Merge branch 'master' into enh-mrtrix3

Author: matteomancini

.mailmap

@@ -1,5 +1,6 @@
 Aimi Watanabe <[email protected]> stymy <[email protected]>
 Aimi Watanabe <[email protected]> stymy <[email protected]>
+Alejandro de la Vega <[email protected]> adelavega <[email protected]>
 Alexander Schaefer <[email protected]> Alexander Schaefer <[email protected]>
 Alexander Schaefer <[email protected]> alexschaefer83 <[email protected]>
 Alexander Schaefer <[email protected]> aschaefer <aschaefer@aschaefer-U36SD.(none)>
@@ -56,11 +57,13 @@ Franz Liem <[email protected]> fliem <franz.liem>
 Gael Varoquaux <[email protected]> GaelVaroquaux
 Gael Varoquaux <[email protected]> GaelVaroquaux <[email protected]>
 Gavin Cooper <[email protected]> gjcooper <[email protected]>
+Gilles de Hollander <[email protected]> Gilles86 <[email protected]>
 Hans Johnson <[email protected]> Hans Johnson <[email protected]>
 Hans Johnson <[email protected]> hjmjohnson <[email protected]>
 Horea Christian <[email protected]> Horea Christian <[email protected]>
 Isaac Schwabacher <[email protected]> ischwabacher <[email protected]>
 James Kent <[email protected]> jdkent <[email protected]>
+Jakub Kaczmarzyk <[email protected]> kaczmarj <[email protected]>
 Jason Wong <[email protected]> Jason <[email protected]>
 Jason Wong <[email protected]> jason <[email protected]>
 Jason Wong <[email protected]> Jason W <[email protected]>
@@ -72,7 +75,9 @@ Joerg Stadler <[email protected]> Jörg Stadler <Stadler@lin-magdeb
 Joke Durnez <[email protected]> jokedurnez <[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]>
+Kevin Sitek <[email protected]> sitek <[email protected]>
 Leonie Lampe <[email protected]> Leonie Lmape <[email protected]>
+Lukas Snoek <[email protected]> Lukas Snoek <[email protected]>
 Mathias Goncalves <[email protected]> mathiasg <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
 Michael Dayan <[email protected]> Michael <[email protected]>
@@ -102,5 +107,6 @@ Steven Giavasis <[email protected]> sgiavasis <[email protected]>
 Tristan Glatard <[email protected]> Tristan Glatard <[email protected]>
 Victor Saase <[email protected]> vsaase <[email protected]>
 William Triplett <[email protected]> William Triplett <[email protected]>
+Wolfgang Pauli <[email protected]> Wolfgang Pauli <[email protected]>
 Yaroslav Halchenko <[email protected]> Yaroslav Halchenko <[email protected]>
 pipolose <[email protected]> pipolose <[email protected]>

.travis.yml

@@ -59,4 +59,4 @@ deploy:
     tags: true
     repo: nipy/nipype
     branch: master
-  distributions: "sdist"
+  distributions: "sdist bdist_wheel"

.zenodo.json

@@ -514,11 +514,6 @@
     {
       "name": "Shachnev, Dmitry"
     },
-    {
-      "affiliation": "MIT, HMS",
-      "name": "Ghosh, Satrajit",
-      "orcid": "0000-0002-5312-6729"
-    },
     {
       "affiliation": "University of Amsterdam",
       "name": "Lukas Snoek",
@@ -540,8 +535,14 @@
       "orcid": "0000-0002-5544-7577"
     },
     {
-      "affiliation": "University College London"
-      "name": "Mancini, Matteo"
+      "affiliation": "MIT, HMS",
+      "name": "Ghosh, Satrajit",
+      "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "University College London",
+      "name": "Mancini, Matteo",
+      "orcid": "0000-0001-7194-4568"
     }
   ],
   "keywords": [

