
     },
-    {
-      "affiliation": "Harvard University - Psychology",
-      "name": "Kastman, Erik",
-      "orcid": "0000-0001-7221-9042"
-    },
     {
       "name": "Ginsburg, Daniel"
     },
@@ -291,6 +286,11 @@
       "name": "Schaefer, Alexander",
       "orcid": "0000-0001-6488-4739"
     },
+    {
+      "affiliation": "Harvard University - Psychology",
+      "name": "Kastman, Erik",
+      "orcid": "0000-0001-7221-9042"
+    },
     {
       "affiliation": "Washington University in St Louis",
       "name": "Acland, Benjamin",
@@ -312,9 +312,6 @@
       "affiliation": "Child Mind Institute",
       "name": "Giavasis, Steven"
     },
-    {
-      "name": "Haselgrove, Christian"
-    },
     {
       "name": "Correa, Carlos"
     },
@@ -336,6 +333,9 @@
     {
       "name": "Blair, Ross"
     },
+    {
+      "name": "Haselgrove, Christian"
+    },
     {
       "affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montr\u00e9al, 3801 University Street, WB-208, H3A 2B4, Qu\u00e9bec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.",
       "name": "Glatard, Tristan",
@@ -385,6 +385,11 @@
       "name": "Chetverikov, Andrey",
       "orcid": "0000-0003-2767-6310"
     },
+    {
+      "affiliation": "GIGA Institute",
+      "name": "Grignard, Martin",
+      "orcid": "0000-0001-5549-1861"
+    },
     {
       "name": "Salvatore, John"
     },
@@ -451,12 +456,6 @@
       "name": "Durnez, Joke",
       "orcid": "0000-0001-9030-2202"
     },
-    {
-      "name": "Mertz, Fred"
-    },
-    {
-      "name": "Haehn, Daniel"
-    },
     {
       "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
       "name": "Geisler, Daniel",
@@ -481,6 +480,9 @@
       "name": "Molina-Romero, Miguel",
       "orcid": "0000-0001-8054-0426"
     },
+    {
+      "name": "Haehn, Daniel"
+    },
     {
       "name": "Weinstein, Alejandro"
     },

README.rst

@@ -11,8 +11,8 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
 .. image:: https://codecov.io/gh/nipy/nipype/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/nipy/nipype
 
-.. image:: https://www.codacy.com/project/badge/182f27944c51474490b369d0a23e2f32
-  :target: https://www.codacy.com/app/krzysztof-gorgolewski/nipy_nipype
+.. image:: https://api.codacy.com/project/badge/Grade/452bfc0d4de342c99b177d2c29abda7b
+  :target: https://www.codacy.com/app/nipype/nipype?utm_source=github.com&utm_medium=referral&utm_content=nipy/nipype&utm_campaign=Badge_Grade
 
 .. image:: https://img.shields.io/pypi/v/nipype.svg
     :target: https://pypi.python.org/pypi/nipype/
@@ -34,8 +34,9 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
     :target: http://gitter.im/nipy/nipype
     :alt: Chat
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.581704.svg
-   :target: https://doi.org/10.5281/zenodo.581704
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.596855.svg
+   :target: https://doi.org/10.5281/zenodo.596855
+   :alt: Citable DOI
 
 Current neuroimaging software offer users an incredible opportunity to
 analyze data using a variety of different algorithms. However, this has

doc/_templates/navbar.html

@@ -1,4 +1,4 @@
-<link rel="stylesheet" href="http://www.google.com/cse/style/look/default.css" type="text/css" />
+<link rel="stylesheet" href="https://www.google.com/cse/style/look/default.css" type="text/css" />
 <style type="text/css">
     a.navbar {
     color: {{ theme_linkcolor }};

