Merge branch 'master' of https://github.com/nipy/nipype into satra_fix_specs

Author: kesshijordan

.circleci/config.yml

@@ -36,9 +36,8 @@ _get_base_image: &get_base_image
       echo "Pulling base image ..."
       docker pull nipype/nipype:base
     elif [ "$GET_BASE" == "BUILD" ]; then
-      e=1 && for i in {1..5}; do
-        docker build -t nipype/nipype:base - < docker/Dockerfile.base  && e=0 && break || sleep 15
-      done && [ "$e" -eq "0" ]
+      tools/retry_cmd.sh -n 5 -s 15 \
+        docker build -t nipype/nipype:base - < docker/Dockerfile.base
     else
       echo "Error: method to get base image not understood"
       exit 1
@@ -48,22 +47,20 @@ _build_main_image_py36: &build_main_image_py36
   name: Build main image (py36)
   no_output_timeout: 60m
   command: |
-    e=1 && for i in {1..5}; do
+    tools/retry_cmd.sh -n 5 -s 15 \
       docker build \
         --rm=false \
         --tag nipype/nipype:latest \
         --tag nipype/nipype:py36 \
         --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
         --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
         --build-arg VERSION="${CIRCLE_TAG}" /home/circleci/nipype \
-      && e=0 && break || sleep 15
-    done && [ "$e" -eq "0" ]
 
 _build_main_image_py27: &build_main_image_py27
   name: Build main image (py27)
   no_output_timeout: 60m
   command: |
-    e=1 && for i in {1..5}; do
+    tools/retry_cmd.sh -n 5 -s 15 \
       docker build \
         --rm=false \
         --tag nipype/nipype:py27 \
@@ -72,8 +69,6 @@ _build_main_image_py27: &build_main_image_py27
         --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
         --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
         --build-arg VERSION="${CIRCLE_TAG}-py27" /home/circleci/nipype \
-      && e=0 && break || sleep 15
-    done && [ "$e" -eq "0" ]
 