CHANGES

@@ -1,6 +1,14 @@
-Upcoming release (0.14.0)
+Upcoming release
 ================
 
+0.14.0 (November 21, 2017)
+==========================
+
+###### [Full changelog](https://github.com/nipy/nipype/milestone/13)
+
+* ENH: Generate Dockerfiles with neurodocker (https://github.com/nipy/nipype/pull/2202)
+* ENH: FLAIR options for recon-all (https://github.com/nipy/nipype/pull/2279)
+* ENH: Config option for setting maxtasksperchild when multiprocessing (https://github.com/nipy/nipype/pull/2284)
 * FIX: Testing maintainance and improvements (https://github.com/nipy/nipype/pull/2252)
 * ENH: Add elapsed_time and final metric_value to ants.Registration (https://github.com/nipy/nipype/pull/1985)
 * ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
@@ -17,7 +25,7 @@ Upcoming release (0.14.0)
 * MAINT: Additional Windows support (https://github.com/nipy/nipype/pull/2085)
 * ENH: Output realignment matrices from TOPUP (https://github.com/nipy/nipype/pull/2084)
 * ENH: Additional AFNI interfaces: 3dZcat, 3dZeropad, 3dedge3, 3dDeconvolve, 3dQwarp, 1dCat, 3dNwarpApply, 3daxialize,
-       3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090, 
+       3dREMLfit, 3dUndump, 3dCM, 3dSynthesize + more (https://github.com/nipy/nipype/pull/2087, https://github.com/nipy/nipype/pull/2090,
        https://github.com/nipy/nipype/pull/2095, https://github.com/nipy/nipype/pull/2099, https://github.com/nipy/nipype/pull/2103,
        https://github.com/nipy/nipype/pull/2114, https://github.com/nipy/nipype/pull/2135, https://github.com/nipy/nipype/pull/2186,
        https://github.com/nipy/nipype/pull/2201, https://github.com/nipy/nipype/pull/2210)

doc/conf.py

@@ -82,7 +82,7 @@
 # The short X.Y version.
 version = nipype.__version__
 # The full version, including alpha/beta/rc tags.
-release = "0.13.1"
+release = "0.14.0-rc1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

nipype/info.py

@@ -10,7 +10,7 @@
 # full release.  '.dev' as a version_extra string means this is a development
 # version
 # Remove -dev for release
-__version__ = '1.0.0-dev'
+__version__ = '0.14.0-rc1'
 
 
 def get_nipype_gitversion():

nipype/interfaces/ants/segmentation.py

@@ -720,17 +720,19 @@ class BrainExtraction(ANTSCommand):
     def _run_interface(self, runtime, correct_return_codes=(0,)):
         # antsBrainExtraction.sh requires ANTSPATH to be defined
         out_environ = self._get_environ()
-        if out_environ.get('ANTSPATH') is None:
-            runtime.environ.update(out_environ)
-            executable_name = self.cmd.split()[0]
-            exist_val, cmd_path = _exists_in_path(executable_name, runtime.environ)
-            if not exist_val:
-                raise IOError("command '%s' could not be found on host %s" %
-                              (self.cmd.split()[0], runtime.hostname))
-
-            # Set the environment variable if found
-            runtime.environ.update({'ANTSPATH': os.path.dirname(cmd_path)})
-
+        ants_path = out_environ.get('ANTSPATH', None) or os.getenv('ANTSPATH', None)
+        if ants_path is None:
+            # Check for antsRegistration, which is under bin/ (the $ANTSPATH) instead of
+            # checking for antsBrainExtraction.sh which is under script/
+            _, cmd_path = _exists_in_path('antsRegistration', runtime.environ)
+            if not cmd_path:
+                raise RuntimeError(
+                    'The environment variable $ANTSPATH is not defined in host "%s", '
+                    'and Nipype could not determine it automatically.' % runtime.hostname)
+            ants_path = os.path.dirname(cmd_path)
+
+        self.inputs.environ.update({'ANTSPATH': ants_path})
+        runtime.environ.update({'ANTSPATH': ants_path})
         runtime = super(BrainExtraction, self)._run_interface(runtime)
 
         # Still, double-check if it didn't found N4
@@ -740,8 +742,8 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
                     tool = line.strip().replace('we cant find the', '').split(' ')[0]
                     break
 
-            errmsg = ('antsBrainExtraction.sh requires %s the environment variable '
-                      'ANTSPATH to be defined' % tool)
+            errmsg = ('antsBrainExtraction.sh requires "%s" to be found in $ANTSPATH '
+                      '($ANTSPATH="%s").') % (tool, ants_path)
             if runtime.stderr is None:
                 runtime.stderr = errmsg
             else:

setup.cfg

@@ -0,0 +1,2 @@
+[bdist_wheel]
+universal=1