Merge pull request #2829 from nipy/rel/1.1.7

REL: 1.1.7

Author: effigies

.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/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 = "1.1.6"
+release = "1.1.7"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

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__ = '1.1.7'
 
 
 def get_nipype_gitversion():

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -6,6 +6,10 @@
 def test_Eddy_inputs():
     input_map = dict(
         args=dict(argstr='%s', ),
+        cnr_maps=dict(
+            argstr='--cnr_maps',
+            min_ver='5.0.10',
+        ),
         dont_peas=dict(argstr='--dont_peas', ),
         dont_sep_offs_move=dict(argstr='--dont_sep_offs_move', ),
         environ=dict(
@@ -71,11 +75,13 @@ def test_Eddy_inputs():
         ),
         output_type=dict(),
         repol=dict(argstr='--repol', ),
+        residuals=dict(
+            argstr='--residuals',
+            min_ver='5.0.10',
+        ),
         session=dict(argstr='--session=%s', ),
         slm=dict(argstr='--slm=%s', ),
         use_cuda=dict(),
-        cnr_maps=dict(argstr='--cnr_maps', min_ver='5.0.10', ),
-        residuals=dict(argstr='--residuals', min_ver='5.0.10', ),
     )
     inputs = Eddy.input_spec()
 
@@ -84,15 +90,15 @@ def test_Eddy_inputs():
             assert getattr(inputs.traits()[key], metakey) == value
 def test_Eddy_outputs():
     output_map = dict(
+        out_cnr_maps=dict(),
         out_corrected=dict(),
         out_movement_rms=dict(),
         out_outlier_report=dict(),
         out_parameter=dict(),
+        out_residuals=dict(),
         out_restricted_movement_rms=dict(),
         out_rotated_bvecs=dict(),
         out_shell_alignment_parameters=dict(),
-        out_cnr_maps=dict(),
-        out_residuals=dict(),
     )
     outputs = Eddy.output_spec()