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Merge pull request #2760 from nipy/rel/1.1.4
REL: 1.1.4
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‎.zenodo.json

+47-47
Original file line numberDiff line numberDiff line change
@@ -74,20 +74,20 @@
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Waskom, Michael"
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},
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{
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"affiliation": "Developer",
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"name": "Clark, Daniel",
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"orcid": "0000-0002-8121-8954"
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},
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{
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"affiliation": "Shattuck Lab, UCLA Brain Mapping Center",
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"name": "Wong, Jason"
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},
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{
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"name": "Modat, Marc"
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},
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{
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"name": "Loney, Fred"
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},
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{
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"name": "Modat, Marc"
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"affiliation": "Developer",
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"name": "Clark, Daniel",
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"orcid": "0000-0002-8121-8954"
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},
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{
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"affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
@@ -141,16 +141,6 @@
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{
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"name": "Berleant, Shoshana"
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},
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{
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"affiliation": "MIT",
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"name": "Kaczmarzyk, Jakub",
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"orcid": "0000-0002-5544-7577"
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},
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{
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"affiliation": "INRIA",
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"name": "Varoquaux, Gael",
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"orcid": "0000-0003-1076-5122"
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},
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{
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"affiliation": "UC San Diego",
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"name": "Cipollini, Ben",
@@ -176,9 +166,24 @@
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"name": "DuPre, Elizabeth",
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"orcid": "0000-0003-1358-196X"
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},
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{
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"affiliation": "MIT",
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"name": "Kaczmarzyk, Jakub",
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"orcid": "0000-0002-5544-7577"
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},
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{
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"name": "Moloney, Brendan"
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},
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{
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"affiliation": "INRIA",
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"name": "Varoquaux, Gael",
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"orcid": "0000-0003-1076-5122"
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},
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{
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"affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
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"name": "Horea, Christian",
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"orcid": "0000-0001-7037-2449"
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},
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{
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"affiliation": "Athena EPI, Inria Sophia-Antipolis",
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"name": "Wassermann , Demian",
@@ -189,11 +194,6 @@
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"name": "Hanke, Michael",
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"orcid": "0000-0001-6398-6370"
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},
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{
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"affiliation": "Institute for Biomedical Engineering, ETH and University of Zurich",
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"name": "Horea, Christian",
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"orcid": "0000-0001-7037-2449"
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},
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{
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"affiliation": "Vrije Universiteit, Amsterdam",
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"name": "Gilles de Hollander",
@@ -268,11 +268,6 @@
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{
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"name": "Cumba, Chad"
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},
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{
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"affiliation": "Harvard University - Psychology",
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"name": "Kastman, Erik",
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"orcid": "0000-0001-7221-9042"
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},
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{
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"affiliation": "SRI International",
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"name": "Nichols, B. Nolan",
@@ -283,6 +278,11 @@
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"name": "Eshaghi, Arman",
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"orcid": "0000-0002-6652-3512"
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},
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{
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"affiliation": "Harvard University - Psychology",
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"name": "Kastman, Erik",
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"orcid": "0000-0001-7221-9042"
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},
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{
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"name": "Ginsburg, Daniel"
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},
@@ -297,8 +297,9 @@
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"orcid": "0000-0001-6392-6634"
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},
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{
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"affiliation": "Child Mind Institute",
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"name": "Giavasis, Steven"
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"affiliation": "University of Zurich",
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"name": "Liem, Franz",
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"orcid": "0000-0003-0646-4810"
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},
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{
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"affiliation": "UniversityHospital Heidelberg, Germany",
@@ -308,7 +309,8 @@
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"name": "Erickson, Drew"
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},
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{
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"name": "K\u00fcttner, Ren\u00e9"
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"affiliation": "Child Mind Institute",
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"name": "Giavasis, Steven"
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},
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{
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"name": "Haselgrove, Christian"
@@ -320,9 +322,7 @@
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"name": "Ghayoor, Ali"
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},
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{
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"affiliation": "University of Zurich",
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"name": "Liem, Franz",
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"orcid": "0000-0003-0646-4810"
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"name": "K\u00fcttner, Ren\u00e9"
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},
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{
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"name": "Millman, Jarrod"
@@ -385,10 +385,6 @@
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"name": "Chetverikov, Andrey",
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"orcid": "0000-0003-2767-6310"
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},
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{
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"affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
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"name": "Weninger, Leon"
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},
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{
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"name": "Salvatore, John"
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},
@@ -403,9 +399,6 @@
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"name": "Craddock, R. Cameron",
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"orcid": "0000-0002-4950-1303"
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},
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{
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"name": "Inati, Souheil"
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},
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{
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"name": "Hinds, Oliver"
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},
@@ -414,6 +407,13 @@
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"name": "Cooper, Gavin",
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"orcid": "0000-0002-7186-5293"
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},
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{
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"affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
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"name": "Weninger, Leon"
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},
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{
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"name": "Inati, Souheil"
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},
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{
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"affiliation": "Boston University",
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"name": "Perkins, L. Nathan"
@@ -443,9 +443,6 @@
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"name": "Floren, Andrew",
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"orcid": "0000-0003-3618-2056"
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},
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{
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"name": "Rothmei, Simon"
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},
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{
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"name": "Urchs, Sebastian"
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},
@@ -465,6 +462,11 @@
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"name": "Geisler, Daniel",
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"orcid": "0000-0003-2076-5329"
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},
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{
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"affiliation": "University of Texas at Austin",
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"name": "De La Vega, Alejandro",
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"orcid": "0000-0001-9062-3778"
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},
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{
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"affiliation": "University of illinois urbana champaign",
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"name": "Sharp, Paul"
@@ -493,6 +495,9 @@
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{
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"name": "Saase, Victor"
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},
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{
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"name": "Rothmei, Simon"
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},
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{
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"affiliation": "University of Helsinki",
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"name": "Andberg, Sami Kristian",
@@ -518,11 +523,6 @@
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{
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"name": "Tarbert, Claire"
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},
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{
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"affiliation": "University of Texas at Austin",
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"name": "De La Vega, Alejandro",
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"orcid": "0000-0001-9062-3778"
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},
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{
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"affiliation": "Vrije Universiteit Amsterdam",
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"name": "Ort, Eduard"