 _download_test_data: &_download_test_data
   name: Download test data

.zenodo.json

@@ -20,16 +20,16 @@
       "name": "Ellis, David Gage",
       "orcid": "0000-0002-3718-6836"
     },
-    {
-      "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland",
-      "name": "Notter, Michael Philipp",
-      "orcid": "0000-0002-5866-047X"
-    },
     {
       "affiliation": "Stanford University",
       "name": "Markiewicz, Christopher J.",
       "orcid": "0000-0002-6533-164X"
     },
+    {
+      "affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland",
+      "name": "Notter, Michael Philipp",
+      "orcid": "0000-0002-5866-047X"
+    },
     {
       "affiliation": "University of Iowa",
       "name": "Johnson, Hans",
@@ -105,11 +105,6 @@
       "name": "Dayan, Michael",
       "orcid": "0000-0002-2666-0969"
     },
-    {
-      "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering",
-      "name": "Keshavan, Anisha",
-      "orcid": "0000-0003-3554-043X"
-    },
     {
       "affiliation": "UC Berkeley",
       "name": "Clark, Dav",
@@ -120,6 +115,11 @@
       "name": "Visconti di Oleggio Castello, Matteo",
       "orcid": "0000-0001-7931-5272"
     },
+    {
+      "affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering",
+      "name": "Keshavan, Anisha",
+      "orcid": "0000-0003-3554-043X"
+    },
     {
       "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay",
       "name": "Gramfort, Alexandre",
@@ -156,14 +156,18 @@
       "name": "Rokem, Ariel",
       "orcid": "0000-0003-0679-1985"
     },
+    {
+      "name": "Moloney, Brendan"
+    },
+    {
+      "affiliation": "Molecular Imaging Research Center, CEA, France",
+      "name": "Bougacha, Salma"
+    },
     {
       "affiliation": "Athena EPI, Inria Sophia-Antipolis",
       "name": "Wassermann , Demian",
       "orcid": "0000-0001-5194-6056"
     },
-    {
-      "name": "Moloney, Brendan"
-    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Halchenko, Yaroslav O.",
@@ -179,10 +183,6 @@
       "name": "Horea, Christian",
       "orcid": "0000-0001-7037-2449"
     },
-    {
-      "affiliation": "Molecular Imaging Research Center, CEA, France",
-      "name": "Bougacha, Salma"
-    },
     {
       "affiliation": "MIT",
       "name": "Kaczmarzyk, Jakub",
@@ -193,6 +193,16 @@
       "name": "Gilles de Hollander",
       "orcid": "0000-0003-1988-5091"
     },
+    {
+      "affiliation": "Montreal Neurological Institute and Hospital",
+      "name": "DuPre, Elizabeth",
+      "orcid": "0000-0003-1358-196X"
+    },
+    {
+      "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"
     },
@@ -229,11 +239,6 @@
       "name": "Malone, Ian B.",
       "orcid": "0000-0001-7512-7856"
     },
-    {
-      "affiliation": "Montreal Neurological Institute and Hospital",
-      "name": "DuPre, Elizabeth",
-      "orcid": "0000-0003-1358-196X"
-    },
     {
       "name": "Dubois, Mathieu"
     },
@@ -259,11 +264,6 @@
       "name": "Huntenburg, Julia M.",
       "orcid": "0000-0003-0579-9811"
     },
-    {
-      "affiliation": "University College London",
-      "name": "Eshaghi, Arman",
-      "orcid": "0000-0002-6652-3512"
-    },
     {
       "affiliation": "Harvard University - Psychology",
       "name": "Kastman, Erik",
@@ -274,6 +274,11 @@
       "name": "Nichols, B. Nolan",
       "orcid": "0000-0003-1099-3328"
     },
+    {
+      "affiliation": "University College London",
+      "name": "Eshaghi, Arman",
+      "orcid": "0000-0002-6652-3512"
+    },
     {
       "name": "Ginsburg, Daniel"
     },
@@ -290,11 +295,6 @@
     {
       "name": "Kent, James"
     },
-    {
-      "affiliation": "Australian eHealth Research Centre, Commonwealth Scientific and Industrial Research Organisation; University of Queensland",
-      "name": "Gillman, Ashley",
-      "orcid": "0000-0001-9130-1092"
-    },
     {
       "affiliation": "Child Mind Institute",
       "name": "Giavasis, Steven"
@@ -356,6 +356,11 @@
       "name": "Kahn, Ari E.",
       "orcid": "0000-0002-2127-0507"
     },
+    {
+      "affiliation": "University College London",
+      "name": "P\u00e9rez-Garc\u00eda, Fernando",
+      "orcid": "0000-0001-9090-3024"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Triplett, William",
@@ -384,9 +389,6 @@
     {
       "name": "Salvatore, John"
     },
-    {
-      "name": "Mertz, Fred"
-    },
     {
       "name": "Park, Anne"
     },
@@ -409,11 +411,6 @@
     {
       "name": "Hinds, Oliver"
     },
-    {
-      "affiliation": "Technical University Munich",
-      "name": "Molina-Romero, Miguel",
-      "orcid": "0000-0001-8054-0426"
-    },
     {
       "affiliation": "University of Newcastle, Australia",
       "name": "Cooper, Gavin",
@@ -467,6 +464,9 @@
       "name": "Durnez, Joke",
       "orcid": "0000-0001-9030-2202"
     },
+    {
+      "name": "Mertz, Fred"
+    },
     {
       "affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
       "name": "Geisler, Daniel",
@@ -476,14 +476,15 @@
       "affiliation": "The University of Texas at Austin",
       "name": "Floren, Andrew",
       "orcid": "0000-0003-3618-2056"
-    },
+      },
     {
       "affiliation": "University of illinois urbana champaign",
       "name": "Sharp, Paul"
     },
     {
-      "affiliation": "Vrije Universiteit Amsterdam",
-      "name": "Ort, Eduard"
+      "affiliation": "Technical University Munich",
+      "name": "Molina-Romero, Miguel",
+      "orcid": "0000-0001-8054-0426"
     },
     {
       "name": "Weinstein, Alejandro"
@@ -558,9 +559,8 @@
       "name": "Flandin, Guillaume"
     },
     {
-      "affiliation": "University College London",
-      "name": "P\u00e9rez-Garc\u00eda, Fernando",
-      "orcid": "0000-0001-9090-3024"
+      "affiliation": "Vrije Universiteit Amsterdam",
+      "name": "Ort, Eduard"
     },
     {
       "name": "Shachnev, Dmitry"