doc/changelog/1.X.X-changelog

@@ -1,3 +1,44 @@
+1.1.7 (December 17, 2018)
+=========================
+
+  * 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)
+  * FIX: Order of SPM.NewSegment channel_info boolean tuple is (Field, Corrected) (https://github.com/nipy/nipype/pull/2817)
+  * FIX: Indices were swapped for memory and cpu profile data (https://github.com/nipy/nipype/pull/2816)
+  * FIX: ``status_callback`` not called with ``stop_on_first_crash`` (https://github.com/nipy/nipype/pull/2810)
+  * FIX: Change undefined ScriptError on LFS plugin to IOError (https://github.com/nipy/nipype/pull/2803)
+  * ENH: Add NaN failure mode to CompCor interfaces (https://github.com/nipy/nipype/pull/2819)
+  * ENH: Enable cnr_maps and residuals outputs for FSL eddy (https://github.com/nipy/nipype/pull/2750)
+  * ENH: Improve ``str2bool`` + doctests (https://github.com/nipy/nipype/pull/2807)
+  * TST: Improve py.test configuration of doctests (https://github.com/nipy/nipype/pull/2802)
+  * DOC: Update DOI badge to point to all versions (https://github.com/nipy/nipype/pull/2804)
+  * MAINT: Offload interfaces with help formatting (https://github.com/nipy/nipype/pull/2797)
+  * MAINT: Reduce minimal code redundancy in filemanip.get_dependencies (https://github.com/nipy/nipype/pull/2782)
+  * MAINT: Delayed imports to reduce import time (https://github.com/nipy/nipype/pull/2809)
+
+
+1.1.6 (November 26, 2018)
+=========================
+
+##### [Full changelog](https://github.com/nipy/nipype/milestone/27?closed=1)
+
+  * FIX: MapNodes fail when ``MultiProcPlugin`` passed by instance (https://github.com/nipy/nipype/pull/2786)
+  * FIX: --fineTune arguments order for MeshFix command (https://github.com/nipy/nipype/pull/2780)
+  * ENH: Add mp_context plugin arg for MultiProc (https://github.com/nipy/nipype/pull/2778)
+  * ENH: Create a crashfile even if 'stop_on_first_crash' is set (https://github.com/nipy/nipype/pull/2774)
+  * ENH: Add ExtractedBrainN4 output to ANTs CorticalThickness interface (https://github.com/nipy/nipype/pull/2784)
+  * STY: Combine split import (https://github.com/nipy/nipype/pull/2801)
+  * DOC: use https in css stylesheet url (https://github.com/nipy/nipype/pull/2779)
+  * MAINT: Outsource ``get_filecopy_info()`` from interfaces (https://github.com/nipy/nipype/pull/2798)
+  * MAINT: Import only Sequence to avoid DeprecationWarning (https://github.com/nipy/nipype/pull/2793)
+  * MAINT: One less DeprecationWarning (configparser) (https://github.com/nipy/nipype/pull/2794)
+  * MAINT: DeprecationWarning: use ``HasTraits.trait_set`` instead (https://github.com/nipy/nipype/pull/2792)
+  * MAINT: Stop using deprecated ``logger.warn()`` (https://github.com/nipy/nipype/pull/2788)
+  * MAINT: Move ``interfaces.base.run_command`` to ``nipype.utils.subprocess`` (https://github.com/nipy/nipype/pull/2777)
+  * MAINT: Force numpy>=1.15.4 when Python>=3.7 (https://github.com/nipy/nipype/pull/2775)
+
+
 1.1.5 (November 08, 2018)
 =========================
 

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "1.1.5"
+release = "1.1.7"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/documentation.rst

@@ -9,7 +9,7 @@ Documentation
    :Release: |version|
    :Date: |today|
 
-Previous versions: `1.1.5 <http://nipype.readthedocs.io/en/1.1.5/>`_ `1.1.4 <http://nipype.readthedocs.io/en/1.1.4/>`_
+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

nipype/algorithms/confounds.py

@@ -10,7 +10,6 @@
 import nibabel as nb
 import numpy as np
 from numpy.polynomial import Legendre
-from scipy import linalg
 
 from .. import config, logging
 from ..external.due import BibTeX
@@ -323,7 +322,7 @@ def _run_interface(self, runtime):
                 tr = self.inputs.series_tr
 
             if self.inputs.normalize and tr is None:
-                IFLOGGER.warn('FD plot cannot be normalized if TR is not set')
+                IFLOGGER.warning('FD plot cannot be normalized if TR is not set')
 
             self._results['out_figure'] = op.abspath(self.inputs.out_figure)
             fig = plot_confound(
@@ -409,6 +408,11 @@ class CompCorInputSpec(BaseInterfaceInputSpec):
         low=0,
         usedefault=True,
         desc='Number of volumes at start of series to ignore')
+    failure_mode = traits.Enum(
+        'error', 'NaN',
+        usedefault=True,
+        desc='When no components are found or convergence fails, raise an error '
+             'or silently return columns of NaNs.')
 
 
 class CompCorOutputSpec(TraitedSpec):
@@ -1182,13 +1186,20 @@ 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."
-        u, _, _ = linalg.svd(M, full_matrices=False)
+        try:
+            u, _, _ = np.linalg.svd(M, full_matrices=False)
+        except np.linalg.LinAlgError:
+            if self.inputs.failure_mode == 'error':
+                raise
+            u = np.ones((M.shape[0], num_components), dtype=np.float32) * np.nan
         if components is None:
             components = u[:, :num_components]
         else:
             components = np.hstack((components, u[:, :num_components]))
     if components is None and num_components > 0:
-        raise ValueError('No components found')
+        if self.inputs.failure_mode == 'error':
+            raise ValueError('No components found')
+        components = np.ones((M.shape[0], num_components), dtype=np.float32) * np.nan
     return components, basis
 
 
@@ -1263,7 +1274,7 @@ def _full_rank(X, cmax=1e15):
     c = smax / smin
     if c < cmax:
         return X, c
-    IFLOGGER.warn('Matrix is singular at working precision, regularizing...')
+    IFLOGGER.warning('Matrix is singular at working precision, regularizing...')
     lda = (smax - cmax * smin) / (cmax - 1)
     s = s + lda
     X = np.dot(U, np.dot(np.diag(s), V))

nipype/algorithms/icc.py

@@ -2,8 +2,8 @@
 import os
 import numpy as np
 from numpy import ones, kron, mean, eye, hstack, dot, tile
+from numpy.linalg import pinv
 import nibabel as nb
-from scipy.linalg import pinv
 from ..interfaces.base import BaseInterfaceInputSpec, TraitedSpec, \
     BaseInterface, traits, File
 from ..utils import NUMPY_MMAP

nipype/algorithms/mesh.py

@@ -418,5 +418,5 @@ class P2PDistance(ComputeMeshWarp):
 
     def __init__(self, **inputs):
         super(P2PDistance, self).__init__(**inputs)
-        IFLOGGER.warn('This interface has been deprecated since 1.0, please '
-                      'use ComputeMeshWarp')
+        IFLOGGER.warning('This interface has been deprecated since 1.0, please '
+                         'use ComputeMeshWarp')