‎doc/changelog/1.X.X-changelog

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@@ -1,3 +1,31 @@
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1.1.4 (October 31, 2018)
2+
========================
3+
4+
##### [Full changelog](https://github.com/nipy/nipype/milestone/25?closed=1)
5+
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* FIX: Python 2.7-3.7.1 compatible NonDaemonPool (https://github.com/nipy/nipype/pull/2754)
7+
* FIX: VRML typo (VMRL) in MeshFix (https://github.com/nipy/nipype/pull/2757)
8+
* FIX: Refine FSL.split output identification (https://github.com/nipy/nipype/pull/2746)
9+
* FIX: Reuse _gen_filename logic in ants.LaplacianThickness (https://github.com/nipy/nipype/pull/2734)
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* FIX: Remove 'reg_term' default from dwi2tensor interface (https://github.com/nipy/nipype/pull/2731)
11+
* FIX: Keep profile files when ``remove_unnecessary_outputs = true`` (https://github.com/nipy/nipype/pull/2718)
12+
* ENH: Add afni.LocalStat and afni.ReHo, update afni.ROIStats inputs (https://github.com/nipy/nipype/pull/2740)
13+
* ENH: Add compression option for bru2nii (https://github.com/nipy/nipype/pull/2762)
14+
* ENH: Add slice_encoding_direction input to TShift (https://github.com/nipy/nipype/pull/2753)
15+
* ENH: Add 'sse' output to FSL DTIFit interface (https://github.com/nipy/nipype/pull/2749)
16+
* ENH: Update ``ants.LaplacianThickness`` to use ``name_source`` (https://github.com/nipy/nipype/pull/2747)
17+
* ENH: Add tab completion for node and interface inputs properties (https://github.com/nipy/nipype/pull/2735)
18+
* ENH: enable/disable resource monitor in the fixture per test (https://github.com/nipy/nipype/pull/2725)
19+
* TEST: Update expected dotfile text for networkx 1.x (https://github.com/nipy/nipype/pull/2730)
20+
* DOC: Move user docs from nipype to nipype_tutorial (https://github.com/nipy/nipype/pull/2726)
21+
* DOC: Use consistent name in reconall workflow docstring (https://github.com/nipy/nipype/pull/2758)
22+
* MAINT: Use neurodocker 0.4.1 + apt install afni (https://github.com/nipy/nipype/pull/2707)
23+
* MAINT: Fix prov and rdflib in nipype (https://github.com/nipy/nipype/pull/2701)
24+
* MAINT: Correct readthedocs build error (https://github.com/nipy/nipype/pull/2723)
25+
* MAINT: Pin codecov to <5.0 so Travis is fixed (https://github.com/nipy/nipype/pull/2728)
26+
* CI: Lock travis pybids 0.6.5 (https://github.com/nipy/nipype/pull/2720)
27+
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1.1.3 (September 24, 2018)
230
==========================
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‎doc/conf.py

+1-1
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@@ -82,7 +82,7 @@
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# The short X.Y version.
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version = nipype.__version__
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# The full version, including alpha/beta/rc tags.
85-
release = "1.1.3"
85+
release = "1.1.4"
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.

