Merge remote-tracking branch 'nipy/master' into fix/mrtrix3-tckgen-option

Author: jguillon

.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",
@@ -380,16 +380,16 @@
     {
       "name": "Hallquist, Michael"
     },
-    {
-      "affiliation": "GIGA Institute",
-      "name": "Grignard, Martin",
-      "orcid": "0000-0001-5549-1861"
-    },
     {
       "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
       "name": "Chetverikov, Andrey",
       "orcid": "0000-0003-2767-6310"
     },
+    {
+      "affiliation": "GIGA Institute",
+      "name": "Grignard, Martin",
+      "orcid": "0000-0001-5549-1861"
+    },
     {
       "name": "Salvatore, John"
     },

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

@@ -1,22 +1,42 @@
+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)
+  * 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: `1.1.6 <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

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>`_.
 
 
     """
@@ -412,6 +422,11 @@ 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):
@@ -1185,13 +1200,20 @@ 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, _, _ = np.linalg.svd(M, full_matrices=False)
+        try:
+            u, _, _ = fallback_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
 
 
@@ -1261,7 +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:

nipype/algorithms/tests/test_auto_ACompCor.py

@@ -6,6 +6,7 @@
 def test_ACompCor_inputs():
     input_map = dict(
         components_file=dict(usedefault=True, ),
+        failure_mode=dict(usedefault=True, ),
         header_prefix=dict(),
         high_pass_cutoff=dict(usedefault=True, ),
         ignore_initial_volumes=dict(usedefault=True, ),

nipype/algorithms/tests/test_auto_TCompCor.py

@@ -6,6 +6,7 @@
 def test_TCompCor_inputs():
     input_map = dict(
         components_file=dict(usedefault=True, ),
+        failure_mode=dict(usedefault=True, ),
         header_prefix=dict(),
         high_pass_cutoff=dict(usedefault=True, ),
         ignore_initial_volumes=dict(usedefault=True, ),

nipype/info.py

@@ -11,7 +11,7 @@
 # full release.  '.dev' as a version_extra string means this is a development
 # version
 # Remove -dev for release
-__version__ = '1.1.7-dev'
+__version__ = '1.1.8-dev'
 
 
 def get_nipype_gitversion():
@@ -108,7 +108,7 @@ def get_nipype_gitversion():
 SCIPY_MIN_VERSION = '0.14'
 TRAITS_MIN_VERSION = '4.6'
 DATEUTIL_MIN_VERSION = '2.2'
-PYTEST_MIN_VERSION = '3.0'
+PYTEST_MIN_VERSION = '3.6'
 FUTURE_MIN_VERSION = '0.16.0'
 SIMPLEJSON_MIN_VERSION = '3.8.0'
 PROV_VERSION = '1.5.2'
@@ -147,8 +147,6 @@ 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,
@@ -159,7 +157,14 @@ def get_nipype_gitversion():
 if sys.version_info <= (3, 4):
     REQUIRES.append('configparser')
 
-TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-env', 'coverage<5']
+TESTS_REQUIRES = [
+    'pytest>=%s' % PYTEST_MIN_VERSION,
+    'pytest-xdist',
+    'pytest-cov',
+    'codecov',
+    'pytest-env',
+    'coverage<5'
+]
 
 EXTRA_REQUIRES = {
     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],

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,