doc/changelog/1.X.X-changelog

@@ -1,3 +1,26 @@
+1.0.2 (March 27, 2018)
+======================
+
+###### [Full changelog](https://github.com/nipy/nipype/milestone/16?closed=1)
+
+  * FIX: dcm2niix interface (https://github.com/nipy/nipype/pull/2498)
+  * FIX: mark .niml.dset as special extension in utils.filemanip (https://github.com/nipy/nipype/pull/2495)
+  * FIX: handle automatic module creation, name extraction, default value (https://github.com/nipy/nipype/pull/2490)
+  * FIX: Check and report mount table parsing failures (https://github.com/nipy/nipype/pull/2476)
+  * FIX: Check against full node name when reconnecting JoinNodes (https://github.com/nipy/nipype/pull/2479)
+  * DOC: Add tutorials, porcupine to users TOC (https://github.com/nipy/nipype/pull/2503
+  * DOC: Contributing and testing (https://github.com/nipy/nipype/pull/2482)
+  * DOC: Describe 'orphaned' tag in CONTRIBUTING (https://github.com/nipy/nipype/pull/2481)
+  * DOC: Add details for dcm2niix output filename pattern (https://github.com/nipy/nipype/pull/2512)
+  * ENH: Add interface for AFNI 3dNwarpAdjust (https://github.com/nipy/nipype/pull/2450)
+  * ENH: Update SSHDataGrabber to fetch related files (https://github.com/nipy/nipype/pull/2104)
+  * ENH: Add interpolation order parameter to NiftyReg's RegTools (https://github.com/nipy/nipype/pull/2471)
+  * MAINT: Stray warnings and exceptions (https://github.com/nipy/nipype/pull/2478)
+  * MAINT: Add dev install option, update CONTRIBUTING (https://github.com/nipy/nipype/pull/2477)
+  * MAINT: Sync requirements with info.py (https://github.com/nipy/nipype/pull/2472)
+  * CI: Update Travis builds, Docker to use latest miniconda (https://github.com/nipy/nipype/pull/2455)
+  * TEST: Parallelize pytest (https://github.com/nipy/nipype/pull/2469)
+
 1.0.1 (February 27, 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 = "1.0.1"
+release = "1.0.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

nipype/algorithms/tests/test_mesh_ops.py

@@ -21,7 +21,7 @@ def test_ident_distances(tmpdir):
     dist_ident = m.ComputeMeshWarp()
     dist_ident.inputs.surface1 = in_surf
     dist_ident.inputs.surface2 = in_surf
-    dist_ident.inputs.out_file = tmpdir.join('distance.npy')
+    dist_ident.inputs.out_file = tmpdir.join('distance.npy').strpath
     res = dist_ident.run()
     assert res.outputs.distance == 0.0
 
@@ -35,7 +35,7 @@ def test_trans_distances(tmpdir):
     from ...interfaces.vtkbase import tvtk
 
     in_surf = example_data('surf01.vtk')
-    warped_surf = tmpdir.join('warped.vtk')
+    warped_surf = tmpdir.join('warped.vtk').strpath
 
     inc = np.array([0.7, 0.3, -0.2])
 
@@ -51,7 +51,7 @@ def test_trans_distances(tmpdir):
     dist = m.ComputeMeshWarp()
     dist.inputs.surface1 = in_surf
     dist.inputs.surface2 = warped_surf
-    dist.inputs.out_file = tmpdir.join('distance.npy')
+    dist.inputs.out_file = tmpdir.join('distance.npy').strpath
     res = dist.run()
     assert np.allclose(res.outputs.distance, np.linalg.norm(inc), 4)
     dist.inputs.weighting = 'area'

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__ = '1.0.2-dev'
+__version__ = '1.0.3-dev'
 
 
 def get_nipype_gitversion():

nipype/interfaces/dcm2nii.py

@@ -275,7 +275,24 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
         xor=['source_names'])
     out_filename = traits.Str(
         argstr="-f %s",
-        desc="Output filename")
+        desc="Output filename template ("
+             "%a=antenna (coil) number, "
+             "%c=comments, "
+             "%d=description, "
+             "%e=echo number, "
+             "%f=folder name, "
+             "%i=ID of patient, "
+             "%j=seriesInstanceUID, "
+             "%k=studyInstanceUID, "
+             "%m=manufacturer, "
+             "%n=name of patient, "
+             "%p=protocol, "
+             "%s=series number, "
+             "%t=time, "
+             "%u=acquisition number, "
+             "%v=vendor, "
+             "%x=study ID; "
+             "%z=sequence name)")
     output_dir = Directory(
         ".",
         usedefault=True,
@@ -320,7 +337,7 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
         False,
         argstr='-t',
         usedefault=True,
-        desc="Flag if text notes includes private patient details")
+        desc="Flag if text notes include private patient details")
     compression = traits.Enum(
         1, 2, 3, 4, 5, 6, 7, 8, 9,
         argstr='-%d',

nipype/interfaces/fsl/model.py

@@ -217,13 +217,16 @@ def _create_ev_files(self, cwd, runinfo, runidx, ev_parameters,
                 self._create_ev_file(evfname, evinfo)
         # add ev orthogonalization
         for i in range(1, num_evs[0] + 1):
+            initial = ev_ortho.substitute(c0=i, c1=0, orthogonal=1)
             for j in range(0, num_evs[0] + 1):
                 try:
                     orthogonal = int(orthogonalization[i][j])
                 except (KeyError, TypeError, ValueError, IndexError):
                     orthogonal = 0
-                ev_txt += ev_ortho.substitute(
-                    c0=i, c1=j, orthogonal=orthogonal)
+                if orthogonal == 1 and initial not in ev_txt:
+                    ev_txt += initial + "\n"
+                ev_txt += ev_ortho.substitute(c0=i, c1=j,
+                                              orthogonal=orthogonal)
                 ev_txt += "\n"
         # add contrast info to fsf file
         if isdefined(contrasts):