‎nipype/info.py

+1-1
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@@ -11,7 +11,7 @@
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# full release. '.dev' as a version_extra string means this is a development
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# version
1313
# Remove -dev for release
14-
__version__ = '1.1.4-dev'
14+
__version__ = '1.1.4'
1515

1616

1717
def get_nipype_gitversion():

‎nipype/interfaces/afni/tests/test_auto_TShift.py

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@@ -30,6 +30,7 @@ def test_TShift_inputs():
3030
outputtype=dict(),
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rlt=dict(argstr='-rlt', ),
3232
rltplus=dict(argstr='-rlt+', ),
33+
slice_encoding_direction=dict(usedefault=True, ),
3334
slice_timing=dict(
3435
argstr='-tpattern @%s',
3536
xor=['tpattern'],

‎nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -52,8 +52,8 @@ def test_AntsJointFusion_inputs():
5252
hash_files=False,
5353
),
5454
out_label_post_prob_name_format=dict(
55-
requires=['out_label_fusion', 'out_intensity_fusion_name_format'],
56-
),
55+
requires=['out_label_fusion',
56+
'out_intensity_fusion_name_format'], ),
5757
patch_metric=dict(argstr='-m %s', ),
5858
patch_radius=dict(
5959
argstr='-p %s',

‎nipype/interfaces/dipy/tests/test_auto_DTI.py

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@@ -20,6 +20,7 @@ def test_DTI_inputs():
2020
def test_DTI_outputs():
2121
output_map = dict(
2222
ad_file=dict(),
23+
color_fa_file=dict(),
2324
fa_file=dict(),
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md_file=dict(),
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out_file=dict(),

‎nipype/interfaces/fsl/tests/test_auto_DTIFit.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -65,8 +65,8 @@ def test_DTIFit_outputs():
6565
V1=dict(),
6666
V2=dict(),
6767
V3=dict(),
68-
tensor=dict(),
6968
sse=dict(),
69+
tensor=dict(),
7070
)
7171
outputs = DTIFit.output_spec()
7272

‎nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py

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1+
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2+
from __future__ import unicode_literals
3+
from ..preprocess import RealignUnwarp
4+
5+
6+
def test_RealignUnwarp_inputs():
7+
input_map = dict(
8+
est_basis_func=dict(field='uweoptions.basfcn', ),
9+
est_first_order_effects=dict(field='uweoptions.fot', ),
10+
est_jacobian_deformations=dict(field='uweoptions.jm', ),
11+
est_num_of_interations=dict(
12+
field='uweoptions.noi',
13+
maxlen=1,
14+
minlen=1,
15+
usedfault=True,
16+
),
17+
est_re_est_mov_par=dict(field='uweoptions.rem', ),
18+
est_reg_factor=dict(
19+
field='uweoptions.lambda',
20+
maxlen=1,
21+
minlen=1,
22+
usedefault=True,
23+
),
24+
est_reg_order=dict(field='uweoptions.regorder', ),
25+
est_second_order_effects=dict(field='uweoptions.sot', ),
26+
est_taylor_expansion_point=dict(
27+
field='uweoptions.expround',
28+
usedefault=True,
29+
),
30+
est_unwarp_fwhm=dict(field='uweoptions.uwfwhm', ),
31+
fwhm=dict(field='eoptions.fwhm', ),
32+
in_files=dict(
33+
copyfile=True,
34+
field='data.scans',
35+
mandatory=True,
36+
),
37+
interp=dict(field='eoptions.einterp', ),
38+
matlab_cmd=dict(),
39+
mfile=dict(usedefault=True, ),
40+
out_prefix=dict(
41+
field='uwroptions.prefix',
42+
usedefault=True,
43+
),
44+
paths=dict(),
45+
phase_map=dict(
46+
copyfile=False,
47+
field='data.pmscan',
48+
),
49+
quality=dict(field='eoptions.quality', ),
50+
register_to_mean=dict(field='eoptions.rtm', ),
51+
reslice_interp=dict(field='uwroptions.rinterp', ),
52+
reslice_mask=dict(field='uwroptions.mask', ),
53+
reslice_which=dict(
54+
field='uwroptions.uwwhich',
55+
maxlen=2,
56+
minlen=2,
57+
usedefault=True,
58+
),
59+
reslice_wrap=dict(field='uwroptions.wrap', ),
60+
separation=dict(field='eoptions.sep', ),
61+
use_mcr=dict(),
62+
use_v8struct=dict(
63+
min_ver='8',
64+
usedefault=True,
65+
),
66+
weight_img=dict(field='eoptions.weight', ),
67+
wrap=dict(field='eoptions.ewrap', ),
68+
)
69+
inputs = RealignUnwarp.input_spec()
70+
71+
for key, metadata in list(input_map.items()):
72+
for metakey, value in list(metadata.items()):
73+
assert getattr(inputs.traits()[key], metakey) == value
74+
def test_RealignUnwarp_outputs():
75+
output_map = dict(
76+
mean_image=dict(),
77+
modified_in_files=dict(),
78+
realigned_unwarped_files=dict(),
79+
realignment_parameters=dict(),
80+
)
81+
outputs = RealignUnwarp.output_spec()
82+
83+
for key, metadata in list(output_map.items()):
84+
for metakey, value in list(metadata.items()):
85+
assert getattr(outputs.traits()[key], metakey) == value

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